Update upstream source from tag 'v2.1.2+dfsg1'
Update to upstream version '2.1.2+dfsg1'
with Debian dir 2c6d363fd8a5f80e7c2fcff586483079324d5a23
Filippo Rusconi
3 years ago
| 0 | 0 | This file lists *major* changes between releases, for a full list see git log. |
| 1 | 1 | |
| 2 | ||
| 3 | 2.1.2 (R-only release) | |
| 4 | ---------------------------------- | |
| 5 | - Workaround for CRAN threatening to remove package because of C++11 function usage, in spite of C++14 being clearly listed in SystemDependencies | |
| 6 | ||
| 7 | 2.1.1 | |
| 8 | ---------------------------------- | |
| 9 | - Speed improvements | |
| 10 | - Bugfixes | |
| 11 | - Support for calculating basic statistics of FixedEnvelopes | |
| 12 | - Support for negative atom counts in formulas in Python. This is useful in conjunction with FASTA argument, to represent protein modification | |
| 2 | 13 | |
| 3 | 14 | 2.1.0 |
| 4 | 15 | ---------------------------------- |
| 12 | 12 | # Basic information about project |
| 13 | 13 | |
| 14 | 14 | project(IsoSpec |
| 15 | DESCRIPTION "A program to calculate isotopic clusters" | |
| 16 | HOMEPAGE_URL "https://github.com/MatteoLacki/IsoSpec") | |
| 15 | DESCRIPTION "A program to calculate isotopic clusters" | |
| 16 | HOMEPAGE_URL "https://github.com/MatteoLacki/IsoSpec") | |
| 17 | 17 | |
| 18 | 18 | set(ISOSPEC_VERSION_MAJOR "2") |
| 19 | 19 | set(ISOSPEC_VERSION_MINOR "1") |
| 35 | 35 | # below, because it roots all the other dirs' configs. |
| 36 | 36 | |
| 37 | 37 | if(NOT CMAKE_INSTALL_PREFIX) |
| 38 | set(CMAKE_INSTALL_PREFIX /usr) | |
| 38 | set(CMAKE_INSTALL_PREFIX /usr) | |
| 39 | 39 | endif() |
| 40 | 40 | |
| 41 | 41 | # This module sets a number of installation directories |
| 75 | 75 | set(CMAKE_EXPORT_COMPILE_COMMANDS 1) |
| 76 | 76 | |
| 77 | 77 | if(EXISTS "${CMAKE_CURRENT_BINARY_DIR}/compile_commands.json" ) |
| 78 | execute_process( COMMAND cmake -E copy_if_different | |
| 79 | ${CMAKE_CURRENT_BINARY_DIR}/compile_commands.json | |
| 80 | ${CMAKE_CURRENT_SOURCE_DIR}/compile_commands.json | |
| 81 | ) | |
| 78 | execute_process( COMMAND cmake -E copy_if_different | |
| 79 | ${CMAKE_CURRENT_BINARY_DIR}/compile_commands.json | |
| 80 | ${CMAKE_CURRENT_SOURCE_DIR}/compile_commands.json | |
| 81 | ) | |
| 82 | 82 | endif() |
| 83 | 83 | |
| 84 | 84 | |
| 101 | 101 | add_definitions(-pedantic) |
| 102 | 102 | |
| 103 | 103 | if(WARN_AS_ERROR) |
| 104 | message(STATUS "${BoldYellow}Setting definition -Werror.${ColourReset}") | |
| 105 | add_definitions(-Werror) | |
| 104 | message(STATUS "${BoldYellow}Setting definition -Werror.${ColourReset}") | |
| 105 | add_definitions(-Werror) | |
| 106 | 106 | endif() |
| 107 | 107 | |
| 108 | 108 | message(STATUS "${BoldGreen}CMAKE_SOURCE_DIR: ${CMAKE_SOURCE_DIR}${ColourReset}") |
| 117 | 117 | # to build Win software right into GNU/Linux. |
| 118 | 118 | if(MXE) |
| 119 | 119 | |
| 120 | # Run the following cmake command line: | |
| 121 | # x86_64-w64-mingw32.shared-cmake -DCMAKE_BUILD_TYPE=Release -DMXE=1 ../development | |
| 122 | include(${CMAKE_TOOLCHAINS_PATH}/mxe-toolchain.cmake) | |
| 123 | #include(${CMAKE_TOOLCHAINS_PATH}/mxe-toolchain-olivier.cmake) | |
| 120 | include(${CMAKE_TOOLCHAINS_PATH}/mxe-toolchain.cmake) | |
| 121 | #include(${CMAKE_TOOLCHAINS_PATH}/mxe-toolchain-olivier.cmake) | |
| 124 | 122 | |
| 125 | # Set the name to the systemUname variable because in this situation that name | |
| 126 | # is not found, it it passed as a flag in the command line. | |
| 127 | set(SYSTEM_UNAME_S "mxe") | |
| 123 | # Set the name to the systemUname variable because in this situation that name | |
| 124 | # is not found, it it passed as a flag in the command line. | |
| 125 | set(SYSTEM_UNAME_S "mxe") | |
| 128 | 126 | |
| 129 | 127 | elseif(UNIX AND NOT APPLE) |
| 130 | 128 | |
| 131 | # Run the following cmake command line: | |
| 132 | # cmake -DCMAKE_BUILD_TYPE=Debug ../development | |
| 133 | ||
| 134 | include(${CMAKE_TOOLCHAINS_PATH}/unix-toolchain.cmake) | |
| 129 | include(${CMAKE_TOOLCHAINS_PATH}/unix-toolchain.cmake) | |
| 135 | 130 | |
| 136 | 131 | elseif(WIN32 OR _WIN32) |
| 137 | 132 | |
| 138 | # Run the following cmake command line: | |
| 139 | # cmake -DCMAKE_BUILD_TYPE=Release ../development | |
| 140 | ||
| 141 | include(${CMAKE_TOOLCHAINS_PATH}/win10-mingw64-toolchain.cmake) | |
| 133 | if(WIN10MINGW64) | |
| 134 | include(${CMAKE_TOOLCHAINS_PATH}/win10-mingw64-toolchain.cmake) | |
| 135 | endif() | |
| 142 | 136 | |
| 143 | 137 | elseif(APPLE) |
| 144 | 138 | |
| 145 | # Run the following cmake command line: | |
| 146 | # cmake -DCMAKE_BUILD_TYPE=Release ../development | |
| 147 | ||
| 148 | include(${CMAKE_TOOLCHAINS_PATH}/apple-macport-toolchain.cmake) | |
| 139 | include(${CMAKE_TOOLCHAINS_PATH}/apple-macport-toolchain.cmake) | |
| 149 | 140 | |
| 150 | 141 | endif() |
| 151 | 142 | |
| 159 | 150 | # Essential software configuration |
| 160 | 151 | |
| 161 | 152 | if(NOT CMAKE_BUILD_TYPE) |
| 162 | set(CMAKE_BUILD_TYPE Release CACHE STRING | |
| 163 | "Type of build, options are: None, Debug, Release, RelWithDebInfo, MinSizeRel." | |
| 164 | FORCE) | |
| 153 | set(CMAKE_BUILD_TYPE Release CACHE STRING | |
| 154 | "Type of build, options are: None, Debug, Release, RelWithDebInfo, MinSizeRel." | |
| 155 | FORCE) | |
| 165 | 156 | endif(NOT CMAKE_BUILD_TYPE) |
| 166 | 157 | |
| 167 | 158 | if(CMAKE_BUILD_TYPE MATCHES "Release") |
| 168 | #message(STATUS "Compiling in release mode.") | |
| 169 | add_definitions("-DQT_NO_DEBUG_OUTPUT") | |
| 159 | #message(STATUS "Compiling in release mode.") | |
| 160 | add_definitions("-DQT_NO_DEBUG_OUTPUT") | |
| 170 | 161 | endif() |
| 171 | 162 | |
| 172 | 163 | if(CMAKE_BUILD_TYPE MATCHES "Debug") |
| 173 | #message(STATUS "Compiling in debug mode.") | |
| 174 | message(STATUS "Add definition -ggdb3 to format debug output for GDB.") | |
| 175 | add_definitions(-ggdb3) | |
| 164 | #message(STATUS "Compiling in debug mode.") | |
| 165 | message(STATUS "Add definition -ggdb3 to format debug output for GDB.") | |
| 166 | add_definitions(-ggdb3) | |
| 176 | 167 | endif() |
| 177 | 168 | |
| 178 | 169 | if(CMAKE_BUILD_TYPE MATCHES "RelWithDebInfo") |
| 179 | #message(STATUS "Compiling in release with debug info mode.") | |
| 170 | #message(STATUS "Compiling in release with debug info mode.") | |
| 180 | 171 | endif(CMAKE_BUILD_TYPE MATCHES "RelWithDebInfo") |
| 181 | 172 | |
| 182 | 173 | message(STATUS "${BoldYellow}CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}.${ColourReset}") |
| 50 | 50 | # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy |
| 51 | 51 | # the logo to the output directory. |
| 52 | 52 | |
| 53 | PROJECT_LOGO = man/images/isospec_logo2_high_versioned.png | |
| 53 | PROJECT_LOGO = images/isospec_logo2_high_versioned.png | |
| 54 | 54 | |
| 55 | 55 | # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path |
| 56 | 56 | # into which the generated documentation will be written. If a relative path is |
| 57 | 57 | # entered, it will be relative to the location where doxygen was started. If |
| 58 | 58 | # left blank the current directory will be used. |
| 59 | 59 | |
| 60 | OUTPUT_DIRECTORY = man | |
| 60 | OUTPUT_DIRECTORY = ./ | |
| 61 | 61 | |
| 62 | 62 | # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- |
| 63 | 63 | # directories (in 2 levels) under the output directory of each output format and |
| 790 | 790 | # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING |
| 791 | 791 | # Note: If this tag is empty the current directory is searched. |
| 792 | 792 | |
| 793 | INPUT = IsoSpec++ | |
| 793 | INPUT = ../IsoSpec++ | |
| 794 | 794 | |
| 795 | 795 | # This tag can be used to specify the character encoding of the source files |
| 796 | 796 | # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses |
| 0 | prefix=${CMAKE_INSTALL_PREFIX} | |
| 0 | prefix=@CMAKE_INSTALL_PREFIX@ | |
| 1 | 1 | exec_prefix=${prefix} |
| 2 | libdir=${CMAKE_INSTALL_LIBDIR} | |
| 3 | includedir=${CMAKE_INSTALL_INCLUDEDIR} | |
| 2 | libdir=${prefix}/lib/@CMAKE_LIBRARY_ARCHITECTURE@ | |
| 3 | includedir=${prefix}/include | |
| 4 | 4 | |
| 5 | 5 | Name: libIsoSpec++ |
| 6 | 6 | Description: IsoSpec++ library for calculating isotopic clusters |
| 7 | Version: 3.0.0 | |
| 7 | Version: @VERSION@ | |
| 8 | 8 | Libs: -lIsoSpec++ |
| 9 | 9 | Cflags: -I${includedir}/IsoSpec++ -I${includedir} |
| 10 | 10 | Requires: |
| 4 | 4 | |
| 5 | 5 | execute_process(COMMAND uname -s OUTPUT_VARIABLE SYSTEM_UNAME_S) |
| 6 | 6 | |
| 7 | if(${SYSTEM_UNAME_S} MATCHES "^.*MINGW64.*") | |
| 8 | message(STATUS "System detected as Windows, setting WIN64") | |
| 9 | set(WIN64 1) | |
| 7 | if(${SYSTEM_UNAME_S} MATCHES "MINGW64_NT-10.*") | |
| 8 | message(STATUS "System detected as Windows10 with MINGW64, setting WIN32 AND WIN10MINGW64") | |
| 9 | # Note that WIN32 is set even on 64 bits systems. | |
| 10 | set(WIN32 1) | |
| 11 | set(WIN10MINGW64 1) | |
| 10 | 12 | #else() |
| 11 | 13 | #message(STATUS "System is not Windows.") |
| 12 | 14 | endif() |
| 11 | 11 | ## platform dependent compiler flags: |
| 12 | 12 | include(CheckCXXCompilerFlag) |
| 13 | 13 | |
| 14 | if (WITH_FPIC) | |
| 14 | if(WITH_FPIC) | |
| 15 | 15 | add_definitions(-fPIC) |
| 16 | 16 | endif() |
| 17 | 17 | |
| 20 | 20 | DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/isospec++) |
| 21 | 21 | |
| 22 | 22 | # Install cmake config |
| 23 | configure_file (${CMAKE_MODULE_PATH}/IsoSpec++Config.cmake.in | |
| 23 | configure_file(${CMAKE_MODULE_PATH}/IsoSpec++Config.cmake.in | |
| 24 | 24 | ${CMAKE_BINARY_DIR}/IsoSpec++Config.cmake) |
| 25 | 25 | install(FILES ${CMAKE_BINARY_DIR}/IsoSpec++Config.cmake |
| 26 | 26 | DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/isospec++) |
| 27 | 27 | |
| 28 | # Install the PkgConfig config file | |
| 29 | configure_file (${CMAKE_MODULE_PATH}/pkgconfig/libisospec++.pc.in | |
| 30 | ${CMAKE_BINARY_DIR}/libisospec++.pc) | |
| 28 | # Install the PkgConfig config file (only substitute the @VAR@ | |
| 29 | # because we need to preserve all the ${prefix} strings like | |
| 30 | # they are. | |
| 31 | configure_file(${CMAKE_MODULE_PATH}/pkgconfig/libisospec++.pc.in | |
| 32 | ${CMAKE_BINARY_DIR}/libisospec++.pc @ONLY) | |
| 31 | 33 | install(FILES ${CMAKE_BINARY_DIR}/libisospec++.pc |
| 32 | 34 | DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) |
| 33 | 35 | |
| 34 | # Prepare the logo picture files with the right version (configure_file) | |
| 36 | # Now deal with the manual doc stuff | |
| 37 | add_subdirectory(man) | |
| 35 | 38 | |
| 36 | configure_file(${CMAKE_SOURCE_DIR}/CMakeStuff/isospec_logo2_high.svg.in | |
| 37 | ${CMAKE_SOURCE_DIR}/man/images/isospec_logo2_high_versioned.svg @ONLY) | |
| 39 | # Now deal with the example stuff | |
| 40 | add_subdirectory(Examples) | |
| 38 | 41 | |
| 39 | configure_file(${CMAKE_SOURCE_DIR}/CMakeStuff/isospec_logo2_long.svg.in | |
| 40 | ${CMAKE_SOURCE_DIR}/man/images/isospec_logo2_long_versioned.svg @ONLY) | |
| 41 | ||
| 42 | # Make the conversion of the svg file into a png, but only on GNU/Linux | |
| 43 | # Produce a file with respected aspect ratio, 200 pixels wide. | |
| 44 | ||
| 45 | if(UNIX AND NOT APPLE) | |
| 46 | execute_process(COMMAND gm convert -geometry 200x | |
| 47 | ${CMAKE_SOURCE_DIR}/man/images/isospec_logo2_high_versioned.svg | |
| 48 | ${CMAKE_SOURCE_DIR}/man/images/isospec_logo2_high_versioned.png) | |
| 49 | endif() | |
| 50 | ||
| 51 | ||
| 52 | if(UNIX AND NOT APPLE) | |
| 53 | execute_process(COMMAND gm convert -geometry 200x | |
| 54 | ${CMAKE_SOURCE_DIR}/man/images/isospec_logo2_long_versioned.svg | |
| 55 | ${CMAKE_SOURCE_DIR}/man/images/isospec_logo2_long_versioned.png) | |
| 56 | endif() | |
| 57 | ||
| 58 | # Ensure that the doxyfile configuration file for Doxygen has always | |
| 59 | # the proper version number! | |
| 60 | ||
| 61 | configure_file(${CMAKE_SOURCE_DIR}/CMakeStuff/doxyfile.in | |
| 62 | ${CMAKE_SOURCE_DIR}/man/doxyfile @ONLY) | |
| 63 | ||
| 64 | # Command: | |
| 65 | # make doc | |
| 66 | add_custom_target(doc | |
| 67 | COMMAND doxygen man/doxyfile | |
| 68 | WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} | |
| 69 | COMMENT "Doxygen-based developer documentation generation") | |
| 70 | ||
| 71 | ||
| 8 | 8 | |
| 9 | 9 | |
| 10 | 10 | # On Win10 all the code is relocatable. |
| 11 | remove_definitions(-fPIC -Wall -pedantic -Wextra) | |
| 11 | message(STATUS "Removing definitions -fPic.") | |
| 12 | remove_definitions(-fPIC) | |
| 12 | 13 |
| 0 | message("") | |
| 1 | message(STATUS "${BoldGreen}Starting configuration for the example material for ${PROJECT_NAME} ${ColourReset}") | |
| 2 | message("") | |
| 3 | ||
| 4 | ||
| 5 | ############### | |
| 6 | # install stuff | |
| 7 | ||
| 8 | install(DIRECTORY C++ Python R | |
| 9 | DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec/examples) | |
| 10 | ||
| 11 | message("") | |
| 12 | message(STATUS "${BoldGreen}Finished configuration for the example material.${ColourReset}") | |
| 13 | message("") | |
| 14 | ||
| 15 |
| 0 | from IsoSpecPy.IsoSpecPy import IsoTotalProb, IsoThreshold | |
| 1 | from IsoSpecPy.PeriodicTbl import symbol_to_masses | |
| 2 | ||
| 3 | ||
| 4 | # Suppose we want to simulate the spectrum of | |
| 5 | # C100H200Ag46 | |
| 6 | # except that the isotope counts of silver in each molecule | |
| 7 | # are fixed: each molecule contains exactly 44 atoms of 107Ag, | |
| 8 | # and 2 atoms of 109Ag. The carbon and hydrogen follow their | |
| 9 | # natural distributions. | |
| 10 | ||
| 11 | # Here's how to do that: | |
| 12 | ||
| 13 | # We start by defining two artificial elements, each representing | |
| 14 | # one isotope of silver. The element is going to be monoisotopic, | |
| 15 | # with proper mass retrieved from the periodic table. | |
| 16 | # The new elements will be passed to Iso* methods using the | |
| 17 | # atomCounts, isotopeMasses, isotopeProbabilities parameters, | |
| 18 | # and the rest of the formula - using standard "formula" | |
| 19 | # argument. | |
| 20 | ||
| 21 | # defining extra elements | |
| 22 | # 44 107Ag atoms and 2 109Ag | |
| 23 | atomCounts = [44, 2] | |
| 24 | ||
| 25 | # Retrieving the isotope masses from IsoSpec's builtin periodic table | |
| 26 | # (one could input them manually too) | |
| 27 | M107Ag, M109Ag = symbol_to_masses['Ag'] | |
| 28 | ||
| 29 | # The masses are passed as list of masses for each new element: | |
| 30 | # we have two elements, each has one isotope, hence the following | |
| 31 | # list structure | |
| 32 | isotopeMasses = [[M107Ag], [M109Ag]] | |
| 33 | ||
| 34 | # The single isotope of each new element occurs with 1.0 probability | |
| 35 | isotopeProbabilities = [[1.0], [1.0]] | |
| 36 | ||
| 37 | ||
| 38 | # peaks above .001 threshold | |
| 39 | print("Here is the list of peaks above 0.001 intensity threshold for C100H200[107Ag]44[109Ag]2") | |
| 40 | MZI_thr = IsoThreshold(.001, | |
| 41 | 'C100H200', # the remaining part of the formula | |
| 42 | get_confs=True, | |
| 43 | atomCounts=atomCounts, | |
| 44 | isotopeMasses=isotopeMasses, | |
| 45 | isotopeProbabilities=isotopeProbabilities) | |
| 46 | ||
| 47 | print("Masses list:", list(MZI_thr.masses)) | |
| 48 | print("Probabilities list:", list(MZI_thr.probs)) | |
| 49 | print("Configurations list:", list(MZI_thr.confs)) | |
| 50 | ||
| 51 | print() | |
| 52 | print() | |
| 53 | ||
| 54 | # Alternatively: peaks that make 99.9% of the isotopic distribution | |
| 55 | print("Here is the list of peaks that comprise at least 99.9% of total intensity for C100H200[107Ag]44[109Ag]2") | |
| 56 | MZI_opt = IsoTotalProb(.999, | |
| 57 | 'C100H200', # the remaining part of the formula | |
| 58 | get_confs=True, | |
| 59 | atomCounts=atomCounts, | |
| 60 | isotopeMasses=isotopeMasses, | |
| 61 | isotopeProbabilities=isotopeProbabilities) | |
| 62 | ||
| 63 | print("Masses list:", list(MZI_opt.masses)) | |
| 64 | print("Probabilities list:", list(MZI_opt.probs)) | |
| 65 | print("Configurations list:", list(MZI_opt.confs)) |
| 0 | from IsoSpecPy.IsoSpecPy import IsoTotalProb | |
| 1 | ||
| 2 | # isotopic distribution of protein with fasta sequence AAAPPGQAAC | |
| 3 | MZI_opt = IsoTotalProb(.999, | |
| 4 | fasta='AAAPPGQAAC') | |
| 5 | ||
| 6 | # isotopic distribution of protein with fasta sequence AAAPPGQAAC, | |
| 7 | # with thioglycinie modification | |
| 8 | MZI_opt2 = IsoTotalProb(.999, | |
| 9 | formula='O-1S1', | |
| 10 | fasta='AAAPPGQAAC') | |
| 11 | print("Masses and probabilities in AAAPPGQAAC with thioglycine modification:") | |
| 12 | print([(m, p) for (m, p) in zip(MZI_opt2.masses, MZI_opt2.probs)]) | |
| 13 |
| 31 | 31 | isotopeMasses = (radiolabelled_carbon_masses,), |
| 32 | 32 | isotopeProbabilities = (radiolabelled_carbon_probs,), |
| 33 | 33 | # And the rest of parameters for configuration |
| 34 | prob_to_cover = 0.99, | |
| 34 | prob_to_cover = 0.99, | |
| 35 | 35 | get_confs=True) |
| 36 | 36 | |
| 37 | 37 | # Radiolabelling (or isotopic labelling) with more than one element looks like this: |
| 0 | 0 | OPTFLAGS=-O3 -march=native -mtune=native |
| 1 | DEBUGFLAGS=-O0 -g -Werror | |
| 2 | CXXFLAGS=-std=c++17 -Wall -pedantic -Wextra -Wshadow | |
| 1 | DEBUGFLAGS=-O0 -g -Werror -DISOSPEC_DEBUG -DDEBUG -D_GLIBCXX_DEBUG | |
| 2 | CXXFLAGS=-std=c++17 -Wall -pedantic -Wextra -Wshadow -Wcast-align -Wcast-qual -Wctor-dtor-privacy -Wdisabled-optimization -Wformat=2 -Winit-self -Wmissing-include-dirs -Wno-old-style-cast -Woverloaded-virtual -Wredundant-decls -Wshadow -Wno-sign-conversion -Wsign-promo -Wswitch-default -Wundef -Werror | |
| 3 | 3 | SRCFILES=cwrapper.cpp allocator.cpp dirtyAllocator.cpp isoSpec++.cpp isoMath.cpp marginalTrek++.cpp operators.cpp element_tables.cpp misc.cpp mman.cpp fixedEnvelopes.cpp fasta.cpp |
| 4 | 4 | |
| 5 | 5 | all: unitylib |
| 20 | 20 | { |
| 21 | 21 | |
| 22 | 22 | template <typename T> |
| 23 | Allocator<T>::Allocator(const int dim_, const int tabSize_): currentId(-1), dim(dim_), tabSize(tabSize_) | |
| 24 | { | |
| 25 | currentTab = new T[dim * tabSize]; | |
| 26 | } | |
| 23 | Allocator<T>::Allocator(const int dim_, const int tabSize_): currentTab(new T[dim_ * tabSize_]), currentId(-1), dim(dim_), tabSize(tabSize_) {} | |
| 24 | ||
| 27 | 25 | |
| 28 | 26 | template <typename T> |
| 29 | 27 | Allocator<T>::~Allocator() |
| 30 | 28 | { |
| 31 | for(unsigned int i = 0; i < prevTabs.size(); ++i) | |
| 29 | if(prevTabs.size() == 0 || currentTab != prevTabs.back()) | |
| 32 | 30 | { |
| 33 | delete [] prevTabs[i]; | |
| 31 | // It will be equal only if shiftTables throws during new[] | |
| 32 | // Make sure we don't del currentTab twice in that case | |
| 33 | delete [] currentTab; | |
| 34 | 34 | } |
| 35 | 35 | |
| 36 | delete [] currentTab; | |
| 36 | for(unsigned int i = 0; i < prevTabs.size(); ++i) | |
| 37 | delete [] prevTabs[i]; | |
| 37 | 38 | } |
| 38 | 39 | |
| 39 | 40 | template <typename T> |
| 15 | 15 | |
| 16 | 16 | #pragma once |
| 17 | 17 | |
| 18 | #include <vector> | |
| 19 | 18 | #include <cstring> |
| 20 | 19 | #include "conf.h" |
| 20 | #include "pod_vector.h" | |
| 21 | 21 | |
| 22 | 22 | namespace IsoSpec |
| 23 | 23 | { |
| 35 | 35 | T* currentTab; |
| 36 | 36 | int currentId; |
| 37 | 37 | const int dim, tabSize; |
| 38 | std::vector<T*> prevTabs; | |
| 38 | pod_vector<T*> prevTabs; | |
| 39 | 39 | |
| 40 | 40 | public: |
| 41 | 41 | explicit Allocator(const int dim, const int tabSize = 10000); |
| 20 | 20 | |
| 21 | 21 | typedef int* Conf; |
| 22 | 22 | |
| 23 | } | |
| 23 | struct ProbAndConfPtr | |
| 24 | { | |
| 25 | // For some reason std::pair isn't trivially copyable... | |
| 26 | double first; | |
| 27 | Conf second; | |
| 24 | 28 | |
| 29 | ProbAndConfPtr(double p, Conf c) : first(p), second(c) {} | |
| 30 | ||
| 31 | bool operator<(const ProbAndConfPtr& other) const | |
| 32 | { | |
| 33 | return first < other.first; | |
| 34 | } | |
| 35 | }; | |
| 36 | ||
| 37 | } // namespace IsoSpec |
| 98 | 98 | { |
| 99 | 99 | Iso* i = reinterpret_cast<Iso*>(iso); |
| 100 | 100 | double* ret = reinterpret_cast<double*>(malloc(sizeof(double)*i->getDimNumber())); |
| 101 | i->saveMarginalLogSizeEstimates(ret, target_total_prob); | |
| 101 | if(ret != nullptr) | |
| 102 | i->saveMarginalLogSizeEstimates(ret, target_total_prob); | |
| 102 | 103 | return ret; |
| 103 | 104 | } |
| 104 | 105 | |
| 264 | 265 | return reinterpret_cast<FixedEnvelope*>(tabulator)->confs_no(); |
| 265 | 266 | } |
| 266 | 267 | |
| 268 | double empiricAverageMass(void* tabulator) | |
| 269 | { | |
| 270 | return reinterpret_cast<FixedEnvelope*>(tabulator)->empiric_average_mass(); | |
| 271 | } | |
| 272 | ||
| 273 | double empiricVariance(void* tabulator) | |
| 274 | { | |
| 275 | return reinterpret_cast<FixedEnvelope*>(tabulator)->empiric_variance(); | |
| 276 | } | |
| 277 | ||
| 278 | double empiricStddev(void* tabulator) | |
| 279 | { | |
| 280 | return reinterpret_cast<FixedEnvelope*>(tabulator)->empiric_stddev(); | |
| 281 | } | |
| 282 | ||
| 267 | 283 | double wassersteinDistance(void* tabulator1, void* tabulator2) |
| 268 | 284 | { |
| 269 | 285 | try |
| 348 | 364 | // Same thing, only this time with C linkage |
| 349 | 365 | parse_fasta(fasta, atomCounts); |
| 350 | 366 | } |
| 351 | ||
| 352 | 367 | } // extern "C" ends here |
| 117 | 117 | const int* confsFixedEnvelope(void* tabulator); |
| 118 | 118 | int confs_noFixedEnvelope(void* tabulator); |
| 119 | 119 | |
| 120 | double empiricAverageMass(void* tabulator); | |
| 121 | double empiricVariance(void* tabulator); | |
| 122 | double empiricStddev(void* tabulator); | |
| 123 | ||
| 120 | 124 | double wassersteinDistance(void* tabulator1, void* tabulator2); |
| 121 | 125 | double orientedWassersteinDistance(void* tabulator1, void* tabulator2); |
| 122 | 126 | void* addEnvelopes(void* tabulator1, void* tabulator2); |
| 14 | 14 | */ |
| 15 | 15 | |
| 16 | 16 | |
| 17 | #include <stdlib.h> | |
| 17 | #include <cstdlib> | |
| 18 | 18 | #include "dirtyAllocator.h" |
| 19 | 19 | |
| 20 | 20 | namespace IsoSpec |
| 29 | 29 | if(cellSize % sizeof(double) != 0) |
| 30 | 30 | cellSize += sizeof(double) - cellSize % sizeof(double); |
| 31 | 31 | currentTab = malloc( cellSize * tabSize ); |
| 32 | if(currentTab == NULL) | |
| 33 | throw std::bad_alloc(); | |
| 32 | 34 | currentConf = currentTab; |
| 33 | 35 | endOfTablePtr = reinterpret_cast<char*>(currentTab) + cellSize*tabSize; |
| 34 | 36 | } |
| 46 | 48 | |
| 47 | 49 | currentTab = malloc( cellSize * tabSize ); |
| 48 | 50 | currentConf = currentTab; |
| 51 | if(currentTab == NULL) | |
| 52 | throw std::bad_alloc(); | |
| 49 | 53 | endOfTablePtr = reinterpret_cast<char*>(currentTab) + cellSize*tabSize; |
| 50 | 54 | } |
| 51 | 55 | |
| 15 | 15 | |
| 16 | 16 | #pragma once |
| 17 | 17 | |
| 18 | #include <vector> | |
| 19 | 18 | #include <cstring> |
| 19 | #include "pod_vector.h" | |
| 20 | 20 | |
| 21 | 21 | namespace IsoSpec |
| 22 | 22 | { |
| 29 | 29 | void* endOfTablePtr; |
| 30 | 30 | const int tabSize; |
| 31 | 31 | int cellSize; |
| 32 | std::vector<void*> prevTabs; | |
| 32 | pod_vector<void*> prevTabs; | |
| 33 | 33 | |
| 34 | 34 | public: |
| 35 | 35 | explicit DirtyAllocator(const int dim, const int tabSize = 10000); |
| 128 | 128 | /* Code: 71 ASCII char: G */ 2, 3, 1, 1, 0, 0, |
| 129 | 129 | /* Code: 72 ASCII char: H */ 6, 7, 3, 1, 0, 0, |
| 130 | 130 | /* Code: 73 ASCII char: I */ 6, 11, 1, 1, 0, 0, |
| 131 | /* Code: 74 ASCII char: J */ 0, 0, 0, 0, 0, 0, | |
| 131 | /* Code: 74 ASCII char: J */ 6, 11, 1, 1, 0, 0, | |
| 132 | 132 | /* Code: 75 ASCII char: K */ 6, 12, 2, 1, 0, 0, |
| 133 | 133 | /* Code: 76 ASCII char: L */ 6, 11, 1, 1, 0, 0, |
| 134 | 134 | /* Code: 77 ASCII char: M */ 5, 9, 1, 1, 1, 0, |
| 160 | 160 | /* Code: 103 ASCII char: g */ 2, 3, 1, 1, 0, 0, |
| 161 | 161 | /* Code: 104 ASCII char: h */ 6, 7, 3, 1, 0, 0, |
| 162 | 162 | /* Code: 105 ASCII char: i */ 6, 11, 1, 1, 0, 0, |
| 163 | /* Code: 106 ASCII char: j */ 0, 0, 0, 0, 0, 0, | |
| 163 | /* Code: 106 ASCII char: j */ 6, 11, 1, 1, 0, 0, | |
| 164 | 164 | /* Code: 107 ASCII char: k */ 6, 12, 2, 1, 0, 0, |
| 165 | 165 | /* Code: 108 ASCII char: l */ 6, 11, 1, 1, 0, 0, |
| 166 | 166 | /* Code: 109 ASCII char: m */ 5, 9, 1, 1, 1, 0, |
| 593 | 593 | template void FixedEnvelope::total_prob_init<false>(Iso&& iso, double target_total_prob, bool optimize); |
| 594 | 594 | |
| 595 | 595 | |
| 596 | double FixedEnvelope::empiric_average_mass() | |
| 597 | { | |
| 598 | double ret = 0.0; | |
| 599 | for(size_t ii = 0; ii < _confs_no; ii++) | |
| 600 | { | |
| 601 | ret += _masses[ii] * _probs[ii]; | |
| 602 | } | |
| 603 | return ret / get_total_prob(); | |
| 604 | } | |
| 605 | ||
| 606 | double FixedEnvelope::empiric_variance() | |
| 607 | { | |
| 608 | double ret = 0.0; | |
| 609 | double avg = empiric_average_mass(); | |
| 610 | for(size_t ii = 0; ii < _confs_no; ii++) | |
| 611 | { | |
| 612 | double msq = _masses[ii] - avg; | |
| 613 | ret += msq * msq * _probs[ii]; | |
| 614 | } | |
| 615 | ||
| 616 | return ret / get_total_prob(); | |
| 617 | } | |
| 618 | ||
| 596 | 619 | } // namespace IsoSpec |
| 95 | 95 | void scale(double factor); |
| 96 | 96 | void normalize(); |
| 97 | 97 | |
| 98 | double empiric_average_mass(); | |
| 99 | double empiric_variance(); | |
| 100 | double empiric_stddev() { return sqrt(empiric_variance()); } | |
| 101 | ||
| 98 | 102 | double WassersteinDistance(FixedEnvelope& other); |
| 99 | 103 | double OrientedWassersteinDistance(FixedEnvelope& other); |
| 100 | 104 |
| 96 | 96 | { |
| 97 | 97 | delete[] isotopeNumbers; |
| 98 | 98 | delete[] atomCounts; |
| 99 | // Since we're throwing in a constructor, the destructor won't run, and we don't need to NULL these. | |
| 100 | // However, this is not the fast code path and we can afford two unneeded instructions to keep | |
| 101 | // some static analysis tools happy. | |
| 102 | isotopeNumbers = nullptr; | |
| 103 | atomCounts = nullptr; | |
| 99 | // Since we're throwing in a constructor, the destructor won't run, and we don't need to NULL these. | |
| 100 | // However, this is not the fast code path and we can afford two unneeded instructions to keep | |
| 101 | // some static analysis tools happy. | |
| 102 | isotopeNumbers = nullptr; | |
| 103 | atomCounts = nullptr; | |
| 104 | 104 | throw; |
| 105 | 105 | } |
| 106 | 106 | } |
| 127 | 127 | { |
| 128 | 128 | delete[] isotopeNumbers; |
| 129 | 129 | delete[] atomCounts; |
| 130 | // Since we're throwing in a constructor, the destructor won't run, and we don't need to NULL these. | |
| 131 | // However, this is not the fast code path and we can afford two unneeded instructions to keep | |
| 132 | // some static analysis tools happy. | |
| 133 | isotopeNumbers = nullptr; | |
| 134 | atomCounts = nullptr; | |
| 130 | // Since we're throwing in a constructor, the destructor won't run, and we don't need to NULL these. | |
| 131 | // However, this is not the fast code path and we can afford two unneeded instructions to keep | |
| 132 | // some static analysis tools happy. | |
| 133 | isotopeNumbers = nullptr; | |
| 134 | atomCounts = nullptr; | |
| 135 | 135 | throw; |
| 136 | 136 | } |
| 137 | 137 | } |
| 822 | 822 | for(int i = 0; i < dimNumber; i++) |
| 823 | 823 | marginalResults[i] = new MarginalTrek(std::move(*(marginals[i])), _tabSize, _hashSize); |
| 824 | 824 | |
| 825 | logProbs = new const std::vector<double>*[dimNumber]; | |
| 826 | masses = new const std::vector<double>*[dimNumber]; | |
| 827 | marginalConfs = new const std::vector<int*>*[dimNumber]; | |
| 825 | logProbs = new const pod_vector<double>*[dimNumber]; | |
| 826 | masses = new const pod_vector<double>*[dimNumber]; | |
| 827 | marginalConfs = new const pod_vector<int*>*[dimNumber]; | |
| 828 | 828 | |
| 829 | 829 | for(int i = 0; i < dimNumber; i++) |
| 830 | 830 | { |
| 102 | 102 | |
| 103 | 103 | //! Constructor (named) from aminoacid FASTA sequence as C string. |
| 104 | 104 | /*! |
| 105 | \param fasta An aminoacid FASTA sequence. May be upper/lower/mixed case, may contain selenocystein (U). Subisotopologues will be in order: CHNOS, possibly with Se added at an end if present. | |
| 105 | \param fasta An aminoacid FASTA sequence. May be upper/lower/mixed case, may contain selenocystein (U) or xleucine (J). | |
| 106 | Other characters, including FASTA codes of indeterminate chemical formula (X, *, -, B, ...) are silently ignored. | |
| 107 | That means "AEDA", "AE-DA", "EAXXDA", "AE DA" will all result in the same chemical formula. | |
| 108 | Subisotopologues will be in order: CHNOS, possibly with Se added at an end if present. | |
| 106 | 109 | \use_nominal_masses Whether to use nucleon number instead of the real mass of each isotope during calculations. |
| 107 | 110 | \add_water Whether the chain should have the terminating -H and -OH groups at the N and C terminus, respectively. |
| 108 | 111 | */ |
| 233 | 236 | { |
| 234 | 237 | private: |
| 235 | 238 | MarginalTrek** marginalResults; /*!< Table of pointers to marginal distributions of subisotopologues. */ |
| 236 | std::priority_queue<void*, std::vector<void*>, ConfOrder> pq; /*!< The priority queue used to generate isotopologues ordered by descending probability. */ | |
| 239 | std::priority_queue<void*, pod_vector<void*>, ConfOrder> pq; /*!< The priority queue used to generate isotopologues ordered by descending probability. */ | |
| 237 | 240 | void* topConf; /*!< Most probable configuration. */ |
| 238 | 241 | DirtyAllocator allocator; /*!< Structure used for alocating memory for isotopologues. */ |
| 239 | const std::vector<double>** logProbs; /*!< Obtained log-probabilities. */ | |
| 240 | const std::vector<double>** masses; /*!< Obtained masses. */ | |
| 241 | const std::vector<int*>** marginalConfs; /*!< Obtained counts of isotopes. */ | |
| 242 | const pod_vector<double>** logProbs; /*!< Obtained log-probabilities. */ | |
| 243 | const pod_vector<double>** masses; /*!< Obtained masses. */ | |
| 244 | const pod_vector<Conf>** marginalConfs; /*!< Obtained counts of isotopes. */ | |
| 242 | 245 | double currentLProb; /*!< The log-probability of the current isotopologue. */ |
| 243 | 246 | double currentMass; /*!< The mass of the current isotopologue. */ |
| 244 | 247 | double currentProb; /*!< The probability of the current isotopologue. */ |
| 18 | 18 | #include <algorithm> |
| 19 | 19 | #include <vector> |
| 20 | 20 | #include <cstdlib> |
| 21 | #include <unordered_map> | |
| 22 | #include <unordered_set> | |
| 23 | 21 | #include <queue> |
| 24 | 22 | #include <utility> |
| 25 | 23 | #include <cstring> |
| 26 | 24 | #include <string> |
| 27 | 25 | #include <limits> |
| 26 | #include <memory> | |
| 28 | 27 | #include "platform.h" |
| 29 | 28 | #include "marginalTrek++.h" |
| 30 | 29 | #include "conf.h" |
| 323 | 322 | MarginalTrek::MarginalTrek( |
| 324 | 323 | Marginal&& m, |
| 325 | 324 | int tabSize, |
| 326 | int hashSize | |
| 325 | int | |
| 327 | 326 | ) : |
| 328 | 327 | Marginal(std::move(m)), |
| 329 | 328 | current_count(0), |
| 330 | keyHasher(isotopeNo), | |
| 331 | equalizer(isotopeNo), | |
| 332 | 329 | orderMarginal(atom_lProbs, isotopeNo), |
| 333 | visited(hashSize, keyHasher, equalizer), | |
| 334 | pq(orderMarginal), | |
| 335 | totalProb(), | |
| 336 | candidate(new int[isotopeNo]), | |
| 330 | pq(), | |
| 337 | 331 | allocator(isotopeNo, tabSize) |
| 338 | 332 | { |
| 339 | 333 | int* initialConf = allocator.makeCopy(mode_conf); |
| 340 | 334 | |
| 341 | pq.push(initialConf); | |
| 342 | visited[initialConf] = 0; | |
| 343 | ||
| 344 | totalProb = Summator(); | |
| 335 | pq.push({unnormalized_logProb(mode_conf), initialConf}); | |
| 345 | 336 | |
| 346 | 337 | current_count = 0; |
| 347 | 338 | |
| 357 | 348 | */ |
| 358 | 349 | if(pq.size() < 1) return false; |
| 359 | 350 | |
| 360 | Conf topConf = pq.top(); | |
| 351 | double logprob = pq.top().first + loggamma_nominator; | |
| 352 | Conf topConf = pq.top().second; | |
| 353 | ||
| 361 | 354 | pq.pop(); |
| 362 | 355 | ++current_count; |
| 363 | visited[topConf] = current_count; | |
| 364 | 356 | |
| 365 | 357 | _confs.push_back(topConf); |
| 358 | ||
| 366 | 359 | _conf_masses.push_back(calc_mass(topConf, atom_masses, isotopeNo)); |
| 367 | double logprob = logProb(topConf); | |
| 368 | 360 | _conf_lprobs.push_back(logprob); |
| 369 | 361 | |
| 370 | ||
| 371 | totalProb.add( exp( logprob ) ); | |
| 372 | ||
| 373 | for( unsigned int i = 0; i < isotopeNo; ++i ) | |
| 374 | { | |
| 375 | for( unsigned int j = 0; j < isotopeNo; ++j ) | |
| 362 | for( unsigned int j = 0; j < isotopeNo; ++j ) | |
| 363 | { | |
| 364 | if( topConf[j] > mode_conf[j]) | |
| 365 | continue; | |
| 366 | ||
| 367 | if( topConf[j] > 0 ) | |
| 376 | 368 | { |
| 377 | // Growing index different than decreasing one AND | |
| 378 | // Remain on simplex condition. | |
| 379 | if( i != j && topConf[j] > 0 ){ | |
| 380 | copyConf(topConf, candidate, isotopeNo); | |
| 381 | ||
| 382 | ++candidate[i]; | |
| 383 | --candidate[j]; | |
| 384 | ||
| 385 | // candidate should not have been already visited. | |
| 386 | if( visited.count( candidate ) == 0 ) | |
| 387 | { | |
| 388 | Conf acceptedCandidate = allocator.makeCopy(candidate); | |
| 389 | pq.push(acceptedCandidate); | |
| 390 | ||
| 391 | visited[acceptedCandidate] = 0; | |
| 369 | for( unsigned int i = 0; i < isotopeNo; ++i ) | |
| 370 | { | |
| 371 | if( topConf[i] < mode_conf[i] ) | |
| 372 | continue; | |
| 373 | // Growing index different than decreasing one AND | |
| 374 | // Remain on simplex condition. | |
| 375 | if( i != j ){ | |
| 376 | Conf acceptedCandidate = allocator.makeCopy(topConf); | |
| 377 | ||
| 378 | ++acceptedCandidate[i]; | |
| 379 | --acceptedCandidate[j]; | |
| 380 | ||
| 381 | double new_prob = unnormalized_logProb(acceptedCandidate); | |
| 382 | ||
| 383 | pq.push({new_prob, acceptedCandidate}); | |
| 392 | 384 | } |
| 385 | ||
| 386 | if( topConf[i] > mode_conf[i] ) | |
| 387 | break; | |
| 393 | 388 | } |
| 394 | 389 | } |
| 390 | if( topConf[j] < mode_conf[j] ) | |
| 391 | break; | |
| 395 | 392 | } |
| 396 | 393 | |
| 397 | 394 | return true; |
| 398 | 395 | } |
| 399 | 396 | |
| 400 | int MarginalTrek::processUntilCutoff(double cutoff) | |
| 401 | { | |
| 402 | Summator s; | |
| 403 | int last_idx = -1; | |
| 404 | for(unsigned int i = 0; i < _conf_lprobs.size(); i++) | |
| 405 | { | |
| 406 | s.add(_conf_lprobs[i]); | |
| 407 | if(s.get() >= cutoff) | |
| 408 | { | |
| 409 | last_idx = i; | |
| 410 | break; | |
| 411 | } | |
| 412 | } | |
| 413 | if(last_idx > -1) | |
| 414 | return last_idx; | |
| 415 | ||
| 416 | while(totalProb.get() < cutoff && add_next_conf()) {} | |
| 417 | return _conf_lprobs.size(); | |
| 418 | } | |
| 419 | ||
| 420 | 397 | |
| 421 | 398 | MarginalTrek::~MarginalTrek() |
| 422 | 399 | { |
| 423 | delete[] candidate; | |
| 424 | } | |
| 425 | ||
| 400 | } | |
| 426 | 401 | |
| 427 | 402 | |
| 428 | 403 | |
| 430 | 405 | double lCutOff, |
| 431 | 406 | bool sort, |
| 432 | 407 | int tabSize, |
| 433 | int hashSize | |
| 408 | int | |
| 434 | 409 | ) : Marginal(std::move(m)), |
| 435 | 410 | allocator(isotopeNo, tabSize) |
| 436 | 411 | { |
| 437 | const ConfEqual equalizer(isotopeNo); | |
| 438 | const KeyHasher keyHasher(isotopeNo); | |
| 439 | const ConfOrderMarginalDescending orderMarginal(atom_lProbs, isotopeNo); | |
| 440 | ||
| 441 | lCutOff -= loggamma_nominator; | |
| 442 | ||
| 443 | std::unordered_set<Conf, KeyHasher, ConfEqual> visited(hashSize, keyHasher, equalizer); | |
| 444 | ||
| 445 | 412 | Conf currentConf = allocator.makeCopy(mode_conf); |
| 446 | if(unnormalized_logProb(currentConf) >= lCutOff) | |
| 447 | { | |
| 448 | // create a copy and store a ptr to the *same* copy in both structures | |
| 449 | // (save some space and time) | |
| 450 | auto tmp = allocator.makeCopy(currentConf); | |
| 451 | configurations.push_back(tmp); | |
| 452 | visited.insert(tmp); | |
| 413 | if(logProb(currentConf) >= lCutOff) | |
| 414 | { | |
| 415 | configurations.push_back(currentConf); | |
| 416 | lProbs.push_back(mode_lprob); | |
| 453 | 417 | } |
| 454 | 418 | |
| 455 | 419 | unsigned int idx = 0; |
| 456 | 420 | |
| 421 | std::unique_ptr<double[]> prob_partials(new double[isotopeNo]); | |
| 422 | std::unique_ptr<double[]> prob_part_acc(new double[isotopeNo+1]); | |
| 423 | prob_part_acc[0] = loggamma_nominator; | |
| 424 | ||
| 457 | 425 | while(idx < configurations.size()) |
| 458 | 426 | { |
| 459 | memcpy(currentConf, configurations[idx], sizeof(int)*isotopeNo); | |
| 427 | currentConf = configurations[idx]; | |
| 460 | 428 | idx++; |
| 429 | ||
| 430 | for(size_t ii = 0; ii < isotopeNo; ii++) | |
| 431 | prob_partials[ii] = minuslogFactorial(currentConf[ii]) + currentConf[ii] * atom_lProbs[ii]; | |
| 432 | ||
| 461 | 433 | for(unsigned int ii = 0; ii < isotopeNo; ii++ ) |
| 462 | 434 | { |
| 463 | currentConf[ii]++; | |
| 464 | for(unsigned int jj = 0; jj < isotopeNo; jj++ ) | |
| 435 | if(currentConf[ii] > mode_conf[ii]) | |
| 436 | continue; | |
| 437 | ||
| 438 | if(currentConf[ii] != 0) | |
| 465 | 439 | { |
| 466 | if( ii != jj && currentConf[jj] > 0) | |
| 440 | double prev_partial_ii = prob_partials[ii]; | |
| 441 | currentConf[ii]--; | |
| 442 | prob_partials[ii] = minuslogFactorial(currentConf[ii]) + currentConf[ii] * atom_lProbs[ii]; | |
| 443 | ||
| 444 | for(unsigned int jj = 0; jj < isotopeNo; jj++ ) | |
| 467 | 445 | { |
| 468 | currentConf[jj]--; | |
| 469 | ||
| 470 | if (visited.count(currentConf) == 0 && unnormalized_logProb(currentConf) >= lCutOff) | |
| 446 | prob_part_acc[jj+1] = prob_part_acc[jj] + prob_partials[jj]; | |
| 447 | ||
| 448 | if(currentConf[jj] < mode_conf[jj]) | |
| 449 | continue; | |
| 450 | ||
| 451 | if( ii != jj ) | |
| 471 | 452 | { |
| 472 | // create a copy and store a ptr to the *same* copy in | |
| 473 | // both structures (save some space and time) | |
| 474 | auto tmp = allocator.makeCopy(currentConf); | |
| 475 | visited.insert(tmp); | |
| 476 | configurations.push_back(tmp); | |
| 477 | // std::cout << " V: "; for (auto it : visited) std::cout << it << " "; std::cout << std::endl; | |
| 453 | double logp = prob_part_acc[jj] + minuslogFactorial(1+currentConf[jj]) + (1+currentConf[jj]) * atom_lProbs[jj]; | |
| 454 | for(size_t kk = jj+1; kk < isotopeNo; kk++) | |
| 455 | logp += prob_partials[kk]; | |
| 456 | ||
| 457 | if (logp >= lCutOff) | |
| 458 | { | |
| 459 | auto tmp = allocator.makeCopy(currentConf); | |
| 460 | tmp[jj]++; | |
| 461 | configurations.push_back(tmp); | |
| 462 | lProbs.push_back(logp); | |
| 463 | } | |
| 478 | 464 | } |
| 479 | ||
| 480 | currentConf[jj]++; | |
| 465 | else | |
| 466 | prob_part_acc[jj+1] = prob_part_acc[jj] + prob_partials[jj]; | |
| 467 | ||
| 468 | if (currentConf[jj] > mode_conf[jj]) | |
| 469 | break; | |
| 481 | 470 | } |
| 471 | currentConf[ii]++; | |
| 472 | prob_partials[ii] = prev_partial_ii; | |
| 482 | 473 | } |
| 483 | currentConf[ii]--; | |
| 474 | ||
| 475 | if(currentConf[ii] < mode_conf[ii]) | |
| 476 | break; | |
| 484 | 477 | } |
| 485 | 478 | } |
| 486 | 479 | |
| 487 | // orderMarginal defines the order of configurations (compares their logprobs) | |
| 488 | // akin to key in Python sort. | |
| 489 | if(sort) | |
| 490 | std::sort(configurations.begin(), configurations.end(), orderMarginal); | |
| 491 | ||
| 492 | ||
| 493 | confs = &configurations[0]; | |
| 494 | 480 | no_confs = configurations.size(); |
| 495 | lProbs = new double[no_confs+1]; | |
| 481 | confs = configurations.data(); | |
| 482 | ||
| 483 | if(sort && no_confs > 0) | |
| 484 | { | |
| 485 | std::unique_ptr<size_t[]> order_arr(get_inverse_order(lProbs.data(), no_confs)); | |
| 486 | impose_order(order_arr.get(), no_confs, lProbs.data(), confs); | |
| 487 | } | |
| 488 | ||
| 496 | 489 | probs = new double[no_confs]; |
| 497 | 490 | masses = new double[no_confs]; |
| 498 | 491 | |
| 499 | 492 | |
| 500 | 493 | for(unsigned int ii = 0; ii < no_confs; ii++) |
| 501 | 494 | { |
| 502 | lProbs[ii] = logProb(confs[ii]); | |
| 503 | 495 | probs[ii] = exp(lProbs[ii]); |
| 504 | 496 | masses[ii] = calc_mass(confs[ii], atom_masses, isotopeNo); |
| 505 | 497 | } |
| 506 | lProbs[no_confs] = -std::numeric_limits<double>::infinity(); | |
| 498 | ||
| 499 | lProbs.push_back(-std::numeric_limits<double>::infinity()); | |
| 507 | 500 | } |
| 508 | 501 | |
| 509 | 502 | |
| 510 | 503 | PrecalculatedMarginal::~PrecalculatedMarginal() |
| 511 | 504 | { |
| 512 | if(lProbs != nullptr) | |
| 513 | delete[] lProbs; | |
| 514 | 505 | if(masses != nullptr) |
| 515 | 506 | delete[] masses; |
| 516 | 507 | if(probs != nullptr) |
| 523 | 514 | |
| 524 | 515 | |
| 525 | 516 | |
| 526 | LayeredMarginal::LayeredMarginal(Marginal&& m, int tabSize, int _hashSize) | |
| 517 | LayeredMarginal::LayeredMarginal(Marginal&& m, int tabSize, int) | |
| 527 | 518 | : Marginal(std::move(m)), current_threshold(1.0), allocator(isotopeNo, tabSize), |
| 528 | equalizer(isotopeNo), keyHasher(isotopeNo), orderMarginal(atom_lProbs, isotopeNo), hashSize(_hashSize) | |
| 519 | equalizer(isotopeNo), keyHasher(isotopeNo) | |
| 529 | 520 | { |
| 530 | 521 | fringe.push_back(mode_conf); |
| 531 | 522 | lProbs.push_back(std::numeric_limits<double>::infinity()); |
| 523 | fringe_unn_lprobs.push_back(unnormalized_logProb(mode_conf)); | |
| 532 | 524 | lProbs.push_back(-std::numeric_limits<double>::infinity()); |
| 533 | 525 | guarded_lProbs = lProbs.data()+1; |
| 534 | 526 | } |
| 535 | 527 | |
| 536 | 528 | bool LayeredMarginal::extend(double new_threshold, bool do_sort) |
| 537 | 529 | { |
| 530 | new_threshold -= loggamma_nominator; | |
| 538 | 531 | if(fringe.empty()) |
| 539 | 532 | return false; |
| 540 | 533 | |
| 541 | std::vector<Conf> new_fringe; | |
| 542 | std::unordered_set<Conf, KeyHasher, ConfEqual> visited(hashSize, keyHasher, equalizer); | |
| 543 | ||
| 544 | for(unsigned int ii = 0; ii < fringe.size(); ii++) | |
| 545 | visited.insert(fringe[ii]); | |
| 546 | ||
| 547 | Conf currentConf; | |
| 534 | lProbs.pop_back(); // Remove the +inf guardian | |
| 535 | ||
| 536 | pod_vector<Conf> new_fringe; | |
| 537 | pod_vector<double> new_fringe_unn_lprobs; | |
| 538 | ||
| 548 | 539 | while(!fringe.empty()) |
| 549 | 540 | { |
| 550 | currentConf = fringe.back(); | |
| 541 | Conf currentConf = fringe.back(); | |
| 551 | 542 | fringe.pop_back(); |
| 552 | 543 | |
| 553 | double opc = logProb(currentConf); | |
| 554 | ||
| 544 | double opc = fringe_unn_lprobs.back(); | |
| 545 | ||
| 546 | fringe_unn_lprobs.pop_back(); | |
| 555 | 547 | if(opc < new_threshold) |
| 548 | { | |
| 556 | 549 | new_fringe.push_back(currentConf); |
| 550 | new_fringe_unn_lprobs.push_back(opc); | |
| 551 | } | |
| 557 | 552 | |
| 558 | 553 | else |
| 559 | 554 | { |
| 560 | 555 | configurations.push_back(currentConf); |
| 556 | lProbs.push_back(opc+loggamma_nominator); | |
| 561 | 557 | for(unsigned int ii = 0; ii < isotopeNo; ii++ ) |
| 562 | 558 | { |
| 563 | currentConf[ii]++; | |
| 564 | for(unsigned int jj = 0; jj < isotopeNo; jj++ ) | |
| 559 | if(currentConf[ii] > mode_conf[ii]) | |
| 560 | continue; | |
| 561 | ||
| 562 | if(currentConf[ii] > 0) | |
| 565 | 563 | { |
| 566 | if( ii != jj && currentConf[jj] > 0 ) | |
| 564 | currentConf[ii]--; | |
| 565 | for(unsigned int jj = 0; jj < isotopeNo; jj++ ) | |
| 567 | 566 | { |
| 568 | currentConf[jj]--; | |
| 569 | ||
| 570 | double lpc = logProb(currentConf); | |
| 571 | ||
| 572 | if (lpc < current_threshold && | |
| 573 | (opc > lpc || (opc == lpc && ii > jj)) && visited.count(currentConf) == 0) | |
| 567 | if(currentConf[jj] < mode_conf[jj]) | |
| 568 | continue; | |
| 569 | ||
| 570 | if( ii != jj ) | |
| 574 | 571 | { |
| 575 | 572 | Conf nc = allocator.makeCopy(currentConf); |
| 576 | currentConf[ii]--; | |
| 577 | currentConf[jj]++; | |
| 578 | visited.insert(nc); | |
| 579 | currentConf[ii]++; | |
| 573 | nc[jj]++; | |
| 574 | ||
| 575 | double lpc = unnormalized_logProb(nc); | |
| 580 | 576 | if(lpc >= new_threshold) |
| 577 | { | |
| 581 | 578 | fringe.push_back(nc); |
| 579 | fringe_unn_lprobs.push_back(lpc); | |
| 580 | } | |
| 582 | 581 | else |
| 582 | { | |
| 583 | 583 | new_fringe.push_back(nc); |
| 584 | new_fringe_unn_lprobs.push_back(lpc); | |
| 585 | } | |
| 584 | 586 | } |
| 585 | else | |
| 586 | { | |
| 587 | currentConf[jj]++; | |
| 588 | } | |
| 587 | ||
| 588 | if(currentConf[jj] > mode_conf[jj]) | |
| 589 | break; | |
| 589 | 590 | } |
| 591 | currentConf[ii]++; | |
| 590 | 592 | } |
| 591 | currentConf[ii]--; | |
| 593 | ||
| 594 | if(currentConf[ii] < mode_conf[ii]) | |
| 595 | break; | |
| 592 | 596 | } |
| 593 | 597 | } |
| 594 | 598 | } |
| 595 | 599 | |
| 596 | 600 | current_threshold = new_threshold; |
| 597 | 601 | fringe.swap(new_fringe); |
| 602 | fringe_unn_lprobs.swap(new_fringe_unn_lprobs); | |
| 598 | 603 | |
| 599 | 604 | if(do_sort) |
| 600 | std::sort(configurations.begin()+probs.size(), configurations.end(), orderMarginal); | |
| 601 | ||
| 602 | if(lProbs.capacity() * 2 < configurations.size() + 2) | |
| 605 | { | |
| 606 | size_t to_sort_size = configurations.size() - probs.size(); | |
| 607 | if(to_sort_size > 0) | |
| 608 | { | |
| 609 | std::unique_ptr<size_t[]> order_arr(get_inverse_order(lProbs.data()+1+probs.size(), to_sort_size)); | |
| 610 | double* P = lProbs.data()+1+probs.size(); | |
| 611 | Conf* C = configurations.data()+probs.size(); | |
| 612 | size_t* O = order_arr.get(); | |
| 613 | impose_order(O, to_sort_size, P, C); | |
| 614 | } | |
| 615 | } | |
| 616 | ||
| 617 | if(probs.capacity() * 2 < configurations.size() + 2) | |
| 603 | 618 | { |
| 604 | 619 | // Reserve space for new values |
| 605 | lProbs.reserve(configurations.size()+2); | |
| 606 | 620 | probs.reserve(configurations.size()); |
| 607 | 621 | masses.reserve(configurations.size()); |
| 608 | 622 | } // Otherwise we're growing slowly enough that standard reallocations on push_back work better - we waste some extra memory |
| 609 | 623 | // but don't reallocate on every call |
| 610 | 624 | |
| 611 | lProbs.pop_back(); // The guardian... | |
| 612 | ||
| 625 | // printVector(lProbs); | |
| 613 | 626 | for(unsigned int ii = probs.size(); ii < configurations.size(); ii++) |
| 614 | 627 | { |
| 615 | lProbs.push_back(logProb(configurations[ii])); | |
| 616 | probs.push_back(exp(lProbs.back())); | |
| 628 | probs.push_back(exp(lProbs[ii+1])); | |
| 617 | 629 | masses.push_back(calc_mass(configurations[ii], atom_masses, isotopeNo)); |
| 618 | 630 | } |
| 619 | 631 | |
| 628 | 640 | double LayeredMarginal::get_min_mass() const |
| 629 | 641 | { |
| 630 | 642 | double ret = std::numeric_limits<double>::infinity(); |
| 631 | for(std::vector<double>::const_iterator it = masses.begin(); it != masses.end(); ++it) | |
| 643 | for(pod_vector<double>::const_iterator it = masses.cbegin(); it != masses.cend(); ++it) | |
| 632 | 644 | if(*it < ret) |
| 633 | 645 | ret = *it; |
| 634 | 646 | return ret; |
| 638 | 650 | double LayeredMarginal::get_max_mass() const |
| 639 | 651 | { |
| 640 | 652 | double ret = -std::numeric_limits<double>::infinity(); |
| 641 | for(std::vector<double>::const_iterator it = masses.begin(); it != masses.end(); ++it) | |
| 653 | for(pod_vector<double>::const_iterator it = masses.cbegin(); it != masses.cend(); ++it) | |
| 642 | 654 | if(*it > ret) |
| 643 | 655 | ret = *it; |
| 644 | 656 | return ret; |
| 15 | 15 | |
| 16 | 16 | #pragma once |
| 17 | 17 | |
| 18 | #include <unordered_map> | |
| 19 | 18 | #include <queue> |
| 20 | 19 | #include <algorithm> |
| 21 | 20 | #include <vector> |
| 21 | #include <functional> | |
| 22 | #include <utility> | |
| 22 | 23 | #include "conf.h" |
| 23 | 24 | #include "allocator.h" |
| 24 | 25 | #include "operators.h" |
| 25 | 26 | #include "summator.h" |
| 27 | #include "pod_vector.h" | |
| 26 | 28 | |
| 27 | 29 | |
| 28 | 30 | namespace IsoSpec |
| 173 | 175 | { |
| 174 | 176 | private: |
| 175 | 177 | int current_count; |
| 176 | const KeyHasher keyHasher; | |
| 177 | const ConfEqual equalizer; | |
| 178 | 178 | const ConfOrderMarginal orderMarginal; |
| 179 | std::unordered_map<Conf, int, KeyHasher, ConfEqual> visited; | |
| 180 | std::priority_queue<Conf, std::vector<Conf>, ConfOrderMarginal> pq; | |
| 181 | Summator totalProb; | |
| 182 | Conf candidate; | |
| 179 | std::priority_queue<ProbAndConfPtr, pod_vector<ProbAndConfPtr> > pq; | |
| 183 | 180 | Allocator<int> allocator; |
| 184 | std::vector<double> _conf_lprobs; | |
| 185 | std::vector<double> _conf_masses; | |
| 186 | std::vector<int*> _confs; | |
| 181 | pod_vector<double> _conf_lprobs; | |
| 182 | pod_vector<double> _conf_masses; | |
| 183 | pod_vector<int*> _confs; | |
| 187 | 184 | |
| 188 | 185 | //! Proceed to the next configuration and memoize it (as it will be surely needed). |
| 189 | 186 | bool add_next_conf(); |
| 225 | 222 | inline double getModeLProb() const { return mode_lprob; } |
| 226 | 223 | |
| 227 | 224 | |
| 228 | //! Calculate subisotopologues with probability above or equal to the cut-off. | |
| 229 | /*! | |
| 230 | \param cutoff The probability cut-off | |
| 231 | \return The number of the last subisotopologue above the cut-off. | |
| 232 | */ | |
| 233 | int processUntilCutoff(double cutoff); | |
| 234 | ||
| 235 | inline const std::vector<double>& conf_lprobs() const { return _conf_lprobs; } | |
| 236 | inline const std::vector<double>& conf_masses() const { return _conf_masses; } | |
| 237 | inline const std::vector<int*>& confs() const { return _confs; } | |
| 225 | inline const pod_vector<double>& conf_lprobs() const { return _conf_lprobs; } | |
| 226 | inline const pod_vector<double>& conf_masses() const { return _conf_masses; } | |
| 227 | inline const pod_vector<Conf>& confs() const { return _confs; } | |
| 238 | 228 | |
| 239 | 229 | |
| 240 | 230 | virtual ~MarginalTrek(); |
| 253 | 243 | class PrecalculatedMarginal : public Marginal |
| 254 | 244 | { |
| 255 | 245 | protected: |
| 256 | std::vector<Conf> configurations; | |
| 246 | pod_vector<Conf> configurations; | |
| 257 | 247 | Conf* confs; |
| 258 | 248 | unsigned int no_confs; |
| 259 | 249 | double* masses; |
| 260 | double* lProbs; | |
| 250 | pod_vector<double> lProbs; | |
| 261 | 251 | double* probs; |
| 262 | 252 | Allocator<int> allocator; |
| 263 | 253 | public: |
| 314 | 304 | /*! |
| 315 | 305 | \return Pointer to the first element in the table storing log-probabilities of subisotopologues. |
| 316 | 306 | */ |
| 317 | inline const double* get_lProbs_ptr() const { return lProbs; } | |
| 307 | inline const double* get_lProbs_ptr() const { return lProbs.data(); } | |
| 318 | 308 | |
| 319 | 309 | //! Get the table of the masses of subisotopologues. |
| 320 | 310 | /*! |
| 353 | 343 | { |
| 354 | 344 | private: |
| 355 | 345 | double current_threshold; |
| 356 | std::vector<Conf> configurations; | |
| 357 | std::vector<Conf> fringe; | |
| 346 | pod_vector<Conf> configurations; | |
| 347 | pod_vector<Conf> fringe; | |
| 348 | pod_vector<double> fringe_unn_lprobs; | |
| 358 | 349 | Allocator<int> allocator; |
| 359 | 350 | const ConfEqual equalizer; |
| 360 | 351 | const KeyHasher keyHasher; |
| 361 | const ConfOrderMarginalDescending orderMarginal; | |
| 362 | std::vector<double> lProbs; | |
| 363 | std::vector<double> probs; | |
| 364 | std::vector<double> masses; | |
| 352 | pod_vector<double> lProbs; | |
| 353 | pod_vector<double> probs; | |
| 354 | pod_vector<double> masses; | |
| 365 | 355 | double* guarded_lProbs; |
| 366 | const int hashSize; | |
| 367 | 356 | |
| 368 | 357 | public: |
| 369 | 358 | //! Move constructor: specializes the Marginal class. |
| 18 | 18 | #include <iostream> |
| 19 | 19 | #include <vector> |
| 20 | 20 | #include <cstring> |
| 21 | #include <algorithm> | |
| 21 | 22 | #include "isoMath.h" |
| 23 | #include "pod_vector.h" | |
| 22 | 24 | |
| 23 | 25 | namespace IsoSpec |
| 24 | 26 | { |
| 25 | 27 | |
| 26 | 28 | inline double combinedSum( |
| 27 | 29 | const int* conf, const std::vector<double>** valuesContainer, int dimNumber |
| 30 | ){ | |
| 31 | double res = 0.0; | |
| 32 | for(int i = 0; i < dimNumber; i++) | |
| 33 | res += (*(valuesContainer[i]))[conf[i]]; | |
| 34 | return res; | |
| 35 | } | |
| 36 | ||
| 37 | inline double combinedSum( | |
| 38 | const int* conf, const pod_vector<double>** valuesContainer, int dimNumber | |
| 28 | 39 | ){ |
| 29 | 40 | double res = 0.0; |
| 30 | 41 | for(int i = 0; i < dimNumber; i++) |
| 136 | 147 | *array = newT; |
| 137 | 148 | } |
| 138 | 149 | |
| 150 | template<typename T> size_t* get_order(T* order_array, size_t N) | |
| 151 | { | |
| 152 | size_t* arr = new size_t[N]; | |
| 153 | for(size_t ii = 0; ii < N; ii++) | |
| 154 | arr[ii] = ii; | |
| 155 | ||
| 156 | std::sort(arr, arr + N, [&](int i, int j) { return order_array[i] < order_array[j]; }); | |
| 157 | ||
| 158 | return arr; | |
| 159 | } | |
| 160 | ||
| 161 | template<typename T> size_t* get_inverse_order(T* order_array, size_t N) | |
| 162 | { | |
| 163 | size_t* arr = new size_t[N]; | |
| 164 | for(size_t ii = 0; ii < N; ii++) | |
| 165 | arr[ii] = ii; | |
| 166 | ||
| 167 | std::sort(arr, arr + N, [&](int i, int j) { return order_array[i] > order_array[j]; }); | |
| 168 | ||
| 169 | return arr; | |
| 170 | } | |
| 171 | ||
| 172 | template<typename TA, typename TB> void impose_order(size_t* O, size_t N, TA* A, TB* B) | |
| 173 | { | |
| 174 | for(size_t ii = 0; ii < N; ii++) | |
| 175 | { | |
| 176 | if(ii != O[ii]) | |
| 177 | { | |
| 178 | size_t curr_ii = ii; | |
| 179 | TA ta = A[ii]; | |
| 180 | TB tb = B[ii]; | |
| 181 | size_t next_ii = O[ii]; | |
| 182 | while(next_ii != ii) | |
| 183 | { | |
| 184 | A[curr_ii] = A[next_ii]; | |
| 185 | B[curr_ii] = B[next_ii]; | |
| 186 | O[curr_ii] = curr_ii; | |
| 187 | curr_ii = next_ii; | |
| 188 | next_ii = O[next_ii]; | |
| 189 | } | |
| 190 | A[curr_ii] = ta; | |
| 191 | B[curr_ii] = tb; | |
| 192 | O[curr_ii] = curr_ii; | |
| 193 | } | |
| 194 | } | |
| 195 | } | |
| 196 | ||
| 197 | ||
| 139 | 198 | } // namespace IsoSpec |
| 92 | 92 | #define ISOSPEC_FORCE_INLINE inline |
| 93 | 93 | #endif |
| 94 | 94 | |
| 95 | #if ISOSPEC_DEBUG | |
| 95 | #ifdef ISOSPEC_DEBUG | |
| 96 | 96 | #undef ISOSPEC_IMPOSSIBLE |
| 97 | 97 | #include <cassert> |
| 98 | 98 | #define ISOSPEC_IMPOSSIBLE(condition) assert(!(condition)); |
| 0 | /*! | |
| 1 | Copyright (C) 2015-2020 Mateusz Łącki and Michał Startek. | |
| 2 | ||
| 3 | This file is part of IsoSpec. | |
| 4 | ||
| 5 | IsoSpec is free software: you can redistribute it and/or modify | |
| 6 | it under the terms of the Simplified ("2-clause") BSD licence. | |
| 7 | ||
| 8 | IsoSpec is distributed in the hope that it will be useful, | |
| 9 | but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 10 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. | |
| 11 | ||
| 12 | You should have received a copy of the Simplified BSD Licence | |
| 13 | along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>. | |
| 14 | */ | |
| 15 | ||
| 16 | #pragma once | |
| 17 | ||
| 18 | #include <type_traits> | |
| 19 | #include <cstdlib> | |
| 20 | #include <utility> | |
| 21 | #include <new> | |
| 22 | #include <algorithm> | |
| 23 | #include "platform.h" | |
| 24 | ||
| 25 | ||
| 26 | ||
| 27 | template<typename T> class unsafe_pod_vector; | |
| 28 | ||
| 29 | template<typename T> class pod_vector | |
| 30 | { | |
| 31 | #if !ISOSPEC_BUILDING_R | |
| 32 | static_assert(std::is_trivially_copyable<T>::value, "Cannot use a pod_vector with a non-Plain Old Data type."); | |
| 33 | #endif | |
| 34 | ||
| 35 | T* backend_past_end; | |
| 36 | T* first_free; | |
| 37 | T* store; | |
| 38 | ||
| 39 | public: | |
| 40 | explicit pod_vector(size_t initial_size = 16) | |
| 41 | { | |
| 42 | store = reinterpret_cast<T*>(malloc(sizeof(T) * initial_size)); | |
| 43 | if(store == NULL) | |
| 44 | throw std::bad_alloc(); | |
| 45 | first_free = store; | |
| 46 | backend_past_end = store + initial_size; | |
| 47 | } | |
| 48 | ||
| 49 | pod_vector(const pod_vector<T>& other) = delete; | |
| 50 | pod_vector& operator=(const pod_vector<T>& other) = delete; | |
| 51 | ||
| 52 | pod_vector(pod_vector<T>&& other) | |
| 53 | { | |
| 54 | backend_past_end = other.backend_past_end; | |
| 55 | first_free = other.first_free; | |
| 56 | store = other.store; | |
| 57 | other.backend_past_end = other.first_free = other.store = NULL; | |
| 58 | } | |
| 59 | ||
| 60 | ~pod_vector() { free(store); } | |
| 61 | ||
| 62 | explicit pod_vector(unsafe_pod_vector<T>&& other) | |
| 63 | { | |
| 64 | backend_past_end = other.backend_past_end; | |
| 65 | first_free = other.first_free; | |
| 66 | store = other.store; | |
| 67 | } | |
| 68 | ||
| 69 | void fast_reserve(size_t n) | |
| 70 | { | |
| 71 | ISOSPEC_IMPOSSIBLE(n < static_cast<size_t>(backend_past_end - store)); | |
| 72 | T* new_store = reinterpret_cast<T*>(realloc(store, n * sizeof(T))); | |
| 73 | if(new_store == NULL) | |
| 74 | throw std::bad_alloc(); | |
| 75 | first_free = new_store + (first_free - store); | |
| 76 | backend_past_end = new_store + n; | |
| 77 | store = new_store; | |
| 78 | } | |
| 79 | ||
| 80 | void reserve(size_t n) | |
| 81 | { | |
| 82 | if (n > static_cast<size_t>(backend_past_end - store)) | |
| 83 | fast_reserve(n); | |
| 84 | } | |
| 85 | ||
| 86 | ISOSPEC_FORCE_INLINE void nocheck_push_back(const T& val) noexcept | |
| 87 | { | |
| 88 | ISOSPEC_IMPOSSIBLE(first_free >= backend_past_end); | |
| 89 | *first_free = val; | |
| 90 | first_free++; | |
| 91 | } | |
| 92 | ||
| 93 | ISOSPEC_FORCE_INLINE void push_back(const T& val) | |
| 94 | { | |
| 95 | if(first_free >= backend_past_end) | |
| 96 | fast_reserve((std::max<std::ptrdiff_t>)(4, (backend_past_end-store)) * 2); | |
| 97 | *first_free = val; | |
| 98 | first_free++; | |
| 99 | } | |
| 100 | ||
| 101 | ISOSPEC_FORCE_INLINE T& operator[](size_t n) noexcept | |
| 102 | { | |
| 103 | ISOSPEC_IMPOSSIBLE(store + n >= first_free); | |
| 104 | return store[n]; | |
| 105 | } | |
| 106 | ||
| 107 | ISOSPEC_FORCE_INLINE const T& operator[](size_t n) const noexcept | |
| 108 | { | |
| 109 | ISOSPEC_IMPOSSIBLE(store + n >= first_free); | |
| 110 | return store[n]; | |
| 111 | } | |
| 112 | ||
| 113 | ISOSPEC_FORCE_INLINE size_t size() const noexcept | |
| 114 | { | |
| 115 | return first_free - store; | |
| 116 | } | |
| 117 | ||
| 118 | ISOSPEC_FORCE_INLINE size_t capacity() const noexcept | |
| 119 | { | |
| 120 | return backend_past_end - store; | |
| 121 | } | |
| 122 | ||
| 123 | ISOSPEC_FORCE_INLINE T* data() noexcept | |
| 124 | { | |
| 125 | return store; | |
| 126 | } | |
| 127 | ||
| 128 | ISOSPEC_FORCE_INLINE const T* data() const noexcept | |
| 129 | { | |
| 130 | return store; | |
| 131 | } | |
| 132 | ||
| 133 | ISOSPEC_FORCE_INLINE bool empty() const noexcept | |
| 134 | { | |
| 135 | return first_free == store; | |
| 136 | } | |
| 137 | ||
| 138 | ISOSPEC_FORCE_INLINE const T& back() const noexcept | |
| 139 | { | |
| 140 | ISOSPEC_IMPOSSIBLE(first_free > backend_past_end); | |
| 141 | return *(first_free-1); | |
| 142 | } | |
| 143 | ||
| 144 | ISOSPEC_FORCE_INLINE void pop_back() noexcept | |
| 145 | { | |
| 146 | // Unlike std::vector we do not ever shrink backend storage unless explicitly requested. | |
| 147 | ISOSPEC_IMPOSSIBLE(first_free == store); | |
| 148 | first_free--; | |
| 149 | } | |
| 150 | ||
| 151 | void swap(pod_vector<T>& other) noexcept | |
| 152 | { | |
| 153 | std::swap(backend_past_end, other.backend_past_end); | |
| 154 | std::swap(first_free, other.first_free); | |
| 155 | std::swap(store, other.store); | |
| 156 | } | |
| 157 | ||
| 158 | typedef T* iterator; | |
| 159 | typedef const T* const_iterator; | |
| 160 | typedef T value_type; | |
| 161 | typedef size_t size_type; | |
| 162 | typedef T& reference; | |
| 163 | typedef const T& const_reference; | |
| 164 | ||
| 165 | iterator begin() noexcept { return store; }; | |
| 166 | const_iterator begin() const noexcept { return store; } | |
| 167 | const_iterator cbegin() const noexcept { return store; } | |
| 168 | iterator end() noexcept { return first_free; } | |
| 169 | const_iterator end() const noexcept { return first_free; } | |
| 170 | const_iterator cend() const noexcept { return first_free; } | |
| 171 | ||
| 172 | ISOSPEC_FORCE_INLINE const T& front() const noexcept | |
| 173 | { | |
| 174 | ISOSPEC_IMPOSSIBLE(store == first_free); | |
| 175 | return *store; | |
| 176 | } | |
| 177 | ||
| 178 | void clear() | |
| 179 | { | |
| 180 | free(store); | |
| 181 | first_free = store = backend_past_end = NULL; | |
| 182 | } | |
| 183 | ||
| 184 | friend class unsafe_pod_vector<T>; | |
| 185 | }; | |
| 186 | ||
| 187 | ||
| 188 | template<typename T> class unsafe_pod_vector | |
| 189 | { | |
| 190 | #if !ISOSPEC_BUILDING_R | |
| 191 | static_assert(std::is_trivially_copyable<T>::value, "Cannot use a pod_vector with a non-Plain Old Data type."); | |
| 192 | static_assert(std::is_trivially_copyable<unsafe_pod_vector<T> >::value, "Cannot use a pod_vector with a non-Plain Old Data type."); | |
| 193 | #endif | |
| 194 | ||
| 195 | T* backend_past_end; | |
| 196 | T* first_free; | |
| 197 | T* store; | |
| 198 | ||
| 199 | public: | |
| 200 | unsafe_pod_vector() = default; | |
| 201 | ||
| 202 | void init() { memset(this, 0, sizeof(*this)); } | |
| 203 | ||
| 204 | void init(size_t initial_size) | |
| 205 | { | |
| 206 | store = reinterpret_cast<T*>(malloc(sizeof(T) * initial_size)); | |
| 207 | if(store == NULL) | |
| 208 | throw std::bad_alloc(); | |
| 209 | first_free = store; | |
| 210 | backend_past_end = store + initial_size; | |
| 211 | } | |
| 212 | ||
| 213 | unsafe_pod_vector(const pod_vector<T>& other) = delete; // NOLINT(runtime/explicit) - seriously? Deleted constructors have to be marked explicit? | |
| 214 | unsafe_pod_vector& operator=(const pod_vector<T>& other) = delete; | |
| 215 | ||
| 216 | unsafe_pod_vector(unsafe_pod_vector<T>&& other) | |
| 217 | { | |
| 218 | memcpy(this, *other, sizeof(*this)); | |
| 219 | } | |
| 220 | ||
| 221 | ~unsafe_pod_vector() = default; | |
| 222 | ||
| 223 | void free() { free(store); } | |
| 224 | ||
| 225 | void fast_reserve(size_t n) | |
| 226 | { | |
| 227 | ISOSPEC_IMPOSSIBLE(n < static_cast<size_t>(backend_past_end - store)); | |
| 228 | T* new_store = reinterpret_cast<T*>(realloc(store, n * sizeof(T))); | |
| 229 | if(new_store == NULL) | |
| 230 | throw std::bad_alloc(); | |
| 231 | first_free = new_store + (first_free - store); | |
| 232 | backend_past_end = new_store + n; | |
| 233 | store = new_store; | |
| 234 | } | |
| 235 | ||
| 236 | void reserve(size_t n) | |
| 237 | { | |
| 238 | if (n > backend_past_end - store) | |
| 239 | fast_reserve(n); | |
| 240 | } | |
| 241 | ||
| 242 | void resize(size_t new_size) | |
| 243 | { | |
| 244 | ISOSPEC_IMPOSSIBLE(new_size < first_free - store); | |
| 245 | size_t cap = capacity(); | |
| 246 | if(cap < new_size) | |
| 247 | { | |
| 248 | do { | |
| 249 | cap = cap * 2; | |
| 250 | } while(cap < new_size); | |
| 251 | fast_reserve(cap); | |
| 252 | } | |
| 253 | first_free = store + new_size; | |
| 254 | } | |
| 255 | ||
| 256 | void resize_and_wipe(size_t new_size) | |
| 257 | { | |
| 258 | size_t old_size = size(); | |
| 259 | ISOSPEC_IMPOSSIBLE(new_size < old_size); | |
| 260 | resize(new_size); | |
| 261 | memset(store+old_size, 0, (new_size-old_size) * sizeof(T)); | |
| 262 | } | |
| 263 | ||
| 264 | ISOSPEC_FORCE_INLINE void nocheck_push_back(const T& val) noexcept | |
| 265 | { | |
| 266 | ISOSPEC_IMPOSSIBLE(first_free >= backend_past_end); | |
| 267 | *first_free = val; | |
| 268 | first_free++; | |
| 269 | } | |
| 270 | ||
| 271 | ISOSPEC_FORCE_INLINE void push_back(const T& val) | |
| 272 | { | |
| 273 | if(first_free >= backend_past_end) | |
| 274 | fast_reserve((std::max<std::ptrdiff_t>)(4, (backend_past_end-store)) * 2); | |
| 275 | *first_free = val; | |
| 276 | first_free++; | |
| 277 | } | |
| 278 | ||
| 279 | ISOSPEC_FORCE_INLINE T& operator[](size_t n) noexcept | |
| 280 | { | |
| 281 | ISOSPEC_IMPOSSIBLE(store + n >= first_free); | |
| 282 | return store[n]; | |
| 283 | } | |
| 284 | ||
| 285 | ISOSPEC_FORCE_INLINE const T& operator[](size_t n) const noexcept | |
| 286 | { | |
| 287 | ISOSPEC_IMPOSSIBLE(store + n >= first_free); | |
| 288 | return store[n]; | |
| 289 | } | |
| 290 | ||
| 291 | ISOSPEC_FORCE_INLINE size_t size() const noexcept | |
| 292 | { | |
| 293 | return first_free - store; | |
| 294 | } | |
| 295 | ||
| 296 | ISOSPEC_FORCE_INLINE size_t capacity() const noexcept | |
| 297 | { | |
| 298 | return backend_past_end - store; | |
| 299 | } | |
| 300 | ||
| 301 | ISOSPEC_FORCE_INLINE T* data() noexcept | |
| 302 | { | |
| 303 | return store; | |
| 304 | } | |
| 305 | ||
| 306 | ISOSPEC_FORCE_INLINE const T* data() const noexcept | |
| 307 | { | |
| 308 | return store; | |
| 309 | } | |
| 310 | ||
| 311 | ISOSPEC_FORCE_INLINE bool empty() const noexcept | |
| 312 | { | |
| 313 | return first_free == store; | |
| 314 | } | |
| 315 | ||
| 316 | ISOSPEC_FORCE_INLINE const T& back() const noexcept | |
| 317 | { | |
| 318 | ISOSPEC_IMPOSSIBLE(first_free > backend_past_end); | |
| 319 | return *(first_free-1); | |
| 320 | } | |
| 321 | ||
| 322 | ISOSPEC_FORCE_INLINE void pop_back() noexcept | |
| 323 | { | |
| 324 | // Unlike std::vector we do not ever shrink backend storage unless explicitly requested. | |
| 325 | ISOSPEC_IMPOSSIBLE(first_free == store); | |
| 326 | first_free--; | |
| 327 | } | |
| 328 | ||
| 329 | void swap(pod_vector<T>& other) noexcept | |
| 330 | { | |
| 331 | std::swap(backend_past_end, other.backend_past_end); | |
| 332 | std::swap(first_free, other.first_free); | |
| 333 | std::swap(store, other.store); | |
| 334 | } | |
| 335 | ||
| 336 | typedef T* iterator; | |
| 337 | typedef const T* const_iterator; | |
| 338 | typedef T value_type; | |
| 339 | typedef size_t size_type; | |
| 340 | typedef T& reference; | |
| 341 | typedef const T& const_reference; | |
| 342 | ||
| 343 | iterator begin() noexcept { return store; }; | |
| 344 | const_iterator begin() const noexcept { return store; } | |
| 345 | const_iterator cbegin() const noexcept { return store; } | |
| 346 | iterator end() noexcept { return first_free; } | |
| 347 | const_iterator end() const noexcept { return first_free; } | |
| 348 | const_iterator cend() const noexcept { return first_free; } | |
| 349 | ||
| 350 | ISOSPEC_FORCE_INLINE const T& front() const noexcept | |
| 351 | { | |
| 352 | ISOSPEC_IMPOSSIBLE(store == first_free); | |
| 353 | return *store; | |
| 354 | } | |
| 355 | ||
| 356 | void clear() | |
| 357 | { | |
| 358 | free(store); | |
| 359 | first_free = store = backend_past_end = NULL; | |
| 360 | } | |
| 361 | ||
| 362 | friend class pod_vector<T>; | |
| 363 | }; | |
| 364 |
| 27 | 27 | except NameError: |
| 28 | 28 | xrange = range |
| 29 | 29 | |
| 30 | regex_pattern = re.compile('([A-Z][a-z]?)([0-9]*)') | |
| 30 | regex_pattern = re.compile('([A-Z][a-z]?)(-?[0-9]*)') | |
| 31 | 31 | ParsedFormula = namedtuple('ParsedFormula', 'atomCounts masses probs elems') |
| 32 | 32 | |
| 33 | 33 | |
| 145 | 145 | for symbol, count in df.items(): |
| 146 | 146 | molecule[symbol] = molecule.get(symbol, 0) + count |
| 147 | 147 | |
| 148 | for sym, cnt in molecule.items(): | |
| 149 | if cnt < 0: | |
| 150 | raise Exception("Negative count of element " + sym + ": " + str(cnt)) | |
| 148 | 151 | |
| 149 | 152 | if len(molecule) == 0 and not all([atomCounts, isotopeMasses, isotopeProbabilities]): |
| 150 | 153 | raise Exception("Either formula, fasta or ALL of: atomCounts, isotopeMasses, isotopeProbabilities must not be None") |
| 383 | 386 | self._total_prob = float('nan') |
| 384 | 387 | self.mass_sorted = False |
| 385 | 388 | self.prob_sorted = False |
| 389 | ||
| 390 | def empiric_average_mass(self): | |
| 391 | co = self._get_cobject() | |
| 392 | ret = isoFFI.clib.empiricAverageMass(co) | |
| 393 | isoFFI.clib.deleteFixedEnvelope(co, True) | |
| 394 | return ret | |
| 395 | ||
| 396 | def empiric_variance(self): | |
| 397 | co = self._get_cobject() | |
| 398 | ret = isoFFI.clib.empiricVariance(co) | |
| 399 | isoFFI.clib.deleteFixedEnvelope(co, True) | |
| 400 | return ret | |
| 401 | ||
| 402 | def empiric_stddev(self): | |
| 403 | co = self._get_cobject() | |
| 404 | ret = isoFFI.clib.empiricStddev(co) | |
| 405 | isoFFI.clib.deleteFixedEnvelope(co, True) | |
| 406 | return ret | |
| 386 | 407 | |
| 387 | 408 | def wassersteinDistance(self, other): |
| 388 | 409 | x = self._get_cobject() |
| 0 | 0 | from .IsoSpecPy import * |
| 1 | 1 | |
| 2 | 2 | |
| 3 | __version__ = "2.1.0" | |
| 3 | __version__ = "2.1.1" | |
| 4 | 4 | |
| 5 | 5 | # Old, deprecated name, for compatibility with 1.9.X only |
| 6 | 6 | IsoLayered = IsoTotalProb |
| 74 | 74 | const int* confsFixedEnvelope(void* tabulator); |
| 75 | 75 | int confs_noFixedEnvelope(void* tabulator); |
| 76 | 76 | |
| 77 | double empiricAverageMass(void* tabulator); | |
| 78 | double empiricVariance(void* tabulator); | |
| 79 | double empiricStddev(void* tabulator); | |
| 80 | ||
| 77 | 81 | double wassersteinDistance(void* tabulator1, void* tabulator2); |
| 78 | 82 | double orientedWassersteinDistance(void* tabulator1, void* tabulator2); |
| 79 | 83 | |
| 142 | 146 | |
| 143 | 147 | paths_to_check = sum(map(glob.glob, paths_to_check), []) |
| 144 | 148 | |
| 149 | try: | |
| 150 | import importlib | |
| 151 | paths_to_check.insert(0, importlib.util.find_spec("IsoSpecCppPy").origin) | |
| 152 | except (ImportError, AttributeError): | |
| 153 | pass | |
| 154 | ||
| 145 | 155 | errors = [] |
| 146 | 156 | |
| 147 | 157 | self.clib = None |
| 52 | 52 | # Versions should comply with PEP440. For a discussion on single-sourcing |
| 53 | 53 | # the version across setup.py and the project code, see |
| 54 | 54 | # https://packaging.python.org/en/latest/single_source_version.html |
| 55 | 'version': '2.1.0', | |
| 55 | 'version': '2.1.1', | |
| 56 | 56 | |
| 57 | 57 | 'description': 'Python interface to IsoSpec++ isotopic envelope calculator library', |
| 58 | 58 | 'long_description': 'Python interface to IsoSpec++ isotopic envelope calculator library', |
| 1 | 1 | Package: IsoSpecR |
| 2 | 2 | Type: Package |
| 3 | 3 | Title: The IsoSpec Algorithm |
| 4 | Version: 2.1.0 | |
| 5 | Date: 2020-05-27 | |
| 4 | Version: 2.1.2 | |
| 5 | Date: 2020-07-14 | |
| 6 | 6 | Author: Mateusz Krzysztof Lacki and Michal Startek |
| 7 | 7 | Maintainer: Matteo Lacki <matteo.lacki@gmail.com> |
| 8 | 8 | Description: IsoSpec is a fine structure calculator used for obtaining the most |
| 0 | 0 | citHeader("To cite IsoSpecR in publications use:") |
| 1 | ||
| 2 | citEntry(entry = "Article", | |
| 3 | title = "{IsoSpec2}: Ultrafast Fine Structure Calculator", | |
| 4 | author = personList(as.person("Mateusz K. Łącki"), as.person("Dirk Valkenborg"), as.person("Michał Startek")), | |
| 5 | year = "2020", | |
| 6 | journal = "Analytical Chemistry", | |
| 7 | volume = "Published online ahead of print", | |
| 8 | doi = "10.1021/acs.analchem.0c00959", | |
| 9 | url = "https://doi.org/10.1021/acs.analchem.0c00959", | |
| 10 | ||
| 11 | textVersion = paste("Mateusz K. Łącki, Dirk Valkenborg, Michał Startek (2020).", | |
| 12 | "IsoSpec2: Ultrafast Fine Structure Calculator", | |
| 13 | "Analytical Chemistry, Published online ahead of print", | |
| 14 | "URL https://doi.org/10.1021/acs.analchem.0c00959") | |
| 15 | ) | |
| 1 | 16 | |
| 2 | 17 | citEntry(entry = "Article", |
| 3 | 18 | title = "{IsoSpec}: Hyperfast Fine Structure Calculator", |
| 20 | 20 | { |
| 21 | 21 | |
| 22 | 22 | template <typename T> |
| 23 | Allocator<T>::Allocator(const int dim_, const int tabSize_): currentId(-1), dim(dim_), tabSize(tabSize_) | |
| 24 | { | |
| 25 | currentTab = new T[dim * tabSize]; | |
| 26 | } | |
| 23 | Allocator<T>::Allocator(const int dim_, const int tabSize_): currentTab(new T[dim_ * tabSize_]), currentId(-1), dim(dim_), tabSize(tabSize_) {} | |
| 24 | ||
| 27 | 25 | |
| 28 | 26 | template <typename T> |
| 29 | 27 | Allocator<T>::~Allocator() |
| 30 | 28 | { |
| 31 | for(unsigned int i = 0; i < prevTabs.size(); ++i) | |
| 29 | if(prevTabs.size() == 0 || currentTab != prevTabs.back()) | |
| 32 | 30 | { |
| 33 | delete [] prevTabs[i]; | |
| 31 | // It will be equal only if shiftTables throws during new[] | |
| 32 | // Make sure we don't del currentTab twice in that case | |
| 33 | delete [] currentTab; | |
| 34 | 34 | } |
| 35 | 35 | |
| 36 | delete [] currentTab; | |
| 36 | for(unsigned int i = 0; i < prevTabs.size(); ++i) | |
| 37 | delete [] prevTabs[i]; | |
| 37 | 38 | } |
| 38 | 39 | |
| 39 | 40 | template <typename T> |
| 15 | 15 | |
| 16 | 16 | #pragma once |
| 17 | 17 | |
| 18 | #include <vector> | |
| 19 | 18 | #include <cstring> |
| 20 | 19 | #include "conf.h" |
| 20 | #include "pod_vector.h" | |
| 21 | 21 | |
| 22 | 22 | namespace IsoSpec |
| 23 | 23 | { |
| 35 | 35 | T* currentTab; |
| 36 | 36 | int currentId; |
| 37 | 37 | const int dim, tabSize; |
| 38 | std::vector<T*> prevTabs; | |
| 38 | pod_vector<T*> prevTabs; | |
| 39 | 39 | |
| 40 | 40 | public: |
| 41 | 41 | explicit Allocator(const int dim, const int tabSize = 10000); |
| 20 | 20 | |
| 21 | 21 | typedef int* Conf; |
| 22 | 22 | |
| 23 | } | |
| 23 | struct ProbAndConfPtr | |
| 24 | { | |
| 25 | // For some reason std::pair isn't trivially copyable... | |
| 26 | double first; | |
| 27 | Conf second; | |
| 24 | 28 | |
| 29 | ProbAndConfPtr(double p, Conf c) : first(p), second(c) {} | |
| 30 | ||
| 31 | bool operator<(const ProbAndConfPtr& other) const | |
| 32 | { | |
| 33 | return first < other.first; | |
| 34 | } | |
| 35 | }; | |
| 36 | ||
| 37 | } // namespace IsoSpec |
| 98 | 98 | { |
| 99 | 99 | Iso* i = reinterpret_cast<Iso*>(iso); |
| 100 | 100 | double* ret = reinterpret_cast<double*>(malloc(sizeof(double)*i->getDimNumber())); |
| 101 | i->saveMarginalLogSizeEstimates(ret, target_total_prob); | |
| 101 | if(ret != nullptr) | |
| 102 | i->saveMarginalLogSizeEstimates(ret, target_total_prob); | |
| 102 | 103 | return ret; |
| 103 | 104 | } |
| 104 | 105 | |
| 264 | 265 | return reinterpret_cast<FixedEnvelope*>(tabulator)->confs_no(); |
| 265 | 266 | } |
| 266 | 267 | |
| 268 | double empiricAverageMass(void* tabulator) | |
| 269 | { | |
| 270 | return reinterpret_cast<FixedEnvelope*>(tabulator)->empiric_average_mass(); | |
| 271 | } | |
| 272 | ||
| 273 | double empiricVariance(void* tabulator) | |
| 274 | { | |
| 275 | return reinterpret_cast<FixedEnvelope*>(tabulator)->empiric_variance(); | |
| 276 | } | |
| 277 | ||
| 278 | double empiricStddev(void* tabulator) | |
| 279 | { | |
| 280 | return reinterpret_cast<FixedEnvelope*>(tabulator)->empiric_stddev(); | |
| 281 | } | |
| 282 | ||
| 267 | 283 | double wassersteinDistance(void* tabulator1, void* tabulator2) |
| 268 | 284 | { |
| 269 | 285 | try |
| 348 | 364 | // Same thing, only this time with C linkage |
| 349 | 365 | parse_fasta(fasta, atomCounts); |
| 350 | 366 | } |
| 351 | ||
| 352 | 367 | } // extern "C" ends here |
| 117 | 117 | const int* confsFixedEnvelope(void* tabulator); |
| 118 | 118 | int confs_noFixedEnvelope(void* tabulator); |
| 119 | 119 | |
| 120 | double empiricAverageMass(void* tabulator); | |
| 121 | double empiricVariance(void* tabulator); | |
| 122 | double empiricStddev(void* tabulator); | |
| 123 | ||
| 120 | 124 | double wassersteinDistance(void* tabulator1, void* tabulator2); |
| 121 | 125 | double orientedWassersteinDistance(void* tabulator1, void* tabulator2); |
| 122 | 126 | void* addEnvelopes(void* tabulator1, void* tabulator2); |
| 14 | 14 | */ |
| 15 | 15 | |
| 16 | 16 | |
| 17 | #include <stdlib.h> | |
| 17 | #include <cstdlib> | |
| 18 | 18 | #include "dirtyAllocator.h" |
| 19 | 19 | |
| 20 | 20 | namespace IsoSpec |
| 29 | 29 | if(cellSize % sizeof(double) != 0) |
| 30 | 30 | cellSize += sizeof(double) - cellSize % sizeof(double); |
| 31 | 31 | currentTab = malloc( cellSize * tabSize ); |
| 32 | if(currentTab == NULL) | |
| 33 | throw std::bad_alloc(); | |
| 32 | 34 | currentConf = currentTab; |
| 33 | 35 | endOfTablePtr = reinterpret_cast<char*>(currentTab) + cellSize*tabSize; |
| 34 | 36 | } |
| 46 | 48 | |
| 47 | 49 | currentTab = malloc( cellSize * tabSize ); |
| 48 | 50 | currentConf = currentTab; |
| 51 | if(currentTab == NULL) | |
| 52 | throw std::bad_alloc(); | |
| 49 | 53 | endOfTablePtr = reinterpret_cast<char*>(currentTab) + cellSize*tabSize; |
| 50 | 54 | } |
| 51 | 55 | |
| 15 | 15 | |
| 16 | 16 | #pragma once |
| 17 | 17 | |
| 18 | #include <vector> | |
| 19 | 18 | #include <cstring> |
| 19 | #include "pod_vector.h" | |
| 20 | 20 | |
| 21 | 21 | namespace IsoSpec |
| 22 | 22 | { |
| 29 | 29 | void* endOfTablePtr; |
| 30 | 30 | const int tabSize; |
| 31 | 31 | int cellSize; |
| 32 | std::vector<void*> prevTabs; | |
| 32 | pod_vector<void*> prevTabs; | |
| 33 | 33 | |
| 34 | 34 | public: |
| 35 | 35 | explicit DirtyAllocator(const int dim, const int tabSize = 10000); |
| 128 | 128 | /* Code: 71 ASCII char: G */ 2, 3, 1, 1, 0, 0, |
| 129 | 129 | /* Code: 72 ASCII char: H */ 6, 7, 3, 1, 0, 0, |
| 130 | 130 | /* Code: 73 ASCII char: I */ 6, 11, 1, 1, 0, 0, |
| 131 | /* Code: 74 ASCII char: J */ 0, 0, 0, 0, 0, 0, | |
| 131 | /* Code: 74 ASCII char: J */ 6, 11, 1, 1, 0, 0, | |
| 132 | 132 | /* Code: 75 ASCII char: K */ 6, 12, 2, 1, 0, 0, |
| 133 | 133 | /* Code: 76 ASCII char: L */ 6, 11, 1, 1, 0, 0, |
| 134 | 134 | /* Code: 77 ASCII char: M */ 5, 9, 1, 1, 1, 0, |
| 160 | 160 | /* Code: 103 ASCII char: g */ 2, 3, 1, 1, 0, 0, |
| 161 | 161 | /* Code: 104 ASCII char: h */ 6, 7, 3, 1, 0, 0, |
| 162 | 162 | /* Code: 105 ASCII char: i */ 6, 11, 1, 1, 0, 0, |
| 163 | /* Code: 106 ASCII char: j */ 0, 0, 0, 0, 0, 0, | |
| 163 | /* Code: 106 ASCII char: j */ 6, 11, 1, 1, 0, 0, | |
| 164 | 164 | /* Code: 107 ASCII char: k */ 6, 12, 2, 1, 0, 0, |
| 165 | 165 | /* Code: 108 ASCII char: l */ 6, 11, 1, 1, 0, 0, |
| 166 | 166 | /* Code: 109 ASCII char: m */ 5, 9, 1, 1, 1, 0, |
| 593 | 593 | template void FixedEnvelope::total_prob_init<false>(Iso&& iso, double target_total_prob, bool optimize); |
| 594 | 594 | |
| 595 | 595 | |
| 596 | double FixedEnvelope::empiric_average_mass() | |
| 597 | { | |
| 598 | double ret = 0.0; | |
| 599 | for(size_t ii = 0; ii < _confs_no; ii++) | |
| 600 | { | |
| 601 | ret += _masses[ii] * _probs[ii]; | |
| 602 | } | |
| 603 | return ret / get_total_prob(); | |
| 604 | } | |
| 605 | ||
| 606 | double FixedEnvelope::empiric_variance() | |
| 607 | { | |
| 608 | double ret = 0.0; | |
| 609 | double avg = empiric_average_mass(); | |
| 610 | for(size_t ii = 0; ii < _confs_no; ii++) | |
| 611 | { | |
| 612 | double msq = _masses[ii] - avg; | |
| 613 | ret += msq * msq * _probs[ii]; | |
| 614 | } | |
| 615 | ||
| 616 | return ret / get_total_prob(); | |
| 617 | } | |
| 618 | ||
| 596 | 619 | } // namespace IsoSpec |
| 95 | 95 | void scale(double factor); |
| 96 | 96 | void normalize(); |
| 97 | 97 | |
| 98 | double empiric_average_mass(); | |
| 99 | double empiric_variance(); | |
| 100 | double empiric_stddev() { return sqrt(empiric_variance()); } | |
| 101 | ||
| 98 | 102 | double WassersteinDistance(FixedEnvelope& other); |
| 99 | 103 | double OrientedWassersteinDistance(FixedEnvelope& other); |
| 100 | 104 |
| 96 | 96 | { |
| 97 | 97 | delete[] isotopeNumbers; |
| 98 | 98 | delete[] atomCounts; |
| 99 | // Since we're throwing in a constructor, the destructor won't run, and we don't need to NULL these. | |
| 100 | // However, this is not the fast code path and we can afford two unneeded instructions to keep | |
| 101 | // some static analysis tools happy. | |
| 102 | isotopeNumbers = nullptr; | |
| 103 | atomCounts = nullptr; | |
| 99 | // Since we're throwing in a constructor, the destructor won't run, and we don't need to NULL these. | |
| 100 | // However, this is not the fast code path and we can afford two unneeded instructions to keep | |
| 101 | // some static analysis tools happy. | |
| 102 | isotopeNumbers = nullptr; | |
| 103 | atomCounts = nullptr; | |
| 104 | 104 | throw; |
| 105 | 105 | } |
| 106 | 106 | } |
| 127 | 127 | { |
| 128 | 128 | delete[] isotopeNumbers; |
| 129 | 129 | delete[] atomCounts; |
| 130 | // Since we're throwing in a constructor, the destructor won't run, and we don't need to NULL these. | |
| 131 | // However, this is not the fast code path and we can afford two unneeded instructions to keep | |
| 132 | // some static analysis tools happy. | |
| 133 | isotopeNumbers = nullptr; | |
| 134 | atomCounts = nullptr; | |
| 130 | // Since we're throwing in a constructor, the destructor won't run, and we don't need to NULL these. | |
| 131 | // However, this is not the fast code path and we can afford two unneeded instructions to keep | |
| 132 | // some static analysis tools happy. | |
| 133 | isotopeNumbers = nullptr; | |
| 134 | atomCounts = nullptr; | |
| 135 | 135 | throw; |
| 136 | 136 | } |
| 137 | 137 | } |
| 822 | 822 | for(int i = 0; i < dimNumber; i++) |
| 823 | 823 | marginalResults[i] = new MarginalTrek(std::move(*(marginals[i])), _tabSize, _hashSize); |
| 824 | 824 | |
| 825 | logProbs = new const std::vector<double>*[dimNumber]; | |
| 826 | masses = new const std::vector<double>*[dimNumber]; | |
| 827 | marginalConfs = new const std::vector<int*>*[dimNumber]; | |
| 825 | logProbs = new const pod_vector<double>*[dimNumber]; | |
| 826 | masses = new const pod_vector<double>*[dimNumber]; | |
| 827 | marginalConfs = new const pod_vector<int*>*[dimNumber]; | |
| 828 | 828 | |
| 829 | 829 | for(int i = 0; i < dimNumber; i++) |
| 830 | 830 | { |
| 102 | 102 | |
| 103 | 103 | //! Constructor (named) from aminoacid FASTA sequence as C string. |
| 104 | 104 | /*! |
| 105 | \param fasta An aminoacid FASTA sequence. May be upper/lower/mixed case, may contain selenocystein (U). Subisotopologues will be in order: CHNOS, possibly with Se added at an end if present. | |
| 105 | \param fasta An aminoacid FASTA sequence. May be upper/lower/mixed case, may contain selenocystein (U) or xleucine (J). | |
| 106 | Other characters, including FASTA codes of indeterminate chemical formula (X, *, -, B, ...) are silently ignored. | |
| 107 | That means "AEDA", "AE-DA", "EAXXDA", "AE DA" will all result in the same chemical formula. | |
| 108 | Subisotopologues will be in order: CHNOS, possibly with Se added at an end if present. | |
| 106 | 109 | \use_nominal_masses Whether to use nucleon number instead of the real mass of each isotope during calculations. |
| 107 | 110 | \add_water Whether the chain should have the terminating -H and -OH groups at the N and C terminus, respectively. |
| 108 | 111 | */ |
| 233 | 236 | { |
| 234 | 237 | private: |
| 235 | 238 | MarginalTrek** marginalResults; /*!< Table of pointers to marginal distributions of subisotopologues. */ |
| 236 | std::priority_queue<void*, std::vector<void*>, ConfOrder> pq; /*!< The priority queue used to generate isotopologues ordered by descending probability. */ | |
| 239 | std::priority_queue<void*, pod_vector<void*>, ConfOrder> pq; /*!< The priority queue used to generate isotopologues ordered by descending probability. */ | |
| 237 | 240 | void* topConf; /*!< Most probable configuration. */ |
| 238 | 241 | DirtyAllocator allocator; /*!< Structure used for alocating memory for isotopologues. */ |
| 239 | const std::vector<double>** logProbs; /*!< Obtained log-probabilities. */ | |
| 240 | const std::vector<double>** masses; /*!< Obtained masses. */ | |
| 241 | const std::vector<int*>** marginalConfs; /*!< Obtained counts of isotopes. */ | |
| 242 | const pod_vector<double>** logProbs; /*!< Obtained log-probabilities. */ | |
| 243 | const pod_vector<double>** masses; /*!< Obtained masses. */ | |
| 244 | const pod_vector<Conf>** marginalConfs; /*!< Obtained counts of isotopes. */ | |
| 242 | 245 | double currentLProb; /*!< The log-probability of the current isotopologue. */ |
| 243 | 246 | double currentMass; /*!< The mass of the current isotopologue. */ |
| 244 | 247 | double currentProb; /*!< The probability of the current isotopologue. */ |
| 18 | 18 | #include <algorithm> |
| 19 | 19 | #include <vector> |
| 20 | 20 | #include <cstdlib> |
| 21 | #include <unordered_map> | |
| 22 | #include <unordered_set> | |
| 23 | 21 | #include <queue> |
| 24 | 22 | #include <utility> |
| 25 | 23 | #include <cstring> |
| 26 | 24 | #include <string> |
| 27 | 25 | #include <limits> |
| 26 | #include <memory> | |
| 28 | 27 | #include "platform.h" |
| 29 | 28 | #include "marginalTrek++.h" |
| 30 | 29 | #include "conf.h" |
| 323 | 322 | MarginalTrek::MarginalTrek( |
| 324 | 323 | Marginal&& m, |
| 325 | 324 | int tabSize, |
| 326 | int hashSize | |
| 325 | int | |
| 327 | 326 | ) : |
| 328 | 327 | Marginal(std::move(m)), |
| 329 | 328 | current_count(0), |
| 330 | keyHasher(isotopeNo), | |
| 331 | equalizer(isotopeNo), | |
| 332 | 329 | orderMarginal(atom_lProbs, isotopeNo), |
| 333 | visited(hashSize, keyHasher, equalizer), | |
| 334 | pq(orderMarginal), | |
| 335 | totalProb(), | |
| 336 | candidate(new int[isotopeNo]), | |
| 330 | pq(), | |
| 337 | 331 | allocator(isotopeNo, tabSize) |
| 338 | 332 | { |
| 339 | 333 | int* initialConf = allocator.makeCopy(mode_conf); |
| 340 | 334 | |
| 341 | pq.push(initialConf); | |
| 342 | visited[initialConf] = 0; | |
| 343 | ||
| 344 | totalProb = Summator(); | |
| 335 | pq.push({unnormalized_logProb(mode_conf), initialConf}); | |
| 345 | 336 | |
| 346 | 337 | current_count = 0; |
| 347 | 338 | |
| 357 | 348 | */ |
| 358 | 349 | if(pq.size() < 1) return false; |
| 359 | 350 | |
| 360 | Conf topConf = pq.top(); | |
| 351 | double logprob = pq.top().first + loggamma_nominator; | |
| 352 | Conf topConf = pq.top().second; | |
| 353 | ||
| 361 | 354 | pq.pop(); |
| 362 | 355 | ++current_count; |
| 363 | visited[topConf] = current_count; | |
| 364 | 356 | |
| 365 | 357 | _confs.push_back(topConf); |
| 358 | ||
| 366 | 359 | _conf_masses.push_back(calc_mass(topConf, atom_masses, isotopeNo)); |
| 367 | double logprob = logProb(topConf); | |
| 368 | 360 | _conf_lprobs.push_back(logprob); |
| 369 | 361 | |
| 370 | ||
| 371 | totalProb.add( exp( logprob ) ); | |
| 372 | ||
| 373 | for( unsigned int i = 0; i < isotopeNo; ++i ) | |
| 374 | { | |
| 375 | for( unsigned int j = 0; j < isotopeNo; ++j ) | |
| 362 | for( unsigned int j = 0; j < isotopeNo; ++j ) | |
| 363 | { | |
| 364 | if( topConf[j] > mode_conf[j]) | |
| 365 | continue; | |
| 366 | ||
| 367 | if( topConf[j] > 0 ) | |
| 376 | 368 | { |
| 377 | // Growing index different than decreasing one AND | |
| 378 | // Remain on simplex condition. | |
| 379 | if( i != j && topConf[j] > 0 ){ | |
| 380 | copyConf(topConf, candidate, isotopeNo); | |
| 381 | ||
| 382 | ++candidate[i]; | |
| 383 | --candidate[j]; | |
| 384 | ||
| 385 | // candidate should not have been already visited. | |
| 386 | if( visited.count( candidate ) == 0 ) | |
| 387 | { | |
| 388 | Conf acceptedCandidate = allocator.makeCopy(candidate); | |
| 389 | pq.push(acceptedCandidate); | |
| 390 | ||
| 391 | visited[acceptedCandidate] = 0; | |
| 369 | for( unsigned int i = 0; i < isotopeNo; ++i ) | |
| 370 | { | |
| 371 | if( topConf[i] < mode_conf[i] ) | |
| 372 | continue; | |
| 373 | // Growing index different than decreasing one AND | |
| 374 | // Remain on simplex condition. | |
| 375 | if( i != j ){ | |
| 376 | Conf acceptedCandidate = allocator.makeCopy(topConf); | |
| 377 | ||
| 378 | ++acceptedCandidate[i]; | |
| 379 | --acceptedCandidate[j]; | |
| 380 | ||
| 381 | double new_prob = unnormalized_logProb(acceptedCandidate); | |
| 382 | ||
| 383 | pq.push({new_prob, acceptedCandidate}); | |
| 392 | 384 | } |
| 385 | ||
| 386 | if( topConf[i] > mode_conf[i] ) | |
| 387 | break; | |
| 393 | 388 | } |
| 394 | 389 | } |
| 390 | if( topConf[j] < mode_conf[j] ) | |
| 391 | break; | |
| 395 | 392 | } |
| 396 | 393 | |
| 397 | 394 | return true; |
| 398 | 395 | } |
| 399 | 396 | |
| 400 | int MarginalTrek::processUntilCutoff(double cutoff) | |
| 401 | { | |
| 402 | Summator s; | |
| 403 | int last_idx = -1; | |
| 404 | for(unsigned int i = 0; i < _conf_lprobs.size(); i++) | |
| 405 | { | |
| 406 | s.add(_conf_lprobs[i]); | |
| 407 | if(s.get() >= cutoff) | |
| 408 | { | |
| 409 | last_idx = i; | |
| 410 | break; | |
| 411 | } | |
| 412 | } | |
| 413 | if(last_idx > -1) | |
| 414 | return last_idx; | |
| 415 | ||
| 416 | while(totalProb.get() < cutoff && add_next_conf()) {} | |
| 417 | return _conf_lprobs.size(); | |
| 418 | } | |
| 419 | ||
| 420 | 397 | |
| 421 | 398 | MarginalTrek::~MarginalTrek() |
| 422 | 399 | { |
| 423 | delete[] candidate; | |
| 424 | } | |
| 425 | ||
| 400 | } | |
| 426 | 401 | |
| 427 | 402 | |
| 428 | 403 | |
| 430 | 405 | double lCutOff, |
| 431 | 406 | bool sort, |
| 432 | 407 | int tabSize, |
| 433 | int hashSize | |
| 408 | int | |
| 434 | 409 | ) : Marginal(std::move(m)), |
| 435 | 410 | allocator(isotopeNo, tabSize) |
| 436 | 411 | { |
| 437 | const ConfEqual equalizer(isotopeNo); | |
| 438 | const KeyHasher keyHasher(isotopeNo); | |
| 439 | const ConfOrderMarginalDescending orderMarginal(atom_lProbs, isotopeNo); | |
| 440 | ||
| 441 | lCutOff -= loggamma_nominator; | |
| 442 | ||
| 443 | std::unordered_set<Conf, KeyHasher, ConfEqual> visited(hashSize, keyHasher, equalizer); | |
| 444 | ||
| 445 | 412 | Conf currentConf = allocator.makeCopy(mode_conf); |
| 446 | if(unnormalized_logProb(currentConf) >= lCutOff) | |
| 447 | { | |
| 448 | // create a copy and store a ptr to the *same* copy in both structures | |
| 449 | // (save some space and time) | |
| 450 | auto tmp = allocator.makeCopy(currentConf); | |
| 451 | configurations.push_back(tmp); | |
| 452 | visited.insert(tmp); | |
| 413 | if(logProb(currentConf) >= lCutOff) | |
| 414 | { | |
| 415 | configurations.push_back(currentConf); | |
| 416 | lProbs.push_back(mode_lprob); | |
| 453 | 417 | } |
| 454 | 418 | |
| 455 | 419 | unsigned int idx = 0; |
| 456 | 420 | |
| 421 | std::unique_ptr<double[]> prob_partials(new double[isotopeNo]); | |
| 422 | std::unique_ptr<double[]> prob_part_acc(new double[isotopeNo+1]); | |
| 423 | prob_part_acc[0] = loggamma_nominator; | |
| 424 | ||
| 457 | 425 | while(idx < configurations.size()) |
| 458 | 426 | { |
| 459 | memcpy(currentConf, configurations[idx], sizeof(int)*isotopeNo); | |
| 427 | currentConf = configurations[idx]; | |
| 460 | 428 | idx++; |
| 429 | ||
| 430 | for(size_t ii = 0; ii < isotopeNo; ii++) | |
| 431 | prob_partials[ii] = minuslogFactorial(currentConf[ii]) + currentConf[ii] * atom_lProbs[ii]; | |
| 432 | ||
| 461 | 433 | for(unsigned int ii = 0; ii < isotopeNo; ii++ ) |
| 462 | 434 | { |
| 463 | currentConf[ii]++; | |
| 464 | for(unsigned int jj = 0; jj < isotopeNo; jj++ ) | |
| 435 | if(currentConf[ii] > mode_conf[ii]) | |
| 436 | continue; | |
| 437 | ||
| 438 | if(currentConf[ii] != 0) | |
| 465 | 439 | { |
| 466 | if( ii != jj && currentConf[jj] > 0) | |
| 440 | double prev_partial_ii = prob_partials[ii]; | |
| 441 | currentConf[ii]--; | |
| 442 | prob_partials[ii] = minuslogFactorial(currentConf[ii]) + currentConf[ii] * atom_lProbs[ii]; | |
| 443 | ||
| 444 | for(unsigned int jj = 0; jj < isotopeNo; jj++ ) | |
| 467 | 445 | { |
| 468 | currentConf[jj]--; | |
| 469 | ||
| 470 | if (visited.count(currentConf) == 0 && unnormalized_logProb(currentConf) >= lCutOff) | |
| 446 | prob_part_acc[jj+1] = prob_part_acc[jj] + prob_partials[jj]; | |
| 447 | ||
| 448 | if(currentConf[jj] < mode_conf[jj]) | |
| 449 | continue; | |
| 450 | ||
| 451 | if( ii != jj ) | |
| 471 | 452 | { |
| 472 | // create a copy and store a ptr to the *same* copy in | |
| 473 | // both structures (save some space and time) | |
| 474 | auto tmp = allocator.makeCopy(currentConf); | |
| 475 | visited.insert(tmp); | |
| 476 | configurations.push_back(tmp); | |
| 477 | // std::cout << " V: "; for (auto it : visited) std::cout << it << " "; std::cout << std::endl; | |
| 453 | double logp = prob_part_acc[jj] + minuslogFactorial(1+currentConf[jj]) + (1+currentConf[jj]) * atom_lProbs[jj]; | |
| 454 | for(size_t kk = jj+1; kk < isotopeNo; kk++) | |
| 455 | logp += prob_partials[kk]; | |
| 456 | ||
| 457 | if (logp >= lCutOff) | |
| 458 | { | |
| 459 | auto tmp = allocator.makeCopy(currentConf); | |
| 460 | tmp[jj]++; | |
| 461 | configurations.push_back(tmp); | |
| 462 | lProbs.push_back(logp); | |
| 463 | } | |
| 478 | 464 | } |
| 479 | ||
| 480 | currentConf[jj]++; | |
| 465 | else | |
| 466 | prob_part_acc[jj+1] = prob_part_acc[jj] + prob_partials[jj]; | |
| 467 | ||
| 468 | if (currentConf[jj] > mode_conf[jj]) | |
| 469 | break; | |
| 481 | 470 | } |
| 471 | currentConf[ii]++; | |
| 472 | prob_partials[ii] = prev_partial_ii; | |
| 482 | 473 | } |
| 483 | currentConf[ii]--; | |
| 474 | ||
| 475 | if(currentConf[ii] < mode_conf[ii]) | |
| 476 | break; | |
| 484 | 477 | } |
| 485 | 478 | } |
| 486 | 479 | |
| 487 | // orderMarginal defines the order of configurations (compares their logprobs) | |
| 488 | // akin to key in Python sort. | |
| 489 | if(sort) | |
| 490 | std::sort(configurations.begin(), configurations.end(), orderMarginal); | |
| 491 | ||
| 492 | ||
| 493 | confs = &configurations[0]; | |
| 494 | 480 | no_confs = configurations.size(); |
| 495 | lProbs = new double[no_confs+1]; | |
| 481 | confs = configurations.data(); | |
| 482 | ||
| 483 | if(sort && no_confs > 0) | |
| 484 | { | |
| 485 | std::unique_ptr<size_t[]> order_arr(get_inverse_order(lProbs.data(), no_confs)); | |
| 486 | impose_order(order_arr.get(), no_confs, lProbs.data(), confs); | |
| 487 | } | |
| 488 | ||
| 496 | 489 | probs = new double[no_confs]; |
| 497 | 490 | masses = new double[no_confs]; |
| 498 | 491 | |
| 499 | 492 | |
| 500 | 493 | for(unsigned int ii = 0; ii < no_confs; ii++) |
| 501 | 494 | { |
| 502 | lProbs[ii] = logProb(confs[ii]); | |
| 503 | 495 | probs[ii] = exp(lProbs[ii]); |
| 504 | 496 | masses[ii] = calc_mass(confs[ii], atom_masses, isotopeNo); |
| 505 | 497 | } |
| 506 | lProbs[no_confs] = -std::numeric_limits<double>::infinity(); | |
| 498 | ||
| 499 | lProbs.push_back(-std::numeric_limits<double>::infinity()); | |
| 507 | 500 | } |
| 508 | 501 | |
| 509 | 502 | |
| 510 | 503 | PrecalculatedMarginal::~PrecalculatedMarginal() |
| 511 | 504 | { |
| 512 | if(lProbs != nullptr) | |
| 513 | delete[] lProbs; | |
| 514 | 505 | if(masses != nullptr) |
| 515 | 506 | delete[] masses; |
| 516 | 507 | if(probs != nullptr) |
| 523 | 514 | |
| 524 | 515 | |
| 525 | 516 | |
| 526 | LayeredMarginal::LayeredMarginal(Marginal&& m, int tabSize, int _hashSize) | |
| 517 | LayeredMarginal::LayeredMarginal(Marginal&& m, int tabSize, int) | |
| 527 | 518 | : Marginal(std::move(m)), current_threshold(1.0), allocator(isotopeNo, tabSize), |
| 528 | equalizer(isotopeNo), keyHasher(isotopeNo), orderMarginal(atom_lProbs, isotopeNo), hashSize(_hashSize) | |
| 519 | equalizer(isotopeNo), keyHasher(isotopeNo) | |
| 529 | 520 | { |
| 530 | 521 | fringe.push_back(mode_conf); |
| 531 | 522 | lProbs.push_back(std::numeric_limits<double>::infinity()); |
| 523 | fringe_unn_lprobs.push_back(unnormalized_logProb(mode_conf)); | |
| 532 | 524 | lProbs.push_back(-std::numeric_limits<double>::infinity()); |
| 533 | 525 | guarded_lProbs = lProbs.data()+1; |
| 534 | 526 | } |
| 535 | 527 | |
| 536 | 528 | bool LayeredMarginal::extend(double new_threshold, bool do_sort) |
| 537 | 529 | { |
| 530 | new_threshold -= loggamma_nominator; | |
| 538 | 531 | if(fringe.empty()) |
| 539 | 532 | return false; |
| 540 | 533 | |
| 541 | std::vector<Conf> new_fringe; | |
| 542 | std::unordered_set<Conf, KeyHasher, ConfEqual> visited(hashSize, keyHasher, equalizer); | |
| 543 | ||
| 544 | for(unsigned int ii = 0; ii < fringe.size(); ii++) | |
| 545 | visited.insert(fringe[ii]); | |
| 546 | ||
| 547 | Conf currentConf; | |
| 534 | lProbs.pop_back(); // Remove the +inf guardian | |
| 535 | ||
| 536 | pod_vector<Conf> new_fringe; | |
| 537 | pod_vector<double> new_fringe_unn_lprobs; | |
| 538 | ||
| 548 | 539 | while(!fringe.empty()) |
| 549 | 540 | { |
| 550 | currentConf = fringe.back(); | |
| 541 | Conf currentConf = fringe.back(); | |
| 551 | 542 | fringe.pop_back(); |
| 552 | 543 | |
| 553 | double opc = logProb(currentConf); | |
| 554 | ||
| 544 | double opc = fringe_unn_lprobs.back(); | |
| 545 | ||
| 546 | fringe_unn_lprobs.pop_back(); | |
| 555 | 547 | if(opc < new_threshold) |
| 548 | { | |
| 556 | 549 | new_fringe.push_back(currentConf); |
| 550 | new_fringe_unn_lprobs.push_back(opc); | |
| 551 | } | |
| 557 | 552 | |
| 558 | 553 | else |
| 559 | 554 | { |
| 560 | 555 | configurations.push_back(currentConf); |
| 556 | lProbs.push_back(opc+loggamma_nominator); | |
| 561 | 557 | for(unsigned int ii = 0; ii < isotopeNo; ii++ ) |
| 562 | 558 | { |
| 563 | currentConf[ii]++; | |
| 564 | for(unsigned int jj = 0; jj < isotopeNo; jj++ ) | |
| 559 | if(currentConf[ii] > mode_conf[ii]) | |
| 560 | continue; | |
| 561 | ||
| 562 | if(currentConf[ii] > 0) | |
| 565 | 563 | { |
| 566 | if( ii != jj && currentConf[jj] > 0 ) | |
| 564 | currentConf[ii]--; | |
| 565 | for(unsigned int jj = 0; jj < isotopeNo; jj++ ) | |
| 567 | 566 | { |
| 568 | currentConf[jj]--; | |
| 569 | ||
| 570 | double lpc = logProb(currentConf); | |
| 571 | ||
| 572 | if (lpc < current_threshold && | |
| 573 | (opc > lpc || (opc == lpc && ii > jj)) && visited.count(currentConf) == 0) | |
| 567 | if(currentConf[jj] < mode_conf[jj]) | |
| 568 | continue; | |
| 569 | ||
| 570 | if( ii != jj ) | |
| 574 | 571 | { |
| 575 | 572 | Conf nc = allocator.makeCopy(currentConf); |
| 576 | currentConf[ii]--; | |
| 577 | currentConf[jj]++; | |
| 578 | visited.insert(nc); | |
| 579 | currentConf[ii]++; | |
| 573 | nc[jj]++; | |
| 574 | ||
| 575 | double lpc = unnormalized_logProb(nc); | |
| 580 | 576 | if(lpc >= new_threshold) |
| 577 | { | |
| 581 | 578 | fringe.push_back(nc); |
| 579 | fringe_unn_lprobs.push_back(lpc); | |
| 580 | } | |
| 582 | 581 | else |
| 582 | { | |
| 583 | 583 | new_fringe.push_back(nc); |
| 584 | new_fringe_unn_lprobs.push_back(lpc); | |
| 585 | } | |
| 584 | 586 | } |
| 585 | else | |
| 586 | { | |
| 587 | currentConf[jj]++; | |
| 588 | } | |
| 587 | ||
| 588 | if(currentConf[jj] > mode_conf[jj]) | |
| 589 | break; | |
| 589 | 590 | } |
| 591 | currentConf[ii]++; | |
| 590 | 592 | } |
| 591 | currentConf[ii]--; | |
| 593 | ||
| 594 | if(currentConf[ii] < mode_conf[ii]) | |
| 595 | break; | |
| 592 | 596 | } |
| 593 | 597 | } |
| 594 | 598 | } |
| 595 | 599 | |
| 596 | 600 | current_threshold = new_threshold; |
| 597 | 601 | fringe.swap(new_fringe); |
| 602 | fringe_unn_lprobs.swap(new_fringe_unn_lprobs); | |
| 598 | 603 | |
| 599 | 604 | if(do_sort) |
| 600 | std::sort(configurations.begin()+probs.size(), configurations.end(), orderMarginal); | |
| 601 | ||
| 602 | if(lProbs.capacity() * 2 < configurations.size() + 2) | |
| 605 | { | |
| 606 | size_t to_sort_size = configurations.size() - probs.size(); | |
| 607 | if(to_sort_size > 0) | |
| 608 | { | |
| 609 | std::unique_ptr<size_t[]> order_arr(get_inverse_order(lProbs.data()+1+probs.size(), to_sort_size)); | |
| 610 | double* P = lProbs.data()+1+probs.size(); | |
| 611 | Conf* C = configurations.data()+probs.size(); | |
| 612 | size_t* O = order_arr.get(); | |
| 613 | impose_order(O, to_sort_size, P, C); | |
| 614 | } | |
| 615 | } | |
| 616 | ||
| 617 | if(probs.capacity() * 2 < configurations.size() + 2) | |
| 603 | 618 | { |
| 604 | 619 | // Reserve space for new values |
| 605 | lProbs.reserve(configurations.size()+2); | |
| 606 | 620 | probs.reserve(configurations.size()); |
| 607 | 621 | masses.reserve(configurations.size()); |
| 608 | 622 | } // Otherwise we're growing slowly enough that standard reallocations on push_back work better - we waste some extra memory |
| 609 | 623 | // but don't reallocate on every call |
| 610 | 624 | |
| 611 | lProbs.pop_back(); // The guardian... | |
| 612 | ||
| 625 | // printVector(lProbs); | |
| 613 | 626 | for(unsigned int ii = probs.size(); ii < configurations.size(); ii++) |
| 614 | 627 | { |
| 615 | lProbs.push_back(logProb(configurations[ii])); | |
| 616 | probs.push_back(exp(lProbs.back())); | |
| 628 | probs.push_back(exp(lProbs[ii+1])); | |
| 617 | 629 | masses.push_back(calc_mass(configurations[ii], atom_masses, isotopeNo)); |
| 618 | 630 | } |
| 619 | 631 | |
| 628 | 640 | double LayeredMarginal::get_min_mass() const |
| 629 | 641 | { |
| 630 | 642 | double ret = std::numeric_limits<double>::infinity(); |
| 631 | for(std::vector<double>::const_iterator it = masses.begin(); it != masses.end(); ++it) | |
| 643 | for(pod_vector<double>::const_iterator it = masses.cbegin(); it != masses.cend(); ++it) | |
| 632 | 644 | if(*it < ret) |
| 633 | 645 | ret = *it; |
| 634 | 646 | return ret; |
| 638 | 650 | double LayeredMarginal::get_max_mass() const |
| 639 | 651 | { |
| 640 | 652 | double ret = -std::numeric_limits<double>::infinity(); |
| 641 | for(std::vector<double>::const_iterator it = masses.begin(); it != masses.end(); ++it) | |
| 653 | for(pod_vector<double>::const_iterator it = masses.cbegin(); it != masses.cend(); ++it) | |
| 642 | 654 | if(*it > ret) |
| 643 | 655 | ret = *it; |
| 644 | 656 | return ret; |
| 15 | 15 | |
| 16 | 16 | #pragma once |
| 17 | 17 | |
| 18 | #include <unordered_map> | |
| 19 | 18 | #include <queue> |
| 20 | 19 | #include <algorithm> |
| 21 | 20 | #include <vector> |
| 21 | #include <functional> | |
| 22 | #include <utility> | |
| 22 | 23 | #include "conf.h" |
| 23 | 24 | #include "allocator.h" |
| 24 | 25 | #include "operators.h" |
| 25 | 26 | #include "summator.h" |
| 27 | #include "pod_vector.h" | |
| 26 | 28 | |
| 27 | 29 | |
| 28 | 30 | namespace IsoSpec |
| 173 | 175 | { |
| 174 | 176 | private: |
| 175 | 177 | int current_count; |
| 176 | const KeyHasher keyHasher; | |
| 177 | const ConfEqual equalizer; | |
| 178 | 178 | const ConfOrderMarginal orderMarginal; |
| 179 | std::unordered_map<Conf, int, KeyHasher, ConfEqual> visited; | |
| 180 | std::priority_queue<Conf, std::vector<Conf>, ConfOrderMarginal> pq; | |
| 181 | Summator totalProb; | |
| 182 | Conf candidate; | |
| 179 | std::priority_queue<ProbAndConfPtr, pod_vector<ProbAndConfPtr> > pq; | |
| 183 | 180 | Allocator<int> allocator; |
| 184 | std::vector<double> _conf_lprobs; | |
| 185 | std::vector<double> _conf_masses; | |
| 186 | std::vector<int*> _confs; | |
| 181 | pod_vector<double> _conf_lprobs; | |
| 182 | pod_vector<double> _conf_masses; | |
| 183 | pod_vector<int*> _confs; | |
| 187 | 184 | |
| 188 | 185 | //! Proceed to the next configuration and memoize it (as it will be surely needed). |
| 189 | 186 | bool add_next_conf(); |
| 225 | 222 | inline double getModeLProb() const { return mode_lprob; } |
| 226 | 223 | |
| 227 | 224 | |
| 228 | //! Calculate subisotopologues with probability above or equal to the cut-off. | |
| 229 | /*! | |
| 230 | \param cutoff The probability cut-off | |
| 231 | \return The number of the last subisotopologue above the cut-off. | |
| 232 | */ | |
| 233 | int processUntilCutoff(double cutoff); | |
| 234 | ||
| 235 | inline const std::vector<double>& conf_lprobs() const { return _conf_lprobs; } | |
| 236 | inline const std::vector<double>& conf_masses() const { return _conf_masses; } | |
| 237 | inline const std::vector<int*>& confs() const { return _confs; } | |
| 225 | inline const pod_vector<double>& conf_lprobs() const { return _conf_lprobs; } | |
| 226 | inline const pod_vector<double>& conf_masses() const { return _conf_masses; } | |
| 227 | inline const pod_vector<Conf>& confs() const { return _confs; } | |
| 238 | 228 | |
| 239 | 229 | |
| 240 | 230 | virtual ~MarginalTrek(); |
| 253 | 243 | class PrecalculatedMarginal : public Marginal |
| 254 | 244 | { |
| 255 | 245 | protected: |
| 256 | std::vector<Conf> configurations; | |
| 246 | pod_vector<Conf> configurations; | |
| 257 | 247 | Conf* confs; |
| 258 | 248 | unsigned int no_confs; |
| 259 | 249 | double* masses; |
| 260 | double* lProbs; | |
| 250 | pod_vector<double> lProbs; | |
| 261 | 251 | double* probs; |
| 262 | 252 | Allocator<int> allocator; |
| 263 | 253 | public: |
| 314 | 304 | /*! |
| 315 | 305 | \return Pointer to the first element in the table storing log-probabilities of subisotopologues. |
| 316 | 306 | */ |
| 317 | inline const double* get_lProbs_ptr() const { return lProbs; } | |
| 307 | inline const double* get_lProbs_ptr() const { return lProbs.data(); } | |
| 318 | 308 | |
| 319 | 309 | //! Get the table of the masses of subisotopologues. |
| 320 | 310 | /*! |
| 353 | 343 | { |
| 354 | 344 | private: |
| 355 | 345 | double current_threshold; |
| 356 | std::vector<Conf> configurations; | |
| 357 | std::vector<Conf> fringe; | |
| 346 | pod_vector<Conf> configurations; | |
| 347 | pod_vector<Conf> fringe; | |
| 348 | pod_vector<double> fringe_unn_lprobs; | |
| 358 | 349 | Allocator<int> allocator; |
| 359 | 350 | const ConfEqual equalizer; |
| 360 | 351 | const KeyHasher keyHasher; |
| 361 | const ConfOrderMarginalDescending orderMarginal; | |
| 362 | std::vector<double> lProbs; | |
| 363 | std::vector<double> probs; | |
| 364 | std::vector<double> masses; | |
| 352 | pod_vector<double> lProbs; | |
| 353 | pod_vector<double> probs; | |
| 354 | pod_vector<double> masses; | |
| 365 | 355 | double* guarded_lProbs; |
| 366 | const int hashSize; | |
| 367 | 356 | |
| 368 | 357 | public: |
| 369 | 358 | //! Move constructor: specializes the Marginal class. |
| 18 | 18 | #include <iostream> |
| 19 | 19 | #include <vector> |
| 20 | 20 | #include <cstring> |
| 21 | #include <algorithm> | |
| 21 | 22 | #include "isoMath.h" |
| 23 | #include "pod_vector.h" | |
| 22 | 24 | |
| 23 | 25 | namespace IsoSpec |
| 24 | 26 | { |
| 25 | 27 | |
| 26 | 28 | inline double combinedSum( |
| 27 | 29 | const int* conf, const std::vector<double>** valuesContainer, int dimNumber |
| 30 | ){ | |
| 31 | double res = 0.0; | |
| 32 | for(int i = 0; i < dimNumber; i++) | |
| 33 | res += (*(valuesContainer[i]))[conf[i]]; | |
| 34 | return res; | |
| 35 | } | |
| 36 | ||
| 37 | inline double combinedSum( | |
| 38 | const int* conf, const pod_vector<double>** valuesContainer, int dimNumber | |
| 28 | 39 | ){ |
| 29 | 40 | double res = 0.0; |
| 30 | 41 | for(int i = 0; i < dimNumber; i++) |
| 136 | 147 | *array = newT; |
| 137 | 148 | } |
| 138 | 149 | |
| 150 | template<typename T> size_t* get_order(T* order_array, size_t N) | |
| 151 | { | |
| 152 | size_t* arr = new size_t[N]; | |
| 153 | for(size_t ii = 0; ii < N; ii++) | |
| 154 | arr[ii] = ii; | |
| 155 | ||
| 156 | std::sort(arr, arr + N, [&](int i, int j) { return order_array[i] < order_array[j]; }); | |
| 157 | ||
| 158 | return arr; | |
| 159 | } | |
| 160 | ||
| 161 | template<typename T> size_t* get_inverse_order(T* order_array, size_t N) | |
| 162 | { | |
| 163 | size_t* arr = new size_t[N]; | |
| 164 | for(size_t ii = 0; ii < N; ii++) | |
| 165 | arr[ii] = ii; | |
| 166 | ||
| 167 | std::sort(arr, arr + N, [&](int i, int j) { return order_array[i] > order_array[j]; }); | |
| 168 | ||
| 169 | return arr; | |
| 170 | } | |
| 171 | ||
| 172 | template<typename TA, typename TB> void impose_order(size_t* O, size_t N, TA* A, TB* B) | |
| 173 | { | |
| 174 | for(size_t ii = 0; ii < N; ii++) | |
| 175 | { | |
| 176 | if(ii != O[ii]) | |
| 177 | { | |
| 178 | size_t curr_ii = ii; | |
| 179 | TA ta = A[ii]; | |
| 180 | TB tb = B[ii]; | |
| 181 | size_t next_ii = O[ii]; | |
| 182 | while(next_ii != ii) | |
| 183 | { | |
| 184 | A[curr_ii] = A[next_ii]; | |
| 185 | B[curr_ii] = B[next_ii]; | |
| 186 | O[curr_ii] = curr_ii; | |
| 187 | curr_ii = next_ii; | |
| 188 | next_ii = O[next_ii]; | |
| 189 | } | |
| 190 | A[curr_ii] = ta; | |
| 191 | B[curr_ii] = tb; | |
| 192 | O[curr_ii] = curr_ii; | |
| 193 | } | |
| 194 | } | |
| 195 | } | |
| 196 | ||
| 197 | ||
| 139 | 198 | } // namespace IsoSpec |
| 92 | 92 | #define ISOSPEC_FORCE_INLINE inline |
| 93 | 93 | #endif |
| 94 | 94 | |
| 95 | #if ISOSPEC_DEBUG | |
| 95 | #ifdef ISOSPEC_DEBUG | |
| 96 | 96 | #undef ISOSPEC_IMPOSSIBLE |
| 97 | 97 | #include <cassert> |
| 98 | 98 | #define ISOSPEC_IMPOSSIBLE(condition) assert(!(condition)); |
| 0 | /*! | |
| 1 | Copyright (C) 2015-2020 Mateusz Łącki and Michał Startek. | |
| 2 | ||
| 3 | This file is part of IsoSpec. | |
| 4 | ||
| 5 | IsoSpec is free software: you can redistribute it and/or modify | |
| 6 | it under the terms of the Simplified ("2-clause") BSD licence. | |
| 7 | ||
| 8 | IsoSpec is distributed in the hope that it will be useful, | |
| 9 | but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 10 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. | |
| 11 | ||
| 12 | You should have received a copy of the Simplified BSD Licence | |
| 13 | along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>. | |
| 14 | */ | |
| 15 | ||
| 16 | #pragma once | |
| 17 | ||
| 18 | #include <type_traits> | |
| 19 | #include <cstdlib> | |
| 20 | #include <utility> | |
| 21 | #include <new> | |
| 22 | #include <algorithm> | |
| 23 | #include "platform.h" | |
| 24 | ||
| 25 | ||
| 26 | ||
| 27 | template<typename T> class unsafe_pod_vector; | |
| 28 | ||
| 29 | template<typename T> class pod_vector | |
| 30 | { | |
| 31 | #if !ISOSPEC_BUILDING_R | |
| 32 | static_assert(std::is_trivially_copyable<T>::value, "Cannot use a pod_vector with a non-Plain Old Data type."); | |
| 33 | #endif | |
| 34 | ||
| 35 | T* backend_past_end; | |
| 36 | T* first_free; | |
| 37 | T* store; | |
| 38 | ||
| 39 | public: | |
| 40 | explicit pod_vector(size_t initial_size = 16) | |
| 41 | { | |
| 42 | store = reinterpret_cast<T*>(malloc(sizeof(T) * initial_size)); | |
| 43 | if(store == NULL) | |
| 44 | throw std::bad_alloc(); | |
| 45 | first_free = store; | |
| 46 | backend_past_end = store + initial_size; | |
| 47 | } | |
| 48 | ||
| 49 | pod_vector(const pod_vector<T>& other) = delete; | |
| 50 | pod_vector& operator=(const pod_vector<T>& other) = delete; | |
| 51 | ||
| 52 | pod_vector(pod_vector<T>&& other) | |
| 53 | { | |
| 54 | backend_past_end = other.backend_past_end; | |
| 55 | first_free = other.first_free; | |
| 56 | store = other.store; | |
| 57 | other.backend_past_end = other.first_free = other.store = NULL; | |
| 58 | } | |
| 59 | ||
| 60 | ~pod_vector() { free(store); } | |
| 61 | ||
| 62 | explicit pod_vector(unsafe_pod_vector<T>&& other) | |
| 63 | { | |
| 64 | backend_past_end = other.backend_past_end; | |
| 65 | first_free = other.first_free; | |
| 66 | store = other.store; | |
| 67 | } | |
| 68 | ||
| 69 | void fast_reserve(size_t n) | |
| 70 | { | |
| 71 | ISOSPEC_IMPOSSIBLE(n < static_cast<size_t>(backend_past_end - store)); | |
| 72 | T* new_store = reinterpret_cast<T*>(realloc(store, n * sizeof(T))); | |
| 73 | if(new_store == NULL) | |
| 74 | throw std::bad_alloc(); | |
| 75 | first_free = new_store + (first_free - store); | |
| 76 | backend_past_end = new_store + n; | |
| 77 | store = new_store; | |
| 78 | } | |
| 79 | ||
| 80 | void reserve(size_t n) | |
| 81 | { | |
| 82 | if (n > static_cast<size_t>(backend_past_end - store)) | |
| 83 | fast_reserve(n); | |
| 84 | } | |
| 85 | ||
| 86 | ISOSPEC_FORCE_INLINE void nocheck_push_back(const T& val) noexcept | |
| 87 | { | |
| 88 | ISOSPEC_IMPOSSIBLE(first_free >= backend_past_end); | |
| 89 | *first_free = val; | |
| 90 | first_free++; | |
| 91 | } | |
| 92 | ||
| 93 | ISOSPEC_FORCE_INLINE void push_back(const T& val) | |
| 94 | { | |
| 95 | if(first_free >= backend_past_end) | |
| 96 | fast_reserve((std::max<std::ptrdiff_t>)(4, (backend_past_end-store)) * 2); | |
| 97 | *first_free = val; | |
| 98 | first_free++; | |
| 99 | } | |
| 100 | ||
| 101 | ISOSPEC_FORCE_INLINE T& operator[](size_t n) noexcept | |
| 102 | { | |
| 103 | ISOSPEC_IMPOSSIBLE(store + n >= first_free); | |
| 104 | return store[n]; | |
| 105 | } | |
| 106 | ||
| 107 | ISOSPEC_FORCE_INLINE const T& operator[](size_t n) const noexcept | |
| 108 | { | |
| 109 | ISOSPEC_IMPOSSIBLE(store + n >= first_free); | |
| 110 | return store[n]; | |
| 111 | } | |
| 112 | ||
| 113 | ISOSPEC_FORCE_INLINE size_t size() const noexcept | |
| 114 | { | |
| 115 | return first_free - store; | |
| 116 | } | |
| 117 | ||
| 118 | ISOSPEC_FORCE_INLINE size_t capacity() const noexcept | |
| 119 | { | |
| 120 | return backend_past_end - store; | |
| 121 | } | |
| 122 | ||
| 123 | ISOSPEC_FORCE_INLINE T* data() noexcept | |
| 124 | { | |
| 125 | return store; | |
| 126 | } | |
| 127 | ||
| 128 | ISOSPEC_FORCE_INLINE const T* data() const noexcept | |
| 129 | { | |
| 130 | return store; | |
| 131 | } | |
| 132 | ||
| 133 | ISOSPEC_FORCE_INLINE bool empty() const noexcept | |
| 134 | { | |
| 135 | return first_free == store; | |
| 136 | } | |
| 137 | ||
| 138 | ISOSPEC_FORCE_INLINE const T& back() const noexcept | |
| 139 | { | |
| 140 | ISOSPEC_IMPOSSIBLE(first_free > backend_past_end); | |
| 141 | return *(first_free-1); | |
| 142 | } | |
| 143 | ||
| 144 | ISOSPEC_FORCE_INLINE void pop_back() noexcept | |
| 145 | { | |
| 146 | // Unlike std::vector we do not ever shrink backend storage unless explicitly requested. | |
| 147 | ISOSPEC_IMPOSSIBLE(first_free == store); | |
| 148 | first_free--; | |
| 149 | } | |
| 150 | ||
| 151 | void swap(pod_vector<T>& other) noexcept | |
| 152 | { | |
| 153 | std::swap(backend_past_end, other.backend_past_end); | |
| 154 | std::swap(first_free, other.first_free); | |
| 155 | std::swap(store, other.store); | |
| 156 | } | |
| 157 | ||
| 158 | typedef T* iterator; | |
| 159 | typedef const T* const_iterator; | |
| 160 | typedef T value_type; | |
| 161 | typedef size_t size_type; | |
| 162 | typedef T& reference; | |
| 163 | typedef const T& const_reference; | |
| 164 | ||
| 165 | iterator begin() noexcept { return store; }; | |
| 166 | const_iterator begin() const noexcept { return store; } | |
| 167 | const_iterator cbegin() const noexcept { return store; } | |
| 168 | iterator end() noexcept { return first_free; } | |
| 169 | const_iterator end() const noexcept { return first_free; } | |
| 170 | const_iterator cend() const noexcept { return first_free; } | |
| 171 | ||
| 172 | ISOSPEC_FORCE_INLINE const T& front() const noexcept | |
| 173 | { | |
| 174 | ISOSPEC_IMPOSSIBLE(store == first_free); | |
| 175 | return *store; | |
| 176 | } | |
| 177 | ||
| 178 | void clear() | |
| 179 | { | |
| 180 | free(store); | |
| 181 | first_free = store = backend_past_end = NULL; | |
| 182 | } | |
| 183 | ||
| 184 | friend class unsafe_pod_vector<T>; | |
| 185 | }; | |
| 186 | ||
| 187 | ||
| 188 | template<typename T> class unsafe_pod_vector | |
| 189 | { | |
| 190 | #if !ISOSPEC_BUILDING_R | |
| 191 | static_assert(std::is_trivially_copyable<T>::value, "Cannot use a pod_vector with a non-Plain Old Data type."); | |
| 192 | static_assert(std::is_trivially_copyable<unsafe_pod_vector<T> >::value, "Cannot use a pod_vector with a non-Plain Old Data type."); | |
| 193 | #endif | |
| 194 | ||
| 195 | T* backend_past_end; | |
| 196 | T* first_free; | |
| 197 | T* store; | |
| 198 | ||
| 199 | public: | |
| 200 | unsafe_pod_vector() = default; | |
| 201 | ||
| 202 | void init() { memset(this, 0, sizeof(*this)); } | |
| 203 | ||
| 204 | void init(size_t initial_size) | |
| 205 | { | |
| 206 | store = reinterpret_cast<T*>(malloc(sizeof(T) * initial_size)); | |
| 207 | if(store == NULL) | |
| 208 | throw std::bad_alloc(); | |
| 209 | first_free = store; | |
| 210 | backend_past_end = store + initial_size; | |
| 211 | } | |
| 212 | ||
| 213 | unsafe_pod_vector(const pod_vector<T>& other) = delete; // NOLINT(runtime/explicit) - seriously? Deleted constructors have to be marked explicit? | |
| 214 | unsafe_pod_vector& operator=(const pod_vector<T>& other) = delete; | |
| 215 | ||
| 216 | unsafe_pod_vector(unsafe_pod_vector<T>&& other) | |
| 217 | { | |
| 218 | memcpy(this, *other, sizeof(*this)); | |
| 219 | } | |
| 220 | ||
| 221 | ~unsafe_pod_vector() = default; | |
| 222 | ||
| 223 | void free() { free(store); } | |
| 224 | ||
| 225 | void fast_reserve(size_t n) | |
| 226 | { | |
| 227 | ISOSPEC_IMPOSSIBLE(n < static_cast<size_t>(backend_past_end - store)); | |
| 228 | T* new_store = reinterpret_cast<T*>(realloc(store, n * sizeof(T))); | |
| 229 | if(new_store == NULL) | |
| 230 | throw std::bad_alloc(); | |
| 231 | first_free = new_store + (first_free - store); | |
| 232 | backend_past_end = new_store + n; | |
| 233 | store = new_store; | |
| 234 | } | |
| 235 | ||
| 236 | void reserve(size_t n) | |
| 237 | { | |
| 238 | if (n > backend_past_end - store) | |
| 239 | fast_reserve(n); | |
| 240 | } | |
| 241 | ||
| 242 | void resize(size_t new_size) | |
| 243 | { | |
| 244 | ISOSPEC_IMPOSSIBLE(new_size < first_free - store); | |
| 245 | size_t cap = capacity(); | |
| 246 | if(cap < new_size) | |
| 247 | { | |
| 248 | do { | |
| 249 | cap = cap * 2; | |
| 250 | } while(cap < new_size); | |
| 251 | fast_reserve(cap); | |
| 252 | } | |
| 253 | first_free = store + new_size; | |
| 254 | } | |
| 255 | ||
| 256 | void resize_and_wipe(size_t new_size) | |
| 257 | { | |
| 258 | size_t old_size = size(); | |
| 259 | ISOSPEC_IMPOSSIBLE(new_size < old_size); | |
| 260 | resize(new_size); | |
| 261 | memset(store+old_size, 0, (new_size-old_size) * sizeof(T)); | |
| 262 | } | |
| 263 | ||
| 264 | ISOSPEC_FORCE_INLINE void nocheck_push_back(const T& val) noexcept | |
| 265 | { | |
| 266 | ISOSPEC_IMPOSSIBLE(first_free >= backend_past_end); | |
| 267 | *first_free = val; | |
| 268 | first_free++; | |
| 269 | } | |
| 270 | ||
| 271 | ISOSPEC_FORCE_INLINE void push_back(const T& val) | |
| 272 | { | |
| 273 | if(first_free >= backend_past_end) | |
| 274 | fast_reserve((std::max<std::ptrdiff_t>)(4, (backend_past_end-store)) * 2); | |
| 275 | *first_free = val; | |
| 276 | first_free++; | |
| 277 | } | |
| 278 | ||
| 279 | ISOSPEC_FORCE_INLINE T& operator[](size_t n) noexcept | |
| 280 | { | |
| 281 | ISOSPEC_IMPOSSIBLE(store + n >= first_free); | |
| 282 | return store[n]; | |
| 283 | } | |
| 284 | ||
| 285 | ISOSPEC_FORCE_INLINE const T& operator[](size_t n) const noexcept | |
| 286 | { | |
| 287 | ISOSPEC_IMPOSSIBLE(store + n >= first_free); | |
| 288 | return store[n]; | |
| 289 | } | |
| 290 | ||
| 291 | ISOSPEC_FORCE_INLINE size_t size() const noexcept | |
| 292 | { | |
| 293 | return first_free - store; | |
| 294 | } | |
| 295 | ||
| 296 | ISOSPEC_FORCE_INLINE size_t capacity() const noexcept | |
| 297 | { | |
| 298 | return backend_past_end - store; | |
| 299 | } | |
| 300 | ||
| 301 | ISOSPEC_FORCE_INLINE T* data() noexcept | |
| 302 | { | |
| 303 | return store; | |
| 304 | } | |
| 305 | ||
| 306 | ISOSPEC_FORCE_INLINE const T* data() const noexcept | |
| 307 | { | |
| 308 | return store; | |
| 309 | } | |
| 310 | ||
| 311 | ISOSPEC_FORCE_INLINE bool empty() const noexcept | |
| 312 | { | |
| 313 | return first_free == store; | |
| 314 | } | |
| 315 | ||
| 316 | ISOSPEC_FORCE_INLINE const T& back() const noexcept | |
| 317 | { | |
| 318 | ISOSPEC_IMPOSSIBLE(first_free > backend_past_end); | |
| 319 | return *(first_free-1); | |
| 320 | } | |
| 321 | ||
| 322 | ISOSPEC_FORCE_INLINE void pop_back() noexcept | |
| 323 | { | |
| 324 | // Unlike std::vector we do not ever shrink backend storage unless explicitly requested. | |
| 325 | ISOSPEC_IMPOSSIBLE(first_free == store); | |
| 326 | first_free--; | |
| 327 | } | |
| 328 | ||
| 329 | void swap(pod_vector<T>& other) noexcept | |
| 330 | { | |
| 331 | std::swap(backend_past_end, other.backend_past_end); | |
| 332 | std::swap(first_free, other.first_free); | |
| 333 | std::swap(store, other.store); | |
| 334 | } | |
| 335 | ||
| 336 | typedef T* iterator; | |
| 337 | typedef const T* const_iterator; | |
| 338 | typedef T value_type; | |
| 339 | typedef size_t size_type; | |
| 340 | typedef T& reference; | |
| 341 | typedef const T& const_reference; | |
| 342 | ||
| 343 | iterator begin() noexcept { return store; }; | |
| 344 | const_iterator begin() const noexcept { return store; } | |
| 345 | const_iterator cbegin() const noexcept { return store; } | |
| 346 | iterator end() noexcept { return first_free; } | |
| 347 | const_iterator end() const noexcept { return first_free; } | |
| 348 | const_iterator cend() const noexcept { return first_free; } | |
| 349 | ||
| 350 | ISOSPEC_FORCE_INLINE const T& front() const noexcept | |
| 351 | { | |
| 352 | ISOSPEC_IMPOSSIBLE(store == first_free); | |
| 353 | return *store; | |
| 354 | } | |
| 355 | ||
| 356 | void clear() | |
| 357 | { | |
| 358 | free(store); | |
| 359 | first_free = store = backend_past_end = NULL; | |
| 360 | } | |
| 361 | ||
| 362 | friend class pod_vector<T>; | |
| 363 | }; | |
| 364 |
| 11 | 11 | you require other licensing terms, please contact the authors. See |
| 12 | 12 | LICENCE file for more details. |
| 13 | 13 | |
| 14 | More details about the program may be found in the Analytical Chemistry | |
| 15 | publication: | |
| 14 | More details about the program may be found in the following Analytical | |
| 15 | Chemistry publications: | |
| 16 | 16 | |
| 17 | http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b01459 | |
| 17 | https://pubs.acs.org/doi/10.1021/acs.analchem.0c00959 | |
| 18 | https://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b01459 | |
| 18 | 19 | |
| 19 | 20 | See especially the Supporting Information for details about the algorithm. |
| 20 | ||
| 21 | ||
| 22 |
| 0 | #include <iostream> | |
| 1 | #include "../../IsoSpec++/unity-build.cpp" | |
| 2 | #include <cassert> | |
| 3 | ||
| 4 | using namespace IsoSpec; | |
| 5 | ||
| 6 | #ifndef ISOSPEC_TESTS_SKIP_MAIN | |
| 7 | ||
| 8 | size_t test_threshold_simple(const char* formula, int count, bool print_confs); | |
| 9 | ||
| 10 | int main(int argc, char** argv) | |
| 11 | { | |
| 12 | if(argc < 3) | |
| 13 | { | |
| 14 | std::cout << "Proper usage (for example): ./from_formula_threshold C10000H1000O1000N1000 0.01" << std::endl; | |
| 15 | std::cout << "...will the configurations with probability above 0.01 for the above molecule" << std::endl; | |
| 16 | return -1; | |
| 17 | } | |
| 18 | ||
| 19 | bool print_confs = true; | |
| 20 | ||
| 21 | if(argc > 3) | |
| 22 | print_confs = (strcmp(argv[3], "true") == 0); | |
| 23 | ||
| 24 | size_t no_visited = test_threshold_simple(argv[1], atof(argv[2]), print_confs); | |
| 25 | ||
| 26 | std::cout << "The number of visited configurations is:" << no_visited << std::endl; | |
| 27 | ||
| 28 | } | |
| 29 | #endif /* ISOSPEC_TESTS_SKIP_MAIN */ | |
| 30 | ||
| 31 | ||
| 32 | size_t test_threshold_simple(const char* formula, int count, bool print_confs) | |
| 33 | { | |
| 34 | ||
| 35 | std::cout << "selection" << std::endl; | |
| 36 | Iso molecule(formula); | |
| 37 | double threshold = exp(molecule.getModeLProb()); | |
| 38 | ||
| 39 | double thr_ratio = 1.25;//64.0; | |
| 40 | int last_confs = 0; | |
| 41 | int confs = 1; | |
| 42 | while(confs < count) | |
| 43 | { | |
| 44 | confs = 1; | |
| 45 | threshold = threshold / thr_ratio; | |
| 46 | last_confs = confs; | |
| 47 | confs = IsoThresholdGenerator(Iso(molecule, false), threshold, true).count_confs(); | |
| 48 | std::cout << confs << " " << threshold << std::endl; | |
| 49 | } | |
| 50 | ||
| 51 | std::cout << confs << " " << count << " ratio: " << ((double)confs)/count << std::endl; | |
| 52 | std::cout << "binsearch" << std::endl; | |
| 53 | ||
| 54 | IsoThresholdGenerator ITG(formula, threshold); | |
| 55 | double left_thr = threshold * thr_ratio; | |
| 56 | while(confs != count) | |
| 57 | { | |
| 58 | double mid_thr = (left_thr + threshold)/2.0; | |
| 59 | ITG.new_threshold(mid_thr); | |
| 60 | ITG.reset(); | |
| 61 | int mid_count = ITG.count_confs(); | |
| 62 | std::cout << mid_count << " " << " " << count << std::endl; | |
| 63 | if(mid_count < count) | |
| 64 | left_thr = mid_thr; | |
| 65 | else | |
| 66 | threshold = mid_thr; | |
| 67 | confs = mid_count; | |
| 68 | } | |
| 69 | std::cout << "accumulation..." << std::endl; | |
| 70 | IsoThresholdGenerator i(formula, threshold, true, 10, 10, false); | |
| 71 | double total_prob = 0.0; | |
| 72 | double* probs = new double[confs]; | |
| 73 | double* masses = new double[confs]; | |
| 74 | ||
| 75 | int idx = 0; | |
| 76 | while(i.advanceToNextConfiguration()) | |
| 77 | { | |
| 78 | probs[idx] = i.prob(); | |
| 79 | masses[idx] = i.mass(); | |
| 80 | } | |
| 81 | std::cout << "selection..." << std::endl; | |
| 82 | std::nth_element(probs, probs+count, probs+confs); | |
| 83 | // total_prob += i.prob(); | |
| 84 | // std::cout << "Done! total prob: " << total_prob << std::endl; | |
| 85 | return confs; | |
| 86 | } |
| 0 | ||
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| 32 | configure_file(${CMAKE_SOURCE_DIR}/CMakeStuff/doxyfile.in | |
| 33 | ${CMAKE_CURRENT_SOURCE_DIR}/doxyfile @ONLY) | |
| 34 | ||
| 35 | add_custom_target(html_doc | |
| 36 | COMMAND doxygen doxyfile | |
| 37 | WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} | |
| 38 | COMMENT "Doxygen-based developer html documentation generation") | |
| 39 | ||
| 40 | add_custom_target(pdf_doc | |
| 41 | COMMAND make | |
| 42 | WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/latex | |
| 43 | COMMENT "Doxygen-based developer pdf documentation generation") | |
| 44 | ||
| 45 | ||
| 46 | ############### | |
| 47 | # install stuff | |
| 48 | ||
| 49 | install(DIRECTORY images | |
| 50 | DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec) | |
| 51 | ||
| 52 | install(DIRECTORY html | |
| 53 | DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec) | |
| 54 | ||
| 55 | install(FILES latex/refman.pdf | |
| 56 | DESTINATION ${CMAKE_INSTALL_FULL_DATAROOTDIR}/doc/isospec/pdf) | |
| 57 | ||
| 58 | file(GLOB man3_pages "man/man3/*") | |
| 59 | ||
| 60 | install(FILES ${man3_pages} | |
| 61 | DESTINATION ${CMAKE_INSTALL_FULL_MANDIR}/man3) | |
| 62 | ||
| 63 | message("") | |
| 64 | message(STATUS "${BoldGreen}Finished configuration of the doc material.${ColourReset}") | |
| 65 | message("") | |
| 66 |
| 0 | \documentclass{article} | |
| 1 | \usepackage{epsfig} | |
| 2 | \pagestyle{empty} | |
| 3 | \begin{document} | |
| 4 | $ \prod_{e\in\mathcal{E}} \frac{n_e!}{n_{e0},\dots,n_{e,i_e-1}} p_{e,0}^{n_{e,0}} \dots p_{e,i_e-1}^{n_{e,i_e-1}} $ | |
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| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">allocator.cpp</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> </div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <iostream></span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include "allocator.h"</span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> </div><div class="line"><a name="l00021"></a><span class="lineno"><a class="line" href="namespace_iso_spec.html"> 21</a></span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> {</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> </div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="keyword">template</span> <<span class="keyword">typename</span> T></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <a class="code" href="class_iso_spec_1_1_allocator.html">Allocator<T>::Allocator</a>(<span class="keyword">const</span> <span class="keywordtype">int</span> dim, <span class="keyword">const</span> <span class="keywordtype">int</span> tabSize): currentId(-1), dim(dim), tabSize(tabSize)</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> {</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  currentTab = <span class="keyword">new</span> T[dim * tabSize];</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> }</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> </div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="keyword">template</span> <<span class="keyword">typename</span> T></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <a class="code" href="class_iso_spec_1_1_allocator.html">Allocator<T>::~Allocator</a>()</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> {</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 0; i < prevTabs.size(); ++i)</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  {</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keyword">delete</span> [] prevTabs[i];</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  }</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> </div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keyword">delete</span> [] currentTab;</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> }</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> </div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="keyword">template</span> <<span class="keyword">typename</span> T></div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="keywordtype">void</span> <a class="code" href="class_iso_spec_1_1_allocator.html">Allocator<T>::shiftTables</a>()</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> {</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  prevTabs.push_back(currentTab);</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  currentTab = <span class="keyword">new</span> T[dim * tabSize];</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  currentId = 0;</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> }</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="keyword">template</span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_allocator.html">Allocator<int></a>;</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> }</div><div class="ttc" id="class_iso_spec_1_1_allocator_html"><div class="ttname"><a href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8h_source.html#l00034">allocator.h:34</a></div></div> | |
| 80 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <iostream></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <string.h></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include "conf.h"</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> </div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> {</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> </div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="keyword">template</span> <<span class="keyword">typename</span> T> <span class="keyword">inline</span> <span class="keywordtype">void</span> copyConf(</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  <span class="keyword">const</span> T* source, T* destination,</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordtype">int</span> dim</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> ){</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  memcpy(destination, source, dim*<span class="keyword">sizeof</span>(T));</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> }</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_allocator.html"> 34</a></span> <span class="keyword">template</span> <<span class="keyword">typename</span> T> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_allocator.html">Allocator</a>{</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  T* currentTab;</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordtype">int</span> currentId;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> dim, tabSize;</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  std::vector<T*> prevTabs;</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <a class="code" href="class_iso_spec_1_1_allocator.html">Allocator</a>(<span class="keyword">const</span> <span class="keywordtype">int</span> dim, <span class="keyword">const</span> <span class="keywordtype">int</span> tabSize = 10000);</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  ~<a class="code" href="class_iso_spec_1_1_allocator.html">Allocator</a>();</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordtype">void</span> shiftTables();</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keyword">inline</span> T* newConf()</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  {</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  currentId++;</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordflow">if</span> (currentId >= tabSize)</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  shiftTables();</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keywordflow">return</span> &(currentTab[ currentId * dim ]);</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  }</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keyword">inline</span> T* makeCopy(<span class="keyword">const</span> T* conf)</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  {</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  T* currentPlace = newConf();</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  copyConf<T>( conf, currentPlace, dim );</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordflow">return</span> currentPlace;</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  }</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keyword">inline</span> T* makeExternalCopy(<span class="keyword">const</span> T* conf)</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  {</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  T* res = <span class="keyword">new</span> T[dim];</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  copyConf( conf, res, dim );</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keywordflow">return</span> res;</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  }</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> };</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> }</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div><div class="ttc" id="class_iso_spec_1_1_allocator_html"><div class="ttname"><a href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8h_source.html#l00034">allocator.h:34</a></div></div> | |
| 80 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
| 81 | </div><!-- fragment --></div><!-- contents --> | |
| 82 | <!-- start footer part --> | |
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| 84 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 86 | </a> 1.8.14 | |
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| 89 | </html> |
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| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
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| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
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| 58 | onmouseover="return searchBox.OnSearchSelectShow()" | |
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| 67 | </iframe> | |
| 68 | </div> | |
| 69 | ||
| 70 | <div class="header"> | |
| 71 | <div class="headertitle"> | |
| 72 | <div class="title">Class List</div> </div> | |
| 73 | </div><!--header--> | |
| 74 | <div class="contents"> | |
| 75 | <div class="textblock">Here are the classes, structs, unions and interfaces with brief descriptions:</div><div class="directory"> | |
| 76 | <div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span>]</div><table class="directory"> | |
| 77 | <tr id="row_0_" class="even"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_0_" class="arrow" onclick="toggleFolder('0_')">▼</span><span class="icona"><span class="icon">N</span></span><a class="el" href="namespace_iso_spec.html" target="_self">IsoSpec</a></td><td class="desc"></td></tr> | |
| 78 | <tr id="row_0_0_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_allocator.html" target="_self">Allocator</a></td><td class="desc"></td></tr> | |
| 79 | <tr id="row_0_1_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_conf_equal.html" target="_self">ConfEqual</a></td><td class="desc"></td></tr> | |
| 80 | <tr id="row_0_2_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_conf_order.html" target="_self">ConfOrder</a></td><td class="desc"></td></tr> | |
| 81 | <tr id="row_0_3_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_conf_order_marginal.html" target="_self">ConfOrderMarginal</a></td><td class="desc"></td></tr> | |
| 82 | <tr id="row_0_4_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_conf_order_marginal_descending.html" target="_self">ConfOrderMarginalDescending</a></td><td class="desc"></td></tr> | |
| 83 | <tr id="row_0_5_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_dirty_allocator.html" target="_self">DirtyAllocator</a></td><td class="desc"></td></tr> | |
| 84 | <tr id="row_0_6_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_iso.html" target="_self">Iso</a></td><td class="desc">For the calculation of the isotopic distribution </td></tr> | |
| 85 | <tr id="row_0_7_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_iso_generator.html" target="_self">IsoGenerator</a></td><td class="desc">The generator of isotopologues </td></tr> | |
| 86 | <tr id="row_0_8_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html" target="_self">IsoLayeredGenerator</a></td><td class="desc">The class that represents isotopologues above a given joint probability value </td></tr> | |
| 87 | <tr id="row_0_9_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html" target="_self">IsoOrderedGenerator</a></td><td class="desc">The generator of isotopologues sorted by their probability of occurrence </td></tr> | |
| 88 | <tr id="row_0_10_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html" target="_self">IsoThresholdGenerator</a></td><td class="desc">The generator of isotopologues above a given threshold value </td></tr> | |
| 89 | <tr id="row_0_11_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_key_hasher.html" target="_self">KeyHasher</a></td><td class="desc"></td></tr> | |
| 90 | <tr id="row_0_12_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_marginal.html" target="_self">Marginal</a></td><td class="desc">The marginal distribution class (a subisotopologue) </td></tr> | |
| 91 | <tr id="row_0_13_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_marginal_trek.html" target="_self">MarginalTrek</a></td><td class="desc">The marginal distribution class (a subisotopologue) </td></tr> | |
| 92 | <tr id="row_0_14_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html" target="_self">OrderMarginalsBySizeDecresing</a></td><td class="desc"></td></tr> | |
| 93 | <tr id="row_0_15_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html" target="_self">PrecalculatedMarginal</a></td><td class="desc">Precalculated <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class </td></tr> | |
| 94 | <tr id="row_0_16_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_reverse_order.html" target="_self">ReverseOrder</a></td><td class="desc"></td></tr> | |
| 95 | <tr id="row_0_17_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_s_summator.html" target="_self">SSummator</a></td><td class="desc"></td></tr> | |
| 96 | <tr id="row_0_18_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_summator.html" target="_self">Summator</a></td><td class="desc"></td></tr> | |
| 97 | <tr id="row_0_19_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_table_order.html" target="_self">TableOrder</a></td><td class="desc"></td></tr> | |
| 98 | <tr id="row_0_20_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_tabulator.html" target="_self">Tabulator</a></td><td class="desc"></td></tr> | |
| 99 | <tr id="row_0_21_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_t_summator.html" target="_self">TSummator</a></td><td class="desc"></td></tr> | |
| 100 | </table> | |
| 101 | </div><!-- directory --> | |
| 102 | </div><!-- contents --> | |
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| 105 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 107 | </a> 1.8.14 | |
| 108 | </small></address> | |
| 109 | </body> | |
| 110 | </html> |
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| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_allocator.html">Allocator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::Allocator< T > Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>Allocator</b>(const int dim, const int tabSize=10000) (defined in <a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a></td><td class="entry"></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>makeCopy</b>(const T *conf) (defined in <a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 84 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>makeExternalCopy</b>(const T *conf) (defined in <a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 85 | <tr bgcolor="#f0f0f0"><td class="entry"><b>newConf</b>() (defined in <a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 86 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>shiftTables</b>() (defined in <a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a></td><td class="entry"></td></tr> | |
| 87 | <tr bgcolor="#f0f0f0"><td class="entry"><b>~Allocator</b>() (defined in <a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< T ></a></td><td class="entry"></td></tr> | |
| 88 | </table></div><!-- contents --> | |
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| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
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| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::Allocator< T > Class Template Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a30f7d0aedcf0cf85e958d66aa7ce0ec7"><td class="memItemLeft" align="right" valign="top"><a id="a30f7d0aedcf0cf85e958d66aa7ce0ec7"></a> | |
| 86 |  </td><td class="memItemRight" valign="bottom"><b>Allocator</b> (const int dim, const int tabSize=10000)</td></tr> | |
| 87 | <tr class="separator:a30f7d0aedcf0cf85e958d66aa7ce0ec7"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:afee0ae1b40ebb05545e7ca29a8319989"><td class="memItemLeft" align="right" valign="top"><a id="afee0ae1b40ebb05545e7ca29a8319989"></a> | |
| 89 | void </td><td class="memItemRight" valign="bottom"><b>shiftTables</b> ()</td></tr> | |
| 90 | <tr class="separator:afee0ae1b40ebb05545e7ca29a8319989"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | <tr class="memitem:aca2253867d95eb50e170d00a01fb6507"><td class="memItemLeft" align="right" valign="top"><a id="aca2253867d95eb50e170d00a01fb6507"></a> | |
| 92 | T * </td><td class="memItemRight" valign="bottom"><b>newConf</b> ()</td></tr> | |
| 93 | <tr class="separator:aca2253867d95eb50e170d00a01fb6507"><td class="memSeparator" colspan="2"> </td></tr> | |
| 94 | <tr class="memitem:a4845b8c1c32e1828903fb71af604a2b1"><td class="memItemLeft" align="right" valign="top"><a id="a4845b8c1c32e1828903fb71af604a2b1"></a> | |
| 95 | T * </td><td class="memItemRight" valign="bottom"><b>makeCopy</b> (const T *conf)</td></tr> | |
| 96 | <tr class="separator:a4845b8c1c32e1828903fb71af604a2b1"><td class="memSeparator" colspan="2"> </td></tr> | |
| 97 | <tr class="memitem:ada9bd9a7168a79c53214fdb0fc66ecf5"><td class="memItemLeft" align="right" valign="top"><a id="ada9bd9a7168a79c53214fdb0fc66ecf5"></a> | |
| 98 | T * </td><td class="memItemRight" valign="bottom"><b>makeExternalCopy</b> (const T *conf)</td></tr> | |
| 99 | <tr class="separator:ada9bd9a7168a79c53214fdb0fc66ecf5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 100 | </table> | |
| 101 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 102 | <div class="textblock"><h3>template<typename T><br /> | |
| 103 | class IsoSpec::Allocator< T ></h3> | |
| 104 | ||
| 105 | ||
| 106 | <p class="definition">Definition at line <a class="el" href="allocator_8h_source.html#l00034">34</a> of file <a class="el" href="allocator_8h_source.html">allocator.h</a>.</p> | |
| 107 | </div><hr/>The documentation for this class was generated from the following files:<ul> | |
| 108 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="allocator_8h_source.html">allocator.h</a></li> | |
| 109 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="allocator_8cpp_source.html">allocator.cpp</a></li> | |
| 110 | </ul> | |
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| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_conf_equal.html">ConfEqual</a></li> </ul> | |
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| 74 | <div class="header"> | |
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| 76 | <div class="title">IsoSpec::ConfEqual Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_conf_equal.html">IsoSpec::ConfEqual</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>ConfEqual</b>(int dim) (defined in <a class="el" href="class_iso_spec_1_1_conf_equal.html">IsoSpec::ConfEqual</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_conf_equal.html">IsoSpec::ConfEqual</a></td><td class="entry"></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>operator()</b>(const int *conf1, const int *conf2) const (defined in <a class="el" href="class_iso_spec_1_1_conf_equal.html">IsoSpec::ConfEqual</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_conf_equal.html">IsoSpec::ConfEqual</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_conf_equal.html">ConfEqual</a></li> </ul> | |
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| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::ConfEqual Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a1e64267307db788516b6dfc98614d4a8"><td class="memItemLeft" align="right" valign="top"><a id="a1e64267307db788516b6dfc98614d4a8"></a> | |
| 86 |  </td><td class="memItemRight" valign="bottom"><b>ConfEqual</b> (int dim)</td></tr> | |
| 87 | <tr class="separator:a1e64267307db788516b6dfc98614d4a8"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:a3efc7320ba25aa916b98066d387890e0"><td class="memItemLeft" align="right" valign="top"><a id="a3efc7320ba25aa916b98066d387890e0"></a> | |
| 89 | bool </td><td class="memItemRight" valign="bottom"><b>operator()</b> (const int *conf1, const int *conf2) const</td></tr> | |
| 90 | <tr class="separator:a3efc7320ba25aa916b98066d387890e0"><td class="memSeparator" colspan="2"> </td></tr> | |
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| 92 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 93 | <div class="textblock"> | |
| 94 | <p class="definition">Definition at line <a class="el" href="operators_8h_source.html#l00045">45</a> of file <a class="el" href="operators_8h_source.html">operators.h</a>.</p> | |
| 95 | </div><hr/>The documentation for this class was generated from the following files:<ul> | |
| 96 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8h_source.html">operators.h</a></li> | |
| 97 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8cpp_source.html">operators.cpp</a></li> | |
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| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_conf_order.html">ConfOrder</a></li> </ul> | |
| 72 | </div> | |
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| 74 | <div class="header"> | |
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| 76 | <div class="title">IsoSpec::ConfOrder Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_conf_order.html">IsoSpec::ConfOrder</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>operator()</b>(void *conf1, void *conf2) const (defined in <a class="el" href="class_iso_spec_1_1_conf_order.html">IsoSpec::ConfOrder</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_conf_order.html">IsoSpec::ConfOrder</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
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| 86 | bool </td><td class="memItemRight" valign="bottom"><b>operator()</b> (void *conf1, void *conf2) const</td></tr> | |
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| 89 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 90 | <div class="textblock"> | |
| 91 | <p class="definition">Definition at line <a class="el" href="operators_8h_source.html#l00066">66</a> of file <a class="el" href="operators_8h_source.html">operators.h</a>.</p> | |
| 92 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 93 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8h_source.html">operators.h</a></li> | |
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| 72 | </div> | |
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| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::ConfOrderMarginal Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_conf_order_marginal.html">IsoSpec::ConfOrderMarginal</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>ConfOrderMarginal</b>(const double *logProbs, int dim) (defined in <a class="el" href="class_iso_spec_1_1_conf_order_marginal.html">IsoSpec::ConfOrderMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_conf_order_marginal.html">IsoSpec::ConfOrderMarginal</a></td><td class="entry"></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>operator()</b>(const Conf conf1, const Conf conf2) (defined in <a class="el" href="class_iso_spec_1_1_conf_order_marginal.html">IsoSpec::ConfOrderMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_conf_order_marginal.html">IsoSpec::ConfOrderMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 86 |  </td><td class="memItemRight" valign="bottom"><b>ConfOrderMarginal</b> (const double *logProbs, int dim)</td></tr> | |
| 87 | <tr class="separator:a91c7b8d57bcd751f08f064802f3c8b87"><td class="memSeparator" colspan="2"> </td></tr> | |
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| 89 | bool </td><td class="memItemRight" valign="bottom"><b>operator()</b> (const Conf conf1, const Conf conf2)</td></tr> | |
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| 94 | <p class="definition">Definition at line <a class="el" href="operators_8h_source.html#l00078">78</a> of file <a class="el" href="operators_8h_source.html">operators.h</a>.</p> | |
| 95 | </div><hr/>The documentation for this class was generated from the following files:<ul> | |
| 96 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8h_source.html">operators.h</a></li> | |
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| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_conf_order_marginal_descending.html">IsoSpec::ConfOrderMarginalDescending</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>ConfOrderMarginalDescending</b>(const double *logProbs, int dim) (defined in <a class="el" href="class_iso_spec_1_1_conf_order_marginal_descending.html">IsoSpec::ConfOrderMarginalDescending</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_conf_order_marginal_descending.html">IsoSpec::ConfOrderMarginalDescending</a></td><td class="entry"></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>operator()</b>(const Conf conf1, const Conf conf2) (defined in <a class="el" href="class_iso_spec_1_1_conf_order_marginal_descending.html">IsoSpec::ConfOrderMarginalDescending</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_conf_order_marginal_descending.html">IsoSpec::ConfOrderMarginalDescending</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 86 |  </td><td class="memItemRight" valign="bottom"><b>ConfOrderMarginalDescending</b> (const double *logProbs, int dim)</td></tr> | |
| 87 | <tr class="separator:a331cca614490a25d2bf4d48e04a1eba3"><td class="memSeparator" colspan="2"> </td></tr> | |
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| 89 | bool </td><td class="memItemRight" valign="bottom"><b>operator()</b> (const Conf conf1, const Conf conf2)</td></tr> | |
| 90 | <tr class="separator:ab393a338e6a2dedb75d4cc84b54ca1f1"><td class="memSeparator" colspan="2"> </td></tr> | |
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| 92 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 93 | <div class="textblock"> | |
| 94 | <p class="definition">Definition at line <a class="el" href="operators_8h_source.html#l00092">92</a> of file <a class="el" href="operators_8h_source.html">operators.h</a>.</p> | |
| 95 | </div><hr/>The documentation for this class was generated from the following files:<ul> | |
| 96 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8h_source.html">operators.h</a></li> | |
| 97 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8cpp_source.html">operators.cpp</a></li> | |
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| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_dirty_allocator.html">DirtyAllocator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::DirtyAllocator Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>DirtyAllocator</b>(const int dim, const int tabSize=10000) (defined in <a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a></td><td class="entry"></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>makeCopy</b>(const void *conf) (defined in <a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 84 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>makeExternalCopy</b>(const void *conf) (defined in <a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 85 | <tr bgcolor="#f0f0f0"><td class="entry"><b>newConf</b>() (defined in <a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 86 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>shiftTables</b>() (defined in <a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a></td><td class="entry"></td></tr> | |
| 87 | <tr bgcolor="#f0f0f0"><td class="entry"><b>~DirtyAllocator</b>() (defined in <a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a></td><td class="entry"></td></tr> | |
| 88 | </table></div><!-- contents --> | |
| 89 | <!-- start footer part --> | |
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| 91 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 92 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 93 | </a> 1.8.14 | |
| 94 | </small></address> | |
| 95 | </body> | |
| 96 | </html> |
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| 7 | <title>IsoSpec: IsoSpec::DirtyAllocator Class Reference</title> | |
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| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
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| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_dirty_allocator.html">DirtyAllocator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_dirty_allocator-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::DirtyAllocator Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a0a2cec7004fa67775b209688fef5c566"><td class="memItemLeft" align="right" valign="top"><a id="a0a2cec7004fa67775b209688fef5c566"></a> | |
| 86 |  </td><td class="memItemRight" valign="bottom"><b>DirtyAllocator</b> (const int dim, const int tabSize=10000)</td></tr> | |
| 87 | <tr class="separator:a0a2cec7004fa67775b209688fef5c566"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:afcaa8b5465f58d8a55dcd15a95921e4f"><td class="memItemLeft" align="right" valign="top"><a id="afcaa8b5465f58d8a55dcd15a95921e4f"></a> | |
| 89 | void </td><td class="memItemRight" valign="bottom"><b>shiftTables</b> ()</td></tr> | |
| 90 | <tr class="separator:afcaa8b5465f58d8a55dcd15a95921e4f"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | <tr class="memitem:a345a18940d01c2943f232591e87fe654"><td class="memItemLeft" align="right" valign="top"><a id="a345a18940d01c2943f232591e87fe654"></a> | |
| 92 | void * </td><td class="memItemRight" valign="bottom"><b>newConf</b> ()</td></tr> | |
| 93 | <tr class="separator:a345a18940d01c2943f232591e87fe654"><td class="memSeparator" colspan="2"> </td></tr> | |
| 94 | <tr class="memitem:ae3e30ff9aeb6649c8f01b07282711ac9"><td class="memItemLeft" align="right" valign="top"><a id="ae3e30ff9aeb6649c8f01b07282711ac9"></a> | |
| 95 | void * </td><td class="memItemRight" valign="bottom"><b>makeCopy</b> (const void *conf)</td></tr> | |
| 96 | <tr class="separator:ae3e30ff9aeb6649c8f01b07282711ac9"><td class="memSeparator" colspan="2"> </td></tr> | |
| 97 | <tr class="memitem:af13586082e8269f496c80183c6eb7703"><td class="memItemLeft" align="right" valign="top"><a id="af13586082e8269f496c80183c6eb7703"></a> | |
| 98 | void * </td><td class="memItemRight" valign="bottom"><b>makeExternalCopy</b> (const void *conf)</td></tr> | |
| 99 | <tr class="separator:af13586082e8269f496c80183c6eb7703"><td class="memSeparator" colspan="2"> </td></tr> | |
| 100 | </table> | |
| 101 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 102 | <div class="textblock"> | |
| 103 | <p class="definition">Definition at line <a class="el" href="dirty_allocator_8h_source.html#l00026">26</a> of file <a class="el" href="dirty_allocator_8h_source.html">dirtyAllocator.h</a>.</p> | |
| 104 | </div><hr/>The documentation for this class was generated from the following files:<ul> | |
| 105 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="dirty_allocator_8h_source.html">dirtyAllocator.h</a></li> | |
| 106 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="dirty_allocator_8cpp_source.html">dirtyAllocator.cpp</a></li> | |
| 107 | </ul> | |
| 108 | </div><!-- contents --> | |
| 109 | <!-- start footer part --> | |
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| 111 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 112 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 113 | </a> 1.8.14 | |
| 114 | </small></address> | |
| 115 | </body> | |
| 116 | </html> |
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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
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| 39 | <!-- Generated by Doxygen 1.8.14 --> | |
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| 56 | <div id="MSearchSelectWindow" | |
| 57 | onmouseover="return searchBox.OnSearchSelectShow()" | |
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| 61 | ||
| 62 | <!-- iframe showing the search results (closed by default) --> | |
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| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso.html">Iso</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::Iso Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 86 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 87 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 88 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 89 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a>(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a>(const char *formula)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a>(Iso &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a>(const Iso &other, bool fullcopy)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 96 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 99 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
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| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso.html">Iso</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="#pub-attribs">Public Attributes</a> | | |
| 78 | <a href="#pro-attribs">Protected Attributes</a> | | |
| 79 | <a href="class_iso_spec_1_1_iso-members.html">List of all members</a> </div> | |
| 80 | <div class="headertitle"> | |
| 81 | <div class="title">IsoSpec::Iso Class Reference</div> </div> | |
| 82 | </div><!--header--> | |
| 83 | <div class="contents"> | |
| 84 | ||
| 85 | <p>The <a class="el" href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. ">Iso</a> class for the calculation of the isotopic distribution. | |
| 86 | <a href="class_iso_spec_1_1_iso.html#details">More...</a></p> | |
| 87 | ||
| 88 | <p><code>#include <<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>></code></p> | |
| 89 | <div class="dynheader"> | |
| 90 | Inheritance diagram for IsoSpec::Iso:</div> | |
| 91 | <div class="dyncontent"> | |
| 92 | <div class="center"> | |
| 93 | <img src="class_iso_spec_1_1_iso.png" usemap="#IsoSpec::Iso_map" alt=""/> | |
| 94 | <map id="IsoSpec::Iso_map" name="IsoSpec::Iso_map"> | |
| 95 | <area href="class_iso_spec_1_1_iso_generator.html" title="The generator of isotopologues. " alt="IsoSpec::IsoGenerator" shape="rect" coords="202,56,394,80"/> | |
| 96 | <area href="class_iso_spec_1_1_iso_layered_generator.html" title="The class that represents isotopologues above a given joint probability value. " alt="IsoSpec::IsoLayeredGenerator" shape="rect" coords="0,112,192,136"/> | |
| 97 | <area href="class_iso_spec_1_1_iso_ordered_generator.html" title="The generator of isotopologues sorted by their probability of occurrence. " alt="IsoSpec::IsoOrderedGenerator" shape="rect" coords="202,112,394,136"/> | |
| 98 | <area href="class_iso_spec_1_1_iso_threshold_generator.html" title="The generator of isotopologues above a given threshold value. " alt="IsoSpec::IsoThresholdGenerator" shape="rect" coords="404,112,596,136"/> | |
| 99 | </map> | |
| 100 | </div></div> | |
| 101 | <table class="memberdecls"> | |
| 102 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 103 | Public Member Functions</h2></td></tr> | |
| 104 | <tr class="memitem:a5ff1fafd079a866e9d61bc7d859842ea"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a> (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td></tr> | |
| 105 | <tr class="memdesc:a5ff1fafd079a866e9d61bc7d859842ea"><td class="mdescLeft"> </td><td class="mdescRight">General constructror. <a href="#a5ff1fafd079a866e9d61bc7d859842ea">More...</a><br /></td></tr> | |
| 106 | <tr class="separator:a5ff1fafd079a866e9d61bc7d859842ea"><td class="memSeparator" colspan="2"> </td></tr> | |
| 107 | <tr class="memitem:ad389effb319e9ed73db9ed5749868b81"><td class="memItemLeft" align="right" valign="top"><a id="ad389effb319e9ed73db9ed5749868b81"></a> | |
| 108 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a> (const char *formula)</td></tr> | |
| 109 | <tr class="memdesc:ad389effb319e9ed73db9ed5749868b81"><td class="mdescLeft"> </td><td class="mdescRight">Constructor from the formula object. <br /></td></tr> | |
| 110 | <tr class="separator:ad389effb319e9ed73db9ed5749868b81"><td class="memSeparator" colspan="2"> </td></tr> | |
| 111 | <tr class="memitem:a6c93ecb77a11bc831cc7600797fbf837"><td class="memItemLeft" align="right" valign="top"><a id="a6c93ecb77a11bc831cc7600797fbf837"></a> | |
| 112 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&other)</td></tr> | |
| 113 | <tr class="memdesc:a6c93ecb77a11bc831cc7600797fbf837"><td class="mdescLeft"> </td><td class="mdescRight">The move constructor. <br /></td></tr> | |
| 114 | <tr class="separator:a6c93ecb77a11bc831cc7600797fbf837"><td class="memSeparator" colspan="2"> </td></tr> | |
| 115 | <tr class="memitem:a485cba7555fbdc64bbea19690f202b13"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a> (const <a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &other, bool fullcopy)</td></tr> | |
| 116 | <tr class="memdesc:a485cba7555fbdc64bbea19690f202b13"><td class="mdescLeft"> </td><td class="mdescRight">The copy constructor. <a href="#a485cba7555fbdc64bbea19690f202b13">More...</a><br /></td></tr> | |
| 117 | <tr class="separator:a485cba7555fbdc64bbea19690f202b13"><td class="memSeparator" colspan="2"> </td></tr> | |
| 118 | <tr class="memitem:a8cf8f90338bfc3e5117f5b491f7b523f"><td class="memItemLeft" align="right" valign="top"><a id="a8cf8f90338bfc3e5117f5b491f7b523f"></a> | |
| 119 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a> ()</td></tr> | |
| 120 | <tr class="memdesc:a8cf8f90338bfc3e5117f5b491f7b523f"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 121 | <tr class="separator:a8cf8f90338bfc3e5117f5b491f7b523f"><td class="memSeparator" colspan="2"> </td></tr> | |
| 122 | <tr class="memitem:a7541599fbc29dd374bb60e5eb8fc047d"><td class="memItemLeft" align="right" valign="top"><a id="a7541599fbc29dd374bb60e5eb8fc047d"></a> | |
| 123 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a> () const</td></tr> | |
| 124 | <tr class="memdesc:a7541599fbc29dd374bb60e5eb8fc047d"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest peak in the isotopic distribution. <br /></td></tr> | |
| 125 | <tr class="separator:a7541599fbc29dd374bb60e5eb8fc047d"><td class="memSeparator" colspan="2"> </td></tr> | |
| 126 | <tr class="memitem:a1ede5e34e5bbbb22ae89b362ce2c6faf"><td class="memItemLeft" align="right" valign="top"><a id="a1ede5e34e5bbbb22ae89b362ce2c6faf"></a> | |
| 127 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a> () const</td></tr> | |
| 128 | <tr class="memdesc:a1ede5e34e5bbbb22ae89b362ce2c6faf"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest peak in the isotopic distribution. <br /></td></tr> | |
| 129 | <tr class="separator:a1ede5e34e5bbbb22ae89b362ce2c6faf"><td class="memSeparator" colspan="2"> </td></tr> | |
| 130 | <tr class="memitem:a9035d076cec8f937d971e3fd972aa83f"><td class="memItemLeft" align="right" valign="top"><a id="a9035d076cec8f937d971e3fd972aa83f"></a> | |
| 131 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a> () const</td></tr> | |
| 132 | <tr class="memdesc:a9035d076cec8f937d971e3fd972aa83f"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode-configuration (if there are many modes, they share this value). <br /></td></tr> | |
| 133 | <tr class="separator:a9035d076cec8f937d971e3fd972aa83f"><td class="memSeparator" colspan="2"> </td></tr> | |
| 134 | <tr class="memitem:a62b17f48d86f62b5ed38ffb296a9daa5"><td class="memItemLeft" align="right" valign="top"><a id="a62b17f48d86f62b5ed38ffb296a9daa5"></a> | |
| 135 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a> () const</td></tr> | |
| 136 | <tr class="memdesc:a62b17f48d86f62b5ed38ffb296a9daa5"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of elements in the chemical formula of the molecule. <br /></td></tr> | |
| 137 | <tr class="separator:a62b17f48d86f62b5ed38ffb296a9daa5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 138 | <tr class="memitem:a656a37dd84a6c0534b2373210ed5a091"><td class="memItemLeft" align="right" valign="top"><a id="a656a37dd84a6c0534b2373210ed5a091"></a> | |
| 139 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a> () const</td></tr> | |
| 140 | <tr class="memdesc:a656a37dd84a6c0534b2373210ed5a091"><td class="mdescLeft"> </td><td class="mdescRight">Get the total number of isotopes of elements present in a chemical formula. <br /></td></tr> | |
| 141 | <tr class="separator:a656a37dd84a6c0534b2373210ed5a091"><td class="memSeparator" colspan="2"> </td></tr> | |
| 142 | </table><table class="memberdecls"> | |
| 143 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-attribs"></a> | |
| 144 | Public Attributes</h2></td></tr> | |
| 145 | <tr class="memitem:ad2a353f2c746648b08a9ad31ff775766"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td></tr> | |
| 146 | <tr class="separator:ad2a353f2c746648b08a9ad31ff775766"><td class="memSeparator" colspan="2"> </td></tr> | |
| 147 | </table><table class="memberdecls"> | |
| 148 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a> | |
| 149 | Protected Attributes</h2></td></tr> | |
| 150 | <tr class="memitem:a90245f9bc318f12720c134f61bbe0db0"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td></tr> | |
| 151 | <tr class="separator:a90245f9bc318f12720c134f61bbe0db0"><td class="memSeparator" colspan="2"> </td></tr> | |
| 152 | <tr class="memitem:a7235f0afc56dccd13937791a630c45da"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td></tr> | |
| 153 | <tr class="separator:a7235f0afc56dccd13937791a630c45da"><td class="memSeparator" colspan="2"> </td></tr> | |
| 154 | <tr class="memitem:ab01939334b6c3e69f65a36f9965971a2"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td></tr> | |
| 155 | <tr class="separator:ab01939334b6c3e69f65a36f9965971a2"><td class="memSeparator" colspan="2"> </td></tr> | |
| 156 | <tr class="memitem:a89ed144bf2495fa25840aca90a31b425"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td></tr> | |
| 157 | <tr class="separator:a89ed144bf2495fa25840aca90a31b425"><td class="memSeparator" colspan="2"> </td></tr> | |
| 158 | <tr class="memitem:a8dd2c443706935b582979b13f935115c"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td></tr> | |
| 159 | <tr class="separator:a8dd2c443706935b582979b13f935115c"><td class="memSeparator" colspan="2"> </td></tr> | |
| 160 | <tr class="memitem:aea98a8331a2f8a1a6bbcace6124fcfae"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> ** </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td></tr> | |
| 161 | <tr class="separator:aea98a8331a2f8a1a6bbcace6124fcfae"><td class="memSeparator" colspan="2"> </td></tr> | |
| 162 | <tr class="memitem:ab51c157b23ae6a6b521667b6f0e8a208"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td></tr> | |
| 163 | <tr class="separator:ab51c157b23ae6a6b521667b6f0e8a208"><td class="memSeparator" colspan="2"> </td></tr> | |
| 164 | </table> | |
| 165 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 166 | <div class="textblock"><p>The <a class="el" href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. ">Iso</a> class for the calculation of the isotopic distribution. </p> | |
| 167 | <p>It contains full description of the molecule for which one would like to calculate the isotopic distribution. </p> | |
| 168 | ||
| 169 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00052">52</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 170 | </div><h2 class="groupheader">Constructor & Destructor Documentation</h2> | |
| 171 | <a id="a5ff1fafd079a866e9d61bc7d859842ea"></a> | |
| 172 | <h2 class="memtitle"><span class="permalink"><a href="#a5ff1fafd079a866e9d61bc7d859842ea">◆ </a></span>Iso() <span class="overload">[1/2]</span></h2> | |
| 173 | ||
| 174 | <div class="memitem"> | |
| 175 | <div class="memproto"> | |
| 176 | <table class="memname"> | |
| 177 | <tr> | |
| 178 | <td class="memname">IsoSpec::Iso::Iso </td> | |
| 179 | <td>(</td> | |
| 180 | <td class="paramtype">int </td> | |
| 181 | <td class="paramname"><em>_dimNumber</em>, </td> | |
| 182 | </tr> | |
| 183 | <tr> | |
| 184 | <td class="paramkey"></td> | |
| 185 | <td></td> | |
| 186 | <td class="paramtype">const int * </td> | |
| 187 | <td class="paramname"><em>_isotopeNumbers</em>, </td> | |
| 188 | </tr> | |
| 189 | <tr> | |
| 190 | <td class="paramkey"></td> | |
| 191 | <td></td> | |
| 192 | <td class="paramtype">const int * </td> | |
| 193 | <td class="paramname"><em>_atomCounts</em>, </td> | |
| 194 | </tr> | |
| 195 | <tr> | |
| 196 | <td class="paramkey"></td> | |
| 197 | <td></td> | |
| 198 | <td class="paramtype">const double *const * </td> | |
| 199 | <td class="paramname"><em>_isotopeMasses</em>, </td> | |
| 200 | </tr> | |
| 201 | <tr> | |
| 202 | <td class="paramkey"></td> | |
| 203 | <td></td> | |
| 204 | <td class="paramtype">const double *const * </td> | |
| 205 | <td class="paramname"><em>_isotopeProbabilities</em> </td> | |
| 206 | </tr> | |
| 207 | <tr> | |
| 208 | <td></td> | |
| 209 | <td>)</td> | |
| 210 | <td></td><td></td> | |
| 211 | </tr> | |
| 212 | </table> | |
| 213 | </div><div class="memdoc"> | |
| 214 | ||
| 215 | <p>General constructror. </p> | |
| 216 | <dl class="params"><dt>Parameters</dt><dd> | |
| 217 | <table class="params"> | |
| 218 | <tr><td class="paramname">_dimNumber</td><td>The number of elements in the formula, e.g. for C100H202 it would be 2, as there are only carbon and hydrogen atoms. </td></tr> | |
| 219 | <tr><td class="paramname">_isotopeNumbers</td><td>A table with numbers of isotopes for each element, e.g. for C100H202 it would be {2, 2}, because both C and H have two stable isotopes. </td></tr> | |
| 220 | <tr><td class="paramname">_atomCounts</td><td>Number of atoms of each element in the formula, e.g. for C100H202 corresponds to {100, 202}. </td></tr> | |
| 221 | <tr><td class="paramname">_isotopeMasses</td><td>A table of masses of isotopes of the elements in the chemical formula, e.g. {12.0, 13.003355, 1.007825, 2.014102} for C100H202. </td></tr> | |
| 222 | <tr><td class="paramname">_isotopeProbabilities</td><td>A table of isotope frequencies of the elements in the chemical formula, e.g. {.989212, .010788, .999885, .000115} for C100H202. </td></tr> | |
| 223 | </table> | |
| 224 | </dd> | |
| 225 | </dl> | |
| 226 | ||
| 227 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8cpp_source.html#l00051">51</a> of file <a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a>.</p> | |
| 228 | ||
| 229 | </div> | |
| 230 | </div> | |
| 231 | <a id="a485cba7555fbdc64bbea19690f202b13"></a> | |
| 232 | <h2 class="memtitle"><span class="permalink"><a href="#a485cba7555fbdc64bbea19690f202b13">◆ </a></span>Iso() <span class="overload">[2/2]</span></h2> | |
| 233 | ||
| 234 | <div class="memitem"> | |
| 235 | <div class="memproto"> | |
| 236 | <table class="memname"> | |
| 237 | <tr> | |
| 238 | <td class="memname">IsoSpec::Iso::Iso </td> | |
| 239 | <td>(</td> | |
| 240 | <td class="paramtype">const <a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> & </td> | |
| 241 | <td class="paramname"><em>other</em>, </td> | |
| 242 | </tr> | |
| 243 | <tr> | |
| 244 | <td class="paramkey"></td> | |
| 245 | <td></td> | |
| 246 | <td class="paramtype">bool </td> | |
| 247 | <td class="paramname"><em>fullcopy</em> </td> | |
| 248 | </tr> | |
| 249 | <tr> | |
| 250 | <td></td> | |
| 251 | <td>)</td> | |
| 252 | <td></td><td></td> | |
| 253 | </tr> | |
| 254 | </table> | |
| 255 | </div><div class="memdoc"> | |
| 256 | ||
| 257 | <p>The copy constructor. </p> | |
| 258 | <dl class="params"><dt>Parameters</dt><dd> | |
| 259 | <table class="params"> | |
| 260 | <tr><td class="paramname">other</td><td>The other instance of the <a class="el" href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. ">Iso</a> class. </td></tr> | |
| 261 | <tr><td class="paramname">fullcopy</td><td>If false, copy only the number of atoms in the formula, the size of the configuration, the total number of isotopes, and the probability of the mode isotopologue. </td></tr> | |
| 262 | </table> | |
| 263 | </dd> | |
| 264 | </dl> | |
| 265 | ||
| 266 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8cpp_source.html#l00084">84</a> of file <a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a>.</p> | |
| 267 | ||
| 268 | </div> | |
| 269 | </div> | |
| 270 | <h2 class="groupheader">Member Data Documentation</h2> | |
| 271 | <a id="a8dd2c443706935b582979b13f935115c"></a> | |
| 272 | <h2 class="memtitle"><span class="permalink"><a href="#a8dd2c443706935b582979b13f935115c">◆ </a></span>allDim</h2> | |
| 273 | ||
| 274 | <div class="memitem"> | |
| 275 | <div class="memproto"> | |
| 276 | <table class="mlabels"> | |
| 277 | <tr> | |
| 278 | <td class="mlabels-left"> | |
| 279 | <table class="memname"> | |
| 280 | <tr> | |
| 281 | <td class="memname">int IsoSpec::Iso::allDim</td> | |
| 282 | </tr> | |
| 283 | </table> | |
| 284 | </td> | |
| 285 | <td class="mlabels-right"> | |
| 286 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 287 | </tr> | |
| 288 | </table> | |
| 289 | </div><div class="memdoc"> | |
| 290 | <p>The total number of isotopes of elements present in a chemical formula, e.g. for H20 it is 2+3=5. </p> | |
| 291 | ||
| 292 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00071">71</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 293 | ||
| 294 | </div> | |
| 295 | </div> | |
| 296 | <a id="ab01939334b6c3e69f65a36f9965971a2"></a> | |
| 297 | <h2 class="memtitle"><span class="permalink"><a href="#ab01939334b6c3e69f65a36f9965971a2">◆ </a></span>atomCounts</h2> | |
| 298 | ||
| 299 | <div class="memitem"> | |
| 300 | <div class="memproto"> | |
| 301 | <table class="mlabels"> | |
| 302 | <tr> | |
| 303 | <td class="mlabels-left"> | |
| 304 | <table class="memname"> | |
| 305 | <tr> | |
| 306 | <td class="memname">int* IsoSpec::Iso::atomCounts</td> | |
| 307 | </tr> | |
| 308 | </table> | |
| 309 | </td> | |
| 310 | <td class="mlabels-right"> | |
| 311 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 312 | </tr> | |
| 313 | </table> | |
| 314 | </div><div class="memdoc"> | |
| 315 | <p>A table with numbers of isotopes for each element. </p> | |
| 316 | ||
| 317 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00069">69</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 318 | ||
| 319 | </div> | |
| 320 | </div> | |
| 321 | <a id="a89ed144bf2495fa25840aca90a31b425"></a> | |
| 322 | <h2 class="memtitle"><span class="permalink"><a href="#a89ed144bf2495fa25840aca90a31b425">◆ </a></span>confSize</h2> | |
| 323 | ||
| 324 | <div class="memitem"> | |
| 325 | <div class="memproto"> | |
| 326 | <table class="mlabels"> | |
| 327 | <tr> | |
| 328 | <td class="mlabels-left"> | |
| 329 | <table class="memname"> | |
| 330 | <tr> | |
| 331 | <td class="memname">unsigned int IsoSpec::Iso::confSize</td> | |
| 332 | </tr> | |
| 333 | </table> | |
| 334 | </td> | |
| 335 | <td class="mlabels-right"> | |
| 336 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 337 | </tr> | |
| 338 | </table> | |
| 339 | </div><div class="memdoc"> | |
| 340 | <p>The number of bytes needed to represent the counts of isotopes present in the extended chemical formula. </p> | |
| 341 | ||
| 342 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00070">70</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 343 | ||
| 344 | </div> | |
| 345 | </div> | |
| 346 | <a id="a90245f9bc318f12720c134f61bbe0db0"></a> | |
| 347 | <h2 class="memtitle"><span class="permalink"><a href="#a90245f9bc318f12720c134f61bbe0db0">◆ </a></span>dimNumber</h2> | |
| 348 | ||
| 349 | <div class="memitem"> | |
| 350 | <div class="memproto"> | |
| 351 | <table class="mlabels"> | |
| 352 | <tr> | |
| 353 | <td class="mlabels-left"> | |
| 354 | <table class="memname"> | |
| 355 | <tr> | |
| 356 | <td class="memname">int IsoSpec::Iso::dimNumber</td> | |
| 357 | </tr> | |
| 358 | </table> | |
| 359 | </td> | |
| 360 | <td class="mlabels-right"> | |
| 361 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 362 | </tr> | |
| 363 | </table> | |
| 364 | </div><div class="memdoc"> | |
| 365 | <p>The number of elements in the chemical formula of the molecule. </p> | |
| 366 | ||
| 367 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00067">67</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 368 | ||
| 369 | </div> | |
| 370 | </div> | |
| 371 | <a id="ad2a353f2c746648b08a9ad31ff775766"></a> | |
| 372 | <h2 class="memtitle"><span class="permalink"><a href="#ad2a353f2c746648b08a9ad31ff775766">◆ </a></span>disowned</h2> | |
| 373 | ||
| 374 | <div class="memitem"> | |
| 375 | <div class="memproto"> | |
| 376 | <table class="memname"> | |
| 377 | <tr> | |
| 378 | <td class="memname">bool IsoSpec::Iso::disowned</td> | |
| 379 | </tr> | |
| 380 | </table> | |
| 381 | </div><div class="memdoc"> | |
| 382 | <p>A variable showing if the <a class="el" href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. ">Iso</a> class was specialized by its child-class. If so, then the description of the molecules has been transfered there and <a class="el" href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. ">Iso</a> is a carcass class, dead as a dodo, an ex-class if you will. </p> | |
| 383 | ||
| 384 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00065">65</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 385 | ||
| 386 | </div> | |
| 387 | </div> | |
| 388 | <a id="a7235f0afc56dccd13937791a630c45da"></a> | |
| 389 | <h2 class="memtitle"><span class="permalink"><a href="#a7235f0afc56dccd13937791a630c45da">◆ </a></span>isotopeNumbers</h2> | |
| 390 | ||
| 391 | <div class="memitem"> | |
| 392 | <div class="memproto"> | |
| 393 | <table class="mlabels"> | |
| 394 | <tr> | |
| 395 | <td class="mlabels-left"> | |
| 396 | <table class="memname"> | |
| 397 | <tr> | |
| 398 | <td class="memname">int* IsoSpec::Iso::isotopeNumbers</td> | |
| 399 | </tr> | |
| 400 | </table> | |
| 401 | </td> | |
| 402 | <td class="mlabels-right"> | |
| 403 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 404 | </tr> | |
| 405 | </table> | |
| 406 | </div><div class="memdoc"> | |
| 407 | <p>A table with numbers of isotopes for each element. </p> | |
| 408 | ||
| 409 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00068">68</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 410 | ||
| 411 | </div> | |
| 412 | </div> | |
| 413 | <a id="aea98a8331a2f8a1a6bbcace6124fcfae"></a> | |
| 414 | <h2 class="memtitle"><span class="permalink"><a href="#aea98a8331a2f8a1a6bbcace6124fcfae">◆ </a></span>marginals</h2> | |
| 415 | ||
| 416 | <div class="memitem"> | |
| 417 | <div class="memproto"> | |
| 418 | <table class="mlabels"> | |
| 419 | <tr> | |
| 420 | <td class="mlabels-left"> | |
| 421 | <table class="memname"> | |
| 422 | <tr> | |
| 423 | <td class="memname"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a>** IsoSpec::Iso::marginals</td> | |
| 424 | </tr> | |
| 425 | </table> | |
| 426 | </td> | |
| 427 | <td class="mlabels-right"> | |
| 428 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 429 | </tr> | |
| 430 | </table> | |
| 431 | </div><div class="memdoc"> | |
| 432 | <p>The table of pointers to the distributions of individual subisotopologues. </p> | |
| 433 | ||
| 434 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00072">72</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 435 | ||
| 436 | </div> | |
| 437 | </div> | |
| 438 | <a id="ab51c157b23ae6a6b521667b6f0e8a208"></a> | |
| 439 | <h2 class="memtitle"><span class="permalink"><a href="#ab51c157b23ae6a6b521667b6f0e8a208">◆ </a></span>modeLProb</h2> | |
| 440 | ||
| 441 | <div class="memitem"> | |
| 442 | <div class="memproto"> | |
| 443 | <table class="mlabels"> | |
| 444 | <tr> | |
| 445 | <td class="mlabels-left"> | |
| 446 | <table class="memname"> | |
| 447 | <tr> | |
| 448 | <td class="memname">double IsoSpec::Iso::modeLProb</td> | |
| 449 | </tr> | |
| 450 | </table> | |
| 451 | </td> | |
| 452 | <td class="mlabels-right"> | |
| 453 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 454 | </tr> | |
| 455 | </table> | |
| 456 | </div><div class="memdoc"> | |
| 457 | <p>The log-probability of the mode of the isotopic distribution. </p> | |
| 458 | ||
| 459 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00073">73</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 460 | ||
| 461 | </div> | |
| 462 | </div> | |
| 463 | <hr/>The documentation for this class was generated from the following files:<ul> | |
| 464 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a></li> | |
| 465 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a></li> | |
| 466 | </ul> | |
| 467 | </div><!-- contents --> | |
| 468 | <!-- start footer part --> | |
| 469 | <hr class="footer"/><address class="footer"><small> | |
| 470 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 471 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 472 | </a> 1.8.14 | |
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| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
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| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a></li> </ul> | |
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| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::IsoGenerator Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a20f48ba18c6aecc57d73b2c3ec3a11dd">advanceToNextConfiguration</a>()=0</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 86 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 87 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 88 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_conf_signature</b>(int *space) const =0 (defined in <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr> | |
| 89 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a>(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a>(const char *formula)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 96 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a>(Iso &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a>(const Iso &other, bool fullcopy)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoGenerator</a>(Iso &&iso, bool alloc_partials=true)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"></td></tr> | |
| 99 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 100 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">lprob</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 101 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 102 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">mass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 103 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 104 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 105 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 106 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 107 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">prob</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 108 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 109 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">~IsoGenerator</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 110 | </table></div><!-- contents --> | |
| 111 | <!-- start footer part --> | |
| 112 | <hr class="footer"/><address class="footer"><small> | |
| 113 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 115 | </a> 1.8.14 | |
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| 118 | </html> |
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| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="#pro-attribs">Protected Attributes</a> | | |
| 78 | <a href="class_iso_spec_1_1_iso_generator-members.html">List of all members</a> </div> | |
| 79 | <div class="headertitle"> | |
| 80 | <div class="title">IsoSpec::IsoGenerator Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span></div> </div> | |
| 81 | </div><!--header--> | |
| 82 | <div class="contents"> | |
| 83 | ||
| 84 | <p>The generator of isotopologues. | |
| 85 | <a href="class_iso_spec_1_1_iso_generator.html#details">More...</a></p> | |
| 86 | ||
| 87 | <p><code>#include <<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>></code></p> | |
| 88 | <div class="dynheader"> | |
| 89 | Inheritance diagram for IsoSpec::IsoGenerator:</div> | |
| 90 | <div class="dyncontent"> | |
| 91 | <div class="center"> | |
| 92 | <img src="class_iso_spec_1_1_iso_generator.png" usemap="#IsoSpec::IsoGenerator_map" alt=""/> | |
| 93 | <map id="IsoSpec::IsoGenerator_map" name="IsoSpec::IsoGenerator_map"> | |
| 94 | <area href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. " alt="IsoSpec::Iso" shape="rect" coords="202,0,394,24"/> | |
| 95 | <area href="class_iso_spec_1_1_iso_layered_generator.html" title="The class that represents isotopologues above a given joint probability value. " alt="IsoSpec::IsoLayeredGenerator" shape="rect" coords="0,112,192,136"/> | |
| 96 | <area href="class_iso_spec_1_1_iso_ordered_generator.html" title="The generator of isotopologues sorted by their probability of occurrence. " alt="IsoSpec::IsoOrderedGenerator" shape="rect" coords="202,112,394,136"/> | |
| 97 | <area href="class_iso_spec_1_1_iso_threshold_generator.html" title="The generator of isotopologues above a given threshold value. " alt="IsoSpec::IsoThresholdGenerator" shape="rect" coords="404,112,596,136"/> | |
| 98 | </map> | |
| 99 | </div></div> | |
| 100 | <table class="memberdecls"> | |
| 101 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 102 | Public Member Functions</h2></td></tr> | |
| 103 | <tr class="memitem:a20f48ba18c6aecc57d73b2c3ec3a11dd"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a20f48ba18c6aecc57d73b2c3ec3a11dd">advanceToNextConfiguration</a> ()=0</td></tr> | |
| 104 | <tr class="memdesc:a20f48ba18c6aecc57d73b2c3ec3a11dd"><td class="mdescLeft"> </td><td class="mdescRight">Advance to the next, not yet visited, most probable isotopologue. <a href="#a20f48ba18c6aecc57d73b2c3ec3a11dd">More...</a><br /></td></tr> | |
| 105 | <tr class="separator:a20f48ba18c6aecc57d73b2c3ec3a11dd"><td class="memSeparator" colspan="2"> </td></tr> | |
| 106 | <tr class="memitem:ae8e24abbce51a4c93994f630acfdf383"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">lprob</a> () const</td></tr> | |
| 107 | <tr class="memdesc:ae8e24abbce51a4c93994f630acfdf383"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the current isotopologue. <a href="#ae8e24abbce51a4c93994f630acfdf383">More...</a><br /></td></tr> | |
| 108 | <tr class="separator:ae8e24abbce51a4c93994f630acfdf383"><td class="memSeparator" colspan="2"> </td></tr> | |
| 109 | <tr class="memitem:a34173228ef73e272e2ff0ae6ce58092d"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">mass</a> () const</td></tr> | |
| 110 | <tr class="memdesc:a34173228ef73e272e2ff0ae6ce58092d"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the current isotopologue. <a href="#a34173228ef73e272e2ff0ae6ce58092d">More...</a><br /></td></tr> | |
| 111 | <tr class="separator:a34173228ef73e272e2ff0ae6ce58092d"><td class="memSeparator" colspan="2"> </td></tr> | |
| 112 | <tr class="memitem:aecf1b3292fcc0857a86efe619a37fff0"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">prob</a> () const</td></tr> | |
| 113 | <tr class="memdesc:aecf1b3292fcc0857a86efe619a37fff0"><td class="mdescLeft"> </td><td class="mdescRight">Get the probability of the current isotopologue. <a href="#aecf1b3292fcc0857a86efe619a37fff0">More...</a><br /></td></tr> | |
| 114 | <tr class="separator:aecf1b3292fcc0857a86efe619a37fff0"><td class="memSeparator" colspan="2"> </td></tr> | |
| 115 | <tr class="memitem:a19ca8af7dd97f8f37756d4267d49d91d"><td class="memItemLeft" align="right" valign="top"><a id="a19ca8af7dd97f8f37756d4267d49d91d"></a> | |
| 116 | virtual void </td><td class="memItemRight" valign="bottom"><b>get_conf_signature</b> (int *space) const =0</td></tr> | |
| 117 | <tr class="separator:a19ca8af7dd97f8f37756d4267d49d91d"><td class="memSeparator" colspan="2"> </td></tr> | |
| 118 | <tr class="memitem:a89b5b851fbc67f79ed165af0b9b2a188"><td class="memItemLeft" align="right" valign="top"><a id="a89b5b851fbc67f79ed165af0b9b2a188"></a> | |
| 119 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoGenerator</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&iso, bool alloc_partials=true)</td></tr> | |
| 120 | <tr class="memdesc:a89b5b851fbc67f79ed165af0b9b2a188"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 121 | <tr class="separator:a89b5b851fbc67f79ed165af0b9b2a188"><td class="memSeparator" colspan="2"> </td></tr> | |
| 122 | <tr class="memitem:a28442c8072a2e85faf5ff04f5feffd76"><td class="memItemLeft" align="right" valign="top"><a id="a28442c8072a2e85faf5ff04f5feffd76"></a> | |
| 123 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">~IsoGenerator</a> ()</td></tr> | |
| 124 | <tr class="memdesc:a28442c8072a2e85faf5ff04f5feffd76"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 125 | <tr class="separator:a28442c8072a2e85faf5ff04f5feffd76"><td class="memSeparator" colspan="2"> </td></tr> | |
| 126 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 127 | <tr class="memitem:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a> (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td></tr> | |
| 128 | <tr class="memdesc:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">General constructror. <a href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">More...</a><br /></td></tr> | |
| 129 | <tr class="separator:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 130 | <tr class="memitem:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="ad389effb319e9ed73db9ed5749868b81"></a> | |
| 131 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a> (const char *formula)</td></tr> | |
| 132 | <tr class="memdesc:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Constructor from the formula object. <br /></td></tr> | |
| 133 | <tr class="separator:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 134 | <tr class="memitem:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a6c93ecb77a11bc831cc7600797fbf837"></a> | |
| 135 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&other)</td></tr> | |
| 136 | <tr class="memdesc:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">The move constructor. <br /></td></tr> | |
| 137 | <tr class="separator:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 138 | <tr class="memitem:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a> (const <a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &other, bool fullcopy)</td></tr> | |
| 139 | <tr class="memdesc:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">The copy constructor. <a href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">More...</a><br /></td></tr> | |
| 140 | <tr class="separator:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 141 | <tr class="memitem:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a8cf8f90338bfc3e5117f5b491f7b523f"></a> | |
| 142 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a> ()</td></tr> | |
| 143 | <tr class="memdesc:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 144 | <tr class="separator:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 145 | <tr class="memitem:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a7541599fbc29dd374bb60e5eb8fc047d"></a> | |
| 146 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a> () const</td></tr> | |
| 147 | <tr class="memdesc:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest peak in the isotopic distribution. <br /></td></tr> | |
| 148 | <tr class="separator:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 149 | <tr class="memitem:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a1ede5e34e5bbbb22ae89b362ce2c6faf"></a> | |
| 150 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a> () const</td></tr> | |
| 151 | <tr class="memdesc:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest peak in the isotopic distribution. <br /></td></tr> | |
| 152 | <tr class="separator:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 153 | <tr class="memitem:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a9035d076cec8f937d971e3fd972aa83f"></a> | |
| 154 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a> () const</td></tr> | |
| 155 | <tr class="memdesc:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode-configuration (if there are many modes, they share this value). <br /></td></tr> | |
| 156 | <tr class="separator:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 157 | <tr class="memitem:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a62b17f48d86f62b5ed38ffb296a9daa5"></a> | |
| 158 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a> () const</td></tr> | |
| 159 | <tr class="memdesc:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of elements in the chemical formula of the molecule. <br /></td></tr> | |
| 160 | <tr class="separator:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 161 | <tr class="memitem:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a656a37dd84a6c0534b2373210ed5a091"></a> | |
| 162 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a> () const</td></tr> | |
| 163 | <tr class="memdesc:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the total number of isotopes of elements present in a chemical formula. <br /></td></tr> | |
| 164 | <tr class="separator:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 165 | </table><table class="memberdecls"> | |
| 166 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a> | |
| 167 | Protected Attributes</h2></td></tr> | |
| 168 | <tr class="memitem:a54a39b847a71aa08d1207d0666dd62bc"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a></td></tr> | |
| 169 | <tr class="separator:a54a39b847a71aa08d1207d0666dd62bc"><td class="memSeparator" colspan="2"> </td></tr> | |
| 170 | <tr class="memitem:af5654fcdba8199cbd60668af5de89a53"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a></td></tr> | |
| 171 | <tr class="separator:af5654fcdba8199cbd60668af5de89a53"><td class="memSeparator" colspan="2"> </td></tr> | |
| 172 | <tr class="memitem:ac18406df84b4b220bcb1974000c192b2"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a></td></tr> | |
| 173 | <tr class="separator:ac18406df84b4b220bcb1974000c192b2"><td class="memSeparator" colspan="2"> </td></tr> | |
| 174 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 175 | <tr class="memitem:a90245f9bc318f12720c134f61bbe0db0 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td></tr> | |
| 176 | <tr class="separator:a90245f9bc318f12720c134f61bbe0db0 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 177 | <tr class="memitem:a7235f0afc56dccd13937791a630c45da inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td></tr> | |
| 178 | <tr class="separator:a7235f0afc56dccd13937791a630c45da inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 179 | <tr class="memitem:ab01939334b6c3e69f65a36f9965971a2 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td></tr> | |
| 180 | <tr class="separator:ab01939334b6c3e69f65a36f9965971a2 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 181 | <tr class="memitem:a89ed144bf2495fa25840aca90a31b425 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td></tr> | |
| 182 | <tr class="separator:a89ed144bf2495fa25840aca90a31b425 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 183 | <tr class="memitem:a8dd2c443706935b582979b13f935115c inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td></tr> | |
| 184 | <tr class="separator:a8dd2c443706935b582979b13f935115c inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 185 | <tr class="memitem:aea98a8331a2f8a1a6bbcace6124fcfae inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> ** </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td></tr> | |
| 186 | <tr class="separator:aea98a8331a2f8a1a6bbcace6124fcfae inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 187 | <tr class="memitem:ab51c157b23ae6a6b521667b6f0e8a208 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td></tr> | |
| 188 | <tr class="separator:ab51c157b23ae6a6b521667b6f0e8a208 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 189 | </table><table class="memberdecls"> | |
| 190 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a> | |
| 191 | Additional Inherited Members</h2></td></tr> | |
| 192 | <tr class="inherit_header pub_attribs_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pub_attribs_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Public Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 193 | <tr class="memitem:ad2a353f2c746648b08a9ad31ff775766 inherit pub_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td></tr> | |
| 194 | <tr class="separator:ad2a353f2c746648b08a9ad31ff775766 inherit pub_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 195 | </table> | |
| 196 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 197 | <div class="textblock"><p>The generator of isotopologues. </p> | |
| 198 | <p>This class provides the common interface for all isotopic generators. </p> | |
| 199 | ||
| 200 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00129">129</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 201 | </div><h2 class="groupheader">Member Function Documentation</h2> | |
| 202 | <a id="a20f48ba18c6aecc57d73b2c3ec3a11dd"></a> | |
| 203 | <h2 class="memtitle"><span class="permalink"><a href="#a20f48ba18c6aecc57d73b2c3ec3a11dd">◆ </a></span>advanceToNextConfiguration()</h2> | |
| 204 | ||
| 205 | <div class="memitem"> | |
| 206 | <div class="memproto"> | |
| 207 | <table class="mlabels"> | |
| 208 | <tr> | |
| 209 | <td class="mlabels-left"> | |
| 210 | <table class="memname"> | |
| 211 | <tr> | |
| 212 | <td class="memname">virtual bool IsoSpec::IsoGenerator::advanceToNextConfiguration </td> | |
| 213 | <td>(</td> | |
| 214 | <td class="paramname"></td><td>)</td> | |
| 215 | <td></td> | |
| 216 | </tr> | |
| 217 | </table> | |
| 218 | </td> | |
| 219 | <td class="mlabels-right"> | |
| 220 | <span class="mlabels"><span class="mlabel">pure virtual</span></span> </td> | |
| 221 | </tr> | |
| 222 | </table> | |
| 223 | </div><div class="memdoc"> | |
| 224 | ||
| 225 | <p>Advance to the next, not yet visited, most probable isotopologue. </p> | |
| 226 | <dl class="section return"><dt>Returns</dt><dd>Return false if it is not possible to advance. </dd></dl> | |
| 227 | ||
| 228 | <p>Implemented in <a class="el" href="class_iso_spec_1_1_iso_layered_generator.html#abce0871ac279fd54a0344ceb80126b66">IsoSpec::IsoLayeredGenerator</a>, <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a7164a6476b84665967c4a667a91d3f3e">IsoSpec::IsoThresholdGenerator</a>, and <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#aa2438bb81fb1d68eda1637d67e9cb36d">IsoSpec::IsoOrderedGenerator</a>.</p> | |
| 229 | ||
| 230 | </div> | |
| 231 | </div> | |
| 232 | <a id="ae8e24abbce51a4c93994f630acfdf383"></a> | |
| 233 | <h2 class="memtitle"><span class="permalink"><a href="#ae8e24abbce51a4c93994f630acfdf383">◆ </a></span>lprob()</h2> | |
| 234 | ||
| 235 | <div class="memitem"> | |
| 236 | <div class="memproto"> | |
| 237 | <table class="mlabels"> | |
| 238 | <tr> | |
| 239 | <td class="mlabels-left"> | |
| 240 | <table class="memname"> | |
| 241 | <tr> | |
| 242 | <td class="memname">virtual double IsoSpec::IsoGenerator::lprob </td> | |
| 243 | <td>(</td> | |
| 244 | <td class="paramname"></td><td>)</td> | |
| 245 | <td> const</td> | |
| 246 | </tr> | |
| 247 | </table> | |
| 248 | </td> | |
| 249 | <td class="mlabels-right"> | |
| 250 | <span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">virtual</span></span> </td> | |
| 251 | </tr> | |
| 252 | </table> | |
| 253 | </div><div class="memdoc"> | |
| 254 | ||
| 255 | <p>Get the log-probability of the current isotopologue. </p> | |
| 256 | <dl class="section return"><dt>Returns</dt><dd>The log-probability of the current isotopologue. </dd></dl> | |
| 257 | ||
| 258 | <p>Reimplemented in <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a4aeebde03e385404d0175fd5696ff529">IsoSpec::IsoThresholdGenerator</a>.</p> | |
| 259 | ||
| 260 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00147">147</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 261 | ||
| 262 | </div> | |
| 263 | </div> | |
| 264 | <a id="a34173228ef73e272e2ff0ae6ce58092d"></a> | |
| 265 | <h2 class="memtitle"><span class="permalink"><a href="#a34173228ef73e272e2ff0ae6ce58092d">◆ </a></span>mass()</h2> | |
| 266 | ||
| 267 | <div class="memitem"> | |
| 268 | <div class="memproto"> | |
| 269 | <table class="mlabels"> | |
| 270 | <tr> | |
| 271 | <td class="mlabels-left"> | |
| 272 | <table class="memname"> | |
| 273 | <tr> | |
| 274 | <td class="memname">virtual double IsoSpec::IsoGenerator::mass </td> | |
| 275 | <td>(</td> | |
| 276 | <td class="paramname"></td><td>)</td> | |
| 277 | <td> const</td> | |
| 278 | </tr> | |
| 279 | </table> | |
| 280 | </td> | |
| 281 | <td class="mlabels-right"> | |
| 282 | <span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">virtual</span></span> </td> | |
| 283 | </tr> | |
| 284 | </table> | |
| 285 | </div><div class="memdoc"> | |
| 286 | ||
| 287 | <p>Get the mass of the current isotopologue. </p> | |
| 288 | <dl class="section return"><dt>Returns</dt><dd>The mass of the current isotopologue. </dd></dl> | |
| 289 | ||
| 290 | <p>Reimplemented in <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ae2236accc7dc7a25a723e3c7317659b6">IsoSpec::IsoThresholdGenerator</a>.</p> | |
| 291 | ||
| 292 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00153">153</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 293 | ||
| 294 | </div> | |
| 295 | </div> | |
| 296 | <a id="aecf1b3292fcc0857a86efe619a37fff0"></a> | |
| 297 | <h2 class="memtitle"><span class="permalink"><a href="#aecf1b3292fcc0857a86efe619a37fff0">◆ </a></span>prob()</h2> | |
| 298 | ||
| 299 | <div class="memitem"> | |
| 300 | <div class="memproto"> | |
| 301 | <table class="mlabels"> | |
| 302 | <tr> | |
| 303 | <td class="mlabels-left"> | |
| 304 | <table class="memname"> | |
| 305 | <tr> | |
| 306 | <td class="memname">virtual double IsoSpec::IsoGenerator::prob </td> | |
| 307 | <td>(</td> | |
| 308 | <td class="paramname"></td><td>)</td> | |
| 309 | <td> const</td> | |
| 310 | </tr> | |
| 311 | </table> | |
| 312 | </td> | |
| 313 | <td class="mlabels-right"> | |
| 314 | <span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">virtual</span></span> </td> | |
| 315 | </tr> | |
| 316 | </table> | |
| 317 | </div><div class="memdoc"> | |
| 318 | ||
| 319 | <p>Get the probability of the current isotopologue. </p> | |
| 320 | <dl class="section return"><dt>Returns</dt><dd>The probability of the current isotopologue. </dd></dl> | |
| 321 | ||
| 322 | <p>Reimplemented in <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a998d987f81b2ca7ed610294f6a5f8df5">IsoSpec::IsoThresholdGenerator</a>.</p> | |
| 323 | ||
| 324 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00159">159</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 325 | ||
| 326 | </div> | |
| 327 | </div> | |
| 328 | <h2 class="groupheader">Member Data Documentation</h2> | |
| 329 | <a id="a54a39b847a71aa08d1207d0666dd62bc"></a> | |
| 330 | <h2 class="memtitle"><span class="permalink"><a href="#a54a39b847a71aa08d1207d0666dd62bc">◆ </a></span>partialLProbs</h2> | |
| 331 | ||
| 332 | <div class="memitem"> | |
| 333 | <div class="memproto"> | |
| 334 | <table class="mlabels"> | |
| 335 | <tr> | |
| 336 | <td class="mlabels-left"> | |
| 337 | <table class="memname"> | |
| 338 | <tr> | |
| 339 | <td class="memname">double* IsoSpec::IsoGenerator::partialLProbs</td> | |
| 340 | </tr> | |
| 341 | </table> | |
| 342 | </td> | |
| 343 | <td class="mlabels-right"> | |
| 344 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 345 | </tr> | |
| 346 | </table> | |
| 347 | </div><div class="memdoc"> | |
| 348 | <p>The prefix sum of the log-probabilities of the current isotopologue. </p> | |
| 349 | ||
| 350 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00132">132</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 351 | ||
| 352 | </div> | |
| 353 | </div> | |
| 354 | <a id="af5654fcdba8199cbd60668af5de89a53"></a> | |
| 355 | <h2 class="memtitle"><span class="permalink"><a href="#af5654fcdba8199cbd60668af5de89a53">◆ </a></span>partialMasses</h2> | |
| 356 | ||
| 357 | <div class="memitem"> | |
| 358 | <div class="memproto"> | |
| 359 | <table class="mlabels"> | |
| 360 | <tr> | |
| 361 | <td class="mlabels-left"> | |
| 362 | <table class="memname"> | |
| 363 | <tr> | |
| 364 | <td class="memname">double* IsoSpec::IsoGenerator::partialMasses</td> | |
| 365 | </tr> | |
| 366 | </table> | |
| 367 | </td> | |
| 368 | <td class="mlabels-right"> | |
| 369 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 370 | </tr> | |
| 371 | </table> | |
| 372 | </div><div class="memdoc"> | |
| 373 | <p>The prefix sum of the masses of the current isotopologue. </p> | |
| 374 | ||
| 375 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00133">133</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 376 | ||
| 377 | </div> | |
| 378 | </div> | |
| 379 | <a id="ac18406df84b4b220bcb1974000c192b2"></a> | |
| 380 | <h2 class="memtitle"><span class="permalink"><a href="#ac18406df84b4b220bcb1974000c192b2">◆ </a></span>partialProbs</h2> | |
| 381 | ||
| 382 | <div class="memitem"> | |
| 383 | <div class="memproto"> | |
| 384 | <table class="mlabels"> | |
| 385 | <tr> | |
| 386 | <td class="mlabels-left"> | |
| 387 | <table class="memname"> | |
| 388 | <tr> | |
| 389 | <td class="memname">double* IsoSpec::IsoGenerator::partialProbs</td> | |
| 390 | </tr> | |
| 391 | </table> | |
| 392 | </td> | |
| 393 | <td class="mlabels-right"> | |
| 394 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 395 | </tr> | |
| 396 | </table> | |
| 397 | </div><div class="memdoc"> | |
| 398 | <p>The prefix product of the probabilities of the current isotopologue. </p> | |
| 399 | ||
| 400 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00134">134</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 401 | ||
| 402 | </div> | |
| 403 | </div> | |
| 404 | <hr/>The documentation for this class was generated from the following files:<ul> | |
| 405 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a></li> | |
| 406 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a></li> | |
| 407 | </ul> | |
| 408 | </div><!-- contents --> | |
| 409 | <!-- start footer part --> | |
| 410 | <hr class="footer"/><address class="footer"><small> | |
| 411 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 412 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 413 | </a> 1.8.14 | |
| 414 | </small></address> | |
| 415 | </body> | |
| 416 | </html> |
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| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
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| 62 | <!-- iframe showing the search results (closed by default) --> | |
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| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoLayeredGenerator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::IsoLayeredGenerator Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html#abce0871ac279fd54a0344ceb80126b66">advanceToNextConfiguration</a>() override final</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 86 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 87 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 88 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_conf_signature</b>(int *space) const override final (defined in <a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 89 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a>(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a>(const char *formula)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 96 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a>(Iso &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a>(const Iso &other, bool fullcopy)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoGenerator</a>(Iso &&iso, bool alloc_partials=true)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"></td></tr> | |
| 99 | <tr bgcolor="#f0f0f0"><td class="entry"><b>IsoLayeredGenerator</b>(Iso &&iso, double _targetCoverage, double _percentageToExpand, int _tabSize=1000, int _hashSize=1000, bool trim=false) (defined in <a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a></td><td class="entry"></td></tr> | |
| 100 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 101 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">lprob</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 102 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 103 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">mass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 104 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 105 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 106 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 107 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 108 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">prob</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 109 | <tr bgcolor="#f0f0f0"><td class="entry"><b>terminate_search</b>() (defined in <a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a></td><td class="entry"></td></tr> | |
| 110 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 111 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">~IsoGenerator</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 112 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~IsoLayeredGenerator</b>() (defined in <a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 113 | </table></div><!-- contents --> | |
| 114 | <!-- start footer part --> | |
| 115 | <hr class="footer"/><address class="footer"><small> | |
| 116 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 118 | </a> 1.8.14 | |
| 119 | </small></address> | |
| 120 | </body> | |
| 121 | </html> |
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| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
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| 42 | var searchBox = new SearchBox("searchBox", "search",false,'Search'); | |
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| 57 | onmouseover="return searchBox.OnSearchSelectShow()" | |
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| 59 | onkeydown="return searchBox.OnSearchSelectKey(event)"> | |
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| 61 | ||
| 62 | <!-- iframe showing the search results (closed by default) --> | |
| 63 | <div id="MSearchResultsWindow"> | |
| 64 | <iframe src="javascript:void(0)" frameborder="0" | |
| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoLayeredGenerator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_iso_layered_generator-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoLayeredGenerator Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p>The class that represents isotopologues above a given joint probability value. | |
| 84 | <a href="class_iso_spec_1_1_iso_layered_generator.html#details">More...</a></p> | |
| 85 | ||
| 86 | <p><code>#include <<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>></code></p> | |
| 87 | <div class="dynheader"> | |
| 88 | Inheritance diagram for IsoSpec::IsoLayeredGenerator:</div> | |
| 89 | <div class="dyncontent"> | |
| 90 | <div class="center"> | |
| 91 | <img src="class_iso_spec_1_1_iso_layered_generator.png" usemap="#IsoSpec::IsoLayeredGenerator_map" alt=""/> | |
| 92 | <map id="IsoSpec::IsoLayeredGenerator_map" name="IsoSpec::IsoLayeredGenerator_map"> | |
| 93 | <area href="class_iso_spec_1_1_iso_generator.html" title="The generator of isotopologues. " alt="IsoSpec::IsoGenerator" shape="rect" coords="0,56,183,80"/> | |
| 94 | <area href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. " alt="IsoSpec::Iso" shape="rect" coords="0,0,183,24"/> | |
| 95 | </map> | |
| 96 | </div></div> | |
| 97 | <table class="memberdecls"> | |
| 98 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 99 | Public Member Functions</h2></td></tr> | |
| 100 | <tr class="memitem:abce0871ac279fd54a0344ceb80126b66"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html#abce0871ac279fd54a0344ceb80126b66">advanceToNextConfiguration</a> () override final</td></tr> | |
| 101 | <tr class="memdesc:abce0871ac279fd54a0344ceb80126b66"><td class="mdescLeft"> </td><td class="mdescRight">Advance to the next, not yet visited, most probable isotopologue. <a href="#abce0871ac279fd54a0344ceb80126b66">More...</a><br /></td></tr> | |
| 102 | <tr class="separator:abce0871ac279fd54a0344ceb80126b66"><td class="memSeparator" colspan="2"> </td></tr> | |
| 103 | <tr class="memitem:ab63cbae392f88528e5b7421dada4abef"><td class="memItemLeft" align="right" valign="top"><a id="ab63cbae392f88528e5b7421dada4abef"></a> | |
| 104 | void </td><td class="memItemRight" valign="bottom"><b>get_conf_signature</b> (int *space) const override final</td></tr> | |
| 105 | <tr class="separator:ab63cbae392f88528e5b7421dada4abef"><td class="memSeparator" colspan="2"> </td></tr> | |
| 106 | <tr class="memitem:a746fc9fe13cca843a0f0f1993aee970a"><td class="memItemLeft" align="right" valign="top"><a id="a746fc9fe13cca843a0f0f1993aee970a"></a> | |
| 107 |  </td><td class="memItemRight" valign="bottom"><b>IsoLayeredGenerator</b> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&iso, double _targetCoverage, double _percentageToExpand, int _tabSize=1000, int _hashSize=1000, bool trim=false)</td></tr> | |
| 108 | <tr class="separator:a746fc9fe13cca843a0f0f1993aee970a"><td class="memSeparator" colspan="2"> </td></tr> | |
| 109 | <tr class="memitem:a6c4ea5906136d802859f47cd1b5add8d"><td class="memItemLeft" align="right" valign="top"><a id="a6c4ea5906136d802859f47cd1b5add8d"></a> | |
| 110 | void </td><td class="memItemRight" valign="bottom"><b>terminate_search</b> ()</td></tr> | |
| 111 | <tr class="separator:a6c4ea5906136d802859f47cd1b5add8d"><td class="memSeparator" colspan="2"> </td></tr> | |
