[med-svn] [Git][med-team/libbpp-raa][master] 3 commits: New upstream version 2.4.1
Julien Y. Dutheil
gitlab at salsa.debian.org
Wed Aug 22 08:12:16 BST 2018
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-raa
Commits:
7506d6dd by Julien Y. Dutheil at 2018-08-22T07:04:21Z
New upstream version 2.4.1
- - - - -
43ec7b6d by Julien Y. Dutheil at 2018-08-22T07:04:22Z
Update upstream source from tag 'upstream/2.4.1'
Update to upstream version '2.4.1'
with Debian dir af59c05c7f52956e6fa7501633b0593503cc9a8c
- - - - -
49529bac by Julien Y. Dutheil at 2018-08-22T07:11:36Z
Version 2.4.1.
- - - - -
8 changed files:
- CMakeLists.txt
- Doxyfile
- bpp-raa.spec
- debian/changelog
- debian/control
- debian/libbpp-raa4.symbols
- − header.html
- src/Bpp/Raa/RAA.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -104,10 +104,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-raa")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Remote Acnuc Access library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=====================================
Doxyfile
=====================================
--- a/Doxyfile
+++ b/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-raa
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = 2.4.0
+PROJECT_NUMBER = 2.4.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
=====================================
bpp-raa.spec
=====================================
--- a/bpp-raa.spec
+++ b/bpp-raa.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP/bpp-raa
Name: bpp-raa
-Version: 2.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -90,8 +90,10 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/include/*
%changelog
+* Mon Aug 13 2018 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.4.1-1
+- Compatibility gcc8.
* Mon Feb 26 2018 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.4.0-1
-- Increased interface number
+- Increased interface number.
- Removed dynamic exceptions specifications.
* Tue Jun 06 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.1-1
- Increased interface number
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+libbpp-raa (2.4.1-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Wed, 22 Aug 2018 09:04:28 +0200
+
libbpp-raa (2.4.0-2) unstable; urgency=medium
[ Julien Dutheil ]
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 11~),
cmake,
d-shlibs (>= 0.80),
zlib1g-dev,
- libbpp-seq-dev (>= 2.4.0)
+ libbpp-seq-dev (>= 2.4.1)
Standards-Version: 4.1.3
Vcs-Browser: https://salsa.debian.org/med-team/libbpp-raa
Vcs-Git: https://salsa.debian.org/med-team/libbpp-raa.git
@@ -19,7 +19,7 @@ Architecture: any
Section: libdevel
Depends: libbpp-raa4 (= ${binary:Version}),
${misc:Depends},
- libbpp-seq-dev (>= 2.4.0)
+ libbpp-seq-dev (>= 2.4.1)
Description: Bio++ Remote Acnuc Access library development files
This library contains utilitary and classes to query public databases
(GenBank, EMBL, SwissProt, etc) using acnuc.
=====================================
debian/libbpp-raa4.symbols
=====================================
--- a/debian/libbpp-raa4.symbols
+++ b/debian/libbpp-raa4.symbols
@@ -1,184 +1,184 @@
libbpp-raa.so.4 libbpp-raa4 #MINVER#
