Commit upstream/2.4.0 - libbpp-raa

+7

-5

CMakeLists.txt less more

35	35	# library implements.
36	36	# In other words, the library implements all the interface numbers in the
37	37	# range from number current - age to current.
38		SET(${PROJECT_NAME}_VERSION_CURRENT "3")
	38	SET(${PROJECT_NAME}_VERSION_CURRENT "4")
39	39	SET(${PROJECT_NAME}_VERSION_REVISION "0")
40	40	SET(${PROJECT_NAME}_VERSION_AGE "0")
41	41

53	53	endif (CMAKE_INSTALL_PREFIX)
54	54
55	55	include (GNUInstallDirs)
56		find_package (bpp-seq 11.0.0 REQUIRED)
	56	find_package (bpp-seq 12.0.0 REQUIRED)
57	57
58	58	# Find the zlib installation (define zlib imported target)
59	59	find_package(ZLIB REQUIRED)

103	103	# Packager
104	104	SET(CPACK_PACKAGE_NAME "libbpp-raa")
105	105	SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
106		SET(CPACK_PACKAGE_VERSION "2.3.1")
	106	SET(CPACK_PACKAGE_VERSION "2.4.0")
107	107	SET(CPACK_PACKAGE_VERSION_MAJOR "2")
108		SET(CPACK_PACKAGE_VERSION_MINOR "3")
109		SET(CPACK_PACKAGE_VERSION_PATCH "1")
	108	SET(CPACK_PACKAGE_VERSION_MINOR "4")
	109	SET(CPACK_PACKAGE_VERSION_PATCH "0")
110	110	SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Remote Acnuc Access library")
111	111	SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
112	112	SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")

115	115	# /!\ This assumes that an external build is used
116	116	SET(CPACK_SOURCE_IGNORE_FILES
117	117	"/build/"
	118	"/html/"
	119	"/BppRaa.tag"
118	120	"/\\\\.git/"
119	121	"/\\\\.gitignore"
120	122	${CPACK_SOURCE_IGNORE_FILES}

+7

-0

ChangeLog less more

	0	25/02/18 -- version 2.4.0 --
	1
	2	25/02/18 Julien Dutheil
	3
	4	* Removed all dynamic exception specifications
	5	* Increased inerface number to 4.
	6
0	7	10/05/17 -- version 2.3.0 --
1	8
2	9	28/09/14 -- Version 2.2.0 --

+1

-1

Doxyfile less more

37	37	# could be handy for archiving the generated documentation or if some version
38	38	# control system is used.
39	39
40		PROJECT_NUMBER = 2.3.0
	40	PROJECT_NUMBER = 2.4.0
41	41
42	42	# Using the PROJECT_BRIEF tag one can provide an optional one line description
43	43	# for a project that appears at the top of each page and should give viewer a

+28

-26

bpp-raa.spec less more

0		%define _basename bpp-raa
1		%define _version 2.3.1
2		%define _release 1
3	0	%define _prefix /usr
4	1
5		URL: http://biopp.univ-montp2.fr/
	2	URL: https://github.com/BioPP/bpp-raa
6	3
7		Name: %{_basename}
8		Version: %{_version}
9		Release: %{_release}
	4	Name: bpp-raa
	5	Version: 2.4.0
	6	Release: 1%{?dist}
10	7	License: CECILL-2.0
11	8	Vendor: The Bio++ Project
12		Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz
	9	Source: %{name}-%{version}.tar.gz
13	10	Summary: Bio++ Remote Acnuc Access library
14	11	Group: Development/Libraries/C and C++
15		Requires: bpp-core = %{_version}
16		Requires: bpp-seq = %{_version}
	12	Requires: bpp-core = %{version}
	13	Requires: bpp-seq = %{version}
17	14
18		BuildRoot: %{_builddir}/%{_basename}-root
	15	BuildRoot: %{_builddir}/%{name}-root
19	16	BuildRequires: cmake >= 2.8.11
20	17	BuildRequires: gcc-c++ >= 4.7.0
21		BuildRequires: libbpp-core3 = %{_version}
22		BuildRequires: libbpp-core-devel = %{_version}
23		BuildRequires: libbpp-seq11 = %{_version}
24		BuildRequires: libbpp-seq-devel = %{_version}
	18	BuildRequires: libbpp-core4 = %{version}
	19	BuildRequires: libbpp-core-devel = %{version}
	20	BuildRequires: libbpp-seq12 = %{version}
	21	BuildRequires: libbpp-seq-devel = %{version}
25	22	BuildRequires: zlib >= 1.2.3
26	23	BuildRequires: zlib-devel >= 1.2.3
27	24