| 112 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_iso_generator"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_iso_generator')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td></tr> | |
| 113 | <tr class="memitem:ae8e24abbce51a4c93994f630acfdf383 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">lprob</a> () const</td></tr> | |
| 114 | <tr class="memdesc:ae8e24abbce51a4c93994f630acfdf383 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the current isotopologue. <a href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">More...</a><br /></td></tr> | |
| 115 | <tr class="separator:ae8e24abbce51a4c93994f630acfdf383 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 116 | <tr class="memitem:a34173228ef73e272e2ff0ae6ce58092d inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">mass</a> () const</td></tr> | |
| 117 | <tr class="memdesc:a34173228ef73e272e2ff0ae6ce58092d inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the current isotopologue. <a href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">More...</a><br /></td></tr> | |
| 118 | <tr class="separator:a34173228ef73e272e2ff0ae6ce58092d inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 119 | <tr class="memitem:aecf1b3292fcc0857a86efe619a37fff0 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">prob</a> () const</td></tr> | |
| 120 | <tr class="memdesc:aecf1b3292fcc0857a86efe619a37fff0 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Get the probability of the current isotopologue. <a href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">More...</a><br /></td></tr> | |
| 121 | <tr class="separator:aecf1b3292fcc0857a86efe619a37fff0 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 122 | <tr class="memitem:a89b5b851fbc67f79ed165af0b9b2a188 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top"><a id="a89b5b851fbc67f79ed165af0b9b2a188"></a> | |
| 123 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoGenerator</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&iso, bool alloc_partials=true)</td></tr> | |
| 124 | <tr class="memdesc:a89b5b851fbc67f79ed165af0b9b2a188 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 125 | <tr class="separator:a89b5b851fbc67f79ed165af0b9b2a188 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 126 | <tr class="memitem:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top"><a id="a28442c8072a2e85faf5ff04f5feffd76"></a> | |
| 127 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">~IsoGenerator</a> ()</td></tr> | |
| 128 | <tr class="memdesc:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 129 | <tr class="separator:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 130 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 131 | <tr class="memitem:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a> (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td></tr> | |
| 132 | <tr class="memdesc:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">General constructror. <a href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">More...</a><br /></td></tr> | |
| 133 | <tr class="separator:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 134 | <tr class="memitem:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="ad389effb319e9ed73db9ed5749868b81"></a> | |
| 135 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a> (const char *formula)</td></tr> | |
| 136 | <tr class="memdesc:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Constructor from the formula object. <br /></td></tr> | |
| 137 | <tr class="separator:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 138 | <tr class="memitem:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a6c93ecb77a11bc831cc7600797fbf837"></a> | |
| 139 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&other)</td></tr> | |
| 140 | <tr class="memdesc:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">The move constructor. <br /></td></tr> | |
| 141 | <tr class="separator:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 142 | <tr class="memitem:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a> (const <a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &other, bool fullcopy)</td></tr> | |
| 143 | <tr class="memdesc:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">The copy constructor. <a href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">More...</a><br /></td></tr> | |
| 144 | <tr class="separator:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 145 | <tr class="memitem:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a8cf8f90338bfc3e5117f5b491f7b523f"></a> | |
| 146 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a> ()</td></tr> | |
| 147 | <tr class="memdesc:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 148 | <tr class="separator:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 149 | <tr class="memitem:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a7541599fbc29dd374bb60e5eb8fc047d"></a> | |
| 150 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a> () const</td></tr> | |
| 151 | <tr class="memdesc:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest peak in the isotopic distribution. <br /></td></tr> | |
| 152 | <tr class="separator:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 153 | <tr class="memitem:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a1ede5e34e5bbbb22ae89b362ce2c6faf"></a> | |
| 154 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a> () const</td></tr> | |
| 155 | <tr class="memdesc:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest peak in the isotopic distribution. <br /></td></tr> | |
| 156 | <tr class="separator:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 157 | <tr class="memitem:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a9035d076cec8f937d971e3fd972aa83f"></a> | |
| 158 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a> () const</td></tr> | |
| 159 | <tr class="memdesc:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode-configuration (if there are many modes, they share this value). <br /></td></tr> | |
| 160 | <tr class="separator:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 161 | <tr class="memitem:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a62b17f48d86f62b5ed38ffb296a9daa5"></a> | |
| 162 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a> () const</td></tr> | |
| 163 | <tr class="memdesc:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of elements in the chemical formula of the molecule. <br /></td></tr> | |
| 164 | <tr class="separator:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 165 | <tr class="memitem:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a656a37dd84a6c0534b2373210ed5a091"></a> | |
| 166 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a> () const</td></tr> | |
| 167 | <tr class="memdesc:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the total number of isotopes of elements present in a chemical formula. <br /></td></tr> | |
| 168 | <tr class="separator:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 169 | </table><table class="memberdecls"> | |
| 170 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a> | |
| 171 | Additional Inherited Members</h2></td></tr> | |
| 172 | <tr class="inherit_header pub_attribs_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pub_attribs_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Public Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 173 | <tr class="memitem:ad2a353f2c746648b08a9ad31ff775766 inherit pub_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td></tr> | |
| 174 | <tr class="separator:ad2a353f2c746648b08a9ad31ff775766 inherit pub_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 175 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_iso_generator"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_iso_generator')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td></tr> | |
| 176 | <tr class="memitem:a54a39b847a71aa08d1207d0666dd62bc inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a></td></tr> | |
| 177 | <tr class="separator:a54a39b847a71aa08d1207d0666dd62bc inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 178 | <tr class="memitem:af5654fcdba8199cbd60668af5de89a53 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a></td></tr> | |
| 179 | <tr class="separator:af5654fcdba8199cbd60668af5de89a53 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 180 | <tr class="memitem:ac18406df84b4b220bcb1974000c192b2 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a></td></tr> | |
| 181 | <tr class="separator:ac18406df84b4b220bcb1974000c192b2 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 182 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 183 | <tr class="memitem:a90245f9bc318f12720c134f61bbe0db0 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td></tr> | |
| 184 | <tr class="separator:a90245f9bc318f12720c134f61bbe0db0 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 185 | <tr class="memitem:a7235f0afc56dccd13937791a630c45da inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td></tr> | |
| 186 | <tr class="separator:a7235f0afc56dccd13937791a630c45da inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 187 | <tr class="memitem:ab01939334b6c3e69f65a36f9965971a2 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td></tr> | |
| 188 | <tr class="separator:ab01939334b6c3e69f65a36f9965971a2 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 189 | <tr class="memitem:a89ed144bf2495fa25840aca90a31b425 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td></tr> | |
| 190 | <tr class="separator:a89ed144bf2495fa25840aca90a31b425 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 191 | <tr class="memitem:a8dd2c443706935b582979b13f935115c inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td></tr> | |
| 192 | <tr class="separator:a8dd2c443706935b582979b13f935115c inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 193 | <tr class="memitem:aea98a8331a2f8a1a6bbcace6124fcfae inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> ** </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td></tr> | |
| 194 | <tr class="separator:aea98a8331a2f8a1a6bbcace6124fcfae inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 195 | <tr class="memitem:ab51c157b23ae6a6b521667b6f0e8a208 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td></tr> | |
| 196 | <tr class="separator:ab51c157b23ae6a6b521667b6f0e8a208 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 197 | </table> | |
| 198 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 199 | <div class="textblock"><p>The class that represents isotopologues above a given joint probability value. </p> | |
| 200 | <p>This class generates subsequent isotopologues that ARE NOT GUARANTEED TO BE ORDERED BY probability. The overal set of isotopologues is guaranteed to surpass a given threshold of probability contained in the isotopic distribution. This calculations are performed in O(N) operations, where N is the total number of the output isotopologues.</p> | |
| 201 | <p>This class is not a true generator yet - the generator methods have been implemented for compatibility, but the class actually performs all computations during the initialization and stores them, and the generator methods only walk through the array of precomputed values. . It will be reimplemented as a true generator in 2.0. </p> | |
| 202 | ||
| 203 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00383">383</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 204 | </div><h2 class="groupheader">Member Function Documentation</h2> | |
| 205 | <a id="abce0871ac279fd54a0344ceb80126b66"></a> | |
| 206 | <h2 class="memtitle"><span class="permalink"><a href="#abce0871ac279fd54a0344ceb80126b66">◆ </a></span>advanceToNextConfiguration()</h2> | |
| 207 | ||
| 208 | <div class="memitem"> | |
| 209 | <div class="memproto"> | |
| 210 | <table class="mlabels"> | |
| 211 | <tr> | |
| 212 | <td class="mlabels-left"> | |
| 213 | <table class="memname"> | |
| 214 | <tr> | |
| 215 | <td class="memname">bool IsoSpec::IsoLayeredGenerator::advanceToNextConfiguration </td> | |
| 216 | <td>(</td> | |
| 217 | <td class="paramname"></td><td>)</td> | |
| 218 | <td></td> | |
| 219 | </tr> | |
| 220 | </table> | |
| 221 | </td> | |
| 222 | <td class="mlabels-right"> | |
| 223 | <span class="mlabels"><span class="mlabel">final</span><span class="mlabel">override</span><span class="mlabel">virtual</span></span> </td> | |
| 224 | </tr> | |
| 225 | </table> | |
| 226 | </div><div class="memdoc"> | |
| 227 | ||
| 228 | <p>Advance to the next, not yet visited, most probable isotopologue. </p> | |
| 229 | <dl class="section return"><dt>Returns</dt><dd>Return false if it is not possible to advance. </dd></dl> | |
| 230 | ||
| 231 | <p>Implements <a class="el" href="class_iso_spec_1_1_iso_generator.html#a20f48ba18c6aecc57d73b2c3ec3a11dd">IsoSpec::IsoGenerator</a>.</p> | |
| 232 | ||
| 233 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8cpp_source.html#l00773">773</a> of file <a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a>.</p> | |
| 234 | ||
| 235 | </div> | |
| 236 | </div> | |
| 237 | <hr/>The documentation for this class was generated from the following files:<ul> | |
| 238 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a></li> | |
| 239 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a></li> | |
| 240 | </ul> | |
| 241 | </div><!-- contents --> | |
| 242 | <!-- start footer part --> | |
| 243 | <hr class="footer"/><address class="footer"><small> | |
| 244 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 245 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 246 | </a> 1.8.14 | |
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| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoOrderedGenerator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::IsoOrderedGenerator Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoSpec::IsoOrderedGenerator</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#aa2438bb81fb1d68eda1637d67e9cb36d">advanceToNextConfiguration</a>() override final</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoSpec::IsoOrderedGenerator</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 86 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 87 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 88 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#af5d638985fd24c03bfe1f3d61e1b25c6">get_conf_signature</a>(int *space) const override final</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoSpec::IsoOrderedGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 89 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a>(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a>(const char *formula)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 96 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a>(Iso &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a>(const Iso &other, bool fullcopy)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoGenerator</a>(Iso &&iso, bool alloc_partials=true)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"></td></tr> | |
| 99 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#afaf81ff3a758cd59629db323560e263d">IsoOrderedGenerator</a>(Iso &&iso, int _tabSize=1000, int _hashSize=1000)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoSpec::IsoOrderedGenerator</a></td><td class="entry"></td></tr> | |
| 100 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 101 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">lprob</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 102 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 103 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">mass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 104 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 105 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 106 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 107 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 108 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">prob</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 109 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 110 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">~IsoGenerator</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 111 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#a030c118b9a6131130684cd2710371842">~IsoOrderedGenerator</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoSpec::IsoOrderedGenerator</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 112 | </table></div><!-- contents --> | |
| 113 | <!-- start footer part --> | |
| 114 | <hr class="footer"/><address class="footer"><small> | |
| 115 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 116 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 117 | </a> 1.8.14 | |
| 118 | </small></address> | |
| 119 | </body> | |
| 120 | </html> |
| 0 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> | |
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| 7 | <title>IsoSpec: IsoSpec::IsoOrderedGenerator Class Reference</title> | |
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| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
| 37 | </div> | |
| 38 | <!-- end header part --> | |
| 39 | <!-- Generated by Doxygen 1.8.14 --> | |
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| 42 | var searchBox = new SearchBox("searchBox", "search",false,'Search'); | |
| 43 | /* @license-end */ | |
| 44 | </script> | |
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| 57 | onmouseover="return searchBox.OnSearchSelectShow()" | |
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| 59 | onkeydown="return searchBox.OnSearchSelectKey(event)"> | |
| 60 | </div> | |
| 61 | ||
| 62 | <!-- iframe showing the search results (closed by default) --> | |
| 63 | <div id="MSearchResultsWindow"> | |
| 64 | <iframe src="javascript:void(0)" frameborder="0" | |
| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoOrderedGenerator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_iso_ordered_generator-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoOrderedGenerator Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p>The generator of isotopologues sorted by their probability of occurrence. | |
| 84 | <a href="class_iso_spec_1_1_iso_ordered_generator.html#details">More...</a></p> | |
| 85 | ||
| 86 | <p><code>#include <<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>></code></p> | |
| 87 | <div class="dynheader"> | |
| 88 | Inheritance diagram for IsoSpec::IsoOrderedGenerator:</div> | |
| 89 | <div class="dyncontent"> | |
| 90 | <div class="center"> | |
| 91 | <img src="class_iso_spec_1_1_iso_ordered_generator.png" usemap="#IsoSpec::IsoOrderedGenerator_map" alt=""/> | |
| 92 | <map id="IsoSpec::IsoOrderedGenerator_map" name="IsoSpec::IsoOrderedGenerator_map"> | |
| 93 | <area href="class_iso_spec_1_1_iso_generator.html" title="The generator of isotopologues. " alt="IsoSpec::IsoGenerator" shape="rect" coords="0,56,184,80"/> | |
| 94 | <area href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. " alt="IsoSpec::Iso" shape="rect" coords="0,0,184,24"/> | |
| 95 | </map> | |
| 96 | </div></div> | |
| 97 | <table class="memberdecls"> | |
| 98 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 99 | Public Member Functions</h2></td></tr> | |
| 100 | <tr class="memitem:aa2438bb81fb1d68eda1637d67e9cb36d"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#aa2438bb81fb1d68eda1637d67e9cb36d">advanceToNextConfiguration</a> () override final</td></tr> | |
| 101 | <tr class="memdesc:aa2438bb81fb1d68eda1637d67e9cb36d"><td class="mdescLeft"> </td><td class="mdescRight">Advance to the next, not yet visited, most probable isotopologue. <a href="#aa2438bb81fb1d68eda1637d67e9cb36d">More...</a><br /></td></tr> | |
| 102 | <tr class="separator:aa2438bb81fb1d68eda1637d67e9cb36d"><td class="memSeparator" colspan="2"> </td></tr> | |
| 103 | <tr class="memitem:af5d638985fd24c03bfe1f3d61e1b25c6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#af5d638985fd24c03bfe1f3d61e1b25c6">get_conf_signature</a> (int *space) const override final</td></tr> | |
| 104 | <tr class="memdesc:af5d638985fd24c03bfe1f3d61e1b25c6"><td class="mdescLeft"> </td><td class="mdescRight">Save the counts of isotopes in the space. <a href="#af5d638985fd24c03bfe1f3d61e1b25c6">More...</a><br /></td></tr> | |
| 105 | <tr class="separator:af5d638985fd24c03bfe1f3d61e1b25c6"><td class="memSeparator" colspan="2"> </td></tr> | |
| 106 | <tr class="memitem:afaf81ff3a758cd59629db323560e263d"><td class="memItemLeft" align="right" valign="top"><a id="afaf81ff3a758cd59629db323560e263d"></a> | |
| 107 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#afaf81ff3a758cd59629db323560e263d">IsoOrderedGenerator</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&iso, int _tabSize=1000, int _hashSize=1000)</td></tr> | |
| 108 | <tr class="memdesc:afaf81ff3a758cd59629db323560e263d"><td class="mdescLeft"> </td><td class="mdescRight">The move-contstructor. <br /></td></tr> | |
| 109 | <tr class="separator:afaf81ff3a758cd59629db323560e263d"><td class="memSeparator" colspan="2"> </td></tr> | |
| 110 | <tr class="memitem:a030c118b9a6131130684cd2710371842"><td class="memItemLeft" align="right" valign="top"><a id="a030c118b9a6131130684cd2710371842"></a> | |
| 111 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#a030c118b9a6131130684cd2710371842">~IsoOrderedGenerator</a> ()</td></tr> | |
| 112 | <tr class="memdesc:a030c118b9a6131130684cd2710371842"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 113 | <tr class="separator:a030c118b9a6131130684cd2710371842"><td class="memSeparator" colspan="2"> </td></tr> | |
| 114 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_iso_generator"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_iso_generator')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td></tr> | |
| 115 | <tr class="memitem:ae8e24abbce51a4c93994f630acfdf383 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">lprob</a> () const</td></tr> | |
| 116 | <tr class="memdesc:ae8e24abbce51a4c93994f630acfdf383 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the current isotopologue. <a href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">More...</a><br /></td></tr> | |
| 117 | <tr class="separator:ae8e24abbce51a4c93994f630acfdf383 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 118 | <tr class="memitem:a34173228ef73e272e2ff0ae6ce58092d inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">mass</a> () const</td></tr> | |
| 119 | <tr class="memdesc:a34173228ef73e272e2ff0ae6ce58092d inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the current isotopologue. <a href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">More...</a><br /></td></tr> | |
| 120 | <tr class="separator:a34173228ef73e272e2ff0ae6ce58092d inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 121 | <tr class="memitem:aecf1b3292fcc0857a86efe619a37fff0 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">prob</a> () const</td></tr> | |
| 122 | <tr class="memdesc:aecf1b3292fcc0857a86efe619a37fff0 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Get the probability of the current isotopologue. <a href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">More...</a><br /></td></tr> | |
| 123 | <tr class="separator:aecf1b3292fcc0857a86efe619a37fff0 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 124 | <tr class="memitem:a89b5b851fbc67f79ed165af0b9b2a188 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top"><a id="a89b5b851fbc67f79ed165af0b9b2a188"></a> | |
| 125 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoGenerator</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&iso, bool alloc_partials=true)</td></tr> | |
| 126 | <tr class="memdesc:a89b5b851fbc67f79ed165af0b9b2a188 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 127 | <tr class="separator:a89b5b851fbc67f79ed165af0b9b2a188 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 128 | <tr class="memitem:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top"><a id="a28442c8072a2e85faf5ff04f5feffd76"></a> | |
| 129 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">~IsoGenerator</a> ()</td></tr> | |
| 130 | <tr class="memdesc:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 131 | <tr class="separator:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 132 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 133 | <tr class="memitem:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a> (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td></tr> | |
| 134 | <tr class="memdesc:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">General constructror. <a href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">More...</a><br /></td></tr> | |
| 135 | <tr class="separator:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 136 | <tr class="memitem:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="ad389effb319e9ed73db9ed5749868b81"></a> | |
| 137 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a> (const char *formula)</td></tr> | |
| 138 | <tr class="memdesc:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Constructor from the formula object. <br /></td></tr> | |
| 139 | <tr class="separator:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 140 | <tr class="memitem:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a6c93ecb77a11bc831cc7600797fbf837"></a> | |
| 141 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&other)</td></tr> | |
| 142 | <tr class="memdesc:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">The move constructor. <br /></td></tr> | |
| 143 | <tr class="separator:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 144 | <tr class="memitem:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a> (const <a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &other, bool fullcopy)</td></tr> | |
| 145 | <tr class="memdesc:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">The copy constructor. <a href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">More...</a><br /></td></tr> | |
| 146 | <tr class="separator:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 147 | <tr class="memitem:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a8cf8f90338bfc3e5117f5b491f7b523f"></a> | |
| 148 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a> ()</td></tr> | |
| 149 | <tr class="memdesc:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 150 | <tr class="separator:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 151 | <tr class="memitem:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a7541599fbc29dd374bb60e5eb8fc047d"></a> | |
| 152 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a> () const</td></tr> | |
| 153 | <tr class="memdesc:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest peak in the isotopic distribution. <br /></td></tr> | |
| 154 | <tr class="separator:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 155 | <tr class="memitem:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a1ede5e34e5bbbb22ae89b362ce2c6faf"></a> | |
| 156 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a> () const</td></tr> | |
| 157 | <tr class="memdesc:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest peak in the isotopic distribution. <br /></td></tr> | |
| 158 | <tr class="separator:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 159 | <tr class="memitem:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a9035d076cec8f937d971e3fd972aa83f"></a> | |
| 160 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a> () const</td></tr> | |
| 161 | <tr class="memdesc:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode-configuration (if there are many modes, they share this value). <br /></td></tr> | |
| 162 | <tr class="separator:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 163 | <tr class="memitem:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a62b17f48d86f62b5ed38ffb296a9daa5"></a> | |
| 164 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a> () const</td></tr> | |
| 165 | <tr class="memdesc:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of elements in the chemical formula of the molecule. <br /></td></tr> | |
| 166 | <tr class="separator:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 167 | <tr class="memitem:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a656a37dd84a6c0534b2373210ed5a091"></a> | |
| 168 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a> () const</td></tr> | |
| 169 | <tr class="memdesc:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the total number of isotopes of elements present in a chemical formula. <br /></td></tr> | |
| 170 | <tr class="separator:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 171 | </table><table class="memberdecls"> | |
| 172 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a> | |
| 173 | Additional Inherited Members</h2></td></tr> | |
| 174 | <tr class="inherit_header pub_attribs_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pub_attribs_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Public Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 175 | <tr class="memitem:ad2a353f2c746648b08a9ad31ff775766 inherit pub_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td></tr> | |
| 176 | <tr class="separator:ad2a353f2c746648b08a9ad31ff775766 inherit pub_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 177 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_iso_generator"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_iso_generator')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td></tr> | |
| 178 | <tr class="memitem:a54a39b847a71aa08d1207d0666dd62bc inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a></td></tr> | |
| 179 | <tr class="separator:a54a39b847a71aa08d1207d0666dd62bc inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 180 | <tr class="memitem:af5654fcdba8199cbd60668af5de89a53 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a></td></tr> | |
| 181 | <tr class="separator:af5654fcdba8199cbd60668af5de89a53 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 182 | <tr class="memitem:ac18406df84b4b220bcb1974000c192b2 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a></td></tr> | |
| 183 | <tr class="separator:ac18406df84b4b220bcb1974000c192b2 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 184 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 185 | <tr class="memitem:a90245f9bc318f12720c134f61bbe0db0 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td></tr> | |
| 186 | <tr class="separator:a90245f9bc318f12720c134f61bbe0db0 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 187 | <tr class="memitem:a7235f0afc56dccd13937791a630c45da inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td></tr> | |
| 188 | <tr class="separator:a7235f0afc56dccd13937791a630c45da inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 189 | <tr class="memitem:ab01939334b6c3e69f65a36f9965971a2 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td></tr> | |
| 190 | <tr class="separator:ab01939334b6c3e69f65a36f9965971a2 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 191 | <tr class="memitem:a89ed144bf2495fa25840aca90a31b425 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td></tr> | |
| 192 | <tr class="separator:a89ed144bf2495fa25840aca90a31b425 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 193 | <tr class="memitem:a8dd2c443706935b582979b13f935115c inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td></tr> | |
| 194 | <tr class="separator:a8dd2c443706935b582979b13f935115c inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 195 | <tr class="memitem:aea98a8331a2f8a1a6bbcace6124fcfae inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> ** </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td></tr> | |
| 196 | <tr class="separator:aea98a8331a2f8a1a6bbcace6124fcfae inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 197 | <tr class="memitem:ab51c157b23ae6a6b521667b6f0e8a208 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td></tr> | |
| 198 | <tr class="separator:ab51c157b23ae6a6b521667b6f0e8a208 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 199 | </table> | |
| 200 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 201 | <div class="textblock"><p>The generator of isotopologues sorted by their probability of occurrence. </p> | |
| 202 | <p>The subsequent isotopologues are generated with diminishing probability, starting from the mode. This algorithm take O(N*log(N)) to compute the N isotopologues because of using the Priority Queue data structure. Obtaining the N isotopologues can be achieved in O(N) if they are not required to be spit out in the descending order. </p> | |
| 203 | ||
| 204 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00179">179</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 205 | </div><h2 class="groupheader">Member Function Documentation</h2> | |
| 206 | <a id="aa2438bb81fb1d68eda1637d67e9cb36d"></a> | |
| 207 | <h2 class="memtitle"><span class="permalink"><a href="#aa2438bb81fb1d68eda1637d67e9cb36d">◆ </a></span>advanceToNextConfiguration()</h2> | |
| 208 | ||
| 209 | <div class="memitem"> | |
| 210 | <div class="memproto"> | |
| 211 | <table class="mlabels"> | |
| 212 | <tr> | |
| 213 | <td class="mlabels-left"> | |
| 214 | <table class="memname"> | |
| 215 | <tr> | |
| 216 | <td class="memname">bool IsoSpec::IsoOrderedGenerator::advanceToNextConfiguration </td> | |
| 217 | <td>(</td> | |
| 218 | <td class="paramname"></td><td>)</td> | |
| 219 | <td></td> | |
| 220 | </tr> | |
| 221 | </table> | |
| 222 | </td> | |
| 223 | <td class="mlabels-right"> | |
| 224 | <span class="mlabels"><span class="mlabel">final</span><span class="mlabel">override</span><span class="mlabel">virtual</span></span> </td> | |
| 225 | </tr> | |
| 226 | </table> | |
| 227 | </div><div class="memdoc"> | |
| 228 | ||
| 229 | <p>Advance to the next, not yet visited, most probable isotopologue. </p> | |
| 230 | <dl class="section return"><dt>Returns</dt><dd>Return false if it is not possible to advance. </dd></dl> | |
| 231 | ||
| 232 | <p>Implements <a class="el" href="class_iso_spec_1_1_iso_generator.html#a20f48ba18c6aecc57d73b2c3ec3a11dd">IsoSpec::IsoGenerator</a>.</p> | |
| 233 | ||
| 234 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8cpp_source.html#l00461">461</a> of file <a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a>.</p> | |
| 235 | ||
| 236 | </div> | |
| 237 | </div> | |
| 238 | <a id="af5d638985fd24c03bfe1f3d61e1b25c6"></a> | |
| 239 | <h2 class="memtitle"><span class="permalink"><a href="#af5d638985fd24c03bfe1f3d61e1b25c6">◆ </a></span>get_conf_signature()</h2> | |
| 240 | ||
| 241 | <div class="memitem"> | |
| 242 | <div class="memproto"> | |
| 243 | <table class="mlabels"> | |
| 244 | <tr> | |
| 245 | <td class="mlabels-left"> | |
| 246 | <table class="memname"> | |
| 247 | <tr> | |
| 248 | <td class="memname">void IsoSpec::IsoOrderedGenerator::get_conf_signature </td> | |
| 249 | <td>(</td> | |
| 250 | <td class="paramtype">int * </td> | |
| 251 | <td class="paramname"><em>space</em></td><td>)</td> | |
| 252 | <td> const</td> | |
| 253 | </tr> | |
| 254 | </table> | |
| 255 | </td> | |
| 256 | <td class="mlabels-right"> | |
| 257 | <span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">final</span><span class="mlabel">override</span><span class="mlabel">virtual</span></span> </td> | |
| 258 | </tr> | |
| 259 | </table> | |
| 260 | </div><div class="memdoc"> | |
| 261 | ||
| 262 | <p>Save the counts of isotopes in the space. </p> | |
| 263 | <dl class="params"><dt>Parameters</dt><dd> | |
| 264 | <table class="params"> | |
| 265 | <tr><td class="paramname">space</td><td>An array where counts of isotopes shall be written. Must be as big as the overall number of isotopes. </td></tr> | |
| 266 | </table> | |
| 267 | </dd> | |
| 268 | </dl> | |
| 269 | ||
| 270 | <p>Implements <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a>.</p> | |
| 271 | ||
| 272 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00202">202</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 273 | ||
| 274 | </div> | |
| 275 | </div> | |
| 276 | <hr/>The documentation for this class was generated from the following files:<ul> | |
| 277 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a></li> | |
| 278 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a></li> | |
| 279 | </ul> | |
| 280 | </div><!-- contents --> | |
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| 283 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 285 | </a> 1.8.14 | |
| 286 | </small></address> | |
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| 288 | </html> |
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| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><b>IsoSpec</b></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_equal.html">ConfEqual</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::IsoSpec::ConfEqual Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_equal.html">IsoSpec::IsoSpec::ConfEqual</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
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| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><b>IsoSpec</b></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_equal.html">ConfEqual</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_iso_spec_1_1_conf_equal-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoSpec::ConfEqual Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p>The equality of configurations operator. | |
| 84 | <a href="class_iso_spec_1_1_iso_spec_1_1_conf_equal.html#details">More...</a></p> | |
| 85 | <table class="memberdecls"> | |
| 86 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 87 | Public Member Functions</h2></td></tr> | |
| 88 | <tr class="memitem:a1e64267307db788516b6dfc98614d4a8"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_equal.html#a1e64267307db788516b6dfc98614d4a8">ConfEqual</a> (int dim)</td></tr> | |
| 89 | <tr class="memdesc:a1e64267307db788516b6dfc98614d4a8"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a1e64267307db788516b6dfc98614d4a8">More...</a><br /></td></tr> | |
| 90 | <tr class="separator:a1e64267307db788516b6dfc98614d4a8"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | <tr class="memitem:ad9d7fb4a033b947a983b302cb3e0c735"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_equal.html#ad9d7fb4a033b947a983b302cb3e0c735">operator()</a> (const int *conf1, const int *conf2) const</td></tr> | |
| 92 | <tr class="memdesc:ad9d7fb4a033b947a983b302cb3e0c735"><td class="mdescLeft"> </td><td class="mdescRight">The <b>call</b> operator. <a href="#ad9d7fb4a033b947a983b302cb3e0c735">More...</a><br /></td></tr> | |
| 93 | <tr class="separator:ad9d7fb4a033b947a983b302cb3e0c735"><td class="memSeparator" colspan="2"> </td></tr> | |
| 94 | </table> | |
| 95 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 96 | <div class="textblock"><p>The equality of configurations operator. </p> | |
| 97 | <p>Needed for the unordered-map. </p> | |
| 98 | ||
| 99 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00062">62</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 100 | </div><h2 class="groupheader">Constructor & Destructor Documentation</h2> | |
| 101 | <a id="a1e64267307db788516b6dfc98614d4a8"></a> | |
| 102 | <h2 class="memtitle"><span class="permalink"><a href="#a1e64267307db788516b6dfc98614d4a8">◆ </a></span>ConfEqual()</h2> | |
| 103 | ||
| 104 | <div class="memitem"> | |
| 105 | <div class="memproto"> | |
| 106 | <table class="memname"> | |
| 107 | <tr> | |
| 108 | <td class="memname">IsoSpec::ConfEqual::ConfEqual </td> | |
| 109 | <td>(</td> | |
| 110 | <td class="paramtype">int </td> | |
| 111 | <td class="paramname"><em>dim</em></td><td>)</td> | |
| 112 | <td></td> | |
| 113 | </tr> | |
| 114 | </table> | |
| 115 | </div><div class="memdoc"> | |
| 116 | ||
| 117 | <p>Constructor. </p> | |
| 118 | <dl class="params"><dt>Parameters</dt><dd> | |
| 119 | <table class="params"> | |
| 120 | <tr><td class="paramname">dim</td><td>the number of the ints that make up a configuration. </td></tr> | |
| 121 | </table> | |
| 122 | </dd> | |
| 123 | </dl> | |
| 124 | ||
| 125 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00026">26</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 126 | ||
| 127 | </div> | |
| 128 | </div> | |
| 129 | <h2 class="groupheader">Member Function Documentation</h2> | |
| 130 | <a id="ad9d7fb4a033b947a983b302cb3e0c735"></a> | |
| 131 | <h2 class="memtitle"><span class="permalink"><a href="#ad9d7fb4a033b947a983b302cb3e0c735">◆ </a></span>operator()()</h2> | |
| 132 | ||
| 133 | <div class="memitem"> | |
| 134 | <div class="memproto"> | |
| 135 | <table class="mlabels"> | |
| 136 | <tr> | |
| 137 | <td class="mlabels-left"> | |
| 138 | <table class="memname"> | |
| 139 | <tr> | |
| 140 | <td class="memname">bool IsoSpec::IsoSpec::ConfEqual::operator() </td> | |
| 141 | <td>(</td> | |
| 142 | <td class="paramtype">const int * </td> | |
| 143 | <td class="paramname"><em>conf1</em>, </td> | |
| 144 | </tr> | |
| 145 | <tr> | |
| 146 | <td class="paramkey"></td> | |
| 147 | <td></td> | |
| 148 | <td class="paramtype">const int * </td> | |
| 149 | <td class="paramname"><em>conf2</em> </td> | |
| 150 | </tr> | |
| 151 | <tr> | |
| 152 | <td></td> | |
| 153 | <td>)</td> | |
| 154 | <td></td><td> const</td> | |
| 155 | </tr> | |
| 156 | </table> | |
| 157 | </td> | |
| 158 | <td class="mlabels-right"> | |
| 159 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 160 | </tr> | |
| 161 | </table> | |
| 162 | </div><div class="memdoc"> | |
| 163 | ||
| 164 | <p>The <b>call</b> operator. </p> | |
| 165 | <p>Let us quote the sacred MAN of memcmp: "The memcmp() function returns zero if the two strings are identical, otherwise returns the difference between the first two differing bytes (treated as unsigned char values, so that ‘\200’ is greater than ‘\0’, for example). Zero-length strings are always identical. This behavior is not required by C and portable code should only depend on the sign of the returned value."</p> | |
| 166 | <dl class="params"><dt>Parameters</dt><dd> | |
| 167 | <table class="params"> | |
| 168 | <tr><td class="paramname">conf1</td><td>An array of integer counts. </td></tr> | |
| 169 | <tr><td class="paramname">conf2</td><td>An array of integer counts. </td></tr> | |
| 170 | </table> | |
| 171 | </dd> | |
| 172 | </dl> | |
| 173 | <dl class="section return"><dt>Returns</dt><dd>Are conf1 and conf2 the same configuration? </dd></dl> | |
| 174 | ||
| 175 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00087">87</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 176 | ||
| 177 | </div> | |
| 178 | </div> | |
| 179 | <hr/>The documentation for this class was generated from the following file:<ul> | |
| 180 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8cpp_source.html">operators.cpp</a></li> | |
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| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order.html">IsoSpec::IsoSpec::ConfOrder</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>operator()</b>(void *conf1, void *conf2) const (defined in <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order.html">IsoSpec::IsoSpec::ConfOrder</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order.html">IsoSpec::IsoSpec::ConfOrder</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoSpec::ConfOrder Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p>The class used for comparing the position of configurations in the order of descending probabilities. | |
| 84 | <a href="class_iso_spec_1_1_iso_spec_1_1_conf_order.html#details">More...</a></p> | |
| 85 | <table class="memberdecls"> | |
| 86 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 87 | Public Member Functions</h2></td></tr> | |
| 88 | <tr class="memitem:adfed4b9c4e5dbd910de88057eb27fdf4"><td class="memItemLeft" align="right" valign="top"><a id="adfed4b9c4e5dbd910de88057eb27fdf4"></a> | |
| 89 | bool </td><td class="memItemRight" valign="bottom"><b>operator()</b> (void *conf1, void *conf2) const</td></tr> | |
| 90 | <tr class="separator:adfed4b9c4e5dbd910de88057eb27fdf4"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | </table> | |
| 92 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 93 | <div class="textblock"><p>The class used for comparing the position of configurations in the order of descending probabilities. </p> | |
| 94 | <p>Needed for the priority queue. </p> | |
| 95 | ||
| 96 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00098">98</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 97 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 98 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8cpp_source.html">operators.cpp</a></li> | |
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| 76 | <div class="title">IsoSpec::IsoSpec::ConfOrderMarginal Member List</div> </div> | |
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| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal.html">IsoSpec::IsoSpec::ConfOrderMarginal</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal.html#a91c7b8d57bcd751f08f064802f3c8b87">ConfOrderMarginal</a>(const double *logProbs, int dim)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal.html">IsoSpec::IsoSpec::ConfOrderMarginal</a></td><td class="entry"></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal.html#a617a19a4c112750abde2153276c90612">operator()</a>(const Conf conf1, const Conf conf2)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal.html">IsoSpec::IsoSpec::ConfOrderMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><b>IsoSpec</b></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal.html">ConfOrderMarginal</a></li> </ul> | |
| 72 | </div> | |
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| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoSpec::ConfOrderMarginal Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p>The class used for comparing the position of subisotopologues in the order of descending probabilities. | |
| 84 | <a href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal.html#details">More...</a></p> | |
| 85 | <table class="memberdecls"> | |
| 86 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 87 | Public Member Functions</h2></td></tr> | |
| 88 | <tr class="memitem:a91c7b8d57bcd751f08f064802f3c8b87"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal.html#a91c7b8d57bcd751f08f064802f3c8b87">ConfOrderMarginal</a> (const double *logProbs, int dim)</td></tr> | |
| 89 | <tr class="memdesc:a91c7b8d57bcd751f08f064802f3c8b87"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a91c7b8d57bcd751f08f064802f3c8b87">More...</a><br /></td></tr> | |
| 90 | <tr class="separator:a91c7b8d57bcd751f08f064802f3c8b87"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | <tr class="memitem:a617a19a4c112750abde2153276c90612"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal.html#a617a19a4c112750abde2153276c90612">operator()</a> (const Conf conf1, const Conf conf2)</td></tr> | |
| 92 | <tr class="memdesc:a617a19a4c112750abde2153276c90612"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a617a19a4c112750abde2153276c90612">More...</a><br /></td></tr> | |
| 93 | <tr class="separator:a617a19a4c112750abde2153276c90612"><td class="memSeparator" colspan="2"> </td></tr> | |
| 94 | </table> | |
| 95 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 96 | <div class="textblock"><p>The class used for comparing the position of subisotopologues in the order of descending probabilities. </p> | |
| 97 | <p>Needed for the priority queue. </p> | |
| 98 | ||
| 99 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00112">112</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 100 | </div><h2 class="groupheader">Constructor & Destructor Documentation</h2> | |
| 101 | <a id="a91c7b8d57bcd751f08f064802f3c8b87"></a> | |
| 102 | <h2 class="memtitle"><span class="permalink"><a href="#a91c7b8d57bcd751f08f064802f3c8b87">◆ </a></span>ConfOrderMarginal()</h2> | |
| 103 | ||
| 104 | <div class="memitem"> | |
| 105 | <div class="memproto"> | |
| 106 | <table class="memname"> | |
| 107 | <tr> | |
| 108 | <td class="memname">IsoSpec::ConfOrderMarginal::ConfOrderMarginal </td> | |
| 109 | <td>(</td> | |
| 110 | <td class="paramtype">const double * </td> | |
| 111 | <td class="paramname"><em>logProbs</em>, </td> | |
| 112 | </tr> | |
| 113 | <tr> | |
| 114 | <td class="paramkey"></td> | |
| 115 | <td></td> | |
| 116 | <td class="paramtype">int </td> | |
| 117 | <td class="paramname"><em>dim</em> </td> | |
| 118 | </tr> | |
| 119 | <tr> | |
| 120 | <td></td> | |
| 121 | <td>)</td> | |
| 122 | <td></td><td></td> | |
| 123 | </tr> | |
| 124 | </table> | |
| 125 | </div><div class="memdoc"> | |
| 126 | ||
| 127 | <p>Constructor. </p> | |
| 128 | <dl class="params"><dt>Parameters</dt><dd> | |
| 129 | <table class="params"> | |
| 130 | <tr><td class="paramname">logProbs</td><td></td></tr> | |
| 131 | <tr><td class="paramname">dim</td><td>The number of isotopes. </td></tr> | |
| 132 | </table> | |
| 133 | </dd> | |
| 134 | </dl> | |
| 135 | ||
| 136 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00030">30</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 137 | ||
| 138 | </div> | |
| 139 | </div> | |
| 140 | <h2 class="groupheader">Member Function Documentation</h2> | |
| 141 | <a id="a617a19a4c112750abde2153276c90612"></a> | |
| 142 | <h2 class="memtitle"><span class="permalink"><a href="#a617a19a4c112750abde2153276c90612">◆ </a></span>operator()()</h2> | |
| 143 | ||
| 144 | <div class="memitem"> | |
| 145 | <div class="memproto"> | |
| 146 | <table class="mlabels"> | |
| 147 | <tr> | |
| 148 | <td class="mlabels-left"> | |
| 149 | <table class="memname"> | |
| 150 | <tr> | |
| 151 | <td class="memname">bool IsoSpec::IsoSpec::ConfOrderMarginal::operator() </td> | |
| 152 | <td>(</td> | |
| 153 | <td class="paramtype">const Conf </td> | |
| 154 | <td class="paramname"><em>conf1</em>, </td> | |
| 155 | </tr> | |
| 156 | <tr> | |
| 157 | <td class="paramkey"></td> | |
| 158 | <td></td> | |
| 159 | <td class="paramtype">const Conf </td> | |
| 160 | <td class="paramname"><em>conf2</em> </td> | |
| 161 | </tr> | |
| 162 | <tr> | |
| 163 | <td></td> | |
| 164 | <td>)</td> | |
| 165 | <td></td><td></td> | |
| 166 | </tr> | |
| 167 | </table> | |
| 168 | </td> | |
| 169 | <td class="mlabels-right"> | |
| 170 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 171 | </tr> | |
| 172 | </table> | |
| 173 | </div><div class="memdoc"> | |
| 174 | ||
| 175 | <p>Constructor. </p> | |
| 176 | <dl class="params"><dt>Parameters</dt><dd> | |
| 177 | <table class="params"> | |
| 178 | <tr><td class="paramname">conf1</td><td>An array of integer counts. </td></tr> | |
| 179 | <tr><td class="paramname">conf2</td><td>An array of integer counts. </td></tr> | |
| 180 | </table> | |
| 181 | </dd> | |
| 182 | </dl> | |
| 183 | <dl class="section return"><dt>Returns</dt><dd>True if conf1 is less probable than conf2. </dd></dl> | |
| 184 | ||
| 185 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00130">130</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 186 | ||
| 187 | </div> | |
| 188 | </div> | |
| 189 | <hr/>The documentation for this class was generated from the following file:<ul> | |
| 190 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8cpp_source.html">operators.cpp</a></li> | |
| 191 | </ul> | |
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| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending.html">IsoSpec::IsoSpec::ConfOrderMarginalDescending</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending.html#a331cca614490a25d2bf4d48e04a1eba3">ConfOrderMarginalDescending</a>(const double *logProbs, int dim)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending.html">IsoSpec::IsoSpec::ConfOrderMarginalDescending</a></td><td class="entry"></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending.html#a24753a23a4484aa1247606e15362dee0">operator()</a>(const Conf conf1, const Conf conf2)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending.html">IsoSpec::IsoSpec::ConfOrderMarginalDescending</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><b>IsoSpec</b></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending.html">ConfOrderMarginalDescending</a></li> </ul> | |
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| 74 | <div class="header"> | |
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| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoSpec::ConfOrderMarginalDescending Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p>The class used for comparing the position of subisotopologues in the order of descending probabilities. | |
| 84 | <a href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending.html#details">More...</a></p> | |
| 85 | <table class="memberdecls"> | |
| 86 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 87 | Public Member Functions</h2></td></tr> | |
| 88 | <tr class="memitem:a331cca614490a25d2bf4d48e04a1eba3"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending.html#a331cca614490a25d2bf4d48e04a1eba3">ConfOrderMarginalDescending</a> (const double *logProbs, int dim)</td></tr> | |
| 89 | <tr class="memdesc:a331cca614490a25d2bf4d48e04a1eba3"><td class="mdescLeft"> </td><td class="mdescRight">Contstructor. <a href="#a331cca614490a25d2bf4d48e04a1eba3">More...</a><br /></td></tr> | |
| 90 | <tr class="separator:a331cca614490a25d2bf4d48e04a1eba3"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | <tr class="memitem:a24753a23a4484aa1247606e15362dee0"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending.html#a24753a23a4484aa1247606e15362dee0">operator()</a> (const Conf conf1, const Conf conf2)</td></tr> | |
| 92 | <tr class="memdesc:a24753a23a4484aa1247606e15362dee0"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a24753a23a4484aa1247606e15362dee0">More...</a><br /></td></tr> | |
| 93 | <tr class="separator:a24753a23a4484aa1247606e15362dee0"><td class="memSeparator" colspan="2"> </td></tr> | |
| 94 | </table> | |
| 95 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 96 | <div class="textblock"><p>The class used for comparing the position of subisotopologues in the order of descending probabilities. </p> | |
| 97 | <p>Needed for the priority queue. </p> | |
| 98 | ||
| 99 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00141">141</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 100 | </div><h2 class="groupheader">Constructor & Destructor Documentation</h2> | |
| 101 | <a id="a331cca614490a25d2bf4d48e04a1eba3"></a> | |
| 102 | <h2 class="memtitle"><span class="permalink"><a href="#a331cca614490a25d2bf4d48e04a1eba3">◆ </a></span>ConfOrderMarginalDescending()</h2> | |
| 103 | ||
| 104 | <div class="memitem"> | |
| 105 | <div class="memproto"> | |
| 106 | <table class="memname"> | |
| 107 | <tr> | |
| 108 | <td class="memname">IsoSpec::ConfOrderMarginalDescending::ConfOrderMarginalDescending </td> | |
| 109 | <td>(</td> | |
| 110 | <td class="paramtype">const double * </td> | |
| 111 | <td class="paramname"><em>logProbs</em>, </td> | |
| 112 | </tr> | |
| 113 | <tr> | |
| 114 | <td class="paramkey"></td> | |
| 115 | <td></td> | |
| 116 | <td class="paramtype">int </td> | |
| 117 | <td class="paramname"><em>dim</em> </td> | |
| 118 | </tr> | |
| 119 | <tr> | |
| 120 | <td></td> | |
| 121 | <td>)</td> | |
| 122 | <td></td><td></td> | |
| 123 | </tr> | |
| 124 | </table> | |
| 125 | </div><div class="memdoc"> | |
| 126 | ||
| 127 | <p>Contstructor. </p> | |
| 128 | <dl class="params"><dt>Parameters</dt><dd> | |
| 129 | <table class="params"> | |
| 130 | <tr><td class="paramname">logProbs</td><td></td></tr> | |
| 131 | <tr><td class="paramname">dim</td><td>The number of isotopes. </td></tr> | |
| 132 | </table> | |
| 133 | </dd> | |
| 134 | </dl> | |
| 135 | ||
| 136 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00034">34</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 137 | ||
| 138 | </div> | |
| 139 | </div> | |
| 140 | <h2 class="groupheader">Member Function Documentation</h2> | |
| 141 | <a id="a24753a23a4484aa1247606e15362dee0"></a> | |
| 142 | <h2 class="memtitle"><span class="permalink"><a href="#a24753a23a4484aa1247606e15362dee0">◆ </a></span>operator()()</h2> | |
| 143 | ||
| 144 | <div class="memitem"> | |
| 145 | <div class="memproto"> | |
| 146 | <table class="mlabels"> | |
| 147 | <tr> | |
| 148 | <td class="mlabels-left"> | |
| 149 | <table class="memname"> | |
| 150 | <tr> | |
| 151 | <td class="memname">bool IsoSpec::IsoSpec::ConfOrderMarginalDescending::operator() </td> | |
| 152 | <td>(</td> | |
| 153 | <td class="paramtype">const Conf </td> | |
| 154 | <td class="paramname"><em>conf1</em>, </td> | |
| 155 | </tr> | |
| 156 | <tr> | |
| 157 | <td class="paramkey"></td> | |
| 158 | <td></td> | |
| 159 | <td class="paramtype">const Conf </td> | |
| 160 | <td class="paramname"><em>conf2</em> </td> | |
| 161 | </tr> | |
| 162 | <tr> | |
| 163 | <td></td> | |
| 164 | <td>)</td> | |
| 165 | <td></td><td></td> | |
| 166 | </tr> | |
| 167 | </table> | |
| 168 | </td> | |
| 169 | <td class="mlabels-right"> | |
| 170 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 171 | </tr> | |
| 172 | </table> | |
| 173 | </div><div class="memdoc"> | |
| 174 | ||
| 175 | <p>Constructor. </p> | |
| 176 | <dl class="params"><dt>Parameters</dt><dd> | |
| 177 | <table class="params"> | |
| 178 | <tr><td class="paramname">conf1</td><td>An array of integer counts. </td></tr> | |
| 179 | <tr><td class="paramname">conf2</td><td>An array of integer counts. </td></tr> | |
| 180 | </table> | |
| 181 | </dd> | |
| 182 | </dl> | |
| 183 | <dl class="section return"><dt>Returns</dt><dd>True if conf1 is more probable than conf2. </dd></dl> | |
| 184 | ||
| 185 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00160">160</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 186 | ||
| 187 | </div> | |
| 188 | </div> | |
| 189 | <hr/>The documentation for this class was generated from the following file:<ul> | |
| 190 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8cpp_source.html">operators.cpp</a></li> | |
| 191 | </ul> | |
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| 76 | <div class="title">IsoSpec::IsoSpec::KeyHasher Member List</div> </div> | |
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| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_key_hasher.html">IsoSpec::IsoSpec::KeyHasher</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_key_hasher.html#a094e6c2b6a3c9fa09b81187cbdf50de3">KeyHasher</a>(int dim)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_key_hasher.html">IsoSpec::IsoSpec::KeyHasher</a></td><td class="entry"></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_key_hasher.html#a4e3d55fd75979e5b725ad0112052f046">operator()</a>(const int *conf) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_key_hasher.html">IsoSpec::IsoSpec::KeyHasher</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><b>IsoSpec</b></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_key_hasher.html">KeyHasher</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_iso_spec_1_1_key_hasher-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoSpec::KeyHasher Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p>The hash function class. | |
| 84 | <a href="class_iso_spec_1_1_iso_spec_1_1_key_hasher.html#details">More...</a></p> | |
| 85 | <table class="memberdecls"> | |
| 86 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 87 | Public Member Functions</h2></td></tr> | |
| 88 | <tr class="memitem:a094e6c2b6a3c9fa09b81187cbdf50de3"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_key_hasher.html#a094e6c2b6a3c9fa09b81187cbdf50de3">KeyHasher</a> (int dim)</td></tr> | |
| 89 | <tr class="memdesc:a094e6c2b6a3c9fa09b81187cbdf50de3"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a094e6c2b6a3c9fa09b81187cbdf50de3">More...</a><br /></td></tr> | |
| 90 | <tr class="separator:a094e6c2b6a3c9fa09b81187cbdf50de3"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | <tr class="memitem:a4e3d55fd75979e5b725ad0112052f046"><td class="memItemLeft" align="right" valign="top">std::size_t </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_key_hasher.html#a4e3d55fd75979e5b725ad0112052f046">operator()</a> (const int *conf) const</td></tr> | |
| 92 | <tr class="memdesc:a4e3d55fd75979e5b725ad0112052f046"><td class="mdescLeft"> </td><td class="mdescRight">The <b>call</b> operator. <a href="#a4e3d55fd75979e5b725ad0112052f046">More...</a><br /></td></tr> | |
| 93 | <tr class="separator:a4e3d55fd75979e5b725ad0112052f046"><td class="memSeparator" colspan="2"> </td></tr> | |
| 94 | </table> | |
| 95 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 96 | <div class="textblock"><p>The hash function class. </p> | |
| 97 | <p>Needed for the unordered-map. </p> | |
| 98 | ||
| 99 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00031">31</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 100 | </div><h2 class="groupheader">Constructor & Destructor Documentation</h2> | |
| 101 | <a id="a094e6c2b6a3c9fa09b81187cbdf50de3"></a> | |
| 102 | <h2 class="memtitle"><span class="permalink"><a href="#a094e6c2b6a3c9fa09b81187cbdf50de3">◆ </a></span>KeyHasher()</h2> | |
| 103 | ||
| 104 | <div class="memitem"> | |
| 105 | <div class="memproto"> | |
| 106 | <table class="memname"> | |
| 107 | <tr> | |
| 108 | <td class="memname">IsoSpec::KeyHasher::KeyHasher </td> | |
| 109 | <td>(</td> | |
| 110 | <td class="paramtype">int </td> | |
| 111 | <td class="paramname"><em>dim</em></td><td>)</td> | |
| 112 | <td></td> | |
| 113 | </tr> | |
| 114 | </table> | |
| 115 | </div><div class="memdoc"> | |
| 116 | ||
| 117 | <p>Constructor. </p> | |
| 118 | <dl class="params"><dt>Parameters</dt><dd> | |
| 119 | <table class="params"> | |
| 120 | <tr><td class="paramname">dim</td><td>the number of the ints that make up a configuration. </td></tr> | |
| 121 | </table> | |
| 122 | </dd> | |
| 123 | </dl> | |
| 124 | ||
| 125 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00022">22</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 126 | ||
| 127 | </div> | |
| 128 | </div> | |
| 129 | <h2 class="groupheader">Member Function Documentation</h2> | |
| 130 | <a id="a4e3d55fd75979e5b725ad0112052f046"></a> | |
| 131 | <h2 class="memtitle"><span class="permalink"><a href="#a4e3d55fd75979e5b725ad0112052f046">◆ </a></span>operator()()</h2> | |
| 132 | ||
| 133 | <div class="memitem"> | |
| 134 | <div class="memproto"> | |
| 135 | <table class="mlabels"> | |
| 136 | <tr> | |
| 137 | <td class="mlabels-left"> | |
| 138 | <table class="memname"> | |
| 139 | <tr> | |
| 140 | <td class="memname">std::size_t IsoSpec::IsoSpec::KeyHasher::operator() </td> | |
| 141 | <td>(</td> | |
| 142 | <td class="paramtype">const int * </td> | |
| 143 | <td class="paramname"><em>conf</em></td><td>)</td> | |
| 144 | <td> const</td> | |
| 145 | </tr> | |
| 146 | </table> | |
| 147 | </td> | |
| 148 | <td class="mlabels-right"> | |
| 149 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 150 | </tr> | |
| 151 | </table> | |
| 152 | </div><div class="memdoc"> | |
| 153 | ||
| 154 | <p>The <b>call</b> operator. </p> | |
| 155 | <dl class="params"><dt>Parameters</dt><dd> | |
| 156 | <table class="params"> | |
| 157 | <tr><td class="paramname">conf</td><td>An array of integer counts. </td></tr> | |
| 158 | </table> | |
| 159 | </dd> | |
| 160 | </dl> | |
| 161 | <dl class="section return"><dt>Returns</dt><dd>The hash for counts. </dd></dl> | |
| 162 | ||
| 163 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00047">47</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 164 | ||
| 165 | </div> | |
| 166 | </div> | |
| 167 | <hr/>The documentation for this class was generated from the following file:<ul> | |
| 168 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8cpp_source.html">operators.cpp</a></li> | |
| 169 | </ul> | |
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| 69 | <div id="nav-path" class="navpath"> | |
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| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><b>IsoSpec</b></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_reverse_order.html">ReverseOrder</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::IsoSpec::ReverseOrder< T > Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_reverse_order.html">IsoSpec::IsoSpec::ReverseOrder< T ></a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>operator()</b>(const T a, const T b) const (defined in <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_reverse_order.html">IsoSpec::IsoSpec::ReverseOrder< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_reverse_order.html">IsoSpec::IsoSpec::ReverseOrder< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>ReverseOrder</b>() (defined in <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_reverse_order.html">IsoSpec::IsoSpec::ReverseOrder< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_reverse_order.html">IsoSpec::IsoSpec::ReverseOrder< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
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| 72 | </div> | |
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| 74 | <div class="header"> | |
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| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_iso_spec_1_1_reverse_order-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoSpec::ReverseOrder< T > Class Template Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a39761f0beb165c285ed1ed4b494e35a4"><td class="memItemLeft" align="right" valign="top"><a id="a39761f0beb165c285ed1ed4b494e35a4"></a> | |
| 86 | bool </td><td class="memItemRight" valign="bottom"><b>operator()</b> (const T a, const T b) const</td></tr> | |
| 87 | <tr class="separator:a39761f0beb165c285ed1ed4b494e35a4"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | </table> | |
| 89 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 90 | <div class="textblock"><h3>template<typename T><br /> | |
| 91 | class IsoSpec::IsoSpec::ReverseOrder< T ></h3> | |
| 92 | ||
| 93 | ||
| 94 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00167">167</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 95 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 96 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8cpp_source.html">operators.cpp</a></li> | |
| 97 | </ul> | |
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| 66 | </iframe> | |
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| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><b>IsoSpec</b></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_table_order.html">TableOrder</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::IsoSpec::TableOrder< T > Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_table_order.html">IsoSpec::IsoSpec::TableOrder< T ></a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>operator()</b>(unsigned int i, unsigned int j) (defined in <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_table_order.html">IsoSpec::IsoSpec::TableOrder< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_table_order.html">IsoSpec::IsoSpec::TableOrder< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>TableOrder</b>(const T *_tbl) (defined in <a class="el" href="class_iso_spec_1_1_iso_spec_1_1_table_order.html">IsoSpec::IsoSpec::TableOrder< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_table_order.html">IsoSpec::IsoSpec::TableOrder< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 51 | $(document).ready(function() { init_search(); }); | |
| 52 | }); | |
| 53 | /* @license-end */</script> | |
| 54 | <div id="main-nav"></div> | |
| 55 | <!-- window showing the filter options --> | |
| 56 | <div id="MSearchSelectWindow" | |
| 57 | onmouseover="return searchBox.OnSearchSelectShow()" | |
| 58 | onmouseout="return searchBox.OnSearchSelectHide()" | |
| 59 | onkeydown="return searchBox.OnSearchSelectKey(event)"> | |
| 60 | </div> | |
| 61 | ||
| 62 | <!-- iframe showing the search results (closed by default) --> | |
| 63 | <div id="MSearchResultsWindow"> | |
| 64 | <iframe src="javascript:void(0)" frameborder="0" | |
| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><b>IsoSpec</b></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_spec_1_1_table_order.html">TableOrder</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_iso_spec_1_1_table_order-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoSpec::TableOrder< T > Class Template Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:ad7f7ff01c71c3ba7308f8576dc7226c6"><td class="memItemLeft" align="right" valign="top"><a id="ad7f7ff01c71c3ba7308f8576dc7226c6"></a> | |
| 86 |  </td><td class="memItemRight" valign="bottom"><b>TableOrder</b> (const T *_tbl)</td></tr> | |
| 87 | <tr class="separator:ad7f7ff01c71c3ba7308f8576dc7226c6"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:a0b952830050570f97ffd71137548c431"><td class="memItemLeft" align="right" valign="top"><a id="a0b952830050570f97ffd71137548c431"></a> | |
| 89 | bool </td><td class="memItemRight" valign="bottom"><b>operator()</b> (unsigned int i, unsigned int j)</td></tr> | |
| 90 | <tr class="separator:a0b952830050570f97ffd71137548c431"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | </table> | |
| 92 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 93 | <div class="textblock"><h3>template<typename T><br /> | |
| 94 | class IsoSpec::IsoSpec::TableOrder< T ></h3> | |
| 95 | ||
| 96 | ||
| 97 | <p class="definition">Definition at line <a class="el" href="operators_8cpp_source.html#l00174">174</a> of file <a class="el" href="operators_8cpp_source.html">operators.cpp</a>.</p> | |
| 98 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 99 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8cpp_source.html">operators.cpp</a></li> | |
| 100 | </ul> | |
| 101 | </div><!-- contents --> | |
| 102 | <!-- start footer part --> | |
| 103 | <hr class="footer"/><address class="footer"><small> | |
| 104 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 105 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 106 | </a> 1.8.14 | |
| 107 | </small></address> | |
| 108 | </body> | |
| 109 | </html> |
| 0 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> | |
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| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
| 37 | </div> | |
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| 39 | <!-- Generated by Doxygen 1.8.14 --> | |
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| 51 | $(document).ready(function() { init_search(); }); | |
| 52 | }); | |
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| 55 | <!-- window showing the filter options --> | |
| 56 | <div id="MSearchSelectWindow" | |
| 57 | onmouseover="return searchBox.OnSearchSelectShow()" | |
| 58 | onmouseout="return searchBox.OnSearchSelectHide()" | |
| 59 | onkeydown="return searchBox.OnSearchSelectKey(event)"> | |
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| 61 | ||
| 62 | <!-- iframe showing the search results (closed by default) --> | |
| 63 | <div id="MSearchResultsWindow"> | |
| 64 | <iframe src="javascript:void(0)" frameborder="0" | |
| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::IsoThresholdGenerator Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a7164a6476b84665967c4a667a91d3f3e">advanceToNextConfiguration</a>() override final</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 86 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ad29d8761174bca7b1846ddec03b33528">count_confs</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></td><td class="entry"></td></tr> | |
| 87 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 88 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 89 | <tr bgcolor="#f0f0f0"><td class="entry"><b>get_conf_signature</b>(int *space) const override final (defined in <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a>(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 96 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a>(const char *formula)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a>(Iso &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a>(const Iso &other, bool fullcopy)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 99 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoGenerator</a>(Iso &&iso, bool alloc_partials=true)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"></td></tr> | |
| 100 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a3abbcf1d810b6cad9400bd2552c3faf1">IsoThresholdGenerator</a>(Iso &&iso, double _threshold, bool _absolute=true, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></td><td class="entry"></td></tr> | |
| 101 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 102 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a4aeebde03e385404d0175fd5696ff529">lprob</a>() const override final</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 103 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 104 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ae2236accc7dc7a25a723e3c7317659b6">mass</a>() const override final</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 105 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 106 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 107 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 108 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 109 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a998d987f81b2ca7ed610294f6a5f8df5">prob</a>() const override final</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 110 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ab830ffa21469df45a513ff1dcaf5d9e7">reset</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></td><td class="entry"></td></tr> | |
| 111 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ac6aa2fff002a76b0beae1995f34ae5f6">terminate_search</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></td><td class="entry"></td></tr> | |
| 112 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 113 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">~IsoGenerator</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 114 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~IsoThresholdGenerator</b>() (defined in <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 115 | </table></div><!-- contents --> | |
| 116 | <!-- start footer part --> | |
| 117 | <hr class="footer"/><address class="footer"><small> | |
| 118 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 119 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 120 | </a> 1.8.14 | |
| 121 | </small></address> | |
| 122 | </body> | |
| 123 | </html> |
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| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
| 37 | </div> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_iso_threshold_generator-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoThresholdGenerator Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p>The generator of isotopologues above a given threshold value. | |
| 84 | <a href="class_iso_spec_1_1_iso_threshold_generator.html#details">More...</a></p> | |
| 85 | ||
| 86 | <p><code>#include <<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>></code></p> | |
| 87 | <div class="dynheader"> | |
| 88 | Inheritance diagram for IsoSpec::IsoThresholdGenerator:</div> | |
| 89 | <div class="dyncontent"> | |
| 90 | <div class="center"> | |
| 91 | <img src="class_iso_spec_1_1_iso_threshold_generator.png" usemap="#IsoSpec::IsoThresholdGenerator_map" alt=""/> | |
| 92 | <map id="IsoSpec::IsoThresholdGenerator_map" name="IsoSpec::IsoThresholdGenerator_map"> | |
| 93 | <area href="class_iso_spec_1_1_iso_generator.html" title="The generator of isotopologues. " alt="IsoSpec::IsoGenerator" shape="rect" coords="0,56,192,80"/> | |
| 94 | <area href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. " alt="IsoSpec::Iso" shape="rect" coords="0,0,192,24"/> | |
| 95 | </map> | |
| 96 | </div></div> | |
| 97 | <table class="memberdecls"> | |
| 98 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 99 | Public Member Functions</h2></td></tr> | |
| 100 | <tr class="memitem:a58699c4e68a846b979b8163bc6982e2c"><td class="memItemLeft" align="right" valign="top"><a id="a58699c4e68a846b979b8163bc6982e2c"></a> | |
| 101 | void </td><td class="memItemRight" valign="bottom"><b>get_conf_signature</b> (int *space) const override final</td></tr> | |
| 102 | <tr class="separator:a58699c4e68a846b979b8163bc6982e2c"><td class="memSeparator" colspan="2"> </td></tr> | |
| 103 | <tr class="memitem:a3abbcf1d810b6cad9400bd2552c3faf1"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a3abbcf1d810b6cad9400bd2552c3faf1">IsoThresholdGenerator</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&iso, double _threshold, bool _absolute=true, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true)</td></tr> | |
| 104 | <tr class="memdesc:a3abbcf1d810b6cad9400bd2552c3faf1"><td class="mdescLeft"> </td><td class="mdescRight">The move-constructor. <a href="#a3abbcf1d810b6cad9400bd2552c3faf1">More...</a><br /></td></tr> | |
| 105 | <tr class="separator:a3abbcf1d810b6cad9400bd2552c3faf1"><td class="memSeparator" colspan="2"> </td></tr> | |
| 106 | <tr class="memitem:a7164a6476b84665967c4a667a91d3f3e"><td class="memItemLeft" align="right" valign="top">ISOSPEC_FORCE_INLINE bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a7164a6476b84665967c4a667a91d3f3e">advanceToNextConfiguration</a> () override final</td></tr> | |
| 107 | <tr class="memdesc:a7164a6476b84665967c4a667a91d3f3e"><td class="mdescLeft"> </td><td class="mdescRight">Advance to the next, not yet visited, most probable isotopologue. <a href="#a7164a6476b84665967c4a667a91d3f3e">More...</a><br /></td></tr> | |
| 108 | <tr class="separator:a7164a6476b84665967c4a667a91d3f3e"><td class="memSeparator" colspan="2"> </td></tr> | |
| 109 | <tr class="memitem:a4aeebde03e385404d0175fd5696ff529"><td class="memItemLeft" align="right" valign="top">ISOSPEC_FORCE_INLINE double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a4aeebde03e385404d0175fd5696ff529">lprob</a> () const override final</td></tr> | |
| 110 | <tr class="memdesc:a4aeebde03e385404d0175fd5696ff529"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the current isotopologue. <a href="#a4aeebde03e385404d0175fd5696ff529">More...</a><br /></td></tr> | |
| 111 | <tr class="separator:a4aeebde03e385404d0175fd5696ff529"><td class="memSeparator" colspan="2"> </td></tr> | |
| 112 | <tr class="memitem:ae2236accc7dc7a25a723e3c7317659b6"><td class="memItemLeft" align="right" valign="top">ISOSPEC_FORCE_INLINE double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ae2236accc7dc7a25a723e3c7317659b6">mass</a> () const override final</td></tr> | |
| 113 | <tr class="memdesc:ae2236accc7dc7a25a723e3c7317659b6"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the current isotopologue. <a href="#ae2236accc7dc7a25a723e3c7317659b6">More...</a><br /></td></tr> | |
| 114 | <tr class="separator:ae2236accc7dc7a25a723e3c7317659b6"><td class="memSeparator" colspan="2"> </td></tr> | |
| 115 | <tr class="memitem:a998d987f81b2ca7ed610294f6a5f8df5"><td class="memItemLeft" align="right" valign="top">ISOSPEC_FORCE_INLINE double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a998d987f81b2ca7ed610294f6a5f8df5">prob</a> () const override final</td></tr> | |
| 116 | <tr class="memdesc:a998d987f81b2ca7ed610294f6a5f8df5"><td class="mdescLeft"> </td><td class="mdescRight">Get the probability of the current isotopologue. <a href="#a998d987f81b2ca7ed610294f6a5f8df5">More...</a><br /></td></tr> | |
| 117 | <tr class="separator:a998d987f81b2ca7ed610294f6a5f8df5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 118 | <tr class="memitem:ac6aa2fff002a76b0beae1995f34ae5f6"><td class="memItemLeft" align="right" valign="top"><a id="ac6aa2fff002a76b0beae1995f34ae5f6"></a> | |
| 119 | void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ac6aa2fff002a76b0beae1995f34ae5f6">terminate_search</a> ()</td></tr> | |
| 120 | <tr class="memdesc:ac6aa2fff002a76b0beae1995f34ae5f6"><td class="mdescLeft"> </td><td class="mdescRight">Block the subsequent search of isotopologues. <br /></td></tr> | |
| 121 | <tr class="separator:ac6aa2fff002a76b0beae1995f34ae5f6"><td class="memSeparator" colspan="2"> </td></tr> | |
| 122 | <tr class="memitem:ab830ffa21469df45a513ff1dcaf5d9e7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ab830ffa21469df45a513ff1dcaf5d9e7">reset</a> ()</td></tr> | |
| 123 | <tr class="separator:ab830ffa21469df45a513ff1dcaf5d9e7"><td class="memSeparator" colspan="2"> </td></tr> | |
| 124 | <tr class="memitem:ad29d8761174bca7b1846ddec03b33528"><td class="memItemLeft" align="right" valign="top">size_t </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ad29d8761174bca7b1846ddec03b33528">count_confs</a> ()</td></tr> | |
| 125 | <tr class="separator:ad29d8761174bca7b1846ddec03b33528"><td class="memSeparator" colspan="2"> </td></tr> | |
| 126 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_iso_generator"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_iso_generator')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td></tr> | |
| 127 | <tr class="memitem:a89b5b851fbc67f79ed165af0b9b2a188 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top"><a id="a89b5b851fbc67f79ed165af0b9b2a188"></a> | |
| 128 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoGenerator</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&iso, bool alloc_partials=true)</td></tr> | |
| 129 | <tr class="memdesc:a89b5b851fbc67f79ed165af0b9b2a188 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 130 | <tr class="separator:a89b5b851fbc67f79ed165af0b9b2a188 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 131 | <tr class="memitem:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top"><a id="a28442c8072a2e85faf5ff04f5feffd76"></a> | |
| 132 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">~IsoGenerator</a> ()</td></tr> | |
| 133 | <tr class="memdesc:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 134 | <tr class="separator:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 135 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 136 | <tr class="memitem:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a> (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td></tr> | |
| 137 | <tr class="memdesc:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">General constructror. <a href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">More...</a><br /></td></tr> | |
| 138 | <tr class="separator:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 139 | <tr class="memitem:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="ad389effb319e9ed73db9ed5749868b81"></a> | |
| 140 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a> (const char *formula)</td></tr> | |
| 141 | <tr class="memdesc:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Constructor from the formula object. <br /></td></tr> | |
| 142 | <tr class="separator:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 143 | <tr class="memitem:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a6c93ecb77a11bc831cc7600797fbf837"></a> | |
| 144 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&other)</td></tr> | |
| 145 | <tr class="memdesc:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">The move constructor. <br /></td></tr> | |
| 146 | <tr class="separator:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 147 | <tr class="memitem:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a> (const <a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &other, bool fullcopy)</td></tr> | |
| 148 | <tr class="memdesc:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">The copy constructor. <a href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">More...</a><br /></td></tr> | |
| 149 | <tr class="separator:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 150 | <tr class="memitem:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a8cf8f90338bfc3e5117f5b491f7b523f"></a> | |
| 151 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a> ()</td></tr> | |
| 152 | <tr class="memdesc:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 153 | <tr class="separator:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 154 | <tr class="memitem:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a7541599fbc29dd374bb60e5eb8fc047d"></a> | |
| 155 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a> () const</td></tr> | |
| 156 | <tr class="memdesc:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest peak in the isotopic distribution. <br /></td></tr> | |
| 157 | <tr class="separator:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 158 | <tr class="memitem:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a1ede5e34e5bbbb22ae89b362ce2c6faf"></a> | |
| 159 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a> () const</td></tr> | |
| 160 | <tr class="memdesc:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest peak in the isotopic distribution. <br /></td></tr> | |
| 161 | <tr class="separator:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 162 | <tr class="memitem:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a9035d076cec8f937d971e3fd972aa83f"></a> | |
| 163 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a> () const</td></tr> | |
| 164 | <tr class="memdesc:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode-configuration (if there are many modes, they share this value). <br /></td></tr> | |
| 165 | <tr class="separator:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 166 | <tr class="memitem:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a62b17f48d86f62b5ed38ffb296a9daa5"></a> | |
| 167 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a> () const</td></tr> | |
| 168 | <tr class="memdesc:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of elements in the chemical formula of the molecule. <br /></td></tr> | |
| 169 | <tr class="separator:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 170 | <tr class="memitem:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a656a37dd84a6c0534b2373210ed5a091"></a> | |
| 171 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a> () const</td></tr> | |
| 172 | <tr class="memdesc:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the total number of isotopes of elements present in a chemical formula. <br /></td></tr> | |
| 173 | <tr class="separator:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 174 | </table><table class="memberdecls"> | |
| 175 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a> | |
| 176 | Additional Inherited Members</h2></td></tr> | |
| 177 | <tr class="inherit_header pub_attribs_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pub_attribs_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Public Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 178 | <tr class="memitem:ad2a353f2c746648b08a9ad31ff775766 inherit pub_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td></tr> | |
| 179 | <tr class="separator:ad2a353f2c746648b08a9ad31ff775766 inherit pub_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 180 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_iso_generator"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_iso_generator')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td></tr> | |
| 181 | <tr class="memitem:a54a39b847a71aa08d1207d0666dd62bc inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a></td></tr> | |
| 182 | <tr class="separator:a54a39b847a71aa08d1207d0666dd62bc inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 183 | <tr class="memitem:af5654fcdba8199cbd60668af5de89a53 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a></td></tr> | |
| 184 | <tr class="separator:af5654fcdba8199cbd60668af5de89a53 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 185 | <tr class="memitem:ac18406df84b4b220bcb1974000c192b2 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a></td></tr> | |
| 186 | <tr class="separator:ac18406df84b4b220bcb1974000c192b2 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 187 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 188 | <tr class="memitem:a90245f9bc318f12720c134f61bbe0db0 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td></tr> | |
| 189 | <tr class="separator:a90245f9bc318f12720c134f61bbe0db0 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 190 | <tr class="memitem:a7235f0afc56dccd13937791a630c45da inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td></tr> | |
| 191 | <tr class="separator:a7235f0afc56dccd13937791a630c45da inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 192 | <tr class="memitem:ab01939334b6c3e69f65a36f9965971a2 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td></tr> | |
| 193 | <tr class="separator:ab01939334b6c3e69f65a36f9965971a2 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 194 | <tr class="memitem:a89ed144bf2495fa25840aca90a31b425 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td></tr> | |
| 195 | <tr class="separator:a89ed144bf2495fa25840aca90a31b425 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 196 | <tr class="memitem:a8dd2c443706935b582979b13f935115c inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td></tr> | |
| 197 | <tr class="separator:a8dd2c443706935b582979b13f935115c inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 198 | <tr class="memitem:aea98a8331a2f8a1a6bbcace6124fcfae inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> ** </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td></tr> | |
| 199 | <tr class="separator:aea98a8331a2f8a1a6bbcace6124fcfae inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 200 | <tr class="memitem:ab51c157b23ae6a6b521667b6f0e8a208 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td></tr> | |
| 201 | <tr class="separator:ab51c157b23ae6a6b521667b6f0e8a208 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 202 | </table> | |
| 203 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 204 | <div class="textblock"><p>The generator of isotopologues above a given threshold value. </p> | |
| 205 | <p>Attention: the calculated configurations are only partially ordeded and the user should not assume they will be ordered. This algorithm computes N isotopologues in O(N). It is a considerable advantage w.r.t. the <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html" title="The generator of isotopologues sorted by their probability of occurrence. ">IsoOrderedGenerator</a>. </p> | |
| 206 | ||
| 207 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00235">235</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 208 | </div><h2 class="groupheader">Constructor & Destructor Documentation</h2> | |
| 209 | <a id="a3abbcf1d810b6cad9400bd2552c3faf1"></a> | |
| 210 | <h2 class="memtitle"><span class="permalink"><a href="#a3abbcf1d810b6cad9400bd2552c3faf1">◆ </a></span>IsoThresholdGenerator()</h2> | |
| 211 | ||
| 212 | <div class="memitem"> | |
| 213 | <div class="memproto"> | |
| 214 | <table class="memname"> | |
| 215 | <tr> | |
| 216 | <td class="memname">IsoSpec::IsoThresholdGenerator::IsoThresholdGenerator </td> | |
| 217 | <td>(</td> | |
| 218 | <td class="paramtype"><a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> && </td> | |
| 219 | <td class="paramname"><em>iso</em>, </td> | |
| 220 | </tr> | |
| 221 | <tr> | |
| 222 | <td class="paramkey"></td> | |
| 223 | <td></td> | |
| 224 | <td class="paramtype">double </td> | |
| 225 | <td class="paramname"><em>_threshold</em>, </td> | |
| 226 | </tr> | |
| 227 | <tr> | |
| 228 | <td class="paramkey"></td> | |
| 229 | <td></td> | |
| 230 | <td class="paramtype">bool </td> | |
| 231 | <td class="paramname"><em>_absolute</em> = <code>true</code>, </td> | |
| 232 | </tr> | |
| 233 | <tr> | |
| 234 | <td class="paramkey"></td> | |
| 235 | <td></td> | |
| 236 | <td class="paramtype">int </td> | |
| 237 | <td class="paramname"><em>_tabSize</em> = <code>1000</code>, </td> | |
| 238 | </tr> | |
| 239 | <tr> | |
| 240 | <td class="paramkey"></td> | |
| 241 | <td></td> | |
| 242 | <td class="paramtype">int </td> | |
| 243 | <td class="paramname"><em>_hashSize</em> = <code>1000</code>, </td> | |
| 244 | </tr> | |
| 245 | <tr> | |
| 246 | <td class="paramkey"></td> | |
| 247 | <td></td> | |
| 248 | <td class="paramtype">bool </td> | |
| 249 | <td class="paramname"><em>reorder_marginals</em> = <code>true</code> </td> | |
| 250 | </tr> | |
| 251 | <tr> | |
| 252 | <td></td> | |
| 253 | <td>)</td> | |
| 254 | <td></td><td></td> | |
| 255 | </tr> | |
| 256 | </table> | |
| 257 | </div><div class="memdoc"> | |
| 258 | ||
| 259 | <p>The move-constructor. </p> | |
| 260 | <dl class="params"><dt>Parameters</dt><dd> | |
| 261 | <table class="params"> | |
| 262 | <tr><td class="paramname">iso</td><td>An instance of the <a class="el" href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. ">Iso</a> class. </td></tr> | |
| 263 | <tr><td class="paramname">_threshold</td><td>The threshold value. </td></tr> | |
| 264 | <tr><td class="paramname">_absolute</td><td>If true, the _threshold is interpreted as the absolute minimal peak height for the isotopologues. If false, the _threshold is the fraction of the heighest peak's probability. </td></tr> | |
| 265 | <tr><td class="paramname">tabSize</td><td>The size of the extension of the table with configurations. </td></tr> | |
| 266 | <tr><td class="paramname">hashSize</td><td>The size of the hash-table used to store subisotopologues and check if they have been already calculated. </td></tr> | |
| 267 | </table> | |
| 268 | </dd> | |
| 269 | </dl> | |
| 270 | ||
| 271 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8cpp_source.html#l00286">286</a> of file <a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a>.</p> | |
| 272 | ||
| 273 | </div> | |
| 274 | </div> | |
| 275 | <h2 class="groupheader">Member Function Documentation</h2> | |
| 276 | <a id="a7164a6476b84665967c4a667a91d3f3e"></a> | |
| 277 | <h2 class="memtitle"><span class="permalink"><a href="#a7164a6476b84665967c4a667a91d3f3e">◆ </a></span>advanceToNextConfiguration()</h2> | |
| 278 | ||
| 279 | <div class="memitem"> | |
| 280 | <div class="memproto"> | |
| 281 | <table class="mlabels"> | |
| 282 | <tr> | |
| 283 | <td class="mlabels-left"> | |
| 284 | <table class="memname"> | |
| 285 | <tr> | |
| 286 | <td class="memname">ISOSPEC_FORCE_INLINE bool IsoSpec::IsoThresholdGenerator::advanceToNextConfiguration </td> | |
| 287 | <td>(</td> | |
| 288 | <td class="paramname"></td><td>)</td> | |
| 289 | <td></td> | |
| 290 | </tr> | |
| 291 | </table> | |
| 292 | </td> | |
| 293 | <td class="mlabels-right"> | |
| 294 | <span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">final</span><span class="mlabel">override</span><span class="mlabel">virtual</span></span> </td> | |
| 295 | </tr> | |
| 296 | </table> | |
| 297 | </div><div class="memdoc"> | |
| 298 | ||
| 299 | <p>Advance to the next, not yet visited, most probable isotopologue. </p> | |
| 300 | <dl class="section return"><dt>Returns</dt><dd>Return false if it is not possible to advance. </dd></dl> | |
| 301 | ||
| 302 | <p>Implements <a class="el" href="class_iso_spec_1_1_iso_generator.html#a20f48ba18c6aecc57d73b2c3ec3a11dd">IsoSpec::IsoGenerator</a>.</p> | |
| 303 | ||
| 304 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00296">296</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 305 | ||
| 306 | </div> | |
| 307 | </div> | |
| 308 | <a id="ad29d8761174bca7b1846ddec03b33528"></a> | |
| 309 | <h2 class="memtitle"><span class="permalink"><a href="#ad29d8761174bca7b1846ddec03b33528">◆ </a></span>count_confs()</h2> | |
| 310 | ||
| 311 | <div class="memitem"> | |
| 312 | <div class="memproto"> | |
| 313 | <table class="memname"> | |
| 314 | <tr> | |
| 315 | <td class="memname">size_t IsoSpec::IsoThresholdGenerator::count_confs </td> | |
| 316 | <td>(</td> | |
| 317 | <td class="paramname"></td><td>)</td> | |
| 318 | <td></td> | |
| 319 | </tr> | |
| 320 | </table> | |
| 321 | </div><div class="memdoc"> | |
| 322 | <p>Count the number of configurations in the distribution. This can be used to pre-allocate enough memory to store it (e.g. std::vector's reserve() method - this is faster than depending on the vector's dynamic resizing, even though it means that the configuration space is walked through twice. This method has to be called before the first call to advanceToNextConfiguration and has undefined results (incl. segfaults) otherwise. </p> | |
| 323 | ||
| 324 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8cpp_source.html#l00376">376</a> of file <a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a>.</p> | |
| 325 | ||
| 326 | </div> | |
| 327 | </div> | |
| 328 | <a id="a4aeebde03e385404d0175fd5696ff529"></a> | |
| 329 | <h2 class="memtitle"><span class="permalink"><a href="#a4aeebde03e385404d0175fd5696ff529">◆ </a></span>lprob()</h2> | |
| 330 | ||
| 331 | <div class="memitem"> | |
| 332 | <div class="memproto"> | |
| 333 | <table class="mlabels"> | |
| 334 | <tr> | |
| 335 | <td class="mlabels-left"> | |
| 336 | <table class="memname"> | |
| 337 | <tr> | |
| 338 | <td class="memname">ISOSPEC_FORCE_INLINE double IsoSpec::IsoThresholdGenerator::lprob </td> | |
| 339 | <td>(</td> | |
| 340 | <td class="paramname"></td><td>)</td> | |
| 341 | <td> const</td> | |
| 342 | </tr> | |
| 343 | </table> | |
| 344 | </td> | |
| 345 | <td class="mlabels-right"> | |
| 346 | <span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">final</span><span class="mlabel">override</span><span class="mlabel">virtual</span></span> </td> | |
| 347 | </tr> | |
| 348 | </table> | |
| 349 | </div><div class="memdoc"> | |
| 350 | ||
| 351 | <p>Get the log-probability of the current isotopologue. </p> | |
| 352 | <dl class="section return"><dt>Returns</dt><dd>The log-probability of the current isotopologue. </dd></dl> | |
| 353 | ||
| 354 | <p>Reimplemented from <a class="el" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">IsoSpec::IsoGenerator</a>.</p> | |
| 355 | ||
| 356 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00335">335</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 357 | ||
| 358 | </div> | |
| 359 | </div> | |
| 360 | <a id="ae2236accc7dc7a25a723e3c7317659b6"></a> | |
| 361 | <h2 class="memtitle"><span class="permalink"><a href="#ae2236accc7dc7a25a723e3c7317659b6">◆ </a></span>mass()</h2> | |
| 362 | ||
| 363 | <div class="memitem"> | |
| 364 | <div class="memproto"> | |
| 365 | <table class="mlabels"> | |
| 366 | <tr> | |
| 367 | <td class="mlabels-left"> | |
| 368 | <table class="memname"> | |
| 369 | <tr> | |
| 370 | <td class="memname">ISOSPEC_FORCE_INLINE double IsoSpec::IsoThresholdGenerator::mass </td> | |
| 371 | <td>(</td> | |
| 372 | <td class="paramname"></td><td>)</td> | |
| 373 | <td> const</td> | |
| 374 | </tr> | |
| 375 | </table> | |
| 376 | </td> | |
| 377 | <td class="mlabels-right"> | |
| 378 | <span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">final</span><span class="mlabel">override</span><span class="mlabel">virtual</span></span> </td> | |
| 379 | </tr> | |
| 380 | </table> | |
| 381 | </div><div class="memdoc"> | |
| 382 | ||
| 383 | <p>Get the mass of the current isotopologue. </p> | |
| 384 | <dl class="section return"><dt>Returns</dt><dd>The mass of the current isotopologue. </dd></dl> | |
| 385 | ||
| 386 | <p>Reimplemented from <a class="el" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">IsoSpec::IsoGenerator</a>.</p> | |
| 387 | ||
| 388 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00336">336</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 389 | ||
| 390 | </div> | |
| 391 | </div> | |
| 392 | <a id="a998d987f81b2ca7ed610294f6a5f8df5"></a> | |
| 393 | <h2 class="memtitle"><span class="permalink"><a href="#a998d987f81b2ca7ed610294f6a5f8df5">◆ </a></span>prob()</h2> | |
| 394 | ||
| 395 | <div class="memitem"> | |
| 396 | <div class="memproto"> | |
| 397 | <table class="mlabels"> | |
| 398 | <tr> | |
| 399 | <td class="mlabels-left"> | |
| 400 | <table class="memname"> | |
| 401 | <tr> | |
| 402 | <td class="memname">ISOSPEC_FORCE_INLINE double IsoSpec::IsoThresholdGenerator::prob </td> | |
| 403 | <td>(</td> | |
| 404 | <td class="paramname"></td><td>)</td> | |
| 405 | <td> const</td> | |
| 406 | </tr> | |
| 407 | </table> | |
| 408 | </td> | |
| 409 | <td class="mlabels-right"> | |
| 410 | <span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">final</span><span class="mlabel">override</span><span class="mlabel">virtual</span></span> </td> | |
| 411 | </tr> | |
| 412 | </table> | |
| 413 | </div><div class="memdoc"> | |
| 414 | ||
| 415 | <p>Get the probability of the current isotopologue. </p> | |
| 416 | <dl class="section return"><dt>Returns</dt><dd>The probability of the current isotopologue. </dd></dl> | |
| 417 | ||
| 418 | <p>Reimplemented from <a class="el" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">IsoSpec::IsoGenerator</a>.</p> | |
| 419 | ||
| 420 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00337">337</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 421 | ||
| 422 | </div> | |
| 423 | </div> | |
| 424 | <a id="ab830ffa21469df45a513ff1dcaf5d9e7"></a> | |
| 425 | <h2 class="memtitle"><span class="permalink"><a href="#ab830ffa21469df45a513ff1dcaf5d9e7">◆ </a></span>reset()</h2> | |
| 426 | ||
| 427 | <div class="memitem"> | |
| 428 | <div class="memproto"> | |
| 429 | <table class="memname"> | |
| 430 | <tr> | |
| 431 | <td class="memname">void IsoSpec::IsoThresholdGenerator::reset </td> | |
| 432 | <td>(</td> | |
| 433 | <td class="paramname"></td><td>)</td> | |
| 434 | <td></td> | |
| 435 | </tr> | |
| 436 | </table> | |
| 437 | </div><div class="memdoc"> | |
| 438 | <p>Reset the generator to the beginning of the sequence. Allows it to be reused, eg. to go through the conf space once, calculate the amount of space needed to store configurations, then to allocate that memory, and go through it again, this time saving configurations (and <em>is</em> in fact faster than allocating a std::vector and depending on it to grow as needed. This is cheaper than throwing away the generator and making a new one too: marginal distributions don't need to be recalculated. </p> | |
| 439 | ||
| 440 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8cpp_source.html#l00386">386</a> of file <a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a>.</p> | |
| 441 | ||
| 442 | </div> | |
| 443 | </div> | |
| 444 | <hr/>The documentation for this class was generated from the following files:<ul> | |
| 445 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a></li> | |
| 446 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a></li> | |
| 447 | </ul> | |
| 448 | </div><!-- contents --> | |
| 449 | <!-- start footer part --> | |
| 450 | <hr class="footer"/><address class="footer"><small> | |
| 451 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 452 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 453 | </a> 1.8.14 | |
| 454 | </small></address> | |
| 455 | </body> | |
| 456 | </html> |
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| 6 | Node4 [label="IsoSpec::IsoGenerator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso_generator.html",tooltip="The generator of isotopologues. "]; | |
| 7 | Node5 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; | |
| 8 | Node5 [label="IsoSpec::Iso",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso.html",tooltip="The Iso class for the calculation of the isotopic distribution. "]; | |
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| 7 | Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; | |
| 8 | Node2 [label="IsoSpec::Iso",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso.html",tooltip="The Iso class for the calculation of the isotopic distribution. "]; | |
| 9 | } |
| 0 | cad1bb76e0da3f0b127af03fb31f4734⏎ |
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| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
| 37 | </div> | |
| 38 | <!-- end header part --> | |
| 39 | <!-- Generated by Doxygen 1.8.14 --> | |
| 40 | <script type="text/javascript"> | |
| 41 | /* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&dn=gpl-2.0.txt GPL-v2 */ | |
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| 51 | $(document).ready(function() { init_search(); }); | |
| 52 | }); | |
| 53 | /* @license-end */</script> | |
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| 55 | <!-- window showing the filter options --> | |
| 56 | <div id="MSearchSelectWindow" | |
| 57 | onmouseover="return searchBox.OnSearchSelectShow()" | |
| 58 | onmouseout="return searchBox.OnSearchSelectHide()" | |
| 59 | onkeydown="return searchBox.OnSearchSelectKey(event)"> | |
| 60 | </div> | |
| 61 | ||
| 62 | <!-- iframe showing the search results (closed by default) --> | |
| 63 | <div id="MSearchResultsWindow"> | |
| 64 | <iframe src="javascript:void(0)" frameborder="0" | |
| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html">IsoThresholdGeneratorMT</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::IsoThresholdGeneratorMT Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html">IsoSpec::IsoThresholdGeneratorMT</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#ab82a60de126aa926b2baf67c49015c22">advanceToNextConfiguration</a>() override final</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html">IsoSpec::IsoThresholdGeneratorMT</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 86 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 87 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 88 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a4f31d79f36d3974004843059f6f19040">eprob</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 89 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#a7c398ea67338f0d446de73ec6670dbf5">get_conf_signature</a>(int *space) const override final</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html">IsoSpec::IsoThresholdGeneratorMT</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a211c8383b3c0ed6a91a112a36d7dff89">get_MT_marginal_set</a>(double Lcutoff, bool absolute, int tabSize, int hashSize)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 96 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a>(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a>(const char *formula)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a>(Iso &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 99 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a>(const Iso &other, bool fullcopy)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"></td></tr> | |
| 100 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a3cda46cec95eefbf4fcb7be97894bfde">IsoGenerator</a>(Iso &&iso)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"></td></tr> | |
| 101 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#a557fc9c693ddd9980151ff6250f80fc0">IsoThresholdGeneratorMT</a>(Iso &&iso, double _threshold, PrecalculatedMarginal **marginals, bool _absolute=true)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html">IsoSpec::IsoThresholdGeneratorMT</a></td><td class="entry"></td></tr> | |
| 102 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 103 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac9f120acfe8495c487f5d73cef141d1b">lprob</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 104 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 105 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a114f352ce4e3665b2c4fe4b56d30a205">mass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 106 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 107 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac38a8eb006e2732c1f0adb58609e397a">partialExpProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 108 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 109 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 110 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#a43d32039cf98798ea3b0b347673fe6ad">terminate_search</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html">IsoSpec::IsoThresholdGeneratorMT</a></td><td class="entry"></td></tr> | |
| 111 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 112 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">~IsoGenerator</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 113 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#a761bc9e2421c3098cf55c800ddc9908c">~IsoThresholdGeneratorMT</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html">IsoSpec::IsoThresholdGeneratorMT</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr> | |
| 114 | </table></div><!-- contents --> | |
| 115 | <!-- start footer part --> | |
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| 117 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 119 | </a> 1.8.14 | |
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| 122 | </html> |
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| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html">IsoThresholdGeneratorMT</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_iso_threshold_generator_m_t-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::IsoThresholdGeneratorMT Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p>The multi-threaded version of the generator of isotopologues. | |
| 84 | <a href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#details">More...</a></p> | |
| 85 | ||
| 86 | <p><code>#include <<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>></code></p> | |
| 87 | <div class="dynheader"> | |
| 88 | Inheritance diagram for IsoSpec::IsoThresholdGeneratorMT:</div> | |
| 89 | <div class="dyncontent"> | |
| 90 | <div class="center"> | |
| 91 | <img src="class_iso_spec_1_1_iso_threshold_generator_m_t.png" usemap="#IsoSpec::IsoThresholdGeneratorMT_map" alt=""/> | |
| 92 | <map id="IsoSpec::IsoThresholdGeneratorMT_map" name="IsoSpec::IsoThresholdGeneratorMT_map"> | |
| 93 | <area href="class_iso_spec_1_1_iso_generator.html" title="The generator of isotopologues. " alt="IsoSpec::IsoGenerator" shape="rect" coords="0,56,210,80"/> | |
| 94 | <area href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. " alt="IsoSpec::Iso" shape="rect" coords="0,0,210,24"/> | |
| 95 | </map> | |
| 96 | </div></div> | |
| 97 | <table class="memberdecls"> | |
| 98 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 99 | Public Member Functions</h2></td></tr> | |
| 100 | <tr class="memitem:ab82a60de126aa926b2baf67c49015c22"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#ab82a60de126aa926b2baf67c49015c22">advanceToNextConfiguration</a> () override final</td></tr> | |
| 101 | <tr class="memdesc:ab82a60de126aa926b2baf67c49015c22"><td class="mdescLeft"> </td><td class="mdescRight">Advance to the next, not yet visited, most probable isotopologue. <a href="#ab82a60de126aa926b2baf67c49015c22">More...</a><br /></td></tr> | |
| 102 | <tr class="separator:ab82a60de126aa926b2baf67c49015c22"><td class="memSeparator" colspan="2"> </td></tr> | |
| 103 | <tr class="memitem:a7c398ea67338f0d446de73ec6670dbf5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#a7c398ea67338f0d446de73ec6670dbf5">get_conf_signature</a> (int *space) const override final</td></tr> | |
| 104 | <tr class="memdesc:a7c398ea67338f0d446de73ec6670dbf5"><td class="mdescLeft"> </td><td class="mdescRight">Save the counts of isotopes in the space. <a href="#a7c398ea67338f0d446de73ec6670dbf5">More...</a><br /></td></tr> | |
| 105 | <tr class="separator:a7c398ea67338f0d446de73ec6670dbf5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 106 | <tr class="memitem:a557fc9c693ddd9980151ff6250f80fc0"><td class="memItemLeft" align="right" valign="top"><a id="a557fc9c693ddd9980151ff6250f80fc0"></a> | |
| 107 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#a557fc9c693ddd9980151ff6250f80fc0">IsoThresholdGeneratorMT</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&iso, double _threshold, <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a> **<a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>, bool _absolute=true)</td></tr> | |
| 108 | <tr class="memdesc:a557fc9c693ddd9980151ff6250f80fc0"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 109 | <tr class="separator:a557fc9c693ddd9980151ff6250f80fc0"><td class="memSeparator" colspan="2"> </td></tr> | |
| 110 | <tr class="memitem:a761bc9e2421c3098cf55c800ddc9908c"><td class="memItemLeft" align="right" valign="top"><a id="a761bc9e2421c3098cf55c800ddc9908c"></a> | |
| 111 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#a761bc9e2421c3098cf55c800ddc9908c">~IsoThresholdGeneratorMT</a> ()</td></tr> | |
| 112 | <tr class="memdesc:a761bc9e2421c3098cf55c800ddc9908c"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 113 | <tr class="separator:a761bc9e2421c3098cf55c800ddc9908c"><td class="memSeparator" colspan="2"> </td></tr> | |
| 114 | <tr class="memitem:a43d32039cf98798ea3b0b347673fe6ad"><td class="memItemLeft" align="right" valign="top"><a id="a43d32039cf98798ea3b0b347673fe6ad"></a> | |
| 115 | void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator_m_t.html#a43d32039cf98798ea3b0b347673fe6ad">terminate_search</a> ()</td></tr> | |
| 116 | <tr class="memdesc:a43d32039cf98798ea3b0b347673fe6ad"><td class="mdescLeft"> </td><td class="mdescRight">Block the subsequent search of isotopologues. <br /></td></tr> | |
| 117 | <tr class="separator:a43d32039cf98798ea3b0b347673fe6ad"><td class="memSeparator" colspan="2"> </td></tr> | |
| 118 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_iso_generator"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_iso_generator')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td></tr> | |
| 119 | <tr class="memitem:ac9f120acfe8495c487f5d73cef141d1b inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac9f120acfe8495c487f5d73cef141d1b">lprob</a> () const</td></tr> | |
| 120 | <tr class="memdesc:ac9f120acfe8495c487f5d73cef141d1b inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the current isotopologue. <a href="class_iso_spec_1_1_iso_generator.html#ac9f120acfe8495c487f5d73cef141d1b">More...</a><br /></td></tr> | |
| 121 | <tr class="separator:ac9f120acfe8495c487f5d73cef141d1b inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 122 | <tr class="memitem:a114f352ce4e3665b2c4fe4b56d30a205 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a114f352ce4e3665b2c4fe4b56d30a205">mass</a> () const</td></tr> | |
| 123 | <tr class="memdesc:a114f352ce4e3665b2c4fe4b56d30a205 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the current isotopologue. <a href="class_iso_spec_1_1_iso_generator.html#a114f352ce4e3665b2c4fe4b56d30a205">More...</a><br /></td></tr> | |
| 124 | <tr class="separator:a114f352ce4e3665b2c4fe4b56d30a205 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 125 | <tr class="memitem:a4f31d79f36d3974004843059f6f19040 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a4f31d79f36d3974004843059f6f19040">eprob</a> () const</td></tr> | |
| 126 | <tr class="memdesc:a4f31d79f36d3974004843059f6f19040 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Get the probability of the current isotopologue. <a href="class_iso_spec_1_1_iso_generator.html#a4f31d79f36d3974004843059f6f19040">More...</a><br /></td></tr> | |
| 127 | <tr class="separator:a4f31d79f36d3974004843059f6f19040 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 128 | <tr class="memitem:a3cda46cec95eefbf4fcb7be97894bfde inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top"><a id="a3cda46cec95eefbf4fcb7be97894bfde"></a> | |
| 129 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a3cda46cec95eefbf4fcb7be97894bfde">IsoGenerator</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&iso)</td></tr> | |
| 130 | <tr class="memdesc:a3cda46cec95eefbf4fcb7be97894bfde inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 131 | <tr class="separator:a3cda46cec95eefbf4fcb7be97894bfde inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 132 | <tr class="memitem:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top"><a id="a28442c8072a2e85faf5ff04f5feffd76"></a> | |
| 133 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">~IsoGenerator</a> ()</td></tr> | |
| 134 | <tr class="memdesc:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 135 | <tr class="separator:a28442c8072a2e85faf5ff04f5feffd76 inherit pub_methods_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 136 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 137 | <tr class="memitem:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso</a> (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</td></tr> | |
| 138 | <tr class="memdesc:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">General constructror. <a href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">More...</a><br /></td></tr> | |
| 139 | <tr class="separator:a5ff1fafd079a866e9d61bc7d859842ea inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 140 | <tr class="memitem:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="ad389effb319e9ed73db9ed5749868b81"></a> | |
| 141 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81">Iso</a> (const char *formula)</td></tr> | |
| 142 | <tr class="memdesc:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Constructor from the formula object. <br /></td></tr> | |
| 143 | <tr class="separator:ad389effb319e9ed73db9ed5749868b81 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 144 | <tr class="memitem:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a6c93ecb77a11bc831cc7600797fbf837"></a> | |
| 145 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837">Iso</a> (<a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &&other)</td></tr> | |
| 146 | <tr class="memdesc:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">The move constructor. <br /></td></tr> | |
| 147 | <tr class="separator:a6c93ecb77a11bc831cc7600797fbf837 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 148 | <tr class="memitem:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">Iso</a> (const <a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> &other, bool fullcopy)</td></tr> | |
| 149 | <tr class="memdesc:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">The copy constructor. <a href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13">More...</a><br /></td></tr> | |
| 150 | <tr class="separator:a485cba7555fbdc64bbea19690f202b13 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 151 | <tr class="memitem:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a8cf8f90338bfc3e5117f5b491f7b523f"></a> | |
| 152 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">~Iso</a> ()</td></tr> | |
| 153 | <tr class="memdesc:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 154 | <tr class="separator:a8cf8f90338bfc3e5117f5b491f7b523f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 155 | <tr class="memitem:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a7541599fbc29dd374bb60e5eb8fc047d"></a> | |
| 156 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">getLightestPeakMass</a> () const</td></tr> | |
| 157 | <tr class="memdesc:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest peak in the isotopic distribution. <br /></td></tr> | |
| 158 | <tr class="separator:a7541599fbc29dd374bb60e5eb8fc047d inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 159 | <tr class="memitem:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a1ede5e34e5bbbb22ae89b362ce2c6faf"></a> | |
| 160 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">getHeaviestPeakMass</a> () const</td></tr> | |
| 161 | <tr class="memdesc:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest peak in the isotopic distribution. <br /></td></tr> | |
| 162 | <tr class="separator:a1ede5e34e5bbbb22ae89b362ce2c6faf inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 163 | <tr class="memitem:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a9035d076cec8f937d971e3fd972aa83f"></a> | |
| 164 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a> () const</td></tr> | |
| 165 | <tr class="memdesc:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode-configuration (if there are many modes, they share this value). <br /></td></tr> | |
| 166 | <tr class="separator:a9035d076cec8f937d971e3fd972aa83f inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 167 | <tr class="memitem:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a62b17f48d86f62b5ed38ffb296a9daa5"></a> | |
| 168 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a> () const</td></tr> | |
| 169 | <tr class="memdesc:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of elements in the chemical formula of the molecule. <br /></td></tr> | |
| 170 | <tr class="separator:a62b17f48d86f62b5ed38ffb296a9daa5 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 171 | <tr class="memitem:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a id="a656a37dd84a6c0534b2373210ed5a091"></a> | |
| 172 | int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a> () const</td></tr> | |
| 173 | <tr class="memdesc:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the total number of isotopes of elements present in a chemical formula. <br /></td></tr> | |
| 174 | <tr class="separator:a656a37dd84a6c0534b2373210ed5a091 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 175 | <tr class="memitem:a211c8383b3c0ed6a91a112a36d7dff89 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a> ** </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a211c8383b3c0ed6a91a112a36d7dff89">get_MT_marginal_set</a> (double Lcutoff, bool absolute, int tabSize, int hashSize)</td></tr> | |
| 176 | <tr class="memdesc:a211c8383b3c0ed6a91a112a36d7dff89 inherit pub_methods_class_iso_spec_1_1_iso"><td class="mdescLeft"> </td><td class="mdescRight">Get the marginal distributions of subisotopologues. <a href="class_iso_spec_1_1_iso.html#a211c8383b3c0ed6a91a112a36d7dff89">More...</a><br /></td></tr> | |
| 177 | <tr class="separator:a211c8383b3c0ed6a91a112a36d7dff89 inherit pub_methods_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 178 | </table><table class="memberdecls"> | |
| 179 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a> | |
| 180 | Additional Inherited Members</h2></td></tr> | |
| 181 | <tr class="inherit_header pub_attribs_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pub_attribs_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Public Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 182 | <tr class="memitem:ad2a353f2c746648b08a9ad31ff775766 inherit pub_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a></td></tr> | |
| 183 | <tr class="separator:ad2a353f2c746648b08a9ad31ff775766 inherit pub_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 184 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_iso_generator"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_iso_generator')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></td></tr> | |
| 185 | <tr class="memitem:a54a39b847a71aa08d1207d0666dd62bc inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a></td></tr> | |
| 186 | <tr class="separator:a54a39b847a71aa08d1207d0666dd62bc inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 187 | <tr class="memitem:af5654fcdba8199cbd60668af5de89a53 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a></td></tr> | |
| 188 | <tr class="separator:af5654fcdba8199cbd60668af5de89a53 inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 189 | <tr class="memitem:ac38a8eb006e2732c1f0adb58609e397a inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html#ac38a8eb006e2732c1f0adb58609e397a">partialExpProbs</a></td></tr> | |
| 190 | <tr class="separator:ac38a8eb006e2732c1f0adb58609e397a inherit pro_attribs_class_iso_spec_1_1_iso_generator"><td class="memSeparator" colspan="2"> </td></tr> | |
| 191 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_iso"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_iso')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></td></tr> | |
| 192 | <tr class="memitem:a90245f9bc318f12720c134f61bbe0db0 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></td></tr> | |
| 193 | <tr class="separator:a90245f9bc318f12720c134f61bbe0db0 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 194 | <tr class="memitem:a7235f0afc56dccd13937791a630c45da inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a></td></tr> | |
| 195 | <tr class="separator:a7235f0afc56dccd13937791a630c45da inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 196 | <tr class="memitem:ab01939334b6c3e69f65a36f9965971a2 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a></td></tr> | |
| 197 | <tr class="separator:ab01939334b6c3e69f65a36f9965971a2 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 198 | <tr class="memitem:a89ed144bf2495fa25840aca90a31b425 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a></td></tr> | |
| 199 | <tr class="separator:a89ed144bf2495fa25840aca90a31b425 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 200 | <tr class="memitem:a8dd2c443706935b582979b13f935115c inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a></td></tr> | |
| 201 | <tr class="separator:a8dd2c443706935b582979b13f935115c inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 202 | <tr class="memitem:aea98a8331a2f8a1a6bbcace6124fcfae inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> ** </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a></td></tr> | |
| 203 | <tr class="separator:aea98a8331a2f8a1a6bbcace6124fcfae inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 204 | <tr class="memitem:ab51c157b23ae6a6b521667b6f0e8a208 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a></td></tr> | |
| 205 | <tr class="separator:ab51c157b23ae6a6b521667b6f0e8a208 inherit pro_attribs_class_iso_spec_1_1_iso"><td class="memSeparator" colspan="2"> </td></tr> | |
| 206 | </table> | |
| 207 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 208 | <div class="textblock"><p>The multi-threaded version of the generator of isotopologues. </p> | |
| 209 | <p>Attention: this code is experimental. </p> | |
| 210 | ||
| 211 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00305">305</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 212 | </div><h2 class="groupheader">Member Function Documentation</h2> | |
| 213 | <a id="ab82a60de126aa926b2baf67c49015c22"></a> | |
| 214 | <h2 class="memtitle"><span class="permalink"><a href="#ab82a60de126aa926b2baf67c49015c22">◆ </a></span>advanceToNextConfiguration()</h2> | |
| 215 | ||
| 216 | <div class="memitem"> | |
| 217 | <div class="memproto"> | |
| 218 | <table class="mlabels"> | |
| 219 | <tr> | |
| 220 | <td class="mlabels-left"> | |
| 221 | <table class="memname"> | |
| 222 | <tr> | |
| 223 | <td class="memname">bool IsoSpec::IsoThresholdGeneratorMT::advanceToNextConfiguration </td> | |
| 224 | <td>(</td> | |
| 225 | <td class="paramname"></td><td>)</td> | |
| 226 | <td></td> | |
| 227 | </tr> | |
| 228 | </table> | |
| 229 | </td> | |
| 230 | <td class="mlabels-right"> | |
| 231 | <span class="mlabels"><span class="mlabel">final</span><span class="mlabel">override</span><span class="mlabel">virtual</span></span> </td> | |
| 232 | </tr> | |
| 233 | </table> | |
| 234 | </div><div class="memdoc"> | |
| 235 | ||
| 236 | <p>Advance to the next, not yet visited, most probable isotopologue. </p> | |
| 237 | <dl class="section return"><dt>Returns</dt><dd>Return false if it is not possible to advance. </dd></dl> | |
| 238 | ||
| 239 | <p>Implements <a class="el" href="class_iso_spec_1_1_iso_generator.html#a20f48ba18c6aecc57d73b2c3ec3a11dd">IsoSpec::IsoGenerator</a>.</p> | |
| 240 | ||
| 241 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8cpp_source.html#l00354">354</a> of file <a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a>.</p> | |
| 242 | ||
| 243 | </div> | |
| 244 | </div> | |
| 245 | <a id="a7c398ea67338f0d446de73ec6670dbf5"></a> | |
| 246 | <h2 class="memtitle"><span class="permalink"><a href="#a7c398ea67338f0d446de73ec6670dbf5">◆ </a></span>get_conf_signature()</h2> | |
| 247 | ||
| 248 | <div class="memitem"> | |
| 249 | <div class="memproto"> | |
| 250 | <table class="mlabels"> | |
| 251 | <tr> | |
| 252 | <td class="mlabels-left"> | |
| 253 | <table class="memname"> | |
| 254 | <tr> | |
| 255 | <td class="memname">void IsoSpec::IsoThresholdGeneratorMT::get_conf_signature </td> | |
| 256 | <td>(</td> | |
| 257 | <td class="paramtype">int * </td> | |
| 258 | <td class="paramname"><em>space</em></td><td>)</td> | |
| 259 | <td> const</td> | |
| 260 | </tr> | |
| 261 | </table> | |
| 262 | </td> | |
| 263 | <td class="mlabels-right"> | |
| 264 | <span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">final</span><span class="mlabel">override</span><span class="mlabel">virtual</span></span> </td> | |
| 265 | </tr> | |
| 266 | </table> | |
| 267 | </div><div class="memdoc"> | |
| 268 | ||
| 269 | <p>Save the counts of isotopes in the space. </p> | |
| 270 | <dl class="params"><dt>Parameters</dt><dd> | |
| 271 | <table class="params"> | |
| 272 | <tr><td class="paramname">space</td><td>An array where counts of isotopes shall be written. Must be as big as the overall number of isotopes. </td></tr> | |
| 273 | </table> | |
| 274 | </dd> | |
| 275 | </dl> | |
| 276 | ||
| 277 | <p>Implements <a class="el" href="class_iso_spec_1_1_iso_generator.html#a19ca8af7dd97f8f37756d4267d49d91d">IsoSpec::IsoGenerator</a>.</p> | |
| 278 | ||
| 279 | <p class="definition">Definition at line <a class="el" href="iso_spec_09_09_8h_source.html#l00316">316</a> of file <a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a>.</p> | |
| 280 | ||
| 281 | </div> | |
| 282 | </div> | |
| 283 | <hr/>The documentation for this class was generated from the following files:<ul> | |
| 284 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8h_source.html">isoSpec++.h</a></li> | |
| 285 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="iso_spec_09_09_8cpp_source.html">isoSpec++.cpp</a></li> | |
| 286 | </ul> | |
| 287 | </div><!-- contents --> | |
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| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
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| 33 | </td> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_key_hasher.html">KeyHasher</a></li> </ul> | |
| 72 | </div> | |
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| 74 | <div class="header"> | |
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| 76 | <div class="title">IsoSpec::KeyHasher Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_key_hasher.html">IsoSpec::KeyHasher</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>KeyHasher</b>(int dim) (defined in <a class="el" href="class_iso_spec_1_1_key_hasher.html">IsoSpec::KeyHasher</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_key_hasher.html">IsoSpec::KeyHasher</a></td><td class="entry"></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>operator()</b>(const int *conf) const (defined in <a class="el" href="class_iso_spec_1_1_key_hasher.html">IsoSpec::KeyHasher</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_key_hasher.html">IsoSpec::KeyHasher</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 55 | <!-- window showing the filter options --> | |
| 56 | <div id="MSearchSelectWindow" | |
| 57 | onmouseover="return searchBox.OnSearchSelectShow()" | |
| 58 | onmouseout="return searchBox.OnSearchSelectHide()" | |
| 59 | onkeydown="return searchBox.OnSearchSelectKey(event)"> | |
| 60 | </div> | |
| 61 | ||
| 62 | <!-- iframe showing the search results (closed by default) --> | |
| 63 | <div id="MSearchResultsWindow"> | |
| 64 | <iframe src="javascript:void(0)" frameborder="0" | |
| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_key_hasher.html">KeyHasher</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_key_hasher-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::KeyHasher Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a094e6c2b6a3c9fa09b81187cbdf50de3"><td class="memItemLeft" align="right" valign="top"><a id="a094e6c2b6a3c9fa09b81187cbdf50de3"></a> | |
| 86 |  </td><td class="memItemRight" valign="bottom"><b>KeyHasher</b> (int dim)</td></tr> | |
| 87 | <tr class="separator:a094e6c2b6a3c9fa09b81187cbdf50de3"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:a32c10222b6c45a5f0f290821c476e83f"><td class="memItemLeft" align="right" valign="top"><a id="a32c10222b6c45a5f0f290821c476e83f"></a> | |
| 89 | std::size_t </td><td class="memItemRight" valign="bottom"><b>operator()</b> (const int *conf) const</td></tr> | |
| 90 | <tr class="separator:a32c10222b6c45a5f0f290821c476e83f"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | </table> | |
| 92 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 93 | <div class="textblock"> | |
| 94 | <p class="definition">Definition at line <a class="el" href="operators_8h_source.html#l00027">27</a> of file <a class="el" href="operators_8h_source.html">operators.h</a>.</p> | |
| 95 | </div><hr/>The documentation for this class was generated from the following files:<ul> | |
| 96 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8h_source.html">operators.h</a></li> | |
| 97 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8cpp_source.html">operators.cpp</a></li> | |
| 98 | </ul> | |
| 99 | </div><!-- contents --> | |
| 100 | <!-- start footer part --> | |
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| 102 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 104 | </a> 1.8.14 | |
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| 107 | </html> |
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| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
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| 61 | ||
| 62 | <!-- iframe showing the search results (closed by default) --> | |
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| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_layered_marginal.html">LayeredMarginal</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::LayeredMarginal Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_layered_marginal.html">IsoSpec::LayeredMarginal</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#ab8b66ed79bad27183f98a9ae34c3b944">extend</a>(double new_threshold)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html">IsoSpec::LayeredMarginal</a></td><td class="entry"></td></tr> | |
| 86 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#abfb6c79d8bdcf4b50f8942f7f8a21de5">get_conf</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html">IsoSpec::LayeredMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 87 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#a3c0a5ce02f00680fc67211c66761e887">get_eProb</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html">IsoSpec::LayeredMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 88 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 89 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#aec04c0f0e00a24d151be39ab46267b4c">get_lProb</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html">IsoSpec::LayeredMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#a0323521e0435172c1f4a4ccd0168668d">get_mass</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html">IsoSpec::LayeredMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#aa15967c22941783e5e59f20544434fb1">get_no_confs</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html">IsoSpec::LayeredMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a1bef0f9020a436652628244533cca61b">getModeEProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 96 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 99 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#af062d180664c9c856b4cc72e3457ca9d">LayeredMarginal</a>(Marginal &&m, int tabSize=1000, int hashSize=1000)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_layered_marginal.html">IsoSpec::LayeredMarginal</a></td><td class="entry"></td></tr> | |
| 100 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 101 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a>(Conf conf) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 102 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a>(const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 103 | <tr bgcolor="#f0f0f0"><td class="entry"><b>Marginal</b>(Marginal &other)=delete (defined in <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 104 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e">Marginal</a>(Marginal &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 105 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 106 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a7cd29141c34e293f0e3257d73baab0ac">mode_eprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 107 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 108 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 109 | <tr bgcolor="#f0f0f0"><td class="entry"><b>operator=</b>(const Marginal &other)=delete (defined in <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 110 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 111 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 112 | </table></div><!-- contents --> | |
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| 117 | </a> 1.8.14 | |
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| 62 | <!-- iframe showing the search results (closed by default) --> | |
| 63 | <div id="MSearchResultsWindow"> | |
| 64 | <iframe src="javascript:void(0)" frameborder="0" | |
| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_layered_marginal.html">LayeredMarginal</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_layered_marginal-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::LayeredMarginal Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p><a class="el" href="class_iso_spec_1_1_layered_marginal.html" title="LayeredMarginal class. ">LayeredMarginal</a> class. | |
| 84 | <a href="class_iso_spec_1_1_layered_marginal.html#details">More...</a></p> | |
| 85 | ||
| 86 | <p><code>#include <<a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>></code></p> | |
| 87 | <div class="dynheader"> | |
| 88 | Inheritance diagram for IsoSpec::LayeredMarginal:</div> | |
| 89 | <div class="dyncontent"> | |
| 90 | <div class="center"> | |
| 91 | <img src="class_iso_spec_1_1_layered_marginal.png" usemap="#IsoSpec::LayeredMarginal_map" alt=""/> | |
| 92 | <map id="IsoSpec::LayeredMarginal_map" name="IsoSpec::LayeredMarginal_map"> | |
| 93 | <area href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). " alt="IsoSpec::Marginal" shape="rect" coords="0,0,160,24"/> | |
| 94 | </map> | |
| 95 | </div></div> | |
| 96 | <table class="memberdecls"> | |
| 97 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 98 | Public Member Functions</h2></td></tr> | |
| 99 | <tr class="memitem:af062d180664c9c856b4cc72e3457ca9d"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#af062d180664c9c856b4cc72e3457ca9d">LayeredMarginal</a> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &&m, int tabSize=1000, int hashSize=1000)</td></tr> | |
| 100 | <tr class="memdesc:af062d180664c9c856b4cc72e3457ca9d"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor: specializes the <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class. <a href="#af062d180664c9c856b4cc72e3457ca9d">More...</a><br /></td></tr> | |
| 101 | <tr class="separator:af062d180664c9c856b4cc72e3457ca9d"><td class="memSeparator" colspan="2"> </td></tr> | |
| 102 | <tr class="memitem:ab8b66ed79bad27183f98a9ae34c3b944"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#ab8b66ed79bad27183f98a9ae34c3b944">extend</a> (double new_threshold)</td></tr> | |
| 103 | <tr class="memdesc:ab8b66ed79bad27183f98a9ae34c3b944"><td class="mdescLeft"> </td><td class="mdescRight">Extend the set of computed subisotopologues to those above the new threshold. <a href="#ab8b66ed79bad27183f98a9ae34c3b944">More...</a><br /></td></tr> | |
| 104 | <tr class="separator:ab8b66ed79bad27183f98a9ae34c3b944"><td class="memSeparator" colspan="2"> </td></tr> | |
| 105 | <tr class="memitem:aec04c0f0e00a24d151be39ab46267b4c"><td class="memItemLeft" align="right" valign="top"><a id="aec04c0f0e00a24d151be39ab46267b4c"></a> | |
| 106 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#aec04c0f0e00a24d151be39ab46267b4c">get_lProb</a> (int idx) const</td></tr> | |
| 107 | <tr class="memdesc:aec04c0f0e00a24d151be39ab46267b4c"><td class="mdescLeft"> </td><td class="mdescRight">get the log-probability of the idx-th subisotopologue, see details in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">PrecalculatedMarginal::get_lProb</a>. <br /></td></tr> | |
| 108 | <tr class="separator:aec04c0f0e00a24d151be39ab46267b4c"><td class="memSeparator" colspan="2"> </td></tr> | |
| 109 | <tr class="memitem:a3c0a5ce02f00680fc67211c66761e887"><td class="memItemLeft" align="right" valign="top"><a id="a3c0a5ce02f00680fc67211c66761e887"></a> | |
| 110 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#a3c0a5ce02f00680fc67211c66761e887">get_eProb</a> (int idx) const</td></tr> | |
| 111 | <tr class="memdesc:a3c0a5ce02f00680fc67211c66761e887"><td class="mdescLeft"> </td><td class="mdescRight">get the probability of the idx-th subisotopologue, see details in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">PrecalculatedMarginal::get_eProb</a>. <br /></td></tr> | |
| 112 | <tr class="separator:a3c0a5ce02f00680fc67211c66761e887"><td class="memSeparator" colspan="2"> </td></tr> | |
| 113 | <tr class="memitem:a0323521e0435172c1f4a4ccd0168668d"><td class="memItemLeft" align="right" valign="top"><a id="a0323521e0435172c1f4a4ccd0168668d"></a> | |
| 114 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#a0323521e0435172c1f4a4ccd0168668d">get_mass</a> (int idx) const</td></tr> | |
| 115 | <tr class="memdesc:a0323521e0435172c1f4a4ccd0168668d"><td class="mdescLeft"> </td><td class="mdescRight">get the mass of the idx-th subisotopologue, see details in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">PrecalculatedMarginal::get_mass</a>. <br /></td></tr> | |
| 116 | <tr class="separator:a0323521e0435172c1f4a4ccd0168668d"><td class="memSeparator" colspan="2"> </td></tr> | |
| 117 | <tr class="memitem:abfb6c79d8bdcf4b50f8942f7f8a21de5"><td class="memItemLeft" align="right" valign="top"><a id="abfb6c79d8bdcf4b50f8942f7f8a21de5"></a> | |
| 118 | const Conf & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#abfb6c79d8bdcf4b50f8942f7f8a21de5">get_conf</a> (int idx) const</td></tr> | |
| 119 | <tr class="memdesc:abfb6c79d8bdcf4b50f8942f7f8a21de5"><td class="mdescLeft"> </td><td class="mdescRight">get the counts of isotopes that define the subisotopologue, see details in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff">PrecalculatedMarginal::get_conf</a>. <br /></td></tr> | |
| 120 | <tr class="separator:abfb6c79d8bdcf4b50f8942f7f8a21de5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 121 | <tr class="memitem:aa15967c22941783e5e59f20544434fb1"><td class="memItemLeft" align="right" valign="top"><a id="aa15967c22941783e5e59f20544434fb1"></a> | |
| 122 | unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_layered_marginal.html#aa15967c22941783e5e59f20544434fb1">get_no_confs</a> () const</td></tr> | |
| 123 | <tr class="memdesc:aa15967c22941783e5e59f20544434fb1"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of precomputed subisotopologues, see details in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">PrecalculatedMarginal::get_no_confs</a>. <br /></td></tr> | |
| 124 | <tr class="separator:aa15967c22941783e5e59f20544434fb1"><td class="memSeparator" colspan="2"> </td></tr> | |
| 125 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_marginal"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_marginal')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td></tr> | |
| 126 | <tr class="memitem:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a> (const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</td></tr> | |
| 127 | <tr class="memdesc:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Class constructor. <a href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">More...</a><br /></td></tr> | |
| 128 | <tr class="separator:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 129 | <tr class="memitem:a02e8f92f8f9add352840f5dba8de5e06 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a02e8f92f8f9add352840f5dba8de5e06"></a> | |
| 130 |  </td><td class="memItemRight" valign="bottom"><b>Marginal</b> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &other)=delete</td></tr> | |
| 131 | <tr class="separator:a02e8f92f8f9add352840f5dba8de5e06 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 132 | <tr class="memitem:a9120cad240058afc3705951d80d28a10 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a9120cad240058afc3705951d80d28a10"></a> | |
| 133 | <a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> & </td><td class="memItemRight" valign="bottom"><b>operator=</b> (const <a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &other)=delete</td></tr> | |
| 134 | <tr class="separator:a9120cad240058afc3705951d80d28a10 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 135 | <tr class="memitem:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="ad60fff17fa2c68ea2cd7f183a635379e"></a> | |
| 136 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e">Marginal</a> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &&other)</td></tr> | |
| 137 | <tr class="memdesc:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 138 | <tr class="separator:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 139 | <tr class="memitem:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="ad44004fa1e83c4a53d431ca403ce3ae4"></a> | |
| 140 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a> ()</td></tr> | |
| 141 | <tr class="memdesc:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 142 | <tr class="separator:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 143 | <tr class="memitem:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a> () const</td></tr> | |
| 144 | <tr class="memdesc:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of isotopes of the investigated element. <a href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">More...</a><br /></td></tr> | |
| 145 | <tr class="separator:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 146 | <tr class="memitem:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a> () const</td></tr> | |
| 147 | <tr class="memdesc:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">More...</a><br /></td></tr> | |
| 148 | <tr class="separator:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 149 | <tr class="memitem:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a> () const</td></tr> | |
| 150 | <tr class="memdesc:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">More...</a><br /></td></tr> | |
| 151 | <tr class="separator:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 152 | <tr class="memitem:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a> () const</td></tr> | |
| 153 | <tr class="memdesc:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">More...</a><br /></td></tr> | |
| 154 | <tr class="separator:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 155 | <tr class="memitem:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a> () const</td></tr> | |
| 156 | <tr class="memdesc:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the mass of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">More...</a><br /></td></tr> | |
| 157 | <tr class="separator:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 158 | <tr class="memitem:a1bef0f9020a436652628244533cca61b inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a1bef0f9020a436652628244533cca61b">getModeEProb</a> () const</td></tr> | |
| 159 | <tr class="memdesc:a1bef0f9020a436652628244533cca61b inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the probability of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a1bef0f9020a436652628244533cca61b">More...</a><br /></td></tr> | |
| 160 | <tr class="separator:a1bef0f9020a436652628244533cca61b inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 161 | <tr class="memitem:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a> () const</td></tr> | |
| 162 | <tr class="memdesc:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the log-probability of the lightest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">More...</a><br /></td></tr> | |
| 163 | <tr class="separator:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 164 | <tr class="memitem:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a> (Conf conf) const</td></tr> | |
| 165 | <tr class="memdesc:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the log-probability of a given subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">More...</a><br /></td></tr> | |
| 166 | <tr class="separator:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 167 | </table><table class="memberdecls"> | |
| 168 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a> | |
| 169 | Additional Inherited Members</h2></td></tr> | |
| 170 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_marginal"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_marginal')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td></tr> | |
| 171 | <tr class="memitem:a8dd6415882661f7b9ceedbe09bc200e3 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a></td></tr> | |
| 172 | <tr class="separator:a8dd6415882661f7b9ceedbe09bc200e3 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 173 | <tr class="memitem:a53c2af7dcb84aa9d5e0e0918fe7875cd inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a></td></tr> | |
| 174 | <tr class="separator:a53c2af7dcb84aa9d5e0e0918fe7875cd inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 175 | <tr class="memitem:a91265e07f5bb65314995f816f5a9c729 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double *const </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a></td></tr> | |
| 176 | <tr class="separator:a91265e07f5bb65314995f816f5a9c729 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 177 | <tr class="memitem:af059df011e707781fdd4c1d7b70bd91a inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double *const </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a></td></tr> | |
| 178 | <tr class="separator:af059df011e707781fdd4c1d7b70bd91a inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 179 | <tr class="memitem:aa3fb5ed3a9b63a855d6270287aed7417 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a></td></tr> | |
| 180 | <tr class="separator:aa3fb5ed3a9b63a855d6270287aed7417 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 181 | <tr class="memitem:a640f3b44605b510ee556a25e35a2e095 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const Conf </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a></td></tr> | |
| 182 | <tr class="separator:a640f3b44605b510ee556a25e35a2e095 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 183 | <tr class="memitem:a38238e7581f59f08d0faf8ab5eabc0dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a></td></tr> | |
| 184 | <tr class="separator:a38238e7581f59f08d0faf8ab5eabc0dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 185 | <tr class="memitem:a3bfea931e5e1ec1e7d90e8e096c38eb7 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a></td></tr> | |
| 186 | <tr class="separator:a3bfea931e5e1ec1e7d90e8e096c38eb7 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 187 | <tr class="memitem:a7cd29141c34e293f0e3257d73baab0ac inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a7cd29141c34e293f0e3257d73baab0ac">mode_eprob</a></td></tr> | |
| 188 | <tr class="separator:a7cd29141c34e293f0e3257d73baab0ac inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 189 | <tr class="memitem:a2abd05ba9351e21cd99e2783e26bd6dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a></td></tr> | |
| 190 | <tr class="separator:a2abd05ba9351e21cd99e2783e26bd6dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 191 | </table> | |
| 192 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 193 | <div class="textblock"><p><a class="el" href="class_iso_spec_1_1_layered_marginal.html" title="LayeredMarginal class. ">LayeredMarginal</a> class. </p> | |
| 194 | <p>An extendable version of the <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html" title="Precalculated Marginal class. ">PrecalculatedMarginal</a>, where you can extend the threshold at will. </p> | |
| 195 | ||
| 196 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00337">337</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 197 | </div><h2 class="groupheader">Constructor & Destructor Documentation</h2> | |
| 198 | <a id="af062d180664c9c856b4cc72e3457ca9d"></a> | |
| 199 | <h2 class="memtitle"><span class="permalink"><a href="#af062d180664c9c856b4cc72e3457ca9d">◆ </a></span>LayeredMarginal()</h2> | |
| 200 | ||
| 201 | <div class="memitem"> | |
| 202 | <div class="memproto"> | |
| 203 | <table class="memname"> | |
| 204 | <tr> | |
| 205 | <td class="memname">IsoSpec::LayeredMarginal::LayeredMarginal </td> | |
| 206 | <td>(</td> | |
| 207 | <td class="paramtype"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> && </td> | |
| 208 | <td class="paramname"><em>m</em>, </td> | |
| 209 | </tr> | |
| 210 | <tr> | |
| 211 | <td class="paramkey"></td> | |
| 212 | <td></td> | |
| 213 | <td class="paramtype">int </td> | |
| 214 | <td class="paramname"><em>tabSize</em> = <code>1000</code>, </td> | |
| 215 | </tr> | |
| 216 | <tr> | |
| 217 | <td class="paramkey"></td> | |
| 218 | <td></td> | |
| 219 | <td class="paramtype">int </td> | |
| 220 | <td class="paramname"><em>hashSize</em> = <code>1000</code> </td> | |
| 221 | </tr> | |
| 222 | <tr> | |
| 223 | <td></td> | |
| 224 | <td>)</td> | |
| 225 | <td></td><td></td> | |
| 226 | </tr> | |
| 227 | </table> | |
| 228 | </div><div class="memdoc"> | |
| 229 | ||
| 230 | <p>Move constructor: specializes the <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class. </p> | |
| 231 | <dl class="params"><dt>Parameters</dt><dd> | |
| 232 | <table class="params"> | |
| 233 | <tr><td class="paramname">tabSize</td><td>The size of the table used to store configurations in the allocator. </td></tr> | |
| 234 | <tr><td class="paramname">hashSize</td><td>The size of the hash table used to store visited subisotopologues. </td></tr> | |
| 235 | </table> | |
| 236 | </dd> | |
| 237 | </dl> | |
| 238 | ||
| 239 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8cpp_source.html#l00445">445</a> of file <a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a>.</p> | |
| 240 | ||
| 241 | </div> | |
| 242 | </div> | |
| 243 | <h2 class="groupheader">Member Function Documentation</h2> | |
| 244 | <a id="ab8b66ed79bad27183f98a9ae34c3b944"></a> | |
| 245 | <h2 class="memtitle"><span class="permalink"><a href="#ab8b66ed79bad27183f98a9ae34c3b944">◆ </a></span>extend()</h2> | |
| 246 | ||
| 247 | <div class="memitem"> | |
| 248 | <div class="memproto"> | |
| 249 | <table class="memname"> | |
| 250 | <tr> | |
| 251 | <td class="memname">bool IsoSpec::LayeredMarginal::extend </td> | |
| 252 | <td>(</td> | |
| 253 | <td class="paramtype">double </td> | |
| 254 | <td class="paramname"><em>new_threshold</em></td><td>)</td> | |
| 255 | <td></td> | |
| 256 | </tr> | |
| 257 | </table> | |
| 258 | </div><div class="memdoc"> | |
| 259 | ||
| 260 | <p>Extend the set of computed subisotopologues to those above the new threshold. </p> | |
| 261 | <dl class="params"><dt>Parameters</dt><dd> | |
| 262 | <table class="params"> | |
| 263 | <tr><td class="paramname">new_threshold</td><td>The new log-probability limiting the subisotopologues from below. </td></tr> | |
| 264 | </table> | |
| 265 | </dd> | |
| 266 | </dl> | |
| 267 | <dl class="section return"><dt>Returns</dt><dd>Returns false, if there are no fringe-subisotopologues (subisotopologues that were neighbours of the previously calculated subisotopologues, with log-probability below the previous threshold). </dd></dl> | |
| 268 | ||
| 269 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8cpp_source.html#l00455">455</a> of file <a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a>.</p> | |
| 270 | ||
| 271 | </div> | |
| 272 | </div> | |
| 273 | <hr/>The documentation for this class was generated from the following files:<ul> | |
| 274 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a></li> | |
| 275 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a></li> | |
| 276 | </ul> | |
| 277 | </div><!-- contents --> | |
| 278 | <!-- start footer part --> | |
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| 280 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 282 | </a> 1.8.14 | |
| 283 | </small></address> | |
| 284 | </body> | |
| 285 | </html> |
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| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
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| 33 | </td> | |
| 34 | </tr> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::Marginal Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 86 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 87 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 88 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 89 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">getModeProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a>(Conf conf) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a>(const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 96 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>Marginal</b>(Marginal &other)=delete (defined in <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e">Marginal</a>(Marginal &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 99 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 100 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 101 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">mode_prob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 102 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>operator=</b>(const Marginal &other)=delete (defined in <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 103 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 104 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
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| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a></li> </ul> | |
| 72 | </div> | |
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| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="#pro-attribs">Protected Attributes</a> | | |
| 78 | <a href="class_iso_spec_1_1_marginal-members.html">List of all members</a> </div> | |
| 79 | <div class="headertitle"> | |
| 80 | <div class="title">IsoSpec::Marginal Class Reference</div> </div> | |
| 81 | </div><!--header--> | |
| 82 | <div class="contents"> | |
| 83 | ||
| 84 | <p>The marginal distribution class (a subisotopologue). | |
| 85 | <a href="class_iso_spec_1_1_marginal.html#details">More...</a></p> | |
| 86 | ||
| 87 | <p><code>#include <<a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>></code></p> | |
| 88 | <div class="dynheader"> | |
| 89 | Inheritance diagram for IsoSpec::Marginal:</div> | |
| 90 | <div class="dyncontent"> | |
| 91 | <div class="center"> | |
| 92 | <img src="class_iso_spec_1_1_marginal.png" usemap="#IsoSpec::Marginal_map" alt=""/> | |
| 93 | <map id="IsoSpec::Marginal_map" name="IsoSpec::Marginal_map"> | |
| 94 | <area href="class_iso_spec_1_1_marginal_trek.html" title="The marginal distribution class (a subisotopologue). " alt="IsoSpec::MarginalTrek" shape="rect" coords="0,56,191,80"/> | |
| 95 | <area href="class_iso_spec_1_1_precalculated_marginal.html" title="Precalculated Marginal class. " alt="IsoSpec::PrecalculatedMarginal" shape="rect" coords="201,56,392,80"/> | |
| 96 | </map> | |
| 97 | </div></div> | |
| 98 | <table class="memberdecls"> | |
| 99 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 100 | Public Member Functions</h2></td></tr> | |
| 101 | <tr class="memitem:a46be0c1cf5b169a54056997ba404183c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a> (const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</td></tr> | |
| 102 | <tr class="memdesc:a46be0c1cf5b169a54056997ba404183c"><td class="mdescLeft"> </td><td class="mdescRight">Class constructor. <a href="#a46be0c1cf5b169a54056997ba404183c">More...</a><br /></td></tr> | |
| 103 | <tr class="separator:a46be0c1cf5b169a54056997ba404183c"><td class="memSeparator" colspan="2"> </td></tr> | |
| 104 | <tr class="memitem:a02e8f92f8f9add352840f5dba8de5e06"><td class="memItemLeft" align="right" valign="top"><a id="a02e8f92f8f9add352840f5dba8de5e06"></a> | |
| 105 |  </td><td class="memItemRight" valign="bottom"><b>Marginal</b> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &other)=delete</td></tr> | |
| 106 | <tr class="separator:a02e8f92f8f9add352840f5dba8de5e06"><td class="memSeparator" colspan="2"> </td></tr> | |
| 107 | <tr class="memitem:a9120cad240058afc3705951d80d28a10"><td class="memItemLeft" align="right" valign="top"><a id="a9120cad240058afc3705951d80d28a10"></a> | |
| 108 | <a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> & </td><td class="memItemRight" valign="bottom"><b>operator=</b> (const <a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &other)=delete</td></tr> | |
| 109 | <tr class="separator:a9120cad240058afc3705951d80d28a10"><td class="memSeparator" colspan="2"> </td></tr> | |
| 110 | <tr class="memitem:ad60fff17fa2c68ea2cd7f183a635379e"><td class="memItemLeft" align="right" valign="top"><a id="ad60fff17fa2c68ea2cd7f183a635379e"></a> | |
| 111 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e">Marginal</a> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &&other)</td></tr> | |
| 112 | <tr class="memdesc:ad60fff17fa2c68ea2cd7f183a635379e"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 113 | <tr class="separator:ad60fff17fa2c68ea2cd7f183a635379e"><td class="memSeparator" colspan="2"> </td></tr> | |
| 114 | <tr class="memitem:ad44004fa1e83c4a53d431ca403ce3ae4"><td class="memItemLeft" align="right" valign="top"><a id="ad44004fa1e83c4a53d431ca403ce3ae4"></a> | |
| 115 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a> ()</td></tr> | |
| 116 | <tr class="memdesc:ad44004fa1e83c4a53d431ca403ce3ae4"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 117 | <tr class="separator:ad44004fa1e83c4a53d431ca403ce3ae4"><td class="memSeparator" colspan="2"> </td></tr> | |
| 118 | <tr class="memitem:a05aa80c3fa77a0406102731934db1a83"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a> () const</td></tr> | |
| 119 | <tr class="memdesc:a05aa80c3fa77a0406102731934db1a83"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of isotopes of the investigated element. <a href="#a05aa80c3fa77a0406102731934db1a83">More...</a><br /></td></tr> | |
| 120 | <tr class="separator:a05aa80c3fa77a0406102731934db1a83"><td class="memSeparator" colspan="2"> </td></tr> | |
| 121 | <tr class="memitem:a8b67c507263973da53e533d804e23ac9"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a> () const</td></tr> | |
| 122 | <tr class="memdesc:a8b67c507263973da53e533d804e23ac9"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest subisotopologue. <a href="#a8b67c507263973da53e533d804e23ac9">More...</a><br /></td></tr> | |
| 123 | <tr class="separator:a8b67c507263973da53e533d804e23ac9"><td class="memSeparator" colspan="2"> </td></tr> | |
| 124 | <tr class="memitem:aa5598b4d2b31b5daec1c2bac653d0aff"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a> () const</td></tr> | |
| 125 | <tr class="memdesc:aa5598b4d2b31b5daec1c2bac653d0aff"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest subisotopologue. <a href="#aa5598b4d2b31b5daec1c2bac653d0aff">More...</a><br /></td></tr> | |
| 126 | <tr class="separator:aa5598b4d2b31b5daec1c2bac653d0aff"><td class="memSeparator" colspan="2"> </td></tr> | |
| 127 | <tr class="memitem:ac9408957145d2aa63af32f6647c8ea49"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a> () const</td></tr> | |
| 128 | <tr class="memdesc:ac9408957145d2aa63af32f6647c8ea49"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode subisotopologue. <a href="#ac9408957145d2aa63af32f6647c8ea49">More...</a><br /></td></tr> | |
| 129 | <tr class="separator:ac9408957145d2aa63af32f6647c8ea49"><td class="memSeparator" colspan="2"> </td></tr> | |
| 130 | <tr class="memitem:ad2121802133075a87f0987dc27d0617f"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a> () const</td></tr> | |
| 131 | <tr class="memdesc:ad2121802133075a87f0987dc27d0617f"><td class="mdescLeft"> </td><td class="mdescRight">The the mass of the mode subisotopologue. <a href="#ad2121802133075a87f0987dc27d0617f">More...</a><br /></td></tr> | |
| 132 | <tr class="separator:ad2121802133075a87f0987dc27d0617f"><td class="memSeparator" colspan="2"> </td></tr> | |
| 133 | <tr class="memitem:a7bc1eeba342977de3a77c3c7e6ca55b0"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">getModeProb</a> () const</td></tr> | |
| 134 | <tr class="memdesc:a7bc1eeba342977de3a77c3c7e6ca55b0"><td class="mdescLeft"> </td><td class="mdescRight">The the probability of the mode subisotopologue. <a href="#a7bc1eeba342977de3a77c3c7e6ca55b0">More...</a><br /></td></tr> | |
| 135 | <tr class="separator:a7bc1eeba342977de3a77c3c7e6ca55b0"><td class="memSeparator" colspan="2"> </td></tr> | |
| 136 | <tr class="memitem:a3f9607f51efcfdac1ca58a1467e3a5dc"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a> () const</td></tr> | |
| 137 | <tr class="memdesc:a3f9607f51efcfdac1ca58a1467e3a5dc"><td class="mdescLeft"> </td><td class="mdescRight">The the log-probability of the lightest subisotopologue. <a href="#a3f9607f51efcfdac1ca58a1467e3a5dc">More...</a><br /></td></tr> | |
| 138 | <tr class="separator:a3f9607f51efcfdac1ca58a1467e3a5dc"><td class="memSeparator" colspan="2"> </td></tr> | |
| 139 | <tr class="memitem:a1974bb030ce70178da569214b4b93cb8"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a> (Conf conf) const</td></tr> | |
| 140 | <tr class="memdesc:a1974bb030ce70178da569214b4b93cb8"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the log-probability of a given subisotopologue. <a href="#a1974bb030ce70178da569214b4b93cb8">More...</a><br /></td></tr> | |
| 141 | <tr class="separator:a1974bb030ce70178da569214b4b93cb8"><td class="memSeparator" colspan="2"> </td></tr> | |
| 142 | </table><table class="memberdecls"> | |
| 143 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a> | |
| 144 | Protected Attributes</h2></td></tr> | |
| 145 | <tr class="memitem:a8dd6415882661f7b9ceedbe09bc200e3"><td class="memItemLeft" align="right" valign="top">const unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a></td></tr> | |
| 146 | <tr class="separator:a8dd6415882661f7b9ceedbe09bc200e3"><td class="memSeparator" colspan="2"> </td></tr> | |
| 147 | <tr class="memitem:a53c2af7dcb84aa9d5e0e0918fe7875cd"><td class="memItemLeft" align="right" valign="top">const unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a></td></tr> | |
| 148 | <tr class="separator:a53c2af7dcb84aa9d5e0e0918fe7875cd"><td class="memSeparator" colspan="2"> </td></tr> | |
| 149 | <tr class="memitem:a91265e07f5bb65314995f816f5a9c729"><td class="memItemLeft" align="right" valign="top">const double *const </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a></td></tr> | |
| 150 | <tr class="separator:a91265e07f5bb65314995f816f5a9c729"><td class="memSeparator" colspan="2"> </td></tr> | |
| 151 | <tr class="memitem:af059df011e707781fdd4c1d7b70bd91a"><td class="memItemLeft" align="right" valign="top">const double *const </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a></td></tr> | |
| 152 | <tr class="separator:af059df011e707781fdd4c1d7b70bd91a"><td class="memSeparator" colspan="2"> </td></tr> | |
| 153 | <tr class="memitem:aa3fb5ed3a9b63a855d6270287aed7417"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a></td></tr> | |
| 154 | <tr class="separator:aa3fb5ed3a9b63a855d6270287aed7417"><td class="memSeparator" colspan="2"> </td></tr> | |
| 155 | <tr class="memitem:a640f3b44605b510ee556a25e35a2e095"><td class="memItemLeft" align="right" valign="top">const Conf </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a></td></tr> | |
| 156 | <tr class="separator:a640f3b44605b510ee556a25e35a2e095"><td class="memSeparator" colspan="2"> </td></tr> | |
| 157 | <tr class="memitem:a38238e7581f59f08d0faf8ab5eabc0dc"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a></td></tr> | |
| 158 | <tr class="separator:a38238e7581f59f08d0faf8ab5eabc0dc"><td class="memSeparator" colspan="2"> </td></tr> | |
| 159 | <tr class="memitem:a3bfea931e5e1ec1e7d90e8e096c38eb7"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a></td></tr> | |
| 160 | <tr class="separator:a3bfea931e5e1ec1e7d90e8e096c38eb7"><td class="memSeparator" colspan="2"> </td></tr> | |
| 161 | <tr class="memitem:a75315ec4c470be5f82b903172f7c43ae"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">mode_prob</a></td></tr> | |
| 162 | <tr class="separator:a75315ec4c470be5f82b903172f7c43ae"><td class="memSeparator" colspan="2"> </td></tr> | |
| 163 | <tr class="memitem:a2abd05ba9351e21cd99e2783e26bd6dc"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a></td></tr> | |
| 164 | <tr class="separator:a2abd05ba9351e21cd99e2783e26bd6dc"><td class="memSeparator" colspan="2"> </td></tr> | |
| 165 | </table> | |
| 166 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 167 | <div class="textblock"><p>The marginal distribution class (a subisotopologue). </p> | |
| 168 | <p>This class mostly provides some basic common API for subclasses, but itself is not abstract. This class represents the probability distribution generated by one element only – a subisotopologue. For instance, it might be the distribution of C200, that might be part of, say, C200H402. It corresponds to the multinomial distribution, where each configuration can also be attributed a precise mass. The constructor method perform initial hill-climbing to find the most probable sub-isotopologue (the mode). </p> | |
| 169 | ||
| 170 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00045">45</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 171 | </div><h2 class="groupheader">Constructor & Destructor Documentation</h2> | |
| 172 | <a id="a46be0c1cf5b169a54056997ba404183c"></a> | |
| 173 | <h2 class="memtitle"><span class="permalink"><a href="#a46be0c1cf5b169a54056997ba404183c">◆ </a></span>Marginal()</h2> | |
| 174 | ||
| 175 | <div class="memitem"> | |
| 176 | <div class="memproto"> | |
| 177 | <table class="memname"> | |
| 178 | <tr> | |
| 179 | <td class="memname">IsoSpec::Marginal::Marginal </td> | |
| 180 | <td>(</td> | |
| 181 | <td class="paramtype">const double * </td> | |
| 182 | <td class="paramname"><em>_masses</em>, </td> | |
| 183 | </tr> | |
| 184 | <tr> | |
| 185 | <td class="paramkey"></td> | |
| 186 | <td></td> | |
| 187 | <td class="paramtype">const double * </td> | |
| 188 | <td class="paramname"><em>_probs</em>, </td> | |
| 189 | </tr> | |
| 190 | <tr> | |
| 191 | <td class="paramkey"></td> | |
| 192 | <td></td> | |
| 193 | <td class="paramtype">int </td> | |
| 194 | <td class="paramname"><em>_isotopeNo</em>, </td> | |
| 195 | </tr> | |
| 196 | <tr> | |
| 197 | <td class="paramkey"></td> | |
| 198 | <td></td> | |
| 199 | <td class="paramtype">int </td> | |
| 200 | <td class="paramname"><em>_atomCnt</em> </td> | |
| 201 | </tr> | |
| 202 | <tr> | |
| 203 | <td></td> | |
| 204 | <td>)</td> | |
| 205 | <td></td><td></td> | |
| 206 | </tr> | |
| 207 | </table> | |
| 208 | </div><div class="memdoc"> | |
| 209 | ||
| 210 | <p>Class constructor. </p> | |
| 211 | <dl class="params"><dt>Parameters</dt><dd> | |
| 212 | <table class="params"> | |
| 213 | <tr><td class="paramname">_masses</td><td>A table of masses of the stable isotopes of the investigated element, e.g. for C10 it is 2: C12 and C13. </td></tr> | |
| 214 | <tr><td class="paramname">_probs</td><td>A table of natural frequencies of the stable isotopes of the investigated element, see IUPAC at <a href="https://iupac.org/isotopesmatter/">https://iupac.org/isotopesmatter/</a> </td></tr> | |
| 215 | <tr><td class="paramname">_isotopeNo</td><td>Number of isotopes of a given element. </td></tr> | |
| 216 | <tr><td class="paramname">_atomCnt</td><td>The number of atoms of the given element, e.g. 10 for C10. </td></tr> | |
| 217 | </table> | |
| 218 | </dd> | |
| 219 | </dl> | |
| 220 | <dl class="section return"><dt>Returns</dt><dd>An instance of the <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class. </dd></dl> | |
| 221 | ||
| 222 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8cpp_source.html#l00187">187</a> of file <a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a>.</p> | |
| 223 | ||
| 224 | </div> | |
| 225 | </div> | |
| 226 | <h2 class="groupheader">Member Function Documentation</h2> | |
| 227 | <a id="a05aa80c3fa77a0406102731934db1a83"></a> | |
| 228 | <h2 class="memtitle"><span class="permalink"><a href="#a05aa80c3fa77a0406102731934db1a83">◆ </a></span>get_isotopeNo()</h2> | |
| 229 | ||
| 230 | <div class="memitem"> | |
| 231 | <div class="memproto"> | |
| 232 | <table class="mlabels"> | |
| 233 | <tr> | |
| 234 | <td class="mlabels-left"> | |
| 235 | <table class="memname"> | |
| 236 | <tr> | |
| 237 | <td class="memname">int IsoSpec::Marginal::get_isotopeNo </td> | |
| 238 | <td>(</td> | |
| 239 | <td class="paramname"></td><td>)</td> | |
| 240 | <td> const</td> | |
| 241 | </tr> | |
| 242 | </table> | |
| 243 | </td> | |
| 244 | <td class="mlabels-right"> | |
| 245 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 246 | </tr> | |
| 247 | </table> | |
| 248 | </div><div class="memdoc"> | |
| 249 | ||
| 250 | <p>Get the number of isotopes of the investigated element. </p> | |
| 251 | <dl class="section return"><dt>Returns</dt><dd>The integer number of isotopes of the investigated element. </dd></dl> | |
| 252 | ||
| 253 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00092">92</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 254 | ||
| 255 | </div> | |
| 256 | </div> | |
| 257 | <a id="aa5598b4d2b31b5daec1c2bac653d0aff"></a> | |
| 258 | <h2 class="memtitle"><span class="permalink"><a href="#aa5598b4d2b31b5daec1c2bac653d0aff">◆ </a></span>getHeaviestConfMass()</h2> | |
| 259 | ||
| 260 | <div class="memitem"> | |
| 261 | <div class="memproto"> | |
| 262 | <table class="memname"> | |
| 263 | <tr> | |
| 264 | <td class="memname">double IsoSpec::Marginal::getHeaviestConfMass </td> | |
| 265 | <td>(</td> | |
| 266 | <td class="paramname"></td><td>)</td> | |
| 267 | <td> const</td> | |
| 268 | </tr> | |
| 269 | </table> | |
| 270 | </div><div class="memdoc"> | |
| 271 | ||
| 272 | <p>Get the mass of the heaviest subisotopologue. </p> | |
| 273 | <p>This is trivially obtained by considering all atomNo atoms to be the heaviest isotope possible. </p><dl class="section return"><dt>Returns</dt><dd>The mass of the heaviest subisotopologue. </dd></dl> | |
| 274 | ||
| 275 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8cpp_source.html#l00246">246</a> of file <a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a>.</p> | |
| 276 | ||
| 277 | </div> | |
| 278 | </div> | |
| 279 | <a id="a8b67c507263973da53e533d804e23ac9"></a> | |
| 280 | <h2 class="memtitle"><span class="permalink"><a href="#a8b67c507263973da53e533d804e23ac9">◆ </a></span>getLightestConfMass()</h2> | |
| 281 | ||
| 282 | <div class="memitem"> | |
| 283 | <div class="memproto"> | |
| 284 | <table class="memname"> | |
| 285 | <tr> | |
| 286 | <td class="memname">double IsoSpec::Marginal::getLightestConfMass </td> | |
| 287 | <td>(</td> | |
| 288 | <td class="paramname"></td><td>)</td> | |
| 289 | <td> const</td> | |
| 290 | </tr> | |
| 291 | </table> | |
| 292 | </div><div class="memdoc"> | |
| 293 | ||
| 294 | <p>Get the mass of the lightest subisotopologue. </p> | |
| 295 | <p>This is trivially obtained by considering all atomNo atoms to be the lightest isotope possible. </p><dl class="section return"><dt>Returns</dt><dd>The mass of the lightiest subisotopologue. </dd></dl> | |
| 296 | ||
| 297 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8cpp_source.html#l00237">237</a> of file <a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a>.</p> | |
| 298 | ||
| 299 | </div> | |
| 300 | </div> | |
| 301 | <a id="ac9408957145d2aa63af32f6647c8ea49"></a> | |
| 302 | <h2 class="memtitle"><span class="permalink"><a href="#ac9408957145d2aa63af32f6647c8ea49">◆ </a></span>getModeLProb()</h2> | |
| 303 | ||
| 304 | <div class="memitem"> | |
| 305 | <div class="memproto"> | |
| 306 | <table class="mlabels"> | |
| 307 | <tr> | |
| 308 | <td class="mlabels-left"> | |
| 309 | <table class="memname"> | |
| 310 | <tr> | |
| 311 | <td class="memname">double IsoSpec::Marginal::getModeLProb </td> | |
| 312 | <td>(</td> | |
| 313 | <td class="paramname"></td><td>)</td> | |
| 314 | <td> const</td> | |
| 315 | </tr> | |
| 316 | </table> | |
| 317 | </td> | |
| 318 | <td class="mlabels-right"> | |
| 319 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 320 | </tr> | |
| 321 | </table> | |
| 322 | </div><div class="memdoc"> | |
| 323 | ||
| 324 | <p>Get the log-probability of the mode subisotopologue. </p> | |
| 325 | <dl class="section return"><dt>Returns</dt><dd>The log-probability of a/the most probable subisotopologue. </dd></dl> | |
| 326 | ||
| 327 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00110">110</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 328 | ||
| 329 | </div> | |
| 330 | </div> | |
| 331 | <a id="ad2121802133075a87f0987dc27d0617f"></a> | |
| 332 | <h2 class="memtitle"><span class="permalink"><a href="#ad2121802133075a87f0987dc27d0617f">◆ </a></span>getModeMass()</h2> | |
| 333 | ||
| 334 | <div class="memitem"> | |
| 335 | <div class="memproto"> | |
| 336 | <table class="mlabels"> | |
| 337 | <tr> | |
| 338 | <td class="mlabels-left"> | |
| 339 | <table class="memname"> | |
| 340 | <tr> | |
| 341 | <td class="memname">double IsoSpec::Marginal::getModeMass </td> | |
| 342 | <td>(</td> | |
| 343 | <td class="paramname"></td><td>)</td> | |
| 344 | <td> const</td> | |
| 345 | </tr> | |
| 346 | </table> | |
| 347 | </td> | |
| 348 | <td class="mlabels-right"> | |
| 349 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 350 | </tr> | |
| 351 | </table> | |
| 352 | </div><div class="memdoc"> | |
| 353 | ||
| 354 | <p>The the mass of the mode subisotopologue. </p> | |
| 355 | <dl class="section return"><dt>Returns</dt><dd>The mass of one of the most probable subisotopologues. </dd></dl> | |
| 356 | ||
| 357 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00116">116</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 358 | ||
| 359 | </div> | |
| 360 | </div> | |
| 361 | <a id="a7bc1eeba342977de3a77c3c7e6ca55b0"></a> | |
| 362 | <h2 class="memtitle"><span class="permalink"><a href="#a7bc1eeba342977de3a77c3c7e6ca55b0">◆ </a></span>getModeProb()</h2> | |
| 363 | ||
| 364 | <div class="memitem"> | |
| 365 | <div class="memproto"> | |
| 366 | <table class="mlabels"> | |
| 367 | <tr> | |
| 368 | <td class="mlabels-left"> | |
| 369 | <table class="memname"> | |
| 370 | <tr> | |
| 371 | <td class="memname">double IsoSpec::Marginal::getModeProb </td> | |
| 372 | <td>(</td> | |
| 373 | <td class="paramname"></td><td>)</td> | |
| 374 | <td> const</td> | |
| 375 | </tr> | |
| 376 | </table> | |
| 377 | </td> | |
| 378 | <td class="mlabels-right"> | |
| 379 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 380 | </tr> | |
| 381 | </table> | |
| 382 | </div><div class="memdoc"> | |
| 383 | ||
| 384 | <p>The the probability of the mode subisotopologue. </p> | |
| 385 | <dl class="section return"><dt>Returns</dt><dd>The probability of a/the most probable subisotopologue. </dd></dl> | |
| 386 | ||
| 387 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00122">122</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 388 | ||
| 389 | </div> | |
| 390 | </div> | |
| 391 | <a id="a3f9607f51efcfdac1ca58a1467e3a5dc"></a> | |
| 392 | <h2 class="memtitle"><span class="permalink"><a href="#a3f9607f51efcfdac1ca58a1467e3a5dc">◆ </a></span>getSmallestLProb()</h2> | |
| 393 | ||
| 394 | <div class="memitem"> | |
| 395 | <div class="memproto"> | |
| 396 | <table class="mlabels"> | |
| 397 | <tr> | |
| 398 | <td class="mlabels-left"> | |
| 399 | <table class="memname"> | |
| 400 | <tr> | |
| 401 | <td class="memname">double IsoSpec::Marginal::getSmallestLProb </td> | |
| 402 | <td>(</td> | |
| 403 | <td class="paramname"></td><td>)</td> | |
| 404 | <td> const</td> | |
| 405 | </tr> | |
| 406 | </table> | |
| 407 | </td> | |
| 408 | <td class="mlabels-right"> | |
| 409 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 410 | </tr> | |
| 411 | </table> | |
| 412 | </div><div class="memdoc"> | |
| 413 | ||
| 414 | <p>The the log-probability of the lightest subisotopologue. </p> | |
| 415 | <dl class="section return"><dt>Returns</dt><dd>The logarithm of the smallest non-zero probability of a subisotopologue. </dd></dl> | |
| 416 | ||
| 417 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00129">129</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 418 | ||
| 419 | </div> | |
| 420 | </div> | |
| 421 | <a id="a1974bb030ce70178da569214b4b93cb8"></a> | |
| 422 | <h2 class="memtitle"><span class="permalink"><a href="#a1974bb030ce70178da569214b4b93cb8">◆ </a></span>logProb()</h2> | |
| 423 | ||
| 424 | <div class="memitem"> | |
| 425 | <div class="memproto"> | |
| 426 | <table class="mlabels"> | |
| 427 | <tr> | |
| 428 | <td class="mlabels-left"> | |
| 429 | <table class="memname"> | |
| 430 | <tr> | |
| 431 | <td class="memname">double IsoSpec::Marginal::logProb </td> | |
| 432 | <td>(</td> | |
| 433 | <td class="paramtype">Conf </td> | |
| 434 | <td class="paramname"><em>conf</em></td><td>)</td> | |
| 435 | <td> const</td> | |
| 436 | </tr> | |
| 437 | </table> | |
| 438 | </td> | |
| 439 | <td class="mlabels-right"> | |
| 440 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 441 | </tr> | |
| 442 | </table> | |
| 443 | </div><div class="memdoc"> | |
| 444 | ||
| 445 | <p>Calculate the log-probability of a given subisotopologue. </p> | |
| 446 | <dl class="params"><dt>Parameters</dt><dd> | |
| 447 | <table class="params"> | |
| 448 | <tr><td class="paramname">conf</td><td>A subisotopologue (a table of integers describing subsequent isotope-counts). </td></tr> | |
| 449 | </table> | |
| 450 | </dd> | |
| 451 | </dl> | |
| 452 | <dl class="section return"><dt>Returns</dt><dd>The log-probability of the input subisotopologue. </dd></dl> | |
| 453 | ||
| 454 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00136">136</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 455 | ||
| 456 | </div> | |
| 457 | </div> | |
| 458 | <h2 class="groupheader">Member Data Documentation</h2> | |
| 459 | <a id="af059df011e707781fdd4c1d7b70bd91a"></a> | |
| 460 | <h2 class="memtitle"><span class="permalink"><a href="#af059df011e707781fdd4c1d7b70bd91a">◆ </a></span>atom_lProbs</h2> | |
| 461 | ||
| 462 | <div class="memitem"> | |
| 463 | <div class="memproto"> | |
| 464 | <table class="mlabels"> | |
| 465 | <tr> | |
| 466 | <td class="mlabels-left"> | |
| 467 | <table class="memname"> | |
| 468 | <tr> | |
| 469 | <td class="memname">const double* const IsoSpec::Marginal::atom_lProbs</td> | |
| 470 | </tr> | |
| 471 | </table> | |
| 472 | </td> | |
| 473 | <td class="mlabels-right"> | |
| 474 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 475 | </tr> | |
| 476 | </table> | |
| 477 | </div><div class="memdoc"> | |
| 478 | <p>Table of log-probabilities of all the isotopeNo isotopes. </p> | |
| 479 | ||
| 480 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00053">53</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 481 | ||
| 482 | </div> | |
| 483 | </div> | |
| 484 | <a id="a91265e07f5bb65314995f816f5a9c729"></a> | |
| 485 | <h2 class="memtitle"><span class="permalink"><a href="#a91265e07f5bb65314995f816f5a9c729">◆ </a></span>atom_masses</h2> | |
| 486 | ||
| 487 | <div class="memitem"> | |
| 488 | <div class="memproto"> | |
| 489 | <table class="mlabels"> | |
| 490 | <tr> | |
| 491 | <td class="mlabels-left"> | |
| 492 | <table class="memname"> | |
| 493 | <tr> | |
| 494 | <td class="memname">const double* const IsoSpec::Marginal::atom_masses</td> | |
| 495 | </tr> | |
| 496 | </table> | |
| 497 | </td> | |
| 498 | <td class="mlabels-right"> | |
| 499 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 500 | </tr> | |
| 501 | </table> | |
| 502 | </div><div class="memdoc"> | |
| 503 | <p>Table of atomic masses of all the isotopeNo isotopes. </p> | |
| 504 | ||
| 505 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00052">52</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 506 | ||
| 507 | </div> | |
| 508 | </div> | |
| 509 | <a id="a53c2af7dcb84aa9d5e0e0918fe7875cd"></a> | |
| 510 | <h2 class="memtitle"><span class="permalink"><a href="#a53c2af7dcb84aa9d5e0e0918fe7875cd">◆ </a></span>atomCnt</h2> | |
| 511 | ||
| 512 | <div class="memitem"> | |
| 513 | <div class="memproto"> | |
| 514 | <table class="mlabels"> | |
| 515 | <tr> | |
| 516 | <td class="mlabels-left"> | |
| 517 | <table class="memname"> | |
| 518 | <tr> | |
| 519 | <td class="memname">const unsigned int IsoSpec::Marginal::atomCnt</td> | |
| 520 | </tr> | |
| 521 | </table> | |
| 522 | </td> | |
| 523 | <td class="mlabels-right"> | |
| 524 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 525 | </tr> | |
| 526 | </table> | |
| 527 | </div><div class="memdoc"> | |
| 528 | <p>The number of atoms of the given element. </p> | |
| 529 | ||
| 530 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00051">51</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 531 | ||
| 532 | </div> | |
| 533 | </div> | |
| 534 | <a id="a8dd6415882661f7b9ceedbe09bc200e3"></a> | |
| 535 | <h2 class="memtitle"><span class="permalink"><a href="#a8dd6415882661f7b9ceedbe09bc200e3">◆ </a></span>isotopeNo</h2> | |
| 536 | ||
| 537 | <div class="memitem"> | |
| 538 | <div class="memproto"> | |
| 539 | <table class="mlabels"> | |
| 540 | <tr> | |
| 541 | <td class="mlabels-left"> | |
| 542 | <table class="memname"> | |
| 543 | <tr> | |
| 544 | <td class="memname">const unsigned int IsoSpec::Marginal::isotopeNo</td> | |
| 545 | </tr> | |
| 546 | </table> | |
| 547 | </td> | |
| 548 | <td class="mlabels-right"> | |
| 549 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 550 | </tr> | |
| 551 | </table> | |
| 552 | </div><div class="memdoc"> | |
| 553 | <p>The number of isotopes of the given element. </p> | |
| 554 | ||
| 555 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00050">50</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 556 | ||
| 557 | </div> | |
| 558 | </div> | |
| 559 | <a id="aa3fb5ed3a9b63a855d6270287aed7417"></a> | |
| 560 | <h2 class="memtitle"><span class="permalink"><a href="#aa3fb5ed3a9b63a855d6270287aed7417">◆ </a></span>loggamma_nominator</h2> | |
| 561 | ||
| 562 | <div class="memitem"> | |
| 563 | <div class="memproto"> | |
| 564 | <table class="mlabels"> | |
| 565 | <tr> | |
| 566 | <td class="mlabels-left"> | |
| 567 | <table class="memname"> | |
| 568 | <tr> | |
| 569 | <td class="memname">const double IsoSpec::Marginal::loggamma_nominator</td> | |
| 570 | </tr> | |
| 571 | </table> | |
| 572 | </td> | |
| 573 | <td class="mlabels-right"> | |
| 574 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 575 | </tr> | |
| 576 | </table> | |
| 577 | </div><div class="memdoc"> | |
| 578 | <p>The constant nominator that appears in the expressions for the multinomial probabilities. </p> | |
| 579 | ||
| 580 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00054">54</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 581 | ||
| 582 | </div> | |
| 583 | </div> | |
| 584 | <a id="a640f3b44605b510ee556a25e35a2e095"></a> | |
| 585 | <h2 class="memtitle"><span class="permalink"><a href="#a640f3b44605b510ee556a25e35a2e095">◆ </a></span>mode_conf</h2> | |
| 586 | ||
| 587 | <div class="memitem"> | |
| 588 | <div class="memproto"> | |
| 589 | <table class="mlabels"> | |
| 590 | <tr> | |
| 591 | <td class="mlabels-left"> | |
| 592 | <table class="memname"> | |
| 593 | <tr> | |
| 594 | <td class="memname">const Conf IsoSpec::Marginal::mode_conf</td> | |
| 595 | </tr> | |
| 596 | </table> | |
| 597 | </td> | |
| 598 | <td class="mlabels-right"> | |
| 599 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 600 | </tr> | |
| 601 | </table> | |
| 602 | </div><div class="memdoc"> | |
| 603 | <p>A subisotopologue with most probability. If not unique, one of the representatives of that class of subisotopologues. </p> | |
| 604 | ||
| 605 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00055">55</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 606 | ||
| 607 | </div> | |
| 608 | </div> | |
| 609 | <a id="a38238e7581f59f08d0faf8ab5eabc0dc"></a> | |
| 610 | <h2 class="memtitle"><span class="permalink"><a href="#a38238e7581f59f08d0faf8ab5eabc0dc">◆ </a></span>mode_lprob</h2> | |
| 611 | ||
| 612 | <div class="memitem"> | |
| 613 | <div class="memproto"> | |
| 614 | <table class="mlabels"> | |
| 615 | <tr> | |
| 616 | <td class="mlabels-left"> | |
| 617 | <table class="memname"> | |
| 618 | <tr> | |
| 619 | <td class="memname">const double IsoSpec::Marginal::mode_lprob</td> | |
| 620 | </tr> | |
| 621 | </table> | |
| 622 | </td> | |
| 623 | <td class="mlabels-right"> | |
| 624 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 625 | </tr> | |
| 626 | </table> | |
| 627 | </div><div class="memdoc"> | |
| 628 | <p>The log-probability of the mode subisotopologue. </p> | |
| 629 | ||
| 630 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00056">56</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 631 | ||
| 632 | </div> | |
| 633 | </div> | |
| 634 | <a id="a3bfea931e5e1ec1e7d90e8e096c38eb7"></a> | |
| 635 | <h2 class="memtitle"><span class="permalink"><a href="#a3bfea931e5e1ec1e7d90e8e096c38eb7">◆ </a></span>mode_mass</h2> | |
| 636 | ||
| 637 | <div class="memitem"> | |
| 638 | <div class="memproto"> | |
| 639 | <table class="mlabels"> | |
| 640 | <tr> | |
| 641 | <td class="mlabels-left"> | |
| 642 | <table class="memname"> | |
| 643 | <tr> | |
| 644 | <td class="memname">const double IsoSpec::Marginal::mode_mass</td> | |
| 645 | </tr> | |
| 646 | </table> | |
| 647 | </td> | |
| 648 | <td class="mlabels-right"> | |
| 649 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 650 | </tr> | |
| 651 | </table> | |
| 652 | </div><div class="memdoc"> | |
| 653 | <p>The mass of the mode subisotopologue. </p> | |
| 654 | ||
| 655 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00057">57</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 656 | ||
| 657 | </div> | |
| 658 | </div> | |
| 659 | <a id="a75315ec4c470be5f82b903172f7c43ae"></a> | |
| 660 | <h2 class="memtitle"><span class="permalink"><a href="#a75315ec4c470be5f82b903172f7c43ae">◆ </a></span>mode_prob</h2> | |
| 661 | ||
| 662 | <div class="memitem"> | |
| 663 | <div class="memproto"> | |
| 664 | <table class="mlabels"> | |
| 665 | <tr> | |
| 666 | <td class="mlabels-left"> | |
| 667 | <table class="memname"> | |
| 668 | <tr> | |
| 669 | <td class="memname">const double IsoSpec::Marginal::mode_prob</td> | |
| 670 | </tr> | |
| 671 | </table> | |
| 672 | </td> | |
| 673 | <td class="mlabels-right"> | |
| 674 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 675 | </tr> | |
| 676 | </table> | |
| 677 | </div><div class="memdoc"> | |
| 678 | <p>The probability of the mode subisotopologue. </p> | |
| 679 | ||
| 680 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00058">58</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 681 | ||
| 682 | </div> | |
| 683 | </div> | |
| 684 | <a id="a2abd05ba9351e21cd99e2783e26bd6dc"></a> | |
| 685 | <h2 class="memtitle"><span class="permalink"><a href="#a2abd05ba9351e21cd99e2783e26bd6dc">◆ </a></span>smallest_lprob</h2> | |
| 686 | ||
| 687 | <div class="memitem"> | |
| 688 | <div class="memproto"> | |
| 689 | <table class="mlabels"> | |
| 690 | <tr> | |
| 691 | <td class="mlabels-left"> | |
| 692 | <table class="memname"> | |
| 693 | <tr> | |
| 694 | <td class="memname">const double IsoSpec::Marginal::smallest_lprob</td> | |
| 695 | </tr> | |
| 696 | </table> | |
| 697 | </td> | |
| 698 | <td class="mlabels-right"> | |
| 699 | <span class="mlabels"><span class="mlabel">protected</span></span> </td> | |
| 700 | </tr> | |
| 701 | </table> | |
| 702 | </div><div class="memdoc"> | |
| 703 | <p>The smallest-achievable log-probability in the distribution of subisotopologues. </p> | |
| 704 | ||
| 705 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00059">59</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 706 | ||
| 707 | </div> | |
| 708 | </div> | |
| 709 | <hr/>The documentation for this class was generated from the following files:<ul> | |
| 710 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a></li> | |
| 711 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a></li> | |
| 712 | </ul> | |
| 713 | </div><!-- contents --> | |
| 714 | <!-- start footer part --> | |
| 715 | <hr class="footer"/><address class="footer"><small> | |
| 716 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 717 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 718 | </a> 1.8.14 | |
| 719 | </small></address> | |
| 720 | </body> | |
| 721 | </html> |
| 0 | digraph "IsoSpec::Marginal" | |
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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">MarginalTrek</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::MarginalTrek Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr bgcolor="#f0f0f0"><td class="entry"><b>conf_lprobs</b>() const (defined in <a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 86 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>conf_masses</b>() const (defined in <a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 87 | <tr bgcolor="#f0f0f0"><td class="entry"><b>confs</b>() const (defined in <a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 88 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 89 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">getModeProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 96 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a>(Conf conf) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a>(const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 99 | <tr bgcolor="#f0f0f0"><td class="entry"><b>Marginal</b>(Marginal &other)=delete (defined in <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 100 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e">Marginal</a>(Marginal &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 101 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal_trek.html#a83e70d522174e4e6724116941fd9c99e">MarginalTrek</a>(Marginal &&m, int tabSize=1000, int hashSize=1000)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a></td><td class="entry"></td></tr> | |
| 102 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 103 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 104 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 105 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">mode_prob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 106 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>operator=</b>(const Marginal &other)=delete (defined in <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 107 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal_trek.html#a4db6041328b818d123a017dda3c8b8ae">probeConfigurationIdx</a>(int idx)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 108 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal_trek.html#a04f3e495a805a3ea242059c963c5b129">processUntilCutoff</a>(double cutoff)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a></td><td class="entry"></td></tr> | |
| 109 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 110 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 111 | <tr bgcolor="#f0f0f0"><td class="entry"><b>~MarginalTrek</b>() (defined in <a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
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| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">MarginalTrek</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_marginal_trek-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::MarginalTrek Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | ||
| 83 | <p>The marginal distribution class (a subisotopologue). | |
| 84 | <a href="class_iso_spec_1_1_marginal_trek.html#details">More...</a></p> | |
| 85 | ||
| 86 | <p><code>#include <<a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>></code></p> | |
| 87 | <div class="dynheader"> | |
| 88 | Inheritance diagram for IsoSpec::MarginalTrek:</div> | |
| 89 | <div class="dyncontent"> | |
| 90 | <div class="center"> | |
| 91 | <img src="class_iso_spec_1_1_marginal_trek.png" usemap="#IsoSpec::MarginalTrek_map" alt=""/> | |
| 92 | <map id="IsoSpec::MarginalTrek_map" name="IsoSpec::MarginalTrek_map"> | |
| 93 | <area href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). " alt="IsoSpec::Marginal" shape="rect" coords="0,0,138,24"/> | |
| 94 | </map> | |
| 95 | </div></div> | |
| 96 | <table class="memberdecls"> | |
| 97 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 98 | Public Member Functions</h2></td></tr> | |
| 99 | <tr class="memitem:a83e70d522174e4e6724116941fd9c99e"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal_trek.html#a83e70d522174e4e6724116941fd9c99e">MarginalTrek</a> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &&m, int tabSize=1000, int hashSize=1000)</td></tr> | |
| 100 | <tr class="memdesc:a83e70d522174e4e6724116941fd9c99e"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor: specializes the <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class. <a href="#a83e70d522174e4e6724116941fd9c99e">More...</a><br /></td></tr> | |
| 101 | <tr class="separator:a83e70d522174e4e6724116941fd9c99e"><td class="memSeparator" colspan="2"> </td></tr> | |
| 102 | <tr class="memitem:a4db6041328b818d123a017dda3c8b8ae"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal_trek.html#a4db6041328b818d123a017dda3c8b8ae">probeConfigurationIdx</a> (int idx)</td></tr> | |
| 103 | <tr class="memdesc:a4db6041328b818d123a017dda3c8b8ae"><td class="mdescLeft"> </td><td class="mdescRight">Check if the table of computed subisotopologues does not have to be extended. <a href="#a4db6041328b818d123a017dda3c8b8ae">More...</a><br /></td></tr> | |
| 104 | <tr class="separator:a4db6041328b818d123a017dda3c8b8ae"><td class="memSeparator" colspan="2"> </td></tr> | |
| 105 | <tr class="memitem:a04f3e495a805a3ea242059c963c5b129"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal_trek.html#a04f3e495a805a3ea242059c963c5b129">processUntilCutoff</a> (double cutoff)</td></tr> | |
| 106 | <tr class="memdesc:a04f3e495a805a3ea242059c963c5b129"><td class="mdescLeft"> </td><td class="mdescRight">Calculate subisotopologues with probability above or equal to the cut-off. <a href="#a04f3e495a805a3ea242059c963c5b129">More...</a><br /></td></tr> | |
| 107 | <tr class="separator:a04f3e495a805a3ea242059c963c5b129"><td class="memSeparator" colspan="2"> </td></tr> | |
| 108 | <tr class="memitem:a802aa5dfd06d560b4f867240bb6c9d10"><td class="memItemLeft" align="right" valign="top"><a id="a802aa5dfd06d560b4f867240bb6c9d10"></a> | |
| 109 | const std::vector< double > & </td><td class="memItemRight" valign="bottom"><b>conf_lprobs</b> () const</td></tr> | |
| 110 | <tr class="separator:a802aa5dfd06d560b4f867240bb6c9d10"><td class="memSeparator" colspan="2"> </td></tr> | |
| 111 | <tr class="memitem:a8b31b886749c0bb07756ae367a4c31cd"><td class="memItemLeft" align="right" valign="top"><a id="a8b31b886749c0bb07756ae367a4c31cd"></a> | |
| 112 | const std::vector< double > & </td><td class="memItemRight" valign="bottom"><b>conf_masses</b> () const</td></tr> | |
| 113 | <tr class="separator:a8b31b886749c0bb07756ae367a4c31cd"><td class="memSeparator" colspan="2"> </td></tr> | |
| 114 | <tr class="memitem:a05df43d45dda1a7f80b711eec016c40c"><td class="memItemLeft" align="right" valign="top"><a id="a05df43d45dda1a7f80b711eec016c40c"></a> | |
| 115 | const std::vector< int * > & </td><td class="memItemRight" valign="bottom"><b>confs</b> () const</td></tr> | |
| 116 | <tr class="separator:a05df43d45dda1a7f80b711eec016c40c"><td class="memSeparator" colspan="2"> </td></tr> | |
| 117 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_marginal"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_marginal')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td></tr> | |
| 118 | <tr class="memitem:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a> (const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</td></tr> | |
| 119 | <tr class="memdesc:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Class constructor. <a href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">More...</a><br /></td></tr> | |
| 120 | <tr class="separator:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 121 | <tr class="memitem:a02e8f92f8f9add352840f5dba8de5e06 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a02e8f92f8f9add352840f5dba8de5e06"></a> | |
| 122 |  </td><td class="memItemRight" valign="bottom"><b>Marginal</b> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &other)=delete</td></tr> | |
| 123 | <tr class="separator:a02e8f92f8f9add352840f5dba8de5e06 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 124 | <tr class="memitem:a9120cad240058afc3705951d80d28a10 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a9120cad240058afc3705951d80d28a10"></a> | |
| 125 | <a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> & </td><td class="memItemRight" valign="bottom"><b>operator=</b> (const <a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &other)=delete</td></tr> | |
| 126 | <tr class="separator:a9120cad240058afc3705951d80d28a10 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 127 | <tr class="memitem:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="ad60fff17fa2c68ea2cd7f183a635379e"></a> | |
| 128 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e">Marginal</a> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &&other)</td></tr> | |
| 129 | <tr class="memdesc:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 130 | <tr class="separator:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 131 | <tr class="memitem:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="ad44004fa1e83c4a53d431ca403ce3ae4"></a> | |
| 132 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a> ()</td></tr> | |
| 133 | <tr class="memdesc:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 134 | <tr class="separator:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 135 | <tr class="memitem:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a> () const</td></tr> | |
| 136 | <tr class="memdesc:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of isotopes of the investigated element. <a href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">More...</a><br /></td></tr> | |
| 137 | <tr class="separator:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 138 | <tr class="memitem:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a> () const</td></tr> | |
| 139 | <tr class="memdesc:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">More...</a><br /></td></tr> | |
| 140 | <tr class="separator:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 141 | <tr class="memitem:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a> () const</td></tr> | |
| 142 | <tr class="memdesc:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">More...</a><br /></td></tr> | |
| 143 | <tr class="separator:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 144 | <tr class="memitem:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a> () const</td></tr> | |
| 145 | <tr class="memdesc:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">More...</a><br /></td></tr> | |
| 146 | <tr class="separator:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 147 | <tr class="memitem:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a> () const</td></tr> | |
| 148 | <tr class="memdesc:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the mass of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">More...</a><br /></td></tr> | |
| 149 | <tr class="separator:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 150 | <tr class="memitem:a7bc1eeba342977de3a77c3c7e6ca55b0 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">getModeProb</a> () const</td></tr> | |
| 151 | <tr class="memdesc:a7bc1eeba342977de3a77c3c7e6ca55b0 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the probability of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">More...</a><br /></td></tr> | |
| 152 | <tr class="separator:a7bc1eeba342977de3a77c3c7e6ca55b0 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 153 | <tr class="memitem:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a> () const</td></tr> | |
| 154 | <tr class="memdesc:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the log-probability of the lightest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">More...</a><br /></td></tr> | |
| 155 | <tr class="separator:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 156 | <tr class="memitem:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a> (Conf conf) const</td></tr> | |
| 157 | <tr class="memdesc:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the log-probability of a given subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">More...</a><br /></td></tr> | |
| 158 | <tr class="separator:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 159 | </table><table class="memberdecls"> | |
| 160 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a> | |
| 161 | Additional Inherited Members</h2></td></tr> | |
| 162 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_marginal"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_marginal')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td></tr> | |
| 163 | <tr class="memitem:a8dd6415882661f7b9ceedbe09bc200e3 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a></td></tr> | |
| 164 | <tr class="separator:a8dd6415882661f7b9ceedbe09bc200e3 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 165 | <tr class="memitem:a53c2af7dcb84aa9d5e0e0918fe7875cd inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a></td></tr> | |
| 166 | <tr class="separator:a53c2af7dcb84aa9d5e0e0918fe7875cd inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 167 | <tr class="memitem:a91265e07f5bb65314995f816f5a9c729 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double *const </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a></td></tr> | |
| 168 | <tr class="separator:a91265e07f5bb65314995f816f5a9c729 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 169 | <tr class="memitem:af059df011e707781fdd4c1d7b70bd91a inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double *const </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a></td></tr> | |
| 170 | <tr class="separator:af059df011e707781fdd4c1d7b70bd91a inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 171 | <tr class="memitem:aa3fb5ed3a9b63a855d6270287aed7417 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a></td></tr> | |
| 172 | <tr class="separator:aa3fb5ed3a9b63a855d6270287aed7417 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 173 | <tr class="memitem:a640f3b44605b510ee556a25e35a2e095 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const Conf </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a></td></tr> | |
| 174 | <tr class="separator:a640f3b44605b510ee556a25e35a2e095 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 175 | <tr class="memitem:a38238e7581f59f08d0faf8ab5eabc0dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a></td></tr> | |
| 176 | <tr class="separator:a38238e7581f59f08d0faf8ab5eabc0dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 177 | <tr class="memitem:a3bfea931e5e1ec1e7d90e8e096c38eb7 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a></td></tr> | |
| 178 | <tr class="separator:a3bfea931e5e1ec1e7d90e8e096c38eb7 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 179 | <tr class="memitem:a75315ec4c470be5f82b903172f7c43ae inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">mode_prob</a></td></tr> | |
| 180 | <tr class="separator:a75315ec4c470be5f82b903172f7c43ae inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 181 | <tr class="memitem:a2abd05ba9351e21cd99e2783e26bd6dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a></td></tr> | |
| 182 | <tr class="separator:a2abd05ba9351e21cd99e2783e26bd6dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 183 | </table> | |
| 184 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 185 | <div class="textblock"><p>The marginal distribution class (a subisotopologue). </p> | |
| 186 | ||
| 187 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00141">141</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 188 | </div><h2 class="groupheader">Constructor & Destructor Documentation</h2> | |
| 189 | <a id="a83e70d522174e4e6724116941fd9c99e"></a> | |
| 190 | <h2 class="memtitle"><span class="permalink"><a href="#a83e70d522174e4e6724116941fd9c99e">◆ </a></span>MarginalTrek()</h2> | |
| 191 | ||
| 192 | <div class="memitem"> | |
| 193 | <div class="memproto"> | |
| 194 | <table class="memname"> | |
| 195 | <tr> | |
| 196 | <td class="memname">IsoSpec::MarginalTrek::MarginalTrek </td> | |
| 197 | <td>(</td> | |
| 198 | <td class="paramtype"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> && </td> | |
| 199 | <td class="paramname"><em>m</em>, </td> | |
| 200 | </tr> | |
| 201 | <tr> | |
| 202 | <td class="paramkey"></td> | |
| 203 | <td></td> | |
| 204 | <td class="paramtype">int </td> | |
| 205 | <td class="paramname"><em>tabSize</em> = <code>1000</code>, </td> | |
| 206 | </tr> | |
| 207 | <tr> | |
| 208 | <td class="paramkey"></td> | |
| 209 | <td></td> | |
| 210 | <td class="paramtype">int </td> | |
| 211 | <td class="paramname"><em>hashSize</em> = <code>1000</code> </td> | |
| 212 | </tr> | |
| 213 | <tr> | |
| 214 | <td></td> | |
| 215 | <td>)</td> | |
| 216 | <td></td><td></td> | |
| 217 | </tr> | |
| 218 | </table> | |
| 219 | </div><div class="memdoc"> | |
| 220 | ||
| 221 | <p>Move constructor: specializes the <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class. </p> | |
| 222 | <dl class="params"><dt>Parameters</dt><dd> | |
| 223 | <table class="params"> | |
| 224 | <tr><td class="paramname">tabSize</td><td>The size of the table used to store configurations in the allocator. </td></tr> | |
| 225 | <tr><td class="paramname">hashSize</td><td>The size of the hash table used to store visited subisotopologues. </td></tr> | |
| 226 | </table> | |
| 227 | </dd> | |
| 228 | </dl> | |
| 229 | ||
| 230 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8cpp_source.html#l00256">256</a> of file <a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a>.</p> | |
| 231 | ||
| 232 | </div> | |
| 233 | </div> | |
| 234 | <h2 class="groupheader">Member Function Documentation</h2> | |
| 235 | <a id="a4db6041328b818d123a017dda3c8b8ae"></a> | |
| 236 | <h2 class="memtitle"><span class="permalink"><a href="#a4db6041328b818d123a017dda3c8b8ae">◆ </a></span>probeConfigurationIdx()</h2> | |
| 237 | ||
| 238 | <div class="memitem"> | |
| 239 | <div class="memproto"> | |
| 240 | <table class="mlabels"> | |
| 241 | <tr> | |
| 242 | <td class="mlabels-left"> | |
| 243 | <table class="memname"> | |
| 244 | <tr> | |
| 245 | <td class="memname">bool IsoSpec::MarginalTrek::probeConfigurationIdx </td> | |
| 246 | <td>(</td> | |
| 247 | <td class="paramtype">int </td> | |
| 248 | <td class="paramname"><em>idx</em></td><td>)</td> | |
| 249 | <td></td> | |
| 250 | </tr> | |
| 251 | </table> | |
| 252 | </td> | |
| 253 | <td class="mlabels-right"> | |
| 254 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 255 | </tr> | |
| 256 | </table> | |
| 257 | </div><div class="memdoc"> | |
| 258 | ||
| 259 | <p>Check if the table of computed subisotopologues does not have to be extended. </p> | |
| 260 | <p>This function checks if the idx-th most probable subisotopologue was memoized and if not, computes it and memoizes it.</p> | |
| 261 | <dl class="params"><dt>Parameters</dt><dd> | |
| 262 | <table class="params"> | |
| 263 | <tr><td class="paramname">idx</td><td>The number of the idx-th most probable subisotopologue. </td></tr> | |
| 264 | </table> | |
| 265 | </dd> | |
| 266 | </dl> | |
| 267 | <dl class="section return"><dt>Returns</dt><dd>Returns false if it the provided idx exceeds the total number of subisotopologues. </dd></dl> | |
| 268 | ||
| 269 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00179">179</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 270 | ||
| 271 | </div> | |
| 272 | </div> | |
| 273 | <a id="a04f3e495a805a3ea242059c963c5b129"></a> | |
| 274 | <h2 class="memtitle"><span class="permalink"><a href="#a04f3e495a805a3ea242059c963c5b129">◆ </a></span>processUntilCutoff()</h2> | |
| 275 | ||
| 276 | <div class="memitem"> | |
| 277 | <div class="memproto"> | |
| 278 | <table class="memname"> | |
| 279 | <tr> | |
| 280 | <td class="memname">int IsoSpec::MarginalTrek::processUntilCutoff </td> | |
| 281 | <td>(</td> | |
| 282 | <td class="paramtype">double </td> | |
| 283 | <td class="paramname"><em>cutoff</em></td><td>)</td> | |
| 284 | <td></td> | |
| 285 | </tr> | |
| 286 | </table> | |
| 287 | </div><div class="memdoc"> | |
| 288 | ||
| 289 | <p>Calculate subisotopologues with probability above or equal to the cut-off. </p> | |
| 290 | <dl class="params"><dt>Parameters</dt><dd> | |
| 291 | <table class="params"> | |
| 292 | <tr><td class="paramname">cutoff</td><td>The probability cut-off </td></tr> | |
| 293 | </table> | |
| 294 | </dd> | |
| 295 | </dl> | |
| 296 | <dl class="section return"><dt>Returns</dt><dd>The number of the last subisotopologue above the cut-off. </dd></dl> | |
| 297 | ||
| 298 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8cpp_source.html#l00333">333</a> of file <a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a>.</p> | |
| 299 | ||
| 300 | </div> | |
| 301 | </div> | |
| 302 | <hr/>The documentation for this class was generated from the following files:<ul> | |
| 303 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a></li> | |
| 304 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a></li> | |
| 305 | </ul> | |