- _ZN3bpp14RaaSpeciesTree10firstChildEi at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree11nextSynonymEi at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree5countEi at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree5labelB5cxx11Ei at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree6getTidEi at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree6parentEi at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree7getNameB5cxx11Ei at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree7isChildEii at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree8findNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree8findNodeEi at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree8getMajorEi at Base 2.4.0
- _ZN3bpp14RaaSpeciesTree9nextChildEii at Base 2.4.0
- _ZN3bpp16BadCharExceptionC1ERKS0_ at Base 2.4.0
- _ZN3bpp16BadCharExceptionC2ERKS0_ at Base 2.4.0
- _ZN3bpp16BadCharExceptionD0Ev at Base 2.4.0
- _ZN3bpp16BadCharExceptionD1Ev at Base 2.4.0
- _ZN3bpp16BadCharExceptionD2Ev at Base 2.4.0
- _ZN3bpp17AlphabetExceptionD0Ev at Base 2.4.0
- _ZN3bpp17AlphabetExceptionD1Ev at Base 2.4.0
- _ZN3bpp17AlphabetExceptionD2Ev at Base 2.4.0
- _ZN3bpp3RAA10deleteListEPNS_7RaaListE at Base 2.4.0
- _ZN3bpp3RAA10getSeqFragERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiRS6_ at Base 2.4.0
- _ZN3bpp3RAA10getSeqFragEiiiRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.0
- _ZN3bpp3RAA11getSeq_bothERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEii at Base 2.4.0
- _ZN3bpp3RAA12openDatabaseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFPcPvESA_ at Base 2.4.0
- _ZN3bpp3RAA12processQueryERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.0
- _ZN3bpp3RAA12translateCDSERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.0
- _ZN3bpp3RAA12translateCDSEi at Base 2.4.0
- _ZN3bpp3RAA13closeDatabaseEv at Base 2.4.0
- _ZN3bpp3RAA13getAttributesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.0
- _ZN3bpp3RAA13getAttributesEi at Base 2.4.0
- _ZN3bpp3RAA14getNextFeatureEPv at Base 2.4.0
- _ZN3bpp3RAA14keywordPatternERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.0
- _ZN3bpp3RAA14knownDatabasesERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EESA_ at Base 2.4.0
- _ZN3bpp3RAA15createEmptyListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.0
- _ZN3bpp3RAA15freeSpeciesTreeEPNS_14RaaSpeciesTreeE at Base 2.4.0
- _ZN3bpp3RAA15loadSpeciesTreeEb at Base 2.4.0
- _ZN3bpp3RAA16getDirectFeatureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_S8_S8_ at Base 2.4.0
- _ZN3bpp3RAA16getNextAnnotLineB5cxx11Ev at Base 2.4.0
- _ZN3bpp3RAA17getFirstAnnotLineB5cxx11Ei at Base 2.4.0
- _ZN3bpp3RAA18listAllFeatureKeysB5cxx11Ev at Base 2.4.0
- _ZN3bpp3RAA18translateInitCodonEi at Base 2.4.0
- _ZN3bpp3RAA19nextMatchingKeywordERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.0
- _ZN3bpp3RAA20prepareGetAnyFeatureEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.0
- _ZN3bpp3RAA21getAnnotLineAtAddressB5cxx11ENS_10RaaAddressE at Base 2.4.0
- _ZN3bpp3RAA21listDirectFeatureKeysB5cxx11Ev at Base 2.4.0
- _ZN3bpp3RAA22getCurrentAnnotAddressEv at Base 2.4.0
- _ZN3bpp3RAA22interruptGetAnyFeatureEPv at Base 2.4.0
- _ZN3bpp3RAA6getSeqERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi at Base 2.4.0
- _ZN3bpp3RAA6getSeqEii at Base 2.4.0
- _ZN3bpp3RAAC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiS8_ at Base 2.4.0
- _ZN3bpp3RAAC1EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.0
- _ZN3bpp3RAAC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiS8_ at Base 2.4.0
- _ZN3bpp3RAAC2EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.0
- _ZN3bpp3RAAD1Ev at Base 2.4.0
- _ZN3bpp3RAAD2Ev at Base 2.4.0
- _ZN3bpp7RaaList10addElementEi at Base 2.4.0
