Commit 5e3c874baa4af43b0412e3bd0ce2d49bfaf5663b - minexpert2

+123

-0

BUILD less more

	0	INSTALLATION ON DEBIAN/UBUNTU
	1	=============================
	2
	3	sudo apt install minexpert2
	4
	5	#optionally install the user manual (HTML and PDF formats).
	6	sudo apt install minexpert2-doc
	7
	8
	9	BUILDING MINEXPERT2
	10	===================
	11
	12	The mineXpert2 software build is under the control of the CMake build system.
	13	There are a number of dependencies to install prior to trying to build the
	14	software, as described below.
	15
	16
	17	DEPENDENCIES
	18	============
	19
	20	The dependencies to be installed are listed here with package names matching the
	21	packages that are in Debian/Ubuntu. In other RPM-based software, most often the
	22	package names are similar, albeit with some slight differences.
	23
	24	# The build system
	25	cmake (>= 3.12),
	26
	27	# For the conversion of svg files to png.
	28	graphicsmagick-imagemagick-compat,
	29
	30	# For the parallel computations
	31	libgomp1,
	32
	33	# For the isotopic cluster calculations
	34	libisospec++-dev (>=2.1.2),
	35
	36	# For all the raw mass calculations like
	37	# the data model, the mass spectral combinations...
	38	libpappsomspp-dev (>= 0.8.8),
	39	libpappsomspp-widget-dev (>= 0.8.8),
	40
	41	# For all the plotting
	42	libqcustomplot-dev(>= 2.0),
	43
	44	# For the C++ objects (GUI and non-GUI)
	45	qtbase5-dev (>= 5.11.3),
	46	libqt5svg5-dev (>= 5.11.3),
	47	qttools5-dev-tools,
	48	qtchooser
	49
	50	# For the man page
	51	docbook-to-man,
	52
	53	# For the documentation (optional, with -DMAKE_USER_MANUAL=1 as a flag to the
	54	# cmake call, see below.
	55	daps (>= 3.0.0)
	56	libjeuclid-core-java,
	57	libjeuclid-fop-java,
	58	docbook-mathml,
	59	libjs-jquery,
	60	libjs-highlight.js,
	61	libjs-mathjax,
	62	fonts-mathjax,
	63	fonts-mathjax-extras,
	64	texlive-fonts-extra,
	65	fonts-ebgaramond-extra,
	66
	67
	68	GETTING THE SOURCE TARBALL
	69	==========================
	70
	71	In the example below, the version of the software to be installed is 7.3.0.
	72	Replace that version with any latest version of interest, which can be looked
	73	for at https://gitlab.com/msxpertsuite/minexpert2/-/releases.
	74
	75
	76	Using git
	77	---------
	78
	79	The rather convoluted command below only downloads the branch of interest. The
	80	whole git repos is very large...
	81
	82	git clone https://gitlab.com/msxpertsuite/minexpert2.git --branch master/7.3.0-1 --single-branch minexpert2-7.3.0
	83
	84	Using wget to download the tarball
	85	----------------------------------
	86
	87	wget https://gitlab.com/msxpertsuite/minexpert2/-/archive/7.3.0/minexpert2-7.3.0.tar.gz
	88
	89	Untar the tarball:
	90
	91	tar xvzf minexpert2-7.3.0.tar.gz
	92
	93	Now start using the source tree to build the software
	94	-----------------------------------------------------
	95
	96	Change directory:
	97
	98	cd minexpert2-7.3.0
	99
	100	Create a build directory:
	101
	102	mkdir build
	103
	104	Change directory:
	105
	106	cd build
	107
	108	Configure the build:
	109
	110	cmake ../ -DCMAKE_BUILD_TYPE=Release
	111
	112	Build the software:
	113
	114	make
	115
	116	Run the software:
	117
	118	src/minexpert2
	119
	120
	121
	122

+12

-3

CMakeLists.txt less more

7	7	# Basic information about project
8	8
9	9	project(mineXpert2
10		DESCRIPTION "A program to visualize and mine mass spectrometric data"
	10	DESCRIPTION "A program to visualize and explore mass spectrometric data"
11	11	HOMEPAGE_URL "http://wwww.msxpertsuite.org/minexpert2")
12	12
13		set(VERSION 7.3.0)
	13	set(VERSION 7.4.0)
14	14
15	15	# Set additional project information
16	16	set(COMPANY "msXpertSuite.org")

235	235	#############################################################
236	236	####################
237	237	# BUILD OF THE TESTS
238		if(TESTS)
	238	if(MAKE_TESTS)
	239	#MESSAGE("MAKE_TEST was set to ${MAKE_TEST}")
	240	enable_testing()
	241	include(CTest)
	242
	243	if(BUILD_TESTING)
	244
239	245	add_subdirectory(tests)
	246
	247	endif(BUILD_TESTING)
	248
240	249	endif()
241	250
242	251

+1

-1

CMakeStuff/toolchains/unix-toolchain.cmake less more

51	51
52	52	if(PappsoMSpp_FOUND)
53	53
54		message(STATUS "PappsoMSpp was found at: ${PappsoMSpp_LIBRARY}")
	54	message(STATUS "PappsoMSpp and PappsoMSppWidget were found at: ${PappsoMSpp_LIBRARY}")
55	55	message(STATUS "Include dir for PappsoMSpp is at: ${PappsoMSpp_INCLUDE_DIRS}")
56	56
57	57	endif()

+0

-5

compile_commands.json less more

192	192	"directory": "/home/rusconi/devel/minexpert2/build-area/unix/src",
193	193	"command": "/usr/bin/c++ -DQCUSTOMPLOT_USE_LIBRARY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_PRINTSUPPORT_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/home/rusconi/devel/minexpert2/build-area/unix/src -I/home/rusconi/devel/minexpert2/development/src -I/home/rusconi/devel/minexpert2/build-area/unix/src/minexpert2_autogen/include -I/home/rusconi/devel/minexpert2/build-area/unix -I/home/rusconi/devel/minexpert2/development -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtSvg -isystem /usr/include/x86_64-linux-gnu/qt5/QtPrintSupport -isystem /usr/include/IsoSpec++ -isystem /usr/include/pappsomspp -fopenmp -g -Wno-unknown-pragmas -Wall -pedantic -Wextra -ggdb3 -fPIC -std=gnu++17 -o CMakeFiles/minexpert2.dir/nongui/ProcessingType.cpp.o -c /home/rusconi/devel/minexpert2/development/src/nongui/ProcessingType.cpp",
194	194	"file": "/home/rusconi/devel/minexpert2/development/src/nongui/ProcessingType.cpp"
195		},
196		{
197		"directory": "/home/rusconi/devel/minexpert2/build-area/unix/src",
198		"command": "/usr/bin/c++ -DQCUSTOMPLOT_USE_LIBRARY -DQT_CORE_LIB -DQT_GUI_LIB -DQT_PRINTSUPPORT_LIB -DQT_SVG_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB -I/home/rusconi/devel/minexpert2/build-area/unix/src -I/home/rusconi/devel/minexpert2/development/src -I/home/rusconi/devel/minexpert2/build-area/unix/src/minexpert2_autogen/include -I/home/rusconi/devel/minexpert2/build-area/unix -I/home/rusconi/devel/minexpert2/development -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtSvg -isystem /usr/include/x86_64-linux-gnu/qt5/QtPrintSupport -isystem /usr/include/IsoSpec++ -isystem /usr/include/pappsomspp -fopenmp -g -Wno-unknown-pragmas -Wall -pedantic -Wextra -ggdb3 -fPIC -std=gnu++17 -o CMakeFiles/minexpert2.dir/nongui/MzIntegrationParams.cpp.o -c /home/rusconi/devel/minexpert2/development/src/nongui/MzIntegrationParams.cpp",
199		"file": "/home/rusconi/devel/minexpert2/development/src/nongui/MzIntegrationParams.cpp"
200	195	},
201	196	{
202	197	"directory": "/home/rusconi/devel/minexpert2/build-area/unix/src",

+14

-15

doc/user-manual/xml/MAIN-minexpert2-user-manual.xml less more

29	29
30	30	</dedication>
31	31
32		<xi:include href="preface.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
33		</xi:include>
	32	<!--<xi:include href="preface.xml" xmlns:xi="http://www.w3.org/2001/XInclude">-->
	33	<!--</xi:include>-->
34	34
35		<xi:include href="generalities.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
36		</xi:include>
	35	<!--<xi:include href="generalities.xml" xmlns:xi="http://www.w3.org/2001/XInclude">-->
	36	<!--</xi:include>-->
37	37
38	38	<xi:include href="graphical-user-interface.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
39	39	</xi:include>

41	41	<xi:include href="mass-data-integrations.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
42	42	</xi:include>
43	43
44		<xi:include href="mass-spectral-deconvolutions.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
45		</xi:include>
	44	<!--<xi:include href="mass-spectral-deconvolutions.xml" xmlns:xi="http://www.w3.org/2001/XInclude">-->
	45	<!--</xi:include>-->
46	46
47		<xi:include href="isotopic-cluster-computations.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
48		</xi:include>
	47	<!--<xi:include href="isotopic-cluster-computations.xml" xmlns:xi="http://www.w3.org/2001/XInclude">-->
	48	<!--</xi:include>-->
49	49
50	50	<!--<xi:include href="processing-flows.xml" xmlns:xi="http://www.w3.org/2001/XInclude">-->
	51
	52	<!--<xi:include href="record-data-mining-discoveries.xml" xmlns:xi="http://www.w3.org/2001/XInclude">-->
51	53	<!--</xi:include>-->
52	54
53		<xi:include href="record-data-mining-discoveries.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
54		</xi:include>
	55	<!--<xi:include href="gpl-3.0.xml" xmlns:xi="http://www.w3.org/2001/XInclude">-->
	56	<!--</xi:include>-->
55	57
56		<xi:include href="gpl-3.0.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
57		</xi:include>
58
59		<xi:include href="colophon.xml" xmlns:xi="http://www.w3.org/2001/XInclude">
60		</xi:include>
	58	<!--<xi:include href="colophon.xml" xmlns:xi="http://www.w3.org/2001/XInclude">-->
	59	<!--</xi:include>-->
61	60
62	61	<!--<xi:include href="feedback.xml" xmlns:xi="http://www.w3.org/2001/XInclude">-->
63	62	<!--</xi:include>-->

+1

-1

doc/user-manual/xml/book-info.xml less more

17	17	<title>&PRODUCT; User Manual</title>
18	18	<productnumber>&VERSION;</productnumber>
19	19	<productname>&PRODUCT;</productname>
20		<subtitle>Visualizing, analyzing and mining of MS<superscript>n</superscript> mass spectrometric data</subtitle>
	20	<subtitle>Visualization, exploration and analysis of MS<superscript>n</superscript> mass spectrometric data</subtitle>
21	21	<releaseinfo>&VERSION;</releaseinfo>
22	22	<date>
23	23	<?dbtimestamp format="B d, Y"?>