| 306 | </div><!-- contents --> | |
| 307 | <!-- start footer part --> | |
| 308 | <hr class="footer"/><address class="footer"><small> | |
| 309 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 310 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 311 | </a> 1.8.14 | |
| 312 | </small></address> | |
| 313 | </body> | |
| 314 | </html> |
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| 0 | c8a1fe4bd879c35ab3bb7ff006c1a0e1⏎ |
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| 76 | <div class="title">IsoSpec::OrderMarginalsBySizeDecresing Member List</div> </div> | |
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| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">IsoSpec::OrderMarginalsBySizeDecresing</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>operator()</b>(int m1, int m2) (defined in <a class="el" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">IsoSpec::OrderMarginalsBySizeDecresing</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">IsoSpec::OrderMarginalsBySizeDecresing</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>OrderMarginalsBySizeDecresing</b>(PrecalculatedMarginal const *const *_T) (defined in <a class="el" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">IsoSpec::OrderMarginalsBySizeDecresing</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">IsoSpec::OrderMarginalsBySizeDecresing</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::OrderMarginalsBySizeDecresing Class Reference</div> </div> | |
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| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a2530a398df14766242b936e5c83e0f37"><td class="memItemLeft" align="right" valign="top"><a id="a2530a398df14766242b936e5c83e0f37"></a> | |
| 86 |  </td><td class="memItemRight" valign="bottom"><b>OrderMarginalsBySizeDecresing</b> (<a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a> const *const *_T)</td></tr> | |
| 87 | <tr class="separator:a2530a398df14766242b936e5c83e0f37"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:a43312dd35580f579c9e64b32e06edb63"><td class="memItemLeft" align="right" valign="top"><a id="a43312dd35580f579c9e64b32e06edb63"></a> | |
| 89 | bool </td><td class="memItemRight" valign="bottom"><b>operator()</b> (int m1, int m2)</td></tr> | |
| 90 | <tr class="separator:a43312dd35580f579c9e64b32e06edb63"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | </table> | |
| 92 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 93 | <div class="textblock"> | |
| 94 | <p class="definition">Definition at line <a class="el" href="operators_8h_source.html#l00128">128</a> of file <a class="el" href="operators_8h_source.html">operators.h</a>.</p> | |
| 95 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 96 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8h_source.html">operators.h</a></li> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::PrecalculatedMarginal Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>allocator</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 86 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>configurations</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 87 | <tr bgcolor="#f0f0f0"><td class="entry"><b>confs</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 88 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>eProbs</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 89 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff">get_conf</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">get_eProb</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">get_lProb</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">get_lProbs_ptr</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">get_mass</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a9a768b90299ea16c447a392dbe1123b5">get_masses_ptr</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 96 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">get_no_confs</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 99 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 100 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 101 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">getModeProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 102 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 103 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a942b30ace039f80c50125360be4ed4d2">inRange</a>(unsigned int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 104 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 105 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 106 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a>(Conf conf) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 107 | <tr bgcolor="#f0f0f0"><td class="entry"><b>lProbs</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 108 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a>(const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 109 | <tr bgcolor="#f0f0f0"><td class="entry"><b>Marginal</b>(Marginal &other)=delete (defined in <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 110 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e">Marginal</a>(Marginal &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 111 | <tr bgcolor="#f0f0f0"><td class="entry"><b>masses</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 112 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 113 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 114 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 115 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">mode_prob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 116 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>no_confs</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 117 | <tr bgcolor="#f0f0f0"><td class="entry"><b>operator=</b>(const Marginal &other)=delete (defined in <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 118 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">PrecalculatedMarginal</a>(Marginal &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"></td></tr> | |
| 119 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 120 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 121 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8">~PrecalculatedMarginal</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
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| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a></li> </ul> | |
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| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="#pro-attribs">Protected Attributes</a> | | |
| 78 | <a href="class_iso_spec_1_1_precalculated_marginal-members.html">List of all members</a> </div> | |
| 79 | <div class="headertitle"> | |
| 80 | <div class="title">IsoSpec::PrecalculatedMarginal Class Reference</div> </div> | |
| 81 | </div><!--header--> | |
| 82 | <div class="contents"> | |
| 83 | ||
| 84 | <p>Precalculated <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class. | |
| 85 | <a href="class_iso_spec_1_1_precalculated_marginal.html#details">More...</a></p> | |
| 86 | ||
| 87 | <p><code>#include <<a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>></code></p> | |
| 88 | <div class="dynheader"> | |
| 89 | Inheritance diagram for IsoSpec::PrecalculatedMarginal:</div> | |
| 90 | <div class="dyncontent"> | |
| 91 | <div class="center"> | |
| 92 | <img src="class_iso_spec_1_1_precalculated_marginal.png" usemap="#IsoSpec::PrecalculatedMarginal_map" alt=""/> | |
| 93 | <map id="IsoSpec::PrecalculatedMarginal_map" name="IsoSpec::PrecalculatedMarginal_map"> | |
| 94 | <area href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). " alt="IsoSpec::Marginal" shape="rect" coords="0,0,191,24"/> | |
| 95 | </map> | |
| 96 | </div></div> | |
| 97 | <table class="memberdecls"> | |
| 98 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 99 | Public Member Functions</h2></td></tr> | |
| 100 | <tr class="memitem:acb84bd7ba582847655c55bd64d64463e"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">PrecalculatedMarginal</a> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000)</td></tr> | |
| 101 | <tr class="memdesc:acb84bd7ba582847655c55bd64d64463e"><td class="mdescLeft"> </td><td class="mdescRight">The move constructor (disowns the <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a>). <a href="#acb84bd7ba582847655c55bd64d64463e">More...</a><br /></td></tr> | |
| 102 | <tr class="separator:acb84bd7ba582847655c55bd64d64463e"><td class="memSeparator" colspan="2"> </td></tr> | |
| 103 | <tr class="memitem:a6b7b30cfe90ffba1d2c9d2f0d87107d8"><td class="memItemLeft" align="right" valign="top"><a id="a6b7b30cfe90ffba1d2c9d2f0d87107d8"></a> | |
| 104 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8">~PrecalculatedMarginal</a> ()</td></tr> | |
| 105 | <tr class="memdesc:a6b7b30cfe90ffba1d2c9d2f0d87107d8"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 106 | <tr class="separator:a6b7b30cfe90ffba1d2c9d2f0d87107d8"><td class="memSeparator" colspan="2"> </td></tr> | |
| 107 | <tr class="memitem:a942b30ace039f80c50125360be4ed4d2"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a942b30ace039f80c50125360be4ed4d2">inRange</a> (unsigned int idx) const</td></tr> | |
| 108 | <tr class="memdesc:a942b30ace039f80c50125360be4ed4d2"><td class="mdescLeft"> </td><td class="mdescRight">Is there a subisotopologue with a given number? <a href="#a942b30ace039f80c50125360be4ed4d2">More...</a><br /></td></tr> | |
| 109 | <tr class="separator:a942b30ace039f80c50125360be4ed4d2"><td class="memSeparator" colspan="2"> </td></tr> | |
| 110 | <tr class="memitem:a07eee6d60635c9c1d6f92c181994e06a"><td class="memItemLeft" align="right" valign="top">const double & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">get_lProb</a> (int idx) const</td></tr> | |
| 111 | <tr class="memdesc:a07eee6d60635c9c1d6f92c181994e06a"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the idx-th subisotopologue. <a href="#a07eee6d60635c9c1d6f92c181994e06a">More...</a><br /></td></tr> | |
| 112 | <tr class="separator:a07eee6d60635c9c1d6f92c181994e06a"><td class="memSeparator" colspan="2"> </td></tr> | |
| 113 | <tr class="memitem:a7a38a567eadf16fa2ad41e81c8f55c02"><td class="memItemLeft" align="right" valign="top">const double & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">get_eProb</a> (int idx) const</td></tr> | |
| 114 | <tr class="memdesc:a7a38a567eadf16fa2ad41e81c8f55c02"><td class="mdescLeft"> </td><td class="mdescRight">Get the probability of the idx-th subisotopologue. <a href="#a7a38a567eadf16fa2ad41e81c8f55c02">More...</a><br /></td></tr> | |
| 115 | <tr class="separator:a7a38a567eadf16fa2ad41e81c8f55c02"><td class="memSeparator" colspan="2"> </td></tr> | |
| 116 | <tr class="memitem:ada12caa2e195c1a16c5158a428ea3ed2"><td class="memItemLeft" align="right" valign="top">const double & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">get_mass</a> (int idx) const</td></tr> | |
| 117 | <tr class="memdesc:ada12caa2e195c1a16c5158a428ea3ed2"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the idx-th subisotopologue. <a href="#ada12caa2e195c1a16c5158a428ea3ed2">More...</a><br /></td></tr> | |
| 118 | <tr class="separator:ada12caa2e195c1a16c5158a428ea3ed2"><td class="memSeparator" colspan="2"> </td></tr> | |
| 119 | <tr class="memitem:af5d01500c7efb8cba57399ba11fc7124"><td class="memItemLeft" align="right" valign="top">const double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">get_lProbs_ptr</a> () const</td></tr> | |
| 120 | <tr class="memdesc:af5d01500c7efb8cba57399ba11fc7124"><td class="mdescLeft"> </td><td class="mdescRight">Get the table of the log-probabilities of subisotopologues. <a href="#af5d01500c7efb8cba57399ba11fc7124">More...</a><br /></td></tr> | |
| 121 | <tr class="separator:af5d01500c7efb8cba57399ba11fc7124"><td class="memSeparator" colspan="2"> </td></tr> | |
| 122 | <tr class="memitem:a9a768b90299ea16c447a392dbe1123b5"><td class="memItemLeft" align="right" valign="top">const double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a9a768b90299ea16c447a392dbe1123b5">get_masses_ptr</a> () const</td></tr> | |
| 123 | <tr class="memdesc:a9a768b90299ea16c447a392dbe1123b5"><td class="mdescLeft"> </td><td class="mdescRight">Get the table of the masses of subisotopologues. <a href="#a9a768b90299ea16c447a392dbe1123b5">More...</a><br /></td></tr> | |
| 124 | <tr class="separator:a9a768b90299ea16c447a392dbe1123b5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 125 | <tr class="memitem:a3ecbbf1263a274cc8e3bc71cd96f0bff"><td class="memItemLeft" align="right" valign="top">const Conf & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff">get_conf</a> (int idx) const</td></tr> | |
| 126 | <tr class="memdesc:a3ecbbf1263a274cc8e3bc71cd96f0bff"><td class="mdescLeft"> </td><td class="mdescRight">Get the counts of isotopes that define the subisotopologue. <a href="#a3ecbbf1263a274cc8e3bc71cd96f0bff">More...</a><br /></td></tr> | |
| 127 | <tr class="separator:a3ecbbf1263a274cc8e3bc71cd96f0bff"><td class="memSeparator" colspan="2"> </td></tr> | |
| 128 | <tr class="memitem:a0dbf1ec53eac9953a354c11e1b0803f9"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">get_no_confs</a> () const</td></tr> | |
| 129 | <tr class="memdesc:a0dbf1ec53eac9953a354c11e1b0803f9"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of precomputed subisotopologues. <a href="#a0dbf1ec53eac9953a354c11e1b0803f9">More...</a><br /></td></tr> | |
| 130 | <tr class="separator:a0dbf1ec53eac9953a354c11e1b0803f9"><td class="memSeparator" colspan="2"> </td></tr> | |
| 131 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_marginal"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_marginal')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td></tr> | |
| 132 | <tr class="memitem:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a> (const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</td></tr> | |
| 133 | <tr class="memdesc:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Class constructor. <a href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">More...</a><br /></td></tr> | |
| 134 | <tr class="separator:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 135 | <tr class="memitem:a02e8f92f8f9add352840f5dba8de5e06 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a02e8f92f8f9add352840f5dba8de5e06"></a> | |
| 136 |  </td><td class="memItemRight" valign="bottom"><b>Marginal</b> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &other)=delete</td></tr> | |
| 137 | <tr class="separator:a02e8f92f8f9add352840f5dba8de5e06 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 138 | <tr class="memitem:a9120cad240058afc3705951d80d28a10 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a9120cad240058afc3705951d80d28a10"></a> | |
| 139 | <a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> & </td><td class="memItemRight" valign="bottom"><b>operator=</b> (const <a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &other)=delete</td></tr> | |
| 140 | <tr class="separator:a9120cad240058afc3705951d80d28a10 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 141 | <tr class="memitem:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="ad60fff17fa2c68ea2cd7f183a635379e"></a> | |
| 142 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e">Marginal</a> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &&other)</td></tr> | |
| 143 | <tr class="memdesc:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 144 | <tr class="separator:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 145 | <tr class="memitem:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="ad44004fa1e83c4a53d431ca403ce3ae4"></a> | |
| 146 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a> ()</td></tr> | |
| 147 | <tr class="memdesc:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 148 | <tr class="separator:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 149 | <tr class="memitem:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a> () const</td></tr> | |
| 150 | <tr class="memdesc:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of isotopes of the investigated element. <a href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">More...</a><br /></td></tr> | |
| 151 | <tr class="separator:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 152 | <tr class="memitem:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a> () const</td></tr> | |
| 153 | <tr class="memdesc:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">More...</a><br /></td></tr> | |
| 154 | <tr class="separator:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 155 | <tr class="memitem:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a> () const</td></tr> | |
| 156 | <tr class="memdesc:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">More...</a><br /></td></tr> | |
| 157 | <tr class="separator:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 158 | <tr class="memitem:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a> () const</td></tr> | |
| 159 | <tr class="memdesc:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">More...</a><br /></td></tr> | |
| 160 | <tr class="separator:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 161 | <tr class="memitem:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a> () const</td></tr> | |
| 162 | <tr class="memdesc:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the mass of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">More...</a><br /></td></tr> | |
| 163 | <tr class="separator:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 164 | <tr class="memitem:a7bc1eeba342977de3a77c3c7e6ca55b0 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">getModeProb</a> () const</td></tr> | |
| 165 | <tr class="memdesc:a7bc1eeba342977de3a77c3c7e6ca55b0 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the probability of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">More...</a><br /></td></tr> | |
| 166 | <tr class="separator:a7bc1eeba342977de3a77c3c7e6ca55b0 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 167 | <tr class="memitem:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a> () const</td></tr> | |
| 168 | <tr class="memdesc:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the log-probability of the lightest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">More...</a><br /></td></tr> | |
| 169 | <tr class="separator:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 170 | <tr class="memitem:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a> (Conf conf) const</td></tr> | |
| 171 | <tr class="memdesc:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the log-probability of a given subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">More...</a><br /></td></tr> | |
| 172 | <tr class="separator:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 173 | </table><table class="memberdecls"> | |
| 174 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a> | |
| 175 | Protected Attributes</h2></td></tr> | |
| 176 | <tr class="memitem:adaba0751ea134b2cbd6c3fdf67c327ea"><td class="memItemLeft" align="right" valign="top"><a id="adaba0751ea134b2cbd6c3fdf67c327ea"></a> | |
| 177 | std::vector< Conf > </td><td class="memItemRight" valign="bottom"><b>configurations</b></td></tr> | |
| 178 | <tr class="separator:adaba0751ea134b2cbd6c3fdf67c327ea"><td class="memSeparator" colspan="2"> </td></tr> | |
| 179 | <tr class="memitem:a1197bed742b2139243e9dc71cb8fcdfc"><td class="memItemLeft" align="right" valign="top"><a id="a1197bed742b2139243e9dc71cb8fcdfc"></a> | |
| 180 | Conf * </td><td class="memItemRight" valign="bottom"><b>confs</b></td></tr> | |
| 181 | <tr class="separator:a1197bed742b2139243e9dc71cb8fcdfc"><td class="memSeparator" colspan="2"> </td></tr> | |
| 182 | <tr class="memitem:ad82d7aef36c946ce4f9bbf3ddac70cd1"><td class="memItemLeft" align="right" valign="top"><a id="ad82d7aef36c946ce4f9bbf3ddac70cd1"></a> | |
| 183 | unsigned int </td><td class="memItemRight" valign="bottom"><b>no_confs</b></td></tr> | |
| 184 | <tr class="separator:ad82d7aef36c946ce4f9bbf3ddac70cd1"><td class="memSeparator" colspan="2"> </td></tr> | |
| 185 | <tr class="memitem:a94e78eba4ae89c0d6c811d7bc0085684"><td class="memItemLeft" align="right" valign="top"><a id="a94e78eba4ae89c0d6c811d7bc0085684"></a> | |
| 186 | double * </td><td class="memItemRight" valign="bottom"><b>masses</b></td></tr> | |
| 187 | <tr class="separator:a94e78eba4ae89c0d6c811d7bc0085684"><td class="memSeparator" colspan="2"> </td></tr> | |
| 188 | <tr class="memitem:afd5a4a7b094038f66eda31c6827a66f9"><td class="memItemLeft" align="right" valign="top"><a id="afd5a4a7b094038f66eda31c6827a66f9"></a> | |
| 189 | double * </td><td class="memItemRight" valign="bottom"><b>lProbs</b></td></tr> | |
| 190 | <tr class="separator:afd5a4a7b094038f66eda31c6827a66f9"><td class="memSeparator" colspan="2"> </td></tr> | |
| 191 | <tr class="memitem:abf3e9faabf5011f75cfb8e89cb3cdcca"><td class="memItemLeft" align="right" valign="top"><a id="abf3e9faabf5011f75cfb8e89cb3cdcca"></a> | |
| 192 | double * </td><td class="memItemRight" valign="bottom"><b>eProbs</b></td></tr> | |
| 193 | <tr class="separator:abf3e9faabf5011f75cfb8e89cb3cdcca"><td class="memSeparator" colspan="2"> </td></tr> | |
| 194 | <tr class="memitem:add0495cfc67fd8b9757b93b07d47e6cf"><td class="memItemLeft" align="right" valign="top"><a id="add0495cfc67fd8b9757b93b07d47e6cf"></a> | |
| 195 | <a class="el" href="class_iso_spec_1_1_allocator.html">Allocator</a>< int > </td><td class="memItemRight" valign="bottom"><b>allocator</b></td></tr> | |
| 196 | <tr class="separator:add0495cfc67fd8b9757b93b07d47e6cf"><td class="memSeparator" colspan="2"> </td></tr> | |
| 197 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_marginal"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_marginal')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td></tr> | |
| 198 | <tr class="memitem:a8dd6415882661f7b9ceedbe09bc200e3 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a></td></tr> | |
| 199 | <tr class="separator:a8dd6415882661f7b9ceedbe09bc200e3 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 200 | <tr class="memitem:a53c2af7dcb84aa9d5e0e0918fe7875cd inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a></td></tr> | |
| 201 | <tr class="separator:a53c2af7dcb84aa9d5e0e0918fe7875cd inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 202 | <tr class="memitem:a91265e07f5bb65314995f816f5a9c729 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double *const </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a></td></tr> | |
| 203 | <tr class="separator:a91265e07f5bb65314995f816f5a9c729 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 204 | <tr class="memitem:af059df011e707781fdd4c1d7b70bd91a inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double *const </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a></td></tr> | |
| 205 | <tr class="separator:af059df011e707781fdd4c1d7b70bd91a inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 206 | <tr class="memitem:aa3fb5ed3a9b63a855d6270287aed7417 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a></td></tr> | |
| 207 | <tr class="separator:aa3fb5ed3a9b63a855d6270287aed7417 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 208 | <tr class="memitem:a640f3b44605b510ee556a25e35a2e095 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const Conf </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a></td></tr> | |
| 209 | <tr class="separator:a640f3b44605b510ee556a25e35a2e095 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 210 | <tr class="memitem:a38238e7581f59f08d0faf8ab5eabc0dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a></td></tr> | |
| 211 | <tr class="separator:a38238e7581f59f08d0faf8ab5eabc0dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 212 | <tr class="memitem:a3bfea931e5e1ec1e7d90e8e096c38eb7 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a></td></tr> | |
| 213 | <tr class="separator:a3bfea931e5e1ec1e7d90e8e096c38eb7 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 214 | <tr class="memitem:a75315ec4c470be5f82b903172f7c43ae inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">mode_prob</a></td></tr> | |
| 215 | <tr class="separator:a75315ec4c470be5f82b903172f7c43ae inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 216 | <tr class="memitem:a2abd05ba9351e21cd99e2783e26bd6dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a></td></tr> | |
| 217 | <tr class="separator:a2abd05ba9351e21cd99e2783e26bd6dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 218 | </table> | |
| 219 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 220 | <div class="textblock"><p>Precalculated <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class. </p> | |
| 221 | <p>This class serves to calculate a set of isotopologues that is defined by the minimal probability threshold.</p> | |
| 222 | <p>This works faster than if you did not know the threshold. If you have no idea about the threshold, you would need to call us, to change encode the layered version of the marginal. </p> | |
| 223 | ||
| 224 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00213">213</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 225 | </div><h2 class="groupheader">Constructor & Destructor Documentation</h2> | |
| 226 | <a id="acb84bd7ba582847655c55bd64d64463e"></a> | |
| 227 | <h2 class="memtitle"><span class="permalink"><a href="#acb84bd7ba582847655c55bd64d64463e">◆ </a></span>PrecalculatedMarginal()</h2> | |
| 228 | ||
| 229 | <div class="memitem"> | |
| 230 | <div class="memproto"> | |
| 231 | <table class="memname"> | |
| 232 | <tr> | |
| 233 | <td class="memname">IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal </td> | |
| 234 | <td>(</td> | |
| 235 | <td class="paramtype"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> && </td> | |
| 236 | <td class="paramname"><em>m</em>, </td> | |
| 237 | </tr> | |
| 238 | <tr> | |
| 239 | <td class="paramkey"></td> | |
| 240 | <td></td> | |
| 241 | <td class="paramtype">double </td> | |
| 242 | <td class="paramname"><em>lCutOff</em>, </td> | |
| 243 | </tr> | |
| 244 | <tr> | |
| 245 | <td class="paramkey"></td> | |
| 246 | <td></td> | |
| 247 | <td class="paramtype">bool </td> | |
| 248 | <td class="paramname"><em>sort</em> = <code>true</code>, </td> | |
| 249 | </tr> | |
| 250 | <tr> | |
| 251 | <td class="paramkey"></td> | |
| 252 | <td></td> | |
| 253 | <td class="paramtype">int </td> | |
| 254 | <td class="paramname"><em>tabSize</em> = <code>1000</code>, </td> | |
| 255 | </tr> | |
| 256 | <tr> | |
| 257 | <td class="paramkey"></td> | |
| 258 | <td></td> | |
| 259 | <td class="paramtype">int </td> | |
| 260 | <td class="paramname"><em>hashSize</em> = <code>1000</code> </td> | |
| 261 | </tr> | |
| 262 | <tr> | |
| 263 | <td></td> | |
| 264 | <td>)</td> | |
| 265 | <td></td><td></td> | |
| 266 | </tr> | |
| 267 | </table> | |
| 268 | </div><div class="memdoc"> | |
| 269 | ||
| 270 | <p>The move constructor (disowns the <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a>). </p> | |
| 271 | <p>This constructor memoizes all subisotopologues with log-probability above the provided threshold lCutOff </p><dl class="params"><dt>Parameters</dt><dd> | |
| 272 | <table class="params"> | |
| 273 | <tr><td class="paramname"><a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a></td><td>An instance of the <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class this class is about to disown. </td></tr> | |
| 274 | <tr><td class="paramname">lCutOff</td><td>The lower limit on the log-probability of the precomputed subisotopologues. </td></tr> | |
| 275 | <tr><td class="paramname">sort</td><td>Should the subisotopologues be stored with descending probability ? </td></tr> | |
| 276 | </table> | |
| 277 | </dd> | |
| 278 | </dl> | |
| 279 | <dl class="section return"><dt>Returns</dt><dd>An instance of the <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html" title="Precalculated Marginal class. ">PrecalculatedMarginal</a> class. </dd></dl> | |
| 280 | ||
| 281 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8cpp_source.html#l00362">362</a> of file <a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a>.</p> | |
| 282 | ||
| 283 | </div> | |
| 284 | </div> | |
| 285 | <h2 class="groupheader">Member Function Documentation</h2> | |
| 286 | <a id="a3ecbbf1263a274cc8e3bc71cd96f0bff"></a> | |
| 287 | <h2 class="memtitle"><span class="permalink"><a href="#a3ecbbf1263a274cc8e3bc71cd96f0bff">◆ </a></span>get_conf()</h2> | |
| 288 | ||
| 289 | <div class="memitem"> | |
| 290 | <div class="memproto"> | |
| 291 | <table class="mlabels"> | |
| 292 | <tr> | |
| 293 | <td class="mlabels-left"> | |
| 294 | <table class="memname"> | |
| 295 | <tr> | |
| 296 | <td class="memname">const Conf& IsoSpec::PrecalculatedMarginal::get_conf </td> | |
| 297 | <td>(</td> | |
| 298 | <td class="paramtype">int </td> | |
| 299 | <td class="paramname"><em>idx</em></td><td>)</td> | |
| 300 | <td> const</td> | |
| 301 | </tr> | |
| 302 | </table> | |
| 303 | </td> | |
| 304 | <td class="mlabels-right"> | |
| 305 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 306 | </tr> | |
| 307 | </table> | |
| 308 | </div><div class="memdoc"> | |
| 309 | ||
| 310 | <p>Get the counts of isotopes that define the subisotopologue. </p> | |
| 311 | <dl class="params"><dt>Parameters</dt><dd> | |
| 312 | <table class="params"> | |
| 313 | <tr><td class="paramname">idx</td><td>The number of the considered subisotopologue. </td></tr> | |
| 314 | </table> | |
| 315 | </dd> | |
| 316 | </dl> | |
| 317 | <dl class="section return"><dt>Returns</dt><dd>The counts of isotopes that define the subisotopologue. </dd></dl> | |
| 318 | ||
| 319 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00288">288</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 320 | ||
| 321 | </div> | |
| 322 | </div> | |
| 323 | <a id="a7a38a567eadf16fa2ad41e81c8f55c02"></a> | |
| 324 | <h2 class="memtitle"><span class="permalink"><a href="#a7a38a567eadf16fa2ad41e81c8f55c02">◆ </a></span>get_eProb()</h2> | |
| 325 | ||
| 326 | <div class="memitem"> | |
| 327 | <div class="memproto"> | |
| 328 | <table class="mlabels"> | |
| 329 | <tr> | |
| 330 | <td class="mlabels-left"> | |
| 331 | <table class="memname"> | |
| 332 | <tr> | |
| 333 | <td class="memname">const double& IsoSpec::PrecalculatedMarginal::get_eProb </td> | |
| 334 | <td>(</td> | |
| 335 | <td class="paramtype">int </td> | |
| 336 | <td class="paramname"><em>idx</em></td><td>)</td> | |
| 337 | <td> const</td> | |
| 338 | </tr> | |
| 339 | </table> | |
| 340 | </td> | |
| 341 | <td class="mlabels-right"> | |
| 342 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 343 | </tr> | |
| 344 | </table> | |
| 345 | </div><div class="memdoc"> | |
| 346 | ||
| 347 | <p>Get the probability of the idx-th subisotopologue. </p> | |
| 348 | <dl class="params"><dt>Parameters</dt><dd> | |
| 349 | <table class="params"> | |
| 350 | <tr><td class="paramname">idx</td><td>The number of the considered subisotopologue. </td></tr> | |
| 351 | </table> | |
| 352 | </dd> | |
| 353 | </dl> | |
| 354 | <dl class="section return"><dt>Returns</dt><dd>The probability of the idx-th subisotopologue. </dd></dl> | |
| 355 | ||
| 356 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00261">261</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 357 | ||
| 358 | </div> | |
| 359 | </div> | |
| 360 | <a id="a07eee6d60635c9c1d6f92c181994e06a"></a> | |
| 361 | <h2 class="memtitle"><span class="permalink"><a href="#a07eee6d60635c9c1d6f92c181994e06a">◆ </a></span>get_lProb()</h2> | |
| 362 | ||
| 363 | <div class="memitem"> | |
| 364 | <div class="memproto"> | |
| 365 | <table class="mlabels"> | |
| 366 | <tr> | |
| 367 | <td class="mlabels-left"> | |
| 368 | <table class="memname"> | |
| 369 | <tr> | |
| 370 | <td class="memname">const double& IsoSpec::PrecalculatedMarginal::get_lProb </td> | |
| 371 | <td>(</td> | |
| 372 | <td class="paramtype">int </td> | |
| 373 | <td class="paramname"><em>idx</em></td><td>)</td> | |
| 374 | <td> const</td> | |
| 375 | </tr> | |
| 376 | </table> | |
| 377 | </td> | |
| 378 | <td class="mlabels-right"> | |
| 379 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 380 | </tr> | |
| 381 | </table> | |
| 382 | </div><div class="memdoc"> | |
| 383 | ||
| 384 | <p>Get the log-probability of the idx-th subisotopologue. </p> | |
| 385 | <dl class="params"><dt>Parameters</dt><dd> | |
| 386 | <table class="params"> | |
| 387 | <tr><td class="paramname">idx</td><td>The number of the considered subisotopologue. </td></tr> | |
| 388 | </table> | |
| 389 | </dd> | |
| 390 | </dl> | |
| 391 | <dl class="section return"><dt>Returns</dt><dd>The log-probability of the idx-th subisotopologue. </dd></dl> | |
| 392 | ||
| 393 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00254">254</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 394 | ||
| 395 | </div> | |
| 396 | </div> | |
| 397 | <a id="af5d01500c7efb8cba57399ba11fc7124"></a> | |
| 398 | <h2 class="memtitle"><span class="permalink"><a href="#af5d01500c7efb8cba57399ba11fc7124">◆ </a></span>get_lProbs_ptr()</h2> | |
| 399 | ||
| 400 | <div class="memitem"> | |
| 401 | <div class="memproto"> | |
| 402 | <table class="mlabels"> | |
| 403 | <tr> | |
| 404 | <td class="mlabels-left"> | |
| 405 | <table class="memname"> | |
| 406 | <tr> | |
| 407 | <td class="memname">const double* IsoSpec::PrecalculatedMarginal::get_lProbs_ptr </td> | |
| 408 | <td>(</td> | |
| 409 | <td class="paramname"></td><td>)</td> | |
| 410 | <td> const</td> | |
| 411 | </tr> | |
| 412 | </table> | |
| 413 | </td> | |
| 414 | <td class="mlabels-right"> | |
| 415 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 416 | </tr> | |
| 417 | </table> | |
| 418 | </div><div class="memdoc"> | |
| 419 | ||
| 420 | <p>Get the table of the log-probabilities of subisotopologues. </p> | |
| 421 | <dl class="section return"><dt>Returns</dt><dd>Pointer to the first element in the table storing log-probabilities of subisotopologues. </dd></dl> | |
| 422 | ||
| 423 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00274">274</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 424 | ||
| 425 | </div> | |
| 426 | </div> | |
| 427 | <a id="ada12caa2e195c1a16c5158a428ea3ed2"></a> | |
| 428 | <h2 class="memtitle"><span class="permalink"><a href="#ada12caa2e195c1a16c5158a428ea3ed2">◆ </a></span>get_mass()</h2> | |
| 429 | ||
| 430 | <div class="memitem"> | |
| 431 | <div class="memproto"> | |
| 432 | <table class="mlabels"> | |
| 433 | <tr> | |
| 434 | <td class="mlabels-left"> | |
| 435 | <table class="memname"> | |
| 436 | <tr> | |
| 437 | <td class="memname">const double& IsoSpec::PrecalculatedMarginal::get_mass </td> | |
| 438 | <td>(</td> | |
| 439 | <td class="paramtype">int </td> | |
| 440 | <td class="paramname"><em>idx</em></td><td>)</td> | |
| 441 | <td> const</td> | |
| 442 | </tr> | |
| 443 | </table> | |
| 444 | </td> | |
| 445 | <td class="mlabels-right"> | |
| 446 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 447 | </tr> | |
| 448 | </table> | |
| 449 | </div><div class="memdoc"> | |
| 450 | ||
| 451 | <p>Get the mass of the idx-th subisotopologue. </p> | |
| 452 | <dl class="params"><dt>Parameters</dt><dd> | |
| 453 | <table class="params"> | |
| 454 | <tr><td class="paramname">idx</td><td>The number of the considered subisotopologue. </td></tr> | |
| 455 | </table> | |
| 456 | </dd> | |
| 457 | </dl> | |
| 458 | <dl class="section return"><dt>Returns</dt><dd>The mass of the idx-th subisotopologue. </dd></dl> | |
| 459 | ||
| 460 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00268">268</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 461 | ||
| 462 | </div> | |
| 463 | </div> | |
| 464 | <a id="a9a768b90299ea16c447a392dbe1123b5"></a> | |
| 465 | <h2 class="memtitle"><span class="permalink"><a href="#a9a768b90299ea16c447a392dbe1123b5">◆ </a></span>get_masses_ptr()</h2> | |
| 466 | ||
| 467 | <div class="memitem"> | |
| 468 | <div class="memproto"> | |
| 469 | <table class="mlabels"> | |
| 470 | <tr> | |
| 471 | <td class="mlabels-left"> | |
| 472 | <table class="memname"> | |
| 473 | <tr> | |
| 474 | <td class="memname">const double* IsoSpec::PrecalculatedMarginal::get_masses_ptr </td> | |
| 475 | <td>(</td> | |
| 476 | <td class="paramname"></td><td>)</td> | |
| 477 | <td> const</td> | |
| 478 | </tr> | |
| 479 | </table> | |
| 480 | </td> | |
| 481 | <td class="mlabels-right"> | |
| 482 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 483 | </tr> | |
| 484 | </table> | |
| 485 | </div><div class="memdoc"> | |
| 486 | ||
| 487 | <p>Get the table of the masses of subisotopologues. </p> | |
| 488 | <dl class="section return"><dt>Returns</dt><dd>Pointer to the first element in the table storing masses of subisotopologues. </dd></dl> | |
| 489 | ||
| 490 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00280">280</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 491 | ||
| 492 | </div> | |
| 493 | </div> | |
| 494 | <a id="a0dbf1ec53eac9953a354c11e1b0803f9"></a> | |
| 495 | <h2 class="memtitle"><span class="permalink"><a href="#a0dbf1ec53eac9953a354c11e1b0803f9">◆ </a></span>get_no_confs()</h2> | |
| 496 | ||
| 497 | <div class="memitem"> | |
| 498 | <div class="memproto"> | |
| 499 | <table class="mlabels"> | |
| 500 | <tr> | |
| 501 | <td class="mlabels-left"> | |
| 502 | <table class="memname"> | |
| 503 | <tr> | |
| 504 | <td class="memname">unsigned int IsoSpec::PrecalculatedMarginal::get_no_confs </td> | |
| 505 | <td>(</td> | |
| 506 | <td class="paramname"></td><td>)</td> | |
| 507 | <td> const</td> | |
| 508 | </tr> | |
| 509 | </table> | |
| 510 | </td> | |
| 511 | <td class="mlabels-right"> | |
| 512 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 513 | </tr> | |
| 514 | </table> | |
| 515 | </div><div class="memdoc"> | |
| 516 | ||
| 517 | <p>Get the number of precomputed subisotopologues. </p> | |
| 518 | <dl class="section return"><dt>Returns</dt><dd>The number of precomputed subisotopologues. </dd></dl> | |
| 519 | ||
| 520 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00294">294</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 521 | ||
| 522 | </div> | |
| 523 | </div> | |
| 524 | <a id="a942b30ace039f80c50125360be4ed4d2"></a> | |
| 525 | <h2 class="memtitle"><span class="permalink"><a href="#a942b30ace039f80c50125360be4ed4d2">◆ </a></span>inRange()</h2> | |
| 526 | ||
| 527 | <div class="memitem"> | |
| 528 | <div class="memproto"> | |
| 529 | <table class="mlabels"> | |
| 530 | <tr> | |
| 531 | <td class="mlabels-left"> | |
| 532 | <table class="memname"> | |
| 533 | <tr> | |
| 534 | <td class="memname">bool IsoSpec::PrecalculatedMarginal::inRange </td> | |
| 535 | <td>(</td> | |
| 536 | <td class="paramtype">unsigned int </td> | |
| 537 | <td class="paramname"><em>idx</em></td><td>)</td> | |
| 538 | <td> const</td> | |
| 539 | </tr> | |
| 540 | </table> | |
| 541 | </td> | |
| 542 | <td class="mlabels-right"> | |
| 543 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 544 | </tr> | |
| 545 | </table> | |
| 546 | </div><div class="memdoc"> | |
| 547 | ||
| 548 | <p>Is there a subisotopologue with a given number? </p> | |
| 549 | <dl class="section return"><dt>Returns</dt><dd>Returns true if idx does not exceed the number of pre-computed configurations. </dd></dl> | |
| 550 | ||
| 551 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00247">247</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 552 | ||
| 553 | </div> | |
| 554 | </div> | |
| 555 | <hr/>The documentation for this class was generated from the following files:<ul> | |
| 556 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a></li> | |
| 557 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a></li> | |
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| 69 | <div id="nav-path" class="navpath"> | |
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| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_reverse_order.html">ReverseOrder</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::ReverseOrder< T > Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_reverse_order.html">IsoSpec::ReverseOrder< T ></a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>operator()</b>(const T a, const T b) const (defined in <a class="el" href="class_iso_spec_1_1_reverse_order.html">IsoSpec::ReverseOrder< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_reverse_order.html">IsoSpec::ReverseOrder< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>ReverseOrder</b>() (defined in <a class="el" href="class_iso_spec_1_1_reverse_order.html">IsoSpec::ReverseOrder< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_reverse_order.html">IsoSpec::ReverseOrder< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 92 | </html> |
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| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
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| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_reverse_order.html">ReverseOrder</a></li> </ul> | |
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| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_reverse_order-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::ReverseOrder< T > Class Template Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a350cba89162d701a0f0f4cf1e4424e44"><td class="memItemLeft" align="right" valign="top"><a id="a350cba89162d701a0f0f4cf1e4424e44"></a> | |
| 86 | bool </td><td class="memItemRight" valign="bottom"><b>operator()</b> (const T a, const T b) const</td></tr> | |
| 87 | <tr class="separator:a350cba89162d701a0f0f4cf1e4424e44"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | </table> | |
| 89 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 90 | <div class="textblock"><h3>template<typename T><br /> | |
| 91 | class IsoSpec::ReverseOrder< T ></h3> | |
| 92 | ||
| 93 | ||
| 94 | <p class="definition">Definition at line <a class="el" href="operators_8h_source.html#l00106">106</a> of file <a class="el" href="operators_8h_source.html">operators.h</a>.</p> | |
| 95 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 96 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8h_source.html">operators.h</a></li> | |
| 97 | </ul> | |
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| 104 | </small></address> | |
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| 106 | </html> |
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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_s_summator.html">SSummator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::SSummator Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_s_summator.html">IsoSpec::SSummator</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>add</b>(double x) (defined in <a class="el" href="class_iso_spec_1_1_s_summator.html">IsoSpec::SSummator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_s_summator.html">IsoSpec::SSummator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>get</b>() (defined in <a class="el" href="class_iso_spec_1_1_s_summator.html">IsoSpec::SSummator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_s_summator.html">IsoSpec::SSummator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 84 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>SSummator</b>() (defined in <a class="el" href="class_iso_spec_1_1_s_summator.html">IsoSpec::SSummator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_s_summator.html">IsoSpec::SSummator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 85 | <tr bgcolor="#f0f0f0"><td class="entry"><b>SSummator</b>(SSummator &other) (defined in <a class="el" href="class_iso_spec_1_1_s_summator.html">IsoSpec::SSummator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_s_summator.html">IsoSpec::SSummator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 86 | </table></div><!-- contents --> | |
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| 61 | ||
| 62 | <!-- iframe showing the search results (closed by default) --> | |
| 63 | <div id="MSearchResultsWindow"> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_s_summator.html">SSummator</a></li> </ul> | |
| 72 | </div> | |
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| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_s_summator-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::SSummator Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a5173dbb75fb32ad67bf3abd1ae6f9dc6"><td class="memItemLeft" align="right" valign="top"><a id="a5173dbb75fb32ad67bf3abd1ae6f9dc6"></a> | |
| 86 |  </td><td class="memItemRight" valign="bottom"><b>SSummator</b> (<a class="el" href="class_iso_spec_1_1_s_summator.html">SSummator</a> &other)</td></tr> | |
| 87 | <tr class="separator:a5173dbb75fb32ad67bf3abd1ae6f9dc6"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:aad1c7ce5e38ce2da7d9e39f43e647402"><td class="memItemLeft" align="right" valign="top"><a id="aad1c7ce5e38ce2da7d9e39f43e647402"></a> | |
| 89 | void </td><td class="memItemRight" valign="bottom"><b>add</b> (double x)</td></tr> | |
| 90 | <tr class="separator:aad1c7ce5e38ce2da7d9e39f43e647402"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | <tr class="memitem:ab7b2c53b5e9258aa4c7e7707089fbb6a"><td class="memItemLeft" align="right" valign="top"><a id="ab7b2c53b5e9258aa4c7e7707089fbb6a"></a> | |
| 92 | double </td><td class="memItemRight" valign="bottom"><b>get</b> ()</td></tr> | |
| 93 | <tr class="separator:ab7b2c53b5e9258aa4c7e7707089fbb6a"><td class="memSeparator" colspan="2"> </td></tr> | |
| 94 | </table> | |
| 95 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 96 | <div class="textblock"> | |
| 97 | <p class="definition">Definition at line <a class="el" href="summator_8h_source.html#l00025">25</a> of file <a class="el" href="summator_8h_source.html">summator.h</a>.</p> | |
| 98 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 99 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="summator_8h_source.html">summator.h</a></li> | |
| 100 | </ul> | |
| 101 | </div><!-- contents --> | |
| 102 | <!-- start footer part --> | |
| 103 | <hr class="footer"/><address class="footer"><small> | |
| 104 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 105 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 106 | </a> 1.8.14 | |
| 107 | </small></address> | |
| 108 | </body> | |
| 109 | </html> |
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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
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| 39 | <!-- Generated by Doxygen 1.8.14 --> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_summator.html">Summator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::Summator Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>add</b>(double what) (defined in <a class="el" href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>get</b>() (defined in <a class="el" href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 84 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>Summator</b>() (defined in <a class="el" href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 85 | </table></div><!-- contents --> | |
| 86 | <!-- start footer part --> | |
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| 88 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 89 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 90 | </a> 1.8.14 | |
| 91 | </small></address> | |
| 92 | </body> | |
| 93 | </html> |
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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
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| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
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| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::Summator Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a1b032359eb84e5788ab31c3ad3932008"><td class="memItemLeft" align="right" valign="top"><a id="a1b032359eb84e5788ab31c3ad3932008"></a> | |
| 86 | void </td><td class="memItemRight" valign="bottom"><b>add</b> (double what)</td></tr> | |
| 87 | <tr class="separator:a1b032359eb84e5788ab31c3ad3932008"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:a87f3249839e99b41d3c16aeed75204fa"><td class="memItemLeft" align="right" valign="top"><a id="a87f3249839e99b41d3c16aeed75204fa"></a> | |
| 89 | double </td><td class="memItemRight" valign="bottom"><b>get</b> ()</td></tr> | |
| 90 | <tr class="separator:a87f3249839e99b41d3c16aeed75204fa"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | </table> | |
| 92 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 93 | <div class="textblock"> | |
| 94 | <p class="definition">Definition at line <a class="el" href="summator_8h_source.html#l00076">76</a> of file <a class="el" href="summator_8h_source.html">summator.h</a>.</p> | |
| 95 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 96 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="summator_8h_source.html">summator.h</a></li> | |
| 97 | </ul> | |
| 98 | </div><!-- contents --> | |
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| 101 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 102 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 103 | </a> 1.8.14 | |
| 104 | </small></address> | |
| 105 | </body> | |
| 106 | </html> |
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| 25 | <table cellspacing="0" cellpadding="0"> | |
| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
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| 33 | </td> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_sync_marginal.html">SyncMarginal</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::SyncMarginal Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>allocator</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 85 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 86 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>configurations</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 87 | <tr bgcolor="#f0f0f0"><td class="entry"><b>confs</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 88 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>counter</b> (defined in <a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 89 | <tr bgcolor="#f0f0f0"><td class="entry"><b>eProbs</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 90 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff">get_conf</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 91 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">get_eProb</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 92 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 93 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">get_lProb</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 94 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">get_lProbs_ptr</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 95 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">get_mass</a>(int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 96 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a9a768b90299ea16c447a392dbe1123b5">get_masses_ptr</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 97 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">get_no_confs</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 98 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 99 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 100 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a1bef0f9020a436652628244533cca61b">getModeEProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 101 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 102 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 103 | <tr bgcolor="#f0f0f0"><td class="entry"><b>getNextConfIdx</b>() (defined in <a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 104 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>getNextConfIdxwMass</b>(double mmin, double mmax) (defined in <a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 105 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a>() const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 106 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a942b30ace039f80c50125360be4ed4d2">inRange</a>(unsigned int idx) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 107 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 108 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 109 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a>(Conf conf) const</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 110 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>lProbs</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 111 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a>(const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 112 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>Marginal</b>(Marginal &other)=delete (defined in <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 113 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e">Marginal</a>(Marginal &&other)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 114 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>masses</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 115 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 116 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a7cd29141c34e293f0e3257d73baab0ac">mode_eprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 117 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 118 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 119 | <tr bgcolor="#f0f0f0"><td class="entry"><b>no_confs</b> (defined in <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 120 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>operator=</b>(const Marginal &other)=delete (defined in <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"></td></tr> | |
| 121 | <tr bgcolor="#f0f0f0"><td class="entry"><b>padding</b> (defined in <a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 122 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>padding2</b> (defined in <a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 123 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">PrecalculatedMarginal</a>(Marginal &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"></td></tr> | |
| 124 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a></td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">protected</span></td></tr> | |
| 125 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_sync_marginal.html#a81bb7f17ae1f2618813cf02e4d2b2f8c">SyncMarginal</a>(Marginal &&m, double lCutOff, int tabSize=1000, int hashSize=1000)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_sync_marginal.html">IsoSpec::SyncMarginal</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 126 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 127 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8">~PrecalculatedMarginal</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr> | |
| 128 | </table></div><!-- contents --> | |
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| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_sync_marginal.html">SyncMarginal</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="#pro-attribs">Protected Attributes</a> | | |
| 78 | <a href="class_iso_spec_1_1_sync_marginal-members.html">List of all members</a> </div> | |
| 79 | <div class="headertitle"> | |
| 80 | <div class="title">IsoSpec::SyncMarginal Class Reference</div> </div> | |
| 81 | </div><!--header--> | |
| 82 | <div class="contents"> | |
| 83 | ||
| 84 | <p>Big experiment for multi-threaded version of the algorithm, do not touch. | |
| 85 | <a href="class_iso_spec_1_1_sync_marginal.html#details">More...</a></p> | |
| 86 | ||
| 87 | <p><code>#include <<a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>></code></p> | |
| 88 | <div class="dynheader"> | |
| 89 | Inheritance diagram for IsoSpec::SyncMarginal:</div> | |
| 90 | <div class="dyncontent"> | |
| 91 | <div class="center"> | |
| 92 | <img src="class_iso_spec_1_1_sync_marginal.png" usemap="#IsoSpec::SyncMarginal_map" alt=""/> | |
| 93 | <map id="IsoSpec::SyncMarginal_map" name="IsoSpec::SyncMarginal_map"> | |
| 94 | <area href="class_iso_spec_1_1_precalculated_marginal.html" title="Precalculated Marginal class. " alt="IsoSpec::PrecalculatedMarginal" shape="rect" coords="0,56,191,80"/> | |
| 95 | <area href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). " alt="IsoSpec::Marginal" shape="rect" coords="0,0,191,24"/> | |
| 96 | </map> | |
| 97 | </div></div> | |
| 98 | <table class="memberdecls"> | |
| 99 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 100 | Public Member Functions</h2></td></tr> | |
| 101 | <tr class="memitem:a81bb7f17ae1f2618813cf02e4d2b2f8c"><td class="memItemLeft" align="right" valign="top"><a id="a81bb7f17ae1f2618813cf02e4d2b2f8c"></a> | |
| 102 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_sync_marginal.html#a81bb7f17ae1f2618813cf02e4d2b2f8c">SyncMarginal</a> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &&m, double lCutOff, int tabSize=1000, int hashSize=1000)</td></tr> | |
| 103 | <tr class="memdesc:a81bb7f17ae1f2618813cf02e4d2b2f8c"><td class="mdescLeft"> </td><td class="mdescRight">likewise... <br /></td></tr> | |
| 104 | <tr class="separator:a81bb7f17ae1f2618813cf02e4d2b2f8c"><td class="memSeparator" colspan="2"> </td></tr> | |
| 105 | <tr class="memitem:a2029b97d45da908ab2ee9a1a0d72cbd3"><td class="memItemLeft" align="right" valign="top"><a id="a2029b97d45da908ab2ee9a1a0d72cbd3"></a> | |
| 106 | unsigned int </td><td class="memItemRight" valign="bottom"><b>getNextConfIdx</b> ()</td></tr> | |
| 107 | <tr class="separator:a2029b97d45da908ab2ee9a1a0d72cbd3"><td class="memSeparator" colspan="2"> </td></tr> | |
| 108 | <tr class="memitem:ad52b7503991e3378cb5f645e6a45b665"><td class="memItemLeft" align="right" valign="top"><a id="ad52b7503991e3378cb5f645e6a45b665"></a> | |
| 109 | unsigned int </td><td class="memItemRight" valign="bottom"><b>getNextConfIdxwMass</b> (double mmin, double mmax)</td></tr> | |
| 110 | <tr class="separator:ad52b7503991e3378cb5f645e6a45b665"><td class="memSeparator" colspan="2"> </td></tr> | |
| 111 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_precalculated_marginal"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_precalculated_marginal')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td></tr> | |
| 112 | <tr class="memitem:acb84bd7ba582847655c55bd64d64463e inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">PrecalculatedMarginal</a> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000)</td></tr> | |
| 113 | <tr class="memdesc:acb84bd7ba582847655c55bd64d64463e inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The move constructor (disowns the <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a>). <a href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">More...</a><br /></td></tr> | |
| 114 | <tr class="separator:acb84bd7ba582847655c55bd64d64463e inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 115 | <tr class="memitem:a6b7b30cfe90ffba1d2c9d2f0d87107d8 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a6b7b30cfe90ffba1d2c9d2f0d87107d8"></a> | |
| 116 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8">~PrecalculatedMarginal</a> ()</td></tr> | |
| 117 | <tr class="memdesc:a6b7b30cfe90ffba1d2c9d2f0d87107d8 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 118 | <tr class="separator:a6b7b30cfe90ffba1d2c9d2f0d87107d8 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 119 | <tr class="memitem:a942b30ace039f80c50125360be4ed4d2 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a942b30ace039f80c50125360be4ed4d2">inRange</a> (unsigned int idx) const</td></tr> | |
| 120 | <tr class="memdesc:a942b30ace039f80c50125360be4ed4d2 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Is there a subisotopologue with a given number? <a href="class_iso_spec_1_1_precalculated_marginal.html#a942b30ace039f80c50125360be4ed4d2">More...</a><br /></td></tr> | |
| 121 | <tr class="separator:a942b30ace039f80c50125360be4ed4d2 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 122 | <tr class="memitem:a07eee6d60635c9c1d6f92c181994e06a inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top">const double & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">get_lProb</a> (int idx) const</td></tr> | |
| 123 | <tr class="memdesc:a07eee6d60635c9c1d6f92c181994e06a inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the idx-th subisotopologue. <a href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">More...</a><br /></td></tr> | |
| 124 | <tr class="separator:a07eee6d60635c9c1d6f92c181994e06a inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 125 | <tr class="memitem:a7a38a567eadf16fa2ad41e81c8f55c02 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top">const double & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">get_eProb</a> (int idx) const</td></tr> | |
| 126 | <tr class="memdesc:a7a38a567eadf16fa2ad41e81c8f55c02 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the probability of the idx-th subisotopologue. <a href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">More...</a><br /></td></tr> | |
| 127 | <tr class="separator:a7a38a567eadf16fa2ad41e81c8f55c02 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 128 | <tr class="memitem:ada12caa2e195c1a16c5158a428ea3ed2 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top">const double & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">get_mass</a> (int idx) const</td></tr> | |
| 129 | <tr class="memdesc:ada12caa2e195c1a16c5158a428ea3ed2 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the idx-th subisotopologue. <a href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">More...</a><br /></td></tr> | |
| 130 | <tr class="separator:ada12caa2e195c1a16c5158a428ea3ed2 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 131 | <tr class="memitem:af5d01500c7efb8cba57399ba11fc7124 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top">const double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">get_lProbs_ptr</a> () const</td></tr> | |
| 132 | <tr class="memdesc:af5d01500c7efb8cba57399ba11fc7124 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the table of the log-probabilities of subisotopologues. <a href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">More...</a><br /></td></tr> | |
| 133 | <tr class="separator:af5d01500c7efb8cba57399ba11fc7124 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 134 | <tr class="memitem:a9a768b90299ea16c447a392dbe1123b5 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top">const double * </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a9a768b90299ea16c447a392dbe1123b5">get_masses_ptr</a> () const</td></tr> | |
| 135 | <tr class="memdesc:a9a768b90299ea16c447a392dbe1123b5 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the table of the masses of subisotopologues. <a href="class_iso_spec_1_1_precalculated_marginal.html#a9a768b90299ea16c447a392dbe1123b5">More...</a><br /></td></tr> | |
| 136 | <tr class="separator:a9a768b90299ea16c447a392dbe1123b5 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 137 | <tr class="memitem:a3ecbbf1263a274cc8e3bc71cd96f0bff inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top">const Conf & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff">get_conf</a> (int idx) const</td></tr> | |
| 138 | <tr class="memdesc:a3ecbbf1263a274cc8e3bc71cd96f0bff inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the counts of isotopes that define the subisotopologue. <a href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff">More...</a><br /></td></tr> | |
| 139 | <tr class="separator:a3ecbbf1263a274cc8e3bc71cd96f0bff inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 140 | <tr class="memitem:a0dbf1ec53eac9953a354c11e1b0803f9 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">get_no_confs</a> () const</td></tr> | |
| 141 | <tr class="memdesc:a0dbf1ec53eac9953a354c11e1b0803f9 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of precomputed subisotopologues. <a href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">More...</a><br /></td></tr> | |
| 142 | <tr class="separator:a0dbf1ec53eac9953a354c11e1b0803f9 inherit pub_methods_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 143 | <tr class="inherit_header pub_methods_class_iso_spec_1_1_marginal"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_iso_spec_1_1_marginal')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td></tr> | |
| 144 | <tr class="memitem:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a> (const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</td></tr> | |
| 145 | <tr class="memdesc:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Class constructor. <a href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">More...</a><br /></td></tr> | |
| 146 | <tr class="separator:a46be0c1cf5b169a54056997ba404183c inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 147 | <tr class="memitem:a02e8f92f8f9add352840f5dba8de5e06 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a02e8f92f8f9add352840f5dba8de5e06"></a> | |
| 148 |  </td><td class="memItemRight" valign="bottom"><b>Marginal</b> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &other)=delete</td></tr> | |
| 149 | <tr class="separator:a02e8f92f8f9add352840f5dba8de5e06 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 150 | <tr class="memitem:a9120cad240058afc3705951d80d28a10 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a9120cad240058afc3705951d80d28a10"></a> | |
| 151 | <a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> & </td><td class="memItemRight" valign="bottom"><b>operator=</b> (const <a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &other)=delete</td></tr> | |
| 152 | <tr class="separator:a9120cad240058afc3705951d80d28a10 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 153 | <tr class="memitem:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="ad60fff17fa2c68ea2cd7f183a635379e"></a> | |
| 154 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e">Marginal</a> (<a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> &&other)</td></tr> | |
| 155 | <tr class="memdesc:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Move constructor. <br /></td></tr> | |
| 156 | <tr class="separator:ad60fff17fa2c68ea2cd7f183a635379e inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 157 | <tr class="memitem:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top"><a id="ad44004fa1e83c4a53d431ca403ce3ae4"></a> | |
| 158 | virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a> ()</td></tr> | |
| 159 | <tr class="memdesc:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <br /></td></tr> | |
| 160 | <tr class="separator:ad44004fa1e83c4a53d431ca403ce3ae4 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 161 | <tr class="memitem:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a> () const</td></tr> | |
| 162 | <tr class="memdesc:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the number of isotopes of the investigated element. <a href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">More...</a><br /></td></tr> | |
| 163 | <tr class="separator:a05aa80c3fa77a0406102731934db1a83 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 164 | <tr class="memitem:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a> () const</td></tr> | |
| 165 | <tr class="memdesc:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the lightest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">More...</a><br /></td></tr> | |
| 166 | <tr class="separator:a8b67c507263973da53e533d804e23ac9 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 167 | <tr class="memitem:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a> () const</td></tr> | |
| 168 | <tr class="memdesc:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the mass of the heaviest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">More...</a><br /></td></tr> | |
| 169 | <tr class="separator:aa5598b4d2b31b5daec1c2bac653d0aff inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 170 | <tr class="memitem:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a> () const</td></tr> | |
| 171 | <tr class="memdesc:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Get the log-probability of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">More...</a><br /></td></tr> | |
| 172 | <tr class="separator:ac9408957145d2aa63af32f6647c8ea49 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 173 | <tr class="memitem:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a> () const</td></tr> | |
| 174 | <tr class="memdesc:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the mass of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">More...</a><br /></td></tr> | |
| 175 | <tr class="separator:ad2121802133075a87f0987dc27d0617f inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 176 | <tr class="memitem:a1bef0f9020a436652628244533cca61b inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a1bef0f9020a436652628244533cca61b">getModeEProb</a> () const</td></tr> | |
| 177 | <tr class="memdesc:a1bef0f9020a436652628244533cca61b inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the probability of the mode subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a1bef0f9020a436652628244533cca61b">More...</a><br /></td></tr> | |
| 178 | <tr class="separator:a1bef0f9020a436652628244533cca61b inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 179 | <tr class="memitem:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a> () const</td></tr> | |
| 180 | <tr class="memdesc:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">The the log-probability of the lightest subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">More...</a><br /></td></tr> | |
| 181 | <tr class="separator:a3f9607f51efcfdac1ca58a1467e3a5dc inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 182 | <tr class="memitem:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a> (Conf conf) const</td></tr> | |
| 183 | <tr class="memdesc:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the log-probability of a given subisotopologue. <a href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">More...</a><br /></td></tr> | |
| 184 | <tr class="separator:a1974bb030ce70178da569214b4b93cb8 inherit pub_methods_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 185 | </table><table class="memberdecls"> | |
| 186 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a> | |
| 187 | Protected Attributes</h2></td></tr> | |
| 188 | <tr class="memitem:a1f01c6fe03bdc15928f577f87764b221"><td class="memItemLeft" align="right" valign="top"><a id="a1f01c6fe03bdc15928f577f87764b221"></a> | |
| 189 | char </td><td class="memItemRight" valign="bottom"><b>padding</b> [64]</td></tr> | |
| 190 | <tr class="separator:a1f01c6fe03bdc15928f577f87764b221"><td class="memSeparator" colspan="2"> </td></tr> | |
| 191 | <tr class="memitem:a88c68e76999fb1e95120172ce050b645"><td class="memItemLeft" align="right" valign="top"><a id="a88c68e76999fb1e95120172ce050b645"></a> | |
| 192 | std::atomic< unsigned int > </td><td class="memItemRight" valign="bottom"><b>counter</b></td></tr> | |
| 193 | <tr class="separator:a88c68e76999fb1e95120172ce050b645"><td class="memSeparator" colspan="2"> </td></tr> | |
| 194 | <tr class="memitem:ad8c8fda5c6d7f772ed814fb318d58a58"><td class="memItemLeft" align="right" valign="top"><a id="ad8c8fda5c6d7f772ed814fb318d58a58"></a> | |
| 195 | char </td><td class="memItemRight" valign="bottom"><b>padding2</b> [64]</td></tr> | |
| 196 | <tr class="separator:ad8c8fda5c6d7f772ed814fb318d58a58"><td class="memSeparator" colspan="2"> </td></tr> | |
| 197 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_precalculated_marginal')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></td></tr> | |
| 198 | <tr class="memitem:adaba0751ea134b2cbd6c3fdf67c327ea inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top"><a id="adaba0751ea134b2cbd6c3fdf67c327ea"></a> | |
| 199 | std::vector< Conf > </td><td class="memItemRight" valign="bottom"><b>configurations</b></td></tr> | |
| 200 | <tr class="separator:adaba0751ea134b2cbd6c3fdf67c327ea inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 201 | <tr class="memitem:a1197bed742b2139243e9dc71cb8fcdfc inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a1197bed742b2139243e9dc71cb8fcdfc"></a> | |
| 202 | Conf * </td><td class="memItemRight" valign="bottom"><b>confs</b></td></tr> | |
| 203 | <tr class="separator:a1197bed742b2139243e9dc71cb8fcdfc inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 204 | <tr class="memitem:ad82d7aef36c946ce4f9bbf3ddac70cd1 inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top"><a id="ad82d7aef36c946ce4f9bbf3ddac70cd1"></a> | |
| 205 | unsigned int </td><td class="memItemRight" valign="bottom"><b>no_confs</b></td></tr> | |
| 206 | <tr class="separator:ad82d7aef36c946ce4f9bbf3ddac70cd1 inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 207 | <tr class="memitem:a94e78eba4ae89c0d6c811d7bc0085684 inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top"><a id="a94e78eba4ae89c0d6c811d7bc0085684"></a> | |
| 208 | double * </td><td class="memItemRight" valign="bottom"><b>masses</b></td></tr> | |
| 209 | <tr class="separator:a94e78eba4ae89c0d6c811d7bc0085684 inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 210 | <tr class="memitem:afd5a4a7b094038f66eda31c6827a66f9 inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top"><a id="afd5a4a7b094038f66eda31c6827a66f9"></a> | |
| 211 | double * </td><td class="memItemRight" valign="bottom"><b>lProbs</b></td></tr> | |
| 212 | <tr class="separator:afd5a4a7b094038f66eda31c6827a66f9 inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 213 | <tr class="memitem:abf3e9faabf5011f75cfb8e89cb3cdcca inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top"><a id="abf3e9faabf5011f75cfb8e89cb3cdcca"></a> | |
| 214 | double * </td><td class="memItemRight" valign="bottom"><b>eProbs</b></td></tr> | |
| 215 | <tr class="separator:abf3e9faabf5011f75cfb8e89cb3cdcca inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 216 | <tr class="memitem:add0495cfc67fd8b9757b93b07d47e6cf inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memItemLeft" align="right" valign="top"><a id="add0495cfc67fd8b9757b93b07d47e6cf"></a> | |
| 217 | <a class="el" href="class_iso_spec_1_1_allocator.html">Allocator</a>< int > </td><td class="memItemRight" valign="bottom"><b>allocator</b></td></tr> | |
| 218 | <tr class="separator:add0495cfc67fd8b9757b93b07d47e6cf inherit pro_attribs_class_iso_spec_1_1_precalculated_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 219 | <tr class="inherit_header pro_attribs_class_iso_spec_1_1_marginal"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_class_iso_spec_1_1_marginal')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></td></tr> | |
| 220 | <tr class="memitem:a8dd6415882661f7b9ceedbe09bc200e3 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a></td></tr> | |
| 221 | <tr class="separator:a8dd6415882661f7b9ceedbe09bc200e3 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 222 | <tr class="memitem:a53c2af7dcb84aa9d5e0e0918fe7875cd inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a></td></tr> | |
| 223 | <tr class="separator:a53c2af7dcb84aa9d5e0e0918fe7875cd inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 224 | <tr class="memitem:a91265e07f5bb65314995f816f5a9c729 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double *const </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a></td></tr> | |
| 225 | <tr class="separator:a91265e07f5bb65314995f816f5a9c729 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 226 | <tr class="memitem:af059df011e707781fdd4c1d7b70bd91a inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double *const </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a></td></tr> | |
| 227 | <tr class="separator:af059df011e707781fdd4c1d7b70bd91a inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 228 | <tr class="memitem:aa3fb5ed3a9b63a855d6270287aed7417 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a></td></tr> | |
| 229 | <tr class="separator:aa3fb5ed3a9b63a855d6270287aed7417 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 230 | <tr class="memitem:a640f3b44605b510ee556a25e35a2e095 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const Conf </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a></td></tr> | |
| 231 | <tr class="separator:a640f3b44605b510ee556a25e35a2e095 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 232 | <tr class="memitem:a38238e7581f59f08d0faf8ab5eabc0dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a></td></tr> | |
| 233 | <tr class="separator:a38238e7581f59f08d0faf8ab5eabc0dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 234 | <tr class="memitem:a3bfea931e5e1ec1e7d90e8e096c38eb7 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a></td></tr> | |
| 235 | <tr class="separator:a3bfea931e5e1ec1e7d90e8e096c38eb7 inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 236 | <tr class="memitem:a7cd29141c34e293f0e3257d73baab0ac inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a7cd29141c34e293f0e3257d73baab0ac">mode_eprob</a></td></tr> | |
| 237 | <tr class="separator:a7cd29141c34e293f0e3257d73baab0ac inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 238 | <tr class="memitem:a2abd05ba9351e21cd99e2783e26bd6dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memItemLeft" align="right" valign="top">const double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a></td></tr> | |
| 239 | <tr class="separator:a2abd05ba9351e21cd99e2783e26bd6dc inherit pro_attribs_class_iso_spec_1_1_marginal"><td class="memSeparator" colspan="2"> </td></tr> | |
| 240 | </table> | |
| 241 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 242 | <div class="textblock"><p>Big experiment for multi-threaded version of the algorithm, do not touch. </p> | |
| 243 | ||
| 244 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8h_source.html#l00298">298</a> of file <a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a>.</p> | |
| 245 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 246 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="marginal_trek_09_09_8h_source.html">marginalTrek++.h</a></li> | |
| 247 | </ul> | |
| 248 | </div><!-- contents --> | |
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| 253 | </a> 1.8.14 | |
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| 256 | </html> |
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| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
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| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_t_summator.html">TSummator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::TSummator Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_t_summator.html">IsoSpec::TSummator</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>add</b>(double what) (defined in <a class="el" href="class_iso_spec_1_1_t_summator.html">IsoSpec::TSummator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_t_summator.html">IsoSpec::TSummator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>get</b>() (defined in <a class="el" href="class_iso_spec_1_1_t_summator.html">IsoSpec::TSummator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_t_summator.html">IsoSpec::TSummator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 84 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>TSummator</b>() (defined in <a class="el" href="class_iso_spec_1_1_t_summator.html">IsoSpec::TSummator</a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_t_summator.html">IsoSpec::TSummator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 85 | </table></div><!-- contents --> | |
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| 88 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::TSummator Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
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| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a5645d3fdac4e35f023fe7a08646dc413"><td class="memItemLeft" align="right" valign="top"><a id="a5645d3fdac4e35f023fe7a08646dc413"></a> | |
| 86 | void </td><td class="memItemRight" valign="bottom"><b>add</b> (double what)</td></tr> | |
| 87 | <tr class="separator:a5645d3fdac4e35f023fe7a08646dc413"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:a0db3add5376aae480fcaa3f489898bd7"><td class="memItemLeft" align="right" valign="top"><a id="a0db3add5376aae480fcaa3f489898bd7"></a> | |
| 89 | double </td><td class="memItemRight" valign="bottom"><b>get</b> ()</td></tr> | |
| 90 | <tr class="separator:a0db3add5376aae480fcaa3f489898bd7"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | </table> | |
| 92 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 93 | <div class="textblock"> | |
| 94 | <p class="definition">Definition at line <a class="el" href="summator_8h_source.html#l00099">99</a> of file <a class="el" href="summator_8h_source.html">summator.h</a>.</p> | |
| 95 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 96 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="summator_8h_source.html">summator.h</a></li> | |
| 97 | </ul> | |
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| 69 | <div id="nav-path" class="navpath"> | |
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| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_table_order.html">TableOrder</a></li> </ul> | |
| 72 | </div> | |
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| 74 | <div class="header"> | |
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| 76 | <div class="title">IsoSpec::TableOrder< T > Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_table_order.html">IsoSpec::TableOrder< T ></a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>operator()</b>(unsigned int i, unsigned int j) (defined in <a class="el" href="class_iso_spec_1_1_table_order.html">IsoSpec::TableOrder< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_table_order.html">IsoSpec::TableOrder< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>TableOrder</b>(const T *_tbl) (defined in <a class="el" href="class_iso_spec_1_1_table_order.html">IsoSpec::TableOrder< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_table_order.html">IsoSpec::TableOrder< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
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| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::TableOrder< T > Class Template Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a82a2474a7990bf0a55e269ea2dabada5"><td class="memItemLeft" align="right" valign="top"><a id="a82a2474a7990bf0a55e269ea2dabada5"></a> | |
| 86 |  </td><td class="memItemRight" valign="bottom"><b>TableOrder</b> (const T *_tbl)</td></tr> | |
| 87 | <tr class="separator:a82a2474a7990bf0a55e269ea2dabada5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:a35b990bbb3f8c3ba0551c0938a5145c8"><td class="memItemLeft" align="right" valign="top"><a id="a35b990bbb3f8c3ba0551c0938a5145c8"></a> | |
| 89 | bool </td><td class="memItemRight" valign="bottom"><b>operator()</b> (unsigned int i, unsigned int j)</td></tr> | |
| 90 | <tr class="separator:a35b990bbb3f8c3ba0551c0938a5145c8"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | </table> | |
| 92 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 93 | <div class="textblock"><h3>template<typename T><br /> | |
| 94 | class IsoSpec::TableOrder< T ></h3> | |
| 95 | ||
| 96 | ||
| 97 | <p class="definition">Definition at line <a class="el" href="operators_8h_source.html#l00113">113</a> of file <a class="el" href="operators_8h_source.html">operators.h</a>.</p> | |
| 98 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 99 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="operators_8h_source.html">operators.h</a></li> | |
| 100 | </ul> | |
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| 109 | </html> |
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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_tabulator.html">Tabulator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::Tabulator< T > Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>confs</b>() (defined in <a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 83 | <tr bgcolor="#f0f0f0"><td class="entry"><b>confs_no</b>() (defined in <a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 84 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>lprobs</b>() (defined in <a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 85 | <tr bgcolor="#f0f0f0"><td class="entry"><b>masses</b>() (defined in <a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 86 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>probs</b>() (defined in <a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 87 | <tr bgcolor="#f0f0f0"><td class="entry"><b>Tabulator</b>(T *generator, bool get_masses, bool get_probs, bool get_lprobs, bool get_confs) (defined in <a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a></td><td class="entry"></td></tr> | |
| 88 | <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~Tabulator</b>() (defined in <a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a>)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator< T ></a></td><td class="entry"></td></tr> | |
| 89 | </table></div><!-- contents --> | |
| 90 | <!-- start footer part --> | |
| 91 | <hr class="footer"/><address class="footer"><small> | |
| 92 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 93 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 94 | </a> 1.8.14 | |
| 95 | </small></address> | |
| 96 | </body> | |
| 97 | </html> |
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| 6 | <meta name="viewport" content="width=device-width, initial-scale=1"/> | |
| 7 | <title>IsoSpec: IsoSpec::Tabulator< T > Class Template Reference</title> | |
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| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
| 37 | </div> | |
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| 39 | <!-- Generated by Doxygen 1.8.14 --> | |
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| 62 | <!-- iframe showing the search results (closed by default) --> | |
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| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_tabulator.html">Tabulator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_tabulator-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::Tabulator< T > Class Template Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a57acb4ba7687ac95916c00fd9cd4f4c7"><td class="memItemLeft" align="right" valign="top"><a id="a57acb4ba7687ac95916c00fd9cd4f4c7"></a> | |
| 86 |  </td><td class="memItemRight" valign="bottom"><b>Tabulator</b> (T *generator, bool get_masses, bool get_probs, bool get_lprobs, bool get_confs)</td></tr> | |
| 87 | <tr class="separator:a57acb4ba7687ac95916c00fd9cd4f4c7"><td class="memSeparator" colspan="2"> </td></tr> | |
| 88 | <tr class="memitem:ae256b348fc6c5d24d540c33094a37df9"><td class="memItemLeft" align="right" valign="top"><a id="ae256b348fc6c5d24d540c33094a37df9"></a> | |
| 89 | double * </td><td class="memItemRight" valign="bottom"><b>masses</b> ()</td></tr> | |
| 90 | <tr class="separator:ae256b348fc6c5d24d540c33094a37df9"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | <tr class="memitem:a486be3022d437b81b4932dd61ca4a0e5"><td class="memItemLeft" align="right" valign="top"><a id="a486be3022d437b81b4932dd61ca4a0e5"></a> | |
| 92 | double * </td><td class="memItemRight" valign="bottom"><b>lprobs</b> ()</td></tr> | |
| 93 | <tr class="separator:a486be3022d437b81b4932dd61ca4a0e5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 94 | <tr class="memitem:a0c572de1f59a3c664c55e55760be2f18"><td class="memItemLeft" align="right" valign="top"><a id="a0c572de1f59a3c664c55e55760be2f18"></a> | |
| 95 | double * </td><td class="memItemRight" valign="bottom"><b>probs</b> ()</td></tr> | |
| 96 | <tr class="separator:a0c572de1f59a3c664c55e55760be2f18"><td class="memSeparator" colspan="2"> </td></tr> | |
| 97 | <tr class="memitem:a8000f897020376b6a03fb75dafb997f1"><td class="memItemLeft" align="right" valign="top"><a id="a8000f897020376b6a03fb75dafb997f1"></a> | |
| 98 | int * </td><td class="memItemRight" valign="bottom"><b>confs</b> ()</td></tr> | |
| 99 | <tr class="separator:a8000f897020376b6a03fb75dafb997f1"><td class="memSeparator" colspan="2"> </td></tr> | |
| 100 | <tr class="memitem:acdbd459f1ec95dfd17cc0617cda02fba"><td class="memItemLeft" align="right" valign="top"><a id="acdbd459f1ec95dfd17cc0617cda02fba"></a> | |
| 101 | size_t </td><td class="memItemRight" valign="bottom"><b>confs_no</b> ()</td></tr> | |
| 102 | <tr class="separator:acdbd459f1ec95dfd17cc0617cda02fba"><td class="memSeparator" colspan="2"> </td></tr> | |
| 103 | </table> | |
| 104 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 105 | <div class="textblock"><h3>template<typename T><br /> | |
| 106 | class IsoSpec::Tabulator< T ></h3> | |
| 107 | ||
| 108 | ||
| 109 | <p class="definition">Definition at line <a class="el" href="tabulator_8h_source.html#l00012">12</a> of file <a class="el" href="tabulator_8h_source.html">tabulator.h</a>.</p> | |
| 110 | </div><hr/>The documentation for this class was generated from the following file:<ul> | |
| 111 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="tabulator_8h_source.html">tabulator.h</a></li> | |
| 112 | </ul> | |
| 113 | </div><!-- contents --> | |
| 114 | <!-- start footer part --> | |
| 115 | <hr class="footer"/><address class="footer"><small> | |
| 116 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 117 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 118 | </a> 1.8.14 | |
| 119 | </small></address> | |
| 120 | </body> | |
| 121 | </html> |
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| 6 | <meta name="viewport" content="width=device-width, initial-scale=1"/> | |
| 7 | <title>IsoSpec: Member List</title> | |
| 8 | <link href="tabs.css" rel="stylesheet" type="text/css"/> | |
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| 21 | </head> | |
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| 23 | <div id="top"><!-- do not remove this div, it is closed by doxygen! --> | |
| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
| 37 | </div> | |
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| 39 | <!-- Generated by Doxygen 1.8.14 --> | |
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| 51 | $(document).ready(function() { init_search(); }); | |
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| 53 | /* @license-end */</script> | |
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| 55 | <!-- window showing the filter options --> | |
| 56 | <div id="MSearchSelectWindow" | |
| 57 | onmouseover="return searchBox.OnSearchSelectShow()" | |
| 58 | onmouseout="return searchBox.OnSearchSelectHide()" | |
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| 61 | ||
| 62 | <!-- iframe showing the search results (closed by default) --> | |
| 63 | <div id="MSearchResultsWindow"> | |
| 64 | <iframe src="javascript:void(0)" frameborder="0" | |
| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_thread_summator.html">ThreadSummator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">IsoSpec::ThreadSummator Member List</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | ||
| 80 | <p>This is the complete list of members for <a class="el" href="class_iso_spec_1_1_thread_summator.html">IsoSpec::ThreadSummator</a>, including all inherited members.</p> | |
| 81 | <table class="directory"> | |
| 82 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_thread_summator.html#a744c019ec413dcc8cf8a93d9f3009f21">add</a>(double what)</td><td class="entry"><a class="el" href="class_iso_spec_1_1_thread_summator.html">IsoSpec::ThreadSummator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 83 | <tr><td class="entry"><a class="el" href="class_iso_spec_1_1_thread_summator.html#a55e0601a6f9722b0c2ca7e0394dc00b8">get</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_thread_summator.html">IsoSpec::ThreadSummator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 84 | <tr class="even"><td class="entry"><a class="el" href="class_iso_spec_1_1_thread_summator.html#a81c6246b37dd7f07071d4d561132beae">ThreadSummator</a>()</td><td class="entry"><a class="el" href="class_iso_spec_1_1_thread_summator.html">IsoSpec::ThreadSummator</a></td><td class="entry"><span class="mlabel">inline</span></td></tr> | |
| 85 | </table></div><!-- contents --> | |
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| 88 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 90 | </a> 1.8.14 | |
| 91 | </small></address> | |
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| 93 | </html> |
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| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
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| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
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| 56 | <div id="MSearchSelectWindow" | |
| 57 | onmouseover="return searchBox.OnSearchSelectShow()" | |
| 58 | onmouseout="return searchBox.OnSearchSelectHide()" | |
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| 62 | <!-- iframe showing the search results (closed by default) --> | |
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| 65 | name="MSearchResults" id="MSearchResults"> | |
| 66 | </iframe> | |
| 67 | </div> | |
| 68 | ||
| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="namespace_iso_spec.html">IsoSpec</a></li><li class="navelem"><a class="el" href="class_iso_spec_1_1_thread_summator.html">ThreadSummator</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="summary"> | |
| 76 | <a href="#pub-methods">Public Member Functions</a> | | |
| 77 | <a href="class_iso_spec_1_1_thread_summator-members.html">List of all members</a> </div> | |
| 78 | <div class="headertitle"> | |
| 79 | <div class="title">IsoSpec::ThreadSummator Class Reference</div> </div> | |
| 80 | </div><!--header--> | |
| 81 | <div class="contents"> | |
| 82 | <table class="memberdecls"> | |
| 83 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a> | |
| 84 | Public Member Functions</h2></td></tr> | |
| 85 | <tr class="memitem:a81c6246b37dd7f07071d4d561132beae"><td class="memItemLeft" align="right" valign="top"><a id="a81c6246b37dd7f07071d4d561132beae"></a> | |
| 86 |  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_thread_summator.html#a81c6246b37dd7f07071d4d561132beae">ThreadSummator</a> ()</td></tr> | |
| 87 | <tr class="memdesc:a81c6246b37dd7f07071d4d561132beae"><td class="mdescLeft"> </td><td class="mdescRight">Constructor (sum defaults to zero). <br /></td></tr> | |
| 88 | <tr class="separator:a81c6246b37dd7f07071d4d561132beae"><td class="memSeparator" colspan="2"> </td></tr> | |
| 89 | <tr class="memitem:a744c019ec413dcc8cf8a93d9f3009f21"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_thread_summator.html#a744c019ec413dcc8cf8a93d9f3009f21">add</a> (double what)</td></tr> | |
| 90 | <tr class="memdesc:a744c019ec413dcc8cf8a93d9f3009f21"><td class="mdescLeft"> </td><td class="mdescRight">Add a number to the existing sum. <a href="#a744c019ec413dcc8cf8a93d9f3009f21">More...</a><br /></td></tr> | |
| 91 | <tr class="separator:a744c019ec413dcc8cf8a93d9f3009f21"><td class="memSeparator" colspan="2"> </td></tr> | |
| 92 | <tr class="memitem:a55e0601a6f9722b0c2ca7e0394dc00b8"><td class="memItemLeft" align="right" valign="top"><a id="a55e0601a6f9722b0c2ca7e0394dc00b8"></a> | |
| 93 | double </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_thread_summator.html#a55e0601a6f9722b0c2ca7e0394dc00b8">get</a> ()</td></tr> | |
| 94 | <tr class="memdesc:a55e0601a6f9722b0c2ca7e0394dc00b8"><td class="mdescLeft"> </td><td class="mdescRight">Get the current value of the sum of the added floating point numbers. <br /></td></tr> | |
| 95 | <tr class="separator:a55e0601a6f9722b0c2ca7e0394dc00b8"><td class="memSeparator" colspan="2"> </td></tr> | |
| 96 | </table> | |
| 97 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 98 | <div class="textblock"> | |
| 99 | <p class="definition">Definition at line <a class="el" href="summator_8h_source.html#l00139">139</a> of file <a class="el" href="summator_8h_source.html">summator.h</a>.</p> | |
| 100 | </div><h2 class="groupheader">Member Function Documentation</h2> | |
| 101 | <a id="a744c019ec413dcc8cf8a93d9f3009f21"></a> | |
| 102 | <h2 class="memtitle"><span class="permalink"><a href="#a744c019ec413dcc8cf8a93d9f3009f21">◆ </a></span>add()</h2> | |
| 103 | ||
| 104 | <div class="memitem"> | |
| 105 | <div class="memproto"> | |
| 106 | <table class="mlabels"> | |
| 107 | <tr> | |
| 108 | <td class="mlabels-left"> | |
| 109 | <table class="memname"> | |
| 110 | <tr> | |
| 111 | <td class="memname">void IsoSpec::ThreadSummator::add </td> | |
| 112 | <td>(</td> | |
| 113 | <td class="paramtype">double </td> | |
| 114 | <td class="paramname"><em>what</em></td><td>)</td> | |
| 115 | <td></td> | |
| 116 | </tr> | |
| 117 | </table> | |
| 118 | </td> | |
| 119 | <td class="mlabels-right"> | |
| 120 | <span class="mlabels"><span class="mlabel">inline</span></span> </td> | |
| 121 | </tr> | |
| 122 | </table> | |
| 123 | </div><div class="memdoc"> | |
| 124 | ||
| 125 | <p>Add a number to the existing sum. </p> | |
| 126 | <dl class="params"><dt>Parameters</dt><dd> | |
| 127 | <table class="params"> | |
| 128 | <tr><td class="paramname">x</td><td>A double floating point number to add. </td></tr> | |
| 129 | </table> | |
| 130 | </dd> | |
| 131 | </dl> | |
| 132 | ||
| 133 | <p class="definition">Definition at line <a class="el" href="summator_8h_source.html#l00151">151</a> of file <a class="el" href="summator_8h_source.html">summator.h</a>.</p> | |
| 134 | ||
| 135 | </div> | |
| 136 | </div> | |
| 137 | <hr/>The documentation for this class was generated from the following file:<ul> | |
| 138 | <li>/Users/matteo/Projects/isospec/IsoSpec/IsoSpec++/<a class="el" href="summator_8h_source.html">summator.h</a></li> | |
| 139 | </ul> | |
| 140 | </div><!-- contents --> | |
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| 143 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 145 | </a> 1.8.14 | |
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| 74 | <div class="contents"> | |
| 75 | <div class="qindex"><a class="qindex" href="#letter_a">a</a> | <a class="qindex" href="#letter_c">c</a> | <a class="qindex" href="#letter_d">d</a> | <a class="qindex" href="#letter_i">i</a> | <a class="qindex" href="#letter_k">k</a> | <a class="qindex" href="#letter_m">m</a> | <a class="qindex" href="#letter_o">o</a> | <a class="qindex" href="#letter_p">p</a> | <a class="qindex" href="#letter_r">r</a> | <a class="qindex" href="#letter_s">s</a> | <a class="qindex" href="#letter_t">t</a></div> | |
| 76 | <table class="classindex"> | |
| 77 | <tr><td rowspan="2" valign="bottom"><a name="letter_a"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  a  </div></td></tr></table> | |
| 78 | </td><td rowspan="2" valign="bottom"><a name="letter_d"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  d  </div></td></tr></table> | |
| 79 | </td><td valign="top"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_p"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  p  </div></td></tr></table> | |
| 80 | </td><td valign="top"><a class="el" href="class_iso_spec_1_1_summator.html">Summator</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td></tr> | |
| 81 | <tr><td rowspan="2" valign="bottom"><a name="letter_k"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  k  </div></td></tr></table> | |
| 82 | </td><td rowspan="2" valign="bottom"><a name="letter_t"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  t  </div></td></tr></table> | |
| 83 | </td></tr> | |
| 84 | <tr><td valign="top"><a class="el" href="class_iso_spec_1_1_allocator.html">Allocator</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td valign="top"><a class="el" href="class_iso_spec_1_1_dirty_allocator.html">DirtyAllocator</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td valign="top"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td></tr> | |
| 85 | <tr><td rowspan="2" valign="bottom"><a name="letter_c"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  c  </div></td></tr></table> | |
| 86 | </td><td rowspan="2" valign="bottom"><a name="letter_i"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  i  </div></td></tr></table> | |
| 87 | </td><td valign="top"><a class="el" href="class_iso_spec_1_1_key_hasher.html">KeyHasher</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_r"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  r  </div></td></tr></table> | |
| 88 | </td><td valign="top"><a class="el" href="class_iso_spec_1_1_table_order.html">TableOrder</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td></tr> | |
| 89 | <tr><td rowspan="2" valign="bottom"><a name="letter_m"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  m  </div></td></tr></table> | |
| 90 | </td><td valign="top"><a class="el" href="class_iso_spec_1_1_tabulator.html">Tabulator</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td></tr> | |
| 91 | <tr><td valign="top"><a class="el" href="class_iso_spec_1_1_conf_equal.html">ConfEqual</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td valign="top"><a class="el" href="class_iso_spec_1_1_iso.html">Iso</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td valign="top"><a class="el" href="class_iso_spec_1_1_reverse_order.html">ReverseOrder</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td valign="top"><a class="el" href="class_iso_spec_1_1_t_summator.html">TSummator</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td></tr> | |
| 92 | <tr><td valign="top"><a class="el" href="class_iso_spec_1_1_conf_order.html">ConfOrder</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td valign="top"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td valign="top"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_s"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  s  </div></td></tr></table> | |
| 93 | </td><td></td></tr> | |
| 94 | <tr><td valign="top"><a class="el" href="class_iso_spec_1_1_conf_order_marginal.html">ConfOrderMarginal</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td valign="top"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoLayeredGenerator</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td valign="top"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">MarginalTrek</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td></td></tr> | |
| 95 | <tr><td valign="top"><a class="el" href="class_iso_spec_1_1_conf_order_marginal_descending.html">ConfOrderMarginalDescending</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td valign="top"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoOrderedGenerator</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_o"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  o  </div></td></tr></table> | |
| 96 | </td><td valign="top"><a class="el" href="class_iso_spec_1_1_s_summator.html">SSummator</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td></td></tr> | |
| 97 | <tr><td></td><td></td><td></td><td></td></tr> | |
| 98 | <tr><td></td><td></td><td valign="top"><a class="el" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">OrderMarginalsBySizeDecresing</a> (<a class="el" href="namespace_iso_spec.html">IsoSpec</a>)   </td><td></td><td></td></tr> | |
| 99 | <tr><td></td><td></td><td></td><td></td><td></td></tr> | |
| 100 | </table> | |
| 101 | <div class="qindex"><a class="qindex" href="#letter_a">a</a> | <a class="qindex" href="#letter_c">c</a> | <a class="qindex" href="#letter_d">d</a> | <a class="qindex" href="#letter_i">i</a> | <a class="qindex" href="#letter_k">k</a> | <a class="qindex" href="#letter_m">m</a> | <a class="qindex" href="#letter_o">o</a> | <a class="qindex" href="#letter_p">p</a> | <a class="qindex" href="#letter_r">r</a> | <a class="qindex" href="#letter_s">s</a> | <a class="qindex" href="#letter_t">t</a></div> | |
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| 72 | </div> | |
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| 76 | <div class="title">conf.h</div> </div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> {</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="keyword">typedef</span> <span class="keywordtype">int</span>* Conf;</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> </div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> }</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 76 | <div class="title">cwrapper.cpp</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> </div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <tuple></span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <string.h></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <iostream></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <algorithm></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <stdexcept></span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#include "cwrapper.h"</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#include "misc.h"</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#include "marginalTrek++.h"</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#include "isoSpec++.h"</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor">#include "tabulator.h"</span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keyword">using namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a>;</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> </div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="keyword">extern</span> <span class="stringliteral">"C"</span></div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> {</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="keywordtype">void</span> * setupIso(<span class="keywordtype">int</span> dimNumber,</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>* isotopeNumbers,</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>* atomCounts,</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* isotopeMasses,</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* isotopeProbabilities)</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> {</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>** IM = <span class="keyword">new</span> <span class="keyword">const</span> <span class="keywordtype">double</span>*[dimNumber];</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>** IP = <span class="keyword">new</span> <span class="keyword">const</span> <span class="keywordtype">double</span>*[dimNumber];</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordtype">int</span> idx = 0;</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=0; i<dimNumber; i++)</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  {</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  IM[i] = &isotopeMasses[idx];</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  IP[i] = &isotopeProbabilities[idx];</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  idx += isotopeNumbers[i];</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  }</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="comment">//TODO in place (maybe pass a numpy matrix??)</span></div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>* iso = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>(dimNumber, isotopeNumbers, atomCounts, IM, IP);</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keyword">delete</span>[] IM;</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keyword">delete</span>[] IP;</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><span class="keywordtype">void</span>*<span class="keyword">></span>(iso);</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> }</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="keywordtype">void</span> deleteIso(<span class="keywordtype">void</span>* iso)</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span> {</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keyword">delete</span> <span class="keyword">reinterpret_cast<</span><a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>*<span class="keyword">></span>(iso);</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> }</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="preprocessor">#define C_CODE(generatorType, dataType, method)\</span></div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="preprocessor">dataType method##generatorType(void* generator){ return reinterpret_cast<generatorType*>(generator)->method(); }</span></div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="preprocessor">#define C_CODE_GET_CONF_SIGNATURE(generatorType)\</span></div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> <span class="preprocessor">void get_conf_signature##generatorType(void* generator, int* space)\</span></div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="preprocessor">{ reinterpret_cast<generatorType*>(generator)->get_conf_signature(space); }</span></div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="preprocessor">#define DELETE(generatorType) void delete##generatorType(void* generator){ delete reinterpret_cast<generatorType*>(generator); }</span></div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> <span class="preprocessor">#define C_CODES(generatorType)\</span></div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="preprocessor">C_CODE(generatorType, double, mass) \</span></div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <span class="preprocessor">C_CODE(generatorType, double, lprob) \</span></div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> <span class="preprocessor">C_CODE_GET_CONF_SIGNATURE(generatorType) \</span></div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> <span class="preprocessor">C_CODE(generatorType, bool, advanceToNextConfiguration) \</span></div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> <span class="preprocessor">DELETE(generatorType)</span></div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> <span class="comment">//______________________________________________________THRESHOLD GENERATOR</span></div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> <span class="keywordtype">void</span>* setupIsoThresholdGenerator(<span class="keywordtype">void</span>* iso,</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">double</span> threshold,</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordtype">bool</span> _absolute,</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordtype">int</span> _tabSize,</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordtype">int</span> _hashSize)</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span> {</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a>* iso_tmp = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a>(</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  std::move(*reinterpret_cast<Iso*>(iso)),</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  threshold,</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  _absolute,</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  _tabSize,</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  _hashSize);</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><span class="keywordtype">void</span>*<span class="keyword">></span>(iso_tmp);</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> }</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> C_CODES(<a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a>)</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span> </div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span> <span class="comment">//______________________________________________________LAYERED GENERATOR</span></div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span> <span class="keywordtype">void</span>* setupIsoLayeredGenerator(<span class="keywordtype">void</span>* iso,</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">double</span> _target_coverage,</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  <span class="keywordtype">double</span> _percentage_to_expand,</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordtype">int</span> _tabSize,</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordtype">int</span> _hashSize,</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="keywordtype">bool</span> _do_trim)</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span> {</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <a class="code" href="class_iso_spec_1_1_iso_layered_generator.html">IsoLayeredGenerator</a>* iso_tmp = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_iso_layered_generator.html">IsoLayeredGenerator</a>(</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  std::move(*reinterpret_cast<Iso*>(iso)),</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  _target_coverage,</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  _percentage_to_expand,</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  _tabSize,</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  _hashSize,</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  _do_trim);</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> </div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><span class="keywordtype">void</span>*<span class="keyword">></span>(iso_tmp);</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> }</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> C_CODES(<a class="code" href="class_iso_spec_1_1_iso_layered_generator.html">IsoLayeredGenerator</a>)</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span> </div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> <span class="comment">//______________________________________________________ORDERED GENERATOR</span></div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> <span class="keywordtype">void</span>* setupIsoOrderedGenerator(<span class="keywordtype">void</span>* iso,</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <span class="keywordtype">int</span> _tabSize,</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordtype">int</span> _hashSize)</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> {</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <a class="code" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoOrderedGenerator</a>* iso_tmp = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoOrderedGenerator</a>(</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  std::move(*reinterpret_cast<Iso*>(iso)),</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  _tabSize,</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  _hashSize);</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span> </div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><span class="keywordtype">void</span>*<span class="keyword">></span>(iso_tmp);</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span> }</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span> C_CODES(<a class="code" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoOrderedGenerator</a>)</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span> <span class="comment">//______________________________________________________ Threshold Tabulator 1.0</span></div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span> <span class="keywordtype">void</span>* setupThresholdTabulator(<span class="keywordtype">void</span>* generator,</div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="keywordtype">bool</span> get_masses,</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keywordtype">bool</span> get_probs,</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordtype">bool</span> get_lprobs,</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  <span class="keywordtype">bool</span> get_confs)</div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span> {</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator<IsoThresholdGenerator></a>* tabulator = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator<IsoThresholdGenerator></a>(<span class="keyword">reinterpret_cast<</span><a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a>*<span class="keyword">></span>(generator),</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  get_masses,</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  get_probs,</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  get_lprobs,</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  get_confs);</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span> </div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><span class="keywordtype">void</span>*<span class="keyword">></span>(tabulator);</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span> }</div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span> </div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span> <span class="keywordtype">void</span> deleteThresholdTabulator(<span class="keywordtype">void</span>* t)</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span> {</div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keyword">delete</span> <span class="keyword">reinterpret_cast<</span><a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator<IsoThresholdGenerator></a>*<span class="keyword">></span>(t);</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span> }</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span> </div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span> <span class="keyword">const</span> <span class="keywordtype">double</span>* massesThresholdTabulator(<span class="keywordtype">void</span>* tabulator)</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span> {</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator<IsoThresholdGenerator></a>*<span class="keyword">></span>(tabulator)->masses();</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span> }</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span> <span class="keyword">const</span> <span class="keywordtype">double</span>* lprobsThresholdTabulator(<span class="keywordtype">void</span>* tabulator)</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span> {</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator<IsoThresholdGenerator></a>*<span class="keyword">></span>(tabulator)->lprobs();</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span> }</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span> </div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span> <span class="keyword">const</span> <span class="keywordtype">double</span>* probsThresholdTabulator(<span class="keywordtype">void</span>* tabulator)</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span> {</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator<IsoThresholdGenerator></a>*<span class="keyword">></span>(tabulator)->probs();</div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span> }</div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span> </div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span> <span class="keyword">const</span> <span class="keywordtype">int</span>* confsThresholdTabulator(<span class="keywordtype">void</span>* tabulator)</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span> {</div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator<IsoThresholdGenerator></a>*<span class="keyword">></span>(tabulator)->confs();</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span> }</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span> </div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span> <span class="keywordtype">int</span> confs_noThresholdTabulator(<span class="keywordtype">void</span>* tabulator)</div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span> {</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator<IsoThresholdGenerator></a>*<span class="keyword">></span>(tabulator)->confs_no();</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span> }</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span> </div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span> </div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span> </div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span> } <span class="comment">//extern "C" ends here</span></div><div class="ttc" id="class_iso_spec_1_1_iso_html"><div class="ttname"><a href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></div><div class="ttdoc">The Iso class for the calculation of the isotopic distribution. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00052">isoSpec++.h:52</a></div></div> | |
| 80 | <div class="ttc" id="class_iso_spec_1_1_iso_layered_generator_html"><div class="ttname"><a href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a></div><div class="ttdoc">The class that represents isotopologues above a given joint probability value. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00383">isoSpec++.h:383</a></div></div> | |
| 81 | <div class="ttc" id="class_iso_spec_1_1_tabulator_html"><div class="ttname"><a href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator</a></div><div class="ttdef"><b>Definition:</b> <a href="tabulator_8h_source.html#l00012">tabulator.h:12</a></div></div> | |
| 82 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></div><div class="ttdoc">The generator of isotopologues above a given threshold value. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00235">isoSpec++.h:235</a></div></div> | |
| 83 | <div class="ttc" id="class_iso_spec_1_1_iso_ordered_generator_html"><div class="ttname"><a href="class_iso_spec_1_1_iso_ordered_generator.html">IsoSpec::IsoOrderedGenerator</a></div><div class="ttdoc">The generator of isotopologues sorted by their probability of occurrence. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00179">isoSpec++.h:179</a></div></div> | |
| 84 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 76 | <div class="title">cwrapper.h</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#define ALGO_LAYERED 0</span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#define ALGO_ORDERED 1</span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#define ALGO_THRESHOLD_ABSOLUTE 2</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#define ALGO_THRESHOLD_RELATIVE 3</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#define ALGO_LAYERED_ESTIMATE 4</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#ifdef __cplusplus</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="keyword">extern</span> <span class="stringliteral">"C"</span> {</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor">#include <stdbool.h></span></div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> </div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="keywordtype">void</span> * setupIso(<span class="keywordtype">int</span> dimNumber,</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>* isotopeNumbers,</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>* atomCounts,</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* isotopeMasses,</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* isotopeProbabilities);</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> </div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="keywordtype">void</span> deleteIso(<span class="keywordtype">void</span>* iso);</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#define C_HEADER(generatorType, dataType, method)\</span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">dataType method##generatorType(void* generator);</span></div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#define C_HEADER_GET_CONF_SIGNATURE(generatorType)\</span></div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">void method##generatorType(void* generator);</span></div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#define C_HEADERS(generatorType)\</span></div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">C_HEADER(generatorType, double, mass) \</span></div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">C_HEADER(generatorType, double, lprob) \</span></div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">C_HEADER_GET_CONF_SIGNATURE(generatorType) \</span></div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">C_HEADER(generatorType, bool, advanceToNextConfiguration) \</span></div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">C_HEADER(generatorType, void, delete)</span></div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="comment">//______________________________________________________THRESHOLD GENERATOR</span></div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="keywordtype">void</span>* setupIsoThresholdGenerator(<span class="keywordtype">void</span>* iso,</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordtype">double</span> threshold,</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordtype">bool</span> _absolute,</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordtype">int</span> _tabSize,</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordtype">int</span> _hashSize);</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> C_HEADERS(IsoThresholdGenerator)</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="comment">//______________________________________________________LAYERED GENERATOR</span></div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="keywordtype">void</span>* setupIsoLayeredGenerator(<span class="keywordtype">void</span>* iso,</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordtype">double</span> _target_coverage,</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordtype">double</span> _percentage_to_expand,</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keywordtype">int</span> _tabSize,</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordtype">int</span> _hashSize,</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="keywordtype">bool</span> _do_trim);</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> C_HEADERS(IsoLayeredGenerator)</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> <span class="comment">//______________________________________________________ORDERED GENERATOR</span></div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="keywordtype">void</span>* setupIsoOrderedGenerator(<span class="keywordtype">void</span>* iso,</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordtype">int</span> _tabSize,</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordtype">int</span> _hashSize);</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> C_HEADERS(IsoOrderedGenerator)</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> <span class="comment">// Check if there is bool in CFFI</span></div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> <span class="keywordtype">void</span>* setupThresholdTabulator(<span class="keywordtype">void</span>* generator,</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keywordtype">bool</span> get_masses,</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">bool</span> get_probs,</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordtype">bool</span> get_lprobs,</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordtype">bool</span> get_confs);</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span> <span class="keywordtype">void</span> deleteThresholdTabulator(<span class="keywordtype">void</span>* tabulator);</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> </div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> <span class="keyword">const</span> <span class="keywordtype">double</span>* massesThresholdTabulator(<span class="keywordtype">void</span>* tabulator);</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> <span class="keyword">const</span> <span class="keywordtype">double</span>* lprobsThresholdTabulator(<span class="keywordtype">void</span>* tabulator);</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> <span class="keyword">const</span> <span class="keywordtype">double</span>* probsThresholdTabulator(<span class="keywordtype">void</span>* tabulator);</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> <span class="keyword">const</span> <span class="keywordtype">int</span>* confsThresholdTabulator(<span class="keywordtype">void</span>* tabulator);</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span> <span class="keywordtype">int</span> confs_noThresholdTabulator(<span class="keywordtype">void</span>* tabulator);</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> <span class="preprocessor">#ifdef __cplusplus</span></div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> }</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span> </div></div><!-- fragment --></div><!-- contents --> | |
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| 71 | <li class="navelem"><a class="el" href="dir_7a6499598ddcfcabe96e224cb4a6d834.html">Projects</a></li><li class="navelem"><a class="el" href="dir_b5e01de8d0b5565037a326965003e69a.html">isospec</a></li><li class="navelem"><a class="el" href="dir_d48d5cdc71da00f1af92faf73cdbdfd7.html">IsoSpec</a></li><li class="navelem"><a class="el" href="dir_5010eccf620ec85ba5a1264edcd95342.html">IsoSpec++</a></li> </ul> | |
| 72 | </div> | |
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| 76 | <div class="title">IsoSpec++ Directory Reference</div> </div> | |
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| 72 | </div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> </div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <iostream></span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <stdlib.h></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include "dirtyAllocator.h"</span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> {</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> DirtyAllocator::DirtyAllocator(</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> dim, <span class="keyword">const</span> <span class="keywordtype">int</span> tabSize</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> ): tabSize(tabSize)</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> {</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  cellSize = <span class="keyword">sizeof</span>(double) + <span class="keyword">sizeof</span>(<span class="keywordtype">int</span>) * dim;</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="comment">// Fix memory alignment problems for SPARC</span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keywordflow">if</span>(cellSize % <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>) != 0)</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  cellSize += <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>) - cellSize % <span class="keyword">sizeof</span>(double);</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  currentTab = malloc( cellSize * tabSize );</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  currentConf = currentTab;</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  endOfTablePtr = <span class="keyword">reinterpret_cast<</span><span class="keywordtype">char</span>*<span class="keyword">></span>(currentTab) + cellSize*tabSize;</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> }</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> </div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> DirtyAllocator::~DirtyAllocator()</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> {</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 0; i < prevTabs.size(); ++i) free(prevTabs[i]);</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  free(currentTab);</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> }</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="keywordtype">void</span> DirtyAllocator::shiftTables()</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> {</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  prevTabs.push_back(currentTab);</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  currentTab = malloc( cellSize * tabSize );</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  currentConf = currentTab;</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  endOfTablePtr = <span class="keyword">reinterpret_cast<</span><span class="keywordtype">char</span>*<span class="keyword">></span>(currentTab) + cellSize*tabSize;</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> }</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div><div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <iostream></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <string.h></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> </div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> {</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="line"><a name="l00026"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_dirty_allocator.html"> 26</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_dirty_allocator.html">DirtyAllocator</a>{</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  <span class="keywordtype">void</span>* currentTab;</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordtype">void</span>* currentConf;</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordtype">void</span>* endOfTablePtr;</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> tabSize;</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="keywordtype">int</span> cellSize;</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  std::vector<void*> prevTabs;</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <a class="code" href="class_iso_spec_1_1_dirty_allocator.html">DirtyAllocator</a>(<span class="keyword">const</span> <span class="keywordtype">int</span> dim, <span class="keyword">const</span> <span class="keywordtype">int</span> tabSize = 10000);</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  ~<a class="code" href="class_iso_spec_1_1_dirty_allocator.html">DirtyAllocator</a>();</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> </div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordtype">void</span> shiftTables();</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keyword">inline</span> <span class="keywordtype">void</span>* newConf()</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  {</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordflow">if</span> (currentConf >= endOfTablePtr)</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  {</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  shiftTables();</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  }</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordtype">void</span>* ret = currentConf;</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  currentConf = <span class="keyword">reinterpret_cast<</span><span class="keywordtype">char</span>*<span class="keyword">></span>(currentConf) + cellSize;</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordflow">return</span> ret;</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  }</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keyword">inline</span> <span class="keywordtype">void</span>* makeCopy(<span class="keyword">const</span> <span class="keywordtype">void</span>* conf)</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  {</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordtype">void</span>* currentPlace = newConf();</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  memcpy(currentPlace, conf, cellSize);</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> </div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordflow">return</span> currentPlace;</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  }</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keyword">inline</span> <span class="keywordtype">void</span>* makeExternalCopy(<span class="keyword">const</span> <span class="keywordtype">void</span>* conf)</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  {</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordtype">void</span>* res = malloc(cellSize);</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  memcpy(res, conf, cellSize);</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordflow">return</span> res;</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  }</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> };</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div><div class="ttc" id="class_iso_spec_1_1_dirty_allocator_html"><div class="ttname"><a href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a></div><div class="ttdef"><b>Definition:</b> <a href="dirty_allocator_8h_source.html#l00026">dirtyAllocator.h:26</a></div></div> | |
| 80 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 256 | -webkit-border-radius: .5em; | |
| 257 | -moz-border-radius: .5em; | |
| 258 | box-shadow: 2px 2px 3px #999; | |
| 259 | -webkit-box-shadow: 2px 2px 3px #999; | |
| 260 | -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px; | |
| 261 | background-image: -webkit-gradient(linear, left top, left bottom, from(#eee), to(#000),color-stop(0.3, #444)); | |
| 262 | background-image: -moz-linear-gradient(center top, #eee 0%, #444 40%, #000 110%); | |
| 263 | } | |
| 264 | ||
| 265 | div.classindex ul { | |
| 266 | list-style: none; | |
| 267 | padding-left: 0; | |
| 268 | } | |
| 269 | ||
| 270 | div.classindex span.ai { | |
| 271 | display: inline-block; | |
| 272 | } | |
| 273 | ||
| 274 | div.groupHeader { | |
| 275 | margin-left: 16px; | |
| 276 | margin-top: 12px; | |
| 277 | font-weight: bold; | |
| 278 | } | |
| 279 | ||
| 280 | div.groupText { | |
| 281 | margin-left: 16px; | |
| 282 | font-style: italic; | |
| 283 | } | |
| 284 | ||
| 285 | body { | |
| 286 | background-color: white; | |
| 287 | color: black; | |
| 288 | margin: 0; | |
| 289 | } | |
| 290 | ||
| 291 | div.contents { | |
| 292 | margin-top: 10px; | |
| 293 | margin-left: 12px; | |
| 294 | margin-right: 8px; | |
| 295 | } | |
| 296 | ||
| 297 | td.indexkey { | |
| 298 | background-color: #D7DFE8; | |
| 299 | font-weight: bold; | |
| 300 | border: 1px solid #8FA7BF; | |
| 301 | margin: 2px 0px 2px 0; | |
| 302 | padding: 2px 10px; | |
| 303 | white-space: nowrap; | |
| 304 | vertical-align: top; | |
| 305 | } | |
| 306 | ||
| 307 | td.indexvalue { | |
| 308 | background-color: #D7DFE8; | |
| 309 | border: 1px solid #8FA7BF; | |
| 310 | padding: 2px 10px; | |
| 311 | margin: 2px 0px; | |
| 312 | } | |
| 313 | ||
| 314 | tr.memlist { | |
| 315 | background-color: #DBE3EB; | |
| 316 | } | |
| 317 | ||
| 318 | p.formulaDsp { | |
| 319 | text-align: center; | |
| 320 | } | |
| 321 | ||
| 322 | img.formulaDsp { | |
| 323 | ||
| 324 | } | |
| 325 | ||
| 326 | img.formulaInl { | |
| 327 | vertical-align: middle; | |
| 328 | } | |
| 329 | ||
| 330 | div.center { | |
| 331 | text-align: center; | |
| 332 | margin-top: 0px; | |
| 333 | margin-bottom: 0px; | |
| 334 | padding: 0px; | |
| 335 | } | |
| 336 | ||
| 337 | div.center img { | |
| 338 | border: 0px; | |
| 339 | } | |
| 340 | ||
| 341 | address.footer { | |
| 342 | text-align: right; | |
| 343 | padding-right: 12px; | |
| 344 | } | |
| 345 | ||
| 346 | img.footer { | |
| 347 | border: 0px; | |
| 348 | vertical-align: middle; | |
| 349 | } | |
| 350 | ||
| 351 | /* @group Code Colorization */ | |
| 352 | ||
| 353 | span.keyword { | |
| 354 | color: #008000 | |
| 355 | } | |
| 356 | ||
| 357 | span.keywordtype { | |
| 358 | color: #604020 | |
| 359 | } | |
| 360 | ||
| 361 | span.keywordflow { | |
| 362 | color: #e08000 | |
| 363 | } | |
| 364 | ||
| 365 | span.comment { | |
| 366 | color: #800000 | |
| 367 | } | |
| 368 | ||
| 369 | span.preprocessor { | |
| 370 | color: #806020 | |
| 371 | } | |
| 372 | ||
| 373 | span.stringliteral { | |
| 374 | color: #002080 | |
| 375 | } | |
| 376 | ||
| 377 | span.charliteral { | |
| 378 | color: #008080 | |
| 379 | } | |
| 380 | ||
| 381 | span.vhdldigit { | |
| 382 | color: #ff00ff | |
| 383 | } | |
| 384 | ||
| 385 | span.vhdlchar { | |
| 386 | color: #000000 | |
| 387 | } | |
| 388 | ||
| 389 | span.vhdlkeyword { | |
| 390 | color: #700070 | |
| 391 | } | |
| 392 | ||
| 393 | span.vhdllogic { | |
| 394 | color: #ff0000 | |
| 395 | } | |
| 396 | ||
| 397 | blockquote { | |
| 398 | background-color: #EEF1F5; | |
| 399 | border-left: 2px solid #557698; | |
| 400 | margin: 0 24px 0 4px; | |
| 401 | padding: 0 12px 0 16px; | |
| 402 | } | |
| 403 | ||
| 404 | /* @end */ | |
| 405 | ||
| 406 | /* | |
| 407 | .search { | |
| 408 | color: #003399; | |
| 409 | font-weight: bold; | |
| 410 | } | |
| 411 | ||
| 412 | form.search { | |
| 413 | margin-bottom: 0px; | |
| 414 | margin-top: 0px; | |
| 415 | } | |
| 416 | ||
| 417 | input.search { | |
| 418 | font-size: 75%; | |
| 419 | color: #000080; | |
| 420 | font-weight: normal; | |
| 421 | background-color: #e8eef2; | |
| 422 | } | |
| 423 | */ | |
| 424 | ||
| 425 | td.tiny { | |
| 426 | font-size: 75%; | |
| 427 | } | |
| 428 | ||
| 429 | .dirtab { | |
| 430 | padding: 4px; | |
| 431 | border-collapse: collapse; | |
| 432 | border: 1px solid #5B7FA2; | |
| 433 | } | |
| 434 | ||
| 435 | th.dirtab { | |
| 436 | background: #D7DFE8; | |
| 437 | font-weight: bold; | |
| 438 | } | |
| 439 | ||
| 440 | hr { | |
| 441 | height: 0px; | |
| 442 | border: none; | |
| 443 | border-top: 1px solid #202D3A; | |
| 444 | } | |
| 445 | ||
| 446 | hr.footer { | |
| 447 | height: 1px; | |
| 448 | } | |
| 449 | ||
| 450 | /* @group Member Descriptions */ | |
| 451 | ||
| 452 | table.memberdecls { | |
| 453 | border-spacing: 0px; | |
| 454 | padding: 0px; | |
| 455 | } | |
| 456 | ||
| 457 | .memberdecls td, .fieldtable tr { | |
| 458 | -webkit-transition-property: background-color, box-shadow; | |
| 459 | -webkit-transition-duration: 0.5s; | |
| 460 | -moz-transition-property: background-color, box-shadow; | |
| 461 | -moz-transition-duration: 0.5s; | |
| 462 | -ms-transition-property: background-color, box-shadow; | |
| 463 | -ms-transition-duration: 0.5s; | |
| 464 | -o-transition-property: background-color, box-shadow; | |
| 465 | -o-transition-duration: 0.5s; | |
| 466 | transition-property: background-color, box-shadow; | |
| 467 | transition-duration: 0.5s; | |
| 468 | } | |
| 469 | ||
| 470 | .memberdecls td.glow, .fieldtable tr.glow { | |
| 471 | background-color: cyan; | |
| 472 | box-shadow: 0 0 15px cyan; | |
| 473 | } | |
| 474 | ||
| 475 | .mdescLeft, .mdescRight, | |
| 476 | .memItemLeft, .memItemRight, | |
| 477 | .memTemplItemLeft, .memTemplItemRight, .memTemplParams { | |
| 478 | background-color: #F3F5F8; | |
| 479 | border: none; | |
| 480 | margin: 4px; | |
| 481 | padding: 1px 0 0 8px; | |
| 482 | } | |
| 483 | ||
| 484 | .mdescLeft, .mdescRight { | |
| 485 | padding: 0px 8px 4px 8px; | |
| 486 | color: #555; | |
| 487 | } | |
| 488 | ||
| 489 | .memSeparator { | |
| 490 | border-bottom: 1px solid #DEE4F0; | |
| 491 | line-height: 1px; | |
| 492 | margin: 0px; | |
| 493 | padding: 0px; | |
| 494 | } | |
| 495 | ||
| 496 | .memItemLeft, .memTemplItemLeft { | |
| 497 | white-space: nowrap; | |
| 498 | } | |
| 499 | ||
| 500 | .memItemRight { | |
| 501 | width: 100%; | |
| 502 | } | |
| 503 | ||
| 504 | .memTemplParams { | |
| 505 | color: #1D2833; | |
| 506 | white-space: nowrap; | |
| 507 | font-size: 80%; | |
| 508 | } | |
| 509 | ||
| 510 | /* @end */ | |
| 511 | ||
| 512 | /* @group Member Details */ | |
| 513 | ||
| 514 | /* Styles for detailed member documentation */ | |
| 515 | ||
| 516 | .memtitle { | |
| 517 | padding: 8px; | |
| 518 | border-top: 1px solid #6284A6; | |
| 519 | border-left: 1px solid #6284A6; | |
| 520 | border-right: 1px solid #6284A6; | |
| 521 | border-top-right-radius: 4px; | |
| 522 | border-top-left-radius: 4px; | |
| 523 | margin-bottom: -1px; | |
| 524 | background-image: url('nav_f.png'); | |
| 525 | background-repeat: repeat-x; | |
| 526 | background-color: #C5D2DE; | |
| 527 | line-height: 1.25; | |
| 528 | font-weight: 300; | |
| 529 | float:left; | |
| 530 | } | |
| 531 | ||
| 532 | .permalink | |
| 533 | { | |
| 534 | font-size: 65%; | |
| 535 | display: inline-block; | |
| 536 | vertical-align: middle; | |
| 537 | } | |
| 538 | ||
| 539 | .memtemplate { | |
| 540 | font-size: 80%; | |
| 541 | color: #1D2833; | |
| 542 | font-weight: normal; | |
| 543 | margin-left: 9px; | |
| 544 | } | |
| 545 | ||
| 546 | .memnav { | |
| 547 | background-color: #D7DFE8; | |
| 548 | border: 1px solid #5B7FA2; | |
| 549 | text-align: center; | |
| 550 | margin: 2px; | |
| 551 | margin-right: 15px; | |
| 552 | padding: 2px; | |
| 553 | } | |
| 554 | ||
| 555 | .mempage { | |
| 556 | width: 100%; | |
| 557 | } | |
| 558 | ||
| 559 | .memitem { | |
| 560 | padding: 0; | |
| 561 | margin-bottom: 10px; | |
| 562 | margin-right: 5px; | |
| 563 | -webkit-transition: box-shadow 0.5s linear; | |
| 564 | -moz-transition: box-shadow 0.5s linear; | |
| 565 | -ms-transition: box-shadow 0.5s linear; | |
| 566 | -o-transition: box-shadow 0.5s linear; | |
| 567 | transition: box-shadow 0.5s linear; | |
| 568 | display: table !important; | |
| 569 | width: 100%; | |
| 570 | } | |
| 571 | ||
| 572 | .memitem.glow { | |
| 573 | box-shadow: 0 0 15px cyan; | |
| 574 | } | |
| 575 | ||
| 576 | .memname { | |
| 577 | font-weight: 400; | |
| 578 | margin-left: 6px; | |
| 579 | } | |
| 580 | ||
| 581 | .memname td { | |
| 582 | vertical-align: bottom; | |
| 583 | } | |
| 584 | ||
| 585 | .memproto, dl.reflist dt { | |
| 586 | border-top: 1px solid #6284A6; | |
| 587 | border-left: 1px solid #6284A6; | |
| 588 | border-right: 1px solid #6284A6; | |
| 589 | padding: 6px 0px 6px 0px; | |
| 590 | color: #06080B; | |
| 591 | font-weight: bold; | |
| 592 | text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9); | |
| 593 | background-color: #BECCDA; | |
| 594 | /* opera specific markup */ | |
| 595 | box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15); | |
| 596 | border-top-right-radius: 4px; | |
| 597 | /* firefox specific markup */ | |
| 598 | -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px; | |
| 599 | -moz-border-radius-topright: 4px; | |
| 600 | /* webkit specific markup */ | |
| 601 | -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15); | |
| 602 | -webkit-border-top-right-radius: 4px; | |
| 603 | ||
| 604 | } | |
| 605 | ||
| 606 | .overload { | |
| 607 | font-family: "courier new",courier,monospace; | |
| 608 | font-size: 65%; | |
| 609 | } | |
| 610 | ||
| 611 | .memdoc, dl.reflist dd { | |
| 612 | border-bottom: 1px solid #6284A6; | |
| 613 | border-left: 1px solid #6284A6; | |
| 614 | border-right: 1px solid #6284A6; | |
| 615 | padding: 6px 10px 2px 10px; | |
| 616 | background-color: #F7F9FA; | |
| 617 | border-top-width: 0; | |
| 618 | background-image:url('nav_g.png'); | |
| 619 | background-repeat:repeat-x; | |
| 620 | background-color: #FFFFFF; | |
| 621 | /* opera specific markup */ | |
| 622 | border-bottom-left-radius: 4px; | |
| 623 | border-bottom-right-radius: 4px; | |
| 624 | box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15); | |
| 625 | /* firefox specific markup */ | |
| 626 | -moz-border-radius-bottomleft: 4px; | |
| 627 | -moz-border-radius-bottomright: 4px; | |
| 628 | -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px; | |
| 629 | /* webkit specific markup */ | |
| 630 | -webkit-border-bottom-left-radius: 4px; | |
| 631 | -webkit-border-bottom-right-radius: 4px; | |
| 632 | -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15); | |
| 633 | } | |
| 634 | ||
| 635 | dl.reflist dt { | |
| 636 | padding: 5px; | |
| 637 | } | |
| 638 | ||
| 639 | dl.reflist dd { | |
| 640 | margin: 0px 0px 10px 0px; | |
| 641 | padding: 5px; | |
| 642 | } | |
| 643 | ||
| 644 | .paramkey { | |
| 645 | text-align: right; | |
| 646 | } | |
| 647 | ||
| 648 | .paramtype { | |
| 649 | white-space: nowrap; | |
| 650 | } | |
| 651 | ||
| 652 | .paramname { | |
| 653 | color: #602020; | |
| 654 | white-space: nowrap; | |
| 655 | } | |
| 656 | .paramname em { | |
| 657 | font-style: normal; | |
| 658 | } | |
| 659 | .paramname code { | |
| 660 | line-height: 14px; | |
| 661 | } | |
| 662 | ||
| 663 | .params, .retval, .exception, .tparams { | |
| 664 | margin-left: 0px; | |
| 665 | padding-left: 0px; | |
| 666 | } | |
| 667 | ||
| 668 | .params .paramname, .retval .paramname { | |
| 669 | font-weight: bold; | |
| 670 | vertical-align: top; | |
| 671 | } | |
| 672 | ||
| 673 | .params .paramtype { | |
| 674 | font-style: italic; | |
| 675 | vertical-align: top; | |
| 676 | } | |
| 677 | ||
| 678 | .params .paramdir { | |
| 679 | font-family: "courier new",courier,monospace; | |
| 680 | vertical-align: top; | |
| 681 | } | |
| 682 | ||
| 683 | table.mlabels { | |
| 684 | border-spacing: 0px; | |
| 685 | } | |
| 686 | ||
| 687 | td.mlabels-left { | |
| 688 | width: 100%; | |
| 689 | padding: 0px; | |
| 690 | } | |
| 691 | ||
| 692 | td.mlabels-right { | |
| 693 | vertical-align: bottom; | |
| 694 | padding: 0px; | |
| 695 | white-space: nowrap; | |
| 696 | } | |
| 697 | ||
| 698 | span.mlabels { | |
| 699 | margin-left: 8px; | |
| 700 | } | |
| 701 | ||
| 702 | span.mlabel { | |
| 703 | background-color: #384E63; | |
| 704 | border-top:1px solid #273645; | |
| 705 | border-left:1px solid #273645; | |
| 706 | border-right:1px solid #8FA7BF; | |
| 707 | border-bottom:1px solid #8FA7BF; | |
| 708 | text-shadow: none; | |
| 709 | color: white; | |
| 710 | margin-right: 4px; | |
| 711 | padding: 2px 3px; | |
| 712 | border-radius: 3px; | |
| 713 | font-size: 7pt; | |
| 714 | white-space: nowrap; | |
| 715 | vertical-align: middle; | |
| 716 | } | |
| 717 | ||
| 718 | ||
| 719 | ||
| 720 | /* @end */ | |
| 721 | ||
| 722 | /* these are for tree view inside a (index) page */ | |
| 723 | ||
| 724 | div.directory { | |
| 725 | margin: 10px 0px; | |
| 726 | border-top: 1px solid #557698; | |
| 727 | border-bottom: 1px solid #557698; | |
| 728 | width: 100%; | |
| 729 | } | |
| 730 | ||
| 731 | .directory table { | |
| 732 | border-collapse:collapse; | |
| 733 | } | |
| 734 | ||
| 735 | .directory td { | |
| 736 | margin: 0px; | |
| 737 | padding: 0px; | |
| 738 | vertical-align: top; | |
| 739 | } | |
| 740 | ||
| 741 | .directory td.entry { | |
| 742 | white-space: nowrap; | |
| 743 | padding-right: 6px; | |
| 744 | padding-top: 3px; | |
| 745 | } | |
| 746 | ||
| 747 | .directory td.entry a { | |
| 748 | outline:none; | |
| 749 | } | |
| 750 | ||
| 751 | .directory td.entry a img { | |
| 752 | border: none; | |
| 753 | } | |
| 754 | ||
| 755 | .directory td.desc { | |
| 756 | width: 100%; | |
| 757 | padding-left: 6px; | |
| 758 | padding-right: 6px; | |
| 759 | padding-top: 3px; | |
| 760 | border-left: 1px solid rgba(0,0,0,0.05); | |
| 761 | } | |
| 762 | ||
| 763 | .directory tr.even { | |
| 764 | padding-left: 6px; | |
| 765 | background-color: #EEF1F5; | |
| 766 | } | |
| 767 | ||
| 768 | .directory img { | |
| 769 | vertical-align: -30%; | |
| 770 | } | |
| 771 | ||
| 772 | .directory .levels { | |
| 773 | white-space: nowrap; | |
| 774 | width: 100%; | |
| 775 | text-align: right; | |
| 776 | font-size: 9pt; | |
| 777 | } | |
| 778 | ||
| 779 | .directory .levels span { | |
| 780 | cursor: pointer; | |
| 781 | padding-left: 2px; | |
| 782 | padding-right: 2px; | |
| 783 | color: #141C24; | |
| 784 | } | |
| 785 | ||
| 786 | .arrow { | |
| 787 | color: #557698; | |
| 788 | -webkit-user-select: none; | |
| 789 | -khtml-user-select: none; | |
| 790 | -moz-user-select: none; | |
| 791 | -ms-user-select: none; | |
| 792 | user-select: none; | |
| 793 | cursor: pointer; | |
| 794 | font-size: 80%; | |
| 795 | display: inline-block; | |
| 796 | width: 16px; | |
| 797 | height: 22px; | |
| 798 | } | |
| 799 | ||
| 800 | .icon { | |
| 801 | font-family: Arial, Helvetica; | |
| 802 | font-weight: bold; | |
| 803 | font-size: 12px; | |
| 804 | height: 14px; | |
| 805 | width: 16px; | |
| 806 | display: inline-block; | |
| 807 | background-color: #384E63; | |
| 808 | color: white; | |
| 809 | text-align: center; | |
| 810 | border-radius: 4px; | |
| 811 | margin-left: 2px; | |
| 812 | margin-right: 2px; | |
| 813 | } | |
| 814 | ||
| 815 | .icona { | |
| 816 | width: 24px; | |
| 817 | height: 22px; | |
| 818 | display: inline-block; | |
| 819 | } | |
| 820 | ||
| 821 | .iconfopen { | |
| 822 | width: 24px; | |
| 823 | height: 18px; | |
| 824 | margin-bottom: 4px; | |
| 825 | background-image:url('folderopen.png'); | |
| 826 | background-position: 0px -4px; | |
| 827 | background-repeat: repeat-y; | |
| 828 | vertical-align:top; | |
| 829 | display: inline-block; | |
| 830 | } | |
| 831 | ||
| 832 | .iconfclosed { | |
| 833 | width: 24px; | |
| 834 | height: 18px; | |
| 835 | margin-bottom: 4px; | |
| 836 | background-image:url('folderclosed.png'); | |
| 837 | background-position: 0px -4px; | |
| 838 | background-repeat: repeat-y; | |
| 839 | vertical-align:top; | |
| 840 | display: inline-block; | |
| 841 | } | |
| 842 | ||
| 843 | .icondoc { | |
| 844 | width: 24px; | |
| 845 | height: 18px; | |
| 846 | margin-bottom: 4px; | |
| 847 | background-image:url('doc.png'); | |
| 848 | background-position: 0px -4px; | |
| 849 | background-repeat: repeat-y; | |
| 850 | vertical-align:top; | |
| 851 | display: inline-block; | |
| 852 | } | |
| 853 | ||
| 854 | table.directory { | |
| 855 | font: 400 14px Roboto,sans-serif; | |
| 856 | } | |
| 857 | ||
| 858 | /* @end */ | |
| 859 | ||
| 860 | div.dynheader { | |
| 861 | margin-top: 8px; | |
| 862 | -webkit-touch-callout: none; | |
| 863 | -webkit-user-select: none; | |
| 864 | -khtml-user-select: none; | |
| 865 | -moz-user-select: none; | |
| 866 | -ms-user-select: none; | |
| 867 | user-select: none; | |
| 868 | } | |
| 869 | ||
| 870 | address { | |
| 871 | font-style: normal; | |
| 872 | color: #080C0F; | |
| 873 | } | |
| 874 | ||
| 875 | table.doxtable caption { | |
| 876 | caption-side: top; | |
| 877 | } | |
| 878 | ||
| 879 | table.doxtable { | |
| 880 | border-collapse:collapse; | |
| 881 | margin-top: 4px; | |
| 882 | margin-bottom: 4px; | |
| 883 | } | |
| 884 | ||
| 885 | table.doxtable td, table.doxtable th { | |
| 886 | border: 1px solid #0A0E12; | |
| 887 | padding: 3px 7px 2px; | |
| 888 | } | |
| 889 | ||
| 890 | table.doxtable th { | |
| 891 | background-color: #10171D; | |
| 892 | color: #FFFFFF; | |
| 893 | font-size: 110%; | |
| 894 | padding-bottom: 4px; | |
| 895 | padding-top: 5px; | |
| 896 | } | |
| 897 | ||
| 898 | table.fieldtable { | |
| 899 | /*width: 100%;*/ | |
| 900 | margin-bottom: 10px; | |
| 901 | border: 1px solid #6284A6; | |
| 902 | border-spacing: 0px; | |
| 903 | -moz-border-radius: 4px; | |
| 904 | -webkit-border-radius: 4px; | |
| 905 | border-radius: 4px; | |
| 906 | -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px; | |
| 907 | -webkit-box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15); | |
| 908 | box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15); | |
| 909 | } | |
| 910 | ||
| 911 | .fieldtable td, .fieldtable th { | |
| 912 | padding: 3px 7px 2px; | |
| 913 | } | |
| 914 | ||
| 915 | .fieldtable td.fieldtype, .fieldtable td.fieldname { | |
| 916 | white-space: nowrap; | |
| 917 | border-right: 1px solid #6284A6; | |
| 918 | border-bottom: 1px solid #6284A6; | |
| 919 | vertical-align: top; | |
| 920 | } | |
| 921 | ||
| 922 | .fieldtable td.fieldname { | |
| 923 | padding-top: 3px; | |
| 924 | } | |
| 925 | ||
| 926 | .fieldtable td.fielddoc { | |
| 927 | border-bottom: 1px solid #6284A6; | |
| 928 | /*width: 100%;*/ | |
| 929 | } | |
| 930 | ||
| 931 | .fieldtable td.fielddoc p:first-child { | |
| 932 | margin-top: 0px; | |
| 933 | } | |
| 934 | ||
| 935 | .fieldtable td.fielddoc p:last-child { | |
| 936 | margin-bottom: 2px; | |
| 937 | } | |
| 938 | ||
| 939 | .fieldtable tr:last-child td { | |
| 940 | border-bottom: none; | |
| 941 | } | |
| 942 | ||
| 943 | .fieldtable th { | |
| 944 | background-image:url('nav_f.png'); | |
| 945 | background-repeat:repeat-x; | |
| 946 | background-color: #C5D2DE; | |
| 947 | font-size: 90%; | |
| 948 | color: #06080B; | |
| 949 | padding-bottom: 4px; | |
| 950 | padding-top: 5px; | |
| 951 | text-align:left; | |
| 952 | font-weight: 400; | |
| 953 | -moz-border-radius-topleft: 4px; | |
| 954 | -moz-border-radius-topright: 4px; | |
| 955 | -webkit-border-top-left-radius: 4px; | |
| 956 | -webkit-border-top-right-radius: 4px; | |
| 957 | border-top-left-radius: 4px; | |
| 958 | border-top-right-radius: 4px; | |
| 959 | border-bottom: 1px solid #6284A6; | |
| 960 | } | |
| 961 | ||
| 962 | ||
| 963 | .tabsearch { | |
| 964 | top: 0px; | |
| 965 | left: 10px; | |
| 966 | height: 36px; | |
| 967 | background-image: url('tab_b.png'); | |
| 968 | z-index: 101; | |
| 969 | overflow: hidden; | |
| 970 | font-size: 13px; | |
| 971 | } | |
| 972 | ||
| 973 | .navpath ul | |
| 974 | { | |
| 975 | font-size: 11px; | |
| 976 | background-image:url('tab_b.png'); | |
| 977 | background-repeat:repeat-x; | |
| 978 | background-position: 0 -5px; | |
| 979 | height:30px; | |
| 980 | line-height:30px; | |
| 981 | color:#48647F; | |
| 982 | border:solid 1px #8BA4BD; | |
| 983 | overflow:hidden; | |
| 984 | margin:0px; | |
| 985 | padding:0px; | |
| 986 | } | |
| 987 | ||
| 988 | .navpath li | |
| 989 | { | |
| 990 | list-style-type:none; | |
| 991 | float:left; | |
| 992 | padding-left:10px; | |
| 993 | padding-right:15px; | |
| 994 | background-image:url('bc_s.png'); | |
| 995 | background-repeat:no-repeat; | |
| 996 | background-position:right; | |
| 997 | color:#0F151B; | |
| 998 | } | |
| 999 | ||
| 1000 | .navpath li.navelem a | |
| 1001 | { | |
| 1002 | height:32px; | |
| 1003 | display:block; | |
| 1004 | text-decoration: none; | |
| 1005 | outline: none; | |
| 1006 | color: #070B0E; | |
| 1007 | font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif; | |
| 1008 | text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9); | |
| 1009 | text-decoration: none; | |
| 1010 | } | |
| 1011 | ||
| 1012 | .navpath li.navelem a:hover | |
| 1013 | { | |
| 1014 | color:#324559; | |
| 1015 | } | |
| 1016 | ||
| 1017 | .navpath li.footer | |
| 1018 | { | |
| 1019 | list-style-type:none; | |
| 1020 | float:right; | |
| 1021 | padding-left:10px; | |
| 1022 | padding-right:15px; | |
| 1023 | background-image:none; | |
| 1024 | background-repeat:no-repeat; | |
| 1025 | background-position:right; | |
| 1026 | color:#0F151B; | |
| 1027 | font-size: 8pt; | |
| 1028 | } | |
| 1029 | ||
| 1030 | ||
| 1031 | div.summary | |
| 1032 | { | |
| 1033 | float: right; | |
| 1034 | font-size: 8pt; | |
| 1035 | padding-right: 5px; | |
| 1036 | width: 50%; | |
| 1037 | text-align: right; | |
| 1038 | } | |
| 1039 | ||
| 1040 | div.summary a | |
| 1041 | { | |
| 1042 | white-space: nowrap; | |
| 1043 | } | |
| 1044 | ||
| 1045 | table.classindex | |
| 1046 | { | |
| 1047 | margin: 10px; | |
| 1048 | white-space: nowrap; | |
| 1049 | margin-left: 3%; | |
| 1050 | margin-right: 3%; | |
| 1051 | width: 94%; | |
| 1052 | border: 0; | |
| 1053 | border-spacing: 0; | |
| 1054 | padding: 0; | |
| 1055 | } | |
| 1056 | ||
| 1057 | div.ingroups | |
| 1058 | { | |
| 1059 | font-size: 8pt; | |
| 1060 | width: 50%; | |
| 1061 | text-align: left; | |
| 1062 | } | |
| 1063 | ||
| 1064 | div.ingroups a | |
| 1065 | { | |
| 1066 | white-space: nowrap; | |
| 1067 | } | |
| 1068 | ||
| 1069 | div.header | |
| 1070 | { | |
| 1071 | background-image:url('nav_h.png'); | |
| 1072 | background-repeat:repeat-x; | |
| 1073 | background-color: #F3F5F8; | |
| 1074 | margin: 0px; | |
| 1075 | border-bottom: 1px solid #8FA7BF; | |
| 1076 | } | |
| 1077 | ||
| 1078 | div.headertitle | |
| 1079 | { | |
| 1080 | padding: 5px 5px 5px 10px; | |
| 1081 | } | |
| 1082 | ||
| 1083 | dl | |
| 1084 | { | |
| 1085 | padding: 0 0 0 10px; | |
| 1086 | } | |
| 1087 | ||
| 1088 | /* dl.note, dl.warning, dl.attention, dl.pre, dl.post, dl.invariant, dl.deprecated, dl.todo, dl.test, dl.bug */ | |
| 1089 | dl.section | |
| 1090 | { | |
| 1091 | margin-left: 0px; | |
| 1092 | padding-left: 0px; | |
| 1093 | } | |
| 1094 | ||
| 1095 | dl.note | |
| 1096 | { | |
| 1097 | margin-left:-7px; | |
| 1098 | padding-left: 3px; | |
| 1099 | border-left:4px solid; | |
| 1100 | border-color: #D0C000; | |
| 1101 | } | |
| 1102 | ||
| 1103 | dl.warning, dl.attention | |
| 1104 | { | |
| 1105 | margin-left:-7px; | |
| 1106 | padding-left: 3px; | |
| 1107 | border-left:4px solid; | |
| 1108 | border-color: #FF0000; | |
| 1109 | } | |
| 1110 | ||
| 1111 | dl.pre, dl.post, dl.invariant | |
| 1112 | { | |
| 1113 | margin-left:-7px; | |
| 1114 | padding-left: 3px; | |
| 1115 | border-left:4px solid; | |
| 1116 | border-color: #00D000; | |
| 1117 | } | |
| 1118 | ||
| 1119 | dl.deprecated | |
| 1120 | { | |
| 1121 | margin-left:-7px; | |
| 1122 | padding-left: 3px; | |
| 1123 | border-left:4px solid; | |
| 1124 | border-color: #505050; | |
| 1125 | } | |
| 1126 | ||
| 1127 | dl.todo | |
| 1128 | { | |
| 1129 | margin-left:-7px; | |
| 1130 | padding-left: 3px; | |
| 1131 | border-left:4px solid; | |
| 1132 | border-color: #00C0E0; | |
| 1133 | } | |
| 1134 | ||
| 1135 | dl.test | |
| 1136 | { | |
| 1137 | margin-left:-7px; | |
| 1138 | padding-left: 3px; | |
| 1139 | border-left:4px solid; | |
| 1140 | border-color: #3030E0; | |
| 1141 | } | |
| 1142 | ||
| 1143 | dl.bug | |
| 1144 | { | |
| 1145 | margin-left:-7px; | |
| 1146 | padding-left: 3px; | |
| 1147 | border-left:4px solid; | |
| 1148 | border-color: #C08050; | |
| 1149 | } | |
| 1150 | ||
| 1151 | dl.section dd { | |
| 1152 | margin-bottom: 6px; | |
| 1153 | } | |
| 1154 | ||
| 1155 | ||
| 1156 | #projectlogo | |
| 1157 | { | |
| 1158 | text-align: center; | |
| 1159 | vertical-align: bottom; | |
| 1160 | border-collapse: separate; | |
| 1161 | } | |
| 1162 | ||
| 1163 | #projectlogo img | |
| 1164 | { | |
| 1165 | border: 0px none; | |
| 1166 | } | |
| 1167 | ||
| 1168 | #projectalign | |
| 1169 | { | |
| 1170 | vertical-align: middle; | |
| 1171 | } | |
| 1172 | ||
| 1173 | #projectname | |
| 1174 | { | |
| 1175 | font: 300% Tahoma, Arial,sans-serif; | |
| 1176 | margin: 0px; | |
| 1177 | padding: 2px 0px; | |
| 1178 | } | |
| 1179 | ||
| 1180 | #projectbrief | |
| 1181 | { | |
| 1182 | font: 120% Tahoma, Arial,sans-serif; | |
| 1183 | margin: 0px; | |
| 1184 | padding: 0px; | |
| 1185 | } | |
| 1186 | ||
| 1187 | #projectnumber | |
| 1188 | { | |
| 1189 | font: 50% Tahoma, Arial,sans-serif; | |
| 1190 | margin: 0px; | |
| 1191 | padding: 0px; | |
| 1192 | } | |
| 1193 | ||
| 1194 | #titlearea | |
| 1195 | { | |
| 1196 | padding: 0px; | |
| 1197 | margin: 0px; | |
| 1198 | width: 100%; | |
| 1199 | border-bottom: 1px solid #273645; | |
| 1200 | } | |
| 1201 | ||
| 1202 | .image | |
| 1203 | { | |
| 1204 | text-align: center; | |
| 1205 | } | |
| 1206 | ||
| 1207 | .dotgraph | |
| 1208 | { | |
| 1209 | text-align: center; | |
| 1210 | } | |
| 1211 | ||
| 1212 | .mscgraph | |
| 1213 | { | |
| 1214 | text-align: center; | |
| 1215 | } | |
| 1216 | ||
| 1217 | .plantumlgraph | |
| 1218 | { | |
| 1219 | text-align: center; | |
| 1220 | } | |
| 1221 | ||
| 1222 | .diagraph | |
| 1223 | { | |
| 1224 | text-align: center; | |
| 1225 | } | |
| 1226 | ||
| 1227 | .caption | |
| 1228 | { | |
| 1229 | font-weight: bold; | |
| 1230 | } | |
| 1231 | ||
| 1232 | div.zoom | |
| 1233 | { | |
| 1234 | border: 1px solid #4C6A87; | |
| 1235 | } | |
| 1236 | ||
| 1237 | dl.citelist { | |
| 1238 | margin-bottom:50px; | |
| 1239 | } | |
| 1240 | ||
| 1241 | dl.citelist dt { | |
| 1242 | color:#0D1218; | |
| 1243 | float:left; | |
| 1244 | font-weight:bold; | |
| 1245 | margin-right:10px; | |
| 1246 | padding:5px; | |
| 1247 | } | |
| 1248 | ||
| 1249 | dl.citelist dd { | |
| 1250 | margin:2px 0; | |
| 1251 | padding:5px 0; | |
| 1252 | } | |
| 1253 | ||
| 1254 | div.toc { | |
| 1255 | padding: 14px 25px; | |
| 1256 | background-color: #E9EEF2; | |
| 1257 | border: 1px solid #B2C2D3; | |
| 1258 | border-radius: 7px 7px 7px 7px; | |
| 1259 | float: right; | |
| 1260 | height: auto; | |
| 1261 | margin: 0 8px 10px 10px; | |
| 1262 | width: 200px; | |
| 1263 | } | |
| 1264 | ||
| 1265 | div.toc li { | |
| 1266 | background: url("bdwn.png") no-repeat scroll 0 5px transparent; | |
| 1267 | font: 10px/1.2 Verdana,DejaVu Sans,Geneva,sans-serif; | |
| 1268 | margin-top: 5px; | |
| 1269 | padding-left: 10px; | |
| 1270 | padding-top: 2px; | |
| 1271 | } | |
| 1272 | ||
| 1273 | div.toc h3 { | |
| 1274 | font: bold 12px/1.2 Arial,FreeSans,sans-serif; | |
| 1275 | color: #1D2833; | |
| 1276 | border-bottom: 0 none; | |
| 1277 | margin: 0; | |
| 1278 | } | |
| 1279 | ||
| 1280 | div.toc ul { | |
| 1281 | list-style: none outside none; | |
| 1282 | border: medium none; | |
| 1283 | padding: 0px; | |
| 1284 | } | |
| 1285 | ||
| 1286 | div.toc li.level1 { | |
| 1287 | margin-left: 0px; | |
| 1288 | } | |
| 1289 | ||
| 1290 | div.toc li.level2 { | |
| 1291 | margin-left: 15px; | |
| 1292 | } | |
| 1293 | ||
| 1294 | div.toc li.level3 { | |
| 1295 | margin-left: 30px; | |
| 1296 | } | |
| 1297 | ||
| 1298 | div.toc li.level4 { | |
| 1299 | margin-left: 45px; | |
| 1300 | } | |
| 1301 | ||
| 1302 | .inherit_header { | |
| 1303 | font-weight: bold; | |
| 1304 | color: gray; | |
| 1305 | cursor: pointer; | |
| 1306 | -webkit-touch-callout: none; | |
| 1307 | -webkit-user-select: none; | |
| 1308 | -khtml-user-select: none; | |
| 1309 | -moz-user-select: none; | |
| 1310 | -ms-user-select: none; | |
| 1311 | user-select: none; | |
| 1312 | } | |
| 1313 | ||
| 1314 | .inherit_header td { | |
| 1315 | padding: 6px 0px 2px 5px; | |
| 1316 | } | |
| 1317 | ||
| 1318 | .inherit { | |
| 1319 | display: none; | |
| 1320 | } | |
| 1321 | ||
| 1322 | tr.heading h2 { | |
| 1323 | margin-top: 12px; | |
| 1324 | margin-bottom: 4px; | |
| 1325 | } | |
| 1326 | ||
| 1327 | /* tooltip related style info */ | |
| 1328 | ||
| 1329 | .ttc { | |
| 1330 | position: absolute; | |
| 1331 | display: none; | |
| 1332 | } | |
| 1333 | ||
| 1334 | #powerTip { | |
| 1335 | cursor: default; | |
| 1336 | white-space: nowrap; | |
| 1337 | background-color: white; | |
| 1338 | border: 1px solid gray; | |
| 1339 | border-radius: 4px 4px 4px 4px; | |
| 1340 | box-shadow: 1px 1px 7px gray; | |
| 1341 | display: none; | |
| 1342 | font-size: smaller; | |
| 1343 | max-width: 80%; | |
| 1344 | opacity: 0.9; | |
| 1345 | padding: 1ex 1em 1em; | |
| 1346 | position: absolute; | |
| 1347 | z-index: 2147483647; | |
| 1348 | } | |
| 1349 | ||
| 1350 | #powerTip div.ttdoc { | |
| 1351 | color: grey; | |
| 1352 | font-style: italic; | |
| 1353 | } | |
| 1354 | ||
| 1355 | #powerTip div.ttname a { | |
| 1356 | font-weight: bold; | |
| 1357 | } | |
| 1358 | ||
| 1359 | #powerTip div.ttname { | |
| 1360 | font-weight: bold; | |
| 1361 | } | |
| 1362 | ||
| 1363 | #powerTip div.ttdeci { | |
| 1364 | color: #006318; | |
| 1365 | } | |
| 1366 | ||
| 1367 | #powerTip div { | |
| 1368 | margin: 0px; | |
| 1369 | padding: 0px; | |
| 1370 | font: 12px/16px Roboto,sans-serif; | |
| 1371 | } | |
| 1372 | ||
| 1373 | #powerTip:before, #powerTip:after { | |
| 1374 | content: ""; | |
| 1375 | position: absolute; | |
| 1376 | margin: 0px; | |
| 1377 | } | |
| 1378 | ||
| 1379 | #powerTip.n:after, #powerTip.n:before, | |
| 1380 | #powerTip.s:after, #powerTip.s:before, | |
| 1381 | #powerTip.w:after, #powerTip.w:before, | |
| 1382 | #powerTip.e:after, #powerTip.e:before, | |
| 1383 | #powerTip.ne:after, #powerTip.ne:before, | |
| 1384 | #powerTip.se:after, #powerTip.se:before, | |
| 1385 | #powerTip.nw:after, #powerTip.nw:before, | |
| 1386 | #powerTip.sw:after, #powerTip.sw:before { | |
| 1387 | border: solid transparent; | |
| 1388 | content: " "; | |
| 1389 | height: 0; | |
| 1390 | width: 0; | |
| 1391 | position: absolute; | |
| 1392 | } | |
| 1393 | ||
| 1394 | #powerTip.n:after, #powerTip.s:after, | |
| 1395 | #powerTip.w:after, #powerTip.e:after, | |
| 1396 | #powerTip.nw:after, #powerTip.ne:after, | |
| 1397 | #powerTip.sw:after, #powerTip.se:after { | |
| 1398 | border-color: rgba(255, 255, 255, 0); | |
| 1399 | } | |
| 1400 | ||
| 1401 | #powerTip.n:before, #powerTip.s:before, | |
| 1402 | #powerTip.w:before, #powerTip.e:before, | |
| 1403 | #powerTip.nw:before, #powerTip.ne:before, | |
| 1404 | #powerTip.sw:before, #powerTip.se:before { | |
| 1405 | border-color: rgba(128, 128, 128, 0); | |
| 1406 | } | |
| 1407 | ||
| 1408 | #powerTip.n:after, #powerTip.n:before, | |
| 1409 | #powerTip.ne:after, #powerTip.ne:before, | |
| 1410 | #powerTip.nw:after, #powerTip.nw:before { | |
| 1411 | top: 100%; | |
| 1412 | } | |
| 1413 | ||
| 1414 | #powerTip.n:after, #powerTip.ne:after, #powerTip.nw:after { | |
| 1415 | border-top-color: #ffffff; | |
| 1416 | border-width: 10px; | |
| 1417 | margin: 0px -10px; | |
| 1418 | } | |
| 1419 | #powerTip.n:before { | |
| 1420 | border-top-color: #808080; | |
| 1421 | border-width: 11px; | |
| 1422 | margin: 0px -11px; | |
| 1423 | } | |
| 1424 | #powerTip.n:after, #powerTip.n:before { | |
| 1425 | left: 50%; | |
| 1426 | } | |
| 1427 | ||
| 1428 | #powerTip.nw:after, #powerTip.nw:before { | |
| 1429 | right: 14px; | |
| 1430 | } | |
| 1431 | ||
| 1432 | #powerTip.ne:after, #powerTip.ne:before { | |
| 1433 | left: 14px; | |
| 1434 | } | |
| 1435 | ||
| 1436 | #powerTip.s:after, #powerTip.s:before, | |
| 1437 | #powerTip.se:after, #powerTip.se:before, | |
| 1438 | #powerTip.sw:after, #powerTip.sw:before { | |
| 1439 | bottom: 100%; | |
| 1440 | } | |
| 1441 | ||
| 1442 | #powerTip.s:after, #powerTip.se:after, #powerTip.sw:after { | |
| 1443 | border-bottom-color: #ffffff; | |
| 1444 | border-width: 10px; | |
| 1445 | margin: 0px -10px; | |
| 1446 | } | |
| 1447 | ||
| 1448 | #powerTip.s:before, #powerTip.se:before, #powerTip.sw:before { | |
| 1449 | border-bottom-color: #808080; | |
| 1450 | border-width: 11px; | |
| 1451 | margin: 0px -11px; | |
| 1452 | } | |
| 1453 | ||
| 1454 | #powerTip.s:after, #powerTip.s:before { | |
| 1455 | left: 50%; | |
| 1456 | } | |
| 1457 | ||
| 1458 | #powerTip.sw:after, #powerTip.sw:before { | |
| 1459 | right: 14px; | |
| 1460 | } | |
| 1461 | ||
| 1462 | #powerTip.se:after, #powerTip.se:before { | |
| 1463 | left: 14px; | |
| 1464 | } | |
| 1465 | ||
| 1466 | #powerTip.e:after, #powerTip.e:before { | |
| 1467 | left: 100%; | |
| 1468 | } | |
| 1469 | #powerTip.e:after { | |
| 1470 | border-left-color: #ffffff; | |
| 1471 | border-width: 10px; | |
| 1472 | top: 50%; | |
| 1473 | margin-top: -10px; | |
| 1474 | } | |
| 1475 | #powerTip.e:before { | |
| 1476 | border-left-color: #808080; | |
| 1477 | border-width: 11px; | |
| 1478 | top: 50%; | |
| 1479 | margin-top: -11px; | |
| 1480 | } | |
| 1481 | ||
| 1482 | #powerTip.w:after, #powerTip.w:before { | |
| 1483 | right: 100%; | |
| 1484 | } | |
| 1485 | #powerTip.w:after { | |
| 1486 | border-right-color: #ffffff; | |
| 1487 | border-width: 10px; | |
| 1488 | top: 50%; | |
| 1489 | margin-top: -10px; | |
| 1490 | } | |
| 1491 | #powerTip.w:before { | |
| 1492 | border-right-color: #808080; | |
| 1493 | border-width: 11px; | |
| 1494 | top: 50%; | |
| 1495 | margin-top: -11px; | |
| 1496 | } | |
| 1497 | ||
| 1498 | @media print | |
| 1499 | { | |
| 1500 | #top { display: none; } | |
| 1501 | #side-nav { display: none; } | |
| 1502 | #nav-path { display: none; } | |
| 1503 | body { overflow:visible; } | |
| 1504 | h1, h2, h3, h4, h5, h6 { page-break-after: avoid; } | |
| 1505 | .summary { display: none; } | |
| 1506 | .memitem { page-break-inside: avoid; } | |
| 1507 | #doc-content | |
| 1508 | { | |
| 1509 | margin-left:0 !important; | |
| 1510 | height:auto !important; | |
| 1511 | width:auto !important; | |
| 1512 | overflow:inherit; | |
| 1513 | display:inline; | |
| 1514 | } | |
| 1515 | } | |
| 1516 | ||
| 1517 | /* @group Markdown */ | |
| 1518 | ||
| 1519 | /* | |
| 1520 | table.markdownTable { | |
| 1521 | border-collapse:collapse; | |
| 1522 | margin-top: 4px; | |
| 1523 | margin-bottom: 4px; | |
| 1524 | } | |
| 1525 | ||
| 1526 | table.markdownTable td, table.markdownTable th { | |
| 1527 | border: 1px solid #0A0E12; | |
| 1528 | padding: 3px 7px 2px; | |
| 1529 | } | |
| 1530 | ||
| 1531 | table.markdownTableHead tr { | |
| 1532 | } | |
| 1533 | ||
| 1534 | table.markdownTableBodyLeft td, table.markdownTable th { | |
| 1535 | border: 1px solid #0A0E12; | |
| 1536 | padding: 3px 7px 2px; | |
| 1537 | } | |
| 1538 | ||
| 1539 | th.markdownTableHeadLeft th.markdownTableHeadRight th.markdownTableHeadCenter th.markdownTableHeadNone { | |
| 1540 | background-color: #10171D; | |
| 1541 | color: #FFFFFF; | |
| 1542 | font-size: 110%; | |
| 1543 | padding-bottom: 4px; | |
| 1544 | padding-top: 5px; | |
| 1545 | } | |
| 1546 | ||
| 1547 | th.markdownTableHeadLeft { | |
| 1548 | text-align: left | |
| 1549 | } | |
| 1550 | ||
| 1551 | th.markdownTableHeadRight { | |
| 1552 | text-align: right | |
| 1553 | } | |
| 1554 | ||
| 1555 | th.markdownTableHeadCenter { | |
| 1556 | text-align: center | |
| 1557 | } | |
| 1558 | */ | |
| 1559 | ||
| 1560 | table.markdownTable { | |
| 1561 | border-collapse:collapse; | |
| 1562 | margin-top: 4px; | |
| 1563 | margin-bottom: 4px; | |
| 1564 | } | |
| 1565 | ||
| 1566 | table.markdownTable td, table.markdownTable th { | |
| 1567 | border: 1px solid #0A0E12; | |
| 1568 | padding: 3px 7px 2px; | |
| 1569 | } | |
| 1570 | ||
| 1571 | table.markdownTable tr { | |
| 1572 | } | |
| 1573 | ||
| 1574 | th.markdownTableHeadLeft, th.markdownTableHeadRight, th.markdownTableHeadCenter, th.markdownTableHeadNone { | |
| 1575 | background-color: #374F7F; | |
| 1576 | color: #FFFFFF; | |
| 1577 | font-size: 110%; | |
| 1578 | padding-bottom: 4px; | |
| 1579 | padding-top: 5px; | |
| 1580 | } | |
| 1581 | ||
| 1582 | th.markdownTableHeadLeft, td.markdownTableBodyLeft { | |
| 1583 | text-align: left | |
| 1584 | } | |
| 1585 | ||
| 1586 | th.markdownTableHeadRight, td.markdownTableBodyRight { | |
| 1587 | text-align: right | |
| 1588 | } | |
| 1589 | ||
| 1590 | th.markdownTableHeadCenter, td.markdownTableBodyCenter { | |
| 1591 | text-align: center | |
| 1592 | } | |
| 1593 | ||
| 1594 | ||
| 1595 | /* @end */ |
| 0 | /* | |
| 1 | @licstart The following is the entire license notice for the | |
| 2 | JavaScript code in this file. | |
| 3 | ||
| 4 | Copyright (C) 1997-2017 by Dimitri van Heesch | |
| 5 | ||
| 6 | This program is free software; you can redistribute it and/or modify | |
| 7 | it under the terms of the GNU General Public License as published by | |
| 8 | the Free Software Foundation; either version 2 of the License, or | |
| 9 | (at your option) any later version. | |
| 10 | ||
| 11 | This program is distributed in the hope that it will be useful, | |
| 12 | but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| 14 | GNU General Public License for more details. | |
| 15 | ||
| 16 | You should have received a copy of the GNU General Public License along | |
| 17 | with this program; if not, write to the Free Software Foundation, Inc., | |
| 18 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. | |
| 19 | ||
| 20 | @licend The above is the entire license notice | |
| 21 | for the JavaScript code in this file | |
| 22 | */ | |
| 23 | function toggleVisibility(linkObj) | |
| 24 | { | |
| 25 | var base = $(linkObj).attr('id'); | |
| 26 | var summary = $('#'+base+'-summary'); | |
| 27 | var content = $('#'+base+'-content'); | |
| 28 | var trigger = $('#'+base+'-trigger'); | |
| 29 | var src=$(trigger).attr('src'); | |
| 30 | if (content.is(':visible')===true) { | |
| 31 | content.hide(); | |
| 32 | summary.show(); | |
| 33 | $(linkObj).addClass('closed').removeClass('opened'); | |
| 34 | $(trigger).attr('src',src.substring(0,src.length-8)+'closed.png'); | |
| 35 | } else { | |
| 36 | content.show(); | |
| 37 | summary.hide(); | |
| 38 | $(linkObj).removeClass('closed').addClass('opened'); | |
| 39 | $(trigger).attr('src',src.substring(0,src.length-10)+'open.png'); | |
| 40 | } | |
| 41 | return false; | |
| 42 | } | |
| 43 | ||
| 44 | function updateStripes() | |
| 45 | { | |
| 46 | $('table.directory tr'). | |
| 47 | removeClass('even').filter(':visible:even').addClass('even'); | |
| 48 | } | |
| 49 | ||
| 50 | function toggleLevel(level) | |
| 51 | { | |
| 52 | $('table.directory tr').each(function() { | |
| 53 | var l = this.id.split('_').length-1; | |
| 54 | var i = $('#img'+this.id.substring(3)); | |
| 55 | var a = $('#arr'+this.id.substring(3)); | |
| 56 | if (l<level+1) { | |
| 57 | i.removeClass('iconfopen iconfclosed').addClass('iconfopen'); | |
| 58 | a.html('▼'); | |
| 59 | $(this).show(); | |
| 60 | } else if (l==level+1) { | |
| 61 | i.removeClass('iconfclosed iconfopen').addClass('iconfclosed'); | |
| 62 | a.html('▶'); | |
| 63 | $(this).show(); | |
| 64 | } else { | |
| 65 | $(this).hide(); | |
| 66 | } | |
| 67 | }); | |
| 68 | updateStripes(); | |
| 69 | } | |
| 70 | ||
| 71 | function toggleFolder(id) | |
| 72 | { | |
| 73 | // the clicked row | |
| 74 | var currentRow = $('#row_'+id); | |
| 75 | ||
| 76 | // all rows after the clicked row | |
| 77 | var rows = currentRow.nextAll("tr"); | |
| 78 | ||
| 79 | var re = new RegExp('^row_'+id+'\\d+_$', "i"); //only one sub | |
| 80 | ||
| 81 | // only match elements AFTER this one (can't hide elements before) | |
| 82 | var childRows = rows.filter(function() { return this.id.match(re); }); | |
| 83 | ||
| 84 | // first row is visible we are HIDING | |
| 85 | if (childRows.filter(':first').is(':visible')===true) { | |
| 86 | // replace down arrow by right arrow for current row | |
| 87 | var currentRowSpans = currentRow.find("span"); | |
| 88 | currentRowSpans.filter(".iconfopen").removeClass("iconfopen").addClass("iconfclosed"); | |
| 89 | currentRowSpans.filter(".arrow").html('▶'); | |
| 90 | rows.filter("[id^=row_"+id+"]").hide(); // hide all children | |
| 91 | } else { // we are SHOWING | |
| 92 | // replace right arrow by down arrow for current row | |
| 93 | var currentRowSpans = currentRow.find("span"); | |
| 94 | currentRowSpans.filter(".iconfclosed").removeClass("iconfclosed").addClass("iconfopen"); | |
| 95 | currentRowSpans.filter(".arrow").html('▼'); | |
| 96 | // replace down arrows by right arrows for child rows | |
| 97 | var childRowsSpans = childRows.find("span"); | |
| 98 | childRowsSpans.filter(".iconfopen").removeClass("iconfopen").addClass("iconfclosed"); | |
| 99 | childRowsSpans.filter(".arrow").html('▶'); | |
| 100 | childRows.show(); //show all children | |
| 101 | } | |
| 102 | updateStripes(); | |
| 103 | } | |
| 104 | ||
| 105 | ||
| 106 | function toggleInherit(id) | |
| 107 | { | |
| 108 | var rows = $('tr.inherit.'+id); | |
| 109 | var img = $('tr.inherit_header.'+id+' img'); | |
| 110 | var src = $(img).attr('src'); | |
| 111 | if (rows.filter(':first').is(':visible')===true) { | |
| 112 | rows.css('display','none'); | |
| 113 | $(img).attr('src',src.substring(0,src.length-8)+'closed.png'); | |
| 114 | } else { | |
| 115 | rows.css('display','table-row'); // using show() causes jump in firefox | |
| 116 | $(img).attr('src',src.substring(0,src.length-10)+'open.png'); | |
| 117 | } | |
| 118 | } | |
| 119 | /* @license-end */ | |
| 120 | ||
| 121 | $(document).ready(function() { | |
| 122 | $('.code,.codeRef').each(function() { | |
| 123 | $(this).data('powertip',$('#'+$(this).attr('href').replace(/.*\//,'').replace(/[^a-z_A-Z0-9]/g,'_')).html()); | |
| 124 | $(this).powerTip({ placement: 's', smartPlacement: true, mouseOnToPopup: true }); | |
| 125 | }); | |
| 126 | }); |
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| 1 | <html xmlns="http://www.w3.org/1999/xhtml"> | |
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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
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| 66 | </iframe> | |
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| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="dir_7a6499598ddcfcabe96e224cb4a6d834.html">Projects</a></li><li class="navelem"><a class="el" href="dir_b5e01de8d0b5565037a326965003e69a.html">isospec</a></li><li class="navelem"><a class="el" href="dir_d48d5cdc71da00f1af92faf73cdbdfd7.html">IsoSpec</a></li><li class="navelem"><a class="el" href="dir_5010eccf620ec85ba5a1264edcd95342.html">IsoSpec++</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">element_tables.cpp</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include "element_tables.h"</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> {</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#ifdef __cplusplus</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="keyword">extern</span> <span class="stringliteral">"C"</span> {</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="keyword">const</span> <span class="keywordtype">int</span> elem_table_atomicNo [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> 1,</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> 1,</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> 2,</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> 2,</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> 3,</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> 3,</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> 4,</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> 5,</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> 5,</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> 6,</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> 6,</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> 7,</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> 7,</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> 8,</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> 8,</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> 8,</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> 9,</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> 10,</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> 10,</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> 10,</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> 11,</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> 12,</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> 12,</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> 12,</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> 13,</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> 14,</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> 14,</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> 14,</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> 15,</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> 16,</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> 16,</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> 16,</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span> 16,</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> 17,</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> 17,</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> 18,</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> 18,</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> 18,</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> 19,</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> 19,</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> 19,</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> 20,</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> 20,</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> 20,</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> 20,</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> 20,</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> 20,</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> 21,</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> 22,</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> 22,</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> 22,</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> 22,</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> 22,</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> 23,</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> 23,</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> 24,</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> 24,</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> 24,</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> 24,</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span> 25,</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span> 26,</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> 26,</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span> 26,</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> 26,</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> 27,</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> 28,</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> 28,</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> 28,</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span> 28,</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span> 28,</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> 29,</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> 29,</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> 30,</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span> 30,</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span> 30,</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span> 30,</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span> 30,</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span> 31,</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span> 31,</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span> 32,</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span> 32,</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span> 32,</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span> 32,</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span> 32,</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span> 33,</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span> 34,</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span> 34,</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span> 34,</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span> 34,</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span> 34,</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> 34,</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span> 35,</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> 35,</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> 36,</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span> 36,</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span> 36,</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> 36,</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> 36,</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> 36,</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span> 37,</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> 37,</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span> 38,</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span> 38,</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span> 38,</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span> 38,</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span> 39,</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span> 40,</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span> 40,</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span> 40,</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> 40,</div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span> 40,</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> 41,</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span> 42,</div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span> 42,</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span> 42,</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span> 42,</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span> 42,</div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span> 42,</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span> 42,</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span> 44,</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span> 44,</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span> 44,</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span> 44,</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span> 44,</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span> 44,</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span> 44,</div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span> 45,</div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span> 46,</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span> 46,</div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span> 46,</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span> 46,</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span> 46,</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span> 46,</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span> 47,</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span> 47,</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span> 48,</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span> 48,</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span> 48,</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span> 48,</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span> 48,</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span> 48,</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span> 48,</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span> 48,</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span> 49,</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span> 49,</div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span> 50,</div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span> 50,</div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span> 50,</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span> 50,</div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span> 50,</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span> 50,</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span> 50,</div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span> 50,</div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span> 50,</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span> 50,</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span> 51,</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span> 51,</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span> 52,</div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span> 52,</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span> 52,</div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span> 52,</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span> 52,</div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span> 52,</div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span> 52,</div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span> 52,</div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span> 53,</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span> 54,</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span> 54,</div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span> 54,</div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span> 54,</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span> 54,</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> 54,</div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span> 54,</div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span> 54,</div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span> 54,</div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span> 55,</div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span> 56,</div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span> 56,</div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span> 56,</div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span> 56,</div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span> 56,</div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span> 56,</div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span> 56,</div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span> 57,</div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span> 57,</div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span> 58,</div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span> 58,</div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span> 58,</div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span> 58,</div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span> 59,</div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span> 60,</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span> 60,</div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span> 60,</div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span> 60,</div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span> 60,</div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span> 60,</div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span> 60,</div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span> 62,</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span> 62,</div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span> 62,</div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span> 62,</div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span> 62,</div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span> 62,</div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span> 62,</div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span> 63,</div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span> 63,</div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span> 64,</div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span> 64,</div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span> 64,</div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span> 64,</div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span> 64,</div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span> 64,</div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span> 64,</div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span> 65,</div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span> 66,</div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span> 66,</div><div class="line"><a name="l00243"></a><span class="lineno"> 243</span> 66,</div><div class="line"><a name="l00244"></a><span class="lineno"> 244</span> 66,</div><div class="line"><a name="l00245"></a><span class="lineno"> 245</span> 66,</div><div class="line"><a name="l00246"></a><span class="lineno"> 246</span> 66,</div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span> 66,</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span> 67,</div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span> 68,</div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span> 68,</div><div class="line"><a name="l00251"></a><span class="lineno"> 251</span> 68,</div><div class="line"><a name="l00252"></a><span class="lineno"> 252</span> 68,</div><div class="line"><a name="l00253"></a><span class="lineno"> 253</span> 68,</div><div class="line"><a name="l00254"></a><span class="lineno"> 254</span> 68,</div><div class="line"><a name="l00255"></a><span class="lineno"> 255</span> 69,</div><div class="line"><a name="l00256"></a><span class="lineno"> 256</span> 70,</div><div class="line"><a name="l00257"></a><span class="lineno"> 257</span> 70,</div><div class="line"><a name="l00258"></a><span class="lineno"> 258</span> 70,</div><div class="line"><a name="l00259"></a><span class="lineno"> 259</span> 70,</div><div class="line"><a name="l00260"></a><span class="lineno"> 260</span> 70,</div><div class="line"><a name="l00261"></a><span class="lineno"> 261</span> 70,</div><div class="line"><a name="l00262"></a><span class="lineno"> 262</span> 70,</div><div class="line"><a name="l00263"></a><span class="lineno"> 263</span> 71,</div><div class="line"><a name="l00264"></a><span class="lineno"> 264</span> 71,</div><div class="line"><a name="l00265"></a><span class="lineno"> 265</span> 72,</div><div class="line"><a name="l00266"></a><span class="lineno"> 266</span> 72,</div><div class="line"><a name="l00267"></a><span class="lineno"> 267</span> 72,</div><div class="line"><a name="l00268"></a><span class="lineno"> 268</span> 72,</div><div class="line"><a name="l00269"></a><span class="lineno"> 269</span> 72,</div><div class="line"><a name="l00270"></a><span class="lineno"> 270</span> 72,</div><div class="line"><a name="l00271"></a><span class="lineno"> 271</span> 73,</div><div class="line"><a name="l00272"></a><span class="lineno"> 272</span> 73,</div><div class="line"><a name="l00273"></a><span class="lineno"> 273</span> 74,</div><div class="line"><a name="l00274"></a><span class="lineno"> 274</span> 74,</div><div class="line"><a name="l00275"></a><span class="lineno"> 275</span> 74,</div><div class="line"><a name="l00276"></a><span class="lineno"> 276</span> 74,</div><div class="line"><a name="l00277"></a><span class="lineno"> 277</span> 74,</div><div class="line"><a name="l00278"></a><span class="lineno"> 278</span> 75,</div><div class="line"><a name="l00279"></a><span class="lineno"> 279</span> 75,</div><div class="line"><a name="l00280"></a><span class="lineno"> 280</span> 76,</div><div class="line"><a name="l00281"></a><span class="lineno"> 281</span> 76,</div><div class="line"><a name="l00282"></a><span class="lineno"> 282</span> 76,</div><div class="line"><a name="l00283"></a><span class="lineno"> 283</span> 76,</div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span> 76,</div><div class="line"><a name="l00285"></a><span class="lineno"> 285</span> 76,</div><div class="line"><a name="l00286"></a><span class="lineno"> 286</span> 76,</div><div class="line"><a name="l00287"></a><span class="lineno"> 287</span> 77,</div><div class="line"><a name="l00288"></a><span class="lineno"> 288</span> 77,</div><div class="line"><a name="l00289"></a><span class="lineno"> 289</span> 78,</div><div class="line"><a name="l00290"></a><span class="lineno"> 290</span> 78,</div><div class="line"><a name="l00291"></a><span class="lineno"> 291</span> 78,</div><div class="line"><a name="l00292"></a><span class="lineno"> 292</span> 78,</div><div class="line"><a name="l00293"></a><span class="lineno"> 293</span> 78,</div><div class="line"><a name="l00294"></a><span class="lineno"> 294</span> 78,</div><div class="line"><a name="l00295"></a><span class="lineno"> 295</span> 79,</div><div class="line"><a name="l00296"></a><span class="lineno"> 296</span> 80,</div><div class="line"><a name="l00297"></a><span class="lineno"> 297</span> 80,</div><div class="line"><a name="l00298"></a><span class="lineno"> 298</span> 80,</div><div class="line"><a name="l00299"></a><span class="lineno"> 299</span> 80,</div><div class="line"><a name="l00300"></a><span class="lineno"> 300</span> 80,</div><div class="line"><a name="l00301"></a><span class="lineno"> 301</span> 80,</div><div class="line"><a name="l00302"></a><span class="lineno"> 302</span> 80,</div><div class="line"><a name="l00303"></a><span class="lineno"> 303</span> 81,</div><div class="line"><a name="l00304"></a><span class="lineno"> 304</span> 81,</div><div class="line"><a name="l00305"></a><span class="lineno"> 305</span> 82,</div><div class="line"><a name="l00306"></a><span class="lineno"> 306</span> 82,</div><div class="line"><a name="l00307"></a><span class="lineno"> 307</span> 82,</div><div class="line"><a name="l00308"></a><span class="lineno"> 308</span> 82,</div><div class="line"><a name="l00309"></a><span class="lineno"> 309</span> 83,</div><div class="line"><a name="l00310"></a><span class="lineno"> 310</span> 92,</div><div class="line"><a name="l00311"></a><span class="lineno"> 311</span> 92,</div><div class="line"><a name="l00312"></a><span class="lineno"> 312</span> 92,</div><div class="line"><a name="l00313"></a><span class="lineno"> 313</span> 90,</div><div class="line"><a name="l00314"></a><span class="lineno"> 314</span> 91,</div><div class="line"><a name="l00315"></a><span class="lineno"> 315</span> };</div><div class="line"><a name="l00316"></a><span class="lineno"> 316</span> </div><div class="line"><a name="l00317"></a><span class="lineno"> 317</span> </div><div class="line"><a name="l00318"></a><span class="lineno"> 318</span> <span class="keyword">const</span> <span class="keywordtype">double</span> elem_table_mass [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {</div><div class="line"><a name="l00319"></a><span class="lineno"> 319</span> 1.00782503227,</div><div class="line"><a name="l00320"></a><span class="lineno"> 320</span> 2.01410177819,</div><div class="line"><a name="l00321"></a><span class="lineno"> 321</span> 3.016029322,</div><div class="line"><a name="l00322"></a><span class="lineno"> 322</span> 4.00260325414,</div><div class="line"><a name="l00323"></a><span class="lineno"> 323</span> 6.0151228871,</div><div class="line"><a name="l00324"></a><span class="lineno"> 324</span> 7.016003443,</div><div class="line"><a name="l00325"></a><span class="lineno"> 325</span> 9.01218316,</div><div class="line"><a name="l00326"></a><span class="lineno"> 326</span> 10.0129373,</div><div class="line"><a name="l00327"></a><span class="lineno"> 327</span> 11.0093053,</div><div class="line"><a name="l00328"></a><span class="lineno"> 328</span> 12,</div><div class="line"><a name="l00329"></a><span class="lineno"> 329</span> 13.0033548352,</div><div class="line"><a name="l00330"></a><span class="lineno"> 330</span> 14.0030740042,</div><div class="line"><a name="l00331"></a><span class="lineno"> 331</span> 15.0001088994,</div><div class="line"><a name="l00332"></a><span class="lineno"> 332</span> 15.9949146202,</div><div class="line"><a name="l00333"></a><span class="lineno"> 333</span> 16.9991317576,</div><div class="line"><a name="l00334"></a><span class="lineno"> 334</span> 17.9991596137,</div><div class="line"><a name="l00335"></a><span class="lineno"> 335</span> 18.9984031637,</div><div class="line"><a name="l00336"></a><span class="lineno"> 336</span> 19.992440182,</div><div class="line"><a name="l00337"></a><span class="lineno"> 337</span> 20.99384673,</div><div class="line"><a name="l00338"></a><span class="lineno"> 338</span> 21.99138512,</div><div class="line"><a name="l00339"></a><span class="lineno"> 339</span> 22.989769282,</div><div class="line"><a name="l00340"></a><span class="lineno"> 340</span> 23.985041701,</div><div class="line"><a name="l00341"></a><span class="lineno"> 341</span> 24.98583703,</div><div class="line"><a name="l00342"></a><span class="lineno"> 342</span> 25.98259302,</div><div class="line"><a name="l00343"></a><span class="lineno"> 343</span> 26.98153858,</div><div class="line"><a name="l00344"></a><span class="lineno"> 344</span> 27.9769265353,</div><div class="line"><a name="l00345"></a><span class="lineno"> 345</span> 28.9764946653,</div><div class="line"><a name="l00346"></a><span class="lineno"> 346</span> 29.973770012,</div><div class="line"><a name="l00347"></a><span class="lineno"> 347</span> 30.9737619986,</div><div class="line"><a name="l00348"></a><span class="lineno"> 348</span> 31.9720711741,</div><div class="line"><a name="l00349"></a><span class="lineno"> 349</span> 32.9714589101,</div><div class="line"><a name="l00350"></a><span class="lineno"> 350</span> 33.96786703,</div><div class="line"><a name="l00351"></a><span class="lineno"> 351</span> 35.9670812,</div><div class="line"><a name="l00352"></a><span class="lineno"> 352</span> 34.96885273,</div><div class="line"><a name="l00353"></a><span class="lineno"> 353</span> 36.96590264,</div><div class="line"><a name="l00354"></a><span class="lineno"> 354</span> 35.96754512,</div><div class="line"><a name="l00355"></a><span class="lineno"> 355</span> 37.9627322,</div><div class="line"><a name="l00356"></a><span class="lineno"> 356</span> 39.962383122,</div><div class="line"><a name="l00357"></a><span class="lineno"> 357</span> 38.963706493,</div><div class="line"><a name="l00358"></a><span class="lineno"> 358</span> 39.96399824,</div><div class="line"><a name="l00359"></a><span class="lineno"> 359</span> 40.961825263,</div><div class="line"><a name="l00360"></a><span class="lineno"> 360</span> 39.96259092,</div><div class="line"><a name="l00361"></a><span class="lineno"> 361</span> 41.9586181,</div><div class="line"><a name="l00362"></a><span class="lineno"> 362</span> 42.9587662,</div><div class="line"><a name="l00363"></a><span class="lineno"> 363</span> 43.9554822,</div><div class="line"><a name="l00364"></a><span class="lineno"> 364</span> 45.953692,</div><div class="line"><a name="l00365"></a><span class="lineno"> 365</span> 47.95252289,</div><div class="line"><a name="l00366"></a><span class="lineno"> 366</span> 44.9559086,</div><div class="line"><a name="l00367"></a><span class="lineno"> 367</span> 45.9526283,</div><div class="line"><a name="l00368"></a><span class="lineno"> 368</span> 46.9517593,</div><div class="line"><a name="l00369"></a><span class="lineno"> 369</span> 47.9479423,</div><div class="line"><a name="l00370"></a><span class="lineno"> 370</span> 48.9478663,</div><div class="line"><a name="l00371"></a><span class="lineno"> 371</span> 49.9447873,</div><div class="line"><a name="l00372"></a><span class="lineno"> 372</span> 49.9471567,</div><div class="line"><a name="l00373"></a><span class="lineno"> 373</span> 50.9439577,</div><div class="line"><a name="l00374"></a><span class="lineno"> 374</span> 49.9460427,</div><div class="line"><a name="l00375"></a><span class="lineno"> 375</span> 51.9405064,</div><div class="line"><a name="l00376"></a><span class="lineno"> 376</span> 52.9406484,</div><div class="line"><a name="l00377"></a><span class="lineno"> 377</span> 53.9388794,</div><div class="line"><a name="l00378"></a><span class="lineno"> 378</span> 54.9380443,</div><div class="line"><a name="l00379"></a><span class="lineno"> 379</span> 53.9396093,</div><div class="line"><a name="l00380"></a><span class="lineno"> 380</span> 55.9349363,</div><div class="line"><a name="l00381"></a><span class="lineno"> 381</span> 56.9353933,</div><div class="line"><a name="l00382"></a><span class="lineno"> 382</span> 57.9332743,</div><div class="line"><a name="l00383"></a><span class="lineno"> 383</span> 58.9331944,</div><div class="line"><a name="l00384"></a><span class="lineno"> 384</span> 57.9353423,</div><div class="line"><a name="l00385"></a><span class="lineno"> 385</span> 59.9307863,</div><div class="line"><a name="l00386"></a><span class="lineno"> 386</span> 60.9310563,</div><div class="line"><a name="l00387"></a><span class="lineno"> 387</span> 61.9283454,</div><div class="line"><a name="l00388"></a><span class="lineno"> 388</span> 63.9279674,</div><div class="line"><a name="l00389"></a><span class="lineno"> 389</span> 62.9295984,</div><div class="line"><a name="l00390"></a><span class="lineno"> 390</span> 64.9277906,</div><div class="line"><a name="l00391"></a><span class="lineno"> 391</span> 63.9291426,</div><div class="line"><a name="l00392"></a><span class="lineno"> 392</span> 65.9260347,</div><div class="line"><a name="l00393"></a><span class="lineno"> 393</span> 66.9271287,</div><div class="line"><a name="l00394"></a><span class="lineno"> 394</span> 67.9248457,</div><div class="line"><a name="l00395"></a><span class="lineno"> 395</span> 69.925322,</div><div class="line"><a name="l00396"></a><span class="lineno"> 396</span> 68.9255749,</div><div class="line"><a name="l00397"></a><span class="lineno"> 397</span> 70.9247037,</div><div class="line"><a name="l00398"></a><span class="lineno"> 398</span> 69.9242497,</div><div class="line"><a name="l00399"></a><span class="lineno"> 399</span> 71.92207586,</div><div class="line"><a name="l00400"></a><span class="lineno"> 400</span> 72.92345904,</div><div class="line"><a name="l00401"></a><span class="lineno"> 401</span> 73.921177761,</div><div class="line"><a name="l00402"></a><span class="lineno"> 402</span> 75.92140272,</div><div class="line"><a name="l00403"></a><span class="lineno"> 403</span> 74.9215957,</div><div class="line"><a name="l00404"></a><span class="lineno"> 404</span> 73.92247591,</div><div class="line"><a name="l00405"></a><span class="lineno"> 405</span> 75.91921372,</div><div class="line"><a name="l00406"></a><span class="lineno"> 406</span> 76.91991426,</div><div class="line"><a name="l00407"></a><span class="lineno"> 407</span> 77.9173092,</div><div class="line"><a name="l00408"></a><span class="lineno"> 408</span> 79.9165229,</div><div class="line"><a name="l00409"></a><span class="lineno"> 409</span> 81.9167001,</div><div class="line"><a name="l00410"></a><span class="lineno"> 410</span> 78.9183381,</div><div class="line"><a name="l00411"></a><span class="lineno"> 411</span> 80.9162901,</div><div class="line"><a name="l00412"></a><span class="lineno"> 412</span> 77.9203656,</div><div class="line"><a name="l00413"></a><span class="lineno"> 413</span> 79.9163786,</div><div class="line"><a name="l00414"></a><span class="lineno"> 414</span> 81.9134837,</div><div class="line"><a name="l00415"></a><span class="lineno"> 415</span> 82.9141272,</div><div class="line"><a name="l00416"></a><span class="lineno"> 416</span> 83.911497733,</div><div class="line"><a name="l00417"></a><span class="lineno"> 417</span> 85.910610633,</div><div class="line"><a name="l00418"></a><span class="lineno"> 418</span> 84.911789743,</div><div class="line"><a name="l00419"></a><span class="lineno"> 419</span> 86.909180536,</div><div class="line"><a name="l00420"></a><span class="lineno"> 420</span> 83.9134199,</div><div class="line"><a name="l00421"></a><span class="lineno"> 421</span> 85.9092619,</div><div class="line"><a name="l00422"></a><span class="lineno"> 422</span> 86.9088789,</div><div class="line"><a name="l00423"></a><span class="lineno"> 423</span> 87.9056139,</div><div class="line"><a name="l00424"></a><span class="lineno"> 424</span> 88.905842,</div><div class="line"><a name="l00425"></a><span class="lineno"> 425</span> 89.904702,</div><div class="line"><a name="l00426"></a><span class="lineno"> 426</span> 90.905642,</div><div class="line"><a name="l00427"></a><span class="lineno"> 427</span> 91.905032,</div><div class="line"><a name="l00428"></a><span class="lineno"> 428</span> 93.906312,</div><div class="line"><a name="l00429"></a><span class="lineno"> 429</span> 95.908272,</div><div class="line"><a name="l00430"></a><span class="lineno"> 430</span> 92.906372,</div><div class="line"><a name="l00431"></a><span class="lineno"> 431</span> 91.9068086,</div><div class="line"><a name="l00432"></a><span class="lineno"> 432</span> 93.9050853,</div><div class="line"><a name="l00433"></a><span class="lineno"> 433</span> 94.9058393,</div><div class="line"><a name="l00434"></a><span class="lineno"> 434</span> 95.9046763,</div><div class="line"><a name="l00435"></a><span class="lineno"> 435</span> 96.9060183,</div><div class="line"><a name="l00436"></a><span class="lineno"> 436</span> 97.9054053,</div><div class="line"><a name="l00437"></a><span class="lineno"> 437</span> 99.9074728,</div><div class="line"><a name="l00438"></a><span class="lineno"> 438</span> 95.9075903,</div><div class="line"><a name="l00439"></a><span class="lineno"> 439</span> 97.905296,</div><div class="line"><a name="l00440"></a><span class="lineno"> 440</span> 98.9059348,</div><div class="line"><a name="l00441"></a><span class="lineno"> 441</span> 99.9042148,</div><div class="line"><a name="l00442"></a><span class="lineno"> 442</span> 100.9055779,</div><div class="line"><a name="l00443"></a><span class="lineno"> 443</span> 101.9043449,</div><div class="line"><a name="l00444"></a><span class="lineno"> 444</span> 103.905432,</div><div class="line"><a name="l00445"></a><span class="lineno"> 445</span> 102.905502,</div><div class="line"><a name="l00446"></a><span class="lineno"> 446</span> 101.905602,</div><div class="line"><a name="l00447"></a><span class="lineno"> 447</span> 103.9040311,</div><div class="line"><a name="l00448"></a><span class="lineno"> 448</span> 104.9050809,</div><div class="line"><a name="l00449"></a><span class="lineno"> 449</span> 105.9034809,</div><div class="line"><a name="l00450"></a><span class="lineno"> 450</span> 107.9038929,</div><div class="line"><a name="l00451"></a><span class="lineno"> 451</span> 109.9051726,</div><div class="line"><a name="l00452"></a><span class="lineno"> 452</span> 106.905092,</div><div class="line"><a name="l00453"></a><span class="lineno"> 453</span> 108.9047551,</div><div class="line"><a name="l00454"></a><span class="lineno"> 454</span> 105.9064609,</div><div class="line"><a name="l00455"></a><span class="lineno"> 455</span> 107.9041839,</div><div class="line"><a name="l00456"></a><span class="lineno"> 456</span> 109.9030074,</div><div class="line"><a name="l00457"></a><span class="lineno"> 457</span> 110.9041834,</div><div class="line"><a name="l00458"></a><span class="lineno"> 458</span> 111.9027634,</div><div class="line"><a name="l00459"></a><span class="lineno"> 459</span> 112.9044083,</div><div class="line"><a name="l00460"></a><span class="lineno"> 460</span> 113.9033653,</div><div class="line"><a name="l00461"></a><span class="lineno"> 461</span> 115.9047632,</div><div class="line"><a name="l00462"></a><span class="lineno"> 462</span> 112.9040627,</div><div class="line"><a name="l00463"></a><span class="lineno"> 463</span> 114.903878789,</div><div class="line"><a name="l00464"></a><span class="lineno"> 464</span> 111.9048244,</div><div class="line"><a name="l00465"></a><span class="lineno"> 465</span> 113.9027837,</div><div class="line"><a name="l00466"></a><span class="lineno"> 466</span> 114.90334471,</div><div class="line"><a name="l00467"></a><span class="lineno"> 467</span> 115.9017431,</div><div class="line"><a name="l00468"></a><span class="lineno"> 468</span> 116.9029543,</div><div class="line"><a name="l00469"></a><span class="lineno"> 469</span> 117.9016073,</div><div class="line"><a name="l00470"></a><span class="lineno"> 470</span> 118.9033116,</div><div class="line"><a name="l00471"></a><span class="lineno"> 471</span> 119.9022027,</div><div class="line"><a name="l00472"></a><span class="lineno"> 472</span> 121.903442,</div><div class="line"><a name="l00473"></a><span class="lineno"> 473</span> 123.9052778,</div><div class="line"><a name="l00474"></a><span class="lineno"> 474</span> 120.903812,</div><div class="line"><a name="l00475"></a><span class="lineno"> 475</span> 122.904212,</div><div class="line"><a name="l00476"></a><span class="lineno"> 476</span> 119.904062,</div><div