- _ZN3bpp7RaaList11nextElementEv at Base 2.4.0
- _ZN3bpp7RaaList11parentsOnlyEv at Base 2.4.0
- _ZN3bpp7RaaList12LIST_SPECIESB5cxx11E at Base 2.4.0
- _ZN3bpp7RaaList12firstElementEv at Base 2.4.0
- _ZN3bpp7RaaList12modifyByDateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.0
- _ZN3bpp7RaaList12residueCountB5cxx11Ev at Base 2.4.0
- _ZN3bpp7RaaList13LIST_KEYWORDSB5cxx11E at Base 2.4.0
- _ZN3bpp7RaaList13removeElementEi at Base 2.4.0
- _ZN3bpp7RaaList14LIST_SEQUENCESB5cxx11E at Base 2.4.0
- _ZN3bpp7RaaList14modifyByLengthERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.0
- _ZN3bpp7RaaList7setFromEi at Base 2.4.0
- _ZN3bpp7RaaList8getCountEv at Base 2.4.0
- _ZN3bpp7RaaList8isInListEi at Base 2.4.0
- _ZN3bpp7RaaList8zeroListEv at Base 2.4.0
- _ZN3bpp7RaaListC1Ev at Base 2.4.0
- _ZN3bpp7RaaListC2Ev at Base 2.4.0
- _ZNK3bpp17AlphabetException11getAlphabetEv at Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm at Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.0
- _ZTINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.0
- _ZTSNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.0
- ajout_reponse at Base 2.4.0
- aminoacids at Base 2.4.0
- atoi_u at Base 2.4.0
- calc_codon_number at Base 2.4.0
- chg_acnuc at Base 2.4.0
- clear_reponse at Base 2.4.0
- close_sock_gz_r at Base 2.4.0
- codaa at Base 2.4.0
- compact at Base 2.4.0
- compch at Base 2.4.0
- complementer_base at Base 2.4.0
- complementer_seq at Base 2.4.0
- genetic_code at Base 2.4.0
- get_acnuc_gc_number at Base 2.4.0
- get_code_descr at Base 2.4.0
- get_ncbi_gc_number at Base 2.4.0
- gets_no_echo at Base 2.4.0
- init_codon_to_aa at Base 2.4.0
- initreponse at Base 2.4.0
- majuscules at Base 2.4.0
- mycalloc at Base 2.4.0
- notrail2 at Base 2.4.0
- padtosize at Base 2.4.0
- parse at Base 2.4.0
- prepare_sock_gz_r at Base 2.4.0
- prepch at Base 2.4.0
- print_raa_long at Base 2.4.0
- raa_1_coordinate_set at Base 2.4.0
- raa_MD5String at Base 2.4.0
- raa_acnucclose at Base 2.4.0
- raa_acnucopen at Base 2.4.0
- raa_acnucopen_alt at Base 2.4.0
- raa_alllistranks at Base 2.4.0
- raa_bcount at Base 2.4.0
- raa_bit0 at Base 2.4.0
- raa_bit1 at Base 2.4.0
- raa_btest at Base 2.4.0
- raa_copylist at Base 2.4.0
- raa_countfilles at Base 2.4.0
- raa_decode_address at Base 2.4.0
- raa_error_mess_proc at Base 2.4.0
- raa_fcode at Base 2.4.0
- raa_followshrt2 at Base 2.4.0
- raa_get_taxon_info at Base 2.4.0
- raa_getattributes at Base 2.4.0
- raa_getemptylist at Base 2.4.0
- raa_getlistrank at Base 2.4.0
- raa_getliststate at Base 2.4.0
- raa_gfrag at Base 2.4.0
- raa_ghelp at Base 2.4.0
- raa_iknum at Base 2.4.0
- raa_isenum at Base 2.4.0
- raa_knowndbs at Base 2.4.0
- raa_loadtaxonomy at Base 2.4.0
- raa_modifylist at Base 2.4.0
- raa_next_annots at Base 2.4.0
- raa_nexteltinlist at Base 2.4.0
- raa_nexteltinlist_annots at Base 2.4.0
- raa_nextmatchkey at Base 2.4.0
- raa_open_socket at Base 2.4.0
- raa_opendb at Base 2.4.0
- raa_opendb_pw at Base 2.4.0
- raa_prep_acnuc_query at Base 2.4.0
- raa_prep_coordinates at Base 2.4.0
- raa_proc_query at Base 2.4.0
- raa_read_annots at Base 2.4.0
- raa_read_first_rec at Base 2.4.0
- raa_readacc at Base 2.4.0
- raa_readext at Base 2.4.0
- raa_readkey at Base 2.4.0
- raa_readlng at Base 2.4.0
- raa_readloc at Base 2.4.0
- raa_readshrt at Base 2.4.0
- raa_readsmj at Base 2.4.0
- raa_readspec at Base 2.4.0
- raa_readsub at Base 2.4.0
- raa_readsub_pannots at Base 2.4.0
- raa_releaselist at Base 2.4.0
- raa_residuecount at Base 2.4.0