32	29	This library contains utilitary and classes to query public database (GenBank, EMBL, SwissProt, etc) using acnuc.
33	30	It is part of the Bio++ project.
34	31
35		%package -n libbpp-raa3
	32	%package -n libbpp-raa4
36	33	Summary: Bio++ Remote Acnuc Access library
37	34	Group: Development/Libraries/C and C++
38	35
39		%description -n libbpp-raa3
	36	%description -n libbpp-raa4
40	37	This library contains utilitary and classes to query public database (GenBank, EMBL, SwissProt, etc) using acnuc.
41	38	It is part of the Bio++ project.
42	39
43	40	%package -n libbpp-raa-devel
44	41	Summary: Libraries, includes to develop applications with %{_basename}
45	42	Group: Development/Libraries/C and C++
46		Requires: libbpp-raa3 = %{_version}
47		Requires: libbpp-seq11 = %{_version}
48		Requires: libbpp-seq-devel = %{_version}
49		Requires: libbpp-core3 = %{_version}
50		Requires: libbpp-core-devel = %{_version}
	43	Requires: libbpp-raa4 = %{version}
	44	Requires: libbpp-seq12 = %{version}
	45	Requires: libbpp-seq-devel = %{version}
	46	Requires: libbpp-core4 = %{version}
	47	Requires: libbpp-core-devel = %{version}
51	48	Requires: zlib >= 1.2.3
52	49	Requires: zlib-devel >= 1.2.3
53	50
54	51	%description -n libbpp-raa-devel
55	52	The libbpp-raa-devel package contains the header files and static libraries for
56		building applications which use %{_basename}.
	53	building applications which use %{name}.
	54
	55	%global debug_package %{nil}
57	56
58	57	%prep
59	58	%setup -q

70	69	%clean
71	70	rm -rf $RPM_BUILD_ROOT
72	71
73		%post -n libbpp-raa3 -p /sbin/ldconfig
	72	%post -n libbpp-raa4 -p /sbin/ldconfig
74	73
75		%postun -n libbpp-raa3 -p /sbin/ldconfig
	74	%postun -n libbpp-raa4 -p /sbin/ldconfig
76	75
77		%files -n libbpp-raa3
	76	%files -n libbpp-raa4
78	77	%defattr(-,root,root)
79	78	%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
80	79	%{_prefix}/%{_lib}/lib.so.

90	89	%{_prefix}/include/*
91	90
92	91	%changelog
	92	* Mon Feb 26 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
	93	- Increased interface number
	94	- Removed dynamic exceptions specifications.
93	95	* Tue Jun 06 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.1-1
94	96	- Increased interface number
95	97	* Wed May 10 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.0-1

+7

-7

src/Bpp/Raa/RAA.cpp less more

14	14	using namespace std;
15	15	using namespace bpp;
16	16
17		RAA::RAA(const string& dbname, int port, const string& server) throw (int)
	17	RAA::RAA(const string& dbname, int port, const string& server)
18	18	{
19	19	kw_pattern = NULL;
20	20	current_address.div = -1;

26	26	}
27	27
28	28
29		RAA::RAA(int port, const string& server) throw (int)
	29	RAA::RAA(int port, const string& server)
30	30	{
31	31	kw_pattern = NULL;
32	32	int error = raa_open_socket((char)server.c_str(), port, (char)"Bio++", &raa_data);

240	240	}
241	241
242	242
243		Sequence* RAA::translateCDS(int seqrank) throw (BadCharException)
	243	Sequence* RAA::translateCDS(int seqrank)
244	244	{
245	245	char* descript;
246	246	if (seqrank < 2 \|\| seqrank > raa_data->nseq)

275	275	}
276	276
277	277
278		Sequence* RAA::translateCDS(const string& name) throw (BadCharException)
	278	Sequence* RAA::translateCDS(const string& name)
279	279	{
280	280	int rank;
281	281	rank = raa_isenum(raa_data, (char*)name.c_str());

302	302	}
303	303
304	304
305		RaaList* RAA::processQuery(const string& query, const string& listname) throw (string)
	305	RaaList* RAA::processQuery(const string& query, const string& listname)
306	306	{
307	307	char* message;
308	308	int type, rank;