class="line"><a name="l00477"></a><span class="lineno"> 477</span> 121.903041,</div><div class="line"><a name="l00478"></a><span class="lineno"> 478</span> 122.904271,</div><div class="line"><a name="l00479"></a><span class="lineno"> 479</span> 123.902821,</div><div class="line"><a name="l00480"></a><span class="lineno"> 480</span> 124.904431,</div><div class="line"><a name="l00481"></a><span class="lineno"> 481</span> 125.903311,</div><div class="line"><a name="l00482"></a><span class="lineno"> 482</span> 127.9044617,</div><div class="line"><a name="l00483"></a><span class="lineno"> 483</span> 129.906222759,</div><div class="line"><a name="l00484"></a><span class="lineno"> 484</span> 126.904473,</div><div class="line"><a name="l00485"></a><span class="lineno"> 485</span> 123.905892,</div><div class="line"><a name="l00486"></a><span class="lineno"> 486</span> 125.904303,</div><div class="line"><a name="l00487"></a><span class="lineno"> 487</span> 127.9035318,</div><div class="line"><a name="l00488"></a><span class="lineno"> 488</span> 128.904780864,</div><div class="line"><a name="l00489"></a><span class="lineno"> 489</span> 129.90350941,</div><div class="line"><a name="l00490"></a><span class="lineno"> 490</span> 130.9050842,</div><div class="line"><a name="l00491"></a><span class="lineno"> 491</span> 131.904155094,</div><div class="line"><a name="l00492"></a><span class="lineno"> 492</span> 133.9053957,</div><div class="line"><a name="l00493"></a><span class="lineno"> 493</span> 135.907214488,</div><div class="line"><a name="l00494"></a><span class="lineno"> 494</span> 132.905451967,</div><div class="line"><a name="l00495"></a><span class="lineno"> 495</span> 129.906322,</div><div class="line"><a name="l00496"></a><span class="lineno"> 496</span> 131.9050618,</div><div class="line"><a name="l00497"></a><span class="lineno"> 497</span> 133.9045082,</div><div class="line"><a name="l00498"></a><span class="lineno"> 498</span> 134.9056882,</div><div class="line"><a name="l00499"></a><span class="lineno"> 499</span> 135.9045762,</div><div class="line"><a name="l00500"></a><span class="lineno"> 500</span> 136.9058272,</div><div class="line"><a name="l00501"></a><span class="lineno"> 501</span> 137.9052472,</div><div class="line"><a name="l00502"></a><span class="lineno"> 502</span> 137.907123,</div><div class="line"><a name="l00503"></a><span class="lineno"> 503</span> 138.906362,</div><div class="line"><a name="l00504"></a><span class="lineno"> 504</span> 135.9071293,</div><div class="line"><a name="l00505"></a><span class="lineno"> 505</span> 137.905998,</div><div class="line"><a name="l00506"></a><span class="lineno"> 506</span> 139.905442,</div><div class="line"><a name="l00507"></a><span class="lineno"> 507</span> 141.909252,</div><div class="line"><a name="l00508"></a><span class="lineno"> 508</span> 140.907662,</div><div class="line"><a name="l00509"></a><span class="lineno"> 509</span> 141.907732,</div><div class="line"><a name="l00510"></a><span class="lineno"> 510</span> 142.909822,</div><div class="line"><a name="l00511"></a><span class="lineno"> 511</span> 143.910092,</div><div class="line"><a name="l00512"></a><span class="lineno"> 512</span> 144.912582,</div><div class="line"><a name="l00513"></a><span class="lineno"> 513</span> 145.913122,</div><div class="line"><a name="l00514"></a><span class="lineno"> 514</span> 147.916902,</div><div class="line"><a name="l00515"></a><span class="lineno"> 515</span> 149.920902,</div><div class="line"><a name="l00516"></a><span class="lineno"> 516</span> 143.912012,</div><div class="line"><a name="l00517"></a><span class="lineno"> 517</span> 146.914902,</div><div class="line"><a name="l00518"></a><span class="lineno"> 518</span> 147.914832,</div><div class="line"><a name="l00519"></a><span class="lineno"> 519</span> 148.917192,</div><div class="line"><a name="l00520"></a><span class="lineno"> 520</span> 149.917282,</div><div class="line"><a name="l00521"></a><span class="lineno"> 521</span> 151.919742,</div><div class="line"><a name="l00522"></a><span class="lineno"> 522</span> 153.922222,</div><div class="line"><a name="l00523"></a><span class="lineno"> 523</span> 150.919862,</div><div class="line"><a name="l00524"></a><span class="lineno"> 524</span> 152.921242,</div><div class="line"><a name="l00525"></a><span class="lineno"> 525</span> 151.919802,</div><div class="line"><a name="l00526"></a><span class="lineno"> 526</span> 153.920872,</div><div class="line"><a name="l00527"></a><span class="lineno"> 527</span> 154.922632,</div><div class="line"><a name="l00528"></a><span class="lineno"> 528</span> 155.922132,</div><div class="line"><a name="l00529"></a><span class="lineno"> 529</span> 156.923972,</div><div class="line"><a name="l00530"></a><span class="lineno"> 530</span> 157.924112,</div><div class="line"><a name="l00531"></a><span class="lineno"> 531</span> 159.927062,</div><div class="line"><a name="l00532"></a><span class="lineno"> 532</span> 158.925352,</div><div class="line"><a name="l00533"></a><span class="lineno"> 533</span> 155.924282,</div><div class="line"><a name="l00534"></a><span class="lineno"> 534</span> 157.924422,</div><div class="line"><a name="l00535"></a><span class="lineno"> 535</span> 159.925202,</div><div class="line"><a name="l00536"></a><span class="lineno"> 536</span> 160.926942,</div><div class="line"><a name="l00537"></a><span class="lineno"> 537</span> 161.926812,</div><div class="line"><a name="l00538"></a><span class="lineno"> 538</span> 162.928742,</div><div class="line"><a name="l00539"></a><span class="lineno"> 539</span> 163.929182,</div><div class="line"><a name="l00540"></a><span class="lineno"> 540</span> 164.930332,</div><div class="line"><a name="l00541"></a><span class="lineno"> 541</span> 161.928792,</div><div class="line"><a name="l00542"></a><span class="lineno"> 542</span> 163.929212,</div><div class="line"><a name="l00543"></a><span class="lineno"> 543</span> 165.930302,</div><div class="line"><a name="l00544"></a><span class="lineno"> 544</span> 166.932052,</div><div class="line"><a name="l00545"></a><span class="lineno"> 545</span> 167.932382,</div><div class="line"><a name="l00546"></a><span class="lineno"> 546</span> 169.935472,</div><div class="line"><a name="l00547"></a><span class="lineno"> 547</span> 168.934222,</div><div class="line"><a name="l00548"></a><span class="lineno"> 548</span> 167.933892,</div><div class="line"><a name="l00549"></a><span class="lineno"> 549</span> 169.934772,</div><div class="line"><a name="l00550"></a><span class="lineno"> 550</span> 170.936332,</div><div class="line"><a name="l00551"></a><span class="lineno"> 551</span> 171.936392,</div><div class="line"><a name="l00552"></a><span class="lineno"> 552</span> 172.938222,</div><div class="line"><a name="l00553"></a><span class="lineno"> 553</span> 173.938872,</div><div class="line"><a name="l00554"></a><span class="lineno"> 554</span> 175.942582,</div><div class="line"><a name="l00555"></a><span class="lineno"> 555</span> 174.940782,</div><div class="line"><a name="l00556"></a><span class="lineno"> 556</span> 175.942692,</div><div class="line"><a name="l00557"></a><span class="lineno"> 557</span> 173.940052,</div><div class="line"><a name="l00558"></a><span class="lineno"> 558</span> 175.941412,</div><div class="line"><a name="l00559"></a><span class="lineno"> 559</span> 176.943232,</div><div class="line"><a name="l00560"></a><span class="lineno"> 560</span> 177.943712,</div><div class="line"><a name="l00561"></a><span class="lineno"> 561</span> 178.945822,</div><div class="line"><a name="l00562"></a><span class="lineno"> 562</span> 179.946562,</div><div class="line"><a name="l00563"></a><span class="lineno"> 563</span> 179.947462,</div><div class="line"><a name="l00564"></a><span class="lineno"> 564</span> 180.948002,</div><div class="line"><a name="l00565"></a><span class="lineno"> 565</span> 179.946712,</div><div class="line"><a name="l00566"></a><span class="lineno"> 566</span> 181.9482047,</div><div class="line"><a name="l00567"></a><span class="lineno"> 567</span> 182.9502237,</div><div class="line"><a name="l00568"></a><span class="lineno"> 568</span> 183.9509317,</div><div class="line"><a name="l00569"></a><span class="lineno"> 569</span> 185.954362,</div><div class="line"><a name="l00570"></a><span class="lineno"> 570</span> 184.9529559,</div><div class="line"><a name="l00571"></a><span class="lineno"> 571</span> 186.955751,</div><div class="line"><a name="l00572"></a><span class="lineno"> 572</span> 183.9524891,</div><div class="line"><a name="l00573"></a><span class="lineno"> 573</span> 185.953841,</div><div class="line"><a name="l00574"></a><span class="lineno"> 574</span> 186.955751,</div><div class="line"><a name="l00575"></a><span class="lineno"> 575</span> 187.955841,</div><div class="line"><a name="l00576"></a><span class="lineno"> 576</span> 188.958142,</div><div class="line"><a name="l00577"></a><span class="lineno"> 577</span> 189.958442,</div><div class="line"><a name="l00578"></a><span class="lineno"> 578</span> 191.961482,</div><div class="line"><a name="l00579"></a><span class="lineno"> 579</span> 190.960592,</div><div class="line"><a name="l00580"></a><span class="lineno"> 580</span> 192.962922,</div><div class="line"><a name="l00581"></a><span class="lineno"> 581</span> 189.959934,</div><div class="line"><a name="l00582"></a><span class="lineno"> 582</span> 191.961042,</div><div class="line"><a name="l00583"></a><span class="lineno"> 583</span> 193.9626817,</div><div class="line"><a name="l00584"></a><span class="lineno"> 584</span> 194.9647927,</div><div class="line"><a name="l00585"></a><span class="lineno"> 585</span> 195.9649527,</div><div class="line"><a name="l00586"></a><span class="lineno"> 586</span> 197.967892,</div><div class="line"><a name="l00587"></a><span class="lineno"> 587</span> 196.9665696,</div><div class="line"><a name="l00588"></a><span class="lineno"> 588</span> 195.965832,</div><div class="line"><a name="l00589"></a><span class="lineno"> 589</span> 197.9667693,</div><div class="line"><a name="l00590"></a><span class="lineno"> 590</span> 198.9682813,</div><div class="line"><a name="l00591"></a><span class="lineno"> 591</span> 199.9683273,</div><div class="line"><a name="l00592"></a><span class="lineno"> 592</span> 200.9703036,</div><div class="line"><a name="l00593"></a><span class="lineno"> 593</span> 201.9706436,</div><div class="line"><a name="l00594"></a><span class="lineno"> 594</span> 203.9734943,</div><div class="line"><a name="l00595"></a><span class="lineno"> 595</span> 202.9723451,</div><div class="line"><a name="l00596"></a><span class="lineno"> 596</span> 204.9744281,</div><div class="line"><a name="l00597"></a><span class="lineno"> 597</span> 203.9730449,</div><div class="line"><a name="l00598"></a><span class="lineno"> 598</span> 205.9744669,</div><div class="line"><a name="l00599"></a><span class="lineno"> 599</span> 206.9758979,</div><div class="line"><a name="l00600"></a><span class="lineno"> 600</span> 207.9766539,</div><div class="line"><a name="l00601"></a><span class="lineno"> 601</span> 208.980401,</div><div class="line"><a name="l00602"></a><span class="lineno"> 602</span> 234.040952,</div><div class="line"><a name="l00603"></a><span class="lineno"> 603</span> 235.043932,</div><div class="line"><a name="l00604"></a><span class="lineno"> 604</span> 238.050792,</div><div class="line"><a name="l00605"></a><span class="lineno"> 605</span> 232.038062,</div><div class="line"><a name="l00606"></a><span class="lineno"> 606</span> 231.035882,</div><div class="line"><a name="l00607"></a><span class="lineno"> 607</span> };</div><div class="line"><a name="l00608"></a><span class="lineno"> 608</span> </div><div class="line"><a name="l00609"></a><span class="lineno"> 609</span> </div><div class="line"><a name="l00610"></a><span class="lineno"> 610</span> <span class="keyword">const</span> <span class="keywordtype">int</span> elem_table_massNo [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {</div><div class="line"><a name="l00611"></a><span class="lineno"> 611</span> 1,</div><div class="line"><a name="l00612"></a><span class="lineno"> 612</span> 2,</div><div class="line"><a name="l00613"></a><span class="lineno"> 613</span> 3,</div><div class="line"><a name="l00614"></a><span class="lineno"> 614</span> 4,</div><div class="line"><a name="l00615"></a><span class="lineno"> 615</span> 6,</div><div class="line"><a name="l00616"></a><span class="lineno"> 616</span> 7,</div><div class="line"><a name="l00617"></a><span class="lineno"> 617</span> 9,</div><div class="line"><a name="l00618"></a><span class="lineno"> 618</span> 10,</div><div class="line"><a name="l00619"></a><span class="lineno"> 619</span> 11,</div><div class="line"><a name="l00620"></a><span class="lineno"> 620</span> 12,</div><div class="line"><a name="l00621"></a><span class="lineno"> 621</span> 13,</div><div class="line"><a name="l00622"></a><span class="lineno"> 622</span> 14,</div><div class="line"><a name="l00623"></a><span class="lineno"> 623</span> 15,</div><div class="line"><a name="l00624"></a><span class="lineno"> 624</span> 16,</div><div class="line"><a name="l00625"></a><span class="lineno"> 625</span> 17,</div><div class="line"><a name="l00626"></a><span class="lineno"> 626</span> 18,</div><div class="line"><a name="l00627"></a><span class="lineno"> 627</span> 19,</div><div class="line"><a name="l00628"></a><span class="lineno"> 628</span> 20,</div><div class="line"><a name="l00629"></a><span class="lineno"> 629</span> 21,</div><div class="line"><a name="l00630"></a><span class="lineno"> 630</span> 22,</div><div class="line"><a name="l00631"></a><span class="lineno"> 631</span> 23,</div><div class="line"><a name="l00632"></a><span class="lineno"> 632</span> 24,</div><div class="line"><a name="l00633"></a><span class="lineno"> 633</span> 25,</div><div class="line"><a name="l00634"></a><span class="lineno"> 634</span> 26,</div><div class="line"><a name="l00635"></a><span class="lineno"> 635</span> 27,</div><div class="line"><a name="l00636"></a><span class="lineno"> 636</span> 28,</div><div class="line"><a name="l00637"></a><span class="lineno"> 637</span> 29,</div><div class="line"><a name="l00638"></a><span class="lineno"> 638</span> 30,</div><div class="line"><a name="l00639"></a><span class="lineno"> 639</span> 31,</div><div class="line"><a name="l00640"></a><span class="lineno"> 640</span> 32,</div><div class="line"><a name="l00641"></a><span class="lineno"> 641</span> 33,</div><div class="line"><a name="l00642"></a><span class="lineno"> 642</span> 34,</div><div class="line"><a name="l00643"></a><span class="lineno"> 643</span> 36,</div><div class="line"><a name="l00644"></a><span class="lineno"> 644</span> 35,</div><div class="line"><a name="l00645"></a><span class="lineno"> 645</span> 37,</div><div class="line"><a name="l00646"></a><span class="lineno"> 646</span> 36,</div><div class="line"><a name="l00647"></a><span class="lineno"> 647</span> 38,</div><div class="line"><a name="l00648"></a><span class="lineno"> 648</span> 40,</div><div class="line"><a name="l00649"></a><span class="lineno"> 649</span> 39,</div><div class="line"><a name="l00650"></a><span class="lineno"> 650</span> 40,</div><div class="line"><a name="l00651"></a><span class="lineno"> 651</span> 41,</div><div class="line"><a name="l00652"></a><span class="lineno"> 652</span> 40,</div><div class="line"><a name="l00653"></a><span class="lineno"> 653</span> 42,</div><div class="line"><a name="l00654"></a><span class="lineno"> 654</span> 43,</div><div class="line"><a name="l00655"></a><span class="lineno"> 655</span> 44,</div><div class="line"><a name="l00656"></a><span class="lineno"> 656</span> 46,</div><div class="line"><a name="l00657"></a><span class="lineno"> 657</span> 48,</div><div class="line"><a name="l00658"></a><span class="lineno"> 658</span> 45,</div><div class="line"><a name="l00659"></a><span class="lineno"> 659</span> 46,</div><div class="line"><a name="l00660"></a><span class="lineno"> 660</span> 47,</div><div class="line"><a name="l00661"></a><span class="lineno"> 661</span> 48,</div><div class="line"><a name="l00662"></a><span class="lineno"> 662</span> 49,</div><div class="line"><a name="l00663"></a><span class="lineno"> 663</span> 50,</div><div class="line"><a name="l00664"></a><span class="lineno"> 664</span> 50,</div><div class="line"><a name="l00665"></a><span class="lineno"> 665</span> 51,</div><div class="line"><a name="l00666"></a><span class="lineno"> 666</span> 50,</div><div class="line"><a name="l00667"></a><span class="lineno"> 667</span> 52,</div><div class="line"><a name="l00668"></a><span class="lineno"> 668</span> 53,</div><div class="line"><a name="l00669"></a><span class="lineno"> 669</span> 54,</div><div class="line"><a name="l00670"></a><span class="lineno"> 670</span> 55,</div><div class="line"><a name="l00671"></a><span class="lineno"> 671</span> 54,</div><div class="line"><a name="l00672"></a><span class="lineno"> 672</span> 56,</div><div class="line"><a name="l00673"></a><span class="lineno"> 673</span> 57,</div><div class="line"><a name="l00674"></a><span class="lineno"> 674</span> 58,</div><div class="line"><a name="l00675"></a><span class="lineno"> 675</span> 59,</div><div class="line"><a name="l00676"></a><span class="lineno"> 676</span> 58,</div><div class="line"><a name="l00677"></a><span class="lineno"> 677</span> 60,</div><div class="line"><a name="l00678"></a><span class="lineno"> 678</span> 61,</div><div class="line"><a name="l00679"></a><span class="lineno"> 679</span> 62,</div><div class="line"><a name="l00680"></a><span class="lineno"> 680</span> 64,</div><div class="line"><a name="l00681"></a><span class="lineno"> 681</span> 63,</div><div class="line"><a name="l00682"></a><span class="lineno"> 682</span> 65,</div><div class="line"><a name="l00683"></a><span class="lineno"> 683</span> 64,</div><div class="line"><a name="l00684"></a><span class="lineno"> 684</span> 66,</div><div class="line"><a name="l00685"></a><span class="lineno"> 685</span> 67,</div><div class="line"><a name="l00686"></a><span class="lineno"> 686</span> 68,</div><div class="line"><a name="l00687"></a><span class="lineno"> 687</span> 70,</div><div class="line"><a name="l00688"></a><span class="lineno"> 688</span> 69,</div><div class="line"><a name="l00689"></a><span class="lineno"> 689</span> 71,</div><div class="line"><a name="l00690"></a><span class="lineno"> 690</span> 70,</div><div class="line"><a name="l00691"></a><span class="lineno"> 691</span> 72,</div><div class="line"><a name="l00692"></a><span class="lineno"> 692</span> 73,</div><div class="line"><a name="l00693"></a><span class="lineno"> 693</span> 74,</div><div class="line"><a name="l00694"></a><span class="lineno"> 694</span> 76,</div><div class="line"><a name="l00695"></a><span class="lineno"> 695</span> 75,</div><div class="line"><a name="l00696"></a><span class="lineno"> 696</span> 74,</div><div class="line"><a name="l00697"></a><span class="lineno"> 697</span> 76,</div><div class="line"><a name="l00698"></a><span class="lineno"> 698</span> 77,</div><div class="line"><a name="l00699"></a><span class="lineno"> 699</span> 78,</div><div class="line"><a name="l00700"></a><span class="lineno"> 700</span> 80,</div><div class="line"><a name="l00701"></a><span class="lineno"> 701</span> 82,</div><div class="line"><a name="l00702"></a><span class="lineno"> 702</span> 79,</div><div class="line"><a name="l00703"></a><span class="lineno"> 703</span> 81,</div><div class="line"><a name="l00704"></a><span class="lineno"> 704</span> 78,</div><div class="line"><a name="l00705"></a><span class="lineno"> 705</span> 80,</div><div class="line"><a name="l00706"></a><span class="lineno"> 706</span> 82,</div><div class="line"><a name="l00707"></a><span class="lineno"> 707</span> 83,</div><div class="line"><a name="l00708"></a><span class="lineno"> 708</span> 84,</div><div class="line"><a name="l00709"></a><span class="lineno"> 709</span> 86,</div><div class="line"><a name="l00710"></a><span class="lineno"> 710</span> 85,</div><div class="line"><a name="l00711"></a><span class="lineno"> 711</span> 87,</div><div class="line"><a name="l00712"></a><span class="lineno"> 712</span> 84,</div><div class="line"><a name="l00713"></a><span class="lineno"> 713</span> 86,</div><div class="line"><a name="l00714"></a><span class="lineno"> 714</span> 87,</div><div class="line"><a name="l00715"></a><span class="lineno"> 715</span> 88,</div><div class="line"><a name="l00716"></a><span class="lineno"> 716</span> 89,</div><div class="line"><a name="l00717"></a><span class="lineno"> 717</span> 90,</div><div class="line"><a name="l00718"></a><span class="lineno"> 718</span> 91,</div><div class="line"><a name="l00719"></a><span class="lineno"> 719</span> 92,</div><div class="line"><a name="l00720"></a><span class="lineno"> 720</span> 94,</div><div class="line"><a name="l00721"></a><span class="lineno"> 721</span> 96,</div><div class="line"><a name="l00722"></a><span class="lineno"> 722</span> 93,</div><div class="line"><a name="l00723"></a><span class="lineno"> 723</span> 92,</div><div class="line"><a name="l00724"></a><span class="lineno"> 724</span> 94,</div><div class="line"><a name="l00725"></a><span class="lineno"> 725</span> 95,</div><div class="line"><a name="l00726"></a><span class="lineno"> 726</span> 96,</div><div class="line"><a name="l00727"></a><span class="lineno"> 727</span> 97,</div><div class="line"><a name="l00728"></a><span class="lineno"> 728</span> 98,</div><div class="line"><a name="l00729"></a><span class="lineno"> 729</span> 100,</div><div class="line"><a name="l00730"></a><span class="lineno"> 730</span> 96,</div><div class="line"><a name="l00731"></a><span class="lineno"> 731</span> 98,</div><div class="line"><a name="l00732"></a><span class="lineno"> 732</span> 99,</div><div class="line"><a name="l00733"></a><span class="lineno"> 733</span> 100,</div><div class="line"><a name="l00734"></a><span class="lineno"> 734</span> 101,</div><div class="line"><a name="l00735"></a><span class="lineno"> 735</span> 102,</div><div class="line"><a name="l00736"></a><span class="lineno"> 736</span> 104,</div><div class="line"><a name="l00737"></a><span class="lineno"> 737</span> 103,</div><div class="line"><a name="l00738"></a><span class="lineno"> 738</span> 102,</div><div class="line"><a name="l00739"></a><span class="lineno"> 739</span> 104,</div><div class="line"><a name="l00740"></a><span class="lineno"> 740</span> 105,</div><div class="line"><a name="l00741"></a><span class="lineno"> 741</span> 106,</div><div class="line"><a name="l00742"></a><span class="lineno"> 742</span> 108,</div><div class="line"><a name="l00743"></a><span class="lineno"> 743</span> 110,</div><div class="line"><a name="l00744"></a><span class="lineno"> 744</span> 107,</div><div class="line"><a name="l00745"></a><span class="lineno"> 745</span> 109,</div><div class="line"><a name="l00746"></a><span class="lineno"> 746</span> 106,</div><div class="line"><a name="l00747"></a><span class="lineno"> 747</span> 108,</div><div class="line"><a name="l00748"></a><span class="lineno"> 748</span> 110,</div><div class="line"><a name="l00749"></a><span class="lineno"> 749</span> 111,</div><div class="line"><a name="l00750"></a><span class="lineno"> 750</span> 112,</div><div class="line"><a name="l00751"></a><span class="lineno"> 751</span> 113,</div><div class="line"><a name="l00752"></a><span class="lineno"> 752</span> 114,</div><div class="line"><a name="l00753"></a><span class="lineno"> 753</span> 116,</div><div class="line"><a name="l00754"></a><span class="lineno"> 754</span> 113,</div><div class="line"><a name="l00755"></a><span class="lineno"> 755</span> 115,</div><div class="line"><a name="l00756"></a><span class="lineno"> 756</span> 112,</div><div class="line"><a name="l00757"></a><span class="lineno"> 757</span> 114,</div><div class="line"><a name="l00758"></a><span class="lineno"> 758</span> 115,</div><div class="line"><a name="l00759"></a><span class="lineno"> 759</span> 116,</div><div class="line"><a name="l00760"></a><span class="lineno"> 760</span> 117,</div><div class="line"><a name="l00761"></a><span class="lineno"> 761</span> 118,</div><div class="line"><a name="l00762"></a><span class="lineno"> 762</span> 119,</div><div class="line"><a name="l00763"></a><span class="lineno"> 763</span> 120,</div><div class="line"><a name="l00764"></a><span class="lineno"> 764</span> 122,</div><div class="line"><a name="l00765"></a><span class="lineno"> 765</span> 124,</div><div class="line"><a name="l00766"></a><span class="lineno"> 766</span> 121,</div><div class="line"><a name="l00767"></a><span class="lineno"> 767</span> 123,</div><div class="line"><a name="l00768"></a><span class="lineno"> 768</span> 120,</div><div class="line"><a name="l00769"></a><span class="lineno"> 769</span> 122,</div><div class="line"><a name="l00770"></a><span class="lineno"> 770</span> 123,</div><div class="line"><a name="l00771"></a><span class="lineno"> 771</span> 124,</div><div class="line"><a name="l00772"></a><span class="lineno"> 772</span> 125,</div><div class="line"><a name="l00773"></a><span class="lineno"> 773</span> 126,</div><div class="line"><a name="l00774"></a><span class="lineno"> 774</span> 128,</div><div class="line"><a name="l00775"></a><span class="lineno"> 775</span> 130,</div><div class="line"><a name="l00776"></a><span class="lineno"> 776</span> 127,</div><div class="line"><a name="l00777"></a><span class="lineno"> 777</span> 124,</div><div class="line"><a name="l00778"></a><span class="lineno"> 778</span> 126,</div><div class="line"><a name="l00779"></a><span class="lineno"> 779</span> 128,</div><div class="line"><a name="l00780"></a><span class="lineno"> 780</span> 129,</div><div class="line"><a name="l00781"></a><span class="lineno"> 781</span> 130,</div><div class="line"><a name="l00782"></a><span class="lineno"> 782</span> 131,</div><div class="line"><a name="l00783"></a><span class="lineno"> 783</span> 132,</div><div class="line"><a name="l00784"></a><span class="lineno"> 784</span> 134,</div><div class="line"><a name="l00785"></a><span class="lineno"> 785</span> 136,</div><div class="line"><a name="l00786"></a><span class="lineno"> 786</span> 133,</div><div class="line"><a name="l00787"></a><span class="lineno"> 787</span> 130,</div><div class="line"><a name="l00788"></a><span class="lineno"> 788</span> 132,</div><div class="line"><a name="l00789"></a><span class="lineno"> 789</span> 134,</div><div class="line"><a name="l00790"></a><span class="lineno"> 790</span> 135,</div><div class="line"><a name="l00791"></a><span class="lineno"> 791</span> 136,</div><div class="line"><a name="l00792"></a><span class="lineno"> 792</span> 137,</div><div class="line"><a name="l00793"></a><span class="lineno"> 793</span> 138,</div><div class="line"><a name="l00794"></a><span class="lineno"> 794</span> 138,</div><div class="line"><a name="l00795"></a><span class="lineno"> 795</span> 139,</div><div class="line"><a name="l00796"></a><span class="lineno"> 796</span> 136,</div><div class="line"><a name="l00797"></a><span class="lineno"> 797</span> 138,</div><div class="line"><a name="l00798"></a><span class="lineno"> 798</span> 140,</div><div class="line"><a name="l00799"></a><span class="lineno"> 799</span> 142,</div><div class="line"><a name="l00800"></a><span class="lineno"> 800</span> 141,</div><div class="line"><a name="l00801"></a><span class="lineno"> 801</span> 142,</div><div class="line"><a name="l00802"></a><span class="lineno"> 802</span> 143,</div><div class="line"><a name="l00803"></a><span class="lineno"> 803</span> 144,</div><div class="line"><a name="l00804"></a><span class="lineno"> 804</span> 145,</div><div class="line"><a name="l00805"></a><span class="lineno"> 805</span> 146,</div><div class="line"><a name="l00806"></a><span class="lineno"> 806</span> 148,</div><div class="line"><a name="l00807"></a><span class="lineno"> 807</span> 150,</div><div class="line"><a name="l00808"></a><span class="lineno"> 808</span> 144,</div><div class="line"><a name="l00809"></a><span class="lineno"> 809</span> 147,</div><div class="line"><a name="l00810"></a><span class="lineno"> 810</span> 148,</div><div class="line"><a name="l00811"></a><span class="lineno"> 811</span> 149,</div><div class="line"><a name="l00812"></a><span class="lineno"> 812</span> 150,</div><div class="line"><a name="l00813"></a><span class="lineno"> 813</span> 152,</div><div class="line"><a name="l00814"></a><span class="lineno"> 814</span> 154,</div><div class="line"><a name="l00815"></a><span class="lineno"> 815</span> 151,</div><div class="line"><a name="l00816"></a><span class="lineno"> 816</span> 153,</div><div class="line"><a name="l00817"></a><span class="lineno"> 817</span> 152,</div><div class="line"><a name="l00818"></a><span class="lineno"> 818</span> 154,</div><div class="line"><a name="l00819"></a><span class="lineno"> 819</span> 155,</div><div class="line"><a name="l00820"></a><span class="lineno"> 820</span> 156,</div><div class="line"><a name="l00821"></a><span class="lineno"> 821</span> 157,</div><div class="line"><a name="l00822"></a><span class="lineno"> 822</span> 158,</div><div class="line"><a name="l00823"></a><span class="lineno"> 823</span> 160,</div><div class="line"><a name="l00824"></a><span class="lineno"> 824</span> 159,</div><div class="line"><a name="l00825"></a><span class="lineno"> 825</span> 156,</div><div class="line"><a name="l00826"></a><span class="lineno"> 826</span> 158,</div><div class="line"><a name="l00827"></a><span class="lineno"> 827</span> 160,</div><div class="line"><a name="l00828"></a><span class="lineno"> 828</span> 161,</div><div class="line"><a name="l00829"></a><span class="lineno"> 829</span> 162,</div><div class="line"><a name="l00830"></a><span class="lineno"> 830</span> 163,</div><div class="line"><a name="l00831"></a><span class="lineno"> 831</span> 164,</div><div class="line"><a name="l00832"></a><span class="lineno"> 832</span> 165,</div><div class="line"><a name="l00833"></a><span class="lineno"> 833</span> 162,</div><div class="line"><a name="l00834"></a><span class="lineno"> 834</span> 164,</div><div class="line"><a name="l00835"></a><span class="lineno"> 835</span> 166,</div><div class="line"><a name="l00836"></a><span class="lineno"> 836</span> 167,</div><div class="line"><a name="l00837"></a><span class="lineno"> 837</span> 168,</div><div class="line"><a name="l00838"></a><span class="lineno"> 838</span> 170,</div><div class="line"><a name="l00839"></a><span class="lineno"> 839</span> 169,</div><div class="line"><a name="l00840"></a><span class="lineno"> 840</span> 168,</div><div class="line"><a name="l00841"></a><span class="lineno"> 841</span> 170,</div><div class="line"><a name="l00842"></a><span class="lineno"> 842</span> 171,</div><div class="line"><a name="l00843"></a><span class="lineno"> 843</span> 172,</div><div class="line"><a name="l00844"></a><span class="lineno"> 844</span> 173,</div><div class="line"><a name="l00845"></a><span class="lineno"> 845</span> 174,</div><div class="line"><a name="l00846"></a><span class="lineno"> 846</span> 176,</div><div class="line"><a name="l00847"></a><span class="lineno"> 847</span> 175,</div><div class="line"><a name="l00848"></a><span class="lineno"> 848</span> 176,</div><div class="line"><a name="l00849"></a><span class="lineno"> 849</span> 174,</div><div class="line"><a name="l00850"></a><span class="lineno"> 850</span> 176,</div><div class="line"><a name="l00851"></a><span class="lineno"> 851</span> 177,</div><div class="line"><a name="l00852"></a><span class="lineno"> 852</span> 178,</div><div class="line"><a name="l00853"></a><span class="lineno"> 853</span> 179,</div><div class="line"><a name="l00854"></a><span class="lineno"> 854</span> 180,</div><div class="line"><a name="l00855"></a><span class="lineno"> 855</span> 180,</div><div class="line"><a name="l00856"></a><span class="lineno"> 856</span> 181,</div><div class="line"><a name="l00857"></a><span class="lineno"> 857</span> 180,</div><div class="line"><a name="l00858"></a><span class="lineno"> 858</span> 182,</div><div class="line"><a name="l00859"></a><span class="lineno"> 859</span> 183,</div><div class="line"><a name="l00860"></a><span class="lineno"> 860</span> 184,</div><div class="line"><a name="l00861"></a><span class="lineno"> 861</span> 186,</div><div class="line"><a name="l00862"></a><span class="lineno"> 862</span> 185,</div><div class="line"><a name="l00863"></a><span class="lineno"> 863</span> 187,</div><div class="line"><a name="l00864"></a><span class="lineno"> 864</span> 184,</div><div class="line"><a name="l00865"></a><span class="lineno"> 865</span> 186,</div><div class="line"><a name="l00866"></a><span class="lineno"> 866</span> 187,</div><div class="line"><a name="l00867"></a><span class="lineno"> 867</span> 188,</div><div class="line"><a name="l00868"></a><span class="lineno"> 868</span> 189,</div><div class="line"><a name="l00869"></a><span class="lineno"> 869</span> 190,</div><div class="line"><a name="l00870"></a><span class="lineno"> 870</span> 192,</div><div class="line"><a name="l00871"></a><span class="lineno"> 871</span> 191,</div><div class="line"><a name="l00872"></a><span class="lineno"> 872</span> 193,</div><div class="line"><a name="l00873"></a><span class="lineno"> 873</span> 190,</div><div class="line"><a name="l00874"></a><span class="lineno"> 874</span> 192,</div><div class="line"><a name="l00875"></a><span class="lineno"> 875</span> 194,</div><div class="line"><a name="l00876"></a><span class="lineno"> 876</span> 195,</div><div class="line"><a name="l00877"></a><span class="lineno"> 877</span> 196,</div><div class="line"><a name="l00878"></a><span class="lineno"> 878</span> 198,</div><div class="line"><a name="l00879"></a><span class="lineno"> 879</span> 197,</div><div class="line"><a name="l00880"></a><span class="lineno"> 880</span> 196,</div><div class="line"><a name="l00881"></a><span class="lineno"> 881</span> 198,</div><div class="line"><a name="l00882"></a><span class="lineno"> 882</span> 199,</div><div class="line"><a name="l00883"></a><span class="lineno"> 883</span> 200,</div><div class="line"><a name="l00884"></a><span class="lineno"> 884</span> 201,</div><div class="line"><a name="l00885"></a><span class="lineno"> 885</span> 202,</div><div class="line"><a name="l00886"></a><span class="lineno"> 886</span> 204,</div><div class="line"><a name="l00887"></a><span class="lineno"> 887</span> 203,</div><div class="line"><a name="l00888"></a><span class="lineno"> 888</span> 205,</div><div class="line"><a name="l00889"></a><span class="lineno"> 889</span> 204,</div><div class="line"><a name="l00890"></a><span class="lineno"> 890</span> 206,</div><div class="line"><a name="l00891"></a><span class="lineno"> 891</span> 207,</div><div class="line"><a name="l00892"></a><span class="lineno"> 892</span> 208,</div><div class="line"><a name="l00893"></a><span class="lineno"> 893</span> 209,</div><div class="line"><a name="l00894"></a><span class="lineno"> 894</span> 234,</div><div class="line"><a name="l00895"></a><span class="lineno"> 895</span> 235,</div><div class="line"><a name="l00896"></a><span class="lineno"> 896</span> 238,</div><div class="line"><a name="l00897"></a><span class="lineno"> 897</span> 232,</div><div class="line"><a name="l00898"></a><span class="lineno"> 898</span> 231,</div><div class="line"><a name="l00899"></a><span class="lineno"> 899</span> };</div><div class="line"><a name="l00900"></a><span class="lineno"> 900</span> </div><div class="line"><a name="l00901"></a><span class="lineno"> 901</span> </div><div class="line"><a name="l00902"></a><span class="lineno"> 902</span> <span class="keyword">const</span> <span class="keywordtype">int</span> elem_table_extraNeutrons [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {</div><div class="line"><a name="l00903"></a><span class="lineno"> 903</span> 0,</div><div class="line"><a name="l00904"></a><span class="lineno"> 904</span> 1,</div><div class="line"><a name="l00905"></a><span class="lineno"> 905</span> 0,</div><div class="line"><a name="l00906"></a><span class="lineno"> 906</span> 1,</div><div class="line"><a name="l00907"></a><span class="lineno"> 907</span> 0,</div><div class="line"><a name="l00908"></a><span class="lineno"> 908</span> 1,</div><div class="line"><a name="l00909"></a><span class="lineno"> 909</span> 0,</div><div class="line"><a name="l00910"></a><span class="lineno"> 910</span> 0,</div><div class="line"><a name="l00911"></a><span class="lineno"> 911</span> 1,</div><div class="line"><a name="l00912"></a><span class="lineno"> 912</span> 0,</div><div class="line"><a name="l00913"></a><span class="lineno"> 913</span> 1,</div><div class="line"><a name="l00914"></a><span class="lineno"> 914</span> 0,</div><div class="line"><a name="l00915"></a><span class="lineno"> 915</span> 1,</div><div class="line"><a name="l00916"></a><span class="lineno"> 916</span> 0,</div><div class="line"><a name="l00917"></a><span class="lineno"> 917</span> 1,</div><div class="line"><a name="l00918"></a><span class="lineno"> 918</span> 2,</div><div class="line"><a name="l00919"></a><span class="lineno"> 919</span> 0,</div><div class="line"><a name="l00920"></a><span class="lineno"> 920</span> 0,</div><div class="line"><a name="l00921"></a><span class="lineno"> 921</span> 1,</div><div class="line"><a name="l00922"></a><span class="lineno"> 922</span> 2,</div><div class="line"><a name="l00923"></a><span class="lineno"> 923</span> 0,</div><div class="line"><a name="l00924"></a><span class="lineno"> 924</span> 0,</div><div class="line"><a name="l00925"></a><span class="lineno"> 925</span> 1,</div><div class="line"><a name="l00926"></a><span class="lineno"> 926</span> 2,</div><div class="line"><a name="l00927"></a><span class="lineno"> 927</span> 0,</div><div class="line"><a name="l00928"></a><span class="lineno"> 928</span> 0,</div><div class="line"><a name="l00929"></a><span class="lineno"> 929</span> 1,</div><div class="line"><a name="l00930"></a><span class="lineno"> 930</span> 2,</div><div class="line"><a name="l00931"></a><span class="lineno"> 931</span> 0,</div><div class="line"><a name="l00932"></a><span class="lineno"> 932</span> 0,</div><div class="line"><a name="l00933"></a><span class="lineno"> 933</span> 1,</div><div class="line"><a name="l00934"></a><span class="lineno"> 934</span> 2,</div><div class="line"><a name="l00935"></a><span class="lineno"> 935</span> 4,</div><div class="line"><a name="l00936"></a><span class="lineno"> 936</span> 0,</div><div class="line"><a name="l00937"></a><span class="lineno"> 937</span> 2,</div><div class="line"><a name="l00938"></a><span class="lineno"> 938</span> 0,</div><div class="line"><a name="l00939"></a><span class="lineno"> 939</span> 2,</div><div class="line"><a name="l00940"></a><span class="lineno"> 940</span> 4,</div><div class="line"><a name="l00941"></a><span class="lineno"> 941</span> 0,</div><div class="line"><a name="l00942"></a><span class="lineno"> 942</span> 1,</div><div class="line"><a name="l00943"></a><span class="lineno"> 943</span> 2,</div><div class="line"><a name="l00944"></a><span class="lineno"> 944</span> 0,</div><div class="line"><a name="l00945"></a><span class="lineno"> 945</span> 2,</div><div class="line"><a name="l00946"></a><span class="lineno"> 946</span> 3,</div><div class="line"><a name="l00947"></a><span class="lineno"> 947</span> 4,</div><div class="line"><a name="l00948"></a><span class="lineno"> 948</span> 6,</div><div class="line"><a name="l00949"></a><span class="lineno"> 949</span> 8,</div><div class="line"><a name="l00950"></a><span class="lineno"> 950</span> 0,</div><div class="line"><a name="l00951"></a><span class="lineno"> 951</span> 0,</div><div class="line"><a name="l00952"></a><span class="lineno"> 952</span> 1,</div><div class="line"><a name="l00953"></a><span class="lineno"> 953</span> 2,</div><div class="line"><a name="l00954"></a><span class="lineno"> 954</span> 3,</div><div class="line"><a name="l00955"></a><span class="lineno"> 955</span> 4,</div><div class="line"><a name="l00956"></a><span class="lineno"> 956</span> 0,</div><div class="line"><a name="l00957"></a><span class="lineno"> 957</span> 1,</div><div class="line"><a name="l00958"></a><span class="lineno"> 958</span> 0,</div><div class="line"><a name="l00959"></a><span class="lineno"> 959</span> 2,</div><div class="line"><a name="l00960"></a><span class="lineno"> 960</span> 3,</div><div class="line"><a name="l00961"></a><span class="lineno"> 961</span> 4,</div><div class="line"><a name="l00962"></a><span class="lineno"> 962</span> 0,</div><div class="line"><a name="l00963"></a><span class="lineno"> 963</span> 0,</div><div class="line"><a name="l00964"></a><span class="lineno"> 964</span> 2,</div><div class="line"><a name="l00965"></a><span class="lineno"> 965</span> 3,</div><div class="line"><a name="l00966"></a><span class="lineno"> 966</span> 4,</div><div class="line"><a name="l00967"></a><span class="lineno"> 967</span> 0,</div><div class="line"><a name="l00968"></a><span class="lineno"> 968</span> 0,</div><div class="line"><a name="l00969"></a><span class="lineno"> 969</span> 2,</div><div class="line"><a name="l00970"></a><span class="lineno"> 970</span> 3,</div><div class="line"><a name="l00971"></a><span class="lineno"> 971</span> 4,</div><div class="line"><a name="l00972"></a><span class="lineno"> 972</span> 6,</div><div class="line"><a name="l00973"></a><span class="lineno"> 973</span> 0,</div><div class="line"><a name="l00974"></a><span class="lineno"> 974</span> 2,</div><div class="line"><a name="l00975"></a><span class="lineno"> 975</span> 0,</div><div class="line"><a name="l00976"></a><span class="lineno"> 976</span> 2,</div><div class="line"><a name="l00977"></a><span class="lineno"> 977</span> 3,</div><div class="line"><a name="l00978"></a><span class="lineno"> 978</span> 4,</div><div class="line"><a name="l00979"></a><span class="lineno"> 979</span> 6,</div><div class="line"><a name="l00980"></a><span class="lineno"> 980</span> 0,</div><div class="line"><a name="l00981"></a><span class="lineno"> 981</span> 2,</div><div class="line"><a name="l00982"></a><span class="lineno"> 982</span> 0,</div><div class="line"><a name="l00983"></a><span class="lineno"> 983</span> 2,</div><div class="line"><a name="l00984"></a><span class="lineno"> 984</span> 3,</div><div class="line"><a name="l00985"></a><span class="lineno"> 985</span> 4,</div><div class="line"><a name="l00986"></a><span class="lineno"> 986</span> 6,</div><div class="line"><a name="l00987"></a><span class="lineno"> 987</span> 0,</div><div class="line"><a name="l00988"></a><span class="lineno"> 988</span> 0,</div><div class="line"><a name="l00989"></a><span class="lineno"> 989</span> 2,</div><div class="line"><a name="l00990"></a><span class="lineno"> 990</span> 3,</div><div class="line"><a name="l00991"></a><span class="lineno"> 991</span> 4,</div><div class="line"><a name="l00992"></a><span class="lineno"> 992</span> 6,</div><div class="line"><a name="l00993"></a><span class="lineno"> 993</span> 8,</div><div class="line"><a name="l00994"></a><span class="lineno"> 994</span> 0,</div><div class="line"><a name="l00995"></a><span class="lineno"> 995</span> 2,</div><div class="line"><a name="l00996"></a><span class="lineno"> 996</span> 0,</div><div class="line"><a name="l00997"></a><span class="lineno"> 997</span> 2,</div><div class="line"><a name="l00998"></a><span class="lineno"> 998</span> 4,</div><div class="line"><a name="l00999"></a><span class="lineno"> 999</span> 5,</div><div class="line"><a name="l01000"></a><span class="lineno"> 1000</span> 6,</div><div class="line"><a name="l01001"></a><span class="lineno"> 1001</span> 8,</div><div class="line"><a name="l01002"></a><span class="lineno"> 1002</span> 0,</div><div class="line"><a name="l01003"></a><span class="lineno"> 1003</span> 2,</div><div class="line"><a name="l01004"></a><span class="lineno"> 1004</span> 0,</div><div class="line"><a name="l01005"></a><span class="lineno"> 1005</span> 2,</div><div class="line"><a name="l01006"></a><span class="lineno"> 1006</span> 3,</div><div class="line"><a name="l01007"></a><span class="lineno"> 1007</span> 4,</div><div class="line"><a name="l01008"></a><span class="lineno"> 1008</span> 0,</div><div class="line"><a name="l01009"></a><span class="lineno"> 1009</span> 0,</div><div class="line"><a name="l01010"></a><span class="lineno"> 1010</span> 1,</div><div class="line"><a name="l01011"></a><span class="lineno"> 1011</span> 2,</div><div class="line"><a name="l01012"></a><span class="lineno"> 1012</span> 4,</div><div class="line"><a name="l01013"></a><span class="lineno"> 1013</span> 6,</div><div class="line"><a name="l01014"></a><span class="lineno"> 1014</span> 0,</div><div class="line"><a name="l01015"></a><span class="lineno"> 1015</span> 0,</div><div class="line"><a name="l01016"></a><span class="lineno"> 1016</span> 2,</div><div class="line"><a name="l01017"></a><span class="lineno"> 1017</span> 3,</div><div class="line"><a name="l01018"></a><span class="lineno"> 1018</span> 4,</div><div class="line"><a name="l01019"></a><span class="lineno"> 1019</span> 5,</div><div class="line"><a name="l01020"></a><span class="lineno"> 1020</span> 6,</div><div class="line"><a name="l01021"></a><span class="lineno"> 1021</span> 8,</div><div class="line"><a name="l01022"></a><span class="lineno"> 1022</span> 0,</div><div class="line"><a name="l01023"></a><span class="lineno"> 1023</span> 2,</div><div class="line"><a name="l01024"></a><span class="lineno"> 1024</span> 3,</div><div class="line"><a name="l01025"></a><span class="lineno"> 1025</span> 4,</div><div class="line"><a name="l01026"></a><span class="lineno"> 1026</span> 5,</div><div class="line"><a name="l01027"></a><span class="lineno"> 1027</span> 6,</div><div class="line"><a name="l01028"></a><span class="lineno"> 1028</span> 8,</div><div class="line"><a name="l01029"></a><span class="lineno"> 1029</span> 0,</div><div class="line"><a name="l01030"></a><span class="lineno"> 1030</span> 0,</div><div class="line"><a name="l01031"></a><span class="lineno"> 1031</span> 2,</div><div class="line"><a name="l01032"></a><span class="lineno"> 1032</span> 3,</div><div class="line"><a name="l01033"></a><span class="lineno"> 1033</span> 4,</div><div class="line"><a name="l01034"></a><span class="lineno"> 1034</span> 6,</div><div class="line"><a name="l01035"></a><span class="lineno"> 1035</span> 8,</div><div class="line"><a name="l01036"></a><span class="lineno"> 1036</span> 0,</div><div class="line"><a name="l01037"></a><span class="lineno"> 1037</span> 2,</div><div class="line"><a name="l01038"></a><span class="lineno"> 1038</span> 0,</div><div class="line"><a name="l01039"></a><span class="lineno"> 1039</span> 2,</div><div class="line"><a name="l01040"></a><span class="lineno"> 1040</span> 4,</div><div class="line"><a name="l01041"></a><span class="lineno"> 1041</span> 5,</div><div class="line"><a name="l01042"></a><span class="lineno"> 1042</span> 6,</div><div class="line"><a name="l01043"></a><span class="lineno"> 1043</span> 7,</div><div class="line"><a name="l01044"></a><span class="lineno"> 1044</span> 8,</div><div class="line"><a name="l01045"></a><span class="lineno"> 1045</span> 10,</div><div class="line"><a name="l01046"></a><span class="lineno"> 1046</span> 0,</div><div class="line"><a name="l01047"></a><span class="lineno"> 1047</span> 2,</div><div class="line"><a name="l01048"></a><span class="lineno"> 1048</span> 0,</div><div class="line"><a name="l01049"></a><span class="lineno"> 1049</span> 2,</div><div class="line"><a name="l01050"></a><span class="lineno"> 1050</span> 3,</div><div class="line"><a name="l01051"></a><span class="lineno"> 1051</span> 4,</div><div class="line"><a name="l01052"></a><span class="lineno"> 1052</span> 5,</div><div class="line"><a name="l01053"></a><span class="lineno"> 1053</span> 6,</div><div class="line"><a name="l01054"></a><span class="lineno"> 1054</span> 7,</div><div class="line"><a name="l01055"></a><span class="lineno"> 1055</span> 8,</div><div class="line"><a name="l01056"></a><span class="lineno"> 1056</span> 10,</div><div class="line"><a name="l01057"></a><span class="lineno"> 1057</span> 12,</div><div class="line"><a name="l01058"></a><span class="lineno"> 1058</span> 0,</div><div class="line"><a name="l01059"></a><span class="lineno"> 1059</span> 2,</div><div class="line"><a name="l01060"></a><span class="lineno"> 1060</span> 0,</div><div class="line"><a name="l01061"></a><span class="lineno"> 1061</span> 2,</div><div class="line"><a name="l01062"></a><span class="lineno"> 1062</span> 3,</div><div class="line"><a name="l01063"></a><span class="lineno"> 1063</span> 4,</div><div class="line"><a name="l01064"></a><span class="lineno"> 1064</span> 5,</div><div class="line"><a name="l01065"></a><span class="lineno"> 1065</span> 6,</div><div class="line"><a name="l01066"></a><span class="lineno"> 1066</span> 8,</div><div class="line"><a name="l01067"></a><span class="lineno"> 1067</span> 10,</div><div class="line"><a name="l01068"></a><span class="lineno"> 1068</span> 0,</div><div class="line"><a name="l01069"></a><span class="lineno"> 1069</span> 0,</div><div class="line"><a name="l01070"></a><span class="lineno"> 1070</span> 2,</div><div class="line"><a name="l01071"></a><span class="lineno"> 1071</span> 4,</div><div class="line"><a name="l01072"></a><span class="lineno"> 1072</span> 5,</div><div class="line"><a name="l01073"></a><span class="lineno"> 1073</span> 6,</div><div class="line"><a name="l01074"></a><span class="lineno"> 1074</span> 7,</div><div class="line"><a name="l01075"></a><span class="lineno"> 1075</span> 8,</div><div class="line"><a name="l01076"></a><span class="lineno"> 1076</span> 10,</div><div class="line"><a name="l01077"></a><span class="lineno"> 1077</span> 12,</div><div class="line"><a name="l01078"></a><span class="lineno"> 1078</span> 0,</div><div class="line"><a name="l01079"></a><span class="lineno"> 1079</span> 0,</div><div class="line"><a name="l01080"></a><span class="lineno"> 1080</span> 2,</div><div class="line"><a name="l01081"></a><span class="lineno"> 1081</span> 4,</div><div class="line"><a name="l01082"></a><span class="lineno"> 1082</span> 5,</div><div class="line"><a name="l01083"></a><span class="lineno"> 1083</span> 6,</div><div class="line"><a name="l01084"></a><span class="lineno"> 1084</span> 7,</div><div class="line"><a name="l01085"></a><span class="lineno"> 1085</span> 8,</div><div class="line"><a name="l01086"></a><span class="lineno"> 1086</span> 0,</div><div class="line"><a name="l01087"></a><span class="lineno"> 1087</span> 1,</div><div class="line"><a name="l01088"></a><span class="lineno"> 1088</span> 0,</div><div class="line"><a name="l01089"></a><span class="lineno"> 1089</span> 2,</div><div class="line"><a name="l01090"></a><span class="lineno"> 1090</span> 4,</div><div class="line"><a name="l01091"></a><span class="lineno"> 1091</span> 6,</div><div class="line"><a name="l01092"></a><span class="lineno"> 1092</span> 0,</div><div class="line"><a name="l01093"></a><span class="lineno"> 1093</span> 0,</div><div class="line"><a name="l01094"></a><span class="lineno"> 1094</span> 1,</div><div class="line"><a name="l01095"></a><span class="lineno"> 1095</span> 2,</div><div class="line"><a name="l01096"></a><span class="lineno"> 1096</span> 3,</div><div class="line"><a name="l01097"></a><span class="lineno"> 1097</span> 4,</div><div class="line"><a name="l01098"></a><span class="lineno"> 1098</span> 6,</div><div class="line"><a name="l01099"></a><span class="lineno"> 1099</span> 8,</div><div class="line"><a name="l01100"></a><span class="lineno"> 1100</span> 0,</div><div class="line"><a name="l01101"></a><span class="lineno"> 1101</span> 3,</div><div class="line"><a name="l01102"></a><span class="lineno"> 1102</span> 4,</div><div class="line"><a name="l01103"></a><span class="lineno"> 1103</span> 5,</div><div class="line"><a name="l01104"></a><span class="lineno"> 1104</span> 6,</div><div class="line"><a name="l01105"></a><span class="lineno"> 1105</span> 8,</div><div class="line"><a name="l01106"></a><span class="lineno"> 1106</span> 10,</div><div class="line"><a name="l01107"></a><span class="lineno"> 1107</span> 0,</div><div class="line"><a name="l01108"></a><span class="lineno"> 1108</span> 2,</div><div class="line"><a name="l01109"></a><span class="lineno"> 1109</span> 0,</div><div class="line"><a name="l01110"></a><span class="lineno"> 1110</span> 2,</div><div class="line"><a name="l01111"></a><span class="lineno"> 1111</span> 3,</div><div class="line"><a name="l01112"></a><span class="lineno"> 1112</span> 4,</div><div class="line"><a name="l01113"></a><span class="lineno"> 1113</span> 5,</div><div class="line"><a name="l01114"></a><span class="lineno"> 1114</span> 6,</div><div class="line"><a name="l01115"></a><span class="lineno"> 1115</span> 8,</div><div class="line"><a name="l01116"></a><span class="lineno"> 1116</span> 0,</div><div class="line"><a name="l01117"></a><span class="lineno"> 1117</span> 0,</div><div class="line"><a name="l01118"></a><span class="lineno"> 1118</span> 2,</div><div class="line"><a name="l01119"></a><span class="lineno"> 1119</span> 4,</div><div class="line"><a name="l01120"></a><span class="lineno"> 1120</span> 5,</div><div class="line"><a name="l01121"></a><span class="lineno"> 1121</span> 6,</div><div class="line"><a name="l01122"></a><span class="lineno"> 1122</span> 7,</div><div class="line"><a name="l01123"></a><span class="lineno"> 1123</span> 8,</div><div class="line"><a name="l01124"></a><span class="lineno"> 1124</span> 0,</div><div class="line"><a name="l01125"></a><span class="lineno"> 1125</span> 0,</div><div class="line"><a name="l01126"></a><span class="lineno"> 1126</span> 2,</div><div class="line"><a name="l01127"></a><span class="lineno"> 1127</span> 4,</div><div class="line"><a name="l01128"></a><span class="lineno"> 1128</span> 5,</div><div class="line"><a name="l01129"></a><span class="lineno"> 1129</span> 6,</div><div class="line"><a name="l01130"></a><span class="lineno"> 1130</span> 8,</div><div class="line"><a name="l01131"></a><span class="lineno"> 1131</span> 0,</div><div class="line"><a name="l01132"></a><span class="lineno"> 1132</span> 0,</div><div class="line"><a name="l01133"></a><span class="lineno"> 1133</span> 2,</div><div class="line"><a name="l01134"></a><span class="lineno"> 1134</span> 3,</div><div class="line"><a name="l01135"></a><span class="lineno"> 1135</span> 4,</div><div class="line"><a name="l01136"></a><span class="lineno"> 1136</span> 5,</div><div class="line"><a name="l01137"></a><span class="lineno"> 1137</span> 6,</div><div class="line"><a name="l01138"></a><span class="lineno"> 1138</span> 8,</div><div class="line"><a name="l01139"></a><span class="lineno"> 1139</span> 0,</div><div class="line"><a name="l01140"></a><span class="lineno"> 1140</span> 1,</div><div class="line"><a name="l01141"></a><span class="lineno"> 1141</span> 0,</div><div class="line"><a name="l01142"></a><span class="lineno"> 1142</span> 2,</div><div class="line"><a name="l01143"></a><span class="lineno"> 1143</span> 3,</div><div class="line"><a name="l01144"></a><span class="lineno"> 1144</span> 4,</div><div class="line"><a name="l01145"></a><span class="lineno"> 1145</span> 5,</div><div class="line"><a name="l01146"></a><span class="lineno"> 1146</span> 6,</div><div class="line"><a name="l01147"></a><span class="lineno"> 1147</span> 0,</div><div class="line"><a name="l01148"></a><span class="lineno"> 1148</span> 1,</div><div class="line"><a name="l01149"></a><span class="lineno"> 1149</span> 0,</div><div class="line"><a name="l01150"></a><span class="lineno"> 1150</span> 2,</div><div class="line"><a name="l01151"></a><span class="lineno"> 1151</span> 3,</div><div class="line"><a name="l01152"></a><span class="lineno"> 1152</span> 4,</div><div class="line"><a name="l01153"></a><span class="lineno"> 1153</span> 6,</div><div class="line"><a name="l01154"></a><span class="lineno"> 1154</span> 0,</div><div class="line"><a name="l01155"></a><span class="lineno"> 1155</span> 2,</div><div class="line"><a name="l01156"></a><span class="lineno"> 1156</span> 0,</div><div class="line"><a name="l01157"></a><span class="lineno"> 1157</span> 2,</div><div class="line"><a name="l01158"></a><span class="lineno"> 1158</span> 3,</div><div class="line"><a name="l01159"></a><span class="lineno"> 1159</span> 4,</div><div class="line"><a name="l01160"></a><span class="lineno"> 1160</span> 5,</div><div class="line"><a name="l01161"></a><span class="lineno"> 1161</span> 6,</div><div class="line"><a name="l01162"></a><span class="lineno"> 1162</span> 8,</div><div class="line"><a name="l01163"></a><span class="lineno"> 1163</span> 0,</div><div class="line"><a name="l01164"></a><span class="lineno"> 1164</span> 2,</div><div class="line"><a name="l01165"></a><span class="lineno"> 1165</span> 0,</div><div class="line"><a name="l01166"></a><span class="lineno"> 1166</span> 2,</div><div class="line"><a name="l01167"></a><span class="lineno"> 1167</span> 4,</div><div class="line"><a name="l01168"></a><span class="lineno"> 1168</span> 5,</div><div class="line"><a name="l01169"></a><span class="lineno"> 1169</span> 6,</div><div class="line"><a name="l01170"></a><span class="lineno"> 1170</span> 8,</div><div class="line"><a name="l01171"></a><span class="lineno"> 1171</span> 0,</div><div class="line"><a name="l01172"></a><span class="lineno"> 1172</span> 0,</div><div class="line"><a name="l01173"></a><span class="lineno"> 1173</span> 2,</div><div class="line"><a name="l01174"></a><span class="lineno"> 1174</span> 3,</div><div class="line"><a name="l01175"></a><span class="lineno"> 1175</span> 4,</div><div class="line"><a name="l01176"></a><span class="lineno"> 1176</span> 5,</div><div class="line"><a name="l01177"></a><span class="lineno"> 1177</span> 6,</div><div class="line"><a name="l01178"></a><span class="lineno"> 1178</span> 8,</div><div class="line"><a name="l01179"></a><span class="lineno"> 1179</span> 0,</div><div class="line"><a name="l01180"></a><span class="lineno"> 1180</span> 2,</div><div class="line"><a name="l01181"></a><span class="lineno"> 1181</span> 0,</div><div class="line"><a name="l01182"></a><span class="lineno"> 1182</span> 2,</div><div class="line"><a name="l01183"></a><span class="lineno"> 1183</span> 3,</div><div class="line"><a name="l01184"></a><span class="lineno"> 1184</span> 4,</div><div class="line"><a name="l01185"></a><span class="lineno"> 1185</span> 0,</div><div class="line"><a name="l01186"></a><span class="lineno"> 1186</span> 1,</div><div class="line"><a name="l01187"></a><span class="lineno"> 1187</span> 2,</div><div class="line"><a name="l01188"></a><span class="lineno"> 1188</span> 5,</div><div class="line"><a name="l01189"></a><span class="lineno"> 1189</span> 0,</div><div class="line"><a name="l01190"></a><span class="lineno"> 1190</span> 0,</div><div class="line"><a name="l01191"></a><span class="lineno"> 1191</span> };</div><div class="line"><a name="l01192"></a><span class="lineno"> 1192</span> </div><div class="line"><a name="l01193"></a><span class="lineno"> 1193</span> </div><div class="line"><a name="l01194"></a><span class="lineno"> 1194</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* elem_table_element [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {</div><div class="line"><a name="l01195"></a><span class="lineno"> 1195</span> <span class="stringliteral">"hydrogen"</span>,</div><div class="line"><a name="l01196"></a><span class="lineno"> 1196</span> <span class="stringliteral">"hydrogen"</span>,</div><div class="line"><a name="l01197"></a><span class="lineno"> 1197</span> <span class="stringliteral">"helium"</span>,</div><div class="line"><a name="l01198"></a><span class="lineno"> 1198</span> <span class="stringliteral">"helium"</span>,</div><div class="line"><a name="l01199"></a><span class="lineno"> 1199</span> <span class="stringliteral">"lithium"</span>,</div><div class="line"><a name="l01200"></a><span class="lineno"> 1200</span> <span class="stringliteral">"lithium"</span>,</div><div class="line"><a name="l01201"></a><span class="lineno"> 1201</span> <span class="stringliteral">"beryllium"</span>,</div><div class="line"><a name="l01202"></a><span class="lineno"> 1202</span> <span class="stringliteral">"boron"</span>,</div><div class="line"><a name="l01203"></a><span class="lineno"> 1203</span> <span class="stringliteral">"boron"</span>,</div><div class="line"><a name="l01204"></a><span class="lineno"> 1204</span> <span class="stringliteral">"carbon"</span>,</div><div class="line"><a name="l01205"></a><span class="lineno"> 1205</span> <span class="stringliteral">"carbon"</span>,</div><div class="line"><a name="l01206"></a><span class="lineno"> 1206</span> <span class="stringliteral">"nitrogen"</span>,</div><div class="line"><a name="l01207"></a><span class="lineno"> 1207</span> <span class="stringliteral">"nitrogen"</span>,</div><div class="line"><a name="l01208"></a><span class="lineno"> 1208</span> <span class="stringliteral">"oxygen"</span>,</div><div class="line"><a name="l01209"></a><span class="lineno"> 1209</span> <span class="stringliteral">"oxygen"</span>,</div><div class="line"><a name="l01210"></a><span class="lineno"> 1210</span> <span class="stringliteral">"oxygen"</span>,</div><div class="line"><a name="l01211"></a><span class="lineno"> 1211</span> <span class="stringliteral">"fluorine"</span>,</div><div class="line"><a name="l01212"></a><span class="lineno"> 1212</span> <span class="stringliteral">"neon"</span>,</div><div class="line"><a name="l01213"></a><span class="lineno"> 1213</span> <span class="stringliteral">"neon"</span>,</div><div class="line"><a name="l01214"></a><span class="lineno"> 1214</span> <span class="stringliteral">"neon"</span>,</div><div class="line"><a name="l01215"></a><span class="lineno"> 1215</span> <span class="stringliteral">"sodium"</span>,</div><div class="line"><a name="l01216"></a><span class="lineno"> 1216</span> <span class="stringliteral">"magnesium"</span>,</div><div class="line"><a name="l01217"></a><span class="lineno"> 1217</span> <span class="stringliteral">"magnesium"</span>,</div><div class="line"><a name="l01218"></a><span class="lineno"> 1218</span> <span class="stringliteral">"magnesium"</span>,</div><div class="line"><a name="l01219"></a><span class="lineno"> 1219</span> <span class="stringliteral">"aluminium"</span>,</div><div class="line"><a name="l01220"></a><span class="lineno"> 1220</span> <span class="stringliteral">"silicon"</span>,</div><div class="line"><a name="l01221"></a><span class="lineno"> 1221</span> <span class="stringliteral">"silicon"</span>,</div><div class="line"><a name="l01222"></a><span class="lineno"> 1222</span> <span class="stringliteral">"silicon"</span>,</div><div class="line"><a name="l01223"></a><span class="lineno"> 1223</span> <span class="stringliteral">"phosphorus"</span>,</div><div class="line"><a name="l01224"></a><span class="lineno"> 1224</span> <span class="stringliteral">"sulfur"</span>,</div><div class="line"><a name="l01225"></a><span class="lineno"> 1225</span> <span class="stringliteral">"sulfur"</span>,</div><div class="line"><a name="l01226"></a><span class="lineno"> 1226</span> <span class="stringliteral">"sulfur"</span>,</div><div class="line"><a name="l01227"></a><span class="lineno"> 1227</span> <span class="stringliteral">"sulfur"</span>,</div><div class="line"><a name="l01228"></a><span class="lineno"> 1228</span> <span class="stringliteral">"chlorine"</span>,</div><div class="line"><a name="l01229"></a><span class="lineno"> 1229</span> <span class="stringliteral">"chlorine"</span>,</div><div class="line"><a name="l01230"></a><span class="lineno"> 1230</span> <span class="stringliteral">"argon"</span>,</div><div class="line"><a name="l01231"></a><span class="lineno"> 1231</span> <span class="stringliteral">"argon"</span>,</div><div class="line"><a name="l01232"></a><span class="lineno"> 1232</span> <span class="stringliteral">"argon"</span>,</div><div class="line"><a name="l01233"></a><span class="lineno"> 1233</span> <span class="stringliteral">"potassium"</span>,</div><div class="line"><a name="l01234"></a><span class="lineno"> 1234</span> <span class="stringliteral">"potassium"</span>,</div><div class="line"><a name="l01235"></a><span class="lineno"> 1235</span> <span class="stringliteral">"potassium"</span>,</div><div class="line"><a name="l01236"></a><span class="lineno"> 1236</span> <span class="stringliteral">"calcium"</span>,</div><div class="line"><a name="l01237"></a><span class="lineno"> 1237</span> <span class="stringliteral">"calcium"</span>,</div><div class="line"><a name="l01238"></a><span class="lineno"> 1238</span> <span class="stringliteral">"calcium"</span>,</div><div class="line"><a name="l01239"></a><span class="lineno"> 1239</span> <span class="stringliteral">"calcium"</span>,</div><div class="line"><a name="l01240"></a><span class="lineno"> 1240</span> <span class="stringliteral">"calcium"</span>,</div><div class="line"><a name="l01241"></a><span class="lineno"> 1241</span> <span class="stringliteral">"calcium"</span>,</div><div class="line"><a name="l01242"></a><span class="lineno"> 1242</span> <span class="stringliteral">"scandium"</span>,</div><div class="line"><a name="l01243"></a><span class="lineno"> 1243</span> <span class="stringliteral">"titanium"</span>,</div><div class="line"><a name="l01244"></a><span class="lineno"> 1244</span> <span class="stringliteral">"titanium"</span>,</div><div class="line"><a name="l01245"></a><span class="lineno"> 1245</span> <span class="stringliteral">"titanium"</span>,</div><div class="line"><a name="l01246"></a><span class="lineno"> 1246</span> <span class="stringliteral">"titanium"</span>,</div><div class="line"><a name="l01247"></a><span class="lineno"> 1247</span> <span class="stringliteral">"titanium"</span>,</div><div class="line"><a name="l01248"></a><span class="lineno"> 1248</span> <span class="stringliteral">"vanadium"</span>,</div><div class="line"><a name="l01249"></a><span class="lineno"> 1249</span> <span class="stringliteral">"vanadium"</span>,</div><div class="line"><a name="l01250"></a><span class="lineno"> 1250</span> <span class="stringliteral">"chromium"</span>,</div><div class="line"><a name="l01251"></a><span class="lineno"> 1251</span> <span class="stringliteral">"chromium"</span>,</div><div class="line"><a name="l01252"></a><span class="lineno"> 1252</span> <span class="stringliteral">"chromium"</span>,</div><div class="line"><a name="l01253"></a><span class="lineno"> 1253</span> <span class="stringliteral">"chromium"</span>,</div><div class="line"><a name="l01254"></a><span class="lineno"> 1254</span> <span class="stringliteral">"manganese"</span>,</div><div class="line"><a name="l01255"></a><span class="lineno"> 1255</span> <span class="stringliteral">"iron"</span>,</div><div class="line"><a name="l01256"></a><span class="lineno"> 1256</span> <span class="stringliteral">"iron"</span>,</div><div class="line"><a name="l01257"></a><span class="lineno"> 1257</span> <span class="stringliteral">"iron"</span>,</div><div class="line"><a name="l01258"></a><span class="lineno"> 1258</span> <span class="stringliteral">"iron"</span>,</div><div class="line"><a name="l01259"></a><span class="lineno"> 1259</span> <span class="stringliteral">"cobalt"</span>,</div><div class="line"><a name="l01260"></a><span class="lineno"> 1260</span> <span class="stringliteral">"nickel"</span>,</div><div class="line"><a name="l01261"></a><span class="lineno"> 1261</span> <span class="stringliteral">"nickel"</span>,</div><div class="line"><a name="l01262"></a><span class="lineno"> 1262</span> <span class="stringliteral">"nickel"</span>,</div><div class="line"><a name="l01263"></a><span class="lineno"> 1263</span> <span class="stringliteral">"nickel"</span>,</div><div class="line"><a name="l01264"></a><span class="lineno"> 1264</span> <span class="stringliteral">"nickel"</span>,</div><div class="line"><a name="l01265"></a><span class="lineno"> 1265</span> <span class="stringliteral">"copper"</span>,</div><div class="line"><a name="l01266"></a><span class="lineno"> 1266</span> <span class="stringliteral">"copper"</span>,</div><div class="line"><a name="l01267"></a><span class="lineno"> 1267</span> <span class="stringliteral">"zinc"</span>,</div><div class="line"><a name="l01268"></a><span class="lineno"> 1268</span> <span class="stringliteral">"zinc"</span>,</div><div class="line"><a name="l01269"></a><span class="lineno"> 1269</span> <span class="stringliteral">"zinc"</span>,</div><div class="line"><a name="l01270"></a><span class="lineno"> 1270</span> <span class="stringliteral">"zinc"</span>,</div><div class="line"><a name="l01271"></a><span class="lineno"> 1271</span> <span class="stringliteral">"zinc"</span>,</div><div class="line"><a name="l01272"></a><span class="lineno"> 1272</span> <span class="stringliteral">"gallium"</span>,</div><div class="line"><a name="l01273"></a><span class="lineno"> 1273</span> <span class="stringliteral">"gallium"</span>,</div><div class="line"><a name="l01274"></a><span class="lineno"> 1274</span> <span class="stringliteral">"germanium"</span>,</div><div class="line"><a name="l01275"></a><span class="lineno"> 1275</span> <span class="stringliteral">"germanium"</span>,</div><div class="line"><a name="l01276"></a><span class="lineno"> 1276</span> <span class="stringliteral">"germanium"</span>,</div><div class="line"><a name="l01277"></a><span class="lineno"> 1277</span> <span class="stringliteral">"germanium"</span>,</div><div class="line"><a name="l01278"></a><span class="lineno"> 1278</span> <span class="stringliteral">"germanium"</span>,</div><div class="line"><a name="l01279"></a><span class="lineno"> 1279</span> <span class="stringliteral">"arsenic"</span>,</div><div class="line"><a name="l01280"></a><span class="lineno"> 1280</span> <span class="stringliteral">"selenium"</span>,</div><div class="line"><a name="l01281"></a><span class="lineno"> 1281</span> <span class="stringliteral">"selenium"</span>,</div><div class="line"><a name="l01282"></a><span class="lineno"> 1282</span> <span class="stringliteral">"selenium"</span>,</div><div class="line"><a name="l01283"></a><span class="lineno"> 1283</span> <span class="stringliteral">"selenium"</span>,</div><div class="line"><a name="l01284"></a><span class="lineno"> 1284</span> <span class="stringliteral">"selenium"</span>,</div><div class="line"><a name="l01285"></a><span class="lineno"> 1285</span> <span class="stringliteral">"selenium"</span>,</div><div class="line"><a name="l01286"></a><span class="lineno"> 1286</span> <span class="stringliteral">"bromine"</span>,</div><div class="line"><a name="l01287"></a><span class="lineno"> 1287</span> <span class="stringliteral">"bromine"</span>,</div><div class="line"><a name="l01288"></a><span class="lineno"> 1288</span> <span class="stringliteral">"krypton"</span>,</div><div class="line"><a name="l01289"></a><span class="lineno"> 1289</span> <span class="stringliteral">"krypton"</span>,</div><div class="line"><a name="l01290"></a><span class="lineno"> 1290</span> <span class="stringliteral">"krypton"</span>,</div><div class="line"><a name="l01291"></a><span class="lineno"> 1291</span> <span class="stringliteral">"krypton"</span>,</div><div class="line"><a name="l01292"></a><span class="lineno"> 1292</span> <span class="stringliteral">"krypton"</span>,</div><div class="line"><a name="l01293"></a><span class="lineno"> 1293</span> <span class="stringliteral">"krypton"</span>,</div><div class="line"><a name="l01294"></a><span class="lineno"> 1294</span> <span class="stringliteral">"rubidium"</span>,</div><div class="line"><a name="l01295"></a><span class="lineno"> 1295</span> <span class="stringliteral">"rubidium"</span>,</div><div class="line"><a name="l01296"></a><span class="lineno"> 1296</span> <span class="stringliteral">"strontium"</span>,</div><div class="line"><a name="l01297"></a><span class="lineno"> 1297</span> <span class="stringliteral">"strontium"</span>,</div><div class="line"><a name="l01298"></a><span class="lineno"> 1298</span> <span class="stringliteral">"strontium"</span>,</div><div class="line"><a name="l01299"></a><span class="lineno"> 1299</span> <span class="stringliteral">"strontium"</span>,</div><div class="line"><a name="l01300"></a><span class="lineno"> 1300</span> <span class="stringliteral">"yttrium"</span>,</div><div class="line"><a name="l01301"></a><span class="lineno"> 1301</span> <span class="stringliteral">"zirconium"</span>,</div><div class="line"><a name="l01302"></a><span class="lineno"> 1302</span> <span class="stringliteral">"zirconium"</span>,</div><div class="line"><a name="l01303"></a><span class="lineno"> 1303</span> <span class="stringliteral">"zirconium"</span>,</div><div class="line"><a name="l01304"></a><span class="lineno"> 1304</span> <span class="stringliteral">"zirconium"</span>,</div><div class="line"><a name="l01305"></a><span class="lineno"> 1305</span> <span class="stringliteral">"zirconium"</span>,</div><div class="line"><a name="l01306"></a><span class="lineno"> 1306</span> <span class="stringliteral">"niobium"</span>,</div><div class="line"><a name="l01307"></a><span class="lineno"> 1307</span> <span class="stringliteral">"molybdenum"</span>,</div><div class="line"><a name="l01308"></a><span class="lineno"> 1308</span> <span class="stringliteral">"molybdenum"</span>,</div><div class="line"><a name="l01309"></a><span class="lineno"> 1309</span> <span class="stringliteral">"molybdenum"</span>,</div><div class="line"><a name="l01310"></a><span class="lineno"> 1310</span> <span class="stringliteral">"molybdenum"</span>,</div><div class="line"><a name="l01311"></a><span class="lineno"> 1311</span> <span class="stringliteral">"molybdenum"</span>,</div><div class="line"><a name="l01312"></a><span class="lineno"> 1312</span> <span class="stringliteral">"molybdenum"</span>,</div><div class="line"><a name="l01313"></a><span class="lineno"> 1313</span> <span class="stringliteral">"molybdenum"</span>,</div><div class="line"><a name="l01314"></a><span class="lineno"> 1314</span> <span class="stringliteral">"ruthenium"</span>,</div><div class="line"><a name="l01315"></a><span class="lineno"> 1315</span> <span class="stringliteral">"ruthenium"</span>,</div><div class="line"><a name="l01316"></a><span class="lineno"> 1316</span> <span class="stringliteral">"ruthenium"</span>,</div><div class="line"><a name="l01317"></a><span class="lineno"> 1317</span> <span class="stringliteral">"ruthenium"</span>,</div><div class="line"><a name="l01318"></a><span class="lineno"> 1318</span> <span class="stringliteral">"ruthenium"</span>,</div><div class="line"><a name="l01319"></a><span class="lineno"> 1319</span> <span class="stringliteral">"ruthenium"</span>,</div><div class="line"><a name="l01320"></a><span class="lineno"> 1320</span> <span class="stringliteral">"ruthenium"</span>,</div><div class="line"><a name="l01321"></a><span class="lineno"> 1321</span> <span class="stringliteral">"rhodium"</span>,</div><div class="line"><a name="l01322"></a><span class="lineno"> 1322</span> <span class="stringliteral">"palladium"</span>,</div><div class="line"><a name="l01323"></a><span class="lineno"> 1323</span> <span class="stringliteral">"palladium"</span>,</div><div class="line"><a name="l01324"></a><span class="lineno"> 1324</span> <span class="stringliteral">"palladium"</span>,</div><div class="line"><a name="l01325"></a><span class="lineno"> 1325</span> <span class="stringliteral">"palladium"</span>,</div><div class="line"><a name="l01326"></a><span class="lineno"> 1326</span> <span class="stringliteral">"palladium"</span>,</div><div class="line"><a name="l01327"></a><span class="lineno"> 1327</span> <span class="stringliteral">"palladium"</span>,</div><div class="line"><a name="l01328"></a><span class="lineno"> 1328</span> <span class="stringliteral">"silver"</span>,</div><div class="line"><a name="l01329"></a><span class="lineno"> 1329</span> <span class="stringliteral">"silver"</span>,</div><div class="line"><a name="l01330"></a><span class="lineno"> 1330</span> <span class="stringliteral">"cadmium"</span>,</div><div class="line"><a name="l01331"></a><span class="lineno"> 1331</span> <span class="stringliteral">"cadmium"</span>,</div><div class="line"><a name="l01332"></a><span class="lineno"> 1332</span> <span class="stringliteral">"cadmium"</span>,</div><div class="line"><a name="l01333"></a><span class="lineno"> 1333</span> <span class="stringliteral">"cadmium"</span>,</div><div class="line"><a name="l01334"></a><span class="lineno"> 1334</span> <span class="stringliteral">"cadmium"</span>,</div><div class="line"><a name="l01335"></a><span class="lineno"> 1335</span> <span class="stringliteral">"cadmium"</span>,</div><div class="line"><a name="l01336"></a><span class="lineno"> 1336</span> <span class="stringliteral">"cadmium"</span>,</div><div class="line"><a name="l01337"></a><span class="lineno"> 1337</span> <span class="stringliteral">"cadmium"</span>,</div><div class="line"><a name="l01338"></a><span class="lineno"> 1338</span> <span class="stringliteral">"indium"</span>,</div><div class="line"><a name="l01339"></a><span class="lineno"> 1339</span> <span class="stringliteral">"indium"</span>,</div><div class="line"><a name="l01340"></a><span class="lineno"> 1340</span> <span class="stringliteral">"tin"</span>,</div><div class="line"><a name="l01341"></a><span class="lineno"> 1341</span> <span class="stringliteral">"tin"</span>,</div><div class="line"><a name="l01342"></a><span class="lineno"> 1342</span> <span class="stringliteral">"tin"</span>,</div><div class="line"><a name="l01343"></a><span class="lineno"> 1343</span> <span class="stringliteral">"tin"</span>,</div><div class="line"><a name="l01344"></a><span class="lineno"> 1344</span> <span class="stringliteral">"tin"</span>,</div><div class="line"><a name="l01345"></a><span class="lineno"> 1345</span> <span class="stringliteral">"tin"</span>,</div><div class="line"><a name="l01346"></a><span class="lineno"> 1346</span> <span class="stringliteral">"tin"</span>,</div><div class="line"><a name="l01347"></a><span class="lineno"> 1347</span> <span class="stringliteral">"tin"</span>,</div><div class="line"><a name="l01348"></a><span class="lineno"> 1348</span> <span class="stringliteral">"tin"</span>,</div><div class="line"><a name="l01349"></a><span class="lineno"> 1349</span> <span class="stringliteral">"tin"</span>,</div><div class="line"><a name="l01350"></a><span class="lineno"> 1350</span> <span class="stringliteral">"antimony"</span>,</div><div class="line"><a name="l01351"></a><span class="lineno"> 1351</span> <span class="stringliteral">"antimony"</span>,</div><div class="line"><a name="l01352"></a><span class="lineno"> 1352</span> <span class="stringliteral">"tellurium"</span>,</div><div class="line"><a name="l01353"></a><span class="lineno"> 1353</span> <span class="stringliteral">"tellurium"</span>,</div><div class="line"><a name="l01354"></a><span class="lineno"> 1354</span> <span class="stringliteral">"tellurium"</span>,</div><div class="line"><a name="l01355"></a><span class="lineno"> 1355</span> <span class="stringliteral">"tellurium"</span>,</div><div class="line"><a name="l01356"></a><span class="lineno"> 1356</span> <span class="stringliteral">"tellurium"</span>,</div><div class="line"><a name="l01357"></a><span class="lineno"> 1357</span> <span class="stringliteral">"tellurium"</span>,</div><div class="line"><a name="l01358"></a><span class="lineno"> 1358</span> <span class="stringliteral">"tellurium"</span>,</div><div class="line"><a name="l01359"></a><span class="lineno"> 1359</span> <span class="stringliteral">"tellurium"</span>,</div><div class="line"><a name="l01360"></a><span class="lineno"> 1360</span> <span class="stringliteral">"iodine"</span>,</div><div class="line"><a name="l01361"></a><span class="lineno"> 1361</span> <span class="stringliteral">"xenon"</span>,</div><div class="line"><a name="l01362"></a><span class="lineno"> 1362</span> <span class="stringliteral">"xenon"</span>,</div><div class="line"><a name="l01363"></a><span class="lineno"> 1363</span> <span class="stringliteral">"xenon"</span>,</div><div class="line"><a name="l01364"></a><span class="lineno"> 1364</span> <span class="stringliteral">"xenon"</span>,</div><div class="line"><a name="l01365"></a><span class="lineno"> 1365</span> <span class="stringliteral">"xenon"</span>,</div><div class="line"><a name="l01366"></a><span class="lineno"> 1366</span> <span class="stringliteral">"xenon"</span>,</div><div class="line"><a name="l01367"></a><span class="lineno"> 1367</span> <span class="stringliteral">"xenon"</span>,</div><div class="line"><a name="l01368"></a><span class="lineno"> 1368</span> <span class="stringliteral">"xenon"</span>,</div><div class="line"><a name="l01369"></a><span class="lineno"> 1369</span> <span class="stringliteral">"xenon"</span>,</div><div class="line"><a name="l01370"></a><span class="lineno"> 1370</span> <span class="stringliteral">"caesium"</span>,</div><div class="line"><a name="l01371"></a><span class="lineno"> 1371</span> <span class="stringliteral">"barium"</span>,</div><div class="line"><a name="l01372"></a><span class="lineno"> 1372</span> <span class="stringliteral">"barium"</span>,</div><div class="line"><a name="l01373"></a><span class="lineno"> 1373</span> <span class="stringliteral">"barium"</span>,</div><div class="line"><a name="l01374"></a><span class="lineno"> 1374</span> <span class="stringliteral">"barium"</span>,</div><div class="line"><a name="l01375"></a><span class="lineno"> 1375</span> <span class="stringliteral">"barium"</span>,</div><div class="line"><a name="l01376"></a><span class="lineno"> 1376</span> <span class="stringliteral">"barium"</span>,</div><div class="line"><a name="l01377"></a><span class="lineno"> 1377</span> <span class="stringliteral">"barium"</span>,</div><div class="line"><a name="l01378"></a><span class="lineno"> 1378</span> <span class="stringliteral">"lanthanum"</span>,</div><div class="line"><a name="l01379"></a><span class="lineno"> 1379</span> <span class="stringliteral">"lanthanum"</span>,</div><div class="line"><a name="l01380"></a><span class="lineno"> 1380</span> <span class="stringliteral">"cerium"</span>,</div><div class="line"><a name="l01381"></a><span class="lineno"> 1381</span> <span class="stringliteral">"cerium"</span>,</div><div class="line"><a name="l01382"></a><span class="lineno"> 1382</span> <span class="stringliteral">"cerium"</span>,</div><div class="line"><a name="l01383"></a><span class="lineno"> 1383</span> <span class="stringliteral">"cerium"</span>,</div><div class="line"><a name="l01384"></a><span class="lineno"> 1384</span> <span class="stringliteral">"praseodymium"</span>,</div><div class="line"><a name="l01385"></a><span class="lineno"> 1385</span> <span class="stringliteral">"neodymium"</span>,</div><div class="line"><a name="l01386"></a><span class="lineno"> 1386</span> <span class="stringliteral">"neodymium"</span>,</div><div class="line"><a name="l01387"></a><span class="lineno"> 1387</span> <span class="stringliteral">"neodymium"</span>,</div><div class="line"><a name="l01388"></a><span class="lineno"> 1388</span> <span class="stringliteral">"neodymium"</span>,</div><div class="line"><a name="l01389"></a><span class="lineno"> 1389</span> <span class="stringliteral">"neodymium"</span>,</div><div class="line"><a name="l01390"></a><span class="lineno"> 1390</span> <span class="stringliteral">"neodymium"</span>,</div><div class="line"><a name="l01391"></a><span class="lineno"> 1391</span> <span class="stringliteral">"neodymium"</span>,</div><div class="line"><a name="l01392"></a><span class="lineno"> 1392</span> <span class="stringliteral">"samarium"</span>,</div><div class="line"><a name="l01393"></a><span class="lineno"> 1393</span> <span class="stringliteral">"samarium"</span>,</div><div class="line"><a name="l01394"></a><span class="lineno"> 1394</span> <span class="stringliteral">"samarium"</span>,</div><div class="line"><a name="l01395"></a><span class="lineno"> 1395</span> <span class="stringliteral">"samarium"</span>,</div><div class="line"><a name="l01396"></a><span class="lineno"> 1396</span> <span class="stringliteral">"samarium"</span>,</div><div class="line"><a name="l01397"></a><span class="lineno"> 1397</span> <span class="stringliteral">"samarium"</span>,</div><div class="line"><a name="l01398"></a><span class="lineno"> 1398</span> <span class="stringliteral">"samarium"</span>,</div><div class="line"><a name="l01399"></a><span class="lineno"> 1399</span> <span class="stringliteral">"europium"</span>,</div><div class="line"><a name="l01400"></a><span class="lineno"> 1400</span> <span class="stringliteral">"europium"</span>,</div><div class="line"><a name="l01401"></a><span class="lineno"> 1401</span> <span class="stringliteral">"gadolinium"</span>,</div><div class="line"><a name="l01402"></a><span class="lineno"> 1402</span> <span class="stringliteral">"gadolinium"</span>,</div><div class="line"><a name="l01403"></a><span class="lineno"> 1403</span> <span class="stringliteral">"gadolinium"</span>,</div><div class="line"><a name="l01404"></a><span class="lineno"> 1404</span> <span class="stringliteral">"gadolinium"</span>,</div><div class="line"><a name="l01405"></a><span class="lineno"> 1405</span> <span class="stringliteral">"gadolinium"</span>,</div><div class="line"><a name="l01406"></a><span class="lineno"> 1406</span> <span class="stringliteral">"gadolinium"</span>,</div><div class="line"><a name="l01407"></a><span class="lineno"> 1407</span> <span class="stringliteral">"gadolinium"</span>,</div><div class="line"><a name="l01408"></a><span class="lineno"> 1408</span> <span class="stringliteral">"terbium"</span>,</div><div class="line"><a name="l01409"></a><span class="lineno"> 1409</span> <span class="stringliteral">"dysprosium"</span>,</div><div class="line"><a name="l01410"></a><span class="lineno"> 1410</span> <span class="stringliteral">"dysprosium"</span>,</div><div class="line"><a name="l01411"></a><span class="lineno"> 1411</span> <span class="stringliteral">"dysprosium"</span>,</div><div class="line"><a name="l01412"></a><span class="lineno"> 1412</span> <span class="stringliteral">"dysprosium"</span>,</div><div class="line"><a name="l01413"></a><span class="lineno"> 1413</span> <span class="stringliteral">"dysprosium"</span>,</div><div class="line"><a name="l01414"></a><span class="lineno"> 1414</span> <span class="stringliteral">"dysprosium"</span>,</div><div class="line"><a name="l01415"></a><span class="lineno"> 1415</span> <span class="stringliteral">"dysprosium"</span>,</div><div class="line"><a name="l01416"></a><span class="lineno"> 1416</span> <span class="stringliteral">"holmium"</span>,</div><div class="line"><a name="l01417"></a><span class="lineno"> 1417</span> <span class="stringliteral">"erbium"</span>,</div><div class="line"><a name="l01418"></a><span class="lineno"> 1418</span> <span class="stringliteral">"erbium"</span>,</div><div class="line"><a name="l01419"></a><span class="lineno"> 1419</span> <span class="stringliteral">"erbium"</span>,</div><div class="line"><a name="l01420"></a><span class="lineno"> 1420</span> <span class="stringliteral">"erbium"</span>,</div><div class="line"><a name="l01421"></a><span class="lineno"> 1421</span> <span class="stringliteral">"erbium"</span>,</div><div class="line"><a name="l01422"></a><span class="lineno"> 1422</span> <span class="stringliteral">"erbium"</span>,</div><div class="line"><a name="l01423"></a><span class="lineno"> 1423</span> <span class="stringliteral">"thulium"</span>,</div><div class="line"><a name="l01424"></a><span class="lineno"> 1424</span> <span class="stringliteral">"ytterbium"</span>,</div><div class="line"><a name="l01425"></a><span class="lineno"> 1425</span> <span class="stringliteral">"ytterbium"</span>,</div><div class="line"><a name="l01426"></a><span class="lineno"> 1426</span> <span class="stringliteral">"ytterbium"</span>,</div><div class="line"><a name="l01427"></a><span class="lineno"> 1427</span> <span class="stringliteral">"ytterbium"</span>,</div><div class="line"><a name="l01428"></a><span class="lineno"> 1428</span> <span class="stringliteral">"ytterbium"</span>,</div><div class="line"><a name="l01429"></a><span class="lineno"> 1429</span> <span class="stringliteral">"ytterbium"</span>,</div><div class="line"><a name="l01430"></a><span class="lineno"> 1430</span> <span class="stringliteral">"ytterbium"</span>,</div><div class="line"><a name="l01431"></a><span class="lineno"> 1431</span> <span class="stringliteral">"lutetium"</span>,</div><div class="line"><a name="l01432"></a><span class="lineno"> 1432</span> <span class="stringliteral">"lutetium"</span>,</div><div class="line"><a name="l01433"></a><span class="lineno"> 1433</span> <span class="stringliteral">"hafnium"</span>,</div><div class="line"><a name="l01434"></a><span class="lineno"> 1434</span> <span class="stringliteral">"hafnium"</span>,</div><div class="line"><a name="l01435"></a><span class="lineno"> 1435</span> <span class="stringliteral">"hafnium"</span>,</div><div class="line"><a name="l01436"></a><span class="lineno"> 1436</span> <span class="stringliteral">"hafnium"</span>,</div><div class="line"><a name="l01437"></a><span class="lineno"> 1437</span> <span class="stringliteral">"hafnium"</span>,</div><div class="line"><a name="l01438"></a><span class="lineno"> 1438</span> <span class="stringliteral">"hafnium"</span>,</div><div class="line"><a name="l01439"></a><span class="lineno"> 1439</span> <span class="stringliteral">"tantalum"</span>,</div><div class="line"><a name="l01440"></a><span class="lineno"> 1440</span> <span class="stringliteral">"tantalum"</span>,</div><div class="line"><a name="l01441"></a><span class="lineno"> 1441</span> <span class="stringliteral">"tungsten"</span>,</div><div class="line"><a name="l01442"></a><span class="lineno"> 1442</span> <span class="stringliteral">"tungsten"</span>,</div><div class="line"><a name="l01443"></a><span class="lineno"> 1443</span> <span class="stringliteral">"tungsten"</span>,</div><div class="line"><a name="l01444"></a><span class="lineno"> 1444</span> <span class="stringliteral">"tungsten"</span>,</div><div class="line"><a name="l01445"></a><span class="lineno"> 1445</span> <span class="stringliteral">"tungsten"</span>,</div><div class="line"><a name="l01446"></a><span class="lineno"> 1446</span> <span class="stringliteral">"rhenium"</span>,</div><div class="line"><a name="l01447"></a><span class="lineno"> 1447</span> <span class="stringliteral">"rhenium"</span>,</div><div class="line"><a name="l01448"></a><span class="lineno"> 1448</span> <span class="stringliteral">"osmium"</span>,</div><div class="line"><a name="l01449"></a><span class="lineno"> 1449</span> <span class="stringliteral">"osmium"</span>,</div><div class="line"><a name="l01450"></a><span class="lineno"> 1450</span> <span class="stringliteral">"osmium"</span>,</div><div class="line"><a name="l01451"></a><span class="lineno"> 1451</span> <span class="stringliteral">"osmium"</span>,</div><div class="line"><a name="l01452"></a><span class="lineno"> 1452</span> <span class="stringliteral">"osmium"</span>,</div><div class="line"><a name="l01453"></a><span class="lineno"> 1453</span> <span class="stringliteral">"osmium"</span>,</div><div class="line"><a name="l01454"></a><span class="lineno"> 1454</span> <span class="stringliteral">"osmium"</span>,</div><div class="line"><a name="l01455"></a><span class="lineno"> 1455</span> <span class="stringliteral">"iridium"</span>,</div><div class="line"><a name="l01456"></a><span class="lineno"> 1456</span> <span class="stringliteral">"iridium"</span>,</div><div class="line"><a name="l01457"></a><span class="lineno"> 1457</span> <span class="stringliteral">"platinum"</span>,</div><div class="line"><a name="l01458"></a><span class="lineno"> 1458</span> <span class="stringliteral">"platinum"</span>,</div><div class="line"><a name="l01459"></a><span class="lineno"> 1459</span> <span class="stringliteral">"platinum"</span>,</div><div class="line"><a name="l01460"></a><span class="lineno"> 1460</span> <span class="stringliteral">"platinum"</span>,</div><div class="line"><a name="l01461"></a><span class="lineno"> 1461</span> <span class="stringliteral">"platinum"</span>,</div><div class="line"><a name="l01462"></a><span class="lineno"> 1462</span> <span class="stringliteral">"platinum"</span>,</div><div class="line"><a name="l01463"></a><span class="lineno"> 1463</span> <span class="stringliteral">"gold"</span>,</div><div class="line"><a name="l01464"></a><span class="lineno"> 1464</span> <span class="stringliteral">"mercury"</span>,</div><div class="line"><a name="l01465"></a><span class="lineno"> 1465</span> <span class="stringliteral">"mercury"</span>,</div><div class="line"><a name="l01466"></a><span class="lineno"> 1466</span> <span class="stringliteral">"mercury"</span>,</div><div class="line"><a name="l01467"></a><span class="lineno"> 1467</span> <span class="stringliteral">"mercury"</span>,</div><div class="line"><a name="l01468"></a><span class="lineno"> 1468</span> <span class="stringliteral">"mercury"</span>,</div><div class="line"><a name="l01469"></a><span class="lineno"> 1469</span> <span class="stringliteral">"mercury"</span>,</div><div class="line"><a name="l01470"></a><span class="lineno"> 1470</span> <span class="stringliteral">"mercury"</span>,</div><div class="line"><a name="l01471"></a><span class="lineno"> 1471</span> <span class="stringliteral">"thallium"</span>,</div><div class="line"><a name="l01472"></a><span class="lineno"> 1472</span> <span class="stringliteral">"thallium"</span>,</div><div class="line"><a name="l01473"></a><span class="lineno"> 1473</span> <span class="stringliteral">"lead"</span>,</div><div class="line"><a name="l01474"></a><span class="lineno"> 1474</span> <span class="stringliteral">"lead"</span>,</div><div class="line"><a name="l01475"></a><span class="lineno"> 1475</span> <span class="stringliteral">"lead"</span>,</div><div class="line"><a name="l01476"></a><span class="lineno"> 1476</span> <span class="stringliteral">"lead"</span>,</div><div class="line"><a name="l01477"></a><span class="lineno"> 1477</span> <span class="stringliteral">"bismuth"</span>,</div><div class="line"><a name="l01478"></a><span class="lineno"> 1478</span> <span class="stringliteral">"uranium"</span>,</div><div class="line"><a name="l01479"></a><span class="lineno"> 1479</span> <span class="stringliteral">"uranium"</span>,</div><div class="line"><a name="l01480"></a><span class="lineno"> 1480</span> <span class="stringliteral">"uranium"</span>,</div><div class="line"><a name="l01481"></a><span class="lineno"> 1481</span> <span class="stringliteral">"thorium"</span>,</div><div class="line"><a name="l01482"></a><span class="lineno"> 1482</span> <span class="stringliteral">"protactinium"</span>,</div><div class="line"><a name="l01483"></a><span class="lineno"> 1483</span> };</div><div class="line"><a name="l01484"></a><span class="lineno"> 1484</span> </div><div class="line"><a name="l01485"></a><span class="lineno"> 1485</span> </div><div class="line"><a name="l01486"></a><span class="lineno"> 1486</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* elem_table_symbol [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {</div><div class="line"><a name="l01487"></a><span class="lineno"> 1487</span> <span class="stringliteral">"H"</span>,</div><div class="line"><a name="l01488"></a><span class="lineno"> 1488</span> <span class="stringliteral">"H"</span>,</div><div class="line"><a name="l01489"></a><span class="lineno"> 1489</span> <span class="stringliteral">"He"</span>,</div><div class="line"><a name="l01490"></a><span class="lineno"> 1490</span> <span class="stringliteral">"He"</span>,</div><div class="line"><a name="l01491"></a><span class="lineno"> 1491</span> <span class="stringliteral">"Li"</span>,</div><div class="line"><a name="l01492"></a><span class="lineno"> 1492</span> <span class="stringliteral">"Li"</span>,</div><div class="line"><a name="l01493"></a><span class="lineno"> 1493</span> <span class="stringliteral">"Be"</span>,</div><div class="line"><a name="l01494"></a><span class="lineno"> 1494</span> <span class="stringliteral">"B"</span>,</div><div class="line"><a name="l01495"></a><span class="lineno"> 1495</span> <span class="stringliteral">"B"</span>,</div><div class="line"><a name="l01496"></a><span class="lineno"> 1496</span> <span class="stringliteral">"C"</span>,</div><div class="line"><a name="l01497"></a><span class="lineno"> 1497</span> <span class="stringliteral">"C"</span>,</div><div class="line"><a name="l01498"></a><span class="lineno"> 1498</span> <span class="stringliteral">"N"</span>,</div><div class="line"><a name="l01499"></a><span class="lineno"> 1499</span> <span class="stringliteral">"N"</span>,</div><div class="line"><a name="l01500"></a><span class="lineno"> 1500</span> <span class="stringliteral">"O"</span>,</div><div class="line"><a name="l01501"></a><span class="lineno"> 1501</span> <span class="stringliteral">"O"</span>,</div><div class="line"><a name="l01502"></a><span class="lineno"> 1502</span> <span class="stringliteral">"O"</span>,</div><div class="line"><a name="l01503"></a><span class="lineno"> 1503</span> <span class="stringliteral">"F"</span>,</div><div class="line"><a name="l01504"></a><span class="lineno"> 1504</span> <span class="stringliteral">"Ne"</span>,</div><div class="line"><a name="l01505"></a><span class="lineno"> 1505</span> <span class="stringliteral">"Ne"</span>,</div><div class="line"><a name="l01506"></a><span class="lineno"> 1506</span> <span class="stringliteral">"Ne"</span>,</div><div class="line"><a name="l01507"></a><span class="lineno"> 1507</span> <span class="stringliteral">"Na"</span>,</div><div class="line"><a name="l01508"></a><span class="lineno"> 1508</span> <span class="stringliteral">"Mg"</span>,</div><div class="line"><a name="l01509"></a><span class="lineno"> 1509</span> <span class="stringliteral">"Mg"</span>,</div><div class="line"><a name="l01510"></a><span class="lineno"> 1510</span> <span class="stringliteral">"Mg"</span>,</div><div class="line"><a name="l01511"></a><span class="lineno"> 1511</span> <span class="stringliteral">"Al"</span>,</div><div class="line"><a name="l01512"></a><span class="lineno"> 1512</span> <span class="stringliteral">"Si"</span>,</div><div class="line"><a name="l01513"></a><span class="lineno"> 1513</span> <span class="stringliteral">"Si"</span>,</div><div class="line"><a name="l01514"></a><span class="lineno"> 1514</span> <span class="stringliteral">"Si"</span>,</div><div class="line"><a name="l01515"></a><span class="lineno"> 1515</span> <span class="stringliteral">"P"</span>,</div><div class="line"><a name="l01516"></a><span class="lineno"> 1516</span> <span class="stringliteral">"S"</span>,</div><div class="line"><a name="l01517"></a><span class="lineno"> 1517</span> <span class="stringliteral">"S"</span>,</div><div class="line"><a name="l01518"></a><span class="lineno"> 1518</span> <span class="stringliteral">"S"</span>,</div><div class="line"><a name="l01519"></a><span class="lineno"> 1519</span> <span class="stringliteral">"S"</span>,</div><div class="line"><a name="l01520"></a><span class="lineno"> 1520</span> <span class="stringliteral">"Cl"</span>,</div><div class="line"><a name="l01521"></a><span class="lineno"> 1521</span> <span class="stringliteral">"Cl"</span>,</div><div class="line"><a name="l01522"></a><span class="lineno"> 1522</span> <span class="stringliteral">"Ar"</span>,</div><div class="line"><a name="l01523"></a><span class="lineno"> 1523</span> <span class="stringliteral">"Ar"</span>,</div><div class="line"><a name="l01524"></a><span class="lineno"> 1524</span> <span class="stringliteral">"Ar"</span>,</div><div class="line"><a name="l01525"></a><span class="lineno"> 1525</span> <span class="stringliteral">"K"</span>,</div><div class="line"><a name="l01526"></a><span class="lineno"> 1526</span> <span class="stringliteral">"K"</span>,</div><div class="line"><a name="l01527"></a><span class="lineno"> 1527</span> <span class="stringliteral">"K"</span>,</div><div class="line"><a name="l01528"></a><span class="lineno"> 1528</span> <span class="stringliteral">"Ca"</span>,</div><div class="line"><a name="l01529"></a><span class="lineno"> 1529</span> <span class="stringliteral">"Ca"</span>,</div><div class="line"><a name="l01530"></a><span class="lineno"> 1530</span> <span class="stringliteral">"Ca"</span>,</div><div class="line"><a name="l01531"></a><span class="lineno"> 1531</span> <span class="stringliteral">"Ca"</span>,</div><div class="line"><a name="l01532"></a><span class="lineno"> 1532</span> <span class="stringliteral">"Ca"</span>,</div><div class="line"><a name="l01533"></a><span class="lineno"> 1533</span> <span class="stringliteral">"Ca"</span>,</div><div class="line"><a name="l01534"></a><span class="lineno"> 1534</span> <span class="stringliteral">"Sc"</span>,</div><div class="line"><a name="l01535"></a><span class="lineno"> 1535</span> <span class="stringliteral">"Ti"</span>,</div><div class="line"><a name="l01536"></a><span class="lineno"> 1536</span> <span class="stringliteral">"Ti"</span>,</div><div class="line"><a name="l01537"></a><span class="lineno"> 1537</span> <span class="stringliteral">"Ti"</span>,</div><div class="line"><a name="l01538"></a><span class="lineno"> 1538</span> <span class="stringliteral">"Ti"</span>,</div><div class="line"><a name="l01539"></a><span class="lineno"> 1539</span> <span class="stringliteral">"Ti"</span>,</div><div class="line"><a name="l01540"></a><span class="lineno"> 1540</span> <span class="stringliteral">"V"</span>,</div><div class="line"><a name="l01541"></a><span class="lineno"> 1541</span> <span class="stringliteral">"V"</span>,</div><div class="line"><a name="l01542"></a><span class="lineno"> 1542</span> <span class="stringliteral">"Cr"</span>,</div><div class="line"><a name="l01543"></a><span class="lineno"> 1543</span> <span class="stringliteral">"Cr"</span>,</div><div class="line"><a name="l01544"></a><span class="lineno"> 1544</span> <span class="stringliteral">"Cr"</span>,</div><div class="line"><a name="l01545"></a><span class="lineno"> 1545</span> <span class="stringliteral">"Cr"</span>,</div><div class="line"><a name="l01546"></a><span class="lineno"> 1546</span> <span class="stringliteral">"Mn"</span>,</div><div class="line"><a name="l01547"></a><span class="lineno"> 1547</span> <span class="stringliteral">"Fe"</span>,</div><div class="line"><a name="l01548"></a><span class="lineno"> 1548</span> <span class="stringliteral">"Fe"</span>,</div><div class="line"><a name="l01549"></a><span class="lineno"> 1549</span> <span class="stringliteral">"Fe"</span>,</div><div class="line"><a name="l01550"></a><span class="lineno"> 1550</span> <span class="stringliteral">"Fe"</span>,</div><div class="line"><a name="l01551"></a><span class="lineno"> 1551</span> <span class="stringliteral">"Co"</span>,</div><div class="line"><a name="l01552"></a><span class="lineno"> 1552</span> <span class="stringliteral">"Ni"</span>,</div><div class="line"><a name="l01553"></a><span class="lineno"> 1553</span> <span class="stringliteral">"Ni"</span>,</div><div class="line"><a name="l01554"></a><span class="lineno"> 1554</span> <span class="stringliteral">"Ni"</span>,</div><div class="line"><a name="l01555"></a><span class="lineno"> 1555</span> <span class="stringliteral">"Ni"</span>,</div><div class="line"><a name="l01556"></a><span class="lineno"> 1556</span> <span class="stringliteral">"Ni"</span>,</div><div class="line"><a name="l01557"></a><span class="lineno"> 1557</span> <span class="stringliteral">"Cu"</span>,</div><div class="line"><a name="l01558"></a><span class="lineno"> 1558</span> <span class="stringliteral">"Cu"</span>,</div><div class="line"><a name="l01559"></a><span class="lineno"> 1559</span> <span class="stringliteral">"Zn"</span>,</div><div class="line"><a name="l01560"></a><span class="lineno"> 1560</span> <span class="stringliteral">"Zn"</span>,</div><div class="line"><a name="l01561"></a><span class="lineno"> 1561</span> <span class="stringliteral">"Zn"</span>,</div><div class="line"><a name="l01562"></a><span class="lineno"> 1562</span> <span class="stringliteral">"Zn"</span>,</div><div class="line"><a name="l01563"></a><span class="lineno"> 1563</span> <span class="stringliteral">"Zn"</span>,</div><div class="line"><a name="l01564"></a><span class="lineno"> 1564</span> <span class="stringliteral">"Ga"</span>,</div><div class="line"><a name="l01565"></a><span class="lineno"> 1565</span> <span class="stringliteral">"Ga"</span>,</div><div class="line"><a name="l01566"></a><span class="lineno"> 1566</span> <span class="stringliteral">"Ge"</span>,</div><div class="line"><a name="l01567"></a><span class="lineno"> 1567</span> <span class="stringliteral">"Ge"</span>,</div><div class="line"><a name="l01568"></a><span class="lineno"> 1568</span> <span class="stringliteral">"Ge"</span>,</div><div class="line"><a name="l01569"></a><span class="lineno"> 1569</span> <span class="stringliteral">"Ge"</span>,</div><div class="line"><a name="l01570"></a><span class="lineno"> 1570</span> <span class="stringliteral">"Ge"</span>,</div><div class="line"><a name="l01571"></a><span class="lineno"> 1571</span> <span class="stringliteral">"As"</span>,</div><div class="line"><a name="l01572"></a><span class="lineno"> 1572</span> <span class="stringliteral">"Se"</span>,</div><div class="line"><a name="l01573"></a><span class="lineno"> 1573</span> <span class="stringliteral">"Se"</span>,</div><div class="line"><a name="l01574"></a><span class="lineno"> 1574</span> <span class="stringliteral">"Se"</span>,</div><div class="line"><a name="l01575"></a><span class="lineno"> 1575</span> <span class="stringliteral">"Se"</span>,</div><div class="line"><a name="l01576"></a><span class="lineno"> 1576</span> <span class="stringliteral">"Se"</span>,</div><div class="line"><a name="l01577"></a><span class="lineno"> 1577</span> <span class="stringliteral">"Se"</span>,</div><div class="line"><a name="l01578"></a><span class="lineno"> 1578</span> <span class="stringliteral">"Br"</span>,</div><div class="line"><a name="l01579"></a><span class="lineno"> 1579</span> <span class="stringliteral">"Br"</span>,</div><div class="line"><a name="l01580"></a><span class="lineno"> 1580</span> <span class="stringliteral">"Kr"</span>,</div><div class="line"><a name="l01581"></a><span class="lineno"> 1581</span> <span class="stringliteral">"Kr"</span>,</div><div class="line"><a name="l01582"></a><span class="lineno"> 1582</span> <span class="stringliteral">"Kr"</span>,</div><div class="line"><a name="l01583"></a><span class="lineno"> 1583</span> <span class="stringliteral">"Kr"</span>,</div><div class="line"><a name="l01584"></a><span class="lineno"> 1584</span> <span class="stringliteral">"Kr"</span>,</div><div class="line"><a name="l01585"></a><span class="lineno"> 1585</span> <span class="stringliteral">"Kr"</span>,</div><div class="line"><a name="l01586"></a><span class="lineno"> 1586</span> <span class="stringliteral">"Rb"</span>,</div><div class="line"><a name="l01587"></a><span class="lineno"> 1587</span> <span class="stringliteral">"Rb"</span>,</div><div class="line"><a name="l01588"></a><span class="lineno"> 1588</span> <span class="stringliteral">"Sr"</span>,</div><div class="line"><a name="l01589"></a><span class="lineno"> 1589</span> <span class="stringliteral">"Sr"</span>,</div><div class="line"><a name="l01590"></a><span class="lineno"> 1590</span> <span class="stringliteral">"Sr"</span>,</div><div class="line"><a name="l01591"></a><span class="lineno"> 1591</span> <span class="stringliteral">"Sr"</span>,</div><div class="line"><a name="l01592"></a><span class="lineno"> 1592</span> <span class="stringliteral">"Y"</span>,</div><div class="line"><a name="l01593"></a><span class="lineno"> 1593</span> <span class="stringliteral">"Zr"</span>,</div><div class="line"><a name="l01594"></a><span class="lineno"> 1594</span> <span class="stringliteral">"Zr"</span>,</div><div class="line"><a name="l01595"></a><span class="lineno"> 1595</span> <span class="stringliteral">"Zr"</span>,</div><div class="line"><a name="l01596"></a><span class="lineno"> 1596</span> <span class="stringliteral">"Zr"</span>,</div><div class="line"><a name="l01597"></a><span class="lineno"> 1597</span> <span class="stringliteral">"Zr"</span>,</div><div class="line"><a name="l01598"></a><span class="lineno"> 1598</span> <span class="stringliteral">"Nb"</span>,</div><div class="line"><a name="l01599"></a><span class="lineno"> 1599</span> <span class="stringliteral">"Mo"</span>,</div><div class="line"><a name="l01600"></a><span class="lineno"> 1600</span> <span class="stringliteral">"Mo"</span>,</div><div class="line"><a name="l01601"></a><span class="lineno"> 1601</span> <span class="stringliteral">"Mo"</span>,</div><div class="line"><a name="l01602"></a><span class="lineno"> 1602</span> <span class="stringliteral">"Mo"</span>,</div><div class="line"><a name="l01603"></a><span class="lineno"> 1603</span> <span class="stringliteral">"Mo"</span>,</div><div class="line"><a name="l01604"></a><span class="lineno"> 1604</span> <span class="stringliteral">"Mo"</span>,</div><div class="line"><a name="l01605"></a><span class="lineno"> 1605</span> <span class="stringliteral">"Mo"</span>,</div><div class="line"><a name="l01606"></a><span class="lineno"> 1606</span> <span class="stringliteral">"Ru"</span>,</div><div class="line"><a name="l01607"></a><span class="lineno"> 1607</span> <span class="stringliteral">"Ru"</span>,</div><div class="line"><a name="l01608"></a><span class="lineno"> 1608</span> <span class="stringliteral">"Ru"</span>,</div><div class="line"><a name="l01609"></a><span class="lineno"> 1609</span> <span class="stringliteral">"Ru"</span>,</div><div class="line"><a name="l01610"></a><span class="lineno"> 1610</span> <span class="stringliteral">"Ru"</span>,</div><div class="line"><a name="l01611"></a><span class="lineno"> 1611</span> <span class="stringliteral">"Ru"</span>,</div><div class="line"><a name="l01612"></a><span class="lineno"> 1612</span> <span class="stringliteral">"Ru"</span>,</div><div class="line"><a name="l01613"></a><span class="lineno"> 1613</span> <span class="stringliteral">"Rh"</span>,</div><div class="line"><a name="l01614"></a><span class="lineno"> 1614</span> <span class="stringliteral">"Pd"</span>,</div><div class="line"><a name="l01615"></a><span class="lineno"> 1615</span> <span class="stringliteral">"Pd"</span>,</div><div class="line"><a name="l01616"></a><span class="lineno"> 1616</span> <span class="stringliteral">"Pd"</span>,</div><div class="line"><a name="l01617"></a><span class="lineno"> 1617</span> <span class="stringliteral">"Pd"</span>,</div><div class="line"><a name="l01618"></a><span class="lineno"> 1618</span> <span class="stringliteral">"Pd"</span>,</div><div class="line"><a name="l01619"></a><span class="lineno"> 1619</span> <span class="stringliteral">"Pd"</span>,</div><div class="line"><a name="l01620"></a><span class="lineno"> 1620</span> <span class="stringliteral">"Ag"</span>,</div><div class="line"><a name="l01621"></a><span class="lineno"> 1621</span> <span class="stringliteral">"Ag"</span>,</div><div class="line"><a name="l01622"></a><span class="lineno"> 1622</span> <span class="stringliteral">"Cd"</span>,</div><div class="line"><a name="l01623"></a><span class="lineno"> 1623</span> <span class="stringliteral">"Cd"</span>,</div><div class="line"><a name="l01624"></a><span class="lineno"> 1624</span> <span class="stringliteral">"Cd"</span>,</div><div class="line"><a name="l01625"></a><span class="lineno"> 1625</span> <span class="stringliteral">"Cd"</span>,</div><div class="line"><a name="l01626"></a><span class="lineno"> 1626</span> <span class="stringliteral">"Cd"</span>,</div><div class="line"><a name="l01627"></a><span class="lineno"> 1627</span> <span class="stringliteral">"Cd"</span>,</div><div class="line"><a name="l01628"></a><span class="lineno"> 1628</span> <span class="stringliteral">"Cd"</span>,</div><div class="line"><a name="l01629"></a><span class="lineno"> 1629</span> <span class="stringliteral">"Cd"</span>,</div><div class="line"><a name="l01630"></a><span class="lineno"> 1630</span> <span class="stringliteral">"In"</span>,</div><div class="line"><a name="l01631"></a><span class="lineno"> 1631</span> <span class="stringliteral">"In"</span>,</div><div class="line"><a name="l01632"></a><span class="lineno"> 1632</span> <span class="stringliteral">"Sn"</span>,</div><div class="line"><a name="l01633"></a><span class="lineno"> 1633</span> <span class="stringliteral">"Sn"</span>,</div><div class="line"><a name="l01634"></a><span class="lineno"> 1634</span> <span class="stringliteral">"Sn"</span>,</div><div class="line"><a name="l01635"></a><span class="lineno"> 1635</span> <span class="stringliteral">"Sn"</span>,</div><div class="line"><a name="l01636"></a><span class="lineno"> 1636</span> <span class="stringliteral">"Sn"</span>,</div><div class="line"><a name="l01637"></a><span class="lineno"> 1637</span> <span class="stringliteral">"Sn"</span>,</div><div class="line"><a name="l01638"></a><span class="lineno"> 1638</span> <span class="stringliteral">"Sn"</span>,</div><div class="line"><a name="l01639"></a><span class="lineno"> 1639</span> <span class="stringliteral">"Sn"</span>,</div><div class="line"><a name="l01640"></a><span class="lineno"> 1640</span> <span class="stringliteral">"Sn"</span>,</div><div class="line"><a name="l01641"></a><span class="lineno"> 1641</span> <span class="stringliteral">"Sn"</span>,</div><div class="line"><a name="l01642"></a><span class="lineno"> 1642</span> <span class="stringliteral">"Sb"</span>,</div><div class="line"><a name="l01643"></a><span class="lineno"> 1643</span> <span class="stringliteral">"Sb"</span>,</div><div class="line"><a name="l01644"></a><span class="lineno"> 1644</span> <span class="stringliteral">"Te"</span>,</div><div class="line"><a name="l01645"></a><span class="lineno"> 1645</span> <span class="stringliteral">"Te"</span>,</div><div class="line"><a name="l01646"></a><span class="lineno"> 1646</span> <span class="stringliteral">"Te"</span>,</div><div class="line"><a name="l01647"></a><span class="lineno"> 1647</span> <span class="stringliteral">"Te"</span>,</div><div class="line"><a name="l01648"></a><span class="lineno"> 1648</span> <span class="stringliteral">"Te"</span>,</div><div class="line"><a name="l01649"></a><span class="lineno"> 1649</span> <span class="stringliteral">"Te"</span>,</div><div class="line"><a name="l01650"></a><span class="lineno"> 1650</span> <span class="stringliteral">"Te"</span>,</div><div class="line"><a name="l01651"></a><span class="lineno"> 1651</span> <span class="stringliteral">"Te"</span>,</div><div class="line"><a name="l01652"></a><span class="lineno"> 1652</span> <span class="stringliteral">"I"</span>,</div><div class="line"><a name="l01653"></a><span class="lineno"> 1653</span> <span class="stringliteral">"Xe"</span>,</div><div class="line"><a name="l01654"></a><span class="lineno"> 1654</span> <span class="stringliteral">"Xe"</span>,</div><div class="line"><a name="l01655"></a><span class="lineno"> 1655</span> <span class="stringliteral">"Xe"</span>,</div><div class="line"><a name="l01656"></a><span class="lineno"> 1656</span> <span class="stringliteral">"Xe"</span>,</div><div class="line"><a name="l01657"></a><span class="lineno"> 1657</span> <span class="stringliteral">"Xe"</span>,</div><div class="line"><a name="l01658"></a><span class="lineno"> 1658</span> <span class="stringliteral">"Xe"</span>,</div><div class="line"><a name="l01659"></a><span class="lineno"> 1659</span> <span class="stringliteral">"Xe"</span>,</div><div class="line"><a name="l01660"></a><span class="lineno"> 1660</span> <span class="stringliteral">"Xe"</span>,</div><div class="line"><a name="l01661"></a><span class="lineno"> 1661</span> <span class="stringliteral">"Xe"</span>,</div><div class="line"><a name="l01662"></a><span class="lineno"> 1662</span> <span class="stringliteral">"Cs"</span>,</div><div class="line"><a name="l01663"></a><span class="lineno"> 1663</span> <span class="stringliteral">"Ba"</span>,</div><div class="line"><a name="l01664"></a><span class="lineno"> 1664</span> <span class="stringliteral">"Ba"</span>,</div><div class="line"><a name="l01665"></a><span class="lineno"> 1665</span> <span class="stringliteral">"Ba"</span>,</div><div class="line"><a name="l01666"></a><span class="lineno"> 1666</span> <span class="stringliteral">"Ba"</span>,</div><div class="line"><a name="l01667"></a><span class="lineno"> 1667</span> <span class="stringliteral">"Ba"</span>,</div><div class="line"><a name="l01668"></a><span class="lineno"> 1668</span> <span class="stringliteral">"Ba"</span>,</div><div class="line"><a name="l01669"></a><span class="lineno"> 1669</span> <span class="stringliteral">"Ba"</span>,</div><div class="line"><a name="l01670"></a><span class="lineno"> 1670</span> <span class="stringliteral">"La"</span>,</div><div class="line"><a name="l01671"></a><span class="lineno"> 1671</span> <span class="stringliteral">"La"</span>,</div><div class="line"><a name="l01672"></a><span class="lineno"> 1672</span> <span class="stringliteral">"Ce"</span>,</div><div class="line"><a name="l01673"></a><span class="lineno"> 1673</span> <span class="stringliteral">"Ce"</span>,</div><div class="line"><a name="l01674"></a><span class="lineno"> 1674</span> <span class="stringliteral">"Ce"</span>,</div><div class="line"><a name="l01675"></a><span class="lineno"> 1675</span> <span class="stringliteral">"Ce"</span>,</div><div class="line"><a name="l01676"></a><span class="lineno"> 1676</span> <span class="stringliteral">"Pr"</span>,</div><div class="line"><a name="l01677"></a><span class="lineno"> 1677</span> <span class="stringliteral">"Nd"</span>,</div><div class="line"><a name="l01678"></a><span class="lineno"> 1678</span> <span class="stringliteral">"Nd"</span>,</div><div class="line"><a name="l01679"></a><span class="lineno"> 1679</span> <span class="stringliteral">"Nd"</span>,</div><div class="line"><a name="l01680"></a><span class="lineno"> 1680</span> <span class="stringliteral">"Nd"</span>,</div><div class="line"><a name="l01681"></a><span class="lineno"> 1681</span> <span class="stringliteral">"Nd"</span>,</div><div class="line"><a name="l01682"></a><span class="lineno"> 1682</span> <span class="stringliteral">"Nd"</span>,</div><div class="line"><a name="l01683"></a><span class="lineno"> 1683</span> <span class="stringliteral">"Nd"</span>,</div><div class="line"><a name="l01684"></a><span class="lineno"> 1684</span> <span class="stringliteral">"Sm"</span>,</div><div class="line"><a name="l01685"></a><span class="lineno"> 1685</span> <span class="stringliteral">"Sm"</span>,</div><div class="line"><a name="l01686"></a><span class="lineno"> 1686</span> <span class="stringliteral">"Sm"</span>,</div><div class="line"><a name="l01687"></a><span class="lineno"> 1687</span> <span class="stringliteral">"Sm"</span>,</div><div class="line"><a name="l01688"></a><span class="lineno"> 1688</span> <span class="stringliteral">"Sm"</span>,</div><div class="line"><a name="l01689"></a><span class="lineno"> 1689</span> <span class="stringliteral">"Sm"</span>,</div><div class="line"><a name="l01690"></a><span class="lineno"> 1690</span> <span class="stringliteral">"Sm"</span>,</div><div class="line"><a name="l01691"></a><span class="lineno"> 1691</span> <span class="stringliteral">"Eu"</span>,</div><div class="line"><a name="l01692"></a><span class="lineno"> 1692</span> <span class="stringliteral">"Eu"</span>,</div><div class="line"><a name="l01693"></a><span class="lineno"> 1693</span> <span class="stringliteral">"Gd"</span>,</div><div class="line"><a name="l01694"></a><span class="lineno"> 1694</span> <span class="stringliteral">"Gd"</span>,</div><div class="line"><a name="l01695"></a><span class="lineno"> 1695</span> <span class="stringliteral">"Gd"</span>,</div><div class="line"><a name="l01696"></a><span class="lineno"> 1696</span> <span class="stringliteral">"Gd"</span>,</div><div class="line"><a name="l01697"></a><span class="lineno"> 1697</span> <span class="stringliteral">"Gd"</span>,</div><div class="line"><a name="l01698"></a><span class="lineno"> 1698</span> <span class="stringliteral">"Gd"</span>,</div><div class="line"><a name="l01699"></a><span class="lineno"> 1699</span> <span class="stringliteral">"Gd"</span>,</div><div class="line"><a name="l01700"></a><span class="lineno"> 1700</span> <span class="stringliteral">"Tb"</span>,</div><div class="line"><a name="l01701"></a><span class="lineno"> 1701</span> <span class="stringliteral">"Dy"</span>,</div><div class="line"><a name="l01702"></a><span class="lineno"> 1702</span> <span class="stringliteral">"Dy"</span>,</div><div class="line"><a name="l01703"></a><span class="lineno"> 1703</span> <span class="stringliteral">"Dy"</span>,</div><div class="line"><a name="l01704"></a><span class="lineno"> 1704</span> <span class="stringliteral">"Dy"</span>,</div><div class="line"><a name="l01705"></a><span class="lineno"> 1705</span> <span class="stringliteral">"Dy"</span>,</div><div class="line"><a name="l01706"></a><span class="lineno"> 1706</span> <span class="stringliteral">"Dy"</span>,</div><div class="line"><a name="l01707"></a><span class="lineno"> 1707</span> <span class="stringliteral">"Dy"</span>,</div><div class="line"><a name="l01708"></a><span class="lineno"> 1708</span> <span class="stringliteral">"Ho"</span>,</div><div class="line"><a name="l01709"></a><span class="lineno"> 1709</span> <span class="stringliteral">"Er"</span>,</div><div class="line"><a name="l01710"></a><span class="lineno"> 1710</span> <span class="stringliteral">"Er"</span>,</div><div class="line"><a name="l01711"></a><span class="lineno"> 1711</span> <span class="stringliteral">"Er"</span>,</div><div class="line"><a name="l01712"></a><span class="lineno"> 1712</span> <span class="stringliteral">"Er"</span>,</div><div class="line"><a name="l01713"></a><span class="lineno"> 1713</span> <span class="stringliteral">"Er"</span>,</div><div class="line"><a name="l01714"></a><span class="lineno"> 1714</span> <span class="stringliteral">"Er"</span>,</div><div class="line"><a name="l01715"></a><span class="lineno"> 1715</span> <span class="stringliteral">"Tm"</span>,</div><div class="line"><a name="l01716"></a><span class="lineno"> 1716</span> <span class="stringliteral">"Yb"</span>,</div><div class="line"><a name="l01717"></a><span class="lineno"> 1717</span> <span class="stringliteral">"Yb"</span>,</div><div class="line"><a name="l01718"></a><span class="lineno"> 1718</span> <span class="stringliteral">"Yb"</span>,</div><div class="line"><a name="l01719"></a><span class="lineno"> 1719</span> <span class="stringliteral">"Yb"</span>,</div><div class="line"><a name="l01720"></a><span class="lineno"> 1720</span> <span class="stringliteral">"Yb"</span>,</div><div class="line"><a name="l01721"></a><span class="lineno"> 1721</span> <span class="stringliteral">"Yb"</span>,</div><div class="line"><a name="l01722"></a><span class="lineno"> 1722</span> <span class="stringliteral">"Yb"</span>,</div><div class="line"><a name="l01723"></a><span class="lineno"> 1723</span> <span class="stringliteral">"Lu"</span>,</div><div class="line"><a name="l01724"></a><span class="lineno"> 1724</span> <span class="stringliteral">"Lu"</span>,</div><div class="line"><a name="l01725"></a><span class="lineno"> 1725</span> <span class="stringliteral">"Hf"</span>,</div><div class="line"><a name="l01726"></a><span class="lineno"> 1726</span> <span class="stringliteral">"Hf"</span>,</div><div class="line"><a name="l01727"></a><span class="lineno"> 1727</span> <span class="stringliteral">"Hf"</span>,</div><div class="line"><a name="l01728"></a><span class="lineno"> 1728</span> <span class="stringliteral">"Hf"</span>,</div><div class="line"><a name="l01729"></a><span class="lineno"> 1729</span> <span class="stringliteral">"Hf"</span>,</div><div class="line"><a name="l01730"></a><span class="lineno"> 1730</span> <span class="stringliteral">"Hf"</span>,</div><div class="line"><a name="l01731"></a><span class="lineno"> 1731</span> <span class="stringliteral">"Ta"</span>,</div><div class="line"><a name="l01732"></a><span class="lineno"> 1732</span> <span class="stringliteral">"Ta"</span>,</div><div class="line"><a name="l01733"></a><span class="lineno"> 1733</span> <span class="stringliteral">"W"</span>,</div><div class="line"><a name="l01734"></a><span class="lineno"> 1734</span> <span class="stringliteral">"W"</span>,</div><div class="line"><a name="l01735"></a><span class="lineno"> 1735</span> <span class="stringliteral">"W"</span>,</div><div class="line"><a name="l01736"></a><span class="lineno"> 1736</span> <span class="stringliteral">"W"</span>,</div><div class="line"><a name="l01737"></a><span class="lineno"> 1737</span> <span class="stringliteral">"W"</span>,</div><div class="line"><a name="l01738"></a><span class="lineno"> 1738</span> <span class="stringliteral">"Re"</span>,</div><div class="line"><a name="l01739"></a><span class="lineno"> 1739</span> <span class="stringliteral">"Re"</span>,</div><div class="line"><a name="l01740"></a><span class="lineno"> 1740</span> <span class="stringliteral">"Os"</span>,</div><div class="line"><a name="l01741"></a><span class="lineno"> 1741</span> <span class="stringliteral">"Os"</span>,</div><div class="line"><a name="l01742"></a><span class="lineno"> 1742</span> <span class="stringliteral">"Os"</span>,</div><div class="line"><a name="l01743"></a><span class="lineno"> 1743</span> <span class="stringliteral">"Os"</span>,</div><div class="line"><a name="l01744"></a><span class="lineno"> 1744</span> <span class="stringliteral">"Os"</span>,</div><div class="line"><a name="l01745"></a><span class="lineno"> 1745</span> <span class="stringliteral">"Os"</span>,</div><div class="line"><a name="l01746"></a><span class="lineno"> 1746</span> <span class="stringliteral">"Os"</span>,</div><div class="line"><a name="l01747"></a><span class="lineno"> 1747</span> <span class="stringliteral">"Ir"</span>,</div><div class="line"><a name="l01748"></a><span class="lineno"> 1748</span> <span class="stringliteral">"Ir"</span>,</div><div class="line"><a name="l01749"></a><span class="lineno"> 1749</span> <span class="stringliteral">"Pt"</span>,</div><div class="line"><a name="l01750"></a><span class="lineno"> 1750</span> <span class="stringliteral">"Pt"</span>,</div><div class="line"><a name="l01751"></a><span class="lineno"> 1751</span> <span class="stringliteral">"Pt"</span>,</div><div class="line"><a name="l01752"></a><span class="lineno"> 1752</span> <span class="stringliteral">"Pt"</span>,</div><div class="line"><a name="l01753"></a><span class="lineno"> 1753</span> <span class="stringliteral">"Pt"</span>,</div><div class="line"><a name="l01754"></a><span class="lineno"> 1754</span> <span class="stringliteral">"Pt"</span>,</div><div class="line"><a name="l01755"></a><span class="lineno"> 1755</span> <span class="stringliteral">"Au"</span>,</div><div class="line"><a name="l01756"></a><span class="lineno"> 1756</span> <span class="stringliteral">"Hg"</span>,</div><div class="line"><a name="l01757"></a><span class="lineno"> 1757</span> <span class="stringliteral">"Hg"</span>,</div><div class="line"><a name="l01758"></a><span class="lineno"> 1758</span> <span class="stringliteral">"Hg"</span>,</div><div class="line"><a name="l01759"></a><span class="lineno"> 1759</span> <span class="stringliteral">"Hg"</span>,</div><div class="line"><a name="l01760"></a><span class="lineno"> 1760</span> <span class="stringliteral">"Hg"</span>,</div><div class="line"><a name="l01761"></a><span class="lineno"> 1761</span> <span class="stringliteral">"Hg"</span>,</div><div class="line"><a name="l01762"></a><span class="lineno"> 1762</span> <span class="stringliteral">"Hg"</span>,</div><div class="line"><a name="l01763"></a><span class="lineno"> 1763</span> <span class="stringliteral">"Tl"</span>,</div><div class="line"><a name="l01764"></a><span class="lineno"> 1764</span> <span class="stringliteral">"Tl"</span>,</div><div class="line"><a name="l01765"></a><span class="lineno"> 1765</span> <span class="stringliteral">"Pb"</span>,</div><div class="line"><a name="l01766"></a><span class="lineno"> 1766</span> <span class="stringliteral">"Pb"</span>,</div><div class="line"><a name="l01767"></a><span class="lineno"> 1767</span> <span class="stringliteral">"Pb"</span>,</div><div class="line"><a name="l01768"></a><span class="lineno"> 1768</span> <span class="stringliteral">"Pb"</span>,</div><div class="line"><a name="l01769"></a><span class="lineno"> 1769</span> <span class="stringliteral">"Bi"</span>,</div><div class="line"><a name="l01770"></a><span class="lineno"> 1770</span> <span class="stringliteral">"U"</span>,</div><div class="line"><a name="l01771"></a><span class="lineno"> 1771</span> <span class="stringliteral">"U"</span>,</div><div class="line"><a name="l01772"></a><span class="lineno"> 1772</span> <span class="stringliteral">"U"</span>,</div><div class="line"><a name="l01773"></a><span class="lineno"> 1773</span> <span class="stringliteral">"Th"</span>,</div><div class="line"><a name="l01774"></a><span class="lineno"> 1774</span> <span class="stringliteral">"Pa"</span>,</div><div class="line"><a name="l01775"></a><span class="lineno"> 1775</span> };</div><div class="line"><a name="l01776"></a><span class="lineno"> 1776</span> </div><div class="line"><a name="l01777"></a><span class="lineno"> 1777</span> </div><div class="line"><a name="l01778"></a><span class="lineno"> 1778</span> <span class="keyword">const</span> <span class="keywordtype">bool</span> elem_table_Radioactive [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {</div><div class="line"><a name="l01779"></a><span class="lineno"> 1779</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01780"></a><span class="lineno"> 1780</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01781"></a><span class="lineno"> 1781</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01782"></a><span class="lineno"> 1782</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01783"></a><span class="lineno"> 1783</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01784"></a><span class="lineno"> 1784</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01785"></a><span class="lineno"> 1785</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01786"></a><span class="lineno"> 1786</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01787"></a><span class="lineno"> 1787</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01788"></a><span class="lineno"> 1788</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01789"></a><span class="lineno"> 1789</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01790"></a><span class="lineno"> 1790</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01791"></a><span class="lineno"> 1791</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01792"></a><span class="lineno"> 1792</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01793"></a><span class="lineno"> 1793</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01794"></a><span class="lineno"> 1794</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01795"></a><span class="lineno"> 1795</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01796"></a><span class="lineno"> 1796</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01797"></a><span class="lineno"> 1797</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01798"></a><span class="lineno"> 1798</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01799"></a><span class="lineno"> 1799</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01800"></a><span class="lineno"> 1800</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01801"></a><span class="lineno"> 1801</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01802"></a><span class="lineno"> 1802</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01803"></a><span class="lineno"> 1803</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01804"></a><span class="lineno"> 1804</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01805"></a><span class="lineno"> 1805</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01806"></a><span class="lineno"> 1806</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01807"></a><span class="lineno"> 1807</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01808"></a><span class="lineno"> 1808</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01809"></a><span class="lineno"> 1809</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01810"></a><span class="lineno"> 1810</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01811"></a><span class="lineno"> 1811</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01812"></a><span class="lineno"> 1812</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01813"></a><span class="lineno"> 1813</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01814"></a><span class="lineno"> 1814</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01815"></a><span class="lineno"> 1815</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01816"></a><span class="lineno"> 1816</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01817"></a><span class="lineno"> 1817</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01818"></a><span class="lineno"> 1818</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01819"></a><span class="lineno"> 1819</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01820"></a><span class="lineno"> 1820</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01821"></a><span class="lineno"> 1821</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01822"></a><span class="lineno"> 1822</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01823"></a><span class="lineno"> 1823</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01824"></a><span class="lineno"> 1824</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01825"></a><span class="lineno"> 1825</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01826"></a><span class="lineno"> 1826</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01827"></a><span class="lineno"> 1827</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01828"></a><span class="lineno"> 1828</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01829"></a><span class="lineno"> 1829</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01830"></a><span class="lineno"> 1830</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01831"></a><span class="lineno"> 1831</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01832"></a><span class="lineno"> 1832</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01833"></a><span class="lineno"> 1833</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01834"></a><span class="lineno"> 1834</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01835"></a><span class="lineno"> 1835</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01836"></a><span class="lineno"> 1836</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01837"></a><span class="lineno"> 1837</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01838"></a><span class="lineno"> 1838</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01839"></a><span class="lineno"> 1839</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01840"></a><span class="lineno"> 1840</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01841"></a><span class="lineno"> 1841</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01842"></a><span class="lineno"> 1842</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01843"></a><span class="lineno"> 1843</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01844"></a><span class="lineno"> 1844</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01845"></a><span class="lineno"> 1845</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01846"></a><span class="lineno"> 1846</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01847"></a><span class="lineno"> 1847</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01848"></a><span class="lineno"> 1848</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01849"></a><span class="lineno"> 1849</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01850"></a><span class="lineno"> 1850</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01851"></a><span class="lineno"> 1851</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01852"></a><span class="lineno"> 1852</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01853"></a><span class="lineno"> 1853</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01854"></a><span class="lineno"> 1854</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01855"></a><span class="lineno"> 1855</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01856"></a><span class="lineno"> 1856</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01857"></a><span class="lineno"> 1857</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01858"></a><span class="lineno"> 1858</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01859"></a><span class="lineno"> 1859</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01860"></a><span class="lineno"> 1860</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01861"></a><span class="lineno"> 1861</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01862"></a><span class="lineno"> 1862</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01863"></a><span class="lineno"> 1863</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01864"></a><span class="lineno"> 1864</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01865"></a><span class="lineno"> 1865</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01866"></a><span class="lineno"> 1866</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01867"></a><span class="lineno"> 1867</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01868"></a><span class="lineno"> 1868</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01869"></a><span class="lineno"> 1869</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01870"></a><span class="lineno"> 1870</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01871"></a><span class="lineno"> 1871</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01872"></a><span class="lineno"> 1872</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01873"></a><span class="lineno"> 1873</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01874"></a><span class="lineno"> 1874</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01875"></a><span class="lineno"> 1875</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01876"></a><span class="lineno"> 1876</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01877"></a><span class="lineno"> 1877</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01878"></a><span class="lineno"> 1878</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01879"></a><span class="lineno"> 1879</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01880"></a><span class="lineno"> 1880</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01881"></a><span class="lineno"> 1881</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01882"></a><span class="lineno"> 1882</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01883"></a><span class="lineno"> 1883</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01884"></a><span class="lineno"> 1884</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01885"></a><span class="lineno"> 1885</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01886"></a><span class="lineno"> 1886</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01887"></a><span class="lineno"> 1887</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01888"></a><span class="lineno"> 1888</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01889"></a><span class="lineno"> 1889</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01890"></a><span class="lineno"> 1890</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01891"></a><span class="lineno"> 1891</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01892"></a><span class="lineno"> 1892</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01893"></a><span class="lineno"> 1893</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01894"></a><span class="lineno"> 1894</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01895"></a><span class="lineno"> 1895</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01896"></a><span class="lineno"> 1896</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01897"></a><span class="lineno"> 1897</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01898"></a><span class="lineno"> 1898</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01899"></a><span class="lineno"> 1899</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01900"></a><span class="lineno"> 1900</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01901"></a><span class="lineno"> 1901</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01902"></a><span class="lineno"> 1902</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01903"></a><span class="lineno"> 1903</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01904"></a><span class="lineno"> 1904</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01905"></a><span class="lineno"> 1905</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01906"></a><span class="lineno"> 1906</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01907"></a><span class="lineno"> 1907</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01908"></a><span class="lineno"> 1908</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01909"></a><span class="lineno"> 1909</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01910"></a><span class="lineno"> 1910</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01911"></a><span class="lineno"> 1911</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01912"></a><span class="lineno"> 1912</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01913"></a><span class="lineno"> 1913</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01914"></a><span class="lineno"> 1914</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01915"></a><span class="lineno"> 1915</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01916"></a><span class="lineno"> 1916</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01917"></a><span class="lineno"> 1917</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01918"></a><span class="lineno"> 1918</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01919"></a><span class="lineno"> 1919</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01920"></a><span class="lineno"> 1920</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01921"></a><span class="lineno"> 1921</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01922"></a><span class="lineno"> 1922</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01923"></a><span class="lineno"> 1923</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01924"></a><span class="lineno"> 1924</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01925"></a><span class="lineno"> 1925</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01926"></a><span class="lineno"> 1926</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01927"></a><span class="lineno"> 1927</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01928"></a><span class="lineno"> 1928</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01929"></a><span class="lineno"> 1929</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01930"></a><span class="lineno"> 1930</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01931"></a><span class="lineno"> 1931</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01932"></a><span class="lineno"> 1932</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01933"></a><span class="lineno"> 1933</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01934"></a><span class="lineno"> 1934</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01935"></a><span class="lineno"> 1935</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01936"></a><span class="lineno"> 1936</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01937"></a><span class="lineno"> 1937</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01938"></a><span class="lineno"> 1938</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01939"></a><span class="lineno"> 1939</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01940"></a><span class="lineno"> 1940</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01941"></a><span class="lineno"> 1941</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01942"></a><span class="lineno"> 1942</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01943"></a><span class="lineno"> 1943</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01944"></a><span class="lineno"> 1944</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01945"></a><span class="lineno"> 1945</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01946"></a><span class="lineno"> 1946</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01947"></a><span class="lineno"> 1947</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01948"></a><span class="lineno"> 1948</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01949"></a><span class="lineno"> 1949</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01950"></a><span class="lineno"> 1950</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01951"></a><span class="lineno"> 1951</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01952"></a><span class="lineno"> 1952</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01953"></a><span class="lineno"> 1953</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01954"></a><span class="lineno"> 1954</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01955"></a><span class="lineno"> 1955</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01956"></a><span class="lineno"> 1956</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01957"></a><span class="lineno"> 1957</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01958"></a><span class="lineno"> 1958</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01959"></a><span class="lineno"> 1959</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01960"></a><span class="lineno"> 1960</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01961"></a><span class="lineno"> 1961</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01962"></a><span class="lineno"> 1962</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01963"></a><span class="lineno"> 1963</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01964"></a><span class="lineno"> 1964</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01965"></a><span class="lineno"> 1965</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01966"></a><span class="lineno"> 1966</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01967"></a><span class="lineno"> 1967</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01968"></a><span class="lineno"> 1968</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01969"></a><span class="lineno"> 1969</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01970"></a><span class="lineno"> 1970</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01971"></a><span class="lineno"> 1971</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01972"></a><span class="lineno"> 1972</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01973"></a><span class="lineno"> 1973</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01974"></a><span class="lineno"> 1974</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01975"></a><span class="lineno"> 1975</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01976"></a><span class="lineno"> 1976</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01977"></a><span class="lineno"> 1977</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01978"></a><span class="lineno"> 1978</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01979"></a><span class="lineno"> 1979</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01980"></a><span class="lineno"> 1980</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01981"></a><span class="lineno"> 1981</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01982"></a><span class="lineno"> 1982</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01983"></a><span class="lineno"> 1983</span> <span class="keyword">true</span>,</div><div class="line"><a name="l01984"></a><span class="lineno"> 1984</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01985"></a><span class="lineno"> 1985</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01986"></a><span class="lineno"> 1986</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01987"></a><span class="lineno"> 1987</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01988"></a><span class="lineno"> 1988</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01989"></a><span class="lineno"> 1989</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01990"></a><span class="lineno"> 1990</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01991"></a><span class="lineno"> 1991</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01992"></a><span class="lineno"> 1992</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01993"></a><span class="lineno"> 1993</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01994"></a><span class="lineno"> 1994</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01995"></a><span class="lineno"> 1995</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01996"></a><span class="lineno"> 1996</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01997"></a><span class="lineno"> 1997</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01998"></a><span class="lineno"> 1998</span> <span class="keyword">false</span>,</div><div class="line"><a name="l01999"></a><span class="lineno"> 1999</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02000"></a><span class="lineno"> 2000</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02001"></a><span class="lineno"> 2001</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02002"></a><span class="lineno"> 2002</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02003"></a><span class="lineno"> 2003</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02004"></a><span class="lineno"> 2004</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02005"></a><span class="lineno"> 2005</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02006"></a><span class="lineno"> 2006</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02007"></a><span class="lineno"> 2007</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02008"></a><span class="lineno"> 2008</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02009"></a><span class="lineno"> 2009</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02010"></a><span class="lineno"> 2010</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02011"></a><span class="lineno"> 2011</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02012"></a><span class="lineno"> 2012</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02013"></a><span class="lineno"> 2013</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02014"></a><span class="lineno"> 2014</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02015"></a><span class="lineno"> 2015</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02016"></a><span class="lineno"> 2016</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02017"></a><span class="lineno"> 2017</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02018"></a><span class="lineno"> 2018</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02019"></a><span class="lineno"> 2019</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02020"></a><span class="lineno"> 2020</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02021"></a><span class="lineno"> 2021</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02022"></a><span class="lineno"> 2022</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02023"></a><span class="lineno"> 2023</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02024"></a><span class="lineno"> 2024</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02025"></a><span class="lineno"> 2025</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02026"></a><span class="lineno"> 2026</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02027"></a><span class="lineno"> 2027</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02028"></a><span class="lineno"> 2028</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02029"></a><span class="lineno"> 2029</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02030"></a><span class="lineno"> 2030</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02031"></a><span class="lineno"> 2031</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02032"></a><span class="lineno"> 2032</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02033"></a><span class="lineno"> 2033</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02034"></a><span class="lineno"> 2034</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02035"></a><span class="lineno"> 2035</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02036"></a><span class="lineno"> 2036</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02037"></a><span class="lineno"> 2037</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02038"></a><span class="lineno"> 2038</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02039"></a><span class="lineno"> 2039</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02040"></a><span class="lineno"> 2040</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02041"></a><span class="lineno"> 2041</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02042"></a><span class="lineno"> 2042</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02043"></a><span class="lineno"> 2043</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02044"></a><span class="lineno"> 2044</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02045"></a><span class="lineno"> 2045</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02046"></a><span class="lineno"> 2046</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02047"></a><span class="lineno"> 2047</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02048"></a><span class="lineno"> 2048</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02049"></a><span class="lineno"> 2049</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02050"></a><span class="lineno"> 2050</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02051"></a><span class="lineno"> 2051</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02052"></a><span class="lineno"> 2052</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02053"></a><span class="lineno"> 2053</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02054"></a><span class="lineno"> 2054</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02055"></a><span class="lineno"> 2055</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02056"></a><span class="lineno"> 2056</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02057"></a><span class="lineno"> 2057</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02058"></a><span class="lineno"> 2058</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02059"></a><span class="lineno"> 2059</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02060"></a><span class="lineno"> 2060</span> <span class="keyword">false</span>,</div><div class="line"><a name="l02061"></a><span class="lineno"> 2061</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02062"></a><span class="lineno"> 2062</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02063"></a><span class="lineno"> 2063</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02064"></a><span class="lineno"> 2064</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02065"></a><span class="lineno"> 2065</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02066"></a><span class="lineno"> 2066</span> <span class="keyword">true</span>,</div><div class="line"><a name="l02067"></a><span class="lineno"> 2067</span> };</div><div class="line"><a name="l02068"></a><span class="lineno"> 2068</span> </div><div class="line"><a name="l02069"></a><span class="lineno"> 2069</span> </div><div class="line"><a name="l02070"></a><span class="lineno"> 2070</span> <span class="keyword">const</span> <span class="keywordtype">double</span> elem_table_probability [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {</div><div class="line"><a name="l02071"></a><span class="lineno"> 2071</span> 0.999884290164307909520857720053754746913909912109375000000000,</div><div class="line"><a name="l02072"></a><span class="lineno"> 2072</span> 0.000115709835692033314582735648023970043141162022948265075684,</div><div class="line"><a name="l02073"></a><span class="lineno"> 2073</span> 0.000001342999991941999914655050951672876635711872950196266174,</div><div class="line"><a name="l02074"></a><span class="lineno"> 2074</span> 0.999998657000008006612290500925155356526374816894531250000000,</div><div class="line"><a name="l02075"></a><span class="lineno"> 2075</span> 0.075933925285977116326208147256693337112665176391601562500000,</div><div class="line"><a name="l02076"></a><span class="lineno"> 2076</span> 0.924066074714022800407065005856566131114959716796875000000000,</div><div class="line"><a name="l02077"></a><span class="lineno"> 2077</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02078"></a><span class="lineno"> 2078</span> 0.199480830670926506664741850727295968681573867797851562500000,</div><div class="line"><a name="l02079"></a><span class="lineno"> 2079</span> 0.800519169329073410068531302385963499546051025390625000000000,</div><div class="line"><a name="l02080"></a><span class="lineno"> 2080</span> 0.989211941850466902614869013632414862513542175292968750000000,</div><div class="line"><a name="l02081"></a><span class="lineno"> 2081</span> 0.010788058149533083507343178553128382191061973571777343750000,</div><div class="line"><a name="l02082"></a><span class="lineno"> 2082</span> 0.996358014567941707717579902237048372626304626464843750000000,</div><div class="line"><a name="l02083"></a><span class="lineno"> 2083</span> 0.003641985432058271465738386041266494430601596832275390625000,</div><div class="line"><a name="l02084"></a><span class="lineno"> 2084</span> 0.997567609729561044495937949250219389796257019042968750000000,</div><div class="line"><a name="l02085"></a><span class="lineno"> 2085</span> 0.000380998476006095935803702490218825005285907536745071411133,</div><div class="line"><a name="l02086"></a><span class="lineno"> 2086</span> 0.002051391794432822109073288885383590240962803363800048828125,</div><div class="line"><a name="l02087"></a><span class="lineno"> 2087</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02088"></a><span class="lineno"> 2088</span> 0.904766666333356561757739200402284041047096252441406250000000,</div><div class="line"><a name="l02089"></a><span class="lineno"> 2089</span> 0.002709810313278070148523823945652111433446407318115234375000,</div><div class="line"><a name="l02090"></a><span class="lineno"> 2090</span> 0.092523523353365264010328417043638182803988456726074218750000,</div><div class="line"><a name="l02091"></a><span class="lineno"> 2091</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02092"></a><span class="lineno"> 2092</span> 0.789876809855211581279377242026384919881820678710937500000000,</div><div class="line"><a name="l02093"></a><span class="lineno"> 2093</span> 0.100001999840012789633192369365133345127105712890625000000000,</div><div class="line"><a name="l02094"></a><span class="lineno"> 2094</span> 0.110121190304775615209642580794024979695677757263183593750000,</div><div class="line"><a name="l02095"></a><span class="lineno"> 2095</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02096"></a><span class="lineno"> 2096</span> 0.922220833349999713490774411184247583150863647460937500000000,</div><div class="line"><a name="l02097"></a><span class="lineno"> 2097</span> 0.046858437698747611166449900110819726251065731048583984375000,</div><div class="line"><a name="l02098"></a><span class="lineno"> 2098</span> 0.030920728951252581667707985957349592354148626327514648437500,</div><div class="line"><a name="l02099"></a><span class="lineno"> 2099</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02100"></a><span class="lineno"> 2100</span> 0.949850011999040066967836537514813244342803955078125000000000,</div><div class="line"><a name="l02101"></a><span class="lineno"> 2101</span> 0.007519398448124149821059081233443066594190895557403564453125,</div><div class="line"><a name="l02102"></a><span class="lineno"> 2102</span> 0.042520598352131823427502155254842364229261875152587890625000,</div><div class="line"><a name="l02103"></a><span class="lineno"> 2103</span> 0.000109991200703943683199964587160479823069181293249130249023,</div><div class="line"><a name="l02104"></a><span class="lineno"> 2104</span> 0.757594848103037898923162174469325691461563110351562500000000,</div><div class="line"><a name="l02105"></a><span class="lineno"> 2105</span> 0.242405151896962045565686594272847287356853485107421875000000,</div><div class="line"><a name="l02106"></a><span class="lineno"> 2106</span> 0.003336205796380696270847510120916012965608388185501098632812,</div><div class="line"><a name="l02107"></a><span class="lineno"> 2107</span> 0.000629799206452999775149304007015871320618316531181335449219,</div><div class="line"><a name="l02108"></a><span class="lineno"> 2108</span> 0.996033994997166272078459314798237755894660949707031250000000,</div><div class="line"><a name="l02109"></a><span class="lineno"> 2109</span> 0.932580526071084436878777523816097527742385864257812500000000,</div><div class="line"><a name="l02110"></a><span class="lineno"> 2110</span> 0.000117099885242112454345267402722186034225160256028175354004,</div><div class="line"><a name="l02111"></a><span class="lineno"> 2111</span> 0.067302374043673424131029037198459263890981674194335937500000,</div><div class="line"><a name="l02112"></a><span class="lineno"> 2112</span> 0.969400838426726974006442105746828019618988037109375000000000,</div><div class="line"><a name="l02113"></a><span class="lineno"> 2113</span> 0.006472228417153705684605746739634923869743943214416503906250,</div><div class="line"><a name="l02114"></a><span class="lineno"> 2114</span> 0.001350985058105257227353823701321289263432845473289489746094,</div><div class="line"><a name="l02115"></a><span class="lineno"> 2115</span> 0.020860869278785776348428271376178599894046783447265625000000,</div><div class="line"><a name="l02116"></a><span class="lineno"> 2116</span> 0.000042999524425259849917842214228613784143817611038684844971,</div><div class="line"><a name="l02117"></a><span class="lineno"> 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2250</span> 0.065920277116120362670415033790050074458122253417968750000000,</div><div class="line"><a name="l02251"></a><span class="lineno"> 2251</span> 0.078541300421794094099858796198532218113541603088378906250000,</div><div class="line"><a name="l02252"></a><span class="lineno"> 2252</span> 0.112320827508414877726750091824214905500411987304687500000000,</div><div class="line"><a name="l02253"></a><span class="lineno"> 2253</span> 0.716974162361726841119491382414707913994789123535156250000000,</div><div class="line"><a name="l02254"></a><span class="lineno"> 2254</span> 0.000888171872103250392010975744483403104823082685470581054688,</div><div class="line"><a name="l02255"></a><span class="lineno"> 2255</span> 0.999111828127896672846475212281802669167518615722656250000000,</div><div class="line"><a name="l02256"></a><span class="lineno"> 2256</span> 0.001851973331584025024912354417949700291501358151435852050781,</div><div class="line"><a name="l02257"></a><span class="lineno"> 2257</span> 0.002511963827720880421123794690174690913408994674682617187500,</div><div class="line"><a name="l02258"></a><span class="lineno"> 2258</span> 0.884492463308528265031327464384958148002624511718750000000000,</div><div class="line"><a name="l02259"></a><span class="lineno"> 2259</span> 0.111143599532166723053983048430382041260600090026855468750000,</div><div class="line"><a name="l02260"></a><span class="lineno"> 2260</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02261"></a><span class="lineno"> 2261</span> 0.271519166958828106483991859931848011910915374755859375000000,</div><div class="line"><a name="l02262"></a><span class="lineno"> 2262</span> 0.121740433020292235233306143982190405949950218200683593750000,</div><div class="line"><a name="l02263"></a><span class="lineno"> 2263</span> 0.237977663997580829446931716120161581784486770629882812500000,</div><div class="line"><a name="l02264"></a><span class="lineno"> 2264</span> 0.082929723850915446070608538775559281930327415466308593750000,</div><div class="line"><a name="l02265"></a><span class="lineno"> 2265</span> 0.171890140355501652713599014532519504427909851074218750000000,</div><div class="line"><a name="l02266"></a><span class="lineno"> 2266</span> 0.057561075412857647115583148433870519511401653289794921875000,</div><div class="line"><a name="l02267"></a><span class="lineno"> 2267</span> 0.056381796404024006608146635244338540360331535339355468750000,</div><div class="line"><a name="l02268"></a><span class="lineno"> 2268</span> 0.030772522277086666181444840617587033193558454513549804687500,</div><div class="line"><a name="l02269"></a><span class="lineno"> 2269</span> 0.149881578776357327065227309503825381398200988769531250000000,</div><div class="line"><a name="l02270"></a><span class="lineno"> 2270</span> 0.112382691006085513873991033051424892619252204895019531250000,</div><div class="line"><a name="l02271"></a><span class="lineno"> 2271</span> 0.138246406123312015612469849656918086111545562744140625000000,</div><div class="line"><a name="l02272"></a><span class="lineno"> 2272</span> 0.073792068527347848272412988990254234522581100463867187500000,</div><div class="line"><a name="l02273"></a><span class="lineno"> 2273</span> 0.267451009404714612482933944193064235150814056396484375000000,</div><div class="line"><a name="l02274"></a><span class="lineno"> 2274</span> 0.227473723885095902019770619517657905817031860351562500000000,</div><div class="line"><a name="l02275"></a><span class="lineno"> 2275</span> 0.478103065570820051632949798658955842256546020507812500000000,</div><div class="line"><a name="l02276"></a><span class="lineno"> 2276</span> 0.521896934429179837344747738825390115380287170410156250000000,</div><div class="line"><a name="l02277"></a><span class="lineno"> 2277</span> 0.002009636255837693018938550082452820788603276014328002929688,</div><div class="line"><a name="l02278"></a><span class="lineno"> 2278</span> 0.021826049485043207132317633067941642366349697113037109375000,</div><div class="line"><a name="l02279"></a><span class="lineno"> 2279</span> 0.147985214676143617129611129712429828941822052001953125000000,</div><div class="line"><a name="l02280"></a><span class="lineno"> 2280</span> 0.204672954195290635048820604424690827727317810058593750000000,</div><div class="line"><a name="l02281"></a><span class="lineno"> 2281</span> 0.156491675006823760529783839956508018076419830322265625000000,</div><div class="line"><a name="l02282"></a><span class="lineno"> 2282</span> 0.248435033258980114689862261911912355571985244750976562500000,</div><div class="line"><a name="l02283"></a><span class="lineno"> 2283</span> 0.218579437121880937322515592313720844686031341552734375000000,</div><div class="line"><a name="l02284"></a><span class="lineno"> 2284</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02285"></a><span class="lineno"> 2285</span> 0.000562985756460361477619691594753703611786477267742156982422,</div><div class="line"><a name="l02286"></a><span class="lineno"> 2286</span> 0.000952975889709990254573812595850768047966994345188140869141,</div><div class="line"><a name="l02287"></a><span class="lineno"> 2287</span> 0.023291210732368467645203580218549177516251802444458007812500,</div><div class="line"><a name="l02288"></a><span class="lineno"> 2288</span> 0.188889421097646226233024435714469291269779205322265625000000,</div><div class="line"><a name="l02289"></a><span class="lineno"> 2289</span> 0.254747154896981076177553404704667627811431884765625000000000,</div><div class="line"><a name="l02290"></a><span class="lineno"> 2290</span> 0.248957901365095435330943018925609067082405090332031250000000,</div><div class="line"><a name="l02291"></a><span class="lineno"> 2291</span> 0.282598350261738351374418698469526134431362152099609375000000,</div><div class="line"><a name="l02292"></a><span class="lineno"> 2292</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02293"></a><span class="lineno"> 2293</span> 0.001395973476503946332158423437874716910300776362419128417969,</div><div class="line"><a name="l02294"></a><span class="lineno"> 2294</span> 0.016012695758780580435054474719436257146298885345458984375000,</div><div class="line"><a name="l02295"></a><span class="lineno"> 2295</span> 0.335027234482544788995994622382568195462226867675781250000000,</div><div class="line"><a name="l02296"></a><span class="lineno"> 2296</span> 0.228686654953555862368475004586798604577779769897460937500000,</div><div class="line"><a name="l02297"></a><span class="lineno"> 2297</span> 0.269776674243189351631855288360384292900562286376953125000000,</div><div class="line"><a name="l02298"></a><span class="lineno"> 2298</span> 0.149100767085425356395234075534972362220287322998046875000000,</div><div class="line"><a name="l02299"></a><span class="lineno"> 2299</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02300"></a><span class="lineno"> 2300</span> 0.001232929969577727796758992440118163358420133590698242187500,</div><div class="line"><a name="l02301"></a><span class="lineno"> 2301</span> 0.029822206098693591902470956256365752778947353363037109375000,</div><div class="line"><a name="l02302"></a><span class="lineno"> 2302</span> 0.140905996539396560773838018576498143374919891357421875000000,</div><div class="line"><a name="l02303"></a><span class="lineno"> 2303</span> 0.216800685721051017429417129278590437024831771850585937500000,</div><div class="line"><a name="l02304"></a><span class="lineno"> 2304</span> 0.161027253651992552363481081556528806686401367187500000000000,</div><div class="line"><a name="l02305"></a><span class="lineno"> 2305</span> 0.320249909805123023076589561242144554853439331054687500000000,</div><div class="line"><a name="l02306"></a><span class="lineno"> 2306</span> 0.129961018214165419104588750087714288383722305297851562500000,</div><div class="line"><a name="l02307"></a><span class="lineno"> 2307</span> 0.974008767577204226384424146090168505907058715820312500000000,</div><div class="line"><a name="l02308"></a><span class="lineno"> 2308</span> 0.025991232422795697287742910930319339968264102935791015625000,</div><div class="line"><a name="l02309"></a><span class="lineno"> 2309</span> 0.001609652315099938373749166586890169128309935331344604492188,</div><div class="line"><a name="l02310"></a><span class="lineno"> 2310</span> 0.052668623577307296934613134453684324398636817932128906250000,</div><div class="line"><a name="l02311"></a><span class="lineno"> 2311</span> 0.185969830516608397585898160286888014525175094604492187500000,</div><div class="line"><a name="l02312"></a><span class="lineno"> 2312</span> 0.272821070648739838482299546740250661969184875488281250000000,</div><div class="line"><a name="l02313"></a><span class="lineno"> 2313</span> 0.136190582834107815068946933934057597070932388305664062500000,</div><div class="line"><a name="l02314"></a><span class="lineno"> 2314</span> 0.350740240108136591690168870627530850470066070556640625000000,</div><div class="line"><a name="l02315"></a><span class="lineno"> 2315</span> 0.000120131992311552486551486096377772128107608295977115631104,</div><div class="line"><a name="l02316"></a><span class="lineno"> 2316</span> 0.999879868007688354936135510797612369060516357421875000000000,</div><div class="line"><a name="l02317"></a><span class="lineno"> 2317</span> 0.001209872963338849303702171589236513682408258318901062011719,</div><div class="line"><a name="l02318"></a><span class="lineno"> 2318</span> 0.264988176241494621798722164385253563523292541503906250000000,</div><div class="line"><a name="l02319"></a><span class="lineno"> 2319</span> 0.143124971877952811283307710255030542612075805664062500000000,</div><div class="line"><a name="l02320"></a><span class="lineno"> 2320</span> 0.306387829277925793913794905165559612214565277099609375000000,</div><div class="line"><a name="l02321"></a><span class="lineno"> 2321</span> 0.284289149639287863635672692907974123954772949218750000000000,</div><div class="line"><a name="l02322"></a><span class="lineno"> 2322</span> 0.374005039798408045470523575204424560070037841796875000000000,</div><div class="line"><a name="l02323"></a><span class="lineno"> 2323</span> 0.625994960201591843507173962279921397566795349121093750000000,</div><div class="line"><a name="l02324"></a><span class="lineno"> 2324</span> 0.000209947723016968765524098428087995671376120299100875854492,</div><div class="line"><a name="l02325"></a><span class="lineno"> 2325</span> 0.015926034417430057904541129687459033448249101638793945312500,</div><div class="line"><a name="l02326"></a><span class="lineno"> 2326</span> 0.019615115836156795520173190539026109036058187484741210937500,</div><div class="line"><a name="l02327"></a><span class="lineno"> 2327</span> 0.132457018202467580181291850749403238296508789062500000000000,</div><div class="line"><a name="l02328"></a><span class="lineno"> 2328</span> 0.161519781574387955025429164379602298140525817871093750000000,</div><div class="line"><a name="l02329"></a><span class="lineno"> 2329</span> 0.262554623898649197588639481182326562702655792236328125000000,</div><div class="line"><a name="l02330"></a><span class="lineno"> 2330</span> 0.407717478347891348899878494194126687943935394287109375000000,</div><div class="line"><a name="l02331"></a><span class="lineno"> 2331</span> 0.373050779688124722888176165724871680140495300292968750000000,</div><div class="line"><a name="l02332"></a><span class="lineno"> 2332</span> 0.626949220311875166089521371759474277496337890625000000000000,</div><div class="line"><a name="l02333"></a><span class="lineno"> 2333</span> 0.000121987349911814132899338936066868654961581341922283172607,</div><div class="line"><a name="l02334"></a><span class="lineno"> 2334</span> 0.007821588901230941415221309398475568741559982299804687500000,</div><div class="line"><a name="l02335"></a><span class="lineno"> 2335</span> 0.328605923565726210089366077227168716490268707275390625000000,</div><div class="line"><a name="l02336"></a><span class="lineno"> 2336</span> 0.337788971283677852408544595164130441844463348388671875000000,</div><div class="line"><a name="l02337"></a><span class="lineno"> 2337</span> 0.252107856415289710572125159160350449383258819580078125000000,</div><div class="line"><a name="l02338"></a><span class="lineno"> 2338</span> 0.073553672484163390432598816914833150804042816162109375000000,</div><div class="line"><a name="l02339"></a><span class="lineno"> 2339</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02340"></a><span class="lineno"> 2340</span> 0.001509815802472098391837085351596670079743489623069763183594,</div><div class="line"><a name="l02341"></a><span class="lineno"> 2341</span> 0.099707835644051417967048678292485419660806655883789062500000,</div><div class="line"><a name="l02342"></a><span class="lineno"> 2342</span> 0.168701418426951910145561441822792403399944305419921875000000,</div><div class="line"><a name="l02343"></a><span class="lineno"> 2343</span> 0.230990819120067331082779560347262304276227951049804687500000,</div><div class="line"><a name="l02344"></a><span class="lineno"> 2344</span> 0.131793921141620695713925215386552736163139343261718750000000,</div><div class="line"><a name="l02345"></a><span class="lineno"> 2345</span> 0.298589572072207154462830658303573727607727050781250000000000,</div><div class="line"><a name="l02346"></a><span class="lineno"> 2346</span> 0.068706617792629293139938795320631470531225204467773437500000,</div><div class="line"><a name="l02347"></a><span class="lineno"> 2347</span> 0.295204095918081610427918803907232359051704406738281250000000,</div><div class="line"><a name="l02348"></a><span class="lineno"> 2348</span> 0.704795904081918278549778733577113598585128784179687500000000,</div><div class="line"><a name="l02349"></a><span class="lineno"> 2349</span> 0.014094362255097959285565778486670751590281724929809570312500,</div><div class="line"><a name="l02350"></a><span class="lineno"> 2350</span> 0.241003598560575765796798464180028531700372695922851562500000,</div><div class="line"><a name="l02351"></a><span class="lineno"> 2351</span> 0.221011595361855245345239495691203046590089797973632812500000,</div><div class="line"><a name="l02352"></a><span class="lineno"> 2352</span> 0.523890443822470963652904174523428082466125488281250000000000,</div><div class="line"><a name="l02353"></a><span class="lineno"> 2353</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02354"></a><span class="lineno"> 2354</span> 0.000054599923560107009460132254652364736102754250168800354004,</div><div class="line"><a name="l02355"></a><span class="lineno"> 2355</span> 0.007204689913434121108226637630878030904568731784820556640625,</div><div class="line"><a name="l02356"></a><span class="lineno"> 2356</span> 0.992740710163005690702675565262325108051300048828125000000000,</div><div class="line"><a name="l02357"></a><span class="lineno"> 2357</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02358"></a><span class="lineno"> 2358</span> 1.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02359"></a><span class="lineno"> 2359</span> };</div><div class="line"><a name="l02360"></a><span class="lineno"> 2360</span> </div><div class="line"><a name="l02361"></a><span class="lineno"> 2361</span> </div><div class="line"><a name="l02362"></a><span class="lineno"> 2362</span> <span class="keyword">const</span> <span class="keywordtype">double</span> elem_table_log_probability [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] = {</div><div class="line"><a name="l02363"></a><span class="lineno"> 2363</span> -0.000115716530591520062594239337538937206772970966994762420654,</div><div class="line"><a name="l02364"></a><span class="lineno"> 2364</span> -9.064424917075021070900220365729182958602905273437500000000000,</div><div class="line"><a name="l02365"></a><span class="lineno"> 2365</span> -13.520604646423175054792409355286508798599243164062500000000000,</div><div class="line"><a name="l02366"></a><span class="lineno"> 2366</span> -0.000001343000893767296712052561162564767727189973811618983746,</div><div class="line"><a name="l02367"></a><span class="lineno"> 2367</span> -2.577891720978651601825504258158616721630096435546875000000000,</div><div class="line"><a name="l02368"></a><span class="lineno"> 2368</span> -0.078971700466369670889932308455172460526227951049804687500000,</div><div class="line"><a name="l02369"></a><span class="lineno"> 2369</span> 0.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a 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name="l02650"></a><span class="lineno"> 2650</span> 0.000000000000000000000000000000000000000000000000000000000000,</div><div class="line"><a name="l02651"></a><span class="lineno"> 2651</span> };</div><div class="line"><a name="l02652"></a><span class="lineno"> 2652</span> </div><div class="line"><a name="l02653"></a><span class="lineno"> 2653</span> <span class="preprocessor">#ifdef __cplusplus</span></div><div class="line"><a name="l02654"></a><span class="lineno"> 2654</span> }</div><div class="line"><a name="l02655"></a><span class="lineno"> 2655</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l02656"></a><span class="lineno"> 2656</span> </div><div class="line"><a name="l02657"></a><span class="lineno"> 2657</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l02658"></a><span class="lineno"> 2658</span> </div><div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
| 80 | </div><!-- fragment --></div><!-- contents --> | |
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| 83 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 71 | <li class="navelem"><a class="el" href="dir_7a6499598ddcfcabe96e224cb4a6d834.html">Projects</a></li><li class="navelem"><a class="el" href="dir_b5e01de8d0b5565037a326965003e69a.html">isospec</a></li><li class="navelem"><a class="el" href="dir_d48d5cdc71da00f1af92faf73cdbdfd7.html">IsoSpec</a></li><li class="navelem"><a class="el" href="dir_5010eccf620ec85ba5a1264edcd95342.html">IsoSpec++</a></li> </ul> | |
| 72 | </div> | |
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| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">element_tables.h</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> {</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#ifdef __cplusplus</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="keyword">extern</span> <span class="stringliteral">"C"</span> {</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> </div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor">#define ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES 288</span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">int</span> elem_table_atomicNo[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES];</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">double</span> elem_table_probability[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES];</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">double</span> elem_table_mass[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES];</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">int</span> elem_table_massNo[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES];</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">int</span> elem_table_extraNeutrons[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES];</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* elem_table_element[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES];</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* elem_table_symbol[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES];</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">bool</span> elem_table_Radioactive[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES];</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="keyword">extern</span> <span class="keyword">const</span> <span class="keywordtype">double</span> elem_table_log_probability[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES];</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#ifdef __cplusplus</span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> }</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div><div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
| 80 | </div><!-- fragment --></div><!-- contents --> | |
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| 83 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 88 | </html> |
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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
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| 72 | <div class="title">File List</div> </div> | |
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| 74 | <div class="contents"> | |
| 75 | <div class="textblock">Here is a list of all documented files with brief descriptions:</div><div class="directory"> | |
| 76 | <div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span><span onclick="javascript:toggleLevel(4);">4</span><span onclick="javascript:toggleLevel(5);">5</span>]</div><table class="directory"> | |
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| 78 | <tr id="row_0_0_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span id="arr_0_0_" class="arrow" onclick="toggleFolder('0_0_')">▼</span><span id="img_0_0_" class="iconfopen" onclick="toggleFolder('0_0_')"> </span><a class="el" href="dir_b5e01de8d0b5565037a326965003e69a.html" target="_self">isospec</a></td><td class="desc"></td></tr> | |
| 79 | <tr id="row_0_0_0_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span id="arr_0_0_0_" class="arrow" onclick="toggleFolder('0_0_0_')">▼</span><span id="img_0_0_0_" class="iconfopen" onclick="toggleFolder('0_0_0_')"> </span><a class="el" href="dir_d48d5cdc71da00f1af92faf73cdbdfd7.html" target="_self">IsoSpec</a></td><td class="desc"></td></tr> | |
| 80 | <tr id="row_0_0_0_0_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span id="arr_0_0_0_0_" class="arrow" onclick="toggleFolder('0_0_0_0_')">▼</span><span id="img_0_0_0_0_" class="iconfopen" onclick="toggleFolder('0_0_0_0_')"> </span><a class="el" href="dir_5010eccf620ec85ba5a1264edcd95342.html" target="_self">IsoSpec++</a></td><td class="desc"></td></tr> | |
| 81 | <tr id="row_0_0_0_0_0_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="allocator_8cpp_source.html"><span class="icondoc"></span></a><b>allocator.cpp</b></td><td class="desc"></td></tr> | |
| 82 | <tr id="row_0_0_0_0_1_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="allocator_8h_source.html"><span class="icondoc"></span></a><b>allocator.h</b></td><td class="desc"></td></tr> | |
| 83 | <tr id="row_0_0_0_0_2_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="conf_8h_source.html"><span class="icondoc"></span></a><b>conf.h</b></td><td class="desc"></td></tr> | |
| 84 | <tr id="row_0_0_0_0_3_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="cwrapper_8cpp_source.html"><span class="icondoc"></span></a><b>cwrapper.cpp</b></td><td class="desc"></td></tr> | |
| 85 | <tr id="row_0_0_0_0_4_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="cwrapper_8h_source.html"><span class="icondoc"></span></a><b>cwrapper.h</b></td><td class="desc"></td></tr> | |
| 86 | <tr id="row_0_0_0_0_5_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="dirty_allocator_8cpp_source.html"><span class="icondoc"></span></a><b>dirtyAllocator.cpp</b></td><td class="desc"></td></tr> | |
| 87 | <tr id="row_0_0_0_0_6_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="dirty_allocator_8h_source.html"><span class="icondoc"></span></a><b>dirtyAllocator.h</b></td><td class="desc"></td></tr> | |
| 88 | <tr id="row_0_0_0_0_7_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="element__tables_8cpp_source.html"><span class="icondoc"></span></a><b>element_tables.cpp</b></td><td class="desc"></td></tr> | |
| 89 | <tr id="row_0_0_0_0_8_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="element__tables_8h_source.html"><span class="icondoc"></span></a><b>element_tables.h</b></td><td class="desc"></td></tr> | |
| 90 | <tr id="row_0_0_0_0_9_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="iso_math_8cpp_source.html"><span class="icondoc"></span></a><b>isoMath.cpp</b></td><td class="desc"></td></tr> | |
| 91 | <tr id="row_0_0_0_0_10_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="iso_math_8h_source.html"><span class="icondoc"></span></a><b>isoMath.h</b></td><td class="desc"></td></tr> | |
| 92 | <tr id="row_0_0_0_0_11_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="iso_spec_09_09_8cpp_source.html"><span class="icondoc"></span></a><b>isoSpec++.cpp</b></td><td class="desc"></td></tr> | |
| 93 | <tr id="row_0_0_0_0_12_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="iso_spec_09_09_8h_source.html"><span class="icondoc"></span></a><b>isoSpec++.h</b></td><td class="desc"></td></tr> | |
| 94 | <tr id="row_0_0_0_0_13_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="marginal_trek_09_09_8cpp_source.html"><span class="icondoc"></span></a><b>marginalTrek++.cpp</b></td><td class="desc"></td></tr> | |
| 95 | <tr id="row_0_0_0_0_14_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="marginal_trek_09_09_8h_source.html"><span class="icondoc"></span></a><b>marginalTrek++.h</b></td><td class="desc"></td></tr> | |
| 96 | <tr id="row_0_0_0_0_15_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="misc_8cpp_source.html"><span class="icondoc"></span></a><b>misc.cpp</b></td><td class="desc"></td></tr> | |
| 97 | <tr id="row_0_0_0_0_16_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="misc_8h_source.html"><span class="icondoc"></span></a><b>misc.h</b></td><td class="desc"></td></tr> | |
| 98 | <tr id="row_0_0_0_0_17_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="mman_8c_source.html"><span class="icondoc"></span></a><b>mman.c</b></td><td class="desc"></td></tr> | |
| 99 | <tr id="row_0_0_0_0_18_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="mman_8h_source.html"><span class="icondoc"></span></a><b>mman.h</b></td><td class="desc"></td></tr> | |
| 100 | <tr id="row_0_0_0_0_19_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="operators_8cpp_source.html"><span class="icondoc"></span></a><b>operators.cpp</b></td><td class="desc"></td></tr> | |
| 101 | <tr id="row_0_0_0_0_20_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="operators_8h_source.html"><span class="icondoc"></span></a><b>operators.h</b></td><td class="desc"></td></tr> | |
| 102 | <tr id="row_0_0_0_0_21_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="platform_8h_source.html"><span class="icondoc"></span></a><b>platform.h</b></td><td class="desc"></td></tr> | |
| 103 | <tr id="row_0_0_0_0_22_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="summator_8h_source.html"><span class="icondoc"></span></a><b>summator.h</b></td><td class="desc"></td></tr> | |
| 104 | <tr id="row_0_0_0_0_23_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="tabulator_8cpp_source.html"><span class="icondoc"></span></a><b>tabulator.cpp</b></td><td class="desc"></td></tr> | |
| 105 | <tr id="row_0_0_0_0_24_" class="even"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="tabulator_8h_source.html"><span class="icondoc"></span></a><b>tabulator.h</b></td><td class="desc"></td></tr> | |
| 106 | <tr id="row_0_0_0_0_25_"><td class="entry"><span style="width:80px;display:inline-block;"> </span><a href="unity-build_8cpp_source.html"><span class="icondoc"></span></a><b>unity-build.cpp</b></td><td class="desc"></td></tr> | |
| 107 | </table> | |
| 108 | </div><!-- directory --> | |
| 109 | </div><!-- contents --> | |
| 110 | <!-- start footer part --> | |
| 111 | <hr class="footer"/><address class="footer"><small> | |
| 112 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 114 | </a> 1.8.14 | |
| 115 | </small></address> | |
| 116 | </body> | |
| 117 | </html> |
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| 7 | <title>IsoSpec: Class Members</title> | |
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| 23 | <div id="top"><!-- do not remove this div, it is closed by doxygen! --> | |
| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
| 37 | </div> | |
| 38 | <!-- end header part --> | |
| 39 | <!-- Generated by Doxygen 1.8.14 --> | |
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| 67 | </iframe> | |
| 68 | </div> | |
| 69 | ||
| 70 | <div class="contents"> | |
| 71 | <div class="textblock">Here is a list of all documented class members with links to the class documentation for each member:</div> | |
| 72 | ||
| 73 | <h3><a id="index_a"></a>- a -</h3><ul> | |
| 74 | <li>advanceToNextConfiguration() | |
| 75 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#a20f48ba18c6aecc57d73b2c3ec3a11dd">IsoSpec::IsoGenerator</a> | |
| 76 | , <a class="el" href="class_iso_spec_1_1_iso_layered_generator.html#abce0871ac279fd54a0344ceb80126b66">IsoSpec::IsoLayeredGenerator</a> | |
| 77 | , <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#aa2438bb81fb1d68eda1637d67e9cb36d">IsoSpec::IsoOrderedGenerator</a> | |
| 78 | , <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a7164a6476b84665967c4a667a91d3f3e">IsoSpec::IsoThresholdGenerator</a> | |
| 79 | </li> | |
| 80 | <li>allDim | |
| 81 | : <a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">IsoSpec::Iso</a> | |
| 82 | </li> | |
| 83 | <li>atom_lProbs | |
| 84 | : <a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">IsoSpec::Marginal</a> | |
| 85 | </li> | |
| 86 | <li>atom_masses | |
| 87 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">IsoSpec::Marginal</a> | |
| 88 | </li> | |
| 89 | <li>atomCnt | |
| 90 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">IsoSpec::Marginal</a> | |
| 91 | </li> | |
| 92 | <li>atomCounts | |
| 93 | : <a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">IsoSpec::Iso</a> | |
| 94 | </li> | |
| 95 | </ul> | |
| 96 | ||
| 97 | ||
| 98 | <h3><a id="index_c"></a>- c -</h3><ul> | |
| 99 | <li>confSize | |
| 100 | : <a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">IsoSpec::Iso</a> | |
| 101 | </li> | |
| 102 | <li>count_confs() | |
| 103 | : <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ad29d8761174bca7b1846ddec03b33528">IsoSpec::IsoThresholdGenerator</a> | |
| 104 | </li> | |
| 105 | </ul> | |
| 106 | ||
| 107 | ||
| 108 | <h3><a id="index_d"></a>- d -</h3><ul> | |
| 109 | <li>dimNumber | |
| 110 | : <a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">IsoSpec::Iso</a> | |
| 111 | </li> | |
| 112 | <li>disowned | |
| 113 | : <a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">IsoSpec::Iso</a> | |
| 114 | </li> | |
| 115 | </ul> | |
| 116 | ||
| 117 | ||
| 118 | <h3><a id="index_g"></a>- g -</h3><ul> | |
| 119 | <li>get_conf() | |
| 120 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff">IsoSpec::PrecalculatedMarginal</a> | |
| 121 | </li> | |
| 122 | <li>get_conf_signature() | |
| 123 | : <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#af5d638985fd24c03bfe1f3d61e1b25c6">IsoSpec::IsoOrderedGenerator</a> | |
| 124 | </li> | |
| 125 | <li>get_eProb() | |
| 126 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">IsoSpec::PrecalculatedMarginal</a> | |
| 127 | </li> | |
| 128 | <li>get_isotopeNo() | |
| 129 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">IsoSpec::Marginal</a> | |
| 130 | </li> | |
| 131 | <li>get_lProb() | |
| 132 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">IsoSpec::PrecalculatedMarginal</a> | |
| 133 | </li> | |
| 134 | <li>get_lProbs_ptr() | |
| 135 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">IsoSpec::PrecalculatedMarginal</a> | |
| 136 | </li> | |
| 137 | <li>get_mass() | |
| 138 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">IsoSpec::PrecalculatedMarginal</a> | |
| 139 | </li> | |
| 140 | <li>get_masses_ptr() | |
| 141 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a9a768b90299ea16c447a392dbe1123b5">IsoSpec::PrecalculatedMarginal</a> | |
| 142 | </li> | |
| 143 | <li>get_no_confs() | |
| 144 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">IsoSpec::PrecalculatedMarginal</a> | |
| 145 | </li> | |
| 146 | <li>getAllDim() | |
| 147 | : <a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">IsoSpec::Iso</a> | |
| 148 | </li> | |
| 149 | <li>getDimNumber() | |
| 150 | : <a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">IsoSpec::Iso</a> | |
| 151 | </li> | |
| 152 | <li>getHeaviestConfMass() | |
| 153 | : <a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">IsoSpec::Marginal</a> | |
| 154 | </li> | |
| 155 | <li>getHeaviestPeakMass() | |
| 156 | : <a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">IsoSpec::Iso</a> | |
| 157 | </li> | |
| 158 | <li>getLightestConfMass() | |
| 159 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">IsoSpec::Marginal</a> | |
| 160 | </li> | |
| 161 | <li>getLightestPeakMass() | |
| 162 | : <a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">IsoSpec::Iso</a> | |
| 163 | </li> | |
| 164 | <li>getModeLProb() | |
| 165 | : <a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">IsoSpec::Iso</a> | |
| 166 | , <a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">IsoSpec::Marginal</a> | |
| 167 | </li> | |
| 168 | <li>getModeMass() | |
| 169 | : <a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">IsoSpec::Marginal</a> | |
| 170 | </li> | |
| 171 | <li>getModeProb() | |
| 172 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">IsoSpec::Marginal</a> | |
| 173 | </li> | |
| 174 | <li>getSmallestLProb() | |
| 175 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">IsoSpec::Marginal</a> | |
| 176 | </li> | |
| 177 | </ul> | |
| 178 | ||
| 179 | ||
| 180 | <h3><a id="index_i"></a>- i -</h3><ul> | |
| 181 | <li>inRange() | |
| 182 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a942b30ace039f80c50125360be4ed4d2">IsoSpec::PrecalculatedMarginal</a> | |
| 183 | </li> | |
| 184 | <li>Iso() | |
| 185 | : <a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">IsoSpec::Iso</a> | |
| 186 | </li> | |
| 187 | <li>IsoGenerator() | |
| 188 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoSpec::IsoGenerator</a> | |
| 189 | </li> | |
| 190 | <li>IsoOrderedGenerator() | |
| 191 | : <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#afaf81ff3a758cd59629db323560e263d">IsoSpec::IsoOrderedGenerator</a> | |
| 192 | </li> | |
| 193 | <li>IsoThresholdGenerator() | |
| 194 | : <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a3abbcf1d810b6cad9400bd2552c3faf1">IsoSpec::IsoThresholdGenerator</a> | |
| 195 | </li> | |
| 196 | <li>isotopeNo | |
| 197 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">IsoSpec::Marginal</a> | |
| 198 | </li> | |
| 199 | <li>isotopeNumbers | |
| 200 | : <a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">IsoSpec::Iso</a> | |
| 201 | </li> | |
| 202 | </ul> | |
| 203 | ||
| 204 | ||
| 205 | <h3><a id="index_l"></a>- l -</h3><ul> | |
| 206 | <li>loggamma_nominator | |
| 207 | : <a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">IsoSpec::Marginal</a> | |
| 208 | </li> | |
| 209 | <li>logProb() | |
| 210 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">IsoSpec::Marginal</a> | |
| 211 | </li> | |
| 212 | <li>lprob() | |
| 213 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">IsoSpec::IsoGenerator</a> | |
| 214 | , <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a4aeebde03e385404d0175fd5696ff529">IsoSpec::IsoThresholdGenerator</a> | |
| 215 | </li> | |
| 216 | </ul> | |
| 217 | ||
| 218 | ||
| 219 | <h3><a id="index_m"></a>- m -</h3><ul> | |
| 220 | <li>Marginal() | |
| 221 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">IsoSpec::Marginal</a> | |
| 222 | </li> | |
| 223 | <li>marginals | |
| 224 | : <a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">IsoSpec::Iso</a> | |
| 225 | </li> | |
| 226 | <li>MarginalTrek() | |
| 227 | : <a class="el" href="class_iso_spec_1_1_marginal_trek.html#a83e70d522174e4e6724116941fd9c99e">IsoSpec::MarginalTrek</a> | |
| 228 | </li> | |
| 229 | <li>mass() | |
| 230 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">IsoSpec::IsoGenerator</a> | |
| 231 | , <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ae2236accc7dc7a25a723e3c7317659b6">IsoSpec::IsoThresholdGenerator</a> | |
| 232 | </li> | |
| 233 | <li>mode_conf | |
| 234 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">IsoSpec::Marginal</a> | |
| 235 | </li> | |
| 236 | <li>mode_lprob | |
| 237 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">IsoSpec::Marginal</a> | |
| 238 | </li> | |
| 239 | <li>mode_mass | |
| 240 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">IsoSpec::Marginal</a> | |
| 241 | </li> | |
| 242 | <li>mode_prob | |
| 243 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">IsoSpec::Marginal</a> | |
| 244 | </li> | |
| 245 | <li>modeLProb | |
| 246 | : <a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">IsoSpec::Iso</a> | |
| 247 | </li> | |
| 248 | </ul> | |
| 249 | ||
| 250 | ||
| 251 | <h3><a id="index_p"></a>- p -</h3><ul> | |
| 252 | <li>partialLProbs | |
| 253 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">IsoSpec::IsoGenerator</a> | |
| 254 | </li> | |
| 255 | <li>partialMasses | |
| 256 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">IsoSpec::IsoGenerator</a> | |
| 257 | </li> | |
| 258 | <li>partialProbs | |
| 259 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">IsoSpec::IsoGenerator</a> | |
| 260 | </li> | |
| 261 | <li>PrecalculatedMarginal() | |
| 262 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">IsoSpec::PrecalculatedMarginal</a> | |
| 263 | </li> | |
| 264 | <li>prob() | |
| 265 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">IsoSpec::IsoGenerator</a> | |
| 266 | , <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a998d987f81b2ca7ed610294f6a5f8df5">IsoSpec::IsoThresholdGenerator</a> | |
| 267 | </li> | |
| 268 | <li>probeConfigurationIdx() | |
| 269 | : <a class="el" href="class_iso_spec_1_1_marginal_trek.html#a4db6041328b818d123a017dda3c8b8ae">IsoSpec::MarginalTrek</a> | |
| 270 | </li> | |
| 271 | <li>processUntilCutoff() | |
| 272 | : <a class="el" href="class_iso_spec_1_1_marginal_trek.html#a04f3e495a805a3ea242059c963c5b129">IsoSpec::MarginalTrek</a> | |
| 273 | </li> | |
| 274 | </ul> | |
| 275 | ||
| 276 | ||
| 277 | <h3><a id="index_r"></a>- r -</h3><ul> | |
| 278 | <li>reset() | |
| 279 | : <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ab830ffa21469df45a513ff1dcaf5d9e7">IsoSpec::IsoThresholdGenerator</a> | |
| 280 | </li> | |
| 281 | </ul> | |
| 282 | ||
| 283 | ||
| 284 | <h3><a id="index_s"></a>- s -</h3><ul> | |
| 285 | <li>smallest_lprob | |
| 286 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">IsoSpec::Marginal</a> | |
| 287 | </li> | |
| 288 | </ul> | |
| 289 | ||
| 290 | ||
| 291 | <h3><a id="index_t"></a>- t -</h3><ul> | |
| 292 | <li>terminate_search() | |
| 293 | : <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ac6aa2fff002a76b0beae1995f34ae5f6">IsoSpec::IsoThresholdGenerator</a> | |
| 294 | </li> | |
| 295 | </ul> | |
| 296 | ||
| 297 | ||
| 298 | <h3><a id="index_0x7e"></a>- ~ -</h3><ul> | |
| 299 | <li>~Iso() | |
| 300 | : <a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">IsoSpec::Iso</a> | |
| 301 | </li> | |
| 302 | <li>~IsoGenerator() | |
| 303 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">IsoSpec::IsoGenerator</a> | |
| 304 | </li> | |
| 305 | <li>~IsoOrderedGenerator() | |
| 306 | : <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#a030c118b9a6131130684cd2710371842">IsoSpec::IsoOrderedGenerator</a> | |
| 307 | </li> | |
| 308 | <li>~Marginal() | |
| 309 | : <a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">IsoSpec::Marginal</a> | |
| 310 | </li> | |
| 311 | <li>~PrecalculatedMarginal() | |
| 312 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8">IsoSpec::PrecalculatedMarginal</a> | |
| 313 | </li> | |
| 314 | </ul> | |
| 315 | </div><!-- contents --> | |
| 316 | <!-- start footer part --> | |
| 317 | <hr class="footer"/><address class="footer"><small> | |
| 318 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 319 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 320 | </a> 1.8.14 | |
| 321 | </small></address> | |
| 322 | </body> | |
| 323 | </html> |
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| 7 | <title>IsoSpec: Class Members - Functions</title> | |
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| 22 | <body> | |
| 23 | <div id="top"><!-- do not remove this div, it is closed by doxygen! --> | |
| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
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| 62 | ||
| 63 | <!-- iframe showing the search results (closed by default) --> | |
| 64 | <div id="MSearchResultsWindow"> | |
| 65 | <iframe src="javascript:void(0)" frameborder="0" | |
| 66 | name="MSearchResults" id="MSearchResults"> | |
| 67 | </iframe> | |
| 68 | </div> | |
| 69 | ||
| 70 | <div class="contents"> | |
| 71 |   | |
| 72 | ||
| 73 | <h3><a id="index_a"></a>- a -</h3><ul> | |
| 74 | <li>advanceToNextConfiguration() | |
| 75 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#a20f48ba18c6aecc57d73b2c3ec3a11dd">IsoSpec::IsoGenerator</a> | |
| 76 | , <a class="el" href="class_iso_spec_1_1_iso_layered_generator.html#abce0871ac279fd54a0344ceb80126b66">IsoSpec::IsoLayeredGenerator</a> | |
| 77 | , <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#aa2438bb81fb1d68eda1637d67e9cb36d">IsoSpec::IsoOrderedGenerator</a> | |
| 78 | , <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a7164a6476b84665967c4a667a91d3f3e">IsoSpec::IsoThresholdGenerator</a> | |
| 79 | </li> | |
| 80 | </ul> | |
| 81 | ||
| 82 | ||
| 83 | <h3><a id="index_c"></a>- c -</h3><ul> | |
| 84 | <li>count_confs() | |
| 85 | : <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ad29d8761174bca7b1846ddec03b33528">IsoSpec::IsoThresholdGenerator</a> | |
| 86 | </li> | |
| 87 | </ul> | |
| 88 | ||
| 89 | ||
| 90 | <h3><a id="index_g"></a>- g -</h3><ul> | |
| 91 | <li>get_conf() | |
| 92 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff">IsoSpec::PrecalculatedMarginal</a> | |
| 93 | </li> | |
| 94 | <li>get_conf_signature() | |
| 95 | : <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#af5d638985fd24c03bfe1f3d61e1b25c6">IsoSpec::IsoOrderedGenerator</a> | |
| 96 | </li> | |
| 97 | <li>get_eProb() | |
| 98 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">IsoSpec::PrecalculatedMarginal</a> | |
| 99 | </li> | |
| 100 | <li>get_isotopeNo() | |
| 101 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">IsoSpec::Marginal</a> | |
| 102 | </li> | |
| 103 | <li>get_lProb() | |
| 104 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">IsoSpec::PrecalculatedMarginal</a> | |
| 105 | </li> | |
| 106 | <li>get_lProbs_ptr() | |
| 107 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">IsoSpec::PrecalculatedMarginal</a> | |
| 108 | </li> | |
| 109 | <li>get_mass() | |
| 110 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">IsoSpec::PrecalculatedMarginal</a> | |
| 111 | </li> | |
| 112 | <li>get_masses_ptr() | |
| 113 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a9a768b90299ea16c447a392dbe1123b5">IsoSpec::PrecalculatedMarginal</a> | |
| 114 | </li> | |
| 115 | <li>get_no_confs() | |
| 116 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">IsoSpec::PrecalculatedMarginal</a> | |
| 117 | </li> | |
| 118 | <li>getAllDim() | |
| 119 | : <a class="el" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">IsoSpec::Iso</a> | |
| 120 | </li> | |
| 121 | <li>getDimNumber() | |
| 122 | : <a class="el" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">IsoSpec::Iso</a> | |
| 123 | </li> | |
| 124 | <li>getHeaviestConfMass() | |
| 125 | : <a class="el" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">IsoSpec::Marginal</a> | |
| 126 | </li> | |
| 127 | <li>getHeaviestPeakMass() | |
| 128 | : <a class="el" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">IsoSpec::Iso</a> | |
| 129 | </li> | |
| 130 | <li>getLightestConfMass() | |
| 131 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">IsoSpec::Marginal</a> | |
| 132 | </li> | |
| 133 | <li>getLightestPeakMass() | |
| 134 | : <a class="el" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">IsoSpec::Iso</a> | |
| 135 | </li> | |
| 136 | <li>getModeLProb() | |
| 137 | : <a class="el" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">IsoSpec::Iso</a> | |
| 138 | , <a class="el" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">IsoSpec::Marginal</a> | |
| 139 | </li> | |
| 140 | <li>getModeMass() | |
| 141 | : <a class="el" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">IsoSpec::Marginal</a> | |
| 142 | </li> | |
| 143 | <li>getModeProb() | |
| 144 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">IsoSpec::Marginal</a> | |
| 145 | </li> | |
| 146 | <li>getSmallestLProb() | |
| 147 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">IsoSpec::Marginal</a> | |
| 148 | </li> | |
| 149 | </ul> | |
| 150 | ||
| 151 | ||
| 152 | <h3><a id="index_i"></a>- i -</h3><ul> | |
| 153 | <li>inRange() | |
| 154 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a942b30ace039f80c50125360be4ed4d2">IsoSpec::PrecalculatedMarginal</a> | |
| 155 | </li> | |
| 156 | <li>Iso() | |
| 157 | : <a class="el" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">IsoSpec::Iso</a> | |
| 158 | </li> | |
| 159 | <li>IsoGenerator() | |
| 160 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoSpec::IsoGenerator</a> | |
| 161 | </li> | |
| 162 | <li>IsoOrderedGenerator() | |
| 163 | : <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#afaf81ff3a758cd59629db323560e263d">IsoSpec::IsoOrderedGenerator</a> | |
| 164 | </li> | |
| 165 | <li>IsoThresholdGenerator() | |
| 166 | : <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a3abbcf1d810b6cad9400bd2552c3faf1">IsoSpec::IsoThresholdGenerator</a> | |
| 167 | </li> | |
| 168 | </ul> | |
| 169 | ||
| 170 | ||
| 171 | <h3><a id="index_l"></a>- l -</h3><ul> | |
| 172 | <li>logProb() | |
| 173 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">IsoSpec::Marginal</a> | |
| 174 | </li> | |
| 175 | <li>lprob() | |
| 176 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">IsoSpec::IsoGenerator</a> | |
| 177 | , <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a4aeebde03e385404d0175fd5696ff529">IsoSpec::IsoThresholdGenerator</a> | |
| 178 | </li> | |
| 179 | </ul> | |
| 180 | ||
| 181 | ||
| 182 | <h3><a id="index_m"></a>- m -</h3><ul> | |
| 183 | <li>Marginal() | |
| 184 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">IsoSpec::Marginal</a> | |
| 185 | </li> | |
| 186 | <li>MarginalTrek() | |
| 187 | : <a class="el" href="class_iso_spec_1_1_marginal_trek.html#a83e70d522174e4e6724116941fd9c99e">IsoSpec::MarginalTrek</a> | |
| 188 | </li> | |
| 189 | <li>mass() | |
| 190 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">IsoSpec::IsoGenerator</a> | |
| 191 | , <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ae2236accc7dc7a25a723e3c7317659b6">IsoSpec::IsoThresholdGenerator</a> | |
| 192 | </li> | |
| 193 | </ul> | |
| 194 | ||
| 195 | ||
| 196 | <h3><a id="index_p"></a>- p -</h3><ul> | |
| 197 | <li>PrecalculatedMarginal() | |
| 198 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">IsoSpec::PrecalculatedMarginal</a> | |
| 199 | </li> | |
| 200 | <li>prob() | |
| 201 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">IsoSpec::IsoGenerator</a> | |
| 202 | , <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#a998d987f81b2ca7ed610294f6a5f8df5">IsoSpec::IsoThresholdGenerator</a> | |
| 203 | </li> | |
| 204 | <li>probeConfigurationIdx() | |
| 205 | : <a class="el" href="class_iso_spec_1_1_marginal_trek.html#a4db6041328b818d123a017dda3c8b8ae">IsoSpec::MarginalTrek</a> | |
| 206 | </li> | |
| 207 | <li>processUntilCutoff() | |
| 208 | : <a class="el" href="class_iso_spec_1_1_marginal_trek.html#a04f3e495a805a3ea242059c963c5b129">IsoSpec::MarginalTrek</a> | |
| 209 | </li> | |
| 210 | </ul> | |
| 211 | ||
| 212 | ||
| 213 | <h3><a id="index_r"></a>- r -</h3><ul> | |
| 214 | <li>reset() | |
| 215 | : <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ab830ffa21469df45a513ff1dcaf5d9e7">IsoSpec::IsoThresholdGenerator</a> | |
| 216 | </li> | |
| 217 | </ul> | |
| 218 | ||
| 219 | ||
| 220 | <h3><a id="index_t"></a>- t -</h3><ul> | |
| 221 | <li>terminate_search() | |
| 222 | : <a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html#ac6aa2fff002a76b0beae1995f34ae5f6">IsoSpec::IsoThresholdGenerator</a> | |
| 223 | </li> | |
| 224 | </ul> | |
| 225 | ||
| 226 | ||
| 227 | <h3><a id="index_0x7e"></a>- ~ -</h3><ul> | |
| 228 | <li>~Iso() | |
| 229 | : <a class="el" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">IsoSpec::Iso</a> | |
| 230 | </li> | |
| 231 | <li>~IsoGenerator() | |
| 232 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">IsoSpec::IsoGenerator</a> | |
| 233 | </li> | |
| 234 | <li>~IsoOrderedGenerator() | |
| 235 | : <a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html#a030c118b9a6131130684cd2710371842">IsoSpec::IsoOrderedGenerator</a> | |
| 236 | </li> | |
| 237 | <li>~Marginal() | |
| 238 | : <a class="el" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">IsoSpec::Marginal</a> | |
| 239 | </li> | |
| 240 | <li>~PrecalculatedMarginal() | |
| 241 | : <a class="el" href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8">IsoSpec::PrecalculatedMarginal</a> | |
| 242 | </li> | |
| 243 | </ul> | |
| 244 | </div><!-- contents --> | |
| 245 | <!-- start footer part --> | |
| 246 | <hr class="footer"/><address class="footer"><small> | |
| 247 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 248 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 249 | </a> 1.8.14 | |
| 250 | </small></address> | |
| 251 | </body> | |
| 252 | </html> |
| 0 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> | |
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| 5 | <meta name="generator" content="Doxygen 1.8.14"/> | |
| 6 | <meta name="viewport" content="width=device-width, initial-scale=1"/> | |
| 7 | <title>IsoSpec: Class Members - Variables</title> | |
| 8 | <link href="tabs.css" rel="stylesheet" type="text/css"/> | |
| 9 | <script type="text/javascript" src="jquery.js"></script> | |
| 10 | <script type="text/javascript" src="dynsections.js"></script> | |
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| 15 | MathJax.Hub.Config({ | |
| 16 | extensions: ["tex2jax.js"], | |
| 17 | jax: ["input/TeX","output/HTML-CSS"], | |
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| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
| 36 | </table> | |
| 37 | </div> | |
| 38 | <!-- end header part --> | |
| 39 | <!-- Generated by Doxygen 1.8.14 --> | |
| 40 | <script type="text/javascript"> | |
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| 52 | }); | |
| 53 | /* @license-end */</script> | |
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| 55 | </div><!-- top --> | |
| 56 | <!-- window showing the filter options --> | |
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| 58 | onmouseover="return searchBox.OnSearchSelectShow()" | |