+755

-481

doc/user-manual/xml/generalities.xml less more

14	14	]>
15	15
16	16	<chapter
17		xml:id="chap_generalities"
18		xmlns="http://docbook.org/ns/docbook" version="5.0"
19		xmlns:xlink="http://www.w3.org/1999/xlink">
20
21		<info>
22
23		<title>Generalities</title>
24
25		<keywordset>
26		<keyword>general concepts</keyword>
27		<keyword>combinations</keyword>
28		<keyword>integrations</keyword>
29		</keywordset>
30
31		</info>
32
33		<para>In this chapter, I wish to introduce some general concepts around the
34		&mineXp2; program and the way data elements are named in this manual and in
35		the program.</para>
36
37		<para>A mass spectrometry experiment generally involves monitoring the &mz;
38		value of analytes injected in the mass spectrometer along a certain time
39		duration. The &mz; value of each detected analyte is recorded along with the
40		corresponding signal intensity ∫, so that a mass spectrum is nothing but
41		a series of &mzi; pairs recorded along the acquisition duration. All along
42		the acquisition, the precise moment at which a given analyte is detected
43		(and its &mzi; pair is recorded), is called the retention time of that
44		analyte (&rt;). This retention time is not to be misunderstood as the drift
45		time of that analyte in an ion mobility mass spectrometry experiment.
46		</para>
47
48		<sect1>
49
50		<title>General concepts and terminologies</title>
51
52		<para> Most generally, the mass spectrometer acquires an important number of
53		spectra in, say, one second. But all these spectra are
54		<emphasis>combined</emphasis> together, and, on the surface, the massist
55		only sees a <quote>slow</quote> acquisition of 1 spectrum per second.
56		This apparent slow acquisition rate is configurable. At the time of
57		writing, generally 1 spectrum per second is recorded on disk. So, say
58		we record mass spectra for 5 minutes, we would have recorded
59		(5*60) spectra.
60		</para>
61
62		</sect1>
63
64		<sect1>
65
66		<title>Acquiring Mass Data Along Time: To Profile or Not To Profile?</title>
67
68		<para>
69		As a mass spectrometry user, the reader of this manual certainly has used mass
70		spectrometers where mass spectra are acquired and stored in different ways:
71
72		<itemizedlist>
73
74		<listitem>
75
76		<para>Mass spectra are acquired and summed—the next to the
77		previous—in such a manner that one is left, at the end of the
78		acquisition, with a single spectrum of which the various peak
79		intensities have been increasing all along the acquisition. Indeed,
80		in this mode, each new spectrum is actually
81		<emphasis><quote>combined</quote></emphasis> to the previously
82		acquired ones. The resulting mass spectrum that is displayed on
83		screen and that gets ultimately stored on disk is called a
84		<emphasis>combined spectrum</emphasis>. This is typically the way
85		MALDI-TOF mass spectrometers are used when manually acquiring data
86		from samples deposited onto sample plates. We refer to this kind of
87		acquisition as an <quote>accumulation</quote> mode
88		acquisition;</para>
89
90		</listitem>
91
92		<listitem>
93
94		<para>Mass spectra are acquired and stored on disk as a single file
95		containing all the spectra, appended one after the other. There is
96		no combination of the spectra: each time a new spectrum is displayed
97		on screen, that spectrum is appended to the
98		file.<footnote><para>Although there certainly is spectrum
99		combination going on in the guts of the software, because the
100		system actually acquires much more spectra than is visible on
101		screen and each newly displayed spectrum is actually the
102		combination of many spectra acquired under the
103		surface.</para></footnote> This is typically the case when mass
104		spectra are acquired all along a chromatography run and is
105		generally called a <emphasis><quote>profile</quote></emphasis>
106		mode acquisition. Note that this profile mode acquisition must
107		not be mistaken as the profile mass peak type that negates the
108		centroid mass peak type.</para>
109
110		</listitem>
111
112		</itemizedlist>
113
114		</para>
115
116		</sect1>
117
118		<sect1>
119
120		<title>Mass Data Visualisation: To Combine or Not To Combine?</title>
121
122		<para> In the previous section, we mentioned <emphasis>spectrum
123		combination</emphasis> a number of times. What does that mean, that
124		spectra are <emphasis><quote>combined</quote></emphasis> together into
125		a single <emphasis><quote>combined spectrum</quote></emphasis>? Say we
126		have 200 spectra that need to be combined together into a
127		<emphasis>single</emphasis> spectrum that summatively represents the
128		data of these 200 spectra.</para>
129
130		<para>First, a new spectrum would be allocated <emphasis>(result
131		spectrum)</emphasis>, entirely empty at first. Then, the very first
132		spectrum of the 200 spectra is literally copied into that result
133		spectrum. At this point the combination occurs, according to an
134		iterative process that has the following steps:
135
136		<itemizedlist>
137
138		<listitem>
139
140		<para>Pick the next spectrum of the 200-spectra dataset;</para>
141
142
143		<orderedlist>
144
145		<listitem>
146
147		<para> Pick the first &mzi; pair of the currently iterated
148		spectrum;</para>
149
150		</listitem>
151
152		<listitem>
153
154		<para> Look up in the <emphasis>result spectrum</emphasis> if a
155		&mz; value identical to the &mz; value of the current
156		&mzi; pair is already present;</para>
157
158		</listitem>
159
160		<listitem>
161
162		<para> If the &mz; value is found, increment its intensity by
163		the intensity of the &mzi; pair;</para>
164
165		</listitem>
166
167		<listitem>
168
169		<para> Else, if the &mz; value is not found, add the current
170		&mzi; pair to the result spectrum;</para>
171
172		</listitem>
173
174		<listitem>
175
176		<para> Iterate over all the remaining &mzi; pairs of the current
177		spectrum and redo these steps.</para>
178
179		</listitem>
180
181		</orderedlist>
182
183		</listitem>
184
185		<listitem>
186
187		<para>Iterate over all the 198 remaining spectra of the dataset
188		and do the steps above for each single iterated spectrum.</para>
189
190		</listitem>
191
192		</itemizedlist>
193
194		</para>
195
196		<para> At the end of the two nested loops above, the combined spectrum is
197		still a single spectrum that represents—summatively—all the
198		200 spectra. This whole process is very computing-intensive, in particular
199		if:
200
201		<itemizedlist>
202
203		<listitem>
204
205		<para> The &mz; range is large: there are lots of points in
206		each spectrum, which means that for each new &mzi; pair we need
207		to iterate in the long list of &mz; values that make the
208		result spectrum;</para>
209
210		</listitem>
211
212		<listitem>
213
214		<para> The resolving power of the mass spectrometer is high: there
215		are many points per &mz; range unit. </para>
216
217		</listitem>
218
219		</itemizedlist>
220
221		</para>
222
223		<para>When a profile mode acquisition is performed, the user gets an
224		innumerable number of distinct spectra, all appended to a single file.
225		These unitary spectra are virtually unusable if an initial processing is
226		not performed. This initial processing of the spectra is called
227		<emphasis><quote>total ion current chromatogram
228		calculation</quote></emphasis>. What is it? Let's say that the user
229		has performed a profile mode mass spectrometry acquisition on the eluate
230		of a chromatography column. Now, imagine that the spectrometer stores the
231		mass data at a rate of one spectrum per second and that the chromatography
232		gradient develops over 45 min: there would be a total of (45 *
233		60) spectra in that file. The question is:
234		—<emphasis><quote>How can we provide the user with a data
235		representation that might be both meaningful and useful to start
236		mining the data?</quote></emphasis> The conventional way of doing so
237		is to load all the mass spectra and compute the <emphasis><quote>total ion
238		current chromatogram</quote></emphasis> (the TIC chromatogram). The
239		analogy with chromatography is evident: the TIC chromatogram is the same
240		as the UV chromatogram unless optical density is not the physical property
241		that is measured over time; instead, the amount of ions that are detected
242		in the mass spectrometer is measured over time. That amount is actually
243		the sum of the intensities of all the &mzi; pairs detected in each
244		spectrum. When mass data are acquired during a chromatography run, often,
245		the total ion current chromatogram mirrors (mimicks) the UV
246		chromatogram<footnote><para>Unless eluted analytes do absorb UV light but
247		do not either desorb/desolvate or ionize, or both.</para></footnote>.
248		For each retention time (RT) a TIC value is computed by summing the
249		intensities of all the &mzi; pairs detected at that specific RT.</para>
	17	xml:id="chap_generalities"
	18	xmlns="http://docbook.org/ns/docbook" version="5.0"
	19	xmlns:xlink="http://www.w3.org/1999/xlink">
	20
	21	<info>
	22
	23	<title>Generalities</title>
	24
	25	<keywordset>
	26	<keyword>general concepts</keyword>
	27	<keyword>combinations</keyword>
	28	<keyword>integrations</keyword>
	29	</keywordset>
	30
	31	</info>
	32
	33	<para>In this chapter, I wish to introduce some general concepts around the
	34	&mineXp2; program and the way data elements are named in this manual and in
	35	the program.</para>
	36
	37	<para>A mass spectrometry experiment generally involves monitoring the &mz;
	38	value of analytes injected in the mass spectrometer along a certain time
	39	duration. The &mz; value of each detected analyte is recorded along with the
	40	corresponding signal intensity ∫, so that a mass spectrum is nothing but
	41	a series of &mzi; pairs recorded along the acquisition duration. All along
	42	the acquisition, the precise moment at which a given analyte is detected
	43	(and its &mzi; pair is recorded), is called the retention time of that
	44	analyte (&rt;). This retention time is not to be misunderstood as the drift
	45	time of that analyte in an ion mobility mass spectrometry experiment.
	46	</para>
	47
	48	<sect1>
	49
	50	<title>General concepts and terminologies</title>
	51
	52	<para> Most generally, the mass spectrometer acquires an important number of
	53	spectra in, say, one second. But all these spectra are
	54	<emphasis>combined</emphasis> together, and, on the surface, the massist
	55	only sees a <quote>slow</quote> acquisition of 1 spectrum per second.
	56	This apparent slow acquisition rate is configurable. At the time of
	57	writing, generally 1 spectrum per second is recorded on disk. So, say
	58	we record mass spectra for 5 minutes, we would have recorded
	59	(5*60) spectra.
	60	</para>
	61
	62	</sect1>
	63
	64	<sect1>
	65
	66	<title>Acquiring Mass Data Along Time: To Profile or Not To Profile?</title>
	67
	68	<para>
	69	As a mass spectrometry user, the reader of this manual certainly has used mass
	70	spectrometers where mass spectra are acquired and stored in different ways:
	71
	72	<itemizedlist>
	73
	74	<listitem>
	75
	76	<para>Mass spectra are acquired and summed—the next to the
	77	previous—in such a manner that one is left, at the end of the
	78	acquisition, with a single spectrum of which the various peak
	79	intensities have been increasing all along the acquisition. Indeed,
	80	in this mode, each new spectrum is actually
	81	<emphasis><quote>combined</quote></emphasis> to the previously
	82	acquired ones. The resulting mass spectrum that is displayed on
	83	screen and that gets ultimately stored on disk is called a
	84	<emphasis>combined spectrum</emphasis>. This is typically the way
	85	MALDI-TOF mass spectrometers are used when manually acquiring data
	86	from samples deposited onto sample plates. We refer to this kind of
	87	acquisition as an <quote>accumulation</quote> mode
	88	acquisition;</para>
	89
	90	</listitem>
	91
	92	<listitem>
	93
	94	<para>Mass spectra are acquired and stored on disk as a single file
	95	containing all the spectra, appended one after the other. There is
	96	no combination of the spectra: each time a new spectrum is displayed
	97	on screen, that spectrum is appended to the
	98	file.<footnote><para>Although there certainly is spectrum
	99	combination going on in the guts of the software, because the
	100	system actually acquires much more spectra than is visible on
	101	screen and each newly displayed spectrum is actually the
	102	combination of many spectra acquired under the
	103	surface.</para></footnote> This is typically the case when mass
	104	spectra are acquired all along a chromatography run and is
	105	generally called a <emphasis><quote>profile</quote></emphasis>
	106	mode acquisition. Note that this profile mode acquisition must
	107	not be mistaken as the profile mass peak type that negates the
	108	centroid mass peak type.</para>
	109
	110	</listitem>
	111
	112	</itemizedlist>
	113
	114	</para>
	115
	116	</sect1>
	117
	118	<sect1>
	119
	120	<title>Mass Data Visualisation: To Combine or Not To Combine?</title>
	121
	122	<para> In the previous section, we mentioned <emphasis>spectrum
	123	combination</emphasis> a number of times. What does that mean, that
	124	spectra are <emphasis><quote>combined</quote></emphasis> together into
	125	a single <emphasis><quote>combined spectrum</quote></emphasis>? Say we
	126	have 200 spectra that need to be combined together into a
	127	<emphasis>single</emphasis> spectrum that summatively represents the
	128	data of these 200 spectra.</para>
	129
	130	<para>First, a new spectrum would be allocated <emphasis>(result
	131	spectrum)</emphasis>, entirely empty at first. Then, the very first
	132	spectrum of the 200 spectra is literally copied into that result
	133	spectrum. At this point the combination occurs, according to an
	134	iterative process that has the following steps:
	135
	136	<itemizedlist>
	137
	138	<listitem>
	139
	140	<para>Pick the next spectrum of the 200-spectra dataset;</para>
	141
	142
	143	<orderedlist>
	144
	145	<listitem>
	146
	147	<para> Pick the first &mzi; pair of the currently iterated
	148	spectrum;</para>
	149
	150	</listitem>
	151
	152	<listitem>
	153
	154	<para> Look up in the <emphasis>result spectrum</emphasis> if a
	155	&mz; value identical to the &mz; value of the current
	156	&mzi; pair is already present;</para>
	157
	158	</listitem>
	159
	160	<listitem>
	161
	162	<para> If the &mz; value is found, increment its intensity by
	163	the intensity of the &mzi; pair;</para>
	164
	165	</listitem>
	166
	167	<listitem>
	168
	169	<para> Else, if the &mz; value is not found, add the current
	170	&mzi; pair to the result spectrum;</para>
	171
	172	</listitem>
	173
	174	<listitem>
	175
	176	<para> Iterate over all the remaining &mzi; pairs of the current
	177	spectrum and redo these steps.</para>
	178
	179	</listitem>
	180
	181	</orderedlist>
	182
	183	</listitem>
	184
	185	<listitem>
	186
	187	<para>Iterate over all the 198 remaining spectra of the dataset
	188	and do the steps above for each single iterated spectrum.</para>
	189
	190	</listitem>
	191
	192	</itemizedlist>
	193
	194	</para>
	195
	196	<para> At the end of the two nested loops above, the combined spectrum is
	197	still a single spectrum that represents—summatively—all the
	198	200 spectra. This whole process is very computing-intensive, in particular
	199	if:
	200
	201	<itemizedlist>
	202
	203	<listitem>
	204
	205	<para> The &mz; range is large: there are lots of points in
	206	each spectrum, which means that for each new &mzi; pair we need
	207	to iterate in the long list of &mz; values that make the
	208	result spectrum;</para>
	209
	210	</listitem>
	211
	212	<listitem>
	213
	214	<para> The resolving power of the mass spectrometer is high: there
	215	are many points per &mz; range unit. </para>
	216
	217	</listitem>
	218
	219	</itemizedlist>
	220
	221	</para>
	222
	223	<para>When a profile mode acquisition is performed, the user gets an
	224	innumerable number of distinct spectra, all appended to a single file.
	225	These unitary spectra are virtually unusable if an initial processing is
	226	not performed. This initial processing of the spectra is called
	227	<emphasis><quote>total ion current chromatogram
	228	calculation</quote></emphasis>. What is it? Let's say that the user
	229	has performed a profile mode mass spectrometry acquisition on the eluate
	230	of a chromatography column. Now, imagine that the spectrometer stores the
	231	mass data at a rate of one spectrum per second and that the chromatography
	232	gradient develops over 45 min: there would be a total of (45 *
	233	60) spectra in that file. The question is:
	234	—<emphasis><quote>How can we provide the user with a data
	235	representation that might be both meaningful and useful to start
	236	mining the data?</quote></emphasis> The conventional way of doing so
	237	is to load all the mass spectra and compute the <emphasis><quote>total ion
	238	current chromatogram</quote></emphasis> (the TIC chromatogram). The
	239	analogy with chromatography is evident: the TIC chromatogram is the same
	240	as the UV chromatogram unless optical density is not the physical property
	241	that is measured over time; instead, the amount of ions that are detected
	242	in the mass spectrometer is measured over time. That amount is actually
	243	the sum of the intensities of all the &mzi; pairs detected in each
	244	spectrum. When mass data are acquired during a chromatography run, often,
	245	the total ion current chromatogram mirrors (mimicks) the UV
	246	chromatogram<footnote><para>Unless eluted analytes do absorb UV light but
	247	do not either desorb/desolvate or ionize, or both.</para></footnote>.
	248	For each retention time (RT) a TIC value is computed by summing the
	249	intensities of all the &mzi; pairs detected at that specific RT.</para>
250	250
251	251	<para>How is this total ion current chromatogram computed? This is an
252		iterative process: from the first spectrum (retention time value
253		0 s), to the second spectrum (retention time value 1 s) up to
254		the last spectrum (retention time 45 min), the program computes the
255		sum of the intensities of all the spectrum's &mzi; pairs. That
256		computation ends up with a map that relates each RT value with the
257		corresponding TIC value. The TIC chromatogram is nothing but a plot of
258		the TIC values as a function of RT values. In that sense, it is indeed a
	252	iterative process: from the first spectrum (retention time value
	253	0 s), to the second spectrum (retention time value 1 s) up to
	254	the last spectrum (retention time 45 min), the program computes the
	255	sum of the intensities of all the spectrum's &mzi; pairs. That
	256	computation ends up with a map that relates each RT value with the
	257	corresponding TIC value. The TIC chromatogram is nothing but a plot of
	258	the TIC values as a function of RT values. In that sense, it is indeed a
259	259	chromatogram.</para>
260	260
261		<para>&mineXp2; works exactly in this way. When mass spectrometry data are
262		loaded from a file, the TIC chromatogram is computed and displayed. This
263		TIC chromatogram serves as the basis for the mass data mining, as
264		described in this manual. The TIC chromatogram serves as the basis for
265		spectral combinations that can be performed in various ways, and not all
266		formally <emphasis>combinations</emphasis>, which is why I prefer the term
267		<emphasis><quote>integrations</quote></emphasis>. Some of these
268		integrations are described below:
269
270		<itemizedlist>
271
272		<listitem>
273
274		<para>Integrating data from the TIC chromatogram to a single mass
275		spectrum;</para>
276
277		</listitem>
278
279		<listitem>
280
281		<para>Integrating data from the TIC chromatogram to a single drift
282		spectrum;</para>
283
284		</listitem>
285
286		</itemizedlist>
287
288		</para>
289
290		<para>Note that the reverse actions are possible (and indeed necessary for
291		a thorough data mining): selecting a region of a mass spectrum and asking
292		that the TIC chromatogram be reconstituted from there; or selecting a
293		region of a drift spectrum and asking that the TIC chromatogram be
294		reconstituted from there also. Finally, integrations may, of course, be
295		performed from a mass spectrum to a drift spectrum, and reverse.</para>
296
297		</sect1>
298
299		<sect1>
300
301		<title>Examples of Various Mass Spectral Data Integrations</title>
302
303		<para> In the sections below, the inner workings of &mineXp2; are
304		described for some exemplary mass data integrations. For example,
305		when doing ion mobility mass spectrometry data mining, it is
306		essential to be able to characterize most finely the drift time of
307		each and any analyte. Since each analyte is actually defined as one
308		or more &mzi; pairs, it is essential to be able to ask questions
309		like the following:
310
311		<itemizedlist>
312
313		<listitem>
314
315		<para>What is the drift time of the ions below this mass
316		peak?</para>
317
318		</listitem>
319
320		<listitem>
321
322		<para>What are all the drift times of all the analytes going
323		through the mobility cell for a given retention time range?</para>
324
325		</listitem>
326
327		<listitem>
328
329		<para>What are all the ions that are responsible for this
330		shoulder in the drift spectrum?</para>
331
332		</listitem>
333
334		</itemizedlist>
335
336		</para>
337
338		<sect2>
339
340		<title>TIC -> MZ integration</title>
341
342		<para>What computation does actually &mineXp2; do when a mass spectrum
343		is computed starting from a TIC chromatogram region, say between
344		retention time RT minute 7 and
345		RT minute 8.5?</para>
346
347		<orderedlist>
348
349		<listitem>
350
351		<para>List all the mass spectra that were acquired between RT 7
352		and RT 8.5. In this <emphasis>spectral set</emphasis>, there
353		might be many hundreds of spectra that match this criterion, if we
354		think that, in ion mobility mass spectrometry,
355		≈ 200 spectra are acquired and stored individually
356		every second (I mean it, every 1 s time lapse);</para>
357
358		</listitem>
359
360		<listitem>
361
362		<para> Allocate a new empty spectrum—the
363		<emphasis><quote>combined spectrum</quote></emphasis>—and
364		copy into it without modification the first spectrum of the
365		spectral set;</para>
366
367		</listitem>
368
369		<listitem xml:id="each-1-spectrum">
370
371		<para> Go to the next spectrum of the spectral
372		set and iterate into each &mzi; pair:</para>
373
374		<itemizedlist>
375
376		<listitem>
377
378		<para> Check if the &mz; value of the iterated pair is
379		already present in the combined spectrum. If so, increment the
380		combined spectrum's &mzi; pair's intensity value by the
381		intensity of the iterated &mzi; pair's intensity. If not, simply
382		copy the iterated &mzi; pair in the combined spectrum; </para>
383
384		</listitem>
385
386		<listitem>
387
388		<para> Iterate over all the remaining &mzi; pairs and
389		perform the same action as above.</para>
390
391		</listitem>
392
393		</itemizedlist>
394
395		</listitem>
396
397		<listitem>
398
399		<para> Iterate over all the remaining spectra of the spectral set and
400		perform step number <xref linkend="each-1-spectrum"/>.</para>
401
402		</listitem>
403
404		</orderedlist>
405
406		<para> &mineXp2; then displays the combined spectrum.</para>
407
408		</sect2>
409
410		<sect2>
411
412		<title>TIC -> DT integration</title>
413
414		<para> What computation does &mineXp2; actually do when a drift
415		spectrum is computed starting from a given TIC chromatogram region,
416		say between retention time RT minute 7 and
417		RT minute 8.5?</para>
418
419		<para> What is a drift spectrum? A drift spectrum (mobilogram) is a
420		plot where the cumulated ion current of the detected ions is plotted
421		against the drift time at which they were detected. Let's see how
422		that computation is handled in &mineXp2;:
423
424		<orderedlist>
425
426		<listitem>
427
428		<para>Create a map to store all the (drift time, intensity) pairs
429		that are to be computed below, the (dt,i) map;</para>
430
431		</listitem>
432
433		<listitem>
434
435		<para>List all the mass spectra that were acquired between
436		RT 7 and RT 8.5. The obtained list of mass spectra is
437		called the <emphasis><quote>spectral
438		set</quote></emphasis>;</para>
439
440		</listitem>
441
442		<listitem xml:id="each-2-spectrum">
443
444		<para>Go to the first spectrum of the spectral set and compute its
445		TIC value (sum of all the intensities of all the &mzi; pairs of
446		that spectrum). Get the drift time value at which this mass
447		spectrum was acquired. We thus have a value pair: (dt, i), that
448		is, for drift time <emphasis>dt</emphasis>, the intensity of the
449		total ion current is <emphasis>i</emphasis>;</para>
450
451		<para> At this point, we need to do a short digression: we saw
452		earlier that, at the time of this writing, one of the
453		commercial instruments on which the author of these lines does
454		his experiments stores 200 spectra each second. These
455		200 spectra actually correspond to the way the drift
456		cycle is divided into 200 bin (time bins). That means
457		that in the retention time range [7–8.5], there are
458		(1.560) complete drift cycles. And thus there are (1.560)
459		spectra with drift time x, the same amount of spectra
460		with drift time y, and so on for the reminaing
461		198 time bins. Of course, a large number of these
462		spectra might be almost empty, but these spectra are there and
463		we need to cope with them.</para>
464
465		<para>The paragraph above must thus lead to one interrogation about
466		the current (dt,i) pair: —<emphasis><quote>Has the current
467		dt value be seen before, during the previous iterations in
468		this loop?</quote></emphasis>. If not, then create the (dt, i)
469		pair and add it to the (dt,i) map; if yes, get the
470		<emphasis>dt</emphasis> element in the map and increment its
471		intensity value by the TIC value computed above;</para>
472
473		</listitem>
474
475		<listitem>
476
477		<para>Iterate over all the remaining spectra of the spectral set and
478		perform step number <xref linkend="each-2-spectrum"/>.</para>
479
480		</listitem>
481
482		</orderedlist>
483
484		</para>
485
486		<para> At the end of the loop above, we get a map in which each item
487		relates a given drift time with a TIC value. This can be understood
488		this way: —<emphasis><quote>For each drift time value, what is
489		the accumulated ion current of all the ions having that specific
490		drift time?</quote></emphasis>.</para>
491
492		<para>At this point, &mineXp2; displays the drift spectrum
493		(mobilogram).</para>
494
495		</sect2>
496
497		</sect1>
498
499
500		</chapter>
501
	261	<para>&mineXp2; works exactly in this way. When mass spectrometry data are
	262	loaded from a file, the TIC chromatogram is computed and displayed. This
	263	TIC chromatogram serves as the basis for the mass data mining, as
	264	described in this manual. The TIC chromatogram serves as the basis for
	265	spectral combinations that can be performed in various ways, and not all
	266	formally <emphasis>combinations</emphasis>, which is why I prefer the term
	267	<emphasis><quote>integrations</quote></emphasis>. Some of these
	268	integrations are described below:
	269
	270	<itemizedlist>
	271
	272	<listitem>
	273
	274	<para>Integrating data from the TIC chromatogram to a single mass
	275	spectrum;</para>
	276
	277	</listitem>
	278
	279	<listitem>
	280
	281	<para>Integrating data from the TIC chromatogram to a single drift
	282	spectrum;</para>
	283
	284	</listitem>
	285
	286	</itemizedlist>
	287
	288	</para>
	289
	290	<para>Note that the reverse actions are possible (and indeed necessary for
	291	a thorough data mining): selecting a region of a mass spectrum and asking
	292	that the TIC chromatogram be reconstituted from there; or selecting a
	293	region of a drift spectrum and asking that the TIC chromatogram be
	294	reconstituted from there also. Finally, integrations may, of course, be
	295	performed from a mass spectrum to a drift spectrum, and reverse.</para>
	296
	297	</sect1>
	298
	299	<sect1>
	300
	301	<title>Examples of Various Mass Spectral Data Integrations</title>
	302
	303	<para> In the sections below, the inner workings of &mineXp2; are
	304	described for some exemplary mass data integrations. For example,
	305	when doing ion mobility mass spectrometry data mining, it is
	306	essential to be able to characterize most finely the drift time of
	307	each and any analyte. Since each analyte is actually defined as one
	308	or more &mzi; pairs, it is essential to be able to ask questions
	309	like the following:
	310
	311	<itemizedlist>
	312
	313	<listitem>
	314
	315	<para>What is the drift time of the ions below this mass
	316	peak?</para>
	317
	318	</listitem>
	319
	320	<listitem>
	321
	322	<para>What are all the drift times of all the analytes going
	323	through the mobility cell for a given retention time range?</para>
	324
	325	</listitem>
	326
	327	<listitem>
	328
	329	<para>What are all the ions that are responsible for this
	330	shoulder in the drift spectrum?</para>
	331
	332	</listitem>
	333
	334	</itemizedlist>
	335
	336	</para>
	337
	338	<sect2>
	339
	340	<title>TIC -> MZ integration</title>
	341
	342	<para>What computation does actually &mineXp2; do when a mass spectrum
	343	is computed starting from a TIC chromatogram region, say between
	344	retention time RT minute 7 and
	345	RT minute 8.5?</para>
	346
	347	<orderedlist>
	348
	349	<listitem>
	350
	351	<para>List all the mass spectra that were acquired between RT 7
	352	and RT 8.5. In this <emphasis>spectral set</emphasis>, there
	353	might be many hundreds of spectra that match this criterion, if we
	354	think that, in ion mobility mass spectrometry,
	355	≈ 200 spectra are acquired and stored individually
	356	every second (I mean it, every 1 s time lapse);</para>
	357
	358	</listitem>
	359
	360	<listitem>
	361
	362	<para> Allocate a new empty spectrum—the
	363	<emphasis><quote>combined spectrum</quote></emphasis>—and
	364	copy into it without modification the first spectrum of the
	365	spectral set;</para>
	366
	367	</listitem>
	368
	369	<listitem xml:id="each-1-spectrum">
	370
	371	<para> Go to the next spectrum of the spectral
	372	set and iterate into each &mzi; pair:</para>
	373
	374	<itemizedlist>
	375
	376	<listitem>
	377
	378	<para> Check if the &mz; value of the iterated pair is
	379	already present in the combined spectrum. If so, increment the
	380	combined spectrum's &mzi; pair's intensity value by the
	381	intensity of the iterated &mzi; pair's intensity. If not, simply
	382	copy the iterated &mzi; pair in the combined spectrum; </para>
	383
	384	</listitem>
	385
	386	<listitem>
	387
	388	<para> Iterate over all the remaining &mzi; pairs and
	389	perform the same action as above.</para>
	390
	391	</listitem>
	392
	393	</itemizedlist>
	394
	395	</listitem>
	396
	397	<listitem>
	398
	399	<para> Iterate over all the remaining spectra of the spectral set and
	400	perform step number <xref linkend="each-1-spectrum"/>.</para>
	401
	402	</listitem>
	403
	404	</orderedlist>
	405
	406	<para> &mineXp2; then displays the combined spectrum.</para>
	407
	408	</sect2>
	409
	410	<sect2>
	411
	412	<title>TIC -> DT integration</title>
	413
	414	<para> What computation does &mineXp2; actually do when a drift
	415	spectrum is computed starting from a given TIC chromatogram region,
	416	say between retention time RT minute 7 and
	417	RT minute 8.5?</para>
	418
	419	<para> What is a drift spectrum? A drift spectrum (mobilogram) is a
	420	plot where the cumulated ion current of the detected ions is plotted
	421	against the drift time at which they were detected. Let's see how
	422	that computation is handled in &mineXp2;:
	423
	424	<orderedlist>
	425
	426	<listitem>
	427
	428	<para>Create a map to store all the (drift time, intensity) pairs
	429	that are to be computed below, the (dt,i) map;</para>
	430
	431	</listitem>
	432
	433	<listitem>
	434
	435	<para>List all the mass spectra that were acquired between
	436	RT 7 and RT 8.5. The obtained list of mass spectra is
	437	called the <emphasis><quote>spectral
	438	set</quote></emphasis>;</para>
	439
	440	</listitem>
	441
	442	<listitem xml:id="each-2-spectrum">
	443
	444	<para>Go to the first spectrum of the spectral set and compute its
	445	TIC value (sum of all the intensities of all the &mzi; pairs of
	446	that spectrum). Get the drift time value at which this mass
	447	spectrum was acquired. We thus have a value pair: (dt, i), that
	448	is, for drift time <emphasis>dt</emphasis>, the intensity of the
	449	total ion current is <emphasis>i</emphasis>;</para>
	450
	451	<para> At this point, we need to do a short digression: we saw
	452	earlier that, at the time of this writing, one of the
	453	commercial instruments on which the author of these lines does
	454	his experiments stores 200 spectra each second. These
	455	200 spectra actually correspond to the way the drift
	456	cycle is divided into 200 bin (time bins). That means
	457	that in the retention time range [7–8.5], there are
	458	(1.560) complete drift cycles. And thus there are (1.560)
	459	spectra with drift time x, the same amount of spectra
	460	with drift time y, and so on for the reminaing
	461	198 time bins. Of course, a large number of these
	462	spectra might be almost empty, but these spectra are there and
	463	we need to cope with them.</para>
	464
	465	<para>The paragraph above must thus lead to one interrogation about
	466	the current (dt,i) pair: —<emphasis><quote>Has the current
	467	dt value be seen before, during the previous iterations in
	468	this loop?</quote></emphasis>. If not, then create the (dt, i)
	469	pair and add it to the (dt,i) map; if yes, get the
	470	<emphasis>dt</emphasis> element in the map and increment its
	471	intensity value by the TIC value computed above;</para>
	472
	473	</listitem>
	474
	475	<listitem>
	476
	477	<para>Iterate over all the remaining spectra of the spectral set and
	478	perform step number <xref linkend="each-2-spectrum"/>.</para>
	479
	480	</listitem>
	481
	482	</orderedlist>
	483
	484	</para>
	485
	486	<para> At the end of the loop above, we get a map in which each item
	487	relates a given drift time with a TIC value. This can be understood
	488	this way: —<emphasis><quote>For each drift time value, what is
	489	the accumulated ion current of all the ions having that specific
	490	drift time?</quote></emphasis>.</para>
	491
	492	<para>At this point, &mineXp2; displays the drift spectrum
	493	(mobilogram).</para>
	494
	495	</sect2>
	496
	497	</sect1>
	498
	499	<sect1>
	500
	501	<title>Installation of the software</title>
	502
	503	<para>
	504
	505	The installation material is available at <uri
	506	type="website">http://msxpertsuite.org</uri>.
	507
	508	</para>
	509
	510	<para>
	511
	512	The installation of the software is extremely easy on the MS-Windows and
	513	macOS platforms. In both cases, the installator programs are standard and
	514	require no explanation.
	515
	516	</para>
	517
	518	<para>
	519
	520	The installation on GNU/Linux platforms is also extremely easy (even more
	521	than in the above situations) on Debian/Ubuntu systems. &mineXp2; is
	522	indeed packaged for these systems and the only command to run to install
	523	it is:
	524
	525	</para>
	526
	527	<para>
	528
	529	<prompt>$</prompt><footnote><para>The prompt character might be
	530	<keysym>%</keysym> in some shells, like
	531	<application>zsh</application></para></footnote> <command>sudo apt install
	532	<package_name></command>
	533
	534	</para>
	535
	536	<para>
	537
	538	In the command above, the typical <emphasis>package_name</emphasis> is
	539	in the form <filename>minexpert2</filename> for the program package and
	540	<filename>minexpert2-doc</filename> for the user manual package.
	541
	542	</para>
	543
	544	<para>Once the package has been installed the program shows up in the
	545	<emphasis>Science</emphasis> menu. It can also be launched from the shell
	546	using the following command: </para>
	547
	548	<para>
	549
	550	<prompt>$</prompt> <command>minexpert2</command>
	551
	552	</para>
	553
	554	</sect1>
	555
	556	<sect1>
	557
	558	<title>Building the software from source</title>
	559
	560	<para>
	561
	562	The &minexp2; software build is under the control of the
	563	<application>>CMake</application> build system. There are a number of
	564	dependencies to install prior to trying to build the software, as
	565	described below.
	566
	567	</para>
	568
	569	<sect2>
	570
	571	<title>The dependencies required to build &minexp2;</title>
	572
	573	<para>
	574
	575	The dependencies to be installed are listed here with package names
	576	matching the packages that are in <orgname>Debian/Ubuntu</orgname>. In
	577	other RPM-based software, most often the package names are similar, albeit
	578	with some slight differences.
	579
	580	</para>
	581
	582	<variablelist><title>Dependencies</title>
	583
	584	<varlistentry>
	585
	586	<term>The build system</term>
	587
	588	<listitem>
	589	<para>cmake</para>
	590	</listitem>
	591
	592	</varlistentry>
	593
	594	<varlistentry>
	595
	596	<term>Conversion of <filename>svg</filename> files to
	597	<filename>png</filename> files</term>
	598
	599	<listitem>
	600	<para>graphicsmagick-imagemagick-compat</para>
	601	</listitem>
	602
	603	</varlistentry>
	604
	605	<varlistentry>
	606
	607	<term>For the parallel computations</term>
	608
	609	<listitem>
	610	<para>libgomp1</para>
	611	</listitem>
	612
	613	</varlistentry>
	614
	615	<varlistentry>
	616
	617	<term>For the isotopic cluster calculations</term>
	618
	619	<listitem>
	620	<para>libisospec++-dev</para>
	621	</listitem>
	622
	623	</varlistentry>
	624
	625	<varlistentry>
	626
	627	<term>For all the raw mass calculations like the data model, the mass
	628	spectral combinations…</term>
	629
	630	<listitem> <para>libpappsomspp-dev, libpappsomspp-widget-dev</para>
	631	</listitem>
	632
	633	</varlistentry>
	634
	635	<varlistentry>
	636
	637	<term>For all the plotting</term>
	638
	639	<listitem>
	640	<para>libqcustomplot-dev</para>
	641	</listitem>
	642
	643	</varlistentry>
	644
	645	<varlistentry>
	646
	647	<term>For the C++ objects (GUI and non-GUI)</term>
	648
	649	<listitem> <para>qtbase5-dev, libqt5svg5-dev,
	650	qttools5-dev-tools, qtchooser</para> </listitem>
	651
	652	</varlistentry>
	653
	654	<varlistentry>
	655
	656	<term>For the man page</term>
	657
	658	<listitem>
	659	<para>docbook-to-man</para>
	660	</listitem>
	661
	662	</varlistentry>
	663
	664	<varlistentry>
	665
	666	<term>For the documentation (optional, with
	667	<option>-DMAKE_USER_MANUAL=1</option> as a flag to the call of
	668	<application>cmake</application>, see below.)</term>
	669
	670	<listitem> <para>daps, libjeuclid-core-java,
	671	libjeuclid-fop-java, docbook-mathml, libjs-jquery, libjs-highlight.js,
	672	libjs-mathjax, fonts-mathjax, fonts-mathjax-extras, texlive-fonts-extra,
	673	fonts-ebgaramond-extra</para> </listitem>
	674
	675	</varlistentry>
	676
	677	</variablelist>
	678
	679	</sect2>
	680
	681	<sect2>
	682
	683	<title>Getting the source tarball</title>
	684
	685	<para>
	686
	687	In the example below, the version of the software to be installed is
	688	<parameter>7.3.0</parameter>. Replace that version with any latest version
	689	of interest, which can be looked for at
	690	https://gitlab.com/msxpertsuite/minexpert2/-/releases.
	691
	692	</para>
	693
	694	<sect3>
	695
	696	<title> Using git</title>
	697
	698	<para>The rather convoluted command below only downloads the branch of
	699	interest. The whole git repos is very large…</para>
	700
	701	<para>
	702
	703	<command> git clone https://gitlab.com/msxpertsuite/minexpert2.git --branch
	704	master/7.3.0-1 --single-branch minexpert2-7.3.0</command>
	705
	706	</para>
	707
	708	</sect3>
	709
	710	<sect3>
	711
	712	<title> Using wget to download the tarball</title>
	713
	714	<para>
	715
	716	<command>wget
	717	https://gitlab.com/msxpertsuite/minexpert2/-/archive/7.3.0/minexpert2-7.3.0.tar.gz</command>
	718
	719	</para>
	720
	721	<para>
	722
	723	Untar the tarball, which creates the
	724	<filename>minexpert2-7.3.0</filename> directory:
	725
	726	</para>
	727
	728	<para>
	729
	730	<command>tar xvzf minexpert2-7.3.0.tar.gz</command>
	731
	732	</para>
	733
	734	</sect3>
	735
	736	</sect2>
	737
	738	<sect2>
	739
	740	<title> Build the software</title>
	741
	742	<para>
	743
	744	<literallayout language="shell">
	745
	746	Change directory:
	747
	748	<prompt>$</prompt> <command>cd minexpert2-7.3.0</command>
	749
	750	Create a build directory:
	751
	752	<prompt>$</prompt> <command>mkdir build</command>
	753
	754	Change directory:
	755
	756	<prompt>$</prompt> <command>cd build</command>
	757
	758	Configure the build:
	759
	760	<prompt>$</prompt> <command>cmake ../ -DCMAKE_BUILD_TYPE=Release</command>
	761
	762	Build the software:
	763
	764	<prompt>$</prompt> <command>make</command>
	765
	766	</literallayout>
	767
	768	</para>
	769
	770	</sect2>
	771
	772	</sect1>
	773
	774	</chapter>
	775

+5

-4

doc/user-manual/xml/graphical-user-interface.xml less more

98	98
99	99	<title>The Window Layout</title>
100	100
101		<para>The graphical interface of comprises a number of windows where data and
102		informations are displayed. When first started, the program shows the main
103		program window. Upon loading of a MS run data set from file, new windows do show up as
104		described below (see <xref linkend="fig_minexpert-whole-window-set"/>):</para>
	101	<para>The graphical interface of comprises a number of windows where data
	102	and informations are displayed. When first started, the program shows the
	103	main program window. Upon loading of a MS run data set from file, new
	104	windows do show up as described below (see <xref
	105	linkend="fig_minexpert-whole-window-set"/>):</para>
105	106
106	107	<itemizedlist>
107	108

+188

-145

doc/user-manual/xml/revision-history.xml less more

12	12
13	13	<revhistory xmlns="http://docbook.org/ns/docbook" version="5.0">
14	14
15		<revision>
16		<revnumber>7.0.1</revnumber>
17		<date>october 2020</date>
18		<authorinitials>fr</authorinitials>
19
20		<revremark>
	15	<revision>
	16	<revnumber>7.4.0</revnumber>
	17	<date>december 2020</date>
	18	<authorinitials>fr</authorinitials>
	19
	20	<revdescription>
	21
	22	<para>
	23
	24	This revision introduces updates to document the following new features.
	25
	26	<itemizedlist>
	27
	28	<listitem><para>
	29
	30	User-definable limitation of the number of threads usable for the
	31	combination computations (good request from a reviewer of the
	32	article).
	33
	34	</para></listitem>
	35
	36	<listitem><para>
	37
	38	GUI shortcut to the MS level to be targeted for the next
	39	integration (good request from a reviewer of the article).
	40
	41	</para></listitem>
	42
	43	</itemizedlist>
	44
	45	</para>
	46
	47	<para>
	48
	49	Document the build and installation of the software (another good
	50	request from a reviewer).
	51
	52	</para>
	53
	54	</revdescription>
	55
	56	</revision>
	57
	58	<revision>
	59	<revnumber>7.0.1</revnumber>
	60	<date>october 2020</date>
	61	<authorinitials>fr</authorinitials>
	62
	63	<revremark>
21	64
22	65	Update of the user manual to document the new combine+ and combine-
23	66	combinations features.
24	67
25		</revremark>
26
27		</revision>
28
29		<revision>
30		<revnumber>7.0.0</revnumber>
31		<date>september 2020</date>
32		<authorinitials>fr</authorinitials>
33
34		<revremark>
	68	</revremark>
	69
	70	</revision>
	71
	72	<revision>
	73	<revnumber>7.0.0</revnumber>
	74	<date>september 2020</date>
	75	<authorinitials>fr</authorinitials>
	76
	77	<revremark>
35	78
36	79	Update of the user manual to document new features, in particular the
37	80	MS<superscript>n</superscript> mass spectrometric data mining and new mass
38	81	data plotting features.
39	82
40		</revremark>
41
42		</revision>
43
44		<revision>
45		<revnumber>6.0.0</revnumber>
46		<date>january 2020</date>
47		<authorinitials>fr</authorinitials>
48
49		<revremark>
50
51		Full rewrite of the user manual to document the new mineXpert2 software
52		program. The new mineXpert2 version is a full rewrite of the previous
53		version such that it can handle MS<superscript>n</superscript> mass
54		spectrometric data. Major features were included in the new version that
55		are described in detail in this user manual.
56
57		</revremark>
58
59		</revision>
60
61		<revision>
62		<revnumber>5.8.2</revnumber>
63		<date>february 2019</date>
64		<authorinitials>fr</authorinitials>
65
66		<revremark>
67
68		Rework the IsoSpec-based isotopic clust calculations to better describe
69		the three available processes. Also, describe the new FWHM calculation
70		feature in the PeakShaperDlg.
71
72		</revremark>
73
74		</revision>
75
76		<revision>
77		<revnumber>5.8.0</revnumber>
78		<date>end january 2019</date>
79		<authorinitials>fr</authorinitials>
80
81		<revremark>
82
83		Add section to described the newly developed feature about isotopic
84		cluster calculations based on the IsoSpec library;
85
86		</revremark>
87
88		</revision>
89
90		<revision>
91		<revnumber>5.7.0</revnumber>
92		<date>beginning january 2019</date>
93		<authorinitials>fr</authorinitials>
94
95		<revremark>
96
97		Finished porting of the historical LaTeX-based documentation to the
98		DocBook/DAPS/FOP publishing system. Please, see Colophon for details;
99
100		</revremark>
101
102		</revision>
103
104		<revision>
105		<revnumber>not_set</revnumber>
106		<date>september 2018</date>
107		<authorinitials>fr</authorinitials>
108
109		<revremark>Update the document to include new features and to make fixes.
110		Insist on the fact that mineXpert reads mzML data files. </revremark>
111
112		</revision>
113
114		<revision>
115		<revnumber>not_set</revnumber>
116		<date>march 2018</date>
117		<authorinitials>fr</authorinitials>
118
119		<revremark>Update the document to include new m/z~integration features and
120		scripting capabilities.</revremark>
121
122		</revision>
123
124		<revision>
125		<revnumber>not_set</revnumber>
126		<date>december 2016</date>
127		<authorinitials>fr</authorinitials>
128
129		<revremark>Major rewriting of the document to incorporate all the new
130		features. Large chapter on the scripting of mineXpert. </revremark>
131
132		</revision>
133
134		<revision>
135		<revnumber>not_set</revnumber>
136		<date>december 2017</date>
137		<authorinitials>fr</authorinitials>
138
139		<revremark>Refactored document. First version documenting almost all the of
140		current features of the software program. </revremark>
141
142		</revision>
143
144		<revision>
145		<revnumber>not_set</revnumber>
146		<date>may 2017</date>
147		<authorinitials>fr</authorinitials>
148
149		<revremark> Refactored document. First version documenting almost all the of
150		current features of the mineXpert software program. </revremark>
151
152		</revision>
153
154		<revision>
155		<revnumber>not_set</revnumber>
156		<date>november 2016</date>
157		<authorinitials>fr</authorinitials>
158
159		<revremark>Resume writing, with new program name: mineXpert.</revremark>
160
161		</revision>
162
163		<revision>
164		<revnumber>not_set</revnumber>
165		<date>september 2016</date>
166		<authorinitials>fr</authorinitials>
167
168		<revremark>Start of writing.</revremark>
	83	</revremark>
	84
	85	</revision>
	86
	87	<revision>
	88	<revnumber>6.0.0</revnumber>
	89	<date>january 2020</date>
	90	<authorinitials>fr</authorinitials>
	91
	92	<revremark>
	93
	94	Full rewrite of the user manual to document the new mineXpert2 software
	95	program. The new mineXpert2 version is a full rewrite of the previous
	96	version such that it can handle MS<superscript>n</superscript> mass
	97	spectrometric data. Major features were included in the new version that
	98	are described in detail in this user manual.
	99
	100	</revremark>
	101
	102	</revision>
	103
	104	<revision>
	105	<revnumber>5.8.2</revnumber>
	106	<date>february 2019</date>
	107	<authorinitials>fr</authorinitials>
	108
	109	<revremark>
	110
	111	Rework the IsoSpec-based isotopic clust calculations to better describe
	112	the three available processes. Also, describe the new FWHM calculation
	113	feature in the PeakShaperDlg.
	114
	115	</revremark>
	116
	117	</revision>
	118
	119	<revision>
	120	<revnumber>5.8.0</revnumber>
	121	<date>end january 2019</date>
	122	<authorinitials>fr</authorinitials>
	123
	124	<revremark>
	125
	126	Add section to described the newly developed feature about isotopic
	127	cluster calculations based on the IsoSpec library;
	128
	129	</revremark>
	130
	131	</revision>
	132
	133	<revision>
	134	<revnumber>5.7.0</revnumber>
	135	<date>beginning january 2019</date>
	136	<authorinitials>fr</authorinitials>
	137
	138	<revremark>
	139
	140	Finished porting of the historical LaTeX-based documentation to the
	141	DocBook/DAPS/FOP publishing system. Please, see Colophon for details;
	142
	143	</revremark>
	144
	145	</revision>
	146
	147	<revision>
	148	<revnumber>not_set</revnumber>
	149	<date>september 2018</date>
	150	<authorinitials>fr</authorinitials>
	151
	152	<revremark>Update the document to include new features and to make fixes.
	153	Insist on the fact that mineXpert reads mzML data files. </revremark>
	154
	155	</revision>
	156
	157	<revision>
	158	<revnumber>not_set</revnumber>
	159	<date>march 2018</date>
	160	<authorinitials>fr</authorinitials>
	161
	162	<revremark>Update the document to include new m/z~integration features and
	163	scripting capabilities.</revremark>
	164
	165	</revision>
	166
	167	<revision>
	168	<revnumber>not_set</revnumber>
	169	<date>december 2016</date>
	170	<authorinitials>fr</authorinitials>
	171
	172	<revremark>Major rewriting of the document to incorporate all the new
	173	features. Large chapter on the scripting of mineXpert. </revremark>
	174
	175	</revision>
	176
	177	<revision>
	178	<revnumber>not_set</revnumber>
	179	<date>december 2017</date>
	180	<authorinitials>fr</authorinitials>
	181
	182	<revremark>Refactored document. First version documenting almost all the of
	183	current features of the software program. </revremark>
	184
	185	</revision>
	186
	187	<revision>
	188	<revnumber>not_set</revnumber>
	189	<date>may 2017</date>
	190	<authorinitials>fr</authorinitials>
	191
	192	<revremark> Refactored document. First version documenting almost all the of
	193	current features of the mineXpert software program. </revremark>
	194
	195	</revision>
	196
	197	<revision>
	198	<revnumber>not_set</revnumber>
	199	<date>november 2016</date>
	200	<authorinitials>fr</authorinitials>
	201
	202	<revremark>Resume writing, with new program name: mineXpert.</revremark>
	203
	204	</revision>
	205
	206	<revision>
	207	<revnumber>not_set</revnumber>
	208	<date>september 2016</date>
	209	<authorinitials>fr</authorinitials>
	210
	211	<revremark>Start of writing.</revremark>
169	212
170	213	</revision>
171	214