328	328	}
329	329
330	330
331		RaaList* RAA::createEmptyList(const string& listname, const string& kind) throw (int)
	331	RaaList* RAA::createEmptyList(const string& listname, const string& kind)
332	332	{
333	333	int err, lrank;
334	334	char type, * p = 0, * q = 0;

551	551	};
552	552
553	553
554		void* RAA::prepareGetAnyFeature(int seqrank, const string& featurekey) throw (string)
	554	void* RAA::prepareGetAnyFeature(int seqrank, const string& featurekey)
555	555	{
556	556	char* p, * line;
557	557	int l;

+7

-7

src/Bpp/Raa/RAA.h less more

96	96	* 4: database is currently not available for remote connection\n
97	97	* 7: not enough memory
98	98	*/
99		RAA(const std::string& dbname, int port = 5558, const std::string& server = "pbil.univ-lyon1.fr") throw (int);
	99	RAA(const std::string& dbname, int port = 5558, const std::string& server = "pbil.univ-lyon1.fr");
100	100
101	101	/**
102	102	* @brief Direct constructor: opens a network connection to a database server, without specifying a database.

112	112	* 2: cannot create connection with server\n
113	113	* 7: not enough memory
114	114	*/
115		RAA(int port = 5558, const std::string& server = "pbil.univ-lyon1.fr") throw (int);
	115	RAA(int port = 5558, const std::string& server = "pbil.univ-lyon1.fr");
116	116
117	117	/**
118	118	* @brief Destructor: closes both the database access, if any, and the network connection.

271	271	* @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an
272	272	* exception when translated to protein.
273	273	*/
274		Sequence* translateCDS(int seqrank) throw (BadCharException); // TODO add comment to Sequence
	274	Sequence* translateCDS(int seqrank); // TODO add comment to Sequence
275	275
276	276	/**
277	277	* @brief Returns the full protein translation of a protein-coding nucleotide database (sub)sequence.

284	284	* @throw BadCharException In rare cases, the CDS may contain an internal stop codon that raises an
285	285	* exception when translated to protein.
286	286	*/
287		Sequence* translateCDS(const std::string& name) throw (BadCharException);
	287	Sequence* translateCDS(const std::string& name);
288	288
289	289	/**
290	290	* @brief Returns the amino acid translation of the first codon of a protein-coding (sub)sequence.

315	315	* @return The resulting list of matching database elements.
316	316	* @throw string If error, the string is a message describing the error cause.
317	317	*/
318		RaaList* processQuery(const std::string& query, const std::string& listname) throw (std::string);
	318	RaaList* processQuery(const std::string& query, const std::string& listname);
319	319
320	320	/**
321	321	* @brief Creates an empty list with specified name.

327	327	* @throw int 3: a list with same name already existed; it is left unchanged.\n
328	328	* 4: the server cannot create more lists.
329	329	*/
330		RaaList* createEmptyList(const std::string& listname, const std::string& kind = RaaList::LIST_SEQUENCES) throw (int);
	330	RaaList* createEmptyList(const std::string& listname, const std::string& kind = RaaList::LIST_SEQUENCES);
331	331
332	332	/**
333	333	* @brief Deletes a list and calls its destructor.

405	405	* @return An opaque pointer to be transmitted to functions getNextFeature() or interruptGetAnyFeature().
406	406	* @throw string A message indicating the cause of the error.
407	407	*/
408		void* prepareGetAnyFeature(int seqrank, const std::string& featurekey) throw (std::string);
	408	void* prepareGetAnyFeature(int seqrank, const std::string& featurekey);
409	409
410	410	/**
411	411	* @brief Successively returns features specified in a previous prepareGetAnyFeature() call.

+1

-1

src/Bpp/Raa/RAA_acnuc.c less more

3191	3191	char raa_translate_init_codon(raa_db_access* raa_current_db, int numseq)
3192	3192	{
3193	3193	char codon[4];
3194		int point, special_init = TRUE, val, gc, phase, rank = 0;
	3194	int point, special_init = TRUE, val, gc = 0, phase = 0, rank = 0;
3195	3195
3196	3196	if (raa_current_db->num_5_partial == 0)
3197	3197	raa_current_db->num_5_partial = raa_iknum(raa_current_db, "5'-PARTIAL", raa_key);