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| 60 | onkeydown="return searchBox.OnSearchSelectKey(event)"> | |
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| 62 | ||
| 63 | <!-- iframe showing the search results (closed by default) --> | |
| 64 | <div id="MSearchResultsWindow"> | |
| 65 | <iframe src="javascript:void(0)" frameborder="0" | |
| 66 | name="MSearchResults" id="MSearchResults"> | |
| 67 | </iframe> | |
| 68 | </div> | |
| 69 | ||
| 70 | <div class="contents"> | |
| 71 |  <ul> | |
| 72 | <li>allDim | |
| 73 | : <a class="el" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">IsoSpec::Iso</a> | |
| 74 | </li> | |
| 75 | <li>atom_lProbs | |
| 76 | : <a class="el" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">IsoSpec::Marginal</a> | |
| 77 | </li> | |
| 78 | <li>atom_masses | |
| 79 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">IsoSpec::Marginal</a> | |
| 80 | </li> | |
| 81 | <li>atomCnt | |
| 82 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">IsoSpec::Marginal</a> | |
| 83 | </li> | |
| 84 | <li>atomCounts | |
| 85 | : <a class="el" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">IsoSpec::Iso</a> | |
| 86 | </li> | |
| 87 | <li>confSize | |
| 88 | : <a class="el" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">IsoSpec::Iso</a> | |
| 89 | </li> | |
| 90 | <li>dimNumber | |
| 91 | : <a class="el" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">IsoSpec::Iso</a> | |
| 92 | </li> | |
| 93 | <li>disowned | |
| 94 | : <a class="el" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">IsoSpec::Iso</a> | |
| 95 | </li> | |
| 96 | <li>isotopeNo | |
| 97 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">IsoSpec::Marginal</a> | |
| 98 | </li> | |
| 99 | <li>isotopeNumbers | |
| 100 | : <a class="el" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">IsoSpec::Iso</a> | |
| 101 | </li> | |
| 102 | <li>loggamma_nominator | |
| 103 | : <a class="el" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">IsoSpec::Marginal</a> | |
| 104 | </li> | |
| 105 | <li>marginals | |
| 106 | : <a class="el" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">IsoSpec::Iso</a> | |
| 107 | </li> | |
| 108 | <li>mode_conf | |
| 109 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">IsoSpec::Marginal</a> | |
| 110 | </li> | |
| 111 | <li>mode_lprob | |
| 112 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">IsoSpec::Marginal</a> | |
| 113 | </li> | |
| 114 | <li>mode_mass | |
| 115 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">IsoSpec::Marginal</a> | |
| 116 | </li> | |
| 117 | <li>mode_prob | |
| 118 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">IsoSpec::Marginal</a> | |
| 119 | </li> | |
| 120 | <li>modeLProb | |
| 121 | : <a class="el" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">IsoSpec::Iso</a> | |
| 122 | </li> | |
| 123 | <li>partialLProbs | |
| 124 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">IsoSpec::IsoGenerator</a> | |
| 125 | </li> | |
| 126 | <li>partialMasses | |
| 127 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">IsoSpec::IsoGenerator</a> | |
| 128 | </li> | |
| 129 | <li>partialProbs | |
| 130 | : <a class="el" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">IsoSpec::IsoGenerator</a> | |
| 131 | </li> | |
| 132 | <li>smallest_lprob | |
| 133 | : <a class="el" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">IsoSpec::Marginal</a> | |
| 134 | </li> | |
| 135 | </ul> | |
| 136 | </div><!-- contents --> | |
| 137 | <!-- start footer part --> | |
| 138 | <hr class="footer"/><address class="footer"><small> | |
| 139 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 140 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 141 | </a> 1.8.14 | |
| 142 | </small></address> | |
| 143 | </body> | |
| 144 | </html> |
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| 6 | <meta name="viewport" content="width=device-width, initial-scale=1"/> | |
| 7 | <title>IsoSpec: Graph Legend</title> | |
| 8 | <link href="tabs.css" rel="stylesheet" type="text/css"/> | |
| 9 | <script type="text/javascript" src="jquery.js"></script> | |
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| 22 | <td id="projectlogo"><img alt="Logo" src="MANGUSTA.png"/></td> | |
| 23 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 24 | <div id="projectname">IsoSpec | |
| 25 |  <span id="projectnumber">1.95</span> | |
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| 74 | </center><p>The boxes in the above graph have the following meaning: </p> | |
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| 79 | A box with a black border denotes a documented struct or class. </li> | |
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| 81 | A box with a gray border denotes an undocumented struct or class. </li> | |
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| 83 | A box with a red border denotes a documented struct or class forwhich not all inheritance/containment relations are shown. A graph is truncated if it does not fit within the specified boundaries. </li> | |
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| 90 | A dark green arrow is used for protected inheritance. </li> | |
| 91 | <li> | |
| 92 | A dark red arrow is used for private inheritance. </li> | |
| 93 | <li> | |
| 94 | A purple dashed arrow is used if a class is contained or used by another class. The arrow is labelled with the variable(s) through which the pointed class or struct is accessible. </li> | |
| 95 | <li> | |
| 96 | A yellow dashed arrow denotes a relation between a template instance and the template class it was instantiated from. The arrow is labelled with the template parameters of the instance. </li> | |
| 97 | </ul> | |
| 98 | </div><!-- contents --> | |
| 99 | <!-- start footer part --> | |
| 100 | <hr class="footer"/><address class="footer"><small> | |
| 101 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
| 102 | <img class="footer" src="doxygen.png" alt="doxygen"/> | |
| 103 | </a> 1.8.14 | |
| 104 | </small></address> | |
| 105 | </body> | |
| 106 | </html> |
| 0 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> | |
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| 3 | <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> | |
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| 5 | <meta name="generator" content="Doxygen 1.8.14"/> | |
| 6 | <meta name="viewport" content="width=device-width, initial-scale=1"/> | |
| 7 | <title>IsoSpec: Class Hierarchy</title> | |
| 8 | <link href="tabs.css" rel="stylesheet" type="text/css"/> | |
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| 10 | <script type="text/javascript" src="dynsections.js"></script> | |
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| 24 | <div id="titlearea"> | |
| 25 | <table cellspacing="0" cellpadding="0"> | |
| 26 | <tbody> | |
| 27 | <tr style="height: 56px;"> | |
| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
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| 43 | /* @license-end */ | |
| 44 | </script> | |
| 45 | <script type="text/javascript" src="menudata.js"></script> | |
| 46 | <script type="text/javascript" src="menu.js"></script> | |
| 47 | <script type="text/javascript"> | |
| 48 | /* @license magnet:?xt=urn:btih:cf05388f2679ee054f2beb29a391d25f4e673ac3&dn=gpl-2.0.txt GPL-v2 */ | |
| 49 | $(function() { | |
| 50 | initMenu('',true,false,'search.php','Search'); | |
| 51 | $(document).ready(function() { init_search(); }); | |
| 52 | }); | |
| 53 | /* @license-end */</script> | |
| 54 | <div id="main-nav"></div> | |
| 55 | </div><!-- top --> | |
| 56 | <!-- window showing the filter options --> | |
| 57 | <div id="MSearchSelectWindow" | |
| 58 | onmouseover="return searchBox.OnSearchSelectShow()" | |
| 59 | onmouseout="return searchBox.OnSearchSelectHide()" | |
| 60 | onkeydown="return searchBox.OnSearchSelectKey(event)"> | |
| 61 | </div> | |
| 62 | ||
| 63 | <!-- iframe showing the search results (closed by default) --> | |
| 64 | <div id="MSearchResultsWindow"> | |
| 65 | <iframe src="javascript:void(0)" frameborder="0" | |
| 66 | name="MSearchResults" id="MSearchResults"> | |
| 67 | </iframe> | |
| 68 | </div> | |
| 69 | ||
| 70 | <div class="header"> | |
| 71 | <div class="headertitle"> | |
| 72 | <div class="title">Class Hierarchy</div> </div> | |
| 73 | </div><!--header--> | |
| 74 | <div class="contents"> | |
| 75 | <div class="textblock">This inheritance list is sorted roughly, but not completely, alphabetically:</div><div class="directory"> | |
| 76 | <div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span>]</div><table class="directory"> | |
| 77 | <tr id="row_0_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_allocator.html" target="_self">IsoSpec::Allocator< T ></a></td><td class="desc"></td></tr> | |
| 78 | <tr id="row_1_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_allocator.html" target="_self">IsoSpec::Allocator< int ></a></td><td class="desc"></td></tr> | |
| 79 | <tr id="row_2_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_conf_equal.html" target="_self">IsoSpec::ConfEqual</a></td><td class="desc"></td></tr> | |
| 80 | <tr id="row_3_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_conf_order.html" target="_self">IsoSpec::ConfOrder</a></td><td class="desc"></td></tr> | |
| 81 | <tr id="row_4_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_conf_order_marginal.html" target="_self">IsoSpec::ConfOrderMarginal</a></td><td class="desc"></td></tr> | |
| 82 | <tr id="row_5_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_conf_order_marginal_descending.html" target="_self">IsoSpec::ConfOrderMarginalDescending</a></td><td class="desc"></td></tr> | |
| 83 | <tr id="row_6_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_dirty_allocator.html" target="_self">IsoSpec::DirtyAllocator</a></td><td class="desc"></td></tr> | |
| 84 | <tr id="row_7_"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_7_" class="arrow" onclick="toggleFolder('7_')">▼</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_iso.html" target="_self">IsoSpec::Iso</a></td><td class="desc">For the calculation of the isotopic distribution </td></tr> | |
| 85 | <tr id="row_7_0_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span id="arr_7_0_" class="arrow" onclick="toggleFolder('7_0_')">▼</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_iso_generator.html" target="_self">IsoSpec::IsoGenerator</a></td><td class="desc">The generator of isotopologues </td></tr> | |
| 86 | <tr id="row_7_0_0_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html" target="_self">IsoSpec::IsoLayeredGenerator</a></td><td class="desc">The class that represents isotopologues above a given joint probability value </td></tr> | |
| 87 | <tr id="row_7_0_1_" class="even"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html" target="_self">IsoSpec::IsoOrderedGenerator</a></td><td class="desc">The generator of isotopologues sorted by their probability of occurrence </td></tr> | |
| 88 | <tr id="row_7_0_2_"><td class="entry"><span style="width:48px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html" target="_self">IsoSpec::IsoThresholdGenerator</a></td><td class="desc">The generator of isotopologues above a given threshold value </td></tr> | |
| 89 | <tr id="row_8_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_key_hasher.html" target="_self">IsoSpec::KeyHasher</a></td><td class="desc"></td></tr> | |
| 90 | <tr id="row_9_"><td class="entry"><span style="width:0px;display:inline-block;"> </span><span id="arr_9_" class="arrow" onclick="toggleFolder('9_')">▼</span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_marginal.html" target="_self">IsoSpec::Marginal</a></td><td class="desc">The marginal distribution class (a subisotopologue) </td></tr> | |
| 91 | <tr id="row_9_0_" class="even"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_marginal_trek.html" target="_self">IsoSpec::MarginalTrek</a></td><td class="desc">The marginal distribution class (a subisotopologue) </td></tr> | |
| 92 | <tr id="row_9_1_"><td class="entry"><span style="width:32px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html" target="_self">IsoSpec::PrecalculatedMarginal</a></td><td class="desc">Precalculated <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class </td></tr> | |
| 93 | <tr id="row_10_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html" target="_self">IsoSpec::OrderMarginalsBySizeDecresing</a></td><td class="desc"></td></tr> | |
| 94 | <tr id="row_11_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_reverse_order.html" target="_self">IsoSpec::ReverseOrder< T ></a></td><td class="desc"></td></tr> | |
| 95 | <tr id="row_12_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_s_summator.html" target="_self">IsoSpec::SSummator</a></td><td class="desc"></td></tr> | |
| 96 | <tr id="row_13_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_summator.html" target="_self">IsoSpec::Summator</a></td><td class="desc"></td></tr> | |
| 97 | <tr id="row_14_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_table_order.html" target="_self">IsoSpec::TableOrder< T ></a></td><td class="desc"></td></tr> | |
| 98 | <tr id="row_15_"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_tabulator.html" target="_self">IsoSpec::Tabulator< T ></a></td><td class="desc"></td></tr> | |
| 99 | <tr id="row_16_" class="even"><td class="entry"><span style="width:16px;display:inline-block;"> </span><span class="icona"><span class="icon">C</span></span><a class="el" href="class_iso_spec_1_1_t_summator.html" target="_self">IsoSpec::TSummator</a></td><td class="desc"></td></tr> | |
| 100 | </table> | |
| 101 | </div><!-- directory --> | |
| 102 | </div><!-- contents --> | |
| 103 | <!-- start footer part --> | |
| 104 | <hr class="footer"/><address class="footer"><small> | |
| 105 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 107 | </a> 1.8.14 | |
| 108 | </small></address> | |
| 109 | </body> | |
| 110 | </html> |
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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
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| 69 | ||
| 70 | <div class="header"> | |
| 71 | <div class="headertitle"> | |
| 72 | <div class="title">IsoSpec Documentation</div> </div> | |
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| 80 | </a> 1.8.14 | |
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| 83 | </html> |
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| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * This file has been released into public domain by John D. Cook</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> * and is used here with some slight modifications (which are hereby</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * also released into public domain),</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> */</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> </div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor">#include <cmath></span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#include <cstdlib></span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#include "isoMath.h"</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor">#include "platform.h"</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> </div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> {</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="keyword">const</span> <span class="keywordtype">double</span> pi = 3.14159265358979323846264338328;</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="keywordtype">void</span> release_g_lfact_table()</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> {</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#if ISOSPEC_GOT_MMAN</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  munmap(g_lfact_table, ISOSPEC_G_FACT_TABLE_SIZE*<span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  free(g_lfact_table);</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> }</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> </div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="keywordtype">double</span>* alloc_lfact_table()</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> {</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordtype">double</span>* ret;</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="preprocessor"># if ISOSPEC_GOT_MMAN</span></div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  ret = <span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(mmap(<span class="keyword">nullptr</span>, <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>)*ISOSPEC_G_FACT_TABLE_SIZE, PROT_READ | PROT_WRITE, MAP_ANONYMOUS | MAP_PRIVATE, -1, 0));</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  ret = <span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(calloc(ISOSPEC_G_FACT_TABLE_SIZE, <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>)));</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  std::atexit(release_g_lfact_table);</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordflow">return</span> ret;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> }</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keywordtype">double</span>* g_lfact_table = alloc_lfact_table();</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> </div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keywordtype">double</span> RationalApproximation(<span class="keywordtype">double</span> t)</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> {</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="comment">// Abramowitz and Stegun formula 26.2.23.</span></div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="comment">// The absolute value of the error should be less than 4.5 e-4.</span></div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordtype">double</span> c[] = {2.515517, 0.802853, 0.010328};</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keywordtype">double</span> d[] = {1.432788, 0.189269, 0.001308};</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordflow">return</span> t - ((c[2]*t + c[1])*t + c[0]) / </div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  (((d[2]*t + d[1])*t + d[0])*t + 1.0);</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> }</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="keywordtype">double</span> NormalCDFInverse(<span class="keywordtype">double</span> p)</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> {</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordflow">if</span> (p < 0.5)</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keywordflow">return</span> -RationalApproximation( sqrt(-2.0*log(p)) );</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordflow">return</span> RationalApproximation( sqrt(-2.0*log(1-p)) );</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> }</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> <span class="keywordtype">double</span> NormalCDFInverse(<span class="keywordtype">double</span> p, <span class="keywordtype">double</span> mean, <span class="keywordtype">double</span> stdev)</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> {</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">return</span> mean + stdev * NormalCDFInverse(p);</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> }</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="keywordtype">double</span> NormalCDF(<span class="keywordtype">double</span> x, <span class="keywordtype">double</span> mean, <span class="keywordtype">double</span> stdev)</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> {</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  x = (x-mean)/stdev * 0.7071067811865476;</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <span class="comment">// constants</span></div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordtype">double</span> a1 = 0.254829592;</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordtype">double</span> a2 = -0.284496736;</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordtype">double</span> a3 = 1.421413741;</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keywordtype">double</span> a4 = -1.453152027;</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordtype">double</span> a5 = 1.061405429;</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordtype">double</span> p = 0.3275911;</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="comment">// Save the sign of x</span></div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <span class="keywordtype">int</span> sign = 1;</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordflow">if</span> (x < 0)</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  sign = -1;</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  x = fabs(x);</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="comment">// A&S formula 7.1.26</span></div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordtype">double</span> t = 1.0/(1.0 + p*x);</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordtype">double</span> y = 1.0 - (((((a5*t + a4)*t) + a3)*t + a2)*t + a1)*t*exp(-x*x);</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keywordflow">return</span> 0.5*(1.0 + sign*y);</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> }</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> <span class="keywordtype">double</span> NormalPDF(<span class="keywordtype">double</span> x, <span class="keywordtype">double</span> mean, <span class="keywordtype">double</span> stdev)</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> {</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keywordtype">double</span> two_variance = stdev * stdev * 2.0;</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keywordtype">double</span> delta = x-mean;</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keywordflow">return</span> exp( -delta*delta / two_variance ) / sqrt( two_variance * pi );</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> }</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span> </div><div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <cmath></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <fenv.h></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#if !defined(ISOSPEC_G_FACT_TABLE_SIZE)</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// 10M should be enough for anyone, right?</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// Actually, yes. If anyone tries to input a molecule that has more than 10M atoms, </span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// he deserves to get an exception thrown in his face.</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#define ISOSPEC_G_FACT_TABLE_SIZE 1024*1024*10</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> {</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> </div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="keyword">extern</span> <span class="keywordtype">double</span>* g_lfact_table;</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="keyword">static</span> <span class="keyword">inline</span> <span class="keywordtype">double</span> minuslogFactorial(<span class="keywordtype">int</span> n) </div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> { </div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="keywordflow">if</span> (n < 2) </div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordflow">return</span> 0.0;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordflow">if</span> (g_lfact_table[n] == 0.0)</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  g_lfact_table[n] = -lgamma(n+1);</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> </div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordflow">return</span> g_lfact_table[n];</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> }</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keywordtype">double</span> NormalCDFInverse(<span class="keywordtype">double</span> p);</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="keywordtype">double</span> NormalCDFInverse(<span class="keywordtype">double</span> p, <span class="keywordtype">double</span> mean, <span class="keywordtype">double</span> stdev);</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="keywordtype">double</span> NormalCDF(<span class="keywordtype">double</span> x, <span class="keywordtype">double</span> mean, <span class="keywordtype">double</span> stdev);</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="keywordtype">double</span> NormalPDF(<span class="keywordtype">double</span> x, <span class="keywordtype">double</span> mean = 0.0, <span class="keywordtype">double</span> stdev = 1.0);</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div><div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> </div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <cmath></span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <algorithm></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <stdlib.h></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <string.h></span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#include <tuple></span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#include <unordered_map></span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#include <queue></span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#include <utility></span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor">#include <iostream></span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="preprocessor">#include <iomanip></span></div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor">#include <cctype></span></div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor">#include <stdexcept></span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="preprocessor">#include <limits></span></div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor">#include <assert.h></span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="preprocessor">#include <ctype.h></span></div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#include "platform.h"</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#include "conf.h"</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor">#include "dirtyAllocator.h"</span></div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include "operators.h"</span></div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include "summator.h"</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include "marginalTrek++.h"</span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include "isoSpec++.h"</span></div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include "misc.h"</span></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include "element_tables.h"</span></div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="keyword">using namespace </span><a class="code" href="namespacestd.html">std</a>;</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> {</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div><div class="line"><a name="l00051"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea"> 51</a></span> Iso::Iso(</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keywordtype">int</span> _dimNumber,</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>* _isotopeNumbers,</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>* _atomCounts,</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* <span class="keyword">const</span> * _isotopeMasses,</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* <span class="keyword">const</span> * _isotopeProbabilities</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> ) :</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> disowned(false),</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span> dimNumber(_dimNumber),</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> isotopeNumbers(array_copy<int>(_isotopeNumbers, _dimNumber)),</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> atomCounts(array_copy<int>(_atomCounts, _dimNumber)),</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> confSize(_dimNumber * sizeof(int)),</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> allDim(0),</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> marginals(nullptr),</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> modeLProb(0.0)</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> {</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  setupMarginals(_isotopeMasses, _isotopeProbabilities);</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> }</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div><div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a6c93ecb77a11bc831cc7600797fbf837"> 70</a></span> <a class="code" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso::Iso</a>(<a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>&& other) :</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> disowned(other.disowned),</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> dimNumber(other.dimNumber),</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> isotopeNumbers(other.isotopeNumbers),</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> atomCounts(other.atomCounts),</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> confSize(other.confSize),</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> allDim(other.allDim),</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> marginals(other.marginals),</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> modeLProb(other.modeLProb)</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> {</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  other.disowned = <span class="keyword">true</span>;</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> }</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div><div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a485cba7555fbdc64bbea19690f202b13"> 84</a></span> <a class="code" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso::Iso</a>(<span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>& other, <span class="keywordtype">bool</span> fullcopy) :</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> disowned(fullcopy ? throw <a class="code" href="namespacestd.html">std</a>::logic_error(<span class="stringliteral">"Not implemented"</span>) : true),</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span> dimNumber(other.dimNumber),</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span> isotopeNumbers(fullcopy ? array_copy<int>(other.isotopeNumbers, dimNumber) : other.isotopeNumbers),</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> atomCounts(fullcopy ? array_copy<int>(other.atomCounts, dimNumber) : other.atomCounts),</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span> confSize(other.confSize),</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> allDim(other.allDim),</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> marginals(fullcopy ? throw <a class="code" href="namespacestd.html">std</a>::logic_error(<span class="stringliteral">"Not implemented"</span>) : other.marginals),</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> modeLProb(other.modeLProb)</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> {}</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span> <span class="keyword">inline</span> <span class="keywordtype">void</span> Iso::setupMarginals(<span class="keyword">const</span> <span class="keywordtype">double</span>* <span class="keyword">const</span> * _isotopeMasses, <span class="keyword">const</span> <span class="keywordtype">double</span>* <span class="keyword">const</span> * _isotopeProbabilities)</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> {</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keywordflow">if</span> (<a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a> == <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  {</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a> = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=0; i<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>;i++)</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  {</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <a class="code" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a> += <a class="code" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a>[i];</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>[i] = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>(</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  _isotopeMasses[i],</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  _isotopeProbabilities[i],</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <a class="code" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a>[i],</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <a class="code" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a>[i]</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  );</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <a class="code" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a> += <a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>[i]-><a class="code" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a>();</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  }</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  }</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span> }</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span> </div><div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f"> 116</a></span> <a class="code" href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">Iso::~Iso</a>()</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> {</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keywordflow">if</span>(!<a class="code" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a>)</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  {</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordflow">if</span> (<a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a> != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  dealloc_table(<a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>, <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>);</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="keyword">delete</span>[] <a class="code" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a>;</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keyword">delete</span>[] <a class="code" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a>;</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  }</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> }</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span> </div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div><div class="line"><a name="l00128"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d"> 128</a></span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">Iso::getLightestPeakMass</a>()<span class="keyword"> const</span></div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span> <span class="keyword"></span>{</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordtype">double</span> mass = 0.0;</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> ii=0; ii<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; ii++)</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  mass += <a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>[ii]->getLightestConfMass();</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordflow">return</span> mass;</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span> }</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div><div class="line"><a name="l00136"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf"> 136</a></span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">Iso::getHeaviestPeakMass</a>()<span class="keyword"> const</span></div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span> <span class="keyword"></span>{</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="keywordtype">double</span> mass = 0.0;</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> ii=0; ii<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; ii++)</div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  mass += <a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>[ii]->getHeaviestConfMass();</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keywordflow">return</span> mass;</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span> }</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span> </div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span> </div><div class="line"><a name="l00146"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#ad389effb319e9ed73db9ed5749868b81"> 146</a></span> <a class="code" href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">Iso::Iso</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* formula) :</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span> disowned(false),</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span> allDim(0),</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span> marginals(nullptr),</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span> modeLProb(0.0)</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span> {</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  std::vector<const double*> isotope_masses;</div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  std::vector<const double*> isotope_probabilities;</div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a> = parse_formula(formula, isotope_masses, isotope_probabilities, &<a class="code" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a>, &<a class="code" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a>, &<a class="code" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a>);</div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  setupMarginals(isotope_masses.data(), isotope_probabilities.data());</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span> }</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> parse_formula(<span class="keyword">const</span> <span class="keywordtype">char</span>* formula, std::vector<const double*>& isotope_masses, std::vector<const double*>& isotope_probabilities, <span class="keywordtype">int</span>** isotopeNumbers, <span class="keywordtype">int</span>** atomCounts, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>* confSize)</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span> {</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="comment">// This function is NOT guaranteed to be secure against malicious input. It should be used only for debugging.</span></div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  <span class="keywordtype">size_t</span> slen = strlen(formula);</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="comment">// Yes, it would be more elegant to use std::string here, but it's the only promiment place where it would be used in IsoSpec, and avoiding it here</span></div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="comment">// means we can run the whole thing through Clang's memory sanitizer without the need for instrumented libc++/libstdc++. That's worth messing with char pointers a</span></div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="comment">// little bit.</span></div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  std::vector<std::pair<const char*, size_t> > elements;</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  std::vector<int> numbers;</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span> </div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  <span class="keywordflow">if</span>(slen == 0)</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  <span class="keywordflow">throw</span> invalid_argument(<span class="stringliteral">"Invalid formula: can't be empty"</span>);</div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span> </div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordflow">if</span>(!isdigit(formula[slen-1]))</div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="keywordflow">throw</span> invalid_argument(<span class="stringliteral">"Invalid formula: every element must be followed by a number - write H2O1 and not H2O for water"</span>);</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span> </div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  <span class="keywordflow">for</span>(<span class="keywordtype">size_t</span> ii=0; ii<slen; ii++)</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keywordflow">if</span>(!isdigit(formula[ii]) && !isalpha(formula[ii]))</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="keywordflow">throw</span> invalid_argument(<span class="stringliteral">"Ivalid formula: contains invalid (non-digit, non-alpha) character"</span>);</div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span> </div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <span class="keywordtype">size_t</span> position = 0;</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keywordtype">size_t</span> elem_end = 0;</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keywordtype">size_t</span> digit_end = 0;</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span> </div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordflow">while</span>(position < slen)</div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  {</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  elem_end = position;</div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="keywordflow">while</span>(isalpha(formula[elem_end]))</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  elem_end++;</div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  digit_end = elem_end;</div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <span class="keywordflow">while</span>(isdigit(formula[digit_end]))</div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  digit_end++;</div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  elements.emplace_back(&formula[position], elem_end-position);</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  numbers.push_back(atoi(&formula[elem_end]));</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  position = digit_end;</div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  }</div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span> </div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  std::vector<int> element_indexes;</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> </div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span>  <span class="keywordflow">for</span> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i=0; i<elements.size(); i++)</div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  {</div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  <span class="keywordtype">int</span> idx = -1;</div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> j=0; j<ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES; j++)</div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  {</div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keywordflow">if</span> ((strlen(elem_table_symbol[j]) == elements[i].second) && (strncmp(elements[i].first, elem_table_symbol[j], elements[i].second) == 0))</div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  {</div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  idx = j;</div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span>  }</div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  }</div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  <span class="keywordflow">if</span>(idx < 0)</div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="keywordflow">throw</span> invalid_argument(<span class="stringliteral">"Invalid formula"</span>);</div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  element_indexes.push_back(idx);</div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  }</div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span> </div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  vector<int> _isotope_numbers;</div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span> </div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="keywordflow">for</span>(vector<int>::iterator it = element_indexes.begin(); it != element_indexes.end(); ++it)</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  {</div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="keywordtype">int</span> num = 0;</div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="keywordtype">int</span> at_idx = *it;</div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <span class="keywordtype">int</span> atomicNo = elem_table_atomicNo[at_idx];</div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <span class="keywordflow">while</span>(at_idx < ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES && elem_table_atomicNo[at_idx] == atomicNo)</div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  {</div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span>  at_idx++;</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span>  num++;</div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span>  }</div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  _isotope_numbers.push_back(num);</div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  }</div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span> </div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <span class="keywordflow">for</span>(vector<int>::iterator it = element_indexes.begin(); it != element_indexes.end(); ++it)</div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  {</div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  isotope_masses.push_back(&elem_table_mass[*it]);</div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  isotope_probabilities.push_back(&elem_table_probability[*it]);</div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  };</div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span> </div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> dimNumber = elements.size();</div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span> </div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  *isotopeNumbers = array_copy<int>(_isotope_numbers.data(), dimNumber);</div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  *atomCounts = array_copy<int>(numbers.data(), dimNumber);</div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  *confSize = dimNumber * <span class="keyword">sizeof</span>(int);</div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span> </div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keywordflow">return</span> dimNumber;</div><div class="line"><a name="l00243"></a><span class="lineno"> 243</span> </div><div class="line"><a name="l00244"></a><span class="lineno"> 244</span> }</div><div class="line"><a name="l00245"></a><span class="lineno"> 245</span> </div><div class="line"><a name="l00246"></a><span class="lineno"> 246</span> </div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span> <span class="comment">/*</span></div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span> <span class="comment"> * ----------------------------------------------------------------------------------------------------------</span></div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span> <span class="comment"> */</span></div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span> </div><div class="line"><a name="l00251"></a><span class="lineno"> 251</span> </div><div class="line"><a name="l00252"></a><span class="lineno"> 252</span> </div><div class="line"><a name="l00253"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188"> 253</a></span> <a class="code" href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoGenerator::IsoGenerator</a>(<a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>&& iso, <span class="keywordtype">bool</span> alloc_partials) :</div><div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>(<a class="code" href="namespacestd.html">std</a>::move(iso)),</div><div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  partialLProbs(alloc_partials ? new double[dimNumber+1] : nullptr),</div><div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  partialMasses(alloc_partials ? new double[dimNumber+1] : nullptr),</div><div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  partialProbs(alloc_partials ? new double[dimNumber+1] : nullptr)</div><div class="line"><a name="l00258"></a><span class="lineno"> 258</span> {</div><div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordflow">if</span>(alloc_partials)</div><div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  {</div><div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a>[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>] = 0.0;</div><div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a>[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>] = 0.0;</div><div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a>[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>] = 1.0;</div><div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  }</div><div class="line"><a name="l00265"></a><span class="lineno"> 265</span> }</div><div class="line"><a name="l00266"></a><span class="lineno"> 266</span> </div><div class="line"><a name="l00267"></a><span class="lineno"> 267</span> </div><div class="line"><a name="l00268"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76"> 268</a></span> <a class="code" href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">IsoGenerator::~IsoGenerator</a>() </div><div class="line"><a name="l00269"></a><span class="lineno"> 269</span> {</div><div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <span class="keywordflow">if</span>(<a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a> != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <span class="keyword">delete</span>[] <a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a>; </div><div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="keywordflow">if</span>(<a class="code" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a> != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <span class="keyword">delete</span>[] <a class="code" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a>; </div><div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  <span class="keywordflow">if</span>(<a class="code" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a> != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  <span class="keyword">delete</span>[] <a class="code" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a>;</div><div class="line"><a name="l00276"></a><span class="lineno"> 276</span> }</div><div class="line"><a name="l00277"></a><span class="lineno"> 277</span> </div><div class="line"><a name="l00278"></a><span class="lineno"> 278</span> </div><div class="line"><a name="l00279"></a><span class="lineno"> 279</span> </div><div class="line"><a name="l00280"></a><span class="lineno"> 280</span> <span class="comment">/*</span></div><div class="line"><a name="l00281"></a><span class="lineno"> 281</span> <span class="comment"> * ----------------------------------------------------------------------------------------------------------</span></div><div class="line"><a name="l00282"></a><span class="lineno"> 282</span> <span class="comment"> */</span></div><div class="line"><a name="l00283"></a><span class="lineno"> 283</span> </div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span> </div><div class="line"><a name="l00285"></a><span class="lineno"> 285</span> </div><div class="line"><a name="l00286"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_threshold_generator.html#a3abbcf1d810b6cad9400bd2552c3faf1"> 286</a></span> <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#a3abbcf1d810b6cad9400bd2552c3faf1">IsoThresholdGenerator::IsoThresholdGenerator</a>(<a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>&& iso, <span class="keywordtype">double</span> _threshold, <span class="keywordtype">bool</span> _absolute, <span class="keywordtype">int</span> tabSize, <span class="keywordtype">int</span> hashSize, <span class="keywordtype">bool</span> reorder_marginals)</div><div class="line"><a name="l00287"></a><span class="lineno"> 287</span> : <a class="code" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a>(<a class="code" href="namespacestd.html">std</a>::move(iso)),</div><div class="line"><a name="l00288"></a><span class="lineno"> 288</span> Lcutoff(_threshold <= 0.0 ? <a class="code" href="namespacestd.html">std</a>::numeric_limits<double>::lowest() : (_absolute ? log(_threshold) : log(_threshold) + modeLProb))</div><div class="line"><a name="l00289"></a><span class="lineno"> 289</span> {</div><div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  counter = <span class="keyword">new</span> <span class="keywordtype">int</span>[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  maxConfsLPSum = <span class="keyword">new</span> <span class="keywordtype">double</span>[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>-1];</div><div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  marginalResultsUnsorted = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a>*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00293"></a><span class="lineno"> 293</span> </div><div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  empty = <span class="keyword">false</span>;</div><div class="line"><a name="l00295"></a><span class="lineno"> 295</span> </div><div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii=0; ii<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; ii++)</div><div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  {</div><div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  counter[ii] = 0;</div><div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  marginalResultsUnsorted[ii] = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a>(std::move(*(<a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>[ii])),</div><div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  Lcutoff - <a class="code" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a> + <a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>[ii]-><a class="code" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a>(),</div><div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <span class="keyword">true</span>,</div><div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  tabSize,</div><div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  hashSize);</div><div class="line"><a name="l00304"></a><span class="lineno"> 304</span> </div><div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <span class="keywordflow">if</span>(!marginalResultsUnsorted[ii]->inRange(0))</div><div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  empty = <span class="keyword">true</span>;</div><div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  }</div><div class="line"><a name="l00308"></a><span class="lineno"> 308</span> </div><div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  <span class="keywordflow">if</span>(reorder_marginals)</div><div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  {</div><div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <a class="code" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">OrderMarginalsBySizeDecresing</a> comparator(marginalResultsUnsorted);</div><div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="keywordtype">int</span>* tmpMarginalOrder = <span class="keyword">new</span> <span class="keywordtype">int</span>[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00313"></a><span class="lineno"> 313</span> </div><div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii=0; ii<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; ii++)</div><div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  tmpMarginalOrder[ii] = ii;</div><div class="line"><a name="l00316"></a><span class="lineno"> 316</span> </div><div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  std::sort(tmpMarginalOrder, tmpMarginalOrder + <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>, comparator);</div><div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  marginalResults = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a>*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  </div><div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii=0; ii<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; ii++)</div><div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  marginalResults[ii] = marginalResultsUnsorted[tmpMarginalOrder[ii]];</div><div class="line"><a name="l00322"></a><span class="lineno"> 322</span> </div><div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  marginalOrder = <span class="keyword">new</span> <span class="keywordtype">int</span>[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii = 0; ii<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; ii++)</div><div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  marginalOrder[tmpMarginalOrder[ii]] = ii;</div><div class="line"><a name="l00326"></a><span class="lineno"> 326</span> </div><div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  <span class="keyword">delete</span>[] tmpMarginalOrder;</div><div class="line"><a name="l00328"></a><span class="lineno"> 328</span> </div><div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  }</div><div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  {</div><div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  marginalResults = marginalResultsUnsorted;</div><div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  marginalOrder = <span class="keyword">nullptr</span>;</div><div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  }</div><div class="line"><a name="l00335"></a><span class="lineno"> 335</span> </div><div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  lProbs_ptr_start = marginalResults[0]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">get_lProbs_ptr</a>();</div><div class="line"><a name="l00337"></a><span class="lineno"> 337</span> </div><div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  <span class="keywordflow">if</span>(<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a> > 1)</div><div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  maxConfsLPSum[0] = marginalResults[0]-><a class="code" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a>();</div><div class="line"><a name="l00340"></a><span class="lineno"> 340</span> </div><div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii=1; ii<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>-1; ii++)</div><div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  maxConfsLPSum[ii] = maxConfsLPSum[ii-1] + marginalResults[ii]-><a class="code" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a>();</div><div class="line"><a name="l00343"></a><span class="lineno"> 343</span> </div><div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  lProbs_ptr = lProbs_ptr_start;</div><div class="line"><a name="l00345"></a><span class="lineno"> 345</span> </div><div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  partialLProbs_second = <a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a>;</div><div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  partialLProbs_second++;</div><div class="line"><a name="l00348"></a><span class="lineno"> 348</span> </div><div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="keywordflow">if</span>(!empty)</div><div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  {</div><div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  recalc(<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>-1);</div><div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  counter[0]--;</div><div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  lProbs_ptr--;</div><div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  }</div><div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  {</div><div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#ac6aa2fff002a76b0beae1995f34ae5f6">terminate_search</a>();</div><div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  lcfmsv = std::numeric_limits<double>::infinity();</div><div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  }</div><div class="line"><a name="l00360"></a><span class="lineno"> 360</span> </div><div class="line"><a name="l00361"></a><span class="lineno"> 361</span> </div><div class="line"><a name="l00362"></a><span class="lineno"> 362</span> </div><div class="line"><a name="l00363"></a><span class="lineno"> 363</span> }</div><div class="line"><a name="l00364"></a><span class="lineno"> 364</span> </div><div class="line"><a name="l00365"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_threshold_generator.html#ac6aa2fff002a76b0beae1995f34ae5f6"> 365</a></span> <span class="keywordtype">void</span> <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#ac6aa2fff002a76b0beae1995f34ae5f6">IsoThresholdGenerator::terminate_search</a>()</div><div class="line"><a name="l00366"></a><span class="lineno"> 366</span> {</div><div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii=0; ii<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; ii++)</div><div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  {</div><div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  counter[ii] = marginalResults[ii]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">get_no_confs</a>()-1;</div><div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a>[ii] = -std::numeric_limits<double>::infinity();</div><div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  }</div><div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a>[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>] = -std::numeric_limits<double>::infinity();</div><div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  lProbs_ptr = lProbs_ptr_start + marginalResults[0]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">get_no_confs</a>()-1;</div><div class="line"><a name="l00374"></a><span class="lineno"> 374</span> }</div><div class="line"><a name="l00375"></a><span class="lineno"> 375</span> </div><div class="line"><a name="l00376"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_threshold_generator.html#ad29d8761174bca7b1846ddec03b33528"> 376</a></span> <span class="keywordtype">size_t</span> <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#ad29d8761174bca7b1846ddec03b33528">IsoThresholdGenerator::count_confs</a>()</div><div class="line"><a name="l00377"></a><span class="lineno"> 377</span> {</div><div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <span class="comment">// Smarter algorithm forthcoming in 2.0</span></div><div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="keywordtype">size_t</span> ret = 0;</div><div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="keywordflow">while</span>(<a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#a7164a6476b84665967c4a667a91d3f3e">advanceToNextConfiguration</a>())</div><div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  ret++;</div><div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#ab830ffa21469df45a513ff1dcaf5d9e7">reset</a>();</div><div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  <span class="keywordflow">return</span> ret;</div><div class="line"><a name="l00384"></a><span class="lineno"> 384</span> }</div><div class="line"><a name="l00385"></a><span class="lineno"> 385</span> </div><div class="line"><a name="l00386"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_threshold_generator.html#ab830ffa21469df45a513ff1dcaf5d9e7"> 386</a></span> <span class="keywordtype">void</span> <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#ab830ffa21469df45a513ff1dcaf5d9e7">IsoThresholdGenerator::reset</a>()</div><div class="line"><a name="l00387"></a><span class="lineno"> 387</span> {</div><div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  <span class="keywordflow">if</span>(empty)</div><div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  {</div><div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#ac6aa2fff002a76b0beae1995f34ae5f6">terminate_search</a>();</div><div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  <span class="keywordflow">return</span>;</div><div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  }</div><div class="line"><a name="l00393"></a><span class="lineno"> 393</span> </div><div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a>[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>] = 0.0;</div><div class="line"><a name="l00395"></a><span class="lineno"> 395</span> </div><div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  memset(counter, 0, <span class="keyword">sizeof</span>(<span class="keywordtype">int</span>)*<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>);</div><div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  recalc(<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>-1);</div><div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  counter[0]--;</div><div class="line"><a name="l00399"></a><span class="lineno"> 399</span> </div><div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  lProbs_ptr = lProbs_ptr_start - 1;</div><div class="line"><a name="l00401"></a><span class="lineno"> 401</span> }</div><div class="line"><a name="l00402"></a><span class="lineno"> 402</span> </div><div class="line"><a name="l00403"></a><span class="lineno"> 403</span> <span class="comment">/*</span></div><div class="line"><a name="l00404"></a><span class="lineno"> 404</span> <span class="comment"> * ------------------------------------------------------------------------------------------------------------------------</span></div><div class="line"><a name="l00405"></a><span class="lineno"> 405</span> <span class="comment"> */</span></div><div class="line"><a name="l00406"></a><span class="lineno"> 406</span> </div><div class="line"><a name="l00407"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_ordered_generator.html#afaf81ff3a758cd59629db323560e263d"> 407</a></span> <a class="code" href="class_iso_spec_1_1_iso_ordered_generator.html#afaf81ff3a758cd59629db323560e263d">IsoOrderedGenerator::IsoOrderedGenerator</a>(<a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>&& iso, <span class="keywordtype">int</span> _tabSize, <span class="keywordtype">int</span> _hashSize) :</div><div class="line"><a name="l00408"></a><span class="lineno"> 408</span> <a class="code" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a>(<a class="code" href="namespacestd.html">std</a>::move(iso), false), allocator(dimNumber, _tabSize)</div><div class="line"><a name="l00409"></a><span class="lineno"> 409</span> {</div><div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a> = &currentLProb;</div><div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a> = &currentMass;</div><div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a> = &currentProb;</div><div class="line"><a name="l00413"></a><span class="lineno"> 413</span> </div><div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  marginalResults = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_marginal_trek.html">MarginalTrek</a>*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00415"></a><span class="lineno"> 415</span> </div><div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; i++)</div><div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  marginalResults[i] = <span class="keyword">new</span> <a class="code" href="class_iso_spec_1_1_marginal_trek.html">MarginalTrek</a>(std::move(*(<a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>[i])), _tabSize, _hashSize);</div><div class="line"><a name="l00418"></a><span class="lineno"> 418</span> </div><div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  logProbs = <span class="keyword">new</span> <span class="keyword">const</span> vector<double>*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  masses = <span class="keyword">new</span> <span class="keyword">const</span> vector<double>*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  marginalConfs = <span class="keyword">new</span> <span class="keyword">const</span> vector<int*>*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00422"></a><span class="lineno"> 422</span> </div><div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; i++)</div><div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  {</div><div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  masses[i] = &marginalResults[i]->conf_masses();</div><div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  logProbs[i] = &marginalResults[i]->conf_lprobs();</div><div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  marginalConfs[i] = &marginalResults[i]->confs();</div><div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  }</div><div class="line"><a name="l00429"></a><span class="lineno"> 429</span> </div><div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  topConf = allocator.newConf();</div><div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  memset(</div><div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  reinterpret_cast<char*>(topConf) + <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>),</div><div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  0,</div><div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  <span class="keyword">sizeof</span>(<span class="keywordtype">int</span>)*<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></div><div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  );</div><div class="line"><a name="l00436"></a><span class="lineno"> 436</span> </div><div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  *(<span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(topConf)) =</div><div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  combinedSum(</div><div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  getConf(topConf),</div><div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  logProbs,</div><div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></div><div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  );</div><div class="line"><a name="l00443"></a><span class="lineno"> 443</span> </div><div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  pq.push(topConf);</div><div class="line"><a name="l00445"></a><span class="lineno"> 445</span> </div><div class="line"><a name="l00446"></a><span class="lineno"> 446</span> }</div><div class="line"><a name="l00447"></a><span class="lineno"> 447</span> </div><div class="line"><a name="l00448"></a><span class="lineno"> 448</span> </div><div class="line"><a name="l00449"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_ordered_generator.html#a030c118b9a6131130684cd2710371842"> 449</a></span> <a class="code" href="class_iso_spec_1_1_iso_ordered_generator.html#a030c118b9a6131130684cd2710371842">IsoOrderedGenerator::~IsoOrderedGenerator</a>()</div><div class="line"><a name="l00450"></a><span class="lineno"> 450</span> {</div><div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  dealloc_table<MarginalTrek*>(marginalResults, <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>);</div><div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  <span class="keyword">delete</span>[] logProbs;</div><div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="keyword">delete</span>[] masses;</div><div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  <span class="keyword">delete</span>[] marginalConfs;</div><div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a> = <span class="keyword">nullptr</span>;</div><div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a> = <span class="keyword">nullptr</span>;</div><div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a> = <span class="keyword">nullptr</span>;</div><div class="line"><a name="l00458"></a><span class="lineno"> 458</span> }</div><div class="line"><a name="l00459"></a><span class="lineno"> 459</span> </div><div class="line"><a name="l00460"></a><span class="lineno"> 460</span> </div><div class="line"><a name="l00461"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_ordered_generator.html#aa2438bb81fb1d68eda1637d67e9cb36d"> 461</a></span> <span class="keywordtype">bool</span> <a class="code" href="class_iso_spec_1_1_iso_ordered_generator.html#aa2438bb81fb1d68eda1637d67e9cb36d">IsoOrderedGenerator::advanceToNextConfiguration</a>()</div><div class="line"><a name="l00462"></a><span class="lineno"> 462</span> {</div><div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  <span class="keywordflow">if</span>(pq.size() < 1)</div><div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00465"></a><span class="lineno"> 465</span> </div><div class="line"><a name="l00466"></a><span class="lineno"> 466</span> </div><div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  topConf = pq.top();</div><div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  pq.pop();</div><div class="line"><a name="l00469"></a><span class="lineno"> 469</span> </div><div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  <span class="keywordtype">int</span>* topConfIsoCounts = getConf(topConf);</div><div class="line"><a name="l00471"></a><span class="lineno"> 471</span> </div><div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  currentLProb = *(<span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(topConf));</div><div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  currentMass = combinedSum( topConfIsoCounts, masses, <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a> );</div><div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  currentProb = exp(currentLProb);</div><div class="line"><a name="l00475"></a><span class="lineno"> 475</span> </div><div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  ccount = -1;</div><div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> j = 0; j < <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; ++j)</div><div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  {</div><div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  <span class="keywordflow">if</span>(marginalResults[j]->probeConfigurationIdx(topConfIsoCounts[j] + 1))</div><div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  {</div><div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  <span class="keywordflow">if</span>(ccount == -1)</div><div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  {</div><div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  topConfIsoCounts[j]++;</div><div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  *(<span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(topConf)) = combinedSum(topConfIsoCounts, logProbs, <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>);</div><div class="line"><a name="l00485"></a><span class="lineno"> 485</span>  pq.push(topConf);</div><div class="line"><a name="l00486"></a><span class="lineno"> 486</span>  topConfIsoCounts[j]--;</div><div class="line"><a name="l00487"></a><span class="lineno"> 487</span>  ccount = j;</div><div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  }</div><div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  {</div><div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  <span class="keywordtype">void</span>* acceptedCandidate = allocator.newConf();</div><div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  <span class="keywordtype">int</span>* acceptedCandidateIsoCounts = getConf(acceptedCandidate);</div><div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  memcpy(acceptedCandidateIsoCounts, topConfIsoCounts, <a class="code" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a>);</div><div class="line"><a name="l00494"></a><span class="lineno"> 494</span> </div><div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  acceptedCandidateIsoCounts[j]++;</div><div class="line"><a name="l00496"></a><span class="lineno"> 496</span> </div><div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  *(<span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(acceptedCandidate)) = combinedSum(acceptedCandidateIsoCounts, logProbs, <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>);</div><div class="line"><a name="l00498"></a><span class="lineno"> 498</span> </div><div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  pq.push(acceptedCandidate);</div><div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  }</div><div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  }</div><div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  <span class="keywordflow">if</span>(topConfIsoCounts[j] > 0)</div><div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  }</div><div class="line"><a name="l00505"></a><span class="lineno"> 505</span>  <span class="keywordflow">if</span>(ccount >=0)</div><div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  topConfIsoCounts[ccount]++;</div><div class="line"><a name="l00507"></a><span class="lineno"> 507</span> </div><div class="line"><a name="l00508"></a><span class="lineno"> 508</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00509"></a><span class="lineno"> 509</span> }</div><div class="line"><a name="l00510"></a><span class="lineno"> 510</span> </div><div class="line"><a name="l00511"></a><span class="lineno"> 511</span> </div><div class="line"><a name="l00512"></a><span class="lineno"> 512</span> </div><div class="line"><a name="l00513"></a><span class="lineno"> 513</span> <span class="comment">/*</span></div><div class="line"><a name="l00514"></a><span class="lineno"> 514</span> <span class="comment"> * ---------------------------------------------------------------------------------------------------</span></div><div class="line"><a name="l00515"></a><span class="lineno"> 515</span> <span class="comment"> */</span></div><div class="line"><a name="l00516"></a><span class="lineno"> 516</span> </div><div class="line"><a name="l00517"></a><span class="lineno"> 517</span> </div><div class="line"><a name="l00518"></a><span class="lineno"> 518</span> </div><div class="line"><a name="l00519"></a><span class="lineno"> 519</span> </div><div class="line"><a name="l00520"></a><span class="lineno"> 520</span> <span class="preprocessor">#if !ISOSPEC_BUILDING_R</span></div><div class="line"><a name="l00521"></a><span class="lineno"> 521</span> </div><div class="line"><a name="l00522"></a><span class="lineno"> 522</span> <span class="keywordtype">void</span> printConfigurations(</div><div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  <span class="keyword">const</span> std::tuple<double*,double*,int*,int>& results,</div><div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  <span class="keywordtype">int</span> dimNumber,</div><div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  <span class="keywordtype">int</span>* isotopeNumbers</div><div class="line"><a name="l00526"></a><span class="lineno"> 526</span> ){</div><div class="line"><a name="l00527"></a><span class="lineno"> 527</span>  <span class="keywordtype">int</span> m = 0;</div><div class="line"><a name="l00528"></a><span class="lineno"> 528</span> </div><div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=0; i<std::get<3>(results); i++){</div><div class="line"><a name="l00530"></a><span class="lineno"> 530</span> </div><div class="line"><a name="l00531"></a><span class="lineno"> 531</span>  std::cout << <span class="stringliteral">"Mass = "</span> << std::get<0>(results)[i] <<</div><div class="line"><a name="l00532"></a><span class="lineno"> 532</span>  <span class="stringliteral">"\tand log-prob = "</span> << std::get<1>(results)[i] <<</div><div class="line"><a name="l00533"></a><span class="lineno"> 533</span>  <span class="stringliteral">"\tand prob = "</span> << exp(std::get<1>(results)[i]) <<</div><div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  <span class="stringliteral">"\tand configuration =\t"</span>;</div><div class="line"><a name="l00535"></a><span class="lineno"> 535</span> </div><div class="line"><a name="l00536"></a><span class="lineno"> 536</span> </div><div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> j=0; j<dimNumber; j++){</div><div class="line"><a name="l00538"></a><span class="lineno"> 538</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> k=0; k<isotopeNumbers[j]; k++ )</div><div class="line"><a name="l00539"></a><span class="lineno"> 539</span>  {</div><div class="line"><a name="l00540"></a><span class="lineno"> 540</span>  std::cout << std::get<2>(results)[m] << <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  m++;</div><div class="line"><a name="l00542"></a><span class="lineno"> 542</span>  }</div><div class="line"><a name="l00543"></a><span class="lineno"> 543</span>  std::cout << <span class="charliteral">'\t'</span>;</div><div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  }</div><div class="line"><a name="l00545"></a><span class="lineno"> 545</span> </div><div class="line"><a name="l00546"></a><span class="lineno"> 546</span> </div><div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  std::cout << std::endl;</div><div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  }</div><div class="line"><a name="l00549"></a><span class="lineno"> 549</span> }</div><div class="line"><a name="l00550"></a><span class="lineno"> 550</span> </div><div class="line"><a name="l00551"></a><span class="lineno"> 551</span> <span class="preprocessor">#endif </span><span class="comment">/* !ISOSPEC_BUILDING_R */</span><span class="preprocessor"></span></div><div class="line"><a name="l00552"></a><span class="lineno"> 552</span> </div><div class="line"><a name="l00553"></a><span class="lineno"> 553</span> </div><div class="line"><a name="l00554"></a><span class="lineno"> 554</span> </div><div class="line"><a name="l00555"></a><span class="lineno"> 555</span> IsoLayeredGenerator::IsoLayeredGenerator( Iso&& iso,</div><div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  <span class="keywordtype">double</span> _targetCoverage,</div><div class="line"><a name="l00557"></a><span class="lineno"> 557</span>  <span class="keywordtype">double</span> _percentageToExpand,</div><div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  <span class="keywordtype">int</span> _tabSize,</div><div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  <span class="keywordtype">int</span> _hashSize,</div><div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  <span class="keywordtype">bool</span> trim</div><div class="line"><a name="l00561"></a><span class="lineno"> 561</span> ) : IsoGenerator(<a class="code" href="namespacestd.html">std</a>::move(iso)),</div><div class="line"><a name="l00562"></a><span class="lineno"> 562</span> allocator(dimNumber, _tabSize),</div><div class="line"><a name="l00563"></a><span class="lineno"> 563</span> candidate(new int[dimNumber]),</div><div class="line"><a name="l00564"></a><span class="lineno"> 564</span> targetCoverage(_targetCoverage),</div><div class="line"><a name="l00565"></a><span class="lineno"> 565</span> percentageToExpand(_percentageToExpand),</div><div class="line"><a name="l00566"></a><span class="lineno"> 566</span> do_trim(trim),</div><div class="line"><a name="l00567"></a><span class="lineno"> 567</span> layers(0),</div><div class="line"><a name="l00568"></a><span class="lineno"> 568</span> generator_position(-1)</div><div class="line"><a name="l00569"></a><span class="lineno"> 569</span> {</div><div class="line"><a name="l00570"></a><span class="lineno"> 570</span>  marginalResults = <span class="keyword">new</span> MarginalTrek*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00571"></a><span class="lineno"> 571</span> </div><div class="line"><a name="l00572"></a><span class="lineno"> 572</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; i++)</div><div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  marginalResults[i] = <span class="keyword">new</span> MarginalTrek(std::move(*(<a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>[i])), _tabSize, _hashSize);</div><div class="line"><a name="l00574"></a><span class="lineno"> 574</span> </div><div class="line"><a name="l00575"></a><span class="lineno"> 575</span>  logProbs = <span class="keyword">new</span> <span class="keyword">const</span> vector<double>*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  masses = <span class="keyword">new</span> <span class="keyword">const</span> vector<double>*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  marginalConfs = <span class="keyword">new</span> <span class="keyword">const</span> vector<int*>*[<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>];</div><div class="line"><a name="l00578"></a><span class="lineno"> 578</span> </div><div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i<<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; i++)</div><div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  {</div><div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  masses[i] = &marginalResults[i]->conf_masses();</div><div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  logProbs[i] = &marginalResults[i]->conf_lprobs();</div><div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  marginalConfs[i] = &marginalResults[i]->confs();</div><div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  }</div><div class="line"><a name="l00585"></a><span class="lineno"> 585</span> </div><div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  <span class="keywordtype">void</span>* topConf = allocator.newConf();</div><div class="line"><a name="l00587"></a><span class="lineno"> 587</span>  memset(reinterpret_cast<char*>(topConf) + <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>), 0, <span class="keyword">sizeof</span>(<span class="keywordtype">int</span>)*<a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>);</div><div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  *(<span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(topConf)) = combinedSum(getConf(topConf), logProbs, <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>);</div><div class="line"><a name="l00589"></a><span class="lineno"> 589</span> </div><div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  current = <span class="keyword">new</span> std::vector<void*>();</div><div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  next = <span class="keyword">new</span> std::vector<void*>();</div><div class="line"><a name="l00592"></a><span class="lineno"> 592</span> </div><div class="line"><a name="l00593"></a><span class="lineno"> 593</span>  current->push_back(topConf);</div><div class="line"><a name="l00594"></a><span class="lineno"> 594</span> </div><div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  lprobThr = (*<span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(topConf));</div><div class="line"><a name="l00596"></a><span class="lineno"> 596</span> </div><div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  <span class="keywordflow">if</span>(targetCoverage > 0.0)</div><div class="line"><a name="l00598"></a><span class="lineno"> 598</span>  <span class="keywordflow">while</span>(advanceToNextLayer()) {};</div><div class="line"><a name="l00599"></a><span class="lineno"> 599</span> }</div><div class="line"><a name="l00600"></a><span class="lineno"> 600</span> </div><div class="line"><a name="l00601"></a><span class="lineno"> 601</span> </div><div class="line"><a name="l00602"></a><span class="lineno"> 602</span> IsoLayeredGenerator::~IsoLayeredGenerator()</div><div class="line"><a name="l00603"></a><span class="lineno"> 603</span> {</div><div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  <span class="keywordflow">if</span>(current != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00605"></a><span class="lineno"> 605</span>  <span class="keyword">delete</span> current;</div><div class="line"><a name="l00606"></a><span class="lineno"> 606</span>  <span class="keywordflow">if</span>(next != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  <span class="keyword">delete</span> next;</div><div class="line"><a name="l00608"></a><span class="lineno"> 608</span>  <span class="keyword">delete</span>[] logProbs;</div><div class="line"><a name="l00609"></a><span class="lineno"> 609</span>  <span class="keyword">delete</span>[] masses;</div><div class="line"><a name="l00610"></a><span class="lineno"> 610</span>  <span class="keyword">delete</span>[] marginalConfs;</div><div class="line"><a name="l00611"></a><span class="lineno"> 611</span>  <span class="keyword">delete</span>[] candidate;</div><div class="line"><a name="l00612"></a><span class="lineno"> 612</span>  dealloc_table(marginalResults, <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>);</div><div class="line"><a name="l00613"></a><span class="lineno"> 613</span> }</div><div class="line"><a name="l00614"></a><span class="lineno"> 614</span> </div><div class="line"><a name="l00615"></a><span class="lineno"> 615</span> <span class="keywordtype">bool</span> IsoLayeredGenerator::advanceToNextLayer()</div><div class="line"><a name="l00616"></a><span class="lineno"> 616</span> {</div><div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  layers += 1;</div><div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  <span class="keywordtype">double</span> maxFringeLprob = -std::numeric_limits<double>::infinity();</div><div class="line"><a name="l00619"></a><span class="lineno"> 619</span> </div><div class="line"><a name="l00620"></a><span class="lineno"> 620</span>  <span class="keywordflow">if</span>(current == <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00621"></a><span class="lineno"> 621</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  <span class="keywordtype">int</span> accepted_in_this_layer = 0;</div><div class="line"><a name="l00623"></a><span class="lineno"> 623</span>  Summator prob_in_this_layer(totalProb);</div><div class="line"><a name="l00624"></a><span class="lineno"> 624</span> </div><div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  <span class="keywordtype">void</span>* topConf;</div><div class="line"><a name="l00626"></a><span class="lineno"> 626</span> </div><div class="line"><a name="l00627"></a><span class="lineno"> 627</span>  <span class="keywordflow">while</span>(current->size() > 0)</div><div class="line"><a name="l00628"></a><span class="lineno"> 628</span>  {</div><div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  topConf = current->back();</div><div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  current->pop_back();</div><div class="line"><a name="l00631"></a><span class="lineno"> 631</span> </div><div class="line"><a name="l00632"></a><span class="lineno"> 632</span>  <span class="keywordtype">double</span> top_lprob = getLProb(topConf);</div><div class="line"><a name="l00633"></a><span class="lineno"> 633</span> </div><div class="line"><a name="l00634"></a><span class="lineno"> 634</span>  <span class="keywordflow">if</span>(top_lprob >= lprobThr)</div><div class="line"><a name="l00635"></a><span class="lineno"> 635</span>  {</div><div class="line"><a name="l00636"></a><span class="lineno"> 636</span>  newaccepted.push_back(topConf);</div><div class="line"><a name="l00637"></a><span class="lineno"> 637</span>  accepted_in_this_layer++;</div><div class="line"><a name="l00638"></a><span class="lineno"> 638</span>  prob_in_this_layer.add(exp(top_lprob));</div><div class="line"><a name="l00639"></a><span class="lineno"> 639</span>  }</div><div class="line"><a name="l00640"></a><span class="lineno"> 640</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00641"></a><span class="lineno"> 641</span>  {</div><div class="line"><a name="l00642"></a><span class="lineno"> 642</span>  next->push_back(topConf);</div><div class="line"><a name="l00643"></a><span class="lineno"> 643</span>  <span class="keywordflow">continue</span>;</div><div class="line"><a name="l00644"></a><span class="lineno"> 644</span>  }</div><div class="line"><a name="l00645"></a><span class="lineno"> 645</span> </div><div class="line"><a name="l00646"></a><span class="lineno"> 646</span>  <span class="keywordtype">int</span>* topConfIsoCounts = getConf(topConf);</div><div class="line"><a name="l00647"></a><span class="lineno"> 647</span> </div><div class="line"><a name="l00648"></a><span class="lineno"> 648</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> j = 0; j < <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; ++j)</div><div class="line"><a name="l00649"></a><span class="lineno"> 649</span>  {</div><div class="line"><a name="l00650"></a><span class="lineno"> 650</span>  <span class="comment">// candidate cannot refer to a position that is</span></div><div class="line"><a name="l00651"></a><span class="lineno"> 651</span>  <span class="comment">// out of range of the stored marginal distribution.</span></div><div class="line"><a name="l00652"></a><span class="lineno"> 652</span>  <span class="keywordflow">if</span>(marginalResults[j]->probeConfigurationIdx(topConfIsoCounts[j] + 1))</div><div class="line"><a name="l00653"></a><span class="lineno"> 653</span>  {</div><div class="line"><a name="l00654"></a><span class="lineno"> 654</span>  memcpy(candidate, topConfIsoCounts, <a class="code" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a>);</div><div class="line"><a name="l00655"></a><span class="lineno"> 655</span>  candidate[j]++;</div><div class="line"><a name="l00656"></a><span class="lineno"> 656</span> </div><div class="line"><a name="l00657"></a><span class="lineno"> 657</span>  <span class="keywordtype">void</span>* acceptedCandidate = allocator.newConf();</div><div class="line"><a name="l00658"></a><span class="lineno"> 658</span>  <span class="keywordtype">int</span>* acceptedCandidateIsoCounts = getConf(acceptedCandidate);</div><div class="line"><a name="l00659"></a><span class="lineno"> 659</span>  memcpy( acceptedCandidateIsoCounts, candidate, <a class="code" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a>);</div><div class="line"><a name="l00660"></a><span class="lineno"> 660</span> </div><div class="line"><a name="l00661"></a><span class="lineno"> 661</span>  <span class="keywordtype">double</span> newConfProb = combinedSum(</div><div class="line"><a name="l00662"></a><span class="lineno"> 662</span>  candidate,</div><div class="line"><a name="l00663"></a><span class="lineno"> 663</span>  logProbs,</div><div class="line"><a name="l00664"></a><span class="lineno"> 664</span>  <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a></div><div class="line"><a name="l00665"></a><span class="lineno"> 665</span>  );</div><div class="line"><a name="l00666"></a><span class="lineno"> 666</span> </div><div class="line"><a name="l00667"></a><span class="lineno"> 667</span> </div><div class="line"><a name="l00668"></a><span class="lineno"> 668</span> </div><div class="line"><a name="l00669"></a><span class="lineno"> 669</span>  *(<span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(acceptedCandidate)) = newConfProb;</div><div class="line"><a name="l00670"></a><span class="lineno"> 670</span> </div><div class="line"><a name="l00671"></a><span class="lineno"> 671</span>  <span class="keywordflow">if</span>(newConfProb >= lprobThr)</div><div class="line"><a name="l00672"></a><span class="lineno"> 672</span>  current->push_back(acceptedCandidate);</div><div class="line"><a name="l00673"></a><span class="lineno"> 673</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00674"></a><span class="lineno"> 674</span>  {</div><div class="line"><a name="l00675"></a><span class="lineno"> 675</span>  next->push_back(acceptedCandidate);</div><div class="line"><a name="l00676"></a><span class="lineno"> 676</span>  <span class="keywordflow">if</span>(newConfProb > maxFringeLprob)</div><div class="line"><a name="l00677"></a><span class="lineno"> 677</span>  maxFringeLprob = top_lprob;</div><div class="line"><a name="l00678"></a><span class="lineno"> 678</span>  }</div><div class="line"><a name="l00679"></a><span class="lineno"> 679</span>  }</div><div class="line"><a name="l00680"></a><span class="lineno"> 680</span>  <span class="keywordflow">if</span>(topConfIsoCounts[j] > 0)</div><div class="line"><a name="l00681"></a><span class="lineno"> 681</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00682"></a><span class="lineno"> 682</span>  }</div><div class="line"><a name="l00683"></a><span class="lineno"> 683</span>  }</div><div class="line"><a name="l00684"></a><span class="lineno"> 684</span> </div><div class="line"><a name="l00685"></a><span class="lineno"> 685</span>  <span class="keywordflow">if</span>(next == <span class="keyword">nullptr</span> || next->size() < 1)</div><div class="line"><a name="l00686"></a><span class="lineno"> 686</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00687"></a><span class="lineno"> 687</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00688"></a><span class="lineno"> 688</span>  {</div><div class="line"><a name="l00689"></a><span class="lineno"> 689</span>  <span class="keywordflow">if</span>(prob_in_this_layer.get() < targetCoverage)</div><div class="line"><a name="l00690"></a><span class="lineno"> 690</span>  {</div><div class="line"><a name="l00691"></a><span class="lineno"> 691</span>  std::vector<void*>* nnew = current;</div><div class="line"><a name="l00692"></a><span class="lineno"> 692</span>  nnew->clear();</div><div class="line"><a name="l00693"></a><span class="lineno"> 693</span>  current = next;</div><div class="line"><a name="l00694"></a><span class="lineno"> 694</span>  next = nnew;</div><div class="line"><a name="l00695"></a><span class="lineno"> 695</span>  <span class="keywordtype">int</span> howmany = floor(current->size()*percentageToExpand);</div><div class="line"><a name="l00696"></a><span class="lineno"> 696</span>  lprobThr = getLProb(<a class="code" href="namespace_iso_spec.html#acbcd0253dcdabd90c53d008c7e12b95f">quickselect</a>(current->data(), howmany, 0, current->size()));</div><div class="line"><a name="l00697"></a><span class="lineno"> 697</span>  totalProb = prob_in_this_layer;</div><div class="line"><a name="l00698"></a><span class="lineno"> 698</span>  }</div><div class="line"><a name="l00699"></a><span class="lineno"> 699</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00700"></a><span class="lineno"> 700</span>  {</div><div class="line"><a name="l00701"></a><span class="lineno"> 701</span>  <span class="keyword">delete</span> next;</div><div class="line"><a name="l00702"></a><span class="lineno"> 702</span>  next = <span class="keyword">nullptr</span>;</div><div class="line"><a name="l00703"></a><span class="lineno"> 703</span>  <span class="keyword">delete</span> current;</div><div class="line"><a name="l00704"></a><span class="lineno"> 704</span>  current = <span class="keyword">nullptr</span>;</div><div class="line"><a name="l00705"></a><span class="lineno"> 705</span>  <span class="keywordtype">int</span> start = 0;</div><div class="line"><a name="l00706"></a><span class="lineno"> 706</span>  <span class="keywordtype">int</span> end = accepted_in_this_layer - 1;</div><div class="line"><a name="l00707"></a><span class="lineno"> 707</span>  <span class="keywordtype">void</span>* swapspace;</div><div class="line"><a name="l00708"></a><span class="lineno"> 708</span> </div><div class="line"><a name="l00709"></a><span class="lineno"> 709</span>  <span class="keywordflow">if</span>(do_trim)</div><div class="line"><a name="l00710"></a><span class="lineno"> 710</span>  {</div><div class="line"><a name="l00711"></a><span class="lineno"> 711</span>  <span class="keywordtype">void</span>** lastLayer = &(newaccepted.data()[newaccepted.size()-accepted_in_this_layer]);</div><div class="line"><a name="l00712"></a><span class="lineno"> 712</span> </div><div class="line"><a name="l00713"></a><span class="lineno"> 713</span>  Summator qsprob(totalProb);</div><div class="line"><a name="l00714"></a><span class="lineno"> 714</span>  <span class="keywordflow">while</span>(totalProb.get() < targetCoverage)</div><div class="line"><a name="l00715"></a><span class="lineno"> 715</span>  {</div><div class="line"><a name="l00716"></a><span class="lineno"> 716</span>  <span class="keywordflow">if</span>(start == end)</div><div class="line"><a name="l00717"></a><span class="lineno"> 717</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00718"></a><span class="lineno"> 718</span> </div><div class="line"><a name="l00719"></a><span class="lineno"> 719</span>  <span class="comment">// Partition part</span></div><div class="line"><a name="l00720"></a><span class="lineno"> 720</span> </div><div class="line"><a name="l00721"></a><span class="lineno"> 721</span>  <span class="keywordtype">int</span> len = end - start;</div><div class="line"><a name="l00722"></a><span class="lineno"> 722</span> <span class="preprocessor">#ifdef BUILDING_R</span></div><div class="line"><a name="l00723"></a><span class="lineno"> 723</span>  <span class="keywordtype">int</span> pivot = len/2 + start; <span class="comment">// We're very definitely NOT switching to R to use a RNG, and if R sees us use C RNG it complains...</span></div><div class="line"><a name="l00724"></a><span class="lineno"> 724</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00725"></a><span class="lineno"> 725</span>  <span class="keywordtype">int</span> pivot = rand() % len + start;</div><div class="line"><a name="l00726"></a><span class="lineno"> 726</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00727"></a><span class="lineno"> 727</span>  <span class="keywordtype">void</span>* pval = lastLayer[pivot];</div><div class="line"><a name="l00728"></a><span class="lineno"> 728</span>  <span class="keywordtype">double</span> pprob = getLProb(pval);</div><div class="line"><a name="l00729"></a><span class="lineno"> 729</span>  mswap(lastLayer[pivot], lastLayer[end-1]);</div><div class="line"><a name="l00730"></a><span class="lineno"> 730</span>  <span class="keywordtype">int</span> loweridx = start;</div><div class="line"><a name="l00731"></a><span class="lineno"> 731</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=start; i<end-1; i++)</div><div class="line"><a name="l00732"></a><span class="lineno"> 732</span>  {</div><div class="line"><a name="l00733"></a><span class="lineno"> 733</span>  <span class="keywordflow">if</span>(getLProb(lastLayer[i]) > pprob)</div><div class="line"><a name="l00734"></a><span class="lineno"> 734</span>  {</div><div class="line"><a name="l00735"></a><span class="lineno"> 735</span>  mswap(lastLayer[i], lastLayer[loweridx]);</div><div class="line"><a name="l00736"></a><span class="lineno"> 736</span>  loweridx++;</div><div class="line"><a name="l00737"></a><span class="lineno"> 737</span>  }</div><div class="line"><a name="l00738"></a><span class="lineno"> 738</span>  }</div><div class="line"><a name="l00739"></a><span class="lineno"> 739</span>  mswap(lastLayer[end-1], lastLayer[loweridx]);</div><div class="line"><a name="l00740"></a><span class="lineno"> 740</span> </div><div class="line"><a name="l00741"></a><span class="lineno"> 741</span>  <span class="comment">// Selection part</span></div><div class="line"><a name="l00742"></a><span class="lineno"> 742</span> </div><div class="line"><a name="l00743"></a><span class="lineno"> 743</span>  Summator leftProb(qsprob);</div><div class="line"><a name="l00744"></a><span class="lineno"> 744</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=start; i<=loweridx; i++)</div><div class="line"><a name="l00745"></a><span class="lineno"> 745</span>  {</div><div class="line"><a name="l00746"></a><span class="lineno"> 746</span>  leftProb.add(exp(getLProb(lastLayer[i])));</div><div class="line"><a name="l00747"></a><span class="lineno"> 747</span>  }</div><div class="line"><a name="l00748"></a><span class="lineno"> 748</span>  <span class="keywordflow">if</span>(leftProb.get() < targetCoverage)</div><div class="line"><a name="l00749"></a><span class="lineno"> 749</span>  {</div><div class="line"><a name="l00750"></a><span class="lineno"> 750</span>  start = loweridx+1;</div><div class="line"><a name="l00751"></a><span class="lineno"> 751</span>  qsprob = leftProb;</div><div class="line"><a name="l00752"></a><span class="lineno"> 752</span>  }</div><div class="line"><a name="l00753"></a><span class="lineno"> 753</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00754"></a><span class="lineno"> 754</span>  end = loweridx;</div><div class="line"><a name="l00755"></a><span class="lineno"> 755</span>  }</div><div class="line"><a name="l00756"></a><span class="lineno"> 756</span>  <span class="keywordtype">int</span> accend = newaccepted.size()-accepted_in_this_layer+start+1;</div><div class="line"><a name="l00757"></a><span class="lineno"> 757</span> </div><div class="line"><a name="l00758"></a><span class="lineno"> 758</span>  totalProb = qsprob;</div><div class="line"><a name="l00759"></a><span class="lineno"> 759</span>  newaccepted.resize(accend);</div><div class="line"><a name="l00760"></a><span class="lineno"> 760</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00761"></a><span class="lineno"> 761</span>  }</div><div class="line"><a name="l00762"></a><span class="lineno"> 762</span>  <span class="keywordflow">else</span> <span class="comment">// No trimming</span></div><div class="line"><a name="l00763"></a><span class="lineno"> 763</span>  {</div><div class="line"><a name="l00764"></a><span class="lineno"> 764</span>  totalProb = prob_in_this_layer;</div><div class="line"><a name="l00765"></a><span class="lineno"> 765</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00766"></a><span class="lineno"> 766</span>  }</div><div class="line"><a name="l00767"></a><span class="lineno"> 767</span>  }</div><div class="line"><a name="l00768"></a><span class="lineno"> 768</span>  }</div><div class="line"><a name="l00769"></a><span class="lineno"> 769</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00770"></a><span class="lineno"> 770</span> </div><div class="line"><a name="l00771"></a><span class="lineno"> 771</span> }</div><div class="line"><a name="l00772"></a><span class="lineno"> 772</span> </div><div class="line"><a name="l00773"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_layered_generator.html#abce0871ac279fd54a0344ceb80126b66"> 773</a></span> <span class="keywordtype">bool</span> <a class="code" href="class_iso_spec_1_1_iso_layered_generator.html#abce0871ac279fd54a0344ceb80126b66">IsoLayeredGenerator::advanceToNextConfiguration</a>()</div><div class="line"><a name="l00774"></a><span class="lineno"> 774</span> {</div><div class="line"><a name="l00775"></a><span class="lineno"> 775</span>  generator_position++;</div><div class="line"><a name="l00776"></a><span class="lineno"> 776</span>  <span class="keywordflow">if</span>(generator_position < newaccepted.size())</div><div class="line"><a name="l00777"></a><span class="lineno"> 777</span>  {</div><div class="line"><a name="l00778"></a><span class="lineno"> 778</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a>[0] = getLProb(newaccepted[generator_position]);</div><div class="line"><a name="l00779"></a><span class="lineno"> 779</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a>[0] = combinedSum(getConf(newaccepted[generator_position]), masses, <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>);</div><div class="line"><a name="l00780"></a><span class="lineno"> 780</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a>[0] = exp(<a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a>[0]);</div><div class="line"><a name="l00781"></a><span class="lineno"> 781</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00782"></a><span class="lineno"> 782</span>  }</div><div class="line"><a name="l00783"></a><span class="lineno"> 783</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00784"></a><span class="lineno"> 784</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00785"></a><span class="lineno"> 785</span> }</div><div class="line"><a name="l00786"></a><span class="lineno"> 786</span> </div><div class="line"><a name="l00787"></a><span class="lineno"> 787</span> </div><div class="line"><a name="l00788"></a><span class="lineno"> 788</span> </div><div class="line"><a name="l00789"></a><span class="lineno"> 789</span> </div><div class="line"><a name="l00790"></a><span class="lineno"> 790</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00791"></a><span class="lineno"> 791</span> </div><div class="ttc" id="class_iso_spec_1_1_iso_html_a89ed144bf2495fa25840aca90a31b425"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">IsoSpec::Iso::confSize</a></div><div class="ttdeci">unsigned int confSize</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00070">isoSpec++.h:70</a></div></div> | |
| 80 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></div><div class="ttdoc">The generator of isotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00129">isoSpec++.h:129</a></div></div> | |
| 81 | <div class="ttc" id="class_iso_spec_1_1_iso_html"><div class="ttname"><a href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></div><div class="ttdoc">The Iso class for the calculation of the isotopic distribution. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00052">isoSpec++.h:52</a></div></div> | |
| 82 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html_ad29d8761174bca7b1846ddec03b33528"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html#ad29d8761174bca7b1846ddec03b33528">IsoSpec::IsoThresholdGenerator::count_confs</a></div><div class="ttdeci">size_t count_confs()</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00376">isoSpec++.cpp:376</a></div></div> | |
| 83 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a90245f9bc318f12720c134f61bbe0db0"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">IsoSpec::Iso::dimNumber</a></div><div class="ttdeci">int dimNumber</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00067">isoSpec++.h:67</a></div></div> | |
| 84 | <div class="ttc" id="class_iso_spec_1_1_marginal_html"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></div><div class="ttdoc">The marginal distribution class (a subisotopologue). </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00045">marginalTrek++.h:45</a></div></div> | |
| 85 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a7541599fbc29dd374bb60e5eb8fc047d"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a7541599fbc29dd374bb60e5eb8fc047d">IsoSpec::Iso::getLightestPeakMass</a></div><div class="ttdeci">double getLightestPeakMass() const</div><div class="ttdoc">Get the mass of the lightest peak in the isotopic distribution. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00128">isoSpec++.cpp:128</a></div></div> | |
| 86 | <div class="ttc" id="namespacestd_html"><div class="ttname"><a href="namespacestd.html">std</a></div></div> | |
| 87 | <div class="ttc" id="class_iso_spec_1_1_order_marginals_by_size_decresing_html"><div class="ttname"><a href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">IsoSpec::OrderMarginalsBySizeDecresing</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00128">operators.h:128</a></div></div> | |
| 88 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html_a3abbcf1d810b6cad9400bd2552c3faf1"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html#a3abbcf1d810b6cad9400bd2552c3faf1">IsoSpec::IsoThresholdGenerator::IsoThresholdGenerator</a></div><div class="ttdeci">IsoThresholdGenerator(Iso &&iso, double _threshold, bool _absolute=true, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true)</div><div class="ttdoc">The move-constructor. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00286">isoSpec++.cpp:286</a></div></div> | |
| 89 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html_a7164a6476b84665967c4a667a91d3f3e"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html#a7164a6476b84665967c4a667a91d3f3e">IsoSpec::IsoThresholdGenerator::advanceToNextConfiguration</a></div><div class="ttdeci">ISOSPEC_FORCE_INLINE bool advanceToNextConfiguration() override final</div><div class="ttdoc">Advance to the next, not yet visited, most probable isotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00296">isoSpec++.h:296</a></div></div> | |
| 90 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_a28442c8072a2e85faf5ff04f5feffd76"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#a28442c8072a2e85faf5ff04f5feffd76">IsoSpec::IsoGenerator::~IsoGenerator</a></div><div class="ttdeci">virtual ~IsoGenerator()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00268">isoSpec++.cpp:268</a></div></div> | |
| 91 | <div class="ttc" id="class_iso_spec_1_1_iso_ordered_generator_html_a030c118b9a6131130684cd2710371842"><div class="ttname"><a href="class_iso_spec_1_1_iso_ordered_generator.html#a030c118b9a6131130684cd2710371842">IsoSpec::IsoOrderedGenerator::~IsoOrderedGenerator</a></div><div class="ttdeci">virtual ~IsoOrderedGenerator()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00449">isoSpec++.cpp:449</a></div></div> | |
| 92 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a1ede5e34e5bbbb22ae89b362ce2c6faf"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a1ede5e34e5bbbb22ae89b362ce2c6faf">IsoSpec::Iso::getHeaviestPeakMass</a></div><div class="ttdeci">double getHeaviestPeakMass() const</div><div class="ttdoc">Get the mass of the heaviest peak in the isotopic distribution. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00136">isoSpec++.cpp:136</a></div></div> | |
| 93 | <div class="ttc" id="class_iso_spec_1_1_iso_ordered_generator_html_afaf81ff3a758cd59629db323560e263d"><div class="ttname"><a href="class_iso_spec_1_1_iso_ordered_generator.html#afaf81ff3a758cd59629db323560e263d">IsoSpec::IsoOrderedGenerator::IsoOrderedGenerator</a></div><div class="ttdeci">IsoOrderedGenerator(Iso &&iso, int _tabSize=1000, int _hashSize=1000)</div><div class="ttdoc">The move-contstructor. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00407">isoSpec++.cpp:407</a></div></div> | |
| 94 | <div class="ttc" id="class_iso_spec_1_1_iso_layered_generator_html_abce0871ac279fd54a0344ceb80126b66"><div class="ttname"><a href="class_iso_spec_1_1_iso_layered_generator.html#abce0871ac279fd54a0344ceb80126b66">IsoSpec::IsoLayeredGenerator::advanceToNextConfiguration</a></div><div class="ttdeci">bool advanceToNextConfiguration() override final</div><div class="ttdoc">Advance to the next, not yet visited, most probable isotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00773">isoSpec++.cpp:773</a></div></div> | |
| 95 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a9035d076cec8f937d971e3fd972aa83f"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">IsoSpec::Iso::getModeLProb</a></div><div class="ttdeci">double getModeLProb() const</div><div class="ttdoc">Get the log-probability of the mode-configuration (if there are many modes, they share this value)...</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00115">isoSpec++.h:115</a></div></div> | |
| 96 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html_ab830ffa21469df45a513ff1dcaf5d9e7"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html#ab830ffa21469df45a513ff1dcaf5d9e7">IsoSpec::IsoThresholdGenerator::reset</a></div><div class="ttdeci">void reset()</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00386">isoSpec++.cpp:386</a></div></div> | |
| 97 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a8cf8f90338bfc3e5117f5b491f7b523f"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a8cf8f90338bfc3e5117f5b491f7b523f">IsoSpec::Iso::~Iso</a></div><div class="ttdeci">virtual ~Iso()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00116">isoSpec++.cpp:116</a></div></div> | |
| 98 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_af5d01500c7efb8cba57399ba11fc7124"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">IsoSpec::PrecalculatedMarginal::get_lProbs_ptr</a></div><div class="ttdeci">const double * get_lProbs_ptr() const</div><div class="ttdoc">Get the table of the log-probabilities of subisotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00274">marginalTrek++.h:274</a></div></div> | |
| 99 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a0dbf1ec53eac9953a354c11e1b0803f9"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">IsoSpec::PrecalculatedMarginal::get_no_confs</a></div><div class="ttdeci">unsigned int get_no_confs() const</div><div class="ttdoc">Get the number of precomputed subisotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00294">marginalTrek++.h:294</a></div></div> | |
| 100 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_ac9408957145d2aa63af32f6647c8ea49"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">IsoSpec::Marginal::getModeLProb</a></div><div class="ttdeci">double getModeLProb() const</div><div class="ttdoc">Get the log-probability of the mode subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00110">marginalTrek++.h:110</a></div></div> | |
| 101 | <div class="ttc" id="namespace_iso_spec_html_acbcd0253dcdabd90c53d008c7e12b95f"><div class="ttname"><a href="namespace_iso_spec.html#acbcd0253dcdabd90c53d008c7e12b95f">IsoSpec::quickselect</a></div><div class="ttdeci">void * quickselect(void **array, int n, int start, int end)</div><div class="ttdoc">Quickly select the n&#39;th positional statistic, including the weights. </div><div class="ttdef"><b>Definition:</b> <a href="misc_8cpp_source.html#l00028">misc.cpp:28</a></div></div> | |
| 102 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_ac18406df84b4b220bcb1974000c192b2"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">IsoSpec::IsoGenerator::partialProbs</a></div><div class="ttdeci">double * partialProbs</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00134">isoSpec++.h:134</a></div></div> | |
| 103 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a5ff1fafd079a866e9d61bc7d859842ea"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a5ff1fafd079a866e9d61bc7d859842ea">IsoSpec::Iso::Iso</a></div><div class="ttdeci">Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)</div><div class="ttdoc">General constructror. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00051">isoSpec++.cpp:51</a></div></div> | |
| 104 | <div class="ttc" id="class_iso_spec_1_1_iso_ordered_generator_html_aa2438bb81fb1d68eda1637d67e9cb36d"><div class="ttname"><a href="class_iso_spec_1_1_iso_ordered_generator.html#aa2438bb81fb1d68eda1637d67e9cb36d">IsoSpec::IsoOrderedGenerator::advanceToNextConfiguration</a></div><div class="ttdeci">bool advanceToNextConfiguration() override final</div><div class="ttdoc">Advance to the next, not yet visited, most probable isotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00461">isoSpec++.cpp:461</a></div></div> | |
| 105 | <div class="ttc" id="class_iso_spec_1_1_iso_html_aea98a8331a2f8a1a6bbcace6124fcfae"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">IsoSpec::Iso::marginals</a></div><div class="ttdeci">Marginal ** marginals</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00072">isoSpec++.h:72</a></div></div> | |
| 106 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a7235f0afc56dccd13937791a630c45da"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">IsoSpec::Iso::isotopeNumbers</a></div><div class="ttdeci">int * isotopeNumbers</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00068">isoSpec++.h:68</a></div></div> | |
| 107 | <div class="ttc" id="class_iso_spec_1_1_iso_html_ab51c157b23ae6a6b521667b6f0e8a208"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">IsoSpec::Iso::modeLProb</a></div><div class="ttdeci">double modeLProb</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00073">isoSpec++.h:73</a></div></div> | |
| 108 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_af5654fcdba8199cbd60668af5de89a53"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">IsoSpec::IsoGenerator::partialMasses</a></div><div class="ttdeci">double * partialMasses</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00133">isoSpec++.h:133</a></div></div> | |
| 109 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_a89b5b851fbc67f79ed165af0b9b2a188"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#a89b5b851fbc67f79ed165af0b9b2a188">IsoSpec::IsoGenerator::IsoGenerator</a></div><div class="ttdeci">IsoGenerator(Iso &&iso, bool alloc_partials=true)</div><div class="ttdoc">Move constructor. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00253">isoSpec++.cpp:253</a></div></div> | |
| 110 | <div class="ttc" id="class_iso_spec_1_1_iso_html_ad2a353f2c746648b08a9ad31ff775766"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">IsoSpec::Iso::disowned</a></div><div class="ttdeci">bool disowned</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00065">isoSpec++.h:65</a></div></div> | |
| 111 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
| 112 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_a54a39b847a71aa08d1207d0666dd62bc"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">IsoSpec::IsoGenerator::partialLProbs</a></div><div class="ttdeci">double * partialLProbs</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00132">isoSpec++.h:132</a></div></div> | |
| 113 | <div class="ttc" id="class_iso_spec_1_1_iso_html_ab01939334b6c3e69f65a36f9965971a2"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">IsoSpec::Iso::atomCounts</a></div><div class="ttdeci">int * atomCounts</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00069">isoSpec++.h:69</a></div></div> | |
| 114 | <div class="ttc" id="class_iso_spec_1_1_marginal_trek_html"><div class="ttname"><a href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a></div><div class="ttdoc">The marginal distribution class (a subisotopologue). </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00141">marginalTrek++.h:141</a></div></div> | |
| 115 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html_ac6aa2fff002a76b0beae1995f34ae5f6"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html#ac6aa2fff002a76b0beae1995f34ae5f6">IsoSpec::IsoThresholdGenerator::terminate_search</a></div><div class="ttdeci">void terminate_search()</div><div class="ttdoc">Block the subsequent search of isotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8cpp_source.html#l00365">isoSpec++.cpp:365</a></div></div> | |
| 116 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></div><div class="ttdoc">Precalculated Marginal class. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00213">marginalTrek++.h:213</a></div></div> | |
| 117 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a8dd2c443706935b582979b13f935115c"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">IsoSpec::Iso::allDim</a></div><div class="ttdeci">int allDim</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00071">isoSpec++.h:71</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <tuple></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <unordered_map></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <queue></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <limits></span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#include "platform.h"</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#include "dirtyAllocator.h"</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#include "summator.h"</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#include "operators.h"</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor">#include "marginalTrek++.h"</span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> </div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor">#if ISOSPEC_BUILDING_R</span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="preprocessor">#include <Rcpp.h></span></div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="keyword">using namespace </span>Rcpp;</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor">#endif </span><span class="comment">/* ISOSPEC_BUILDING_R */</span><span class="preprocessor"></span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> </div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> {</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="comment">// This function is NOT guaranteed to be secure against malicious input. It should be used only for debugging.</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> parse_formula(<span class="keyword">const</span> <span class="keywordtype">char</span>* formula,</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  std::vector<const double*>& isotope_masses,</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  std::vector<const double*>& isotope_probabilities,</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="keywordtype">int</span>** isotopeNumbers,</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordtype">int</span>** atomCounts,</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>* confSize);</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div><div class="line"><a name="l00052"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html"> 52</a></span> <span class="keyword">class </span>ISOSPEC_EXPORT_SYMBOL <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a> {</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keywordtype">void</span> setupMarginals(<span class="keyword">const</span> <span class="keywordtype">double</span>* <span class="keyword">const</span> * _isotopeMasses,</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* <span class="keyword">const</span> * _isotopeProbabilities);</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766"> 65</a></span>  <span class="keywordtype">bool</span> <a class="code" href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">disowned</a>; </div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="keyword">protected</span>:</div><div class="line"><a name="l00067"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0"> 67</a></span>  <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">dimNumber</a>; </div><div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da"> 68</a></span>  <span class="keywordtype">int</span>* <a class="code" href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">isotopeNumbers</a>; </div><div class="line"><a name="l00069"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2"> 69</a></span>  <span class="keywordtype">int</span>* <a class="code" href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">atomCounts</a>; </div><div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425"> 70</a></span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">confSize</a>; </div><div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c"> 71</a></span>  <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">allDim</a>; </div><div class="line"><a name="l00072"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae"> 72</a></span>  <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>** <a class="code" href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">marginals</a>; </div><div class="line"><a name="l00073"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208"> 73</a></span>  <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">modeLProb</a>; </div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>(</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keywordtype">int</span> _dimNumber,</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>* _isotopeNumbers,</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>* _atomCounts,</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* <span class="keyword">const</span> * _isotopeMasses,</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* <span class="keyword">const</span> * _isotopeProbabilities</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  );</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>(<span class="keyword">const</span> <span class="keywordtype">char</span>* formula);</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>(<a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>&& other);</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>(<span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>& other, <span class="keywordtype">bool</span> fullcopy);</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keyword">virtual</span> ~<a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>();</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span> </div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keywordtype">double</span> getLightestPeakMass() <span class="keyword">const</span>;</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span> </div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordtype">double</span> getHeaviestPeakMass() <span class="keyword">const</span>;</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div><div class="line"><a name="l00115"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f"> 115</a></span>  <span class="keyword">inline</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">getModeLProb</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> modeLProb; };</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div><div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5"> 118</a></span>  <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">getDimNumber</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> dimNumber; };</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div><div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091"> 121</a></span>  <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">getAllDim</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> allDim; };</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span> };</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span> </div><div class="line"><a name="l00129"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_generator.html"> 129</a></span> <span class="keyword">class </span>ISOSPEC_EXPORT_SYMBOL <a class="code" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a> : <span class="keyword">public</span> <a class="code" href="class_iso_spec_1_1_iso.html">Iso</a></div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span> {</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span> <span class="keyword">protected</span>:</div><div class="line"><a name="l00132"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc"> 132</a></span>  <span class="keywordtype">double</span>* <a class="code" href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">partialLProbs</a>; </div><div class="line"><a name="l00133"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53"> 133</a></span>  <span class="keywordtype">double</span>* <a class="code" href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">partialMasses</a>; </div><div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2"> 134</a></span>  <span class="keywordtype">double</span>* <a class="code" href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">partialProbs</a>;</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> advanceToNextConfiguration() = 0;</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span> </div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span> </div><div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383"> 147</a></span>  <span class="keyword">virtual</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">lprob</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> partialLProbs[0]; };</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span> </div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span> </div><div class="line"><a name="l00153"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d"> 153</a></span>  <span class="keyword">virtual</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">mass</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> partialMasses[0]; };</div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span> </div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div><div class="line"><a name="l00159"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0"> 159</a></span>  <span class="keyword">virtual</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">prob</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> partialProbs[0]; };</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span> </div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="comment">//TODO: what is this???</span></div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> get_conf_signature(<span class="keywordtype">int</span>* space) <span class="keyword">const</span> = 0;</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span> </div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <a class="code" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a>(<a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>&& iso, <span class="keywordtype">bool</span> alloc_partials = <span class="keyword">true</span>);</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span> </div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keyword">virtual</span> ~<a class="code" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a>();</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span> };</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span> </div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span> </div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span> </div><div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_ordered_generator.html"> 179</a></span> <span class="keyword">class </span>ISOSPEC_EXPORT_SYMBOL <a class="code" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoOrderedGenerator</a>: <span class="keyword">public</span> <a class="code" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a></div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span> {</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <a class="code" href="class_iso_spec_1_1_marginal_trek.html">MarginalTrek</a>** marginalResults; </div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  std::priority_queue<void*,std::vector<void*>,<a class="code" href="class_iso_spec_1_1_conf_order.html">ConfOrder</a>> pq; </div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordtype">void</span>* topConf; </div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <a class="code" href="class_iso_spec_1_1_dirty_allocator.html">DirtyAllocator</a> allocator; </div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  <span class="keyword">const</span> std::vector<double>** logProbs; </div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  <span class="keyword">const</span> std::vector<double>** masses; </div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="keyword">const</span> std::vector<int*>** marginalConfs; </div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordtype">double</span> currentLProb; </div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <span class="keywordtype">double</span> currentMass; </div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordtype">double</span> currentProb; </div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  <span class="keywordtype">int</span> ccount;</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span> </div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keywordtype">bool</span> advanceToNextConfiguration() <span class="keyword">override</span> <span class="keyword">final</span>;</div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span> </div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> </div><div class="line"><a name="l00202"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_ordered_generator.html#af5d638985fd24c03bfe1f3d61e1b25c6"> 202</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="class_iso_spec_1_1_iso_ordered_generator.html#af5d638985fd24c03bfe1f3d61e1b25c6">get_conf_signature</a>(<span class="keywordtype">int</span>* space) <span class="keyword">const</span> <span class="keyword">override</span> <span class="keyword">final</span></div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  {</div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  <span class="keywordtype">int</span>* c = getConf(topConf);</div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span> </div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="keywordflow">if</span> (ccount >= 0)</div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  c[ccount]--;</div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span> </div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii=0; ii<dimNumber; ii++)</div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span>  {</div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  memcpy(space, marginalResults[ii]->confs()[c[ii]], isotopeNumbers[ii]*<span class="keyword">sizeof</span>(<span class="keywordtype">int</span>));</div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span>  space += isotopeNumbers[ii];</div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  }</div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span> </div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  <span class="keywordflow">if</span> (ccount >= 0)</div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  c[ccount]++;</div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  };</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span> </div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <a class="code" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoOrderedGenerator</a>(<a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>&& iso, <span class="keywordtype">int</span> _tabSize = 1000, <span class="keywordtype">int</span> _hashSize = 1000);</div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span> </div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  <span class="keyword">virtual</span> ~<a class="code" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoOrderedGenerator</a>();</div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span> };</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span> </div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span> </div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span> </div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span> </div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span> </div><div class="line"><a name="l00235"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_threshold_generator.html"> 235</a></span> <span class="keyword">class </span>ISOSPEC_EXPORT_SYMBOL <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a>: <span class="keyword">public</span> <a class="code" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a></div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span> {</div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span> </div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keywordtype">int</span>* counter; </div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="keywordtype">double</span>* maxConfsLPSum; </div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="keyword">const</span> <span class="keywordtype">double</span> Lcutoff; </div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a>** marginalResults;</div><div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a>** marginalResultsUnsorted;</div><div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  <span class="keywordtype">int</span>* marginalOrder;</div><div class="line"><a name="l00245"></a><span class="lineno"> 245</span> </div><div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* lProbs_ptr;</div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* lProbs_ptr_start;</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keywordtype">double</span>* partialLProbs_second;</div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="keywordtype">double</span> partialLProbs_second_val, lcfmsv;</div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="keywordtype">bool</span> empty;</div><div class="line"><a name="l00251"></a><span class="lineno"> 251</span> </div><div class="line"><a name="l00252"></a><span class="lineno"> 252</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> get_conf_signature(<span class="keywordtype">int</span>* space) <span class="keyword">const</span> <span class="keyword">override</span> <span class="keyword">final</span></div><div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  {</div><div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  counter[0] = lProbs_ptr - lProbs_ptr_start;</div><div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keywordflow">if</span>(marginalOrder != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii=0; ii<dimNumber; ii++)</div><div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  {</div><div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordtype">int</span> jj = marginalOrder[ii];</div><div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  memcpy(space, marginalResultsUnsorted[ii]->get_conf(counter[jj]), isotopeNumbers[ii]*<span class="keyword">sizeof</span>(<span class="keywordtype">int</span>));</div><div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  space += isotopeNumbers[ii];</div><div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  }</div><div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii=0; ii<dimNumber; ii++)</div><div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  {</div><div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  memcpy(space, marginalResultsUnsorted[ii]->get_conf(counter[ii]), isotopeNumbers[ii]*<span class="keyword">sizeof</span>(<span class="keywordtype">int</span>));</div><div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  space += isotopeNumbers[ii];</div><div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  }</div><div class="line"><a name="l00269"></a><span class="lineno"> 269</span> </div><div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  };</div><div class="line"><a name="l00271"></a><span class="lineno"> 271</span> </div><div class="line"><a name="l00273"></a><span class="lineno"> 273</span> </div><div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a>(<a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>&& iso, <span class="keywordtype">double</span> _threshold, <span class="keywordtype">bool</span> _absolute=<span class="keyword">true</span>, <span class="keywordtype">int</span> _tabSize=1000, <span class="keywordtype">int</span> _hashSize=1000, <span class="keywordtype">bool</span> reorder_marginals = <span class="keyword">true</span>);</div><div class="line"><a name="l00282"></a><span class="lineno"> 282</span> </div><div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <span class="keyword">inline</span> ~<a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a>()</div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  {</div><div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <span class="keyword">delete</span>[] counter;</div><div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="keyword">delete</span>[] maxConfsLPSum;</div><div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="keywordflow">if</span> (marginalResultsUnsorted != marginalResults)</div><div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="keyword">delete</span>[] marginalResultsUnsorted;</div><div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  dealloc_table(marginalResults, dimNumber); </div><div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <span class="keywordflow">if</span>(marginalOrder != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <span class="keyword">delete</span>[] marginalOrder;</div><div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  };</div><div class="line"><a name="l00293"></a><span class="lineno"> 293</span> </div><div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  <span class="comment">// Perform highly aggressive inling as this function is often called as while(advanceToNextConfiguration()) {}</span></div><div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <span class="comment">// which leads to an extremely tight loop and some compilers miss this (potentially due to the length of the function). </span></div><div class="line"><a name="l00296"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_threshold_generator.html#a7164a6476b84665967c4a667a91d3f3e"> 296</a></span>  ISOSPEC_FORCE_INLINE <span class="keywordtype">bool</span> <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#a7164a6476b84665967c4a667a91d3f3e">advanceToNextConfiguration</a>() override final</div><div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  {</div><div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  lProbs_ptr++;</div><div class="line"><a name="l00299"></a><span class="lineno"> 299</span> </div><div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <span class="keywordflow">if</span>(ISOSPEC_LIKELY(*lProbs_ptr >= lcfmsv))</div><div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  {</div><div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  }</div><div class="line"><a name="l00304"></a><span class="lineno"> 304</span> </div><div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <span class="comment">// If we reached this point, a carry is needed</span></div><div class="line"><a name="l00306"></a><span class="lineno"> 306</span> </div><div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <span class="keywordtype">int</span> idx = 0;</div><div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  lProbs_ptr = lProbs_ptr_start;</div><div class="line"><a name="l00309"></a><span class="lineno"> 309</span> </div><div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  <span class="keywordtype">int</span> * cntr_ptr = counter;</div><div class="line"><a name="l00311"></a><span class="lineno"> 311</span> </div><div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="keywordflow">while</span>(idx<dimNumber-1)</div><div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  {</div><div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <span class="comment">// counter[idx] = 0;</span></div><div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  *cntr_ptr = 0;</div><div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  idx++;</div><div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  cntr_ptr++;</div><div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <span class="comment">// counter[idx]++;</span></div><div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  (*cntr_ptr)++;</div><div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  partialLProbs[idx] = partialLProbs[idx+1] + marginalResults[idx]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">get_lProb</a>(counter[idx]);</div><div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="keywordflow">if</span>(partialLProbs[idx] + maxConfsLPSum[idx-1] >= Lcutoff)</div><div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  {</div><div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  partialMasses[idx] = partialMasses[idx+1] + marginalResults[idx]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">get_mass</a>(counter[idx]);</div><div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  partialProbs[idx] = partialProbs[idx+1] * marginalResults[idx]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">get_eProb</a>(counter[idx]);</div><div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  recalc(idx-1);</div><div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  }</div><div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  }</div><div class="line"><a name="l00329"></a><span class="lineno"> 329</span> </div><div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  terminate_search();</div><div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  }</div><div class="line"><a name="l00333"></a><span class="lineno"> 333</span> </div><div class="line"><a name="l00334"></a><span class="lineno"> 334</span> </div><div class="line"><a name="l00335"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_threshold_generator.html#a4aeebde03e385404d0175fd5696ff529"> 335</a></span>  ISOSPEC_FORCE_INLINE <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#a4aeebde03e385404d0175fd5696ff529">lprob</a>() const override final { <span class="keywordflow">return</span> partialLProbs_second_val + (*(lProbs_ptr)); };</div><div class="line"><a name="l00336"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_threshold_generator.html#ae2236accc7dc7a25a723e3c7317659b6"> 336</a></span>  ISOSPEC_FORCE_INLINE <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#ae2236accc7dc7a25a723e3c7317659b6">mass</a>() const override final { <span class="keywordflow">return</span> partialMasses[1] + marginalResults[0]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">get_mass</a>(lProbs_ptr - lProbs_ptr_start); };</div><div class="line"><a name="l00337"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_threshold_generator.html#a998d987f81b2ca7ed610294f6a5f8df5"> 337</a></span>  ISOSPEC_FORCE_INLINE <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_iso_threshold_generator.html#a998d987f81b2ca7ed610294f6a5f8df5">prob</a>() const override final { <span class="keywordflow">return</span> partialProbs[1] * marginalResults[0]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">get_eProb</a>(lProbs_ptr - lProbs_ptr_start); };</div><div class="line"><a name="l00338"></a><span class="lineno"> 338</span> </div><div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  <span class="keywordtype">void</span> terminate_search();</div><div class="line"><a name="l00341"></a><span class="lineno"> 341</span> </div><div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keywordtype">void</span> reset();</div><div class="line"><a name="l00347"></a><span class="lineno"> 347</span> </div><div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  <span class="keywordtype">size_t</span> count_confs();</div><div class="line"><a name="l00353"></a><span class="lineno"> 353</span> </div><div class="line"><a name="l00354"></a><span class="lineno"> 354</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  ISOSPEC_FORCE_INLINE <span class="keywordtype">void</span> recalc(<span class="keywordtype">int</span> idx)</div><div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  {</div><div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  <span class="keywordflow">for</span>(; idx > 0; idx--)</div><div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  {</div><div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  partialLProbs[idx] = partialLProbs[idx+1] + marginalResults[idx]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">get_lProb</a>(counter[idx]);</div><div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  partialMasses[idx] = partialMasses[idx+1] + marginalResults[idx]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">get_mass</a>(counter[idx]);</div><div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  partialProbs[idx] = partialProbs[idx+1] * marginalResults[idx]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">get_eProb</a>(counter[idx]);</div><div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  }</div><div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  partialLProbs_second_val = *partialLProbs_second;</div><div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  partialLProbs[0] = *partialLProbs_second + marginalResults[0]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">get_lProb</a>(counter[0]);</div><div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  lcfmsv = Lcutoff - partialLProbs_second_val;</div><div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  }</div><div class="line"><a name="l00368"></a><span class="lineno"> 368</span> };</div><div class="line"><a name="l00369"></a><span class="lineno"> 369</span> </div><div class="line"><a name="l00370"></a><span class="lineno"> 370</span> </div><div class="line"><a name="l00371"></a><span class="lineno"> 371</span> </div><div class="line"><a name="l00373"></a><span class="lineno"> 373</span> </div><div class="line"><a name="l00383"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_iso_layered_generator.html"> 383</a></span> <span class="keyword">class </span>ISOSPEC_EXPORT_SYMBOL <a class="code" href="class_iso_spec_1_1_iso_layered_generator.html">IsoLayeredGenerator</a> : <span class="keyword">public</span> <a class="code" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a></div><div class="line"><a name="l00384"></a><span class="lineno"> 384</span> {</div><div class="line"><a name="l00385"></a><span class="lineno"> 385</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  <a class="code" href="class_iso_spec_1_1_summator.html">Summator</a> totalProb;</div><div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  std::vector<void*> newaccepted;</div><div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  <a class="code" href="class_iso_spec_1_1_dirty_allocator.html">DirtyAllocator</a> allocator;</div><div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  <span class="keywordtype">int</span>* candidate;</div><div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  <span class="keyword">const</span> std::vector<double>** logProbs; </div><div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  <span class="keyword">const</span> std::vector<double>** masses; </div><div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  <span class="keyword">const</span> std::vector<int*>** marginalConfs; </div><div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  <a class="code" href="class_iso_spec_1_1_marginal_trek.html">MarginalTrek</a>** marginalResults;</div><div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  std::vector<void*>* current;</div><div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  std::vector<void*>* next;</div><div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  <span class="keywordtype">double</span> lprobThr;</div><div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  <span class="keywordtype">double</span> targetCoverage;</div><div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  <span class="keywordtype">double</span> percentageToExpand;</div><div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  <span class="keywordtype">bool</span> do_trim;</div><div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  <span class="keywordtype">int</span> layers;</div><div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  <span class="keywordtype">size_t</span> generator_position;</div><div class="line"><a name="l00402"></a><span class="lineno"> 402</span> </div><div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  <span class="keywordtype">bool</span> advanceToNextLayer(); </div><div class="line"><a name="l00404"></a><span class="lineno"> 404</span> </div><div class="line"><a name="l00405"></a><span class="lineno"> 405</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  <span class="keywordtype">bool</span> advanceToNextConfiguration() <span class="keyword">override</span> <span class="keyword">final</span>;</div><div class="line"><a name="l00407"></a><span class="lineno"> 407</span> </div><div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> get_conf_signature(<span class="keywordtype">int</span>* space) <span class="keyword">const</span> <span class="keyword">override</span> <span class="keyword">final</span></div><div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  {</div><div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <span class="keywordtype">int</span>* conf = getConf(newaccepted[generator_position]);</div><div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii=0; ii<dimNumber; ii++)</div><div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  {</div><div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  memcpy(space, marginalResults[ii]->confs()[conf[ii]], isotopeNumbers[ii]*<span class="keyword">sizeof</span>(<span class="keywordtype">int</span>));</div><div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  space += isotopeNumbers[ii];</div><div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  }</div><div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  };</div><div class="line"><a name="l00417"></a><span class="lineno"> 417</span> </div><div class="line"><a name="l00418"></a><span class="lineno"> 418</span> </div><div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  <a class="code" href="class_iso_spec_1_1_iso_layered_generator.html">IsoLayeredGenerator</a>(<a class="code" href="class_iso_spec_1_1_iso.html">Iso</a>&& iso, <span class="keywordtype">double</span> _targetCoverage, <span class="keywordtype">double</span> _percentageToExpand, <span class="keywordtype">int</span> _tabSize = 1000, <span class="keywordtype">int</span> _hashSize = 1000, <span class="keywordtype">bool</span> trim = <span class="keyword">false</span>);</div><div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <span class="keyword">virtual</span> ~<a class="code" href="class_iso_spec_1_1_iso_layered_generator.html">IsoLayeredGenerator</a>();</div><div class="line"><a name="l00421"></a><span class="lineno"> 421</span> </div><div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  <span class="keywordtype">void</span> terminate_search();</div><div class="line"><a name="l00423"></a><span class="lineno"> 423</span> </div><div class="line"><a name="l00424"></a><span class="lineno"> 424</span> };</div><div class="line"><a name="l00425"></a><span class="lineno"> 425</span> </div><div class="line"><a name="l00426"></a><span class="lineno"> 426</span> </div><div class="line"><a name="l00427"></a><span class="lineno"> 427</span> </div><div class="line"><a name="l00428"></a><span class="lineno"> 428</span> </div><div class="line"><a name="l00429"></a><span class="lineno"> 429</span> <span class="preprocessor">#if !ISOSPEC_BUILDING_R</span></div><div class="line"><a name="l00430"></a><span class="lineno"> 430</span> </div><div class="line"><a name="l00431"></a><span class="lineno"> 431</span> <span class="keywordtype">void</span> printConfigurations(</div><div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="keyword">const</span> std::tuple<double*,double*,int*,int>& results,</div><div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  <span class="keywordtype">int</span> dimNumber,</div><div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  <span class="keywordtype">int</span>* isotopeNumbers</div><div class="line"><a name="l00435"></a><span class="lineno"> 435</span> );</div><div class="line"><a name="l00436"></a><span class="lineno"> 436</span> <span class="preprocessor">#endif </span><span class="comment">/* !ISOSPEC_BUILDING_R */</span><span class="preprocessor"></span></div><div class="line"><a name="l00437"></a><span class="lineno"> 437</span> </div><div class="line"><a name="l00438"></a><span class="lineno"> 438</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00439"></a><span class="lineno"> 439</span> </div><div class="ttc" id="class_iso_spec_1_1_iso_html_a89ed144bf2495fa25840aca90a31b425"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a89ed144bf2495fa25840aca90a31b425">IsoSpec::Iso::confSize</a></div><div class="ttdeci">unsigned int confSize</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00070">isoSpec++.h:70</a></div></div> | |
| 80 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html">IsoSpec::IsoGenerator</a></div><div class="ttdoc">The generator of isotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00129">isoSpec++.h:129</a></div></div> | |
| 81 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html_a4aeebde03e385404d0175fd5696ff529"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html#a4aeebde03e385404d0175fd5696ff529">IsoSpec::IsoThresholdGenerator::lprob</a></div><div class="ttdeci">ISOSPEC_FORCE_INLINE double lprob() const override final</div><div class="ttdoc">Get the log-probability of the current isotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00335">isoSpec++.h:335</a></div></div> | |
| 82 | <div class="ttc" id="class_iso_spec_1_1_iso_html"><div class="ttname"><a href="class_iso_spec_1_1_iso.html">IsoSpec::Iso</a></div><div class="ttdoc">The Iso class for the calculation of the isotopic distribution. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00052">isoSpec++.h:52</a></div></div> | |
| 83 | <div class="ttc" id="class_iso_spec_1_1_iso_layered_generator_html"><div class="ttname"><a href="class_iso_spec_1_1_iso_layered_generator.html">IsoSpec::IsoLayeredGenerator</a></div><div class="ttdoc">The class that represents isotopologues above a given joint probability value. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00383">isoSpec++.h:383</a></div></div> | |
| 84 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a90245f9bc318f12720c134f61bbe0db0"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a90245f9bc318f12720c134f61bbe0db0">IsoSpec::Iso::dimNumber</a></div><div class="ttdeci">int dimNumber</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00067">isoSpec++.h:67</a></div></div> | |
| 85 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html_ae2236accc7dc7a25a723e3c7317659b6"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html#ae2236accc7dc7a25a723e3c7317659b6">IsoSpec::IsoThresholdGenerator::mass</a></div><div class="ttdeci">ISOSPEC_FORCE_INLINE double mass() const override final</div><div class="ttdoc">Get the mass of the current isotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00336">isoSpec++.h:336</a></div></div> | |
| 86 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a62b17f48d86f62b5ed38ffb296a9daa5"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a62b17f48d86f62b5ed38ffb296a9daa5">IsoSpec::Iso::getDimNumber</a></div><div class="ttdeci">int getDimNumber() const</div><div class="ttdoc">Get the number of elements in the chemical formula of the molecule. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00118">isoSpec++.h:118</a></div></div> | |
| 87 | <div class="ttc" id="class_iso_spec_1_1_marginal_html"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></div><div class="ttdoc">The marginal distribution class (a subisotopologue). </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00045">marginalTrek++.h:45</a></div></div> | |
| 88 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html_a7164a6476b84665967c4a667a91d3f3e"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html#a7164a6476b84665967c4a667a91d3f3e">IsoSpec::IsoThresholdGenerator::advanceToNextConfiguration</a></div><div class="ttdeci">ISOSPEC_FORCE_INLINE bool advanceToNextConfiguration() override final</div><div class="ttdoc">Advance to the next, not yet visited, most probable isotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00296">isoSpec++.h:296</a></div></div> | |
| 89 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a7a38a567eadf16fa2ad41e81c8f55c02"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">IsoSpec::PrecalculatedMarginal::get_eProb</a></div><div class="ttdeci">const double & get_eProb(int idx) const</div><div class="ttdoc">Get the probability of the idx-th subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00261">marginalTrek++.h:261</a></div></div> | |
| 90 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_a34173228ef73e272e2ff0ae6ce58092d"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#a34173228ef73e272e2ff0ae6ce58092d">IsoSpec::IsoGenerator::mass</a></div><div class="ttdeci">virtual double mass() const</div><div class="ttdoc">Get the mass of the current isotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00153">isoSpec++.h:153</a></div></div> | |
| 91 | <div class="ttc" id="class_iso_spec_1_1_summator_html"><div class="ttname"><a href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a></div><div class="ttdef"><b>Definition:</b> <a href="summator_8h_source.html#l00076">summator.h:76</a></div></div> | |
| 92 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a9035d076cec8f937d971e3fd972aa83f"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a9035d076cec8f937d971e3fd972aa83f">IsoSpec::Iso::getModeLProb</a></div><div class="ttdeci">double getModeLProb() const</div><div class="ttdoc">Get the log-probability of the mode-configuration (if there are many modes, they share this value)...</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00115">isoSpec++.h:115</a></div></div> | |
| 93 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a07eee6d60635c9c1d6f92c181994e06a"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">IsoSpec::PrecalculatedMarginal::get_lProb</a></div><div class="ttdeci">const double & get_lProb(int idx) const</div><div class="ttdoc">Get the log-probability of the idx-th subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00254">marginalTrek++.h:254</a></div></div> | |
| 94 | <div class="ttc" id="class_iso_spec_1_1_dirty_allocator_html"><div class="ttname"><a href="class_iso_spec_1_1_dirty_allocator.html">IsoSpec::DirtyAllocator</a></div><div class="ttdef"><b>Definition:</b> <a href="dirty_allocator_8h_source.html#l00026">dirtyAllocator.h:26</a></div></div> | |
| 95 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_aecf1b3292fcc0857a86efe619a37fff0"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#aecf1b3292fcc0857a86efe619a37fff0">IsoSpec::IsoGenerator::prob</a></div><div class="ttdeci">virtual double prob() const</div><div class="ttdoc">Get the probability of the current isotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00159">isoSpec++.h:159</a></div></div> | |
| 96 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_ac18406df84b4b220bcb1974000c192b2"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#ac18406df84b4b220bcb1974000c192b2">IsoSpec::IsoGenerator::partialProbs</a></div><div class="ttdeci">double * partialProbs</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00134">isoSpec++.h:134</a></div></div> | |
| 97 | <div class="ttc" id="class_iso_spec_1_1_iso_html_aea98a8331a2f8a1a6bbcace6124fcfae"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#aea98a8331a2f8a1a6bbcace6124fcfae">IsoSpec::Iso::marginals</a></div><div class="ttdeci">Marginal ** marginals</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00072">isoSpec++.h:72</a></div></div> | |
| 98 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a7235f0afc56dccd13937791a630c45da"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a7235f0afc56dccd13937791a630c45da">IsoSpec::Iso::isotopeNumbers</a></div><div class="ttdeci">int * isotopeNumbers</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00068">isoSpec++.h:68</a></div></div> | |
| 99 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a656a37dd84a6c0534b2373210ed5a091"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a656a37dd84a6c0534b2373210ed5a091">IsoSpec::Iso::getAllDim</a></div><div class="ttdeci">int getAllDim() const</div><div class="ttdoc">Get the total number of isotopes of elements present in a chemical formula. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00121">isoSpec++.h:121</a></div></div> | |
| 100 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_ae8e24abbce51a4c93994f630acfdf383"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#ae8e24abbce51a4c93994f630acfdf383">IsoSpec::IsoGenerator::lprob</a></div><div class="ttdeci">virtual double lprob() const</div><div class="ttdoc">Get the log-probability of the current isotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00147">isoSpec++.h:147</a></div></div> | |
| 101 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_ada12caa2e195c1a16c5158a428ea3ed2"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">IsoSpec::PrecalculatedMarginal::get_mass</a></div><div class="ttdeci">const double & get_mass(int idx) const</div><div class="ttdoc">Get the mass of the idx-th subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00268">marginalTrek++.h:268</a></div></div> | |
| 102 | <div class="ttc" id="class_iso_spec_1_1_iso_html_ab51c157b23ae6a6b521667b6f0e8a208"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#ab51c157b23ae6a6b521667b6f0e8a208">IsoSpec::Iso::modeLProb</a></div><div class="ttdeci">double modeLProb</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00073">isoSpec++.h:73</a></div></div> | |
| 103 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html">IsoSpec::IsoThresholdGenerator</a></div><div class="ttdoc">The generator of isotopologues above a given threshold value. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00235">isoSpec++.h:235</a></div></div> | |
| 104 | <div class="ttc" id="class_iso_spec_1_1_iso_ordered_generator_html"><div class="ttname"><a href="class_iso_spec_1_1_iso_ordered_generator.html">IsoSpec::IsoOrderedGenerator</a></div><div class="ttdoc">The generator of isotopologues sorted by their probability of occurrence. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00179">isoSpec++.h:179</a></div></div> | |
| 105 | <div class="ttc" id="class_iso_spec_1_1_conf_order_html"><div class="ttname"><a href="class_iso_spec_1_1_conf_order.html">IsoSpec::ConfOrder</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00066">operators.h:66</a></div></div> | |
| 106 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_af5654fcdba8199cbd60668af5de89a53"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#af5654fcdba8199cbd60668af5de89a53">IsoSpec::IsoGenerator::partialMasses</a></div><div class="ttdeci">double * partialMasses</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00133">isoSpec++.h:133</a></div></div> | |
| 107 | <div class="ttc" id="class_iso_spec_1_1_iso_html_ad2a353f2c746648b08a9ad31ff775766"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#ad2a353f2c746648b08a9ad31ff775766">IsoSpec::Iso::disowned</a></div><div class="ttdeci">bool disowned</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00065">isoSpec++.h:65</a></div></div> | |
| 108 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
| 109 | <div class="ttc" id="class_iso_spec_1_1_iso_generator_html_a54a39b847a71aa08d1207d0666dd62bc"><div class="ttname"><a href="class_iso_spec_1_1_iso_generator.html#a54a39b847a71aa08d1207d0666dd62bc">IsoSpec::IsoGenerator::partialLProbs</a></div><div class="ttdeci">double * partialLProbs</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00132">isoSpec++.h:132</a></div></div> | |
| 110 | <div class="ttc" id="class_iso_spec_1_1_iso_threshold_generator_html_a998d987f81b2ca7ed610294f6a5f8df5"><div class="ttname"><a href="class_iso_spec_1_1_iso_threshold_generator.html#a998d987f81b2ca7ed610294f6a5f8df5">IsoSpec::IsoThresholdGenerator::prob</a></div><div class="ttdeci">ISOSPEC_FORCE_INLINE double prob() const override final</div><div class="ttdoc">Get the probability of the current isotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00337">isoSpec++.h:337</a></div></div> | |
| 111 | <div class="ttc" id="class_iso_spec_1_1_iso_html_ab01939334b6c3e69f65a36f9965971a2"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#ab01939334b6c3e69f65a36f9965971a2">IsoSpec::Iso::atomCounts</a></div><div class="ttdeci">int * atomCounts</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00069">isoSpec++.h:69</a></div></div> | |
| 112 | <div class="ttc" id="class_iso_spec_1_1_marginal_trek_html"><div class="ttname"><a href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a></div><div class="ttdoc">The marginal distribution class (a subisotopologue). </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00141">marginalTrek++.h:141</a></div></div> | |
| 113 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></div><div class="ttdoc">Precalculated Marginal class. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00213">marginalTrek++.h:213</a></div></div> | |
| 114 | <div class="ttc" id="class_iso_spec_1_1_iso_ordered_generator_html_af5d638985fd24c03bfe1f3d61e1b25c6"><div class="ttname"><a href="class_iso_spec_1_1_iso_ordered_generator.html#af5d638985fd24c03bfe1f3d61e1b25c6">IsoSpec::IsoOrderedGenerator::get_conf_signature</a></div><div class="ttdeci">void get_conf_signature(int *space) const override final</div><div class="ttdoc">Save the counts of isotopes in the space. </div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00202">isoSpec++.h:202</a></div></div> | |
| 115 | <div class="ttc" id="class_iso_spec_1_1_iso_html_a8dd2c443706935b582979b13f935115c"><div class="ttname"><a href="class_iso_spec_1_1_iso.html#a8dd2c443706935b582979b13f935115c">IsoSpec::Iso::allDim</a></div><div class="ttdeci">int allDim</div><div class="ttdef"><b>Definition:</b> <a href="iso_spec_09_09_8h_source.html#l00071">isoSpec++.h:71</a></div></div> | |
| 116 | </div><!-- fragment --></div><!-- contents --> | |
| 117 | <!-- start footer part --> | |
| 118 | <hr class="footer"/><address class="footer"><small> | |
| 119 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 121 | </a> 1.8.14 | |
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| 0 | /* | |
| 1 | @licstart The following is the entire license notice for the | |
| 2 | JavaScript code in this file. | |
| 3 | ||
| 4 | Copyright (C) 1997-2017 by Dimitri van Heesch | |
| 5 | ||
| 6 | Permission is hereby granted, free of charge, to any person obtaining | |
| 7 | a copy of this software and associated documentation files (the | |
| 8 | "Software"), to deal in the Software without restriction, including | |
| 9 | without limitation the rights to use, copy, modify, merge, publish, | |
| 10 | distribute, sublicense, and/or sell copies of the Software, and to | |
| 11 | permit persons to whom the Software is furnished to do so, subject to | |
| 12 | the following conditions: | |
| 13 | ||
| 14 | The above copyright notice and this permission notice shall be included | |
| 15 | in all copies or substantial portions of the Software. | |
| 16 | ||
| 17 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, | |
| 18 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF | |
| 19 | MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. | |
| 20 | IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY | |
| 21 | CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, | |
| 22 | TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE | |
| 23 | SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. | |
| 24 | ||
| 25 | @licend The above is the entire license notice | |
| 26 | for the JavaScript code in this file | |
| 27 | */ | |
| 28 | /*! | |
| 29 | * jQuery JavaScript Library v1.7.1 | |
| 30 | * http://jquery.com/ | |
| 31 | * | |
| 32 | * Copyright 2011, John Resig | |
| 33 | * Dual licensed under the MIT or GPL Version 2 licenses. | |
| 34 | * http://jquery.org/license | |
| 35 | * | |
| 36 | * Includes Sizzle.js | |
| 37 | * http://sizzlejs.com/ | |
| 38 | * Copyright 2011, The Dojo Foundation | |
| 39 | * Released under the MIT, BSD, and GPL Licenses. | |
| 40 | * | |
| 41 | * Date: Mon Nov 21 21:11:03 2011 -0500 | |
| 42 | */ | |
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bx){bx[by]=false}}}}},attrHooks:{type:{set:function(e,bv){if(g.test(e.nodeName)&&e.parentNode){b.error("type property can't be changed")}else{if(!b.support.radioValue&&bv==="radio"&&b.nodeName(e,"input")){var bw=e.value;e.setAttribute("type",bv);if(bw){e.value=bw}return bv}}}},value:{get:function(bv,e){if(be&&b.nodeName(bv,"button")){return be.get(bv,e)}return e in bv?bv.value:null},set:function(bv,bw,e){if(be&&b.nodeName(bv,"button")){return be.set(bv,bw,e)}bv.value=bw}}},propFix:{tabindex:"tabIndex",readonly:"readOnly","for":"htmlFor","class":"className",maxlength:"maxLength",cellspacing:"cellSpacing",cellpadding:"cellPadding",rowspan:"rowSpan",colspan:"colSpan",usemap:"useMap",frameborder:"frameBorder",contenteditable:"contentEditable"},prop:function(bz,bx,bA){var bw,e,by,bv=bz.nodeType;if(!bz||bv===3||bv===8||bv===2){return}by=bv!==1||!b.isXMLDoc(bz);if(by){bx=b.propFix[bx]||bx;e=b.propHooks[bx]}if(bA!==L){if(e&&"set" in e&&(bw=e.set(bz,bA,bx))!==L){return bw}else{return(bz[bx]=bA)}}else{if(e&&"get" in e&&(bw=e.get(bz,bx))!==null){return bw}else{return bz[bx]}}},propHooks:{tabIndex:{get:function(bv){var e=bv.getAttributeNode("tabindex");return e&&e.specified?parseInt(e.value,10):D.test(bv.nodeName)||l.test(bv.nodeName)&&bv.href?0:L}}}});b.attrHooks.tabindex=b.propHooks.tabIndex;aY={get:function(bv,e){var bx,bw=b.prop(bv,e);return bw===true||typeof bw!=="boolean"&&(bx=bv.getAttributeNode(e))&&bx.nodeValue!==false?e.toLowerCase():L},set:function(bv,bx,e){var bw;if(bx===false){b.removeAttr(bv,e)}else{bw=b.propFix[e]||e;if(bw in bv){bv[bw]=true}bv.setAttribute(e,e.toLowerCase())}return e}};if(!F){aF={name:true,id:true};be=b.valHooks.button={get:function(bw,bv){var e;e=bw.getAttributeNode(bv);return e&&(aF[bv]?e.nodeValue!=="":e.specified)?e.nodeValue:L},set:function(bw,bx,bv){var e=bw.getAttributeNode(bv);if(!e){e=av.createAttribute(bv);bw.setAttributeNode(e)}return(e.nodeValue=bx+"")}};b.attrHooks.tabindex.set=be.set;b.each(["width","height"],function(bv,e){b.attrHooks[e]=b.extend(b.attrHooks[e],{set:function(bw,bx){if(bx===""){bw.setAttribute(e,"auto");return bx}}})});b.attrHooks.contenteditable={get:be.get,set:function(bv,bw,e){if(bw===""){bw="false"}be.set(bv,bw,e)}}}if(!b.support.hrefNormalized){b.each(["href","src","width","height"],function(bv,e){b.attrHooks[e]=b.extend(b.attrHooks[e],{get:function(bx){var bw=bx.getAttribute(e,2);return bw===null?L:bw}})})}if(!b.support.style){b.attrHooks.style={get:function(e){return e.style.cssText.toLowerCase()||L},set:function(e,bv){return(e.style.cssText=""+bv)}}}if(!b.support.optSelected){b.propHooks.selected=b.extend(b.propHooks.selected,{get:function(bv){var e=bv.parentNode;if(e){e.selectedIndex;if(e.parentNode){e.parentNode.selectedIndex}}return null}})}if(!b.support.enctype){b.propFix.enctype="encoding"}if(!b.support.checkOn){b.each(["radio","checkbox"],function(){b.valHooks[this]={get:function(e){return e.getAttribute("value")===null?"on":e.value}}})}b.each(["radio","checkbox"],function(){b.valHooks[this]=b.extend(b.valHooks[this],{set:function(e,bv){if(b.isArray(bv)){return(e.checked=b.inArray(b(e).val(),bv)>=0)}}})});var bd=/^(?:textarea|input|select)$/i,n=/^([^\.]*)?(?:\.(.+))?$/,J=/\bhover(\.\S+)?\b/,aO=/^key/,bf=/^(?:mouse|contextmenu)|click/,T=/^(?:focusinfocus|focusoutblur)$/,U=/^(\w*)(?:#([\w\-]+))?(?:\.([\w\-]+))?$/,Y=function(e){var bv=U.exec(e);if(bv){bv[1]=(bv[1]||"").toLowerCase();bv[3]=bv[3]&&new RegExp("(?:^|\\s)"+bv[3]+"(?:\\s|$)")}return bv},j=function(bw,e){var bv=bw.attributes||{};return((!e[1]||bw.nodeName.toLowerCase()===e[1])&&(!e[2]||(bv.id||{}).value===e[2])&&(!e[3]||e[3].test((bv["class"]||{}).value)))},bt=function(e){return b.event.special.hover?e:e.replace(J,"mouseenter$1 mouseleave$1")};b.event={add:function(bx,bC,bJ,bA,by){var bD,bB,bK,bI,bH,bF,e,bG,bv,bz,bw,bE;if(bx.nodeType===3||bx.nodeType===8||!bC||!bJ||!(bD=b._data(bx))){return}if(bJ.handler){bv=bJ;bJ=bv.handler}if(!bJ.guid){bJ.guid=b.guid++}bK=bD.events;if(!bK){bD.events=bK={}}bB=bD.handle;if(!bB){bD.handle=bB=function(bL){return typeof b!=="undefined"&&(!bL||b.event.triggered!==bL.type)?b.event.dispatch.apply(bB.elem,arguments):L};bB.elem=bx}bC=b.trim(bt(bC)).split(" ");for(bI=0;bI<bC.length;bI++){bH=n.exec(bC[bI])||[];bF=bH[1];e=(bH[2]||"").split(".").sort();bE=b.event.special[bF]||{};bF=(by?bE.delegateType:bE.bindType)||bF;bE=b.event.special[bF]||{};bG=b.extend({type:bF,origType:bH[1],data:bA,handler:bJ,guid:bJ.guid,selector:by,quick:Y(by),namespace:e.join(".")},bv);bw=bK[bF];if(!bw){bw=bK[bF]=[];bw.delegateCount=0;if(!bE.setup||bE.setup.call(bx,bA,e,bB)===false){if(bx.addEventListener){bx.addEventListener(bF,bB,false)}else{if(bx.attachEvent){bx.attachEvent("on"+bF,bB)}}}}if(bE.add){bE.add.call(bx,bG);if(!bG.handler.guid){bG.handler.guid=bJ.guid}}if(by){bw.splice(bw.delegateCount++,0,bG)}else{bw.push(bG)}b.event.global[bF]=true}bx=null},global:{},remove:function(bJ,bE,bv,bH,bB){var bI=b.hasData(bJ)&&b._data(bJ),bF,bx,bz,bL,bC,bA,bG,bw,by,bK,bD,e;if(!bI||!(bw=bI.events)){return}bE=b.trim(bt(bE||"")).split(" ");for(bF=0;bF<bE.length;bF++){bx=n.exec(bE[bF])||[];bz=bL=bx[1];bC=bx[2];if(!bz){for(bz in bw){b.event.remove(bJ,bz+bE[bF],bv,bH,true)}continue}by=b.event.special[bz]||{};bz=(bH?by.delegateType:by.bindType)||bz;bD=bw[bz]||[];bA=bD.length;bC=bC?new RegExp("(^|\\.)"+bC.split(".").sort().join("\\.(?:.*\\.)?")+"(\\.|$)"):null;for(bG=0;bG<bD.length;bG++){e=bD[bG];if((bB||bL===e.origType)&&(!bv||bv.guid===e.guid)&&(!bC||bC.test(e.namespace))&&(!bH||bH===e.selector||bH==="**"&&e.selector)){bD.splice(bG--,1);if(e.selector){bD.delegateCount--}if(by.remove){by.remove.call(bJ,e)}}}if(bD.length===0&&bA!==bD.length){if(!by.teardown||by.teardown.call(bJ,bC)===false){b.removeEvent(bJ,bz,bI.handle)}delete bw[bz]}}if(b.isEmptyObject(bw)){bK=bI.handle;if(bK){bK.elem=null}b.removeData(bJ,["events","handle"],true)}},customEvent:{getData:true,setData:true,changeData:true},trigger:function(bv,bD,bA,bJ){if(bA&&(bA.nodeType===3||bA.nodeType===8)){return}var bG=bv.type||bv,bx=[],e,bw,bC,bH,bz,by,bF,bE,bB,bI;if(T.test(bG+b.event.triggered)){return}if(bG.indexOf("!")>=0){bG=bG.slice(0,-1);bw=true}if(bG.indexOf(".")>=0){bx=bG.split(".");bG=bx.shift();bx.sort()}if((!bA||b.event.customEvent[bG])&&!b.event.global[bG]){return}bv=typeof bv==="object"?bv[b.expando]?bv:new b.Event(bG,bv):new b.Event(bG);bv.type=bG;bv.isTrigger=true;bv.exclusive=bw;bv.namespace=bx.join(".");bv.namespace_re=bv.namespace?new RegExp("(^|\\.)"+bx.join("\\.(?:.*\\.)?")+"(\\.|$)"):null;by=bG.indexOf(":")<0?"on"+bG:"";if(!bA){e=b.cache;for(bC in e){if(e[bC].events&&e[bC].events[bG]){b.event.trigger(bv,bD,e[bC].handle.elem,true)}}return}bv.result=L;if(!bv.target){bv.target=bA}bD=bD!=null?b.makeArray(bD):[];bD.unshift(bv);bF=b.event.special[bG]||{};if(bF.trigger&&bF.trigger.apply(bA,bD)===false){return}bB=[[bA,bF.bindType||bG]];if(!bJ&&!bF.noBubble&&!b.isWindow(bA)){bI=bF.delegateType||bG;bH=T.test(bI+bG)?bA:bA.parentNode;bz=null;for(;bH;bH=bH.parentNode){bB.push([bH,bI]);bz=bH}if(bz&&bz===bA.ownerDocument){bB.push([bz.defaultView||bz.parentWindow||bb,bI])}}for(bC=0;bC<bB.length&&!bv.isPropagationStopped();bC++){bH=bB[bC][0];bv.type=bB[bC][1];bE=(b._data(bH,"events")||{})[bv.type]&&b._data(bH,"handle");if(bE){bE.apply(bH,bD)}bE=by&&bH[by];if(bE&&b.acceptData(bH)&&bE.apply(bH,bD)===false){bv.preventDefault()}}bv.type=bG;if(!bJ&&!bv.isDefaultPrevented()){if((!bF._default||bF._default.apply(bA.ownerDocument,bD)===false)&&!(bG==="click"&&b.nodeName(bA,"a"))&&b.acceptData(bA)){if(by&&bA[bG]&&((bG!=="focus"&&bG!=="blur")||bv.target.offsetWidth!==0)&&!b.isWindow(bA)){bz=bA[by];if(bz){bA[by]=null}b.event.triggered=bG;bA[bG]();b.event.triggered=L;if(bz){bA[by]=bz}}}}return bv.result},dispatch:function(e){e=b.event.fix(e||bb.event);var bz=((b._data(this,"events")||{})[e.type]||[]),bA=bz.delegateCount,bG=[].slice.call(arguments,0),by=!e.exclusive&&!e.namespace,bH=[],bC,bB,bK,bx,bF,bE,bv,bD,bI,bw,bJ;bG[0]=e;e.delegateTarget=this;if(bA&&!e.target.disabled&&!(e.button&&e.type==="click")){bx=b(this);bx.context=this.ownerDocument||this;for(bK=e.target;bK!=this;bK=bK.parentNode||this){bE={};bD=[];bx[0]=bK;for(bC=0;bC<bA;bC++){bI=bz[bC];bw=bI.selector;if(bE[bw]===L){bE[bw]=(bI.quick?j(bK,bI.quick):bx.is(bw))}if(bE[bw]){bD.push(bI)}}if(bD.length){bH.push({elem:bK,matches:bD})}}}if(bz.length>bA){bH.push({elem:this,matches:bz.slice(bA)})}for(bC=0;bC<bH.length&&!e.isPropagationStopped();bC++){bv=bH[bC];e.currentTarget=bv.elem;for(bB=0;bB<bv.matches.length&&!e.isImmediatePropagationStopped();bB++){bI=bv.matches[bB];if(by||(!e.namespace&&!bI.namespace)||e.namespace_re&&e.namespace_re.test(bI.namespace)){e.data=bI.data;e.handleObj=bI;bF=((b.event.special[bI.origType]||{}).handle||bI.handler).apply(bv.elem,bG);if(bF!==L){e.result=bF;if(bF===false){e.preventDefault();e.stopPropagation()}}}}}return e.result},props:"attrChange attrName relatedNode srcElement altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),fixHooks:{},keyHooks:{props:"char charCode key keyCode".split(" "),filter:function(bv,e){if(bv.which==null){bv.which=e.charCode!=null?e.charCode:e.keyCode}return bv}},mouseHooks:{props:"button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),filter:function(bx,bw){var by,bz,e,bv=bw.button,bA=bw.fromElement;if(bx.pageX==null&&bw.clientX!=null){by=bx.target.ownerDocument||av;bz=by.documentElement;e=by.body;bx.pageX=bw.clientX+(bz&&bz.scrollLeft||e&&e.scrollLeft||0)-(bz&&bz.clientLeft||e&&e.clientLeft||0);bx.pageY=bw.clientY+(bz&&bz.scrollTop||e&&e.scrollTop||0)-(bz&&bz.clientTop||e&&e.clientTop||0)}if(!bx.relatedTarget&&bA){bx.relatedTarget=bA===bx.target?bw.toElement:bA}if(!bx.which&&bv!==L){bx.which=(bv&1?1:(bv&2?3:(bv&4?2:0)))}return bx}},fix:function(bw){if(bw[b.expando]){return bw}var bv,bz,e=bw,bx=b.event.fixHooks[bw.type]||{},by=bx.props?this.props.concat(bx.props):this.props;bw=b.Event(e);for(bv=by.length;bv;){bz=by[--bv];bw[bz]=e[bz]}if(!bw.target){bw.target=e.srcElement||av}if(bw.target.nodeType===3){bw.target=bw.target.parentNode}if(bw.metaKey===L){bw.metaKey=bw.ctrlKey}return bx.filter?bx.filter(bw,e):bw},special:{ready:{setup:b.bindReady},load:{noBubble:true},focus:{delegateType:"focusin"},blur:{delegateType:"focusout"},beforeunload:{setup:function(bw,bv,e){if(b.isWindow(this)){this.onbeforeunload=e}},teardown:function(bv,e){if(this.onbeforeunload===e){this.onbeforeunload=null}}}},simulate:function(bw,by,bx,bv){var bz=b.extend(new b.Event(),bx,{type:bw,isSimulated:true,originalEvent:{}});if(bv){b.event.trigger(bz,null,by)}else{b.event.dispatch.call(by,bz)}if(bz.isDefaultPrevented()){bx.preventDefault()}}};b.event.handle=b.event.dispatch;b.removeEvent=av.removeEventListener?function(bv,e,bw){if(bv.removeEventListener){bv.removeEventListener(e,bw,false)}}:function(bv,e,bw){if(bv.detachEvent){bv.detachEvent("on"+e,bw)}};b.Event=function(bv,e){if(!(this instanceof b.Event)){return new b.Event(bv,e)}if(bv&&bv.type){this.originalEvent=bv;this.type=bv.type;this.isDefaultPrevented=(bv.defaultPrevented||bv.returnValue===false||bv.getPreventDefault&&bv.getPreventDefault())?i:bk}else{this.type=bv}if(e){b.extend(this,e)}this.timeStamp=bv&&bv.timeStamp||b.now();this[b.expando]=true};function bk(){return false}function i(){return true}b.Event.prototype={preventDefault:function(){this.isDefaultPrevented=i;var bv=this.originalEvent;if(!bv){return}if(bv.preventDefault){bv.preventDefault()}else{bv.returnValue=false}},stopPropagation:function(){this.isPropagationStopped=i;var bv=this.originalEvent;if(!bv){return}if(bv.stopPropagation){bv.stopPropagation()}bv.cancelBubble=true},stopImmediatePropagation:function(){this.isImmediatePropagationStopped=i;this.stopPropagation()},isDefaultPrevented:bk,isPropagationStopped:bk,isImmediatePropagationStopped:bk};b.each({mouseenter:"mouseover",mouseleave:"mouseout"},function(bv,e){b.event.special[bv]={delegateType:e,bindType:e,handle:function(bz){var bB=this,bA=bz.relatedTarget,by=bz.handleObj,bw=by.selector,bx;if(!bA||(bA!==bB&&!b.contains(bB,bA))){bz.type=by.origType;bx=by.handler.apply(this,arguments);bz.type=e}return bx}}});if(!b.support.submitBubbles){b.event.special.submit={setup:function(){if(b.nodeName(this,"form")){return false}b.event.add(this,"click._submit keypress._submit",function(bx){var bw=bx.target,bv=b.nodeName(bw,"input")||b.nodeName(bw,"button")?bw.form:L;if(bv&&!bv._submit_attached){b.event.add(bv,"submit._submit",function(e){if(this.parentNode&&!e.isTrigger){b.event.simulate("submit",this.parentNode,e,true)}});bv._submit_attached=true}})},teardown:function(){if(b.nodeName(this,"form")){return false}b.event.remove(this,"._submit")}}}if(!b.support.changeBubbles){b.event.special.change={setup:function(){if(bd.test(this.nodeName)){if(this.type==="checkbox"||this.type==="radio"){b.event.add(this,"propertychange._change",function(e){if(e.originalEvent.propertyName==="checked"){this._just_changed=true}});b.event.add(this,"click._change",function(e){if(this._just_changed&&!e.isTrigger){this._just_changed=false;b.event.simulate("change",this,e,true)}})}return false}b.event.add(this,"beforeactivate._change",function(bw){var bv=bw.target;if(bd.test(bv.nodeName)&&!bv._change_attached){b.event.add(bv,"change._change",function(e){if(this.parentNode&&!e.isSimulated&&!e.isTrigger){b.event.simulate("change",this.parentNode,e,true)}});bv._change_attached=true}})},handle:function(bv){var e=bv.target;if(this!==e||bv.isSimulated||bv.isTrigger||(e.type!=="radio"&&e.type!=="checkbox")){return bv.handleObj.handler.apply(this,arguments)}},teardown:function(){b.event.remove(this,"._change");return bd.test(this.nodeName)}}}if(!b.support.focusinBubbles){b.each({focus:"focusin",blur:"focusout"},function(bx,e){var bv=0,bw=function(by){b.event.simulate(e,by.target,b.event.fix(by),true)};b.event.special[e]={setup:function(){if(bv++===0){av.addEventListener(bx,bw,true)}},teardown:function(){if(--bv===0){av.removeEventListener(bx,bw,true)}}}})}b.fn.extend({on:function(bw,e,bz,by,bv){var bA,bx;if(typeof bw==="object"){if(typeof e!=="string"){bz=e;e=L}for(bx in bw){this.on(bx,e,bz,bw[bx],bv)}return this}if(bz==null&&by==null){by=e;bz=e=L}else{if(by==null){if(typeof e==="string"){by=bz;bz=L}else{by=bz;bz=e;e=L}}}if(by===false){by=bk}else{if(!by){return this}}if(bv===1){bA=by;by=function(bB){b().off(bB);return bA.apply(this,arguments)};by.guid=bA.guid||(bA.guid=b.guid++)}return this.each(function(){b.event.add(this,bw,by,bz,e)})},one:function(bv,e,bx,bw){return this.on.call(this,bv,e,bx,bw,1)},off:function(bw,e,by){if(bw&&bw.preventDefault&&bw.handleObj){var bv=bw.handleObj;b(bw.delegateTarget).off(bv.namespace?bv.type+"."+bv.namespace:bv.type,bv.selector,bv.handler);return this}if(typeof bw==="object"){for(var bx in bw){this.off(bx,e,bw[bx])}return this}if(e===false||typeof e==="function"){by=e;e=L}if(by===false){by=bk}return this.each(function(){b.event.remove(this,bw,by,e)})},bind:function(e,bw,bv){return this.on(e,null,bw,bv)},unbind:function(e,bv){return this.off(e,null,bv)},live:function(e,bw,bv){b(this.context).on(e,this.selector,bw,bv);return this},die:function(e,bv){b(this.context).off(e,this.selector||"**",bv);return this},delegate:function(e,bv,bx,bw){return this.on(bv,e,bx,bw)},undelegate:function(e,bv,bw){return arguments.length==1?this.off(e,"**"):this.off(bv,e,bw)},trigger:function(e,bv){return this.each(function(){b.event.trigger(e,bv,this)})},triggerHandler:function(e,bv){if(this[0]){return b.event.trigger(e,bv,this[0],true)}},toggle:function(bx){var bv=arguments,e=bx.guid||b.guid++,bw=0,by=function(bz){var bA=(b._data(this,"lastToggle"+bx.guid)||0)%bw;b._data(this,"lastToggle"+bx.guid,bA+1);bz.preventDefault();return bv[bA].apply(this,arguments)||false};by.guid=e;while(bw<bv.length){bv[bw++].guid=e}return this.click(by)},hover:function(e,bv){return this.mouseenter(e).mouseleave(bv||e)}});b.each(("blur focus focusin focusout load resize scroll unload click dblclick mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave change select submit keydown keypress keyup error contextmenu").split(" "),function(bv,e){b.fn[e]=function(bx,bw){if(bw==null){bw=bx;bx=null}return arguments.length>0?this.on(e,null,bx,bw):this.trigger(e)};if(b.attrFn){b.attrFn[e]=true}if(aO.test(e)){b.event.fixHooks[e]=b.event.keyHooks}if(bf.test(e)){b.event.fixHooks[e]=b.event.mouseHooks}}); | |
| 44 | /*! | |
| 45 | * Sizzle CSS Selector Engine | |
| 46 | * Copyright 2011, The Dojo Foundation | |
| 47 | * Released under the MIT, BSD, and GPL Licenses. | |
| 48 | * More information: http://sizzlejs.com/ | |
| 49 | */ | |
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| 51 | * jQuery UI 1.8.18 | |
| 52 | * | |
| 53 | * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about) | |
| 54 | * Dual licensed under the MIT or GPL Version 2 licenses. | |
| 55 | * http://jquery.org/license | |
| 56 | * | |
| 57 | * http://docs.jquery.com/UI | |
| 58 | */ | |
| 59 | (function(a,d){a.ui=a.ui||{};if(a.ui.version){return}a.extend(a.ui,{version:"1.8.18",keyCode:{ALT:18,BACKSPACE:8,CAPS_LOCK:20,COMMA:188,COMMAND:91,COMMAND_LEFT:91,COMMAND_RIGHT:93,CONTROL:17,DELETE:46,DOWN:40,END:35,ENTER:13,ESCAPE:27,HOME:36,INSERT:45,LEFT:37,MENU:93,NUMPAD_ADD:107,NUMPAD_DECIMAL:110,NUMPAD_DIVIDE:111,NUMPAD_ENTER:108,NUMPAD_MULTIPLY:106,NUMPAD_SUBTRACT:109,PAGE_DOWN:34,PAGE_UP:33,PERIOD:190,RIGHT:39,SHIFT:16,SPACE:32,TAB:9,UP:38,WINDOWS:91}});a.fn.extend({propAttr:a.fn.prop||a.fn.attr,_focus:a.fn.focus,focus:function(e,f){return typeof e==="number"?this.each(function(){var g=this;setTimeout(function(){a(g).focus();if(f){f.call(g)}},e)}):this._focus.apply(this,arguments)},scrollParent:function(){var e;if((a.browser.msie&&(/(static|relative)/).test(this.css("position")))||(/absolute/).test(this.css("position"))){e=this.parents().filter(function(){return(/(relative|absolute|fixed)/).test(a.curCSS(this,"position",1))&&(/(auto|scroll)/).test(a.curCSS(this,"overflow",1)+a.curCSS(this,"overflow-y",1)+a.curCSS(this,"overflow-x",1))}).eq(0)}else{e=this.parents().filter(function(){return(/(auto|scroll)/).test(a.curCSS(this,"overflow",1)+a.curCSS(this,"overflow-y",1)+a.curCSS(this,"overflow-x",1))}).eq(0)}return(/fixed/).test(this.css("position"))||!e.length?a(document):e},zIndex:function(h){if(h!==d){return this.css("zIndex",h)}if(this.length){var f=a(this[0]),e,g;while(f.length&&f[0]!==document){e=f.css("position");if(e==="absolute"||e==="relative"||e==="fixed"){g=parseInt(f.css("zIndex"),10);if(!isNaN(g)&&g!==0){return g}}f=f.parent()}}return 0},disableSelection:function(){return this.bind((a.support.selectstart?"selectstart":"mousedown")+".ui-disableSelection",function(e){e.preventDefault()})},enableSelection:function(){return this.unbind(".ui-disableSelection")}});a.each(["Width","Height"],function(g,e){var f=e==="Width"?["Left","Right"]:["Top","Bottom"],h=e.toLowerCase(),k={innerWidth:a.fn.innerWidth,innerHeight:a.fn.innerHeight,outerWidth:a.fn.outerWidth,outerHeight:a.fn.outerHeight};function j(m,l,i,n){a.each(f,function(){l-=parseFloat(a.curCSS(m,"padding"+this,true))||0;if(i){l-=parseFloat(a.curCSS(m,"border"+this+"Width",true))||0}if(n){l-=parseFloat(a.curCSS(m,"margin"+this,true))||0}});return l}a.fn["inner"+e]=function(i){if(i===d){return k["inner"+e].call(this)}return this.each(function(){a(this).css(h,j(this,i)+"px")})};a.fn["outer"+e]=function(i,l){if(typeof i!=="number"){return k["outer"+e].call(this,i)}return this.each(function(){a(this).css(h,j(this,i,true,l)+"px")})}});function c(g,e){var j=g.nodeName.toLowerCase();if("area"===j){var i=g.parentNode,h=i.name,f;if(!g.href||!h||i.nodeName.toLowerCase()!=="map"){return false}f=a("img[usemap=#"+h+"]")[0];return !!f&&b(f)}return(/input|select|textarea|button|object/.test(j)?!g.disabled:"a"==j?g.href||e:e)&&b(g)}function b(e){return !a(e).parents().andSelf().filter(function(){return a.curCSS(this,"visibility")==="hidden"||a.expr.filters.hidden(this)}).length}a.extend(a.expr[":"],{data:function(g,f,e){return !!a.data(g,e[3])},focusable:function(e){return c(e,!isNaN(a.attr(e,"tabindex")))},tabbable:function(g){var e=a.attr(g,"tabindex"),f=isNaN(e);return(f||e>=0)&&c(g,!f)}});a(function(){var e=document.body,f=e.appendChild(f=document.createElement("div"));f.offsetHeight;a.extend(f.style,{minHeight:"100px",height:"auto",padding:0,borderWidth:0});a.support.minHeight=f.offsetHeight===100;a.support.selectstart="onselectstart" in f;e.removeChild(f).style.display="none"});a.extend(a.ui,{plugin:{add:function(f,g,j){var h=a.ui[f].prototype;for(var e in j){h.plugins[e]=h.plugins[e]||[];h.plugins[e].push([g,j[e]])}},call:function(e,g,f){var j=e.plugins[g];if(!j||!e.element[0].parentNode){return}for(var h=0;h<j.length;h++){if(e.options[j[h][0]]){j[h][1].apply(e.element,f)}}}},contains:function(f,e){return document.compareDocumentPosition?f.compareDocumentPosition(e)&16:f!==e&&f.contains(e)},hasScroll:function(h,f){if(a(h).css("overflow")==="hidden"){return false}var e=(f&&f==="left")?"scrollLeft":"scrollTop",g=false;if(h[e]>0){return true}h[e]=1;g=(h[e]>0);h[e]=0;return g},isOverAxis:function(f,e,g){return(f>e)&&(f<(e+g))},isOver:function(j,f,i,h,e,g){return a.ui.isOverAxis(j,i,e)&&a.ui.isOverAxis(f,h,g)}})})(jQuery);/*! | |
| 60 | * jQuery UI Widget 1.8.18 | |
| 61 | * | |
| 62 | * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about) | |
| 63 | * Dual licensed under the MIT or GPL Version 2 licenses. | |
| 64 | * http://jquery.org/license | |
| 65 | * | |
| 66 | * http://docs.jquery.com/UI/Widget | |
| 67 | */ | |
| 68 | (function(b,d){if(b.cleanData){var c=b.cleanData;b.cleanData=function(f){for(var g=0,h;(h=f[g])!=null;g++){try{b(h).triggerHandler("remove")}catch(j){}}c(f)}}else{var a=b.fn.remove;b.fn.remove=function(e,f){return this.each(function(){if(!f){if(!e||b.filter(e,[this]).length){b("*",this).add([this]).each(function(){try{b(this).triggerHandler("remove")}catch(g){}})}}return a.call(b(this),e,f)})}}b.widget=function(f,h,e){var g=f.split(".")[0],j;f=f.split(".")[1];j=g+"-"+f;if(!e){e=h;h=b.Widget}b.expr[":"][j]=function(k){return !!b.data(k,f)};b[g]=b[g]||{};b[g][f]=function(k,l){if(arguments.length){this._createWidget(k,l)}};var i=new h();i.options=b.extend(true,{},i.options);b[g][f].prototype=b.extend(true,i,{namespace:g,widgetName:f,widgetEventPrefix:b[g][f].prototype.widgetEventPrefix||f,widgetBaseClass:j},e);b.widget.bridge(f,b[g][f])};b.widget.bridge=function(f,e){b.fn[f]=function(i){var g=typeof i==="string",h=Array.prototype.slice.call(arguments,1),j=this;i=!g&&h.length?b.extend.apply(null,[true,i].concat(h)):i;if(g&&i.charAt(0)==="_"){return j}if(g){this.each(function(){var k=b.data(this,f),l=k&&b.isFunction(k[i])?k[i].apply(k,h):k;if(l!==k&&l!==d){j=l;return false}})}else{this.each(function(){var k=b.data(this,f);if(k){k.option(i||{})._init()}else{b.data(this,f,new e(i,this))}})}return j}};b.Widget=function(e,f){if(arguments.length){this._createWidget(e,f)}};b.Widget.prototype={widgetName:"widget",widgetEventPrefix:"",options:{disabled:false},_createWidget:function(f,g){b.data(g,this.widgetName,this);this.element=b(g);this.options=b.extend(true,{},this.options,this._getCreateOptions(),f);var e=this;this.element.bind("remove."+this.widgetName,function(){e.destroy()});this._create();this._trigger("create");this._init()},_getCreateOptions:function(){return b.metadata&&b.metadata.get(this.element[0])[this.widgetName]},_create:function(){},_init:function(){},destroy:function(){this.element.unbind("."+this.widgetName).removeData(this.widgetName);this.widget().unbind("."+this.widgetName).removeAttr("aria-disabled").removeClass(this.widgetBaseClass+"-disabled ui-state-disabled")},widget:function(){return this.element},option:function(f,g){var e=f;if(arguments.length===0){return b.extend({},this.options)}if(typeof f==="string"){if(g===d){return this.options[f]}e={};e[f]=g}this._setOptions(e);return this},_setOptions:function(f){var e=this;b.each(f,function(g,h){e._setOption(g,h)});return this},_setOption:function(e,f){this.options[e]=f;if(e==="disabled"){this.widget()[f?"addClass":"removeClass"](this.widgetBaseClass+"-disabled ui-state-disabled").attr("aria-disabled",f)}return this},enable:function(){return this._setOption("disabled",false)},disable:function(){return this._setOption("disabled",true)},_trigger:function(e,f,g){var j,i,h=this.options[e];g=g||{};f=b.Event(f);f.type=(e===this.widgetEventPrefix?e:this.widgetEventPrefix+e).toLowerCase();f.target=this.element[0];i=f.originalEvent;if(i){for(j in i){if(!(j in f)){f[j]=i[j]}}}this.element.trigger(f,g);return !(b.isFunction(h)&&h.call(this.element[0],f,g)===false||f.isDefaultPrevented())}}})(jQuery);/*! | |
| 69 | * jQuery UI Mouse 1.8.18 | |
| 70 | * | |
| 71 | * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about) | |
| 72 | * Dual licensed under the MIT or GPL Version 2 licenses. | |
| 73 | * http://jquery.org/license | |
| 74 | * | |
| 75 | * http://docs.jquery.com/UI/Mouse | |
| 76 | * | |
| 77 | * Depends: | |
| 78 | * jquery.ui.widget.js | |
| 79 | */ | |
| 80 | (function(b,c){var a=false;b(document).mouseup(function(d){a=false});b.widget("ui.mouse",{options:{cancel:":input,option",distance:1,delay:0},_mouseInit:function(){var d=this;this.element.bind("mousedown."+this.widgetName,function(e){return d._mouseDown(e)}).bind("click."+this.widgetName,function(e){if(true===b.data(e.target,d.widgetName+".preventClickEvent")){b.removeData(e.target,d.widgetName+".preventClickEvent");e.stopImmediatePropagation();return false}});this.started=false},_mouseDestroy:function(){this.element.unbind("."+this.widgetName)},_mouseDown:function(f){if(a){return}(this._mouseStarted&&this._mouseUp(f));this._mouseDownEvent=f;var e=this,g=(f.which==1),d=(typeof this.options.cancel=="string"&&f.target.nodeName?b(f.target).closest(this.options.cancel).length:false);if(!g||d||!this._mouseCapture(f)){return true}this.mouseDelayMet=!this.options.delay;if(!this.mouseDelayMet){this._mouseDelayTimer=setTimeout(function(){e.mouseDelayMet=true},this.options.delay)}if(this._mouseDistanceMet(f)&&this._mouseDelayMet(f)){this._mouseStarted=(this._mouseStart(f)!==false);if(!this._mouseStarted){f.preventDefault();return true}}if(true===b.data(f.target,this.widgetName+".preventClickEvent")){b.removeData(f.target,this.widgetName+".preventClickEvent")}this._mouseMoveDelegate=function(h){return e._mouseMove(h)};this._mouseUpDelegate=function(h){return e._mouseUp(h)};b(document).bind("mousemove."+this.widgetName,this._mouseMoveDelegate).bind("mouseup."+this.widgetName,this._mouseUpDelegate);f.preventDefault();a=true;return true},_mouseMove:function(d){if(b.browser.msie&&!(document.documentMode>=9)&&!d.button){return this._mouseUp(d)}if(this._mouseStarted){this._mouseDrag(d);return d.preventDefault()}if(this._mouseDistanceMet(d)&&this._mouseDelayMet(d)){this._mouseStarted=(this._mouseStart(this._mouseDownEvent,d)!==false);(this._mouseStarted?this._mouseDrag(d):this._mouseUp(d))}return !this._mouseStarted},_mouseUp:function(d){b(document).unbind("mousemove."+this.widgetName,this._mouseMoveDelegate).unbind("mouseup."+this.widgetName,this._mouseUpDelegate);if(this._mouseStarted){this._mouseStarted=false;if(d.target==this._mouseDownEvent.target){b.data(d.target,this.widgetName+".preventClickEvent",true)}this._mouseStop(d)}return false},_mouseDistanceMet:function(d){return(Math.max(Math.abs(this._mouseDownEvent.pageX-d.pageX),Math.abs(this._mouseDownEvent.pageY-d.pageY))>=this.options.distance)},_mouseDelayMet:function(d){return this.mouseDelayMet},_mouseStart:function(d){},_mouseDrag:function(d){},_mouseStop:function(d){},_mouseCapture:function(d){return true}})})(jQuery);(function(c,d){c.widget("ui.resizable",c.ui.mouse,{widgetEventPrefix:"resize",options:{alsoResize:false,animate:false,animateDuration:"slow",animateEasing:"swing",aspectRatio:false,autoHide:false,containment:false,ghost:false,grid:false,handles:"e,s,se",helper:false,maxHeight:null,maxWidth:null,minHeight:10,minWidth:10,zIndex:1000},_create:function(){var f=this,k=this.options;this.element.addClass("ui-resizable");c.extend(this,{_aspectRatio:!!(k.aspectRatio),aspectRatio:k.aspectRatio,originalElement:this.element,_proportionallyResizeElements:[],_helper:k.helper||k.ghost||k.animate?k.helper||"ui-resizable-helper":null});if(this.element[0].nodeName.match(/canvas|textarea|input|select|button|img/i)){this.element.wrap(c('<div class="ui-wrapper" style="overflow: hidden;"></div>').css({position:this.element.css("position"),width:this.element.outerWidth(),height:this.element.outerHeight(),top:this.element.css("top"),left:this.element.css("left")}));this.element=this.element.parent().data("resizable",this.element.data("resizable"));this.elementIsWrapper=true;this.element.css({marginLeft:this.originalElement.css("marginLeft"),marginTop:this.originalElement.css("marginTop"),marginRight:this.originalElement.css("marginRight"),marginBottom:this.originalElement.css("marginBottom")});this.originalElement.css({marginLeft:0,marginTop:0,marginRight:0,marginBottom:0});this.originalResizeStyle=this.originalElement.css("resize");this.originalElement.css("resize","none");this._proportionallyResizeElements.push(this.originalElement.css({position:"static",zoom:1,display:"block"}));this.originalElement.css({margin:this.originalElement.css("margin")});this._proportionallyResize()}this.handles=k.handles||(!c(".ui-resizable-handle",this.element).length?"e,s,se":{n:".ui-resizable-n",e:".ui-resizable-e",s:".ui-resizable-s",w:".ui-resizable-w",se:".ui-resizable-se",sw:".ui-resizable-sw",ne:".ui-resizable-ne",nw:".ui-resizable-nw"});if(this.handles.constructor==String){if(this.handles=="all"){this.handles="n,e,s,w,se,sw,ne,nw"}var l=this.handles.split(",");this.handles={};for(var g=0;g<l.length;g++){var j=c.trim(l[g]),e="ui-resizable-"+j;var h=c('<div class="ui-resizable-handle '+e+'"></div>');if(/sw|se|ne|nw/.test(j)){h.css({zIndex:++k.zIndex})}if("se"==j){h.addClass("ui-icon ui-icon-gripsmall-diagonal-se")}this.handles[j]=".ui-resizable-"+j;this.element.append(h)}}this._renderAxis=function(q){q=q||this.element;for(var n in this.handles){if(this.handles[n].constructor==String){this.handles[n]=c(this.handles[n],this.element).show()}if(this.elementIsWrapper&&this.originalElement[0].nodeName.match(/textarea|input|select|button/i)){var o=c(this.handles[n],this.element),p=0;p=/sw|ne|nw|se|n|s/.test(n)?o.outerHeight():o.outerWidth();var m=["padding",/ne|nw|n/.test(n)?"Top":/se|sw|s/.test(n)?"Bottom":/^e$/.test(n)?"Right":"Left"].join("");q.css(m,p);this._proportionallyResize()}if(!c(this.handles[n]).length){continue}}};this._renderAxis(this.element);this._handles=c(".ui-resizable-handle",this.element).disableSelection();this._handles.mouseover(function(){if(!f.resizing){if(this.className){var i=this.className.match(/ui-resizable-(se|sw|ne|nw|n|e|s|w)/i)}f.axis=i&&i[1]?i[1]:"se"}});if(k.autoHide){this._handles.hide();c(this.element).addClass("ui-resizable-autohide").hover(function(){if(k.disabled){return}c(this).removeClass("ui-resizable-autohide");f._handles.show()},function(){if(k.disabled){return}if(!f.resizing){c(this).addClass("ui-resizable-autohide");f._handles.hide()}})}this._mouseInit()},destroy:function(){this._mouseDestroy();var e=function(g){c(g).removeClass("ui-resizable ui-resizable-disabled ui-resizable-resizing").removeData("resizable").unbind(".resizable").find(".ui-resizable-handle").remove()};if(this.elementIsWrapper){e(this.element);var f=this.element;f.after(this.originalElement.css({position:f.css("position"),width:f.outerWidth(),height:f.outerHeight(),top:f.css("top"),left:f.css("left")})).remove()}this.originalElement.css("resize",this.originalResizeStyle);e(this.originalElement);return this},_mouseCapture:function(f){var g=false;for(var e in this.handles){if(c(this.handles[e])[0]==f.target){g=true}}return !this.options.disabled&&g},_mouseStart:function(g){var j=this.options,f=this.element.position(),e=this.element;this.resizing=true;this.documentScroll={top:c(document).scrollTop(),left:c(document).scrollLeft()};if(e.is(".ui-draggable")||(/absolute/).test(e.css("position"))){e.css({position:"absolute",top:f.top,left:f.left})}this._renderProxy();var k=b(this.helper.css("left")),h=b(this.helper.css("top"));if(j.containment){k+=c(j.containment).scrollLeft()||0;h+=c(j.containment).scrollTop()||0}this.offset=this.helper.offset();this.position={left:k,top:h};this.size=this._helper?{width:e.outerWidth(),height:e.outerHeight()}:{width:e.width(),height:e.height()};this.originalSize=this._helper?{width:e.outerWidth(),height:e.outerHeight()}:{width:e.width(),height:e.height()};this.originalPosition={left:k,top:h};this.sizeDiff={width:e.outerWidth()-e.width(),height:e.outerHeight()-e.height()};this.originalMousePosition={left:g.pageX,top:g.pageY};this.aspectRatio=(typeof j.aspectRatio=="number")?j.aspectRatio:((this.originalSize.width/this.originalSize.height)||1);var i=c(".ui-resizable-"+this.axis).css("cursor");c("body").css("cursor",i=="auto"?this.axis+"-resize":i);e.addClass("ui-resizable-resizing");this._propagate("start",g);return true},_mouseDrag:function(e){var h=this.helper,g=this.options,m={},q=this,j=this.originalMousePosition,n=this.axis;var r=(e.pageX-j.left)||0,p=(e.pageY-j.top)||0;var i=this._change[n];if(!i){return false}var l=i.apply(this,[e,r,p]),k=c.browser.msie&&c.browser.version<7,f=this.sizeDiff;this._updateVirtualBoundaries(e.shiftKey);if(this._aspectRatio||e.shiftKey){l=this._updateRatio(l,e)}l=this._respectSize(l,e);this._propagate("resize",e);h.css({top:this.position.top+"px",left:this.position.left+"px",width:this.size.width+"px",height:this.size.height+"px"});if(!this._helper&&this._proportionallyResizeElements.length){this._proportionallyResize()}this._updateCache(l);this._trigger("resize",e,this.ui());return false},_mouseStop:function(h){this.resizing=false;var i=this.options,m=this;if(this._helper){var g=this._proportionallyResizeElements,e=g.length&&(/textarea/i).test(g[0].nodeName),f=e&&c.ui.hasScroll(g[0],"left")?0:m.sizeDiff.height,k=e?0:m.sizeDiff.width;var n={width:(m.helper.width()-k),height:(m.helper.height()-f)},j=(parseInt(m.element.css("left"),10)+(m.position.left-m.originalPosition.left))||null,l=(parseInt(m.element.css("top"),10)+(m.position.top-m.originalPosition.top))||null;if(!i.animate){this.element.css(c.extend(n,{top:l,left:j}))}m.helper.height(m.size.height);m.helper.width(m.size.width);if(this._helper&&!i.animate){this._proportionallyResize()}}c("body").css("cursor","auto");this.element.removeClass("ui-resizable-resizing");this._propagate("stop",h);if(this._helper){this.helper.remove()}return false},_updateVirtualBoundaries:function(g){var j=this.options,i,h,f,k,e;e={minWidth:a(j.minWidth)?j.minWidth:0,maxWidth:a(j.maxWidth)?j.maxWidth:Infinity,minHeight:a(j.minHeight)?j.minHeight:0,maxHeight:a(j.maxHeight)?j.maxHeight:Infinity};if(this._aspectRatio||g){i=e.minHeight*this.aspectRatio;f=e.minWidth/this.aspectRatio;h=e.maxHeight*this.aspectRatio;k=e.maxWidth/this.aspectRatio;if(i>e.minWidth){e.minWidth=i}if(f>e.minHeight){e.minHeight=f}if(h<e.maxWidth){e.maxWidth=h}if(k<e.maxHeight){e.maxHeight=k}}this._vBoundaries=e},_updateCache:function(e){var f=this.options;this.offset=this.helper.offset();if(a(e.left)){this.position.left=e.left}if(a(e.top)){this.position.top=e.top}if(a(e.height)){this.size.height=e.height}if(a(e.width)){this.size.width=e.width}},_updateRatio:function(h,g){var i=this.options,j=this.position,f=this.size,e=this.axis;if(a(h.height)){h.width=(h.height*this.aspectRatio)}else{if(a(h.width)){h.height=(h.width/this.aspectRatio)}}if(e=="sw"){h.left=j.left+(f.width-h.width);h.top=null}if(e=="nw"){h.top=j.top+(f.height-h.height);h.left=j.left+(f.width-h.width)}return h},_respectSize:function(l,g){var j=this.helper,i=this._vBoundaries,r=this._aspectRatio||g.shiftKey,q=this.axis,t=a(l.width)&&i.maxWidth&&(i.maxWidth<l.width),m=a(l.height)&&i.maxHeight&&(i.maxHeight<l.height),h=a(l.width)&&i.minWidth&&(i.minWidth>l.width),s=a(l.height)&&i.minHeight&&(i.minHeight>l.height);if(h){l.width=i.minWidth}if(s){l.height=i.minHeight}if(t){l.width=i.maxWidth}if(m){l.height=i.maxHeight}var f=this.originalPosition.left+this.originalSize.width,p=this.position.top+this.size.height;var k=/sw|nw|w/.test(q),e=/nw|ne|n/.test(q);if(h&&k){l.left=f-i.minWidth}if(t&&k){l.left=f-i.maxWidth}if(s&&e){l.top=p-i.minHeight}if(m&&e){l.top=p-i.maxHeight}var n=!l.width&&!l.height;if(n&&!l.left&&l.top){l.top=null}else{if(n&&!l.top&&l.left){l.left=null}}return l},_proportionallyResize:function(){var k=this.options;if(!this._proportionallyResizeElements.length){return}var g=this.helper||this.element;for(var f=0;f<this._proportionallyResizeElements.length;f++){var h=this._proportionallyResizeElements[f];if(!this.borderDif){var e=[h.css("borderTopWidth"),h.css("borderRightWidth"),h.css("borderBottomWidth"),h.css("borderLeftWidth")],j=[h.css("paddingTop"),h.css("paddingRight"),h.css("paddingBottom"),h.css("paddingLeft")];this.borderDif=c.map(e,function(l,n){var m=parseInt(l,10)||0,o=parseInt(j[n],10)||0;return m+o})}if(c.browser.msie&&!(!(c(g).is(":hidden")||c(g).parents(":hidden").length))){continue}h.css({height:(g.height()-this.borderDif[0]-this.borderDif[2])||0,width:(g.width()-this.borderDif[1]-this.borderDif[3])||0})}},_renderProxy:function(){var 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| 81 | * jQuery hashchange event - v1.3 - 7/21/2010 | |
| 82 | * http://benalman.com/projects/jquery-hashchange-plugin/ | |
| 83 | * | |
| 84 | * Copyright (c) 2010 "Cowboy" Ben Alman | |
| 85 | * Dual licensed under the MIT and GPL licenses. | |
| 86 | * http://benalman.com/about/license/ | |
| 87 | */ | |
| 88 | (function($,e,b){var c="hashchange",h=document,f,g=$.event.special,i=h.documentMode,d="on"+c in e&&(i===b||i>7);function a(j){j=j||location.href;return"#"+j.replace(/^[^#]*#?(.*)$/,"$1")}$.fn[c]=function(j){return j?this.bind(c,j):this.trigger(c)};$.fn[c].delay=50;g[c]=$.extend(g[c],{setup:function(){if(d){return false}$(f.start)},teardown:function(){if(d){return false}$(f.stop)}});f=(function(){var j={},p,m=a(),k=function(q){return q},l=k,o=k;j.start=function(){p||n()};j.stop=function(){p&&clearTimeout(p);p=b};function n(){var r=a(),q=o(m);if(r!==m){l(m=r,q);$(e).trigger(c)}else{if(q!==m){location.href=location.href.replace(/#.*/,"")+q}}p=setTimeout(n,$.fn[c].delay)}$.browser.msie&&!d&&(function(){var q,r;j.start=function(){if(!q){r=$.fn[c].src;r=r&&r+a();q=$('<iframe tabindex="-1" title="empty"/>').hide().one("load",function(){r||l(a());n()}).attr("src",r||"javascript:0").insertAfter("body")[0].contentWindow;h.onpropertychange=function(){try{if(event.propertyName==="title"){q.document.title=h.title}}catch(s){}}}};j.stop=k;o=function(){return a(q.location.href)};l=function(v,s){var u=q.document,t=$.fn[c].domain;if(v!==s){u.title=h.title;u.open();t&&u.write('<script>document.domain="'+t+'"<\/script>');u.close();q.location.hash=v}}})();return j})()})(jQuery,this);(function(c){var a=c.scrollTo=function(f,e,d){c(window).scrollTo(f,e,d)};a.defaults={axis:"xy",duration:parseFloat(c.fn.jquery)>=1.3?0:1};a.window=function(d){return c(window)._scrollable()};c.fn._scrollable=function(){return this.map(function(){var e=this,d=!e.nodeName||c.inArray(e.nodeName.toLowerCase(),["iframe","#document","html","body"])!=-1;if(!d){return e}var f=(e.contentWindow||e).document||e.ownerDocument||e;return c.browser.safari||f.compatMode=="BackCompat"?f.body:f.documentElement})};c.fn.scrollTo=function(f,e,d){if(typeof e=="object"){d=e;e=0}if(typeof d=="function"){d={onAfter:d}}if(f=="max"){f=9000000000}d=c.extend({},a.defaults,d);e=e||d.speed||d.duration;d.queue=d.queue&&d.axis.length>1;if(d.queue){e/=2}d.offset=b(d.offset);d.over=b(d.over);return this._scrollable().each(function(){var l=this,j=c(l),k=f,i,g={},m=j.is("html,body");switch(typeof k){case"number":case"string":if(/^([+-]=)?\d+(\.\d+)?(px|%)?$/.test(k)){k=b(k);break}k=c(k,this);case"object":if(k.is||k.style){i=(k=c(k)).offset()}}c.each(d.axis.split(""),function(q,r){var s=r=="x"?"Left":"Top",u=s.toLowerCase(),p="scroll"+s,o=l[p],n=a.max(l,r);if(i){g[p]=i[u]+(m?0:o-j.offset()[u]);if(d.margin){g[p]-=parseInt(k.css("margin"+s))||0;g[p]-=parseInt(k.css("border"+s+"Width"))||0}g[p]+=d.offset[u]||0;if(d.over[u]){g[p]+=k[r=="x"?"width":"height"]()*d.over[u]}}else{var t=k[u];g[p]=t.slice&&t.slice(-1)=="%"?parseFloat(t)/100*n:t}if(/^\d+$/.test(g[p])){g[p]=g[p]<=0?0:Math.min(g[p],n)}if(!q&&d.queue){if(o!=g[p]){h(d.onAfterFirst)}delete g[p]}});h(d.onAfter);function h(n){j.animate(g,e,d.easing,n&&function(){n.call(this,f,d)})}}).end()};a.max=function(j,i){var h=i=="x"?"Width":"Height",e="scroll"+h;if(!c(j).is("html,body")){return j[e]-c(j)[h.toLowerCase()]()}var g="client"+h,f=j.ownerDocument.documentElement,d=j.ownerDocument.body;return Math.max(f[e],d[e])-Math.min(f[g],d[g])};function b(d){return typeof d=="object"?d:{top:d,left:d}}})(jQuery);/*! | |