images/splashscreen.png less more

Binary diff not shown

+1

-1

images/splashscreen.svg less more

160	160	id="tspan831"
161	161	x="392.0386"
162	162	y="984.63959"
163		style="stroke-width:0.39535946px">version 7.3.0</tspan></text>
	163	style="stroke-width:0.39535946px">version 7.4.0</tspan></text>
164	164	</g>
165	165	</svg>

+1

-1

license-stub.txt less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2019 Filippo Rusconi
	4	* Copyright (C) 2009-2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+0

-2

org.msxpertsuite.minexpert2.desktop less more

16	16	Icon=minexpert2
17	17
18	18	Categories=Science;Chemistry;Biology;Qt
19		Categories[fr]=Science;Chimie;Biologie;Qt
20		Categories[it]=Scienza;Chimica;Biologia;Qt
21	19
22	20	Keywords=Mass spectrometry;Biology;Chemistry
23	21	Keywords[fr]=Spectrométrie de masse;Biologie;Chimie

+0

-1

src/CMakeLists.txt less more

65	65	#
66	66	# The classes that handle the parameters for the various integrations and the
67	67	# display of traces.
68		nongui/MzIntegrationParams.cpp
69	68	nongui/MsFragmentationSpec.cpp
70	69	#
71	70	# Peak-shaping classes (Gaussian Lorentzian peak shapes).

+1

-1

src/gui/AboutDlg.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/AboutDlg.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/AnalysisPreferencesDlg.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/AnalysisPreferencesDlg.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+2

-2

src/gui/Application.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

55	55
56	56	/////////////////////// Local includes
57	57	#include "Application.hpp"
58		#include "nongui/MzIntegrationParams.hpp"
	58	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
59	59	#include "gui/MsRunDataSetTableView.hpp"
60	60	#include "gui/MsRunDataSetTableViewItem.hpp"
61	61	#include "gui/MsRunDataSetTableViewModel.hpp"

+1

-1

src/gui/Application.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/BaseColorMapPlotCompositeWidget.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+2

-2

src/gui/BaseColorMapPlotCompositeWidget.hpp less more

2	2	*
3	3	* msXpertSuite - mass spectrometry software suite
4	4	* -----------------------------------------------
5		* Copyright(C) 2009,...,2018 Filippo Rusconi
	5	* Copyright (C) 2009--2020 Filippo Rusconi
6	6	*
7	7	* http://www.msxpertsuite.org
8	8	*

52	52	#include "BasePlotCompositeWidget.hpp"
53	53	#include "../nongui/MsRunDataSet.hpp"
54	54	#include "../nongui/ProcessingFlow.hpp"
55		#include "../nongui/MzIntegrationParams.hpp"
	55	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
56	56
57	57
58	58	namespace msxps

+97

-17

src/gui/BasePlotCompositeWidget.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

36	36	/////////////////////// Qt includes
37	37	#include <QMessageBox>
38	38	#include <QSvgGenerator>
	39	#include <QSpinBox>
39	40
40	41	/////////////////////// QCustomPlot
41	42

83	84	// to setup the ui so that the widgets are known when we use them below.
84	85	m_ui.setupUi(dynamic_cast<QWidget *>(this));
85	86
	87	// Connect the integrate to Mz pushbutton so that we can show the MS level
	88	// slider.
	89
	90	// connect(m_ui.msLevelSpinBox,
	91	// static_cast<void (QSpinBox::*)(int)>(&QSpinBox::valueChanged),
	92	connect(m_ui.msLevelSpinBox,
	93	QOverload<int>::of(&QSpinBox::valueChanged),
	94	this,
	95	&BasePlotCompositeWidget::msLevelValueChanged);
	96
86	97	// Construct the context menu that will be associated to the main menu push
87	98	// button.
88	99

99	110	m_ui.pushPinPushButton->setShortcut(QKeySequence("Ctrl+T, P"));
100	111	m_ui.pushPinPushButton->setToolTip("Toggle push pin status (Ctrl+T,P)");
101	112
102		m_ui.keepTraceCreateNewPushButton->setToolTip("Overlay new trace onto the other(s) (Ctrl+T, O)");
	113	m_ui.keepTraceCreateNewPushButton->setToolTip(
	114	"Overlay new trace onto the other(s) (Ctrl+T, O)");
103	115	m_ui.keepTraceCreateNewPushButton->setShortcut(QKeySequence("Ctrl+T, O"));
104	116
105		m_ui.eraseTraceCreateNewPushButton->setToolTip("Replace currently selected trace(s) with new one (Ctrl+T, R)");
	117	m_ui.eraseTraceCreateNewPushButton->setToolTip(
	118	"Replace currently selected trace(s) with new one (Ctrl+T, R)");
106	119	m_ui.eraseTraceCreateNewPushButton->setShortcut(QKeySequence("Ctrl+T, R"));
107	120
108	121	// The red cross pixmap plot widget closing button. Clicking this button
109	122	// triggers the signal that is trapped by the containing window that then
110	123	// handle the destruction of the widget.
111	124
112		m_ui.closeCompositePlotWidgetPushButton->setShortcut(QKeySequence("Ctrl+P, C"));
113		m_ui.closeCompositePlotWidgetPushButton->setToolTip("Close the composite plot widget (Ctrl+P,C)");
	125	m_ui.closeCompositePlotWidgetPushButton->setShortcut(
	126	QKeySequence("Ctrl+P, C"));
	127	m_ui.closeCompositePlotWidgetPushButton->setToolTip(
	128	"Close the composite plot widget (Ctrl+P,C)");
114	129	connect(
115	130	m_ui.closeCompositePlotWidgetPushButton, &QPushButton::clicked, [this]() {
116	131	mp_parentWnd->plotCompositeWidgetDestructionRequested(this);

146	161	void
147	162	BasePlotCompositeWidget::createMainMenu()
148	163	{
149		//qDebug() << "ENTER";
	164	// qDebug() << "ENTER";
150	165
151	166	if(mp_mainMenu != nullptr)
152	167	delete mp_mainMenu;

220	235
221	236	mp_mainMenu->addAction(save_plot_to_clipboard_p);
222	237
223		//qDebug() << "EXIT";
	238	// qDebug() << "EXIT";
224	239	}
225	240
226	241

244	259	void
245	260	BasePlotCompositeWidget::mainMenuPushButtonClicked()
246	261	{
247		//qDebug() << "ENTER";
	262	// qDebug() << "ENTER";
248	263
249	264	//// Create the contextual menu that will show when the button is clicked (see
250	265	//// below).

252	267	createMainMenu();
253	268	m_ui.mainMenuPushButton->showMenu();
254	269
255		//qDebug() << "EXIT";
	270	// qDebug() << "EXIT";
256	271	}
257	272
258	273

492	507
493	508
494	509	void
495		BasePlotCompositeWidget::plotWidgetMouseReleaseEvent([
496		[maybe_unused]] const pappso::BasePlotContext &context)
	510	BasePlotCompositeWidget::plotWidgetMouseReleaseEvent(
	511	[[maybe_unused]] const pappso::BasePlotContext &context)
497	512	{
498	513	// qDebug();
499	514

841	856	ProcessingFlow *processing_flow_p =
842	857	getProcessingFlowPtrForPlottable(source_plottable_p);
843	858
	859	// Set the default ms frag spec.
	860	processing_flow_p->setDefaultMsFragmentationSpec(ms_fragmentation_spec);
	861
	862	qDebug() << "Now setting the MS level to the spin box.";
	863
	864	// Change the MS level value in the spinbox.
	865	// But we need to disconnect the spin box' value changed signal, because
	866	// otherwise, the msLevelValueChanged() is called and it will update the ms
	867	// frag spec's ms level again.
	868
	869	disconnect(m_ui.msLevelSpinBox,
	870	QOverload<int>::of(&QSpinBox::valueChanged),
	871	this,
	872	&BasePlotCompositeWidget::msLevelValueChanged);
	873
	874	m_ui.msLevelSpinBox->setValue(ms_fragmentation_spec.getMsLevel());
	875
	876	// And connect back
	877	connect(m_ui.msLevelSpinBox,
	878	QOverload<int>::of(&QSpinBox::valueChanged),
	879	this,
	880	&BasePlotCompositeWidget::msLevelValueChanged);
	881
	882
	883	}
	884
	885
	886	void
	887	BasePlotCompositeWidget::msLevelValueChanged(int value)
	888	{
	889	// The user has selected a new MS level value, we need to ensure that this
	890	// value is record in the MsFragmentationSpec.
	891
	892	qDebug() << "Value: " << value;
	893
	894	QCPAbstractPlottable *source_plottable_p =
	895	plottableToBeUsedAsIntegrationSource();
	896
	897	if(source_plottable_p == nullptr)
	898	{
	899	QMessageBox::information(
	900	this,
	901	"Please select one trace",
	902	"In order to set the MS level for the next integration, the source "
	903	"graph needs to be selected.",
	904	QMessageBox::StandardButton::Ok,
	905	QMessageBox::StandardButton::NoButton);
	906
	907	return;
	908	}
	909
	910	// Next get the processing flow for that specific graph.
	911
	912	ProcessingFlow *processing_flow_p =
	913	getProcessingFlowPtrForPlottable(source_plottable_p);
	914
	915	// Now get the MsFragmentationSpec out of that ProcessingFlow.
	916
	917	MsFragmentationSpec ms_fragmentation_spec =
	918	processing_flow_p->getDefaultMsFragmentationSpec();
	919
	920	// Update the value of the MS level.
	921
	922	ms_fragmentation_spec.setMsLevel(value);
	923
844	924	// And finally set the default ms frag spec.
845	925	processing_flow_p->setDefaultMsFragmentationSpec(ms_fragmentation_spec);
846	926	}
847	927
848	928
849		MzIntegrationParams
	929	pappso::MzIntegrationParams
850	930	BasePlotCompositeWidget::getMzIntegrationParams(
851	931	const QCPAbstractPlottable *plottable_p)
852	932	{

860	940	// Now extract mz integration parameters from where they sit. That might
861	941	// be multiple places.
862	942
863		MzIntegrationParams mz_integration_params;
	943	pappso::MzIntegrationParams mz_integration_params;
864	944
865	945	// First check if the processing flow has default mz integration params.
866	946

871	951	// Check if there is at least one step in the flow that has mz integration
872	952	// params set.
873	953
874		const MzIntegrationParams *most_recent_mz_integration_params_p =
	954	const pappso::MzIntegrationParams *most_recent_mz_integration_params_p =
875	955	processing_flow.mostRecentMzIntegrationParams();
876	956
877	957	if(most_recent_mz_integration_params_p == nullptr)

935	1015	}
936	1016
937	1017	// Get the mz integration params for the plottable.
938		MzIntegrationParams mz_integration_params =
	1018	pappso::MzIntegrationParams mz_integration_params =
939	1019	getMzIntegrationParams(source_plottable_p);
940	1020
941	1021	// qDebug().noquote() << "Found mz integration params:"

972	1052
973	1053	mp_mzIntegrationParamsDlg->show();
974	1054	}
975		} // namespace minexpert
	1055	}
976	1056
977	1057
978	1058	void
979	1059	BasePlotCompositeWidget::mzIntegrationParamsChanged(
980		MzIntegrationParams mz_integration_params)
	1060	pappso::MzIntegrationParams mz_integration_params)
981	1061	{
982	1062	// qDebug();
983	1063

+9

-6

src/gui/BasePlotCompositeWidget.hpp less more

2	2	*
3	3	* msXpertSuite - mass spectrometry software suite
4	4	* -----------------------------------------------
5		* Copyright(C) 2009,...,2018 Filippo Rusconi
	5	* Copyright (C) 2009--2020 Filippo Rusconi
6	6	*
7	7	* http://www.msxpertsuite.org
8	8	*

44	44
45	45	/////////////////////// pappsomspp includes
46	46	#include <pappsomspp/widget/plotwidget/baseplotwidget.h>
	47	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
47	48
48	49
49	50	/////////////////////// Local includes
50	51	#include "ui_BasePlotCompositeWidget.h"
51	52	#include "../nongui/MsRunDataSet.hpp"
52	53	#include "../nongui/ProcessingFlow.hpp"
53		#include "../nongui/MzIntegrationParams.hpp"
54	54	#include "../nongui/AnalysisPreferences.hpp"
	55	#include "MzIntegrationParamsDlg.hpp"
55	56
56	57
57	58	namespace msxps

61	62
62	63	class BasePlotWnd;
63	64	class MsFragmentationSpecDlg;
64		class MzIntegrationParamsDlg;
	65	//class pappso::MzIntegrationParamsDlg;
65	66	class ProcessingFlowViewerDlg;
66	67
67	68

106	107
107	108	virtual void
108	109	msFragmentationSpecReady(const MsFragmentationSpec &ms_fragmentation_spec);
109		void setMzIntegrationParams(const MzIntegrationParams &mz_integration_params);
	110	void setMzIntegrationParams(const pappso::MzIntegrationParams &mz_integration_params);
110	111
111	112	public slots:
112	113

123	124	virtual void plottableSelectionChanged(QCPAbstractPlottable *plottable_p,
124	125	bool is_selected);
125	126
126		void mzIntegrationParamsChanged(MzIntegrationParams mz_integration_params);
	127	void mzIntegrationParamsChanged(pappso::MzIntegrationParams mz_integration_params);
127	128
128	129	virtual void newTicIntensityCalculated(double tic_intensity) const;
129	130	virtual void resetTicIntensity();
130	131
131		MzIntegrationParams
	132	pappso::MzIntegrationParams
132	133	getMzIntegrationParams(const QCPAbstractPlottable *plottable_p);
133	134	void msFragmentationSpecChanged(MsFragmentationSpec ms_fragmentation_spec);
134	135

190	191	QString craftAnalysisStanza(const pappso::BasePlotContext &context);
191	192
192	193	void setPlottingColor(QCPAbstractPlottable *plottable_p, const QColor &color);
	194
	195	void msLevelValueChanged(int value);
193	196
194	197	signals:
195	198

+6

-4

src/gui/BasePlotWnd.cpp less more

485	485	{
486	486	// qDebug();
487	487
488		MzIntegrationParams mz_integration_params;
	488	pappso::MzIntegrationParams mz_integration_params;
489	489
490	490	MzIntegrationParamsDlg *mz_integration_params_dlg_p =
491	491	new MzIntegrationParamsDlg(this, mz_integration_params, Qt::black);

509	509
510	510	void
511	511	BasePlotWnd::mzIntegrationParamsChanged(
512		MzIntegrationParams mz_integration_params)
	512	pappso::MzIntegrationParams mz_integration_params)
513	513	{
514	514	// We now know what are the mz integ params. We need to propagate them to all
515	515	// the pinned-down widgets.

535	535	// know some params like the smallest/greatest m/z bin, for example.
536	536	// Then, we'll update it with the new params set here.
537	537
538		MzIntegrationParams iter_mz_integration_params =
	538	pappso::MzIntegrationParams iter_mz_integration_params =
539	539	processing_flow_p->getDefaultMzIntegrationParams();
540	540
541	541	// Now modify the values according to the new settings:

554	554	processing_flow_p->setDefaultMzIntegrationParams(
555	555	iter_mz_integration_params);
556	556
557		MzIntegrationParams mz_integration_params =
	557	pappso::MzIntegrationParams mz_integration_params =
558	558	processing_flow_p->getDefaultMzIntegrationParams();
559	559
560	560	// qDebug() << "Set the mz integration params to one plottable:"

871	871	new QualifiedMassSpectrumVectorMassDataIntegratorToTicInt(
872	872	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_sp);
873	873
	874	mass_data_integrator_p->setMaxThreadUseCount(mp_programWindow->getMaxThreadUseCount());
	875
874	876	// Ensure the mass data integrator messages are used.
875	877
876	878	connect(

+2

-1

src/gui/BasePlotWnd.hpp less more

40	40
41	41
42	42	/////////////////////// pappsomspp includes
	43	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
43	44
44	45
45	46	/////////////////////// Local includes

122	123	void savePinnedPlotsToGraphicsFile();
123	124
124	125	void setMzIntegrationParamsForAllPlotWidgets();
125		void mzIntegrationParamsChanged(MzIntegrationParams mz_integration_params);
	126	void mzIntegrationParamsChanged(pappso::MzIntegrationParams mz_integration_params);
126	127
127	128	void setMsFragmentationSpecForAllPlotWidgets();
128	129	void msFragmentationSpecChanged(MsFragmentationSpec ms_fragmentation_spec);

+2

-2

src/gui/BaseTracePlotCompositeWidget.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

431	431	// Now we need to set the parameters of the SavGol filter.
432	432
433	433	// Get the mz integration params for the plottable.
434		MzIntegrationParams mz_integration_params =
	434	pappso::MzIntegrationParams mz_integration_params =
435	435	getMzIntegrationParams(source_plottable_p);
436	436
437	437	pappso::SavGolParams sav_gol_params = mz_integration_params.getSavGolParams();

+2

-3

src/gui/BaseTracePlotCompositeWidget.hpp less more

2	2	*
3	3	* msXpertSuite - mass spectrometry software suite
4	4	* -----------------------------------------------
5		* Copyright(C) 2009,...,2018 Filippo Rusconi
	5	* Copyright (C) 2009--2020 Filippo Rusconi
6	6	*
7	7	* http://www.msxpertsuite.org
8	8	*

52	52	#include "BasePlotCompositeWidget.hpp"
53	53	#include "../nongui/MsRunDataSet.hpp"
54	54	#include "../nongui/ProcessingFlow.hpp"
55		#include "../nongui/MzIntegrationParams.hpp"
	55	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
56	56
57	57
58	58	namespace msxps

62	62
63	63	class BaseTracePlotWnd;
64	64	class MsFragmentationSpecDlg;
65		class MzIntegrationParamsDlg;
66	65
67	66
68	67	// The BaseTracePlotCompositeWidget class is aimed at receiving QCPGraph_s, not

+1

-1

src/gui/ConsoleWnd.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/ConsoleWnd.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+5

-5

src/gui/DriftSpecMassSpecColorMapPlotCompositeWidget.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

390	390	// This is a multi-layer work: the graph has a ProcessingFlow associated
391	391	// to it via the m_graphProcessingFlowMap. We have gotten it above.
392	392
393		// Extract from it the default MzIntegrationParams:
394
395		MzIntegrationParams mz_integration_params =
	393	// Extract from it the default pappso::MzIntegrationParams:
	394
	395	pappso::MzIntegrationParams mz_integration_params =
396	396	local_processing_flow.getDefaultMzIntegrationParams();
397	397
398	398	// If it is not valid, then try mz integration params from the various

426	426	if(m_ui.integrateToDtMzPushButton->isChecked() \|\|
427	427	m_ui.integrateToRtMzPushButton->isChecked())
428	428	{
429		mz_integration_params.setBinningType(BinningType::NONE);
	429	mz_integration_params.setBinningType(pappso::BinningType::NONE);
430	430	mz_integration_params.setDecimalPlaces(0);
431	431	}
432	432

+1

-1

src/gui/DriftSpecMassSpecColorMapPlotCompositeWidget.hpp less more

2	2	*
3	3	* msXpertSuite - mass spectrometry software suite
4	4	* -----------------------------------------------
5		* Copyright(C) 2009,...,2018 Filippo Rusconi
	5	* Copyright (C) 2009--2020 Filippo Rusconi
6	6	*
7	7	* http://www.msxpertsuite.org
8	8	*

+2

-0

src/gui/DriftSpecMassSpecColorMapWnd.cpp less more

152	152	*mass_data_integrator_p =
153	153	new QualifiedMassSpectrumVectorMassDataIntegratorToDtRtMz(
154	154	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_sp);
	155
	156	mass_data_integrator_p->setMaxThreadUseCount(mp_programWindow->getMaxThreadUseCount());
155	157
156	158	// Ensure the mass data integrator messages are used.
157	159

+7

-6

src/gui/DriftSpecTracePlotCompositeWidget.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

41	41
42	42	/////////////////////// pappsomspp includes
43	43	#include <pappsomspp/widget/plotwidget/driftspectraceplotwidget.h>
	44	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
44	45
45	46
46	47	/////////////////////// Local includes

315	316	// This is a multi-layer work: the graph has a ProcessingFlow associated
316	317	// to it via the m_graphProcessingFlowMap. We have gotten it above.
317	318
318		// Extract from it the default MzIntegrationParams:
319
320		MzIntegrationParams mz_integration_params =
	319	// Extract from it the default pappso::MzIntegrationParams:
	320
	321	pappso::MzIntegrationParams mz_integration_params =
321	322	local_processing_flow.getDefaultMzIntegrationParams();
322	323
323	324	// If it is not valid, then try mz integration params from the various

350	351	// here. We need to reduce the resolution to integer resolution.
351	352	if(m_ui.integrateToDtMzPushButton->isChecked())
352	353	{
353		mz_integration_params.setBinningType(BinningType::NONE);
	354	mz_integration_params.setBinningType(pappso::BinningType::NONE);
354	355	mz_integration_params.setDecimalPlaces(0);
355	356	}
356	357

452	453
453	454	processing_step_p->newSpec(ProcessingType("DT_TO_MZ"), processing_spec_p);
454	455
455		MzIntegrationParams mz_integration_params =
	456	pappso::MzIntegrationParams mz_integration_params =
456	457	local_processing_flow.getDefaultMzIntegrationParams();
457	458
458	459	// If it is not valid, then try mz integration params from the various

+1

-1

src/gui/DriftSpecTracePlotCompositeWidget.hpp less more

2	2	*
3	3	* msXpertSuite - mass spectrometry software suite
4	4	* -----------------------------------------------
5		* Copyright(C) 2009,...,2018 Filippo Rusconi
	5	* Copyright (C) 2009--2020 Filippo Rusconi
6	6	*
7	7	* http://www.msxpertsuite.org
8	8	*

+2

-0

src/gui/DriftSpecTracePlotWnd.cpp less more

151	151	QualifiedMassSpectrumVectorMassDataIntegratorToDt *mass_data_integrator_p =
152	152	new QualifiedMassSpectrumVectorMassDataIntegratorToDt(
153	153	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_sp);
	154
	155	mass_data_integrator_p->setMaxThreadUseCount(mp_programWindow->getMaxThreadUseCount());
154	156
155	157	// Ensure the mass data integrator messages are used.
156	158

+2

-2

src/gui/IsoSpecDlg.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

659	659	if(match.hasMatch())
660	660	continue;
661	661
662		QStringList dataStringList = line.split("\t", QString::SkipEmptyParts);
	662	QStringList dataStringList = line.split("\t", Qt::SkipEmptyParts);
663	663
664	664	if(dataStringList.size() <
665	665	static_cast<int>(IsoSpecTableViewColumns::TOTAL_COLUMNS))

+1

-1

src/gui/IsoSpecDlg.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/IsoSpecTableView.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/IsoSpecTableView.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/IsoSpecTableViewModel.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/IsoSpecTableViewModel.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+6

-6

src/gui/MassPeakShaperDlg.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

264	264
265	265	QString input_data_string = m_ui.inputDataPointsPlainTextEdit->toPlainText();
266	266	QStringList input_data_string_list =
267		input_data_string.split("\n", QString::SkipEmptyParts);
	267	input_data_string.split("\n", Qt::SkipEmptyParts);
268	268
269	269	QString line;
270	270

335	335
336	336	QString input_data_string = m_ui.inputDataPointsPlainTextEdit->toPlainText();
337	337	QStringList input_data_string_list =
338		input_data_string.split("\n", QString::SkipEmptyParts);
	338	input_data_string.split("\n", Qt::SkipEmptyParts);
339	339
340	340	QString line;
341	341

373	373
374	374	QString input_data_string = m_ui.inputDataPointsPlainTextEdit->toPlainText();
375	375	QStringList input_data_string_list =
376		input_data_string.split("\n", QString::SkipEmptyParts);
	376	input_data_string.split("\n", Qt::SkipEmptyParts);
377	377
378	378	// The stratey is to convert each line into a DataPoint object that is
379	379	// appended to a vector. Then, the vector is sorted on the basis of the

807	807	}
808	808
809	809	m_mzIntegrationParams =
810		MzIntegrationParams(minMz,
	810	pappso::MzIntegrationParams(minMz,
811	811	maxMz,
812		BinningType::ARBITRARY,
	812	pappso::BinningType::ARBITRARY,
813	813	-1,
814	814	pappso::PrecisionFactory::getDaltonInstance(binSize),
815	815	false,