| 89 | PowerTip - v1.2.0 - 2013-04-03 | |
| 90 | http://stevenbenner.github.com/jquery-powertip/ | |
| 91 | Copyright (c) 2013 Steven Benner (http://stevenbenner.com/). | |
| 92 | Released under MIT license. | |
| 93 | https://raw.github.com/stevenbenner/jquery-powertip/master/LICENSE.txt | |
| 94 | */ | |
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O=K.offset(),N=K.outerWidth(),I=K.outerHeight(),M,L;switch(J){case"n":M=O.left+N/2;L=O.top;break;case"e":M=O.left+N;L=O.top+I/2;break;case"s":M=O.left+N/2;L=O.top+I;break;case"w":M=O.left;L=O.top+I/2;break;case"nw":M=O.left;L=O.top;break;case"ne":M=O.left+N;L=O.top;break;case"sw":M=O.left;L=O.top+I;break;case"se":M=O.left+N;L=O.top+I;break}return{top:L,left:M}}function H(O,K){var S=O.closest("svg")[0],N=O[0],W=S.createSVGPoint(),L=N.getBBox(),V=N.getScreenCTM(),M=L.width/2,Q=L.height/2,P=[],I=["nw","n","ne","e","se","s","sw","w"],U,X,R,T;function J(){P.push(W.matrixTransform(V))}W.x=L.x;W.y=L.y;J();W.x+=M;J();W.x+=M;J();W.y+=Q;J();W.y+=Q;J();W.x-=M;J();W.x-=M;J();W.y-=Q;J();if(P[0].y!==P[1].y||P[0].x!==P[7].x){X=Math.atan2(V.b,V.a)*E;R=Math.ceil(((X%360)-22.5)/45);if(R<1){R+=8}while(R--){I.push(I.shift())}}for(T=0;T<P.length;T++){if(I[T]===K){U=P[T];break}}return{top:U.y+c.scrollTop,left:U.x+c.scrollLeft}}this.compute=G}function x(Q){var P=new j(),O=k("#"+Q.popupId);if(O.length===0){O=k("<div/>",{id:Q.popupId});if(w.length===0){w=k("body")}w.append(O)}if(Q.followMouse){if(!O.data(u)){A.on("mousemove",M);s.on("scroll",M);O.data(u,true)}}if(Q.mouseOnToPopup){O.on({mouseenter:function L(){if(O.data(f)){if(c.activeHover){c.activeHover.data(n).cancel()}}},mouseleave:function N(){if(c.activeHover){c.activeHover.data(n).hide()}}})}function I(S){S.data(e,true);O.queue(function R(T){H(S);T()})}function H(S){var U;if(!S.data(e)){return}if(c.isTipOpen){if(!c.isClosing){K(c.activeHover)}O.delay(100).queue(function R(V){H(S);V()});return}S.trigger("powerTipPreRender");U=B(S);if(U){O.empty().append(U)}else{return}S.trigger("powerTipRender");c.activeHover=S;c.isTipOpen=true;O.data(f,Q.mouseOnToPopup);if(!Q.followMouse){G(S);c.isFixedTipOpen=true}else{M()}O.fadeIn(Q.fadeInTime,function T(){if(!c.desyncTimeout){c.desyncTimeout=setInterval(J,500)}S.trigger("powerTipOpen")})}function 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| 96 | * jQuery UI Touch Punch 0.2.3 | |
| 97 | * | |
| 98 | * Copyright 2011–2014, Dave Furfero | |
| 99 | * Dual licensed under the MIT or GPL Version 2 licenses. | |
| 100 | * | |
| 101 | * Depends: | |
| 102 | * jquery.ui.widget.js | |
| 103 | * jquery.ui.mouse.js | |
| 104 | */ | |
| 105 | (function(b){b.support.touch="ontouchend" in document;if(!b.support.touch){return}var d=b.ui.mouse.prototype,f=d._mouseInit,c=d._mouseDestroy,a;function e(h,i){if(h.originalEvent.touches.length>1){return}h.preventDefault();var j=h.originalEvent.changedTouches[0],g=document.createEvent("MouseEvents");g.initMouseEvent(i,true,true,window,1,j.screenX,j.screenY,j.clientX,j.clientY,false,false,false,false,0,null);h.target.dispatchEvent(g)}d._touchStart=function(h){var g=this;if(a||!g._mouseCapture(h.originalEvent.changedTouches[0])){return}a=true;g._touchMoved=false;e(h,"mouseover");e(h,"mousemove");e(h,"mousedown")};d._touchMove=function(g){if(!a){return}this._touchMoved=true;e(g,"mousemove")};d._touchEnd=function(g){if(!a){return}e(g,"mouseup");e(g,"mouseout");if(!this._touchMoved){e(g,"click")}a=false};d._mouseInit=function(){var g=this;g.element.bind({touchstart:b.proxy(g,"_touchStart"),touchmove:b.proxy(g,"_touchMove"),touchend:b.proxy(g,"_touchEnd")});f.call(g)};d._mouseDestroy=function(){var g=this;g.element.unbind({touchstart:b.proxy(g,"_touchStart"),touchmove:b.proxy(g,"_touchMove"),touchend:b.proxy(g,"_touchEnd")});c.call(g)}})(jQuery);/*! | |
| 106 | * SmartMenus jQuery Plugin - v1.0.0 - January 27, 2016 | |
| 107 | * http://www.smartmenus.org/ | |
| 108 | * | |
| 109 | * Copyright Vasil Dinkov, Vadikom Web Ltd. | |
| 110 | * http://vadikom.com | |
| 111 | * | |
| 112 | * Licensed MIT | |
| 113 | */ | |
| 114 | (function(a){if(typeof define==="function"&&define.amd){define(["jquery"],a)}else{if(typeof module==="object"&&typeof module.exports==="object"){module.exports=a(require("jquery"))}else{a(jQuery)}}}(function(a){var b=[],e=!!window.createPopup,f=false,d="ontouchstart" in window,h=false,g=window.requestAnimationFrame||function(l){return setTimeout(l,1000/60)},c=window.cancelAnimationFrame||function(l){clearTimeout(l)};function k(m){var n=".smartmenus_mouse";if(!h&&!m){var o=true,l=null;a(document).bind(i([["mousemove",function(s){var t={x:s.pageX,y:s.pageY,timeStamp:new Date().getTime()};if(l){var q=Math.abs(l.x-t.x),p=Math.abs(l.y-t.y);if((q>0||p>0)&&q<=2&&p<=2&&t.timeStamp-l.timeStamp<=300){f=true;if(o){var r=a(s.target).closest("a");if(r.is("a")){a.each(b,function(){if(a.contains(this.$root[0],r[0])){this.itemEnter({currentTarget:r[0]});return false}})}o=false}}}l=t}],[d?"touchstart":"pointerover pointermove pointerout MSPointerOver MSPointerMove 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p=/(index|default)\.[^#\?\/]*/i,m=/#.*/,q=window.location.href.replace(p,""),o=q.replace(m,"");this.$root.find("a").each(function(){var s=this.href.replace(p,""),t=a(this);if(s==q||s==o){t.addClass("current");if(l.opts.markCurrentTree){t.parentsUntil("[data-smartmenus-id]","ul").each(function(){a(this).dataSM("parent-a").addClass("current")})}}})}this.wasCollapsible=this.isCollapsible()},destroy:function(m){if(!m){var n=".smartmenus";this.$root.removeData("smartmenus").removeAttr("data-smartmenus-id").removeDataSM("level").unbind(n).undelegate(n);n+=this.rootId;a(document).unbind(n);a(window).unbind(n);if(this.opts.subIndicators){this.$subArrow=null}}this.menuHideAll();var l=this;this.$root.find("ul").each(function(){var 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l=m.originalEvent.touches[0];this.lastTouch.x2=l.pageX;this.lastTouch.y2=l.pageY},docTouchStart:function(m){var l=m.originalEvent.touches[0];this.lastTouch={x1:l.pageX,y1:l.pageY,target:l.target}},enable:function(){if(this.disabled){if(this.$disableOverlay){this.$disableOverlay.remove();this.$disableOverlay=null}this.disabled=false}},getClosestMenu:function(m){var l=a(m).closest("ul");while(l.dataSM("in-mega")){l=l.parent().closest("ul")}return l[0]||null},getHeight:function(l){return this.getOffset(l,true)},getOffset:function(n,l){var m;if(n.css("display")=="none"){m={position:n[0].style.position,visibility:n[0].style.visibility};n.css({position:"absolute",visibility:"hidden"}).show()}var o=n[0].getBoundingClientRect&&n[0].getBoundingClientRect(),p=o&&(l?o.height||o.bottom-o.top:o.width||o.right-o.left);if(!p&&p!==0){p=l?n[0].offsetHeight:n[0].offsetWidth}if(m){n.hide().css(m)}return p},getStartZIndex:function(l){var m=parseInt(this[l?"$root":"$firstSub"].css("z-index"));if(!l&&isNaN(m)){m=parseInt(this.$root.css("z-index"))}return !isNaN(m)?m:1},getTouchPoint:function(l){return l.touches&&l.touches[0]||l.changedTouches&&l.changedTouches[0]||l},getViewport:function(l){var m=l?"Height":"Width",o=document.documentElement["client"+m],n=window["inner"+m];if(n){o=Math.min(o,n)}return o},getViewportHeight:function(){return this.getViewport(true)},getViewportWidth:function(){return this.getViewport()},getWidth:function(l){return this.getOffset(l)},handleEvents:function(){return !this.disabled&&this.isCSSOn()},handleItemEvents:function(l){return this.handleEvents()&&!this.isLinkInMegaMenu(l)},isCollapsible:function(){return this.$firstSub.css("position")=="static"},isCSSOn:function(){return this.$firstLink.css("display")=="block"},isFixed:function(){var l=this.$root.css("position")=="fixed";if(!l){this.$root.parentsUntil("body").each(function(){if(a(this).css("position")=="fixed"){l=true;return false}})}return l},isLinkInMegaMenu:function(l){return a(this.getClosestMenu(l[0])).hasClass("mega-menu")},isTouchMode:function(){return !f||this.opts.noMouseOver||this.isCollapsible()},itemActivate:function(p,l){var n=p.closest("ul"),q=n.dataSM("level");if(q>1&&(!this.activatedItems[q-2]||this.activatedItems[q-2][0]!=n.dataSM("parent-a")[0])){var m=this;a(n.parentsUntil("[data-smartmenus-id]","ul").get().reverse()).add(n).each(function(){m.itemActivate(a(this).dataSM("parent-a"))})}if(!this.isCollapsible()||l){this.menuHideSubMenus(!this.activatedItems[q-1]||this.activatedItems[q-1][0]!=p[0]?q-1:q)}this.activatedItems[q-1]=p;if(this.$root.triggerHandler("activate.smapi",p[0])===false){return}var o=p.dataSM("sub");if(o&&(this.isTouchMode()||(!this.opts.showOnClick||this.clickActivated))){this.menuShow(o)}},itemBlur:function(m){var l=a(m.currentTarget);if(!this.handleItemEvents(l)){return}this.$root.triggerHandler("blur.smapi",l[0])},itemClick:function(o){var n=a(o.currentTarget);if(!this.handleItemEvents(n)){return}if(this.$touchScrollingSub&&this.$touchScrollingSub[0]==n.closest("ul")[0]){this.$touchScrollingSub=null;o.stopPropagation();return false}if(this.$root.triggerHandler("click.smapi",n[0])===false){return false}var p=a(o.target).is("span.sub-arrow"),m=n.dataSM("sub"),l=m?m.dataSM("level")==2:false;if(m&&!m.is(":visible")){if(this.opts.showOnClick&&l){this.clickActivated=true}this.itemActivate(n);if(m.is(":visible")){this.focusActivated=true;return false}}else{if(this.isCollapsible()&&p){this.itemActivate(n);this.menuHide(m);return false}}if(this.opts.showOnClick&&l||n.hasClass("disabled")||this.$root.triggerHandler("select.smapi",n[0])===false){return false}},itemDown:function(m){var l=a(m.currentTarget);if(!this.handleItemEvents(l)){return}l.dataSM("mousedown",true)},itemEnter:function(n){var m=a(n.currentTarget);if(!this.handleItemEvents(m)){return}if(!this.isTouchMode()){if(this.showTimeout){clearTimeout(this.showTimeout);this.showTimeout=0}var l=this;this.showTimeout=setTimeout(function(){l.itemActivate(m)},this.opts.showOnClick&&m.closest("ul").dataSM("level")==1?1:this.opts.showTimeout)}this.$root.triggerHandler("mouseenter.smapi",m[0])},itemFocus:function(m){var l=a(m.currentTarget);if(!this.handleItemEvents(l)){return}if(this.focusActivated&&(!this.isTouchMode()||!l.dataSM("mousedown"))&&(!this.activatedItems.length||this.activatedItems[this.activatedItems.length-1][0]!=l[0])){this.itemActivate(l,true)}this.$root.triggerHandler("focus.smapi",l[0])},itemLeave:function(m){var 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| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> </div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include <cmath></span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <algorithm></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <stdlib.h></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <tuple></span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#include <unordered_map></span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#include <unordered_set></span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#include <queue></span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#include <utility></span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor">#include <iostream></span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="preprocessor">#include <string.h></span></div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor">#include <limits></span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="preprocessor">#include <cstdlib></span></div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="preprocessor">#include <fenv.h></span></div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor">#include "platform.h"</span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="preprocessor">#include "marginalTrek++.h"</span></div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#include "conf.h"</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#include "allocator.h"</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor">#include "operators.h"</span></div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include "summator.h"</span></div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include "element_tables.h"</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include "misc.h"</span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> </div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> {</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div><div class="line"><a name="l00055"></a><span class="lineno"><a class="line" href="namespace_iso_spec.html#a9abbd881dd3c9347438361a6dd21cef4"> 55</a></span> Conf <a class="code" href="namespace_iso_spec.html#a9abbd881dd3c9347438361a6dd21cef4">initialConfigure</a>(<span class="keyword">const</span> <span class="keywordtype">int</span> atomCnt, <span class="keyword">const</span> <span class="keywordtype">int</span> isotopeNo, <span class="keyword">const</span> <span class="keywordtype">double</span>* probs, <span class="keyword">const</span> <span class="keywordtype">double</span>* lprobs)</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> {</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  Conf res = <span class="keyword">new</span> <span class="keywordtype">int</span>[isotopeNo];</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="comment">// This approximates the mode (heuristics: the mean is close to the mode).</span></div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i < isotopeNo; ++i )</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  res[i] = <span class="keywordtype">int</span>( atomCnt * probs[i] ) + 1;</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="comment">// The number of assigned atoms above.</span></div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <span class="keywordtype">int</span> s = 0;</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i < isotopeNo; ++i) s += res[i];</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordtype">int</span> diff = atomCnt - s;</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="comment">// Too little: enlarging fist index.</span></div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keywordflow">if</span>( diff > 0 ){</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  res[0] += diff;</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  }</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="comment">// Too much: trying to redistribute the difference: hopefully the first element is the largest.</span></div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordflow">if</span>( diff < 0 ){</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  diff = abs(diff);</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordtype">int</span> i = 0, coordDiff = 0;</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keywordflow">while</span>( diff > 0){</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  coordDiff = res[i] - diff;</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keywordflow">if</span>( coordDiff >= 0 ){</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  res[i] -= diff;</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  diff = 0;</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  res[i] = 0;</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  i++;</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  diff = abs(coordDiff);</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  }</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  }</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  }</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="comment">// What we computed so far will be very close to the mode: hillclimb the rest of the way</span></div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keywordtype">bool</span> modified = <span class="keyword">true</span>;</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="keywordtype">double</span> LP = unnormalized_logProb(res, lprobs, isotopeNo);</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="keywordtype">double</span> NLP;</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="keywordflow">while</span>(modified)</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  {</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  modified = <span class="keyword">false</span>;</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> ii = 0; ii<isotopeNo; ii++)</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> jj = 0; jj<isotopeNo; jj++)</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  <span class="keywordflow">if</span>(ii != jj && res[ii] > 0)</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  {</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  res[ii]--;</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  res[jj]++;</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  NLP = unnormalized_logProb(res, lprobs, isotopeNo);</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordflow">if</span>(NLP>LP || (NLP==LP && ii>jj))</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  {</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  modified = <span class="keyword">true</span>;</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  LP = NLP;</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  }</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  {</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  res[ii]++;</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  res[jj]--;</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  }</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  }</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> </div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  }</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <span class="keywordflow">return</span> res;</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span> }</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span> </div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span> <span class="preprocessor">#if !ISOSPEC_BUILDING_R</span></div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span> <span class="keywordtype">void</span> printMarginal( <span class="keyword">const</span> std::tuple<double*,double*,int*,int>& results, <span class="keywordtype">int</span> dim)</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span> {</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=0; i<std::get<3>(results); i++){</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  std::cout << <span class="stringliteral">"Mass = "</span> << std::get<0>(results)[i] <<</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <span class="stringliteral">" log-prob =\t"</span> << std::get<1>(results)[i] <<</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="stringliteral">" prob =\t"</span> << exp(std::get<1>(results)[i]) <<</div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <span class="stringliteral">"\tand configuration =\t"</span>;</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span> </div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> j=0; j<dim; j++) std::cout << std::get<2>(results)[i*dim + j] << <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span> </div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  std::cout << std::endl;</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  }</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span> }</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span> </div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span> </div><div class="line"><a name="l00150"></a><span class="lineno"><a class="line" href="namespace_iso_spec.html#a4b68cc6e2f1f4f30b189a5d01153daa4"> 150</a></span> <span class="keywordtype">double</span>* <a class="code" href="namespace_iso_spec.html#a4b68cc6e2f1f4f30b189a5d01153daa4">getMLogProbs</a>(<span class="keyword">const</span> <span class="keywordtype">double</span>* probs, <span class="keywordtype">int</span> isoNo)</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span> {</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  <span class="keywordtype">int</span> curr_method = fegetround();</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  fesetround(FE_UPWARD);</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordtype">double</span>* ret = <span class="keyword">new</span> <span class="keywordtype">double</span>[isoNo];</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span> </div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  <span class="comment">// here we change the table of probabilities and log it.</span></div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i < isoNo; i++)</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  {</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  ret[i] = log(probs[i]);</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> j=0; j<ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES; j++)</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <span class="keywordflow">if</span>(elem_table_probability[j] == probs[i])</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  {</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  ret[i] = elem_table_log_probability[j];</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  }</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span>  }</div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  fesetround(curr_method);</div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span>  <span class="keywordflow">return</span> ret;</div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span> }</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span> </div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span> <span class="keywordtype">double</span> get_loggamma_nominator(<span class="keywordtype">int</span> x)</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span> {</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="comment">// calculate log gamma of the nominator calculated in the binomial exression.</span></div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordtype">int</span> curr_method = fegetround();</div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  fesetround(FE_UPWARD);</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keywordtype">double</span> ret = lgamma(x+1);</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  fesetround(curr_method);</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordflow">return</span> ret;</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span> }</div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span> </div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span> </div><div class="line"><a name="l00187"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c"> 187</a></span> <a class="code" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal::Marginal</a>(</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* _masses,</div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* _probs,</div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  <span class="keywordtype">int</span> _isotopeNo,</div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  <span class="keywordtype">int</span> _atomCnt</div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span> ) :</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span> disowned(false),</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span> isotopeNo(_isotopeNo),</div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span> atomCnt(_atomCnt),</div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span> atom_masses(array_copy<double>(_masses, _isotopeNo)),</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span> atom_lProbs(<a class="code" href="namespace_iso_spec.html#a4b68cc6e2f1f4f30b189a5d01153daa4">getMLogProbs</a>(_probs, isotopeNo)),</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> loggamma_nominator(get_loggamma_nominator(_atomCnt)),</div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span> mode_conf(<a class="code" href="namespace_iso_spec.html#a9abbd881dd3c9347438361a6dd21cef4">initialConfigure</a>(atomCnt, isotopeNo, _probs, atom_lProbs)),</div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span> mode_lprob(loggamma_nominator+unnormalized_logProb(mode_conf, atom_lProbs, isotopeNo)),</div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span> mode_mass(mass(mode_conf, atom_masses, isotopeNo)),</div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span> mode_prob(exp(mode_lprob)),</div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span> smallest_lprob(atomCnt * *<a class="code" href="namespacestd.html">std</a>::min_element(atom_lProbs, atom_lProbs+isotopeNo))</div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span> {</div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  <span class="keywordflow">if</span>(ISOSPEC_G_FACT_TABLE_SIZE-1 <= <a class="code" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a>)</div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  <span class="keywordflow">throw</span> std::length_error(<span class="stringliteral">"Subisotopologue too large, size limit (that is, the maximum number of atoms of a single element in a molecule) is: "</span> + std::to_string(ISOSPEC_G_FACT_TABLE_SIZE-1));</div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span> }</div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span> </div><div class="line"><a name="l00209"></a><span class="lineno"> 209</span> <span class="comment">// the move-constructor: used in the specialization of the marginal.</span></div><div class="line"><a name="l00210"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#ad60fff17fa2c68ea2cd7f183a635379e"> 210</a></span> <a class="code" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal::Marginal</a>(<a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>&& other) :</div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span> disowned(other.disowned),</div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span> isotopeNo(other.isotopeNo),</div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span> atomCnt(other.atomCnt),</div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span> atom_masses(other.atom_masses),</div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span> atom_lProbs(other.atom_lProbs),</div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span> loggamma_nominator(other.loggamma_nominator),</div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span> mode_conf(other.mode_conf),</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span> mode_lprob(other.mode_lprob),</div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span> mode_mass(other.mode_mass),</div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span> mode_prob(other.mode_prob),</div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span> smallest_lprob(other.smallest_lprob)</div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span> {</div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span>  other.disowned = <span class="keyword">true</span>;</div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span> }</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span> </div><div class="line"><a name="l00226"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4"> 226</a></span> <a class="code" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">Marginal::~Marginal</a>()</div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span> {</div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  <span class="keywordflow">if</span>(!disowned)</div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  {</div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  <span class="keyword">delete</span>[] <a class="code" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a>;</div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span>  <span class="keyword">delete</span>[] <a class="code" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a>;</div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="keyword">delete</span>[] <a class="code" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a>;</div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  }</div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span> }</div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span> </div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span> </div><div class="line"><a name="l00237"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9"> 237</a></span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">Marginal::getLightestConfMass</a>()<span class="keyword"> const</span></div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span> <span class="keyword"></span>{</div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keywordtype">double</span> ret_mass = std::numeric_limits<double>::infinity();</div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> ii=0; ii < <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>; ii++)</div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="keywordflow">if</span>( ret_mass > <a class="code" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a>[ii] )</div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  ret_mass = <a class="code" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a>[ii];</div><div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  <span class="keywordflow">return</span> ret_mass*<a class="code" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a>;</div><div class="line"><a name="l00244"></a><span class="lineno"> 244</span> }</div><div class="line"><a name="l00245"></a><span class="lineno"> 245</span> </div><div class="line"><a name="l00246"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff"> 246</a></span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">Marginal::getHeaviestConfMass</a>()<span class="keyword"> const</span></div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span> <span class="keyword"></span>{</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  <span class="keywordtype">double</span> ret_mass = 0.0;</div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> ii=0; ii < <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>; ii++)</div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="keywordflow">if</span>( ret_mass < <a class="code" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a>[ii] )</div><div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  ret_mass = <a class="code" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a>[ii];</div><div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  <span class="keywordflow">return</span> ret_mass*<a class="code" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a>;</div><div class="line"><a name="l00253"></a><span class="lineno"> 253</span> }</div><div class="line"><a name="l00254"></a><span class="lineno"> 254</span> </div><div class="line"><a name="l00255"></a><span class="lineno"> 255</span> <span class="comment">// this is roughly an equivalent of IsoSpec-Threshold-Generator</span></div><div class="line"><a name="l00256"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal_trek.html#a83e70d522174e4e6724116941fd9c99e"> 256</a></span> <a class="code" href="class_iso_spec_1_1_marginal_trek.html#a83e70d522174e4e6724116941fd9c99e">MarginalTrek::MarginalTrek</a>(</div><div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>&& m,</div><div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <span class="keywordtype">int</span> tabSize,</div><div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keywordtype">int</span> hashSize</div><div class="line"><a name="l00260"></a><span class="lineno"> 260</span> ) :</div><div class="line"><a name="l00261"></a><span class="lineno"> 261</span> <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>(<a class="code" href="namespacestd.html">std</a>::move(m)),</div><div class="line"><a name="l00262"></a><span class="lineno"> 262</span> current_count(0),</div><div class="line"><a name="l00263"></a><span class="lineno"> 263</span> keyHasher(isotopeNo),</div><div class="line"><a name="l00264"></a><span class="lineno"> 264</span> equalizer(isotopeNo),</div><div class="line"><a name="l00265"></a><span class="lineno"> 265</span> orderMarginal(atom_lProbs, isotopeNo),</div><div class="line"><a name="l00266"></a><span class="lineno"> 266</span> visited(hashSize,keyHasher,equalizer),</div><div class="line"><a name="l00267"></a><span class="lineno"> 267</span> pq(orderMarginal),</div><div class="line"><a name="l00268"></a><span class="lineno"> 268</span> totalProb(),</div><div class="line"><a name="l00269"></a><span class="lineno"> 269</span> candidate(new int[isotopeNo]),</div><div class="line"><a name="l00270"></a><span class="lineno"> 270</span> allocator(isotopeNo, tabSize)</div><div class="line"><a name="l00271"></a><span class="lineno"> 271</span> {</div><div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <span class="keywordtype">int</span>* initialConf = allocator.makeCopy(<a class="code" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a>);</div><div class="line"><a name="l00273"></a><span class="lineno"> 273</span> </div><div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  pq.push(initialConf);</div><div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  visited[initialConf] = 0;</div><div class="line"><a name="l00276"></a><span class="lineno"> 276</span> </div><div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  totalProb = <a class="code" href="class_iso_spec_1_1_summator.html">Summator</a>();</div><div class="line"><a name="l00278"></a><span class="lineno"> 278</span> </div><div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  current_count = 0;</div><div class="line"><a name="l00280"></a><span class="lineno"> 280</span> </div><div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  add_next_conf();</div><div class="line"><a name="l00282"></a><span class="lineno"> 282</span> }</div><div class="line"><a name="l00283"></a><span class="lineno"> 283</span> </div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span> </div><div class="line"><a name="l00285"></a><span class="lineno"> 285</span> <span class="keywordtype">bool</span> MarginalTrek::add_next_conf()</div><div class="line"><a name="l00286"></a><span class="lineno"> 286</span> {</div><div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  <span class="keywordflow">if</span>(pq.size() < 1) <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00292"></a><span class="lineno"> 292</span> </div><div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  Conf topConf = pq.top();</div><div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  pq.pop();</div><div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  ++current_count;</div><div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  visited[topConf] = current_count;</div><div class="line"><a name="l00297"></a><span class="lineno"> 297</span> </div><div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  _confs.push_back(topConf);</div><div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  _conf_masses.push_back(mass(topConf, <a class="code" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a>, <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>));</div><div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <span class="keywordtype">double</span> logprob = <a class="code" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a>(topConf);</div><div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  _conf_lprobs.push_back(logprob);</div><div class="line"><a name="l00302"></a><span class="lineno"> 302</span> </div><div class="line"><a name="l00303"></a><span class="lineno"> 303</span> </div><div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  totalProb.add( exp( logprob ) );</div><div class="line"><a name="l00305"></a><span class="lineno"> 305</span> </div><div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  <span class="keywordflow">for</span>( <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i = 0; i < <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>; ++i )</div><div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  {</div><div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="keywordflow">for</span>( <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j = 0; j < <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>; ++j )</div><div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  {</div><div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  <span class="comment">// Growing index different than decreasing one AND</span></div><div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="comment">// Remain on simplex condition.</span></div><div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="keywordflow">if</span>( i != j && topConf[j] > 0 ){</div><div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  copyConf(topConf, candidate, <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>);</div><div class="line"><a name="l00314"></a><span class="lineno"> 314</span> </div><div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  ++candidate[i];</div><div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  --candidate[j];</div><div class="line"><a name="l00317"></a><span class="lineno"> 317</span> </div><div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <span class="comment">// candidate should not have been already visited.</span></div><div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  <span class="keywordflow">if</span>( visited.count( candidate ) == 0 )</div><div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  {</div><div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  Conf acceptedCandidate = allocator.makeCopy(candidate);</div><div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  pq.push(acceptedCandidate);</div><div class="line"><a name="l00323"></a><span class="lineno"> 323</span> </div><div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  visited[acceptedCandidate] = 0;</div><div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  }</div><div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  }</div><div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  }</div><div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  }</div><div class="line"><a name="l00329"></a><span class="lineno"> 329</span> </div><div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00331"></a><span class="lineno"> 331</span> }</div><div class="line"><a name="l00332"></a><span class="lineno"> 332</span> </div><div class="line"><a name="l00333"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal_trek.html#a04f3e495a805a3ea242059c963c5b129"> 333</a></span> <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_marginal_trek.html#a04f3e495a805a3ea242059c963c5b129">MarginalTrek::processUntilCutoff</a>(<span class="keywordtype">double</span> cutoff)</div><div class="line"><a name="l00334"></a><span class="lineno"> 334</span> {</div><div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <a class="code" href="class_iso_spec_1_1_summator.html">Summator</a> s;</div><div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <span class="keywordtype">int</span> last_idx = -1;</div><div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i=0; i<_conf_lprobs.size(); i++)</div><div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  {</div><div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  s.add(_conf_lprobs[i]);</div><div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  <span class="keywordflow">if</span>(s.get() >= cutoff)</div><div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  {</div><div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  last_idx = i;</div><div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <span class="keywordflow">break</span>;</div><div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  }</div><div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  }</div><div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keywordflow">if</span>(last_idx > -1)</div><div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <span class="keywordflow">return</span> last_idx;</div><div class="line"><a name="l00348"></a><span class="lineno"> 348</span> </div><div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="keywordflow">while</span>(totalProb.get() < cutoff && add_next_conf()) {}</div><div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  <span class="keywordflow">return</span> _conf_lprobs.size();</div><div class="line"><a name="l00351"></a><span class="lineno"> 351</span> }</div><div class="line"><a name="l00352"></a><span class="lineno"> 352</span> </div><div class="line"><a name="l00353"></a><span class="lineno"> 353</span> </div><div class="line"><a name="l00354"></a><span class="lineno"> 354</span> MarginalTrek::~MarginalTrek()</div><div class="line"><a name="l00355"></a><span class="lineno"> 355</span> {</div><div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  <span class="keyword">delete</span>[] candidate;</div><div class="line"><a name="l00357"></a><span class="lineno"> 357</span> }</div><div class="line"><a name="l00358"></a><span class="lineno"> 358</span> </div><div class="line"><a name="l00359"></a><span class="lineno"> 359</span> </div><div class="line"><a name="l00360"></a><span class="lineno"> 360</span> </div><div class="line"><a name="l00361"></a><span class="lineno"> 361</span> </div><div class="line"><a name="l00362"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e"> 362</a></span> <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">PrecalculatedMarginal::PrecalculatedMarginal</a>(<a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>&& m,</div><div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  <span class="keywordtype">double</span> lCutOff,</div><div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  <span class="keywordtype">bool</span> sort,</div><div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  <span class="keywordtype">int</span> tabSize,</div><div class="line"><a name="l00366"></a><span class="lineno"> 366</span>  <span class="keywordtype">int</span> hashSize</div><div class="line"><a name="l00367"></a><span class="lineno"> 367</span> ) : <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>(<a class="code" href="namespacestd.html">std</a>::move(m)),</div><div class="line"><a name="l00368"></a><span class="lineno"> 368</span> allocator(isotopeNo, tabSize)</div><div class="line"><a name="l00369"></a><span class="lineno"> 369</span> {</div><div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_conf_equal.html">ConfEqual</a> equalizer(<a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>);</div><div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_key_hasher.html">KeyHasher</a> keyHasher(<a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>);</div><div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  <span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_conf_order_marginal_descending.html">ConfOrderMarginalDescending</a> orderMarginal(<a class="code" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a>, <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>);</div><div class="line"><a name="l00373"></a><span class="lineno"> 373</span> </div><div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  std::unordered_set<Conf,KeyHasher,ConfEqual> visited(hashSize,keyHasher,equalizer);</div><div class="line"><a name="l00375"></a><span class="lineno"> 375</span> </div><div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  Conf currentConf = allocator.makeCopy(<a class="code" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a>);</div><div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  <span class="keywordflow">if</span>(<a class="code" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a>(currentConf) >= lCutOff)</div><div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  {</div><div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <span class="comment">// create a copy and store a ptr to the *same* copy in both structures</span></div><div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="comment">// (save some space and time)</span></div><div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  <span class="keyword">auto</span> tmp = allocator.makeCopy(currentConf);</div><div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  configurations.push_back(tmp);</div><div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  visited.insert(tmp);</div><div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  }</div><div class="line"><a name="l00385"></a><span class="lineno"> 385</span> </div><div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> idx = 0;</div><div class="line"><a name="l00387"></a><span class="lineno"> 387</span> </div><div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  <span class="keywordflow">while</span>(idx < configurations.size())</div><div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  {</div><div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  memcpy(currentConf, configurations[idx], <span class="keyword">sizeof</span>(<span class="keywordtype">int</span>)*<a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>);</div><div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  idx++;</div><div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> ii = 0; ii < <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>; ii++ )</div><div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> jj = 0; jj < <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>; jj++ )</div><div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  <span class="keywordflow">if</span>( ii != jj && currentConf[jj] > 0)</div><div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  {</div><div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  currentConf[ii]++;</div><div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  currentConf[jj]--;</div><div class="line"><a name="l00398"></a><span class="lineno"> 398</span> </div><div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  <span class="keywordflow">if</span> (visited.count(currentConf) == 0 && <a class="code" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a>(currentConf) >= lCutOff)</div><div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  {</div><div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  <span class="comment">// create a copy and store a ptr to the *same* copy in</span></div><div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  <span class="comment">// both structures (save some space and time)</span></div><div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  <span class="keyword">auto</span> tmp = allocator.makeCopy(currentConf);</div><div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  visited.insert(tmp);</div><div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  configurations.push_back(tmp);</div><div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  <span class="comment">// std::cout << " V: "; for (auto it : visited) std::cout << it << " "; std::cout << std::endl;</span></div><div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  }</div><div class="line"><a name="l00408"></a><span class="lineno"> 408</span> </div><div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  currentConf[ii]--;</div><div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  currentConf[jj]++;</div><div class="line"><a name="l00411"></a><span class="lineno"> 411</span> </div><div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  }</div><div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  }</div><div class="line"><a name="l00414"></a><span class="lineno"> 414</span> </div><div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  <span class="comment">// orderMarginal defines the order of configurations (compares their logprobs)</span></div><div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  <span class="comment">// akin to key in Python sort.</span></div><div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  <span class="keywordflow">if</span>(sort)</div><div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  std::sort(configurations.begin(), configurations.end(), orderMarginal);</div><div class="line"><a name="l00419"></a><span class="lineno"> 419</span> </div><div class="line"><a name="l00420"></a><span class="lineno"> 420</span> </div><div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  confs = &configurations[0];</div><div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  no_confs = configurations.size();</div><div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  lProbs = <span class="keyword">new</span> <span class="keywordtype">double</span>[no_confs+1];</div><div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  eProbs = <span class="keyword">new</span> <span class="keywordtype">double</span>[no_confs];</div><div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  masses = <span class="keyword">new</span> <span class="keywordtype">double</span>[no_confs];</div><div class="line"><a name="l00426"></a><span class="lineno"> 426</span> </div><div class="line"><a name="l00427"></a><span class="lineno"> 427</span> </div><div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  <span class="keywordflow">for</span>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> ii=0; ii < no_confs; ii++)</div><div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  {</div><div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  lProbs[ii] = <a class="code" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a>(confs[ii]);</div><div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  eProbs[ii] = exp(lProbs[ii]);</div><div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  masses[ii] = mass(confs[ii], <a class="code" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a>, <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>);</div><div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  }</div><div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  lProbs[no_confs] = -std::numeric_limits<double>::infinity();</div><div class="line"><a name="l00435"></a><span class="lineno"> 435</span> }</div><div class="line"><a name="l00436"></a><span class="lineno"> 436</span> </div><div class="line"><a name="l00437"></a><span class="lineno"> 437</span> </div><div class="line"><a name="l00438"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8"> 438</a></span> <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8">PrecalculatedMarginal::~PrecalculatedMarginal</a>()</div><div class="line"><a name="l00439"></a><span class="lineno"> 439</span> {</div><div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  <span class="keywordflow">if</span>(lProbs != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <span class="keyword">delete</span>[] lProbs;</div><div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  <span class="keywordflow">if</span>(masses != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  <span class="keyword">delete</span>[] masses;</div><div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  <span class="keywordflow">if</span>(eProbs != <span class="keyword">nullptr</span>)</div><div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  <span class="keyword">delete</span>[] eProbs;</div><div class="line"><a name="l00446"></a><span class="lineno"> 446</span> }</div><div class="line"><a name="l00447"></a><span class="lineno"> 447</span> </div><div class="line"><a name="l00448"></a><span class="lineno"> 448</span> </div><div class="line"><a name="l00449"></a><span class="lineno"> 449</span> </div><div class="line"><a name="l00450"></a><span class="lineno"> 450</span> </div><div class="line"><a name="l00451"></a><span class="lineno"> 451</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00452"></a><span class="lineno"> 452</span> </div><div class="ttc" id="class_iso_spec_1_1_conf_order_marginal_descending_html"><div class="ttname"><a href="class_iso_spec_1_1_conf_order_marginal_descending.html">IsoSpec::ConfOrderMarginalDescending</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00092">operators.h:92</a></div></div> | |
| 80 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a8b67c507263973da53e533d804e23ac9"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">IsoSpec::Marginal::getLightestConfMass</a></div><div class="ttdeci">double getLightestConfMass() const</div><div class="ttdoc">Get the mass of the lightest subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00237">marginalTrek++.cpp:237</a></div></div> | |
| 81 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a6b7b30cfe90ffba1d2c9d2f0d87107d8"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8">IsoSpec::PrecalculatedMarginal::~PrecalculatedMarginal</a></div><div class="ttdeci">virtual ~PrecalculatedMarginal()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00438">marginalTrek++.cpp:438</a></div></div> | |
| 82 | <div class="ttc" id="class_iso_spec_1_1_marginal_html"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></div><div class="ttdoc">The marginal distribution class (a subisotopologue). </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00045">marginalTrek++.h:45</a></div></div> | |
| 83 | <div class="ttc" id="class_iso_spec_1_1_marginal_trek_html_a04f3e495a805a3ea242059c963c5b129"><div class="ttname"><a href="class_iso_spec_1_1_marginal_trek.html#a04f3e495a805a3ea242059c963c5b129">IsoSpec::MarginalTrek::processUntilCutoff</a></div><div class="ttdeci">int processUntilCutoff(double cutoff)</div><div class="ttdoc">Calculate subisotopologues with probability above or equal to the cut-off. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00333">marginalTrek++.cpp:333</a></div></div> | |
| 84 | <div class="ttc" id="class_iso_spec_1_1_marginal_trek_html_a83e70d522174e4e6724116941fd9c99e"><div class="ttname"><a href="class_iso_spec_1_1_marginal_trek.html#a83e70d522174e4e6724116941fd9c99e">IsoSpec::MarginalTrek::MarginalTrek</a></div><div class="ttdeci">MarginalTrek(Marginal &&m, int tabSize=1000, int hashSize=1000)</div><div class="ttdoc">Move constructor: specializes the Marginal class. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00256">marginalTrek++.cpp:256</a></div></div> | |
| 85 | <div class="ttc" id="namespacestd_html"><div class="ttname"><a href="namespacestd.html">std</a></div></div> | |
| 86 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a8dd6415882661f7b9ceedbe09bc200e3"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">IsoSpec::Marginal::isotopeNo</a></div><div class="ttdeci">const unsigned int isotopeNo</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00050">marginalTrek++.h:50</a></div></div> | |
| 87 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a640f3b44605b510ee556a25e35a2e095"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">IsoSpec::Marginal::mode_conf</a></div><div class="ttdeci">const Conf mode_conf</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00055">marginalTrek++.h:55</a></div></div> | |
| 88 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a53c2af7dcb84aa9d5e0e0918fe7875cd"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">IsoSpec::Marginal::atomCnt</a></div><div class="ttdeci">const unsigned int atomCnt</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00051">marginalTrek++.h:51</a></div></div> | |
| 89 | <div class="ttc" id="class_iso_spec_1_1_key_hasher_html"><div class="ttname"><a href="class_iso_spec_1_1_key_hasher.html">IsoSpec::KeyHasher</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00027">operators.h:27</a></div></div> | |
| 90 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_ad44004fa1e83c4a53d431ca403ce3ae4"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">IsoSpec::Marginal::~Marginal</a></div><div class="ttdeci">virtual ~Marginal()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00226">marginalTrek++.cpp:226</a></div></div> | |
| 91 | <div class="ttc" id="class_iso_spec_1_1_summator_html"><div class="ttname"><a href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a></div><div class="ttdef"><b>Definition:</b> <a href="summator_8h_source.html#l00076">summator.h:76</a></div></div> | |
| 92 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_af059df011e707781fdd4c1d7b70bd91a"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">IsoSpec::Marginal::atom_lProbs</a></div><div class="ttdeci">const double *const atom_lProbs</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00053">marginalTrek++.h:53</a></div></div> | |
| 93 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_aa5598b4d2b31b5daec1c2bac653d0aff"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">IsoSpec::Marginal::getHeaviestConfMass</a></div><div class="ttdeci">double getHeaviestConfMass() const</div><div class="ttdoc">Get the mass of the heaviest subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00246">marginalTrek++.cpp:246</a></div></div> | |
| 94 | <div class="ttc" id="class_iso_spec_1_1_conf_equal_html"><div class="ttname"><a href="class_iso_spec_1_1_conf_equal.html">IsoSpec::ConfEqual</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00045">operators.h:45</a></div></div> | |
| 95 | <div class="ttc" id="namespace_iso_spec_html_a9abbd881dd3c9347438361a6dd21cef4"><div class="ttname"><a href="namespace_iso_spec.html#a9abbd881dd3c9347438361a6dd21cef4">IsoSpec::initialConfigure</a></div><div class="ttdeci">Conf initialConfigure(const int atomCnt, const int isotopeNo, const double *probs, const double *lprobs)</div><div class="ttdoc">Find one of the most probable subisotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00055">marginalTrek++.cpp:55</a></div></div> | |
| 96 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a46be0c1cf5b169a54056997ba404183c"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">IsoSpec::Marginal::Marginal</a></div><div class="ttdeci">Marginal(const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</div><div class="ttdoc">Class constructor. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00187">marginalTrek++.cpp:187</a></div></div> | |
| 97 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_acb84bd7ba582847655c55bd64d64463e"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal</a></div><div class="ttdeci">PrecalculatedMarginal(Marginal &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000)</div><div class="ttdoc">The move constructor (disowns the Marginal). </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00362">marginalTrek++.cpp:362</a></div></div> | |
| 98 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
| 99 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a91265e07f5bb65314995f816f5a9c729"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">IsoSpec::Marginal::atom_masses</a></div><div class="ttdeci">const double *const atom_masses</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00052">marginalTrek++.h:52</a></div></div> | |
| 100 | <div class="ttc" id="namespace_iso_spec_html_a4b68cc6e2f1f4f30b189a5d01153daa4"><div class="ttname"><a href="namespace_iso_spec.html#a4b68cc6e2f1f4f30b189a5d01153daa4">IsoSpec::getMLogProbs</a></div><div class="ttdeci">double * getMLogProbs(const double *probs, int isoNo)</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00150">marginalTrek++.cpp:150</a></div></div> | |
| 101 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a1974bb030ce70178da569214b4b93cb8"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">IsoSpec::Marginal::logProb</a></div><div class="ttdeci">double logProb(Conf conf) const</div><div class="ttdoc">Calculate the log-probability of a given subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00136">marginalTrek++.h:136</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <tuple></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <unordered_map></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <queue></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <atomic></span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#include "conf.h"</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#include "allocator.h"</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#include "operators.h"</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#include "summator.h"</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> </div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> {</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> </div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> Conf <a class="code" href="namespace_iso_spec.html#a9abbd881dd3c9347438361a6dd21cef4">initialConfigure</a>(<span class="keywordtype">int</span> atomCnt, <span class="keywordtype">int</span> isotopeNo, <span class="keyword">const</span> <span class="keywordtype">double</span>* probs);</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="keywordtype">void</span> printMarginal(<span class="keyword">const</span> std::tuple<double*,double*,int*,int>& results, <span class="keywordtype">int</span> dim);</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> </div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div><div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html"> 45</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a></div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> {</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keywordtype">bool</span> disowned;</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="keyword">protected</span>:</div><div class="line"><a name="l00050"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3"> 50</a></span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>; </div><div class="line"><a name="l00051"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd"> 51</a></span>  <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">atomCnt</a>; </div><div class="line"><a name="l00052"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729"> 52</a></span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* <span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">atom_masses</a>; </div><div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a"> 53</a></span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* <span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a>; </div><div class="line"><a name="l00054"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417"> 54</a></span>  <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a>; </div><div class="line"><a name="l00055"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095"> 55</a></span>  <span class="keyword">const</span> Conf <a class="code" href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">mode_conf</a>; </div><div class="line"><a name="l00056"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc"> 56</a></span>  <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a>; </div><div class="line"><a name="l00057"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7"> 57</a></span>  <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a>; </div><div class="line"><a name="l00058"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae"> 58</a></span>  <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">mode_prob</a>; </div><div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc"> 59</a></span>  <span class="keyword">const</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a>; </div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <a class="code" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a>(</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* _masses, <span class="comment">// masses size = logProbs size = isotopeNo</span></div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* _probs,</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordtype">int</span> _isotopeNo,</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <span class="keywordtype">int</span> _atomCnt</div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  );</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="comment">// Get rid of the C++ generated copy and assignment constructors.</span></div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <a class="code" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a>(<a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>& other) = <span class="keyword">delete</span>;</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>& operator= (<span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>& other) = <span class="keyword">delete</span>;</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> </div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <a class="code" href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">Marginal</a>(<a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>&& other);</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keyword">virtual</span> <a class="code" href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">~Marginal</a>();</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div><div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83"> 92</a></span>  <span class="keyword">inline</span> <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">get_isotopeNo</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>; };</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">getLightestConfMass</a>() <span class="keyword">const</span>;</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">getHeaviestConfMass</a>() <span class="keyword">const</span>;</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span> </div><div class="line"><a name="l00110"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49"> 110</a></span>  <span class="keyword">inline</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">getModeLProb</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">mode_lprob</a>; };</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div><div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f"> 116</a></span>  <span class="keyword">inline</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">getModeMass</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">mode_mass</a>; };</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> </div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div><div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0"> 122</a></span>  <span class="keyword">inline</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">getModeProb</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">mode_prob</a>; };</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> </div><div class="line"><a name="l00129"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc"> 129</a></span>  <span class="keyword">inline</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">getSmallestLProb</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">smallest_lprob</a>; };</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span> </div><div class="line"><a name="l00136"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8"> 136</a></span>  <span class="keyword">inline</span> <span class="keywordtype">double</span> <a class="code" href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">logProb</a>(Conf conf)<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code" href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">loggamma_nominator</a> + unnormalized_logProb(conf, <a class="code" href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">atom_lProbs</a>, <a class="code" href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">isotopeNo</a>); };</div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span> };</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div><div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal_trek.html"> 141</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_marginal_trek.html">MarginalTrek</a> : <span class="keyword">public</span> <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a></div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span> {</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  <span class="keywordtype">int</span> current_count;</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_key_hasher.html">KeyHasher</a> keyHasher;</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_conf_equal.html">ConfEqual</a> equalizer;</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  <span class="keyword">const</span> <a class="code" href="class_iso_spec_1_1_conf_order_marginal.html">ConfOrderMarginal</a> orderMarginal;</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  std::unordered_map<Conf,int,KeyHasher,ConfEqual> visited;</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span>  std::priority_queue<Conf,std::vector<Conf>,<a class="code" href="class_iso_spec_1_1_conf_order_marginal.html">ConfOrderMarginal</a>> pq;</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  <a class="code" href="class_iso_spec_1_1_summator.html">Summator</a> totalProb;</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  Conf candidate;</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  <a class="code" href="class_iso_spec_1_1_allocator.html">Allocator<int></a> allocator;</div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  std::vector<double> _conf_lprobs;</div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  std::vector<double> _conf_masses;</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  std::vector<int*> _confs;</div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span> </div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="keywordtype">bool</span> add_next_conf();</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span> </div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span> </div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  <a class="code" href="class_iso_spec_1_1_marginal_trek.html#a83e70d522174e4e6724116941fd9c99e">MarginalTrek</a>(</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>&& m,</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  <span class="keywordtype">int</span> tabSize = 1000,</div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="keywordtype">int</span> hashSize = 1000</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span>  );</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span> </div><div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_marginal_trek.html#a4db6041328b818d123a017dda3c8b8ae"> 179</a></span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="class_iso_spec_1_1_marginal_trek.html#a4db6041328b818d123a017dda3c8b8ae">probeConfigurationIdx</a>(<span class="keywordtype">int</span> idx)</div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  {</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span>  <span class="keywordflow">while</span>(current_count <= idx)</div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span>  <span class="keywordflow">if</span>(!add_next_conf())</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span>  <span class="keywordflow">return</span> <span class="keyword">false</span>;</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordflow">return</span> <span class="keyword">true</span>;</div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  }</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span> </div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span> </div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span> </div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_marginal_trek.html#a04f3e495a805a3ea242059c963c5b129">processUntilCutoff</a>(<span class="keywordtype">double</span> cutoff);</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span> </div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span>  <span class="keyword">inline</span> <span class="keyword">const</span> std::vector<double>& conf_lprobs()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> _conf_lprobs; };</div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  <span class="keyword">inline</span> <span class="keyword">const</span> std::vector<double>& conf_masses()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> _conf_masses; };</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  <span class="keyword">inline</span> <span class="keyword">const</span> std::vector<int*>& confs()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> _confs; };</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> </div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span> </div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="keyword">virtual</span> ~<a class="code" href="class_iso_spec_1_1_marginal_trek.html#a83e70d522174e4e6724116941fd9c99e">MarginalTrek</a>();</div><div class="line"><a name="l00201"></a><span class="lineno"> 201</span> };</div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span> </div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span> </div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span> </div><div class="line"><a name="l00213"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html"> 213</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a> : <span class="keyword">public</span> <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a></div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span> {</div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span> <span class="keyword">protected</span>:</div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  std::vector<Conf> configurations;</div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  Conf* confs;</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> no_confs;</div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span>  <span class="keywordtype">double</span>* masses;</div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span>  <span class="keywordtype">double</span>* lProbs;</div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span>  <span class="keywordtype">double</span>* eProbs;</div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span>  <a class="code" href="class_iso_spec_1_1_allocator.html">Allocator<int></a> allocator;</div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span> </div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">PrecalculatedMarginal</a>(</div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  <a class="code" href="class_iso_spec_1_1_marginal.html">Marginal</a>&& m,</div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span>  <span class="keywordtype">double</span> lCutOff,</div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="keywordtype">bool</span> sort = <span class="keyword">true</span>,</div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="keywordtype">int</span> tabSize = 1000,</div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  <span class="keywordtype">int</span> hashSize = 1000</div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  );</div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span> </div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="keyword">virtual</span> <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8">~PrecalculatedMarginal</a>();</div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  </div><div class="line"><a name="l00244"></a><span class="lineno"> 244</span> </div><div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html#a942b30ace039f80c50125360be4ed4d2"> 247</a></span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a942b30ace039f80c50125360be4ed4d2">inRange</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> idx)<span class="keyword"> const </span>{ <span class="keywordflow">return</span> idx < no_confs; };</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span> </div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span> </div><div class="line"><a name="l00254"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a"> 254</a></span>  <span class="keyword">inline</span> <span class="keyword">const</span> <span class="keywordtype">double</span>& <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">get_lProb</a>(<span class="keywordtype">int</span> idx)<span class="keyword"> const </span>{ <span class="keywordflow">return</span> lProbs[idx]; };</div><div class="line"><a name="l00255"></a><span class="lineno"> 255</span> </div><div class="line"><a name="l00257"></a><span class="lineno"> 257</span> </div><div class="line"><a name="l00261"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02"> 261</a></span>  <span class="keyword">inline</span> <span class="keyword">const</span> <span class="keywordtype">double</span>& <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">get_eProb</a>(<span class="keywordtype">int</span> idx)<span class="keyword"> const </span>{ <span class="keywordflow">return</span> eProbs[idx]; };</div><div class="line"><a name="l00262"></a><span class="lineno"> 262</span> </div><div class="line"><a name="l00264"></a><span class="lineno"> 264</span> </div><div class="line"><a name="l00268"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2"> 268</a></span>  <span class="keyword">inline</span> <span class="keyword">const</span> <span class="keywordtype">double</span>& <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">get_mass</a>(<span class="keywordtype">int</span> idx)<span class="keyword"> const </span>{ <span class="keywordflow">return</span> masses[idx]; };</div><div class="line"><a name="l00269"></a><span class="lineno"> 269</span> </div><div class="line"><a name="l00271"></a><span class="lineno"> 271</span> </div><div class="line"><a name="l00274"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124"> 274</a></span>  <span class="keyword">inline</span> <span class="keyword">const</span> <span class="keywordtype">double</span>* <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">get_lProbs_ptr</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> lProbs; };</div><div class="line"><a name="l00275"></a><span class="lineno"> 275</span> </div><div class="line"><a name="l00277"></a><span class="lineno"> 277</span> </div><div class="line"><a name="l00280"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html#a9a768b90299ea16c447a392dbe1123b5"> 280</a></span>  <span class="keyword">inline</span> <span class="keyword">const</span> <span class="keywordtype">double</span>* <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a9a768b90299ea16c447a392dbe1123b5">get_masses_ptr</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> masses; };</div><div class="line"><a name="l00281"></a><span class="lineno"> 281</span> </div><div class="line"><a name="l00282"></a><span class="lineno"> 282</span> </div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span> </div><div class="line"><a name="l00288"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff"> 288</a></span>  <span class="keyword">inline</span> <span class="keyword">const</span> Conf& <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff">get_conf</a>(<span class="keywordtype">int</span> idx)<span class="keyword"> const </span>{ <span class="keywordflow">return</span> confs[idx]; };</div><div class="line"><a name="l00289"></a><span class="lineno"> 289</span> </div><div class="line"><a name="l00291"></a><span class="lineno"> 291</span> </div><div class="line"><a name="l00294"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9"> 294</a></span>  <span class="keyword">inline</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">get_no_confs</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> no_confs; };</div><div class="line"><a name="l00295"></a><span class="lineno"> 295</span> };</div><div class="line"><a name="l00296"></a><span class="lineno"> 296</span> </div><div class="line"><a name="l00297"></a><span class="lineno"> 297</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00298"></a><span class="lineno"> 298</span> </div><div class="ttc" id="class_iso_spec_1_1_marginal_html_a8b67c507263973da53e533d804e23ac9"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a8b67c507263973da53e533d804e23ac9">IsoSpec::Marginal::getLightestConfMass</a></div><div class="ttdeci">double getLightestConfMass() const</div><div class="ttdoc">Get the mass of the lightest subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00237">marginalTrek++.cpp:237</a></div></div> | |
| 80 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a7bc1eeba342977de3a77c3c7e6ca55b0"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a7bc1eeba342977de3a77c3c7e6ca55b0">IsoSpec::Marginal::getModeProb</a></div><div class="ttdeci">double getModeProb() const</div><div class="ttdoc">The the probability of the mode subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00122">marginalTrek++.h:122</a></div></div> | |
| 81 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a942b30ace039f80c50125360be4ed4d2"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a942b30ace039f80c50125360be4ed4d2">IsoSpec::PrecalculatedMarginal::inRange</a></div><div class="ttdeci">bool inRange(unsigned int idx) const</div><div class="ttdoc">Is there a subisotopologue with a given number? </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00247">marginalTrek++.h:247</a></div></div> | |
| 82 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a75315ec4c470be5f82b903172f7c43ae"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a75315ec4c470be5f82b903172f7c43ae">IsoSpec::Marginal::mode_prob</a></div><div class="ttdeci">const double mode_prob</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00058">marginalTrek++.h:58</a></div></div> | |
| 83 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a6b7b30cfe90ffba1d2c9d2f0d87107d8"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a6b7b30cfe90ffba1d2c9d2f0d87107d8">IsoSpec::PrecalculatedMarginal::~PrecalculatedMarginal</a></div><div class="ttdeci">virtual ~PrecalculatedMarginal()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00438">marginalTrek++.cpp:438</a></div></div> | |
| 84 | <div class="ttc" id="class_iso_spec_1_1_marginal_html"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html">IsoSpec::Marginal</a></div><div class="ttdoc">The marginal distribution class (a subisotopologue). </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00045">marginalTrek++.h:45</a></div></div> | |
| 85 | <div class="ttc" id="class_iso_spec_1_1_marginal_trek_html_a04f3e495a805a3ea242059c963c5b129"><div class="ttname"><a href="class_iso_spec_1_1_marginal_trek.html#a04f3e495a805a3ea242059c963c5b129">IsoSpec::MarginalTrek::processUntilCutoff</a></div><div class="ttdeci">int processUntilCutoff(double cutoff)</div><div class="ttdoc">Calculate subisotopologues with probability above or equal to the cut-off. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00333">marginalTrek++.cpp:333</a></div></div> | |
| 86 | <div class="ttc" id="class_iso_spec_1_1_marginal_trek_html_a83e70d522174e4e6724116941fd9c99e"><div class="ttname"><a href="class_iso_spec_1_1_marginal_trek.html#a83e70d522174e4e6724116941fd9c99e">IsoSpec::MarginalTrek::MarginalTrek</a></div><div class="ttdeci">MarginalTrek(Marginal &&m, int tabSize=1000, int hashSize=1000)</div><div class="ttdoc">Move constructor: specializes the Marginal class. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00256">marginalTrek++.cpp:256</a></div></div> | |
| 87 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a8dd6415882661f7b9ceedbe09bc200e3"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a8dd6415882661f7b9ceedbe09bc200e3">IsoSpec::Marginal::isotopeNo</a></div><div class="ttdeci">const unsigned int isotopeNo</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00050">marginalTrek++.h:50</a></div></div> | |
| 88 | <div class="ttc" id="class_iso_spec_1_1_conf_order_marginal_html"><div class="ttname"><a href="class_iso_spec_1_1_conf_order_marginal.html">IsoSpec::ConfOrderMarginal</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00078">operators.h:78</a></div></div> | |
| 89 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a7a38a567eadf16fa2ad41e81c8f55c02"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a7a38a567eadf16fa2ad41e81c8f55c02">IsoSpec::PrecalculatedMarginal::get_eProb</a></div><div class="ttdeci">const double & get_eProb(int idx) const</div><div class="ttdoc">Get the probability of the idx-th subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00261">marginalTrek++.h:261</a></div></div> | |
| 90 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a640f3b44605b510ee556a25e35a2e095"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a640f3b44605b510ee556a25e35a2e095">IsoSpec::Marginal::mode_conf</a></div><div class="ttdeci">const Conf mode_conf</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00055">marginalTrek++.h:55</a></div></div> | |
| 91 | <div class="ttc" id="class_iso_spec_1_1_allocator_html"><div class="ttname"><a href="class_iso_spec_1_1_allocator.html">IsoSpec::Allocator< int ></a></div></div> | |
| 92 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a53c2af7dcb84aa9d5e0e0918fe7875cd"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a53c2af7dcb84aa9d5e0e0918fe7875cd">IsoSpec::Marginal::atomCnt</a></div><div class="ttdeci">const unsigned int atomCnt</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00051">marginalTrek++.h:51</a></div></div> | |
| 93 | <div class="ttc" id="class_iso_spec_1_1_key_hasher_html"><div class="ttname"><a href="class_iso_spec_1_1_key_hasher.html">IsoSpec::KeyHasher</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00027">operators.h:27</a></div></div> | |
| 94 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a05aa80c3fa77a0406102731934db1a83"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a05aa80c3fa77a0406102731934db1a83">IsoSpec::Marginal::get_isotopeNo</a></div><div class="ttdeci">int get_isotopeNo() const</div><div class="ttdoc">Get the number of isotopes of the investigated element. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00092">marginalTrek++.h:92</a></div></div> | |
| 95 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_ad44004fa1e83c4a53d431ca403ce3ae4"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#ad44004fa1e83c4a53d431ca403ce3ae4">IsoSpec::Marginal::~Marginal</a></div><div class="ttdeci">virtual ~Marginal()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00226">marginalTrek++.cpp:226</a></div></div> | |
| 96 | <div class="ttc" id="class_iso_spec_1_1_summator_html"><div class="ttname"><a href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a></div><div class="ttdef"><b>Definition:</b> <a href="summator_8h_source.html#l00076">summator.h:76</a></div></div> | |
| 97 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a07eee6d60635c9c1d6f92c181994e06a"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a07eee6d60635c9c1d6f92c181994e06a">IsoSpec::PrecalculatedMarginal::get_lProb</a></div><div class="ttdeci">const double & get_lProb(int idx) const</div><div class="ttdoc">Get the log-probability of the idx-th subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00254">marginalTrek++.h:254</a></div></div> | |
| 98 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_af059df011e707781fdd4c1d7b70bd91a"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#af059df011e707781fdd4c1d7b70bd91a">IsoSpec::Marginal::atom_lProbs</a></div><div class="ttdeci">const double *const atom_lProbs</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00053">marginalTrek++.h:53</a></div></div> | |
| 99 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_aa5598b4d2b31b5daec1c2bac653d0aff"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#aa5598b4d2b31b5daec1c2bac653d0aff">IsoSpec::Marginal::getHeaviestConfMass</a></div><div class="ttdeci">double getHeaviestConfMass() const</div><div class="ttdoc">Get the mass of the heaviest subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00246">marginalTrek++.cpp:246</a></div></div> | |
| 100 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_aa3fb5ed3a9b63a855d6270287aed7417"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#aa3fb5ed3a9b63a855d6270287aed7417">IsoSpec::Marginal::loggamma_nominator</a></div><div class="ttdeci">const double loggamma_nominator</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00054">marginalTrek++.h:54</a></div></div> | |
| 101 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_af5d01500c7efb8cba57399ba11fc7124"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#af5d01500c7efb8cba57399ba11fc7124">IsoSpec::PrecalculatedMarginal::get_lProbs_ptr</a></div><div class="ttdeci">const double * get_lProbs_ptr() const</div><div class="ttdoc">Get the table of the log-probabilities of subisotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00274">marginalTrek++.h:274</a></div></div> | |
| 102 | <div class="ttc" id="class_iso_spec_1_1_conf_equal_html"><div class="ttname"><a href="class_iso_spec_1_1_conf_equal.html">IsoSpec::ConfEqual</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00045">operators.h:45</a></div></div> | |
| 103 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a0dbf1ec53eac9953a354c11e1b0803f9"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">IsoSpec::PrecalculatedMarginal::get_no_confs</a></div><div class="ttdeci">unsigned int get_no_confs() const</div><div class="ttdoc">Get the number of precomputed subisotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00294">marginalTrek++.h:294</a></div></div> | |
| 104 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_ac9408957145d2aa63af32f6647c8ea49"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#ac9408957145d2aa63af32f6647c8ea49">IsoSpec::Marginal::getModeLProb</a></div><div class="ttdeci">double getModeLProb() const</div><div class="ttdoc">Get the log-probability of the mode subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00110">marginalTrek++.h:110</a></div></div> | |
| 105 | <div class="ttc" id="namespace_iso_spec_html_a9abbd881dd3c9347438361a6dd21cef4"><div class="ttname"><a href="namespace_iso_spec.html#a9abbd881dd3c9347438361a6dd21cef4">IsoSpec::initialConfigure</a></div><div class="ttdeci">Conf initialConfigure(const int atomCnt, const int isotopeNo, const double *probs, const double *lprobs)</div><div class="ttdoc">Find one of the most probable subisotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00055">marginalTrek++.cpp:55</a></div></div> | |
| 106 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a2abd05ba9351e21cd99e2783e26bd6dc"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a2abd05ba9351e21cd99e2783e26bd6dc">IsoSpec::Marginal::smallest_lprob</a></div><div class="ttdeci">const double smallest_lprob</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00059">marginalTrek++.h:59</a></div></div> | |
| 107 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a46be0c1cf5b169a54056997ba404183c"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a46be0c1cf5b169a54056997ba404183c">IsoSpec::Marginal::Marginal</a></div><div class="ttdeci">Marginal(const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)</div><div class="ttdoc">Class constructor. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00187">marginalTrek++.cpp:187</a></div></div> | |
| 108 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_ada12caa2e195c1a16c5158a428ea3ed2"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#ada12caa2e195c1a16c5158a428ea3ed2">IsoSpec::PrecalculatedMarginal::get_mass</a></div><div class="ttdeci">const double & get_mass(int idx) const</div><div class="ttdoc">Get the mass of the idx-th subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00268">marginalTrek++.h:268</a></div></div> | |
| 109 | <div class="ttc" id="class_iso_spec_1_1_marginal_trek_html_a4db6041328b818d123a017dda3c8b8ae"><div class="ttname"><a href="class_iso_spec_1_1_marginal_trek.html#a4db6041328b818d123a017dda3c8b8ae">IsoSpec::MarginalTrek::probeConfigurationIdx</a></div><div class="ttdeci">bool probeConfigurationIdx(int idx)</div><div class="ttdoc">Check if the table of computed subisotopologues does not have to be extended. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00179">marginalTrek++.h:179</a></div></div> | |
| 110 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a38238e7581f59f08d0faf8ab5eabc0dc"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a38238e7581f59f08d0faf8ab5eabc0dc">IsoSpec::Marginal::mode_lprob</a></div><div class="ttdeci">const double mode_lprob</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00056">marginalTrek++.h:56</a></div></div> | |
| 111 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_acb84bd7ba582847655c55bd64d64463e"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#acb84bd7ba582847655c55bd64d64463e">IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal</a></div><div class="ttdeci">PrecalculatedMarginal(Marginal &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000)</div><div class="ttdoc">The move constructor (disowns the Marginal). </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8cpp_source.html#l00362">marginalTrek++.cpp:362</a></div></div> | |
| 112 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
| 113 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a91265e07f5bb65314995f816f5a9c729"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a91265e07f5bb65314995f816f5a9c729">IsoSpec::Marginal::atom_masses</a></div><div class="ttdeci">const double *const atom_masses</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00052">marginalTrek++.h:52</a></div></div> | |
| 114 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a3ecbbf1263a274cc8e3bc71cd96f0bff"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a3ecbbf1263a274cc8e3bc71cd96f0bff">IsoSpec::PrecalculatedMarginal::get_conf</a></div><div class="ttdeci">const Conf & get_conf(int idx) const</div><div class="ttdoc">Get the counts of isotopes that define the subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00288">marginalTrek++.h:288</a></div></div> | |
| 115 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_ad2121802133075a87f0987dc27d0617f"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#ad2121802133075a87f0987dc27d0617f">IsoSpec::Marginal::getModeMass</a></div><div class="ttdeci">double getModeMass() const</div><div class="ttdoc">The the mass of the mode subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00116">marginalTrek++.h:116</a></div></div> | |
| 116 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a3bfea931e5e1ec1e7d90e8e096c38eb7"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a3bfea931e5e1ec1e7d90e8e096c38eb7">IsoSpec::Marginal::mode_mass</a></div><div class="ttdeci">const double mode_mass</div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00057">marginalTrek++.h:57</a></div></div> | |
| 117 | <div class="ttc" id="class_iso_spec_1_1_marginal_trek_html"><div class="ttname"><a href="class_iso_spec_1_1_marginal_trek.html">IsoSpec::MarginalTrek</a></div><div class="ttdoc">The marginal distribution class (a subisotopologue). </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00141">marginalTrek++.h:141</a></div></div> | |
| 118 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></div><div class="ttdoc">Precalculated Marginal class. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00213">marginalTrek++.h:213</a></div></div> | |
| 119 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a3f9607f51efcfdac1ca58a1467e3a5dc"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a3f9607f51efcfdac1ca58a1467e3a5dc">IsoSpec::Marginal::getSmallestLProb</a></div><div class="ttdeci">double getSmallestLProb() const</div><div class="ttdoc">The the log-probability of the lightest subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00129">marginalTrek++.h:129</a></div></div> | |
| 120 | <div class="ttc" id="class_iso_spec_1_1_marginal_html_a1974bb030ce70178da569214b4b93cb8"><div class="ttname"><a href="class_iso_spec_1_1_marginal.html#a1974bb030ce70178da569214b4b93cb8">IsoSpec::Marginal::logProb</a></div><div class="ttdeci">double logProb(Conf conf) const</div><div class="ttdoc">Calculate the log-probability of a given subisotopologue. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00136">marginalTrek++.h:136</a></div></div> | |
| 121 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a9a768b90299ea16c447a392dbe1123b5"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a9a768b90299ea16c447a392dbe1123b5">IsoSpec::PrecalculatedMarginal::get_masses_ptr</a></div><div class="ttdeci">const double * get_masses_ptr() const</div><div class="ttdoc">Get the table of the masses of subisotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00280">marginalTrek++.h:280</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> </div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#include "misc.h"</span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include "platform.h"</span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <stdlib.h></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#define mswap(x, y) swapspace = x; x = y; y=swapspace;</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> </div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> {</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> </div><div class="line"><a name="l00028"></a><span class="lineno"><a class="line" href="namespace_iso_spec.html#acbcd0253dcdabd90c53d008c7e12b95f"> 28</a></span> <span class="keywordtype">void</span>* <a class="code" href="namespace_iso_spec.html#acbcd0253dcdabd90c53d008c7e12b95f">quickselect</a>(<span class="keywordtype">void</span>** array, <span class="keywordtype">int</span> n, <span class="keywordtype">int</span> start, <span class="keywordtype">int</span> end)</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> {</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordtype">void</span>* swapspace;</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> </div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="keywordflow">if</span>(start == end)</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  <span class="keywordflow">return</span> array[start];</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keywordflow">while</span>(<span class="keyword">true</span>)</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  {</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="comment">// Partition part</span></div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordtype">int</span> len = end - start;</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#if ISOSPEC_BUILDING_R</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keywordtype">int</span> pivot = len/2 + start;</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordtype">int</span> pivot = rand() % len + start;</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordtype">void</span>* pval = array[pivot];</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordtype">double</span> pprob = getLProb(pval);</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  mswap(array[pivot], array[end-1]);</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordtype">int</span> loweridx = start;</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=start; i<end-1; i++)</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  {</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keywordflow">if</span>(getLProb(array[i]) < pprob)</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  {</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  mswap(array[i], array[loweridx]);</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  loweridx++;</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  }</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  }</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  mswap(array[end-1], array[loweridx]);</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> </div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="comment">// Selection part</span></div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordflow">if</span>(n==loweridx)</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordflow">return</span> array[n];</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordflow">if</span>(n<loweridx)</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  end = loweridx;</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  start = loweridx+1;</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  };</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> }</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div><div class="ttc" id="namespace_iso_spec_html_acbcd0253dcdabd90c53d008c7e12b95f"><div class="ttname"><a href="namespace_iso_spec.html#acbcd0253dcdabd90c53d008c7e12b95f">IsoSpec::quickselect</a></div><div class="ttdeci">void * quickselect(void **array, int n, int start, int end)</div><div class="ttdoc">Quickly select the n&#39;th positional statistic, including the weights. </div><div class="ttdef"><b>Definition:</b> <a href="misc_8cpp_source.html#l00028">misc.cpp:28</a></div></div> | |
| 80 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <iostream></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <tuple></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include <vector></span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <fenv.h></span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#include "isoMath.h"</span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> {</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> </div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="keyword">inline</span> <span class="keywordtype">double</span> combinedSum(</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keyword">const</span> <span class="keywordtype">int</span>* conf, <span class="keyword">const</span> std::vector<double>** valuesContainer, <span class="keywordtype">int</span> dimNumber</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> ){</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keywordtype">double</span> res = 0.0;</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=0; i<dimNumber;i++)</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  res += (*(valuesContainer[i]))[conf[i]];</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keywordflow">return</span> res;</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> }</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> </div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="keyword">inline</span> <span class="keywordtype">int</span>* getConf(<span class="keywordtype">void</span>* conf)</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> {</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="keywordflow">return</span> <span class="keyword">reinterpret_cast<</span><span class="keywordtype">int</span>*<span class="keyword">></span>(</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keyword">reinterpret_cast<</span><span class="keywordtype">char</span>*<span class="keyword">></span>(conf) + <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>)</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  );</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> }</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="keyword">inline</span> <span class="keywordtype">double</span> getLProb(<span class="keywordtype">void</span>* conf)</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> {</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keywordtype">double</span> ret = *<span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(conf);</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordflow">return</span> ret;</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> }</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="keyword">inline</span> <span class="keywordtype">double</span> unnormalized_logProb(<span class="keyword">const</span> <span class="keywordtype">int</span>* conf, <span class="keyword">const</span> <span class="keywordtype">double</span>* logProbs, <span class="keywordtype">int</span> dim)</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> {</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  <span class="keywordtype">double</span> res = 0.0;</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordtype">int</span> curr_method = fegetround();</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  fesetround(FE_TOWARDZERO);</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> </div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=0; i < dim; i++)</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  res += minuslogFactorial(conf[i]);</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  fesetround(FE_UPWARD);</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=0; i < dim; i++)</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  res += conf[i] * logProbs[i];</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  fesetround(curr_method);</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <span class="keywordflow">return</span> res;</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> }</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="keyword">inline</span> <span class="keywordtype">double</span> mass(<span class="keyword">const</span> <span class="keywordtype">int</span>* conf, <span class="keyword">const</span> <span class="keywordtype">double</span>* masses, <span class="keywordtype">int</span> dim)</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> {</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordtype">double</span> res = 0.0;</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=0; i < dim; i++)</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  {</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  res += conf[i] * masses[i];</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  }</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keywordflow">return</span> res;</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> }</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="keyword">inline</span> <span class="keywordtype">bool</span> tupleCmp(</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  std::tuple<double,double,int*> t1,</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  std::tuple<double,double,int*> t2</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> ){</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keywordflow">return</span> std::get<1>(t1) > std::get<1>(t2);</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> }</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keywordtype">void</span> printArray(<span class="keyword">const</span> T* array, <span class="keywordtype">int</span> size)</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> {</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i=0; i<size; i++)</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  std::cout << array[i] << <span class="stringliteral">" "</span>;</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  std::cout << std::endl;</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> }</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keywordtype">void</span> printVector(<span class="keyword">const</span> std::vector<T>& vec)</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span> {</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  printArray<T>(vec.data(), vec.size());</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span> }</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span> </div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keywordtype">void</span> printNestedArray(<span class="keyword">const</span> T** array, <span class="keyword">const</span> <span class="keywordtype">int</span>* shape, <span class="keywordtype">int</span> size)</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span> {</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i=0; i<size; i++)</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  printArray(array[i], shape[i]);</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  std::cout << std::endl;</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span> }</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span> <span class="preprocessor">#define mswap(x, y) swapspace = x; x = y; y=swapspace;</span></div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span> <span class="keywordtype">void</span>* <a class="code" href="namespace_iso_spec.html#acbcd0253dcdabd90c53d008c7e12b95f">quickselect</a>(<span class="keywordtype">void</span>** array, <span class="keywordtype">int</span> n, <span class="keywordtype">int</span> start, <span class="keywordtype">int</span> end);</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> </div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> <span class="keyword">template</span> <<span class="keyword">typename</span> T> <span class="keyword">inline</span> <span class="keyword">static</span> T* array_copy(<span class="keyword">const</span> T* A, <span class="keywordtype">int</span> size)</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> {</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  T* ret = <span class="keyword">new</span> T[size];</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  memcpy(ret, A, size*<span class="keyword">sizeof</span>(T));</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keywordflow">return</span> ret;</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> }</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> </div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span> <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keywordtype">void</span> dealloc_table(T* tbl, <span class="keywordtype">int</span> dim)</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> {</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=0; i<dim; i++)</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  {</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keyword">delete</span> tbl[i];</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  }</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keyword">delete</span>[] tbl;</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span> }</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span> </div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div><div class="ttc" id="namespace_iso_spec_html_acbcd0253dcdabd90c53d008c7e12b95f"><div class="ttname"><a href="namespace_iso_spec.html#acbcd0253dcdabd90c53d008c7e12b95f">IsoSpec::quickselect</a></div><div class="ttdeci">void * quickselect(void **array, int n, int start, int end)</div><div class="ttdoc">Quickly select the n&#39;th positional statistic, including the weights. </div><div class="ttdef"><b>Definition:</b> <a href="misc_8cpp_source.html#l00028">misc.cpp:28</a></div></div> | |
| 80 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * This file has been included as a part of IsoSpec project, under a MIT licence. It</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> * comes from the repository:</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> *</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> * https://github.com/witwall/mman-win32</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> *</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * which itself is a mirror of:</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * https://code.google.com/archive/p/mman-win32/</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> */</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> </div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor">#include <windows.h></span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include <errno.h></span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include <io.h></span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> </div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include "mman.h"</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> </div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#ifndef FILE_MAP_EXECUTE</span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#define FILE_MAP_EXECUTE 0x0020</span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#endif </span><span class="comment">/* FILE_MAP_EXECUTE */</span><span class="preprocessor"></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="keyword">static</span> <span class="keywordtype">int</span> __map_mman_error(<span class="keyword">const</span> DWORD err, <span class="keyword">const</span> <span class="keywordtype">int</span> deferr)</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> {</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span>  <span class="keywordflow">if</span> (err == 0)</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span>  <span class="comment">//TODO: implement</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <span class="keywordflow">return</span> err;</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> }</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> </div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="keyword">static</span> DWORD __map_mmap_prot_page(<span class="keyword">const</span> <span class="keywordtype">int</span> prot)</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> {</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  DWORD protect = 0;</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keywordflow">if</span> (prot == PROT_NONE)</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keywordflow">return</span> protect;</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  </div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keywordflow">if</span> ((prot & PROT_EXEC) != 0)</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  {</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  protect = ((prot & PROT_WRITE) != 0) ? </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  PAGE_EXECUTE_READWRITE : PAGE_EXECUTE_READ;</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  }</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  {</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  protect = ((prot & PROT_WRITE) != 0) ?</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  PAGE_READWRITE : PAGE_READONLY;</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  }</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  </div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keywordflow">return</span> protect;</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> }</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="keyword">static</span> DWORD __map_mmap_prot_file(<span class="keyword">const</span> <span class="keywordtype">int</span> prot)</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> {</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  DWORD desiredAccess = 0;</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  </div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keywordflow">if</span> (prot == PROT_NONE)</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordflow">return</span> desiredAccess;</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  </div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="keywordflow">if</span> ((prot & PROT_READ) != 0)</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  desiredAccess |= FILE_MAP_READ;</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keywordflow">if</span> ((prot & PROT_WRITE) != 0)</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  desiredAccess |= FILE_MAP_WRITE;</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keywordflow">if</span> ((prot & PROT_EXEC) != 0)</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  desiredAccess |= FILE_MAP_EXECUTE;</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  </div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keywordflow">return</span> desiredAccess;</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> }</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> <span class="keywordtype">void</span>* mmap(<span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len, <span class="keywordtype">int</span> prot, <span class="keywordtype">int</span> flags, <span class="keywordtype">int</span> fildes, OffsetType off)</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> {</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  HANDLE fm, h;</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  </div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordtype">void</span> * map = MAP_FAILED;</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  </div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> <span class="preprocessor">#ifdef _MSC_VER</span></div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="preprocessor">#pragma warning(push)</span></div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <span class="preprocessor">#pragma warning(disable: 4293)</span></div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keyword">const</span> DWORD dwFileOffsetLow = (<span class="keyword">sizeof</span>(OffsetType) <= <span class="keyword">sizeof</span>(DWORD)) ?</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  (DWORD)off : (DWORD)(off & 0xFFFFFFFFL);</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keyword">const</span> DWORD dwFileOffsetHigh = (<span class="keyword">sizeof</span>(OffsetType) <= <span class="keyword">sizeof</span>(DWORD)) ?</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  (DWORD)0 : (DWORD)((off >> 32) & 0xFFFFFFFFL);</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keyword">const</span> DWORD protect = __map_mmap_prot_page(prot);</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keyword">const</span> DWORD desiredAccess = __map_mmap_prot_file(prot);</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keyword">const</span> OffsetType maxSize = off + (OffsetType)len;</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keyword">const</span> DWORD dwMaxSizeLow = (<span class="keyword">sizeof</span>(OffsetType) <= <span class="keyword">sizeof</span>(DWORD)) ?</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  (DWORD)maxSize : (DWORD)(maxSize & 0xFFFFFFFFL);</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <span class="keyword">const</span> DWORD dwMaxSizeHigh = (<span class="keyword">sizeof</span>(OffsetType) <= <span class="keyword">sizeof</span>(DWORD)) ?</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  (DWORD)0 : (DWORD)((maxSize >> 32) & 0xFFFFFFFFL);</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> <span class="preprocessor">#ifdef _MSC_VER</span></div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> <span class="preprocessor">#pragma warning(pop)</span></div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  errno = 0;</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  </div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  <span class="keywordflow">if</span> (len == 0 </div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="comment">/* Unsupported flag combinations */</span></div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  || (flags & MAP_FIXED) != 0</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="comment">/* Usupported protection combinations */</span></div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  || prot == PROT_EXEC)</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  {</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  errno = EINVAL;</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="keywordflow">return</span> MAP_FAILED;</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  }</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  </div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  h = ((flags & MAP_ANONYMOUS) == 0) ? </div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  (HANDLE)_get_osfhandle(fildes) : INVALID_HANDLE_VALUE;</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  <span class="keywordflow">if</span> ((flags & MAP_ANONYMOUS) == 0 && h == INVALID_HANDLE_VALUE)</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  {</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  errno = EBADF;</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keywordflow">return</span> MAP_FAILED;</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  }</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> </div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  fm = CreateFileMapping(h, NULL, protect, dwMaxSizeHigh, dwMaxSizeLow, NULL);</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="keywordflow">if</span> (fm == NULL)</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  {</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  errno = __map_mman_error(GetLastError(), EPERM);</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keywordflow">return</span> MAP_FAILED;</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  }</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  </div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  map = MapViewOfFile(fm, desiredAccess, dwFileOffsetHigh, dwFileOffsetLow, len);</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  CloseHandle(fm);</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  </div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordflow">if</span> (map == NULL)</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  {</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  errno = __map_mman_error(GetLastError(), EPERM);</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keywordflow">return</span> MAP_FAILED;</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  }</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span> </div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="keywordflow">return</span> map;</div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span> }</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span> <span class="keywordtype">int</span> munmap(<span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len)</div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span> {</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <span class="keywordflow">if</span> (UnmapViewOfFile(addr))</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span>  </div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  errno = __map_mman_error(GetLastError(), EPERM);</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  </div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span> }</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span> </div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span> <span class="keywordtype">int</span> _mprotect(<span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len, <span class="keywordtype">int</span> prot)</div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span> {</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  DWORD newProtect = __map_mmap_prot_page(prot);</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  DWORD oldProtect = 0;</div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  </div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  <span class="keywordflow">if</span> (VirtualProtect(addr, len, newProtect, &oldProtect))</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  </div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  errno = __map_mman_error(GetLastError(), EPERM);</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  </div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span> }</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span> </div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span> <span class="keywordtype">int</span> msync(<span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len, <span class="keywordtype">int</span> flags)</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span> {</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span>  <span class="keywordflow">if</span> (FlushViewOfFile(addr, len))</div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span>  </div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span>  errno = __map_mman_error(GetLastError(), EPERM);</div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span>  </div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00170"></a><span class="lineno"> 170</span> }</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span> </div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span> <span class="keywordtype">int</span> mlock(<span class="keyword">const</span> <span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len)</div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span> {</div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  <span class="keywordflow">if</span> (VirtualLock((LPVOID)addr, len))</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  </div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  errno = __map_mman_error(GetLastError(), EPERM);</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  </div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span> }</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span> <span class="keywordtype">int</span> munlock(<span class="keyword">const</span> <span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len)</div><div class="line"><a name="l00183"></a><span class="lineno"> 183</span> {</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span>  <span class="keywordflow">if</span> (VirtualUnlock((LPVOID)addr, len))</div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  <span class="keywordflow">return</span> 0;</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  </div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  errno = __map_mman_error(GetLastError(), EPERM);</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  </div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordflow">return</span> -1;</div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span> }</div></div><!-- fragment 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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
| 34 | </tr> | |
| 35 | </tbody> | |
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| 39 | <!-- Generated by Doxygen 1.8.14 --> | |
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| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="dir_7a6499598ddcfcabe96e224cb4a6d834.html">Projects</a></li><li class="navelem"><a class="el" href="dir_b5e01de8d0b5565037a326965003e69a.html">isospec</a></li><li class="navelem"><a class="el" href="dir_d48d5cdc71da00f1af92faf73cdbdfd7.html">IsoSpec</a></li><li class="navelem"><a class="el" href="dir_5010eccf620ec85ba5a1264edcd95342.html">IsoSpec++</a></li> </ul> | |
| 72 | </div> | |
| 73 | </div><!-- top --> | |
| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">mman.h</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * sys/mman.h</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> * mman-win32</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> *</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> * This file has been included as a part of IsoSpec project, under a MIT licence. It</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * comes from the repository:</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> *</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> * https://github.com/witwall/mman-win32</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> *</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * which itself is a mirror of:</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> *</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> * https://code.google.com/archive/p/mman-win32/</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> */</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> </div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#ifndef _WIN32_WINNT // Allow use of features specific to Windows XP or later. </span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#define _WIN32_WINNT 0x0501 // Change this to the appropriate value to target other versions of Windows.</span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#endif </span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> </div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">/* All the headers include this file. */</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#ifndef _MSC_VER</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#include <_mingw.h></span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#if defined(MMAN_LIBRARY)</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor">#define MMANSHARED_EXPORT __declspec(dllexport)</span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor">#define MMANSHARED_EXPORT __declspec(dllimport)</span></div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> </div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">/* Determine offset type */</span></div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor">#include <stdint.h></span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="preprocessor">#if defined(_WIN64)</span></div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="keyword">typedef</span> int64_t OffsetType;</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="keyword">typedef</span> uint32_t OffsetType;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <sys/types.h></span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> </div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#ifdef __cplusplus</span></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="keyword">extern</span> <span class="stringliteral">"C"</span> {</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#define PROT_NONE 0</span></div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#define PROT_READ 1</span></div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#define PROT_WRITE 2</span></div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#define PROT_EXEC 4</span></div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#define MAP_FILE 0</span></div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="preprocessor">#define MAP_SHARED 1</span></div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#define MAP_PRIVATE 2</span></div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="preprocessor">#define MAP_TYPE 0xf</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="preprocessor">#define MAP_FIXED 0x10</span></div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="preprocessor">#define MAP_ANONYMOUS 0x20</span></div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="preprocessor">#define MAP_ANON MAP_ANONYMOUS</span></div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> </div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span> <span class="preprocessor">#define MAP_FAILED ((void *)-1)</span></div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> <span class="comment">/* Flags for msync. */</span></div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> <span class="preprocessor">#define MS_ASYNC 1</span></div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="preprocessor">#define MS_SYNC 2</span></div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="preprocessor">#define MS_INVALIDATE 4</span></div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> MMANSHARED_EXPORT <span class="keywordtype">void</span>* mmap(<span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len, <span class="keywordtype">int</span> prot, <span class="keywordtype">int</span> flags, <span class="keywordtype">int</span> fildes, OffsetType off);</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> MMANSHARED_EXPORT <span class="keywordtype">int</span> munmap(<span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len);</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> MMANSHARED_EXPORT <span class="keywordtype">int</span> _mprotect(<span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len, <span class="keywordtype">int</span> prot);</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> MMANSHARED_EXPORT <span class="keywordtype">int</span> msync(<span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len, <span class="keywordtype">int</span> flags);</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> MMANSHARED_EXPORT <span class="keywordtype">int</span> mlock(<span class="keyword">const</span> <span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len);</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> MMANSHARED_EXPORT <span class="keywordtype">int</span> munlock(<span class="keyword">const</span> <span class="keywordtype">void</span> *addr, <span class="keywordtype">size_t</span> len);</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> <span class="preprocessor">#ifdef __cplusplus</span></div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> }</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div></div><!-- fragment --></div><!-- contents --> | |
| 80 | <!-- start footer part --> | |
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| 82 | Generated by  <a href="http://www.doxygen.org/index.html"> | |
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| 84 | </a> 1.8.14 | |
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| 28 | <td id="projectlogo"><img alt="Logo" src="logo.pdf"/></td> | |
| 29 | <td id="projectalign" style="padding-left: 0.5em;"> | |
| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
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| 70 | <div class="header"> | |
| 71 | <div class="summary"> | |
| 72 | <a href="#nested-classes">Classes</a> | | |
| 73 | <a href="#typedef-members">Typedefs</a> | | |
| 74 | <a href="#func-members">Functions</a> | | |
| 75 | <a href="#var-members">Variables</a> </div> | |
| 76 | <div class="headertitle"> | |
| 77 | <div class="title">IsoSpec Namespace Reference</div> </div> | |
| 78 | </div><!--header--> | |
| 79 | <div class="contents"> | |
| 80 | <table class="memberdecls"> | |
| 81 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a> | |
| 82 | Classes</h2></td></tr> | |
| 83 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_allocator.html">Allocator</a></td></tr> | |
| 84 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 85 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_conf_equal.html">ConfEqual</a></td></tr> | |
| 86 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 87 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_conf_order.html">ConfOrder</a></td></tr> | |
| 88 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 89 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_conf_order_marginal.html">ConfOrderMarginal</a></td></tr> | |
| 90 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 91 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_conf_order_marginal_descending.html">ConfOrderMarginalDescending</a></td></tr> | |
| 92 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 93 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_dirty_allocator.html">DirtyAllocator</a></td></tr> | |
| 94 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 95 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso.html">Iso</a></td></tr> | |
| 96 | <tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">The <a class="el" href="class_iso_spec_1_1_iso.html" title="The Iso class for the calculation of the isotopic distribution. ">Iso</a> class for the calculation of the isotopic distribution. <a href="class_iso_spec_1_1_iso.html#details">More...</a><br /></td></tr> | |
| 97 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 98 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_generator.html">IsoGenerator</a></td></tr> | |
| 99 | <tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">The generator of isotopologues. <a href="class_iso_spec_1_1_iso_generator.html#details">More...</a><br /></td></tr> | |
| 100 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 101 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_layered_generator.html">IsoLayeredGenerator</a></td></tr> | |
| 102 | <tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">The class that represents isotopologues above a given joint probability value. <a href="class_iso_spec_1_1_iso_layered_generator.html#details">More...</a><br /></td></tr> | |
| 103 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 104 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_ordered_generator.html">IsoOrderedGenerator</a></td></tr> | |
| 105 | <tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">The generator of isotopologues sorted by their probability of occurrence. <a href="class_iso_spec_1_1_iso_ordered_generator.html#details">More...</a><br /></td></tr> | |
| 106 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 107 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_iso_threshold_generator.html">IsoThresholdGenerator</a></td></tr> | |
| 108 | <tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">The generator of isotopologues above a given threshold value. <a href="class_iso_spec_1_1_iso_threshold_generator.html#details">More...</a><br /></td></tr> | |
| 109 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 110 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_key_hasher.html">KeyHasher</a></td></tr> | |
| 111 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 112 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal.html">Marginal</a></td></tr> | |
| 113 | <tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">The marginal distribution class (a subisotopologue). <a href="class_iso_spec_1_1_marginal.html#details">More...</a><br /></td></tr> | |
| 114 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 115 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_marginal_trek.html">MarginalTrek</a></td></tr> | |
| 116 | <tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">The marginal distribution class (a subisotopologue). <a href="class_iso_spec_1_1_marginal_trek.html#details">More...</a><br /></td></tr> | |
| 117 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 118 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">OrderMarginalsBySizeDecresing</a></td></tr> | |
| 119 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 120 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a></td></tr> | |
| 121 | <tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Precalculated <a class="el" href="class_iso_spec_1_1_marginal.html" title="The marginal distribution class (a subisotopologue). ">Marginal</a> class. <a href="class_iso_spec_1_1_precalculated_marginal.html#details">More...</a><br /></td></tr> | |
| 122 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 123 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_reverse_order.html">ReverseOrder</a></td></tr> | |
| 124 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 125 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_s_summator.html">SSummator</a></td></tr> | |
| 126 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 127 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_summator.html">Summator</a></td></tr> | |
| 128 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 129 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_table_order.html">TableOrder</a></td></tr> | |
| 130 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 131 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_tabulator.html">Tabulator</a></td></tr> | |
| 132 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 133 | <tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_iso_spec_1_1_t_summator.html">TSummator</a></td></tr> | |
| 134 | <tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr> | |
| 135 | </table><table class="memberdecls"> | |
| 136 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="typedef-members"></a> | |
| 137 | Typedefs</h2></td></tr> | |
| 138 | <tr class="memitem:a5e5cbcb7f667e0610638d0a4372899c1"><td class="memItemLeft" align="right" valign="top"><a id="a5e5cbcb7f667e0610638d0a4372899c1"></a> | |
| 139 | typedef int * </td><td class="memItemRight" valign="bottom"><b>Conf</b></td></tr> | |
| 140 | <tr class="separator:a5e5cbcb7f667e0610638d0a4372899c1"><td class="memSeparator" colspan="2"> </td></tr> | |
| 141 | </table><table class="memberdecls"> | |
| 142 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a> | |
| 143 | Functions</h2></td></tr> | |
| 144 | <tr class="memitem:a823643c5602bf7f0992eadc3ae472b5a"><td class="memTemplParams" colspan="2"><a id="a823643c5602bf7f0992eadc3ae472b5a"></a> | |
| 145 | template<typename T > </td></tr> | |
| 146 | <tr class="memitem:a823643c5602bf7f0992eadc3ae472b5a"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><b>copyConf</b> (const T *source, T *destination, int dim)</td></tr> | |
| 147 | <tr class="separator:a823643c5602bf7f0992eadc3ae472b5a"><td class="memSeparator" colspan="2"> </td></tr> | |
| 148 | <tr class="memitem:a7f5e7376b35b2e0766dfea0d5917baed"><td class="memItemLeft" align="right" valign="top"><a id="a7f5e7376b35b2e0766dfea0d5917baed"></a> | |
| 149 | void </td><td class="memItemRight" valign="bottom"><b>release_g_lfact_table</b> ()</td></tr> | |
| 150 | <tr class="separator:a7f5e7376b35b2e0766dfea0d5917baed"><td class="memSeparator" colspan="2"> </td></tr> | |
| 151 | <tr class="memitem:a8cd1d93e56c1301eed0d696332fc81a5"><td class="memItemLeft" align="right" valign="top"><a id="a8cd1d93e56c1301eed0d696332fc81a5"></a> | |
| 152 | double * </td><td class="memItemRight" valign="bottom"><b>alloc_lfact_table</b> ()</td></tr> | |
| 153 | <tr class="separator:a8cd1d93e56c1301eed0d696332fc81a5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 154 | <tr class="memitem:ac766fd9337e208d161395836b9fd9249"><td class="memItemLeft" align="right" valign="top"><a id="ac766fd9337e208d161395836b9fd9249"></a> | |
| 155 | double </td><td class="memItemRight" valign="bottom"><b>RationalApproximation</b> (double t)</td></tr> | |
| 156 | <tr class="separator:ac766fd9337e208d161395836b9fd9249"><td class="memSeparator" colspan="2"> </td></tr> | |
| 157 | <tr class="memitem:ac143363e41d73579b72144675ea3ed43"><td class="memItemLeft" align="right" valign="top"><a id="ac143363e41d73579b72144675ea3ed43"></a> | |
| 158 | double </td><td class="memItemRight" valign="bottom"><b>NormalCDFInverse</b> (double p)</td></tr> | |
| 159 | <tr class="separator:ac143363e41d73579b72144675ea3ed43"><td class="memSeparator" colspan="2"> </td></tr> | |
| 160 | <tr class="memitem:a07b909ec7b54fbe3f68c4c3e3cdf9105"><td class="memItemLeft" align="right" valign="top"><a id="a07b909ec7b54fbe3f68c4c3e3cdf9105"></a> | |
| 161 | double </td><td class="memItemRight" valign="bottom"><b>NormalCDFInverse</b> (double p, double mean, double stdev)</td></tr> | |
| 162 | <tr class="separator:a07b909ec7b54fbe3f68c4c3e3cdf9105"><td class="memSeparator" colspan="2"> </td></tr> | |
| 163 | <tr class="memitem:a80f49da9159a9df06ac64e89d3cef4c8"><td class="memItemLeft" align="right" valign="top"><a id="a80f49da9159a9df06ac64e89d3cef4c8"></a> | |
| 164 | double </td><td class="memItemRight" valign="bottom"><b>NormalCDF</b> (double x, double mean, double stdev)</td></tr> | |
| 165 | <tr class="separator:a80f49da9159a9df06ac64e89d3cef4c8"><td class="memSeparator" colspan="2"> </td></tr> | |
| 166 | <tr class="memitem:aaea4e6cc79d5b2185f4b7b905bd2157f"><td class="memItemLeft" align="right" valign="top"><a id="aaea4e6cc79d5b2185f4b7b905bd2157f"></a> | |
| 167 | double </td><td class="memItemRight" valign="bottom"><b>NormalPDF</b> (double x, double mean, double stdev)</td></tr> | |
| 168 | <tr class="separator:aaea4e6cc79d5b2185f4b7b905bd2157f"><td class="memSeparator" colspan="2"> </td></tr> | |
| 169 | <tr class="memitem:a1cde19132fedfa1686da624baa5e5c35"><td class="memItemLeft" align="right" valign="top"><a id="a1cde19132fedfa1686da624baa5e5c35"></a> | |
| 170 | unsigned int </td><td class="memItemRight" valign="bottom"><b>parse_formula</b> (const char *formula, std::vector< const double *> &isotope_masses, std::vector< const double *> &isotope_probabilities, int **isotopeNumbers, int **atomCounts, unsigned int *confSize)</td></tr> | |
| 171 | <tr class="separator:a1cde19132fedfa1686da624baa5e5c35"><td class="memSeparator" colspan="2"> </td></tr> | |
| 172 | <tr class="memitem:a8c0ac7d2f8818b2f4e66b40cf15aebe5"><td class="memItemLeft" align="right" valign="top"><a id="a8c0ac7d2f8818b2f4e66b40cf15aebe5"></a> | |
| 173 | void </td><td class="memItemRight" valign="bottom"><b>printConfigurations</b> (const std::tuple< double *, double *, int *, int > &results, int dimNumber, int *isotopeNumbers)</td></tr> | |
| 174 | <tr class="separator:a8c0ac7d2f8818b2f4e66b40cf15aebe5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 175 | <tr class="memitem:a9abbd881dd3c9347438361a6dd21cef4"><td class="memItemLeft" align="right" valign="top">Conf </td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_iso_spec.html#a9abbd881dd3c9347438361a6dd21cef4">initialConfigure</a> (const int atomCnt, const int isotopeNo, const double *probs, const double *lprobs)</td></tr> | |
| 176 | <tr class="memdesc:a9abbd881dd3c9347438361a6dd21cef4"><td class="mdescLeft"> </td><td class="mdescRight">Find one of the most probable subisotopologues. <a href="#a9abbd881dd3c9347438361a6dd21cef4">More...</a><br /></td></tr> | |
| 177 | <tr class="separator:a9abbd881dd3c9347438361a6dd21cef4"><td class="memSeparator" colspan="2"> </td></tr> | |
| 178 | <tr class="memitem:a90a5da54d5272c212ed36f4117939343"><td class="memItemLeft" align="right" valign="top"><a id="a90a5da54d5272c212ed36f4117939343"></a> | |
| 179 | void </td><td class="memItemRight" valign="bottom"><b>printMarginal</b> (const std::tuple< double *, double *, int *, int > &results, int dim)</td></tr> | |
| 180 | <tr class="separator:a90a5da54d5272c212ed36f4117939343"><td class="memSeparator" colspan="2"> </td></tr> | |
| 181 | <tr class="memitem:a4b68cc6e2f1f4f30b189a5d01153daa4"><td class="memItemLeft" align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_iso_spec.html#a4b68cc6e2f1f4f30b189a5d01153daa4">getMLogProbs</a> (const double *probs, int isoNo)</td></tr> | |
| 182 | <tr class="separator:a4b68cc6e2f1f4f30b189a5d01153daa4"><td class="memSeparator" colspan="2"> </td></tr> | |
| 183 | <tr class="memitem:a01f8cd14080a2713f6e83e9f46322277"><td class="memItemLeft" align="right" valign="top"><a id="a01f8cd14080a2713f6e83e9f46322277"></a> | |
| 184 | double </td><td class="memItemRight" valign="bottom"><b>get_loggamma_nominator</b> (int x)</td></tr> | |
| 185 | <tr class="separator:a01f8cd14080a2713f6e83e9f46322277"><td class="memSeparator" colspan="2"> </td></tr> | |
| 186 | <tr class="memitem:a4e0e801604398f617d64e6822bbc4e03"><td class="memItemLeft" align="right" valign="top"><a id="a4e0e801604398f617d64e6822bbc4e03"></a> | |
| 187 | Conf </td><td class="memItemRight" valign="bottom"><b>initialConfigure</b> (int atomCnt, int isotopeNo, const double *probs)</td></tr> | |
| 188 | <tr class="separator:a4e0e801604398f617d64e6822bbc4e03"><td class="memSeparator" colspan="2"> </td></tr> | |
| 189 | <tr class="memitem:acbcd0253dcdabd90c53d008c7e12b95f"><td class="memItemLeft" align="right" valign="top"><a id="acbcd0253dcdabd90c53d008c7e12b95f"></a> | |
| 190 | void * </td><td class="memItemRight" valign="bottom"><a class="el" href="namespace_iso_spec.html#acbcd0253dcdabd90c53d008c7e12b95f">quickselect</a> (void **array, int n, int start, int end)</td></tr> | |
| 191 | <tr class="memdesc:acbcd0253dcdabd90c53d008c7e12b95f"><td class="mdescLeft"> </td><td class="mdescRight">Quickly select the n'th positional statistic, including the weights. <br /></td></tr> | |
| 192 | <tr class="separator:acbcd0253dcdabd90c53d008c7e12b95f"><td class="memSeparator" colspan="2"> </td></tr> | |
| 193 | <tr class="memitem:a79a88e35ec43cb5066675948fec030cd"><td class="memItemLeft" align="right" valign="top"><a id="a79a88e35ec43cb5066675948fec030cd"></a> | |
| 194 | double </td><td class="memItemRight" valign="bottom"><b>combinedSum</b> (const int *conf, const std::vector< double > **valuesContainer, int dimNumber)</td></tr> | |
| 195 | <tr class="separator:a79a88e35ec43cb5066675948fec030cd"><td class="memSeparator" colspan="2"> </td></tr> | |
| 196 | <tr class="memitem:a82d9acffe9c8d0b1cca7d801233284c3"><td class="memItemLeft" align="right" valign="top"><a id="a82d9acffe9c8d0b1cca7d801233284c3"></a> | |
| 197 | int * </td><td class="memItemRight" valign="bottom"><b>getConf</b> (void *conf)</td></tr> | |
| 198 | <tr class="separator:a82d9acffe9c8d0b1cca7d801233284c3"><td class="memSeparator" colspan="2"> </td></tr> | |
| 199 | <tr class="memitem:a4642b23c34680776d4e55f6b815a6888"><td class="memItemLeft" align="right" valign="top"><a id="a4642b23c34680776d4e55f6b815a6888"></a> | |
| 200 | double </td><td class="memItemRight" valign="bottom"><b>getLProb</b> (void *conf)</td></tr> | |
| 201 | <tr class="separator:a4642b23c34680776d4e55f6b815a6888"><td class="memSeparator" colspan="2"> </td></tr> | |
| 202 | <tr class="memitem:aa105ce846eaa3e14d1db54ca4e21ad05"><td class="memItemLeft" align="right" valign="top"><a id="aa105ce846eaa3e14d1db54ca4e21ad05"></a> | |
| 203 | double </td><td class="memItemRight" valign="bottom"><b>unnormalized_logProb</b> (const int *conf, const double *logProbs, int dim)</td></tr> | |
| 204 | <tr class="separator:aa105ce846eaa3e14d1db54ca4e21ad05"><td class="memSeparator" colspan="2"> </td></tr> | |
| 205 | <tr class="memitem:a0fc35ec359d8411cbdbab3a9e364c7f5"><td class="memItemLeft" align="right" valign="top"><a id="a0fc35ec359d8411cbdbab3a9e364c7f5"></a> | |
| 206 | double </td><td class="memItemRight" valign="bottom"><b>mass</b> (const int *conf, const double *masses, int dim)</td></tr> | |
| 207 | <tr class="separator:a0fc35ec359d8411cbdbab3a9e364c7f5"><td class="memSeparator" colspan="2"> </td></tr> | |
| 208 | <tr class="memitem:a54355fd7cad87694458f8ea19a478a09"><td class="memItemLeft" align="right" valign="top"><a id="a54355fd7cad87694458f8ea19a478a09"></a> | |
| 209 | bool </td><td class="memItemRight" valign="bottom"><b>tupleCmp</b> (std::tuple< double, double, int *> t1, std::tuple< double, double, int *> t2)</td></tr> | |
| 210 | <tr class="separator:a54355fd7cad87694458f8ea19a478a09"><td class="memSeparator" colspan="2"> </td></tr> | |
| 211 | <tr class="memitem:aa6fae021871c7833eb935320e12f7ddc"><td class="memTemplParams" colspan="2"><a id="aa6fae021871c7833eb935320e12f7ddc"></a> | |
| 212 | template<typename T > </td></tr> | |
| 213 | <tr class="memitem:aa6fae021871c7833eb935320e12f7ddc"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><b>printArray</b> (const T *array, int size)</td></tr> | |
| 214 | <tr class="separator:aa6fae021871c7833eb935320e12f7ddc"><td class="memSeparator" colspan="2"> </td></tr> | |
| 215 | <tr class="memitem:ae984eaef367699061a7fd28a8f20c3ec"><td class="memTemplParams" colspan="2"><a id="ae984eaef367699061a7fd28a8f20c3ec"></a> | |
| 216 | template<typename T > </td></tr> | |
| 217 | <tr class="memitem:ae984eaef367699061a7fd28a8f20c3ec"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><b>printVector</b> (const std::vector< T > &vec)</td></tr> | |
| 218 | <tr class="separator:ae984eaef367699061a7fd28a8f20c3ec"><td class="memSeparator" colspan="2"> </td></tr> | |
| 219 | <tr class="memitem:a6e695f7c9f32f0a53a47765ea7369e0b"><td class="memTemplParams" colspan="2"><a id="a6e695f7c9f32f0a53a47765ea7369e0b"></a> | |
| 220 | template<typename T > </td></tr> | |
| 221 | <tr class="memitem:a6e695f7c9f32f0a53a47765ea7369e0b"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><b>printNestedArray</b> (const T **array, const int *shape, int size)</td></tr> | |
| 222 | <tr class="separator:a6e695f7c9f32f0a53a47765ea7369e0b"><td class="memSeparator" colspan="2"> </td></tr> | |
| 223 | <tr class="memitem:ac68241aedabb0a2fb5ee9c744bc12555"><td class="memTemplParams" colspan="2"><a id="ac68241aedabb0a2fb5ee9c744bc12555"></a> | |
| 224 | template<typename T > </td></tr> | |
| 225 | <tr class="memitem:ac68241aedabb0a2fb5ee9c744bc12555"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><b>dealloc_table</b> (T *tbl, int dim)</td></tr> | |
| 226 | <tr class="separator:ac68241aedabb0a2fb5ee9c744bc12555"><td class="memSeparator" colspan="2"> </td></tr> | |
| 227 | <tr class="memitem:a01daa7537f1603ce443013c0a69f5ad3"><td class="memItemLeft" align="right" valign="top"><a id="a01daa7537f1603ce443013c0a69f5ad3"></a> | |
| 228 | void </td><td class="memItemRight" valign="bottom"><b>reallocate</b> (double **array, int new_size)</td></tr> | |
| 229 | <tr class="separator:a01daa7537f1603ce443013c0a69f5ad3"><td class="memSeparator" colspan="2"> </td></tr> | |
| 230 | </table><table class="memberdecls"> | |
| 231 | <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="var-members"></a> | |
| 232 | Variables</h2></td></tr> | |
| 233 | <tr class="memitem:ad8f480cc82f6a8972cf586464d61b328"><td class="memItemLeft" align="right" valign="top"><a id="ad8f480cc82f6a8972cf586464d61b328"></a> | |
| 234 | const int </td><td class="memItemRight" valign="bottom"><b>elem_table_atomicNo</b> [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]</td></tr> | |
| 235 | <tr class="separator:ad8f480cc82f6a8972cf586464d61b328"><td class="memSeparator" colspan="2"> </td></tr> | |
| 236 | <tr class="memitem:a005cf652f6fd989d4c361ec5a78c3d30"><td class="memItemLeft" align="right" valign="top"><a id="a005cf652f6fd989d4c361ec5a78c3d30"></a> | |
| 237 | const double </td><td class="memItemRight" valign="bottom"><b>elem_table_mass</b> [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]</td></tr> | |
| 238 | <tr class="separator:a005cf652f6fd989d4c361ec5a78c3d30"><td class="memSeparator" colspan="2"> </td></tr> | |
| 239 | <tr class="memitem:a967fbb44ff2abf87af634d2342faff44"><td class="memItemLeft" align="right" valign="top"><a id="a967fbb44ff2abf87af634d2342faff44"></a> | |
| 240 | const int </td><td class="memItemRight" valign="bottom"><b>elem_table_massNo</b> [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]</td></tr> | |
| 241 | <tr class="separator:a967fbb44ff2abf87af634d2342faff44"><td class="memSeparator" colspan="2"> </td></tr> | |
| 242 | <tr class="memitem:a933aad6dfcdc5a011338a53dd3699a6d"><td class="memItemLeft" align="right" valign="top"><a id="a933aad6dfcdc5a011338a53dd3699a6d"></a> | |
| 243 | const int </td><td class="memItemRight" valign="bottom"><b>elem_table_extraNeutrons</b> [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]</td></tr> | |
| 244 | <tr class="separator:a933aad6dfcdc5a011338a53dd3699a6d"><td class="memSeparator" colspan="2"> </td></tr> | |
| 245 | <tr class="memitem:a0fbc31be6f3b2728456a9a7345f727e8"><td class="memItemLeft" align="right" valign="top"><a id="a0fbc31be6f3b2728456a9a7345f727e8"></a> | |
| 246 | const char * </td><td class="memItemRight" valign="bottom"><b>elem_table_element</b> [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]</td></tr> | |
| 247 | <tr class="separator:a0fbc31be6f3b2728456a9a7345f727e8"><td class="memSeparator" colspan="2"> </td></tr> | |
| 248 | <tr class="memitem:a917b6e971fd81932bb4703644ede9728"><td class="memItemLeft" align="right" valign="top"><a id="a917b6e971fd81932bb4703644ede9728"></a> | |
| 249 | const char * </td><td class="memItemRight" valign="bottom"><b>elem_table_symbol</b> [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]</td></tr> | |
| 250 | <tr class="separator:a917b6e971fd81932bb4703644ede9728"><td class="memSeparator" colspan="2"> </td></tr> | |
| 251 | <tr class="memitem:aaa9917bfb60e80f214b7c6d238a39082"><td class="memItemLeft" align="right" valign="top"><a id="aaa9917bfb60e80f214b7c6d238a39082"></a> | |
| 252 | const bool </td><td class="memItemRight" valign="bottom"><b>elem_table_Radioactive</b> [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]</td></tr> | |
| 253 | <tr class="separator:aaa9917bfb60e80f214b7c6d238a39082"><td class="memSeparator" colspan="2"> </td></tr> | |
| 254 | <tr class="memitem:a0f9c2f5f409e63672066a692931e189b"><td class="memItemLeft" align="right" valign="top"><a id="a0f9c2f5f409e63672066a692931e189b"></a> | |
| 255 | const double </td><td class="memItemRight" valign="bottom"><b>elem_table_probability</b> [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]</td></tr> | |
| 256 | <tr class="separator:a0f9c2f5f409e63672066a692931e189b"><td class="memSeparator" colspan="2"> </td></tr> | |
| 257 | <tr class="memitem:a9fe61f2f9c36103283bb256a2f59e93a"><td class="memItemLeft" align="right" valign="top"><a id="a9fe61f2f9c36103283bb256a2f59e93a"></a> | |
| 258 | const double </td><td class="memItemRight" valign="bottom"><b>elem_table_log_probability</b> [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]</td></tr> | |
| 259 | <tr class="separator:a9fe61f2f9c36103283bb256a2f59e93a"><td class="memSeparator" colspan="2"> </td></tr> | |
| 260 | <tr class="memitem:acc706853ec222cb50405ee264e9007bf"><td class="memItemLeft" align="right" valign="top"><a id="acc706853ec222cb50405ee264e9007bf"></a> | |
| 261 | const double </td><td class="memItemRight" valign="bottom"><b>pi</b> = 3.14159265358979323846264338328</td></tr> | |
| 262 | <tr class="separator:acc706853ec222cb50405ee264e9007bf"><td class="memSeparator" colspan="2"> </td></tr> | |
| 263 | <tr class="memitem:a8be6485cb575264c4ec7398501f7c99d"><td class="memItemLeft" align="right" valign="top"><a id="a8be6485cb575264c4ec7398501f7c99d"></a> | |
| 264 | double * </td><td class="memItemRight" valign="bottom"><b>g_lfact_table</b> = alloc_lfact_table()</td></tr> | |
| 265 | <tr class="separator:a8be6485cb575264c4ec7398501f7c99d"><td class="memSeparator" colspan="2"> </td></tr> | |
| 266 | </table> | |
| 267 | <a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2> | |
| 268 | <div class="textblock"><p>Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</p> | |
| 269 | <p>This file is part of <a class="el" href="namespace_iso_spec.html">IsoSpec</a>.</p> | |
| 270 | <p><a class="el" href="namespace_iso_spec.html">IsoSpec</a> is free software: you can redistribute it and/or modify it under the terms of the Simplified ("2-clause") BSD licence.</p> | |
| 271 | <p><a class="el" href="namespace_iso_spec.html">IsoSpec</a> is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</p> | |
| 272 | <p>You should have received a copy of the Simplified BSD Licence along with <a class="el" href="namespace_iso_spec.html">IsoSpec</a>. If not, see <a href="https://opensource.org/licenses/BSD-2-Clause">https://opensource.org/licenses/BSD-2-Clause</a>. </p> | |
| 273 | </div><h2 class="groupheader">Function Documentation</h2> | |
| 274 | <a id="a4b68cc6e2f1f4f30b189a5d01153daa4"></a> | |
| 275 | <h2 class="memtitle"><span class="permalink"><a href="#a4b68cc6e2f1f4f30b189a5d01153daa4">◆ </a></span>getMLogProbs()</h2> | |
| 276 | ||
| 277 | <div class="memitem"> | |
| 278 | <div class="memproto"> | |
| 279 | <table class="memname"> | |
| 280 | <tr> | |
| 281 | <td class="memname">double* IsoSpec::getMLogProbs </td> | |
| 282 | <td>(</td> | |
| 283 | <td class="paramtype">const double * </td> | |
| 284 | <td class="paramname"><em>probs</em>, </td> | |
| 285 | </tr> | |
| 286 | <tr> | |
| 287 | <td class="paramkey"></td> | |
| 288 | <td></td> | |
| 289 | <td class="paramtype">int </td> | |
| 290 | <td class="paramname"><em>isoNo</em> </td> | |
| 291 | </tr> | |
| 292 | <tr> | |
| 293 | <td></td> | |
| 294 | <td>)</td> | |
| 295 | <td></td><td></td> | |
| 296 | </tr> | |
| 297 | </table> | |
| 298 | </div><div class="memdoc"> | |
| 299 | <p><br /> | |
| 300 | Here we order the processor to round the numbers up rather than down. Rounding down could result in the algorithm falling in an infinite loop because of the numerical instability of summing.</p> | |
| 301 | ||
| 302 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8cpp_source.html#l00150">150</a> of file <a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a>.</p> | |
| 303 | ||
| 304 | </div> | |
| 305 | </div> | |
| 306 | <a id="a9abbd881dd3c9347438361a6dd21cef4"></a> | |
| 307 | <h2 class="memtitle"><span class="permalink"><a href="#a9abbd881dd3c9347438361a6dd21cef4">◆ </a></span>initialConfigure()</h2> | |
| 308 | ||
| 309 | <div class="memitem"> | |
| 310 | <div class="memproto"> | |
| 311 | <table class="memname"> | |
| 312 | <tr> | |
| 313 | <td class="memname">Conf IsoSpec::initialConfigure </td> | |
| 314 | <td>(</td> | |
| 315 | <td class="paramtype">const int </td> | |
| 316 | <td class="paramname"><em>atomCnt</em>, </td> | |
| 317 | </tr> | |
| 318 | <tr> | |
| 319 | <td class="paramkey"></td> | |
| 320 | <td></td> | |
| 321 | <td class="paramtype">const int </td> | |
| 322 | <td class="paramname"><em>isotopeNo</em>, </td> | |
| 323 | </tr> | |
| 324 | <tr> | |
| 325 | <td class="paramkey"></td> | |
| 326 | <td></td> | |
| 327 | <td class="paramtype">const double * </td> | |
| 328 | <td class="paramname"><em>probs</em>, </td> | |
| 329 | </tr> | |
| 330 | <tr> | |
| 331 | <td class="paramkey"></td> | |
| 332 | <td></td> | |
| 333 | <td class="paramtype">const double * </td> | |
| 334 | <td class="paramname"><em>lprobs</em> </td> | |
| 335 | </tr> | |
| 336 | <tr> | |
| 337 | <td></td> | |
| 338 | <td>)</td> | |
| 339 | <td></td><td></td> | |
| 340 | </tr> | |
| 341 | </table> | |
| 342 | </div><div class="memdoc"> | |
| 343 | ||
| 344 | <p>Find one of the most probable subisotopologues. </p> | |
| 345 | <p>The algorithm uses the hill-climbing algorithm. It starts from a subisotopologue close to the mean of the underlying multinomial distribution. There might be more than one modes, in case of which this function will return only one of them, close to the mean.</p> | |
| 346 | <dl class="params"><dt>Parameters</dt><dd> | |
| 347 | <table class="params"> | |
| 348 | <tr><td class="paramname">atomCnt</td><td></td></tr> | |
| 349 | </table> | |
| 350 | </dd> | |
| 351 | </dl> | |
| 352 | <p><br /> | |
| 353 | Here we perform hill climbing to the mode of the marginal distribution (the subisotopologue distribution). We start from the point close to the mean of the underlying multinomial distribution.</p> | |
| 354 | ||
| 355 | <p class="definition">Definition at line <a class="el" href="marginal_trek_09_09_8cpp_source.html#l00055">55</a> of file <a class="el" href="marginal_trek_09_09_8cpp_source.html">marginalTrek++.cpp</a>.</p> | |
| 356 | ||
| 357 | </div> | |
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| 364 | </a> 1.8.14 | |
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| 31 |  <span id="projectnumber">1.95</span> | |
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| 56 | <!-- window showing the filter options --> | |
| 57 | <div id="MSearchSelectWindow" | |
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| 69 | ||
| 70 | <div class="contents"> | |
| 71 | <div class="textblock">Here is a list of all documented namespace members with links to the namespaces they belong to:</div><ul> | |
| 72 | <li>getMLogProbs() | |
| 73 | : <a class="el" href="namespace_iso_spec.html#a4b68cc6e2f1f4f30b189a5d01153daa4">IsoSpec</a> | |
| 74 | </li> | |
| 75 | <li>initialConfigure() | |
| 76 | : <a class="el" href="namespace_iso_spec.html#a9abbd881dd3c9347438361a6dd21cef4">IsoSpec</a> | |
| 77 | </li> | |
| 78 | <li>quickselect() | |
| 79 | : <a class="el" href="namespace_iso_spec.html#acbcd0253dcdabd90c53d008c7e12b95f">IsoSpec</a> | |
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| 72 | <li>getMLogProbs() | |
| 73 | : <a class="el" href="namespace_iso_spec.html#a4b68cc6e2f1f4f30b189a5d01153daa4">IsoSpec</a> | |
| 74 | </li> | |
| 75 | <li>initialConfigure() | |
| 76 | : <a class="el" href="namespace_iso_spec.html#a9abbd881dd3c9347438361a6dd21cef4">IsoSpec</a> | |
| 77 | </li> | |
| 78 | <li>quickselect() | |
| 79 | : <a class="el" href="namespace_iso_spec.html#acbcd0253dcdabd90c53d008c7e12b95f">IsoSpec</a> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#include "operators.h"</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> {</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> KeyHasher::KeyHasher(<span class="keywordtype">int</span> _dim)</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> : dim(_dim)</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> {}</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> </div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> ConfEqual::ConfEqual(<span class="keywordtype">int</span> dim)</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> : size( dim*sizeof(int) )</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> {}</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> </div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> ConfOrderMarginal::ConfOrderMarginal(<span class="keyword">const</span> <span class="keywordtype">double</span>* _logProbs, <span class="keywordtype">int</span> _dim)</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> : logProbs(_logProbs), dim(_dim)</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> {}</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> ConfOrderMarginalDescending::ConfOrderMarginalDescending(<span class="keyword">const</span> <span class="keywordtype">double</span>* _logProbs, <span class="keywordtype">int</span> _dim)</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> : logProbs(_logProbs), dim(_dim)</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> {}</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> </div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> </div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> </div><div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <string.h></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include "conf.h"</span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include "isoMath.h"</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include "misc.h"</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> </div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> {</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> </div><div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_key_hasher.html"> 27</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_key_hasher.html">KeyHasher</a></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> {</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keywordtype">int</span> dim;</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  <a class="code" href="class_iso_spec_1_1_key_hasher.html">KeyHasher</a>(<span class="keywordtype">int</span> dim);</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keyword">inline</span> std::size_t operator()(<span class="keyword">const</span> <span class="keywordtype">int</span>* conf)<span class="keyword"> const</span></div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="keyword"> </span>{</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="comment">// Following Boost...</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  std::size_t seed = 0;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i = 0; i < dim; ++i )</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  seed ^= conf[i] + 0x9e3779b9 + (seed << 6) + (seed >> 2);</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="keywordflow">return</span> seed;</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  };</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> };</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div><div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_conf_equal.html"> 45</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_conf_equal.html">ConfEqual</a></div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> {</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keywordtype">int</span> size;</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <a class="code" href="class_iso_spec_1_1_conf_equal.html">ConfEqual</a>(<span class="keywordtype">int</span> dim);</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> operator()(<span class="keyword">const</span> <span class="keywordtype">int</span>* conf1, <span class="keyword">const</span> <span class="keywordtype">int</span>* conf2)<span class="keyword"> const</span></div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="keyword"> </span>{</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="comment">// The memcmp() function returns zero if the two strings are identical, oth-</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="comment">// erwise returns the difference between the first two differing bytes</span></div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="comment">// (treated as unsigned char values, so that `\200' is greater than `\0',</span></div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="comment">// for example). Zero-length strings are always identical. This behavior</span></div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  <span class="comment">// is not required by C and portable code should only depend on the sign of</span></div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="comment">// the returned value.</span></div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="comment">// sacred man of memcmp.</span></div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keywordflow">return</span> memcmp(conf1, conf2, size) == 0;</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  }</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> };</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> </div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> </div><div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_conf_order.html"> 66</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_conf_order.html">ConfOrder</a></div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> {</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> <span class="comment">//configurations comparator</span></div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> operator()(<span class="keywordtype">void</span>* conf1,<span class="keywordtype">void</span>* conf2)<span class="keyword"> const</span></div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="keyword"> </span>{</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordflow">return</span> *<span class="keyword">reinterpret_cast<</span><span class="keywordtype">double</span>*<span class="keyword">></span>(conf1) < *reinterpret_cast<double*>(conf2);</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  };</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> };</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> </div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div><div class="line"><a name="l00078"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_conf_order_marginal.html"> 78</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_conf_order_marginal.html">ConfOrderMarginal</a></div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> {</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <span class="comment">//configurations comparator</span></div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* logProbs;</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordtype">int</span> dim;</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <a class="code" href="class_iso_spec_1_1_conf_order_marginal.html">ConfOrderMarginal</a>(<span class="keyword">const</span> <span class="keywordtype">double</span>* logProbs, <span class="keywordtype">int</span> dim);</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> operator()(<span class="keyword">const</span> Conf conf1, <span class="keyword">const</span> Conf conf2)</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  {<span class="comment">// Return true if conf1 is less probable than conf2.</span></div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordflow">return</span> unnormalized_logProb(conf1,logProbs,dim) < unnormalized_logProb(conf2,logProbs,dim);</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  };</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> };</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div><div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_conf_order_marginal_descending.html"> 92</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_conf_order_marginal_descending.html">ConfOrderMarginalDescending</a></div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> {</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> <span class="comment">//configurations comparator</span></div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keyword">const</span> <span class="keywordtype">double</span>* logProbs;</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keywordtype">int</span> dim;</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <a class="code" href="class_iso_spec_1_1_conf_order_marginal_descending.html">ConfOrderMarginalDescending</a>(<span class="keyword">const</span> <span class="keywordtype">double</span>* logProbs, <span class="keywordtype">int</span> dim);</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> operator()(<span class="keyword">const</span> Conf conf1, <span class="keyword">const</span> Conf conf2)</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  {<span class="comment">// Return true if conf1 is less probable than conf2.</span></div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordflow">return</span> unnormalized_logProb(conf1,logProbs,dim) > unnormalized_logProb(conf2,logProbs,dim);</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  };</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span> };</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div><div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_reverse_order.html"> 106</a></span> <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_reverse_order.html">ReverseOrder</a></div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span> {</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="keyword">inline</span> <a class="code" href="class_iso_spec_1_1_reverse_order.html">ReverseOrder</a>() {};</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> operator()(<span class="keyword">const</span> T a,<span class="keyword">const</span> T b)<span class="keyword"> const </span>{ <span class="keywordflow">return</span> a > b; };</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span> };</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span> </div><div class="line"><a name="l00113"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_table_order.html"> 113</a></span> <span class="keyword">template</span><<span class="keyword">typename</span> T> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_table_order.html">TableOrder</a></div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span> {</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  <span class="keyword">const</span> T* tbl;</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  <span class="keyword">inline</span> <a class="code" href="class_iso_spec_1_1_table_order.html">TableOrder</a>(<span class="keyword">const</span> T* _tbl) : tbl(_tbl) {};</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> operator()(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> j) { <span class="keywordflow">return</span> tbl[i] < tbl[j]; };</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> };</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span> </div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> <span class="preprocessor">#include "marginalTrek++.h"</span></div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span> {</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> </div><div class="line"><a name="l00128"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html"> 128</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">OrderMarginalsBySizeDecresing</a></div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span> {</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <a class="code" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a> <span class="keyword">const</span>* <span class="keyword">const</span>* <span class="keyword">const</span> T;</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keyword">inline</span> <a class="code" href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">OrderMarginalsBySizeDecresing</a>(<a class="code" href="class_iso_spec_1_1_precalculated_marginal.html">PrecalculatedMarginal</a> <span class="keyword">const</span>* <span class="keyword">const</span> * _T) : T(_T) {};</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> operator()(<span class="keywordtype">int</span> m1, <span class="keywordtype">int</span> m2)</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  {</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <span class="keywordflow">return</span> T[m1]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">get_no_confs</a>() > T[m2]-><a class="code" href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">get_no_confs</a>();</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  }</div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span> };</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> </div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span> </div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span> </div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span> </div><div class="ttc" id="class_iso_spec_1_1_conf_order_marginal_descending_html"><div class="ttname"><a href="class_iso_spec_1_1_conf_order_marginal_descending.html">IsoSpec::ConfOrderMarginalDescending</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00092">operators.h:92</a></div></div> | |
| 80 | <div class="ttc" id="class_iso_spec_1_1_order_marginals_by_size_decresing_html"><div class="ttname"><a href="class_iso_spec_1_1_order_marginals_by_size_decresing.html">IsoSpec::OrderMarginalsBySizeDecresing</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00128">operators.h:128</a></div></div> | |
| 81 | <div class="ttc" id="class_iso_spec_1_1_conf_order_marginal_html"><div class="ttname"><a href="class_iso_spec_1_1_conf_order_marginal.html">IsoSpec::ConfOrderMarginal</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00078">operators.h:78</a></div></div> | |
| 82 | <div class="ttc" id="class_iso_spec_1_1_key_hasher_html"><div class="ttname"><a href="class_iso_spec_1_1_key_hasher.html">IsoSpec::KeyHasher</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00027">operators.h:27</a></div></div> | |
| 83 | <div class="ttc" id="class_iso_spec_1_1_conf_equal_html"><div class="ttname"><a href="class_iso_spec_1_1_conf_equal.html">IsoSpec::ConfEqual</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00045">operators.h:45</a></div></div> | |
| 84 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html_a0dbf1ec53eac9953a354c11e1b0803f9"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html#a0dbf1ec53eac9953a354c11e1b0803f9">IsoSpec::PrecalculatedMarginal::get_no_confs</a></div><div class="ttdeci">unsigned int get_no_confs() const</div><div class="ttdoc">Get the number of precomputed subisotopologues. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00294">marginalTrek++.h:294</a></div></div> | |
| 85 | <div class="ttc" id="class_iso_spec_1_1_table_order_html"><div class="ttname"><a href="class_iso_spec_1_1_table_order.html">IsoSpec::TableOrder</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00113">operators.h:113</a></div></div> | |
| 86 | <div class="ttc" id="class_iso_spec_1_1_conf_order_html"><div class="ttname"><a href="class_iso_spec_1_1_conf_order.html">IsoSpec::ConfOrder</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00066">operators.h:66</a></div></div> | |
| 87 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
| 88 | <div class="ttc" id="class_iso_spec_1_1_reverse_order_html"><div class="ttname"><a href="class_iso_spec_1_1_reverse_order.html">IsoSpec::ReverseOrder</a></div><div class="ttdef"><b>Definition:</b> <a href="operators_8h_source.html#l00106">operators.h:106</a></div></div> | |
| 89 | <div class="ttc" id="class_iso_spec_1_1_precalculated_marginal_html"><div class="ttname"><a href="class_iso_spec_1_1_precalculated_marginal.html">IsoSpec::PrecalculatedMarginal</a></div><div class="ttdoc">Precalculated Marginal class. </div><div class="ttdef"><b>Definition:</b> <a href="marginal_trek_09_09_8h_source.html#l00213">marginalTrek++.h:213</a></div></div> | |
| 90 | </div><!-- fragment --></div><!-- contents --> | |
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| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
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| 33 | </td> | |
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| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="dir_7a6499598ddcfcabe96e224cb4a6d834.html">Projects</a></li><li class="navelem"><a class="el" href="dir_b5e01de8d0b5565037a326965003e69a.html">isospec</a></li><li class="navelem"><a class="el" href="dir_d48d5cdc71da00f1af92faf73cdbdfd7.html">IsoSpec</a></li><li class="navelem"><a class="el" href="dir_5010eccf620ec85ba5a1264edcd95342.html">IsoSpec++</a></li> </ul> | |
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| 76 | <div class="title">platform.h</div> </div> | |
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| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> </div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> </div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor">#if !defined(ISOSPEC_BUILDING_R)</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#define ISOSPEC_BUILDING_R false</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> </div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor">#if !defined(ISOSPEC_BUILDING_CPP)</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor">#define ISOSPEC_BUILDING_CPP true</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> </div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor">#if !defined(ISOSPEC_BUILDING_PYTHON)</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#define ISOSPEC_BUILDING_PYTHON false</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> </div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#if !defined(ISOSPEC_BUILDING_OPENMS)</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#define ISOSPEC_BUILDING_OPENMS false</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> </div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#if defined(__unix__) || defined(__unix) || \</span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor"> (defined(__APPLE__) && defined(__MACH__))</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#define ISOSPEC_TEST_WE_ARE_ON_UNIX_YAY true</span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#define ISOSPEC_TEST_WE_ARE_ON_WINDOWS false </span><span class="comment">/* CYGWIN doesn't really count as Windows for our purposes, we'll be using UNIX API anyway */</span><span class="preprocessor"></span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="preprocessor">#define ISOSPEC_TEST_GOT_SYSTEM_MMAN true</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="preprocessor">#define ISOSPEC_TEST_GOT_MMAN true</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="preprocessor">#elif defined(__MINGW32__) || defined(_WIN32)</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="preprocessor">#define ISOSPEC_TEST_WE_ARE_ON_UNIX_YAY false</span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="preprocessor">#define ISOSPEC_TEST_WE_ARE_ON_WINDOWS true</span></div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="preprocessor">#define ISOSPEC_TEST_GOT_SYSTEM_MMAN false</span></div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="preprocessor">#define ISOSPEC_TEST_GOT_MMAN true</span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="preprocessor">#define ISOSPEC_TEST_WE_ARE_ON_UNIX_YAY false </span><span class="comment">/* Well, probably... */</span><span class="preprocessor"></span></div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="preprocessor">#define ISOSPEC_TEST_WE_ARE_ON_WINDOWS false</span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="preprocessor">#define ISOSPEC_TEST_GOT_SYSTEM_MMAN false</span></div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#define ISOSPEC_TEST_GOT_MMAN false</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> </div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#if !defined(ISOSPEC_USE_PTHREADS)</span></div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#define ISOSPEC_USE_PTHREADS false </span><span class="comment">/* TODO: possibly put a macro here to detect whether we */</span><span class="preprocessor"></span></div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#endif </span><span class="comment">/* can/should use pthreads - or rip them out altogether.</span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="comment"> * Investigate whether the performance advantage of pthreads on</span></div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="comment"> * some platforms (*cough* CYGWIN *cough*) is still large</span></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="comment"> * enough to justify keeping both implementations around */</span><span class="preprocessor"></span></div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#if !defined(ISOSPEC_WE_ARE_ON_UNIX_YAY)</span></div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#define ISOSPEC_WE_ARE_ON_UNIX_YAY ISOSPEC_TEST_WE_ARE_ON_UNIX_YAY</span></div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> </div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#if !defined(ISOSPEC_WE_ARE_ON_WINDOWS)</span></div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">#define ISOSPEC_WE_ARE_ON_WINDOWS ISOSPEC_TEST_WE_ARE_ON_WINDOWS</span></div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> </div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#if !defined(ISOSPEC_GOT_SYSTEM_MMAN)</span></div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="preprocessor">#define ISOSPEC_GOT_SYSTEM_MMAN ISOSPEC_TEST_GOT_SYSTEM_MMAN</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> </div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="preprocessor">#if !defined(ISOSPEC_GOT_MMAN)</span></div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="preprocessor">#define ISOSPEC_GOT_MMAN ISOSPEC_TEST_GOT_MMAN</span></div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span> </div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> <span class="comment">// Note: __GNUC__ is defined by clang and gcc</span></div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="preprocessor">#ifdef __GNUC__</span></div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="preprocessor">#define ISOSPEC_LIKELY(condition) __builtin_expect(static_cast<bool>(condition), 1)</span></div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="preprocessor">#define ISOSPEC_UNLIKELY(condition) __builtin_expect(static_cast<bool>(condition), 0)</span></div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="comment">// For aggressive inlining </span></div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="preprocessor">#define ISOSPEC_FORCE_INLINE __attribute__ ((always_inline)) inline</span></div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> <span class="preprocessor">#elif defined _MSC_VER</span></div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> <span class="preprocessor">#define ISOSPEC_LIKELY(condition) condition</span></div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="preprocessor">#define ISOSPEC_UNLIKELY(condition) condition</span></div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> <span class="preprocessor">#define ISOSPEC_FORCE_INLINE __forceinline inline</span></div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> <span class="preprocessor">#define ISOSPEC_LIKELY(condition) condition</span></div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> <span class="preprocessor">#define ISOSPEC_UNLIKELY(condition) condition</span></div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="preprocessor">#define ISOSPEC_FORCE_INLINE inline</span></div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> <span class="preprocessor">#if ISOSPEC_GOT_MMAN</span></div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <span class="preprocessor"> #if ISOSPEC_GOT_SYSTEM_MMAN</span></div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> <span class="preprocessor"> #include <sys/mman.h></span></div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> <span class="preprocessor"> #else</span></div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> <span class="preprocessor"> #include "mman.h"</span></div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> <span class="preprocessor"> #endif</span></div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="preprocessor">#else</span></div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span> <span class="preprocessor"> #include <stdlib.h></span> <span class="comment">/* malloc, free, rand */</span></div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> </div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> <span class="preprocessor">#if defined(OPENMS_DLLAPI) </span><span class="comment">/* IsoSpec is being built as a part of OpenMS: use their visibility macros */</span><span class="preprocessor"></span></div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> <span class="preprocessor">#define ISOSPEC_EXPORT_SYMBOL OPENMS_DLLAPI</span></div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> <span class="preprocessor">#else </span><span class="comment">/* it's a can of worms we don't yet want to open ourselves though... */</span><span class="preprocessor"></span></div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> <span class="preprocessor">#define ISOSPEC_EXPORT_SYMBOL</span></div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> <span class="preprocessor">#endif</span></div></div><!-- fragment --></div><!-- contents --> | |
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| 3 | <link rel="stylesheet" type="text/css" href="search.css"/> | |
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| 0 | /*---------------- Search Box */ | |
| 1 | ||
| 2 | #FSearchBox { | |
| 3 | float: left; | |
| 4 | } | |
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| 6 | #MSearchBox { | |
| 7 | white-space : nowrap; | |
| 8 | float: none; | |
| 9 | margin-top: 8px; | |
| 10 | right: 0px; | |
| 11 | width: 170px; | |
| 12 | height: 24px; | |
| 13 | z-index: 102; | |
| 14 | } | |
| 15 | ||
| 16 | #MSearchBox .left | |
| 17 | { | |
| 18 | display:block; | |
| 19 | position:absolute; | |
| 20 | left:10px; | |
| 21 | width:20px; | |
| 22 | height:19px; | |
| 23 | background:url('search_l.png') no-repeat; | |
| 24 | background-position:right; | |
| 25 | } | |
| 26 | ||
| 27 | #MSearchSelect { | |
| 28 | display:block; | |
| 29 | position:absolute; | |
| 30 | width:20px; | |
| 31 | height:19px; | |
| 32 | } | |
| 33 | ||
| 34 | .left #MSearchSelect { | |
| 35 | left:4px; | |
| 36 | } | |
| 37 | ||
| 38 | .right #MSearchSelect { | |
| 39 | right:5px; | |
| 40 | } | |
| 41 | ||
| 42 | #MSearchField { | |
| 43 | display:block; | |
| 44 | position:absolute; | |
| 45 | height:19px; | |
| 46 | background:url('search_m.png') repeat-x; | |
| 47 | border:none; | |
| 48 | width:115px; | |
| 49 | margin-left:20px; | |
| 50 | padding-left:4px; | |
| 51 | color: #909090; | |
| 52 | outline: none; | |
| 53 | font: 9pt Arial, Verdana, sans-serif; | |
| 54 | -webkit-border-radius: 0px; | |
| 55 | } | |
| 56 | ||
| 57 | #FSearchBox #MSearchField { | |
| 58 | margin-left:15px; | |
| 59 | } | |
| 60 | ||
| 61 | #MSearchBox .right { | |
| 62 | display:block; | |
| 63 | position:absolute; | |
| 64 | right:10px; | |
| 65 | top:8px; | |
| 66 | width:20px; | |
| 67 | height:19px; | |
| 68 | background:url('search_r.png') no-repeat; | |
| 69 | background-position:left; | |
| 70 | } | |
| 71 | ||
| 72 | #MSearchClose { | |
| 73 | display: none; | |
| 74 | position: absolute; | |
| 75 | top: 4px; | |
| 76 | background : none; | |
| 77 | border: none; | |
| 78 | margin: 0px 4px 0px 0px; | |
| 79 | padding: 0px 0px; | |
| 80 | outline: none; | |
| 81 | } | |
| 82 | ||
| 83 | .left #MSearchClose { | |
| 84 | left: 6px; | |
| 85 | } | |
| 86 | ||
| 87 | .right #MSearchClose { | |
| 88 | right: 2px; | |
| 89 | } | |
| 90 | ||
| 91 | .MSearchBoxActive #MSearchField { | |
| 92 | color: #000000; | |
| 93 | } | |
| 94 | ||
| 95 | /*---------------- Search filter selection */ | |
| 96 | ||
| 97 | #MSearchSelectWindow { | |
| 98 | display: none; | |
| 99 | position: absolute; | |
| 100 | left: 0; top: 0; | |
| 101 | border: 1px solid #4C6A87; | |
| 102 | background-color: #F3F5F8; | |
| 103 | z-index: 10001; | |
| 104 | padding-top: 4px; | |
| 105 | padding-bottom: 4px; | |
| 106 | -moz-border-radius: 4px; | |
| 107 | -webkit-border-top-left-radius: 4px; | |
| 108 | -webkit-border-top-right-radius: 4px; | |
| 109 | -webkit-border-bottom-left-radius: 4px; | |
| 110 | -webkit-border-bottom-right-radius: 4px; | |
| 111 | -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15); | |
| 112 | } | |
| 113 | ||
| 114 | .SelectItem { | |
| 115 | font: 8pt Arial, Verdana, sans-serif; | |
| 116 | padding-left: 2px; | |
| 117 | padding-right: 12px; | |
| 118 | border: 0px; | |
| 119 | } | |
| 120 | ||
| 121 | span.SelectionMark { | |
| 122 | margin-right: 4px; | |
| 123 | font-family: monospace; | |
| 124 | outline-style: none; | |
| 125 | text-decoration: none; | |
| 126 | } | |
| 127 | ||
| 128 | a.SelectItem { | |
| 129 | display: block; | |
| 130 | outline-style: none; | |
| 131 | color: #000000; | |
| 132 | text-decoration: none; | |
| 133 | padding-left: 6px; | |
| 134 | padding-right: 12px; | |
| 135 | } | |
| 136 | ||
| 137 | a.SelectItem:focus, | |
| 138 | a.SelectItem:active { | |
| 139 | color: #000000; | |
| 140 | outline-style: none; | |
| 141 | text-decoration: none; | |
| 142 | } | |
| 143 | ||
| 144 | a.SelectItem:hover { | |
| 145 | color: #FFFFFF; | |
| 146 | background-color: #141C24; | |
| 147 | outline-style: none; | |
| 148 | text-decoration: none; | |
| 149 | cursor: pointer; | |
| 150 | display: block; | |
| 151 | } | |
| 152 | ||
| 153 | /*---------------- Search results window */ | |
| 154 | ||
| 155 | iframe#MSearchResults { | |
| 156 | width: 60ex; | |
| 157 | height: 15em; | |
| 158 | } | |
| 159 | ||
| 160 | #MSearchResultsWindow { | |
| 161 | display: none; | |
| 162 | position: absolute; | |
| 163 | left: 0; top: 0; | |
| 164 | border: 1px solid #000; | |
| 165 | background-color: #DBE3EB; | |
| 166 | z-index:10000; | |
| 167 | } | |
| 168 | ||
| 169 | /* ----------------------------------- */ | |
| 170 | ||
| 171 | ||
| 172 | #SRIndex { | |
| 173 | clear:both; | |
| 174 | padding-bottom: 15px; | |
| 175 | } | |
| 176 | ||
| 177 | .SREntry { | |
| 178 | font-size: 10pt; | |
| 179 | padding-left: 1ex; | |
| 180 | } | |
| 181 | ||
| 182 | .SRPage .SREntry { | |
| 183 | font-size: 8pt; | |
| 184 | padding: 1px 5px; | |
| 185 | } | |
| 186 | ||
| 187 | body.SRPage { | |
| 188 | margin: 5px 2px; | |
| 189 | } | |
| 190 | ||
| 191 | .SRChildren { | |
| 192 | padding-left: 3ex; padding-bottom: .5em | |
| 193 | } | |
| 194 | ||
| 195 | .SRPage .SRChildren { | |
| 196 | display: none; | |
| 197 | } | |
| 198 | ||
| 199 | .SRSymbol { | |
| 200 | font-weight: bold; | |
| 201 | color: #18222C; | |
| 202 | font-family: Arial, Verdana, sans-serif; | |
| 203 | text-decoration: none; | |
| 204 | outline: none; | |
| 205 | } | |
| 206 | ||
| 207 | a.SRScope { | |
| 208 | display: block; | |
| 209 | color: #18222C; | |
| 210 | font-family: Arial, Verdana, sans-serif; | |
| 211 | text-decoration: none; | |
| 212 | outline: none; | |
| 213 | } | |
| 214 | ||
| 215 | a.SRSymbol:focus, a.SRSymbol:active, | |
| 216 | a.SRScope:focus, a.SRScope:active { | |
| 217 | text-decoration: underline; | |
| 218 | } | |
| 219 | ||
| 220 | span.SRScope { | |
| 221 | padding-left: 4px; | |
| 222 | } | |
| 223 | ||
| 224 | .SRPage .SRStatus { | |
| 225 | padding: 2px 5px; | |
| 226 | font-size: 8pt; | |
| 227 | font-style: italic; | |
| 228 | } | |
| 229 | ||
| 230 | .SRResult { | |
| 231 | display: none; | |
| 232 | } | |
| 233 | ||
| 234 | DIV.searchresults { | |
| 235 | margin-left: 10px; | |
| 236 | margin-right: 10px; | |
| 237 | } | |
| 238 | ||
| 239 | /*---------------- External search page results */ | |
| 240 | ||
| 241 | .searchresult { | |
| 242 | background-color: #E0E7ED; | |
| 243 | } | |
| 244 | ||
| 245 | .pages b { | |
| 246 | color: white; | |
| 247 | padding: 5px 5px 3px 5px; | |
| 248 | background-image: url("../tab_a.png"); | |
| 249 | background-repeat: repeat-x; | |
| 250 | text-shadow: 0 1px 1px #000000; | |
| 251 | } | |
| 252 | ||
| 253 | .pages { | |
| 254 | line-height: 17px; | |
| 255 | margin-left: 4px; | |
| 256 | text-decoration: none; | |
| 257 | } | |
| 258 | ||
| 259 | .hl { | |
| 260 | font-weight: bold; | |
| 261 | } | |
| 262 | ||
| 263 | #searchresults { | |
| 264 | margin-bottom: 20px; | |
| 265 | } | |
| 266 | ||
| 267 | .searchpages { | |
| 268 | margin-top: 10px; | |
| 269 | } | |
| 270 |
| 0 | /* | |
| 1 | @licstart The following is the entire license notice for the | |
| 2 | JavaScript code in this file. | |
| 3 | ||
| 4 | Copyright (C) 1997-2017 by Dimitri van Heesch | |
| 5 | ||
| 6 | This program is free software; you can redistribute it and/or modify | |
| 7 | it under the terms of the GNU General Public License as published by | |
| 8 | the Free Software Foundation; either version 2 of the License, or | |
| 9 | (at your option) any later version. | |
| 10 | ||
| 11 | This program is distributed in the hope that it will be useful, | |
| 12 | but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| 14 | GNU General Public License for more details. | |
| 15 | ||
| 16 | You should have received a copy of the GNU General Public License along | |
| 17 | with this program; if not, write to the Free Software Foundation, Inc., | |
| 18 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. | |
| 19 | ||
| 20 | @licend The above is the entire license notice | |
| 21 | for the JavaScript code in this file | |
| 22 | */ | |
| 23 | function convertToId(search) | |
| 24 | { | |
| 25 | var result = ''; | |
| 26 | for (i=0;i<search.length;i++) | |
| 27 | { | |
| 28 | var c = search.charAt(i); | |
| 29 | var cn = c.charCodeAt(0); | |
| 30 | if (c.match(/[a-z0-9\u0080-\uFFFF]/)) | |
| 31 | { | |
| 32 | result+=c; | |
| 33 | } | |
| 34 | else if (cn<16) | |
| 35 | { | |
| 36 | result+="_0"+cn.toString(16); | |
| 37 | } | |
| 38 | else | |
| 39 | { | |
| 40 | result+="_"+cn.toString(16); | |
| 41 | } | |
| 42 | } | |
| 43 | return result; | |
| 44 | } | |
| 45 | ||
| 46 | function getXPos(item) | |
| 47 | { | |
| 48 | var x = 0; | |
| 49 | if (item.offsetWidth) | |
| 50 | { | |
| 51 | while (item && item!=document.body) | |
| 52 | { | |
| 53 | x += item.offsetLeft; | |
| 54 | item = item.offsetParent; | |
| 55 | } | |
| 56 | } | |
| 57 | return x; | |
| 58 | } | |
| 59 | ||
| 60 | function getYPos(item) | |
| 61 | { | |
| 62 | var y = 0; | |
| 63 | if (item.offsetWidth) | |
| 64 | { | |
| 65 | while (item && item!=document.body) | |
| 66 | { | |
| 67 | y += item.offsetTop; | |
| 68 | item = item.offsetParent; | |
| 69 | } | |
| 70 | } | |
| 71 | return y; | |
| 72 | } | |
| 73 | ||
| 74 | /* A class handling everything associated with the search panel. | |
| 75 | ||
| 76 | Parameters: | |
| 77 | name - The name of the global variable that will be | |
| 78 | storing this instance. Is needed to be able to set timeouts. | |
| 79 | resultPath - path to use for external files | |
| 80 | */ | |
| 81 | function SearchBox(name, resultsPath, inFrame, label) | |
| 82 | { | |
| 83 | if (!name || !resultsPath) { alert("Missing parameters to SearchBox."); } | |
| 84 | ||
| 85 | // ---------- Instance variables | |
| 86 | this.name = name; | |
| 87 | this.resultsPath = resultsPath; | |
| 88 | this.keyTimeout = 0; | |
| 89 | this.keyTimeoutLength = 500; | |
| 90 | this.closeSelectionTimeout = 300; | |
| 91 | this.lastSearchValue = ""; | |
| 92 | this.lastResultsPage = ""; | |
| 93 | this.hideTimeout = 0; | |
| 94 | this.searchIndex = 0; | |
| 95 | this.searchActive = false; | |
| 96 | this.insideFrame = inFrame; | |
| 97 | this.searchLabel = label; | |
| 98 | ||
| 99 | // ----------- DOM Elements | |
| 100 | ||
| 101 | this.DOMSearchField = function() | |
| 102 | { return document.getElementById("MSearchField"); } | |
| 103 | ||
| 104 | this.DOMSearchSelect = function() | |
| 105 | { return document.getElementById("MSearchSelect"); } | |
| 106 | ||
| 107 | this.DOMSearchSelectWindow = function() | |
| 108 | { return document.getElementById("MSearchSelectWindow"); } | |
| 109 | ||
| 110 | this.DOMPopupSearchResults = function() | |
| 111 | { return document.getElementById("MSearchResults"); } | |
| 112 | ||
| 113 | this.DOMPopupSearchResultsWindow = function() | |
| 114 | { return document.getElementById("MSearchResultsWindow"); } | |
| 115 | ||
| 116 | this.DOMSearchClose = function() | |
| 117 | { return document.getElementById("MSearchClose"); } | |
| 118 | ||
| 119 | this.DOMSearchBox = function() | |
| 120 | { return document.getElementById("MSearchBox"); } | |
| 121 | ||
| 122 | // ------------ Event Handlers | |
| 123 | ||
| 124 | // Called when focus is added or removed from the search field. | |
| 125 | this.OnSearchFieldFocus = function(isActive) | |
| 126 | { | |
| 127 | this.Activate(isActive); | |
| 128 | } | |
| 129 | ||
| 130 | this.OnSearchSelectShow = function() | |
| 131 | { | |
| 132 | var searchSelectWindow = this.DOMSearchSelectWindow(); | |
| 133 | var searchField = this.DOMSearchSelect(); | |
| 134 | ||
| 135 | if (this.insideFrame) | |
| 136 | { | |
| 137 | var left = getXPos(searchField); | |
| 138 | var top = getYPos(searchField); | |
| 139 | left += searchField.offsetWidth + 6; | |
| 140 | top += searchField.offsetHeight; | |
| 141 | ||
| 142 | // show search selection popup | |
| 143 | searchSelectWindow.style.display='block'; | |
| 144 | left -= searchSelectWindow.offsetWidth; | |
| 145 | searchSelectWindow.style.left = left + 'px'; | |
| 146 | searchSelectWindow.style.top = top + 'px'; | |
| 147 | } | |
| 148 | else | |
| 149 | { | |
| 150 | var left = getXPos(searchField); | |
| 151 | var top = getYPos(searchField); | |
| 152 | top += searchField.offsetHeight; | |
| 153 | ||
| 154 | // show search selection popup | |
| 155 | searchSelectWindow.style.display='block'; | |
| 156 | searchSelectWindow.style.left = left + 'px'; | |
| 157 | searchSelectWindow.style.top = top + 'px'; | |
| 158 | } | |
| 159 | ||
| 160 | // stop selection hide timer | |
| 161 | if (this.hideTimeout) | |
| 162 | { | |
| 163 | clearTimeout(this.hideTimeout); | |
| 164 | this.hideTimeout=0; | |
| 165 | } | |
| 166 | return false; // to avoid "image drag" default event | |
| 167 | } | |
| 168 | ||
| 169 | this.OnSearchSelectHide = function() | |
| 170 | { | |
| 171 | this.hideTimeout = setTimeout(this.name +".CloseSelectionWindow()", | |
| 172 | this.closeSelectionTimeout); | |
| 173 | } | |
| 174 | ||
| 175 | // Called when the content of the search field is changed. | |
| 176 | this.OnSearchFieldChange = function(evt) | |
| 177 | { | |
| 178 | if (this.keyTimeout) // kill running timer | |
| 179 | { | |
| 180 | clearTimeout(this.keyTimeout); | |
| 181 | this.keyTimeout = 0; | |
| 182 | } | |
| 183 | ||
| 184 | var e = (evt) ? evt : window.event; // for IE | |
| 185 | if (e.keyCode==40 || e.keyCode==13) | |
| 186 | { | |
| 187 | if (e.shiftKey==1) | |
| 188 | { | |
| 189 | this.OnSearchSelectShow(); | |
| 190 | var win=this.DOMSearchSelectWindow(); | |
| 191 | for (i=0;i<win.childNodes.length;i++) | |
| 192 | { | |
| 193 | var child = win.childNodes[i]; // get span within a | |
| 194 | if (child.className=='SelectItem') | |
| 195 | { | |
| 196 | child.focus(); | |
| 197 | return; | |
| 198 | } | |
| 199 | } | |
| 200 | return; | |
| 201 | } | |
| 202 | else if (window.frames.MSearchResults.searchResults) | |
| 203 | { | |
| 204 | var elem = window.frames.MSearchResults.searchResults.NavNext(0); | |
| 205 | if (elem) elem.focus(); | |
| 206 | } | |
| 207 | } | |
| 208 | else if (e.keyCode==27) // Escape out of the search field | |
| 209 | { | |
| 210 | this.DOMSearchField().blur(); | |
| 211 | this.DOMPopupSearchResultsWindow().style.display = 'none'; | |
| 212 | this.DOMSearchClose().style.display = 'none'; | |
| 213 | this.lastSearchValue = ''; | |
| 214 | this.Activate(false); | |
| 215 | return; | |
| 216 | } | |
| 217 | ||
| 218 | // strip whitespaces | |
| 219 | var searchValue = this.DOMSearchField().value.replace(/ +/g, ""); | |
| 220 | ||
| 221 | if (searchValue != this.lastSearchValue) // search value has changed | |
| 222 | { | |
| 223 | if (searchValue != "") // non-empty search | |
| 224 | { | |
| 225 | // set timer for search update | |
| 226 | this.keyTimeout = setTimeout(this.name + '.Search()', | |
| 227 | this.keyTimeoutLength); | |
| 228 | } | |
| 229 | else // empty search field | |
| 230 | { | |
| 231 | this.DOMPopupSearchResultsWindow().style.display = 'none'; | |
| 232 | this.DOMSearchClose().style.display = 'none'; | |
| 233 | this.lastSearchValue = ''; | |
| 234 | } | |
| 235 | } | |
| 236 | } | |
| 237 | ||
| 238 | this.SelectItemCount = function(id) | |
| 239 | { | |
| 240 | var count=0; | |
| 241 | var win=this.DOMSearchSelectWindow(); | |
| 242 | for (i=0;i<win.childNodes.length;i++) | |
| 243 | { | |
| 244 | var child = win.childNodes[i]; // get span within a | |
| 245 | if (child.className=='SelectItem') | |
| 246 | { | |
| 247 | count++; | |
| 248 | } | |
| 249 | } | |
| 250 | return count; | |
| 251 | } | |
| 252 | ||
| 253 | this.SelectItemSet = function(id) | |
| 254 | { | |
| 255 | var i,j=0; | |
| 256 | var win=this.DOMSearchSelectWindow(); | |
| 257 | for (i=0;i<win.childNodes.length;i++) | |
| 258 | { | |
| 259 | var child = win.childNodes[i]; // get span within a | |
| 260 | if (child.className=='SelectItem') | |
| 261 | { | |
| 262 | var node = child.firstChild; | |
| 263 | if (j==id) | |
| 264 | { | |
| 265 | node.innerHTML='•'; | |
| 266 | } | |
| 267 | else | |
| 268 | { | |
| 269 | node.innerHTML=' '; | |
| 270 | } | |
| 271 | j++; | |
| 272 | } | |
| 273 | } | |
| 274 | } | |
| 275 | ||
| 276 | // Called when an search filter selection is made. | |
| 277 | // set item with index id as the active item | |
| 278 | this.OnSelectItem = function(id) | |
| 279 | { | |
| 280 | this.searchIndex = id; | |
| 281 | this.SelectItemSet(id); | |
| 282 | var searchValue = this.DOMSearchField().value.replace(/ +/g, ""); | |
| 283 | if (searchValue!="" && this.searchActive) // something was found -> do a search | |
| 284 | { | |
| 285 | this.Search(); | |
| 286 | } | |
| 287 | } | |
| 288 | ||
| 289 | this.OnSearchSelectKey = function(evt) | |
| 290 | { | |
| 291 | var e = (evt) ? evt : window.event; // for IE | |
| 292 | if (e.keyCode==40 && this.searchIndex<this.SelectItemCount()) // Down | |
| 293 | { | |
| 294 | this.searchIndex++; | |
| 295 | this.OnSelectItem(this.searchIndex); | |
| 296 | } | |
| 297 | else if (e.keyCode==38 && this.searchIndex>0) // Up | |
| 298 | { | |
| 299 | this.searchIndex--; | |
| 300 | this.OnSelectItem(this.searchIndex); | |
| 301 | } | |
| 302 | else if (e.keyCode==13 || e.keyCode==27) | |
| 303 | { | |
| 304 | this.OnSelectItem(this.searchIndex); | |
| 305 | this.CloseSelectionWindow(); | |
| 306 | this.DOMSearchField().focus(); | |
| 307 | } | |
| 308 | return false; | |
| 309 | } | |
| 310 | ||
| 311 | // --------- Actions | |
| 312 | ||
| 313 | // Closes the results window. | |
| 314 | this.CloseResultsWindow = function() | |
| 315 | { | |
| 316 | this.DOMPopupSearchResultsWindow().style.display = 'none'; | |
| 317 | this.DOMSearchClose().style.display = 'none'; | |
| 318 | this.Activate(false); | |
| 319 | } | |
| 320 | ||
| 321 | this.CloseSelectionWindow = function() | |
| 322 | { | |
| 323 | this.DOMSearchSelectWindow().style.display = 'none'; | |
| 324 | } | |
| 325 | ||
| 326 | // Performs a search. | |
| 327 | this.Search = function() | |
| 328 | { | |
| 329 | this.keyTimeout = 0; | |
| 330 | ||
| 331 | // strip leading whitespace | |
| 332 | var searchValue = this.DOMSearchField().value.replace(/^ +/, ""); | |
| 333 | ||
| 334 | var code = searchValue.toLowerCase().charCodeAt(0); | |
| 335 | var idxChar = searchValue.substr(0, 1).toLowerCase(); | |
| 336 | if ( 0xD800 <= code && code <= 0xDBFF && searchValue > 1) // surrogate pair | |
| 337 | { | |
| 338 | idxChar = searchValue.substr(0, 2); | |
| 339 | } | |
| 340 | ||
| 341 | var resultsPage; | |
| 342 | var resultsPageWithSearch; | |
| 343 | var hasResultsPage; | |
| 344 | ||
| 345 | var idx = indexSectionsWithContent[this.searchIndex].indexOf(idxChar); | |
| 346 | if (idx!=-1) | |
| 347 | { | |
| 348 | var hexCode=idx.toString(16); | |
| 349 | resultsPage = this.resultsPath + '/' + indexSectionNames[this.searchIndex] + '_' + hexCode + '.html'; | |
| 350 | resultsPageWithSearch = resultsPage+'?'+escape(searchValue); | |
| 351 | hasResultsPage = true; | |
| 352 | } | |
| 353 | else // nothing available for this search term | |
| 354 | { | |
| 355 | resultsPage = this.resultsPath + '/nomatches.html'; | |
| 356 | resultsPageWithSearch = resultsPage; | |
| 357 | hasResultsPage = false; | |
| 358 | } | |
| 359 | ||
| 360 | window.frames.MSearchResults.location = resultsPageWithSearch; | |
| 361 | var domPopupSearchResultsWindow = this.DOMPopupSearchResultsWindow(); | |
| 362 | ||
| 363 | if (domPopupSearchResultsWindow.style.display!='block') | |
| 364 | { | |
| 365 | var domSearchBox = this.DOMSearchBox(); | |
| 366 | this.DOMSearchClose().style.display = 'inline'; | |
| 367 | if (this.insideFrame) | |
| 368 | { | |
| 369 | var domPopupSearchResults = this.DOMPopupSearchResults(); | |
| 370 | domPopupSearchResultsWindow.style.position = 'relative'; | |
| 371 | domPopupSearchResultsWindow.style.display = 'block'; | |
| 372 | var width = document.body.clientWidth - 8; // the -8 is for IE :-( | |
| 373 | domPopupSearchResultsWindow.style.width = width + 'px'; | |
| 374 | domPopupSearchResults.style.width = width + 'px'; | |
| 375 | } | |
| 376 | else | |
| 377 | { | |
| 378 | var domPopupSearchResults = this.DOMPopupSearchResults(); | |
| 379 | var left = getXPos(domSearchBox) + 150; // domSearchBox.offsetWidth; | |
| 380 | var top = getYPos(domSearchBox) + 20; // domSearchBox.offsetHeight + 1; | |
| 381 | domPopupSearchResultsWindow.style.display = 'block'; | |
| 382 | left -= domPopupSearchResults.offsetWidth; | |
| 383 | domPopupSearchResultsWindow.style.top = top + 'px'; | |
| 384 | domPopupSearchResultsWindow.style.left = left + 'px'; | |
| 385 | } | |
| 386 | } | |
| 387 | ||
| 388 | this.lastSearchValue = searchValue; | |
| 389 | this.lastResultsPage = resultsPage; | |
| 390 | } | |
| 391 | ||
| 392 | // -------- Activation Functions | |
| 393 | ||
| 394 | // Activates or deactivates the search panel, resetting things to | |
| 395 | // their default values if necessary. | |
| 396 | this.Activate = function(isActive) | |
| 397 | { | |
| 398 | if (isActive || // open it | |
| 399 | this.DOMPopupSearchResultsWindow().style.display == 'block' | |
| 400 | ) | |
| 401 | { | |
| 402 | this.DOMSearchBox().className = 'MSearchBoxActive'; | |
| 403 | ||
| 404 | var searchField = this.DOMSearchField(); | |
| 405 | ||
| 406 | if (searchField.value == this.searchLabel) // clear "Search" term upon entry | |
| 407 | { | |
| 408 | searchField.value = ''; | |
| 409 | this.searchActive = true; | |
| 410 | } | |
| 411 | } | |
| 412 | else if (!isActive) // directly remove the panel | |
| 413 | { | |
| 414 | this.DOMSearchBox().className = 'MSearchBoxInactive'; | |
| 415 | this.DOMSearchField().value = this.searchLabel; | |
| 416 | this.searchActive = false; | |
| 417 | this.lastSearchValue = '' | |
| 418 | this.lastResultsPage = ''; | |
| 419 | } | |
| 420 | } | |
| 421 | } | |
| 422 | ||
| 423 | // ----------------------------------------------------------------------- | |
| 424 | ||
| 425 | // The class that handles everything on the search results page. | |
| 426 | function SearchResults(name) | |
| 427 | { | |
| 428 | // The number of matches from the last run of <Search()>. | |
| 429 | this.lastMatchCount = 0; | |
| 430 | this.lastKey = 0; | |
| 431 | this.repeatOn = false; | |
| 432 | ||
| 433 | // Toggles the visibility of the passed element ID. | |
| 434 | this.FindChildElement = function(id) | |
| 435 | { | |
| 436 | var parentElement = document.getElementById(id); | |
| 437 | var element = parentElement.firstChild; | |
| 438 | ||
| 439 | while (element && element!=parentElement) | |
| 440 | { | |
| 441 | if (element.nodeName == 'DIV' && element.className == 'SRChildren') | |
| 442 | { | |
| 443 | return element; | |
| 444 | } | |
| 445 | ||
| 446 | if (element.nodeName == 'DIV' && element.hasChildNodes()) | |
| 447 | { | |
| 448 | element = element.firstChild; | |
| 449 | } | |
| 450 | else if (element.nextSibling) | |
| 451 | { | |
| 452 | element = element.nextSibling; | |
| 453 | } | |
| 454 | else | |
| 455 | { | |
| 456 | do | |
| 457 | { | |
| 458 | element = element.parentNode; | |
| 459 | } | |
| 460 | while (element && element!=parentElement && !element.nextSibling); | |
| 461 | ||
| 462 | if (element && element!=parentElement) | |
| 463 | { | |
| 464 | element = element.nextSibling; | |
| 465 | } | |
| 466 | } | |
| 467 | } | |
| 468 | } | |
| 469 | ||
| 470 | this.Toggle = function(id) | |
| 471 | { | |
| 472 | var element = this.FindChildElement(id); | |
| 473 | if (element) | |
| 474 | { | |
| 475 | if (element.style.display == 'block') | |
| 476 | { | |
| 477 | element.style.display = 'none'; | |
| 478 | } | |
| 479 | else | |
| 480 | { | |
| 481 | element.style.display = 'block'; | |
| 482 | } | |
| 483 | } | |
| 484 | } | |
| 485 | ||
| 486 | // Searches for the passed string. If there is no parameter, | |
| 487 | // it takes it from the URL query. | |
| 488 | // | |
| 489 | // Always returns true, since other documents may try to call it | |
| 490 | // and that may or may not be possible. | |
| 491 | this.Search = function(search) | |
| 492 | { | |
| 493 | if (!search) // get search word from URL | |
| 494 | { | |
| 495 | search = window.location.search; | |
| 496 | search = search.substring(1); // Remove the leading '?' | |
| 497 | search = unescape(search); | |
| 498 | } | |
| 499 | ||
| 500 | search = search.replace(/^ +/, ""); // strip leading spaces | |
| 501 | search = search.replace(/ +$/, ""); // strip trailing spaces | |
| 502 | search = search.toLowerCase(); | |
| 503 | search = convertToId(search); | |
| 504 | ||
| 505 | var resultRows = document.getElementsByTagName("div"); | |
| 506 | var matches = 0; | |
| 507 | ||
| 508 | var i = 0; | |
| 509 | while (i < resultRows.length) | |
| 510 | { | |
| 511 | var row = resultRows.item(i); | |
| 512 | if (row.className == "SRResult") | |
| 513 | { | |
| 514 | var rowMatchName = row.id.toLowerCase(); | |
| 515 | rowMatchName = rowMatchName.replace(/^sr\d*_/, ''); // strip 'sr123_' | |
| 516 | ||
| 517 | if (search.length<=rowMatchName.length && | |
| 518 | rowMatchName.substr(0, search.length)==search) | |
| 519 | { | |
| 520 | row.style.display = 'block'; | |
| 521 | matches++; | |
| 522 | } | |
| 523 | else | |
| 524 | { | |
| 525 | row.style.display = 'none'; | |
| 526 | } | |
| 527 | } | |
| 528 | i++; | |
| 529 | } | |
| 530 | document.getElementById("Searching").style.display='none'; | |
| 531 | if (matches == 0) // no results | |
| 532 | { | |
| 533 | document.getElementById("NoMatches").style.display='block'; | |
| 534 | } | |
| 535 | else // at least one result | |
| 536 | { | |
| 537 | document.getElementById("NoMatches").style.display='none'; | |
| 538 | } | |
| 539 | this.lastMatchCount = matches; | |
| 540 | return true; | |
| 541 | } | |
| 542 | ||
| 543 | // return the first item with index index or higher that is visible | |
| 544 | this.NavNext = function(index) | |
| 545 | { | |
| 546 | var focusItem; | |
| 547 | while (1) | |
| 548 | { | |
| 549 | var focusName = 'Item'+index; | |
| 550 | focusItem = document.getElementById(focusName); | |
| 551 | if (focusItem && focusItem.parentNode.parentNode.style.display=='block') | |
| 552 | { | |
| 553 | break; | |
| 554 | } | |
| 555 | else if (!focusItem) // last element | |
| 556 | { | |
| 557 | break; | |
| 558 | } | |
| 559 | focusItem=null; | |
| 560 | index++; | |
| 561 | } | |
| 562 | return focusItem; | |
| 563 | } | |
| 564 | ||
| 565 | this.NavPrev = function(index) | |
| 566 | { | |
| 567 | var focusItem; | |
| 568 | while (1) | |
| 569 | { | |
| 570 | var focusName = 'Item'+index; | |
| 571 | focusItem = document.getElementById(focusName); | |
| 572 | if (focusItem && focusItem.parentNode.parentNode.style.display=='block') | |
| 573 | { | |
| 574 | break; | |
| 575 | } | |
| 576 | else if (!focusItem) // last element | |
| 577 | { | |
| 578 | break; | |
| 579 | } | |
| 580 | focusItem=null; | |
| 581 | index--; | |
| 582 | } | |
| 583 | return focusItem; | |
| 584 | } | |
| 585 | ||
| 586 | this.ProcessKeys = function(e) | |
| 587 | { | |
| 588 | if (e.type == "keydown") | |
| 589 | { | |
| 590 | this.repeatOn = false; | |
| 591 | this.lastKey = e.keyCode; | |
| 592 | } | |
| 593 | else if (e.type == "keypress") | |
| 594 | { | |
| 595 | if (!this.repeatOn) | |
| 596 | { | |
| 597 | if (this.lastKey) this.repeatOn = true; | |
| 598 | return false; // ignore first keypress after keydown | |
| 599 | } | |
| 600 | } | |
| 601 | else if (e.type == "keyup") | |
| 602 | { | |
| 603 | this.lastKey = 0; | |
| 604 | this.repeatOn = false; | |
| 605 | } | |
| 606 | return this.lastKey!=0; | |
| 607 | } | |
| 608 | ||
| 609 | this.Nav = function(evt,itemIndex) | |
| 610 | { | |
| 611 | var e = (evt) ? evt : window.event; // for IE | |
| 612 | if (e.keyCode==13) return true; | |
| 613 | if (!this.ProcessKeys(e)) return false; | |
| 614 | ||
| 615 | if (this.lastKey==38) // Up | |
| 616 | { | |
| 617 | var newIndex = itemIndex-1; | |
| 618 | var focusItem = this.NavPrev(newIndex); | |
| 619 | if (focusItem) | |
| 620 | { | |
| 621 | var child = this.FindChildElement(focusItem.parentNode.parentNode.id); | |
| 622 | if (child && child.style.display == 'block') // children visible | |
| 623 | { | |
| 624 | var n=0; | |
| 625 | var tmpElem; | |
| 626 | while (1) // search for last child | |
| 627 | { | |
| 628 | tmpElem = document.getElementById('Item'+newIndex+'_c'+n); | |
| 629 | if (tmpElem) | |
| 630 | { | |
| 631 | focusItem = tmpElem; | |
| 632 | } | |
| 633 | else // found it! | |
| 634 | { | |
| 635 | break; | |
| 636 | } | |
| 637 | n++; | |
| 638 | } | |
| 639 | } | |
| 640 | } | |
| 641 | if (focusItem) | |
| 642 | { | |
| 643 | focusItem.focus(); | |
| 644 | } | |
| 645 | else // return focus to search field | |
| 646 | { | |
| 647 | parent.document.getElementById("MSearchField").focus(); | |
| 648 | } | |
| 649 | } | |
| 650 | else if (this.lastKey==40) // Down | |
| 651 | { | |
| 652 | var newIndex = itemIndex+1; | |
| 653 | var focusItem; | |
| 654 | var item = document.getElementById('Item'+itemIndex); | |
| 655 | var elem = this.FindChildElement(item.parentNode.parentNode.id); | |
| 656 | if (elem && elem.style.display == 'block') // children visible | |
| 657 | { | |
| 658 | focusItem = document.getElementById('Item'+itemIndex+'_c0'); | |
| 659 | } | |
| 660 | if (!focusItem) focusItem = this.NavNext(newIndex); | |
| 661 | if (focusItem) focusItem.focus(); | |
| 662 | } | |
| 663 | else if (this.lastKey==39) // Right | |
| 664 | { | |
| 665 | var item = document.getElementById('Item'+itemIndex); | |
| 666 | var elem = this.FindChildElement(item.parentNode.parentNode.id); | |
| 667 | if (elem) elem.style.display = 'block'; | |
| 668 | } | |
| 669 | else if (this.lastKey==37) // Left | |
| 670 | { | |
| 671 | var item = document.getElementById('Item'+itemIndex); | |
| 672 | var elem = this.FindChildElement(item.parentNode.parentNode.id); | |
| 673 | if (elem) elem.style.display = 'none'; | |
| 674 | } | |
| 675 | else if (this.lastKey==27) // Escape | |
| 676 | { | |
| 677 | parent.searchBox.CloseResultsWindow(); | |
| 678 | parent.document.getElementById("MSearchField").focus(); | |
| 679 | } | |
| 680 | else if (this.lastKey==13) // Enter | |
| 681 | { | |
| 682 | return true; | |
| 683 | } | |
| 684 | return false; | |
| 685 | } | |
| 686 | ||
| 687 | this.NavChild = function(evt,itemIndex,childIndex) | |
| 688 | { | |
| 689 | var e = (evt) ? evt : window.event; // for IE | |
| 690 | if (e.keyCode==13) return true; | |
| 691 | if (!this.ProcessKeys(e)) return false; | |
| 692 | ||
| 693 | if (this.lastKey==38) // Up | |
| 694 | { | |
| 695 | if (childIndex>0) | |
| 696 | { | |
| 697 | var newIndex = childIndex-1; | |
| 698 | document.getElementById('Item'+itemIndex+'_c'+newIndex).focus(); | |
| 699 | } | |
| 700 | else // already at first child, jump to parent | |
| 701 | { | |
| 702 | document.getElementById('Item'+itemIndex).focus(); | |
| 703 | } | |
| 704 | } | |
| 705 | else if (this.lastKey==40) // Down | |
| 706 | { | |
| 707 | var newIndex = childIndex+1; | |
| 708 | var elem = document.getElementById('Item'+itemIndex+'_c'+newIndex); | |
| 709 | if (!elem) // last child, jump to parent next parent | |
| 710 | { | |
| 711 | elem = this.NavNext(itemIndex+1); | |
| 712 | } | |
| 713 | if (elem) | |
| 714 | { | |
| 715 | elem.focus(); | |
| 716 | } | |
| 717 | } | |
| 718 | else if (this.lastKey==27) // Escape | |
| 719 | { | |
| 720 | parent.searchBox.CloseResultsWindow(); | |
| 721 | parent.document.getElementById("MSearchField").focus(); | |
| 722 | } | |
| 723 | else if (this.lastKey==13) // Enter | |
| 724 | { | |
| 725 | return true; | |
| 726 | } | |
| 727 | return false; | |
| 728 | } | |
| 729 | } | |
| 730 | ||
| 731 | function setKeyActions(elem,action) | |
| 732 | { | |
| 733 | elem.setAttribute('onkeydown',action); | |
| 734 | elem.setAttribute('onkeypress',action); | |
| 735 | elem.setAttribute('onkeyup',action); | |
| 736 | } | |
| 737 | ||
| 738 | function setClassAttr(elem,attr) | |
| 739 | { | |
| 740 | elem.setAttribute('class',attr); | |
| 741 | elem.setAttribute('className',attr); | |
| 742 | } | |
| 743 | ||
| 744 | function createResults() | |
| 745 | { | |
| 746 | var results = document.getElementById("SRResults"); | |
| 747 | for (var e=0; e<searchData.length; e++) | |
| 748 | { | |
| 749 | var id = searchData[e][0]; | |
| 750 | var srResult = document.createElement('div'); | |
| 751 | srResult.setAttribute('id','SR_'+id); | |
| 752 | setClassAttr(srResult,'SRResult'); | |
| 753 | var srEntry = document.createElement('div'); | |
| 754 | setClassAttr(srEntry,'SREntry'); | |
| 755 | var srLink = document.createElement('a'); | |
| 756 | srLink.setAttribute('id','Item'+e); | |
| 757 | setKeyActions(srLink,'return searchResults.Nav(event,'+e+')'); | |
| 758 | setClassAttr(srLink,'SRSymbol'); | |
| 759 | srLink.innerHTML = searchData[e][1][0]; | |
| 760 | srEntry.appendChild(srLink); | |
| 761 | if (searchData[e][1].length==2) // single result | |
| 762 | { | |
| 763 | srLink.setAttribute('href',searchData[e][1][1][0]); | |
| 764 | if (searchData[e][1][1][1]) | |
| 765 | { | |
| 766 | srLink.setAttribute('target','_parent'); | |
| 767 | } | |
| 768 | var srScope = document.createElement('span'); | |
| 769 | setClassAttr(srScope,'SRScope'); | |
| 770 | srScope.innerHTML = searchData[e][1][1][2]; | |
| 771 | srEntry.appendChild(srScope); | |
| 772 | } | |
| 773 | else // multiple results | |
| 774 | { | |
| 775 | srLink.setAttribute('href','javascript:searchResults.Toggle("SR_'+id+'")'); | |
| 776 | var srChildren = document.createElement('div'); | |
| 777 | setClassAttr(srChildren,'SRChildren'); | |
| 778 | for (var c=0; c<searchData[e][1].length-1; c++) | |
| 779 | { | |
| 780 | var srChild = document.createElement('a'); | |
| 781 | srChild.setAttribute('id','Item'+e+'_c'+c); | |
| 782 | setKeyActions(srChild,'return searchResults.NavChild(event,'+e+','+c+')'); | |
| 783 | setClassAttr(srChild,'SRScope'); | |
| 784 | srChild.setAttribute('href',searchData[e][1][c+1][0]); | |
| 785 | if (searchData[e][1][c+1][1]) | |
| 786 | { | |
| 787 | srChild.setAttribute('target','_parent'); | |
| 788 | } | |
| 789 | srChild.innerHTML = searchData[e][1][c+1][2]; | |
| 790 | srChildren.appendChild(srChild); | |
| 791 | } | |
| 792 | srEntry.appendChild(srChildren); | |
| 793 | } | |
| 794 | srResult.appendChild(srEntry); | |
| 795 | results.appendChild(srResult); | |
| 796 | } | |
| 797 | } | |
| 798 | ||
| 799 | function init_search() | |
| 800 | { | |
| 801 | var results = document.getElementById("MSearchSelectWindow"); | |
| 802 | for (var key in indexSectionLabels) | |
| 803 | { | |
| 804 | var link = document.createElement('a'); | |
| 805 | link.setAttribute('class','SelectItem'); | |
| 806 | link.setAttribute('onclick','searchBox.OnSelectItem('+key+')'); | |
| 807 | link.href='javascript:void(0)'; | |
| 808 | link.innerHTML='<span class="SelectionMark"> </span>'+indexSectionLabels[key]; | |
| 809 | results.appendChild(link); | |
| 810 | } | |
| 811 | searchBox.OnSelectItem(0); | |
| 812 | } | |
| 813 | /* @license-end */ |
| 0 | var indexSectionsWithContent = | |
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| 2 | 0: "acdgiklmopqrst~", | |
| 3 | 1: "acdikmoprst", | |
| 4 | 2: "i", | |
| 5 | 3: "acgilmpqrt~", | |
| 6 | 4: "acdilmps" | |
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| 9 | var indexSectionNames = | |
| 10 | { | |
| 11 | 0: "all", | |
| 12 | 1: "classes", | |
| 13 | 2: "namespaces", | |
| 14 | 3: "functions", | |
| 15 | 4: "variables" | |
| 16 | }; | |
| 17 | ||
| 18 | var indexSectionLabels = | |
| 19 | { | |
| 20 | 0: "All", | |
| 21 | 1: "Classes", | |
| 22 | 2: "Namespaces", | |
| 23 | 3: "Functions", | |
| 24 | 4: "Variables" | |
| 25 | }; | |
| 26 |
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| 7 | </head> | |
| 8 | <body class="SRPage"> | |
| 9 | <div id="SRIndex"> | |
| 10 | <div class="SRStatus" id="Loading">Loading...</div> | |
| 11 | <div id="SRResults"></div> | |
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| 76 | <div class="title">summator.h</div> </div> | |
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| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment"> * Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek.</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> *</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * This file is part of IsoSpec.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * IsoSpec is free software: you can redistribute it and/or modify</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * it under the terms of the Simplified ("2-clause") BSD licence.</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> *</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> * IsoSpec is distributed in the hope that it will be useful,</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * You should have received a copy of the Simplified BSD Licence</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> */</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> </div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#include <cmath></span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="preprocessor">#include <atomic></span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> {</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div><div class="line"><a name="l00025"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_s_summator.html"> 25</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_s_summator.html">SSummator</a></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> {</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <span class="comment">// Shewchuk algorithm</span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  std::vector<double> partials;</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keywordtype">int</span> maxpart;</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keyword">inline</span> <a class="code" href="class_iso_spec_1_1_s_summator.html">SSummator</a>()</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  { maxpart = 0; }</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  <span class="keyword">inline</span> <a class="code" href="class_iso_spec_1_1_s_summator.html">SSummator</a>(<a class="code" href="class_iso_spec_1_1_s_summator.html">SSummator</a>& other)</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  {</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  this->partials = other.partials;</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  this->maxpart = other.maxpart;</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  }</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> add(<span class="keywordtype">double</span> x)</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  {</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> i=0;</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> pidx=0; pidx<maxpart; pidx++)</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  {</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordtype">double</span> y = partials[pidx];</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordflow">if</span>(std::abs(x) < std::abs(y))</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  std::swap(x, y);</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keywordtype">double</span> hi = x+y;</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keywordtype">double</span> lo = y-(hi-x);</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keywordflow">if</span>(lo != 0.0)</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  {</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  partials[i] = lo;</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  i += 1;</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  }</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  x = hi;</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  }</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordflow">while</span>(partials.size() <= i)</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  partials.push_back(0.0);</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  partials[i] = x;</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  maxpart = i+1;</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  }</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">inline</span> <span class="keywordtype">double</span> <span class="keyword">get</span>()</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  {</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  <span class="keywordtype">double</span> ret = 0.0;</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">for</span>(<span class="keywordtype">int</span> i=0; i<maxpart; i++)</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  ret += partials[i];</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordflow">return</span> ret;</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  }</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> };</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> </div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div><div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_summator.html"> 76</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_summator.html">Summator</a>{</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="comment">// Kahan algorithm</span></div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordtype">double</span> sum;</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  <span class="keywordtype">double</span> c;</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keyword">inline</span> <a class="code" href="class_iso_spec_1_1_summator.html">Summator</a>()</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  { sum = 0.0; c = 0.0;}</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> add(<span class="keywordtype">double</span> what)</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  {</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordtype">double</span> y = what - c;</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <span class="keywordtype">double</span> t = sum + y;</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  c = (t - sum) - y;</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  sum = t;</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  }</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <span class="keyword">inline</span> <span class="keywordtype">double</span> <span class="keyword">get</span>()</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  {</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keywordflow">return</span> sum;</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  }</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> };</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> </div><div class="line"><a name="l00099"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_t_summator.html"> 99</a></span> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_t_summator.html">TSummator</a></div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span> {</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <span class="comment">// Trivial algorithm, for testing only</span></div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordtype">double</span> sum;</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keyword">inline</span> <a class="code" href="class_iso_spec_1_1_t_summator.html">TSummator</a>()</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  { sum = 0.0; }</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> add(<span class="keywordtype">double</span> what)</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span>  {</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  sum += what;</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  }</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  <span class="keyword">inline</span> <span class="keywordtype">double</span> <span class="keyword">get</span>()</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span>  {</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordflow">return</span> sum;</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span>  }</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span> };</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span> </div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> </div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div><div class="ttc" id="class_iso_spec_1_1_t_summator_html"><div class="ttname"><a href="class_iso_spec_1_1_t_summator.html">IsoSpec::TSummator</a></div><div class="ttdef"><b>Definition:</b> <a href="summator_8h_source.html#l00099">summator.h:99</a></div></div> | |
| 80 | <div class="ttc" id="class_iso_spec_1_1_summator_html"><div class="ttname"><a href="class_iso_spec_1_1_summator.html">IsoSpec::Summator</a></div><div class="ttdef"><b>Definition:</b> <a href="summator_8h_source.html#l00076">summator.h:76</a></div></div> | |
| 81 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
| 82 | <div class="ttc" id="class_iso_spec_1_1_s_summator_html"><div class="ttname"><a href="class_iso_spec_1_1_s_summator.html">IsoSpec::SSummator</a></div><div class="ttdef"><b>Definition:</b> <a href="summator_8h_source.html#l00025">summator.h:25</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#include "tabulator.h"</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> </div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> </div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> {</div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="keyword">template</span> <span class="keyword">class </span>Tabulator<IsoThresholdGenerator>;</div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">//template class Tabulator<IsoLayeredGenerator>;</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> } <span class="comment">// namespace IsoSpec</span></div><div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
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| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#pragma once</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> </div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#include <stdlib.h></span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> </div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#include "isoSpec++.h"</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> </div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#define ISOSPEC_INIT_TABLE_SIZE 1024</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> </div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="keyword">namespace </span><a class="code" href="namespace_iso_spec.html">IsoSpec</a></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> {</div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> </div><div class="line"><a name="l00012"></a><span class="lineno"><a class="line" href="class_iso_spec_1_1_tabulator.html"> 12</a></span> <span class="keyword">template</span> <<span class="keyword">typename</span> T> <span class="keyword">class </span><a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator</a></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> {</div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="keyword">private</span>:</div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span>  <span class="keywordtype">double</span>* _masses;</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span>  <span class="keywordtype">double</span>* _lprobs;</div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span>  <span class="keywordtype">double</span>* _probs;</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span>  <span class="keywordtype">int</span>* _confs;</div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span>  <span class="keywordtype">size_t</span> _confs_no;</div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="keyword">public</span>:</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span>  <a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator</a>(T* generator,</div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span>  <span class="keywordtype">bool</span> get_masses, <span class="keywordtype">bool</span> get_probs,</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span>  <span class="keywordtype">bool</span> get_lprobs, <span class="keywordtype">bool</span> get_confs);</div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span>  ~<a class="code" href="class_iso_spec_1_1_tabulator.html">Tabulator</a>();</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> </div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span>  <span class="keyword">inline</span> <span class="keywordtype">double</span>* masses() { <span class="keywordflow">return</span> _masses; };</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span>  <span class="keyword">inline</span> <span class="keywordtype">double</span>* lprobs() { <span class="keywordflow">return</span> _lprobs; };</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="keyword">inline</span> <span class="keywordtype">double</span>* probs() { <span class="keywordflow">return</span> _probs; };</div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span>  <span class="keyword">inline</span> <span class="keywordtype">int</span>* confs() { <span class="keywordflow">return</span> _confs; };</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  <span class="keyword">inline</span> <span class="keywordtype">size_t</span> confs_no() { <span class="keywordflow">return</span> _confs_no; };</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> };</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> </div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="keywordtype">void</span> reallocate(<span class="keywordtype">double</span> **array, <span class="keywordtype">int</span> new_size){</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  <span class="keywordflow">if</span>( *array != <span class="keyword">nullptr</span> ){</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  *array = (<span class="keywordtype">double</span> *) realloc(*array, new_size);</div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  }</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span> }</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="keyword">template</span> <<span class="keyword">typename</span> T> Tabulator<T>::Tabulator(T* generator,</div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keywordtype">bool</span> get_masses, <span class="keywordtype">bool</span> get_probs,</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span>  <span class="keywordtype">bool</span> get_lprobs, <span class="keywordtype">bool</span> get_confs )</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> {</div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span>  <span class="keywordtype">size_t</span> current_size = ISOSPEC_INIT_TABLE_SIZE;</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="keywordtype">int</span> confs_tbl_idx = 0;</div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  _confs_no = 0;</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keyword">const</span> <span class="keywordtype">int</span> allDimSizeOfInt = <span class="keyword">sizeof</span>(int)*generator->getAllDim();</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> </div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  _masses = get_masses ? (<span class="keywordtype">double</span> *) malloc(ISOSPEC_INIT_TABLE_SIZE * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>)) : <span class="keyword">nullptr</span>;</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  _lprobs = get_lprobs ? (<span class="keywordtype">double</span> *) malloc(ISOSPEC_INIT_TABLE_SIZE * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>)) : <span class="keyword">nullptr</span>;</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  _probs = get_probs ? (<span class="keywordtype">double</span> *) malloc(ISOSPEC_INIT_TABLE_SIZE * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>)) : <span class="keyword">nullptr</span>;</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span>  _confs = get_confs ? (<span class="keywordtype">int</span> *) malloc(ISOSPEC_INIT_TABLE_SIZE * allDimSizeOfInt): nullptr;</div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keywordflow">while</span>(generator->advanceToNextConfiguration()){</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keywordflow">if</span>( _confs_no == current_size )</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  {</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  current_size *= 2;</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> </div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="comment">// FIXME: Handle overflow gracefully here. It definitely could happen for people still stuck on 32 bits...</span></div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  reallocate(&_masses, current_size * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  reallocate(&_lprobs, current_size * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  reallocate(&_probs, current_size * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  <span class="keywordflow">if</span>( _confs != <span class="keyword">nullptr</span> ){</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  _confs = (<span class="keywordtype">int</span> *) realloc(_confs, current_size * allDimSizeOfInt);</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  }</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  }</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> </div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <span class="keywordflow">if</span>(_masses != <span class="keyword">nullptr</span>) _masses[_confs_no] = generator->mass();</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> </div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <span class="keywordflow">if</span>(_lprobs != <span class="keyword">nullptr</span>) _lprobs[_confs_no] = generator->lprob();</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordflow">if</span>(_probs != <span class="keyword">nullptr</span>) _probs[_confs_no] = generator->prob();</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> </div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordflow">if</span>(_confs != <span class="keyword">nullptr</span>){</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  generator->get_conf_signature(_confs + confs_tbl_idx);</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span>  confs_tbl_idx += generator->getAllDim();</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span>  }</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> </div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  _confs_no++;</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  }</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  _masses = (<span class="keywordtype">double</span> *) realloc(_masses, _confs_no * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  _lprobs = (<span class="keywordtype">double</span> *) realloc(_lprobs, _confs_no * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  _probs = (<span class="keywordtype">double</span> *) realloc(_probs, _confs_no * <span class="keyword">sizeof</span>(<span class="keywordtype">double</span>));</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  _confs = (<span class="keywordtype">int</span> *) realloc(_confs, confs_tbl_idx * <span class="keyword">sizeof</span>(<span class="keywordtype">int</span>));</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> }</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> </div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> <span class="keyword">template</span> <<span class="keyword">typename</span> T> Tabulator<T>::~Tabulator()</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> {</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keywordflow">if</span>( _masses != <span class="keyword">nullptr</span> ) free(_masses);</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keywordflow">if</span>( _lprobs != <span class="keyword">nullptr</span> ) free(_lprobs);</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  <span class="keywordflow">if</span>( _probs != <span class="keyword">nullptr</span> ) free(_probs);</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  <span class="keywordflow">if</span>( _confs != <span class="keyword">nullptr</span> ) free(_confs);</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> }</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span> } <span class="comment">// namespace IsoSpec</span></div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div><div class="ttc" id="class_iso_spec_1_1_tabulator_html"><div class="ttname"><a href="class_iso_spec_1_1_tabulator.html">IsoSpec::Tabulator</a></div><div class="ttdef"><b>Definition:</b> <a href="tabulator_8h_source.html#l00012">tabulator.h:12</a></div></div> | |
| 80 | <div class="ttc" id="namespace_iso_spec_html"><div class="ttname"><a href="namespace_iso_spec.html">IsoSpec</a></div><div class="ttdef"><b>Definition:</b> <a href="allocator_8cpp_source.html#l00021">allocator.cpp:21</a></div></div> | |
| 81 | </div><!-- fragment --></div><!-- contents --> | |
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| 30 | <div id="projectname">IsoSpec | |
| 31 |  <span id="projectnumber">1.95</span> | |
| 32 | </div> | |
| 33 | </td> | |
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| 69 | <div id="nav-path" class="navpath"> | |
| 70 | <ul> | |
| 71 | <li class="navelem"><a class="el" href="dir_7a6499598ddcfcabe96e224cb4a6d834.html">Projects</a></li><li class="navelem"><a class="el" href="dir_b5e01de8d0b5565037a326965003e69a.html">isospec</a></li><li class="navelem"><a class="el" href="dir_d48d5cdc71da00f1af92faf73cdbdfd7.html">IsoSpec</a></li><li class="navelem"><a class="el" href="dir_5010eccf620ec85ba5a1264edcd95342.html">IsoSpec++</a></li> </ul> | |
| 72 | </div> | |
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| 74 | <div class="header"> | |
| 75 | <div class="headertitle"> | |
| 76 | <div class="title">unity-build.cpp</div> </div> | |
| 77 | </div><!--header--> | |
| 78 | <div class="contents"> | |
| 79 | <div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="preprocessor">#include "platform.h"</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> </div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="preprocessor">#if !ISOSPEC_GOT_SYSTEM_MMAN && ISOSPEC_GOT_MMAN</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="preprocessor"> #include "mman.c"</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="preprocessor">#endif</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> </div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="preprocessor">#include "allocator.cpp"</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="preprocessor">#include "dirtyAllocator.cpp"</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="preprocessor">#include "isoSpec++.cpp"</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="preprocessor">#include "isoMath.cpp"</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="preprocessor">#include "marginalTrek++.cpp"</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="preprocessor">#include "operators.cpp"</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="preprocessor">#include "element_tables.cpp"</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="preprocessor">#include "cwrapper.cpp"</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="preprocessor">#include "tabulator.cpp"</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="preprocessor">#include "misc.cpp"</span></div></div><!-- fragment --></div><!-- contents --> | |
| 80 | <!-- start footer part --> | |
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| 0 | all: refman.pdf | |
| 1 | ||
| 2 | pdf: refman.pdf | |
| 3 | ||
| 4 | refman.pdf: clean refman.tex | |
| 5 | pdflatex refman | |
| 6 | makeindex refman.idx | |
| 7 | pdflatex refman | |
| 8 | latex_count=8 ; \ | |
| 9 | while egrep -s 'Rerun (LaTeX|to get cross-references right)' refman.log && [ $$latex_count -gt 0 ] ;\ | |
| 10 | do \ | |
| 11 | echo "Rerunning latex...." ;\ | |
| 12 | pdflatex refman ;\ | |
| 13 | latex_count=`expr $$latex_count - 1` ;\ | |
| 14 | done | |
| 15 | makeindex refman.idx | |
| 16 | pdflatex refman | |
| 17 | ||
| 18 | ||
| 19 | clean: | |
| 20 | rm -f *.ps *.dvi *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl refman.pdf |
| 0 | \section{Class List} | |
| 1 | Here are the classes, structs, unions and interfaces with brief descriptions\+:\begin{DoxyCompactList} | |
| 2 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_allocator}{Iso\+Spec\+::\+Allocator$<$ T $>$}} }{\pageref{class_iso_spec_1_1_allocator}}{} | |
| 3 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_conf_equal}{Iso\+Spec\+::\+Conf\+Equal}} }{\pageref{class_iso_spec_1_1_conf_equal}}{} | |
| 4 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_conf_order}{Iso\+Spec\+::\+Conf\+Order}} }{\pageref{class_iso_spec_1_1_conf_order}}{} | |
| 5 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_conf_order_marginal}{Iso\+Spec\+::\+Conf\+Order\+Marginal}} }{\pageref{class_iso_spec_1_1_conf_order_marginal}}{} | |
| 6 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_conf_order_marginal_descending}{Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}} }{\pageref{class_iso_spec_1_1_conf_order_marginal_descending}}{} | |
| 7 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_dirty_allocator}{Iso\+Spec\+::\+Dirty\+Allocator}} }{\pageref{class_iso_spec_1_1_dirty_allocator}}{} | |
| 8 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso\+Spec\+::\+Iso}} \\*For the calculation of the isotopic distribution }{\pageref{class_iso_spec_1_1_iso}}{} | |
| 9 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_iso_generator}{Iso\+Spec\+::\+Iso\+Generator}} \\*The generator of isotopologues }{\pageref{class_iso_spec_1_1_iso_generator}}{} | |
| 10 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_iso_layered_generator}{Iso\+Spec\+::\+Iso\+Layered\+Generator}} \\*The class that represents isotopologues above a given joint probability value }{\pageref{class_iso_spec_1_1_iso_layered_generator}}{} | |
| 11 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_iso_ordered_generator}{Iso\+Spec\+::\+Iso\+Ordered\+Generator}} \\*The generator of isotopologues sorted by their probability of occurrence }{\pageref{class_iso_spec_1_1_iso_ordered_generator}}{} | |
| 12 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator}{Iso\+Spec\+::\+Iso\+Threshold\+Generator}} \\*The generator of isotopologues above a given threshold value }{\pageref{class_iso_spec_1_1_iso_threshold_generator}}{} | |
| 13 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_key_hasher}{Iso\+Spec\+::\+Key\+Hasher}} }{\pageref{class_iso_spec_1_1_key_hasher}}{} | |
| 14 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_marginal}{Iso\+Spec\+::\+Marginal}} \\*The marginal distribution class (a subisotopologue) }{\pageref{class_iso_spec_1_1_marginal}}{} | |
| 15 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_marginal_trek}{Iso\+Spec\+::\+Marginal\+Trek}} \\*The marginal distribution class (a subisotopologue) }{\pageref{class_iso_spec_1_1_marginal_trek}}{} | |
| 16 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_order_marginals_by_size_decresing}{Iso\+Spec\+::\+Order\+Marginals\+By\+Size\+Decresing}} }{\pageref{class_iso_spec_1_1_order_marginals_by_size_decresing}}{} | |
| 17 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal}{Iso\+Spec\+::\+Precalculated\+Marginal}} \\*Precalculated \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} class }{\pageref{class_iso_spec_1_1_precalculated_marginal}}{} | |
| 18 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_reverse_order}{Iso\+Spec\+::\+Reverse\+Order$<$ T $>$}} }{\pageref{class_iso_spec_1_1_reverse_order}}{} | |
| 19 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_s_summator}{Iso\+Spec\+::\+S\+Summator}} }{\pageref{class_iso_spec_1_1_s_summator}}{} | |
| 20 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_summator}{Iso\+Spec\+::\+Summator}} }{\pageref{class_iso_spec_1_1_summator}}{} | |
| 21 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_table_order}{Iso\+Spec\+::\+Table\+Order$<$ T $>$}} }{\pageref{class_iso_spec_1_1_table_order}}{} | |
| 22 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_tabulator}{Iso\+Spec\+::\+Tabulator$<$ T $>$}} }{\pageref{class_iso_spec_1_1_tabulator}}{} | |
| 23 | \item\contentsline{section}{\mbox{\hyperlink{class_iso_spec_1_1_t_summator}{Iso\+Spec\+::\+T\+Summator}} }{\pageref{class_iso_spec_1_1_t_summator}}{} | |
| 24 | \end{DoxyCompactList} |
| 0 | \hypertarget{class_iso_spec_1_1_allocator}{}\section{Iso\+Spec\+:\+:Allocator$<$ T $>$ Class Template Reference} | |
| 1 | \label{class_iso_spec_1_1_allocator}\index{Iso\+Spec\+::\+Allocator$<$ T $>$@{Iso\+Spec\+::\+Allocator$<$ T $>$}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_allocator_a30f7d0aedcf0cf85e958d66aa7ce0ec7}\label{class_iso_spec_1_1_allocator_a30f7d0aedcf0cf85e958d66aa7ce0ec7}} | |
| 6 | {\bfseries Allocator} (const int dim, const int tab\+Size=10000) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_allocator_afee0ae1b40ebb05545e7ca29a8319989}\label{class_iso_spec_1_1_allocator_afee0ae1b40ebb05545e7ca29a8319989}} | |
| 9 | void {\bfseries shift\+Tables} () | |
| 10 | \item | |
| 11 | \mbox{\Hypertarget{class_iso_spec_1_1_allocator_aca2253867d95eb50e170d00a01fb6507}\label{class_iso_spec_1_1_allocator_aca2253867d95eb50e170d00a01fb6507}} | |
| 12 | T $\ast$ {\bfseries new\+Conf} () | |
| 13 | \item | |
| 14 | \mbox{\Hypertarget{class_iso_spec_1_1_allocator_a4845b8c1c32e1828903fb71af604a2b1}\label{class_iso_spec_1_1_allocator_a4845b8c1c32e1828903fb71af604a2b1}} | |
| 15 | T $\ast$ {\bfseries make\+Copy} (const T $\ast$conf) | |
| 16 | \item | |
| 17 | \mbox{\Hypertarget{class_iso_spec_1_1_allocator_ada9bd9a7168a79c53214fdb0fc66ecf5}\label{class_iso_spec_1_1_allocator_ada9bd9a7168a79c53214fdb0fc66ecf5}} | |
| 18 | T $\ast$ {\bfseries make\+External\+Copy} (const T $\ast$conf) | |
| 19 | \end{DoxyCompactItemize} | |
| 20 | ||
| 21 | ||
| 22 | \subsection{Detailed Description} | |
| 23 | \subsubsection*{template$<$typename T$>$\newline | |
| 24 | class Iso\+Spec\+::\+Allocator$<$ T $>$} | |
| 25 | ||
| 26 | ||
| 27 | ||
| 28 | Definition at line 34 of file allocator.\+h. | |
| 29 | ||
| 30 | ||
| 31 | ||
| 32 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 33 | \item | |
| 34 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/allocator.\+h\item | |
| 35 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/allocator.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_conf_equal}{}\section{Iso\+Spec\+:\+:Conf\+Equal Class Reference} | |
| 1 | \label{class_iso_spec_1_1_conf_equal}\index{Iso\+Spec\+::\+Conf\+Equal@{Iso\+Spec\+::\+Conf\+Equal}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_conf_equal_a1e64267307db788516b6dfc98614d4a8}\label{class_iso_spec_1_1_conf_equal_a1e64267307db788516b6dfc98614d4a8}} | |
| 6 | {\bfseries Conf\+Equal} (int dim) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_conf_equal_a3efc7320ba25aa916b98066d387890e0}\label{class_iso_spec_1_1_conf_equal_a3efc7320ba25aa916b98066d387890e0}} | |
| 9 | bool {\bfseries operator()} (const int $\ast$conf1, const int $\ast$conf2) const | |
| 10 | \end{DoxyCompactItemize} | |
| 11 | ||
| 12 | ||
| 13 | \subsection{Detailed Description} | |
| 14 | ||
| 15 | ||
| 16 | Definition at line 45 of file operators.\+h. | |
| 17 | ||
| 18 | ||
| 19 | ||
| 20 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 21 | \item | |
| 22 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+h\item | |
| 23 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_conf_order}{}\section{Iso\+Spec\+:\+:Conf\+Order Class Reference} | |
| 1 | \label{class_iso_spec_1_1_conf_order}\index{Iso\+Spec\+::\+Conf\+Order@{Iso\+Spec\+::\+Conf\+Order}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_conf_order_a5ab8109685af0925b461ce532fa45a74}\label{class_iso_spec_1_1_conf_order_a5ab8109685af0925b461ce532fa45a74}} | |
| 6 | bool {\bfseries operator()} (void $\ast$conf1, void $\ast$conf2) const | |
| 7 | \end{DoxyCompactItemize} | |
| 8 | ||
| 9 | ||
| 10 | \subsection{Detailed Description} | |
| 11 | ||
| 12 | ||
| 13 | Definition at line 66 of file operators.\+h. | |
| 14 | ||
| 15 | ||
| 16 | ||
| 17 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 18 | \item | |
| 19 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+h\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_conf_order_marginal}{}\section{Iso\+Spec\+:\+:Conf\+Order\+Marginal Class Reference} | |
| 1 | \label{class_iso_spec_1_1_conf_order_marginal}\index{Iso\+Spec\+::\+Conf\+Order\+Marginal@{Iso\+Spec\+::\+Conf\+Order\+Marginal}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_conf_order_marginal_a91c7b8d57bcd751f08f064802f3c8b87}\label{class_iso_spec_1_1_conf_order_marginal_a91c7b8d57bcd751f08f064802f3c8b87}} | |
| 6 | {\bfseries Conf\+Order\+Marginal} (const double $\ast$log\+Probs, int dim) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_conf_order_marginal_a3506b5b6289592e63983b3d9143462dc}\label{class_iso_spec_1_1_conf_order_marginal_a3506b5b6289592e63983b3d9143462dc}} | |
| 9 | bool {\bfseries operator()} (const Conf conf1, const Conf conf2) | |
| 10 | \end{DoxyCompactItemize} | |
| 11 | ||
| 12 | ||
| 13 | \subsection{Detailed Description} | |
| 14 | ||
| 15 | ||
| 16 | Definition at line 78 of file operators.\+h. | |
| 17 | ||
| 18 | ||
| 19 | ||
| 20 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 21 | \item | |
| 22 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+h\item | |
| 23 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_conf_order_marginal_descending}{}\section{Iso\+Spec\+:\+:Conf\+Order\+Marginal\+Descending Class Reference} | |
| 1 | \label{class_iso_spec_1_1_conf_order_marginal_descending}\index{Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending@{Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_conf_order_marginal_descending_a331cca614490a25d2bf4d48e04a1eba3}\label{class_iso_spec_1_1_conf_order_marginal_descending_a331cca614490a25d2bf4d48e04a1eba3}} | |
| 6 | {\bfseries Conf\+Order\+Marginal\+Descending} (const double $\ast$log\+Probs, int dim) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_conf_order_marginal_descending_ab393a338e6a2dedb75d4cc84b54ca1f1}\label{class_iso_spec_1_1_conf_order_marginal_descending_ab393a338e6a2dedb75d4cc84b54ca1f1}} | |
| 9 | bool {\bfseries operator()} (const Conf conf1, const Conf conf2) | |
| 10 | \end{DoxyCompactItemize} | |
| 11 | ||
| 12 | ||
| 13 | \subsection{Detailed Description} | |
| 14 | ||
| 15 | ||
| 16 | Definition at line 92 of file operators.\+h. | |
| 17 | ||
| 18 | ||
| 19 | ||
| 20 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 21 | \item | |
| 22 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+h\item | |
| 23 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_dirty_allocator}{}\section{Iso\+Spec\+:\+:Dirty\+Allocator Class Reference} | |
| 1 | \label{class_iso_spec_1_1_dirty_allocator}\index{Iso\+Spec\+::\+Dirty\+Allocator@{Iso\+Spec\+::\+Dirty\+Allocator}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_dirty_allocator_a0a2cec7004fa67775b209688fef5c566}\label{class_iso_spec_1_1_dirty_allocator_a0a2cec7004fa67775b209688fef5c566}} | |
| 6 | {\bfseries Dirty\+Allocator} (const int dim, const int tab\+Size=10000) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_dirty_allocator_afcaa8b5465f58d8a55dcd15a95921e4f}\label{class_iso_spec_1_1_dirty_allocator_afcaa8b5465f58d8a55dcd15a95921e4f}} | |
| 9 | void {\bfseries shift\+Tables} () | |
| 10 | \item | |
| 11 | \mbox{\Hypertarget{class_iso_spec_1_1_dirty_allocator_a345a18940d01c2943f232591e87fe654}\label{class_iso_spec_1_1_dirty_allocator_a345a18940d01c2943f232591e87fe654}} | |
| 12 | void $\ast$ {\bfseries new\+Conf} () | |
| 13 | \item | |
| 14 | \mbox{\Hypertarget{class_iso_spec_1_1_dirty_allocator_ae3e30ff9aeb6649c8f01b07282711ac9}\label{class_iso_spec_1_1_dirty_allocator_ae3e30ff9aeb6649c8f01b07282711ac9}} | |
| 15 | void $\ast$ {\bfseries make\+Copy} (const void $\ast$conf) | |
| 16 | \item | |
| 17 | \mbox{\Hypertarget{class_iso_spec_1_1_dirty_allocator_af13586082e8269f496c80183c6eb7703}\label{class_iso_spec_1_1_dirty_allocator_af13586082e8269f496c80183c6eb7703}} | |
| 18 | void $\ast$ {\bfseries make\+External\+Copy} (const void $\ast$conf) | |
| 19 | \end{DoxyCompactItemize} | |
| 20 | ||
| 21 | ||
| 22 | \subsection{Detailed Description} | |
| 23 | ||
| 24 | ||
| 25 | Definition at line 26 of file dirty\+Allocator.\+h. | |
| 26 | ||
| 27 | ||
| 28 | ||
| 29 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 30 | \item | |
| 31 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/dirty\+Allocator.\+h\item | |
| 32 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/dirty\+Allocator.\+cpp\end{DoxyCompactItemize} |
| 0 | %!PS-Adobe-2.0 EPSF-2.0 | |
| 1 | %%Title: ClassName | |
| 2 | %%Creator: Doxygen | |
| 3 | %%CreationDate: Time | |
| 4 | %%For: | |
| 5 | %Magnification: 1.00 | |
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| 8 | %%Pages: 0 | |
| 9 | %%BeginSetup | |
| 10 | %%EndSetup | |
| 11 | %%EndComments | |
| 12 | ||
| 13 | % ----- variables ----- | |
| 14 | ||
| 15 | /boxwidth 0 def | |
| 16 | /boxheight 40 def | |
| 17 | /fontheight 24 def | |
| 18 | /marginwidth 10 def | |
| 19 | /distx 20 def | |
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| 22 | /boundx 500 def | |
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| 27 | /cols 3 def | |
| 28 | /scalefactor 0 def | |
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| 30 | ||
| 31 | % ----- procedures ----- | |
| 32 | ||
| 33 | /dotted { [1 4] 0 setdash } def | |
| 34 | /dashed { [5] 0 setdash } def | |
| 35 | /solid { [] 0 setdash } def | |
| 36 | ||
| 37 | /max % result = MAX(arg1,arg2) | |
| 38 | { | |
| 39 | /a exch def | |
| 40 | /b exch def | |
| 41 | a b gt {a} {b} ifelse | |
| 42 | } def | |
| 43 | ||
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| 45 | { | |
| 46 | 0 scalefactor boxwidth cols mul distx cols 1 sub mul add sub 2 div max | |
| 47 | } def | |
| 48 | ||
| 49 | /cw % boxwidth = MAX(boxwidth, stringwidth(arg1)) | |
| 50 | { | |
| 51 | /str exch def | |
| 52 | /boxwidth boxwidth str stringwidth pop max def | |
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| 74 | { newpath | |
| 75 | exch xspacing mul xoffset add boxwidth add | |
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| 78 | 0 boxheight 4 div rlineto | |
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| 86 | { newpath | |
| 87 | moveto | |
| 88 | 3 -8 rlineto | |
| 89 | -6 0 rlineto | |
| 90 | 3 8 rlineto | |
| 91 | closepath | |
| 92 | eofill | |
| 93 | stroke | |
| 94 | } def | |
| 95 | ||
| 96 | /out % draws an output connector for the block at (arg1,arg2) | |
| 97 | { | |
| 98 | newpath | |
| 99 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 100 | exch yspacing mul boxheight add | |
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| 104 | 0 disty 2 div rlineto | |
| 105 | stroke | |
| 106 | 1 eq { x y disty 2 div add arrow } if | |
| 107 | } def | |
| 108 | ||
| 109 | /in % draws an input connector for the block at (arg1,arg2) | |
| 110 | { | |
| 111 | newpath | |
| 112 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 113 | exch yspacing mul disty 2 div sub | |
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| 117 | 0 disty 2 div rlineto | |
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| 119 | 1 eq { x y disty 2 div add arrow } if | |
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| 121 | ||
| 122 | /hedge | |
| 123 | { | |
| 124 | exch xspacing mul xoffset add boxwidth 2 div add | |
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| 133 | { newpath x boxwidth 2 div distx add add y moveto | |
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| 140 | } if | |
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| 144 | { | |
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| 154 | stroke | |
| 155 | } def | |
| 156 | ||
| 157 | /conn % connections the blocks from col `arg1' to `arg2' of row `arg3' | |
| 158 | { | |
| 159 | /ys exch def | |
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| 163 | xs xspacing mul xoffset add boxwidth 2 div add | |
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| 170 | ||
| 171 | % ----- main ------ | |
| 172 | ||
| 173 | boxfont setfont | |
| 174 | 1 boundaspect scale | |
| 175 | (IsoSpec::Iso) cw | |
| 176 | (IsoSpec::IsoGenerator) cw | |
| 177 | (IsoSpec::IsoLayeredGenerator) cw | |
| 178 | (IsoSpec::IsoOrderedGenerator) cw | |
| 179 | (IsoSpec::IsoThresholdGenerator) cw | |
| 180 | /boxwidth boxwidth marginwidth 2 mul add def | |
| 181 | /xspacing boxwidth distx add def | |
| 182 | /yspacing boxheight disty add def | |
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| 184 | boxwidth cols mul distx cols 1 sub mul add | |
| 185 | boxheight rows mul disty rows 1 sub mul add boundaspect mul | |
| 186 | max def | |
| 187 | boundx scalefactor div boundy scalefactor div scale | |
| 188 | ||
| 189 | % ----- classes ----- | |
| 190 | ||
| 191 | (IsoSpec::Iso) 1.000000 2.000000 box | |
| 192 | (IsoSpec::IsoGenerator) 1.000000 1.000000 box | |
| 193 | (IsoSpec::IsoLayeredGenerator) 0.000000 0.000000 box | |
| 194 | (IsoSpec::IsoOrderedGenerator) 1.000000 0.000000 box | |
| 195 | (IsoSpec::IsoThresholdGenerator) 2.000000 0.000000 box | |
| 196 | ||
| 197 | % ----- relations ----- | |
| 198 | ||
| 199 | solid | |
| 200 | 1 1.000000 1.250000 out | |
| 201 | solid | |
| 202 | 0 1.000000 1.750000 in | |
| 203 | solid | |
| 204 | 1 1.000000 0.250000 out | |
| 205 | solid | |
| 206 | 0.000000 2.000000 1.000000 conn | |
| 207 | solid | |
| 208 | 0 0.000000 0.750000 in | |
| 209 | solid | |
| 210 | 0 1.000000 0.750000 in | |
| 211 | solid | |
| 212 | 0 2.000000 0.750000 in |
| 0 | \hypertarget{class_iso_spec_1_1_iso}{}\section{Iso\+Spec\+:\+:Iso Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso}\index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 2 | ||
| 3 | ||
| 4 | The \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} class for the calculation of the isotopic distribution. | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$iso\+Spec++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Iso\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=2.800000cm]{class_iso_spec_1_1_iso} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | \mbox{\hyperlink{class_iso_spec_1_1_iso_a5ff1fafd079a866e9d61bc7d859842ea}{Iso}} (int \+\_\+dim\+Number, const int $\ast$\+\_\+isotope\+Numbers, const int $\ast$\+\_\+atom\+Counts, const double $\ast$const $\ast$\+\_\+isotope\+Masses, const double $\ast$const $\ast$\+\_\+isotope\+Probabilities) | |
| 21 | \begin{DoxyCompactList}\small\item\em General constructror. \end{DoxyCompactList}\item | |
| 22 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_ad389effb319e9ed73db9ed5749868b81}\label{class_iso_spec_1_1_iso_ad389effb319e9ed73db9ed5749868b81}} | |
| 23 | \mbox{\hyperlink{class_iso_spec_1_1_iso_ad389effb319e9ed73db9ed5749868b81}{Iso}} (const char $\ast$formula) | |
| 24 | \begin{DoxyCompactList}\small\item\em Constructor from the formula object. \end{DoxyCompactList}\item | |
| 25 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a6c93ecb77a11bc831cc7600797fbf837}\label{class_iso_spec_1_1_iso_a6c93ecb77a11bc831cc7600797fbf837}} | |
| 26 | \mbox{\hyperlink{class_iso_spec_1_1_iso_a6c93ecb77a11bc831cc7600797fbf837}{Iso}} (\mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&\&other) | |
| 27 | \begin{DoxyCompactList}\small\item\em The move constructor. \end{DoxyCompactList}\item | |
| 28 | \mbox{\hyperlink{class_iso_spec_1_1_iso_a485cba7555fbdc64bbea19690f202b13}{Iso}} (const \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&other, bool fullcopy) | |
| 29 | \begin{DoxyCompactList}\small\item\em The copy constructor. \end{DoxyCompactList}\item | |
| 30 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a8cf8f90338bfc3e5117f5b491f7b523f}\label{class_iso_spec_1_1_iso_a8cf8f90338bfc3e5117f5b491f7b523f}} | |
| 31 | virtual \mbox{\hyperlink{class_iso_spec_1_1_iso_a8cf8f90338bfc3e5117f5b491f7b523f}{$\sim$\+Iso}} () | |
| 32 | \begin{DoxyCompactList}\small\item\em Destructor. \end{DoxyCompactList}\item | |
| 33 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a7541599fbc29dd374bb60e5eb8fc047d}\label{class_iso_spec_1_1_iso_a7541599fbc29dd374bb60e5eb8fc047d}} | |
| 34 | double \mbox{\hyperlink{class_iso_spec_1_1_iso_a7541599fbc29dd374bb60e5eb8fc047d}{get\+Lightest\+Peak\+Mass}} () const | |
| 35 | \begin{DoxyCompactList}\small\item\em Get the mass of the lightest peak in the isotopic distribution. \end{DoxyCompactList}\item | |
| 36 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a1ede5e34e5bbbb22ae89b362ce2c6faf}\label{class_iso_spec_1_1_iso_a1ede5e34e5bbbb22ae89b362ce2c6faf}} | |
| 37 | double \mbox{\hyperlink{class_iso_spec_1_1_iso_a1ede5e34e5bbbb22ae89b362ce2c6faf}{get\+Heaviest\+Peak\+Mass}} () const | |
| 38 | \begin{DoxyCompactList}\small\item\em Get the mass of the heaviest peak in the isotopic distribution. \end{DoxyCompactList}\item | |
| 39 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a9035d076cec8f937d971e3fd972aa83f}\label{class_iso_spec_1_1_iso_a9035d076cec8f937d971e3fd972aa83f}} | |
| 40 | double \mbox{\hyperlink{class_iso_spec_1_1_iso_a9035d076cec8f937d971e3fd972aa83f}{get\+Mode\+L\+Prob}} () const | |
| 41 | \begin{DoxyCompactList}\small\item\em Get the log-\/probability of the mode-\/configuration (if there are many modes, they share this value). \end{DoxyCompactList}\item | |
| 42 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a62b17f48d86f62b5ed38ffb296a9daa5}\label{class_iso_spec_1_1_iso_a62b17f48d86f62b5ed38ffb296a9daa5}} | |
| 43 | int \mbox{\hyperlink{class_iso_spec_1_1_iso_a62b17f48d86f62b5ed38ffb296a9daa5}{get\+Dim\+Number}} () const | |
| 44 | \begin{DoxyCompactList}\small\item\em Get the number of elements in the chemical formula of the molecule. \end{DoxyCompactList}\item | |
| 45 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a656a37dd84a6c0534b2373210ed5a091}\label{class_iso_spec_1_1_iso_a656a37dd84a6c0534b2373210ed5a091}} | |
| 46 | int \mbox{\hyperlink{class_iso_spec_1_1_iso_a656a37dd84a6c0534b2373210ed5a091}{get\+All\+Dim}} () const | |
| 47 | \begin{DoxyCompactList}\small\item\em Get the total number of isotopes of elements present in a chemical formula. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 48 | \subsection*{Public Attributes} | |
| 49 | \begin{DoxyCompactItemize} | |
| 50 | \item | |
| 51 | bool \mbox{\hyperlink{class_iso_spec_1_1_iso_ad2a353f2c746648b08a9ad31ff775766}{disowned}} | |
| 52 | \end{DoxyCompactItemize} | |
| 53 | \subsection*{Protected Attributes} | |
| 54 | \begin{DoxyCompactItemize} | |
| 55 | \item | |
| 56 | int \mbox{\hyperlink{class_iso_spec_1_1_iso_a90245f9bc318f12720c134f61bbe0db0}{dim\+Number}} | |
| 57 | \item | |
| 58 | int $\ast$ \mbox{\hyperlink{class_iso_spec_1_1_iso_a7235f0afc56dccd13937791a630c45da}{isotope\+Numbers}} | |
| 59 | \item | |
| 60 | int $\ast$ \mbox{\hyperlink{class_iso_spec_1_1_iso_ab01939334b6c3e69f65a36f9965971a2}{atom\+Counts}} | |
| 61 | \item | |
| 62 | unsigned int \mbox{\hyperlink{class_iso_spec_1_1_iso_a89ed144bf2495fa25840aca90a31b425}{conf\+Size}} | |
| 63 | \item | |
| 64 | int \mbox{\hyperlink{class_iso_spec_1_1_iso_a8dd2c443706935b582979b13f935115c}{all\+Dim}} | |
| 65 | \item | |
| 66 | \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} $\ast$$\ast$ \mbox{\hyperlink{class_iso_spec_1_1_iso_aea98a8331a2f8a1a6bbcace6124fcfae}{marginals}} | |
| 67 | \item | |
| 68 | double \mbox{\hyperlink{class_iso_spec_1_1_iso_ab51c157b23ae6a6b521667b6f0e8a208}{mode\+L\+Prob}} | |
| 69 | \end{DoxyCompactItemize} | |
| 70 | ||
| 71 | ||
| 72 | \subsection{Detailed Description} | |
| 73 | The \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} class for the calculation of the isotopic distribution. | |
| 74 | ||
| 75 | It contains full description of the molecule for which one would like to calculate the isotopic distribution. | |
| 76 | ||
| 77 | Definition at line 52 of file iso\+Spec++.\+h. | |
| 78 | ||
| 79 | ||
| 80 | ||
| 81 | \subsection{Constructor \& Destructor Documentation} | |
| 82 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a5ff1fafd079a866e9d61bc7d859842ea}\label{class_iso_spec_1_1_iso_a5ff1fafd079a866e9d61bc7d859842ea}} | |
| 83 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!Iso@{Iso}} | |
| 84 | \index{Iso@{Iso}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 85 | \subsubsection{\texorpdfstring{Iso()}{Iso()}\hspace{0.1cm}{\footnotesize\ttfamily [1/2]}} | |
| 86 | {\footnotesize\ttfamily Iso\+Spec\+::\+Iso\+::\+Iso (\begin{DoxyParamCaption}\item[{int}]{\+\_\+dim\+Number, }\item[{const int $\ast$}]{\+\_\+isotope\+Numbers, }\item[{const int $\ast$}]{\+\_\+atom\+Counts, }\item[{const double $\ast$const $\ast$}]{\+\_\+isotope\+Masses, }\item[{const double $\ast$const $\ast$}]{\+\_\+isotope\+Probabilities }\end{DoxyParamCaption})} | |
| 87 | ||
| 88 | ||
| 89 | ||
| 90 | General constructror. | |
| 91 | ||
| 92 | ||
| 93 | \begin{DoxyParams}{Parameters} | |
| 94 | {\em \+\_\+dim\+Number} & The number of elements in the formula, e.\+g. for C100\+H202 it would be 2, as there are only carbon and hydrogen atoms. \\ | |
| 95 | \hline | |
| 96 | {\em \+\_\+isotope\+Numbers} & A table with numbers of isotopes for each element, e.\+g. for C100\+H202 it would be \{2, 2\}, because both C and H have two stable isotopes. \\ | |
| 97 | \hline | |
| 98 | {\em \+\_\+atom\+Counts} & Number of atoms of each element in the formula, e.\+g. for C100\+H202 corresponds to \{100, 202\}. \\ | |
| 99 | \hline | |
| 100 | {\em \+\_\+isotope\+Masses} & A table of masses of isotopes of the elements in the chemical formula, e.\+g. \{12.\+0, 13.\+003355, 1.\+007825, 2.\+014102\} for C100\+H202. \\ | |
| 101 | \hline | |
| 102 | {\em \+\_\+isotope\+Probabilities} & A table of isotope frequencies of the elements in the chemical formula, e.\+g. \{.989212, .010788, .999885, .000115\} for C100\+H202. \\ | |
| 103 | \hline | |
| 104 | \end{DoxyParams} | |
| 105 | ||
| 106 | ||
| 107 | Definition at line 51 of file iso\+Spec++.\+cpp. | |
| 108 | ||
| 109 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a485cba7555fbdc64bbea19690f202b13}\label{class_iso_spec_1_1_iso_a485cba7555fbdc64bbea19690f202b13}} | |
| 110 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!Iso@{Iso}} | |
| 111 | \index{Iso@{Iso}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 112 | \subsubsection{\texorpdfstring{Iso()}{Iso()}\hspace{0.1cm}{\footnotesize\ttfamily [2/2]}} | |
| 113 | {\footnotesize\ttfamily Iso\+Spec\+::\+Iso\+::\+Iso (\begin{DoxyParamCaption}\item[{const \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&}]{other, }\item[{bool}]{fullcopy }\end{DoxyParamCaption})} | |
| 114 | ||
| 115 | ||
| 116 | ||
| 117 | The copy constructor. | |
| 118 | ||
| 119 | ||
| 120 | \begin{DoxyParams}{Parameters} | |
| 121 | {\em other} & The other instance of the \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} class. \\ | |
| 122 | \hline | |
| 123 | {\em fullcopy} & If false, copy only the number of atoms in the formula, the size of the configuration, the total number of isotopes, and the probability of the mode isotopologue. \\ | |
| 124 | \hline | |
| 125 | \end{DoxyParams} | |
| 126 | ||
| 127 | ||
| 128 | Definition at line 84 of file iso\+Spec++.\+cpp. | |
| 129 | ||
| 130 | ||
| 131 | ||
| 132 | \subsection{Member Data Documentation} | |
| 133 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a8dd2c443706935b582979b13f935115c}\label{class_iso_spec_1_1_iso_a8dd2c443706935b582979b13f935115c}} | |
| 134 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!all\+Dim@{all\+Dim}} | |
| 135 | \index{all\+Dim@{all\+Dim}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 136 | \subsubsection{\texorpdfstring{all\+Dim}{allDim}} | |
| 137 | {\footnotesize\ttfamily int Iso\+Spec\+::\+Iso\+::all\+Dim\hspace{0.3cm}{\ttfamily [protected]}} | |
| 138 | ||
| 139 | The total number of isotopes of elements present in a chemical formula, e.\+g. for H20 it is 2+3=5. | |
| 140 | ||
| 141 | Definition at line 71 of file iso\+Spec++.\+h. | |
| 142 | ||
| 143 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_ab01939334b6c3e69f65a36f9965971a2}\label{class_iso_spec_1_1_iso_ab01939334b6c3e69f65a36f9965971a2}} | |
| 144 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!atom\+Counts@{atom\+Counts}} | |
| 145 | \index{atom\+Counts@{atom\+Counts}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 146 | \subsubsection{\texorpdfstring{atom\+Counts}{atomCounts}} | |
| 147 | {\footnotesize\ttfamily int$\ast$ Iso\+Spec\+::\+Iso\+::atom\+Counts\hspace{0.3cm}{\ttfamily [protected]}} | |
| 148 | ||
| 149 | A table with numbers of isotopes for each element. | |
| 150 | ||
| 151 | Definition at line 69 of file iso\+Spec++.\+h. | |
| 152 | ||
| 153 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a89ed144bf2495fa25840aca90a31b425}\label{class_iso_spec_1_1_iso_a89ed144bf2495fa25840aca90a31b425}} | |
| 154 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!conf\+Size@{conf\+Size}} | |
| 155 | \index{conf\+Size@{conf\+Size}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 156 | \subsubsection{\texorpdfstring{conf\+Size}{confSize}} | |
| 157 | {\footnotesize\ttfamily unsigned int Iso\+Spec\+::\+Iso\+::conf\+Size\hspace{0.3cm}{\ttfamily [protected]}} | |
| 158 | ||
| 159 | The number of bytes needed to represent the counts of isotopes present in the extended chemical formula. | |
| 160 | ||
| 161 | Definition at line 70 of file iso\+Spec++.\+h. | |
| 162 | ||
| 163 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a90245f9bc318f12720c134f61bbe0db0}\label{class_iso_spec_1_1_iso_a90245f9bc318f12720c134f61bbe0db0}} | |
| 164 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!dim\+Number@{dim\+Number}} | |
| 165 | \index{dim\+Number@{dim\+Number}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 166 | \subsubsection{\texorpdfstring{dim\+Number}{dimNumber}} | |
| 167 | {\footnotesize\ttfamily int Iso\+Spec\+::\+Iso\+::dim\+Number\hspace{0.3cm}{\ttfamily [protected]}} | |
| 168 | ||
| 169 | The number of elements in the chemical formula of the molecule. | |
| 170 | ||
| 171 | Definition at line 67 of file iso\+Spec++.\+h. | |
| 172 | ||
| 173 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_ad2a353f2c746648b08a9ad31ff775766}\label{class_iso_spec_1_1_iso_ad2a353f2c746648b08a9ad31ff775766}} | |
| 174 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!disowned@{disowned}} | |
| 175 | \index{disowned@{disowned}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 176 | \subsubsection{\texorpdfstring{disowned}{disowned}} | |
| 177 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Iso\+::disowned} | |
| 178 | ||
| 179 | A variable showing if the \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} class was specialized by its child-\/class. If so, then the description of the molecules has been transfered there and \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} is a carcass class, dead as a dodo, an ex-\/class if you will. | |
| 180 | ||
| 181 | Definition at line 65 of file iso\+Spec++.\+h. | |
| 182 | ||
| 183 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a7235f0afc56dccd13937791a630c45da}\label{class_iso_spec_1_1_iso_a7235f0afc56dccd13937791a630c45da}} | |
| 184 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!isotope\+Numbers@{isotope\+Numbers}} | |
| 185 | \index{isotope\+Numbers@{isotope\+Numbers}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 186 | \subsubsection{\texorpdfstring{isotope\+Numbers}{isotopeNumbers}} | |
| 187 | {\footnotesize\ttfamily int$\ast$ Iso\+Spec\+::\+Iso\+::isotope\+Numbers\hspace{0.3cm}{\ttfamily [protected]}} | |
| 188 | ||
| 189 | A table with numbers of isotopes for each element. | |
| 190 | ||
| 191 | Definition at line 68 of file iso\+Spec++.\+h. | |
| 192 | ||
| 193 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_aea98a8331a2f8a1a6bbcace6124fcfae}\label{class_iso_spec_1_1_iso_aea98a8331a2f8a1a6bbcace6124fcfae}} | |
| 194 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!marginals@{marginals}} | |
| 195 | \index{marginals@{marginals}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 196 | \subsubsection{\texorpdfstring{marginals}{marginals}} | |
| 197 | {\footnotesize\ttfamily \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}}$\ast$$\ast$ Iso\+Spec\+::\+Iso\+::marginals\hspace{0.3cm}{\ttfamily [protected]}} | |
| 198 | ||
| 199 | The table of pointers to the distributions of individual subisotopologues. | |
| 200 | ||
| 201 | Definition at line 72 of file iso\+Spec++.\+h. | |
| 202 | ||
| 203 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_ab51c157b23ae6a6b521667b6f0e8a208}\label{class_iso_spec_1_1_iso_ab51c157b23ae6a6b521667b6f0e8a208}} | |
| 204 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!mode\+L\+Prob@{mode\+L\+Prob}} | |
| 205 | \index{mode\+L\+Prob@{mode\+L\+Prob}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 206 | \subsubsection{\texorpdfstring{mode\+L\+Prob}{modeLProb}} | |
| 207 | {\footnotesize\ttfamily double Iso\+Spec\+::\+Iso\+::mode\+L\+Prob\hspace{0.3cm}{\ttfamily [protected]}} | |
| 208 | ||
| 209 | The log-\/probability of the mode of the isotopic distribution. | |
| 210 | ||
| 211 | Definition at line 73 of file iso\+Spec++.\+h. | |
| 212 | ||
| 213 | ||
| 214 | ||
| 215 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 216 | \item | |
| 217 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+h\item | |
| 218 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_iso}{}\section{Iso\+Spec\+:\+:Iso Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso}\index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 2 | ||
| 3 | ||
| 4 | The \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} class for the calculation of the isotopic distribution. | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$iso\+Spec++.\+h$>$} | |
| 10 | ||
| 11 | ||
| 12 | ||
| 13 | Inheritance diagram for Iso\+Spec\+:\+:Iso\+: | |
| 14 | % FIG 0 | |
| 15 | ||
| 16 | ||
| 17 | Collaboration diagram for Iso\+Spec\+:\+:Iso\+: | |
| 18 | % FIG 1 | |
| 19 | \subsection*{Public Member Functions} | |
| 20 | \begin{DoxyCompactItemize} | |
| 21 | \item | |
| 22 | \mbox{\hyperlink{class_iso_spec_1_1_iso_a5ff1fafd079a866e9d61bc7d859842ea}{Iso}} (int \+\_\+dim\+Number, const int $\ast$\+\_\+isotope\+Numbers, const int $\ast$\+\_\+atom\+Counts, const double $\ast$const $\ast$\+\_\+isotope\+Masses, const double $\ast$const $\ast$\+\_\+isotope\+Probabilities) | |
| 23 | \begin{DoxyCompactList}\small\item\em General constructror. \end{DoxyCompactList}\item | |
| 24 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_ad389effb319e9ed73db9ed5749868b81}\label{class_iso_spec_1_1_iso_ad389effb319e9ed73db9ed5749868b81}} | |
| 25 | \mbox{\hyperlink{class_iso_spec_1_1_iso_ad389effb319e9ed73db9ed5749868b81}{Iso}} (const char $\ast$formula) | |
| 26 | \begin{DoxyCompactList}\small\item\em Constructor from the formula object. \end{DoxyCompactList}\item | |
| 27 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a6c93ecb77a11bc831cc7600797fbf837}\label{class_iso_spec_1_1_iso_a6c93ecb77a11bc831cc7600797fbf837}} | |
| 28 | {\bfseries Iso} (\mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&\&other) | |
| 29 | \item | |
| 30 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a485cba7555fbdc64bbea19690f202b13}\label{class_iso_spec_1_1_iso_a485cba7555fbdc64bbea19690f202b13}} | |
| 31 | {\bfseries Iso} (const \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&other, bool fullcopy) | |
| 32 | \item | |
| 33 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a7541599fbc29dd374bb60e5eb8fc047d}\label{class_iso_spec_1_1_iso_a7541599fbc29dd374bb60e5eb8fc047d}} | |
| 34 | double \mbox{\hyperlink{class_iso_spec_1_1_iso_a7541599fbc29dd374bb60e5eb8fc047d}{get\+Lightest\+Peak\+Mass}} () const | |
| 35 | \begin{DoxyCompactList}\small\item\em Get the mass of the lightest peak in the isotopic distribution. \end{DoxyCompactList}\item | |
| 36 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a1ede5e34e5bbbb22ae89b362ce2c6faf}\label{class_iso_spec_1_1_iso_a1ede5e34e5bbbb22ae89b362ce2c6faf}} | |
| 37 | double \mbox{\hyperlink{class_iso_spec_1_1_iso_a1ede5e34e5bbbb22ae89b362ce2c6faf}{get\+Heaviest\+Peak\+Mass}} () const | |
| 38 | \begin{DoxyCompactList}\small\item\em Get the mass of the heaviest peak in the isotopic distribution. \end{DoxyCompactList}\item | |
| 39 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a9035d076cec8f937d971e3fd972aa83f}\label{class_iso_spec_1_1_iso_a9035d076cec8f937d971e3fd972aa83f}} | |
| 40 | double \mbox{\hyperlink{class_iso_spec_1_1_iso_a9035d076cec8f937d971e3fd972aa83f}{get\+Mode\+L\+Prob}} () const | |
| 41 | \begin{DoxyCompactList}\small\item\em Get the log-\/probability of the mode-\/configuration (if there are many modes, they share this value). \end{DoxyCompactList}\item | |
| 42 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a62b17f48d86f62b5ed38ffb296a9daa5}\label{class_iso_spec_1_1_iso_a62b17f48d86f62b5ed38ffb296a9daa5}} | |
| 43 | int \mbox{\hyperlink{class_iso_spec_1_1_iso_a62b17f48d86f62b5ed38ffb296a9daa5}{get\+Dim\+Number}} () const | |
| 44 | \begin{DoxyCompactList}\small\item\em Get the number of elements in the chemical formula of the molecule. \end{DoxyCompactList}\item | |
| 45 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a656a37dd84a6c0534b2373210ed5a091}\label{class_iso_spec_1_1_iso_a656a37dd84a6c0534b2373210ed5a091}} | |
| 46 | int \mbox{\hyperlink{class_iso_spec_1_1_iso_a656a37dd84a6c0534b2373210ed5a091}{get\+All\+Dim}} () const | |
| 47 | \begin{DoxyCompactList}\small\item\em Get the total number of isotopes of elements present in a chemical formula. \end{DoxyCompactList}\item | |
| 48 | \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal}{Precalculated\+Marginal}} $\ast$$\ast$ \mbox{\hyperlink{class_iso_spec_1_1_iso_ab360d8afe0b1ea916939703de8c1eb84}{get\+\_\+\+M\+T\+\_\+marginal\+\_\+set}} (double Lcutoff, bool absolute, int tab\+Size, int hash\+Size) | |
| 49 | \begin{DoxyCompactList}\small\item\em Get the marginal distributions of subisotopologues. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 50 | \subsection*{Public Attributes} | |
| 51 | \begin{DoxyCompactItemize} | |
| 52 | \item | |
| 53 | bool \mbox{\hyperlink{class_iso_spec_1_1_iso_ad2a353f2c746648b08a9ad31ff775766}{disowned}} | |
| 54 | \end{DoxyCompactItemize} | |
| 55 | \subsection*{Protected Attributes} | |
| 56 | \begin{DoxyCompactItemize} | |
| 57 | \item | |
| 58 | int \mbox{\hyperlink{class_iso_spec_1_1_iso_a90245f9bc318f12720c134f61bbe0db0}{dim\+Number}} | |
| 59 | \item | |
| 60 | int $\ast$ \mbox{\hyperlink{class_iso_spec_1_1_iso_a7235f0afc56dccd13937791a630c45da}{isotope\+Numbers}} | |
| 61 | \item | |
| 62 | int $\ast$ \mbox{\hyperlink{class_iso_spec_1_1_iso_ab01939334b6c3e69f65a36f9965971a2}{atom\+Counts}} | |
| 63 | \item | |
| 64 | unsigned int \mbox{\hyperlink{class_iso_spec_1_1_iso_a89ed144bf2495fa25840aca90a31b425}{conf\+Size}} | |
| 65 | \item | |
| 66 | int \mbox{\hyperlink{class_iso_spec_1_1_iso_a8dd2c443706935b582979b13f935115c}{all\+Dim}} | |
| 67 | \item | |
| 68 | \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} $\ast$$\ast$ \mbox{\hyperlink{class_iso_spec_1_1_iso_aea98a8331a2f8a1a6bbcace6124fcfae}{marginals}} | |
| 69 | \item | |
| 70 | double \mbox{\hyperlink{class_iso_spec_1_1_iso_ab51c157b23ae6a6b521667b6f0e8a208}{mode\+L\+Prob}} | |
| 71 | \end{DoxyCompactItemize} | |
| 72 | ||
| 73 | ||
| 74 | \subsection{Detailed Description} | |
| 75 | The \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} class for the calculation of the isotopic distribution. | |
| 76 | ||
| 77 | It contains full description of the molecule for which one would like to calculate the isotopic distribution. | |
| 78 | ||
| 79 | \subsection{Constructor \& Destructor Documentation} | |
| 80 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a5ff1fafd079a866e9d61bc7d859842ea}\label{class_iso_spec_1_1_iso_a5ff1fafd079a866e9d61bc7d859842ea}} | |
| 81 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!Iso@{Iso}} | |
| 82 | \index{Iso@{Iso}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 83 | \subsubsection{\texorpdfstring{Iso()}{Iso()}} | |
| 84 | {\footnotesize\ttfamily Iso\+Spec\+::\+Iso\+::\+Iso (\begin{DoxyParamCaption}\item[{int}]{\+\_\+dim\+Number, }\item[{const int $\ast$}]{\+\_\+isotope\+Numbers, }\item[{const int $\ast$}]{\+\_\+atom\+Counts, }\item[{const double $\ast$const $\ast$}]{\+\_\+isotope\+Masses, }\item[{const double $\ast$const $\ast$}]{\+\_\+isotope\+Probabilities }\end{DoxyParamCaption})} | |
| 85 | ||
| 86 | ||
| 87 | ||
| 88 | General constructror. | |
| 89 | ||
| 90 | ||
| 91 | \begin{DoxyParams}{Parameters} | |
| 92 | {\em \+\_\+dim\+Number} & The number of elements in the formula, e.\+g. for C100\+H202 it would be 2, as there are only carbon and hydrogen atoms. \\ | |
| 93 | \hline | |
| 94 | {\em \+\_\+isotope\+Numbers} & A table with numbers of isotopes for each element, e.\+g. for C100\+H202 it would be \{2, 2\}, because both C and H have two stable isotopes. \\ | |
| 95 | \hline | |
| 96 | {\em \+\_\+atom\+Counts} & Number of atoms of each element in the formula, e.\+g. for C100\+H202 corresponds to \{100, 202\}. \\ | |
| 97 | \hline | |
| 98 | {\em \+\_\+isotope\+Masses} & A table of masses of isotopes of the elements in the chemical formula, e.\+g. \{12.\+0, 13.\+003355, 1.\+007825, 2.\+014102\} for C100\+H202. \\ | |
| 99 | \hline | |
| 100 | {\em \+\_\+isotope\+Probabilities} & A table of isotope frequencies of the elements in the chemical formula, e.\+g. \{.989212, .010788, .999885, .000115\} for C100\+H202. \\ | |
| 101 | \hline | |
| 102 | \end{DoxyParams} | |
| 103 | ||
| 104 | ||
| 105 | \subsection{Member Function Documentation} | |
| 106 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_ab360d8afe0b1ea916939703de8c1eb84}\label{class_iso_spec_1_1_iso_ab360d8afe0b1ea916939703de8c1eb84}} | |
| 107 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!get\+\_\+\+M\+T\+\_\+marginal\+\_\+set@{get\+\_\+\+M\+T\+\_\+marginal\+\_\+set}} | |
| 108 | \index{get\+\_\+\+M\+T\+\_\+marginal\+\_\+set@{get\+\_\+\+M\+T\+\_\+marginal\+\_\+set}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 109 | \subsubsection{\texorpdfstring{get\+\_\+\+M\+T\+\_\+marginal\+\_\+set()}{get\_MT\_marginal\_set()}} | |
| 110 | {\footnotesize\ttfamily \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal}{Precalculated\+Marginal}}$\ast$$\ast$ Iso\+Spec\+::\+Iso\+::get\+\_\+\+M\+T\+\_\+marginal\+\_\+set (\begin{DoxyParamCaption}\item[{double}]{Lcutoff, }\item[{bool}]{absolute, }\item[{int}]{tab\+Size, }\item[{int}]{hash\+Size }\end{DoxyParamCaption})} | |
| 111 | ||
| 112 | ||
| 113 | ||
| 114 | Get the marginal distributions of subisotopologues. | |
| 115 | ||
| 116 | ||
| 117 | \begin{DoxyParams}{Parameters} | |
| 118 | {\em Lcutoff} & The logarithm of the cut off value. \\ | |
| 119 | \hline | |
| 120 | {\em absolute} & Should the cutoff be in terms of absolute height of the peak, or relative to the height/probability of the mode. \\ | |
| 121 | \hline | |
| 122 | {\em tab\+Size} & The size of the extension of the table with configurations. \\ | |
| 123 | \hline | |
| 124 | {\em hash\+Size} & The size of the hash-\/table used to store subisotopologues and check if they have been already calculated. \\ | |
| 125 | \hline | |
| 126 | \end{DoxyParams} | |
| 127 | ||
| 128 | ||
| 129 | \subsection{Member Data Documentation} | |
| 130 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_a8dd2c443706935b582979b13f935115c}\label{class_iso_spec_1_1_iso_a8dd2c443706935b582979b13f935115c}} | |
| 131 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!all\+Dim@{all\+Dim}} | |
| 132 | \index{all\+Dim@{all\+Dim}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 133 | \subsubsection{\texorpdfstring{all\+Dim}{allDim}} | |
| 134 | {\footnotesize\ttfamily int Iso\+Spec\+::\+Iso\+::all\+Dim\hspace{0.3cm}{\ttfamily [protected]}} | |
| 135 | ||
| 136 | The total number of isotopes of elements present in a chemical formula, e.\+g. for H20 it is 2+3=5. \mbox{\Hypertarget{class_iso_spec_1_1_iso_ab01939334b6c3e69f65a36f9965971a2}\label{class_iso_spec_1_1_iso_ab01939334b6c3e69f65a36f9965971a2}} | |
| 137 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!atom\+Counts@{atom\+Counts}} | |
| 138 | \index{atom\+Counts@{atom\+Counts}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 139 | \subsubsection{\texorpdfstring{atom\+Counts}{atomCounts}} | |
| 140 | {\footnotesize\ttfamily int$\ast$ Iso\+Spec\+::\+Iso\+::atom\+Counts\hspace{0.3cm}{\ttfamily [protected]}} | |
| 141 | ||
| 142 | A table with numbers of isotopes for each element. \mbox{\Hypertarget{class_iso_spec_1_1_iso_a89ed144bf2495fa25840aca90a31b425}\label{class_iso_spec_1_1_iso_a89ed144bf2495fa25840aca90a31b425}} | |
| 143 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!conf\+Size@{conf\+Size}} | |
| 144 | \index{conf\+Size@{conf\+Size}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 145 | \subsubsection{\texorpdfstring{conf\+Size}{confSize}} | |
| 146 | {\footnotesize\ttfamily unsigned int Iso\+Spec\+::\+Iso\+::conf\+Size\hspace{0.3cm}{\ttfamily [protected]}} | |
| 147 | ||
| 148 | The number of bytes needed to represent the counts of isotopes present in the extended chemical formula. \mbox{\Hypertarget{class_iso_spec_1_1_iso_a90245f9bc318f12720c134f61bbe0db0}\label{class_iso_spec_1_1_iso_a90245f9bc318f12720c134f61bbe0db0}} | |
| 149 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!dim\+Number@{dim\+Number}} | |
| 150 | \index{dim\+Number@{dim\+Number}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 151 | \subsubsection{\texorpdfstring{dim\+Number}{dimNumber}} | |
| 152 | {\footnotesize\ttfamily int Iso\+Spec\+::\+Iso\+::dim\+Number\hspace{0.3cm}{\ttfamily [protected]}} | |
| 153 | ||
| 154 | The number of elements in the chemical formula of the molecule. \mbox{\Hypertarget{class_iso_spec_1_1_iso_ad2a353f2c746648b08a9ad31ff775766}\label{class_iso_spec_1_1_iso_ad2a353f2c746648b08a9ad31ff775766}} | |
| 155 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!disowned@{disowned}} | |
| 156 | \index{disowned@{disowned}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 157 | \subsubsection{\texorpdfstring{disowned}{disowned}} | |
| 158 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Iso\+::disowned} | |
| 159 | ||
| 160 | A variable showing if the \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} class was specialized by its child-\/class. If so, then the description of the molecules has been transfered there and \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} is a carcass class, dead as a dodo, an ex-\/class if you will. \mbox{\Hypertarget{class_iso_spec_1_1_iso_a7235f0afc56dccd13937791a630c45da}\label{class_iso_spec_1_1_iso_a7235f0afc56dccd13937791a630c45da}} | |
| 161 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!isotope\+Numbers@{isotope\+Numbers}} | |
| 162 | \index{isotope\+Numbers@{isotope\+Numbers}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 163 | \subsubsection{\texorpdfstring{isotope\+Numbers}{isotopeNumbers}} | |
| 164 | {\footnotesize\ttfamily int$\ast$ Iso\+Spec\+::\+Iso\+::isotope\+Numbers\hspace{0.3cm}{\ttfamily [protected]}} | |
| 165 | ||
| 166 | A table with numbers of isotopes for each element. \mbox{\Hypertarget{class_iso_spec_1_1_iso_aea98a8331a2f8a1a6bbcace6124fcfae}\label{class_iso_spec_1_1_iso_aea98a8331a2f8a1a6bbcace6124fcfae}} | |
| 167 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!marginals@{marginals}} | |
| 168 | \index{marginals@{marginals}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 169 | \subsubsection{\texorpdfstring{marginals}{marginals}} | |
| 170 | {\footnotesize\ttfamily \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}}$\ast$$\ast$ Iso\+Spec\+::\+Iso\+::marginals\hspace{0.3cm}{\ttfamily [protected]}} | |
| 171 | ||
| 172 | The table of pointers to the distributions of individual subisotopologues. \mbox{\Hypertarget{class_iso_spec_1_1_iso_ab51c157b23ae6a6b521667b6f0e8a208}\label{class_iso_spec_1_1_iso_ab51c157b23ae6a6b521667b6f0e8a208}} | |
| 173 | \index{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!mode\+L\+Prob@{mode\+L\+Prob}} | |
| 174 | \index{mode\+L\+Prob@{mode\+L\+Prob}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}} | |
| 175 | \subsubsection{\texorpdfstring{mode\+L\+Prob}{modeLProb}} | |
| 176 | {\footnotesize\ttfamily double Iso\+Spec\+::\+Iso\+::mode\+L\+Prob\hspace{0.3cm}{\ttfamily [protected]}} | |
| 177 | ||
| 178 | The log-\/probability of the mode of the isotopic distribution. | |
| 179 | ||
| 180 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 181 | \item | |
| 182 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+h\item | |
| 183 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+cpp\end{DoxyCompactItemize} |
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| 175 | (IsoSpec::IsoGenerator) cw | |
| 176 | (IsoSpec::Iso) cw | |
| 177 | (IsoSpec::IsoLayeredGenerator) cw | |
| 178 | (IsoSpec::IsoOrderedGenerator) cw | |
| 179 | (IsoSpec::IsoThresholdGenerator) cw | |
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| 194 | (IsoSpec::IsoOrderedGenerator) 1.000000 0.000000 box | |
| 195 | (IsoSpec::IsoThresholdGenerator) 2.000000 0.000000 box | |
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| 0 | \hypertarget{class_iso_spec_1_1_iso_generator}{}\section{Iso\+Spec\+:\+:Iso\+Generator Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_generator}\index{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}} | |
| 2 | ||
| 3 | ||
| 4 | The generator of isotopologues. | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$iso\+Spec++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Iso\+Generator\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=2.800000cm]{class_iso_spec_1_1_iso_generator} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | virtual bool \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a20f48ba18c6aecc57d73b2c3ec3a11dd}{advance\+To\+Next\+Configuration}} ()=0 | |
| 21 | \begin{DoxyCompactList}\small\item\em Advance to the next, not yet visited, most probable isotopologue. \end{DoxyCompactList}\item | |
| 22 | virtual double \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_ae8e24abbce51a4c93994f630acfdf383}{lprob}} () const | |
| 23 | \begin{DoxyCompactList}\small\item\em Get the log-\/probability of the current isotopologue. \end{DoxyCompactList}\item | |
| 24 | virtual double \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a34173228ef73e272e2ff0ae6ce58092d}{mass}} () const | |
| 25 | \begin{DoxyCompactList}\small\item\em Get the mass of the current isotopologue. \end{DoxyCompactList}\item | |
| 26 | virtual double \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_aecf1b3292fcc0857a86efe619a37fff0}{prob}} () const | |
| 27 | \begin{DoxyCompactList}\small\item\em Get the probability of the current isotopologue. \end{DoxyCompactList}\item | |
| 28 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_generator_a19ca8af7dd97f8f37756d4267d49d91d}\label{class_iso_spec_1_1_iso_generator_a19ca8af7dd97f8f37756d4267d49d91d}} | |
| 29 | virtual void {\bfseries get\+\_\+conf\+\_\+signature} (int $\ast$space) const =0 | |
| 30 | \item | |
| 31 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_generator_a89b5b851fbc67f79ed165af0b9b2a188}\label{class_iso_spec_1_1_iso_generator_a89b5b851fbc67f79ed165af0b9b2a188}} | |
| 32 | \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a89b5b851fbc67f79ed165af0b9b2a188}{Iso\+Generator}} (\mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&\&iso, bool alloc\+\_\+partials=true) | |
| 33 | \begin{DoxyCompactList}\small\item\em Move constructor. \end{DoxyCompactList}\item | |
| 34 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_generator_a28442c8072a2e85faf5ff04f5feffd76}\label{class_iso_spec_1_1_iso_generator_a28442c8072a2e85faf5ff04f5feffd76}} | |
| 35 | virtual \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a28442c8072a2e85faf5ff04f5feffd76}{$\sim$\+Iso\+Generator}} () | |
| 36 | \begin{DoxyCompactList}\small\item\em Destructor. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 37 | \subsection*{Protected Attributes} | |
| 38 | \begin{DoxyCompactItemize} | |
| 39 | \item | |
| 40 | double $\ast$ \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a54a39b847a71aa08d1207d0666dd62bc}{partial\+L\+Probs}} | |
| 41 | \item | |
| 42 | double $\ast$ \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_af5654fcdba8199cbd60668af5de89a53}{partial\+Masses}} | |
| 43 | \item | |
| 44 | double $\ast$ \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_ac18406df84b4b220bcb1974000c192b2}{partial\+Probs}} | |
| 45 | \end{DoxyCompactItemize} | |
| 46 | \subsection*{Additional Inherited Members} | |
| 47 | ||
| 48 | ||
| 49 | \subsection{Detailed Description} | |
| 50 | The generator of isotopologues. | |
| 51 | ||
| 52 | This class provides the common interface for all isotopic generators. | |
| 53 | ||
| 54 | Definition at line 129 of file iso\+Spec++.\+h. | |
| 55 | ||
| 56 | ||
| 57 | ||
| 58 | \subsection{Member Function Documentation} | |
| 59 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_generator_a20f48ba18c6aecc57d73b2c3ec3a11dd}\label{class_iso_spec_1_1_iso_generator_a20f48ba18c6aecc57d73b2c3ec3a11dd}} | |
| 60 | \index{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}!advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}} | |
| 61 | \index{advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}!Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}} | |
| 62 | \subsubsection{\texorpdfstring{advance\+To\+Next\+Configuration()}{advanceToNextConfiguration()}} | |
| 63 | {\footnotesize\ttfamily virtual bool Iso\+Spec\+::\+Iso\+Generator\+::advance\+To\+Next\+Configuration (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [pure virtual]}} | |
| 64 | ||
| 65 | ||
| 66 | ||
| 67 | Advance to the next, not yet visited, most probable isotopologue. | |
| 68 | ||
| 69 | \begin{DoxyReturn}{Returns} | |
| 70 | Return false if it is not possible to advance. | |
| 71 | \end{DoxyReturn} | |
| 72 | ||
| 73 | ||
| 74 | Implemented in \mbox{\hyperlink{class_iso_spec_1_1_iso_layered_generator_abce0871ac279fd54a0344ceb80126b66}{Iso\+Spec\+::\+Iso\+Layered\+Generator}}, \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_a7164a6476b84665967c4a667a91d3f3e}{Iso\+Spec\+::\+Iso\+Threshold\+Generator}}, and \mbox{\hyperlink{class_iso_spec_1_1_iso_ordered_generator_aa2438bb81fb1d68eda1637d67e9cb36d}{Iso\+Spec\+::\+Iso\+Ordered\+Generator}}. | |
| 75 | ||
| 76 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_generator_ae8e24abbce51a4c93994f630acfdf383}\label{class_iso_spec_1_1_iso_generator_ae8e24abbce51a4c93994f630acfdf383}} | |
| 77 | \index{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}!lprob@{lprob}} | |
| 78 | \index{lprob@{lprob}!Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}} | |
| 79 | \subsubsection{\texorpdfstring{lprob()}{lprob()}} | |
| 80 | {\footnotesize\ttfamily virtual double Iso\+Spec\+::\+Iso\+Generator\+::lprob (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}, {\ttfamily [virtual]}} | |
| 81 | ||
| 82 | ||
| 83 | ||
| 84 | Get the log-\/probability of the current isotopologue. | |
| 85 | ||
| 86 | \begin{DoxyReturn}{Returns} | |
| 87 | The log-\/probability of the current isotopologue. | |
| 88 | \end{DoxyReturn} | |
| 89 | ||
| 90 | ||
| 91 | Reimplemented in \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_a4aeebde03e385404d0175fd5696ff529}{Iso\+Spec\+::\+Iso\+Threshold\+Generator}}. | |
| 92 | ||
| 93 | ||
| 94 | ||
| 95 | Definition at line 147 of file iso\+Spec++.\+h. | |
| 96 | ||
| 97 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_generator_a34173228ef73e272e2ff0ae6ce58092d}\label{class_iso_spec_1_1_iso_generator_a34173228ef73e272e2ff0ae6ce58092d}} | |
| 98 | \index{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}!mass@{mass}} | |
| 99 | \index{mass@{mass}!Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}} | |
| 100 | \subsubsection{\texorpdfstring{mass()}{mass()}} | |
| 101 | {\footnotesize\ttfamily virtual double Iso\+Spec\+::\+Iso\+Generator\+::mass (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}, {\ttfamily [virtual]}} | |
| 102 | ||
| 103 | ||
| 104 | ||
| 105 | Get the mass of the current isotopologue. | |
| 106 | ||
| 107 | \begin{DoxyReturn}{Returns} | |
| 108 | The mass of the current isotopologue. | |
| 109 | \end{DoxyReturn} | |
| 110 | ||
| 111 | ||
| 112 | Reimplemented in \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_ae2236accc7dc7a25a723e3c7317659b6}{Iso\+Spec\+::\+Iso\+Threshold\+Generator}}. | |
| 113 | ||
| 114 | ||
| 115 | ||
| 116 | Definition at line 153 of file iso\+Spec++.\+h. | |
| 117 | ||
| 118 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_generator_aecf1b3292fcc0857a86efe619a37fff0}\label{class_iso_spec_1_1_iso_generator_aecf1b3292fcc0857a86efe619a37fff0}} | |
| 119 | \index{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}!prob@{prob}} | |
| 120 | \index{prob@{prob}!Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}} | |
| 121 | \subsubsection{\texorpdfstring{prob()}{prob()}} | |
| 122 | {\footnotesize\ttfamily virtual double Iso\+Spec\+::\+Iso\+Generator\+::prob (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}, {\ttfamily [virtual]}} | |
| 123 | ||
| 124 | ||
| 125 | ||
| 126 | Get the probability of the current isotopologue. | |
| 127 | ||
| 128 | \begin{DoxyReturn}{Returns} | |
| 129 | The probability of the current isotopologue. | |
| 130 | \end{DoxyReturn} | |
| 131 | ||
| 132 | ||
| 133 | Reimplemented in \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_a998d987f81b2ca7ed610294f6a5f8df5}{Iso\+Spec\+::\+Iso\+Threshold\+Generator}}. | |
| 134 | ||
| 135 | ||
| 136 | ||
| 137 | Definition at line 159 of file iso\+Spec++.\+h. | |
| 138 | ||
| 139 | ||
| 140 | ||
| 141 | \subsection{Member Data Documentation} | |
| 142 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_generator_a54a39b847a71aa08d1207d0666dd62bc}\label{class_iso_spec_1_1_iso_generator_a54a39b847a71aa08d1207d0666dd62bc}} | |
| 143 | \index{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}!partial\+L\+Probs@{partial\+L\+Probs}} | |
| 144 | \index{partial\+L\+Probs@{partial\+L\+Probs}!Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}} | |
| 145 | \subsubsection{\texorpdfstring{partial\+L\+Probs}{partialLProbs}} | |
| 146 | {\footnotesize\ttfamily double$\ast$ Iso\+Spec\+::\+Iso\+Generator\+::partial\+L\+Probs\hspace{0.3cm}{\ttfamily [protected]}} | |
| 147 | ||
| 148 | The prefix sum of the log-\/probabilities of the current isotopologue. | |
| 149 | ||
| 150 | Definition at line 132 of file iso\+Spec++.\+h. | |
| 151 | ||
| 152 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_generator_af5654fcdba8199cbd60668af5de89a53}\label{class_iso_spec_1_1_iso_generator_af5654fcdba8199cbd60668af5de89a53}} | |
| 153 | \index{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}!partial\+Masses@{partial\+Masses}} | |
| 154 | \index{partial\+Masses@{partial\+Masses}!Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}} | |
| 155 | \subsubsection{\texorpdfstring{partial\+Masses}{partialMasses}} | |
| 156 | {\footnotesize\ttfamily double$\ast$ Iso\+Spec\+::\+Iso\+Generator\+::partial\+Masses\hspace{0.3cm}{\ttfamily [protected]}} | |
| 157 | ||
| 158 | The prefix sum of the masses of the current isotopologue. | |
| 159 | ||
| 160 | Definition at line 133 of file iso\+Spec++.\+h. | |
| 161 | ||
| 162 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_generator_ac18406df84b4b220bcb1974000c192b2}\label{class_iso_spec_1_1_iso_generator_ac18406df84b4b220bcb1974000c192b2}} | |
| 163 | \index{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}!partial\+Probs@{partial\+Probs}} | |
| 164 | \index{partial\+Probs@{partial\+Probs}!Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}} | |
| 165 | \subsubsection{\texorpdfstring{partial\+Probs}{partialProbs}} | |
| 166 | {\footnotesize\ttfamily double$\ast$ Iso\+Spec\+::\+Iso\+Generator\+::partial\+Probs\hspace{0.3cm}{\ttfamily [protected]}} | |
| 167 | ||
| 168 | The prefix product of the probabilities of the current isotopologue. | |
| 169 | ||
| 170 | Definition at line 134 of file iso\+Spec++.\+h. | |
| 171 | ||
| 172 | ||
| 173 | ||
| 174 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 175 | \item | |
| 176 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+h\item | |
| 177 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+cpp\end{DoxyCompactItemize} |
| 0 | digraph "IsoSpec::IsoGenerator" | |
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| 7 | Node7 -> Node6 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" marginals" ]; | |
| 8 | Node7 [label="IsoSpec::Marginal",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_marginal.html"]; | |
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| 0 | 8983a489c6f749fa26550459fcc8d3c5⏎ |
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| 10 | Node0 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid"]; | |
| 11 | Node3 [label="IsoSpec::IsoOrderedGenerator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso_ordered_generator.html",tooltip="The generator of isotopologues sorted by their probability of occurrence. "]; | |
| 12 | Node0 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid"]; | |
| 13 | Node4 [label="IsoSpec::IsoThresholdGenerator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso_threshold_generator.html"]; | |
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| 0 | 0e4642420494ca1dce77b5d72dd5ad71⏎ |
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| 38 | { | |
| 39 | /a exch def | |
| 40 | /b exch def | |
| 41 | a b gt {a} {b} ifelse | |
| 42 | } def | |
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| 45 | { | |
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| 47 | } def | |
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| 51 | /str exch def | |
| 52 | /boxwidth boxwidth str stringwidth pop max def | |
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| 112 | exch xspacing mul xoffset add boxwidth 2 div add | |
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| 117 | 0 disty 2 div rlineto | |
| 118 | stroke | |
| 119 | 1 eq { x y disty 2 div add arrow } if | |
| 120 | } def | |
| 121 | ||
| 122 | /hedge | |
| 123 | { | |
| 124 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 125 | exch yspacing mul boxheight 2 div sub | |
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| 130 | boxwidth 2 div distx add 0 rlineto | |
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| 156 | ||
| 157 | /conn % connections the blocks from col `arg1' to `arg2' of row `arg3' | |
| 158 | { | |
| 159 | /ys exch def | |
| 160 | /xe exch def | |
| 161 | /xs exch def | |
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| 170 | ||
| 171 | % ----- main ------ | |
| 172 | ||
| 173 | boxfont setfont | |
| 174 | 1 boundaspect scale | |
| 175 | (IsoSpec::IsoLayeredGenerator) cw | |
| 176 | (IsoSpec::IsoGenerator) cw | |
| 177 | (IsoSpec::Iso) cw | |
| 178 | /boxwidth boxwidth marginwidth 2 mul add def | |
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| 180 | /yspacing boxheight disty add def | |
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| 182 | boxwidth cols mul distx cols 1 sub mul add | |
| 183 | boxheight rows mul disty rows 1 sub mul add boundaspect mul | |
| 184 | max def | |
| 185 | boundx scalefactor div boundy scalefactor div scale | |
| 186 | ||
| 187 | % ----- classes ----- | |
| 188 | ||
| 189 | (IsoSpec::IsoLayeredGenerator) 0.000000 0.000000 box | |
| 190 | (IsoSpec::IsoGenerator) 0.000000 1.000000 box | |
| 191 | (IsoSpec::Iso) 0.000000 2.000000 box | |
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| 193 | % ----- relations ----- | |
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| 0 | \hypertarget{class_iso_spec_1_1_iso_layered_generator}{}\section{Iso\+Spec\+:\+:Iso\+Layered\+Generator Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_layered_generator}\index{Iso\+Spec\+::\+Iso\+Layered\+Generator@{Iso\+Spec\+::\+Iso\+Layered\+Generator}} | |
| 2 | ||
| 3 | ||
| 4 | The class that represents isotopologues above a given joint probability value. | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$iso\+Spec++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Iso\+Layered\+Generator\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=3.000000cm]{class_iso_spec_1_1_iso_layered_generator} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | bool \mbox{\hyperlink{class_iso_spec_1_1_iso_layered_generator_abce0871ac279fd54a0344ceb80126b66}{advance\+To\+Next\+Configuration}} () override final | |
| 21 | \begin{DoxyCompactList}\small\item\em Advance to the next, not yet visited, most probable isotopologue. \end{DoxyCompactList}\item | |
| 22 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_layered_generator_ab63cbae392f88528e5b7421dada4abef}\label{class_iso_spec_1_1_iso_layered_generator_ab63cbae392f88528e5b7421dada4abef}} | |
| 23 | void {\bfseries get\+\_\+conf\+\_\+signature} (int $\ast$space) const override final | |
| 24 | \item | |
| 25 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_layered_generator_a746fc9fe13cca843a0f0f1993aee970a}\label{class_iso_spec_1_1_iso_layered_generator_a746fc9fe13cca843a0f0f1993aee970a}} | |
| 26 | {\bfseries Iso\+Layered\+Generator} (\mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&\&iso, double \+\_\+target\+Coverage, double \+\_\+percentage\+To\+Expand, int \+\_\+tab\+Size=1000, int \+\_\+hash\+Size=1000, bool trim=false) | |
| 27 | \item | |
| 28 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_layered_generator_a6c4ea5906136d802859f47cd1b5add8d}\label{class_iso_spec_1_1_iso_layered_generator_a6c4ea5906136d802859f47cd1b5add8d}} | |
| 29 | void {\bfseries terminate\+\_\+search} () | |
| 30 | \end{DoxyCompactItemize} | |
| 31 | \subsection*{Additional Inherited Members} | |
| 32 | ||
| 33 | ||
| 34 | \subsection{Detailed Description} | |
| 35 | The class that represents isotopologues above a given joint probability value. | |
| 36 | ||
| 37 | This class generates subsequent isotopologues that A\+RE N\+OT G\+U\+A\+R\+A\+N\+T\+E\+ED TO BE O\+R\+D\+E\+R\+ED BY probability. The overal set of isotopologues is guaranteed to surpass a given threshold of probability contained in the isotopic distribution. This calculations are performed in O(\+N) operations, where N is the total number of the output isotopologues. | |
| 38 | ||
| 39 | This class is not a true generator yet -\/ the generator methods have been implemented for compatibility, but the class actually performs all computations during the initialization and stores them, and the generator methods only walk through the array of precomputed values. . It will be reimplemented as a true generator in 2.\+0. | |
| 40 | ||
| 41 | Definition at line 383 of file iso\+Spec++.\+h. | |
| 42 | ||
| 43 | ||
| 44 | ||
| 45 | \subsection{Member Function Documentation} | |
| 46 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_layered_generator_abce0871ac279fd54a0344ceb80126b66}\label{class_iso_spec_1_1_iso_layered_generator_abce0871ac279fd54a0344ceb80126b66}} | |
| 47 | \index{Iso\+Spec\+::\+Iso\+Layered\+Generator@{Iso\+Spec\+::\+Iso\+Layered\+Generator}!advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}} | |
| 48 | \index{advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}!Iso\+Spec\+::\+Iso\+Layered\+Generator@{Iso\+Spec\+::\+Iso\+Layered\+Generator}} | |
| 49 | \subsubsection{\texorpdfstring{advance\+To\+Next\+Configuration()}{advanceToNextConfiguration()}} | |
| 50 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Iso\+Layered\+Generator\+::advance\+To\+Next\+Configuration (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [final]}, {\ttfamily [override]}, {\ttfamily [virtual]}} | |
| 51 | ||
| 52 | ||
| 53 | ||
| 54 | Advance to the next, not yet visited, most probable isotopologue. | |
| 55 | ||
| 56 | \begin{DoxyReturn}{Returns} | |
| 57 | Return false if it is not possible to advance. | |
| 58 | \end{DoxyReturn} | |
| 59 | ||
| 60 | ||
| 61 | Implements \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a20f48ba18c6aecc57d73b2c3ec3a11dd}{Iso\+Spec\+::\+Iso\+Generator}}. | |
| 62 | ||
| 63 | ||
| 64 | ||
| 65 | Definition at line 773 of file iso\+Spec++.\+cpp. | |
| 66 | ||
| 67 | ||
| 68 | ||
| 69 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 70 | \item | |
| 71 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+h\item | |
| 72 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+cpp\end{DoxyCompactItemize} |
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| 8 | Node5 [label="IsoSpec::Iso",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso.html",tooltip="The Iso class for the calculation of the isotopic distribution. "]; | |
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| 11 | } |
| 0 | 67a1eea9dee54f4b4a0f71a556e6b0d9⏎ |
| 0 | digraph "IsoSpec::IsoLayeredGenerator" | |
| 1 | { | |
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| 6 | Node1 [label="IsoSpec::IsoGenerator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso_generator.html",tooltip="The generator of isotopologues. "]; | |
| 7 | Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid"]; | |
| 8 | Node2 [label="IsoSpec::Iso",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso.html",tooltip="The Iso class for the calculation of the isotopic distribution. "]; | |
| 9 | } |
| 0 | 4b38cc722d390b6ab9eaf90a61a124f9⏎ |
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| 18 | /marginwidth 10 def | |
| 19 | /distx 20 def | |
| 20 | /disty 40 def | |
| 21 | /boundaspect 1.600000 def % aspect ratio of the BoundingBox (width/height) | |
| 22 | /boundx 500 def | |
| 23 | /boundy boundx boundaspect div def | |
| 24 | /xspacing 0 def | |
| 25 | /yspacing 0 def | |
| 26 | /rows 3 def | |
| 27 | /cols 1 def | |
| 28 | /scalefactor 0 def | |
| 29 | /boxfont /Times-Roman findfont fontheight scalefont def | |
| 30 | ||
| 31 | % ----- procedures ----- | |
| 32 | ||
| 33 | /dotted { [1 4] 0 setdash } def | |
| 34 | /dashed { [5] 0 setdash } def | |
| 35 | /solid { [] 0 setdash } def | |
| 36 | ||
| 37 | /max % result = MAX(arg1,arg2) | |
| 38 | { | |
| 39 | /a exch def | |
| 40 | /b exch def | |
| 41 | a b gt {a} {b} ifelse | |
| 42 | } def | |
| 43 | ||
| 44 | /xoffset % result = MAX(0,(scalefactor-(boxwidth*cols+distx*(cols-1)))/2) | |
| 45 | { | |
| 46 | 0 scalefactor boxwidth cols mul distx cols 1 sub mul add sub 2 div max | |
| 47 | } def | |
| 48 | ||
| 49 | /cw % boxwidth = MAX(boxwidth, stringwidth(arg1)) | |
| 50 | { | |
| 51 | /str exch def | |
| 52 | /boxwidth boxwidth str stringwidth pop max def | |
| 53 | } def | |
| 54 | ||
| 55 | /box % draws a box with text `arg1' at grid pos (arg2,arg3) | |
| 56 | { gsave | |
| 57 | 2 setlinewidth | |
| 58 | newpath | |
| 59 | exch xspacing mul xoffset add | |
| 60 | exch yspacing mul | |
| 61 | moveto | |
| 62 | boxwidth 0 rlineto | |
| 63 | 0 boxheight rlineto | |
| 64 | boxwidth neg 0 rlineto | |
| 65 | 0 boxheight neg rlineto | |
| 66 | closepath | |
| 67 | dup stringwidth pop neg boxwidth add 2 div | |
| 68 | boxheight fontheight 2 div sub 2 div | |
| 69 | rmoveto show stroke | |
| 70 | grestore | |
| 71 | } def | |
| 72 | ||
| 73 | /mark | |
| 74 | { newpath | |
| 75 | exch xspacing mul xoffset add boxwidth add | |
| 76 | exch yspacing mul | |
| 77 | moveto | |
| 78 | 0 boxheight 4 div rlineto | |
| 79 | boxheight neg 4 div boxheight neg 4 div rlineto | |
| 80 | closepath | |
| 81 | eofill | |
| 82 | stroke | |
| 83 | } def | |
| 84 | ||
| 85 | /arrow | |
| 86 | { newpath | |
| 87 | moveto | |
| 88 | 3 -8 rlineto | |
| 89 | -6 0 rlineto | |
| 90 | 3 8 rlineto | |
| 91 | closepath | |
| 92 | eofill | |
| 93 | stroke | |
| 94 | } def | |
| 95 | ||
| 96 | /out % draws an output connector for the block at (arg1,arg2) | |
| 97 | { | |
| 98 | newpath | |
| 99 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 100 | exch yspacing mul boxheight add | |
| 101 | /y exch def | |
| 102 | /x exch def | |
| 103 | x y moveto | |
| 104 | 0 disty 2 div rlineto | |
| 105 | stroke | |
| 106 | 1 eq { x y disty 2 div add arrow } if | |
| 107 | } def | |
| 108 | ||
| 109 | /in % draws an input connector for the block at (arg1,arg2) | |
| 110 | { | |
| 111 | newpath | |
| 112 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 113 | exch yspacing mul disty 2 div sub | |
| 114 | /y exch def | |
| 115 | /x exch def | |
| 116 | x y moveto | |
| 117 | 0 disty 2 div rlineto | |
| 118 | stroke | |
| 119 | 1 eq { x y disty 2 div add arrow } if | |
| 120 | } def | |
| 121 | ||
| 122 | /hedge | |
| 123 | { | |
| 124 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 125 | exch yspacing mul boxheight 2 div sub | |
| 126 | /y exch def | |
| 127 | /x exch def | |
| 128 | newpath | |
| 129 | x y moveto | |
| 130 | boxwidth 2 div distx add 0 rlineto | |
| 131 | stroke | |
| 132 | 1 eq | |
| 133 | { newpath x boxwidth 2 div distx add add y moveto | |
| 134 | -8 3 rlineto | |
| 135 | 0 -6 rlineto | |
| 136 | 8 3 rlineto | |
| 137 | closepath | |
| 138 | eofill | |
| 139 | stroke | |
| 140 | } if | |
| 141 | } def | |
| 142 | ||
| 143 | /vedge | |
| 144 | { | |
| 145 | /ye exch def | |
| 146 | /ys exch def | |
| 147 | /xs exch def | |
| 148 | newpath | |
| 149 | xs xspacing mul xoffset add boxwidth 2 div add dup | |
| 150 | ys yspacing mul boxheight 2 div sub | |
| 151 | moveto | |
| 152 | ye yspacing mul boxheight 2 div sub | |
| 153 | lineto | |
| 154 | stroke | |
| 155 | } def | |
| 156 | ||
| 157 | /conn % connections the blocks from col `arg1' to `arg2' of row `arg3' | |
| 158 | { | |
| 159 | /ys exch def | |
| 160 | /xe exch def | |
| 161 | /xs exch def | |
| 162 | newpath | |
| 163 | xs xspacing mul xoffset add boxwidth 2 div add | |
| 164 | ys yspacing mul disty 2 div sub | |
| 165 | moveto | |
| 166 | xspacing xe xs sub mul 0 | |
| 167 | rlineto | |
| 168 | stroke | |
| 169 | } def | |
| 170 | ||
| 171 | % ----- main ------ | |
| 172 | ||
| 173 | boxfont setfont | |
| 174 | 1 boundaspect scale | |
| 175 | (IsoSpec::IsoOrderedGenerator) cw | |
| 176 | (IsoSpec::IsoGenerator) cw | |
| 177 | (IsoSpec::Iso) cw | |
| 178 | /boxwidth boxwidth marginwidth 2 mul add def | |
| 179 | /xspacing boxwidth distx add def | |
| 180 | /yspacing boxheight disty add def | |
| 181 | /scalefactor | |
| 182 | boxwidth cols mul distx cols 1 sub mul add | |
| 183 | boxheight rows mul disty rows 1 sub mul add boundaspect mul | |
| 184 | max def | |
| 185 | boundx scalefactor div boundy scalefactor div scale | |
| 186 | ||
| 187 | % ----- classes ----- | |
| 188 | ||
| 189 | (IsoSpec::IsoOrderedGenerator) 0.000000 0.000000 box | |
| 190 | (IsoSpec::IsoGenerator) 0.000000 1.000000 box | |
| 191 | (IsoSpec::Iso) 0.000000 2.000000 box | |
| 192 | ||
| 193 | % ----- relations ----- | |
| 194 | ||
| 195 | solid | |
| 196 | 0 0.000000 0.000000 out | |
| 197 | solid | |
| 198 | 1 0.000000 1.000000 in | |
| 199 | solid | |
| 200 | 0 0.000000 1.000000 out | |
| 201 | solid | |
| 202 | 1 0.000000 2.000000 in |
| 0 | \hypertarget{class_iso_spec_1_1_iso_ordered_generator}{}\section{Iso\+Spec\+:\+:Iso\+Ordered\+Generator Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_ordered_generator}\index{Iso\+Spec\+::\+Iso\+Ordered\+Generator@{Iso\+Spec\+::\+Iso\+Ordered\+Generator}} | |
| 2 | ||
| 3 | ||
| 4 | The generator of isotopologues sorted by their probability of occurrence. | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$iso\+Spec++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Iso\+Ordered\+Generator\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=3.000000cm]{class_iso_spec_1_1_iso_ordered_generator} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | bool \mbox{\hyperlink{class_iso_spec_1_1_iso_ordered_generator_aa2438bb81fb1d68eda1637d67e9cb36d}{advance\+To\+Next\+Configuration}} () override final | |
| 21 | \begin{DoxyCompactList}\small\item\em Advance to the next, not yet visited, most probable isotopologue. \end{DoxyCompactList}\item | |
| 22 | void \mbox{\hyperlink{class_iso_spec_1_1_iso_ordered_generator_af5d638985fd24c03bfe1f3d61e1b25c6}{get\+\_\+conf\+\_\+signature}} (int $\ast$space) const override final | |
| 23 | \begin{DoxyCompactList}\small\item\em Save the counts of isotopes in the space. \end{DoxyCompactList}\item | |
| 24 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_ordered_generator_afaf81ff3a758cd59629db323560e263d}\label{class_iso_spec_1_1_iso_ordered_generator_afaf81ff3a758cd59629db323560e263d}} | |
| 25 | \mbox{\hyperlink{class_iso_spec_1_1_iso_ordered_generator_afaf81ff3a758cd59629db323560e263d}{Iso\+Ordered\+Generator}} (\mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&\&iso, int \+\_\+tab\+Size=1000, int \+\_\+hash\+Size=1000) | |
| 26 | \begin{DoxyCompactList}\small\item\em The move-\/contstructor. \end{DoxyCompactList}\item | |
| 27 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_ordered_generator_a030c118b9a6131130684cd2710371842}\label{class_iso_spec_1_1_iso_ordered_generator_a030c118b9a6131130684cd2710371842}} | |
| 28 | virtual \mbox{\hyperlink{class_iso_spec_1_1_iso_ordered_generator_a030c118b9a6131130684cd2710371842}{$\sim$\+Iso\+Ordered\+Generator}} () | |
| 29 | \begin{DoxyCompactList}\small\item\em Destructor. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 30 | \subsection*{Additional Inherited Members} | |
| 31 | ||
| 32 | ||
| 33 | \subsection{Detailed Description} | |
| 34 | The generator of isotopologues sorted by their probability of occurrence. | |
| 35 | ||
| 36 | The subsequent isotopologues are generated with diminishing probability, starting from the mode. This algorithm take O(\+N$\ast$log(\+N)) to compute the N isotopologues because of using the Priority Queue data structure. Obtaining the N isotopologues can be achieved in O(\+N) if they are not required to be spit out in the descending order. | |
| 37 | ||
| 38 | Definition at line 179 of file iso\+Spec++.\+h. | |
| 39 | ||
| 40 | ||
| 41 | ||
| 42 | \subsection{Member Function Documentation} | |
| 43 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_ordered_generator_aa2438bb81fb1d68eda1637d67e9cb36d}\label{class_iso_spec_1_1_iso_ordered_generator_aa2438bb81fb1d68eda1637d67e9cb36d}} | |
| 44 | \index{Iso\+Spec\+::\+Iso\+Ordered\+Generator@{Iso\+Spec\+::\+Iso\+Ordered\+Generator}!advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}} | |
| 45 | \index{advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}!Iso\+Spec\+::\+Iso\+Ordered\+Generator@{Iso\+Spec\+::\+Iso\+Ordered\+Generator}} | |
| 46 | \subsubsection{\texorpdfstring{advance\+To\+Next\+Configuration()}{advanceToNextConfiguration()}} | |
| 47 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Iso\+Ordered\+Generator\+::advance\+To\+Next\+Configuration (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [final]}, {\ttfamily [override]}, {\ttfamily [virtual]}} | |
| 48 | ||
| 49 | ||
| 50 | ||
| 51 | Advance to the next, not yet visited, most probable isotopologue. | |
| 52 | ||
| 53 | \begin{DoxyReturn}{Returns} | |
| 54 | Return false if it is not possible to advance. | |
| 55 | \end{DoxyReturn} | |
| 56 | ||
| 57 | ||
| 58 | Implements \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a20f48ba18c6aecc57d73b2c3ec3a11dd}{Iso\+Spec\+::\+Iso\+Generator}}. | |
| 59 | ||
| 60 | ||
| 61 | ||
| 62 | Definition at line 461 of file iso\+Spec++.\+cpp. | |
| 63 | ||
| 64 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_ordered_generator_af5d638985fd24c03bfe1f3d61e1b25c6}\label{class_iso_spec_1_1_iso_ordered_generator_af5d638985fd24c03bfe1f3d61e1b25c6}} | |
| 65 | \index{Iso\+Spec\+::\+Iso\+Ordered\+Generator@{Iso\+Spec\+::\+Iso\+Ordered\+Generator}!get\+\_\+conf\+\_\+signature@{get\+\_\+conf\+\_\+signature}} | |
| 66 | \index{get\+\_\+conf\+\_\+signature@{get\+\_\+conf\+\_\+signature}!Iso\+Spec\+::\+Iso\+Ordered\+Generator@{Iso\+Spec\+::\+Iso\+Ordered\+Generator}} | |
| 67 | \subsubsection{\texorpdfstring{get\+\_\+conf\+\_\+signature()}{get\_conf\_signature()}} | |
| 68 | {\footnotesize\ttfamily void Iso\+Spec\+::\+Iso\+Ordered\+Generator\+::get\+\_\+conf\+\_\+signature (\begin{DoxyParamCaption}\item[{int $\ast$}]{space }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}, {\ttfamily [final]}, {\ttfamily [override]}, {\ttfamily [virtual]}} | |
| 69 | ||
| 70 | ||
| 71 | ||
| 72 | Save the counts of isotopes in the space. | |
| 73 | ||
| 74 | ||
| 75 | \begin{DoxyParams}{Parameters} | |
| 76 | {\em space} & An array where counts of isotopes shall be written. Must be as big as the overall number of isotopes. \\ | |
| 77 | \hline | |
| 78 | \end{DoxyParams} | |
| 79 | ||
| 80 | ||
| 81 | Implements \mbox{\hyperlink{class_iso_spec_1_1_iso_generator}{Iso\+Spec\+::\+Iso\+Generator}}. | |
| 82 | ||
| 83 | ||
| 84 | ||
| 85 | Definition at line 202 of file iso\+Spec++.\+h. | |
| 86 | ||
| 87 | ||
| 88 | ||
| 89 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 90 | \item | |
| 91 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+h\item | |
| 92 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+cpp\end{DoxyCompactItemize} |
| 0 | digraph "IsoSpec::IsoOrderedGenerator" | |
| 1 | { | |
| 2 | edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; | |
| 3 | node [fontname="Helvetica",fontsize="10",shape=record]; | |
| 4 | Node3 [label="IsoSpec::IsoOrderedGenerator",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; | |
| 5 | Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid"]; | |
| 6 | Node4 [label="IsoSpec::IsoGenerator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso_generator.html",tooltip="The generator of isotopologues. "]; | |
| 7 | Node5 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid"]; | |
| 8 | Node5 [label="IsoSpec::Iso",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso.html",tooltip="The Iso class for the calculation of the isotopic distribution. "]; | |
| 9 | Node6 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" marginals" ]; | |
| 10 | Node6 [label="IsoSpec::Marginal",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_marginal.html"]; | |
| 11 | } |
| 0 | 0a3fea285b82a31a0b2745fd8dc60fd3⏎ |
| 0 | digraph "IsoSpec::IsoOrderedGenerator" | |
| 1 | { | |
| 2 | edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; | |
| 3 | node [fontname="Helvetica",fontsize="10",shape=record]; | |
| 4 | Node0 [label="IsoSpec::IsoOrderedGenerator",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; | |
| 5 | Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid"]; | |
| 6 | Node1 [label="IsoSpec::IsoGenerator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso_generator.html",tooltip="The generator of isotopologues. "]; | |
| 7 | Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid"]; | |
| 8 | Node2 [label="IsoSpec::Iso",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_iso.html",tooltip="The Iso class for the calculation of the isotopic distribution. "]; | |
| 9 | } |
| 0 | 156b9a37f79303511a74bc589a0d085a⏎ |
| 0 | \hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_equal}{}\section{Iso\+Spec\+:\+:Iso\+Spec\+:\+:Conf\+Equal Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_spec_1_1_conf_equal}\index{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal}} | |
| 2 | ||
| 3 | ||
| 4 | The equality of configurations operator. | |
| 5 | ||
| 6 | ||
| 7 | \subsection*{Public Member Functions} | |
| 8 | \begin{DoxyCompactItemize} | |
| 9 | \item | |
| 10 | \mbox{\hyperlink{class_iso_spec_1_1_iso_spec_1_1_conf_equal_a1e64267307db788516b6dfc98614d4a8}{Conf\+Equal}} (int dim) | |
| 11 | \begin{DoxyCompactList}\small\item\em Constructor. \end{DoxyCompactList}\item | |
| 12 | bool \mbox{\hyperlink{class_iso_spec_1_1_iso_spec_1_1_conf_equal_ad9d7fb4a033b947a983b302cb3e0c735}{operator()}} (const int $\ast$conf1, const int $\ast$conf2) const | |
| 13 | \begin{DoxyCompactList}\small\item\em The {\bfseries call} operator. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 14 | ||
| 15 | ||
| 16 | \subsection{Detailed Description} | |
| 17 | The equality of configurations operator. | |
| 18 | ||
| 19 | Needed for the unordered-\/map. | |
| 20 | ||
| 21 | Definition at line 62 of file operators.\+cpp. | |
| 22 | ||
| 23 | ||
| 24 | ||
| 25 | \subsection{Constructor \& Destructor Documentation} | |
| 26 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_equal_a1e64267307db788516b6dfc98614d4a8}\label{class_iso_spec_1_1_iso_spec_1_1_conf_equal_a1e64267307db788516b6dfc98614d4a8}} | |
| 27 | \index{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal}!Conf\+Equal@{Conf\+Equal}} | |
| 28 | \index{Conf\+Equal@{Conf\+Equal}!Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal}} | |
| 29 | \subsubsection{\texorpdfstring{Conf\+Equal()}{ConfEqual()}} | |
| 30 | {\footnotesize\ttfamily Iso\+Spec\+::\+Conf\+Equal\+::\+Conf\+Equal (\begin{DoxyParamCaption}\item[{int}]{dim }\end{DoxyParamCaption})} | |
| 31 | ||
| 32 | ||
| 33 | ||
| 34 | Constructor. | |
| 35 | ||
| 36 | ||
| 37 | \begin{DoxyParams}{Parameters} | |
| 38 | {\em dim} & the number of the ints that make up a configuration. \\ | |
| 39 | \hline | |
| 40 | \end{DoxyParams} | |
| 41 | ||
| 42 | ||
| 43 | Definition at line 26 of file operators.\+cpp. | |
| 44 | ||
| 45 | ||
| 46 | ||
| 47 | \subsection{Member Function Documentation} | |
| 48 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_equal_ad9d7fb4a033b947a983b302cb3e0c735}\label{class_iso_spec_1_1_iso_spec_1_1_conf_equal_ad9d7fb4a033b947a983b302cb3e0c735}} | |
| 49 | \index{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal}!operator()@{operator()}} | |
| 50 | \index{operator()@{operator()}!Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal}} | |
| 51 | \subsubsection{\texorpdfstring{operator()()}{operator()()}} | |
| 52 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal\+::operator() (\begin{DoxyParamCaption}\item[{const int $\ast$}]{conf1, }\item[{const int $\ast$}]{conf2 }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 53 | ||
| 54 | ||
| 55 | ||
| 56 | The {\bfseries call} operator. | |
| 57 | ||
| 58 | Let us quote the sacred M\+AN of memcmp\+: "The memcmp() function returns zero if the two strings are identical, otherwise returns the difference between the first two differing bytes (treated as unsigned char values, so that `\textbackslash{}200' is greater than `\textbackslash{}0', for example). Zero-\/length strings are always identical. This behavior is not required by C and portable code should only depend on the sign of the returned value." | |
| 59 | ||
| 60 | ||
| 61 | \begin{DoxyParams}{Parameters} | |
| 62 | {\em conf1} & An array of integer counts. \\ | |
| 63 | \hline | |
| 64 | {\em conf2} & An array of integer counts. \\ | |
| 65 | \hline | |
| 66 | \end{DoxyParams} | |
| 67 | \begin{DoxyReturn}{Returns} | |
| 68 | Are conf1 and conf2 the same configuration? | |
| 69 | \end{DoxyReturn} | |
| 70 | ||
| 71 | ||
| 72 | Definition at line 87 of file operators.\+cpp. | |
| 73 | ||
| 74 | ||
| 75 | ||
| 76 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 77 | \item | |
| 78 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_order}{}\section{Iso\+Spec\+:\+:Iso\+Spec\+:\+:Conf\+Order Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_spec_1_1_conf_order}\index{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order}} | |
| 2 | ||
| 3 | ||
| 4 | The class used for comparing the position of configurations in the order of descending probabilities. | |
| 5 | ||
| 6 | ||
| 7 | \subsection*{Public Member Functions} | |
| 8 | \begin{DoxyCompactItemize} | |
| 9 | \item | |
| 10 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_order_adfed4b9c4e5dbd910de88057eb27fdf4}\label{class_iso_spec_1_1_iso_spec_1_1_conf_order_adfed4b9c4e5dbd910de88057eb27fdf4}} | |
| 11 | bool {\bfseries operator()} (void $\ast$conf1, void $\ast$conf2) const | |
| 12 | \end{DoxyCompactItemize} | |
| 13 | ||
| 14 | ||
| 15 | \subsection{Detailed Description} | |
| 16 | The class used for comparing the position of configurations in the order of descending probabilities. | |
| 17 | ||
| 18 | Needed for the priority queue. | |
| 19 | ||
| 20 | Definition at line 98 of file operators.\+cpp. | |
| 21 | ||
| 22 | ||
| 23 | ||
| 24 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 25 | \item | |
| 26 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal}{}\section{Iso\+Spec\+:\+:Iso\+Spec\+:\+:Conf\+Order\+Marginal Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal}\index{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal}} | |
| 2 | ||
| 3 | ||
| 4 | The class used for comparing the position of subisotopologues in the order of descending probabilities. | |
| 5 | ||
| 6 | ||
| 7 | \subsection*{Public Member Functions} | |
| 8 | \begin{DoxyCompactItemize} | |
| 9 | \item | |
| 10 | \mbox{\hyperlink{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_a91c7b8d57bcd751f08f064802f3c8b87}{Conf\+Order\+Marginal}} (const double $\ast$log\+Probs, int dim) | |
| 11 | \begin{DoxyCompactList}\small\item\em Constructor. \end{DoxyCompactList}\item | |
| 12 | bool \mbox{\hyperlink{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_a617a19a4c112750abde2153276c90612}{operator()}} (const Conf conf1, const Conf conf2) | |
| 13 | \begin{DoxyCompactList}\small\item\em Constructor. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 14 | ||
| 15 | ||
| 16 | \subsection{Detailed Description} | |
| 17 | The class used for comparing the position of subisotopologues in the order of descending probabilities. | |
| 18 | ||
| 19 | Needed for the priority queue. | |
| 20 | ||
| 21 | Definition at line 112 of file operators.\+cpp. | |
| 22 | ||
| 23 | ||
| 24 | ||
| 25 | \subsection{Constructor \& Destructor Documentation} | |
| 26 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_a91c7b8d57bcd751f08f064802f3c8b87}\label{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_a91c7b8d57bcd751f08f064802f3c8b87}} | |
| 27 | \index{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal}!Conf\+Order\+Marginal@{Conf\+Order\+Marginal}} | |
| 28 | \index{Conf\+Order\+Marginal@{Conf\+Order\+Marginal}!Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal}} | |
| 29 | \subsubsection{\texorpdfstring{Conf\+Order\+Marginal()}{ConfOrderMarginal()}} | |
| 30 | {\footnotesize\ttfamily Iso\+Spec\+::\+Conf\+Order\+Marginal\+::\+Conf\+Order\+Marginal (\begin{DoxyParamCaption}\item[{const double $\ast$}]{log\+Probs, }\item[{int}]{dim }\end{DoxyParamCaption})} | |
| 31 | ||
| 32 | ||
| 33 | ||
| 34 | Constructor. | |
| 35 | ||
| 36 | ||
| 37 | \begin{DoxyParams}{Parameters} | |
| 38 | {\em log\+Probs} & \\ | |
| 39 | \hline | |
| 40 | {\em dim} & The number of isotopes. \\ | |
| 41 | \hline | |
| 42 | \end{DoxyParams} | |
| 43 | ||
| 44 | ||
| 45 | Definition at line 30 of file operators.\+cpp. | |
| 46 | ||
| 47 | ||
| 48 | ||
| 49 | \subsection{Member Function Documentation} | |
| 50 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_a617a19a4c112750abde2153276c90612}\label{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_a617a19a4c112750abde2153276c90612}} | |
| 51 | \index{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal}!operator()@{operator()}} | |
| 52 | \index{operator()@{operator()}!Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal}} | |
| 53 | \subsubsection{\texorpdfstring{operator()()}{operator()()}} | |
| 54 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+::operator() (\begin{DoxyParamCaption}\item[{const Conf}]{conf1, }\item[{const Conf}]{conf2 }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} | |
| 55 | ||
| 56 | ||
| 57 | ||
| 58 | Constructor. | |
| 59 | ||
| 60 | ||
| 61 | \begin{DoxyParams}{Parameters} | |
| 62 | {\em conf1} & An array of integer counts. \\ | |
| 63 | \hline | |
| 64 | {\em conf2} & An array of integer counts. \\ | |
| 65 | \hline | |
| 66 | \end{DoxyParams} | |
| 67 | \begin{DoxyReturn}{Returns} | |
| 68 | True if conf1 is less probable than conf2. | |
| 69 | \end{DoxyReturn} | |
| 70 | ||
| 71 | ||
| 72 | Definition at line 130 of file operators.\+cpp. | |
| 73 | ||
| 74 | ||
| 75 | ||
| 76 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 77 | \item | |
| 78 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending}{}\section{Iso\+Spec\+:\+:Iso\+Spec\+:\+:Conf\+Order\+Marginal\+Descending Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending}\index{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}} | |
| 2 | ||
| 3 | ||
| 4 | The class used for comparing the position of subisotopologues in the order of descending probabilities. | |
| 5 | ||
| 6 | ||
| 7 | \subsection*{Public Member Functions} | |
| 8 | \begin{DoxyCompactItemize} | |
| 9 | \item | |
| 10 | \mbox{\hyperlink{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending_a331cca614490a25d2bf4d48e04a1eba3}{Conf\+Order\+Marginal\+Descending}} (const double $\ast$log\+Probs, int dim) | |
| 11 | \begin{DoxyCompactList}\small\item\em Contstructor. \end{DoxyCompactList}\item | |
| 12 | bool \mbox{\hyperlink{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending_a24753a23a4484aa1247606e15362dee0}{operator()}} (const Conf conf1, const Conf conf2) | |
| 13 | \begin{DoxyCompactList}\small\item\em Constructor. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 14 | ||
| 15 | ||
| 16 | \subsection{Detailed Description} | |
| 17 | The class used for comparing the position of subisotopologues in the order of descending probabilities. | |
| 18 | ||
| 19 | Needed for the priority queue. | |
| 20 | ||
| 21 | Definition at line 141 of file operators.\+cpp. | |
| 22 | ||
| 23 | ||
| 24 | ||
| 25 | \subsection{Constructor \& Destructor Documentation} | |
| 26 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending_a331cca614490a25d2bf4d48e04a1eba3}\label{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending_a331cca614490a25d2bf4d48e04a1eba3}} | |
| 27 | \index{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}!Conf\+Order\+Marginal\+Descending@{Conf\+Order\+Marginal\+Descending}} | |
| 28 | \index{Conf\+Order\+Marginal\+Descending@{Conf\+Order\+Marginal\+Descending}!Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}} | |
| 29 | \subsubsection{\texorpdfstring{Conf\+Order\+Marginal\+Descending()}{ConfOrderMarginalDescending()}} | |
| 30 | {\footnotesize\ttfamily Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending\+::\+Conf\+Order\+Marginal\+Descending (\begin{DoxyParamCaption}\item[{const double $\ast$}]{log\+Probs, }\item[{int}]{dim }\end{DoxyParamCaption})} | |
| 31 | ||
| 32 | ||
| 33 | ||
| 34 | Contstructor. | |
| 35 | ||
| 36 | ||
| 37 | \begin{DoxyParams}{Parameters} | |
| 38 | {\em log\+Probs} & \\ | |
| 39 | \hline | |
| 40 | {\em dim} & The number of isotopes. \\ | |
| 41 | \hline | |
| 42 | \end{DoxyParams} | |
| 43 | ||
| 44 | ||
| 45 | Definition at line 34 of file operators.\+cpp. | |
| 46 | ||
| 47 | ||
| 48 | ||
| 49 | \subsection{Member Function Documentation} | |
| 50 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending_a24753a23a4484aa1247606e15362dee0}\label{class_iso_spec_1_1_iso_spec_1_1_conf_order_marginal_descending_a24753a23a4484aa1247606e15362dee0}} | |
| 51 | \index{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}!operator()@{operator()}} | |
| 52 | \index{operator()@{operator()}!Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}} | |
| 53 | \subsubsection{\texorpdfstring{operator()()}{operator()()}} | |
| 54 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending\+::operator() (\begin{DoxyParamCaption}\item[{const Conf}]{conf1, }\item[{const Conf}]{conf2 }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} | |
| 55 | ||
| 56 | ||
| 57 | ||
| 58 | Constructor. | |
| 59 | ||
| 60 | ||
| 61 | \begin{DoxyParams}{Parameters} | |
| 62 | {\em conf1} & An array of integer counts. \\ | |
| 63 | \hline | |
| 64 | {\em conf2} & An array of integer counts. \\ | |
| 65 | \hline | |
| 66 | \end{DoxyParams} | |
| 67 | \begin{DoxyReturn}{Returns} | |
| 68 | True if conf1 is more probable than conf2. | |
| 69 | \end{DoxyReturn} | |
| 70 | ||
| 71 | ||
| 72 | Definition at line 160 of file operators.\+cpp. | |
| 73 | ||
| 74 | ||
| 75 | ||
| 76 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 77 | \item | |
| 78 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_iso_spec_1_1_key_hasher}{}\section{Iso\+Spec\+:\+:Iso\+Spec\+:\+:Key\+Hasher Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_spec_1_1_key_hasher}\index{Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher@{Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher}} | |
| 2 | ||
| 3 | ||
| 4 | The hash function class. | |
| 5 | ||
| 6 | ||
| 7 | \subsection*{Public Member Functions} | |
| 8 | \begin{DoxyCompactItemize} | |
| 9 | \item | |
| 10 | \mbox{\hyperlink{class_iso_spec_1_1_iso_spec_1_1_key_hasher_a094e6c2b6a3c9fa09b81187cbdf50de3}{Key\+Hasher}} (int dim) | |
| 11 | \begin{DoxyCompactList}\small\item\em Constructor. \end{DoxyCompactList}\item | |
| 12 | std\+::size\+\_\+t \mbox{\hyperlink{class_iso_spec_1_1_iso_spec_1_1_key_hasher_a4e3d55fd75979e5b725ad0112052f046}{operator()}} (const int $\ast$conf) const | |
| 13 | \begin{DoxyCompactList}\small\item\em The {\bfseries call} operator. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 14 | ||
| 15 | ||
| 16 | \subsection{Detailed Description} | |
| 17 | The hash function class. | |
| 18 | ||
| 19 | Needed for the unordered-\/map. | |
| 20 | ||
| 21 | Definition at line 31 of file operators.\+cpp. | |
| 22 | ||
| 23 | ||
| 24 | ||
| 25 | \subsection{Constructor \& Destructor Documentation} | |
| 26 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_key_hasher_a094e6c2b6a3c9fa09b81187cbdf50de3}\label{class_iso_spec_1_1_iso_spec_1_1_key_hasher_a094e6c2b6a3c9fa09b81187cbdf50de3}} | |
| 27 | \index{Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher@{Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher}!Key\+Hasher@{Key\+Hasher}} | |
| 28 | \index{Key\+Hasher@{Key\+Hasher}!Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher@{Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher}} | |
| 29 | \subsubsection{\texorpdfstring{Key\+Hasher()}{KeyHasher()}} | |
| 30 | {\footnotesize\ttfamily Iso\+Spec\+::\+Key\+Hasher\+::\+Key\+Hasher (\begin{DoxyParamCaption}\item[{int}]{dim }\end{DoxyParamCaption})} | |
| 31 | ||
| 32 | ||
| 33 | ||
| 34 | Constructor. | |
| 35 | ||
| 36 | ||
| 37 | \begin{DoxyParams}{Parameters} | |
| 38 | {\em dim} & the number of the ints that make up a configuration. \\ | |
| 39 | \hline | |
| 40 | \end{DoxyParams} | |
| 41 | ||
| 42 | ||
| 43 | Definition at line 22 of file operators.\+cpp. | |
| 44 | ||
| 45 | ||
| 46 | ||
| 47 | \subsection{Member Function Documentation} | |
| 48 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_key_hasher_a4e3d55fd75979e5b725ad0112052f046}\label{class_iso_spec_1_1_iso_spec_1_1_key_hasher_a4e3d55fd75979e5b725ad0112052f046}} | |
| 49 | \index{Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher@{Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher}!operator()@{operator()}} | |
| 50 | \index{operator()@{operator()}!Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher@{Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher}} | |
| 51 | \subsubsection{\texorpdfstring{operator()()}{operator()()}} | |
| 52 | {\footnotesize\ttfamily std\+::size\+\_\+t Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher\+::operator() (\begin{DoxyParamCaption}\item[{const int $\ast$}]{conf }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 53 | ||
| 54 | ||
| 55 | ||
| 56 | The {\bfseries call} operator. | |
| 57 | ||
| 58 | ||
| 59 | \begin{DoxyParams}{Parameters} | |
| 60 | {\em conf} & An array of integer counts. \\ | |
| 61 | \hline | |
| 62 | \end{DoxyParams} | |
| 63 | \begin{DoxyReturn}{Returns} | |
| 64 | The hash for counts. | |
| 65 | \end{DoxyReturn} | |
| 66 | ||
| 67 | ||
| 68 | Definition at line 47 of file operators.\+cpp. | |
| 69 | ||
| 70 | ||
| 71 | ||
| 72 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 73 | \item | |
| 74 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_iso_spec_1_1_reverse_order}{}\section{Iso\+Spec\+:\+:Iso\+Spec\+:\+:Reverse\+Order$<$ T $>$ Class Template Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_spec_1_1_reverse_order}\index{Iso\+Spec\+::\+Iso\+Spec\+::\+Reverse\+Order$<$ T $>$@{Iso\+Spec\+::\+Iso\+Spec\+::\+Reverse\+Order$<$ T $>$}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_reverse_order_a39761f0beb165c285ed1ed4b494e35a4}\label{class_iso_spec_1_1_iso_spec_1_1_reverse_order_a39761f0beb165c285ed1ed4b494e35a4}} | |
| 6 | bool {\bfseries operator()} (const T a, const T b) const | |
| 7 | \end{DoxyCompactItemize} | |
| 8 | ||
| 9 | ||
| 10 | \subsection{Detailed Description} | |
| 11 | \subsubsection*{template$<$typename T$>$\newline | |
| 12 | class Iso\+Spec\+::\+Iso\+Spec\+::\+Reverse\+Order$<$ T $>$} | |
| 13 | ||
| 14 | ||
| 15 | ||
| 16 | Definition at line 167 of file operators.\+cpp. | |
| 17 | ||
| 18 | ||
| 19 | ||
| 20 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 21 | \item | |
| 22 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_iso_spec_1_1_table_order}{}\section{Iso\+Spec\+:\+:Iso\+Spec\+:\+:Table\+Order$<$ T $>$ Class Template Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_spec_1_1_table_order}\index{Iso\+Spec\+::\+Iso\+Spec\+::\+Table\+Order$<$ T $>$@{Iso\+Spec\+::\+Iso\+Spec\+::\+Table\+Order$<$ T $>$}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_table_order_ad7f7ff01c71c3ba7308f8576dc7226c6}\label{class_iso_spec_1_1_iso_spec_1_1_table_order_ad7f7ff01c71c3ba7308f8576dc7226c6}} | |
| 6 | {\bfseries Table\+Order} (const T $\ast$\+\_\+tbl) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_spec_1_1_table_order_a0b952830050570f97ffd71137548c431}\label{class_iso_spec_1_1_iso_spec_1_1_table_order_a0b952830050570f97ffd71137548c431}} | |
| 9 | bool {\bfseries operator()} (unsigned int i, unsigned int j) | |
| 10 | \end{DoxyCompactItemize} | |
| 11 | ||
| 12 | ||
| 13 | \subsection{Detailed Description} | |
| 14 | \subsubsection*{template$<$typename T$>$\newline | |
| 15 | class Iso\+Spec\+::\+Iso\+Spec\+::\+Table\+Order$<$ T $>$} | |
| 16 | ||
| 17 | ||
| 18 | ||
| 19 | Definition at line 174 of file operators.\+cpp. | |
| 20 | ||
| 21 | ||
| 22 | ||
| 23 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 24 | \item | |
| 25 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
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| 143 | /vedge | |
| 144 | { | |
| 145 | /ye exch def | |
| 146 | /ys exch def | |
| 147 | /xs exch def | |
| 148 | newpath | |
| 149 | xs xspacing mul xoffset add boxwidth 2 div add dup | |
| 150 | ys yspacing mul boxheight 2 div sub | |
| 151 | moveto | |
| 152 | ye yspacing mul boxheight 2 div sub | |
| 153 | lineto | |
| 154 | stroke | |
| 155 | } def | |
| 156 | ||
| 157 | /conn % connections the blocks from col `arg1' to `arg2' of row `arg3' | |
| 158 | { | |
| 159 | /ys exch def | |
| 160 | /xe exch def | |
| 161 | /xs exch def | |
| 162 | newpath | |
| 163 | xs xspacing mul xoffset add boxwidth 2 div add | |
| 164 | ys yspacing mul disty 2 div sub | |
| 165 | moveto | |
| 166 | xspacing xe xs sub mul 0 | |
| 167 | rlineto | |
| 168 | stroke | |
| 169 | } def | |
| 170 | ||
| 171 | % ----- main ------ | |
| 172 | ||
| 173 | boxfont setfont | |
| 174 | 1 boundaspect scale | |
| 175 | (IsoSpec::IsoThresholdGenerator) cw | |
| 176 | (IsoSpec::IsoGenerator) cw | |
| 177 | (IsoSpec::Iso) cw | |
| 178 | /boxwidth boxwidth marginwidth 2 mul add def | |
| 179 | /xspacing boxwidth distx add def | |
| 180 | /yspacing boxheight disty add def | |
| 181 | /scalefactor | |
| 182 | boxwidth cols mul distx cols 1 sub mul add | |
| 183 | boxheight rows mul disty rows 1 sub mul add boundaspect mul | |
| 184 | max def | |
| 185 | boundx scalefactor div boundy scalefactor div scale | |
| 186 | ||
| 187 | % ----- classes ----- | |
| 188 | ||
| 189 | (IsoSpec::IsoThresholdGenerator) 0.000000 0.000000 box | |
| 190 | (IsoSpec::IsoGenerator) 0.000000 1.000000 box | |
| 191 | (IsoSpec::Iso) 0.000000 2.000000 box | |
| 192 | ||
| 193 | % ----- relations ----- | |
| 194 | ||
| 195 | solid | |
| 196 | 0 0.000000 0.000000 out | |
| 197 | solid | |
| 198 | 1 0.000000 1.000000 in | |
| 199 | solid | |
| 200 | 0 0.000000 1.000000 out | |
| 201 | solid | |
| 202 | 1 0.000000 2.000000 in |
| 0 | \hypertarget{class_iso_spec_1_1_iso_threshold_generator}{}\section{Iso\+Spec\+:\+:Iso\+Threshold\+Generator Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_threshold_generator}\index{Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}} | |
| 2 | ||
| 3 | ||
| 4 | The generator of isotopologues above a given threshold value. | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$iso\+Spec++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Iso\+Threshold\+Generator\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=3.000000cm]{class_iso_spec_1_1_iso_threshold_generator} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_a58699c4e68a846b979b8163bc6982e2c}\label{class_iso_spec_1_1_iso_threshold_generator_a58699c4e68a846b979b8163bc6982e2c}} | |
| 21 | void {\bfseries get\+\_\+conf\+\_\+signature} (int $\ast$space) const override final | |
| 22 | \item | |
| 23 | \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_a3abbcf1d810b6cad9400bd2552c3faf1}{Iso\+Threshold\+Generator}} (\mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&\&iso, double \+\_\+threshold, bool \+\_\+absolute=true, int \+\_\+tab\+Size=1000, int \+\_\+hash\+Size=1000, bool reorder\+\_\+marginals=true) | |
| 24 | \begin{DoxyCompactList}\small\item\em The move-\/constructor. \end{DoxyCompactList}\item | |
| 25 | I\+S\+O\+S\+P\+E\+C\+\_\+\+F\+O\+R\+C\+E\+\_\+\+I\+N\+L\+I\+NE bool \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_a7164a6476b84665967c4a667a91d3f3e}{advance\+To\+Next\+Configuration}} () override final | |
| 26 | \begin{DoxyCompactList}\small\item\em Advance to the next, not yet visited, most probable isotopologue. \end{DoxyCompactList}\item | |
| 27 | I\+S\+O\+S\+P\+E\+C\+\_\+\+F\+O\+R\+C\+E\+\_\+\+I\+N\+L\+I\+NE double \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_a4aeebde03e385404d0175fd5696ff529}{lprob}} () const override final | |
| 28 | \begin{DoxyCompactList}\small\item\em Get the log-\/probability of the current isotopologue. \end{DoxyCompactList}\item | |
| 29 | I\+S\+O\+S\+P\+E\+C\+\_\+\+F\+O\+R\+C\+E\+\_\+\+I\+N\+L\+I\+NE double \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_ae2236accc7dc7a25a723e3c7317659b6}{mass}} () const override final | |
| 30 | \begin{DoxyCompactList}\small\item\em Get the mass of the current isotopologue. \end{DoxyCompactList}\item | |
| 31 | I\+S\+O\+S\+P\+E\+C\+\_\+\+F\+O\+R\+C\+E\+\_\+\+I\+N\+L\+I\+NE double \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_a998d987f81b2ca7ed610294f6a5f8df5}{prob}} () const override final | |
| 32 | \begin{DoxyCompactList}\small\item\em Get the probability of the current isotopologue. \end{DoxyCompactList}\item | |
| 33 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_ac6aa2fff002a76b0beae1995f34ae5f6}\label{class_iso_spec_1_1_iso_threshold_generator_ac6aa2fff002a76b0beae1995f34ae5f6}} | |
| 34 | void \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_ac6aa2fff002a76b0beae1995f34ae5f6}{terminate\+\_\+search}} () | |
| 35 | \begin{DoxyCompactList}\small\item\em Block the subsequent search of isotopologues. \end{DoxyCompactList}\item | |
| 36 | void \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_ab830ffa21469df45a513ff1dcaf5d9e7}{reset}} () | |
| 37 | \item | |
| 38 | size\+\_\+t \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_ad29d8761174bca7b1846ddec03b33528}{count\+\_\+confs}} () | |
| 39 | \end{DoxyCompactItemize} | |
| 40 | \subsection*{Additional Inherited Members} | |
| 41 | ||
| 42 | ||
| 43 | \subsection{Detailed Description} | |
| 44 | The generator of isotopologues above a given threshold value. | |
| 45 | ||
| 46 | Attention\+: the calculated configurations are only partially ordeded and the user should not assume they will be ordered. This algorithm computes N isotopologues in O(\+N). It is a considerable advantage w.\+r.\+t. the \mbox{\hyperlink{class_iso_spec_1_1_iso_ordered_generator}{Iso\+Ordered\+Generator}}. | |
| 47 | ||
| 48 | Definition at line 235 of file iso\+Spec++.\+h. | |
| 49 | ||
| 50 | ||
| 51 | ||
| 52 | \subsection{Constructor \& Destructor Documentation} | |
| 53 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_a3abbcf1d810b6cad9400bd2552c3faf1}\label{class_iso_spec_1_1_iso_threshold_generator_a3abbcf1d810b6cad9400bd2552c3faf1}} | |
| 54 | \index{Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}!Iso\+Threshold\+Generator@{Iso\+Threshold\+Generator}} | |
| 55 | \index{Iso\+Threshold\+Generator@{Iso\+Threshold\+Generator}!Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}} | |
| 56 | \subsubsection{\texorpdfstring{Iso\+Threshold\+Generator()}{IsoThresholdGenerator()}} | |
| 57 | {\footnotesize\ttfamily Iso\+Spec\+::\+Iso\+Threshold\+Generator\+::\+Iso\+Threshold\+Generator (\begin{DoxyParamCaption}\item[{\mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&\&}]{iso, }\item[{double}]{\+\_\+threshold, }\item[{bool}]{\+\_\+absolute = {\ttfamily true}, }\item[{int}]{\+\_\+tab\+Size = {\ttfamily 1000}, }\item[{int}]{\+\_\+hash\+Size = {\ttfamily 1000}, }\item[{bool}]{reorder\+\_\+marginals = {\ttfamily true} }\end{DoxyParamCaption})} | |
| 58 | ||
| 59 | ||
| 60 | ||
| 61 | The move-\/constructor. | |
| 62 | ||
| 63 | ||
| 64 | \begin{DoxyParams}{Parameters} | |
| 65 | {\em iso} & An instance of the \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} class. \\ | |
| 66 | \hline | |
| 67 | {\em \+\_\+threshold} & The threshold value. \\ | |
| 68 | \hline | |
| 69 | {\em \+\_\+absolute} & If true, the \+\_\+threshold is interpreted as the absolute minimal peak height for the isotopologues. If false, the \+\_\+threshold is the fraction of the heighest peak\textquotesingle{}s probability. \\ | |
| 70 | \hline | |
| 71 | {\em tab\+Size} & The size of the extension of the table with configurations. \\ | |
| 72 | \hline | |
| 73 | {\em hash\+Size} & The size of the hash-\/table used to store subisotopologues and check if they have been already calculated. \\ | |
| 74 | \hline | |
| 75 | \end{DoxyParams} | |
| 76 | ||
| 77 | ||
| 78 | Definition at line 286 of file iso\+Spec++.\+cpp. | |
| 79 | ||
| 80 | ||
| 81 | ||
| 82 | \subsection{Member Function Documentation} | |
| 83 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_a7164a6476b84665967c4a667a91d3f3e}\label{class_iso_spec_1_1_iso_threshold_generator_a7164a6476b84665967c4a667a91d3f3e}} | |
| 84 | \index{Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}!advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}} | |
| 85 | \index{advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}!Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}} | |
| 86 | \subsubsection{\texorpdfstring{advance\+To\+Next\+Configuration()}{advanceToNextConfiguration()}} | |
| 87 | {\footnotesize\ttfamily I\+S\+O\+S\+P\+E\+C\+\_\+\+F\+O\+R\+C\+E\+\_\+\+I\+N\+L\+I\+NE bool Iso\+Spec\+::\+Iso\+Threshold\+Generator\+::advance\+To\+Next\+Configuration (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}, {\ttfamily [final]}, {\ttfamily [override]}, {\ttfamily [virtual]}} | |
| 88 | ||
| 89 | ||
| 90 | ||
| 91 | Advance to the next, not yet visited, most probable isotopologue. | |
| 92 | ||
| 93 | \begin{DoxyReturn}{Returns} | |
| 94 | Return false if it is not possible to advance. | |
| 95 | \end{DoxyReturn} | |
| 96 | ||
| 97 | ||
| 98 | Implements \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a20f48ba18c6aecc57d73b2c3ec3a11dd}{Iso\+Spec\+::\+Iso\+Generator}}. | |
| 99 | ||
| 100 | ||
| 101 | ||
| 102 | Definition at line 296 of file iso\+Spec++.\+h. | |
| 103 | ||
| 104 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_ad29d8761174bca7b1846ddec03b33528}\label{class_iso_spec_1_1_iso_threshold_generator_ad29d8761174bca7b1846ddec03b33528}} | |
| 105 | \index{Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}!count\+\_\+confs@{count\+\_\+confs}} | |
| 106 | \index{count\+\_\+confs@{count\+\_\+confs}!Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}} | |
| 107 | \subsubsection{\texorpdfstring{count\+\_\+confs()}{count\_confs()}} | |
| 108 | {\footnotesize\ttfamily size\+\_\+t Iso\+Spec\+::\+Iso\+Threshold\+Generator\+::count\+\_\+confs (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption})} | |
| 109 | ||
| 110 | Count the number of configurations in the distribution. This can be used to pre-\/allocate enough memory to store it (e.\+g. std\+::vector\textquotesingle{}s reserve() method -\/ this is faster than depending on the vector\textquotesingle{}s dynamic resizing, even though it means that the configuration space is walked through twice. This method has to be called before the first call to advance\+To\+Next\+Configuration and has undefined results (incl. segfaults) otherwise. | |
| 111 | ||
| 112 | Definition at line 376 of file iso\+Spec++.\+cpp. | |
| 113 | ||
| 114 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_a4aeebde03e385404d0175fd5696ff529}\label{class_iso_spec_1_1_iso_threshold_generator_a4aeebde03e385404d0175fd5696ff529}} | |
| 115 | \index{Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}!lprob@{lprob}} | |
| 116 | \index{lprob@{lprob}!Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}} | |
| 117 | \subsubsection{\texorpdfstring{lprob()}{lprob()}} | |
| 118 | {\footnotesize\ttfamily I\+S\+O\+S\+P\+E\+C\+\_\+\+F\+O\+R\+C\+E\+\_\+\+I\+N\+L\+I\+NE double Iso\+Spec\+::\+Iso\+Threshold\+Generator\+::lprob (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}, {\ttfamily [final]}, {\ttfamily [override]}, {\ttfamily [virtual]}} | |
| 119 | ||
| 120 | ||
| 121 | ||
| 122 | Get the log-\/probability of the current isotopologue. | |
| 123 | ||
| 124 | \begin{DoxyReturn}{Returns} | |
| 125 | The log-\/probability of the current isotopologue. | |
| 126 | \end{DoxyReturn} | |
| 127 | ||
| 128 | ||
| 129 | Reimplemented from \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_ae8e24abbce51a4c93994f630acfdf383}{Iso\+Spec\+::\+Iso\+Generator}}. | |
| 130 | ||
| 131 | ||
| 132 | ||
| 133 | Definition at line 335 of file iso\+Spec++.\+h. | |
| 134 | ||
| 135 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_ae2236accc7dc7a25a723e3c7317659b6}\label{class_iso_spec_1_1_iso_threshold_generator_ae2236accc7dc7a25a723e3c7317659b6}} | |
| 136 | \index{Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}!mass@{mass}} | |
| 137 | \index{mass@{mass}!Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}} | |
| 138 | \subsubsection{\texorpdfstring{mass()}{mass()}} | |
| 139 | {\footnotesize\ttfamily I\+S\+O\+S\+P\+E\+C\+\_\+\+F\+O\+R\+C\+E\+\_\+\+I\+N\+L\+I\+NE double Iso\+Spec\+::\+Iso\+Threshold\+Generator\+::mass (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}, {\ttfamily [final]}, {\ttfamily [override]}, {\ttfamily [virtual]}} | |
| 140 | ||
| 141 | ||
| 142 | ||
| 143 | Get the mass of the current isotopologue. | |
| 144 | ||
| 145 | \begin{DoxyReturn}{Returns} | |
| 146 | The mass of the current isotopologue. | |
| 147 | \end{DoxyReturn} | |
| 148 | ||
| 149 | ||
| 150 | Reimplemented from \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a34173228ef73e272e2ff0ae6ce58092d}{Iso\+Spec\+::\+Iso\+Generator}}. | |
| 151 | ||
| 152 | ||
| 153 | ||
| 154 | Definition at line 336 of file iso\+Spec++.\+h. | |
| 155 | ||
| 156 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_a998d987f81b2ca7ed610294f6a5f8df5}\label{class_iso_spec_1_1_iso_threshold_generator_a998d987f81b2ca7ed610294f6a5f8df5}} | |
| 157 | \index{Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}!prob@{prob}} | |
| 158 | \index{prob@{prob}!Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}} | |
| 159 | \subsubsection{\texorpdfstring{prob()}{prob()}} | |
| 160 | {\footnotesize\ttfamily I\+S\+O\+S\+P\+E\+C\+\_\+\+F\+O\+R\+C\+E\+\_\+\+I\+N\+L\+I\+NE double Iso\+Spec\+::\+Iso\+Threshold\+Generator\+::prob (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}, {\ttfamily [final]}, {\ttfamily [override]}, {\ttfamily [virtual]}} | |
| 161 | ||
| 162 | ||
| 163 | ||
| 164 | Get the probability of the current isotopologue. | |
| 165 | ||
| 166 | \begin{DoxyReturn}{Returns} | |
| 167 | The probability of the current isotopologue. | |
| 168 | \end{DoxyReturn} | |
| 169 | ||
| 170 | ||
| 171 | Reimplemented from \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_aecf1b3292fcc0857a86efe619a37fff0}{Iso\+Spec\+::\+Iso\+Generator}}. | |
| 172 | ||
| 173 | ||
| 174 | ||
| 175 | Definition at line 337 of file iso\+Spec++.\+h. | |
| 176 | ||
| 177 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_ab830ffa21469df45a513ff1dcaf5d9e7}\label{class_iso_spec_1_1_iso_threshold_generator_ab830ffa21469df45a513ff1dcaf5d9e7}} | |
| 178 | \index{Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}!reset@{reset}} | |
| 179 | \index{reset@{reset}!Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}} | |
| 180 | \subsubsection{\texorpdfstring{reset()}{reset()}} | |
| 181 | {\footnotesize\ttfamily void Iso\+Spec\+::\+Iso\+Threshold\+Generator\+::reset (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption})} | |
| 182 | ||
| 183 | Reset the generator to the beginning of the sequence. Allows it to be reused, eg. to go through the conf space once, calculate the amount of space needed to store configurations, then to allocate that memory, and go through it again, this time saving configurations (and {\itshape is} in fact faster than allocating a std\+::vector and depending on it to grow as needed. This is cheaper than throwing away the generator and making a new one too\+: marginal distributions don\textquotesingle{}t need to be recalculated. | |
| 184 | ||
| 185 | Definition at line 386 of file iso\+Spec++.\+cpp. | |
| 186 | ||
| 187 | ||
| 188 | ||
| 189 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 190 | \item | |
| 191 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+h\item | |
| 192 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+cpp\end{DoxyCompactItemize} |
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| 12 | ||
| 13 | % ----- variables ----- | |
| 14 | ||
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| 16 | /boxheight 40 def | |
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| 19 | /distx 20 def | |
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| 58 | newpath | |
| 59 | exch xspacing mul xoffset add | |
| 60 | exch yspacing mul | |
| 61 | moveto | |
| 62 | boxwidth 0 rlineto | |
| 63 | 0 boxheight rlineto | |
| 64 | boxwidth neg 0 rlineto | |
| 65 | 0 boxheight neg rlineto | |
| 66 | closepath | |
| 67 | dup stringwidth pop neg boxwidth add 2 div | |
| 68 | boxheight fontheight 2 div sub 2 div | |
| 69 | rmoveto show stroke | |
| 70 | grestore | |
| 71 | } def | |
| 72 | ||
| 73 | /mark | |
| 74 | { newpath | |
| 75 | exch xspacing mul xoffset add boxwidth add | |
| 76 | exch yspacing mul | |
| 77 | moveto | |
| 78 | 0 boxheight 4 div rlineto | |
| 79 | boxheight neg 4 div boxheight neg 4 div rlineto | |
| 80 | closepath | |
| 81 | eofill | |
| 82 | stroke | |
| 83 | } def | |
| 84 | ||
| 85 | /arrow | |
| 86 | { newpath | |
| 87 | moveto | |
| 88 | 3 -8 rlineto | |
| 89 | -6 0 rlineto | |
| 90 | 3 8 rlineto | |
| 91 | closepath | |
| 92 | eofill | |
| 93 | stroke | |
| 94 | } def | |
| 95 | ||
| 96 | /out % draws an output connector for the block at (arg1,arg2) | |
| 97 | { | |
| 98 | newpath | |
| 99 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 100 | exch yspacing mul boxheight add | |
| 101 | /y exch def | |
| 102 | /x exch def | |
| 103 | x y moveto | |
| 104 | 0 disty 2 div rlineto | |
| 105 | stroke | |
| 106 | 1 eq { x y disty 2 div add arrow } if | |
| 107 | } def | |
| 108 | ||
| 109 | /in % draws an input connector for the block at (arg1,arg2) | |
| 110 | { | |
| 111 | newpath | |
| 112 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 113 | exch yspacing mul disty 2 div sub | |
| 114 | /y exch def | |
| 115 | /x exch def | |
| 116 | x y moveto | |
| 117 | 0 disty 2 div rlineto | |
| 118 | stroke | |
| 119 | 1 eq { x y disty 2 div add arrow } if | |
| 120 | } def | |
| 121 | ||
| 122 | /hedge | |
| 123 | { | |
| 124 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 125 | exch yspacing mul boxheight 2 div sub | |
| 126 | /y exch def | |
| 127 | /x exch def | |
| 128 | newpath | |
| 129 | x y moveto | |
| 130 | boxwidth 2 div distx add 0 rlineto | |
| 131 | stroke | |
| 132 | 1 eq | |
| 133 | { newpath x boxwidth 2 div distx add add y moveto | |
| 134 | -8 3 rlineto | |
| 135 | 0 -6 rlineto | |
| 136 | 8 3 rlineto | |
| 137 | closepath | |
| 138 | eofill | |
| 139 | stroke | |
| 140 | } if | |
| 141 | } def | |
| 142 | ||
| 143 | /vedge | |
| 144 | { | |
| 145 | /ye exch def | |
| 146 | /ys exch def | |
| 147 | /xs exch def | |
| 148 | newpath | |
| 149 | xs xspacing mul xoffset add boxwidth 2 div add dup | |
| 150 | ys yspacing mul boxheight 2 div sub | |
| 151 | moveto | |
| 152 | ye yspacing mul boxheight 2 div sub | |
| 153 | lineto | |
| 154 | stroke | |
| 155 | } def | |
| 156 | ||
| 157 | /conn % connections the blocks from col `arg1' to `arg2' of row `arg3' | |
| 158 | { | |
| 159 | /ys exch def | |
| 160 | /xe exch def | |
| 161 | /xs exch def | |
| 162 | newpath | |
| 163 | xs xspacing mul xoffset add boxwidth 2 div add | |
| 164 | ys yspacing mul disty 2 div sub | |
| 165 | moveto | |
| 166 | xspacing xe xs sub mul 0 | |
| 167 | rlineto | |
| 168 | stroke | |
| 169 | } def | |
| 170 | ||
| 171 | % ----- main ------ | |
| 172 | ||
| 173 | boxfont setfont | |
| 174 | 1 boundaspect scale | |
| 175 | (IsoSpec::IsoThresholdGeneratorMT) cw | |
| 176 | (IsoSpec::IsoGenerator) cw | |
| 177 | (IsoSpec::Iso) cw | |
| 178 | /boxwidth boxwidth marginwidth 2 mul add def | |
| 179 | /xspacing boxwidth distx add def | |
| 180 | /yspacing boxheight disty add def | |
| 181 | /scalefactor | |
| 182 | boxwidth cols mul distx cols 1 sub mul add | |
| 183 | boxheight rows mul disty rows 1 sub mul add boundaspect mul | |
| 184 | max def | |
| 185 | boundx scalefactor div boundy scalefactor div scale | |
| 186 | ||
| 187 | % ----- classes ----- | |
| 188 | ||
| 189 | (IsoSpec::IsoThresholdGeneratorMT) 0.000000 0.000000 box | |
| 190 | (IsoSpec::IsoGenerator) 0.000000 1.000000 box | |
| 191 | (IsoSpec::Iso) 0.000000 2.000000 box | |
| 192 | ||
| 193 | % ----- relations ----- | |
| 194 | ||
| 195 | solid | |
| 196 | 0 0.000000 0.000000 out | |
| 197 | solid | |
| 198 | 1 0.000000 1.000000 in | |
| 199 | solid | |
| 200 | 0 0.000000 1.000000 out | |
| 201 | solid | |
| 202 | 1 0.000000 2.000000 in |
| 0 | \hypertarget{class_iso_spec_1_1_iso_threshold_generator_m_t}{}\section{Iso\+Spec\+:\+:Iso\+Threshold\+Generator\+MT Class Reference} | |
| 1 | \label{class_iso_spec_1_1_iso_threshold_generator_m_t}\index{Iso\+Spec\+::\+Iso\+Threshold\+Generator\+MT@{Iso\+Spec\+::\+Iso\+Threshold\+Generator\+MT}} | |
| 2 | ||
| 3 | ||
| 4 | The multi-\/threaded version of the generator of isotopologues. | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$iso\+Spec++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Iso\+Threshold\+Generator\+MT\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=3.000000cm]{class_iso_spec_1_1_iso_threshold_generator_m_t} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | bool \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_m_t_ab82a60de126aa926b2baf67c49015c22}{advance\+To\+Next\+Configuration}} () override final | |
| 21 | \begin{DoxyCompactList}\small\item\em Advance to the next, not yet visited, most probable isotopologue. \end{DoxyCompactList}\item | |
| 22 | void \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_m_t_a7c398ea67338f0d446de73ec6670dbf5}{get\+\_\+conf\+\_\+signature}} (int $\ast$space) const override final | |
| 23 | \begin{DoxyCompactList}\small\item\em Save the counts of isotopes in the space. \end{DoxyCompactList}\item | |
| 24 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_m_t_a557fc9c693ddd9980151ff6250f80fc0}\label{class_iso_spec_1_1_iso_threshold_generator_m_t_a557fc9c693ddd9980151ff6250f80fc0}} | |
| 25 | \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_m_t_a557fc9c693ddd9980151ff6250f80fc0}{Iso\+Threshold\+Generator\+MT}} (\mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} \&\&iso, double \+\_\+threshold, \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal}{Precalculated\+Marginal}} $\ast$$\ast$\mbox{\hyperlink{class_iso_spec_1_1_iso_aea98a8331a2f8a1a6bbcace6124fcfae}{marginals}}, bool \+\_\+absolute=true) | |
| 26 | \begin{DoxyCompactList}\small\item\em Move constructor. \end{DoxyCompactList}\item | |
| 27 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_m_t_a761bc9e2421c3098cf55c800ddc9908c}\label{class_iso_spec_1_1_iso_threshold_generator_m_t_a761bc9e2421c3098cf55c800ddc9908c}} | |
| 28 | virtual \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_m_t_a761bc9e2421c3098cf55c800ddc9908c}{$\sim$\+Iso\+Threshold\+Generator\+MT}} () | |
| 29 | \begin{DoxyCompactList}\small\item\em Destructor. \end{DoxyCompactList}\item | |
| 30 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_m_t_a43d32039cf98798ea3b0b347673fe6ad}\label{class_iso_spec_1_1_iso_threshold_generator_m_t_a43d32039cf98798ea3b0b347673fe6ad}} | |
| 31 | void \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator_m_t_a43d32039cf98798ea3b0b347673fe6ad}{terminate\+\_\+search}} () | |
| 32 | \begin{DoxyCompactList}\small\item\em Block the subsequent search of isotopologues. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 33 | \subsection*{Additional Inherited Members} | |
| 34 | ||
| 35 | ||
| 36 | \subsection{Detailed Description} | |
| 37 | The multi-\/threaded version of the generator of isotopologues. | |
| 38 | ||
| 39 | Attention\+: this code is experimental. | |
| 40 | ||
| 41 | Definition at line 305 of file iso\+Spec++.\+h. | |
| 42 | ||
| 43 | ||
| 44 | ||
| 45 | \subsection{Member Function Documentation} | |
| 46 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_m_t_ab82a60de126aa926b2baf67c49015c22}\label{class_iso_spec_1_1_iso_threshold_generator_m_t_ab82a60de126aa926b2baf67c49015c22}} | |
| 47 | \index{Iso\+Spec\+::\+Iso\+Threshold\+Generator\+MT@{Iso\+Spec\+::\+Iso\+Threshold\+Generator\+MT}!advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}} | |
| 48 | \index{advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}!Iso\+Spec\+::\+Iso\+Threshold\+Generator\+MT@{Iso\+Spec\+::\+Iso\+Threshold\+Generator\+MT}} | |
| 49 | \subsubsection{\texorpdfstring{advance\+To\+Next\+Configuration()}{advanceToNextConfiguration()}} | |
| 50 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Iso\+Threshold\+Generator\+M\+T\+::advance\+To\+Next\+Configuration (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [final]}, {\ttfamily [override]}, {\ttfamily [virtual]}} | |
| 51 | ||
| 52 | ||
| 53 | ||
| 54 | Advance to the next, not yet visited, most probable isotopologue. | |
| 55 | ||
| 56 | \begin{DoxyReturn}{Returns} | |
| 57 | Return false if it is not possible to advance. | |
| 58 | \end{DoxyReturn} | |
| 59 | ||
| 60 | ||
| 61 | Implements \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a20f48ba18c6aecc57d73b2c3ec3a11dd}{Iso\+Spec\+::\+Iso\+Generator}}. | |
| 62 | ||
| 63 | ||
| 64 | ||
| 65 | Definition at line 354 of file iso\+Spec++.\+cpp. | |
| 66 | ||
| 67 | \mbox{\Hypertarget{class_iso_spec_1_1_iso_threshold_generator_m_t_a7c398ea67338f0d446de73ec6670dbf5}\label{class_iso_spec_1_1_iso_threshold_generator_m_t_a7c398ea67338f0d446de73ec6670dbf5}} | |
| 68 | \index{Iso\+Spec\+::\+Iso\+Threshold\+Generator\+MT@{Iso\+Spec\+::\+Iso\+Threshold\+Generator\+MT}!get\+\_\+conf\+\_\+signature@{get\+\_\+conf\+\_\+signature}} | |
| 69 | \index{get\+\_\+conf\+\_\+signature@{get\+\_\+conf\+\_\+signature}!Iso\+Spec\+::\+Iso\+Threshold\+Generator\+MT@{Iso\+Spec\+::\+Iso\+Threshold\+Generator\+MT}} | |
| 70 | \subsubsection{\texorpdfstring{get\+\_\+conf\+\_\+signature()}{get\_conf\_signature()}} | |
| 71 | {\footnotesize\ttfamily void Iso\+Spec\+::\+Iso\+Threshold\+Generator\+M\+T\+::get\+\_\+conf\+\_\+signature (\begin{DoxyParamCaption}\item[{int $\ast$}]{space }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}, {\ttfamily [final]}, {\ttfamily [override]}, {\ttfamily [virtual]}} | |
| 72 | ||
| 73 | ||
| 74 | ||
| 75 | Save the counts of isotopes in the space. | |
| 76 | ||
| 77 | ||
| 78 | \begin{DoxyParams}{Parameters} | |
| 79 | {\em space} & An array where counts of isotopes shall be written. Must be as big as the overall number of isotopes. \\ | |
| 80 | \hline | |
| 81 | \end{DoxyParams} | |
| 82 | ||
| 83 | ||
| 84 | Implements \mbox{\hyperlink{class_iso_spec_1_1_iso_generator_a19ca8af7dd97f8f37756d4267d49d91d}{Iso\+Spec\+::\+Iso\+Generator}}. | |
| 85 | ||
| 86 | ||
| 87 | ||
| 88 | Definition at line 316 of file iso\+Spec++.\+h. | |
| 89 | ||
| 90 | ||
| 91 | ||
| 92 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 93 | \item | |
| 94 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+h\item | |
| 95 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/iso\+Spec++.\+cpp\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_key_hasher}{}\section{Iso\+Spec\+:\+:Key\+Hasher Class Reference} | |
| 1 | \label{class_iso_spec_1_1_key_hasher}\index{Iso\+Spec\+::\+Key\+Hasher@{Iso\+Spec\+::\+Key\+Hasher}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_key_hasher_a094e6c2b6a3c9fa09b81187cbdf50de3}\label{class_iso_spec_1_1_key_hasher_a094e6c2b6a3c9fa09b81187cbdf50de3}} | |
| 6 | {\bfseries Key\+Hasher} (int dim) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_key_hasher_a32c10222b6c45a5f0f290821c476e83f}\label{class_iso_spec_1_1_key_hasher_a32c10222b6c45a5f0f290821c476e83f}} | |
| 9 | std\+::size\+\_\+t {\bfseries operator()} (const int $\ast$conf) const | |
| 10 | \end{DoxyCompactItemize} | |
| 11 | ||
| 12 | ||
| 13 | \subsection{Detailed Description} | |
| 14 | ||
| 15 | ||
| 16 | Definition at line 27 of file operators.\+h. | |
| 17 | ||
| 18 | ||
| 19 | ||
| 20 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 21 | \item | |
| 22 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+h\item | |
| 23 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+cpp\end{DoxyCompactItemize} |
| 0 | %!PS-Adobe-2.0 EPSF-2.0 | |
| 1 | %%Title: ClassName | |
| 2 | %%Creator: Doxygen | |
| 3 | %%CreationDate: Time | |
| 4 | %%For: | |
| 5 | %Magnification: 1.00 | |
| 6 | %%Orientation: Portrait | |
| 7 | %%BoundingBox: 0 0 500 238.095238 | |
| 8 | %%Pages: 0 | |
| 9 | %%BeginSetup | |
| 10 | %%EndSetup | |
| 11 | %%EndComments | |
| 12 | ||
| 13 | % ----- variables ----- | |
| 14 | ||
| 15 | /boxwidth 0 def | |
| 16 | /boxheight 40 def | |
| 17 | /fontheight 24 def | |
| 18 | /marginwidth 10 def | |
| 19 | /distx 20 def | |
| 20 | /disty 40 def | |
| 21 | /boundaspect 2.100000 def % aspect ratio of the BoundingBox (width/height) | |
| 22 | /boundx 500 def | |
| 23 | /boundy boundx boundaspect div def | |
| 24 | /xspacing 0 def | |
| 25 | /yspacing 0 def | |
| 26 | /rows 2 def | |
| 27 | /cols 1 def | |
| 28 | /scalefactor 0 def | |
| 29 | /boxfont /Times-Roman findfont fontheight scalefont def | |
| 30 | ||
| 31 | % ----- procedures ----- | |
| 32 | ||
| 33 | /dotted { [1 4] 0 setdash } def | |
| 34 | /dashed { [5] 0 setdash } def | |
| 35 | /solid { [] 0 setdash } def | |
| 36 | ||
| 37 | /max % result = MAX(arg1,arg2) | |
| 38 | { | |
| 39 | /a exch def | |
| 40 | /b exch def | |
| 41 | a b gt {a} {b} ifelse | |
| 42 | } def | |
| 43 | ||
| 44 | /xoffset % result = MAX(0,(scalefactor-(boxwidth*cols+distx*(cols-1)))/2) | |
| 45 | { | |
| 46 | 0 scalefactor boxwidth cols mul distx cols 1 sub mul add sub 2 div max | |
| 47 | } def | |
| 48 | ||
| 49 | /cw % boxwidth = MAX(boxwidth, stringwidth(arg1)) | |
| 50 | { | |
| 51 | /str exch def | |
| 52 | /boxwidth boxwidth str stringwidth pop max def | |
| 53 | } def | |
| 54 | ||
| 55 | /box % draws a box with text `arg1' at grid pos (arg2,arg3) | |
| 56 | { gsave | |
| 57 | 2 setlinewidth | |
| 58 | newpath | |
| 59 | exch xspacing mul xoffset add | |
| 60 | exch yspacing mul | |
| 61 | moveto | |
| 62 | boxwidth 0 rlineto | |
| 63 | 0 boxheight rlineto | |
| 64 | boxwidth neg 0 rlineto | |
| 65 | 0 boxheight neg rlineto | |
| 66 | closepath | |
| 67 | dup stringwidth pop neg boxwidth add 2 div | |
| 68 | boxheight fontheight 2 div sub 2 div | |
| 69 | rmoveto show stroke | |
| 70 | grestore | |
| 71 | } def | |
| 72 | ||
| 73 | /mark | |
| 74 | { newpath | |
| 75 | exch xspacing mul xoffset add boxwidth add | |
| 76 | exch yspacing mul | |
| 77 | moveto | |
| 78 | 0 boxheight 4 div rlineto | |
| 79 | boxheight neg 4 div boxheight neg 4 div rlineto | |
| 80 | closepath | |
| 81 | eofill | |
| 82 | stroke | |
| 83 | } def | |
| 84 | ||
| 85 | /arrow | |
| 86 | { newpath | |
| 87 | moveto | |
| 88 | 3 -8 rlineto | |
| 89 | -6 0 rlineto | |
| 90 | 3 8 rlineto | |
| 91 | closepath | |
| 92 | eofill | |
| 93 | stroke | |
| 94 | } def | |
| 95 | ||
| 96 | /out % draws an output connector for the block at (arg1,arg2) | |
| 97 | { | |
| 98 | newpath | |
| 99 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 100 | exch yspacing mul boxheight add | |
| 101 | /y exch def | |
| 102 | /x exch def | |
| 103 | x y moveto | |
| 104 | 0 disty 2 div rlineto | |
| 105 | stroke | |
| 106 | 1 eq { x y disty 2 div add arrow } if | |
| 107 | } def | |
| 108 | ||
| 109 | /in % draws an input connector for the block at (arg1,arg2) | |
| 110 | { | |
| 111 | newpath | |
| 112 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 113 | exch yspacing mul disty 2 div sub | |
| 114 | /y exch def | |
| 115 | /x exch def | |
| 116 | x y moveto | |
| 117 | 0 disty 2 div rlineto | |
| 118 | stroke | |
| 119 | 1 eq { x y disty 2 div add arrow } if | |
| 120 | } def | |
| 121 | ||
| 122 | /hedge | |
| 123 | { | |
| 124 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 125 | exch yspacing mul boxheight 2 div sub | |
| 126 | /y exch def | |
| 127 | /x exch def | |
| 128 | newpath | |
| 129 | x y moveto | |
| 130 | boxwidth 2 div distx add 0 rlineto | |
| 131 | stroke | |
| 132 | 1 eq | |
| 133 | { newpath x boxwidth 2 div distx add add y moveto | |
| 134 | -8 3 rlineto | |
| 135 | 0 -6 rlineto | |
| 136 | 8 3 rlineto | |
| 137 | closepath | |
| 138 | eofill | |
| 139 | stroke | |
| 140 | } if | |
| 141 | } def | |
| 142 | ||
| 143 | /vedge | |
| 144 | { | |
| 145 | /ye exch def | |
| 146 | /ys exch def | |
| 147 | /xs exch def | |
| 148 | newpath | |
| 149 | xs xspacing mul xoffset add boxwidth 2 div add dup | |
| 150 | ys yspacing mul boxheight 2 div sub | |
| 151 | moveto | |
| 152 | ye yspacing mul boxheight 2 div sub | |
| 153 | lineto | |
| 154 | stroke | |
| 155 | } def | |
| 156 | ||
| 157 | /conn % connections the blocks from col `arg1' to `arg2' of row `arg3' | |
| 158 | { | |
| 159 | /ys exch def | |
| 160 | /xe exch def | |
| 161 | /xs exch def | |
| 162 | newpath | |
| 163 | xs xspacing mul xoffset add boxwidth 2 div add | |
| 164 | ys yspacing mul disty 2 div sub | |
| 165 | moveto | |
| 166 | xspacing xe xs sub mul 0 | |
| 167 | rlineto | |
| 168 | stroke | |
| 169 | } def | |
| 170 | ||
| 171 | % ----- main ------ | |
| 172 | ||
| 173 | boxfont setfont | |
| 174 | 1 boundaspect scale | |
| 175 | (IsoSpec::LayeredMarginal) cw | |
| 176 | (IsoSpec::Marginal) cw | |
| 177 | /boxwidth boxwidth marginwidth 2 mul add def | |
| 178 | /xspacing boxwidth distx add def | |
| 179 | /yspacing boxheight disty add def | |
| 180 | /scalefactor | |
| 181 | boxwidth cols mul distx cols 1 sub mul add | |
| 182 | boxheight rows mul disty rows 1 sub mul add boundaspect mul | |
| 183 | max def | |
| 184 | boundx scalefactor div boundy scalefactor div scale | |
| 185 | ||
| 186 | % ----- classes ----- | |
| 187 | ||
| 188 | (IsoSpec::LayeredMarginal) 0.000000 0.000000 box | |
| 189 | (IsoSpec::Marginal) 0.000000 1.000000 box | |
| 190 | ||
| 191 | % ----- relations ----- | |
| 192 | ||
| 193 | solid | |
| 194 | 0 0.000000 0.000000 out | |
| 195 | solid | |
| 196 | 1 0.000000 1.000000 in |
| 0 | \hypertarget{class_iso_spec_1_1_layered_marginal}{}\section{Iso\+Spec\+:\+:Layered\+Marginal Class Reference} | |
| 1 | \label{class_iso_spec_1_1_layered_marginal}\index{Iso\+Spec\+::\+Layered\+Marginal@{Iso\+Spec\+::\+Layered\+Marginal}} | |
| 2 | ||
| 3 | ||
| 4 | \mbox{\hyperlink{class_iso_spec_1_1_layered_marginal}{Layered\+Marginal}} class. | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$marginal\+Trek++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Layered\+Marginal\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=2.000000cm]{class_iso_spec_1_1_layered_marginal} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | \mbox{\hyperlink{class_iso_spec_1_1_layered_marginal_af062d180664c9c856b4cc72e3457ca9d}{Layered\+Marginal}} (\mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \&\&m, int tab\+Size=1000, int hash\+Size=1000) | |
| 21 | \begin{DoxyCompactList}\small\item\em Move constructor\+: specializes the \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} class. \end{DoxyCompactList}\item | |
| 22 | bool \mbox{\hyperlink{class_iso_spec_1_1_layered_marginal_ab8b66ed79bad27183f98a9ae34c3b944}{extend}} (double new\+\_\+threshold) | |
| 23 | \begin{DoxyCompactList}\small\item\em Extend the set of computed subisotopologues to those above the new threshold. \end{DoxyCompactList}\item | |
| 24 | \mbox{\Hypertarget{class_iso_spec_1_1_layered_marginal_aec04c0f0e00a24d151be39ab46267b4c}\label{class_iso_spec_1_1_layered_marginal_aec04c0f0e00a24d151be39ab46267b4c}} | |
| 25 | double \mbox{\hyperlink{class_iso_spec_1_1_layered_marginal_aec04c0f0e00a24d151be39ab46267b4c}{get\+\_\+l\+Prob}} (int idx) const | |
| 26 | \begin{DoxyCompactList}\small\item\em get the log-\/probability of the idx-\/th subisotopologue, see details in \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a07eee6d60635c9c1d6f92c181994e06a}{Precalculated\+Marginal\+::get\+\_\+l\+Prob}}. \end{DoxyCompactList}\item | |
| 27 | \mbox{\Hypertarget{class_iso_spec_1_1_layered_marginal_a3c0a5ce02f00680fc67211c66761e887}\label{class_iso_spec_1_1_layered_marginal_a3c0a5ce02f00680fc67211c66761e887}} | |
| 28 | double \mbox{\hyperlink{class_iso_spec_1_1_layered_marginal_a3c0a5ce02f00680fc67211c66761e887}{get\+\_\+e\+Prob}} (int idx) const | |
| 29 | \begin{DoxyCompactList}\small\item\em get the probability of the idx-\/th subisotopologue, see details in \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a7a38a567eadf16fa2ad41e81c8f55c02}{Precalculated\+Marginal\+::get\+\_\+e\+Prob}}. \end{DoxyCompactList}\item | |
| 30 | \mbox{\Hypertarget{class_iso_spec_1_1_layered_marginal_a0323521e0435172c1f4a4ccd0168668d}\label{class_iso_spec_1_1_layered_marginal_a0323521e0435172c1f4a4ccd0168668d}} | |
| 31 | double \mbox{\hyperlink{class_iso_spec_1_1_layered_marginal_a0323521e0435172c1f4a4ccd0168668d}{get\+\_\+mass}} (int idx) const | |
| 32 | \begin{DoxyCompactList}\small\item\em get the mass of the idx-\/th subisotopologue, see details in \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_ada12caa2e195c1a16c5158a428ea3ed2}{Precalculated\+Marginal\+::get\+\_\+mass}}. \end{DoxyCompactList}\item | |
| 33 | \mbox{\Hypertarget{class_iso_spec_1_1_layered_marginal_abfb6c79d8bdcf4b50f8942f7f8a21de5}\label{class_iso_spec_1_1_layered_marginal_abfb6c79d8bdcf4b50f8942f7f8a21de5}} | |
| 34 | const Conf \& \mbox{\hyperlink{class_iso_spec_1_1_layered_marginal_abfb6c79d8bdcf4b50f8942f7f8a21de5}{get\+\_\+conf}} (int idx) const | |
| 35 | \begin{DoxyCompactList}\small\item\em get the counts of isotopes that define the subisotopologue, see details in \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a3ecbbf1263a274cc8e3bc71cd96f0bff}{Precalculated\+Marginal\+::get\+\_\+conf}}. \end{DoxyCompactList}\item | |
| 36 | \mbox{\Hypertarget{class_iso_spec_1_1_layered_marginal_aa15967c22941783e5e59f20544434fb1}\label{class_iso_spec_1_1_layered_marginal_aa15967c22941783e5e59f20544434fb1}} | |
| 37 | unsigned int \mbox{\hyperlink{class_iso_spec_1_1_layered_marginal_aa15967c22941783e5e59f20544434fb1}{get\+\_\+no\+\_\+confs}} () const | |
| 38 | \begin{DoxyCompactList}\small\item\em Get the number of precomputed subisotopologues, see details in \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a0dbf1ec53eac9953a354c11e1b0803f9}{Precalculated\+Marginal\+::get\+\_\+no\+\_\+confs}}. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 39 | \subsection*{Additional Inherited Members} | |
| 40 | ||
| 41 | ||
| 42 | \subsection{Detailed Description} | |
| 43 | \mbox{\hyperlink{class_iso_spec_1_1_layered_marginal}{Layered\+Marginal}} class. | |
| 44 | ||
| 45 | An extendable version of the \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal}{Precalculated\+Marginal}}, where you can extend the threshold at will. | |
| 46 | ||
| 47 | Definition at line 337 of file marginal\+Trek++.\+h. | |
| 48 | ||
| 49 | ||
| 50 | ||
| 51 | \subsection{Constructor \& Destructor Documentation} | |
| 52 | \mbox{\Hypertarget{class_iso_spec_1_1_layered_marginal_af062d180664c9c856b4cc72e3457ca9d}\label{class_iso_spec_1_1_layered_marginal_af062d180664c9c856b4cc72e3457ca9d}} | |
| 53 | \index{Iso\+Spec\+::\+Layered\+Marginal@{Iso\+Spec\+::\+Layered\+Marginal}!Layered\+Marginal@{Layered\+Marginal}} | |
| 54 | \index{Layered\+Marginal@{Layered\+Marginal}!Iso\+Spec\+::\+Layered\+Marginal@{Iso\+Spec\+::\+Layered\+Marginal}} | |
| 55 | \subsubsection{\texorpdfstring{Layered\+Marginal()}{LayeredMarginal()}} | |
| 56 | {\footnotesize\ttfamily Iso\+Spec\+::\+Layered\+Marginal\+::\+Layered\+Marginal (\begin{DoxyParamCaption}\item[{\mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \&\&}]{m, }\item[{int}]{tab\+Size = {\ttfamily 1000}, }\item[{int}]{hash\+Size = {\ttfamily 1000} }\end{DoxyParamCaption})} | |
| 57 | ||
| 58 | ||
| 59 | ||
| 60 | Move constructor\+: specializes the \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} class. | |
| 61 | ||
| 62 | ||
| 63 | \begin{DoxyParams}{Parameters} | |
| 64 | {\em tab\+Size} & The size of the table used to store configurations in the allocator. \\ | |
| 65 | \hline | |
| 66 | {\em hash\+Size} & The size of the hash table used to store visited subisotopologues. \\ | |
| 67 | \hline | |
| 68 | \end{DoxyParams} | |
| 69 | ||
| 70 | ||
| 71 | Definition at line 445 of file marginal\+Trek++.\+cpp. | |
| 72 | ||
| 73 | ||
| 74 | ||
| 75 | \subsection{Member Function Documentation} | |
| 76 | \mbox{\Hypertarget{class_iso_spec_1_1_layered_marginal_ab8b66ed79bad27183f98a9ae34c3b944}\label{class_iso_spec_1_1_layered_marginal_ab8b66ed79bad27183f98a9ae34c3b944}} | |
| 77 | \index{Iso\+Spec\+::\+Layered\+Marginal@{Iso\+Spec\+::\+Layered\+Marginal}!extend@{extend}} | |
| 78 | \index{extend@{extend}!Iso\+Spec\+::\+Layered\+Marginal@{Iso\+Spec\+::\+Layered\+Marginal}} | |
| 79 | \subsubsection{\texorpdfstring{extend()}{extend()}} | |
| 80 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Layered\+Marginal\+::extend (\begin{DoxyParamCaption}\item[{double}]{new\+\_\+threshold }\end{DoxyParamCaption})} | |
| 81 | ||
| 82 | ||
| 83 | ||
| 84 | Extend the set of computed subisotopologues to those above the new threshold. | |
| 85 | ||
| 86 | ||
| 87 | \begin{DoxyParams}{Parameters} | |
| 88 | {\em new\+\_\+threshold} & The new log-\/probability limiting the subisotopologues from below. \\ | |
| 89 | \hline | |
| 90 | \end{DoxyParams} | |
| 91 | \begin{DoxyReturn}{Returns} | |
| 92 | Returns false, if there are no fringe-\/subisotopologues (subisotopologues that were neighbours of the previously calculated subisotopologues, with log-\/probability below the previous threshold). | |
| 93 | \end{DoxyReturn} | |
| 94 | ||
| 95 | ||
| 96 | Definition at line 455 of file marginal\+Trek++.\+cpp. | |
| 97 | ||
| 98 | ||
| 99 | ||
| 100 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 101 | \item | |
| 102 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/marginal\+Trek++.\+h\item | |
| 103 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/marginal\+Trek++.\+cpp\end{DoxyCompactItemize} |
| 0 | %!PS-Adobe-2.0 EPSF-2.0 | |
| 1 | %%Title: ClassName | |
| 2 | %%Creator: Doxygen | |
| 3 | %%CreationDate: Time | |
| 4 | %%For: | |
| 5 | %Magnification: 1.00 | |
| 6 | %%Orientation: Portrait | |
| 7 | %%BoundingBox: 0 0 500 100.502513 | |
| 8 | %%Pages: 0 | |
| 9 | %%BeginSetup | |
| 10 | %%EndSetup | |
| 11 | %%EndComments | |
| 12 | ||
| 13 | % ----- variables ----- | |
| 14 | ||
| 15 | /boxwidth 0 def | |
| 16 | /boxheight 40 def | |
| 17 | /fontheight 24 def | |
| 18 | /marginwidth 10 def | |
| 19 | /distx 20 def | |
| 20 | /disty 40 def | |
| 21 | /boundaspect 4.975000 def % aspect ratio of the BoundingBox (width/height) | |
| 22 | /boundx 500 def | |
| 23 | /boundy boundx boundaspect div def | |
| 24 | /xspacing 0 def | |
| 25 | /yspacing 0 def | |
| 26 | /rows 2 def | |
| 27 | /cols 2 def | |
| 28 | /scalefactor 0 def | |
| 29 | /boxfont /Times-Roman findfont fontheight scalefont def | |
| 30 | ||
| 31 | % ----- procedures ----- | |
| 32 | ||
| 33 | /dotted { [1 4] 0 setdash } def | |
| 34 | /dashed { [5] 0 setdash } def | |
| 35 | /solid { [] 0 setdash } def | |
| 36 | ||
| 37 | /max % result = MAX(arg1,arg2) | |
| 38 | { | |
| 39 | /a exch def | |
| 40 | /b exch def | |
| 41 | a b gt {a} {b} ifelse | |
| 42 | } def | |
| 43 | ||
| 44 | /xoffset % result = MAX(0,(scalefactor-(boxwidth*cols+distx*(cols-1)))/2) | |
| 45 | { | |
| 46 | 0 scalefactor boxwidth cols mul distx cols 1 sub mul add sub 2 div max | |
| 47 | } def | |
| 48 | ||
| 49 | /cw % boxwidth = MAX(boxwidth, stringwidth(arg1)) | |
| 50 | { | |
| 51 | /str exch def | |
| 52 | /boxwidth boxwidth str stringwidth pop max def | |
| 53 | } def | |
| 54 | ||
| 55 | /box % draws a box with text `arg1' at grid pos (arg2,arg3) | |
| 56 | { gsave | |
| 57 | 2 setlinewidth | |
| 58 | newpath | |
| 59 | exch xspacing mul xoffset add | |
| 60 | exch yspacing mul | |
| 61 | moveto | |
| 62 | boxwidth 0 rlineto | |
| 63 | 0 boxheight rlineto | |
| 64 | boxwidth neg 0 rlineto | |
| 65 | 0 boxheight neg rlineto | |
| 66 | closepath | |
| 67 | dup stringwidth pop neg boxwidth add 2 div | |
| 68 | boxheight fontheight 2 div sub 2 div | |
| 69 | rmoveto show stroke | |
| 70 | grestore | |
| 71 | } def | |
| 72 | ||
| 73 | /mark | |
| 74 | { newpath | |
| 75 | exch xspacing mul xoffset add boxwidth add | |
| 76 | exch yspacing mul | |
| 77 | moveto | |
| 78 | 0 boxheight 4 div rlineto | |
| 79 | boxheight neg 4 div boxheight neg 4 div rlineto | |
| 80 | closepath | |
| 81 | eofill | |
| 82 | stroke | |
| 83 | } def | |
| 84 | ||
| 85 | /arrow | |
| 86 | { newpath | |
| 87 | moveto | |
| 88 | 3 -8 rlineto | |
| 89 | -6 0 rlineto | |
| 90 | 3 8 rlineto | |
| 91 | closepath | |
| 92 | eofill | |
| 93 | stroke | |
| 94 | } def | |
| 95 | ||
| 96 | /out % draws an output connector for the block at (arg1,arg2) | |
| 97 | { | |
| 98 | newpath | |
| 99 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 100 | exch yspacing mul boxheight add | |
| 101 | /y exch def | |
| 102 | /x exch def | |
| 103 | x y moveto | |
| 104 | 0 disty 2 div rlineto | |
| 105 | stroke | |
| 106 | 1 eq { x y disty 2 div add arrow } if | |
| 107 | } def | |
| 108 | ||
| 109 | /in % draws an input connector for the block at (arg1,arg2) | |
| 110 | { | |
| 111 | newpath | |
| 112 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 113 | exch yspacing mul disty 2 div sub | |
| 114 | /y exch def | |
| 115 | /x exch def | |
| 116 | x y moveto | |
| 117 | 0 disty 2 div rlineto | |
| 118 | stroke | |
| 119 | 1 eq { x y disty 2 div add arrow } if | |
| 120 | } def | |
| 121 | ||
| 122 | /hedge | |
| 123 | { | |
| 124 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 125 | exch yspacing mul boxheight 2 div sub | |
| 126 | /y exch def | |
| 127 | /x exch def | |
| 128 | newpath | |
| 129 | x y moveto | |
| 130 | boxwidth 2 div distx add 0 rlineto | |
| 131 | stroke | |
| 132 | 1 eq | |
| 133 | { newpath x boxwidth 2 div distx add add y moveto | |
| 134 | -8 3 rlineto | |
| 135 | 0 -6 rlineto | |
| 136 | 8 3 rlineto | |
| 137 | closepath | |
| 138 | eofill | |
| 139 | stroke | |
| 140 | } if | |
| 141 | } def | |
| 142 | ||
| 143 | /vedge | |
| 144 | { | |
| 145 | /ye exch def | |
| 146 | /ys exch def | |
| 147 | /xs exch def | |
| 148 | newpath | |
| 149 | xs xspacing mul xoffset add boxwidth 2 div add dup | |
| 150 | ys yspacing mul boxheight 2 div sub | |
| 151 | moveto | |
| 152 | ye yspacing mul boxheight 2 div sub | |
| 153 | lineto | |
| 154 | stroke | |
| 155 | } def | |
| 156 | ||
| 157 | /conn % connections the blocks from col `arg1' to `arg2' of row `arg3' | |
| 158 | { | |
| 159 | /ys exch def | |
| 160 | /xe exch def | |
| 161 | /xs exch def | |
| 162 | newpath | |
| 163 | xs xspacing mul xoffset add boxwidth 2 div add | |
| 164 | ys yspacing mul disty 2 div sub | |
| 165 | moveto | |
| 166 | xspacing xe xs sub mul 0 | |
| 167 | rlineto | |
| 168 | stroke | |
| 169 | } def | |
| 170 | ||
| 171 | % ----- main ------ | |
| 172 | ||
| 173 | boxfont setfont | |
| 174 | 1 boundaspect scale | |
| 175 | (IsoSpec::Marginal) cw | |
| 176 | (IsoSpec::MarginalTrek) cw | |
| 177 | (IsoSpec::PrecalculatedMarginal) cw | |
| 178 | /boxwidth boxwidth marginwidth 2 mul add def | |
| 179 | /xspacing boxwidth distx add def | |
| 180 | /yspacing boxheight disty add def | |
| 181 | /scalefactor | |
| 182 | boxwidth cols mul distx cols 1 sub mul add | |
| 183 | boxheight rows mul disty rows 1 sub mul add boundaspect mul | |
| 184 | max def | |
| 185 | boundx scalefactor div boundy scalefactor div scale | |
| 186 | ||
| 187 | % ----- classes ----- | |
| 188 | ||
| 189 | (IsoSpec::Marginal) 0.500000 1.000000 box | |
| 190 | (IsoSpec::MarginalTrek) 0.000000 0.000000 box | |
| 191 | (IsoSpec::PrecalculatedMarginal) 1.000000 0.000000 box | |
| 192 | ||
| 193 | % ----- relations ----- | |
| 194 | ||
| 195 | solid | |
| 196 | 1 0.500000 0.250000 out | |
| 197 | solid | |
| 198 | 0.000000 1.000000 1.000000 conn | |
| 199 | solid | |
| 200 | 0 0.000000 0.750000 in | |
| 201 | solid | |
| 202 | 0 1.000000 0.750000 in |
| 0 | \hypertarget{class_iso_spec_1_1_marginal}{}\section{Iso\+Spec\+:\+:Marginal Class Reference} | |
| 1 | \label{class_iso_spec_1_1_marginal}\index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 2 | ||
| 3 | ||
| 4 | The marginal distribution class (a subisotopologue). | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$marginal\+Trek++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Marginal\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=2.000000cm]{class_iso_spec_1_1_marginal} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | \mbox{\hyperlink{class_iso_spec_1_1_marginal_a46be0c1cf5b169a54056997ba404183c}{Marginal}} (const double $\ast$\+\_\+masses, const double $\ast$\+\_\+probs, int \+\_\+isotope\+No, int \+\_\+atom\+Cnt) | |
| 21 | \begin{DoxyCompactList}\small\item\em Class constructor. \end{DoxyCompactList}\item | |
| 22 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a02e8f92f8f9add352840f5dba8de5e06}\label{class_iso_spec_1_1_marginal_a02e8f92f8f9add352840f5dba8de5e06}} | |
| 23 | {\bfseries Marginal} (\mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \&other)=delete | |
| 24 | \item | |
| 25 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a9120cad240058afc3705951d80d28a10}\label{class_iso_spec_1_1_marginal_a9120cad240058afc3705951d80d28a10}} | |
| 26 | \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \& {\bfseries operator=} (const \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \&other)=delete | |
| 27 | \item | |
| 28 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_ad60fff17fa2c68ea2cd7f183a635379e}\label{class_iso_spec_1_1_marginal_ad60fff17fa2c68ea2cd7f183a635379e}} | |
| 29 | \mbox{\hyperlink{class_iso_spec_1_1_marginal_ad60fff17fa2c68ea2cd7f183a635379e}{Marginal}} (\mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \&\&other) | |
| 30 | \begin{DoxyCompactList}\small\item\em Move constructor. \end{DoxyCompactList}\item | |
| 31 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_ad44004fa1e83c4a53d431ca403ce3ae4}\label{class_iso_spec_1_1_marginal_ad44004fa1e83c4a53d431ca403ce3ae4}} | |
| 32 | virtual \mbox{\hyperlink{class_iso_spec_1_1_marginal_ad44004fa1e83c4a53d431ca403ce3ae4}{$\sim$\+Marginal}} () | |
| 33 | \begin{DoxyCompactList}\small\item\em Destructor. \end{DoxyCompactList}\item | |
| 34 | int \mbox{\hyperlink{class_iso_spec_1_1_marginal_a05aa80c3fa77a0406102731934db1a83}{get\+\_\+isotope\+No}} () const | |
| 35 | \begin{DoxyCompactList}\small\item\em Get the number of isotopes of the investigated element. \end{DoxyCompactList}\item | |
| 36 | double \mbox{\hyperlink{class_iso_spec_1_1_marginal_a8b67c507263973da53e533d804e23ac9}{get\+Lightest\+Conf\+Mass}} () const | |
| 37 | \begin{DoxyCompactList}\small\item\em Get the mass of the lightest subisotopologue. \end{DoxyCompactList}\item | |
| 38 | double \mbox{\hyperlink{class_iso_spec_1_1_marginal_aa5598b4d2b31b5daec1c2bac653d0aff}{get\+Heaviest\+Conf\+Mass}} () const | |
| 39 | \begin{DoxyCompactList}\small\item\em Get the mass of the heaviest subisotopologue. \end{DoxyCompactList}\item | |
| 40 | double \mbox{\hyperlink{class_iso_spec_1_1_marginal_ac9408957145d2aa63af32f6647c8ea49}{get\+Mode\+L\+Prob}} () const | |
| 41 | \begin{DoxyCompactList}\small\item\em Get the log-\/probability of the mode subisotopologue. \end{DoxyCompactList}\item | |
| 42 | double \mbox{\hyperlink{class_iso_spec_1_1_marginal_ad2121802133075a87f0987dc27d0617f}{get\+Mode\+Mass}} () const | |
| 43 | \begin{DoxyCompactList}\small\item\em The the mass of the mode subisotopologue. \end{DoxyCompactList}\item | |
| 44 | double \mbox{\hyperlink{class_iso_spec_1_1_marginal_a7bc1eeba342977de3a77c3c7e6ca55b0}{get\+Mode\+Prob}} () const | |
| 45 | \begin{DoxyCompactList}\small\item\em The the probability of the mode subisotopologue. \end{DoxyCompactList}\item | |
| 46 | double \mbox{\hyperlink{class_iso_spec_1_1_marginal_a3f9607f51efcfdac1ca58a1467e3a5dc}{get\+Smallest\+L\+Prob}} () const | |
| 47 | \begin{DoxyCompactList}\small\item\em The the log-\/probability of the lightest subisotopologue. \end{DoxyCompactList}\item | |
| 48 | double \mbox{\hyperlink{class_iso_spec_1_1_marginal_a1974bb030ce70178da569214b4b93cb8}{log\+Prob}} (Conf conf) const | |
| 49 | \begin{DoxyCompactList}\small\item\em Calculate the log-\/probability of a given subisotopologue. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 50 | \subsection*{Protected Attributes} | |
| 51 | \begin{DoxyCompactItemize} | |
| 52 | \item | |
| 53 | const unsigned int \mbox{\hyperlink{class_iso_spec_1_1_marginal_a8dd6415882661f7b9ceedbe09bc200e3}{isotope\+No}} | |
| 54 | \item | |
| 55 | const unsigned int \mbox{\hyperlink{class_iso_spec_1_1_marginal_a53c2af7dcb84aa9d5e0e0918fe7875cd}{atom\+Cnt}} | |
| 56 | \item | |
| 57 | const double $\ast$const \mbox{\hyperlink{class_iso_spec_1_1_marginal_a91265e07f5bb65314995f816f5a9c729}{atom\+\_\+masses}} | |
| 58 | \item | |
| 59 | const double $\ast$const \mbox{\hyperlink{class_iso_spec_1_1_marginal_af059df011e707781fdd4c1d7b70bd91a}{atom\+\_\+l\+Probs}} | |
| 60 | \item | |
| 61 | const double \mbox{\hyperlink{class_iso_spec_1_1_marginal_aa3fb5ed3a9b63a855d6270287aed7417}{loggamma\+\_\+nominator}} | |
| 62 | \item | |
| 63 | const Conf \mbox{\hyperlink{class_iso_spec_1_1_marginal_a640f3b44605b510ee556a25e35a2e095}{mode\+\_\+conf}} | |
| 64 | \item | |
| 65 | const double \mbox{\hyperlink{class_iso_spec_1_1_marginal_a38238e7581f59f08d0faf8ab5eabc0dc}{mode\+\_\+lprob}} | |
| 66 | \item | |
| 67 | const double \mbox{\hyperlink{class_iso_spec_1_1_marginal_a3bfea931e5e1ec1e7d90e8e096c38eb7}{mode\+\_\+mass}} | |
| 68 | \item | |
| 69 | const double \mbox{\hyperlink{class_iso_spec_1_1_marginal_a75315ec4c470be5f82b903172f7c43ae}{mode\+\_\+prob}} | |
| 70 | \item | |
| 71 | const double \mbox{\hyperlink{class_iso_spec_1_1_marginal_a2abd05ba9351e21cd99e2783e26bd6dc}{smallest\+\_\+lprob}} | |
| 72 | \end{DoxyCompactItemize} | |
| 73 | ||
| 74 | ||
| 75 | \subsection{Detailed Description} | |
| 76 | The marginal distribution class (a subisotopologue). | |
| 77 | ||
| 78 | This class mostly provides some basic common A\+PI for subclasses, but itself is not abstract. This class represents the probability distribution generated by one element only -- a subisotopologue. For instance, it might be the distribution of C200, that might be part of, say, C200\+H402. It corresponds to the multinomial distribution, where each configuration can also be attributed a precise mass. The constructor method perform initial hill-\/climbing to find the most probable sub-\/isotopologue (the mode). | |
| 79 | ||
| 80 | Definition at line 45 of file marginal\+Trek++.\+h. | |
| 81 | ||
| 82 | ||
| 83 | ||
| 84 | \subsection{Constructor \& Destructor Documentation} | |
| 85 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a46be0c1cf5b169a54056997ba404183c}\label{class_iso_spec_1_1_marginal_a46be0c1cf5b169a54056997ba404183c}} | |
| 86 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!Marginal@{Marginal}} | |
| 87 | \index{Marginal@{Marginal}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 88 | \subsubsection{\texorpdfstring{Marginal()}{Marginal()}} | |
| 89 | {\footnotesize\ttfamily Iso\+Spec\+::\+Marginal\+::\+Marginal (\begin{DoxyParamCaption}\item[{const double $\ast$}]{\+\_\+masses, }\item[{const double $\ast$}]{\+\_\+probs, }\item[{int}]{\+\_\+isotope\+No, }\item[{int}]{\+\_\+atom\+Cnt }\end{DoxyParamCaption})} | |
| 90 | ||
| 91 | ||
| 92 | ||
| 93 | Class constructor. | |
| 94 | ||
| 95 | ||
| 96 | \begin{DoxyParams}{Parameters} | |
| 97 | {\em \+\_\+masses} & A table of masses of the stable isotopes of the investigated element, e.\+g. for C10 it is 2\+: C12 and C13. \\ | |
| 98 | \hline | |
| 99 | {\em \+\_\+probs} & A table of natural frequencies of the stable isotopes of the investigated element, see I\+U\+P\+AC at \href{https://iupac.org/isotopesmatter/}{\tt https\+://iupac.\+org/isotopesmatter/} \\ | |
| 100 | \hline | |
| 101 | {\em \+\_\+isotope\+No} & Number of isotopes of a given element. \\ | |
| 102 | \hline | |
| 103 | {\em \+\_\+atom\+Cnt} & The number of atoms of the given element, e.\+g. 10 for C10. \\ | |
| 104 | \hline | |
| 105 | \end{DoxyParams} | |
| 106 | \begin{DoxyReturn}{Returns} | |
| 107 | An instance of the \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} class. | |
| 108 | \end{DoxyReturn} | |
| 109 | ||
| 110 | ||
| 111 | Definition at line 187 of file marginal\+Trek++.\+cpp. | |
| 112 | ||
| 113 | ||
| 114 | ||
| 115 | \subsection{Member Function Documentation} | |
| 116 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a05aa80c3fa77a0406102731934db1a83}\label{class_iso_spec_1_1_marginal_a05aa80c3fa77a0406102731934db1a83}} | |
| 117 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!get\+\_\+isotope\+No@{get\+\_\+isotope\+No}} | |
| 118 | \index{get\+\_\+isotope\+No@{get\+\_\+isotope\+No}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 119 | \subsubsection{\texorpdfstring{get\+\_\+isotope\+No()}{get\_isotopeNo()}} | |
| 120 | {\footnotesize\ttfamily int Iso\+Spec\+::\+Marginal\+::get\+\_\+isotope\+No (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 121 | ||
| 122 | ||
| 123 | ||
| 124 | Get the number of isotopes of the investigated element. | |
| 125 | ||
| 126 | \begin{DoxyReturn}{Returns} | |
| 127 | The integer number of isotopes of the investigated element. | |
| 128 | \end{DoxyReturn} | |
| 129 | ||
| 130 | ||
| 131 | Definition at line 92 of file marginal\+Trek++.\+h. | |
| 132 | ||
| 133 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_aa5598b4d2b31b5daec1c2bac653d0aff}\label{class_iso_spec_1_1_marginal_aa5598b4d2b31b5daec1c2bac653d0aff}} | |
| 134 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!get\+Heaviest\+Conf\+Mass@{get\+Heaviest\+Conf\+Mass}} | |
| 135 | \index{get\+Heaviest\+Conf\+Mass@{get\+Heaviest\+Conf\+Mass}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 136 | \subsubsection{\texorpdfstring{get\+Heaviest\+Conf\+Mass()}{getHeaviestConfMass()}} | |
| 137 | {\footnotesize\ttfamily double Iso\+Spec\+::\+Marginal\+::get\+Heaviest\+Conf\+Mass (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const} | |
| 138 | ||
| 139 | ||
| 140 | ||
| 141 | Get the mass of the heaviest subisotopologue. | |
| 142 | ||
| 143 | This is trivially obtained by considering all atom\+No atoms to be the heaviest isotope possible. \begin{DoxyReturn}{Returns} | |
| 144 | The mass of the heaviest subisotopologue. | |
| 145 | \end{DoxyReturn} | |
| 146 | ||
| 147 | ||
| 148 | Definition at line 246 of file marginal\+Trek++.\+cpp. | |
| 149 | ||
| 150 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a8b67c507263973da53e533d804e23ac9}\label{class_iso_spec_1_1_marginal_a8b67c507263973da53e533d804e23ac9}} | |
| 151 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!get\+Lightest\+Conf\+Mass@{get\+Lightest\+Conf\+Mass}} | |
| 152 | \index{get\+Lightest\+Conf\+Mass@{get\+Lightest\+Conf\+Mass}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 153 | \subsubsection{\texorpdfstring{get\+Lightest\+Conf\+Mass()}{getLightestConfMass()}} | |
| 154 | {\footnotesize\ttfamily double Iso\+Spec\+::\+Marginal\+::get\+Lightest\+Conf\+Mass (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const} | |
| 155 | ||
| 156 | ||
| 157 | ||
| 158 | Get the mass of the lightest subisotopologue. | |
| 159 | ||
| 160 | This is trivially obtained by considering all atom\+No atoms to be the lightest isotope possible. \begin{DoxyReturn}{Returns} | |
| 161 | The mass of the lightiest subisotopologue. | |
| 162 | \end{DoxyReturn} | |
| 163 | ||
| 164 | ||
| 165 | Definition at line 237 of file marginal\+Trek++.\+cpp. | |
| 166 | ||
| 167 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_ac9408957145d2aa63af32f6647c8ea49}\label{class_iso_spec_1_1_marginal_ac9408957145d2aa63af32f6647c8ea49}} | |
| 168 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!get\+Mode\+L\+Prob@{get\+Mode\+L\+Prob}} | |
| 169 | \index{get\+Mode\+L\+Prob@{get\+Mode\+L\+Prob}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 170 | \subsubsection{\texorpdfstring{get\+Mode\+L\+Prob()}{getModeLProb()}} | |
| 171 | {\footnotesize\ttfamily double Iso\+Spec\+::\+Marginal\+::get\+Mode\+L\+Prob (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 172 | ||
| 173 | ||
| 174 | ||
| 175 | Get the log-\/probability of the mode subisotopologue. | |
| 176 | ||
| 177 | \begin{DoxyReturn}{Returns} | |
| 178 | The log-\/probability of a/the most probable subisotopologue. | |
| 179 | \end{DoxyReturn} | |
| 180 | ||
| 181 | ||
| 182 | Definition at line 110 of file marginal\+Trek++.\+h. | |
| 183 | ||
| 184 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_ad2121802133075a87f0987dc27d0617f}\label{class_iso_spec_1_1_marginal_ad2121802133075a87f0987dc27d0617f}} | |
| 185 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!get\+Mode\+Mass@{get\+Mode\+Mass}} | |
| 186 | \index{get\+Mode\+Mass@{get\+Mode\+Mass}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 187 | \subsubsection{\texorpdfstring{get\+Mode\+Mass()}{getModeMass()}} | |
| 188 | {\footnotesize\ttfamily double Iso\+Spec\+::\+Marginal\+::get\+Mode\+Mass (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 189 | ||
| 190 | ||
| 191 | ||
| 192 | The the mass of the mode subisotopologue. | |
| 193 | ||
| 194 | \begin{DoxyReturn}{Returns} | |
| 195 | The mass of one of the most probable subisotopologues. | |
| 196 | \end{DoxyReturn} | |
| 197 | ||
| 198 | ||
| 199 | Definition at line 116 of file marginal\+Trek++.\+h. | |
| 200 | ||
| 201 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a7bc1eeba342977de3a77c3c7e6ca55b0}\label{class_iso_spec_1_1_marginal_a7bc1eeba342977de3a77c3c7e6ca55b0}} | |
| 202 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!get\+Mode\+Prob@{get\+Mode\+Prob}} | |
| 203 | \index{get\+Mode\+Prob@{get\+Mode\+Prob}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 204 | \subsubsection{\texorpdfstring{get\+Mode\+Prob()}{getModeProb()}} | |
| 205 | {\footnotesize\ttfamily double Iso\+Spec\+::\+Marginal\+::get\+Mode\+Prob (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 206 | ||
| 207 | ||
| 208 | ||
| 209 | The the probability of the mode subisotopologue. | |
| 210 | ||
| 211 | \begin{DoxyReturn}{Returns} | |
| 212 | The probability of a/the most probable subisotopologue. | |
| 213 | \end{DoxyReturn} | |
| 214 | ||
| 215 | ||
| 216 | Definition at line 122 of file marginal\+Trek++.\+h. | |
| 217 | ||
| 218 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a3f9607f51efcfdac1ca58a1467e3a5dc}\label{class_iso_spec_1_1_marginal_a3f9607f51efcfdac1ca58a1467e3a5dc}} | |
| 219 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!get\+Smallest\+L\+Prob@{get\+Smallest\+L\+Prob}} | |
| 220 | \index{get\+Smallest\+L\+Prob@{get\+Smallest\+L\+Prob}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 221 | \subsubsection{\texorpdfstring{get\+Smallest\+L\+Prob()}{getSmallestLProb()}} | |
| 222 | {\footnotesize\ttfamily double Iso\+Spec\+::\+Marginal\+::get\+Smallest\+L\+Prob (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 223 | ||
| 224 | ||
| 225 | ||
| 226 | The the log-\/probability of the lightest subisotopologue. | |
| 227 | ||
| 228 | \begin{DoxyReturn}{Returns} | |
| 229 | The logarithm of the smallest non-\/zero probability of a subisotopologue. | |
| 230 | \end{DoxyReturn} | |
| 231 | ||
| 232 | ||
| 233 | Definition at line 129 of file marginal\+Trek++.\+h. | |
| 234 | ||
| 235 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a1974bb030ce70178da569214b4b93cb8}\label{class_iso_spec_1_1_marginal_a1974bb030ce70178da569214b4b93cb8}} | |
| 236 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!log\+Prob@{log\+Prob}} | |
| 237 | \index{log\+Prob@{log\+Prob}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 238 | \subsubsection{\texorpdfstring{log\+Prob()}{logProb()}} | |
| 239 | {\footnotesize\ttfamily double Iso\+Spec\+::\+Marginal\+::log\+Prob (\begin{DoxyParamCaption}\item[{Conf}]{conf }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 240 | ||
| 241 | ||
| 242 | ||
| 243 | Calculate the log-\/probability of a given subisotopologue. | |
| 244 | ||
| 245 | ||
| 246 | \begin{DoxyParams}{Parameters} | |
| 247 | {\em conf} & A subisotopologue (a table of integers describing subsequent isotope-\/counts). \\ | |
| 248 | \hline | |
| 249 | \end{DoxyParams} | |
| 250 | \begin{DoxyReturn}{Returns} | |
| 251 | The log-\/probability of the input subisotopologue. | |
| 252 | \end{DoxyReturn} | |
| 253 | ||
| 254 | ||
| 255 | Definition at line 136 of file marginal\+Trek++.\+h. | |
| 256 | ||
| 257 | ||
| 258 | ||
| 259 | \subsection{Member Data Documentation} | |
| 260 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_af059df011e707781fdd4c1d7b70bd91a}\label{class_iso_spec_1_1_marginal_af059df011e707781fdd4c1d7b70bd91a}} | |
| 261 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!atom\+\_\+l\+Probs@{atom\+\_\+l\+Probs}} | |
| 262 | \index{atom\+\_\+l\+Probs@{atom\+\_\+l\+Probs}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 263 | \subsubsection{\texorpdfstring{atom\+\_\+l\+Probs}{atom\_lProbs}} | |
| 264 | {\footnotesize\ttfamily const double$\ast$ const Iso\+Spec\+::\+Marginal\+::atom\+\_\+l\+Probs\hspace{0.3cm}{\ttfamily [protected]}} | |
| 265 | ||
| 266 | Table of log-\/probabilities of all the isotope\+No isotopes. | |
| 267 | ||
| 268 | Definition at line 53 of file marginal\+Trek++.\+h. | |
| 269 | ||
| 270 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a91265e07f5bb65314995f816f5a9c729}\label{class_iso_spec_1_1_marginal_a91265e07f5bb65314995f816f5a9c729}} | |
| 271 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!atom\+\_\+masses@{atom\+\_\+masses}} | |
| 272 | \index{atom\+\_\+masses@{atom\+\_\+masses}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 273 | \subsubsection{\texorpdfstring{atom\+\_\+masses}{atom\_masses}} | |
| 274 | {\footnotesize\ttfamily const double$\ast$ const Iso\+Spec\+::\+Marginal\+::atom\+\_\+masses\hspace{0.3cm}{\ttfamily [protected]}} | |
| 275 | ||
| 276 | Table of atomic masses of all the isotope\+No isotopes. | |
| 277 | ||
| 278 | Definition at line 52 of file marginal\+Trek++.\+h. | |
| 279 | ||
| 280 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a53c2af7dcb84aa9d5e0e0918fe7875cd}\label{class_iso_spec_1_1_marginal_a53c2af7dcb84aa9d5e0e0918fe7875cd}} | |
| 281 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!atom\+Cnt@{atom\+Cnt}} | |
| 282 | \index{atom\+Cnt@{atom\+Cnt}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 283 | \subsubsection{\texorpdfstring{atom\+Cnt}{atomCnt}} | |
| 284 | {\footnotesize\ttfamily const unsigned int Iso\+Spec\+::\+Marginal\+::atom\+Cnt\hspace{0.3cm}{\ttfamily [protected]}} | |
| 285 | ||
| 286 | The number of atoms of the given element. | |
| 287 | ||
| 288 | Definition at line 51 of file marginal\+Trek++.\+h. | |
| 289 | ||
| 290 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a8dd6415882661f7b9ceedbe09bc200e3}\label{class_iso_spec_1_1_marginal_a8dd6415882661f7b9ceedbe09bc200e3}} | |
| 291 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!isotope\+No@{isotope\+No}} | |
| 292 | \index{isotope\+No@{isotope\+No}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 293 | \subsubsection{\texorpdfstring{isotope\+No}{isotopeNo}} | |
| 294 | {\footnotesize\ttfamily const unsigned int Iso\+Spec\+::\+Marginal\+::isotope\+No\hspace{0.3cm}{\ttfamily [protected]}} | |
| 295 | ||
| 296 | The number of isotopes of the given element. | |
| 297 | ||
| 298 | Definition at line 50 of file marginal\+Trek++.\+h. | |
| 299 | ||
| 300 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_aa3fb5ed3a9b63a855d6270287aed7417}\label{class_iso_spec_1_1_marginal_aa3fb5ed3a9b63a855d6270287aed7417}} | |
| 301 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!loggamma\+\_\+nominator@{loggamma\+\_\+nominator}} | |
| 302 | \index{loggamma\+\_\+nominator@{loggamma\+\_\+nominator}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 303 | \subsubsection{\texorpdfstring{loggamma\+\_\+nominator}{loggamma\_nominator}} | |
| 304 | {\footnotesize\ttfamily const double Iso\+Spec\+::\+Marginal\+::loggamma\+\_\+nominator\hspace{0.3cm}{\ttfamily [protected]}} | |
| 305 | ||
| 306 | The constant nominator that appears in the expressions for the multinomial probabilities. | |
| 307 | ||
| 308 | Definition at line 54 of file marginal\+Trek++.\+h. | |
| 309 | ||
| 310 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a640f3b44605b510ee556a25e35a2e095}\label{class_iso_spec_1_1_marginal_a640f3b44605b510ee556a25e35a2e095}} | |
| 311 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!mode\+\_\+conf@{mode\+\_\+conf}} | |
| 312 | \index{mode\+\_\+conf@{mode\+\_\+conf}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 313 | \subsubsection{\texorpdfstring{mode\+\_\+conf}{mode\_conf}} | |
| 314 | {\footnotesize\ttfamily const Conf Iso\+Spec\+::\+Marginal\+::mode\+\_\+conf\hspace{0.3cm}{\ttfamily [protected]}} | |
| 315 | ||
| 316 | A subisotopologue with most probability. If not unique, one of the representatives of that class of subisotopologues. | |
| 317 | ||
| 318 | Definition at line 55 of file marginal\+Trek++.\+h. | |
| 319 | ||
| 320 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a38238e7581f59f08d0faf8ab5eabc0dc}\label{class_iso_spec_1_1_marginal_a38238e7581f59f08d0faf8ab5eabc0dc}} | |
| 321 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!mode\+\_\+lprob@{mode\+\_\+lprob}} | |
| 322 | \index{mode\+\_\+lprob@{mode\+\_\+lprob}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 323 | \subsubsection{\texorpdfstring{mode\+\_\+lprob}{mode\_lprob}} | |
| 324 | {\footnotesize\ttfamily const double Iso\+Spec\+::\+Marginal\+::mode\+\_\+lprob\hspace{0.3cm}{\ttfamily [protected]}} | |
| 325 | ||
| 326 | The log-\/probability of the mode subisotopologue. | |
| 327 | ||
| 328 | Definition at line 56 of file marginal\+Trek++.\+h. | |
| 329 | ||
| 330 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a3bfea931e5e1ec1e7d90e8e096c38eb7}\label{class_iso_spec_1_1_marginal_a3bfea931e5e1ec1e7d90e8e096c38eb7}} | |
| 331 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!mode\+\_\+mass@{mode\+\_\+mass}} | |
| 332 | \index{mode\+\_\+mass@{mode\+\_\+mass}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 333 | \subsubsection{\texorpdfstring{mode\+\_\+mass}{mode\_mass}} | |
| 334 | {\footnotesize\ttfamily const double Iso\+Spec\+::\+Marginal\+::mode\+\_\+mass\hspace{0.3cm}{\ttfamily [protected]}} | |
| 335 | ||
| 336 | The mass of the mode subisotopologue. | |
| 337 | ||
| 338 | Definition at line 57 of file marginal\+Trek++.\+h. | |
| 339 | ||
| 340 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a75315ec4c470be5f82b903172f7c43ae}\label{class_iso_spec_1_1_marginal_a75315ec4c470be5f82b903172f7c43ae}} | |
| 341 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!mode\+\_\+prob@{mode\+\_\+prob}} | |
| 342 | \index{mode\+\_\+prob@{mode\+\_\+prob}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 343 | \subsubsection{\texorpdfstring{mode\+\_\+prob}{mode\_prob}} | |
| 344 | {\footnotesize\ttfamily const double Iso\+Spec\+::\+Marginal\+::mode\+\_\+prob\hspace{0.3cm}{\ttfamily [protected]}} | |
| 345 | ||
| 346 | The probability of the mode subisotopologue. | |
| 347 | ||
| 348 | Definition at line 58 of file marginal\+Trek++.\+h. | |
| 349 | ||
| 350 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_a2abd05ba9351e21cd99e2783e26bd6dc}\label{class_iso_spec_1_1_marginal_a2abd05ba9351e21cd99e2783e26bd6dc}} | |
| 351 | \index{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}!smallest\+\_\+lprob@{smallest\+\_\+lprob}} | |
| 352 | \index{smallest\+\_\+lprob@{smallest\+\_\+lprob}!Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}} | |
| 353 | \subsubsection{\texorpdfstring{smallest\+\_\+lprob}{smallest\_lprob}} | |
| 354 | {\footnotesize\ttfamily const double Iso\+Spec\+::\+Marginal\+::smallest\+\_\+lprob\hspace{0.3cm}{\ttfamily [protected]}} | |
| 355 | ||
| 356 | The smallest-\/achievable log-\/probability in the distribution of subisotopologues. | |
| 357 | ||
| 358 | Definition at line 59 of file marginal\+Trek++.\+h. | |
| 359 | ||
| 360 | ||
| 361 | ||
| 362 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 363 | \item | |
| 364 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/marginal\+Trek++.\+h\item | |
| 365 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/marginal\+Trek++.\+cpp\end{DoxyCompactItemize} |
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| 90 | 3 8 rlineto | |
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| 97 | { | |
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| 100 | exch yspacing mul boxheight add | |
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| 104 | 0 disty 2 div rlineto | |
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| 108 | ||
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| 119 | 1 eq { x y disty 2 div add arrow } if | |
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| 121 | ||
| 122 | /hedge | |
| 123 | { | |
| 124 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 125 | exch yspacing mul boxheight 2 div sub | |
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| 127 | /x exch def | |
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| 129 | x y moveto | |
| 130 | boxwidth 2 div distx add 0 rlineto | |
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| 132 | 1 eq | |
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| 134 | -8 3 rlineto | |
| 135 | 0 -6 rlineto | |
| 136 | 8 3 rlineto | |
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| 138 | eofill | |
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| 140 | } if | |
| 141 | } def | |
| 142 | ||
| 143 | /vedge | |
| 144 | { | |
| 145 | /ye exch def | |
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| 151 | moveto | |
| 152 | ye yspacing mul boxheight 2 div sub | |
| 153 | lineto | |
| 154 | stroke | |
| 155 | } def | |
| 156 | ||
| 157 | /conn % connections the blocks from col `arg1' to `arg2' of row `arg3' | |
| 158 | { | |
| 159 | /ys exch def | |
| 160 | /xe exch def | |
| 161 | /xs exch def | |
| 162 | newpath | |
| 163 | xs xspacing mul xoffset add boxwidth 2 div add | |
| 164 | ys yspacing mul disty 2 div sub | |
| 165 | moveto | |
| 166 | xspacing xe xs sub mul 0 | |
| 167 | rlineto | |
| 168 | stroke | |
| 169 | } def | |
| 170 | ||
| 171 | % ----- main ------ | |
| 172 | ||
| 173 | boxfont setfont | |
| 174 | 1 boundaspect scale | |
| 175 | (IsoSpec::MarginalTrek) cw | |
| 176 | (IsoSpec::Marginal) cw | |
| 177 | /boxwidth boxwidth marginwidth 2 mul add def | |
| 178 | /xspacing boxwidth distx add def | |
| 179 | /yspacing boxheight disty add def | |
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| 181 | boxwidth cols mul distx cols 1 sub mul add | |
| 182 | boxheight rows mul disty rows 1 sub mul add boundaspect mul | |
| 183 | max def | |
| 184 | boundx scalefactor div boundy scalefactor div scale | |
| 185 | ||
| 186 | % ----- classes ----- | |
| 187 | ||
| 188 | (IsoSpec::MarginalTrek) 0.000000 0.000000 box | |
| 189 | (IsoSpec::Marginal) 0.000000 1.000000 box | |
| 190 | ||
| 191 | % ----- relations ----- | |
| 192 | ||
| 193 | solid | |
| 194 | 0 0.000000 0.000000 out | |
| 195 | solid | |
| 196 | 1 0.000000 1.000000 in |
| 0 | \hypertarget{class_iso_spec_1_1_marginal_trek}{}\section{Iso\+Spec\+:\+:Marginal\+Trek Class Reference} | |
| 1 | \label{class_iso_spec_1_1_marginal_trek}\index{Iso\+Spec\+::\+Marginal\+Trek@{Iso\+Spec\+::\+Marginal\+Trek}} | |
| 2 | ||
| 3 | ||
| 4 | The marginal distribution class (a subisotopologue). | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$marginal\+Trek++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Marginal\+Trek\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=2.000000cm]{class_iso_spec_1_1_marginal_trek} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | \mbox{\hyperlink{class_iso_spec_1_1_marginal_trek_a83e70d522174e4e6724116941fd9c99e}{Marginal\+Trek}} (\mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \&\&m, int tab\+Size=1000, int hash\+Size=1000) | |