+3

-3

src/gui/MassPeakShaperDlg.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

44	44	/////////////////////// pappsomspp includes
45	45	#include <pappsomspp/trace/trace.h>
46	46	#include <pappsomspp/trace/maptrace.h>
	47	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
47	48
48	49
49	50	/////////////////////// Local includes
50	51	#include "ui_MassPeakShaperDlg.h"
51	52	#include "../nongui/MassPeakShaper.hpp"
52	53	#include "../nongui/MassPeakShaperConfig.hpp"
53		#include "../nongui/MzIntegrationParams.hpp"
54	54
55	55
56	56	namespace msxps

89	89
90	90	pappso::MapTrace m_mapTrace;
91	91
92		MzIntegrationParams m_mzIntegrationParams;
	92	pappso::MzIntegrationParams m_mzIntegrationParams;
93	93
94	94	// Each (m/z,i) pair (the i is in fact a probability that can later be
95	95	// converted to a relative intensity) in the text edit widget will be

+10

-10

src/gui/MassSpecTracePlotCompositeWidget.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

949	949	// This is a multi-layer work: the graph has a ProcessingFlow associated
950	950	// to it via the m_graphProcessingFlowMap. We have gotten it above.
951	951
952		// Extract from it the default MzIntegrationParams:
953
954		MzIntegrationParams mz_integration_params =
	952	// Extract from it the default pappso::MzIntegrationParams:
	953
	954	pappso::MzIntegrationParams mz_integration_params =
955	955	local_processing_flow.getDefaultMzIntegrationParams();
956	956
957	957	// If it is not valid, then try mz integration params from the various

986	986	if(m_ui.integrateToDtMzPushButton->isChecked() \|\|
987	987	m_ui.integrateToRtMzPushButton->isChecked())
988	988	{
989		mz_integration_params.setBinningType(BinningType::NONE);
	989	mz_integration_params.setBinningType(pappso::BinningType::NONE);
990	990	mz_integration_params.setDecimalPlaces(0);
991	991	}
992	992

1152	1152	// Since we are asked that an integration to a mass spectrum be
1153	1153	// performed, there must be a non-nullptr mz integration pointer in
1154	1154	// the step.
1155		const MzIntegrationParams *mz_integration_params_p =
	1155	const pappso::MzIntegrationParams *mz_integration_params_p =
1156	1156	processing_flow.mostRecentMzIntegrationParams();
1157	1157
1158	1158	if(mz_integration_params_p == nullptr)

1161	1161	"integration "
1162	1162	"params are not available in the processing flow.");
1163	1163
1164		if(mz_integration_params_p->getBinningType() == BinningType::NONE)
	1164	if(mz_integration_params_p->getBinningType() == pappso::BinningType::NONE)
1165	1165	{
1166	1166	pappso::TraceMinusCombiner trace_minus_combiner;
1167	1167	pappso::TracePlusCombiner trace_plus_combiner;

1229	1229	}
1230	1230	}
1231	1231	else if(mz_integration_params_p->getBinningType() ==
1232		BinningType::ARBITRARY)
	1232	pappso::BinningType::ARBITRARY)
1233	1233	{
1234	1234	pappso::MassSpectrumMinusCombiner mass_spectrum_minus_combiner;
1235	1235	pappso::MassSpectrumPlusCombiner mass_spectrum_plus_combiner;

1243	1243	// flow we get as parameters. Make a copy of them as we'll need
1244	1244	// to set the mz smallest and greatest values to them.
1245	1245
1246		const MzIntegrationParams *mz_integration_params_p =
	1246	const pappso::MzIntegrationParams *mz_integration_params_p =
1247	1247	processing_flow.mostRecentMzIntegrationParams();
1248	1248
1249	1249	if(mz_integration_params_p == nullptr)

1251	1251	"Pointer to the returned mz integration parameters cannot be "
1252	1252	"nullptr.");
1253	1253
1254		MzIntegrationParams copy_mz_integration_params =
	1254	pappso::MzIntegrationParams copy_mz_integration_params =
1255	1255	*processing_flow.mostRecentMzIntegrationParams();
1256	1256
1257	1257	// Because we are making an integration to a mass spectrum plot

+1

-1

src/gui/MassSpecTracePlotCompositeWidget.hpp less more

2	2	*
3	3	* msXpertSuite - mass spectrometry software suite
4	4	* -----------------------------------------------
5		* Copyright(C) 2009,...,2018 Filippo Rusconi
	5	* Copyright (C) 2009--2020 Filippo Rusconi
6	6	*
7	7	* http://www.msxpertsuite.org
8	8	*

+8

-6

src/gui/MassSpecTracePlotWnd.cpp less more

195	195
196	196	#if 0
197	197	// NO BINNING
198		MzIntegrationParams mz_integration_params(
	198	pappso::MzIntegrationParams mz_integration_params(
199	199	std::numeric_limits<double>::max(), // smallest m/z
200	200	std::numeric_limits<double>::min(), // greatest m/z
201		BinningType::NONE,
	201	pappso::BinningType::NONE,
202	202	-1, // decimal_places
203	203	pappso::PrecisionFactory::getDaltonInstance(0.05),
204	204	false, // apply_mz_shift

207	207	#endif
208	208	#if 0
209	209	// ARBITRARY BINNING
210		MzIntegrationParams mz_integration_params(
	210	pappso::MzIntegrationParams mz_integration_params(
211	211	std::numeric_limits<double>::max(),
212	212	std::numeric_limits<double>::min(),
213		BinningType::ARBITRARY,
	213	pappso::BinningType::ARBITRARY,
214	214	-1,
215	215	// pappso::PrecisionFactory::getDaltonInstance(0.05),
216	216	pappso::PrecisionFactory::getDaltonInstance(0.1),

231	231	// integration params.
232	232
233	233	// Set aside an object for later use.
234		const MzIntegrationParams *mz_integration_params_p =
	234	const pappso::MzIntegrationParams *mz_integration_params_p =
235	235	processing_flow.mostRecentStep()->getMzIntegrationParamsPtr();
236	236
237	237	if(mz_integration_params_p == nullptr \|\| !mz_integration_params_p->isValid())

495	495	// integration params.
496	496
497	497	// Set aside an object for later use.
498		const MzIntegrationParams *mz_integration_params_p =
	498	const pappso::MzIntegrationParams *mz_integration_params_p =
499	499	processing_flow.mostRecentStep()->getMzIntegrationParamsPtr();
500	500
501	501	if(mz_integration_params_p == nullptr \|\| !mz_integration_params_p->isValid())

521	521	QualifiedMassSpectrumVectorMassDataIntegratorToMz *mass_data_integrator_p =
522	522	new QualifiedMassSpectrumVectorMassDataIntegratorToMz(
523	523	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_sp);
	524
	525	mass_data_integrator_p->setMaxThreadUseCount(mp_programWindow->getMaxThreadUseCount());
524	526
525	527	// Ensure the mass data integrator messages are used.
526	528

+1

-1

src/gui/MsRunDataSetTableView.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/MsRunDataSetTableView.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/MsRunDataSetTableViewItem.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/MsRunDataSetTableViewItem.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/MsRunDataSetTableViewModel.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/MsRunDataSetTableViewModel.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+7

-7

src/gui/MsRunDataSetTableViewProxyModel.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

1102	1102	// single-element list containing this string.
1103	1103
1104	1104	QStringList mz_value_string_list(
1105		data.split(';', QString::SkipEmptyParts));
	1105	data.split(';', Qt::SkipEmptyParts));
1106	1106
1107	1107	if(!mz_value_string_list.isEmpty())
1108	1108	{

1212	1212	// single-element list containing this string.
1213	1213
1214	1214	QStringList cell_data_z_value_string_list(
1215		cell_data.split(';', QString::SkipEmptyParts));
	1215	cell_data.split(';', Qt::SkipEmptyParts));
1216	1216
1217	1217	if(!cell_data_z_value_string_list.isEmpty())
1218	1218	{

1323	1323	// single-element list containing this string.
1324	1324
1325	1325	QStringList z_value_list_left(
1326		leftData.toString().split(';', QString::SkipEmptyParts));
	1326	leftData.toString().split(';', Qt::SkipEmptyParts));
1327	1327
1328	1328	// qDebug() << "left_value_string_list:" << z_value_list_left;
1329	1329

1335	1335	// qDebug() << "left_value_string:" << left_value_string;
1336	1336
1337	1337	QStringList z_value_list_right(
1338		rightData.toString().split(';', QString::SkipEmptyParts));
	1338	rightData.toString().split(';', Qt::SkipEmptyParts));
1339	1339
1340	1340	if(z_value_list_right.isEmpty())
1341	1341	return false;

1389	1389	// single-element list containing this string.
1390	1390
1391	1391	QStringList mz_value_list_left(
1392		leftData.toString().split(';', QString::SkipEmptyParts));
	1392	leftData.toString().split(';', Qt::SkipEmptyParts));
1393	1393
1394	1394	// qDebug() << "left_value_string_list:" << mz_value_list_left;
1395	1395

1401	1401	// qDebug() << "left_value_string:" << left_value_string;
1402	1402
1403	1403	QStringList mz_value_list_right(
1404		rightData.toString().split(';', QString::SkipEmptyParts));
	1404	rightData.toString().split(';', Qt::SkipEmptyParts));
1405	1405
1406	1406	if(mz_value_list_right.isEmpty())
1407	1407	return false;

+1

-1

src/gui/MsRunDataSetTableViewProxyModel.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+2

-2

src/gui/MsRunDataSetTableViewWnd.cpp less more

410	410
411	411	void
412	412	MsRunDataSetTableViewWnd::mzIntegrationParamsChanged(
413		MzIntegrationParams mz_integration_params)
	413	pappso::MzIntegrationParams mz_integration_params)
414	414	{
415	415	// qDebug().noquote() << "The validated mz integration parameters:"
416	416	//<< mz_integration_params.toString();

420	420	// ms run data set upon creation of this window.
421	421
422	422	// Create a local copy of the processing flow's default mz integration params.
423		MzIntegrationParams local_mz_integration_params =
	423	pappso::MzIntegrationParams local_mz_integration_params =
424	424	m_processingFlow.getDefaultMzIntegrationParams();
425	425
426	426	// Update some of the values with the params after change.

+3

-3

src/gui/MsRunDataSetTableViewWnd.hpp less more

45	45	#include <pappsomspp/msrun/msrundatasettree.h>
46	46	#include <pappsomspp/massspectrum/qualifiedmassspectrum.h>
47	47	#include <pappsomspp/widget/precisionwidget/precisionwidget.h>
	48	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
48	49
49	50
50	51	/////////////////////// Local includes

53	54	#include "MsRunDataSetTableViewModel.hpp"
54	55	#include "MsRunDataSetTableViewProxyModel.hpp"
55	56	#include "../nongui/MsRunDataSet.hpp"
56		#include "../nongui/MzIntegrationParams.hpp"
57	57	#include "../nongui/ProcessingFlow.hpp"
	58	#include "MzIntegrationParamsDlg.hpp"
58	59
59	60
60	61	namespace msxps

66	67	class MsRunDataSet;
67	68	class ProgramWindow;
68	69	class MsFragmentationSpecDlg;
69		class MzIntegrationParamsDlg;
70	70
71	71
72	72	class MsRunDataSetTableViewWnd : public QMainWindow

92	92	void executeFilteringPushButtonClicked();
93	93
94	94	void showMzIntegrationParamsDlg();
95		void mzIntegrationParamsChanged(MzIntegrationParams mz_integration_params);
	95	void mzIntegrationParamsChanged(pappso::MzIntegrationParams mz_integration_params);
96	96
97	97	public slots:
98	98

+21

-22

src/gui/MzIntegrationParamsDlg.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

65	65
66	66	MzIntegrationParamsDlg::MzIntegrationParamsDlg(
67	67	QWidget *parent,
68		const MzIntegrationParams &mz_integration_params,
	68	const pappso::MzIntegrationParams &mz_integration_params,
69	69	const QColor &color)
70	70	: QDialog(parent),
71	71	m_mzIntegrationParams(mz_integration_params),

161	161	m_ui.arbitraryBinningRadioButton->setChecked(true);
162	162	});
163	163
164		m_ui.noBinningRadioButton->setChecked(m_mzIntegrationParams.m_binningType ==
165		BinningType::NONE);
	164	m_ui.noBinningRadioButton->setChecked(m_mzIntegrationParams.getBinningType() ==
	165	pappso::BinningType::NONE);
166	166	m_ui.arbitraryBinningRadioButton->setChecked(
167		m_mzIntegrationParams.m_binningType == BinningType::ARBITRARY);
	167	m_mzIntegrationParams.getBinningType() == pappso::BinningType::ARBITRARY);
168	168
169	169	connect(m_ui.arbitraryBinningRadioButton,
170	170	&QRadioButton::toggled,
171	171	[this](bool checked) { mp_precisionWidget->setEnabled(checked); });
172	172
173	173	m_ui.removeZeroValueCheckBox->setCheckState(
174		m_mzIntegrationParams.m_removeZeroValDataPoints ? Qt::Checked
	174	m_mzIntegrationParams.isRemoveZeroValDataPoints() ? Qt::Checked
175	175	: Qt::Unchecked);
176	176
177	177	/******* Savitzky-Golay parameters ********/

179	179	m_ui.savitzkyGolayGroupBox->setChecked(
180	180	m_mzIntegrationParams.isApplySavGolFilter());
181	181
182		m_ui.nlSpinBox->setValue(m_mzIntegrationParams.m_savGolParams.nL);
183		m_ui.nrSpinBox->setValue(m_mzIntegrationParams.m_savGolParams.nR);
184		m_ui.mSpinBox->setValue(m_mzIntegrationParams.m_savGolParams.m);
185		m_ui.ldSpinBox->setValue(m_mzIntegrationParams.m_savGolParams.lD);
	182	m_ui.nlSpinBox->setValue(m_mzIntegrationParams.getSavGolParams().nL);
	183	m_ui.nrSpinBox->setValue(m_mzIntegrationParams.getSavGolParams().nR);
	184	m_ui.mSpinBox->setValue(m_mzIntegrationParams.getSavGolParams().m);
	185	m_ui.ldSpinBox->setValue(m_mzIntegrationParams.getSavGolParams().lD);
186	186
187	187	connect(m_ui.applyPushButton,
188	188	&QPushButton::clicked,

201	201	if(radioButton == m_ui.noBinningRadioButton)
202	202	{
203	203	if(checked == true)
204		m_mzIntegrationParams.m_binningType = BinningType::NONE;
	204	m_mzIntegrationParams.setBinningType(pappso::BinningType::NONE);
205	205	}
206	206	else if(radioButton == m_ui.arbitraryBinningRadioButton)
207	207	{
208	208	if(checked == true)
209		m_mzIntegrationParams.m_binningType = BinningType::ARBITRARY;
	209	m_mzIntegrationParams.setBinningType(pappso::BinningType::ARBITRARY);
210	210	}
211	211	else
212	212	qFatal("Programming error.");

221	221
222	222
223	223	void
224		MzIntegrationParamsDlg::setBinningType(BinningType binningType)
225		{
226		if(binningType == BinningType::NONE)
	224	MzIntegrationParamsDlg::setBinningType(pappso::BinningType binningType)
	225	{
	226	if(binningType == pappso::BinningType::NONE)
227	227	m_ui.noBinningRadioButton->setChecked(true);
228		else if(binningType == BinningType::ARBITRARY)
	228	else if(binningType == pappso::BinningType::ARBITRARY)
229	229	m_ui.arbitraryBinningRadioButton->setChecked(true);
230	230	else
231	231	qFatal("Programming error.");

282	282	// qDebug();
283	283
284	284	// We need to check all the widgets, extract their information and then craft
285		// a MzIntegrationParams instance that we'll pass to any widget (the trace
	285	// a pappso::MzIntegrationParams instance that we'll pass to any widget (the trace
286	286	// plot composite widget) that might be listening. We make a new instance by
287	287	// copying the member instance because that member instance has data that are
288	288	// not configured in this dialog. We would loose those data if we created a
289	289	// default mz integration params instance.
290	290
291		MzIntegrationParams mz_integration_params(m_mzIntegrationParams);
	291	pappso::MzIntegrationParams mz_integration_params(m_mzIntegrationParams);
292	292
293	293	// qDebug().noquote() << "Before reading all the widgets' values::"
294	294	//<< mz_integration_params.toString();
295	295
296	296	if(m_ui.noBinningRadioButton->isChecked())
297		mz_integration_params.m_binningType = BinningType::NONE;
	297	mz_integration_params.setBinningType(pappso::BinningType::NONE);
298	298	else if(m_ui.arbitraryBinningRadioButton->isChecked())
299		mz_integration_params.m_binningType = BinningType::ARBITRARY;
	299	mz_integration_params.setBinningType(pappso::BinningType::ARBITRARY);
300	300
301	301	mz_integration_params.setPrecision(mp_precision);
302	302
303	303	mz_integration_params.setDecimalPlaces(m_ui.decimalPlacesSpinBox->value());
304	304
305		mz_integration_params.m_removeZeroValDataPoints =
306		m_ui.removeZeroValueCheckBox->isChecked();
	305	mz_integration_params.setRemoveZeroValDataPoints(m_ui.removeZeroValueCheckBox->isChecked());
307	306
308	307	if(m_ui.savitzkyGolayGroupBox->isChecked())
309	308	{

+6

-6

src/gui/MzIntegrationParamsDlg.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

47	47
48	48	/////////////////////// Local includes
49	49	#include "ui_MzIntegrationParamsDlg.h"
50		#include "../nongui/MzIntegrationParams.hpp"
	50	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
51	51
52	52
53	53	namespace msxps

63	63	public:
64	64	MzIntegrationParamsDlg(QWidget *parent = nullptr);
65	65	MzIntegrationParamsDlg(QWidget *parent,
66		const MzIntegrationParams &mz_integration_params,
	66	const pappso::MzIntegrationParams &mz_integration_params,
67	67	const QColor &color);
68	68	~MzIntegrationParamsDlg();
69	69

73	73	void keyPressEvent(QKeyEvent *event);
74	74
75	75	void show();
76		void setBinningType(BinningType binningType);
	76	void setBinningType(pappso::BinningType binningType);
77	77	void setBinSizePrecisionPtr(pappso::PrecisionPtr bin_size_precsion_p);
78	78	void setDecimalPlaces(int decimal_places);
79	79	void setRemoveZeroValDataPoints(bool apply);

87	87	void binningRadioButtonToggled(bool checked);
88	88
89	89	signals:
90		void mzIntegrationParamsChangedSignal(MzIntegrationParams params);
	90	void mzIntegrationParamsChangedSignal(pappso::MzIntegrationParams params);
91	91	void mzIntegrationParamsDlgShouldBeDestroyedSignal();
92	92
93	93	protected:
94	94	Ui::MzIntegrationParamsDlg m_ui;
95		MzIntegrationParams m_mzIntegrationParams;
	95	pappso::MzIntegrationParams m_mzIntegrationParams;
96	96	pappso::PrecisionWidget *mp_precisionWidget;
97	97	pappso::PrecisionPtr mp_precision =
98	98	pappso::PrecisionFactory::getDaltonInstance(0.05);

+1

-1

src/gui/OpenMsRunDataSetsDlg.cpp less more

662	662	std::vector<MsRunDataSetCstSPtr> vector_of_ms_run_data_set_csp;
663	663
664	664	QList<QListWidgetItem *> item_list =
665		m_ui.openMsRunDataSetsListWidget->findItems(".*", Qt::MatchRegExp);
	665	m_ui.openMsRunDataSetsListWidget->findItems(".*", Qt::MatchRegularExpression);
666	666
667	667	for(int iter = 0; iter < item_list.size(); ++iter)
668	668	{

+1

-1

src/gui/ProcessingFlowViewerDlg.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/ProcessingFlowViewerDlg.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+50

-1

src/gui/ProgramWindow.cpp less more

65	65	#include "MsRunDataSetTableViewProxyModel.hpp"
66	66	#include "../nongui/globals.hpp"
67	67	#include "MsRunReadTask.hpp"
68		#include "../nongui/MzIntegrationParams.hpp"
	68	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
69	69	#include "../nongui/MassDataIntegrator.hpp"
70	70	#include "ColorSelector.hpp"
71	71	#include "MsRunSelectorDlg.hpp"

426	426
427	427	mp_utilitiesMenu->addAction(action_p);
428	428
	429
	430	// Preferences menu
	431	mp_preferencesMenu = menuBar()->addMenu("&Preferences");
	432
	433	action_p =
	434	new QAction("Set max. thread count", dynamic_cast<QObject *>(this));
	435	action_p->setStatusTip("Set the maximum number of threads to be used for the integrations");
	436	action_p->setShortcut(tr("Ctrl+P, T"));
	437
	438	connect(
	439	action_p, &QAction::triggered, [this]()
	440	{
	441	std::size_t ideal_thread_count = QThread::idealThreadCount();
	442
	443	m_maxThreadUseCount = QInputDialog::getInt(this, "Set max. thread count",
	444	"Count", ideal_thread_count, 1, ideal_thread_count, 1);
	445
	446	//qDebug() << "Set the max. thread use count to : " << m_maxThreadUseCount;
	447	});
	448
	449	mp_preferencesMenu->addAction(action_p);
	450
	451
429	452	// Help menu
430	453	mp_helpMenu = menuBar()->addMenu("&Help");
431	454

477	500	dlg->show();
478	501
479	502	return dlg;
	503	}
	504
	505
	506	void
	507	ProgramWindow::setMaxThreadUseCount(std::size_t count)
	508	{
	509	m_maxThreadUseCount = count;
	510	}
	511
	512
	513	std::size_t
	514	ProgramWindow::getMaxThreadUseCount()
	515	{
	516	return m_maxThreadUseCount;
480	517	}
481	518
482	519

1372	1409	new QualifiedMassSpectrumVectorMassDataIntegratorToRt(
1373	1410	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_vector_sp);
1374	1411
	1412	mass_data_integrator_p->setMaxThreadUseCount(m_maxThreadUseCount);
	1413
1375	1414	MassDataIntegratorTask *mass_data_integrator_task_p =
1376	1415	new MassDataIntegratorTask();
1377	1416

1560	1599	ms_run_data_set_csp,
1561	1600	processing_flow,
1562	1601	vector_of_qualified_mass_spectra_sp);
	1602
	1603	mass_data_integrator_p->setMaxThreadUseCount(m_maxThreadUseCount);
1563	1604
1564	1605	MassDataIntegratorTask *mass_data_integrator_task_p =
1565	1606	new MassDataIntegratorTask();

1730	1771	new QualifiedMassSpectrumVectorMassDataIntegratorToMz(
1731	1772	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_vector_sp);
1732	1773
	1774	mass_data_integrator_p->setMaxThreadUseCount(m_maxThreadUseCount);
	1775
1733	1776	// qDebug() << "Receiving processing flow:" << processing_flow.toString();
1734	1777
1735	1778	MassDataIntegratorTask *mass_data_integrator_task_p =

1919	1962	new QualifiedMassSpectrumVectorMassDataIntegratorToTicInt(
1920	1963	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_vector_sp);
1921	1964
	1965	mass_data_integrator_p->setMaxThreadUseCount(m_maxThreadUseCount);
	1966
1922	1967	MassDataIntegratorTask *mass_data_integrator_task_p =
1923	1968	new MassDataIntegratorTask();
1924	1969

2114	2159	*mass_data_integrator_p =
2115	2160	new QualifiedMassSpectrumVectorMassDataIntegratorToDtRtMz(
2116	2161	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_vector_sp);
	2162
	2163	mass_data_integrator_p->setMaxThreadUseCount(m_maxThreadUseCount);
2117	2164
2118	2165	MassDataIntegratorTask *mass_data_integrator_task_p =
2119	2166	new MassDataIntegratorTask();

2375	2422	new QualifiedMassSpectrumVectorMassDataIntegratorToRtDt(
2376	2423	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_vector_sp);
2377	2424
	2425	mass_data_integrator_p->setMaxThreadUseCount(m_maxThreadUseCount);
	2426
2378	2427	MassDataIntegratorTask *mass_data_integrator_task_p =
2379	2428	new MassDataIntegratorTask();
2380	2429

+11

-4

src/gui/ProgramWindow.hpp less more

124	124	virtual ~ProgramWindow();
125	125
126	126	const QString &moduleName() const;
	127
	128	void setMaxThreadUseCount(std::size_t count);
	129	std::size_t getMaxThreadUseCount();
127	130
128	131	bool openMassSpectrometryFileDlg(const QString &dir_name = QDir::homePath(),
129	132	bool full_in_memory = false);

324	327	*mass_data_integrator_p);
325	328
326	329	void integrateQualifiedMassSpectrumVectorToRtDtSignal(
327		QualifiedMassSpectrumVectorMassDataIntegratorToRtDt
328		*mass_data_integrator_p,
	330	QualifiedMassSpectrumVectorMassDataIntegratorToRtDt *mass_data_integrator_p,
329	331	pappso::DataKind data_kind);
330	332
331	333	void integrateQualifiedMassSpectrumVectorToDtRtMzSignal(

347	349
348	350	int m_selectedMsRunIndex = -1;
349	351
	352	// The user can limit the max number of threads to use. 0 is no limitation
	353	// (all the available threads are going to be used).
	354	std::size_t m_maxThreadUseCount = 0;
	355
350	356	// We need to track all the plot widgets and plottables. This tree aims at
351	357	// storing the structure of all the plottables in all the plot widgets, in all
352	358	// the windows, for all the ms run data sets.

363	369	MassSpecTracePlotWnd *mp_massSpecPlotWnd = nullptr;
364	370	DriftSpecTracePlotWnd *mp_driftSpecPlotWnd = nullptr;
365	371
366		DriftSpecMassSpecColorMapWnd *mp_driftSpecMassSpecColorMapWnd = nullptr;
367		TicXicChromMassSpecColorMapWnd *mp_ticXicChromMassSpecColorMapWnd = nullptr;
	372	DriftSpecMassSpecColorMapWnd *mp_driftSpecMassSpecColorMapWnd = nullptr;
	373	TicXicChromMassSpecColorMapWnd *mp_ticXicChromMassSpecColorMapWnd = nullptr;
368	374	TicXicChromDriftSpecColorMapWnd *mp_ticXicChromDriftSpecColorMapWnd = nullptr;
369	375
370	376	XicExtractionWnd *mp_xicExtractionWnd = nullptr;

397	403	QMenu *mp_fileMenu = nullptr;
398	404	QMenu *mp_windowsMenu = nullptr;
399	405	QMenu *mp_utilitiesMenu = nullptr;
	406	QMenu *mp_preferencesMenu = nullptr;
400	407	QMenu *mp_helpMenu = nullptr;
401	408	QAction *mp_openFullMsFileAct = nullptr;
402	409	QAction *mp_openStreamedMsFileAct = nullptr;

+1

-1

src/gui/SaveToGraphicsFileDlg.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/SaveToGraphicsFileDlg.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+14

-10

src/gui/TaskMonitorCompositeWidget.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

402	402
403	403	{
404	404
405		//#if 0
	405	bool result = true;
	406
	407	//#if 0
406	408	std::chrono::time_point<std::chrono::system_clock> now =
407	409	std::chrono::system_clock::now();
408	410

412	414	if(time_lag.count() >= m_timeLag)
413	415	{
414	416	m_lastTimePoint = now;
415		return true;
416		}
417
418		return false;
419		//#endif
420
421		// return true;
	417	result = true;
	418	}
	419
	420	//qDebug() << "Returning:" << result;
	421	//#endif
	422
	423	return result;
422	424	}
423	425
424	426

557	559	void
558	560	TaskMonitorCompositeWidget::setStatusText(QString text)
559	561	{
	562	//qDebug() << "m_isLocked:" << m_isLocked << "shouldUpdate:" << shouldUpdate();
	563
560	564	if(!m_isLocked && shouldUpdate())
561	565	m_ui.statusLineEdit->setText(text);
562	566	}

673	677	return text;
674	678	}
675	679
676		QStringList string_list = text.split("%c", QString::KeepEmptyParts);
	680	QStringList string_list = text.split("%c", Qt::KeepEmptyParts);
677	681
678	682	QString new_text;
679	683

+2

-2

src/gui/TaskMonitorCompositeWidget.hpp less more

2	2	*
3	3	* msXpertSuite - mass spectrometry software suite
4	4	* -----------------------------------------------
5		* Copyright(C) 2009,...,2018 Filippo Rusconi
	5	* Copyright (C) 2009--2020 Filippo Rusconi
6	6	*
7	7	* http://www.msxpertsuite.org
8	8	*

134	134	// Start with an unlocked widget.
135	135	bool m_isLocked = false;
136	136
137		double m_timeLag = 100; /* milliseconds */
	137	double m_timeLag = 50; /* milliseconds */
138	138	std::chrono::system_clock::time_point m_lastTimePoint;
139	139	double m_currentValue = 0;
140	140	QString craftStringIfFormattedText(const QString &text) const;

+5

-5

src/gui/TicXicChromDriftSpecColorMapPlotCompositeWidget.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

405	405	// This is a multi-layer work: the graph has a ProcessingFlow associated
406	406	// to it via the m_graphProcessingFlowMap. We have gotten it above.
407	407
408		// Extract from it the default MzIntegrationParams:
409
410		MzIntegrationParams mz_integration_params =
	408	// Extract from it the default pappso::MzIntegrationParams:
	409
	410	pappso::MzIntegrationParams mz_integration_params =
411	411	local_processing_flow.getDefaultMzIntegrationParams();
412	412
413	413	// If it is not valid, then try mz integration params from the various

441	441	if(m_ui.integrateToDtMzPushButton->isChecked() \|\|
442	442	m_ui.integrateToRtMzPushButton->isChecked())
443	443	{
444		mz_integration_params.setBinningType(BinningType::NONE);
	444	mz_integration_params.setBinningType(pappso::BinningType::NONE);
445	445	mz_integration_params.setDecimalPlaces(0);
446	446	}
447	447

+1

-1

src/gui/TicXicChromDriftSpecColorMapPlotCompositeWidget.hpp less more

2	2	*
3	3	* msXpertSuite - mass spectrometry software suite
4	4	* -----------------------------------------------
5		* Copyright(C) 2009,...,2018 Filippo Rusconi
	5	* Copyright (C) 2009--2020 Filippo Rusconi
6	6	*
7	7	* http://www.msxpertsuite.org
8	8	*

+2

-0

src/gui/TicXicChromDriftSpecColorMapWnd.cpp less more

161	161	QualifiedMassSpectrumVectorMassDataIntegratorToRtDt *mass_data_integrator_p =
162	162	new QualifiedMassSpectrumVectorMassDataIntegratorToRtDt(
163	163	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_sp);
	164
	165	mass_data_integrator_p->setMaxThreadUseCount(mp_programWindow->getMaxThreadUseCount());
164	166
165	167	// Ensure the mass data integrator messages are used.
166	168

+5

-5

src/gui/TicXicChromMassSpecColorMapPlotCompositeWidget.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

395	395	// This is a multi-layer work: the graph has a ProcessingFlow associated
396	396	// to it via the m_graphProcessingFlowMap. We have gotten it above.
397	397
398		// Extract from it the default MzIntegrationParams:
399
400		MzIntegrationParams mz_integration_params =
	398	// Extract from it the default pappso::MzIntegrationParams:
	399
	400	pappso::MzIntegrationParams mz_integration_params =
401	401	local_processing_flow.getDefaultMzIntegrationParams();
402	402
403	403	// If it is not valid, then try mz integration params from the various

431	431	if(m_ui.integrateToDtMzPushButton->isChecked() \|\|
432	432	m_ui.integrateToRtMzPushButton->isChecked())
433	433	{
434		mz_integration_params.setBinningType(BinningType::NONE);
	434	mz_integration_params.setBinningType(pappso::BinningType::NONE);
435	435	mz_integration_params.setDecimalPlaces(0);
436	436	}
437	437

+1

-1

src/gui/TicXicChromMassSpecColorMapPlotCompositeWidget.hpp less more

2	2	*
3	3	* msXpertSuite - mass spectrometry software suite
4	4	* -----------------------------------------------
5		* Copyright(C) 2009,...,2018 Filippo Rusconi
	5	* Copyright (C) 2009--2020 Filippo Rusconi
6	6	*
7	7	* http://www.msxpertsuite.org
8	8	*

+2

-0

src/gui/TicXicChromMassSpecColorMapWnd.cpp less more

150	150	*mass_data_integrator_p =
151	151	new QualifiedMassSpectrumVectorMassDataIntegratorToDtRtMz(
152	152	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_sp);
	153
	154	mass_data_integrator_p->setMaxThreadUseCount(mp_programWindow->getMaxThreadUseCount());
153	155
154	156	// Ensure the mass data integrator messages are used.
155	157

+6

-6

src/gui/TicXicChromTracePlotCompositeWidget.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

399	399	// This is a multi-layer work: the graph has a ProcessingFlow associated
400	400	// to it via the m_graphProcessingFlowMap. We have gotten it above.
401	401
402		// Extract from it the default MzIntegrationParams:
403
404		MzIntegrationParams mz_integration_params =
	402	// Extract from it the default pappso::MzIntegrationParams:
	403
	404	pappso::MzIntegrationParams mz_integration_params =
405	405	local_processing_flow.getDefaultMzIntegrationParams();
406	406
407	407	// If it is not valid, then try mz integration params from the various

411	411	// qDebug()
412	412	//<< "The processing flow's default mz integ params are not valid.";
413	413
414		const MzIntegrationParams *mz_integration_params_p =
	414	const pappso::MzIntegrationParams *mz_integration_params_p =
415	415	local_processing_flow.mostRecentMzIntegrationParams();
416	416
417	417	if(mz_integration_params_p != nullptr)

438	438	if(m_ui.integrateToDtMzPushButton->isChecked() \|\|
439	439	m_ui.integrateToRtMzPushButton->isChecked())
440	440	{
441		mz_integration_params.setBinningType(BinningType::NONE);
	441	mz_integration_params.setBinningType(pappso::BinningType::NONE);
442	442	mz_integration_params.setDecimalPlaces(0);
443	443	}
444	444

+1

-1

src/gui/TicXicChromTracePlotCompositeWidget.hpp less more

2	2	*
3	3	* msXpertSuite - mass spectrometry software suite
4	4	* -----------------------------------------------
5		* Copyright(C) 2009,...,2018 Filippo Rusconi
	5	* Copyright (C) 2009--2020 Filippo Rusconi
6	6	*
7	7	* http://www.msxpertsuite.org
8	8	*

+6

-4

src/gui/TicXicChromTracePlotWnd.cpp less more

497	497	qualified_mass_spectra_sp,
498	498	const ProcessingFlow &processing_flow)
499	499	{
500		qDebug().noquote() << "Integrating to RT with processing flow:"
501		<< processing_flow.toString();
	500	//qDebug().noquote() << "Integrating to RT with processing flow:"
	501	//<< processing_flow.toString();
502	502
503	503	// Get the ms run data set that for the graph we are going to base the
504	504	// integration on.

526	526	if(!qualified_mass_spectra_count)
527	527	return;
528	528
529		qDebug() << "The number of remaining mass spectra:"
530		<< qualified_mass_spectra_count;
	529	//qDebug() << "The number of remaining mass spectra:"
	530	//<< qualified_mass_spectra_count;
531	531
532	532	// Now start the actual integration work.
533	533

536	536	QualifiedMassSpectrumVectorMassDataIntegratorToRt *mass_data_integrator_p =
537	537	new QualifiedMassSpectrumVectorMassDataIntegratorToRt(
538	538	ms_run_data_set_csp, processing_flow, qualified_mass_spectra_sp);
	539
	540	mass_data_integrator_p->setMaxThreadUseCount(mp_programWindow->getMaxThreadUseCount());
539	541
540	542	// Ensure the mass data integrator messages are used.
541	543

+1

-1

src/gui/XicExtractionWnd.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/gui/XicExtractionWnd.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+288

-266

src/gui/ui/BasePlotCompositeWidget.ui less more

423	423	<property name="spacing">
424	424	<number>1</number>
425	425	</property>
426		<item row="8" column="0">
427		<widget class="QPushButton" name="integrateToDtMzPushButton">
428		<property name="sizePolicy">
429		<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
430		<horstretch>0</horstretch>
431		<verstretch>0</verstretch>
432		</sizepolicy>
433		</property>
434		<property name="minimumSize">
435		<size>
436		<width>20</width>
437		<height>20</height>
438		</size>
439		</property>
440		<property name="toolTip">
441		<string>Integration will generate a mass spectrum /drift spectrum colormap</string>
442		</property>
443		<property name="text">
444		<string/>
445		</property>
446		<property name="icon">
447		<iconset resource="../../../minexpert2.qrc">
448		<normaloff>:/images/integrate-to-dt-mz-pushbutton-32x32.png</normaloff>:/images/integrate-to-dt-mz-pushbutton-32x32.png</iconset>
449		</property>
450		<property name="iconSize">
451		<size>
452		<width>16</width>
453		<height>16</height>
454		</size>
455		</property>
456		<property name="shortcut">
457		<string>Ctrl+O, Ctrl+D, Ctrl+C</string>
458		</property>
459		<property name="checkable">
460		<bool>true</bool>
461		</property>
462		<property name="autoExclusive">
463		<bool>true</bool>
464		</property>
465		<property name="flat">
466		<bool>true</bool>
467		</property>
468		</widget>
469		</item>
470		<item row="5" column="0">
471		<widget class="QPushButton" name="integrateToRtPushButton">
472		<property name="sizePolicy">
473		<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
474		<horstretch>0</horstretch>
475		<verstretch>0</verstretch>
476		</sizepolicy>
477		</property>
478		<property name="minimumSize">
479		<size>
480		<width>20</width>
481		<height>20</height>
482		</size>
483		</property>
484		<property name="toolTip">
485		<string>Integration will generate a TIC/XIC chromatogram trace (Ctrl-O,Ctrl-R)</string>
486		</property>
487		<property name="text">
488		<string/>
489		</property>
490		<property name="icon">
491		<iconset resource="../../../minexpert2.qrc">
492		<normaloff>:/images/integrate-to-rt-pushbutton-32x32.png</normaloff>:/images/integrate-to-rt-pushbutton-32x32.png</iconset>
493		</property>
494		<property name="iconSize">
495		<size>
496		<width>16</width>
497		<height>16</height>
498		</size>
499		</property>
500		<property name="shortcut">
501		<string>Ctrl+O, Ctrl+R</string>
502		</property>
503		<property name="checkable">
504		<bool>true</bool>
505		</property>
506		<property name="autoExclusive">
507		<bool>true</bool>
508		</property>
509		<property name="flat">
510		<bool>true</bool>
511		</property>
512		</widget>
513		</item>
514		<item row="0" column="0">
515		<widget class="QPushButton" name="duplicateTracePushButton">
516		<property name="enabled">
517		<bool>true</bool>
518		</property>
519		<property name="sizePolicy">
520		<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
521		<horstretch>0</horstretch>
522		<verstretch>0</verstretch>
523		</sizepolicy>
524		</property>
525		<property name="minimumSize">
526		<size>
527		<width>20</width>
528		<height>20</height>
529		</size>
530		</property>
531		<property name="maximumSize">
532		<size>
533		<width>32</width>
534		<height>32</height>
535		</size>
536		</property>
537		<property name="focusPolicy">
538		<enum>Qt::NoFocus</enum>
539		</property>
540		<property name="toolTip">
541		<string>Duplication of the trace (Ctrl-O,Ctrl-U)</string>
542		</property>
543		<property name="text">
544		<string/>
545		</property>
546		<property name="icon">
547		<iconset resource="../../../minexpert2.qrc">
548		<normaloff>:/images/duplicate-trace-pushbutton-32x32.png</normaloff>:/images/duplicate-trace-pushbutton-32x32.png</iconset>
549		</property>
550		<property name="iconSize">
551		<size>
552		<width>16</width>
553		<height>16</height>
554		</size>
555		</property>
556		<property name="shortcut">
557		<string>Ctrl+O, Ctrl+U</string>
558		</property>
559		<property name="checkable">
560		<bool>false</bool>
561		</property>
562		<property name="autoExclusive">
563		<bool>false</bool>
564		</property>
565		<property name="flat">
566		<bool>false</bool>
567		</property>
568		</widget>
569		</item>
570		<item row="7" column="0">
571		<widget class="QPushButton" name="integrateToRtMzPushButton">
572		<property name="sizePolicy">
573		<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
574		<horstretch>0</horstretch>
575		<verstretch>0</verstretch>
576		</sizepolicy>
577		</property>
578		<property name="minimumSize">
579		<size>
580		<width>20</width>
581		<height>20</height>
582		</size>
583		</property>
584		<property name="toolTip">
585		<string>Integration will generate a TIC\|XIC chromatogram / mass spectrum colormap</string>
586		</property>
587		<property name="text">
588		<string/>
589		</property>
590		<property name="icon">
591		<iconset resource="../../../minexpert2.qrc">
592		<normaloff>:/images/integrate-to-rt-mz-pushbutton-32x32.png</normaloff>:/images/integrate-to-rt-mz-pushbutton-32x32.png</iconset>
593		</property>
594		<property name="iconSize">
595		<size>
596		<width>16</width>
597		<height>16</height>
598		</size>
599		</property>
600		<property name="shortcut">
601		<string>Ctrl+O, Ctrl+R, Ctrl+C</string>
602		</property>
603		<property name="checkable">
604		<bool>true</bool>
605		</property>
606		<property name="autoExclusive">
607		<bool>true</bool>
608		</property>
609		<property name="flat">
610		<bool>true</bool>
611		</property>
612		</widget>
613		</item>
614		<item row="10" column="0">
	426	<item row="2" column="0">
	427	<widget class="QPushButton" name="integrateToMzPushButton">
	428	<property name="sizePolicy">
	429	<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	430	<horstretch>0</horstretch>
	431	<verstretch>0</verstretch>
	432	</sizepolicy>
	433	</property>
	434	<property name="minimumSize">
	435	<size>
	436	<width>20</width>
	437	<height>20</height>
	438	</size>
	439	</property>
	440	<property name="toolTip">
	441	<string>Integration will generate a mass spectrum trace (Ctrl-O,Ctrl-M)</string>
	442	</property>
	443	<property name="text">
	444	<string/>
	445	</property>
	446	<property name="icon">
	447	<iconset resource="../../../minexpert2.qrc">
	448	<normaloff>:/images/integrate-to-mz-pushbutton-32x32.png</normaloff>:/images/integrate-to-mz-pushbutton-32x32.png</iconset>
	449	</property>
	450	<property name="iconSize">
	451	<size>
	452	<width>16</width>
	453	<height>16</height>
	454	</size>
	455	</property>
	456	<property name="shortcut">
	457	<string>Ctrl+O, Ctrl+M</string>
	458	</property>
	459	<property name="checkable">
	460	<bool>true</bool>
	461	</property>
	462	<property name="autoExclusive">
	463	<bool>true</bool>
	464	</property>
	465	<property name="flat">
	466	<bool>true</bool>
	467	</property>
	468	</widget>
	469	</item>
	470	<item row="4" column="0">
	471	<widget class="QPushButton" name="integrateToDtPushButton">
	472	<property name="sizePolicy">
	473	<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	474	<horstretch>0</horstretch>
	475	<verstretch>0</verstretch>
	476	</sizepolicy>
	477	</property>
	478	<property name="minimumSize">
	479	<size>
	480	<width>20</width>
	481	<height>20</height>
	482	</size>
	483	</property>
	484	<property name="toolTip">
	485	<string>Integration will generate a drift spectrum trace (Ctrl-O,Ctrl-D)</string>
	486	</property>
	487	<property name="text">
	488	<string/>
	489	</property>
	490	<property name="icon">
	491	<iconset resource="../../../minexpert2.qrc">
	492	<normaloff>:/images/integrate-to-dt-pushbutton-32x32.png</normaloff>:/images/integrate-to-dt-pushbutton-32x32.png</iconset>
	493	</property>
	494	<property name="iconSize">
	495	<size>
	496	<width>16</width>
	497	<height>16</height>
	498	</size>
	499	</property>
	500	<property name="shortcut">
	501	<string>Ctrl+O, Ctrl+D</string>
	502	</property>
	503	<property name="checkable">
	504	<bool>true</bool>
	505	</property>
	506	<property name="autoExclusive">
	507	<bool>true</bool>
	508	</property>
	509	<property name="flat">
	510	<bool>true</bool>
	511	</property>
	512	</widget>
	513	</item>
	514	<item row="11" column="0">
615	515	<spacer name="verticalSpacer5">
616	516	<property name="orientation">
617	517	<enum>Qt::Vertical</enum>

624	524	</property>
625	525	</spacer>
626	526	</item>
627		<item row="3" column="0">
628		<widget class="QPushButton" name="integrateToDtPushButton">
629		<property name="sizePolicy">
630		<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
631		<horstretch>0</horstretch>
632		<verstretch>0</verstretch>
633		</sizepolicy>
634		</property>
635		<property name="minimumSize">
636		<size>
637		<width>20</width>
638		<height>20</height>
639		</size>
640		</property>
641		<property name="toolTip">
642		<string>Integration will generate a drift spectrum trace (Ctrl-O,Ctrl-D)</string>
643		</property>
644		<property name="text">
645		<string/>
646		</property>
647		<property name="icon">
648		<iconset resource="../../../minexpert2.qrc">
649		<normaloff>:/images/integrate-to-dt-pushbutton-32x32.png</normaloff>:/images/integrate-to-dt-pushbutton-32x32.png</iconset>
650		</property>
651		<property name="iconSize">
652		<size>
653		<width>16</width>
654		<height>16</height>
655		</size>
656		</property>
657		<property name="shortcut">
658		<string>Ctrl+O, Ctrl+D</string>
	527	<item row="9" column="0">
	528	<widget class="QPushButton" name="integrateToDtMzPushButton">
	529	<property name="sizePolicy">
	530	<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	531	<horstretch>0</horstretch>
	532	<verstretch>0</verstretch>
	533	</sizepolicy>
	534	</property>
	535	<property name="minimumSize">
	536	<size>
	537	<width>20</width>
	538	<height>20</height>
	539	</size>
	540	</property>
	541	<property name="toolTip">
	542	<string>Integration will generate a mass spectrum /drift spectrum colormap</string>
	543	</property>
	544	<property name="text">
	545	<string/>
	546	</property>
	547	<property name="icon">
	548	<iconset resource="../../../minexpert2.qrc">
	549	<normaloff>:/images/integrate-to-dt-mz-pushbutton-32x32.png</normaloff>:/images/integrate-to-dt-mz-pushbutton-32x32.png</iconset>
	550	</property>
	551	<property name="iconSize">
	552	<size>
	553	<width>16</width>
	554	<height>16</height>
	555	</size>
	556	</property>
	557	<property name="shortcut">
	558	<string>Ctrl+O, Ctrl+D, Ctrl+C</string>
	559	</property>
	560	<property name="checkable">
	561	<bool>true</bool>
	562	</property>
	563	<property name="autoExclusive">
	564	<bool>true</bool>
	565	</property>
	566	<property name="flat">
	567	<bool>true</bool>
	568	</property>
	569	</widget>
	570	</item>
	571	<item row="6" column="0">
	572	<widget class="QPushButton" name="integrateToRtPushButton">
	573	<property name="sizePolicy">
	574	<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	575	<horstretch>0</horstretch>
	576	<verstretch>0</verstretch>
	577	</sizepolicy>
	578	</property>
	579	<property name="minimumSize">
	580	<size>
	581	<width>20</width>
	582	<height>20</height>
	583	</size>
	584	</property>
	585	<property name="toolTip">
	586	<string>Integration will generate a TIC/XIC chromatogram trace (Ctrl-O,Ctrl-R)</string>
	587	</property>
	588	<property name="text">
	589	<string/>
	590	</property>
	591	<property name="icon">
	592	<iconset resource="../../../minexpert2.qrc">
	593	<normaloff>:/images/integrate-to-rt-pushbutton-32x32.png</normaloff>:/images/integrate-to-rt-pushbutton-32x32.png</iconset>
	594	</property>
	595	<property name="iconSize">
	596	<size>
	597	<width>16</width>
	598	<height>16</height>
	599	</size>
	600	</property>
	601	<property name="shortcut">
	602	<string>Ctrl+O, Ctrl+R</string>
	603	</property>
	604	<property name="checkable">
	605	<bool>true</bool>
	606	</property>
	607	<property name="autoExclusive">
	608	<bool>true</bool>
	609	</property>
	610	<property name="flat">
	611	<bool>true</bool>
	612	</property>
	613	</widget>
	614	</item>
	615	<item row="8" column="0">
	616	<widget class="QPushButton" name="integrateToRtMzPushButton">
	617	<property name="sizePolicy">
	618	<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	619	<horstretch>0</horstretch>
	620	<verstretch>0</verstretch>
	621	</sizepolicy>
	622	</property>
	623	<property name="minimumSize">
	624	<size>
	625	<width>20</width>
	626	<height>20</height>
	627	</size>
	628	</property>
	629	<property name="toolTip">
	630	<string>Integration will generate a TIC\|XIC chromatogram / mass spectrum colormap</string>
	631	</property>
	632	<property name="text">
	633	<string/>
	634	</property>
	635	<property name="icon">
	636	<iconset resource="../../../minexpert2.qrc">
	637	<normaloff>:/images/integrate-to-rt-mz-pushbutton-32x32.png</normaloff>:/images/integrate-to-rt-mz-pushbutton-32x32.png</iconset>
	638	</property>
	639	<property name="iconSize">
	640	<size>
	641	<width>16</width>
	642	<height>16</height>
	643	</size>
	644	</property>
	645	<property name="shortcut">
	646	<string>Ctrl+O, Ctrl+R, Ctrl+C</string>
659	647	</property>
660	648	<property name="checkable">
661	649	<bool>true</bool>

669	657	</widget>
670	658	</item>
671	659	<item row="1" column="0">
672		<widget class="QPushButton" name="integrateToMzPushButton">
673		<property name="sizePolicy">
674		<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
675		<horstretch>0</horstretch>
676		<verstretch>0</verstretch>
677		</sizepolicy>
678		</property>
679		<property name="minimumSize">
680		<size>
681		<width>20</width>
682		<height>20</height>
683		</size>
684		</property>
685		<property name="toolTip">
686		<string>Integration will generate a mass spectrum trace (Ctrl-O,Ctrl-M)</string>
687		</property>
688		<property name="text">
689		<string/>
690		</property>
691		<property name="icon">
692		<iconset resource="../../../minexpert2.qrc">
693		<normaloff>:/images/integrate-to-mz-pushbutton-32x32.png</normaloff>:/images/integrate-to-mz-pushbutton-32x32.png</iconset>
694		</property>
695		<property name="iconSize">
696		<size>
697		<width>16</width>
698		<height>16</height>
699		</size>
700		</property>
701		<property name="shortcut">
702		<string>Ctrl+O, Ctrl+M</string>
703		</property>
704		<property name="checkable">
705		<bool>true</bool>
706		</property>
707		<property name="autoExclusive">
708		<bool>true</bool>
709		</property>
710		<property name="flat">
711		<bool>true</bool>
712		</property>
713		</widget>
714		</item>
715		<item row="6" column="0">
	660	<widget class="QPushButton" name="duplicateTracePushButton">
	661	<property name="enabled">
	662	<bool>true</bool>
	663	</property>
	664	<property name="sizePolicy">
	665	<sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	666	<horstretch>0</horstretch>
	667	<verstretch>0</verstretch>
	668	</sizepolicy>
	669	</property>
	670	<property name="minimumSize">
	671	<size>
	672	<width>20</width>
	673	<height>20</height>
	674	</size>
	675	</property>
	676	<property name="maximumSize">
	677	<size>
	678	<width>32</width>
	679	<height>32</height>
	680	</size>
	681	</property>
	682	<property name="focusPolicy">
	683	<enum>Qt::NoFocus</enum>
	684	</property>
	685	<property name="toolTip">
	686	<string>Duplication of the trace (Ctrl-O,Ctrl-U)</string>
	687	</property>
	688	<property name="text">
	689	<string/>
	690	</property>
	691	<property name="icon">
	692	<iconset resource="../../../minexpert2.qrc">
	693	<normaloff>:/images/duplicate-trace-pushbutton-32x32.png</normaloff>:/images/duplicate-trace-pushbutton-32x32.png</iconset>
	694	</property>
	695	<property name="iconSize">
	696	<size>
	697	<width>16</width>
	698	<height>16</height>
	699	</size>
	700	</property>
	701	<property name="shortcut">
	702	<string>Ctrl+O, Ctrl+U</string>
	703	</property>
	704	<property name="checkable">
	705	<bool>false</bool>
	706	</property>
	707	<property name="autoExclusive">
	708	<bool>false</bool>
	709	</property>
	710	<property name="flat">
	711	<bool>false</bool>
	712	</property>
	713	</widget>
	714	</item>
	715	<item row="7" column="0">
716	716	<widget class="QPushButton" name="integrateToIntPushButton">
717	717	<property name="sizePolicy">
718	718	<sizepolicy hsizetype="Fixed" vsizetype="Fixed">

756	756	</property>
757	757	</widget>
758	758	</item>
759		<item row="9" column="0">
	759	<item row="10" column="0">
760	760	<widget class="QPushButton" name="integrateToRtDtPushButton">
761	761	<property name="sizePolicy">
762	762	<sizepolicy hsizetype="Fixed" vsizetype="Fixed">

797	797	</property>
798	798	<property name="flat">
799	799	<bool>true</bool>
	800	</property>
	801	</widget>
	802	</item>
	803	<item row="0" column="0">
	804	<widget class="QSpinBox" name="msLevelSpinBox">
	805	<property name="toolTip">
	806	<string>Set MS level for next integration</string>
	807	</property>
	808	<property name="wrapping">
	809	<bool>false</bool>
	810	</property>
	811	<property name="buttonSymbols">
	812	<enum>QAbstractSpinBox::UpDownArrows</enum>
	813	</property>
	814	<property name="prefix">
	815	<string/>
	816	</property>
	817	<property name="minimum">
	818	<number>0</number>
	819	</property>
	820	<property name="maximum">
	821	<number>11</number>
800	822	</property>
801	823	</widget>
802	824	</item>

+29

-28

src/nongui/About_gpl_v30.hpp less more

0		/* BEGIN software license
1		*
2		* msXpertSuite - mass spectrometry software suite
3		* -----------------------------------------------
4		* Copyright(C) 2009, 2017 Filippo Rusconi
5		*
6		* http://www.msxpertsuite.org
7		*
8		* This file is part of the msXpertSuite project.
9		*
10		* The msXpertSuite project is the successor of the massXpert project. This
11		* project now includes various independent modules:
12		*
13		* - massXpert, model polymer chemistries and simulate mass spectrometric data;
14		* - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
15		*
16		* This program is free software: you can redistribute it and/or modify
17		* it under the terms of the GNU General Public License as published by
18		* the Free Software Foundation, either version 3 of the License, or
19		* (at your option) any later version.
20		*
21		* This program is distributed in the hope that it will be useful,
22		* but WITHOUT ANY WARRANTY; without even the implied warranty of
23		* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
24		* GNU General Public License for more details.
25		*
26		* You should have received a copy of the GNU General Public License
27		* along with this program. If not, see <http://www.gnu.org/licenses/>.
	0	/* BEGIN software license
	1	*
	2	* msXpertSuite - mass spectrometry software suite
	3	* -----------------------------------------------
	4	* Copyright (C) 2009--2020 Filippo Rusconi
	5	*
	6	* http://www.msxpertsuite.org
	7	*
	8	* This file is part of the msXpertSuite project.
	9	*
	10	* The msXpertSuite project is the successor of the massXpert project. This
	11	* project now includes various independent modules:
	12	*
	13	* - massXpert, model polymer chemistries and simulate mass spectrometric data;
	14	* - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
	15	*
	16	* This program is free software: you can redistribute it and/or modify
	17	* it under the terms of the GNU General Public License as published by
	18	* the Free Software Foundation, either version 3 of the License, or
	19	* (at your option) any later version.
	20	*
	21	* This program is distributed in the hope that it will be useful,
	22	* but WITHOUT ANY WARRANTY; without even the implied warranty of
	23	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	24	* GNU General Public License for more details.
	25	*
	26	* You should have received a copy of the GNU General Public License
	27	* along with this program. If not, see <http://www.gnu.org/licenses/>.
28	28	*
29	29	* END software license
30	30	*/
	31
31	32
32	33
33	34	namespace msxps

+1

-1

src/nongui/AnalysisPreferences.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/AnalysisPreferences.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/Atom.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/Atom.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+31