| 21 | \begin{DoxyCompactList}\small\item\em Move constructor\+: specializes the \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} class. \end{DoxyCompactList}\item | |
| 22 | bool \mbox{\hyperlink{class_iso_spec_1_1_marginal_trek_a4db6041328b818d123a017dda3c8b8ae}{probe\+Configuration\+Idx}} (int idx) | |
| 23 | \begin{DoxyCompactList}\small\item\em Check if the table of computed subisotopologues does not have to be extended. \end{DoxyCompactList}\item | |
| 24 | int \mbox{\hyperlink{class_iso_spec_1_1_marginal_trek_a04f3e495a805a3ea242059c963c5b129}{process\+Until\+Cutoff}} (double cutoff) | |
| 25 | \begin{DoxyCompactList}\small\item\em Calculate subisotopologues with probability above or equal to the cut-\/off. \end{DoxyCompactList}\item | |
| 26 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_trek_a802aa5dfd06d560b4f867240bb6c9d10}\label{class_iso_spec_1_1_marginal_trek_a802aa5dfd06d560b4f867240bb6c9d10}} | |
| 27 | const std\+::vector$<$ double $>$ \& {\bfseries conf\+\_\+lprobs} () const | |
| 28 | \item | |
| 29 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_trek_a8b31b886749c0bb07756ae367a4c31cd}\label{class_iso_spec_1_1_marginal_trek_a8b31b886749c0bb07756ae367a4c31cd}} | |
| 30 | const std\+::vector$<$ double $>$ \& {\bfseries conf\+\_\+masses} () const | |
| 31 | \item | |
| 32 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_trek_a05df43d45dda1a7f80b711eec016c40c}\label{class_iso_spec_1_1_marginal_trek_a05df43d45dda1a7f80b711eec016c40c}} | |
| 33 | const std\+::vector$<$ int $\ast$ $>$ \& {\bfseries confs} () const | |
| 34 | \end{DoxyCompactItemize} | |
| 35 | \subsection*{Additional Inherited Members} | |
| 36 | ||
| 37 | ||
| 38 | \subsection{Detailed Description} | |
| 39 | The marginal distribution class (a subisotopologue). | |
| 40 | ||
| 41 | Definition at line 141 of file marginal\+Trek++.\+h. | |
| 42 | ||
| 43 | ||
| 44 | ||
| 45 | \subsection{Constructor \& Destructor Documentation} | |
| 46 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_trek_a83e70d522174e4e6724116941fd9c99e}\label{class_iso_spec_1_1_marginal_trek_a83e70d522174e4e6724116941fd9c99e}} | |
| 47 | \index{Iso\+Spec\+::\+Marginal\+Trek@{Iso\+Spec\+::\+Marginal\+Trek}!Marginal\+Trek@{Marginal\+Trek}} | |
| 48 | \index{Marginal\+Trek@{Marginal\+Trek}!Iso\+Spec\+::\+Marginal\+Trek@{Iso\+Spec\+::\+Marginal\+Trek}} | |
| 49 | \subsubsection{\texorpdfstring{Marginal\+Trek()}{MarginalTrek()}} | |
| 50 | {\footnotesize\ttfamily Iso\+Spec\+::\+Marginal\+Trek\+::\+Marginal\+Trek (\begin{DoxyParamCaption}\item[{\mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \&\&}]{m, }\item[{int}]{tab\+Size = {\ttfamily 1000}, }\item[{int}]{hash\+Size = {\ttfamily 1000} }\end{DoxyParamCaption})} | |
| 51 | ||
| 52 | ||
| 53 | ||
| 54 | Move constructor\+: specializes the \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} class. | |
| 55 | ||
| 56 | ||
| 57 | \begin{DoxyParams}{Parameters} | |
| 58 | {\em tab\+Size} & The size of the table used to store configurations in the allocator. \\ | |
| 59 | \hline | |
| 60 | {\em hash\+Size} & The size of the hash table used to store visited subisotopologues. \\ | |
| 61 | \hline | |
| 62 | \end{DoxyParams} | |
| 63 | ||
| 64 | ||
| 65 | Definition at line 256 of file marginal\+Trek++.\+cpp. | |
| 66 | ||
| 67 | ||
| 68 | ||
| 69 | \subsection{Member Function Documentation} | |
| 70 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_trek_a4db6041328b818d123a017dda3c8b8ae}\label{class_iso_spec_1_1_marginal_trek_a4db6041328b818d123a017dda3c8b8ae}} | |
| 71 | \index{Iso\+Spec\+::\+Marginal\+Trek@{Iso\+Spec\+::\+Marginal\+Trek}!probe\+Configuration\+Idx@{probe\+Configuration\+Idx}} | |
| 72 | \index{probe\+Configuration\+Idx@{probe\+Configuration\+Idx}!Iso\+Spec\+::\+Marginal\+Trek@{Iso\+Spec\+::\+Marginal\+Trek}} | |
| 73 | \subsubsection{\texorpdfstring{probe\+Configuration\+Idx()}{probeConfigurationIdx()}} | |
| 74 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Marginal\+Trek\+::probe\+Configuration\+Idx (\begin{DoxyParamCaption}\item[{int}]{idx }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} | |
| 75 | ||
| 76 | ||
| 77 | ||
| 78 | Check if the table of computed subisotopologues does not have to be extended. | |
| 79 | ||
| 80 | This function checks if the idx-\/th most probable subisotopologue was memoized and if not, computes it and memoizes it. | |
| 81 | ||
| 82 | ||
| 83 | \begin{DoxyParams}{Parameters} | |
| 84 | {\em idx} & The number of the idx-\/th most probable subisotopologue. \\ | |
| 85 | \hline | |
| 86 | \end{DoxyParams} | |
| 87 | \begin{DoxyReturn}{Returns} | |
| 88 | Returns false if it the provided idx exceeds the total number of subisotopologues. | |
| 89 | \end{DoxyReturn} | |
| 90 | ||
| 91 | ||
| 92 | Definition at line 179 of file marginal\+Trek++.\+h. | |
| 93 | ||
| 94 | \mbox{\Hypertarget{class_iso_spec_1_1_marginal_trek_a04f3e495a805a3ea242059c963c5b129}\label{class_iso_spec_1_1_marginal_trek_a04f3e495a805a3ea242059c963c5b129}} | |
| 95 | \index{Iso\+Spec\+::\+Marginal\+Trek@{Iso\+Spec\+::\+Marginal\+Trek}!process\+Until\+Cutoff@{process\+Until\+Cutoff}} | |
| 96 | \index{process\+Until\+Cutoff@{process\+Until\+Cutoff}!Iso\+Spec\+::\+Marginal\+Trek@{Iso\+Spec\+::\+Marginal\+Trek}} | |
| 97 | \subsubsection{\texorpdfstring{process\+Until\+Cutoff()}{processUntilCutoff()}} | |
| 98 | {\footnotesize\ttfamily int Iso\+Spec\+::\+Marginal\+Trek\+::process\+Until\+Cutoff (\begin{DoxyParamCaption}\item[{double}]{cutoff }\end{DoxyParamCaption})} | |
| 99 | ||
| 100 | ||
| 101 | ||
| 102 | Calculate subisotopologues with probability above or equal to the cut-\/off. | |
| 103 | ||
| 104 | ||
| 105 | \begin{DoxyParams}{Parameters} | |
| 106 | {\em cutoff} & The probability cut-\/off \\ | |
| 107 | \hline | |
| 108 | \end{DoxyParams} | |
| 109 | \begin{DoxyReturn}{Returns} | |
| 110 | The number of the last subisotopologue above the cut-\/off. | |
| 111 | \end{DoxyReturn} | |
| 112 | ||
| 113 | ||
| 114 | Definition at line 333 of file marginal\+Trek++.\+cpp. | |
| 115 | ||
| 116 | ||
| 117 | ||
| 118 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 119 | \item | |
| 120 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/marginal\+Trek++.\+h\item | |
| 121 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/marginal\+Trek++.\+cpp\end{DoxyCompactItemize} |
| 0 | digraph "IsoSpec::MarginalTrek" | |
| 1 | { | |
| 2 | edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; | |
| 3 | node [fontname="Helvetica",fontsize="10",shape=record]; | |
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| 6 | Node3 [label="IsoSpec::Marginal",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_marginal.html"]; | |
| 7 | } |
| 0 | 9f0594eeacbcc0b6c455caca14bd94bf⏎ |
| 0 | digraph "IsoSpec::MarginalTrek" | |
| 1 | { | |
| 2 | edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; | |
| 3 | node [fontname="Helvetica",fontsize="10",shape=record]; | |
| 4 | Node0 [label="IsoSpec::MarginalTrek",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; | |
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| 6 | Node1 [label="IsoSpec::Marginal",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_marginal.html"]; | |
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| 0 | 163fb9c54a04cb44177f30c6fa782fe4⏎ |
| 0 | \hypertarget{class_iso_spec_1_1_order_marginals_by_size_decresing}{}\section{Iso\+Spec\+:\+:Order\+Marginals\+By\+Size\+Decresing Class Reference} | |
| 1 | \label{class_iso_spec_1_1_order_marginals_by_size_decresing}\index{Iso\+Spec\+::\+Order\+Marginals\+By\+Size\+Decresing@{Iso\+Spec\+::\+Order\+Marginals\+By\+Size\+Decresing}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_order_marginals_by_size_decresing_a2530a398df14766242b936e5c83e0f37}\label{class_iso_spec_1_1_order_marginals_by_size_decresing_a2530a398df14766242b936e5c83e0f37}} | |
| 6 | {\bfseries Order\+Marginals\+By\+Size\+Decresing} (\mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal}{Precalculated\+Marginal}} const $\ast$const $\ast$\+\_\+T) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_order_marginals_by_size_decresing_a43312dd35580f579c9e64b32e06edb63}\label{class_iso_spec_1_1_order_marginals_by_size_decresing_a43312dd35580f579c9e64b32e06edb63}} | |
| 9 | bool {\bfseries operator()} (int m1, int m2) | |
| 10 | \end{DoxyCompactItemize} | |
| 11 | ||
| 12 | ||
| 13 | \subsection{Detailed Description} | |
| 14 | ||
| 15 | ||
| 16 | Definition at line 128 of file operators.\+h. | |
| 17 | ||
| 18 | ||
| 19 | ||
| 20 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 21 | \item | |
| 22 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+h\end{DoxyCompactItemize} |
Binary diff not shown
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| 1 | %%Title: ClassName | |
| 2 | %%Creator: Doxygen | |
| 3 | %%CreationDate: Time | |
| 4 | %%For: | |
| 5 | %Magnification: 1.00 | |
| 6 | %%Orientation: Portrait | |
| 7 | %%BoundingBox: 0 0 500 201.005025 | |
| 8 | %%Pages: 0 | |
| 9 | %%BeginSetup | |
| 10 | %%EndSetup | |
| 11 | %%EndComments | |
| 12 | ||
| 13 | % ----- variables ----- | |
| 14 | ||
| 15 | /boxwidth 0 def | |
| 16 | /boxheight 40 def | |
| 17 | /fontheight 24 def | |
| 18 | /marginwidth 10 def | |
| 19 | /distx 20 def | |
| 20 | /disty 40 def | |
| 21 | /boundaspect 2.487500 def % aspect ratio of the BoundingBox (width/height) | |
| 22 | /boundx 500 def | |
| 23 | /boundy boundx boundaspect div def | |
| 24 | /xspacing 0 def | |
| 25 | /yspacing 0 def | |
| 26 | /rows 2 def | |
| 27 | /cols 1 def | |
| 28 | /scalefactor 0 def | |
| 29 | /boxfont /Times-Roman findfont fontheight scalefont def | |
| 30 | ||
| 31 | % ----- procedures ----- | |
| 32 | ||
| 33 | /dotted { [1 4] 0 setdash } def | |
| 34 | /dashed { [5] 0 setdash } def | |
| 35 | /solid { [] 0 setdash } def | |
| 36 | ||
| 37 | /max % result = MAX(arg1,arg2) | |
| 38 | { | |
| 39 | /a exch def | |
| 40 | /b exch def | |
| 41 | a b gt {a} {b} ifelse | |
| 42 | } def | |
| 43 | ||
| 44 | /xoffset % result = MAX(0,(scalefactor-(boxwidth*cols+distx*(cols-1)))/2) | |
| 45 | { | |
| 46 | 0 scalefactor boxwidth cols mul distx cols 1 sub mul add sub 2 div max | |
| 47 | } def | |
| 48 | ||
| 49 | /cw % boxwidth = MAX(boxwidth, stringwidth(arg1)) | |
| 50 | { | |
| 51 | /str exch def | |
| 52 | /boxwidth boxwidth str stringwidth pop max def | |
| 53 | } def | |
| 54 | ||
| 55 | /box % draws a box with text `arg1' at grid pos (arg2,arg3) | |
| 56 | { gsave | |
| 57 | 2 setlinewidth | |
| 58 | newpath | |
| 59 | exch xspacing mul xoffset add | |
| 60 | exch yspacing mul | |
| 61 | moveto | |
| 62 | boxwidth 0 rlineto | |
| 63 | 0 boxheight rlineto | |
| 64 | boxwidth neg 0 rlineto | |
| 65 | 0 boxheight neg rlineto | |
| 66 | closepath | |
| 67 | dup stringwidth pop neg boxwidth add 2 div | |
| 68 | boxheight fontheight 2 div sub 2 div | |
| 69 | rmoveto show stroke | |
| 70 | grestore | |
| 71 | } def | |
| 72 | ||
| 73 | /mark | |
| 74 | { newpath | |
| 75 | exch xspacing mul xoffset add boxwidth add | |
| 76 | exch yspacing mul | |
| 77 | moveto | |
| 78 | 0 boxheight 4 div rlineto | |
| 79 | boxheight neg 4 div boxheight neg 4 div rlineto | |
| 80 | closepath | |
| 81 | eofill | |
| 82 | stroke | |
| 83 | } def | |
| 84 | ||
| 85 | /arrow | |
| 86 | { newpath | |
| 87 | moveto | |
| 88 | 3 -8 rlineto | |
| 89 | -6 0 rlineto | |
| 90 | 3 8 rlineto | |
| 91 | closepath | |
| 92 | eofill | |
| 93 | stroke | |
| 94 | } def | |
| 95 | ||
| 96 | /out % draws an output connector for the block at (arg1,arg2) | |
| 97 | { | |
| 98 | newpath | |
| 99 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 100 | exch yspacing mul boxheight add | |
| 101 | /y exch def | |
| 102 | /x exch def | |
| 103 | x y moveto | |
| 104 | 0 disty 2 div rlineto | |
| 105 | stroke | |
| 106 | 1 eq { x y disty 2 div add arrow } if | |
| 107 | } def | |
| 108 | ||
| 109 | /in % draws an input connector for the block at (arg1,arg2) | |
| 110 | { | |
| 111 | newpath | |
| 112 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 113 | exch yspacing mul disty 2 div sub | |
| 114 | /y exch def | |
| 115 | /x exch def | |
| 116 | x y moveto | |
| 117 | 0 disty 2 div rlineto | |
| 118 | stroke | |
| 119 | 1 eq { x y disty 2 div add arrow } if | |
| 120 | } def | |
| 121 | ||
| 122 | /hedge | |
| 123 | { | |
| 124 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 125 | exch yspacing mul boxheight 2 div sub | |
| 126 | /y exch def | |
| 127 | /x exch def | |
| 128 | newpath | |
| 129 | x y moveto | |
| 130 | boxwidth 2 div distx add 0 rlineto | |
| 131 | stroke | |
| 132 | 1 eq | |
| 133 | { newpath x boxwidth 2 div distx add add y moveto | |
| 134 | -8 3 rlineto | |
| 135 | 0 -6 rlineto | |
| 136 | 8 3 rlineto | |
| 137 | closepath | |
| 138 | eofill | |
| 139 | stroke | |
| 140 | } if | |
| 141 | } def | |
| 142 | ||
| 143 | /vedge | |
| 144 | { | |
| 145 | /ye exch def | |
| 146 | /ys exch def | |
| 147 | /xs exch def | |
| 148 | newpath | |
| 149 | xs xspacing mul xoffset add boxwidth 2 div add dup | |
| 150 | ys yspacing mul boxheight 2 div sub | |
| 151 | moveto | |
| 152 | ye yspacing mul boxheight 2 div sub | |
| 153 | lineto | |
| 154 | stroke | |
| 155 | } def | |
| 156 | ||
| 157 | /conn % connections the blocks from col `arg1' to `arg2' of row `arg3' | |
| 158 | { | |
| 159 | /ys exch def | |
| 160 | /xe exch def | |
| 161 | /xs exch def | |
| 162 | newpath | |
| 163 | xs xspacing mul xoffset add boxwidth 2 div add | |
| 164 | ys yspacing mul disty 2 div sub | |
| 165 | moveto | |
| 166 | xspacing xe xs sub mul 0 | |
| 167 | rlineto | |
| 168 | stroke | |
| 169 | } def | |
| 170 | ||
| 171 | % ----- main ------ | |
| 172 | ||
| 173 | boxfont setfont | |
| 174 | 1 boundaspect scale | |
| 175 | (IsoSpec::PrecalculatedMarginal) cw | |
| 176 | (IsoSpec::Marginal) cw | |
| 177 | /boxwidth boxwidth marginwidth 2 mul add def | |
| 178 | /xspacing boxwidth distx add def | |
| 179 | /yspacing boxheight disty add def | |
| 180 | /scalefactor | |
| 181 | boxwidth cols mul distx cols 1 sub mul add | |
| 182 | boxheight rows mul disty rows 1 sub mul add boundaspect mul | |
| 183 | max def | |
| 184 | boundx scalefactor div boundy scalefactor div scale | |
| 185 | ||
| 186 | % ----- classes ----- | |
| 187 | ||
| 188 | (IsoSpec::PrecalculatedMarginal) 0.000000 0.000000 box | |
| 189 | (IsoSpec::Marginal) 0.000000 1.000000 box | |
| 190 | ||
| 191 | % ----- relations ----- | |
| 192 | ||
| 193 | solid | |
| 194 | 0 0.000000 0.000000 out | |
| 195 | solid | |
| 196 | 1 0.000000 1.000000 in |
| 0 | \hypertarget{class_iso_spec_1_1_precalculated_marginal}{}\section{Iso\+Spec\+:\+:Precalculated\+Marginal Class Reference} | |
| 1 | \label{class_iso_spec_1_1_precalculated_marginal}\index{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}} | |
| 2 | ||
| 3 | ||
| 4 | Precalculated \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} class. | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$marginal\+Trek++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Precalculated\+Marginal\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=2.000000cm]{class_iso_spec_1_1_precalculated_marginal} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_acb84bd7ba582847655c55bd64d64463e}{Precalculated\+Marginal}} (\mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \&\&m, double l\+Cut\+Off, bool sort=true, int tab\+Size=1000, int hash\+Size=1000) | |
| 21 | \begin{DoxyCompactList}\small\item\em The move constructor (disowns the \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}}). \end{DoxyCompactList}\item | |
| 22 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_a6b7b30cfe90ffba1d2c9d2f0d87107d8}\label{class_iso_spec_1_1_precalculated_marginal_a6b7b30cfe90ffba1d2c9d2f0d87107d8}} | |
| 23 | virtual \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a6b7b30cfe90ffba1d2c9d2f0d87107d8}{$\sim$\+Precalculated\+Marginal}} () | |
| 24 | \begin{DoxyCompactList}\small\item\em Destructor. \end{DoxyCompactList}\item | |
| 25 | bool \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a942b30ace039f80c50125360be4ed4d2}{in\+Range}} (unsigned int idx) const | |
| 26 | \begin{DoxyCompactList}\small\item\em Is there a subisotopologue with a given number? \end{DoxyCompactList}\item | |
| 27 | const double \& \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a07eee6d60635c9c1d6f92c181994e06a}{get\+\_\+l\+Prob}} (int idx) const | |
| 28 | \begin{DoxyCompactList}\small\item\em Get the log-\/probability of the idx-\/th subisotopologue. \end{DoxyCompactList}\item | |
| 29 | const double \& \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a7a38a567eadf16fa2ad41e81c8f55c02}{get\+\_\+e\+Prob}} (int idx) const | |
| 30 | \begin{DoxyCompactList}\small\item\em Get the probability of the idx-\/th subisotopologue. \end{DoxyCompactList}\item | |
| 31 | const double \& \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_ada12caa2e195c1a16c5158a428ea3ed2}{get\+\_\+mass}} (int idx) const | |
| 32 | \begin{DoxyCompactList}\small\item\em Get the mass of the idx-\/th subisotopologue. \end{DoxyCompactList}\item | |
| 33 | const double $\ast$ \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_af5d01500c7efb8cba57399ba11fc7124}{get\+\_\+l\+Probs\+\_\+ptr}} () const | |
| 34 | \begin{DoxyCompactList}\small\item\em Get the table of the log-\/probabilities of subisotopologues. \end{DoxyCompactList}\item | |
| 35 | const double $\ast$ \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a9a768b90299ea16c447a392dbe1123b5}{get\+\_\+masses\+\_\+ptr}} () const | |
| 36 | \begin{DoxyCompactList}\small\item\em Get the table of the masses of subisotopologues. \end{DoxyCompactList}\item | |
| 37 | const Conf \& \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a3ecbbf1263a274cc8e3bc71cd96f0bff}{get\+\_\+conf}} (int idx) const | |
| 38 | \begin{DoxyCompactList}\small\item\em Get the counts of isotopes that define the subisotopologue. \end{DoxyCompactList}\item | |
| 39 | unsigned int \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal_a0dbf1ec53eac9953a354c11e1b0803f9}{get\+\_\+no\+\_\+confs}} () const | |
| 40 | \begin{DoxyCompactList}\small\item\em Get the number of precomputed subisotopologues. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 41 | \subsection*{Protected Attributes} | |
| 42 | \begin{DoxyCompactItemize} | |
| 43 | \item | |
| 44 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_adaba0751ea134b2cbd6c3fdf67c327ea}\label{class_iso_spec_1_1_precalculated_marginal_adaba0751ea134b2cbd6c3fdf67c327ea}} | |
| 45 | std\+::vector$<$ Conf $>$ {\bfseries configurations} | |
| 46 | \item | |
| 47 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_a1197bed742b2139243e9dc71cb8fcdfc}\label{class_iso_spec_1_1_precalculated_marginal_a1197bed742b2139243e9dc71cb8fcdfc}} | |
| 48 | Conf $\ast$ {\bfseries confs} | |
| 49 | \item | |
| 50 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_ad82d7aef36c946ce4f9bbf3ddac70cd1}\label{class_iso_spec_1_1_precalculated_marginal_ad82d7aef36c946ce4f9bbf3ddac70cd1}} | |
| 51 | unsigned int {\bfseries no\+\_\+confs} | |
| 52 | \item | |
| 53 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_a94e78eba4ae89c0d6c811d7bc0085684}\label{class_iso_spec_1_1_precalculated_marginal_a94e78eba4ae89c0d6c811d7bc0085684}} | |
| 54 | double $\ast$ {\bfseries masses} | |
| 55 | \item | |
| 56 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_afd5a4a7b094038f66eda31c6827a66f9}\label{class_iso_spec_1_1_precalculated_marginal_afd5a4a7b094038f66eda31c6827a66f9}} | |
| 57 | double $\ast$ {\bfseries l\+Probs} | |
| 58 | \item | |
| 59 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_abf3e9faabf5011f75cfb8e89cb3cdcca}\label{class_iso_spec_1_1_precalculated_marginal_abf3e9faabf5011f75cfb8e89cb3cdcca}} | |
| 60 | double $\ast$ {\bfseries e\+Probs} | |
| 61 | \item | |
| 62 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_add0495cfc67fd8b9757b93b07d47e6cf}\label{class_iso_spec_1_1_precalculated_marginal_add0495cfc67fd8b9757b93b07d47e6cf}} | |
| 63 | \mbox{\hyperlink{class_iso_spec_1_1_allocator}{Allocator}}$<$ int $>$ {\bfseries allocator} | |
| 64 | \end{DoxyCompactItemize} | |
| 65 | ||
| 66 | ||
| 67 | \subsection{Detailed Description} | |
| 68 | Precalculated \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} class. | |
| 69 | ||
| 70 | This class serves to calculate a set of isotopologues that is defined by the minimal probability threshold. | |
| 71 | ||
| 72 | This works faster than if you did not know the threshold. If you have no idea about the threshold, you would need to call us, to change encode the layered version of the marginal. | |
| 73 | ||
| 74 | Definition at line 213 of file marginal\+Trek++.\+h. | |
| 75 | ||
| 76 | ||
| 77 | ||
| 78 | \subsection{Constructor \& Destructor Documentation} | |
| 79 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_acb84bd7ba582847655c55bd64d64463e}\label{class_iso_spec_1_1_precalculated_marginal_acb84bd7ba582847655c55bd64d64463e}} | |
| 80 | \index{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}!Precalculated\+Marginal@{Precalculated\+Marginal}} | |
| 81 | \index{Precalculated\+Marginal@{Precalculated\+Marginal}!Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}} | |
| 82 | \subsubsection{\texorpdfstring{Precalculated\+Marginal()}{PrecalculatedMarginal()}} | |
| 83 | {\footnotesize\ttfamily Iso\+Spec\+::\+Precalculated\+Marginal\+::\+Precalculated\+Marginal (\begin{DoxyParamCaption}\item[{\mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \&\&}]{m, }\item[{double}]{l\+Cut\+Off, }\item[{bool}]{sort = {\ttfamily true}, }\item[{int}]{tab\+Size = {\ttfamily 1000}, }\item[{int}]{hash\+Size = {\ttfamily 1000} }\end{DoxyParamCaption})} | |
| 84 | ||
| 85 | ||
| 86 | ||
| 87 | The move constructor (disowns the \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}}). | |
| 88 | ||
| 89 | This constructor memoizes all subisotopologues with log-\/probability above the provided threshold l\+Cut\+Off | |
| 90 | \begin{DoxyParams}{Parameters} | |
| 91 | {\em \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}}} & An instance of the \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} class this class is about to disown. \\ | |
| 92 | \hline | |
| 93 | {\em l\+Cut\+Off} & The lower limit on the log-\/probability of the precomputed subisotopologues. \\ | |
| 94 | \hline | |
| 95 | {\em sort} & Should the subisotopologues be stored with descending probability ? \\ | |
| 96 | \hline | |
| 97 | \end{DoxyParams} | |
| 98 | \begin{DoxyReturn}{Returns} | |
| 99 | An instance of the \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal}{Precalculated\+Marginal}} class. | |
| 100 | \end{DoxyReturn} | |
| 101 | ||
| 102 | ||
| 103 | Definition at line 362 of file marginal\+Trek++.\+cpp. | |
| 104 | ||
| 105 | ||
| 106 | ||
| 107 | \subsection{Member Function Documentation} | |
| 108 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_a3ecbbf1263a274cc8e3bc71cd96f0bff}\label{class_iso_spec_1_1_precalculated_marginal_a3ecbbf1263a274cc8e3bc71cd96f0bff}} | |
| 109 | \index{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}!get\+\_\+conf@{get\+\_\+conf}} | |
| 110 | \index{get\+\_\+conf@{get\+\_\+conf}!Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}} | |
| 111 | \subsubsection{\texorpdfstring{get\+\_\+conf()}{get\_conf()}} | |
| 112 | {\footnotesize\ttfamily const Conf\& Iso\+Spec\+::\+Precalculated\+Marginal\+::get\+\_\+conf (\begin{DoxyParamCaption}\item[{int}]{idx }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 113 | ||
| 114 | ||
| 115 | ||
| 116 | Get the counts of isotopes that define the subisotopologue. | |
| 117 | ||
| 118 | ||
| 119 | \begin{DoxyParams}{Parameters} | |
| 120 | {\em idx} & The number of the considered subisotopologue. \\ | |
| 121 | \hline | |
| 122 | \end{DoxyParams} | |
| 123 | \begin{DoxyReturn}{Returns} | |
| 124 | The counts of isotopes that define the subisotopologue. | |
| 125 | \end{DoxyReturn} | |
| 126 | ||
| 127 | ||
| 128 | Definition at line 288 of file marginal\+Trek++.\+h. | |
| 129 | ||
| 130 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_a7a38a567eadf16fa2ad41e81c8f55c02}\label{class_iso_spec_1_1_precalculated_marginal_a7a38a567eadf16fa2ad41e81c8f55c02}} | |
| 131 | \index{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}!get\+\_\+e\+Prob@{get\+\_\+e\+Prob}} | |
| 132 | \index{get\+\_\+e\+Prob@{get\+\_\+e\+Prob}!Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}} | |
| 133 | \subsubsection{\texorpdfstring{get\+\_\+e\+Prob()}{get\_eProb()}} | |
| 134 | {\footnotesize\ttfamily const double\& Iso\+Spec\+::\+Precalculated\+Marginal\+::get\+\_\+e\+Prob (\begin{DoxyParamCaption}\item[{int}]{idx }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 135 | ||
| 136 | ||
| 137 | ||
| 138 | Get the probability of the idx-\/th subisotopologue. | |
| 139 | ||
| 140 | ||
| 141 | \begin{DoxyParams}{Parameters} | |
| 142 | {\em idx} & The number of the considered subisotopologue. \\ | |
| 143 | \hline | |
| 144 | \end{DoxyParams} | |
| 145 | \begin{DoxyReturn}{Returns} | |
| 146 | The probability of the idx-\/th subisotopologue. | |
| 147 | \end{DoxyReturn} | |
| 148 | ||
| 149 | ||
| 150 | Definition at line 261 of file marginal\+Trek++.\+h. | |
| 151 | ||
| 152 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_a07eee6d60635c9c1d6f92c181994e06a}\label{class_iso_spec_1_1_precalculated_marginal_a07eee6d60635c9c1d6f92c181994e06a}} | |
| 153 | \index{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}!get\+\_\+l\+Prob@{get\+\_\+l\+Prob}} | |
| 154 | \index{get\+\_\+l\+Prob@{get\+\_\+l\+Prob}!Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}} | |
| 155 | \subsubsection{\texorpdfstring{get\+\_\+l\+Prob()}{get\_lProb()}} | |
| 156 | {\footnotesize\ttfamily const double\& Iso\+Spec\+::\+Precalculated\+Marginal\+::get\+\_\+l\+Prob (\begin{DoxyParamCaption}\item[{int}]{idx }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 157 | ||
| 158 | ||
| 159 | ||
| 160 | Get the log-\/probability of the idx-\/th subisotopologue. | |
| 161 | ||
| 162 | ||
| 163 | \begin{DoxyParams}{Parameters} | |
| 164 | {\em idx} & The number of the considered subisotopologue. \\ | |
| 165 | \hline | |
| 166 | \end{DoxyParams} | |
| 167 | \begin{DoxyReturn}{Returns} | |
| 168 | The log-\/probability of the idx-\/th subisotopologue. | |
| 169 | \end{DoxyReturn} | |
| 170 | ||
| 171 | ||
| 172 | Definition at line 254 of file marginal\+Trek++.\+h. | |
| 173 | ||
| 174 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_af5d01500c7efb8cba57399ba11fc7124}\label{class_iso_spec_1_1_precalculated_marginal_af5d01500c7efb8cba57399ba11fc7124}} | |
| 175 | \index{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}!get\+\_\+l\+Probs\+\_\+ptr@{get\+\_\+l\+Probs\+\_\+ptr}} | |
| 176 | \index{get\+\_\+l\+Probs\+\_\+ptr@{get\+\_\+l\+Probs\+\_\+ptr}!Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}} | |
| 177 | \subsubsection{\texorpdfstring{get\+\_\+l\+Probs\+\_\+ptr()}{get\_lProbs\_ptr()}} | |
| 178 | {\footnotesize\ttfamily const double$\ast$ Iso\+Spec\+::\+Precalculated\+Marginal\+::get\+\_\+l\+Probs\+\_\+ptr (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 179 | ||
| 180 | ||
| 181 | ||
| 182 | Get the table of the log-\/probabilities of subisotopologues. | |
| 183 | ||
| 184 | \begin{DoxyReturn}{Returns} | |
| 185 | Pointer to the first element in the table storing log-\/probabilities of subisotopologues. | |
| 186 | \end{DoxyReturn} | |
| 187 | ||
| 188 | ||
| 189 | Definition at line 274 of file marginal\+Trek++.\+h. | |
| 190 | ||
| 191 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_ada12caa2e195c1a16c5158a428ea3ed2}\label{class_iso_spec_1_1_precalculated_marginal_ada12caa2e195c1a16c5158a428ea3ed2}} | |
| 192 | \index{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}!get\+\_\+mass@{get\+\_\+mass}} | |
| 193 | \index{get\+\_\+mass@{get\+\_\+mass}!Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}} | |
| 194 | \subsubsection{\texorpdfstring{get\+\_\+mass()}{get\_mass()}} | |
| 195 | {\footnotesize\ttfamily const double\& Iso\+Spec\+::\+Precalculated\+Marginal\+::get\+\_\+mass (\begin{DoxyParamCaption}\item[{int}]{idx }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 196 | ||
| 197 | ||
| 198 | ||
| 199 | Get the mass of the idx-\/th subisotopologue. | |
| 200 | ||
| 201 | ||
| 202 | \begin{DoxyParams}{Parameters} | |
| 203 | {\em idx} & The number of the considered subisotopologue. \\ | |
| 204 | \hline | |
| 205 | \end{DoxyParams} | |
| 206 | \begin{DoxyReturn}{Returns} | |
| 207 | The mass of the idx-\/th subisotopologue. | |
| 208 | \end{DoxyReturn} | |
| 209 | ||
| 210 | ||
| 211 | Definition at line 268 of file marginal\+Trek++.\+h. | |
| 212 | ||
| 213 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_a9a768b90299ea16c447a392dbe1123b5}\label{class_iso_spec_1_1_precalculated_marginal_a9a768b90299ea16c447a392dbe1123b5}} | |
| 214 | \index{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}!get\+\_\+masses\+\_\+ptr@{get\+\_\+masses\+\_\+ptr}} | |
| 215 | \index{get\+\_\+masses\+\_\+ptr@{get\+\_\+masses\+\_\+ptr}!Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}} | |
| 216 | \subsubsection{\texorpdfstring{get\+\_\+masses\+\_\+ptr()}{get\_masses\_ptr()}} | |
| 217 | {\footnotesize\ttfamily const double$\ast$ Iso\+Spec\+::\+Precalculated\+Marginal\+::get\+\_\+masses\+\_\+ptr (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 218 | ||
| 219 | ||
| 220 | ||
| 221 | Get the table of the masses of subisotopologues. | |
| 222 | ||
| 223 | \begin{DoxyReturn}{Returns} | |
| 224 | Pointer to the first element in the table storing masses of subisotopologues. | |
| 225 | \end{DoxyReturn} | |
| 226 | ||
| 227 | ||
| 228 | Definition at line 280 of file marginal\+Trek++.\+h. | |
| 229 | ||
| 230 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_a0dbf1ec53eac9953a354c11e1b0803f9}\label{class_iso_spec_1_1_precalculated_marginal_a0dbf1ec53eac9953a354c11e1b0803f9}} | |
| 231 | \index{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}!get\+\_\+no\+\_\+confs@{get\+\_\+no\+\_\+confs}} | |
| 232 | \index{get\+\_\+no\+\_\+confs@{get\+\_\+no\+\_\+confs}!Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}} | |
| 233 | \subsubsection{\texorpdfstring{get\+\_\+no\+\_\+confs()}{get\_no\_confs()}} | |
| 234 | {\footnotesize\ttfamily unsigned int Iso\+Spec\+::\+Precalculated\+Marginal\+::get\+\_\+no\+\_\+confs (\begin{DoxyParamCaption}{ }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 235 | ||
| 236 | ||
| 237 | ||
| 238 | Get the number of precomputed subisotopologues. | |
| 239 | ||
| 240 | \begin{DoxyReturn}{Returns} | |
| 241 | The number of precomputed subisotopologues. | |
| 242 | \end{DoxyReturn} | |
| 243 | ||
| 244 | ||
| 245 | Definition at line 294 of file marginal\+Trek++.\+h. | |
| 246 | ||
| 247 | \mbox{\Hypertarget{class_iso_spec_1_1_precalculated_marginal_a942b30ace039f80c50125360be4ed4d2}\label{class_iso_spec_1_1_precalculated_marginal_a942b30ace039f80c50125360be4ed4d2}} | |
| 248 | \index{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}!in\+Range@{in\+Range}} | |
| 249 | \index{in\+Range@{in\+Range}!Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}} | |
| 250 | \subsubsection{\texorpdfstring{in\+Range()}{inRange()}} | |
| 251 | {\footnotesize\ttfamily bool Iso\+Spec\+::\+Precalculated\+Marginal\+::in\+Range (\begin{DoxyParamCaption}\item[{unsigned int}]{idx }\end{DoxyParamCaption}) const\hspace{0.3cm}{\ttfamily [inline]}} | |
| 252 | ||
| 253 | ||
| 254 | ||
| 255 | Is there a subisotopologue with a given number? | |
| 256 | ||
| 257 | \begin{DoxyReturn}{Returns} | |
| 258 | Returns true if idx does not exceed the number of pre-\/computed configurations. | |
| 259 | \end{DoxyReturn} | |
| 260 | ||
| 261 | ||
| 262 | Definition at line 247 of file marginal\+Trek++.\+h. | |
| 263 | ||
| 264 | ||
| 265 | ||
| 266 | The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize} | |
| 267 | \item | |
| 268 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/marginal\+Trek++.\+h\item | |
| 269 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/marginal\+Trek++.\+cpp\end{DoxyCompactItemize} |
| 0 | digraph "IsoSpec::PrecalculatedMarginal" | |
| 1 | { | |
| 2 | edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; | |
| 3 | node [fontname="Helvetica",fontsize="10",shape=record]; | |
| 4 | Node2 [label="IsoSpec::PrecalculatedMarginal",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; | |
| 5 | Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid"]; | |
| 6 | Node3 [label="IsoSpec::Marginal",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_marginal.html"]; | |
| 7 | Node4 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" allocator" ]; | |
| 8 | Node4 [label="IsoSpec::Allocator\l\< int \>",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_allocator.html"]; | |
| 9 | } |
| 0 | 370f0997aff4a92279b0a33957b4ec2e⏎ |
| 0 | digraph "IsoSpec::PrecalculatedMarginal" | |
| 1 | { | |
| 2 | edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; | |
| 3 | node [fontname="Helvetica",fontsize="10",shape=record]; | |
| 4 | Node0 [label="IsoSpec::PrecalculatedMarginal",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; | |
| 5 | Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid"]; | |
| 6 | Node1 [label="IsoSpec::Marginal",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$class_iso_spec_1_1_marginal.html"]; | |
| 7 | } |
| 0 | 7bdbf77a07d1dbe61d90a7b1a74d2730⏎ |
| 0 | \hypertarget{class_iso_spec_1_1_reverse_order}{}\section{Iso\+Spec\+:\+:Reverse\+Order$<$ T $>$ Class Template Reference} | |
| 1 | \label{class_iso_spec_1_1_reverse_order}\index{Iso\+Spec\+::\+Reverse\+Order$<$ T $>$@{Iso\+Spec\+::\+Reverse\+Order$<$ T $>$}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_reverse_order_a350cba89162d701a0f0f4cf1e4424e44}\label{class_iso_spec_1_1_reverse_order_a350cba89162d701a0f0f4cf1e4424e44}} | |
| 6 | bool {\bfseries operator()} (const T a, const T b) const | |
| 7 | \end{DoxyCompactItemize} | |
| 8 | ||
| 9 | ||
| 10 | \subsection{Detailed Description} | |
| 11 | \subsubsection*{template$<$typename T$>$\newline | |
| 12 | class Iso\+Spec\+::\+Reverse\+Order$<$ T $>$} | |
| 13 | ||
| 14 | ||
| 15 | ||
| 16 | Definition at line 106 of file operators.\+h. | |
| 17 | ||
| 18 | ||
| 19 | ||
| 20 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 21 | \item | |
| 22 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+h\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_s_summator}{}\section{Iso\+Spec\+:\+:S\+Summator Class Reference} | |
| 1 | \label{class_iso_spec_1_1_s_summator}\index{Iso\+Spec\+::\+S\+Summator@{Iso\+Spec\+::\+S\+Summator}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_s_summator_a5173dbb75fb32ad67bf3abd1ae6f9dc6}\label{class_iso_spec_1_1_s_summator_a5173dbb75fb32ad67bf3abd1ae6f9dc6}} | |
| 6 | {\bfseries S\+Summator} (\mbox{\hyperlink{class_iso_spec_1_1_s_summator}{S\+Summator}} \&other) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_s_summator_aad1c7ce5e38ce2da7d9e39f43e647402}\label{class_iso_spec_1_1_s_summator_aad1c7ce5e38ce2da7d9e39f43e647402}} | |
| 9 | void {\bfseries add} (double x) | |
| 10 | \item | |
| 11 | \mbox{\Hypertarget{class_iso_spec_1_1_s_summator_ab7b2c53b5e9258aa4c7e7707089fbb6a}\label{class_iso_spec_1_1_s_summator_ab7b2c53b5e9258aa4c7e7707089fbb6a}} | |
| 12 | double {\bfseries get} () | |
| 13 | \end{DoxyCompactItemize} | |
| 14 | ||
| 15 | ||
| 16 | \subsection{Detailed Description} | |
| 17 | ||
| 18 | ||
| 19 | Definition at line 25 of file summator.\+h. | |
| 20 | ||
| 21 | ||
| 22 | ||
| 23 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 24 | \item | |
| 25 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/summator.\+h\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_summator}{}\section{Iso\+Spec\+:\+:Summator Class Reference} | |
| 1 | \label{class_iso_spec_1_1_summator}\index{Iso\+Spec\+::\+Summator@{Iso\+Spec\+::\+Summator}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_summator_a1b032359eb84e5788ab31c3ad3932008}\label{class_iso_spec_1_1_summator_a1b032359eb84e5788ab31c3ad3932008}} | |
| 6 | void {\bfseries add} (double what) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_summator_a87f3249839e99b41d3c16aeed75204fa}\label{class_iso_spec_1_1_summator_a87f3249839e99b41d3c16aeed75204fa}} | |
| 9 | double {\bfseries get} () | |
| 10 | \end{DoxyCompactItemize} | |
| 11 | ||
| 12 | ||
| 13 | \subsection{Detailed Description} | |
| 14 | ||
| 15 | ||
| 16 | Definition at line 76 of file summator.\+h. | |
| 17 | ||
| 18 | ||
| 19 | ||
| 20 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 21 | \item | |
| 22 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/summator.\+h\end{DoxyCompactItemize} |
| 0 | %!PS-Adobe-2.0 EPSF-2.0 | |
| 1 | %%Title: ClassName | |
| 2 | %%Creator: Doxygen | |
| 3 | %%CreationDate: Time | |
| 4 | %%For: | |
| 5 | %Magnification: 1.00 | |
| 6 | %%Orientation: Portrait | |
| 7 | %%BoundingBox: 0 0 500 301.507538 | |
| 8 | %%Pages: 0 | |
| 9 | %%BeginSetup | |
| 10 | %%EndSetup | |
| 11 | %%EndComments | |
| 12 | ||
| 13 | % ----- variables ----- | |
| 14 | ||
| 15 | /boxwidth 0 def | |
| 16 | /boxheight 40 def | |
| 17 | /fontheight 24 def | |
| 18 | /marginwidth 10 def | |
| 19 | /distx 20 def | |
| 20 | /disty 40 def | |
| 21 | /boundaspect 1.658333 def % aspect ratio of the BoundingBox (width/height) | |
| 22 | /boundx 500 def | |
| 23 | /boundy boundx boundaspect div def | |
| 24 | /xspacing 0 def | |
| 25 | /yspacing 0 def | |
| 26 | /rows 3 def | |
| 27 | /cols 1 def | |
| 28 | /scalefactor 0 def | |
| 29 | /boxfont /Times-Roman findfont fontheight scalefont def | |
| 30 | ||
| 31 | % ----- procedures ----- | |
| 32 | ||
| 33 | /dotted { [1 4] 0 setdash } def | |
| 34 | /dashed { [5] 0 setdash } def | |
| 35 | /solid { [] 0 setdash } def | |
| 36 | ||
| 37 | /max % result = MAX(arg1,arg2) | |
| 38 | { | |
| 39 | /a exch def | |
| 40 | /b exch def | |
| 41 | a b gt {a} {b} ifelse | |
| 42 | } def | |
| 43 | ||
| 44 | /xoffset % result = MAX(0,(scalefactor-(boxwidth*cols+distx*(cols-1)))/2) | |
| 45 | { | |
| 46 | 0 scalefactor boxwidth cols mul distx cols 1 sub mul add sub 2 div max | |
| 47 | } def | |
| 48 | ||
| 49 | /cw % boxwidth = MAX(boxwidth, stringwidth(arg1)) | |
| 50 | { | |
| 51 | /str exch def | |
| 52 | /boxwidth boxwidth str stringwidth pop max def | |
| 53 | } def | |
| 54 | ||
| 55 | /box % draws a box with text `arg1' at grid pos (arg2,arg3) | |
| 56 | { gsave | |
| 57 | 2 setlinewidth | |
| 58 | newpath | |
| 59 | exch xspacing mul xoffset add | |
| 60 | exch yspacing mul | |
| 61 | moveto | |
| 62 | boxwidth 0 rlineto | |
| 63 | 0 boxheight rlineto | |
| 64 | boxwidth neg 0 rlineto | |
| 65 | 0 boxheight neg rlineto | |
| 66 | closepath | |
| 67 | dup stringwidth pop neg boxwidth add 2 div | |
| 68 | boxheight fontheight 2 div sub 2 div | |
| 69 | rmoveto show stroke | |
| 70 | grestore | |
| 71 | } def | |
| 72 | ||
| 73 | /mark | |
| 74 | { newpath | |
| 75 | exch xspacing mul xoffset add boxwidth add | |
| 76 | exch yspacing mul | |
| 77 | moveto | |
| 78 | 0 boxheight 4 div rlineto | |
| 79 | boxheight neg 4 div boxheight neg 4 div rlineto | |
| 80 | closepath | |
| 81 | eofill | |
| 82 | stroke | |
| 83 | } def | |
| 84 | ||
| 85 | /arrow | |
| 86 | { newpath | |
| 87 | moveto | |
| 88 | 3 -8 rlineto | |
| 89 | -6 0 rlineto | |
| 90 | 3 8 rlineto | |
| 91 | closepath | |
| 92 | eofill | |
| 93 | stroke | |
| 94 | } def | |
| 95 | ||
| 96 | /out % draws an output connector for the block at (arg1,arg2) | |
| 97 | { | |
| 98 | newpath | |
| 99 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 100 | exch yspacing mul boxheight add | |
| 101 | /y exch def | |
| 102 | /x exch def | |
| 103 | x y moveto | |
| 104 | 0 disty 2 div rlineto | |
| 105 | stroke | |
| 106 | 1 eq { x y disty 2 div add arrow } if | |
| 107 | } def | |
| 108 | ||
| 109 | /in % draws an input connector for the block at (arg1,arg2) | |
| 110 | { | |
| 111 | newpath | |
| 112 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 113 | exch yspacing mul disty 2 div sub | |
| 114 | /y exch def | |
| 115 | /x exch def | |
| 116 | x y moveto | |
| 117 | 0 disty 2 div rlineto | |
| 118 | stroke | |
| 119 | 1 eq { x y disty 2 div add arrow } if | |
| 120 | } def | |
| 121 | ||
| 122 | /hedge | |
| 123 | { | |
| 124 | exch xspacing mul xoffset add boxwidth 2 div add | |
| 125 | exch yspacing mul boxheight 2 div sub | |
| 126 | /y exch def | |
| 127 | /x exch def | |
| 128 | newpath | |
| 129 | x y moveto | |
| 130 | boxwidth 2 div distx add 0 rlineto | |
| 131 | stroke | |
| 132 | 1 eq | |
| 133 | { newpath x boxwidth 2 div distx add add y moveto | |
| 134 | -8 3 rlineto | |
| 135 | 0 -6 rlineto | |
| 136 | 8 3 rlineto | |
| 137 | closepath | |
| 138 | eofill | |
| 139 | stroke | |
| 140 | } if | |
| 141 | } def | |
| 142 | ||
| 143 | /vedge | |
| 144 | { | |
| 145 | /ye exch def | |
| 146 | /ys exch def | |
| 147 | /xs exch def | |
| 148 | newpath | |
| 149 | xs xspacing mul xoffset add boxwidth 2 div add dup | |
| 150 | ys yspacing mul boxheight 2 div sub | |
| 151 | moveto | |
| 152 | ye yspacing mul boxheight 2 div sub | |
| 153 | lineto | |
| 154 | stroke | |
| 155 | } def | |
| 156 | ||
| 157 | /conn % connections the blocks from col `arg1' to `arg2' of row `arg3' | |
| 158 | { | |
| 159 | /ys exch def | |
| 160 | /xe exch def | |
| 161 | /xs exch def | |
| 162 | newpath | |
| 163 | xs xspacing mul xoffset add boxwidth 2 div add | |
| 164 | ys yspacing mul disty 2 div sub | |
| 165 | moveto | |
| 166 | xspacing xe xs sub mul 0 | |
| 167 | rlineto | |
| 168 | stroke | |
| 169 | } def | |
| 170 | ||
| 171 | % ----- main ------ | |
| 172 | ||
| 173 | boxfont setfont | |
| 174 | 1 boundaspect scale | |
| 175 | (IsoSpec::SyncMarginal) cw | |
| 176 | (IsoSpec::PrecalculatedMarginal) cw | |
| 177 | (IsoSpec::Marginal) cw | |
| 178 | /boxwidth boxwidth marginwidth 2 mul add def | |
| 179 | /xspacing boxwidth distx add def | |
| 180 | /yspacing boxheight disty add def | |
| 181 | /scalefactor | |
| 182 | boxwidth cols mul distx cols 1 sub mul add | |
| 183 | boxheight rows mul disty rows 1 sub mul add boundaspect mul | |
| 184 | max def | |
| 185 | boundx scalefactor div boundy scalefactor div scale | |
| 186 | ||
| 187 | % ----- classes ----- | |
| 188 | ||
| 189 | (IsoSpec::SyncMarginal) 0.000000 0.000000 box | |
| 190 | (IsoSpec::PrecalculatedMarginal) 0.000000 1.000000 box | |
| 191 | (IsoSpec::Marginal) 0.000000 2.000000 box | |
| 192 | ||
| 193 | % ----- relations ----- | |
| 194 | ||
| 195 | solid | |
| 196 | 0 0.000000 0.000000 out | |
| 197 | solid | |
| 198 | 1 0.000000 1.000000 in | |
| 199 | solid | |
| 200 | 0 0.000000 1.000000 out | |
| 201 | solid | |
| 202 | 1 0.000000 2.000000 in |
| 0 | \hypertarget{class_iso_spec_1_1_sync_marginal}{}\section{Iso\+Spec\+:\+:Sync\+Marginal Class Reference} | |
| 1 | \label{class_iso_spec_1_1_sync_marginal}\index{Iso\+Spec\+::\+Sync\+Marginal@{Iso\+Spec\+::\+Sync\+Marginal}} | |
| 2 | ||
| 3 | ||
| 4 | Big experiment for multi-\/threaded version of the algorithm, do not touch. | |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | ||
| 9 | {\ttfamily \#include $<$marginal\+Trek++.\+h$>$} | |
| 10 | ||
| 11 | Inheritance diagram for Iso\+Spec\+:\+:Sync\+Marginal\+:\begin{figure}[H] | |
| 12 | \begin{center} | |
| 13 | \leavevmode | |
| 14 | \includegraphics[height=3.000000cm]{class_iso_spec_1_1_sync_marginal} | |
| 15 | \end{center} | |
| 16 | \end{figure} | |
| 17 | \subsection*{Public Member Functions} | |
| 18 | \begin{DoxyCompactItemize} | |
| 19 | \item | |
| 20 | \mbox{\Hypertarget{class_iso_spec_1_1_sync_marginal_a81bb7f17ae1f2618813cf02e4d2b2f8c}\label{class_iso_spec_1_1_sync_marginal_a81bb7f17ae1f2618813cf02e4d2b2f8c}} | |
| 21 | \mbox{\hyperlink{class_iso_spec_1_1_sync_marginal_a81bb7f17ae1f2618813cf02e4d2b2f8c}{Sync\+Marginal}} (\mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} \&\&m, double l\+Cut\+Off, int tab\+Size=1000, int hash\+Size=1000) | |
| 22 | \begin{DoxyCompactList}\small\item\em likewise... \end{DoxyCompactList}\item | |
| 23 | \mbox{\Hypertarget{class_iso_spec_1_1_sync_marginal_a2029b97d45da908ab2ee9a1a0d72cbd3}\label{class_iso_spec_1_1_sync_marginal_a2029b97d45da908ab2ee9a1a0d72cbd3}} | |
| 24 | unsigned int {\bfseries get\+Next\+Conf\+Idx} () | |
| 25 | \item | |
| 26 | \mbox{\Hypertarget{class_iso_spec_1_1_sync_marginal_ad52b7503991e3378cb5f645e6a45b665}\label{class_iso_spec_1_1_sync_marginal_ad52b7503991e3378cb5f645e6a45b665}} | |
| 27 | unsigned int {\bfseries get\+Next\+Conf\+Idxw\+Mass} (double mmin, double mmax) | |
| 28 | \end{DoxyCompactItemize} | |
| 29 | \subsection*{Protected Attributes} | |
| 30 | \begin{DoxyCompactItemize} | |
| 31 | \item | |
| 32 | \mbox{\Hypertarget{class_iso_spec_1_1_sync_marginal_a1f01c6fe03bdc15928f577f87764b221}\label{class_iso_spec_1_1_sync_marginal_a1f01c6fe03bdc15928f577f87764b221}} | |
| 33 | char {\bfseries padding} \mbox{[}64\mbox{]} | |
| 34 | \item | |
| 35 | \mbox{\Hypertarget{class_iso_spec_1_1_sync_marginal_a88c68e76999fb1e95120172ce050b645}\label{class_iso_spec_1_1_sync_marginal_a88c68e76999fb1e95120172ce050b645}} | |
| 36 | std\+::atomic$<$ unsigned int $>$ {\bfseries counter} | |
| 37 | \item | |
| 38 | \mbox{\Hypertarget{class_iso_spec_1_1_sync_marginal_ad8c8fda5c6d7f772ed814fb318d58a58}\label{class_iso_spec_1_1_sync_marginal_ad8c8fda5c6d7f772ed814fb318d58a58}} | |
| 39 | char {\bfseries padding2} \mbox{[}64\mbox{]} | |
| 40 | \end{DoxyCompactItemize} | |
| 41 | ||
| 42 | ||
| 43 | \subsection{Detailed Description} | |
| 44 | Big experiment for multi-\/threaded version of the algorithm, do not touch. | |
| 45 | ||
| 46 | Definition at line 298 of file marginal\+Trek++.\+h. | |
| 47 | ||
| 48 | ||
| 49 | ||
| 50 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 51 | \item | |
| 52 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/marginal\+Trek++.\+h\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_t_summator}{}\section{Iso\+Spec\+:\+:T\+Summator Class Reference} | |
| 1 | \label{class_iso_spec_1_1_t_summator}\index{Iso\+Spec\+::\+T\+Summator@{Iso\+Spec\+::\+T\+Summator}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_t_summator_a5645d3fdac4e35f023fe7a08646dc413}\label{class_iso_spec_1_1_t_summator_a5645d3fdac4e35f023fe7a08646dc413}} | |
| 6 | void {\bfseries add} (double what) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_t_summator_a0db3add5376aae480fcaa3f489898bd7}\label{class_iso_spec_1_1_t_summator_a0db3add5376aae480fcaa3f489898bd7}} | |
| 9 | double {\bfseries get} () | |
| 10 | \end{DoxyCompactItemize} | |
| 11 | ||
| 12 | ||
| 13 | \subsection{Detailed Description} | |
| 14 | ||
| 15 | ||
| 16 | Definition at line 99 of file summator.\+h. | |
| 17 | ||
| 18 | ||
| 19 | ||
| 20 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 21 | \item | |
| 22 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/summator.\+h\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_table_order}{}\section{Iso\+Spec\+:\+:Table\+Order$<$ T $>$ Class Template Reference} | |
| 1 | \label{class_iso_spec_1_1_table_order}\index{Iso\+Spec\+::\+Table\+Order$<$ T $>$@{Iso\+Spec\+::\+Table\+Order$<$ T $>$}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_table_order_a82a2474a7990bf0a55e269ea2dabada5}\label{class_iso_spec_1_1_table_order_a82a2474a7990bf0a55e269ea2dabada5}} | |
| 6 | {\bfseries Table\+Order} (const T $\ast$\+\_\+tbl) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_table_order_a35b990bbb3f8c3ba0551c0938a5145c8}\label{class_iso_spec_1_1_table_order_a35b990bbb3f8c3ba0551c0938a5145c8}} | |
| 9 | bool {\bfseries operator()} (unsigned int i, unsigned int j) | |
| 10 | \end{DoxyCompactItemize} | |
| 11 | ||
| 12 | ||
| 13 | \subsection{Detailed Description} | |
| 14 | \subsubsection*{template$<$typename T$>$\newline | |
| 15 | class Iso\+Spec\+::\+Table\+Order$<$ T $>$} | |
| 16 | ||
| 17 | ||
| 18 | ||
| 19 | Definition at line 113 of file operators.\+h. | |
| 20 | ||
| 21 | ||
| 22 | ||
| 23 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 24 | \item | |
| 25 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/operators.\+h\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_tabulator}{}\section{Iso\+Spec\+:\+:Tabulator$<$ T $>$ Class Template Reference} | |
| 1 | \label{class_iso_spec_1_1_tabulator}\index{Iso\+Spec\+::\+Tabulator$<$ T $>$@{Iso\+Spec\+::\+Tabulator$<$ T $>$}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_tabulator_a57acb4ba7687ac95916c00fd9cd4f4c7}\label{class_iso_spec_1_1_tabulator_a57acb4ba7687ac95916c00fd9cd4f4c7}} | |
| 6 | {\bfseries Tabulator} (T $\ast$generator, bool get\+\_\+masses, bool get\+\_\+probs, bool get\+\_\+lprobs, bool get\+\_\+confs) | |
| 7 | \item | |
| 8 | \mbox{\Hypertarget{class_iso_spec_1_1_tabulator_ae256b348fc6c5d24d540c33094a37df9}\label{class_iso_spec_1_1_tabulator_ae256b348fc6c5d24d540c33094a37df9}} | |
| 9 | double $\ast$ {\bfseries masses} () | |
| 10 | \item | |
| 11 | \mbox{\Hypertarget{class_iso_spec_1_1_tabulator_a486be3022d437b81b4932dd61ca4a0e5}\label{class_iso_spec_1_1_tabulator_a486be3022d437b81b4932dd61ca4a0e5}} | |
| 12 | double $\ast$ {\bfseries lprobs} () | |
| 13 | \item | |
| 14 | \mbox{\Hypertarget{class_iso_spec_1_1_tabulator_a0c572de1f59a3c664c55e55760be2f18}\label{class_iso_spec_1_1_tabulator_a0c572de1f59a3c664c55e55760be2f18}} | |
| 15 | double $\ast$ {\bfseries probs} () | |
| 16 | \item | |
| 17 | \mbox{\Hypertarget{class_iso_spec_1_1_tabulator_a8000f897020376b6a03fb75dafb997f1}\label{class_iso_spec_1_1_tabulator_a8000f897020376b6a03fb75dafb997f1}} | |
| 18 | int $\ast$ {\bfseries confs} () | |
| 19 | \item | |
| 20 | \mbox{\Hypertarget{class_iso_spec_1_1_tabulator_acdbd459f1ec95dfd17cc0617cda02fba}\label{class_iso_spec_1_1_tabulator_acdbd459f1ec95dfd17cc0617cda02fba}} | |
| 21 | size\+\_\+t {\bfseries confs\+\_\+no} () | |
| 22 | \end{DoxyCompactItemize} | |
| 23 | ||
| 24 | ||
| 25 | \subsection{Detailed Description} | |
| 26 | \subsubsection*{template$<$typename T$>$\newline | |
| 27 | class Iso\+Spec\+::\+Tabulator$<$ T $>$} | |
| 28 | ||
| 29 | ||
| 30 | ||
| 31 | Definition at line 12 of file tabulator.\+h. | |
| 32 | ||
| 33 | ||
| 34 | ||
| 35 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 36 | \item | |
| 37 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/tabulator.\+h\end{DoxyCompactItemize} |
| 0 | \hypertarget{class_iso_spec_1_1_thread_summator}{}\section{Iso\+Spec\+:\+:Thread\+Summator Class Reference} | |
| 1 | \label{class_iso_spec_1_1_thread_summator}\index{Iso\+Spec\+::\+Thread\+Summator@{Iso\+Spec\+::\+Thread\+Summator}} | |
| 2 | \subsection*{Public Member Functions} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | \mbox{\Hypertarget{class_iso_spec_1_1_thread_summator_a81c6246b37dd7f07071d4d561132beae}\label{class_iso_spec_1_1_thread_summator_a81c6246b37dd7f07071d4d561132beae}} | |
| 6 | \mbox{\hyperlink{class_iso_spec_1_1_thread_summator_a81c6246b37dd7f07071d4d561132beae}{Thread\+Summator}} () | |
| 7 | \begin{DoxyCompactList}\small\item\em Constructor (sum defaults to zero). \end{DoxyCompactList}\item | |
| 8 | void \mbox{\hyperlink{class_iso_spec_1_1_thread_summator_a744c019ec413dcc8cf8a93d9f3009f21}{add}} (double what) | |
| 9 | \begin{DoxyCompactList}\small\item\em Add a number to the existing sum. \end{DoxyCompactList}\item | |
| 10 | \mbox{\Hypertarget{class_iso_spec_1_1_thread_summator_a55e0601a6f9722b0c2ca7e0394dc00b8}\label{class_iso_spec_1_1_thread_summator_a55e0601a6f9722b0c2ca7e0394dc00b8}} | |
| 11 | double \mbox{\hyperlink{class_iso_spec_1_1_thread_summator_a55e0601a6f9722b0c2ca7e0394dc00b8}{get}} () | |
| 12 | \begin{DoxyCompactList}\small\item\em Get the current value of the sum of the added floating point numbers. \end{DoxyCompactList}\end{DoxyCompactItemize} | |
| 13 | ||
| 14 | ||
| 15 | \subsection{Detailed Description} | |
| 16 | ||
| 17 | ||
| 18 | Definition at line 139 of file summator.\+h. | |
| 19 | ||
| 20 | ||
| 21 | ||
| 22 | \subsection{Member Function Documentation} | |
| 23 | \mbox{\Hypertarget{class_iso_spec_1_1_thread_summator_a744c019ec413dcc8cf8a93d9f3009f21}\label{class_iso_spec_1_1_thread_summator_a744c019ec413dcc8cf8a93d9f3009f21}} | |
| 24 | \index{Iso\+Spec\+::\+Thread\+Summator@{Iso\+Spec\+::\+Thread\+Summator}!add@{add}} | |
| 25 | \index{add@{add}!Iso\+Spec\+::\+Thread\+Summator@{Iso\+Spec\+::\+Thread\+Summator}} | |
| 26 | \subsubsection{\texorpdfstring{add()}{add()}} | |
| 27 | {\footnotesize\ttfamily void Iso\+Spec\+::\+Thread\+Summator\+::add (\begin{DoxyParamCaption}\item[{double}]{what }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} | |
| 28 | ||
| 29 | ||
| 30 | ||
| 31 | Add a number to the existing sum. | |
| 32 | ||
| 33 | ||
| 34 | \begin{DoxyParams}{Parameters} | |
| 35 | {\em x} & A double floating point number to add. \\ | |
| 36 | \hline | |
| 37 | \end{DoxyParams} | |
| 38 | ||
| 39 | ||
| 40 | Definition at line 151 of file summator.\+h. | |
| 41 | ||
| 42 | ||
| 43 | ||
| 44 | The documentation for this class was generated from the following file\+:\begin{DoxyCompactItemize} | |
| 45 | \item | |
| 46 | /\+Users/matteo/\+Projects/isospec/\+Iso\+Spec/\+Iso\+Spec++/summator.\+h\end{DoxyCompactItemize} |
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| 408 | }% | |
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| 436 | ||
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| 454 | }{% | |
| 455 | \unskip% | |
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| 458 | ||
| 459 | % Used when hyperlinks are turned off | |
| 460 | \newcommand{\doxyref}[3]{% | |
| 461 | \textbf{#1} (\textnormal{#2}\,\pageref{#3})% | |
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| 463 | ||
| 464 | % Used to link to a table when hyperlinks are turned on | |
| 465 | \newcommand{\doxytablelink}[2]{% | |
| 466 | \ref{#1}% | |
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| 468 | ||
| 469 | % Used to link to a table when hyperlinks are turned off | |
| 470 | \newcommand{\doxytableref}[3]{% | |
| 471 | \ref{#3}% | |
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| 473 | ||
| 474 | % Used by @addindex | |
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| 491 | % Color used for table heading | |
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| 494 | % Version of hypertarget with correct landing location | |
| 495 | \newcommand{\Hypertarget}[1]{\Hy@raisedlink{\hypertarget{#1}{}}} | |
| 496 | ||
| 497 | % Define caption that is also suitable in a table | |
| 498 | \makeatletter | |
| 499 | \def\doxyfigcaption{% | |
| 500 | \refstepcounter{figure}% | |
| 501 | \@dblarg{\@caption{figure}}} | |
| 502 | \makeatother |
| 0 | \section{Class Hierarchy} | |
| 1 | This inheritance list is sorted roughly, but not completely, alphabetically\+:\begin{DoxyCompactList} | |
| 2 | \item \contentsline{section}{Iso\+Spec\+:\+:Allocator$<$ T $>$}{\pageref{class_iso_spec_1_1_allocator}}{} | |
| 3 | \item \contentsline{section}{Iso\+Spec\+:\+:Allocator$<$ int $>$}{\pageref{class_iso_spec_1_1_allocator}}{} | |
| 4 | \item \contentsline{section}{Iso\+Spec\+:\+:Conf\+Equal}{\pageref{class_iso_spec_1_1_conf_equal}}{} | |
| 5 | \item \contentsline{section}{Iso\+Spec\+:\+:Conf\+Order}{\pageref{class_iso_spec_1_1_conf_order}}{} | |
| 6 | \item \contentsline{section}{Iso\+Spec\+:\+:Conf\+Order\+Marginal}{\pageref{class_iso_spec_1_1_conf_order_marginal}}{} | |
| 7 | \item \contentsline{section}{Iso\+Spec\+:\+:Conf\+Order\+Marginal\+Descending}{\pageref{class_iso_spec_1_1_conf_order_marginal_descending}}{} | |
| 8 | \item \contentsline{section}{Iso\+Spec\+:\+:Dirty\+Allocator}{\pageref{class_iso_spec_1_1_dirty_allocator}}{} | |
| 9 | \item \contentsline{section}{Iso\+Spec\+:\+:Iso}{\pageref{class_iso_spec_1_1_iso}}{} | |
| 10 | \begin{DoxyCompactList} | |
| 11 | \item \contentsline{section}{Iso\+Spec\+:\+:Iso\+Generator}{\pageref{class_iso_spec_1_1_iso_generator}}{} | |
| 12 | \begin{DoxyCompactList} | |
| 13 | \item \contentsline{section}{Iso\+Spec\+:\+:Iso\+Layered\+Generator}{\pageref{class_iso_spec_1_1_iso_layered_generator}}{} | |
| 14 | \item \contentsline{section}{Iso\+Spec\+:\+:Iso\+Ordered\+Generator}{\pageref{class_iso_spec_1_1_iso_ordered_generator}}{} | |
| 15 | \item \contentsline{section}{Iso\+Spec\+:\+:Iso\+Threshold\+Generator}{\pageref{class_iso_spec_1_1_iso_threshold_generator}}{} | |
| 16 | \end{DoxyCompactList} | |
| 17 | \end{DoxyCompactList} | |
| 18 | \item \contentsline{section}{Iso\+Spec\+:\+:Key\+Hasher}{\pageref{class_iso_spec_1_1_key_hasher}}{} | |
| 19 | \item \contentsline{section}{Iso\+Spec\+:\+:Marginal}{\pageref{class_iso_spec_1_1_marginal}}{} | |
| 20 | \begin{DoxyCompactList} | |
| 21 | \item \contentsline{section}{Iso\+Spec\+:\+:Marginal\+Trek}{\pageref{class_iso_spec_1_1_marginal_trek}}{} | |
| 22 | \item \contentsline{section}{Iso\+Spec\+:\+:Precalculated\+Marginal}{\pageref{class_iso_spec_1_1_precalculated_marginal}}{} | |
| 23 | \end{DoxyCompactList} | |
| 24 | \item \contentsline{section}{Iso\+Spec\+:\+:Order\+Marginals\+By\+Size\+Decresing}{\pageref{class_iso_spec_1_1_order_marginals_by_size_decresing}}{} | |
| 25 | \item \contentsline{section}{Iso\+Spec\+:\+:Reverse\+Order$<$ T $>$}{\pageref{class_iso_spec_1_1_reverse_order}}{} | |
| 26 | \item \contentsline{section}{Iso\+Spec\+:\+:S\+Summator}{\pageref{class_iso_spec_1_1_s_summator}}{} | |
| 27 | \item \contentsline{section}{Iso\+Spec\+:\+:Summator}{\pageref{class_iso_spec_1_1_summator}}{} | |
| 28 | \item \contentsline{section}{Iso\+Spec\+:\+:Table\+Order$<$ T $>$}{\pageref{class_iso_spec_1_1_table_order}}{} | |
| 29 | \item \contentsline{section}{Iso\+Spec\+:\+:Tabulator$<$ T $>$}{\pageref{class_iso_spec_1_1_tabulator}}{} | |
| 30 | \item \contentsline{section}{Iso\+Spec\+:\+:T\+Summator}{\pageref{class_iso_spec_1_1_t_summator}}{} | |
| 31 | \end{DoxyCompactList} |
| 0 | \hypertarget{namespace_iso_spec}{}\section{Iso\+Spec Namespace Reference} | |
| 1 | \label{namespace_iso_spec}\index{Iso\+Spec@{Iso\+Spec}} | |
| 2 | \subsection*{Classes} | |
| 3 | \begin{DoxyCompactItemize} | |
| 4 | \item | |
| 5 | class \mbox{\hyperlink{class_iso_spec_1_1_allocator}{Allocator}} | |
| 6 | \item | |
| 7 | class \mbox{\hyperlink{class_iso_spec_1_1_conf_equal}{Conf\+Equal}} | |
| 8 | \item | |
| 9 | class \mbox{\hyperlink{class_iso_spec_1_1_conf_order}{Conf\+Order}} | |
| 10 | \item | |
| 11 | class \mbox{\hyperlink{class_iso_spec_1_1_conf_order_marginal}{Conf\+Order\+Marginal}} | |
| 12 | \item | |
| 13 | class \mbox{\hyperlink{class_iso_spec_1_1_conf_order_marginal_descending}{Conf\+Order\+Marginal\+Descending}} | |
| 14 | \item | |
| 15 | class \mbox{\hyperlink{class_iso_spec_1_1_dirty_allocator}{Dirty\+Allocator}} | |
| 16 | \item | |
| 17 | class \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} | |
| 18 | \begin{DoxyCompactList}\small\item\em The \mbox{\hyperlink{class_iso_spec_1_1_iso}{Iso}} class for the calculation of the isotopic distribution. \end{DoxyCompactList}\item | |
| 19 | class \mbox{\hyperlink{class_iso_spec_1_1_iso_generator}{Iso\+Generator}} | |
| 20 | \begin{DoxyCompactList}\small\item\em The generator of isotopologues. \end{DoxyCompactList}\item | |
| 21 | class \mbox{\hyperlink{class_iso_spec_1_1_iso_layered_generator}{Iso\+Layered\+Generator}} | |
| 22 | \begin{DoxyCompactList}\small\item\em The class that represents isotopologues above a given joint probability value. \end{DoxyCompactList}\item | |
| 23 | class \mbox{\hyperlink{class_iso_spec_1_1_iso_ordered_generator}{Iso\+Ordered\+Generator}} | |
| 24 | \begin{DoxyCompactList}\small\item\em The generator of isotopologues sorted by their probability of occurrence. \end{DoxyCompactList}\item | |
| 25 | class \mbox{\hyperlink{class_iso_spec_1_1_iso_threshold_generator}{Iso\+Threshold\+Generator}} | |
| 26 | \begin{DoxyCompactList}\small\item\em The generator of isotopologues above a given threshold value. \end{DoxyCompactList}\item | |
| 27 | class \mbox{\hyperlink{class_iso_spec_1_1_key_hasher}{Key\+Hasher}} | |
| 28 | \item | |
| 29 | class \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} | |
| 30 | \begin{DoxyCompactList}\small\item\em The marginal distribution class (a subisotopologue). \end{DoxyCompactList}\item | |
| 31 | class \mbox{\hyperlink{class_iso_spec_1_1_marginal_trek}{Marginal\+Trek}} | |
| 32 | \begin{DoxyCompactList}\small\item\em The marginal distribution class (a subisotopologue). \end{DoxyCompactList}\item | |
| 33 | class \mbox{\hyperlink{class_iso_spec_1_1_order_marginals_by_size_decresing}{Order\+Marginals\+By\+Size\+Decresing}} | |
| 34 | \item | |
| 35 | class \mbox{\hyperlink{class_iso_spec_1_1_precalculated_marginal}{Precalculated\+Marginal}} | |
| 36 | \begin{DoxyCompactList}\small\item\em Precalculated \mbox{\hyperlink{class_iso_spec_1_1_marginal}{Marginal}} class. \end{DoxyCompactList}\item | |
| 37 | class \mbox{\hyperlink{class_iso_spec_1_1_reverse_order}{Reverse\+Order}} | |
| 38 | \item | |
| 39 | class \mbox{\hyperlink{class_iso_spec_1_1_s_summator}{S\+Summator}} | |
| 40 | \item | |
| 41 | class \mbox{\hyperlink{class_iso_spec_1_1_summator}{Summator}} | |
| 42 | \item | |
| 43 | class \mbox{\hyperlink{class_iso_spec_1_1_table_order}{Table\+Order}} | |
| 44 | \item | |
| 45 | class \mbox{\hyperlink{class_iso_spec_1_1_tabulator}{Tabulator}} | |
| 46 | \item | |
| 47 | class \mbox{\hyperlink{class_iso_spec_1_1_t_summator}{T\+Summator}} | |
| 48 | \end{DoxyCompactItemize} | |
| 49 | \subsection*{Typedefs} | |
| 50 | \begin{DoxyCompactItemize} | |
| 51 | \item | |
| 52 | \mbox{\Hypertarget{namespace_iso_spec_a5e5cbcb7f667e0610638d0a4372899c1}\label{namespace_iso_spec_a5e5cbcb7f667e0610638d0a4372899c1}} | |
| 53 | typedef int $\ast$ {\bfseries Conf} | |
| 54 | \end{DoxyCompactItemize} | |
| 55 | \subsection*{Functions} | |
| 56 | \begin{DoxyCompactItemize} | |
| 57 | \item | |
| 58 | \mbox{\Hypertarget{namespace_iso_spec_a823643c5602bf7f0992eadc3ae472b5a}\label{namespace_iso_spec_a823643c5602bf7f0992eadc3ae472b5a}} | |
| 59 | {\footnotesize template$<$typename T $>$ }\\void {\bfseries copy\+Conf} (const T $\ast$source, T $\ast$destination, int dim) | |
| 60 | \item | |
| 61 | \mbox{\Hypertarget{namespace_iso_spec_a7f5e7376b35b2e0766dfea0d5917baed}\label{namespace_iso_spec_a7f5e7376b35b2e0766dfea0d5917baed}} | |
| 62 | void {\bfseries release\+\_\+g\+\_\+lfact\+\_\+table} () | |
| 63 | \item | |
| 64 | \mbox{\Hypertarget{namespace_iso_spec_a8cd1d93e56c1301eed0d696332fc81a5}\label{namespace_iso_spec_a8cd1d93e56c1301eed0d696332fc81a5}} | |
| 65 | double $\ast$ {\bfseries alloc\+\_\+lfact\+\_\+table} () | |
| 66 | \item | |
| 67 | \mbox{\Hypertarget{namespace_iso_spec_ac766fd9337e208d161395836b9fd9249}\label{namespace_iso_spec_ac766fd9337e208d161395836b9fd9249}} | |
| 68 | double {\bfseries Rational\+Approximation} (double t) | |
| 69 | \item | |
| 70 | \mbox{\Hypertarget{namespace_iso_spec_ac143363e41d73579b72144675ea3ed43}\label{namespace_iso_spec_ac143363e41d73579b72144675ea3ed43}} | |
| 71 | double {\bfseries Normal\+C\+D\+F\+Inverse} (double p) | |
| 72 | \item | |
| 73 | \mbox{\Hypertarget{namespace_iso_spec_a07b909ec7b54fbe3f68c4c3e3cdf9105}\label{namespace_iso_spec_a07b909ec7b54fbe3f68c4c3e3cdf9105}} | |
| 74 | double {\bfseries Normal\+C\+D\+F\+Inverse} (double p, double mean, double stdev) | |
| 75 | \item | |
| 76 | \mbox{\Hypertarget{namespace_iso_spec_a80f49da9159a9df06ac64e89d3cef4c8}\label{namespace_iso_spec_a80f49da9159a9df06ac64e89d3cef4c8}} | |
| 77 | double {\bfseries Normal\+C\+DF} (double x, double mean, double stdev) | |
| 78 | \item | |
| 79 | \mbox{\Hypertarget{namespace_iso_spec_aaea4e6cc79d5b2185f4b7b905bd2157f}\label{namespace_iso_spec_aaea4e6cc79d5b2185f4b7b905bd2157f}} | |
| 80 | double {\bfseries Normal\+P\+DF} (double x, double mean, double stdev) | |
| 81 | \item | |
| 82 | \mbox{\Hypertarget{namespace_iso_spec_a1cde19132fedfa1686da624baa5e5c35}\label{namespace_iso_spec_a1cde19132fedfa1686da624baa5e5c35}} | |
| 83 | unsigned int {\bfseries parse\+\_\+formula} (const char $\ast$formula, std\+::vector$<$ const double $\ast$$>$ \&isotope\+\_\+masses, std\+::vector$<$ const double $\ast$$>$ \&isotope\+\_\+probabilities, int $\ast$$\ast$isotope\+Numbers, int $\ast$$\ast$atom\+Counts, unsigned int $\ast$conf\+Size) | |
| 84 | \item | |
| 85 | \mbox{\Hypertarget{namespace_iso_spec_a8c0ac7d2f8818b2f4e66b40cf15aebe5}\label{namespace_iso_spec_a8c0ac7d2f8818b2f4e66b40cf15aebe5}} | |
| 86 | void {\bfseries print\+Configurations} (const std\+::tuple$<$ double $\ast$, double $\ast$, int $\ast$, int $>$ \&results, int dim\+Number, int $\ast$isotope\+Numbers) | |
| 87 | \item | |
| 88 | Conf \mbox{\hyperlink{namespace_iso_spec_a9abbd881dd3c9347438361a6dd21cef4}{initial\+Configure}} (const int atom\+Cnt, const int isotope\+No, const double $\ast$probs, const double $\ast$lprobs) | |
| 89 | \begin{DoxyCompactList}\small\item\em Find one of the most probable subisotopologues. \end{DoxyCompactList}\item | |
| 90 | \mbox{\Hypertarget{namespace_iso_spec_a90a5da54d5272c212ed36f4117939343}\label{namespace_iso_spec_a90a5da54d5272c212ed36f4117939343}} | |
| 91 | void {\bfseries print\+Marginal} (const std\+::tuple$<$ double $\ast$, double $\ast$, int $\ast$, int $>$ \&results, int dim) | |
| 92 | \item | |
| 93 | double $\ast$ \mbox{\hyperlink{namespace_iso_spec_a4b68cc6e2f1f4f30b189a5d01153daa4}{get\+M\+Log\+Probs}} (const double $\ast$probs, int iso\+No) | |
| 94 | \item | |
| 95 | \mbox{\Hypertarget{namespace_iso_spec_a01f8cd14080a2713f6e83e9f46322277}\label{namespace_iso_spec_a01f8cd14080a2713f6e83e9f46322277}} | |
| 96 | double {\bfseries get\+\_\+loggamma\+\_\+nominator} (int x) | |
| 97 | \item | |
| 98 | \mbox{\Hypertarget{namespace_iso_spec_a4e0e801604398f617d64e6822bbc4e03}\label{namespace_iso_spec_a4e0e801604398f617d64e6822bbc4e03}} | |
| 99 | Conf {\bfseries initial\+Configure} (int atom\+Cnt, int isotope\+No, const double $\ast$probs) | |
| 100 | \item | |
| 101 | \mbox{\Hypertarget{namespace_iso_spec_acbcd0253dcdabd90c53d008c7e12b95f}\label{namespace_iso_spec_acbcd0253dcdabd90c53d008c7e12b95f}} | |
| 102 | void $\ast$ \mbox{\hyperlink{namespace_iso_spec_acbcd0253dcdabd90c53d008c7e12b95f}{quickselect}} (void $\ast$$\ast$array, int n, int start, int end) | |
| 103 | \begin{DoxyCompactList}\small\item\em Quickly select the n\textquotesingle{}th positional statistic, including the weights. \end{DoxyCompactList}\item | |
| 104 | \mbox{\Hypertarget{namespace_iso_spec_a79a88e35ec43cb5066675948fec030cd}\label{namespace_iso_spec_a79a88e35ec43cb5066675948fec030cd}} | |
| 105 | double {\bfseries combined\+Sum} (const int $\ast$conf, const std\+::vector$<$ double $>$ $\ast$$\ast$values\+Container, int dim\+Number) | |
| 106 | \item | |
| 107 | \mbox{\Hypertarget{namespace_iso_spec_a82d9acffe9c8d0b1cca7d801233284c3}\label{namespace_iso_spec_a82d9acffe9c8d0b1cca7d801233284c3}} | |
| 108 | int $\ast$ {\bfseries get\+Conf} (void $\ast$conf) | |
| 109 | \item | |
| 110 | \mbox{\Hypertarget{namespace_iso_spec_a4642b23c34680776d4e55f6b815a6888}\label{namespace_iso_spec_a4642b23c34680776d4e55f6b815a6888}} | |
| 111 | double {\bfseries get\+L\+Prob} (void $\ast$conf) | |
| 112 | \item | |
| 113 | \mbox{\Hypertarget{namespace_iso_spec_aa105ce846eaa3e14d1db54ca4e21ad05}\label{namespace_iso_spec_aa105ce846eaa3e14d1db54ca4e21ad05}} | |
| 114 | double {\bfseries unnormalized\+\_\+log\+Prob} (const int $\ast$conf, const double $\ast$log\+Probs, int dim) | |
| 115 | \item | |
| 116 | \mbox{\Hypertarget{namespace_iso_spec_a0fc35ec359d8411cbdbab3a9e364c7f5}\label{namespace_iso_spec_a0fc35ec359d8411cbdbab3a9e364c7f5}} | |
| 117 | double {\bfseries mass} (const int $\ast$conf, const double $\ast$masses, int dim) | |
| 118 | \item | |
| 119 | \mbox{\Hypertarget{namespace_iso_spec_a54355fd7cad87694458f8ea19a478a09}\label{namespace_iso_spec_a54355fd7cad87694458f8ea19a478a09}} | |
| 120 | bool {\bfseries tuple\+Cmp} (std\+::tuple$<$ double, double, int $\ast$$>$ t1, std\+::tuple$<$ double, double, int $\ast$$>$ t2) | |
| 121 | \item | |
| 122 | \mbox{\Hypertarget{namespace_iso_spec_aa6fae021871c7833eb935320e12f7ddc}\label{namespace_iso_spec_aa6fae021871c7833eb935320e12f7ddc}} | |
| 123 | {\footnotesize template$<$typename T $>$ }\\void {\bfseries print\+Array} (const T $\ast$array, int size) | |
| 124 | \item | |
| 125 | \mbox{\Hypertarget{namespace_iso_spec_ae984eaef367699061a7fd28a8f20c3ec}\label{namespace_iso_spec_ae984eaef367699061a7fd28a8f20c3ec}} | |
| 126 | {\footnotesize template$<$typename T $>$ }\\void {\bfseries print\+Vector} (const std\+::vector$<$ T $>$ \&vec) | |
| 127 | \item | |
| 128 | \mbox{\Hypertarget{namespace_iso_spec_a6e695f7c9f32f0a53a47765ea7369e0b}\label{namespace_iso_spec_a6e695f7c9f32f0a53a47765ea7369e0b}} | |
| 129 | {\footnotesize template$<$typename T $>$ }\\void {\bfseries print\+Nested\+Array} (const T $\ast$$\ast$array, const int $\ast$shape, int size) | |
| 130 | \item | |
| 131 | \mbox{\Hypertarget{namespace_iso_spec_ac68241aedabb0a2fb5ee9c744bc12555}\label{namespace_iso_spec_ac68241aedabb0a2fb5ee9c744bc12555}} | |
| 132 | {\footnotesize template$<$typename T $>$ }\\void {\bfseries dealloc\+\_\+table} (T $\ast$tbl, int dim) | |
| 133 | \item | |
| 134 | \mbox{\Hypertarget{namespace_iso_spec_a01daa7537f1603ce443013c0a69f5ad3}\label{namespace_iso_spec_a01daa7537f1603ce443013c0a69f5ad3}} | |
| 135 | void {\bfseries reallocate} (double $\ast$$\ast$array, int new\+\_\+size) | |
| 136 | \end{DoxyCompactItemize} | |
| 137 | \subsection*{Variables} | |
| 138 | \begin{DoxyCompactItemize} | |
| 139 | \item | |
| 140 | \mbox{\Hypertarget{namespace_iso_spec_ad8f480cc82f6a8972cf586464d61b328}\label{namespace_iso_spec_ad8f480cc82f6a8972cf586464d61b328}} | |
| 141 | const int {\bfseries elem\+\_\+table\+\_\+atomic\+No} \mbox{[}I\+S\+O\+S\+P\+E\+C\+\_\+\+N\+U\+M\+B\+E\+R\+\_\+\+O\+F\+\_\+\+I\+S\+O\+T\+O\+P\+I\+C\+\_\+\+E\+N\+T\+R\+I\+ES\mbox{]} | |
| 142 | \item | |
| 143 | \mbox{\Hypertarget{namespace_iso_spec_a005cf652f6fd989d4c361ec5a78c3d30}\label{namespace_iso_spec_a005cf652f6fd989d4c361ec5a78c3d30}} | |
| 144 | const double {\bfseries elem\+\_\+table\+\_\+mass} \mbox{[}I\+S\+O\+S\+P\+E\+C\+\_\+\+N\+U\+M\+B\+E\+R\+\_\+\+O\+F\+\_\+\+I\+S\+O\+T\+O\+P\+I\+C\+\_\+\+E\+N\+T\+R\+I\+ES\mbox{]} | |
| 145 | \item | |
| 146 | \mbox{\Hypertarget{namespace_iso_spec_a967fbb44ff2abf87af634d2342faff44}\label{namespace_iso_spec_a967fbb44ff2abf87af634d2342faff44}} | |
| 147 | const int {\bfseries elem\+\_\+table\+\_\+mass\+No} \mbox{[}I\+S\+O\+S\+P\+E\+C\+\_\+\+N\+U\+M\+B\+E\+R\+\_\+\+O\+F\+\_\+\+I\+S\+O\+T\+O\+P\+I\+C\+\_\+\+E\+N\+T\+R\+I\+ES\mbox{]} | |
| 148 | \item | |
| 149 | \mbox{\Hypertarget{namespace_iso_spec_a933aad6dfcdc5a011338a53dd3699a6d}\label{namespace_iso_spec_a933aad6dfcdc5a011338a53dd3699a6d}} | |
| 150 | const int {\bfseries elem\+\_\+table\+\_\+extra\+Neutrons} \mbox{[}I\+S\+O\+S\+P\+E\+C\+\_\+\+N\+U\+M\+B\+E\+R\+\_\+\+O\+F\+\_\+\+I\+S\+O\+T\+O\+P\+I\+C\+\_\+\+E\+N\+T\+R\+I\+ES\mbox{]} | |
| 151 | \item | |
| 152 | \mbox{\Hypertarget{namespace_iso_spec_a0fbc31be6f3b2728456a9a7345f727e8}\label{namespace_iso_spec_a0fbc31be6f3b2728456a9a7345f727e8}} | |
| 153 | const char $\ast$ {\bfseries elem\+\_\+table\+\_\+element} \mbox{[}I\+S\+O\+S\+P\+E\+C\+\_\+\+N\+U\+M\+B\+E\+R\+\_\+\+O\+F\+\_\+\+I\+S\+O\+T\+O\+P\+I\+C\+\_\+\+E\+N\+T\+R\+I\+ES\mbox{]} | |
| 154 | \item | |
| 155 | \mbox{\Hypertarget{namespace_iso_spec_a917b6e971fd81932bb4703644ede9728}\label{namespace_iso_spec_a917b6e971fd81932bb4703644ede9728}} | |
| 156 | const char $\ast$ {\bfseries elem\+\_\+table\+\_\+symbol} \mbox{[}I\+S\+O\+S\+P\+E\+C\+\_\+\+N\+U\+M\+B\+E\+R\+\_\+\+O\+F\+\_\+\+I\+S\+O\+T\+O\+P\+I\+C\+\_\+\+E\+N\+T\+R\+I\+ES\mbox{]} | |
| 157 | \item | |
| 158 | \mbox{\Hypertarget{namespace_iso_spec_aaa9917bfb60e80f214b7c6d238a39082}\label{namespace_iso_spec_aaa9917bfb60e80f214b7c6d238a39082}} | |
| 159 | const bool {\bfseries elem\+\_\+table\+\_\+\+Radioactive} \mbox{[}I\+S\+O\+S\+P\+E\+C\+\_\+\+N\+U\+M\+B\+E\+R\+\_\+\+O\+F\+\_\+\+I\+S\+O\+T\+O\+P\+I\+C\+\_\+\+E\+N\+T\+R\+I\+ES\mbox{]} | |
| 160 | \item | |
| 161 | \mbox{\Hypertarget{namespace_iso_spec_a0f9c2f5f409e63672066a692931e189b}\label{namespace_iso_spec_a0f9c2f5f409e63672066a692931e189b}} | |
| 162 | const double {\bfseries elem\+\_\+table\+\_\+probability} \mbox{[}I\+S\+O\+S\+P\+E\+C\+\_\+\+N\+U\+M\+B\+E\+R\+\_\+\+O\+F\+\_\+\+I\+S\+O\+T\+O\+P\+I\+C\+\_\+\+E\+N\+T\+R\+I\+ES\mbox{]} | |
| 163 | \item | |
| 164 | \mbox{\Hypertarget{namespace_iso_spec_a9fe61f2f9c36103283bb256a2f59e93a}\label{namespace_iso_spec_a9fe61f2f9c36103283bb256a2f59e93a}} | |
| 165 | const double {\bfseries elem\+\_\+table\+\_\+log\+\_\+probability} \mbox{[}I\+S\+O\+S\+P\+E\+C\+\_\+\+N\+U\+M\+B\+E\+R\+\_\+\+O\+F\+\_\+\+I\+S\+O\+T\+O\+P\+I\+C\+\_\+\+E\+N\+T\+R\+I\+ES\mbox{]} | |
| 166 | \item | |
| 167 | \mbox{\Hypertarget{namespace_iso_spec_acc706853ec222cb50405ee264e9007bf}\label{namespace_iso_spec_acc706853ec222cb50405ee264e9007bf}} | |
| 168 | const double {\bfseries pi} = 3.\+14159265358979323846264338328 | |
| 169 | \item | |
| 170 | \mbox{\Hypertarget{namespace_iso_spec_a8be6485cb575264c4ec7398501f7c99d}\label{namespace_iso_spec_a8be6485cb575264c4ec7398501f7c99d}} | |
| 171 | double $\ast$ {\bfseries g\+\_\+lfact\+\_\+table} = alloc\+\_\+lfact\+\_\+table() | |
| 172 | \end{DoxyCompactItemize} | |
| 173 | ||
| 174 | ||
| 175 | \subsection{Detailed Description} | |
| 176 | Copyright (C) 2015-\/2018 Mateusz Łącki and Michał Startek. | |
| 177 | ||
| 178 | This file is part of \mbox{\hyperlink{namespace_iso_spec}{Iso\+Spec}}. | |
| 179 | ||
| 180 | \mbox{\hyperlink{namespace_iso_spec}{Iso\+Spec}} is free software\+: you can redistribute it and/or modify it under the terms of the Simplified (\char`\"{}2-\/clause\char`\"{}) B\+SD licence. | |
| 181 | ||
| 182 | \mbox{\hyperlink{namespace_iso_spec}{Iso\+Spec}} is distributed in the hope that it will be useful, but W\+I\+T\+H\+O\+UT A\+NY W\+A\+R\+R\+A\+N\+TY; without even the implied warranty of M\+E\+R\+C\+H\+A\+N\+T\+A\+B\+I\+L\+I\+TY or F\+I\+T\+N\+E\+SS F\+OR A P\+A\+R\+T\+I\+C\+U\+L\+AR P\+U\+R\+P\+O\+SE. | |
| 183 | ||
| 184 | You should have received a copy of the Simplified B\+SD Licence along with \mbox{\hyperlink{namespace_iso_spec}{Iso\+Spec}}. If not, see \href{https://opensource.org/licenses/BSD-2-Clause}{\tt https\+://opensource.\+org/licenses/\+B\+S\+D-\/2-\/\+Clause}. | |
| 185 | ||
| 186 | \subsection{Function Documentation} | |
| 187 | \mbox{\Hypertarget{namespace_iso_spec_a4b68cc6e2f1f4f30b189a5d01153daa4}\label{namespace_iso_spec_a4b68cc6e2f1f4f30b189a5d01153daa4}} | |
| 188 | \index{Iso\+Spec@{Iso\+Spec}!get\+M\+Log\+Probs@{get\+M\+Log\+Probs}} | |
| 189 | \index{get\+M\+Log\+Probs@{get\+M\+Log\+Probs}!Iso\+Spec@{Iso\+Spec}} | |
| 190 | \subsubsection{\texorpdfstring{get\+M\+Log\+Probs()}{getMLogProbs()}} | |
| 191 | {\footnotesize\ttfamily double$\ast$ Iso\+Spec\+::get\+M\+Log\+Probs (\begin{DoxyParamCaption}\item[{const double $\ast$}]{probs, }\item[{int}]{iso\+No }\end{DoxyParamCaption})} | |
| 192 | ||
| 193 | ~\newline | |
| 194 | Here we order the processor to round the numbers up rather than down. Rounding down could result in the algorithm falling in an infinite loop because of the numerical instability of summing. | |
| 195 | ||
| 196 | Definition at line 150 of file marginal\+Trek++.\+cpp. | |
| 197 | ||
| 198 | \mbox{\Hypertarget{namespace_iso_spec_a9abbd881dd3c9347438361a6dd21cef4}\label{namespace_iso_spec_a9abbd881dd3c9347438361a6dd21cef4}} | |
| 199 | \index{Iso\+Spec@{Iso\+Spec}!initial\+Configure@{initial\+Configure}} | |
| 200 | \index{initial\+Configure@{initial\+Configure}!Iso\+Spec@{Iso\+Spec}} | |
| 201 | \subsubsection{\texorpdfstring{initial\+Configure()}{initialConfigure()}} | |
| 202 | {\footnotesize\ttfamily Conf Iso\+Spec\+::initial\+Configure (\begin{DoxyParamCaption}\item[{const int}]{atom\+Cnt, }\item[{const int}]{isotope\+No, }\item[{const double $\ast$}]{probs, }\item[{const double $\ast$}]{lprobs }\end{DoxyParamCaption})} | |
| 203 | ||
| 204 | ||
| 205 | ||
| 206 | Find one of the most probable subisotopologues. | |
| 207 | ||
| 208 | The algorithm uses the hill-\/climbing algorithm. It starts from a subisotopologue close to the mean of the underlying multinomial distribution. There might be more than one modes, in case of which this function will return only one of them, close to the mean. | |
| 209 | ||
| 210 | ||
| 211 | \begin{DoxyParams}{Parameters} | |
| 212 | {\em atom\+Cnt} & \\ | |
| 213 | \hline | |
| 214 | \end{DoxyParams} | |
| 215 | ~\newline | |
| 216 | Here we perform hill climbing to the mode of the marginal distribution (the subisotopologue distribution). We start from the point close to the mean of the underlying multinomial distribution. | |
| 217 | ||
| 218 | Definition at line 55 of file marginal\+Trek++.\+cpp. | |
| 219 |
| 0 | \section{Namespace List} | |
| 1 | Here is a list of all documented namespaces with brief descriptions\+:\begin{DoxyCompactList} | |
| 2 | \item\contentsline{section}{\mbox{\hyperlink{namespace_iso_spec}{Iso\+Spec}} }{\pageref{namespace_iso_spec}}{} | |
| 3 | \end{DoxyCompactList} |
| 0 | \relax | |
| 1 | \providecommand\hyper@newdestlabel[2]{} | |
| 2 | \providecommand\HyperFirstAtBeginDocument{\AtBeginDocument} | |
| 3 | \HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined | |
| 4 | \global\let\oldcontentsline\contentsline | |
| 5 | \gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}} | |
| 6 | \global\let\oldnewlabel\newlabel | |
| 7 | \gdef\newlabel#1#2{\newlabelxx{#1}#2} | |
| 8 | \gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} | |
| 9 | \AtEndDocument{\ifx\hyper@anchor\@undefined | |
| 10 | \let\contentsline\oldcontentsline | |
| 11 | \let\newlabel\oldnewlabel | |
| 12 | \fi} | |
| 13 | \fi} | |
| 14 | \global\let\hyper@last\relax | |
| 15 | \gdef\HyperFirstAtBeginDocument#1{#1} | |
| 16 | \providecommand\HyField@AuxAddToFields[1]{} | |
| 17 | \providecommand\HyField@AuxAddToCoFields[2]{} | |
| 18 | \providecommand \oddpage@label [2]{} | |
| 19 | \@writefile{toc}{\contentsline {chapter}{\numberline {1}Namespace Index}{1}{chapter.1}} | |
| 20 | \@writefile{lof}{\addvspace {10\p@ }} | |
| 21 | \@writefile{lot}{\addvspace {10\p@ }} | |
| 22 | \@writefile{toc}{\contentsline {section}{\numberline {1.1}Namespace List}{1}{section.1.1}} | |
| 23 | \@writefile{toc}{\contentsline {chapter}{\numberline {2}Hierarchical Index}{3}{chapter.2}} | |
| 24 | \@writefile{lof}{\addvspace {10\p@ }} | |
| 25 | \@writefile{lot}{\addvspace {10\p@ }} | |
| 26 | \@writefile{toc}{\contentsline {section}{\numberline {2.1}Class Hierarchy}{3}{section.2.1}} | |
| 27 | \@writefile{toc}{\contentsline {chapter}{\numberline {3}Class Index}{5}{chapter.3}} | |
| 28 | \@writefile{lof}{\addvspace {10\p@ }} | |
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| 30 | \@writefile{toc}{\contentsline {section}{\numberline {3.1}Class List}{5}{section.3.1}} | |
| 31 | \@writefile{toc}{\contentsline {chapter}{\numberline {4}Namespace Documentation}{7}{chapter.4}} | |
| 32 | \@writefile{lof}{\addvspace {10\p@ }} | |
| 33 | \@writefile{lot}{\addvspace {10\p@ }} | |
| 34 | \@writefile{toc}{\contentsline {section}{\numberline {4.1}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec Namespace Reference}{7}{section.4.1}} | |
| 35 | \newlabel{namespace_iso_spec}{{4.1}{7}{Iso\+Spec Namespace Reference}{section.4.1}{}} | |
| 36 | \newlabel{namespace_iso_spec_a5e5cbcb7f667e0610638d0a4372899c1}{{4.1}{7}{Typedefs}{section*.3}{}} | |
| 37 | \newlabel{namespace_iso_spec_a823643c5602bf7f0992eadc3ae472b5a}{{4.1}{8}{Functions}{section*.4}{}} | |
| 38 | \newlabel{namespace_iso_spec_ac766fd9337e208d161395836b9fd9249}{{4.1}{8}{Functions}{section*.4}{}} | |
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| 71 | \@writefile{toc}{\contentsline {subsection}{\numberline {4.1.1}Detailed Description}{9}{subsection.4.1.1}} | |
| 72 | \@writefile{toc}{\contentsline {subsection}{\numberline {4.1.2}Function Documentation}{9}{subsection.4.1.2}} | |
| 73 | \newlabel{namespace_iso_spec_a4b68cc6e2f1f4f30b189a5d01153daa4}{{4.1.2}{9}{Function Documentation}{subsection.4.1.2}{}} | |
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| 75 | \newlabel{namespace_iso_spec_a9abbd881dd3c9347438361a6dd21cef4}{{4.1.2.1}{9}{\texorpdfstring {get\+M\+Log\+Probs()}{getMLogProbs()}}{subsubsection.4.1.2.1}{}} | |
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| 77 | \@writefile{toc}{\contentsline {chapter}{\numberline {5}Class Documentation}{11}{chapter.5}} | |
| 78 | \@writefile{lof}{\addvspace {10\p@ }} | |
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| 81 | \newlabel{class_iso_spec_1_1_allocator}{{5.1}{11}{Iso\+Spec\+:\+:Allocator$<$ T $>$ Class Template Reference}{section.5.1}{}} | |
| 82 | \newlabel{class_iso_spec_1_1_allocator_a30f7d0aedcf0cf85e958d66aa7ce0ec7}{{5.1}{11}{Public Member Functions}{section*.6}{}} | |
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| 87 | \@writefile{toc}{\contentsline {section}{\numberline {5.2}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Conf\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Equal Class Reference}{11}{section.5.2}} | |
| 88 | \newlabel{class_iso_spec_1_1_conf_equal}{{5.2}{11}{Iso\+Spec\+:\+:Conf\+Equal Class Reference}{section.5.2}{}} | |
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| 282 | \newlabel{class_iso_spec_1_1_summator_a87f3249839e99b41d3c16aeed75204fa}{{5.24}{24}{Public Member Functions}{section*.47}{}} | |
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| 284 | \newlabel{class_iso_spec_1_1_table_order}{{5.25}{25}{Iso\+Spec\+:\+:Table\+Order$<$ T $>$ Class Template Reference}{section.5.25}{}} | |
| 285 | \newlabel{class_iso_spec_1_1_table_order_a82a2474a7990bf0a55e269ea2dabada5}{{5.25}{25}{Public Member Functions}{section*.48}{}} | |
| 286 | \newlabel{class_iso_spec_1_1_table_order_a35b990bbb3f8c3ba0551c0938a5145c8}{{5.25}{25}{Public Member Functions}{section*.48}{}} | |
| 287 | \@writefile{toc}{\contentsline {section}{\numberline {5.26}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Table\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order$<$ T $>$ Class Template Reference}{25}{section.5.26}} | |
| 288 | \newlabel{class_iso_spec_1_1_iso_spec_1_1_table_order}{{5.26}{25}{Iso\+Spec\+:\+:Iso\+Spec\+:\+:Table\+Order$<$ T $>$ Class Template Reference}{section.5.26}{}} | |
| 289 | \newlabel{class_iso_spec_1_1_iso_spec_1_1_table_order_ad7f7ff01c71c3ba7308f8576dc7226c6}{{5.26}{25}{Public Member Functions}{section*.49}{}} | |
| 290 | \newlabel{class_iso_spec_1_1_iso_spec_1_1_table_order_a0b952830050570f97ffd71137548c431}{{5.26}{25}{Public Member Functions}{section*.49}{}} | |
| 291 | \@writefile{toc}{\contentsline {section}{\numberline {5.27}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Tabulator$<$ T $>$ Class Template Reference}{25}{section.5.27}} | |
| 292 | \newlabel{class_iso_spec_1_1_tabulator}{{5.27}{25}{Iso\+Spec\+:\+:Tabulator$<$ T $>$ Class Template Reference}{section.5.27}{}} | |
| 293 | \newlabel{class_iso_spec_1_1_tabulator_a57acb4ba7687ac95916c00fd9cd4f4c7}{{5.27}{25}{Public Member Functions}{section*.50}{}} | |
| 294 | \newlabel{class_iso_spec_1_1_tabulator_ae256b348fc6c5d24d540c33094a37df9}{{5.27}{25}{Public Member Functions}{section*.50}{}} | |
| 295 | \newlabel{class_iso_spec_1_1_tabulator_a486be3022d437b81b4932dd61ca4a0e5}{{5.27}{25}{Public Member Functions}{section*.50}{}} | |
| 296 | \newlabel{class_iso_spec_1_1_tabulator_a0c572de1f59a3c664c55e55760be2f18}{{5.27}{25}{Public Member Functions}{section*.50}{}} | |
| 297 | \newlabel{class_iso_spec_1_1_tabulator_a8000f897020376b6a03fb75dafb997f1}{{5.27}{25}{Public Member Functions}{section*.50}{}} | |
| 298 | \newlabel{class_iso_spec_1_1_tabulator_acdbd459f1ec95dfd17cc0617cda02fba}{{5.27}{25}{Public Member Functions}{section*.50}{}} | |
| 299 | \@writefile{toc}{\contentsline {section}{\numberline {5.28}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Thread\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Summator Class Reference}{25}{section.5.28}} | |
| 300 | \newlabel{class_iso_spec_1_1_thread_summator}{{5.28}{25}{Iso\+Spec\+:\+:Thread\+Summator Class Reference}{section.5.28}{}} | |
| 301 | \newlabel{class_iso_spec_1_1_thread_summator_a744c019ec413dcc8cf8a93d9f3009f21}{{5.28}{25}{Public Member Functions}{section*.51}{}} | |
| 302 | \newlabel{class_iso_spec_1_1_thread_summator_a55e0601a6f9722b0c2ca7e0394dc00b8}{{5.28}{25}{Public Member Functions}{section*.51}{}} | |
| 303 | \@writefile{toc}{\contentsline {section}{\numberline {5.29}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:T\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Summator Class Reference}{26}{section.5.29}} | |
| 304 | \newlabel{class_iso_spec_1_1_t_summator}{{5.29}{26}{Iso\+Spec\+:\+:T\+Summator Class Reference}{section.5.29}{}} | |
| 305 | \newlabel{class_iso_spec_1_1_t_summator_a5645d3fdac4e35f023fe7a08646dc413}{{5.29}{26}{Public Member Functions}{section*.52}{}} | |
| 306 | \newlabel{class_iso_spec_1_1_t_summator_a0db3add5376aae480fcaa3f489898bd7}{{5.29}{26}{Public Member Functions}{section*.52}{}} | |
| 307 | \@writefile{toc}{\contentsline {chapter}{Index}{27}{section*.53}} |
| 0 | \indexentry{Iso\+Spec@{Iso\+Spec}|hyperpage}{7} | |
| 1 | \indexentry{Iso\+Spec@{Iso\+Spec}!get\+M\+Log\+Probs@{get\+M\+Log\+Probs}|hyperpage}{9} | |
| 2 | \indexentry{get\+M\+Log\+Probs@{get\+M\+Log\+Probs}!Iso\+Spec@{Iso\+Spec}|hyperpage}{9} | |
| 3 | \indexentry{Iso\+Spec@{Iso\+Spec}!initial\+Configure@{initial\+Configure}|hyperpage}{9} | |
| 4 | \indexentry{initial\+Configure@{initial\+Configure}!Iso\+Spec@{Iso\+Spec}|hyperpage}{9} | |
| 5 | \indexentry{Iso\+Spec\+::\+Allocator$<$ T $>$@{Iso\+Spec\+::\+Allocator$<$ T $>$}|hyperpage}{11} | |
| 6 | \indexentry{Iso\+Spec\+::\+Conf\+Equal@{Iso\+Spec\+::\+Conf\+Equal}|hyperpage}{11} | |
| 7 | \indexentry{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal}|hyperpage}{11} | |
| 8 | \indexentry{Iso\+Spec\+::\+Conf\+Order@{Iso\+Spec\+::\+Conf\+Order}|hyperpage}{12} | |
| 9 | \indexentry{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order}|hyperpage}{12} | |
| 10 | \indexentry{Iso\+Spec\+::\+Conf\+Order\+Marginal@{Iso\+Spec\+::\+Conf\+Order\+Marginal}|hyperpage}{12} | |
| 11 | \indexentry{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal}|hyperpage}{12} | |
| 12 | \indexentry{Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending@{Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}|hyperpage}{13} | |
| 13 | \indexentry{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending@{Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}|hyperpage}{13} | |
| 14 | \indexentry{Iso\+Spec\+::\+Dirty\+Allocator@{Iso\+Spec\+::\+Dirty\+Allocator}|hyperpage}{13} | |
| 15 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{13} | |
| 16 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!Iso@{Iso}|hyperpage}{14} | |
| 17 | \indexentry{Iso@{Iso}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{14} | |
| 18 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!get\+\_\+\+M\+T\+\_\+marginal\+\_\+set@{get\+\_\+\+M\+T\+\_\+marginal\+\_\+set}|hyperpage}{15} | |
| 19 | \indexentry{get\+\_\+\+M\+T\+\_\+marginal\+\_\+set@{get\+\_\+\+M\+T\+\_\+marginal\+\_\+set}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{15} | |
| 20 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!all\+Dim@{all\+Dim}|hyperpage}{15} | |
| 21 | \indexentry{all\+Dim@{all\+Dim}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{15} | |
| 22 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!atom\+Counts@{atom\+Counts}|hyperpage}{15} | |
| 23 | \indexentry{atom\+Counts@{atom\+Counts}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{15} | |
| 24 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!conf\+Size@{conf\+Size}|hyperpage}{16} | |
| 25 | \indexentry{conf\+Size@{conf\+Size}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{16} | |
| 26 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!dim\+Number@{dim\+Number}|hyperpage}{16} | |
| 27 | \indexentry{dim\+Number@{dim\+Number}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{16} | |
| 28 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!disowned@{disowned}|hyperpage}{16} | |
| 29 | \indexentry{disowned@{disowned}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{16} | |
| 30 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!isotope\+Numbers@{isotope\+Numbers}|hyperpage}{16} | |
| 31 | \indexentry{isotope\+Numbers@{isotope\+Numbers}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{16} | |
| 32 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!marginals@{marginals}|hyperpage}{16} | |
| 33 | \indexentry{marginals@{marginals}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{16} | |
| 34 | \indexentry{Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}!mode\+L\+Prob@{mode\+L\+Prob}|hyperpage}{16} | |
| 35 | \indexentry{mode\+L\+Prob@{mode\+L\+Prob}!Iso\+Spec\+::\+Iso@{Iso\+Spec\+::\+Iso}|hyperpage}{16} | |
| 36 | \indexentry{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}|hyperpage}{17} | |
| 37 | \indexentry{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}!advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}|hyperpage}{17} | |
| 38 | \indexentry{advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}!Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}|hyperpage}{17} | |
| 39 | \indexentry{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}!partial\+Exp\+Probs@{partial\+Exp\+Probs}|hyperpage}{18} | |
| 40 | \indexentry{partial\+Exp\+Probs@{partial\+Exp\+Probs}!Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}|hyperpage}{18} | |
| 41 | \indexentry{Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}!partial\+Masses@{partial\+Masses}|hyperpage}{18} | |
| 42 | \indexentry{partial\+Masses@{partial\+Masses}!Iso\+Spec\+::\+Iso\+Generator@{Iso\+Spec\+::\+Iso\+Generator}|hyperpage}{18} | |
| 43 | \indexentry{Iso\+Spec\+::\+Iso\+Layered\+Generator@{Iso\+Spec\+::\+Iso\+Layered\+Generator}|hyperpage}{18} | |
| 44 | \indexentry{Iso\+Spec\+::\+Iso\+Layered\+Generator@{Iso\+Spec\+::\+Iso\+Layered\+Generator}!advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}|hyperpage}{18} | |
| 45 | \indexentry{advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}!Iso\+Spec\+::\+Iso\+Layered\+Generator@{Iso\+Spec\+::\+Iso\+Layered\+Generator}|hyperpage}{18} | |
| 46 | \indexentry{Iso\+Spec\+::\+Iso\+Ordered\+Generator@{Iso\+Spec\+::\+Iso\+Ordered\+Generator}|hyperpage}{19} | |
| 47 | \indexentry{Iso\+Spec\+::\+Iso\+Ordered\+Generator@{Iso\+Spec\+::\+Iso\+Ordered\+Generator}!advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}|hyperpage}{19} | |
| 48 | \indexentry{advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}!Iso\+Spec\+::\+Iso\+Ordered\+Generator@{Iso\+Spec\+::\+Iso\+Ordered\+Generator}|hyperpage}{19} | |
| 49 | \indexentry{Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}|hyperpage}{20} | |
| 50 | \indexentry{Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}!advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}|hyperpage}{20} | |
| 51 | \indexentry{advance\+To\+Next\+Configuration@{advance\+To\+Next\+Configuration}!Iso\+Spec\+::\+Iso\+Threshold\+Generator@{Iso\+Spec\+::\+Iso\+Threshold\+Generator}|hyperpage}{20} | |
| 52 | \indexentry{Iso\+Spec\+::\+Key\+Hasher@{Iso\+Spec\+::\+Key\+Hasher}|hyperpage}{21} | |
| 53 | \indexentry{Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher@{Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher}|hyperpage}{21} | |
| 54 | \indexentry{Iso\+Spec\+::\+Marginal@{Iso\+Spec\+::\+Marginal}|hyperpage}{21} | |
| 55 | \indexentry{Iso\+Spec\+::\+Marginal\+Trek@{Iso\+Spec\+::\+Marginal\+Trek}|hyperpage}{22} | |
| 56 | \indexentry{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}|hyperpage}{23} | |
| 57 | \indexentry{Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}!configurations@{configurations}|hyperpage}{23} | |
| 58 | \indexentry{configurations@{configurations}!Iso\+Spec\+::\+Precalculated\+Marginal@{Iso\+Spec\+::\+Precalculated\+Marginal}|hyperpage}{23} | |
| 59 | \indexentry{Iso\+Spec\+::\+Iso\+Spec\+::\+Reverse\+Order$<$ T $>$@{Iso\+Spec\+::\+Iso\+Spec\+::\+Reverse\+Order$<$ T $>$}|hyperpage}{24} | |
| 60 | \indexentry{Iso\+Spec\+::\+Reverse\+Order$<$ T $>$@{Iso\+Spec\+::\+Reverse\+Order$<$ T $>$}|hyperpage}{24} | |
| 61 | \indexentry{Iso\+Spec\+::\+S\+Summator@{Iso\+Spec\+::\+S\+Summator}|hyperpage}{24} | |
| 62 | \indexentry{Iso\+Spec\+::\+Summator@{Iso\+Spec\+::\+Summator}|hyperpage}{24} | |
| 63 | \indexentry{Iso\+Spec\+::\+Table\+Order$<$ T $>$@{Iso\+Spec\+::\+Table\+Order$<$ T $>$}|hyperpage}{25} | |
| 64 | \indexentry{Iso\+Spec\+::\+Iso\+Spec\+::\+Table\+Order$<$ T $>$@{Iso\+Spec\+::\+Iso\+Spec\+::\+Table\+Order$<$ T $>$}|hyperpage}{25} | |
| 65 | \indexentry{Iso\+Spec\+::\+Tabulator$<$ T $>$@{Iso\+Spec\+::\+Tabulator$<$ T $>$}|hyperpage}{25} | |
| 66 | \indexentry{Iso\+Spec\+::\+Thread\+Summator@{Iso\+Spec\+::\+Thread\+Summator}|hyperpage}{25} | |
| 67 | \indexentry{Iso\+Spec\+::\+T\+Summator@{Iso\+Spec\+::\+T\+Summator}|hyperpage}{26} |
| 0 | This is makeindex, version 2.15 [TeX Live 2018] (kpathsea + Thai support). | |
| 1 | Scanning input file refman.idx....done (68 entries accepted, 0 rejected). | |
| 2 | Sorting entries....done (433 comparisons). | |
| 3 | Generating output file refman.ind....done (111 lines written, 0 warnings). | |
| 4 | Output written in refman.ind. | |
| 5 | Transcript written in refman.ilg. |
| 0 | \begin{theindex} | |
| 1 | ||
| 2 | \item {advance\+To\+Next\+Configuration} | |
| 3 | \subitem {Iso\+Spec\+::\+Iso\+Generator}, \hyperpage{17} | |
| 4 | \subitem {Iso\+Spec\+::\+Iso\+Layered\+Generator}, \hyperpage{18} | |
| 5 | \subitem {Iso\+Spec\+::\+Iso\+Ordered\+Generator}, \hyperpage{19} | |
| 6 | \subitem {Iso\+Spec\+::\+Iso\+Threshold\+Generator}, \hyperpage{20} | |
| 7 | \item {all\+Dim} | |
| 8 | \subitem {Iso\+Spec\+::\+Iso}, \hyperpage{15} | |
| 9 | \item {atom\+Counts} | |
| 10 | \subitem {Iso\+Spec\+::\+Iso}, \hyperpage{15} | |
| 11 | ||
| 12 | \indexspace | |
| 13 | ||
| 14 | \item {conf\+Size} | |
| 15 | \subitem {Iso\+Spec\+::\+Iso}, \hyperpage{16} | |
| 16 | \item {configurations} | |
| 17 | \subitem {Iso\+Spec\+::\+Precalculated\+Marginal}, \hyperpage{23} | |
| 18 | ||
| 19 | \indexspace | |
| 20 | ||
| 21 | \item {dim\+Number} | |
| 22 | \subitem {Iso\+Spec\+::\+Iso}, \hyperpage{16} | |
| 23 | \item {disowned} | |
| 24 | \subitem {Iso\+Spec\+::\+Iso}, \hyperpage{16} | |
| 25 | ||
| 26 | \indexspace | |
| 27 | ||
| 28 | \item {get\+\_\+\+M\+T\+\_\+marginal\+\_\+set} | |
| 29 | \subitem {Iso\+Spec\+::\+Iso}, \hyperpage{15} | |
| 30 | \item {get\+M\+Log\+Probs} | |
| 31 | \subitem {Iso\+Spec}, \hyperpage{9} | |
| 32 | ||
| 33 | \indexspace | |
| 34 | ||
| 35 | \item {initial\+Configure} | |
| 36 | \subitem {Iso\+Spec}, \hyperpage{9} | |
| 37 | \item {Iso} | |
| 38 | \subitem {Iso\+Spec\+::\+Iso}, \hyperpage{14} | |
| 39 | \item {Iso\+Spec}, \hyperpage{7} | |
| 40 | \subitem {get\+M\+Log\+Probs}, \hyperpage{9} | |
| 41 | \subitem {initial\+Configure}, \hyperpage{9} | |
| 42 | \item {Iso\+Spec\+::\+Allocator$<$ T $>$}, \hyperpage{11} | |
| 43 | \item {Iso\+Spec\+::\+Conf\+Equal}, \hyperpage{11} | |
| 44 | \item {Iso\+Spec\+::\+Conf\+Order}, \hyperpage{12} | |
| 45 | \item {Iso\+Spec\+::\+Conf\+Order\+Marginal}, \hyperpage{12} | |
| 46 | \item {Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}, | |
| 47 | \hyperpage{13} | |
| 48 | \item {Iso\+Spec\+::\+Dirty\+Allocator}, \hyperpage{13} | |
| 49 | \item {Iso\+Spec\+::\+Iso}, \hyperpage{13} | |
| 50 | \subitem {all\+Dim}, \hyperpage{15} | |
| 51 | \subitem {atom\+Counts}, \hyperpage{15} | |
| 52 | \subitem {conf\+Size}, \hyperpage{16} | |
| 53 | \subitem {dim\+Number}, \hyperpage{16} | |
| 54 | \subitem {disowned}, \hyperpage{16} | |
| 55 | \subitem {get\+\_\+\+M\+T\+\_\+marginal\+\_\+set}, \hyperpage{15} | |
| 56 | \subitem {Iso}, \hyperpage{14} | |
| 57 | \subitem {isotope\+Numbers}, \hyperpage{16} | |
| 58 | \subitem {marginals}, \hyperpage{16} | |
| 59 | \subitem {mode\+L\+Prob}, \hyperpage{16} | |
| 60 | \item {Iso\+Spec\+::\+Iso\+Generator}, \hyperpage{17} | |
| 61 | \subitem {advance\+To\+Next\+Configuration}, \hyperpage{17} | |
| 62 | \subitem {partial\+Exp\+Probs}, \hyperpage{18} | |
| 63 | \subitem {partial\+Masses}, \hyperpage{18} | |
| 64 | \item {Iso\+Spec\+::\+Iso\+Layered\+Generator}, \hyperpage{18} | |
| 65 | \subitem {advance\+To\+Next\+Configuration}, \hyperpage{18} | |
| 66 | \item {Iso\+Spec\+::\+Iso\+Ordered\+Generator}, \hyperpage{19} | |
| 67 | \subitem {advance\+To\+Next\+Configuration}, \hyperpage{19} | |
| 68 | \item {Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Equal}, \hyperpage{11} | |
| 69 | \item {Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order}, \hyperpage{12} | |
| 70 | \item {Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal}, | |
| 71 | \hyperpage{12} | |
| 72 | \item {Iso\+Spec\+::\+Iso\+Spec\+::\+Conf\+Order\+Marginal\+Descending}, | |
| 73 | \hyperpage{13} | |
| 74 | \item {Iso\+Spec\+::\+Iso\+Spec\+::\+Key\+Hasher}, \hyperpage{21} | |
| 75 | \item {Iso\+Spec\+::\+Iso\+Spec\+::\+Reverse\+Order$<$ T $>$}, | |
| 76 | \hyperpage{24} | |
| 77 | \item {Iso\+Spec\+::\+Iso\+Spec\+::\+Table\+Order$<$ T $>$}, | |
| 78 | \hyperpage{25} | |
| 79 | \item {Iso\+Spec\+::\+Iso\+Threshold\+Generator}, \hyperpage{20} | |
| 80 | \subitem {advance\+To\+Next\+Configuration}, \hyperpage{20} | |
| 81 | \item {Iso\+Spec\+::\+Key\+Hasher}, \hyperpage{21} | |
| 82 | \item {Iso\+Spec\+::\+Marginal}, \hyperpage{21} | |
| 83 | \item {Iso\+Spec\+::\+Marginal\+Trek}, \hyperpage{22} | |
| 84 | \item {Iso\+Spec\+::\+Precalculated\+Marginal}, \hyperpage{23} | |
| 85 | \subitem {configurations}, \hyperpage{23} | |
| 86 | \item {Iso\+Spec\+::\+Reverse\+Order$<$ T $>$}, \hyperpage{24} | |
| 87 | \item {Iso\+Spec\+::\+S\+Summator}, \hyperpage{24} | |
| 88 | \item {Iso\+Spec\+::\+Summator}, \hyperpage{24} | |
| 89 | \item {Iso\+Spec\+::\+T\+Summator}, \hyperpage{26} | |
| 90 | \item {Iso\+Spec\+::\+Table\+Order$<$ T $>$}, \hyperpage{25} | |
| 91 | \item {Iso\+Spec\+::\+Tabulator$<$ T $>$}, \hyperpage{25} | |
| 92 | \item {Iso\+Spec\+::\+Thread\+Summator}, \hyperpage{25} | |
| 93 | \item {isotope\+Numbers} | |
| 94 | \subitem {Iso\+Spec\+::\+Iso}, \hyperpage{16} | |
| 95 | ||
| 96 | \indexspace | |
| 97 | ||
| 98 | \item {marginals} | |
| 99 | \subitem {Iso\+Spec\+::\+Iso}, \hyperpage{16} | |
| 100 | \item {mode\+L\+Prob} | |
| 101 | \subitem {Iso\+Spec\+::\+Iso}, \hyperpage{16} | |
| 102 | ||
| 103 | \indexspace | |
| 104 | ||
| 105 | \item {partial\+Exp\+Probs} | |
| 106 | \subitem {Iso\+Spec\+::\+Iso\+Generator}, \hyperpage{18} | |
| 107 | \item {partial\+Masses} | |
| 108 | \subitem {Iso\+Spec\+::\+Iso\+Generator}, \hyperpage{18} | |
| 109 | ||
| 110 | \end{theindex} |
| 0 | This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex 2018.9.10) 10 OCT 2018 16:33 | |
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| 357 | defining Unicode char U+2022 (decimal 8226) | |
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| 359 | defining Unicode char U+2031 (decimal 8241) | |
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| 378 | defining Unicode char U+2126 (decimal 8486) | |
| 379 | defining Unicode char U+2127 (decimal 8487) | |
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| 381 | defining Unicode char U+2190 (decimal 8592) | |
| 382 | defining Unicode char U+2191 (decimal 8593) | |
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| 389 | defining Unicode char U+25EF (decimal 9711) | |
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| 984 | Chapter 5. | |
| 985 | (./class_iso_spec_1_1_allocator.tex | |
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| 0 | \documentclass[twoside]{book} | |
| 1 | ||
| 2 | % Packages required by doxygen | |
| 3 | \usepackage{fixltx2e} | |
| 4 | \usepackage{calc} | |
| 5 | \usepackage{doxygen} | |
| 6 | \usepackage[export]{adjustbox} % also loads graphicx | |
| 7 | \usepackage{graphicx} | |
| 8 | \usepackage[utf8]{inputenc} | |
| 9 | \usepackage{makeidx} | |
| 10 | \usepackage{multicol} | |
| 11 | \usepackage{multirow} | |
| 12 | \PassOptionsToPackage{warn}{textcomp} | |
| 13 | \usepackage{textcomp} | |
| 14 | \usepackage[nointegrals]{wasysym} | |
| 15 | \usepackage[table]{xcolor} | |
| 16 | ||
| 17 | % Font selection | |
| 18 | \usepackage[T1]{fontenc} | |
| 19 | \usepackage[scaled=.90]{helvet} | |
| 20 | \usepackage{courier} | |
| 21 | \usepackage{amssymb} | |
| 22 | \usepackage{sectsty} | |
| 23 | \renewcommand{\familydefault}{\sfdefault} | |
| 24 | \allsectionsfont{% | |
| 25 | \fontseries{bc}\selectfont% | |
| 26 | \color{darkgray}% | |
| 27 | } | |
| 28 | \renewcommand{\DoxyLabelFont}{% | |
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| 30 | \color{darkgray}% | |
| 31 | } | |
| 32 | \newcommand{\+}{\discretionary{\mbox{\scriptsize$\hookleftarrow$}}{}{}} | |
| 33 | ||
| 34 | % Page & text layout | |
| 35 | \usepackage{geometry} | |
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| 44 | \hfuzz=15pt | |
| 45 | \hbadness=750 | |
| 46 | \setlength{\emergencystretch}{15pt} | |
| 47 | \setlength{\parindent}{0cm} | |
| 48 | \setlength{\parskip}{3ex plus 2ex minus 2ex} | |
| 49 | \makeatletter | |
| 50 | \renewcommand{\paragraph}{% | |
| 51 | \@startsection{paragraph}{4}{0ex}{-1.0ex}{1.0ex}{% | |
| 52 | \normalfont\normalsize\bfseries\SS@parafont% | |
| 53 | }% | |
| 54 | } | |
| 55 | \renewcommand{\subparagraph}{% | |
| 56 | \@startsection{subparagraph}{5}{0ex}{-1.0ex}{1.0ex}{% | |
| 57 | \normalfont\normalsize\bfseries\SS@subparafont% | |
| 58 | }% | |
| 59 | } | |
| 60 | \makeatother | |
| 61 | ||
| 62 | % Headers & footers | |
| 63 | \usepackage{fancyhdr} | |
| 64 | \pagestyle{fancyplain} | |
| 65 | \fancyhead[LE]{\fancyplain{}{\bfseries\thepage}} | |
| 66 | \fancyhead[CE]{\fancyplain{}{}} | |
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| 75 | \fancyfoot[CO]{\fancyplain{}{}} | |
| 76 | \fancyfoot[RO]{\fancyplain{}{}} | |
| 77 | \renewcommand{\footrulewidth}{0.4pt} | |
| 78 | \renewcommand{\chaptermark}[1]{% | |
| 79 | \markboth{#1}{}% | |
| 80 | } | |
| 81 | \renewcommand{\sectionmark}[1]{% | |
| 82 | \markright{\thesection\ #1}% | |
| 83 | } | |
| 84 | ||
| 85 | % Indices & bibliography | |
| 86 | \usepackage{natbib} | |
| 87 | \usepackage[titles]{tocloft} | |
| 88 | \setcounter{tocdepth}{3} | |
| 89 | \setcounter{secnumdepth}{5} | |
| 90 | \makeindex | |
| 91 | ||
| 92 | % Hyperlinks (required, but should be loaded last) | |
| 93 | \usepackage{ifpdf} | |
| 94 | \ifpdf | |
| 95 | \usepackage[pdftex,pagebackref=true]{hyperref} | |
| 96 | \else | |
| 97 | \usepackage[ps2pdf,pagebackref=true]{hyperref} | |
| 98 | \fi | |
| 99 | \hypersetup{% | |
| 100 | colorlinks=true,% | |
| 101 | linkcolor=blue,% | |
| 102 | citecolor=blue,% | |
| 103 | unicode% | |
| 104 | } | |
| 105 | ||
| 106 | % Custom commands | |
| 107 | \newcommand{\clearemptydoublepage}{% | |
| 108 | \newpage{\pagestyle{empty}\cleardoublepage}% | |
| 109 | } | |
| 110 | ||
| 111 | \usepackage{caption} | |
| 112 | \captionsetup{labelsep=space,justification=centering,font={bf},singlelinecheck=off,skip=4pt,position=top} | |
| 113 | ||
| 114 | %===== C O N T E N T S ===== | |
| 115 | ||
| 116 | \begin{document} | |
| 117 | ||
| 118 | % Titlepage & ToC | |
| 119 | \hypersetup{pageanchor=false, | |
| 120 | bookmarksnumbered=true, | |
| 121 | pdfencoding=unicode | |
| 122 | } | |
| 123 | \pagenumbering{alph} | |
| 124 | \begin{titlepage} | |
| 125 | \vspace*{7cm} | |
| 126 | \begin{center}% | |
| 127 | {\Large Iso\+Spec \\[1ex]\large 1.\+95 }\\ | |
| 128 | \vspace*{1cm} | |
| 129 | {\large Generated by Doxygen 1.8.14}\\ | |
| 130 | \end{center} | |
| 131 | \end{titlepage} | |
| 132 | \clearemptydoublepage | |
| 133 | \pagenumbering{roman} | |
| 134 | \tableofcontents | |
| 135 | \clearemptydoublepage | |
| 136 | \pagenumbering{arabic} | |
| 137 | \hypersetup{pageanchor=true} | |
| 138 | ||
| 139 | %--- Begin generated contents --- | |
| 140 | \chapter{Namespace Index} | |
| 141 | \input{namespaces} | |
| 142 | \chapter{Hierarchical Index} | |
| 143 | \input{hierarchy} | |
| 144 | \chapter{Class Index} | |
| 145 | \input{annotated} | |
| 146 | \chapter{Namespace Documentation} | |
| 147 | \input{namespace_iso_spec} | |
| 148 | \chapter{Class Documentation} | |
| 149 | \input{class_iso_spec_1_1_allocator} | |
| 150 | \input{class_iso_spec_1_1_conf_equal} | |
| 151 | \input{class_iso_spec_1_1_conf_order} | |
| 152 | \input{class_iso_spec_1_1_conf_order_marginal} | |
| 153 | \input{class_iso_spec_1_1_conf_order_marginal_descending} | |
| 154 | \input{class_iso_spec_1_1_dirty_allocator} | |
| 155 | \input{class_iso_spec_1_1_iso} | |
| 156 | \input{class_iso_spec_1_1_iso_generator} | |
| 157 | \input{class_iso_spec_1_1_iso_layered_generator} | |
| 158 | \input{class_iso_spec_1_1_iso_ordered_generator} | |
| 159 | \input{class_iso_spec_1_1_iso_threshold_generator} | |
| 160 | \input{class_iso_spec_1_1_key_hasher} | |
| 161 | \input{class_iso_spec_1_1_marginal} | |
| 162 | \input{class_iso_spec_1_1_marginal_trek} | |
| 163 | \input{class_iso_spec_1_1_order_marginals_by_size_decresing} | |
| 164 | \input{class_iso_spec_1_1_precalculated_marginal} | |
| 165 | \input{class_iso_spec_1_1_reverse_order} | |
| 166 | \input{class_iso_spec_1_1_s_summator} | |
| 167 | \input{class_iso_spec_1_1_summator} | |
| 168 | \input{class_iso_spec_1_1_table_order} | |
| 169 | \input{class_iso_spec_1_1_tabulator} | |
| 170 | \input{class_iso_spec_1_1_t_summator} | |
| 171 | %--- End generated contents --- | |
| 172 | ||
| 173 | % Index | |
| 174 | \backmatter | |
| 175 | \newpage | |
| 176 | \phantomsection | |
| 177 | \clearemptydoublepage | |
| 178 | \addcontentsline{toc}{chapter}{Index} | |
| 179 | \printindex | |
| 180 | ||
| 181 | \end{document} |
| 0 | \contentsline {chapter}{\numberline {1}Namespace Index}{1}{chapter.1} | |
| 1 | \contentsline {section}{\numberline {1.1}Namespace List}{1}{section.1.1} | |
| 2 | \contentsline {chapter}{\numberline {2}Hierarchical Index}{3}{chapter.2} | |
| 3 | \contentsline {section}{\numberline {2.1}Class Hierarchy}{3}{section.2.1} | |
| 4 | \contentsline {chapter}{\numberline {3}Class Index}{5}{chapter.3} | |
| 5 | \contentsline {section}{\numberline {3.1}Class List}{5}{section.3.1} | |
| 6 | \contentsline {chapter}{\numberline {4}Namespace Documentation}{7}{chapter.4} | |
| 7 | \contentsline {section}{\numberline {4.1}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec Namespace Reference}{7}{section.4.1} | |
| 8 | \contentsline {subsection}{\numberline {4.1.1}Detailed Description}{9}{subsection.4.1.1} | |
| 9 | \contentsline {subsection}{\numberline {4.1.2}Function Documentation}{9}{subsection.4.1.2} | |
| 10 | \contentsline {subsubsection}{\numberline {4.1.2.1}get\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}M\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Log\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Probs()}{9}{subsubsection.4.1.2.1} | |
| 11 | \contentsline {subsubsection}{\numberline {4.1.2.2}initial\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Configure()}{9}{subsubsection.4.1.2.2} | |
| 12 | \contentsline {chapter}{\numberline {5}Class Documentation}{11}{chapter.5} | |
| 13 | \contentsline {section}{\numberline {5.1}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Allocator$<$ T $>$ Class Template Reference}{11}{section.5.1} | |
| 14 | \contentsline {section}{\numberline {5.2}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Conf\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Equal Class Reference}{11}{section.5.2} | |
| 15 | \contentsline {section}{\numberline {5.3}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Conf\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Equal Class Reference}{11}{section.5.3} | |
| 16 | \contentsline {section}{\numberline {5.4}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Conf\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order Class Reference}{12}{section.5.4} | |
| 17 | \contentsline {section}{\numberline {5.5}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Conf\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order Class Reference}{12}{section.5.5} | |
| 18 | \contentsline {section}{\numberline {5.6}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Conf\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Marginal Class Reference}{12}{section.5.6} | |
| 19 | \contentsline {section}{\numberline {5.7}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Conf\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Marginal Class Reference}{12}{section.5.7} | |
| 20 | \contentsline {section}{\numberline {5.8}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Conf\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Marginal\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Descending Class Reference}{13}{section.5.8} | |
| 21 | \contentsline {section}{\numberline {5.9}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Conf\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Marginal\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Descending Class Reference}{13}{section.5.9} | |
| 22 | \contentsline {section}{\numberline {5.10}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Dirty\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Allocator Class Reference}{13}{section.5.10} | |
| 23 | \contentsline {section}{\numberline {5.11}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso Class Reference}{13}{section.5.11} | |
| 24 | \contentsline {subsection}{\numberline {5.11.1}Detailed Description}{14}{subsection.5.11.1} | |
| 25 | \contentsline {subsection}{\numberline {5.11.2}Constructor \& Destructor Documentation}{14}{subsection.5.11.2} | |
| 26 | \contentsline {subsubsection}{\numberline {5.11.2.1}Iso()}{14}{subsubsection.5.11.2.1} | |
| 27 | \contentsline {subsection}{\numberline {5.11.3}Member Function Documentation}{15}{subsection.5.11.3} | |
| 28 | \contentsline {subsubsection}{\numberline {5.11.3.1}get\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}\_\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}M\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}T\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}\_\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}marginal\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}\_\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}set()}{15}{subsubsection.5.11.3.1} | |
| 29 | \contentsline {subsection}{\numberline {5.11.4}Member Data Documentation}{15}{subsection.5.11.4} | |
| 30 | \contentsline {subsubsection}{\numberline {5.11.4.1}all\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Dim}{15}{subsubsection.5.11.4.1} | |
| 31 | \contentsline {subsubsection}{\numberline {5.11.4.2}atom\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Counts}{16}{subsubsection.5.11.4.2} | |
| 32 | \contentsline {subsubsection}{\numberline {5.11.4.3}conf\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Size}{16}{subsubsection.5.11.4.3} | |
| 33 | \contentsline {subsubsection}{\numberline {5.11.4.4}dim\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Number}{16}{subsubsection.5.11.4.4} | |
| 34 | \contentsline {subsubsection}{\numberline {5.11.4.5}disowned}{16}{subsubsection.5.11.4.5} | |
| 35 | \contentsline {subsubsection}{\numberline {5.11.4.6}isotope\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Numbers}{16}{subsubsection.5.11.4.6} | |
| 36 | \contentsline {subsubsection}{\numberline {5.11.4.7}marginals}{16}{subsubsection.5.11.4.7} | |
| 37 | \contentsline {subsubsection}{\numberline {5.11.4.8}mode\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}L\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Prob}{16}{subsubsection.5.11.4.8} | |
| 38 | \contentsline {section}{\numberline {5.12}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Generator Class Reference}{17}{section.5.12} | |
| 39 | \contentsline {subsection}{\numberline {5.12.1}Detailed Description}{17}{subsection.5.12.1} | |
| 40 | \contentsline {subsection}{\numberline {5.12.2}Member Function Documentation}{17}{subsection.5.12.2} | |
| 41 | \contentsline {subsubsection}{\numberline {5.12.2.1}advance\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}To\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Next\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Configuration()}{17}{subsubsection.5.12.2.1} | |
| 42 | \contentsline {subsection}{\numberline {5.12.3}Member Data Documentation}{18}{subsection.5.12.3} | |
| 43 | \contentsline {subsubsection}{\numberline {5.12.3.1}partial\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Exp\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Probs}{18}{subsubsection.5.12.3.1} | |
| 44 | \contentsline {subsubsection}{\numberline {5.12.3.2}partial\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Masses}{18}{subsubsection.5.12.3.2} | |
| 45 | \contentsline {section}{\numberline {5.13}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Layered\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Generator Class Reference}{18}{section.5.13} | |
| 46 | \contentsline {subsection}{\numberline {5.13.1}Member Function Documentation}{18}{subsection.5.13.1} | |
| 47 | \contentsline {subsubsection}{\numberline {5.13.1.1}advance\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}To\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Next\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Configuration()}{19}{subsubsection.5.13.1.1} | |
| 48 | \contentsline {section}{\numberline {5.14}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Ordered\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Generator Class Reference}{19}{section.5.14} | |
| 49 | \contentsline {subsection}{\numberline {5.14.1}Detailed Description}{19}{subsection.5.14.1} | |
| 50 | \contentsline {subsection}{\numberline {5.14.2}Member Function Documentation}{19}{subsection.5.14.2} | |
| 51 | \contentsline {subsubsection}{\numberline {5.14.2.1}advance\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}To\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Next\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Configuration()}{20}{subsubsection.5.14.2.1} | |
| 52 | \contentsline {section}{\numberline {5.15}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Threshold\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Generator Class Reference}{20}{section.5.15} | |
| 53 | \contentsline {subsection}{\numberline {5.15.1}Member Function Documentation}{20}{subsection.5.15.1} | |
| 54 | \contentsline {subsubsection}{\numberline {5.15.1.1}advance\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}To\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Next\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Configuration()}{20}{subsubsection.5.15.1.1} | |
| 55 | \contentsline {section}{\numberline {5.16}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Key\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Hasher Class Reference}{21}{section.5.16} | |
| 56 | \contentsline {section}{\numberline {5.17}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Key\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Hasher Class Reference}{21}{section.5.17} | |
| 57 | \contentsline {section}{\numberline {5.18}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Marginal Class Reference}{21}{section.5.18} | |
| 58 | \contentsline {section}{\numberline {5.19}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Marginal\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Trek Class Reference}{22}{section.5.19} | |
| 59 | \contentsline {section}{\numberline {5.20}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Precalculated\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Marginal Class Reference}{23}{section.5.20} | |
| 60 | \contentsline {subsection}{\numberline {5.20.1}Member Data Documentation}{23}{subsection.5.20.1} | |
| 61 | \contentsline {subsubsection}{\numberline {5.20.1.1}configurations}{23}{subsubsection.5.20.1.1} | |
| 62 | \contentsline {section}{\numberline {5.21}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Reverse\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order$<$ T $>$ Class Template Reference}{24}{section.5.21} | |
| 63 | \contentsline {section}{\numberline {5.22}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Reverse\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order$<$ T $>$ Class Template Reference}{24}{section.5.22} | |
| 64 | \contentsline {section}{\numberline {5.23}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:S\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Summator Class Reference}{24}{section.5.23} | |
| 65 | \contentsline {section}{\numberline {5.24}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Summator Class Reference}{24}{section.5.24} | |
| 66 | \contentsline {section}{\numberline {5.25}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Table\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order$<$ T $>$ Class Template Reference}{25}{section.5.25} | |
| 67 | \contentsline {section}{\numberline {5.26}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Table\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Order$<$ T $>$ Class Template Reference}{25}{section.5.26} | |
| 68 | \contentsline {section}{\numberline {5.27}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Tabulator$<$ T $>$ Class Template Reference}{25}{section.5.27} | |
| 69 | \contentsline {section}{\numberline {5.28}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:Thread\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Summator Class Reference}{25}{section.5.28} | |
| 70 | \contentsline {section}{\numberline {5.29}Iso\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Spec\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}:T\discretionary {\unhbox \voidb@x \hbox {\relax \fontsize {7}{8}\selectfont $\leftarrow \joinrel \rhook $}}{}{}Summator Class Reference}{26}{section.5.29} | |
| 71 | \contentsline {chapter}{Index}{27}{section*.53} |
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| 0 | .TH "IsoSpec" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Classes" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "class \fBAllocator\fP" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "class \fBConfEqual\fP" | |
| 16 | .br | |
| 17 | .ti -1c | |
| 18 | .RI "class \fBConfOrder\fP" | |
| 19 | .br | |
| 20 | .ti -1c | |
| 21 | .RI "class \fBConfOrderMarginal\fP" | |
| 22 | .br | |
| 23 | .ti -1c | |
| 24 | .RI "class \fBConfOrderMarginalDescending\fP" | |
| 25 | .br | |
| 26 | .ti -1c | |
| 27 | .RI "class \fBDirtyAllocator\fP" | |
| 28 | .br | |
| 29 | .ti -1c | |
| 30 | .RI "class \fBIso\fP" | |
| 31 | .br | |
| 32 | .RI "The \fBIso\fP class for the calculation of the isotopic distribution\&. " | |
| 33 | .ti -1c | |
| 34 | .RI "class \fBIsoGenerator\fP" | |
| 35 | .br | |
| 36 | .RI "The generator of isotopologues\&. " | |
| 37 | .ti -1c | |
| 38 | .RI "class \fBIsoLayeredGenerator\fP" | |
| 39 | .br | |
| 40 | .RI "The class that represents isotopologues above a given joint probability value\&. " | |
| 41 | .ti -1c | |
| 42 | .RI "class \fBIsoOrderedGenerator\fP" | |
| 43 | .br | |
| 44 | .RI "The generator of isotopologues sorted by their probability of occurrence\&. " | |
| 45 | .ti -1c | |
| 46 | .RI "class \fBIsoThresholdGenerator\fP" | |
| 47 | .br | |
| 48 | .RI "The generator of isotopologues above a given threshold value\&. " | |
| 49 | .ti -1c | |
| 50 | .RI "class \fBKeyHasher\fP" | |
| 51 | .br | |
| 52 | .ti -1c | |
| 53 | .RI "class \fBMarginal\fP" | |
| 54 | .br | |
| 55 | .RI "The marginal distribution class (a subisotopologue)\&. " | |
| 56 | .ti -1c | |
| 57 | .RI "class \fBMarginalTrek\fP" | |
| 58 | .br | |
| 59 | .RI "The marginal distribution class (a subisotopologue)\&. " | |
| 60 | .ti -1c | |
| 61 | .RI "class \fBOrderMarginalsBySizeDecresing\fP" | |
| 62 | .br | |
| 63 | .ti -1c | |
| 64 | .RI "class \fBPrecalculatedMarginal\fP" | |
| 65 | .br | |
| 66 | .RI "Precalculated \fBMarginal\fP class\&. " | |
| 67 | .ti -1c | |
| 68 | .RI "class \fBReverseOrder\fP" | |
| 69 | .br | |
| 70 | .ti -1c | |
| 71 | .RI "class \fBSSummator\fP" | |
| 72 | .br | |
| 73 | .ti -1c | |
| 74 | .RI "class \fBSummator\fP" | |
| 75 | .br | |
| 76 | .ti -1c | |
| 77 | .RI "class \fBTableOrder\fP" | |
| 78 | .br | |
| 79 | .ti -1c | |
| 80 | .RI "class \fBTabulator\fP" | |
| 81 | .br | |
| 82 | .ti -1c | |
| 83 | .RI "class \fBTSummator\fP" | |
| 84 | .br | |
| 85 | .in -1c | |
| 86 | .SS "Typedefs" | |
| 87 | ||
| 88 | .in +1c | |
| 89 | .ti -1c | |
| 90 | .RI "typedef int * \fBConf\fP" | |
| 91 | .br | |
| 92 | .in -1c | |
| 93 | .SS "Functions" | |
| 94 | ||
| 95 | .in +1c | |
| 96 | .ti -1c | |
| 97 | .RI "template<typename T > void \fBcopyConf\fP (const T *source, T *destination, int dim)" | |
| 98 | .br | |
| 99 | .ti -1c | |
| 100 | .RI "void \fBrelease_g_lfact_table\fP ()" | |
| 101 | .br | |
| 102 | .ti -1c | |
| 103 | .RI "double * \fBalloc_lfact_table\fP ()" | |
| 104 | .br | |
| 105 | .ti -1c | |
| 106 | .RI "double \fBRationalApproximation\fP (double t)" | |
| 107 | .br | |
| 108 | .ti -1c | |
| 109 | .RI "double \fBNormalCDFInverse\fP (double p)" | |
| 110 | .br | |
| 111 | .ti -1c | |
| 112 | .RI "double \fBNormalCDFInverse\fP (double p, double mean, double stdev)" | |
| 113 | .br | |
| 114 | .ti -1c | |
| 115 | .RI "double \fBNormalCDF\fP (double x, double mean, double stdev)" | |
| 116 | .br | |
| 117 | .ti -1c | |
| 118 | .RI "double \fBNormalPDF\fP (double x, double mean, double stdev)" | |
| 119 | .br | |
| 120 | .ti -1c | |
| 121 | .RI "unsigned int \fBparse_formula\fP (const char *formula, std::vector< const double *> &isotope_masses, std::vector< const double *> &isotope_probabilities, int **isotopeNumbers, int **atomCounts, unsigned int *confSize)" | |
| 122 | .br | |
| 123 | .ti -1c | |
| 124 | .RI "void \fBprintConfigurations\fP (const std::tuple< double *, double *, int *, int > &results, int dimNumber, int *isotopeNumbers)" | |
| 125 | .br | |
| 126 | .ti -1c | |
| 127 | .RI "Conf \fBinitialConfigure\fP (const int atomCnt, const int isotopeNo, const double *probs, const double *lprobs)" | |
| 128 | .br | |
| 129 | .RI "Find one of the most probable subisotopologues\&. " | |
| 130 | .ti -1c | |
| 131 | .RI "void \fBprintMarginal\fP (const std::tuple< double *, double *, int *, int > &results, int dim)" | |
| 132 | .br | |
| 133 | .ti -1c | |
| 134 | .RI "double * \fBgetMLogProbs\fP (const double *probs, int isoNo)" | |
| 135 | .br | |
| 136 | .ti -1c | |
| 137 | .RI "double \fBget_loggamma_nominator\fP (int x)" | |
| 138 | .br | |
| 139 | .ti -1c | |
| 140 | .RI "Conf \fBinitialConfigure\fP (int atomCnt, int isotopeNo, const double *probs)" | |
| 141 | .br | |
| 142 | .ti -1c | |
| 143 | .RI "void * \fBquickselect\fP (void **array, int n, int start, int end)" | |
| 144 | .br | |
| 145 | .RI "Quickly select the n'th positional statistic, including the weights\&. " | |
| 146 | .ti -1c | |
| 147 | .RI "double \fBcombinedSum\fP (const int *conf, const std::vector< double > **valuesContainer, int dimNumber)" | |
| 148 | .br | |
| 149 | .ti -1c | |
| 150 | .RI "int * \fBgetConf\fP (void *conf)" | |
| 151 | .br | |
| 152 | .ti -1c | |
| 153 | .RI "double \fBgetLProb\fP (void *conf)" | |
| 154 | .br | |
| 155 | .ti -1c | |
| 156 | .RI "double \fBunnormalized_logProb\fP (const int *conf, const double *logProbs, int dim)" | |
| 157 | .br | |
| 158 | .ti -1c | |
| 159 | .RI "double \fBmass\fP (const int *conf, const double *masses, int dim)" | |
| 160 | .br | |
| 161 | .ti -1c | |
| 162 | .RI "bool \fBtupleCmp\fP (std::tuple< double, double, int *> t1, std::tuple< double, double, int *> t2)" | |
| 163 | .br | |
| 164 | .ti -1c | |
| 165 | .RI "template<typename T > void \fBprintArray\fP (const T *array, int size)" | |
| 166 | .br | |
| 167 | .ti -1c | |
| 168 | .RI "template<typename T > void \fBprintVector\fP (const std::vector< T > &vec)" | |
| 169 | .br | |
| 170 | .ti -1c | |
| 171 | .RI "template<typename T > void \fBprintNestedArray\fP (const T **array, const int *shape, int size)" | |
| 172 | .br | |
| 173 | .ti -1c | |
| 174 | .RI "template<typename T > void \fBdealloc_table\fP (T *tbl, int dim)" | |
| 175 | .br | |
| 176 | .ti -1c | |
| 177 | .RI "void \fBreallocate\fP (double **array, int new_size)" | |
| 178 | .br | |
| 179 | .in -1c | |
| 180 | .SS "Variables" | |
| 181 | ||
| 182 | .in +1c | |
| 183 | .ti -1c | |
| 184 | .RI "const int \fBelem_table_atomicNo\fP [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]" | |
| 185 | .br | |
| 186 | .ti -1c | |
| 187 | .RI "const double \fBelem_table_mass\fP [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]" | |
| 188 | .br | |
| 189 | .ti -1c | |
| 190 | .RI "const int \fBelem_table_massNo\fP [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]" | |
| 191 | .br | |
| 192 | .ti -1c | |
| 193 | .RI "const int \fBelem_table_extraNeutrons\fP [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]" | |
| 194 | .br | |
| 195 | .ti -1c | |
| 196 | .RI "const char * \fBelem_table_element\fP [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]" | |
| 197 | .br | |
| 198 | .ti -1c | |
| 199 | .RI "const char * \fBelem_table_symbol\fP [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]" | |
| 200 | .br | |
| 201 | .ti -1c | |
| 202 | .RI "const bool \fBelem_table_Radioactive\fP [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]" | |
| 203 | .br | |
| 204 | .ti -1c | |
| 205 | .RI "const double \fBelem_table_probability\fP [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]" | |
| 206 | .br | |
| 207 | .ti -1c | |
| 208 | .RI "const double \fBelem_table_log_probability\fP [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]" | |
| 209 | .br | |
| 210 | .ti -1c | |
| 211 | .RI "const double \fBpi\fP = 3\&.14159265358979323846264338328" | |
| 212 | .br | |
| 213 | .ti -1c | |
| 214 | .RI "double * \fBg_lfact_table\fP = alloc_lfact_table()" | |
| 215 | .br | |
| 216 | .in -1c | |
| 217 | .SH "Detailed Description" | |
| 218 | .PP | |
| 219 | Copyright (C) 2015-2018 Mateusz Łącki and Michał Startek\&. | |
| 220 | .PP | |
| 221 | This file is part of \fBIsoSpec\fP\&. | |
| 222 | .PP | |
| 223 | \fBIsoSpec\fP is free software: you can redistribute it and/or modify it under the terms of the Simplified ('2-clause') BSD licence\&. | |
| 224 | .PP | |
| 225 | \fBIsoSpec\fP is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE\&. | |
| 226 | .PP | |
| 227 | You should have received a copy of the Simplified BSD Licence along with \fBIsoSpec\fP\&. If not, see https://opensource.org/licenses/BSD-2-Clause\&. | |
| 228 | .SH "Function Documentation" | |
| 229 | .PP | |
| 230 | .SS "double* IsoSpec::getMLogProbs (const double * probs, int isoNo)" | |
| 231 | ||
| 232 | .br | |
| 233 | Here we order the processor to round the numbers up rather than down\&. Rounding down could result in the algorithm falling in an infinite loop because of the numerical instability of summing\&. | |
| 234 | .PP | |
| 235 | Definition at line 150 of file marginalTrek++\&.cpp\&. | |
| 236 | .SS "Conf IsoSpec::initialConfigure (const int atomCnt, const int isotopeNo, const double * probs, const double * lprobs)" | |
| 237 | ||
| 238 | .PP | |
| 239 | Find one of the most probable subisotopologues\&. The algorithm uses the hill-climbing algorithm\&. It starts from a subisotopologue close to the mean of the underlying multinomial distribution\&. There might be more than one modes, in case of which this function will return only one of them, close to the mean\&. | |
| 240 | .PP | |
| 241 | \fBParameters:\fP | |
| 242 | .RS 4 | |
| 243 | \fIatomCnt\fP | |
| 244 | .RE | |
| 245 | .PP | |
| 246 | ||
| 247 | .br | |
| 248 | Here we perform hill climbing to the mode of the marginal distribution (the subisotopologue distribution)\&. We start from the point close to the mean of the underlying multinomial distribution\&. | |
| 249 | .PP | |
| 250 | Definition at line 55 of file marginalTrek++\&.cpp\&. | |
| 251 | .SH "Author" | |
| 252 | .PP | |
| 253 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::Allocator< T >" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::Allocator< T > | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBAllocator\fP (const int dim, const int tabSize=10000)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "void \fBshiftTables\fP ()" | |
| 16 | .br | |
| 17 | .ti -1c | |
| 18 | .RI "T * \fBnewConf\fP ()" | |
| 19 | .br | |
| 20 | .ti -1c | |
| 21 | .RI "T * \fBmakeCopy\fP (const T *conf)" | |
| 22 | .br | |
| 23 | .ti -1c | |
| 24 | .RI "T * \fBmakeExternalCopy\fP (const T *conf)" | |
| 25 | .br | |
| 26 | .in -1c | |
| 27 | .SH "Detailed Description" | |
| 28 | .PP | |
| 29 | ||
| 30 | .SS "template<typename T> | |
| 31 | .br | |
| 32 | class IsoSpec::Allocator< T >" | |
| 33 | ||
| 34 | .PP | |
| 35 | Definition at line 34 of file allocator\&.h\&. | |
| 36 | ||
| 37 | .SH "Author" | |
| 38 | .PP | |
| 39 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::ConfEqual" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::ConfEqual | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBConfEqual\fP (int dim)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "bool \fBoperator()\fP (const int *conf1, const int *conf2) const" | |
| 16 | .br | |
| 17 | .in -1c | |
| 18 | .SH "Detailed Description" | |
| 19 | .PP | |
| 20 | Definition at line 45 of file operators\&.h\&. | |
| 21 | ||
| 22 | .SH "Author" | |
| 23 | .PP | |
| 24 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::ConfOrder" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::ConfOrder | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "bool \fBoperator()\fP (void *conf1, void *conf2) const" | |
| 13 | .br | |
| 14 | .in -1c | |
| 15 | .SH "Detailed Description" | |
| 16 | .PP | |
| 17 | Definition at line 66 of file operators\&.h\&. | |
| 18 | ||
| 19 | .SH "Author" | |
| 20 | .PP | |
| 21 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::ConfOrderMarginal" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::ConfOrderMarginal | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBConfOrderMarginal\fP (const double *logProbs, int dim)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "bool \fBoperator()\fP (const Conf conf1, const Conf conf2)" | |
| 16 | .br | |
| 17 | .in -1c | |
| 18 | .SH "Detailed Description" | |
| 19 | .PP | |
| 20 | Definition at line 78 of file operators\&.h\&. | |
| 21 | ||
| 22 | .SH "Author" | |
| 23 | .PP | |
| 24 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::ConfOrderMarginalDescending" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::ConfOrderMarginalDescending | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBConfOrderMarginalDescending\fP (const double *logProbs, int dim)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "bool \fBoperator()\fP (const Conf conf1, const Conf conf2)" | |
| 16 | .br | |
| 17 | .in -1c | |
| 18 | .SH "Detailed Description" | |
| 19 | .PP | |
| 20 | Definition at line 92 of file operators\&.h\&. | |
| 21 | ||
| 22 | .SH "Author" | |
| 23 | .PP | |
| 24 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::DirtyAllocator" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::DirtyAllocator | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBDirtyAllocator\fP (const int dim, const int tabSize=10000)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "void \fBshiftTables\fP ()" | |
| 16 | .br | |
| 17 | .ti -1c | |
| 18 | .RI "void * \fBnewConf\fP ()" | |
| 19 | .br | |
| 20 | .ti -1c | |
| 21 | .RI "void * \fBmakeCopy\fP (const void *conf)" | |
| 22 | .br | |
| 23 | .ti -1c | |
| 24 | .RI "void * \fBmakeExternalCopy\fP (const void *conf)" | |
| 25 | .br | |
| 26 | .in -1c | |
| 27 | .SH "Detailed Description" | |
| 28 | .PP | |
| 29 | Definition at line 26 of file dirtyAllocator\&.h\&. | |
| 30 | ||
| 31 | .SH "Author" | |
| 32 | .PP | |
| 33 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::Iso" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::Iso \- The \fBIso\fP class for the calculation of the isotopic distribution\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <isoSpec++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherited by \fBIsoSpec::IsoGenerator\fP\&. | |
| 13 | .SS "Public Member Functions" | |
| 14 | ||
| 15 | .in +1c | |
| 16 | .ti -1c | |
| 17 | .RI "\fBIso\fP (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)" | |
| 18 | .br | |
| 19 | .RI "General constructror\&. " | |
| 20 | .ti -1c | |
| 21 | .RI "\fBIso\fP (const char *formula)" | |
| 22 | .br | |
| 23 | .RI "Constructor from the formula object\&. " | |
| 24 | .ti -1c | |
| 25 | .RI "\fBIso\fP (\fBIso\fP &&other)" | |
| 26 | .br | |
| 27 | .RI "The move constructor\&. " | |
| 28 | .ti -1c | |
| 29 | .RI "\fBIso\fP (const \fBIso\fP &other, bool fullcopy)" | |
| 30 | .br | |
| 31 | .RI "The copy constructor\&. " | |
| 32 | .ti -1c | |
| 33 | .RI "virtual \fB~Iso\fP ()" | |
| 34 | .br | |
| 35 | .RI "Destructor\&. " | |
| 36 | .ti -1c | |
| 37 | .RI "double \fBgetLightestPeakMass\fP () const" | |
| 38 | .br | |
| 39 | .RI "Get the mass of the lightest peak in the isotopic distribution\&. " | |
| 40 | .ti -1c | |
| 41 | .RI "double \fBgetHeaviestPeakMass\fP () const" | |
| 42 | .br | |
| 43 | .RI "Get the mass of the heaviest peak in the isotopic distribution\&. " | |
| 44 | .ti -1c | |
| 45 | .RI "double \fBgetModeLProb\fP () const" | |
| 46 | .br | |
| 47 | .RI "Get the log-probability of the mode-configuration (if there are many modes, they share this value)\&. " | |
| 48 | .ti -1c | |
| 49 | .RI "int \fBgetDimNumber\fP () const" | |
| 50 | .br | |
| 51 | .RI "Get the number of elements in the chemical formula of the molecule\&. " | |
| 52 | .ti -1c | |
| 53 | .RI "int \fBgetAllDim\fP () const" | |
| 54 | .br | |
| 55 | .RI "Get the total number of isotopes of elements present in a chemical formula\&. " | |
| 56 | .in -1c | |
| 57 | .SS "Public Attributes" | |
| 58 | ||
| 59 | .in +1c | |
| 60 | .ti -1c | |
| 61 | .RI "bool \fBdisowned\fP" | |
| 62 | .br | |
| 63 | .in -1c | |
| 64 | .SS "Protected Attributes" | |
| 65 | ||
| 66 | .in +1c | |
| 67 | .ti -1c | |
| 68 | .RI "int \fBdimNumber\fP" | |
| 69 | .br | |
| 70 | .ti -1c | |
| 71 | .RI "int * \fBisotopeNumbers\fP" | |
| 72 | .br | |
| 73 | .ti -1c | |
| 74 | .RI "int * \fBatomCounts\fP" | |
| 75 | .br | |
| 76 | .ti -1c | |
| 77 | .RI "unsigned int \fBconfSize\fP" | |
| 78 | .br | |
| 79 | .ti -1c | |
| 80 | .RI "int \fBallDim\fP" | |
| 81 | .br | |
| 82 | .ti -1c | |
| 83 | .RI "\fBMarginal\fP ** \fBmarginals\fP" | |
| 84 | .br | |
| 85 | .ti -1c | |
| 86 | .RI "double \fBmodeLProb\fP" | |
| 87 | .br | |
| 88 | .in -1c | |
| 89 | .SH "Detailed Description" | |
| 90 | .PP | |
| 91 | The \fBIso\fP class for the calculation of the isotopic distribution\&. | |
| 92 | ||
| 93 | It contains full description of the molecule for which one would like to calculate the isotopic distribution\&. | |
| 94 | .PP | |
| 95 | Definition at line 52 of file isoSpec++\&.h\&. | |
| 96 | .SH "Constructor & Destructor Documentation" | |
| 97 | .PP | |
| 98 | .SS "IsoSpec::Iso::Iso (int _dimNumber, const int * _isotopeNumbers, const int * _atomCounts, const double *const * _isotopeMasses, const double *const * _isotopeProbabilities)" | |
| 99 | ||
| 100 | .PP | |
| 101 | General constructror\&. | |
| 102 | .PP | |
| 103 | \fBParameters:\fP | |
| 104 | .RS 4 | |
| 105 | \fI_dimNumber\fP The number of elements in the formula, e\&.g\&. for C100H202 it would be 2, as there are only carbon and hydrogen atoms\&. | |
| 106 | .br | |
| 107 | \fI_isotopeNumbers\fP A table with numbers of isotopes for each element, e\&.g\&. for C100H202 it would be {2, 2}, because both C and H have two stable isotopes\&. | |
| 108 | .br | |
| 109 | \fI_atomCounts\fP Number of atoms of each element in the formula, e\&.g\&. for C100H202 corresponds to {100, 202}\&. | |
| 110 | .br | |
| 111 | \fI_isotopeMasses\fP A table of masses of isotopes of the elements in the chemical formula, e\&.g\&. {12\&.0, 13\&.003355, 1\&.007825, 2\&.014102} for C100H202\&. | |
| 112 | .br | |
| 113 | \fI_isotopeProbabilities\fP A table of isotope frequencies of the elements in the chemical formula, e\&.g\&. {\&.989212, \&.010788, \&.999885, \&.000115} for C100H202\&. | |
| 114 | .RE | |
| 115 | .PP | |
| 116 | ||
| 117 | .PP | |
| 118 | Definition at line 51 of file isoSpec++\&.cpp\&. | |
| 119 | .SS "IsoSpec::Iso::Iso (const \fBIso\fP & other, bool fullcopy)" | |
| 120 | ||
| 121 | .PP | |
| 122 | The copy constructor\&. | |
| 123 | .PP | |
| 124 | \fBParameters:\fP | |
| 125 | .RS 4 | |
| 126 | \fIother\fP The other instance of the \fBIso\fP class\&. | |
| 127 | .br | |
| 128 | \fIfullcopy\fP If false, copy only the number of atoms in the formula, the size of the configuration, the total number of isotopes, and the probability of the mode isotopologue\&. | |
| 129 | .RE | |
| 130 | .PP | |
| 131 | ||
| 132 | .PP | |
| 133 | Definition at line 84 of file isoSpec++\&.cpp\&. | |
| 134 | .SH "Member Data Documentation" | |
| 135 | .PP | |
| 136 | .SS "int IsoSpec::Iso::allDim\fC [protected]\fP" | |
| 137 | The total number of isotopes of elements present in a chemical formula, e\&.g\&. for H20 it is 2+3=5\&. | |
| 138 | .PP | |
| 139 | Definition at line 71 of file isoSpec++\&.h\&. | |
| 140 | .SS "int* IsoSpec::Iso::atomCounts\fC [protected]\fP" | |
| 141 | A table with numbers of isotopes for each element\&. | |
| 142 | .PP | |
| 143 | Definition at line 69 of file isoSpec++\&.h\&. | |
| 144 | .SS "unsigned int IsoSpec::Iso::confSize\fC [protected]\fP" | |
| 145 | The number of bytes needed to represent the counts of isotopes present in the extended chemical formula\&. | |
| 146 | .PP | |
| 147 | Definition at line 70 of file isoSpec++\&.h\&. | |
| 148 | .SS "int IsoSpec::Iso::dimNumber\fC [protected]\fP" | |
| 149 | The number of elements in the chemical formula of the molecule\&. | |
| 150 | .PP | |
| 151 | Definition at line 67 of file isoSpec++\&.h\&. | |
| 152 | .SS "bool IsoSpec::Iso::disowned" | |
| 153 | A variable showing if the \fBIso\fP class was specialized by its child-class\&. If so, then the description of the molecules has been transfered there and \fBIso\fP is a carcass class, dead as a dodo, an ex-class if you will\&. | |
| 154 | .PP | |
| 155 | Definition at line 65 of file isoSpec++\&.h\&. | |
| 156 | .SS "int* IsoSpec::Iso::isotopeNumbers\fC [protected]\fP" | |
| 157 | A table with numbers of isotopes for each element\&. | |
| 158 | .PP | |
| 159 | Definition at line 68 of file isoSpec++\&.h\&. | |
| 160 | .SS "\fBMarginal\fP** IsoSpec::Iso::marginals\fC [protected]\fP" | |
| 161 | The table of pointers to the distributions of individual subisotopologues\&. | |
| 162 | .PP | |
| 163 | Definition at line 72 of file isoSpec++\&.h\&. | |
| 164 | .SS "double IsoSpec::Iso::modeLProb\fC [protected]\fP" | |
| 165 | The log-probability of the mode of the isotopic distribution\&. | |
| 166 | .PP | |
| 167 | Definition at line 73 of file isoSpec++\&.h\&. | |
| 168 | ||
| 169 | .SH "Author" | |
| 170 | .PP | |
| 171 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoGenerator" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoGenerator \- The generator of isotopologues\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <isoSpec++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherits \fBIsoSpec::Iso\fP\&. | |
| 13 | .PP | |
| 14 | Inherited by \fBIsoSpec::IsoLayeredGenerator\fP, \fBIsoSpec::IsoOrderedGenerator\fP, and \fBIsoSpec::IsoThresholdGenerator\fP\&. | |
| 15 | .SS "Public Member Functions" | |
| 16 | ||
| 17 | .in +1c | |
| 18 | .ti -1c | |
| 19 | .RI "virtual bool \fBadvanceToNextConfiguration\fP ()=0" | |
| 20 | .br | |
| 21 | .RI "Advance to the next, not yet visited, most probable isotopologue\&. " | |
| 22 | .ti -1c | |
| 23 | .RI "virtual double \fBlprob\fP () const" | |
| 24 | .br | |
| 25 | .RI "Get the log-probability of the current isotopologue\&. " | |
| 26 | .ti -1c | |
| 27 | .RI "virtual double \fBmass\fP () const" | |
| 28 | .br | |
| 29 | .RI "Get the mass of the current isotopologue\&. " | |
| 30 | .ti -1c | |
| 31 | .RI "virtual double \fBprob\fP () const" | |
| 32 | .br | |
| 33 | .RI "Get the probability of the current isotopologue\&. " | |
| 34 | .ti -1c | |
| 35 | .RI "virtual void \fBget_conf_signature\fP (int *space) const =0" | |
| 36 | .br | |
| 37 | .ti -1c | |
| 38 | .RI "\fBIsoGenerator\fP (\fBIso\fP &&iso, bool alloc_partials=true)" | |
| 39 | .br | |
| 40 | .RI "Move constructor\&. " | |
| 41 | .ti -1c | |
| 42 | .RI "virtual \fB~IsoGenerator\fP ()" | |
| 43 | .br | |
| 44 | .RI "Destructor\&. " | |
| 45 | .in -1c | |
| 46 | .SS "Protected Attributes" | |
| 47 | ||
| 48 | .in +1c | |
| 49 | .ti -1c | |
| 50 | .RI "double * \fBpartialLProbs\fP" | |
| 51 | .br | |
| 52 | .ti -1c | |
| 53 | .RI "double * \fBpartialMasses\fP" | |
| 54 | .br | |
| 55 | .ti -1c | |
| 56 | .RI "double * \fBpartialProbs\fP" | |
| 57 | .br | |
| 58 | .in -1c | |
| 59 | .SS "Additional Inherited Members" | |
| 60 | .SH "Detailed Description" | |
| 61 | .PP | |
| 62 | The generator of isotopologues\&. | |
| 63 | ||
| 64 | This class provides the common interface for all isotopic generators\&. | |
| 65 | .PP | |
| 66 | Definition at line 129 of file isoSpec++\&.h\&. | |
| 67 | .SH "Member Function Documentation" | |
| 68 | .PP | |
| 69 | .SS "virtual bool IsoSpec::IsoGenerator::advanceToNextConfiguration ()\fC [pure virtual]\fP" | |
| 70 | ||
| 71 | .PP | |
| 72 | Advance to the next, not yet visited, most probable isotopologue\&. | |
| 73 | .PP | |
| 74 | \fBReturns:\fP | |
| 75 | .RS 4 | |
| 76 | Return false if it is not possible to advance\&. | |
| 77 | .RE | |
| 78 | .PP | |
| 79 | ||
| 80 | .PP | |
| 81 | Implemented in \fBIsoSpec::IsoLayeredGenerator\fP, \fBIsoSpec::IsoThresholdGenerator\fP, and \fBIsoSpec::IsoOrderedGenerator\fP\&. | |
| 82 | .SS "virtual double IsoSpec::IsoGenerator::lprob () const\fC [inline]\fP, \fC [virtual]\fP" | |
| 83 | ||
| 84 | .PP | |
| 85 | Get the log-probability of the current isotopologue\&. | |
| 86 | .PP | |
| 87 | \fBReturns:\fP | |
| 88 | .RS 4 | |
| 89 | The log-probability of the current isotopologue\&. | |
| 90 | .RE | |
| 91 | .PP | |
| 92 | ||
| 93 | .PP | |
| 94 | Reimplemented in \fBIsoSpec::IsoThresholdGenerator\fP\&. | |
| 95 | .PP | |
| 96 | Definition at line 147 of file isoSpec++\&.h\&. | |
| 97 | .SS "virtual double IsoSpec::IsoGenerator::mass () const\fC [inline]\fP, \fC [virtual]\fP" | |
| 98 | ||
| 99 | .PP | |
| 100 | Get the mass of the current isotopologue\&. | |
| 101 | .PP | |
| 102 | \fBReturns:\fP | |
| 103 | .RS 4 | |
| 104 | The mass of the current isotopologue\&. | |
| 105 | .RE | |
| 106 | .PP | |
| 107 | ||
| 108 | .PP | |
| 109 | Reimplemented in \fBIsoSpec::IsoThresholdGenerator\fP\&. | |
| 110 | .PP | |
| 111 | Definition at line 153 of file isoSpec++\&.h\&. | |
| 112 | .SS "virtual double IsoSpec::IsoGenerator::prob () const\fC [inline]\fP, \fC [virtual]\fP" | |
| 113 | ||
| 114 | .PP | |
| 115 | Get the probability of the current isotopologue\&. | |
| 116 | .PP | |
| 117 | \fBReturns:\fP | |
| 118 | .RS 4 | |
| 119 | The probability of the current isotopologue\&. | |
| 120 | .RE | |
| 121 | .PP | |
| 122 | ||
| 123 | .PP | |
| 124 | Reimplemented in \fBIsoSpec::IsoThresholdGenerator\fP\&. | |
| 125 | .PP | |
| 126 | Definition at line 159 of file isoSpec++\&.h\&. | |
| 127 | .SH "Member Data Documentation" | |
| 128 | .PP | |
| 129 | .SS "double* IsoSpec::IsoGenerator::partialLProbs\fC [protected]\fP" | |
| 130 | The prefix sum of the log-probabilities of the current isotopologue\&. | |
| 131 | .PP | |
| 132 | Definition at line 132 of file isoSpec++\&.h\&. | |
| 133 | .SS "double* IsoSpec::IsoGenerator::partialMasses\fC [protected]\fP" | |
| 134 | The prefix sum of the masses of the current isotopologue\&. | |
| 135 | .PP | |
| 136 | Definition at line 133 of file isoSpec++\&.h\&. | |
| 137 | .SS "double* IsoSpec::IsoGenerator::partialProbs\fC [protected]\fP" | |
| 138 | The prefix product of the probabilities of the current isotopologue\&. | |
| 139 | .PP | |
| 140 | Definition at line 134 of file isoSpec++\&.h\&. | |
| 141 | ||
| 142 | .SH "Author" | |
| 143 | .PP | |
| 144 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoLayeredGenerator" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoLayeredGenerator \- The class that represents isotopologues above a given joint probability value\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <isoSpec++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherits \fBIsoSpec::IsoGenerator\fP\&. | |
| 13 | .SS "Public Member Functions" | |
| 14 | ||
| 15 | .in +1c | |
| 16 | .ti -1c | |
| 17 | .RI "bool \fBadvanceToNextConfiguration\fP () override final" | |
| 18 | .br | |
| 19 | .RI "Advance to the next, not yet visited, most probable isotopologue\&. " | |
| 20 | .ti -1c | |
| 21 | .RI "void \fBget_conf_signature\fP (int *space) const override final" | |
| 22 | .br | |
| 23 | .ti -1c | |
| 24 | .RI "\fBIsoLayeredGenerator\fP (\fBIso\fP &&iso, double _targetCoverage, double _percentageToExpand, int _tabSize=1000, int _hashSize=1000, bool trim=false)" | |
| 25 | .br | |
| 26 | .ti -1c | |
| 27 | .RI "void \fBterminate_search\fP ()" | |
| 28 | .br | |
| 29 | .in -1c | |
| 30 | .SS "Additional Inherited Members" | |
| 31 | .SH "Detailed Description" | |
| 32 | .PP | |
| 33 | The class that represents isotopologues above a given joint probability value\&. | |
| 34 | ||
| 35 | This class generates subsequent isotopologues that ARE NOT GUARANTEED TO BE ORDERED BY probability\&. The overal set of isotopologues is guaranteed to surpass a given threshold of probability contained in the isotopic distribution\&. This calculations are performed in O(N) operations, where N is the total number of the output isotopologues\&. | |
| 36 | .PP | |
| 37 | This class is not a true generator yet - the generator methods have been implemented for compatibility, but the class actually performs all computations during the initialization and stores them, and the generator methods only walk through the array of precomputed values\&. \&. It will be reimplemented as a true generator in 2\&.0\&. | |
| 38 | .PP | |
| 39 | Definition at line 383 of file isoSpec++\&.h\&. | |
| 40 | .SH "Member Function Documentation" | |
| 41 | .PP | |
| 42 | .SS "bool IsoSpec::IsoLayeredGenerator::advanceToNextConfiguration ()\fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP" | |
| 43 | ||
| 44 | .PP | |
| 45 | Advance to the next, not yet visited, most probable isotopologue\&. | |
| 46 | .PP | |
| 47 | \fBReturns:\fP | |
| 48 | .RS 4 | |
| 49 | Return false if it is not possible to advance\&. | |
| 50 | .RE | |
| 51 | .PP | |
| 52 | ||
| 53 | .PP | |
| 54 | Implements \fBIsoSpec::IsoGenerator\fP\&. | |
| 55 | .PP | |
| 56 | Definition at line 773 of file isoSpec++\&.cpp\&. | |
| 57 | ||
| 58 | .SH "Author" | |
| 59 | .PP | |
| 60 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoOrderedGenerator" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoOrderedGenerator \- The generator of isotopologues sorted by their probability of occurrence\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <isoSpec++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherits \fBIsoSpec::IsoGenerator\fP\&. | |
| 13 | .SS "Public Member Functions" | |
| 14 | ||
| 15 | .in +1c | |
| 16 | .ti -1c | |
| 17 | .RI "bool \fBadvanceToNextConfiguration\fP () override final" | |
| 18 | .br | |
| 19 | .RI "Advance to the next, not yet visited, most probable isotopologue\&. " | |
| 20 | .ti -1c | |
| 21 | .RI "void \fBget_conf_signature\fP (int *space) const override final" | |
| 22 | .br | |
| 23 | .RI "Save the counts of isotopes in the space\&. " | |
| 24 | .ti -1c | |
| 25 | .RI "\fBIsoOrderedGenerator\fP (\fBIso\fP &&iso, int _tabSize=1000, int _hashSize=1000)" | |
| 26 | .br | |
| 27 | .RI "The move-contstructor\&. " | |
| 28 | .ti -1c | |
| 29 | .RI "virtual \fB~IsoOrderedGenerator\fP ()" | |
| 30 | .br | |
| 31 | .RI "Destructor\&. " | |
| 32 | .in -1c | |
| 33 | .SS "Additional Inherited Members" | |
| 34 | .SH "Detailed Description" | |
| 35 | .PP | |
| 36 | The generator of isotopologues sorted by their probability of occurrence\&. | |
| 37 | ||
| 38 | The subsequent isotopologues are generated with diminishing probability, starting from the mode\&. This algorithm take O(N*log(N)) to compute the N isotopologues because of using the Priority Queue data structure\&. Obtaining the N isotopologues can be achieved in O(N) if they are not required to be spit out in the descending order\&. | |
| 39 | .PP | |
| 40 | Definition at line 179 of file isoSpec++\&.h\&. | |
| 41 | .SH "Member Function Documentation" | |
| 42 | .PP | |
| 43 | .SS "bool IsoSpec::IsoOrderedGenerator::advanceToNextConfiguration ()\fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP" | |
| 44 | ||
| 45 | .PP | |
| 46 | Advance to the next, not yet visited, most probable isotopologue\&. | |
| 47 | .PP | |
| 48 | \fBReturns:\fP | |
| 49 | .RS 4 | |
| 50 | Return false if it is not possible to advance\&. | |
| 51 | .RE | |
| 52 | .PP | |
| 53 | ||
| 54 | .PP | |
| 55 | Implements \fBIsoSpec::IsoGenerator\fP\&. | |
| 56 | .PP | |
| 57 | Definition at line 461 of file isoSpec++\&.cpp\&. | |
| 58 | .SS "void IsoSpec::IsoOrderedGenerator::get_conf_signature (int * space) const\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP" | |
| 59 | ||
| 60 | .PP | |
| 61 | Save the counts of isotopes in the space\&. | |
| 62 | .PP | |
| 63 | \fBParameters:\fP | |
| 64 | .RS 4 | |
| 65 | \fIspace\fP An array where counts of isotopes shall be written\&. Must be as big as the overall number of isotopes\&. | |
| 66 | .RE | |
| 67 | .PP | |
| 68 | ||
| 69 | .PP | |
| 70 | Implements \fBIsoSpec::IsoGenerator\fP\&. | |
| 71 | .PP | |
| 72 | Definition at line 202 of file isoSpec++\&.h\&. | |
| 73 | ||
| 74 | .SH "Author" | |
| 75 | .PP | |
| 76 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoSpec::ConfEqual" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoSpec::ConfEqual \- The equality of configurations operator\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .SS "Public Member Functions" | |
| 10 | ||
| 11 | .in +1c | |
| 12 | .ti -1c | |
| 13 | .RI "\fBConfEqual\fP (int dim)" | |
| 14 | .br | |
| 15 | .RI "Constructor\&. " | |
| 16 | .ti -1c | |
| 17 | .RI "bool \fBoperator()\fP (const int *conf1, const int *conf2) const" | |
| 18 | .br | |
| 19 | .RI "The \fBcall\fP operator\&. " | |
| 20 | .in -1c | |
| 21 | .SH "Detailed Description" | |
| 22 | .PP | |
| 23 | The equality of configurations operator\&. | |
| 24 | ||
| 25 | Needed for the unordered-map\&. | |
| 26 | .PP | |
| 27 | Definition at line 62 of file operators\&.cpp\&. | |
| 28 | .SH "Constructor & Destructor Documentation" | |
| 29 | .PP | |
| 30 | .SS "IsoSpec::ConfEqual::ConfEqual (int dim)" | |
| 31 | ||
| 32 | .PP | |
| 33 | Constructor\&. | |
| 34 | .PP | |
| 35 | \fBParameters:\fP | |
| 36 | .RS 4 | |
| 37 | \fIdim\fP the number of the ints that make up a configuration\&. | |
| 38 | .RE | |
| 39 | .PP | |
| 40 | ||
| 41 | .PP | |
| 42 | Definition at line 26 of file operators\&.cpp\&. | |
| 43 | .SH "Member Function Documentation" | |
| 44 | .PP | |
| 45 | .SS "bool IsoSpec::IsoSpec::ConfEqual::operator() (const int * conf1, const int * conf2) const\fC [inline]\fP" | |
| 46 | ||
| 47 | .PP | |
| 48 | The \fBcall\fP operator\&. Let us quote the sacred MAN of memcmp: "The memcmp() function returns zero if the two strings are identical, otherwise returns the difference between the first two differing bytes (treated as unsigned char values, so that `\\200' is greater than `\\0', for example)\&. Zero-length strings are always identical\&. This behavior is not required by C and portable code should only depend on the sign of the returned value\&." | |
| 49 | .PP | |
| 50 | \fBParameters:\fP | |
| 51 | .RS 4 | |
| 52 | \fIconf1\fP An array of integer counts\&. | |
| 53 | .br | |
| 54 | \fIconf2\fP An array of integer counts\&. | |
| 55 | .RE | |
| 56 | .PP | |
| 57 | \fBReturns:\fP | |
| 58 | .RS 4 | |
| 59 | Are conf1 and conf2 the same configuration? | |
| 60 | .RE | |
| 61 | .PP | |
| 62 | ||
| 63 | .PP | |
| 64 | Definition at line 87 of file operators\&.cpp\&. | |
| 65 | ||
| 66 | .SH "Author" | |
| 67 | .PP | |
| 68 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoSpec::ConfOrder" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoSpec::ConfOrder \- The class used for comparing the position of configurations in the order of descending probabilities\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .SS "Public Member Functions" | |
| 10 | ||
| 11 | .in +1c | |
| 12 | .ti -1c | |
| 13 | .RI "bool \fBoperator()\fP (void *conf1, void *conf2) const" | |
| 14 | .br | |
| 15 | .in -1c | |
| 16 | .SH "Detailed Description" | |
| 17 | .PP | |
| 18 | The class used for comparing the position of configurations in the order of descending probabilities\&. | |
| 19 | ||
| 20 | Needed for the priority queue\&. | |
| 21 | .PP | |
| 22 | Definition at line 98 of file operators\&.cpp\&. | |
| 23 | ||
| 24 | .SH "Author" | |
| 25 | .PP | |
| 26 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoSpec::ConfOrderMarginal" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoSpec::ConfOrderMarginal \- The class used for comparing the position of subisotopologues in the order of descending probabilities\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .SS "Public Member Functions" | |
| 10 | ||
| 11 | .in +1c | |
| 12 | .ti -1c | |
| 13 | .RI "\fBConfOrderMarginal\fP (const double *logProbs, int dim)" | |
| 14 | .br | |
| 15 | .RI "Constructor\&. " | |
| 16 | .ti -1c | |
| 17 | .RI "bool \fBoperator()\fP (const Conf conf1, const Conf conf2)" | |
| 18 | .br | |
| 19 | .RI "Constructor\&. " | |
| 20 | .in -1c | |
| 21 | .SH "Detailed Description" | |
| 22 | .PP | |
| 23 | The class used for comparing the position of subisotopologues in the order of descending probabilities\&. | |
| 24 | ||
| 25 | Needed for the priority queue\&. | |
| 26 | .PP | |
| 27 | Definition at line 112 of file operators\&.cpp\&. | |
| 28 | .SH "Constructor & Destructor Documentation" | |
| 29 | .PP | |
| 30 | .SS "IsoSpec::ConfOrderMarginal::ConfOrderMarginal (const double * logProbs, int dim)" | |
| 31 | ||
| 32 | .PP | |
| 33 | Constructor\&. | |
| 34 | .PP | |
| 35 | \fBParameters:\fP | |
| 36 | .RS 4 | |
| 37 | \fIlogProbs\fP | |
| 38 | .br | |
| 39 | \fIdim\fP The number of isotopes\&. | |
| 40 | .RE | |
| 41 | .PP | |
| 42 | ||
| 43 | .PP | |
| 44 | Definition at line 30 of file operators\&.cpp\&. | |
| 45 | .SH "Member Function Documentation" | |
| 46 | .PP | |
| 47 | .SS "bool IsoSpec::IsoSpec::ConfOrderMarginal::operator() (const Conf conf1, const Conf conf2)\fC [inline]\fP" | |
| 48 | ||
| 49 | .PP | |
| 50 | Constructor\&. | |
| 51 | .PP | |
| 52 | \fBParameters:\fP | |
| 53 | .RS 4 | |
| 54 | \fIconf1\fP An array of integer counts\&. | |
| 55 | .br | |
| 56 | \fIconf2\fP An array of integer counts\&. | |
| 57 | .RE | |
| 58 | .PP | |
| 59 | \fBReturns:\fP | |
| 60 | .RS 4 | |
| 61 | True if conf1 is less probable than conf2\&. | |
| 62 | .RE | |
| 63 | .PP | |
| 64 | ||
| 65 | .PP | |
| 66 | Definition at line 130 of file operators\&.cpp\&. | |
| 67 | ||
| 68 | .SH "Author" | |
| 69 | .PP | |
| 70 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoSpec::ConfOrderMarginalDescending" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoSpec::ConfOrderMarginalDescending \- The class used for comparing the position of subisotopologues in the order of descending probabilities\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .SS "Public Member Functions" | |
| 10 | ||
| 11 | .in +1c | |
| 12 | .ti -1c | |
| 13 | .RI "\fBConfOrderMarginalDescending\fP (const double *logProbs, int dim)" | |
| 14 | .br | |
| 15 | .RI "Contstructor\&. " | |
| 16 | .ti -1c | |
| 17 | .RI "bool \fBoperator()\fP (const Conf conf1, const Conf conf2)" | |
| 18 | .br | |
| 19 | .RI "Constructor\&. " | |
| 20 | .in -1c | |
| 21 | .SH "Detailed Description" | |
| 22 | .PP | |
| 23 | The class used for comparing the position of subisotopologues in the order of descending probabilities\&. | |
| 24 | ||
| 25 | Needed for the priority queue\&. | |
| 26 | .PP | |
| 27 | Definition at line 141 of file operators\&.cpp\&. | |
| 28 | .SH "Constructor & Destructor Documentation" | |
| 29 | .PP | |
| 30 | .SS "IsoSpec::ConfOrderMarginalDescending::ConfOrderMarginalDescending (const double * logProbs, int dim)" | |
| 31 | ||
| 32 | .PP | |
| 33 | Contstructor\&. | |
| 34 | .PP | |
| 35 | \fBParameters:\fP | |
| 36 | .RS 4 | |
| 37 | \fIlogProbs\fP | |
| 38 | .br | |
| 39 | \fIdim\fP The number of isotopes\&. | |
| 40 | .RE | |
| 41 | .PP | |
| 42 | ||
| 43 | .PP | |
| 44 | Definition at line 34 of file operators\&.cpp\&. | |
| 45 | .SH "Member Function Documentation" | |
| 46 | .PP | |
| 47 | .SS "bool IsoSpec::IsoSpec::ConfOrderMarginalDescending::operator() (const Conf conf1, const Conf conf2)\fC [inline]\fP" | |
| 48 | ||
| 49 | .PP | |
| 50 | Constructor\&. | |
| 51 | .PP | |
| 52 | \fBParameters:\fP | |
| 53 | .RS 4 | |
| 54 | \fIconf1\fP An array of integer counts\&. | |
| 55 | .br | |
| 56 | \fIconf2\fP An array of integer counts\&. | |
| 57 | .RE | |
| 58 | .PP | |
| 59 | \fBReturns:\fP | |
| 60 | .RS 4 | |
| 61 | True if conf1 is more probable than conf2\&. | |
| 62 | .RE | |
| 63 | .PP | |
| 64 | ||
| 65 | .PP | |
| 66 | Definition at line 160 of file operators\&.cpp\&. | |
| 67 | ||
| 68 | .SH "Author" | |
| 69 | .PP | |
| 70 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoSpec::KeyHasher" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoSpec::KeyHasher \- The hash function class\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .SS "Public Member Functions" | |
| 10 | ||
| 11 | .in +1c | |
| 12 | .ti -1c | |
| 13 | .RI "\fBKeyHasher\fP (int dim)" | |
| 14 | .br | |
| 15 | .RI "Constructor\&. " | |
| 16 | .ti -1c | |
| 17 | .RI "std::size_t \fBoperator()\fP (const int *conf) const" | |
| 18 | .br | |
| 19 | .RI "The \fBcall\fP operator\&. " | |
| 20 | .in -1c | |
| 21 | .SH "Detailed Description" | |
| 22 | .PP | |
| 23 | The hash function class\&. | |
| 24 | ||
| 25 | Needed for the unordered-map\&. | |
| 26 | .PP | |
| 27 | Definition at line 31 of file operators\&.cpp\&. | |
| 28 | .SH "Constructor & Destructor Documentation" | |
| 29 | .PP | |
| 30 | .SS "IsoSpec::KeyHasher::KeyHasher (int dim)" | |
| 31 | ||
| 32 | .PP | |
| 33 | Constructor\&. | |
| 34 | .PP | |
| 35 | \fBParameters:\fP | |
| 36 | .RS 4 | |
| 37 | \fIdim\fP the number of the ints that make up a configuration\&. | |
| 38 | .RE | |
| 39 | .PP | |
| 40 | ||
| 41 | .PP | |
| 42 | Definition at line 22 of file operators\&.cpp\&. | |
| 43 | .SH "Member Function Documentation" | |
| 44 | .PP | |
| 45 | .SS "std::size_t IsoSpec::IsoSpec::KeyHasher::operator() (const int * conf) const\fC [inline]\fP" | |
| 46 | ||
| 47 | .PP | |
| 48 | The \fBcall\fP operator\&. | |
| 49 | .PP | |
| 50 | \fBParameters:\fP | |
| 51 | .RS 4 | |
| 52 | \fIconf\fP An array of integer counts\&. | |
| 53 | .RE | |
| 54 | .PP | |
| 55 | \fBReturns:\fP | |
| 56 | .RS 4 | |
| 57 | The hash for counts\&. | |
| 58 | .RE | |
| 59 | .PP | |
| 60 | ||
| 61 | .PP | |
| 62 | Definition at line 47 of file operators\&.cpp\&. | |
| 63 | ||
| 64 | .SH "Author" | |
| 65 | .PP | |
| 66 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoSpec::ReverseOrder< T >" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoSpec::ReverseOrder< T > | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "bool \fBoperator()\fP (const T a, const T b) const" | |
| 13 | .br | |
| 14 | .in -1c | |
| 15 | .SH "Detailed Description" | |
| 16 | .PP | |
| 17 | ||
| 18 | .SS "template<typename T> | |
| 19 | .br | |
| 20 | class IsoSpec::IsoSpec::ReverseOrder< T >" | |
| 21 | ||
| 22 | .PP | |
| 23 | Definition at line 167 of file operators\&.cpp\&. | |
| 24 | ||
| 25 | .SH "Author" | |
| 26 | .PP | |
| 27 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoSpec::TableOrder< T >" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoSpec::TableOrder< T > | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBTableOrder\fP (const T *_tbl)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "bool \fBoperator()\fP (unsigned int i, unsigned int j)" | |
| 16 | .br | |
| 17 | .in -1c | |
| 18 | .SH "Detailed Description" | |
| 19 | .PP | |
| 20 | ||
| 21 | .SS "template<typename T> | |
| 22 | .br | |
| 23 | class IsoSpec::IsoSpec::TableOrder< T >" | |
| 24 | ||
| 25 | .PP | |
| 26 | Definition at line 174 of file operators\&.cpp\&. | |
| 27 | ||
| 28 | .SH "Author" | |
| 29 | .PP | |
| 30 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoThresholdGenerator" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoThresholdGenerator \- The generator of isotopologues above a given threshold value\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <isoSpec++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherits \fBIsoSpec::IsoGenerator\fP\&. | |
| 13 | .SS "Public Member Functions" | |
| 14 | ||
| 15 | .in +1c | |
| 16 | .ti -1c | |
| 17 | .RI "void \fBget_conf_signature\fP (int *space) const override final" | |
| 18 | .br | |
| 19 | .ti -1c | |
| 20 | .RI "\fBIsoThresholdGenerator\fP (\fBIso\fP &&iso, double _threshold, bool _absolute=true, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true)" | |
| 21 | .br | |
| 22 | .RI "The move-constructor\&. " | |
| 23 | .ti -1c | |
| 24 | .RI "ISOSPEC_FORCE_INLINE bool \fBadvanceToNextConfiguration\fP () override final" | |
| 25 | .br | |
| 26 | .RI "Advance to the next, not yet visited, most probable isotopologue\&. " | |
| 27 | .ti -1c | |
| 28 | .RI "ISOSPEC_FORCE_INLINE double \fBlprob\fP () const override final" | |
| 29 | .br | |
| 30 | .RI "Get the log-probability of the current isotopologue\&. " | |
| 31 | .ti -1c | |
| 32 | .RI "ISOSPEC_FORCE_INLINE double \fBmass\fP () const override final" | |
| 33 | .br | |
| 34 | .RI "Get the mass of the current isotopologue\&. " | |
| 35 | .ti -1c | |
| 36 | .RI "ISOSPEC_FORCE_INLINE double \fBprob\fP () const override final" | |
| 37 | .br | |
| 38 | .RI "Get the probability of the current isotopologue\&. " | |
| 39 | .ti -1c | |
| 40 | .RI "void \fBterminate_search\fP ()" | |
| 41 | .br | |
| 42 | .RI "Block the subsequent search of isotopologues\&. " | |
| 43 | .ti -1c | |
| 44 | .RI "void \fBreset\fP ()" | |
| 45 | .br | |
| 46 | .ti -1c | |
| 47 | .RI "size_t \fBcount_confs\fP ()" | |
| 48 | .br | |
| 49 | .in -1c | |
| 50 | .SS "Additional Inherited Members" | |
| 51 | .SH "Detailed Description" | |
| 52 | .PP | |
| 53 | The generator of isotopologues above a given threshold value\&. | |
| 54 | ||
| 55 | Attention: the calculated configurations are only partially ordeded and the user should not assume they will be ordered\&. This algorithm computes N isotopologues in O(N)\&. It is a considerable advantage w\&.r\&.t\&. the \fBIsoOrderedGenerator\fP\&. | |
| 56 | .PP | |
| 57 | Definition at line 235 of file isoSpec++\&.h\&. | |
| 58 | .SH "Constructor & Destructor Documentation" | |
| 59 | .PP | |
| 60 | .SS "IsoSpec::IsoThresholdGenerator::IsoThresholdGenerator (\fBIso\fP && iso, double _threshold, bool _absolute = \fCtrue\fP, int _tabSize = \fC1000\fP, int _hashSize = \fC1000\fP, bool reorder_marginals = \fCtrue\fP)" | |
| 61 | ||
| 62 | .PP | |
| 63 | The move-constructor\&. | |
| 64 | .PP | |
| 65 | \fBParameters:\fP | |
| 66 | .RS 4 | |
| 67 | \fIiso\fP An instance of the \fBIso\fP class\&. | |
| 68 | .br | |
| 69 | \fI_threshold\fP The threshold value\&. | |
| 70 | .br | |
| 71 | \fI_absolute\fP If true, the _threshold is interpreted as the absolute minimal peak height for the isotopologues\&. If false, the _threshold is the fraction of the heighest peak's probability\&. | |
| 72 | .br | |
| 73 | \fItabSize\fP The size of the extension of the table with configurations\&. | |
| 74 | .br | |
| 75 | \fIhashSize\fP The size of the hash-table used to store subisotopologues and check if they have been already calculated\&. | |
| 76 | .RE | |
| 77 | .PP | |
| 78 | ||
| 79 | .PP | |
| 80 | Definition at line 286 of file isoSpec++\&.cpp\&. | |
| 81 | .SH "Member Function Documentation" | |
| 82 | .PP | |
| 83 | .SS "ISOSPEC_FORCE_INLINE bool IsoSpec::IsoThresholdGenerator::advanceToNextConfiguration ()\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP" | |
| 84 | ||
| 85 | .PP | |
| 86 | Advance to the next, not yet visited, most probable isotopologue\&. | |
| 87 | .PP | |
| 88 | \fBReturns:\fP | |
| 89 | .RS 4 | |
| 90 | Return false if it is not possible to advance\&. | |
| 91 | .RE | |
| 92 | .PP | |
| 93 | ||
| 94 | .PP | |
| 95 | Implements \fBIsoSpec::IsoGenerator\fP\&. | |
| 96 | .PP | |
| 97 | Definition at line 296 of file isoSpec++\&.h\&. | |
| 98 | .SS "size_t IsoSpec::IsoThresholdGenerator::count_confs ()" | |
| 99 | Count the number of configurations in the distribution\&. This can be used to pre-allocate enough memory to store it (e\&.g\&. std::vector's reserve() method - this is faster than depending on the vector's dynamic resizing, even though it means that the configuration space is walked through twice\&. This method has to be called before the first call to advanceToNextConfiguration and has undefined results (incl\&. segfaults) otherwise\&. | |
| 100 | .PP | |
| 101 | Definition at line 376 of file isoSpec++\&.cpp\&. | |
| 102 | .SS "ISOSPEC_FORCE_INLINE double IsoSpec::IsoThresholdGenerator::lprob () const\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP" | |
| 103 | ||
| 104 | .PP | |
| 105 | Get the log-probability of the current isotopologue\&. | |
| 106 | .PP | |
| 107 | \fBReturns:\fP | |
| 108 | .RS 4 | |
| 109 | The log-probability of the current isotopologue\&. | |
| 110 | .RE | |
| 111 | .PP | |
| 112 | ||
| 113 | .PP | |
| 114 | Reimplemented from \fBIsoSpec::IsoGenerator\fP\&. | |
| 115 | .PP | |
| 116 | Definition at line 335 of file isoSpec++\&.h\&. | |
| 117 | .SS "ISOSPEC_FORCE_INLINE double IsoSpec::IsoThresholdGenerator::mass () const\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP" | |
| 118 | ||
| 119 | .PP | |
| 120 | Get the mass of the current isotopologue\&. | |
| 121 | .PP | |
| 122 | \fBReturns:\fP | |
| 123 | .RS 4 | |
| 124 | The mass of the current isotopologue\&. | |
| 125 | .RE | |
| 126 | .PP | |
| 127 | ||
| 128 | .PP | |
| 129 | Reimplemented from \fBIsoSpec::IsoGenerator\fP\&. | |
| 130 | .PP | |
| 131 | Definition at line 336 of file isoSpec++\&.h\&. | |
| 132 | .SS "ISOSPEC_FORCE_INLINE double IsoSpec::IsoThresholdGenerator::prob () const\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP" | |
| 133 | ||
| 134 | .PP | |
| 135 | Get the probability of the current isotopologue\&. | |
| 136 | .PP | |
| 137 | \fBReturns:\fP | |
| 138 | .RS 4 | |
| 139 | The probability of the current isotopologue\&. | |
| 140 | .RE | |
| 141 | .PP | |
| 142 | ||
| 143 | .PP | |
| 144 | Reimplemented from \fBIsoSpec::IsoGenerator\fP\&. | |
| 145 | .PP | |
| 146 | Definition at line 337 of file isoSpec++\&.h\&. | |
| 147 | .SS "void IsoSpec::IsoThresholdGenerator::reset ()" | |
| 148 | Reset the generator to the beginning of the sequence\&. Allows it to be reused, eg\&. to go through the conf space once, calculate the amount of space needed to store configurations, then to allocate that memory, and go through it again, this time saving configurations (and \fIis\fP in fact faster than allocating a std::vector and depending on it to grow as needed\&. This is cheaper than throwing away the generator and making a new one too: marginal distributions don't need to be recalculated\&. | |
| 149 | .PP | |
| 150 | Definition at line 386 of file isoSpec++\&.cpp\&. | |
| 151 | ||
| 152 | .SH "Author" | |
| 153 | .PP | |
| 154 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::IsoThresholdGeneratorMT" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::IsoThresholdGeneratorMT \- The multi-threaded version of the generator of isotopologues\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <isoSpec++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherits \fBIsoSpec::IsoGenerator\fP\&. | |
| 13 | .SS "Public Member Functions" | |
| 14 | ||
| 15 | .in +1c | |
| 16 | .ti -1c | |
| 17 | .RI "bool \fBadvanceToNextConfiguration\fP () override final" | |
| 18 | .br | |
| 19 | .RI "Advance to the next, not yet visited, most probable isotopologue\&. " | |
| 20 | .ti -1c | |
| 21 | .RI "void \fBget_conf_signature\fP (int *space) const override final" | |
| 22 | .br | |
| 23 | .RI "Save the counts of isotopes in the space\&. " | |
| 24 | .ti -1c | |
| 25 | .RI "\fBIsoThresholdGeneratorMT\fP (\fBIso\fP &&iso, double _threshold, \fBPrecalculatedMarginal\fP **\fBmarginals\fP, bool _absolute=true)" | |
| 26 | .br | |
| 27 | .RI "Move constructor\&. " | |
| 28 | .ti -1c | |
| 29 | .RI "virtual \fB~IsoThresholdGeneratorMT\fP ()" | |
| 30 | .br | |
| 31 | .RI "Destructor\&. " | |
| 32 | .ti -1c | |
| 33 | .RI "void \fBterminate_search\fP ()" | |
| 34 | .br | |
| 35 | .RI "Block the subsequent search of isotopologues\&. " | |
| 36 | .in -1c | |
| 37 | .SS "Additional Inherited Members" | |
| 38 | .SH "Detailed Description" | |
| 39 | .PP | |
| 40 | The multi-threaded version of the generator of isotopologues\&. | |
| 41 | ||
| 42 | Attention: this code is experimental\&. | |
| 43 | .PP | |
| 44 | Definition at line 305 of file isoSpec++\&.h\&. | |
| 45 | .SH "Member Function Documentation" | |
| 46 | .PP | |
| 47 | .SS "bool IsoSpec::IsoThresholdGeneratorMT::advanceToNextConfiguration ()\fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP" | |
| 48 | ||
| 49 | .PP | |
| 50 | Advance to the next, not yet visited, most probable isotopologue\&. | |
| 51 | .PP | |
| 52 | \fBReturns:\fP | |
| 53 | .RS 4 | |
| 54 | Return false if it is not possible to advance\&. | |
| 55 | .RE | |
| 56 | .PP | |
| 57 | ||
| 58 | .PP | |
| 59 | Implements \fBIsoSpec::IsoGenerator\fP\&. | |
| 60 | .PP | |
| 61 | Definition at line 354 of file isoSpec++\&.cpp\&. | |
| 62 | .SS "void IsoSpec::IsoThresholdGeneratorMT::get_conf_signature (int * space) const\fC [inline]\fP, \fC [final]\fP, \fC [override]\fP, \fC [virtual]\fP" | |
| 63 | ||
| 64 | .PP | |
| 65 | Save the counts of isotopes in the space\&. | |
| 66 | .PP | |
| 67 | \fBParameters:\fP | |
| 68 | .RS 4 | |
| 69 | \fIspace\fP An array where counts of isotopes shall be written\&. Must be as big as the overall number of isotopes\&. | |
| 70 | .RE | |
| 71 | .PP | |
| 72 | ||
| 73 | .PP | |
| 74 | Implements \fBIsoSpec::IsoGenerator\fP\&. | |
| 75 | .PP | |
| 76 | Definition at line 316 of file isoSpec++\&.h\&. | |
| 77 | ||
| 78 | .SH "Author" | |
| 79 | .PP | |
| 80 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::KeyHasher" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::KeyHasher | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBKeyHasher\fP (int dim)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "std::size_t \fBoperator()\fP (const int *conf) const" | |
| 16 | .br | |
| 17 | .in -1c | |
| 18 | .SH "Detailed Description" | |
| 19 | .PP | |
| 20 | Definition at line 27 of file operators\&.h\&. | |
| 21 | ||
| 22 | .SH "Author" | |
| 23 | .PP | |
| 24 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::LayeredMarginal" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::LayeredMarginal \- \fBLayeredMarginal\fP class\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <marginalTrek++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherits \fBIsoSpec::Marginal\fP\&. | |
| 13 | .SS "Public Member Functions" | |
| 14 | ||
| 15 | .in +1c | |
| 16 | .ti -1c | |
| 17 | .RI "\fBLayeredMarginal\fP (\fBMarginal\fP &&m, int tabSize=1000, int hashSize=1000)" | |
| 18 | .br | |
| 19 | .RI "Move constructor: specializes the \fBMarginal\fP class\&. " | |
| 20 | .ti -1c | |
| 21 | .RI "bool \fBextend\fP (double new_threshold)" | |
| 22 | .br | |
| 23 | .RI "Extend the set of computed subisotopologues to those above the new threshold\&. " | |
| 24 | .ti -1c | |
| 25 | .RI "double \fBget_lProb\fP (int idx) const" | |
| 26 | .br | |
| 27 | .RI "get the log-probability of the idx-th subisotopologue, see details in \fBPrecalculatedMarginal::get_lProb\fP\&. " | |
| 28 | .ti -1c | |
| 29 | .RI "double \fBget_eProb\fP (int idx) const" | |
| 30 | .br | |
| 31 | .RI "get the probability of the idx-th subisotopologue, see details in \fBPrecalculatedMarginal::get_eProb\fP\&. " | |
| 32 | .ti -1c | |
| 33 | .RI "double \fBget_mass\fP (int idx) const" | |
| 34 | .br | |
| 35 | .RI "get the mass of the idx-th subisotopologue, see details in \fBPrecalculatedMarginal::get_mass\fP\&. " | |
| 36 | .ti -1c | |
| 37 | .RI "const Conf & \fBget_conf\fP (int idx) const" | |
| 38 | .br | |
| 39 | .RI "get the counts of isotopes that define the subisotopologue, see details in \fBPrecalculatedMarginal::get_conf\fP\&. " | |
| 40 | .ti -1c | |
| 41 | .RI "unsigned int \fBget_no_confs\fP () const" | |
| 42 | .br | |
| 43 | .RI "Get the number of precomputed subisotopologues, see details in \fBPrecalculatedMarginal::get_no_confs\fP\&. " | |
| 44 | .in -1c | |
| 45 | .SS "Additional Inherited Members" | |
| 46 | .SH "Detailed Description" | |
| 47 | .PP | |
| 48 | \fBLayeredMarginal\fP class\&. | |
| 49 | ||
| 50 | An extendable version of the \fBPrecalculatedMarginal\fP, where you can extend the threshold at will\&. | |
| 51 | .PP | |
| 52 | Definition at line 337 of file marginalTrek++\&.h\&. | |
| 53 | .SH "Constructor & Destructor Documentation" | |
| 54 | .PP | |
| 55 | .SS "IsoSpec::LayeredMarginal::LayeredMarginal (\fBMarginal\fP && m, int tabSize = \fC1000\fP, int hashSize = \fC1000\fP)" | |
| 56 | ||
| 57 | .PP | |
| 58 | Move constructor: specializes the \fBMarginal\fP class\&. | |
| 59 | .PP | |
| 60 | \fBParameters:\fP | |
| 61 | .RS 4 | |
| 62 | \fItabSize\fP The size of the table used to store configurations in the allocator\&. | |
| 63 | .br | |
| 64 | \fIhashSize\fP The size of the hash table used to store visited subisotopologues\&. | |
| 65 | .RE | |
| 66 | .PP | |
| 67 | ||
| 68 | .PP | |
| 69 | Definition at line 445 of file marginalTrek++\&.cpp\&. | |
| 70 | .SH "Member Function Documentation" | |
| 71 | .PP | |
| 72 | .SS "bool IsoSpec::LayeredMarginal::extend (double new_threshold)" | |
| 73 | ||
| 74 | .PP | |
| 75 | Extend the set of computed subisotopologues to those above the new threshold\&. | |
| 76 | .PP | |
| 77 | \fBParameters:\fP | |
| 78 | .RS 4 | |
| 79 | \fInew_threshold\fP The new log-probability limiting the subisotopologues from below\&. | |
| 80 | .RE | |
| 81 | .PP | |
| 82 | \fBReturns:\fP | |
| 83 | .RS 4 | |
| 84 | Returns false, if there are no fringe-subisotopologues (subisotopologues that were neighbours of the previously calculated subisotopologues, with log-probability below the previous threshold)\&. | |
| 85 | .RE | |
| 86 | .PP | |
| 87 | ||
| 88 | .PP | |
| 89 | Definition at line 455 of file marginalTrek++\&.cpp\&. | |
| 90 | ||
| 91 | .SH "Author" | |
| 92 | .PP | |
| 93 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::Marginal" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::Marginal \- The marginal distribution class (a subisotopologue)\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <marginalTrek++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherited by \fBIsoSpec::MarginalTrek\fP, and \fBIsoSpec::PrecalculatedMarginal\fP\&. | |
| 13 | .SS "Public Member Functions" | |
| 14 | ||
| 15 | .in +1c | |
| 16 | .ti -1c | |
| 17 | .RI "\fBMarginal\fP (const double *_masses, const double *_probs, int _isotopeNo, int _atomCnt)" | |
| 18 | .br | |
| 19 | .RI "Class constructor\&. " | |
| 20 | .ti -1c | |
| 21 | .RI "\fBMarginal\fP (\fBMarginal\fP &other)=delete" | |
| 22 | .br | |
| 23 | .ti -1c | |
| 24 | .RI "\fBMarginal\fP & \fBoperator=\fP (const \fBMarginal\fP &other)=delete" | |
| 25 | .br | |
| 26 | .ti -1c | |
| 27 | .RI "\fBMarginal\fP (\fBMarginal\fP &&other)" | |
| 28 | .br | |
| 29 | .RI "Move constructor\&. " | |
| 30 | .ti -1c | |
| 31 | .RI "virtual \fB~Marginal\fP ()" | |
| 32 | .br | |
| 33 | .RI "Destructor\&. " | |
| 34 | .ti -1c | |
| 35 | .RI "int \fBget_isotopeNo\fP () const" | |
| 36 | .br | |
| 37 | .RI "Get the number of isotopes of the investigated element\&. " | |
| 38 | .ti -1c | |
| 39 | .RI "double \fBgetLightestConfMass\fP () const" | |
| 40 | .br | |
| 41 | .RI "Get the mass of the lightest subisotopologue\&. " | |
| 42 | .ti -1c | |
| 43 | .RI "double \fBgetHeaviestConfMass\fP () const" | |
| 44 | .br | |
| 45 | .RI "Get the mass of the heaviest subisotopologue\&. " | |
| 46 | .ti -1c | |
| 47 | .RI "double \fBgetModeLProb\fP () const" | |
| 48 | .br | |
| 49 | .RI "Get the log-probability of the mode subisotopologue\&. " | |
| 50 | .ti -1c | |
| 51 | .RI "double \fBgetModeMass\fP () const" | |
| 52 | .br | |
| 53 | .RI "The the mass of the mode subisotopologue\&. " | |
| 54 | .ti -1c | |
| 55 | .RI "double \fBgetModeProb\fP () const" | |
| 56 | .br | |
| 57 | .RI "The the probability of the mode subisotopologue\&. " | |
| 58 | .ti -1c | |
| 59 | .RI "double \fBgetSmallestLProb\fP () const" | |
| 60 | .br | |
| 61 | .RI "The the log-probability of the lightest subisotopologue\&. " | |
| 62 | .ti -1c | |
| 63 | .RI "double \fBlogProb\fP (Conf conf) const" | |
| 64 | .br | |
| 65 | .RI "Calculate the log-probability of a given subisotopologue\&. " | |
| 66 | .in -1c | |
| 67 | .SS "Protected Attributes" | |
| 68 | ||
| 69 | .in +1c | |
| 70 | .ti -1c | |
| 71 | .RI "const unsigned int \fBisotopeNo\fP" | |
| 72 | .br | |
| 73 | .ti -1c | |
| 74 | .RI "const unsigned int \fBatomCnt\fP" | |
| 75 | .br | |
| 76 | .ti -1c | |
| 77 | .RI "const double *const \fBatom_masses\fP" | |
| 78 | .br | |
| 79 | .ti -1c | |
| 80 | .RI "const double *const \fBatom_lProbs\fP" | |
| 81 | .br | |
| 82 | .ti -1c | |
| 83 | .RI "const double \fBloggamma_nominator\fP" | |
| 84 | .br | |
| 85 | .ti -1c | |
| 86 | .RI "const Conf \fBmode_conf\fP" | |
| 87 | .br | |
| 88 | .ti -1c | |
| 89 | .RI "const double \fBmode_lprob\fP" | |
| 90 | .br | |
| 91 | .ti -1c | |
| 92 | .RI "const double \fBmode_mass\fP" | |
| 93 | .br | |
| 94 | .ti -1c | |
| 95 | .RI "const double \fBmode_prob\fP" | |
| 96 | .br | |
| 97 | .ti -1c | |
| 98 | .RI "const double \fBsmallest_lprob\fP" | |
| 99 | .br | |
| 100 | .in -1c | |
| 101 | .SH "Detailed Description" | |
| 102 | .PP | |
| 103 | The marginal distribution class (a subisotopologue)\&. | |
| 104 | ||
| 105 | This class mostly provides some basic common API for subclasses, but itself is not abstract\&. This class represents the probability distribution generated by one element only -- a subisotopologue\&. For instance, it might be the distribution of C200, that might be part of, say, C200H402\&. It corresponds to the multinomial distribution, where each configuration can also be attributed a precise mass\&. The constructor method perform initial hill-climbing to find the most probable sub-isotopologue (the mode)\&. | |
| 106 | .PP | |
| 107 | Definition at line 45 of file marginalTrek++\&.h\&. | |
| 108 | .SH "Constructor & Destructor Documentation" | |
| 109 | .PP | |
| 110 | .SS "IsoSpec::Marginal::Marginal (const double * _masses, const double * _probs, int _isotopeNo, int _atomCnt)" | |
| 111 | ||
| 112 | .PP | |
| 113 | Class constructor\&. | |
| 114 | .PP | |
| 115 | \fBParameters:\fP | |
| 116 | .RS 4 | |
| 117 | \fI_masses\fP A table of masses of the stable isotopes of the investigated element, e\&.g\&. for C10 it is 2: C12 and C13\&. | |
| 118 | .br | |
| 119 | \fI_probs\fP A table of natural frequencies of the stable isotopes of the investigated element, see IUPAC at https://iupac.org/isotopesmatter/ | |
| 120 | .br | |
| 121 | \fI_isotopeNo\fP Number of isotopes of a given element\&. | |
| 122 | .br | |
| 123 | \fI_atomCnt\fP The number of atoms of the given element, e\&.g\&. 10 for C10\&. | |
| 124 | .RE | |
| 125 | .PP | |
| 126 | \fBReturns:\fP | |
| 127 | .RS 4 | |
| 128 | An instance of the \fBMarginal\fP class\&. | |
| 129 | .RE | |
| 130 | .PP | |
| 131 | ||
| 132 | .PP | |
| 133 | Definition at line 187 of file marginalTrek++\&.cpp\&. | |
| 134 | .SH "Member Function Documentation" | |
| 135 | .PP | |
| 136 | .SS "int IsoSpec::Marginal::get_isotopeNo () const\fC [inline]\fP" | |
| 137 | ||
| 138 | .PP | |
| 139 | Get the number of isotopes of the investigated element\&. | |
| 140 | .PP | |
| 141 | \fBReturns:\fP | |
| 142 | .RS 4 | |
| 143 | The integer number of isotopes of the investigated element\&. | |
| 144 | .RE | |
| 145 | .PP | |
| 146 | ||
| 147 | .PP | |
| 148 | Definition at line 92 of file marginalTrek++\&.h\&. | |
| 149 | .SS "double IsoSpec::Marginal::getHeaviestConfMass () const" | |
| 150 | ||
| 151 | .PP | |
| 152 | Get the mass of the heaviest subisotopologue\&. This is trivially obtained by considering all atomNo atoms to be the heaviest isotope possible\&. | |
| 153 | .PP | |
| 154 | \fBReturns:\fP | |
| 155 | .RS 4 | |
| 156 | The mass of the heaviest subisotopologue\&. | |
| 157 | .RE | |
| 158 | .PP | |
| 159 | ||
| 160 | .PP | |
| 161 | Definition at line 246 of file marginalTrek++\&.cpp\&. | |
| 162 | .SS "double IsoSpec::Marginal::getLightestConfMass () const" | |
| 163 | ||
| 164 | .PP | |
| 165 | Get the mass of the lightest subisotopologue\&. This is trivially obtained by considering all atomNo atoms to be the lightest isotope possible\&. | |
| 166 | .PP | |
| 167 | \fBReturns:\fP | |
| 168 | .RS 4 | |
| 169 | The mass of the lightiest subisotopologue\&. | |
| 170 | .RE | |
| 171 | .PP | |
| 172 | ||
| 173 | .PP | |
| 174 | Definition at line 237 of file marginalTrek++\&.cpp\&. | |
| 175 | .SS "double IsoSpec::Marginal::getModeLProb () const\fC [inline]\fP" | |
| 176 | ||
| 177 | .PP | |
| 178 | Get the log-probability of the mode subisotopologue\&. | |
| 179 | .PP | |
| 180 | \fBReturns:\fP | |
| 181 | .RS 4 | |
| 182 | The log-probability of a/the most probable subisotopologue\&. | |
| 183 | .RE | |
| 184 | .PP | |
| 185 | ||
| 186 | .PP | |
| 187 | Definition at line 110 of file marginalTrek++\&.h\&. | |
| 188 | .SS "double IsoSpec::Marginal::getModeMass () const\fC [inline]\fP" | |
| 189 | ||
| 190 | .PP | |
| 191 | The the mass of the mode subisotopologue\&. | |
| 192 | .PP | |
| 193 | \fBReturns:\fP | |
| 194 | .RS 4 | |
| 195 | The mass of one of the most probable subisotopologues\&. | |
| 196 | .RE | |
| 197 | .PP | |
| 198 | ||
| 199 | .PP | |
| 200 | Definition at line 116 of file marginalTrek++\&.h\&. | |
| 201 | .SS "double IsoSpec::Marginal::getModeProb () const\fC [inline]\fP" | |
| 202 | ||
| 203 | .PP | |
| 204 | The the probability of the mode subisotopologue\&. | |
| 205 | .PP | |
| 206 | \fBReturns:\fP | |
| 207 | .RS 4 | |
| 208 | The probability of a/the most probable subisotopologue\&. | |
| 209 | .RE | |
| 210 | .PP | |
| 211 | ||
| 212 | .PP | |
| 213 | Definition at line 122 of file marginalTrek++\&.h\&. | |
| 214 | .SS "double IsoSpec::Marginal::getSmallestLProb () const\fC [inline]\fP" | |
| 215 | ||
| 216 | .PP | |
| 217 | The the log-probability of the lightest subisotopologue\&. | |
| 218 | .PP | |
| 219 | \fBReturns:\fP | |
| 220 | .RS 4 | |
| 221 | The logarithm of the smallest non-zero probability of a subisotopologue\&. | |
| 222 | .RE | |
| 223 | .PP | |
| 224 | ||
| 225 | .PP | |
| 226 | Definition at line 129 of file marginalTrek++\&.h\&. | |
| 227 | .SS "double IsoSpec::Marginal::logProb (Conf conf) const\fC [inline]\fP" | |
| 228 | ||
| 229 | .PP | |
| 230 | Calculate the log-probability of a given subisotopologue\&. | |
| 231 | .PP | |
| 232 | \fBParameters:\fP | |
| 233 | .RS 4 | |
| 234 | \fIconf\fP A subisotopologue (a table of integers describing subsequent isotope-counts)\&. | |
| 235 | .RE | |
| 236 | .PP | |
| 237 | \fBReturns:\fP | |
| 238 | .RS 4 | |
| 239 | The log-probability of the input subisotopologue\&. | |
| 240 | .RE | |
| 241 | .PP | |
| 242 | ||
| 243 | .PP | |
| 244 | Definition at line 136 of file marginalTrek++\&.h\&. | |
| 245 | .SH "Member Data Documentation" | |
| 246 | .PP | |
| 247 | .SS "const double* const IsoSpec::Marginal::atom_lProbs\fC [protected]\fP" | |
| 248 | Table of log-probabilities of all the isotopeNo isotopes\&. | |
| 249 | .PP | |
| 250 | Definition at line 53 of file marginalTrek++\&.h\&. | |
| 251 | .SS "const double* const IsoSpec::Marginal::atom_masses\fC [protected]\fP" | |
| 252 | Table of atomic masses of all the isotopeNo isotopes\&. | |
| 253 | .PP | |
| 254 | Definition at line 52 of file marginalTrek++\&.h\&. | |
| 255 | .SS "const unsigned int IsoSpec::Marginal::atomCnt\fC [protected]\fP" | |
| 256 | The number of atoms of the given element\&. | |
| 257 | .PP | |
| 258 | Definition at line 51 of file marginalTrek++\&.h\&. | |
| 259 | .SS "const unsigned int IsoSpec::Marginal::isotopeNo\fC [protected]\fP" | |
| 260 | The number of isotopes of the given element\&. | |
| 261 | .PP | |
| 262 | Definition at line 50 of file marginalTrek++\&.h\&. | |
| 263 | .SS "const double IsoSpec::Marginal::loggamma_nominator\fC [protected]\fP" | |
| 264 | The constant nominator that appears in the expressions for the multinomial probabilities\&. | |
| 265 | .PP | |
| 266 | Definition at line 54 of file marginalTrek++\&.h\&. | |
| 267 | .SS "const Conf IsoSpec::Marginal::mode_conf\fC [protected]\fP" | |
| 268 | A subisotopologue with most probability\&. If not unique, one of the representatives of that class of subisotopologues\&. | |
| 269 | .PP | |
| 270 | Definition at line 55 of file marginalTrek++\&.h\&. | |
| 271 | .SS "const double IsoSpec::Marginal::mode_lprob\fC [protected]\fP" | |
| 272 | The log-probability of the mode subisotopologue\&. | |
| 273 | .PP | |
| 274 | Definition at line 56 of file marginalTrek++\&.h\&. | |
| 275 | .SS "const double IsoSpec::Marginal::mode_mass\fC [protected]\fP" | |
| 276 | The mass of the mode subisotopologue\&. | |
| 277 | .PP | |
| 278 | Definition at line 57 of file marginalTrek++\&.h\&. | |
| 279 | .SS "const double IsoSpec::Marginal::mode_prob\fC [protected]\fP" | |
| 280 | The probability of the mode subisotopologue\&. | |
| 281 | .PP | |
| 282 | Definition at line 58 of file marginalTrek++\&.h\&. | |
| 283 | .SS "const double IsoSpec::Marginal::smallest_lprob\fC [protected]\fP" | |
| 284 | The smallest-achievable log-probability in the distribution of subisotopologues\&. | |
| 285 | .PP | |
| 286 | Definition at line 59 of file marginalTrek++\&.h\&. | |
| 287 | ||
| 288 | .SH "Author" | |
| 289 | .PP | |
| 290 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::MarginalTrek" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::MarginalTrek \- The marginal distribution class (a subisotopologue)\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <marginalTrek++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherits \fBIsoSpec::Marginal\fP\&. | |
| 13 | .SS "Public Member Functions" | |
| 14 | ||
| 15 | .in +1c | |
| 16 | .ti -1c | |
| 17 | .RI "\fBMarginalTrek\fP (\fBMarginal\fP &&m, int tabSize=1000, int hashSize=1000)" | |
| 18 | .br | |
| 19 | .RI "Move constructor: specializes the \fBMarginal\fP class\&. " | |
| 20 | .ti -1c | |
| 21 | .RI "bool \fBprobeConfigurationIdx\fP (int idx)" | |
| 22 | .br | |
| 23 | .RI "Check if the table of computed subisotopologues does not have to be extended\&. " | |
| 24 | .ti -1c | |
| 25 | .RI "int \fBprocessUntilCutoff\fP (double cutoff)" | |
| 26 | .br | |
| 27 | .RI "Calculate subisotopologues with probability above or equal to the cut-off\&. " | |
| 28 | .ti -1c | |
| 29 | .RI "const std::vector< double > & \fBconf_lprobs\fP () const" | |
| 30 | .br | |
| 31 | .ti -1c | |
| 32 | .RI "const std::vector< double > & \fBconf_masses\fP () const" | |
| 33 | .br | |
| 34 | .ti -1c | |
| 35 | .RI "const std::vector< int * > & \fBconfs\fP () const" | |
| 36 | .br | |
| 37 | .in -1c | |
| 38 | .SS "Additional Inherited Members" | |
| 39 | .SH "Detailed Description" | |
| 40 | .PP | |
| 41 | The marginal distribution class (a subisotopologue)\&. | |
| 42 | .PP | |
| 43 | Definition at line 141 of file marginalTrek++\&.h\&. | |
| 44 | .SH "Constructor & Destructor Documentation" | |
| 45 | .PP | |
| 46 | .SS "IsoSpec::MarginalTrek::MarginalTrek (\fBMarginal\fP && m, int tabSize = \fC1000\fP, int hashSize = \fC1000\fP)" | |
| 47 | ||
| 48 | .PP | |
| 49 | Move constructor: specializes the \fBMarginal\fP class\&. | |
| 50 | .PP | |
| 51 | \fBParameters:\fP | |
| 52 | .RS 4 | |
| 53 | \fItabSize\fP The size of the table used to store configurations in the allocator\&. | |
| 54 | .br | |
| 55 | \fIhashSize\fP The size of the hash table used to store visited subisotopologues\&. | |
| 56 | .RE | |
| 57 | .PP | |
| 58 | ||
| 59 | .PP | |
| 60 | Definition at line 256 of file marginalTrek++\&.cpp\&. | |
| 61 | .SH "Member Function Documentation" | |
| 62 | .PP | |
| 63 | .SS "bool IsoSpec::MarginalTrek::probeConfigurationIdx (int idx)\fC [inline]\fP" | |
| 64 | ||
| 65 | .PP | |
| 66 | Check if the table of computed subisotopologues does not have to be extended\&. This function checks if the idx-th most probable subisotopologue was memoized and if not, computes it and memoizes it\&. | |
| 67 | .PP | |
| 68 | \fBParameters:\fP | |
| 69 | .RS 4 | |
| 70 | \fIidx\fP The number of the idx-th most probable subisotopologue\&. | |
| 71 | .RE | |
| 72 | .PP | |
| 73 | \fBReturns:\fP | |
| 74 | .RS 4 | |
| 75 | Returns false if it the provided idx exceeds the total number of subisotopologues\&. | |
| 76 | .RE | |
| 77 | .PP | |
| 78 | ||
| 79 | .PP | |
| 80 | Definition at line 179 of file marginalTrek++\&.h\&. | |
| 81 | .SS "int IsoSpec::MarginalTrek::processUntilCutoff (double cutoff)" | |
| 82 | ||
| 83 | .PP | |
| 84 | Calculate subisotopologues with probability above or equal to the cut-off\&. | |
| 85 | .PP | |
| 86 | \fBParameters:\fP | |
| 87 | .RS 4 | |
| 88 | \fIcutoff\fP The probability cut-off | |
| 89 | .RE | |
| 90 | .PP | |
| 91 | \fBReturns:\fP | |
| 92 | .RS 4 | |
| 93 | The number of the last subisotopologue above the cut-off\&. | |
| 94 | .RE | |
| 95 | .PP | |
| 96 | ||
| 97 | .PP | |
| 98 | Definition at line 333 of file marginalTrek++\&.cpp\&. | |
| 99 | ||
| 100 | .SH "Author" | |
| 101 | .PP | |
| 102 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::OrderMarginalsBySizeDecresing" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::OrderMarginalsBySizeDecresing | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBOrderMarginalsBySizeDecresing\fP (\fBPrecalculatedMarginal\fP const *const *_T)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "bool \fBoperator()\fP (int m1, int m2)" | |
| 16 | .br | |
| 17 | .in -1c | |
| 18 | .SH "Detailed Description" | |
| 19 | .PP | |
| 20 | Definition at line 128 of file operators\&.h\&. | |
| 21 | ||
| 22 | .SH "Author" | |
| 23 | .PP | |
| 24 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::PrecalculatedMarginal" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::PrecalculatedMarginal \- Precalculated \fBMarginal\fP class\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <marginalTrek++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherits \fBIsoSpec::Marginal\fP\&. | |
| 13 | .SS "Public Member Functions" | |
| 14 | ||
| 15 | .in +1c | |
| 16 | .ti -1c | |
| 17 | .RI "\fBPrecalculatedMarginal\fP (\fBMarginal\fP &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000)" | |
| 18 | .br | |
| 19 | .RI "The move constructor (disowns the \fBMarginal\fP)\&. " | |
| 20 | .ti -1c | |
| 21 | .RI "virtual \fB~PrecalculatedMarginal\fP ()" | |
| 22 | .br | |
| 23 | .RI "Destructor\&. " | |
| 24 | .ti -1c | |
| 25 | .RI "bool \fBinRange\fP (unsigned int idx) const" | |
| 26 | .br | |
| 27 | .RI "Is there a subisotopologue with a given number? " | |
| 28 | .ti -1c | |
| 29 | .RI "const double & \fBget_lProb\fP (int idx) const" | |
| 30 | .br | |
| 31 | .RI "Get the log-probability of the idx-th subisotopologue\&. " | |
| 32 | .ti -1c | |
| 33 | .RI "const double & \fBget_eProb\fP (int idx) const" | |
| 34 | .br | |
| 35 | .RI "Get the probability of the idx-th subisotopologue\&. " | |
| 36 | .ti -1c | |
| 37 | .RI "const double & \fBget_mass\fP (int idx) const" | |
| 38 | .br | |
| 39 | .RI "Get the mass of the idx-th subisotopologue\&. " | |
| 40 | .ti -1c | |
| 41 | .RI "const double * \fBget_lProbs_ptr\fP () const" | |
| 42 | .br | |
| 43 | .RI "Get the table of the log-probabilities of subisotopologues\&. " | |
| 44 | .ti -1c | |
| 45 | .RI "const double * \fBget_masses_ptr\fP () const" | |
| 46 | .br | |
| 47 | .RI "Get the table of the masses of subisotopologues\&. " | |
| 48 | .ti -1c | |
| 49 | .RI "const Conf & \fBget_conf\fP (int idx) const" | |
| 50 | .br | |
| 51 | .RI "Get the counts of isotopes that define the subisotopologue\&. " | |
| 52 | .ti -1c | |
| 53 | .RI "unsigned int \fBget_no_confs\fP () const" | |
| 54 | .br | |
| 55 | .RI "Get the number of precomputed subisotopologues\&. " | |
| 56 | .in -1c | |
| 57 | .SS "Protected Attributes" | |
| 58 | ||
| 59 | .in +1c | |
| 60 | .ti -1c | |
| 61 | .RI "std::vector< Conf > \fBconfigurations\fP" | |
| 62 | .br | |
| 63 | .ti -1c | |
| 64 | .RI "Conf * \fBconfs\fP" | |
| 65 | .br | |
| 66 | .ti -1c | |
| 67 | .RI "unsigned int \fBno_confs\fP" | |
| 68 | .br | |
| 69 | .ti -1c | |
| 70 | .RI "double * \fBmasses\fP" | |
| 71 | .br | |
| 72 | .ti -1c | |
| 73 | .RI "double * \fBlProbs\fP" | |
| 74 | .br | |
| 75 | .ti -1c | |
| 76 | .RI "double * \fBeProbs\fP" | |
| 77 | .br | |
| 78 | .ti -1c | |
| 79 | .RI "\fBAllocator\fP< int > \fBallocator\fP" | |
| 80 | .br | |
| 81 | .in -1c | |
| 82 | .SH "Detailed Description" | |
| 83 | .PP | |
| 84 | Precalculated \fBMarginal\fP class\&. | |
| 85 | ||
| 86 | This class serves to calculate a set of isotopologues that is defined by the minimal probability threshold\&. | |
| 87 | .PP | |
| 88 | This works faster than if you did not know the threshold\&. If you have no idea about the threshold, you would need to call us, to change encode the layered version of the marginal\&. | |
| 89 | .PP | |
| 90 | Definition at line 213 of file marginalTrek++\&.h\&. | |
| 91 | .SH "Constructor & Destructor Documentation" | |
| 92 | .PP | |
| 93 | .SS "IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal (\fBMarginal\fP && m, double lCutOff, bool sort = \fCtrue\fP, int tabSize = \fC1000\fP, int hashSize = \fC1000\fP)" | |
| 94 | ||
| 95 | .PP | |
| 96 | The move constructor (disowns the \fBMarginal\fP)\&. This constructor memoizes all subisotopologues with log-probability above the provided threshold lCutOff | |
| 97 | .PP | |
| 98 | \fBParameters:\fP | |
| 99 | .RS 4 | |
| 100 | \fI\fBMarginal\fP\fP An instance of the \fBMarginal\fP class this class is about to disown\&. | |
| 101 | .br | |
| 102 | \fIlCutOff\fP The lower limit on the log-probability of the precomputed subisotopologues\&. | |
| 103 | .br | |
| 104 | \fIsort\fP Should the subisotopologues be stored with descending probability ? | |
| 105 | .RE | |
| 106 | .PP | |
| 107 | \fBReturns:\fP | |
| 108 | .RS 4 | |
| 109 | An instance of the \fBPrecalculatedMarginal\fP class\&. | |
| 110 | .RE | |
| 111 | .PP | |
| 112 | ||
| 113 | .PP | |
| 114 | Definition at line 362 of file marginalTrek++\&.cpp\&. | |
| 115 | .SH "Member Function Documentation" | |
| 116 | .PP | |
| 117 | .SS "const Conf& IsoSpec::PrecalculatedMarginal::get_conf (int idx) const\fC [inline]\fP" | |
| 118 | ||
| 119 | .PP | |
| 120 | Get the counts of isotopes that define the subisotopologue\&. | |
| 121 | .PP | |
| 122 | \fBParameters:\fP | |
| 123 | .RS 4 | |
| 124 | \fIidx\fP The number of the considered subisotopologue\&. | |
| 125 | .RE | |
| 126 | .PP | |
| 127 | \fBReturns:\fP | |
| 128 | .RS 4 | |
| 129 | The counts of isotopes that define the subisotopologue\&. | |
| 130 | .RE | |
| 131 | .PP | |
| 132 | ||
| 133 | .PP | |
| 134 | Definition at line 288 of file marginalTrek++\&.h\&. | |
| 135 | .SS "const double& IsoSpec::PrecalculatedMarginal::get_eProb (int idx) const\fC [inline]\fP" | |
| 136 | ||
| 137 | .PP | |
| 138 | Get the probability of the idx-th subisotopologue\&. | |
| 139 | .PP | |
| 140 | \fBParameters:\fP | |
| 141 | .RS 4 | |
| 142 | \fIidx\fP The number of the considered subisotopologue\&. | |
| 143 | .RE | |
| 144 | .PP | |
| 145 | \fBReturns:\fP | |
| 146 | .RS 4 | |
| 147 | The probability of the idx-th subisotopologue\&. | |
| 148 | .RE | |
| 149 | .PP | |
| 150 | ||
| 151 | .PP | |
| 152 | Definition at line 261 of file marginalTrek++\&.h\&. | |
| 153 | .SS "const double& IsoSpec::PrecalculatedMarginal::get_lProb (int idx) const\fC [inline]\fP" | |
| 154 | ||
| 155 | .PP | |
| 156 | Get the log-probability of the idx-th subisotopologue\&. | |
| 157 | .PP | |
| 158 | \fBParameters:\fP | |
| 159 | .RS 4 | |
| 160 | \fIidx\fP The number of the considered subisotopologue\&. | |
| 161 | .RE | |
| 162 | .PP | |
| 163 | \fBReturns:\fP | |
| 164 | .RS 4 | |
| 165 | The log-probability of the idx-th subisotopologue\&. | |
| 166 | .RE | |
| 167 | .PP | |
| 168 | ||
| 169 | .PP | |
| 170 | Definition at line 254 of file marginalTrek++\&.h\&. | |
| 171 | .SS "const double* IsoSpec::PrecalculatedMarginal::get_lProbs_ptr () const\fC [inline]\fP" | |
| 172 | ||
| 173 | .PP | |
| 174 | Get the table of the log-probabilities of subisotopologues\&. | |
| 175 | .PP | |
| 176 | \fBReturns:\fP | |
| 177 | .RS 4 | |
| 178 | Pointer to the first element in the table storing log-probabilities of subisotopologues\&. | |
| 179 | .RE | |
| 180 | .PP | |
| 181 | ||
| 182 | .PP | |
| 183 | Definition at line 274 of file marginalTrek++\&.h\&. | |
| 184 | .SS "const double& IsoSpec::PrecalculatedMarginal::get_mass (int idx) const\fC [inline]\fP" | |
| 185 | ||
| 186 | .PP | |
| 187 | Get the mass of the idx-th subisotopologue\&. | |
| 188 | .PP | |
| 189 | \fBParameters:\fP | |
| 190 | .RS 4 | |
| 191 | \fIidx\fP The number of the considered subisotopologue\&. | |
| 192 | .RE | |
| 193 | .PP | |
| 194 | \fBReturns:\fP | |
| 195 | .RS 4 | |
| 196 | The mass of the idx-th subisotopologue\&. | |
| 197 | .RE | |
| 198 | .PP | |
| 199 | ||
| 200 | .PP | |
| 201 | Definition at line 268 of file marginalTrek++\&.h\&. | |
| 202 | .SS "const double* IsoSpec::PrecalculatedMarginal::get_masses_ptr () const\fC [inline]\fP" | |
| 203 | ||
| 204 | .PP | |
| 205 | Get the table of the masses of subisotopologues\&. | |
| 206 | .PP | |
| 207 | \fBReturns:\fP | |
| 208 | .RS 4 | |
| 209 | Pointer to the first element in the table storing masses of subisotopologues\&. | |
| 210 | .RE | |
| 211 | .PP | |
| 212 | ||
| 213 | .PP | |
| 214 | Definition at line 280 of file marginalTrek++\&.h\&. | |
| 215 | .SS "unsigned int IsoSpec::PrecalculatedMarginal::get_no_confs () const\fC [inline]\fP" | |
| 216 | ||
| 217 | .PP | |
| 218 | Get the number of precomputed subisotopologues\&. | |
| 219 | .PP | |
| 220 | \fBReturns:\fP | |
| 221 | .RS 4 | |
| 222 | The number of precomputed subisotopologues\&. | |
| 223 | .RE | |
| 224 | .PP | |
| 225 | ||
| 226 | .PP | |
| 227 | Definition at line 294 of file marginalTrek++\&.h\&. | |
| 228 | .SS "bool IsoSpec::PrecalculatedMarginal::inRange (unsigned int idx) const\fC [inline]\fP" | |
| 229 | ||
| 230 | .PP | |
| 231 | Is there a subisotopologue with a given number? | |
| 232 | .PP | |
| 233 | \fBReturns:\fP | |
| 234 | .RS 4 | |
| 235 | Returns true if idx does not exceed the number of pre-computed configurations\&. | |
| 236 | .RE | |
| 237 | .PP | |
| 238 | ||
| 239 | .PP | |
| 240 | Definition at line 247 of file marginalTrek++\&.h\&. | |
| 241 | ||
| 242 | .SH "Author" | |
| 243 | .PP | |
| 244 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::ReverseOrder< T >" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::ReverseOrder< T > | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "bool \fBoperator()\fP (const T a, const T b) const" | |
| 13 | .br | |
| 14 | .in -1c | |
| 15 | .SH "Detailed Description" | |
| 16 | .PP | |
| 17 | ||
| 18 | .SS "template<typename T> | |
| 19 | .br | |
| 20 | class IsoSpec::ReverseOrder< T >" | |
| 21 | ||
| 22 | .PP | |
| 23 | Definition at line 106 of file operators\&.h\&. | |
| 24 | ||
| 25 | .SH "Author" | |
| 26 | .PP | |
| 27 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::SSummator" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::SSummator | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBSSummator\fP (\fBSSummator\fP &other)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "void \fBadd\fP (double x)" | |
| 16 | .br | |
| 17 | .ti -1c | |
| 18 | .RI "double \fBget\fP ()" | |
| 19 | .br | |
| 20 | .in -1c | |
| 21 | .SH "Detailed Description" | |
| 22 | .PP | |
| 23 | Definition at line 25 of file summator\&.h\&. | |
| 24 | ||
| 25 | .SH "Author" | |
| 26 | .PP | |
| 27 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::Summator" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::Summator | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "void \fBadd\fP (double what)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "double \fBget\fP ()" | |
| 16 | .br | |
| 17 | .in -1c | |
| 18 | .SH "Detailed Description" | |
| 19 | .PP | |
| 20 | Definition at line 76 of file summator\&.h\&. | |
| 21 | ||
| 22 | .SH "Author" | |
| 23 | .PP | |
| 24 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::SyncMarginal" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::SyncMarginal \- Big experiment for multi-threaded version of the algorithm, do not touch\&. | |
| 5 | ||
| 6 | .SH SYNOPSIS | |
| 7 | .br | |
| 8 | .PP | |
| 9 | .PP | |
| 10 | \fC#include <marginalTrek++\&.h>\fP | |
| 11 | .PP | |
| 12 | Inherits \fBIsoSpec::PrecalculatedMarginal\fP\&. | |
| 13 | .SS "Public Member Functions" | |
| 14 | ||
| 15 | .in +1c | |
| 16 | .ti -1c | |
| 17 | .RI "\fBSyncMarginal\fP (\fBMarginal\fP &&m, double lCutOff, int tabSize=1000, int hashSize=1000)" | |
| 18 | .br | |
| 19 | .RI "likewise\&.\&.\&. " | |
| 20 | .ti -1c | |
| 21 | .RI "unsigned int \fBgetNextConfIdx\fP ()" | |
| 22 | .br | |
| 23 | .ti -1c | |
| 24 | .RI "unsigned int \fBgetNextConfIdxwMass\fP (double mmin, double mmax)" | |
| 25 | .br | |
| 26 | .in -1c | |
| 27 | .SS "Protected Attributes" | |
| 28 | ||
| 29 | .in +1c | |
| 30 | .ti -1c | |
| 31 | .RI "char \fBpadding\fP [64]" | |
| 32 | .br | |
| 33 | .ti -1c | |
| 34 | .RI "std::atomic< unsigned int > \fBcounter\fP" | |
| 35 | .br | |
| 36 | .ti -1c | |
| 37 | .RI "char \fBpadding2\fP [64]" | |
| 38 | .br | |
| 39 | .in -1c | |
| 40 | .SH "Detailed Description" | |
| 41 | .PP | |
| 42 | Big experiment for multi-threaded version of the algorithm, do not touch\&. | |
| 43 | .PP | |
| 44 | Definition at line 298 of file marginalTrek++\&.h\&. | |
| 45 | ||
| 46 | .SH "Author" | |
| 47 | .PP | |
| 48 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::TSummator" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::TSummator | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "void \fBadd\fP (double what)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "double \fBget\fP ()" | |
| 16 | .br | |
| 17 | .in -1c | |
| 18 | .SH "Detailed Description" | |
| 19 | .PP | |
| 20 | Definition at line 99 of file summator\&.h\&. | |
| 21 | ||
| 22 | .SH "Author" | |
| 23 | .PP | |
| 24 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::TableOrder< T >" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::TableOrder< T > | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBTableOrder\fP (const T *_tbl)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "bool \fBoperator()\fP (unsigned int i, unsigned int j)" | |
| 16 | .br | |
| 17 | .in -1c | |
| 18 | .SH "Detailed Description" | |
| 19 | .PP | |
| 20 | ||
| 21 | .SS "template<typename T> | |
| 22 | .br | |
| 23 | class IsoSpec::TableOrder< T >" | |
| 24 | ||
| 25 | .PP | |
| 26 | Definition at line 113 of file operators\&.h\&. | |
| 27 | ||
| 28 | .SH "Author" | |
| 29 | .PP | |
| 30 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::Tabulator< T >" 3 "Tue Oct 30 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::Tabulator< T > | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBTabulator\fP (T *generator, bool get_masses, bool get_probs, bool get_lprobs, bool get_confs)" | |
| 13 | .br | |
| 14 | .ti -1c | |
| 15 | .RI "double * \fBmasses\fP ()" | |
| 16 | .br | |
| 17 | .ti -1c | |
| 18 | .RI "double * \fBlprobs\fP ()" | |
| 19 | .br | |
| 20 | .ti -1c | |
| 21 | .RI "double * \fBprobs\fP ()" | |
| 22 | .br | |
| 23 | .ti -1c | |
| 24 | .RI "int * \fBconfs\fP ()" | |
| 25 | .br | |
| 26 | .ti -1c | |
| 27 | .RI "size_t \fBconfs_no\fP ()" | |
| 28 | .br | |
| 29 | .in -1c | |
| 30 | .SH "Detailed Description" | |
| 31 | .PP | |
| 32 | ||
| 33 | .SS "template<typename T> | |
| 34 | .br | |
| 35 | class IsoSpec::Tabulator< T >" | |
| 36 | ||
| 37 | .PP | |
| 38 | Definition at line 12 of file tabulator\&.h\&. | |
| 39 | ||
| 40 | .SH "Author" | |
| 41 | .PP | |
| 42 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | .TH "IsoSpec::ThreadSummator" 3 "Thu Oct 11 2018" "Version 1.95" "IsoSpec" \" -*- nroff -*- | |
| 1 | .ad l | |
| 2 | .nh | |
| 3 | .SH NAME | |
| 4 | IsoSpec::ThreadSummator | |
| 5 | .SH SYNOPSIS | |
| 6 | .br | |
| 7 | .PP | |
| 8 | .SS "Public Member Functions" | |
| 9 | ||
| 10 | .in +1c | |
| 11 | .ti -1c | |
| 12 | .RI "\fBThreadSummator\fP ()" | |
| 13 | .br | |
| 14 | .RI "Constructor (sum defaults to zero)\&. " | |
| 15 | .ti -1c | |
| 16 | .RI "void \fBadd\fP (double what)" | |
| 17 | .br | |
| 18 | .RI "Add a number to the existing sum\&. " | |
| 19 | .ti -1c | |
| 20 | .RI "double \fBget\fP ()" | |
| 21 | .br | |
| 22 | .RI "Get the current value of the sum of the added floating point numbers\&. " | |
| 23 | .in -1c | |
| 24 | .SH "Detailed Description" | |
| 25 | .PP | |
| 26 | Definition at line 139 of file summator\&.h\&. | |
| 27 | .SH "Member Function Documentation" | |
| 28 | .PP | |
| 29 | .SS "void IsoSpec::ThreadSummator::add (double what)\fC [inline]\fP" | |
| 30 | ||
| 31 | .PP | |
| 32 | Add a number to the existing sum\&. | |
| 33 | .PP | |
| 34 | \fBParameters:\fP | |
| 35 | .RS 4 | |
| 36 | \fIx\fP A double floating point number to add\&. | |
| 37 | .RE | |
| 38 | .PP | |
| 39 | ||
| 40 | .PP | |
| 41 | Definition at line 151 of file summator\&.h\&. | |
| 42 | ||
| 43 | .SH "Author" | |
| 44 | .PP | |
| 45 | Generated automatically by Doxygen for IsoSpec from the source code\&. |
| 0 | 0 | CXX=clang++ |
| 1 | 1 | OPTFLAGS=-O3 -march=native -mtune=native -g |
| 2 | DEBUGFLAGS=-O0 -g | |
| 2 | DEBUGFLAGS=-O0 -g -DISOSPEC_DEBUG -DDEBUG -D_GLIBCXX_DEBUG | |
| 3 | 3 | TESTFLAGS=-fsanitize=leak,undefined |
| 4 | 4 | TESTMEMFLAGS= $(TESTFLAGS) -fsanitize=memory |
| 5 | 5 | TESTADDRFLAGS= $(TESTFLAGS) -fsanitize=address |
| 32 | 32 | size_t test_layered_tabulator(const char* formula, double total_prob, bool print_confs) |
| 33 | 33 | { |
| 34 | 34 | // IsoLayeredGenerator i(formula, 1000, 1000); |
| 35 | FixedEnvelope t = FixedEnvelope::FromTotalProb(formula, total_prob, false, true); | |
| 35 | FixedEnvelope t = FixedEnvelope::FromTotalProb(formula, total_prob, true, print_confs); | |
| 36 | 36 | const double* probs = t.probs(); |
| 37 | 37 | double* masses = t.release_masses(); |
| 38 | 38 | const int* confs = t.confs(); |
| 39 | 39 | |
| 40 | for(size_t ii = 0; ii<t.confs_no(); ii++) | |
| 41 | { | |
| 42 | if(print_confs) | |
| 43 | { | |
| 44 | std::cout << "PROB: " << probs[ii] << " \tMASS: " << masses[ii] << "\tCONF: "; | |
| 45 | const int* space = confs + ii*t.getAllDim(); | |
| 46 | for(int ii=0; ii<t.getAllDim(); ii++) | |
| 47 | std::cout << space[ii] << " "; | |
| 48 | std::cout << std::endl; | |
| 49 | } | |
| 40 | if(print_confs) | |
| 41 | for(size_t ii = 0; ii<t.confs_no(); ii++) | |
| 42 | { | |
| 43 | std::cout << "PROB: " << probs[ii] << " \tMASS: " << masses[ii] << "\tCONF: "; | |
| 44 | const int* space = confs + ii*t.getAllDim(); | |
| 45 | for(int ii=0; ii<t.getAllDim(); ii++) | |
| 46 | std::cout << space[ii] << " "; | |
| 47 | std::cout << std::endl; | |
| 50 | 48 | |
| 51 | } | |
| 49 | } | |
| 52 | 50 | |
| 53 | 51 | free(masses); |
| 54 | 52 |
| 0 | 0 | #include <iostream> |
| 1 | #include <cassert> | |
| 1 | 2 | #include "isoSpec++.h" |
| 2 | 3 | |
| 3 | 4 | using namespace IsoSpec; |
| 11 | 12 | { |
| 12 | 13 | std::cout << "Proper usage (for example): " << argv[0] << " C10000H1000O1000N1000 0.9999" << std::endl; |
| 13 | 14 | std::cout << "...will print the minimal number of configurations necessary to cover 0.9999 probability of the above molecule" << std::endl; |
| 15 | std::cout << argv[0] << " C10000H1000O1000N1000 0.9999 false" << std::endl; | |
| 16 | std::cout << "will just count them" << std::endl; | |
| 14 | 17 | return -1; |
| 15 | 18 | } |
| 19 | bool print_confs = true; | |
| 20 | ||
| 21 | if(argc > 3) | |
| 22 | print_confs = (strcmp(argv[3], "true") == 0); | |
| 16 | 23 | |
| 17 | 24 | #ifndef ISOSPEC_TESTS_MEMSAN |
| 18 | 25 | size_t no_confs = |
| 19 | 26 | #endif |
| 20 | test_ordered(argv[1], atof(argv[2]), true); | |
| 27 | test_ordered(argv[1], atof(argv[2]), print_confs); | |
| 21 | 28 | |
| 22 | 29 | #ifndef ISOSPEC_TESTS_MEMSAN |
| 23 | 30 | std::cout << "The number of visited configurations is: " << no_confs << std::endl; |
| 34 | 41 | |
| 35 | 42 | size_t no_visited = 0; |
| 36 | 43 | int* space = new int[i.getAllDim()]; |
| 44 | double last_p = 1.0; | |
| 37 | 45 | while(target_prob > 0.0 && i.advanceToNextConfiguration()) |
| 38 | 46 | { |
| 39 | target_prob -= i.prob(); | |
| 47 | double curr_p = i.prob(); | |
| 48 | assert(last_p >= curr_p); | |
| 49 | last_p = curr_p; | |
| 50 | target_prob -= curr_p; | |
| 40 | 51 | no_visited += 1; |
| 41 | 52 | if(print_confs) |
| 42 | 53 | { |
| 36 | 36 | |
| 37 | 37 | IsoThresholdGenerator i(formula, threshold, true, 100, 100, true); |
| 38 | 38 | size_t confs_no = i.count_confs(); |
| 39 | if(print_confs) | |
| 40 | std::cout << "No. confs is: " << confs_no << std::endl; | |
| 39 | //if(print_confs) | |
| 40 | // std::cout << "No. confs is: " << confs_no << std::endl; | |
| 41 | 41 | i.reset(); |
| 42 | 42 | IsoThresholdGenerator i2(formula, threshold, true, 100, 100, true); |
| 43 | 43 | IsoThresholdGenerator i3(formula, threshold, true, 100, 100, false); |
| 39 | 39 | std::cout << "No. confs is: " << confs_no << std::endl; |
| 40 | 40 | i.reset(); |
| 41 | 41 | #endif |
| 42 | int* confspace = new int[i.getAllDim()]; | |
| 42 | int* confspace = print_confs ? new int[i.getAllDim()] : nullptr; | |
| 43 | 43 | size_t no_visited = 0; |
| 44 | 44 | double total_prob = 0.0; |
| 45 | 45 | while(i.advanceToNextConfiguration()) |
| 46 | 46 | { |
| 47 | i.get_conf_signature(confspace); | |
| 48 | if(print_confs) | |
| 49 | { | |
| 50 | std::cout << "lprob: " << i.lprob() << " prob: " << i.prob() << " log(prob): " << log(i.prob()) << " mass: " << i.mass() << " conf: "; | |
| 51 | printArray<int>(confspace, i.getAllDim()); | |
| 52 | } | |
| 53 | no_visited += 1; | |
| 54 | total_prob += i.prob(); | |
| 47 | if(print_confs) | |
| 48 | { | |
| 49 | i.get_conf_signature(confspace); | |
| 50 | std::cout << "lprob: " << i.lprob() << " prob: " << i.prob() << " log(prob): " << log(i.prob()) << " mass: " << i.mass() << " conf: "; | |
| 51 | printArray<int>(confspace, i.getAllDim()); | |
| 52 | } | |
| 53 | no_visited += 1; | |
| 54 | total_prob += i.prob(); | |
| 55 | 55 | } |
| 56 | 56 | delete[] confspace; |
| 57 | 57 | return no_visited; |
| 32 | 32 | assert(zero_ok); |
| 33 | 33 | test_empty_and_print(); |
| 34 | 34 | #if !defined(ISOSPEC_SKIP_SLOW_TESTS) |
| 35 | char test_formulas[] = "P1 P2 H1 H2 O1 O2 H2O1 C0 P0 C100O0P100 C100 P100 C1 H10C10O10N10S5 Se1 Se10 Sn1 Sn4 Sn4C1 C2H6O1 C1000 C1H1O2N2Se1Sn1P1 P1C1Sn1 Se5 Sn5 Se2Sn2C2O2N2S2B2He2U2Na2Cl2"; | |
| 35 | char test_formulas[] = "P1 P2 H1 H2 O1 O2 H2O1 C0 P0 C10000P10 F10C10000P10 P10F10O100 C100O0P100 C100 P100 C1 H10C10O10N10S5 Se1 Se10 Sn1 Sn4 Sn4C1 C2H6O1 C1000 C1H1O2N2Se1Sn1P1 P1C1Sn1 Se5 Sn5 Se2Sn2C2O2N2S2B2He2U2Na2Cl2"; | |
| 36 | 36 | #else |
| 37 | char test_formulas[] = "P1 P2 H1 H2 O1 O2 H2O1 C0 P0 C100O0P100 C100 P100 C1 H3C3O3N3S3 Se1 Se3 Sn1 Sn3C1 C2H6O1 C1000 C1H1O2N2Se1Sn1P1 P1C1Sn1 Se5"; | |
| 37 | char test_formulas[] = "P1 P2 H1 H2 O1 O2 H2O1 C0 P0 C10000P10 F10C10000P10 P10F10O100 C100O0P100 C100 P100 C1 H3C3O3N3S3 Se1 Se3 Sn1 Sn3C1 C2H6O1 C1000 C1H1O2N2Se1Sn1P1 P1C1Sn1 Se5"; | |
| 38 | 38 | #endif |
| 39 | 39 | size_t tf_len = strlen(test_formulas); |
| 40 | 40 | std::vector<const char*> formulas; |
| 75 | 75 | assert math.isclose(WSD, 0.0, abs_tol=1e-7) |
| 76 | 76 | print("OK!") |
| 77 | 77 | |
| 78 | ||
| 79 | print("Checking negative formulas... ", end="") | |
| 80 | try: | |
| 81 | I = Iso(formula="C-10") | |
| 82 | print("FAIL: exception not thrown") | |
| 83 | except Exception as e: | |
| 84 | print("""exception successfully obtained, message: "{}" -> OK!""".format((str(e)))) | |
| 85 | ||
| 86 | ||
| 87 | print("Checking FASTA + negative formulas... ", end="") | |
| 88 | try: | |
| 89 | I = Iso(fasta = "C", formula="C-5") | |
| 90 | print("FAIL: exception not thrown") | |
| 91 | except Exception as e: | |
| 92 | print("""exception successfully obtained, message: "{}" -> OK!""".format((str(e)))) | |
| 93 | ||
| 94 | ||
| 95 | print("Checking FASTA + modification... ", end="") | |
| 96 | # Selenation of methionine | |
| 97 | I = IsoSpecPy.IsoTotalProb(0.999, formula = "C5H9N1O1Se1") | |
| 98 | I2 = IsoSpecPy.IsoTotalProb(0.999, fasta = "M", formula = "S-1Se1") | |
| 99 | WSD = I.wassersteinDistance(I2) | |
| 100 | print(WSD, end="") | |
| 101 | assert(math.isclose(I.wassersteinDistance(I2), 0.0)) | |
| 102 | print(" -> OK!") | |
| 103 | ||
| 104 | ||
| 105 | print("Checking empiric avg mass... ", end="") | |
| 106 | formulas = "C1 P1 H1 H100 P100 N100 O100 C100H100N100 C100O100".split() | |
| 107 | isos = [IsoSpecPy.Iso(formula) for formula in formulas] | |
| 108 | dists = [IsoSpecPy.IsoThreshold(0.0, formula) for formula in formulas] | |
| 109 | diffs = [abs(i.getTheoreticalAverageMass() - d.empiric_average_mass()) for i, d in zip(isos, dists)] | |
| 110 | print(max(diffs), end="") | |
| 111 | assert max(diffs) < 1e-6 | |
| 112 | print(" -> OK!") | |
| 113 | ||
| 114 | ||
| 115 | print("Checking empiric variance... ", end="") | |
| 116 | diffs = [abs(i.variance() - d.empiric_variance()) for i, d in zip(isos, dists)] | |
| 117 | print(max(diffs), end="") | |
| 118 | assert max(diffs) < 1e-6 | |
| 119 | print(" -> OK!") | |
| 120 | ||
| 121 | print("Checking empiric stddev... ", end="") | |
| 122 | diffs = [abs(i.stddev() - d.empiric_stddev()) for i, d in zip(isos, dists)] | |
| 123 | print(max(diffs), end="") | |
| 124 | assert max(diffs) < 1e-6 | |
| 125 | print(" -> OK!") |