-27

src/nongui/AtomCount.cpp less more

0		/* msXpertSuite - mass spectrometry software suite
1		* -----------------------------------------------
2		* Copyright(C) 2016 Filippo Rusconi
3		*
4		* http://www.{site}.org
5		*
6		* This file is part of the msXpertSuite project.
7		*
8		* The msXpertSuite project is the successor of the massXpert project. This
9		* project now includes various independent modules:
10		* - massXpert, the original mass spectrometry environment software (greatly
11		* refactored code);
12		* - mobXpert, a module to process and mine mobility mass spectrometry data;
13		* - viewXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
14		*
15		* This program is free software: you can redistribute it and/or modify
16		* it under the terms of the GNU General Public License as published by
17		* the Free Software Foundation, either version 3 of the License, or
18		* (at your option) any later version.
19		*
20		* This program is distributed in the hope that it will be useful,
21		* but WITHOUT ANY WARRANTY; without even the implied warranty of
22		* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23		* GNU General Public License for more details.
24		*
25		* You should have received a copy of the GNU General Public License
26		* along with this program. If not, see <http://www.gnu.org/licenses/>.
	0	/* BEGIN software license
	1	*
	2	* msXpertSuite - mass spectrometry software suite
	3	* -----------------------------------------------
	4	* Copyright (C) 2009--2020 Filippo Rusconi
	5	*
	6	* http://www.msxpertsuite.org
	7	*
	8	* This file is part of the msXpertSuite project.
	9	*
	10	* The msXpertSuite project is the successor of the massXpert project. This
	11	* project now includes various independent modules:
	12	*
	13	* - massXpert, model polymer chemistries and simulate mass spectrometric data;
	14	* - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
	15	*
	16	* This program is free software: you can redistribute it and/or modify
	17	* it under the terms of the GNU General Public License as published by
	18	* the Free Software Foundation, either version 3 of the License, or
	19	* (at your option) any later version.
	20	*
	21	* This program is distributed in the hope that it will be useful,
	22	* but WITHOUT ANY WARRANTY; without even the implied warranty of
	23	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	24	* GNU General Public License for more details.
	25	*
	26	* You should have received a copy of the GNU General Public License
	27	* along with this program. If not, see <http://www.gnu.org/licenses/>.
	28	*
	29	* END software license
27	30	*/
	31
28	32
29	33
30	34	/////////////////////// Local includes

+25

-21

src/nongui/AtomCount.hpp less more

0		/* msXpertSuite - mass spectrometry software suite
1		* -----------------------------------------------
2		* Copyright(C) 2016 Filippo Rusconi
	0	/* BEGIN software license
3	1	*
4		* http://www.{site}.org
	2	* msXpertSuite - mass spectrometry software suite
	3	* -----------------------------------------------
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6		* This file is part of the msXpertSuite project.
	6	* http://www.msxpertsuite.org
7	7	*
8		* The msXpertSuite project is the successor of the massXpert project. This
9		* project now includes various independent modules:
10		* - massXpert, the original mass spectrometry environment software (greatly
11		* refactored code);
12		* - mobXpert, a module to process and mine mobility mass spectrometry data;
13		* - viewXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
	8	* This file is part of the msXpertSuite project.
14	9	*
15		* This program is free software: you can redistribute it and/or modify
16		* it under the terms of the GNU General Public License as published by
17		* the Free Software Foundation, either version 3 of the License, or
18		* (at your option) any later version.
	10	* The msXpertSuite project is the successor of the massXpert project. This
	11	* project now includes various independent modules:
19	12	*
20		* This program is distributed in the hope that it will be useful,
21		* but WITHOUT ANY WARRANTY; without even the implied warranty of
22		* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23		* GNU General Public License for more details.
	13	* - massXpert, model polymer chemistries and simulate mass spectrometric data;
	14	* - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
24	15	*
25		* You should have received a copy of the GNU General Public License
26		* along with this program. If not, see <http://www.gnu.org/licenses/>.
	16	* This program is free software: you can redistribute it and/or modify
	17	* it under the terms of the GNU General Public License as published by
	18	* the Free Software Foundation, either version 3 of the License, or
	19	* (at your option) any later version.
	20	*
	21	* This program is distributed in the hope that it will be useful,
	22	* but WITHOUT ANY WARRANTY; without even the implied warranty of
	23	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	24	* GNU General Public License for more details.
	25	*
	26	* You should have received a copy of the GNU General Public License
	27	* along with this program. If not, see <http://www.gnu.org/licenses/>.
	28	*
	29	* END software license
27	30	*/
	31
28	32
29	33
30	34	#pragma once

+1

-1

src/nongui/Formula.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/Formula.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/IsoSpecEntity.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/IsoSpecEntity.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/Isotope.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/Isotope.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MassDataIntegrator.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MassDataIntegrator.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MassPeakShaper.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MassPeakShaper.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MassPeakShaperConfig.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MassPeakShaperConfig.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MassSpecDataFileLoader.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MassSpecDataFileLoader.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+3

-3

src/nongui/MassSpectrumTreeNodeCombinerVisitor.cpp less more

66	66	MsRunDataSetCstSPtr ms_run_data_set_csp,
67	67	const ProcessingFlow &processing_flow,
68	68	pappso::MassSpectrumPlusCombinerSPtr &mass_spectrum_combiner_sp,
69		const MzIntegrationParams &mz_integration_params)
	69	const pappso::MzIntegrationParams &mz_integration_params)
70	70	: BaseMsRunDataSetTreeNodeVisitor(ms_run_data_set_csp, processing_flow),
71	71	msp_combiner(mass_spectrum_combiner_sp),
72	72	m_mzIntegrationParams(mz_integration_params)

130	130
131	131	void
132	132	MassSpectrumTreeNodeCombinerVisitor::setMzIntegrationParams(
133		const MzIntegrationParams &mz_integration_params)
	133	const pappso::MzIntegrationParams &mz_integration_params)
134	134	{
135	135	m_mzIntegrationParams = mz_integration_params;
136	136	}
137	137
138	138
139		const MzIntegrationParams &
	139	const pappso::MzIntegrationParams &
140	140	MassSpectrumTreeNodeCombinerVisitor::getMzIntegrationParams()
141	141	{
142	142	return m_mzIntegrationParams;

+5

-5

src/nongui/MassSpectrumTreeNodeCombinerVisitor.hpp less more

49	49	#include "ProcessingFlow.hpp"
50	50	#include "MsRunDataSet.hpp"
51	51	#include "BaseMsRunDataSetTreeNodeVisitor.hpp"
52		#include "MzIntegrationParams.hpp"
	52	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
53	53
54	54
55	55	namespace msxps

80	80	MsRunDataSetCstSPtr ms_run_data_set_csp,
81	81	const ProcessingFlow &processing_flow,
82	82	pappso::MassSpectrumPlusCombinerSPtr &mass_spectrum_combiner_sp,
83		const MzIntegrationParams &mz_integration_params);
	83	const pappso::MzIntegrationParams &mz_integration_params);
84	84
85	85	MassSpectrumTreeNodeCombinerVisitor(
86	86	const MassSpectrumTreeNodeCombinerVisitor &other);

93	93
94	94	const pappso::MapTrace &getMapTrace() const;
95	95
96		void setMzIntegrationParams(const MzIntegrationParams &mz_integration_params);
97		const MzIntegrationParams &getMzIntegrationParams();
	96	void setMzIntegrationParams(const pappso::MzIntegrationParams &mz_integration_params);
	97	const pappso::MzIntegrationParams &getMzIntegrationParams();
98	98
99	99	MassSpectrumTreeNodeCombinerVisitor &
100	100	operator=(const MassSpectrumTreeNodeCombinerVisitor &other);

125	125	protected:
126	126	pappso::MassSpectrumPlusCombinerSPtr msp_combiner;
127	127
128		MzIntegrationParams m_mzIntegrationParams;
	128	pappso::MzIntegrationParams m_mzIntegrationParams;
129	129	pappso::MapTrace m_mapTrace;
130	130
131	131	uint m_verifiedMsFragmentationLevels = 0;

+5

-5

src/nongui/MsRunDataSet.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

44	44
45	45	/////////////////////// pappsomspp includes
46	46	#include <pappsomspp/massspectrum/qualifiedmassspectrum.h>
	47	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
47	48
48	49
49	50	/////////////////////// Local includes
50	51	#include "MsRunDataSet.hpp"
51		#include "MzIntegrationParams.hpp"
52	52
53	53
54	54	int msRunDataSetMetaTypeId = qRegisterMetaType<msxps::minexpert::MsRunDataSet>(

217	217	}
218	218
219	219
220		MzIntegrationParams
	220	pappso::MzIntegrationParams
221	221	MsRunDataSet::craftInitialMzIntegrationParams() const
222	222	{
223		return MzIntegrationParams(
	223	return pappso::MzIntegrationParams(
224	224	// Absolute min m/z value of the whole data set
225	225	m_msRunDataSetStats.m_minMz,
226	226	// Absolute max m/z value of the whole data set
227	227	m_msRunDataSetStats.m_maxMz,
228	228	// Binning type
229		BinningType::ARBITRARY,
	229	pappso::BinningType::ARBITRARY,
230	230	// Decimal places
231	231	3,
232	232	// The size of the m/z bins in Dalton units.

+4

-3

src/nongui/MsRunDataSet.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

48	48	#include <pappsomspp/massspectrum/qualifiedmassspectrum.h>
49	49	#include <pappsomspp/msrun/msrundatasettree.h>
50	50	#include <pappsomspp/msrun/msrundatasettreenode.h>
	51	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
51	52
52	53
53	54	/////////////////////// Local includes

67	68
68	69
69	70	class MsRunDataSetStats;
70		class MzIntegrationParams;
	71	//class pappso::MzIntegrationParams;
71	72
72	73	class MsRunDataSet : public QObject
73	74	{

130	131	void
131	132	mapMassSpectrum(pappso::QualifiedMassSpectrumCstSPtr mass_spectrum_csptr);
132	133
133		MzIntegrationParams craftInitialMzIntegrationParams() const;
	134	pappso::MzIntegrationParams craftInitialMzIntegrationParams() const;
134	135
135	136	using VectorConstIterator =
136	137	std::vector<pappso::MsRunDataSetTreeNode *>::const_iterator;

+1

-1

src/nongui/MsRunDataSetStats.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MsRunDataSetStats.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MsRunDataSetTreeMassDataIntegratorToDt.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MsRunDataSetTreeMassDataIntegratorToDt.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MsRunDataSetTreeMassDataIntegratorToDtRtMz.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MsRunDataSetTreeMassDataIntegratorToDtRtMz.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+8

-8

src/nongui/MsRunDataSetTreeMassDataIntegratorToMz.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

177	177
178	178	// Since we are asked that an integration to a mass spectrum be performed,
179	179	// there must be a non-nullptr mz integration pointer in the step.
180		const MzIntegrationParams *mz_integration_params_p =
	180	const pappso::MzIntegrationParams *mz_integration_params_p =
181	181	processing_step_p->getMzIntegrationParamsPtr();
182	182
183	183	if(mz_integration_params_p == nullptr)

192	192	emit setTaskDescriptionTextSignal(
193	193	"Computing the combination of the appropriate mass spectra");
194	194
195		if(mz_integration_params_p->getBinningType() == BinningType::NONE)
	195	if(mz_integration_params_p->getBinningType() == pappso::BinningType::NONE)
196	196	{
197	197	integrateToMzNoBinning();
198	198	}
199		else if(mz_integration_params_p->getBinningType() == BinningType::ARBITRARY)
	199	else if(mz_integration_params_p->getBinningType() == pappso::BinningType::ARBITRARY)
200	200	{
201	201	integrateToMzArbitraryBinning();
202	202	}

296	296	// Since we are asked that an integration to a mass spectrum be performed,
297	297	// there must be a non-nullptr mz integration pointer in the most recent step.
298	298
299		const MzIntegrationParams *mz_integration_params_p =
	299	const pappso::MzIntegrationParams *mz_integration_params_p =
300	300	m_processingFlow.mostRecentStep()->getMzIntegrationParamsPtr();
301	301
302	302	if(mz_integration_params_p == nullptr)

532	532	// Since we are asked that an integration to a mass spectrum be performed,
533	533	// there must be a non-nullptr mz integration pointer in the most recent step.
534	534
535		const MzIntegrationParams *mz_integration_params_p =
	535	const pappso::MzIntegrationParams *mz_integration_params_p =
536	536	m_processingFlow.mostRecentStep()->getMzIntegrationParamsPtr();
537	537
538	538	if(mz_integration_params_p == nullptr)

542	542	// to establish the bins. Create a local copy that we'll be able to modify
543	543	// before using it.
544	544
545		MzIntegrationParams local_mz_integration_params = *mz_integration_params_p;
	545	pappso::MzIntegrationParams local_mz_integration_params = *mz_integration_params_p;
546	546
547	547	local_mz_integration_params.setSmallestMz(
548	548	mcsp_msRunDataSet->getMsRunDataSetStats().m_minMz);

573	573	{
574	574	// qDebug() << "thread index:" << iter;
575	575
576		if(local_mz_integration_params.getBinningType() != BinningType::ARBITRARY)
	576	if(local_mz_integration_params.getBinningType() != pappso::BinningType::ARBITRARY)
577	577	qFatal("Programming error.");
578	578
579	579	// We are using MassSpectrum combiner visitors because we are going to use

+1

-1

src/nongui/MsRunDataSetTreeMassDataIntegratorToMz.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MsRunDataSetTreeMassDataIntegratorToRt.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MsRunDataSetTreeMassDataIntegratorToRt.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MsRunDataSetTreeMassDataIntegratorToTicInt.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MsRunDataSetTreeMassDataIntegratorToTicInt.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MsRunStatisticsTreeNodeVisitor.hpp less more

47	47	#include "ProcessingFlow.hpp"
48	48	#include "MsRunDataSet.hpp"
49	49	#include "BaseMsRunDataSetTreeNodeVisitor.hpp"
50		#include "MzIntegrationParams.hpp"
	50	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
51	51	#include "MsRunDataSetStats.hpp"
52	52
53	53

+1

-1

src/nongui/MultiTreeNodeCombinerVisitor.hpp less more

49	49	#include "ProcessingFlow.hpp"
50	50	#include "MsRunDataSet.hpp"
51	51	#include "BaseMsRunDataSetTreeNodeVisitor.hpp"
52		#include "MzIntegrationParams.hpp"
	52	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
53	53
54	54
55	55	namespace msxps

+1

-1

src/nongui/MzIntegrationParams.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/MzIntegrationParams.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+2

-1

src/nongui/Ponderable.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

28	28	*
29	29	* END software license
30	30	*/
	31
31	32
32	33
33	34	/////////////////////// Qt includes

+1

-1

src/nongui/Ponderable.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+3

-3

src/nongui/ProcessingFlow.cpp less more

112	112
113	113	void
114	114	ProcessingFlow::setDefaultMzIntegrationParams(
115		const MzIntegrationParams &mz_integration_params)
	115	const pappso::MzIntegrationParams &mz_integration_params)
116	116	{
117	117	m_defaultMzIntegrationParams = mz_integration_params;
118	118	}

128	128	}
129	129
130	130
131		const MzIntegrationParams &
	131	const pappso::MzIntegrationParams &
132	132	ProcessingFlow::getDefaultMzIntegrationParams() const
133	133	{
134	134	return m_defaultMzIntegrationParams;

460	460	}
461	461
462	462
463		const MzIntegrationParams *
	463	const pappso::MzIntegrationParams *
464	464	ProcessingFlow::mostRecentMzIntegrationParams() const
465	465	{
466	466

+5

-5

src/nongui/ProcessingFlow.hpp less more

89	89	const ProcessingStep *mostRecentStep() const;
90	90
91	91	void setDefaultMzIntegrationParams(
92		const MzIntegrationParams &mz_integration_params);
93		const MzIntegrationParams &getDefaultMzIntegrationParams() const;
94		const MzIntegrationParams *mostRecentMzIntegrationParams() const;
	92	const pappso::MzIntegrationParams &mz_integration_params);
	93	const pappso::MzIntegrationParams &getDefaultMzIntegrationParams() const;
	94	const pappso::MzIntegrationParams *mostRecentMzIntegrationParams() const;
95	95
96	96	void setDefaultMsFragmentationSpec(
97	97	const MsFragmentationSpec &ms_fragmentation_spec);

105	105	protected:
106	106	MsRunDataSetCstSPtr mcsp_msRunDataSet = nullptr;
107	107
108		// Note that each step has an optional MzIntegrationParams *. This one is the
	108	// Note that each step has an optional pappso::MzIntegrationParams *. This one is the
109	109	// default one when not a single step has mz integration params. This one is
110	110	// set automatically in the first graph obtained when displaying the TIC
111	111	// chromatogram right after having loaded the ms run from file.
112		MzIntegrationParams m_defaultMzIntegrationParams;
	112	pappso::MzIntegrationParams m_defaultMzIntegrationParams;
113	113
114	114	// Same for MsFragmentationSpec
115	115	MsFragmentationSpec m_defaultMsFragmentationSpec;

+9

-9

src/nongui/ProcessingStep.cpp less more

62	62
63	63	if(other.mpa_mzIntegrationParams != nullptr)
64	64	mpa_mzIntegrationParams =
65		new MzIntegrationParams(*other.mpa_mzIntegrationParams);
	65	new pappso::MzIntegrationParams(*other.mpa_mzIntegrationParams);
66	66
67	67	for(auto &&type_spec_pair : other.m_processingTypeSpecMultiMap)
68	68	{

94	94
95	95	if(other.mpa_mzIntegrationParams != nullptr)
96	96	mpa_mzIntegrationParams =
97		new MzIntegrationParams(*other.mpa_mzIntegrationParams);
	97	new pappso::MzIntegrationParams(*other.mpa_mzIntegrationParams);
98	98
99	99	for(auto &&item : m_processingTypeSpecMultiMap)
100	100	{

109	109
110	110	void
111	111	ProcessingStep::setMzIntegrationParams(
112		const MzIntegrationParams &mz_integration_params)
113		{
114		mpa_mzIntegrationParams = new MzIntegrationParams(mz_integration_params);
115		}
116
117
118		const MzIntegrationParams *
	112	const pappso::MzIntegrationParams &mz_integration_params)
	113	{
	114	mpa_mzIntegrationParams = new pappso::MzIntegrationParams(mz_integration_params);
	115	}
	116
	117
	118	const pappso::MzIntegrationParams *
119	119	ProcessingStep::getMzIntegrationParamsPtr() const
120	120	{
121	121	return mpa_mzIntegrationParams;

+4

-3

src/nongui/ProcessingStep.hpp less more

43	43
44	44
45	45	/////////////////////// pappsomspp includes
	46	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
46	47
47	48
48	49	/////////////////////// Local includes

80	81
81	82	ProcessingStep &operator=(const ProcessingStep &other);
82	83
83		void setMzIntegrationParams(const MzIntegrationParams &mz_integration_params);
84		const MzIntegrationParams *getMzIntegrationParamsPtr() const;
	84	void setMzIntegrationParams(const pappso::MzIntegrationParams &mz_integration_params);
	85	const pappso::MzIntegrationParams *getMzIntegrationParamsPtr() const;
85	86
86	87	void newSpec(ProcessingType processing_type,
87	88	ProcessingSpec *processing_spec_p);

125	126	// class instance allows to do so. Because not all the specs need such
126	127	// parameters, we do not make a member variable of that type, but we provide a
127	128	// means to store a pointer.
128		MzIntegrationParams *mpa_mzIntegrationParams = nullptr;
	129	pappso::MzIntegrationParams *mpa_mzIntegrationParams = nullptr;
129	130	};
130	131
131	132

+23

-3

src/nongui/QualifiedMassSpectrumVectorMassDataIntegrator.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

184	184	}
185	185
186	186
	187	void
	188	QualifiedMassSpectrumVectorMassDataIntegrator::setMaxThreadUseCount(std::size_t number)
	189	{
	190	m_maxThreadUseCount = number;
	191	}
	192
	193
	194	std::size_t
	195	QualifiedMassSpectrumVectorMassDataIntegrator::getMaxThreadUseCount()
	196	{
	197	return m_maxThreadUseCount;
	198	}
	199
	200
187	201	void
188	202	QualifiedMassSpectrumVectorMassDataIntegrator::cancelOperation()
189	203	{
190	204	m_isOperationCancelled = true;
191	205
192		qDebug() << "cancellation asked, setting m_isOperationCancelled to true and "
193		"emitting cancelOperationSignal";
	206	//qDebug() << "cancellation asked, setting m_isOperationCancelled to true and "
	207	//"emitting cancelOperationSignal";
194	208
195	209	emit cancelOperationSignal();
196	210	}

202	216
203	217	std::size_t ideal_thread_count = QThread::idealThreadCount();
204	218	// qDebug() << "ideal_thread_count:" << ideal_thread_count;
	219
	220	// If the user has limited the count of usable threads, then we need to honour
	221	// that limitation. Only if the limitation value is not 0 (in which case there
	222	// is no limitation).
	223	if(m_maxThreadUseCount != 0 && ideal_thread_count > m_maxThreadUseCount)
	224	ideal_thread_count = m_maxThreadUseCount;
205	225
206	226	// Depending on the number of nodes (node_count) and on the number of thread
207	227	// available, we need to compute the right values to parallelize correctly the

+6

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegrator.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

95	95	pappso::QualifiedMassSpectrumCstSPtr &qualified_mass_spectrum_csp);
96	96
97	97	const pappso::MapTrace &getMapTrace() const;
	98
	99	void setMaxThreadUseCount(std::size_t count);
	100	std::size_t getMaxThreadUseCount();
98	101
99	102	public slots:
100	103

131	134	MsRunDataSetCstSPtr mcsp_msRunDataSet = nullptr;
132	135
133	136	ProcessingFlow m_processingFlow;
	137
	138	std::size_t m_maxThreadUseCount = 0;
134	139
135	140	std::pair<double, double> m_rtRange = std::pair<double, double>(
136	141	std::numeric_limits<double>::max(), std::numeric_limits<double>::min());

+3

-3

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToDt.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

303	303	{
304	304
305	305	emit setStatusTextSignal(
306		QString("Consolidating TEST drift spectra from thread %1")
	306	QString("Consolidating drift spectra from thread %1")
307	307	.arg(iter));
308	308
309	309	emit setProgressBarCurrentValueSignal(iter);

661	661	{
662	662
663	663	emit setStatusTextSignal(
664		QString("Consolidating TIC chromatograms from thread %1")
	664	QString("Consolidating drift spectra from thread %1")
665	665	.arg(iter));
666	666
667	667	emit setProgressBarCurrentValueSignal(iter);

+1

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToDt.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToDtRtMz.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToDtRtMz.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+17

-18

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToMz.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

125	125	m_mapTrace.clear();
126	126
127	127	if(m_processingFlow.getDefaultMzIntegrationParams().getBinningType() ==
128		BinningType::NONE)
	128	pappso::BinningType::NONE)
129	129	{
130	130	integrateToMzNoBinning();
131	131	}
132	132	else if(m_processingFlow.getDefaultMzIntegrationParams().getBinningType() ==
133		BinningType::ARBITRARY)
	133	pappso::BinningType::ARBITRARY)
134	134	{
135	135	integrateToMzArbitraryBinning();
136	136	}

252	252	if(m_mzRange.first != std::numeric_limits<double>::max() &&
253	253	m_mzRange.second != std::numeric_limits<double>::min())
254	254	{
255		qDebug() << "The m_mzRange.first:" << m_mzRange.first
256		<< "and m_mzRange.second:" << m_mzRange.second;
	255	//qDebug() << "The m_mzRange.first:" << m_mzRange.first
	256	//<< "and m_mzRange.second:" << m_mzRange.second;
257	257
258	258	trace_plus_combiner.setFilterResampleKeepXRange(
259	259	pappso::FilterResampleKeepXRange(m_mzRange.first,
260	260	m_mzRange.second));
261	261	}
262		else
263		qDebug() << "There is no limitation on the m/z range.";
	262	//else
	263	//qDebug() << "There is no limitation on the m/z range.";
264	264
265	265	while(current_iterator != end_iterator)
266	266	{

414	414	++iter;
415	415
416	416	emit setStatusTextSignal(
417		QString("Consolidating TEST mass spectra from thread %1").arg(iter));
	417	QString("Consolidating mass spectra from thread %1").arg(iter));
418	418
419	419	// qDebug() << "In the consolidating loop, iter:" << iter
420	420	//<< "with a MapTrace of this size : "

441	441	QualifiedMassSpectrumVectorMassDataIntegratorToMz::
442	442	integrateToMzArbitraryBinning()
443	443	{
444		qDebug();
	444	// qDebug();
445	445
446	446	// This function needs to be called by integrateToMz() that has setup all the
447	447	// required parameters.

454	454	if(!m_processingFlow.size())
455	455	qFatal("The processing flow cannot be empty. Program aborted.");
456	456
457		MzIntegrationParams local_mz_integration_params =
	457	pappso::MzIntegrationParams local_mz_integration_params =
458	458	m_processingFlow.getDefaultMzIntegrationParams();
459	459
460	460	if(!local_mz_integration_params.isValid())
461	461	{
462		// qFatal("the mz integration paramas are not valid.");
463		qDebug() << "the mz integration paramas are not valid.";
	462	qDebug() << "The mz integration paramas are not valid.";
464	463
465	464	// If the mz integration params are not valid, then we cannot know the
466	465	// start and end of the bins ! We need to resort to the statistical data

562	561	m_mzRange.second != std::numeric_limits<double>::min())
563	562	{
564	563
565		qDebug() << "The m_mzRange.first:" << m_mzRange.first
566		<< "and m_mzRange.second:" << m_mzRange.second;
	564	// qDebug() << "The m_mzRange.first:" << m_mzRange.first
	565	//<< "and m_mzRange.second:" << m_mzRange.second;
567	566
568	567	mass_spectrum_plus_combiner.setFilterResampleKeepXRange(
569	568	pappso::FilterResampleKeepXRange(m_mzRange.first,
570	569	m_mzRange.second));
571	570	}
572		else
573		qDebug() << "There is no limitation on the m/z range.";
	571	// else
	572	// qDebug() << "There is no limitation on the m/z range.";
574	573
575	574	// Configure the binning mass spectrum combiner.
576	575

748	747
749	748	emit setStatusTextSignal(message);
750	749
751		// qDebug() << message;
	750	//qDebug() << message;
752	751
753	752	mass_spectrum_plus_combiner.combine(m_mapTrace, *current_map_trace_sp);
754	753
755	754	emit setProgressBarCurrentValueSignal(iter);
756	755
757		// qDebug() << "Emitted current value:" << iter;
	756	//qDebug() << "Emitted current value:" << iter;
758	757	}
759	758
760	759	// Write the data to file so that we can check. It works !!!

+1

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToMz.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToRt.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToRt.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToRtDt.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToRtDt.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToTicInt.cpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/QualifiedMassSpectrumVectorMassDataIntegratorToTicInt.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+1

-1

src/nongui/RtDtColorMapTreeNodeCombinerVisitor.hpp less more

49	49	#include "ProcessingFlow.hpp"
50	50	#include "MsRunDataSet.hpp"
51	51	#include "BaseMsRunDataSetTreeNodeVisitor.hpp"
52		#include "MzIntegrationParams.hpp"
	52	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
53	53
54	54
55	55	namespace msxps

+1

-1

src/nongui/RtDtMzColorMapsTreeNodeCombinerVisitor.hpp less more

49	49	#include "ProcessingFlow.hpp"
50	50	#include "MsRunDataSet.hpp"
51	51	#include "BaseMsRunDataSetTreeNodeVisitor.hpp"
52		#include "MzIntegrationParams.hpp"
	52	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
53	53
54	54
55	55	namespace msxps

+3

-3

src/nongui/TraceTreeNodeCombinerVisitor.cpp less more

65	65	MsRunDataSetCstSPtr ms_run_data_set_csp,
66	66	const ProcessingFlow &processing_flow,
67	67	pappso::TracePlusCombinerSPtr &trace_combiner_sp,
68		const MzIntegrationParams &mz_integration_params)
	68	const pappso::MzIntegrationParams &mz_integration_params)
69	69	: BaseMsRunDataSetTreeNodeVisitor(ms_run_data_set_csp, processing_flow),
70	70	msp_combiner(trace_combiner_sp),
71	71	m_mzIntegrationParams(mz_integration_params)

129	129
130	130	void
131	131	TraceTreeNodeCombinerVisitor::setMzIntegrationParams(
132		const MzIntegrationParams &mz_integration_params)
	132	const pappso::MzIntegrationParams &mz_integration_params)
133	133	{
134	134	m_mzIntegrationParams = mz_integration_params;
135	135	}
136	136
137	137
138		const MzIntegrationParams &
	138	const pappso::MzIntegrationParams &
139	139	TraceTreeNodeCombinerVisitor::getMzIntegrationParams()
140	140	{
141	141	return m_mzIntegrationParams;

+5

-5

src/nongui/TraceTreeNodeCombinerVisitor.hpp less more

49	49	#include "ProcessingFlow.hpp"
50	50	#include "MsRunDataSet.hpp"
51	51	#include "BaseMsRunDataSetTreeNodeVisitor.hpp"
52		#include "MzIntegrationParams.hpp"
	52	#include <pappsomspp/processing/combiners/mzintegrationparams.h>
53	53
54	54
55	55	namespace msxps

79	79	MsRunDataSetCstSPtr ms_run_data_set_csp,
80	80	const ProcessingFlow &processing_flow,
81	81	pappso::TracePlusCombinerSPtr &trace_combiner_sp,
82		const MzIntegrationParams &mz_integration_params);
	82	const pappso::MzIntegrationParams &mz_integration_params);
83	83
84	84	TraceTreeNodeCombinerVisitor(const TraceTreeNodeCombinerVisitor &other);
85	85

90	90
91	91	const pappso::MapTrace &getMapTrace() const;
92	92
93		void setMzIntegrationParams(const MzIntegrationParams &mz_integration_params);
94		const MzIntegrationParams &getMzIntegrationParams();
	93	void setMzIntegrationParams(const pappso::MzIntegrationParams &mz_integration_params);
	94	const pappso::MzIntegrationParams &getMzIntegrationParams();
95	95
96	96	TraceTreeNodeCombinerVisitor &
97	97	operator=(const TraceTreeNodeCombinerVisitor &other);

122	122	protected:
123	123	pappso::TracePlusCombinerSPtr msp_combiner;
124	124
125		MzIntegrationParams m_mzIntegrationParams;
	125	pappso::MzIntegrationParams m_mzIntegrationParams;
126	126	pappso::MapTrace m_mapTrace;
127	127	};
128	128

+0

-781

~~src/nongui/about_gpl_v30.hpp~~ less more

0		/* BEGIN software license
1		*
2		* msXpertSuite - mass spectrometry software suite
3		* -----------------------------------------------
4		* Copyright(C) 2009, 2017 Filippo Rusconi
5		*
6		* http://www.msxpertsuite.org
7		*
8		* This file is part of the msXpertSuite project.
9		*
10		* The msXpertSuite project is the successor of the massXpert project. This
11		* project now includes various independent modules:
12		*
13		* - massXpert, model polymer chemistries and simulate mass spectrometric data;
14		* - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
15		*
16		* This program is free software: you can redistribute it and/or modify
17		* it under the terms of the GNU General Public License as published by
18		* the Free Software Foundation, either version 3 of the License, or
19		* (at your option) any later version.
20		*
21		* This program is distributed in the hope that it will be useful,
22		* but WITHOUT ANY WARRANTY; without even the implied warranty of
23		* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
24		* GNU General Public License for more details.
25		*
26		* You should have received a copy of the GNU General Public License
27		* along with this program. If not, see <http://www.gnu.org/licenses/>.
28		*
29		* END software license
30		*/
31
32
33		namespace msxps
34		{
35		namespace minexpert
36		{
37
38		QString gpl(
39		" GNU GENERAL PUBLIC LICENSE\n"
40		" Version 3, 29 June 2007\n"
41		"\n"
42		" Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>\n"
43		" Everyone is permitted to copy and distribute verbatim copies\n"
44		" of this license document, but changing it is not allowed.\n"
45		"\n"
46		" Preamble\n"
47		"\n"
48		" The GNU General Public License is a free, copyleft license for\n"
49		"software and other kinds of works.\n"
50		"\n"
51		" The licenses for most software and other practical works are designed\n"
52		"to take away your freedom to share and change the works. By contrast,\n"
53		"the GNU General Public License is intended to guarantee your freedom to\n"
54		"share and change all versions of a program--to make sure it remains free\n"
55		"software for all its users. We, the Free Software Foundation, use the\n"
56		"GNU General Public License for most of our software; it applies also to\n"
57		"any other work released this way by its authors. You can apply it to\n"
58		"your programs, too.\n"
59		"\n"
60		" When we speak of free software, we are referring to freedom, not\n"
61		"price. Our General Public Licenses are designed to make sure that you\n"
62		"have the freedom to distribute copies of free software (and charge for\n"
63		"them if you wish), that you receive source code or can get it if you\n"
64		"want it, that you can change the software or use pieces of it in new\n"
65		"free programs, and that you know you can do these things.\n"
66		"\n"
67		" To protect your rights, we need to prevent others from denying you\n"
68		"these rights or asking you to surrender the rights. Therefore, you have\n"
69		"certain responsibilities if you distribute copies of the software, or if\n"
70		"you modify it: responsibilities to respect the freedom of others.\n"
71		"\n"
72		" For example, if you distribute copies of such a program, whether\n"
73		"gratis or for a fee, you must pass on to the recipients the same\n"
74		"freedoms that you received. You must make sure that they, too, receive\n"
75		"or can get the source code. And you must show them these terms so they\n"
76		"know their rights.\n"
77		"\n"
78		" Developers that use the GNU GPL protect your rights with two steps:\n"
79		"(1) assert copyright on the software, and (2) offer you this License\n"
80		"giving you legal permission to copy, distribute and/or modify it.\n"
81		"\n"
82		" For the developers' and authors' protection, the GPL clearly explains\n"
83		"that there is no warranty for this free software. For both users' and\n"
84		"authors' sake, the GPL requires that modified versions be marked as\n"
85		"changed, so that their problems will not be attributed erroneously to\n"
86		"authors of previous versions.\n"
87		"\n"
88		" Some devices are designed to deny users access to install or run\n"
89		"modified versions of the software inside them, although the manufacturer\n"
90		"can do so. This is fundamentally incompatible with the aim of\n"
91		"protecting users' freedom to change the software. The systematic\n"
92		"pattern of such abuse occurs in the area of products for individuals to\n"
93		"use, which is precisely where it is most unacceptable. Therefore, we\n"
94		"have designed this version of the GPL to prohibit the practice for those\n"
95		"products. If such problems arise substantially in other domains, we\n"
96		"stand ready to extend this provision to those domains in future versions\n"
97		"of the GPL, as needed to protect the freedom of users.\n"
98		"\n"
99		" Finally, every program is threatened constantly by software patents.\n"
100		"States should not allow patents to restrict development and use of\n"
101		"software on general-purpose computers, but in those that do, we wish to\n"
102		"avoid the special danger that patents applied to a free program could\n"
103		"make it effectively proprietary. To prevent this, the GPL assures that\n"
104		"patents cannot be used to render the program non-free.\n"
105		"\n"
106		" The precise terms and conditions for copying, distribution and\n"
107		"modification follow.\n"
108		"\n"
109		" TERMS AND CONDITIONS\n"
110		"\n"
111		" 0. Definitions.\n"
112		"\n"
113		" \"This License\" refers to version 3 of the GNU General Public "
114		"License.\n"
115		"\n"
116		" \"Copyright\" also means copyright-like laws that apply to other kinds "
117		"of\n"
118		"works, such as semiconductor masks.\n"
119		"\n"
120		" \"The Program\" refers to any copyrightable work licensed under this\n"
121		"License. Each licensee is addressed as \"you\". \"Licensees\" and\n"
122		"\"recipients\" may be individuals or organizations.\n"
123		"\n"
124		" To \"modify\" a work means to copy from or adapt all or part of the "
125		"work\n"
126		"in a fashion requiring copyright permission, other than the making of an\n"
127		"exact copy. The resulting work is called a \"modified version\" of the\n"
128		"earlier work or a work \"based on\" the earlier work.\n"
129		"\n"
130		" A \"covered work\" means either the unmodified Program or a work based\n"
131		"on the Program.\n"
132		"\n"
133		" To \"propagate\" a work means to do anything with it that, without\n"
134		"permission, would make you directly or secondarily liable for\n"
135		"infringement under applicable copyright law, except executing it on a\n"
136		"computer or modifying a private copy. Propagation includes copying,\n"
137		"distribution (with or without modification), making available to the\n"
138		"public, and in some countries other activities as well.\n"
139		"\n"
140		" To \"convey\" a work means any kind of propagation that enables other\n"
141		"parties to make or receive copies. Mere interaction with a user through\n"
142		"a computer network, with no transfer of a copy, is not conveying.\n"
143		"\n"
144		" An interactive user interface displays \"Appropriate Legal Notices\"\n"
145		"to the extent that it includes a convenient and prominently visible\n"
146		"feature that (1) displays an appropriate copyright notice, and (2)\n"
147		"tells the user that there is no warranty for the work (except to the\n"
148		"extent that warranties are provided), that licensees may convey the\n"
149		"work under this License, and how to view a copy of this License. If\n"
150		"the interface presents a list of user commands or options, such as a\n"
151		"menu, a prominent item in the list meets this criterion.\n"
152		"\n"
153		" 1. Source Code.\n"
154		"\n"
155		" The \"source code\" for a work means the preferred form of the work\n"
156		"for making modifications to it. \"Object code\" means any non-source\n"
157		"form of a work.\n"
158		"\n"
159		" A \"Standard Interface\" means an interface that either is an official\n"
160		"standard defined by a recognized standards body, or, in the case of\n"
161		"interfaces specified for a particular programming language, one that\n"
162		"is widely used among developers working in that language.\n"
163		"\n"
164		" The \"System Libraries\" of an executable work include anything, other\n"
165		"than the work as a whole, that (a) is included in the normal form of\n"
166		"packaging a Major Component, but which is not part of that Major\n"
167		"Component, and (b) serves only to enable use of the work with that\n"
168		"Major Component, or to implement a Standard Interface for which an\n"
169		"implementation is available to the public in source code form. A\n"
170		"\"Major Component\", in this context, means a major essential component\n"
171		"(kernel, window system, and so on) of the specific operating system\n"
172		"(if any) on which the executable work runs, or a compiler used to\n"
173		"produce the work, or an object code interpreter used to run it.\n"
174		"\n"
175		" The \"Corresponding Source\" for a work in object code form means all\n"
176		"the source code needed to generate, install, and (for an executable\n"
177		"work) run the object code and to modify the work, including scripts to\n"
178		"control those activities. However, it does not include the work's\n"
179		"System Libraries, or general-purpose tools or generally available free\n"
180		"programs which are used unmodified in performing those activities but\n"
181		"which are not part of the work. For example, Corresponding Source\n"
182		"includes interface definition files associated with source files for\n"
183		"the work, and the source code for shared libraries and dynamically\n"
184		"linked subprograms that the work is specifically designed to require,\n"
185		"such as by intimate data communication or control flow between those\n"
186		"subprograms and other parts of the work.\n"
187		"\n"
188		" The Corresponding Source need not include anything that users\n"
189		"can regenerate automatically from other parts of the Corresponding\n"
190		"Source.\n"
191		"\n"
192		" The Corresponding Source for a work in source code form is that\n"
193		"same work.\n"
194		"\n"
195		" 2. Basic Permissions.\n"
196		"\n"
197		" All rights granted under this License are granted for the term of\n"
198		"copyright on the Program, and are irrevocable provided the stated\n"
199		"conditions are met. This License explicitly affirms your unlimited\n"
200		"permission to run the unmodified Program. The output from running a\n"
201		"covered work is covered by this License only if the output, given its\n"
202		"content, constitutes a covered work. This License acknowledges your\n"
203		"rights of fair use or other equivalent, as provided by copyright law.\n"
204		"\n"
205		" You may make, run and propagate covered works that you do not\n"
206		"convey, without conditions so long as your license otherwise remains\n"
207		"in force. You may convey covered works to others for the sole purpose\n"
208		"of having them make modifications exclusively for you, or provide you\n"
209		"with facilities for running those works, provided that you comply with\n"
210		"the terms of this License in conveying all material for which you do\n"
211		"not control copyright. Those thus making or running the covered works\n"
212		"for you must do so exclusively on your behalf, under your direction\n"
213		"and control, on terms that prohibit them from making any copies of\n"
214		"your copyrighted material outside their relationship with you.\n"
215		"\n"
216		" Conveying under any other circumstances is permitted solely under\n"
217		"the conditions stated below. Sublicensing is not allowed; section 10\n"
218		"makes it unnecessary.\n"
219		"\n"
220		" 3. Protecting Users' Legal Rights From Anti-Circumvention Law.\n"
221		"\n"
222		" No covered work shall be deemed part of an effective technological\n"
223		"measure under any applicable law fulfilling obligations under article\n"
224		"11 of the WIPO copyright treaty adopted on 20 December 1996, or\n"
225		"similar laws prohibiting or restricting circumvention of such\n"
226		"measures.\n"
227		"\n"
228		" When you convey a covered work, you waive any legal power to forbid\n"
229		"circumvention of technological measures to the extent such circumvention\n"
230		"is effected by exercising rights under this License with respect to\n"
231		"the covered work, and you disclaim any intention to limit operation or\n"
232		"modification of the work as a means of enforcing, against the work's\n"
233		"users, your or third parties' legal rights to forbid circumvention of\n"
234		"technological measures.\n"
235		"\n"
236		" 4. Conveying Verbatim Copies.\n"
237		"\n"
238		" You may convey verbatim copies of the Program's source code as you\n"
239		"receive it, in any medium, provided that you conspicuously and\n"
240		"appropriately publish on each copy an appropriate copyright notice;\n"
241		"keep intact all notices stating that this License and any\n"
242		"non-permissive terms added in accord with section 7 apply to the code;\n"
243		"keep intact all notices of the absence of any warranty; and give all\n"
244		"recipients a copy of this License along with the Program.\n"
245		"\n"
246		" You may charge any price or no price for each copy that you convey,\n"
247		"and you may offer support or warranty protection for a fee.\n"
248		"\n"
249		" 5. Conveying Modified Source Versions.\n"
250		"\n"
251		" You may convey a work based on the Program, or the modifications to\n"
252		"produce it from the Program, in the form of source code under the\n"
253		"terms of section 4, provided that you also meet all of these conditions:\n"
254		"\n"
255		" a) The work must carry prominent notices stating that you modified\n"
256		" it, and giving a relevant date.\n"
257		"\n"
258		" b) The work must carry prominent notices stating that it is\n"
259		" released under this License and any conditions added under section\n"
260		" 7. This requirement modifies the requirement in section 4 to\n"
261		" \"keep intact all notices\".\n"
262		"\n"
263		" c) You must license the entire work, as a whole, under this\n"
264		" License to anyone who comes into possession of a copy. This\n"
265		" License will therefore apply, along with any applicable section 7\n"
266		" additional terms, to the whole of the work, and all its parts,\n"
267		" regardless of how they are packaged. This License gives no\n"
268		" permission to license the work in any other way, but it does not\n"
269		" invalidate such permission if you have separately received it.\n"
270		"\n"
271		" d) If the work has interactive user interfaces, each must display\n"
272		" Appropriate Legal Notices; however, if the Program has interactive\n"
273		" interfaces that do not display Appropriate Legal Notices, your\n"
274		" work need not make them do so.\n"
275		"\n"
276		" A compilation of a covered work with other separate and independent\n"
277		"works, which are not by their nature extensions of the covered work,\n"
278		"and which are not combined with it such as to form a larger program,\n"
279		"in or on a volume of a storage or distribution medium, is called an\n"
280		"\"aggregate\" if the compilation and its resulting copyright are not\n"
281		"used to limit the access or legal rights of the compilation's users\n"
282		"beyond what the individual works permit. Inclusion of a covered work\n"
283		"in an aggregate does not cause this License to apply to the other\n"
284		"parts of the aggregate.\n"
285		"\n"
286		" 6. Conveying Non-Source Forms.\n"
287		"\n"
288		" You may convey a covered work in object code form under the terms\n"
289		"of sections 4 and 5, provided that you also convey the\n"
290		"machine-readable Corresponding Source under the terms of this License,\n"
291		"in one of these ways:\n"
292		"\n"
293		" a) Convey the object code in, or embodied in, a physical product\n"
294		" (including a physical distribution medium), accompanied by the\n"
295		" Corresponding Source fixed on a durable physical medium\n"
296		" customarily used for software interchange.\n"
297		"\n"
298		" b) Convey the object code in, or embodied in, a physical product\n"
299		" (including a physical distribution medium), accompanied by a\n"
300		" written offer, valid for at least three years and valid for as\n"
301		" long as you offer spare parts or customer support for that product\n"
302		" model, to give anyone who possesses the object code either (1) a\n"
303		" copy of the Corresponding Source for all the software in the\n"
304		" product that is covered by this License, on a durable physical\n"
305		" medium customarily used for software interchange, for a price no\n"
306		" more than your reasonable cost of physically performing this\n"
307		" conveying of source, or (2) access to copy the\n"
308		" Corresponding Source from a network server at no charge.\n"
309		"\n"
310		" c) Convey individual copies of the object code with a copy of the\n"
311		" written offer to provide the Corresponding Source. This\n"
312		" alternative is allowed only occasionally and noncommercially, and\n"
313		" only if you received the object code with such an offer, in accord\n"
314		" with subsection 6b.\n"
315		"\n"
316		" d) Convey the object code by offering access from a designated\n"
317		" place (gratis or for a charge), and offer equivalent access to the\n"
318		" Corresponding Source in the same way through the same place at no\n"
319		" further charge. You need not require recipients to copy the\n"
320		" Corresponding Source along with the object code. If the place to\n"
321		" copy the object code is a network server, the Corresponding Source\n"
322		" may be on a different server (operated by you or a third party)\n"
323		" that supports equivalent copying facilities, provided you maintain\n"
324		" clear directions next to the object code saying where to find the\n"
325		" Corresponding Source. Regardless of what server hosts the\n"
326		" Corresponding Source, you remain obligated to ensure that it is\n"
327		" available for as long as needed to satisfy these requirements.\n"
328		"\n"
329		" e) Convey the object code using peer-to-peer transmission, provided\n"
330		" you inform other peers where the object code and Corresponding\n"
331		" Source of the work are being offered to the general public at no\n"
332		" charge under subsection 6d.\n"
333		"\n"
334		" A separable portion of the object code, whose source code is excluded\n"
335		"from the Corresponding Source as a System Library, need not be\n"
336		"included in conveying the object code work.\n"
337		"\n"
338		" A \"User Product\" is either (1) a \"consumer product\", which means "
339		"any\n"
340		"tangible personal property which is normally used for personal, family,\n"
341		"or household purposes, or (2) anything designed or sold for "
342		"incorporation\n"
343		"into a dwelling. In determining whether a product is a consumer "
344		"product,\n"
345		"doubtful cases shall be resolved in favor of coverage. For a particular\n"
346		"product received by a particular user, \"normally used\" refers to a\n"
347		"typical or common use of that class of product, regardless of the status\n"
348		"of the particular user or of the way in which the particular user\n"
349		"actually uses, or expects or is expected to use, the product. A product\n"
350		"is a consumer product regardless of whether the product has substantial\n"
351		"commercial, industrial or non-consumer uses, unless such uses represent\n"
352		"the only significant mode of use of the product.\n"
353		"\n"
354		" \"Installation Information\" for a User Product means any methods,\n"
355		"procedures, authorization keys, or other information required to install\n"
356		"and execute modified versions of a covered work in that User Product "
357		"from\n"
358		"a modified version of its Corresponding Source. The information must\n"
359		"suffice to ensure that the continued functioning of the modified object\n"
360		"code is in no case prevented or interfered with solely because\n"
361		"modification has been made.\n"
362		"\n"
363		" If you convey an object code work under this section in, or with, or\n"
364		"specifically for use in, a User Product, and the conveying occurs as\n"
365		"part of a transaction in which the right of possession and use of the\n"
366		"User Product is transferred to the recipient in perpetuity or for a\n"
367		"fixed term (regardless of how the transaction is characterized), the\n"
368		"Corresponding Source conveyed under this section must be accompanied\n"
369		"by the Installation Information. But this requirement does not apply\n"
370		"if neither you nor any third party retains the ability to install\n"
371		"modified object code on the User Product (for example, the work has\n"
372		"been installed in ROM).\n"
373		"\n"
374		" The requirement to provide Installation Information does not include a\n"
375		"requirement to continue to provide support service, warranty, or updates\n"
376		"for a work that has been modified or installed by the recipient, or for\n"
377		"the User Product in which it has been modified or installed. Access to "
378		"a\n"
379		"network may be denied when the modification itself materially and\n"
380		"adversely affects the operation of the network or violates the rules and\n"
381		"protocols for communication across the network.\n"
382		"\n"
383		" Corresponding Source conveyed, and Installation Information provided,\n"
384		"in accord with this section must be in a format that is publicly\n"
385		"documented (and with an implementation available to the public in\n"
386		"source code form), and must require no special password or key for\n"
387		"unpacking, reading or copying.\n"
388		"\n"
389		" 7. Additional Terms.\n"
390		"\n"
391		" \"Additional permissions\" are terms that supplement the terms of this\n"
392		"License by making exceptions from one or more of its conditions.\n"
393		"Additional permissions that are applicable to the entire Program shall\n"
394		"be treated as though they were included in this License, to the extent\n"
395		"that they are valid under applicable law. If additional permissions\n"
396		"apply only to part of the Program, that part may be used separately\n"
397		"under those permissions, but the entire Program remains governed by\n"
398		"this License without regard to the additional permissions.\n"
399		"\n"
400		" When you convey a copy of a covered work, you may at your option\n"
401		"remove any additional permissions from that copy, or from any part of\n"
402		"it. (Additional permissions may be written to require their own\n"
403		"removal in certain cases when you modify the work.) You may place\n"
404		"additional permissions on material, added by you to a covered work,\n"
405		"for which you have or can give appropriate copyright permission.\n"
406		"\n"
407		" Notwithstanding any other provision of this License, for material you\n"
408		"add to a covered work, you may (if authorized by the copyright holders "
409		"of\n"
410		"that material) supplement the terms of this License with terms:\n"
411		"\n"
412		" a) Disclaiming warranty or limiting liability differently from the\n"
413		" terms of sections 15 and 16 of this License; or\n"
414		"\n"
415		" b) Requiring preservation of specified reasonable legal notices or\n"
416		" author attributions in that material or in the Appropriate Legal\n"
417		" Notices displayed by works containing it; or\n"
418		"\n"
419		" c) Prohibiting misrepresentation of the origin of that material, or\n"
420		" requiring that modified versions of such material be marked in\n"
421		" reasonable ways as different from the original version; or\n"
422		"\n"
423		" d) Limiting the use for publicity purposes of names of licensors or\n"
424		" authors of the material; or\n"
425		"\n"
426		" e) Declining to grant rights under trademark law for use of some\n"
427		" trade names, trademarks, or service marks; or\n"
428		"\n"
429		" f) Requiring indemnification of licensors and authors of that\n"
430		" material by anyone who conveys the material (or modified versions of\n"
431		" it) with contractual assumptions of liability to the recipient, for\n"
432		" any liability that these contractual assumptions directly impose on\n"
433		" those licensors and authors.\n"
434		"\n"
435		" All other non-permissive additional terms are considered \"further\n"
436		"restrictions\" within the meaning of section 10. If the Program as you\n"
437		"received it, or any part of it, contains a notice stating that it is\n"
438		"governed by this License along with a term that is a further\n"
439		"restriction, you may remove that term. If a license document contains\n"
440		"a further restriction but permits relicensing or conveying under this\n"
441		"License, you may add to a covered work material governed by the terms\n"
442		"of that license document, provided that the further restriction does\n"
443		"not survive such relicensing or conveying.\n"
444		"\n"
445		" If you add terms to a covered work in accord with this section, you\n"
446		"must place, in the relevant source files, a statement of the\n"
447		"additional terms that apply to those files, or a notice indicating\n"
448		"where to find the applicable terms.\n"
449		"\n"
450		" Additional terms, permissive or non-permissive, may be stated in the\n"
451		"form of a separately written license, or stated as exceptions;\n"
452		"the above requirements apply either way.\n"
453		"\n"
454		" 8. Termination.\n"
455		"\n"
456		" You may not propagate or modify a covered work except as expressly\n"
457		"provided under this License. Any attempt otherwise to propagate or\n"
458		"modify it is void, and will automatically terminate your rights under\n"
459		"this License (including any patent licenses granted under the third\n"
460		"paragraph of section 11).\n"
461		"\n"
462		" However, if you cease all violation of this License, then your\n"
463		"license from a particular copyright holder is reinstated (a)\n"
464		"provisionally, unless and until the copyright holder explicitly and\n"
465		"finally terminates your license, and (b) permanently, if the copyright\n"
466		"holder fails to notify you of the violation by some reasonable means\n"
467		"prior to 60 days after the cessation.\n"
468		"\n"
469		" Moreover, your license from a particular copyright holder is\n"
470		"reinstated permanently if the copyright holder notifies you of the\n"
471		"violation by some reasonable means, this is the first time you have\n"
472		"received notice of violation of this License (for any work) from that\n"
473		"copyright holder, and you cure the violation prior to 30 days after\n"
474		"your receipt of the notice.\n"
475		"\n"
476		" Termination of your rights under this section does not terminate the\n"
477		"licenses of parties who have received copies or rights from you under\n"
478		"this License. If your rights have been terminated and not permanently\n"
479		"reinstated, you do not qualify to receive new licenses for the same\n"
480		"material under section 10.\n"
481		"\n"
482		" 9. Acceptance Not Required for Having Copies.\n"
483		"\n"
484		" You are not required to accept this License in order to receive or\n"
485		"run a copy of the Program. Ancillary propagation of a covered work\n"
486		"occurring solely as a consequence of using peer-to-peer transmission\n"
487		"to receive a copy likewise does not require acceptance. However,\n"
488		"nothing other than this License grants you permission to propagate or\n"
489		"modify any covered work. These actions infringe copyright if you do\n"
490		"not accept this License. Therefore, by modifying or propagating a\n"
491		"covered work, you indicate your acceptance of this License to do so.\n"
492		"\n"
493		" 10. Automatic Licensing of Downstream Recipients.\n"
494		"\n"
495		" Each time you convey a covered work, the recipient automatically\n"
496		"receives a license from the original licensors, to run, modify and\n"
497		"propagate that work, subject to this License. You are not responsible\n"
498		"for enforcing compliance by third parties with this License.\n"
499		"\n"
500		" An \"entity transaction\" is a transaction transferring control of an\n"
501		"organization, or substantially all assets of one, or subdividing an\n"
502		"organization, or merging organizations. If propagation of a covered\n"
503		"work results from an entity transaction, each party to that\n"
504		"transaction who receives a copy of the work also receives whatever\n"
505		"licenses to the work the party's predecessor in interest had or could\n"
506		"give under the previous paragraph, plus a right to possession of the\n"
507		"Corresponding Source of the work from the predecessor in interest, if\n"
508		"the predecessor has it or can get it with reasonable efforts.\n"
509		"\n"
510		" You may not impose any further restrictions on the exercise of the\n"
511		"rights granted or affirmed under this License. For example, you may\n"
512		"not impose a license fee, royalty, or other charge for exercise of\n"
513		"rights granted under this License, and you may not initiate litigation\n"
514		"(including a cross-claim or counterclaim in a lawsuit) alleging that\n"
515		"any patent claim is infringed by making, using, selling, offering for\n"
516		"sale, or importing the Program or any portion of it.\n"
517		"\n"
518		" 11. Patents.\n"
519		"\n"
520		" A \"contributor\" is a copyright holder who authorizes use under this\n"
521		"License of the Program or a work on which the Program is based. The\n"
522		"work thus licensed is called the contributor's \"contributor version\".\n"
523		"\n"
524		" A contributor's \"essential patent claims\" are all patent claims\n"
525		"owned or controlled by the contributor, whether already acquired or\n"
526		"hereafter acquired, that would be infringed by some manner, permitted\n"
527		"by this License, of making, using, or selling its contributor version,\n"
528		"but do not include claims that would be infringed only as a\n"
529		"consequence of further modification of the contributor version. For\n"
530		"purposes of this definition, \"control\" includes the right to grant\n"
531		"patent sublicenses in a manner consistent with the requirements of\n"
532		"this License.\n"
533		"\n"
534		" Each contributor grants you a non-exclusive, worldwide, royalty-free\n"
535		"patent license under the contributor's essential patent claims, to\n"
536		"make, use, sell, offer for sale, import and otherwise run, modify and\n"
537		"propagate the contents of its contributor version.\n"
538		"\n"
539		" In the following three paragraphs, a \"patent license\" is any express\n"
540		"agreement or commitment, however denominated, not to enforce a patent\n"
541		"(such as an express permission to practice a patent or covenant not to\n"
542		"sue for patent infringement). To \"grant\" such a patent license to a\n"
543		"party means to make such an agreement or commitment not to enforce a\n"
544		"patent against the party.\n"
545		"\n"
546		" If you convey a covered work, knowingly relying on a patent license,\n"
547		"and the Corresponding Source of the work is not available for anyone\n"
548		"to copy, free of charge and under the terms of this License, through a\n"
549		"publicly available network server or other readily accessible means,\n"
550		"then you must either (1) cause the Corresponding Source to be so\n"
551		"available, or (2) arrange to deprive yourself of the benefit of the\n"
552		"patent license for this particular work, or (3) arrange, in a manner\n"
553		"consistent with the requirements of this License, to extend the patent\n"
554		"license to downstream recipients. \"Knowingly relying\" means you have\n"
555		"actual knowledge that, but for the patent license, your conveying the\n"
556		"covered work in a country, or your recipient's use of the covered work\n"
557		"in a country, would infringe one or more identifiable patents in that\n"
558		"country that you have reason to believe are valid.\n"
559		"\n"
560		" If, pursuant to or in connection with a single transaction or\n"
561		"arrangement, you convey, or propagate by procuring conveyance of, a\n"
562		"covered work, and grant a patent license to some of the parties\n"
563		"receiving the covered work authorizing them to use, propagate, modify\n"
564		"or convey a specific copy of the covered work, then the patent license\n"
565		"you grant is automatically extended to all recipients of the covered\n"
566		"work and works based on it.\n"
567		"\n"
568		" A patent license is \"discriminatory\" if it does not include within\n"
569		"the scope of its coverage, prohibits the exercise of, or is\n"
570		"conditioned on the non-exercise of one or more of the rights that are\n"
571		"specifically granted under this License. You may not convey a covered\n"
572		"work if you are a party to an arrangement with a third party that is\n"
573		"in the business of distributing software, under which you make payment\n"
574		"to the third party based on the extent of your activity of conveying\n"
575		"the work, and under which the third party grants, to any of the\n"
576		"parties who would receive the covered work from you, a discriminatory\n"
577		"patent license (a) in connection with copies of the covered work\n"
578		"conveyed by you (or copies made from those copies), or (b) primarily\n"
579		"for and in connection with specific products or compilations that\n"
580		"contain the covered work, unless you entered into that arrangement,\n"
581		"or that patent license was granted, prior to 28 March 2007.\n"
582		"\n"
583		" Nothing in this License shall be construed as excluding or limiting\n"
584		"any implied license or other defenses to infringement that may\n"
585		"otherwise be available to you under applicable patent law.\n"
586		"\n"
587		" 12. No Surrender of Others' Freedom.\n"
588		"\n"
589		" If conditions are imposed on you (whether by court order, agreement or\n"
590		"otherwise) that contradict the conditions of this License, they do not\n"
591		"excuse you from the conditions of this License. If you cannot convey a\n"
592		"covered work so as to satisfy simultaneously your obligations under this\n"
593		"License and any other pertinent obligations, then as a consequence you "
594		"may\n"
595		"not convey it at all. For example, if you agree to terms that obligate "
596		"you\n"
597		"to collect a royalty for further conveying from those to whom you convey\n"
598		"the Program, the only way you could satisfy both those terms and this\n"
599		"License would be to refrain entirely from conveying the Program.\n"
600		"\n"
601		" 13. Use with the GNU Affero General Public License.\n"
602		"\n"
603		" Notwithstanding any other provision of this License, you have\n"
604		"permission to link or combine any covered work with a work licensed\n"
605		"under version 3 of the GNU Affero General Public License into a single\n"
606		"combined work, and to convey the resulting work. The terms of this\n"
607		"License will continue to apply to the part which is the covered work,\n"
608		"but the special requirements of the GNU Affero General Public License,\n"
609		"section 13, concerning interaction through a network will apply to the\n"
610		"combination as such.\n"
611		"\n"
612		" 14. Revised Versions of this License.\n"
613		"\n"
614		" The Free Software Foundation may publish revised and/or new versions "
615		"of\n"
616		"the GNU General Public License from time to time. Such new versions "
617		"will\n"
618		"be similar in spirit to the present version, but may differ in detail to\n"
619		"address new problems or concerns.\n"
620		"\n"
621		" Each version is given a distinguishing version number. If the\n"
622		"Program specifies that a certain numbered version of the GNU General\n"
623		"Public License \"or any later version\" applies to it, you have the\n"
624		"option of following the terms and conditions either of that numbered\n"
625		"version or of any later version published by the Free Software\n"
626		"Foundation. If the Program does not specify a version number of the\n"
627		"GNU General Public License, you may choose any version ever published\n"
628		"by the Free Software Foundation.\n"
629		"\n"
630		" If the Program specifies that a proxy can decide which future\n"
631		"versions of the GNU General Public License can be used, that proxy's\n"
632		"public statement of acceptance of a version permanently authorizes you\n"
633		"to choose that version for the Program.\n"
634		"\n"
635		" Later license versions may give you additional or different\n"
636		"permissions. However, no additional obligations are imposed on any\n"
637		"author or copyright holder as a result of your choosing to follow a\n"
638		"later version.\n"
639		"\n"
640		" 15. Disclaimer of Warranty.\n"
641		"\n"
642		" THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY\n"
643		"APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT\n"
644		"HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM \"AS IS\" WITHOUT "
645		"WARRANTY\n"
646		"OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,\n"
647		"THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR\n"
648		"PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE "
649		"PROGRAM\n"
650		"IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF\n"
651		"ALL NECESSARY SERVICING, REPAIR OR CORRECTION.\n"
652		"\n"
653		" 16. Limitation of Liability.\n"
654		"\n"
655		" IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING\n"
656		"WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR "
657		"CONVEYS\n"
658		"THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING "
659		"ANY\n"
660		"GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE\n"
661		"USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS "
662		"OF\n"
663		"DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR "
664		"THIRD\n"
665		"PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),\n"
666		"EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY "
667		"OF\n"
668		"SUCH DAMAGES.\n"
669		"\n"
670		" 17. Interpretation of Sections 15 and 16.\n"
671		"\n"
672		" If the disclaimer of warranty and limitation of liability provided\n"
673		"above cannot be given local legal effect according to their terms,\n"
674		"reviewing courts shall apply local law that most closely approximates\n"
675		"an absolute waiver of all civil liability in connection with the\n"
676		"Program, unless a warranty or assumption of liability accompanies a\n"
677		"copy of the Program in return for a fee.\n"
678		"\n"
679		" END OF TERMS AND CONDITIONS\n"
680		"\n"
681		" How to Apply These Terms to Your New Programs\n"
682		"\n"
683		" If you develop a new program, and you want it to be of the greatest\n"
684		"possible use to the public, the best way to achieve this is to make it\n"
685		"free software which everyone can redistribute and change under these "
686		"terms.\n"
687		"\n"
688		" To do so, attach the following notices to the program. It is safest\n"
689		"to attach them to the start of each source file to most effectively\n"
690		"state the exclusion of warranty; and each file should have at least\n"
691		"the \"copyright\" line and a pointer to where the full notice is found.\n"
692		"\n"
693		" <one line to give the program's name and a brief idea of what it "
694		"does.>\n"
695		" Copyright (C) <year> <name of author>\n"
696		"\n"
697		" This program is free software: you can redistribute it and/or modify\n"
698		" it under the terms of the GNU General Public License as published by\n"
699		" the Free Software Foundation, either version 3 of the License, or\n"
700		" (at your option) any later version.\n"
701		"\n"
702		" This program is distributed in the hope that it will be useful,\n"
703		" but WITHOUT ANY WARRANTY; without even the implied warranty of\n"
704		" MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n"
705		" GNU General Public License for more details.\n"
706		"\n"
707		" You should have received a copy of the GNU General Public License\n"
708		" along with this program. If not, see "
709		"<http://www.gnu.org/licenses/>.\n"
710		"\n"
711		"Also add information on how to contact you by electronic and paper mail.\n"
712		"\n"
713		" If the program does terminal interaction, make it output a short\n"
714		"notice like this when it starts in an interactive mode:\n"
715		"\n"
716		" <program> Copyright (C) <year> <name of author>\n"
717		" This program comes with ABSOLUTELY NO WARRANTY; for details type "
718		"`show w'.\n"
719		" This is free software, and you are welcome to redistribute it\n"
720		" under certain conditions; type `show c' for details.\n"
721		"\n"
722		"The hypothetical commands `show w' and `show c' should show the "
723		"appropriate\n"
724		"parts of the General Public License. Of course, your program's commands\n"
725		"might be different; for a GUI interface, you would use an \"about box\".\n"
726		"\n"
727		" You should also get your employer (if you work as a programmer) or "
728		"school,\n"
729		"if any, to sign a \"copyright disclaimer\" for the program, if "
730		"necessary.\n"
731		"For more information on this, and how to apply and follow the GNU GPL, "
732		"see\n"
733		"<http://www.gnu.org/licenses/>.\n"
734		"\n"
735		" The GNU General Public License does not permit incorporating your "
736		"program\n"
737		"into proprietary programs. If your program is a subroutine library, you\n"
738		"may consider it more useful to permit linking proprietary applications "
739		"with\n"
740		"the library. If this is what you want to do, use the GNU Lesser General\n"
741		"Public License instead of this License. But first, please read\n"
742		"<http://www.gnu.org/philosophy/why-not-lgpl.html>.\n");
743
744
745		QString gplLegalDisclaimerLiabilitySections(
746		" 15. Disclaimer of Warranty.\n"
747		"\n"
748		" THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY\n"
749		"APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT\n"
750		"HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM \"AS IS\" WITHOUT "
751		"WARRANTY\n"
752		"OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,\n"
753		"THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR\n"
754		"PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE "
755		"PROGRAM\n"
756		"IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF\n"
757		"ALL NECESSARY SERVICING, REPAIR OR CORRECTION.\n"
758		"\n"
759		" 16. Limitation of Liability.\n"
760		"\n"
761		" IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING\n"
762		"WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR "
763		"CONVEYS\n"
764		"THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING "
765		"ANY\n"
766		"GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE\n"
767		"USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS "
768		"OF\n"
769		"DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR "
770		"THIRD\n"
771		"PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),\n"
772		"EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY "
773		"OF\n"
774		"SUCH DAMAGES.\n"
775		"\n");
776
777		} // namespace minexpert
778
779		} // namespace msxps
780

+30

-28

src/nongui/globals.cpp less more

0		/* BEGIN software license
1		*
2		* msXpertSuite - mass spectrometry software suite
3		* -----------------------------------------------
4		* Copyright(C) 2009, 2017 Filippo Rusconi
5		*
6		* http://www.msxpertsuite.org
7		*
8		* This file is part of the msXpertSuite project.
9		*
10		* The msXpertSuite project is the successor of the massXpert project. This
11		* project now includes various independent modules:
12		*
13		* - massXpert, model polymer chemistries and simulate mass spectrometric data;
14		* - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
15		*
16		* This program is free software: you can redistribute it and/or modify
17		* it under the terms of the GNU General Public License as published by
18		* the Free Software Foundation, either version 3 of the License, or
19		* (at your option) any later version.
20		*
21		* This program is distributed in the hope that it will be useful,
22		* but WITHOUT ANY WARRANTY; without even the implied warranty of
23		* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
24		* GNU General Public License for more details.
25		*
26		* You should have received a copy of the GNU General Public License
27		* along with this program. If not, see <http://www.gnu.org/licenses/>.
	0	/* BEGIN software license
	1	*
	2	* msXpertSuite - mass spectrometry software suite
	3	* -----------------------------------------------
	4	* Copyright (C) 2009--2020 Filippo Rusconi
	5	*
	6	* http://www.msxpertsuite.org
	7	*
	8	* This file is part of the msXpertSuite project.
	9	*
	10	* The msXpertSuite project is the successor of the massXpert project. This
	11	* project now includes various independent modules:
	12	*
	13	* - massXpert, model polymer chemistries and simulate mass spectrometric data;
	14	* - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner;
	15	*
	16	* This program is free software: you can redistribute it and/or modify
	17	* it under the terms of the GNU General Public License as published by
	18	* the Free Software Foundation, either version 3 of the License, or
	19	* (at your option) any later version.
	20	*
	21	* This program is distributed in the hope that it will be useful,
	22	* but WITHOUT ANY WARRANTY; without even the implied warranty of
	23	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	24	* GNU General Public License for more details.
	25	*
	26	* You should have received a copy of the GNU General Public License
	27	* along with this program. If not, see <http://www.gnu.org/licenses/>.
28	28	*
29	29	* END software license
30	30	*/
	31
	32
31	33
32	34	#include <cmath>
33	35	#include <limits>

+1

-1

src/nongui/globals.hpp less more

1	1	*
2	2	* msXpertSuite - mass spectrometry software suite
3	3	* -----------------------------------------------
4		* Copyright(C) 2009,...,2018 Filippo Rusconi
	4	* Copyright (C) 2009--2020 Filippo Rusconi
5	5	*
6	6	* http://www.msxpertsuite.org
7	7	*

+7

-16

tests/CMakeLists.txt less more

0		if(TESTS AND (UNIX AND NOT APPLE))
	0	if(MAKE_TESTS AND (UNIX AND NOT APPLE))
1	1
2	2	message(\n${BoldRed}"Now configuring src/tests for ${CMAKE_PROJECT_NAME}"${ColourReset}\n)
3	3	message("TARGET is: ${TARGET}")

7	7	########################################################
8	8	# Files
9	9
10		file(GLOB tests_SRCS
11
12		# Files from the main code source tree
13		../src/nongui/MzIntegrationParams.cpp
	10	set(tests_SRCS
14	11
15	12	# The main() of the tests executable file
16	13	testmain.cpp
17	14
18	15	# Files for the tests
19		nongui/DataPoint_test.cpp
20		nongui/Trace_test.cpp
21		nongui/MapTrace_test.cpp
22		nongui/MassSpectrum_test.cpp
23		nongui/TraceCombiner_test.cpp
24		nongui/MassSpectrumCombiner_test.cpp
25		nongui/MzIntegrationParams_test.cpp
26	16	)
27	17
28	18	find_package(Catch2 REQUIRED)

31	21	# Instruct CMake to run moc automatically when needed.
32	22	set(CMAKE_AUTOMOC ON)
33	23
34		find_package(Qt5 COMPONENTS Widgets Xml Svg Sql Script)
	24	find_package(Qt5 COMPONENTS Widgets Xml Svg)
35	25
36	26	qt5_wrap_ui(tests_UIS_H ${${TARGET}_UIS})
37	27

48	38	qt5_use_modules(tests Widgets)
49	39	qt5_use_modules(tests Xml)
50	40	qt5_use_modules(tests Svg)
51		qt5_use_modules(tests Sql)
52		qt5_use_modules(tests Script)
53	41	qt5_use_modules(tests PrintSupport)
54	42
55	43	#message("CMAKE_SOURCE_DIR: ${CMAKE_SOURCE_DIR}")

65	53	${Qt5Widgets_INCLUDE_DIRS}
66	54	${Qt5Xml_INCLUDE_DIRS}
67	55	${Qt5Svg_INCLUDE_DIRS}
68		${Qt5Sql_INCLUDE_DIRS}
69	56	${Qt5PrintSupport_INCLUDE_DIRS}
70	57	)
71	58

88	75	target_link_libraries(tests
89	76	${required_target_link_libraries})
90	77
	78	#add_test(tests "All Catch2-based tests")
	79	add_test(tests "tests")
	80
91	81	message("")
92	82	message(STATUS "${BoldGreen}Finished processing src/tests.${ColourReset}")
93	83	message("")

96	86	message(STATUS "Tests are not built.")
97	87	endif()
98	88
	89

+1

-1

tests/nongui/DataPoint_test.cpp less more

0		#include <catch.hpp>
	0	#include <catch2/catch.hpp>
1	1
2	2	#include <QDebug>
3	3

+1

-1

tests/nongui/MapTrace_test.cpp less more

0		#include <catch.hpp>
	0	#include <catch2/catch.hpp>
1	1
2	2	#include <QDebug>
3	3

+6

-6

tests/nongui/MassSpectrumCombiner_test.cpp less more

0		#include <catch.hpp>
	0	#include <catch2/catch.hpp>
1	1
2	2	#include <QDebug>
3	3

228	228	data_point_vector.push_back(DataPoint("610.07500 15639.6568298340"));
229	229	data_point_vector.push_back(DataPoint("610.12500 55999.7628784180"));
230	230	data_point_vector.push_back(DataPoint("610.17500 9335990.3578681946"));
231		data_point_vector.push_back(DataPoint("610.2200000 635674266.1611375809"));
	231	data_point_vector.push_back(DataPoint("610.22500 635674266.1611375809"));
232	232	data_point_vector.push_back(DataPoint("610.27500 54459.4762458801"));
233	233	data_point_vector.push_back(DataPoint("610.32500 205580.6580276489"));
234	234	data_point_vector.push_back(DataPoint("610.37500 84627.3196716309"));

256	256	// Prepare the bins on the basis of the spectrum.
257	257
258	258	int decimal_places = 5;
	259
	260	// The size of the bins.
259	261	pappso::PrecisionPtr precision_p =
260	262	pappso::PrecisionFactory::getDaltonInstance(0.05);
261	263
262		MzIntegrationParams mz_integration_params(610.02,
	264	MzIntegrationParams mz_integration_params(610.025,
263	265	610.975,
264	266	BinningType::ARBITRARY,
265	267	decimal_places,

268	270	0.0,
269	271	true);
270	272
271		// Check that it does not compute bins, since BinningType::NONE.
272
273	273	std::vector<double> bins = mz_integration_params.createBins();
274	274	REQUIRE(bins.size() == 21);
275		REQUIRE(bins[0] == 610.02000);
	275	REQUIRE(bins[0] == 610.02500);
276	276
277	277	// The last bin matches the last DataPoint of the second spectrum + one bin
278	278	// size.

+6

-6

tests/nongui/MassSpectrum_test.cpp less more

0		#include <catch.hpp>
	0	#include <catch2/catch.hpp>
1	1
2	2	#include <QDebug>
3	3

212	212	REQUIRE(tic == 12963.5715942383 + 15639.6568298340 + 55999.7628784180);
213	213
214	214	tic = mass_spectrum.tic(610.020001, 610.12001);
215		REQUIRE(tic == 15639.6568298340);
	215	REQUIRE(tic == 15639.6568298340 + 55999.7628784180);
216	216	}
217	217
218	218	SECTION("Get the maxIntensityDataPoint from MassSpectrum", "[MassSpectrum]")
219	219	{
220	220	DataPoint datapoint = mass_spectrum.maxIntensityDataPoint();
221		REQUIRE(datapoint.x == 610.2200000);
222		REQUIRE(datapoint.y == 635674266.1611375809);
	221	REQUIRE(datapoint.x == 610.1200000);
	222	REQUIRE(datapoint.y == 55999.7628784180);
223	223	}
224	224
225	225	SECTION("Get the minIntensityDataPoint from MassSpectrum", "[MassSpectrum]")
226	226	{
227	227	DataPoint datapoint = mass_spectrum.minIntensityDataPoint();
228		REQUIRE(datapoint.x == 613.52000);
229		REQUIRE(datapoint.y == 480.5255737305);
	228	REQUIRE(datapoint.x == 610.02000);
	229	REQUIRE(datapoint.y == 12963.5715942383);
230	230	}
231	231	}

+114

-13

tests/nongui/MzIntegrationParams_test.cpp less more

0		#include <catch.hpp>
	0	#include <catch2/catch.hpp>
1	1
2	2	#include <QDebug>
3	3
4	4	#include "../../src/nongui/MzIntegrationParams.hpp"
	5	#include <pappsomspp/utils.h>
5	6
6	7
7	8	using namespace pappso;

115	116	}
116	117	}
117	118
118		TEST_CASE("Create bins", "[MzIntegrationParams]")
119		{
120		double smallestMz = 1800.373856;
121		double greatestMz = 2600.956480;
122		BinningType binningType = BinningType::ARBITRARY;
123		int decimalPlaces = 3;
124		PrecisionPtr precision_p = pappso::PrecisionFactory::getPpmInstance(20);
125		bool applyMzShift = false;
126		double mzShift = 0;
	119
	120	TEST_CASE("Create bins with Da-based bin size", "[MzIntegrationParams]")
	121	{
	122	double smallestMz = 1800.373856;
	123	double greatestMz = 1800.373856;
	124	BinningType binningType = BinningType::ARBITRARY;
	125	int decimalPlaces = 3;
	126	PrecisionPtr precision_p = pappso::PrecisionFactory::getDaltonInstance(0.05);
	127	bool applyMzShift = false;
	128	double mzShift = 0;
127	129	bool removeZeroValDataPoints = true;
128	130
129	131	MzIntegrationParams mz_integration_params(smallestMz,

142	144
143	145	// Do not forget that we round to 3 decimal places:
144	146	REQUIRE(bins.front() == 1800.374);
145		REQUIRE(bins.back() == 2600.957 + precision_p->delta(2600.957));
146		}
147		}
	147
	148	// We create two bins: the first mz value (1800.374) and a new one that is
	149	// that mz value incremented by the delta (that is the size of the bin that
	150	// is created using an increment of 0.05).
	151
	152	REQUIRE(bins.back() == 1800.374 + precision_p->delta(1800.374));
	153	}
	154	}
	155
	156
	157	TEST_CASE("Create bins with ppm-based bin sizes", "[MzIntegrationParams]")
	158	{
	159	double smallestMz = 1800.373856;
	160	double greatestMz = 1800.373856;
	161	BinningType binningType = BinningType::ARBITRARY;
	162	int decimalPlaces = 3;
	163	PrecisionPtr precision_p = pappso::PrecisionFactory::getPpmInstance(20);
	164	bool applyMzShift = false;
	165	double mzShift = 0;
	166	bool removeZeroValDataPoints = true;
	167
	168	MzIntegrationParams mz_integration_params(smallestMz,
	169	greatestMz,
	170	binningType,
	171	decimalPlaces,
	172	precision_p,
	173	applyMzShift,
	174	mzShift,
	175	removeZeroValDataPoints);
	176
	177	SECTION("Create bins in ARBITRARY mode", "[MzIntegrationParams]")
	178	{
	179
	180	std::vector<double> bins = mz_integration_params.createBins();
	181
	182	// Do not forget that we round to 3 decimal places:
	183	REQUIRE(bins.front() == 1800.374);
	184
	185	// Check that the precision delta is computed correctly:
	186	double precision_delta = 1800.374 * 20 / 1000000;
	187	REQUIRE(pappso::Utils::almostEqual(
	188	precision_p->delta(1800.374), precision_delta, /decimal_places/ 15));
	189
	190	double rounded_precision_delta =
	191	ceil((precision_delta * pow(10, decimalPlaces)) - 0.49) /
	192	pow(10, decimalPlaces);
	193
	194	// We create two bins: the first mz value (1800.374) and a new one that is
	195	// that mz value incremented by the delta (that is the size of the bin that
	196	// is created using relative proportion of 20 ppm).
	197
	198	REQUIRE(bins.back() == 1800.374 + rounded_precision_delta);
	199	}
	200	}
	201
	202
	203	TEST_CASE("Create bins with res-based bin sizes", "[MzIntegrationParams]")
	204	{
	205	double smallestMz = 1800.373856;
	206	double greatestMz = 1800.373856;
	207	BinningType binningType = BinningType::ARBITRARY;
	208	int decimalPlaces = 3;
	209	PrecisionPtr precision_p = pappso::PrecisionFactory::getResInstance(20000);
	210	bool applyMzShift = false;
	211	double mzShift = 0;
	212	bool removeZeroValDataPoints = true;
	213
	214	MzIntegrationParams mz_integration_params(smallestMz,
	215	greatestMz,
	216	binningType,
	217	decimalPlaces,
	218	precision_p,
	219	applyMzShift,
	220	mzShift,
	221	removeZeroValDataPoints);
	222
	223	SECTION("Create bins in ARBITRARY mode", "[MzIntegrationParams]")
	224	{
	225
	226	std::vector<double> bins = mz_integration_params.createBins();
	227
	228	// Do not forget that we round to 3 decimal places:
	229	REQUIRE(bins.front() == 1800.374);
	230
	231	// Check that the precision delta is computed correctly:
	232	double precision_delta = 1800.374 / 20000;
	233	REQUIRE(pappso::Utils::almostEqual(
	234	precision_p->delta(1800.374), precision_delta, /decimal_places/ 15));
	235
	236	double rounded_precision_delta =
	237	ceil((precision_delta * pow(10, decimalPlaces)) - 0.49) /
	238	pow(10, decimalPlaces);
	239
	240	// We create two bins: the first mz value (1800.374) and a new one that is
	241	// that mz value incremented by the delta (that is the size of the bin that
	242	// is created using relative proportion of 20 ppm).
	243
	244	REQUIRE(bins.back() == 1800.374 + rounded_precision_delta);
	245	}
	246	}
	247
	248

+1

-1

tests/nongui/TraceCombiner_test.cpp less more

0		#include <catch.hpp>
	0	#include <catch2/catch.hpp>
1	1
2	2	#include <QDebug>
3	3

+18

-18

tests/nongui/Trace_test.cpp less more

0		#include <catch.hpp>
	0	#include <catch2/catch.hpp>
1	1
2	2	#include <QDebug>
3	3

510	510	std::vector<DataPoint> data_point_vector;
511	511
512	512	// clang-format off
513		data_point_vector.push_back(DataPoint("610.02000 55999.00000"));
514		data_point_vector.push_back(DataPoint("610.07000 55999.00000"));
515		data_point_vector.push_back(DataPoint("610.12000 55999.00000"));
516		data_point_vector.push_back(DataPoint("610.17000 55599.00000"));
517		data_point_vector.push_back(DataPoint("610.2200000 635674266.1611375809"));
518		data_point_vector.push_back(DataPoint("610.27000 54459.4762458801"));
519		data_point_vector.push_back(DataPoint("610.32000 205580.6580276489"));
520		data_point_vector.push_back(DataPoint("610.37000 84627.3196716309"));
521		data_point_vector.push_back(DataPoint("610.42000 51061.7636718750"));
522		data_point_vector.push_back(DataPoint("610.47000 20260.0218505859"));
523		data_point_vector.push_back(DataPoint("610.52000 29848.3424072266"));
524		data_point_vector.push_back(DataPoint("610.57000 27266.8031616211"));
	513	data_point_vector.push_back(DataPoint(610.02000, 55999));
	514	data_point_vector.push_back(DataPoint(610.07000, 55999));
	515	data_point_vector.push_back(DataPoint(610.12000, 55999));
	516	data_point_vector.push_back(DataPoint(610.17000, 55599));
	517	data_point_vector.push_back(DataPoint(610.22000, 635674266));
	518	data_point_vector.push_back(DataPoint(610.27000, 54459.4762458801));
	519	data_point_vector.push_back(DataPoint(610.32000, 205580.658027648));
	520	data_point_vector.push_back(DataPoint(610.37000, 84627.3196716309));
	521	data_point_vector.push_back(DataPoint(610.42000, 51061.7636718750));
	522	data_point_vector.push_back(DataPoint(610.47000, 20260.0218505859));
	523	data_point_vector.push_back(DataPoint(610.52000, 29848.3424072266));
	524	data_point_vector.push_back(DataPoint(610.57000, 27266.8031616211));
525	525	// clang-format on
526	526
527	527	Trace trace(data_point_vector);
528	528
529	529	std::vector<DataPoint>::iterator iterator =
530		findDifferentYvalue(trace.begin(), trace.end(), 55999.00000);
531
532		REQUIRE((*iterator).y == 635674266.1611375809);
	530	findDifferentYvalue(trace.begin(), trace.end(), 55999.0);
	531
	532	REQUIRE((*iterator).y == 635674266);
533	533	}
534	534
535	535	SECTION("Test minYDataPoint", "[Trace][filters]")

594	594	{
595	595	// As long as prev datapoint has y value less or equal to next,
596	596	// move along up the container. That is, continue moving if
597		// direction is downhill to the beginning of the container (its front).
	597	// direction is downhill to the beginning of the container (its front)
	598	// or if direction is uphill to the right (its back).
598	599
599	600	std::vector<DataPoint> data_point_vector;
600	601

607	608	data_point_vector.push_back(DataPoint("610.02000 12961.5715942383"));
608	609	data_point_vector.push_back(DataPoint("610.02000 12962.5715942383"));
609	610	data_point_vector.push_back(DataPoint("610.02000 12963.5715942383"));
610		data_point_vector.push_back(DataPoint("610.02000 12963.5715942383"));
611	611	// clang-format on
612	612
613	613	Trace trace(data_point_vector);

+1

-1

tests/testmain.cpp less more

0	0	#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
1	1	// this in one cpp file
2		#include <catch.hpp>
	2	#include <catch2/catch.hpp>