- raa_savelist at Base 2.4.0
- raa_seq_to_annots at Base 2.4.0
- raa_seqrank_attributes at Base 2.4.0
- raa_setlistname at Base 2.4.0
- raa_setliststate at Base 2.4.0
- raa_short_descr at Base 2.4.0
- raa_translate_cds at Base 2.4.0
- raa_translate_init_codon at Base 2.4.0
- raa_zerolist at Base 2.4.0
- read_sock at Base 2.4.0
- read_sock_timeout at Base 2.4.0
- scan_raa_long at Base 2.4.0
- sock_flush at Base 2.4.0
- sock_fputs at Base 2.4.0
- sock_printf at Base 2.4.0
- strcmptrail at Base 2.4.0
- totcodes at Base 2.4.0
- trim_key at Base 2.4.0
- unprotect_quotes at Base 2.4.0
- val at Base 2.4.0
- z_getc at Base 2.4.0
- z_gets at Base 2.4.0
- z_read_sock at Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree10firstChildEi at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree11nextSynonymEi at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree5countEi at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree5labelB5cxx11Ei at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree6getTidEi at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree6parentEi at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree7getNameB5cxx11Ei at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree7isChildEii at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree8findNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree8findNodeEi at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree8getMajorEi at Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree9nextChildEii at Base 2.4.1
+ _ZN3bpp16BadCharExceptionD0Ev at Base 2.4.1
+ _ZN3bpp16BadCharExceptionD1Ev at Base 2.4.1
+ _ZN3bpp16BadCharExceptionD2Ev at Base 2.4.1
+ _ZN3bpp17AlphabetExceptionD0Ev at Base 2.4.1
+ _ZN3bpp17AlphabetExceptionD1Ev at Base 2.4.1
+ _ZN3bpp17AlphabetExceptionD2Ev at Base 2.4.1
+ _ZN3bpp3RAA10deleteListEPNS_7RaaListE at Base 2.4.1
+ _ZN3bpp3RAA10getSeqFragERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiRS6_ at Base 2.4.1
+ _ZN3bpp3RAA10getSeqFragEiiiRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZN3bpp3RAA11getSeq_bothERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEii at Base 2.4.1
+ _ZN3bpp3RAA12openDatabaseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFPcPvESA_ at Base 2.4.1
+ _ZN3bpp3RAA12processQueryERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.1
+ _ZN3bpp3RAA12translateCDSERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZN3bpp3RAA12translateCDSEi at Base 2.4.1
+ _ZN3bpp3RAA13closeDatabaseEv at Base 2.4.1
+ _ZN3bpp3RAA13getAttributesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZN3bpp3RAA13getAttributesEi at Base 2.4.1
+ _ZN3bpp3RAA14getNextFeatureEPv at Base 2.4.1
+ _ZN3bpp3RAA14keywordPatternERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZN3bpp3RAA14knownDatabasesERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EESA_ at Base 2.4.1
+ _ZN3bpp3RAA15createEmptyListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.1
+ _ZN3bpp3RAA15freeSpeciesTreeEPNS_14RaaSpeciesTreeE at Base 2.4.1
+ _ZN3bpp3RAA15loadSpeciesTreeEb at Base 2.4.1
+ _ZN3bpp3RAA16getDirectFeatureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_S8_S8_ at Base 2.4.1
+ _ZN3bpp3RAA16getNextAnnotLineB5cxx11Ev at Base 2.4.1
+ _ZN3bpp3RAA17getFirstAnnotLineB5cxx11Ei at Base 2.4.1
+ _ZN3bpp3RAA18listAllFeatureKeysB5cxx11Ev at Base 2.4.1
+ _ZN3bpp3RAA18translateInitCodonEi at Base 2.4.1
+ _ZN3bpp3RAA19nextMatchingKeywordERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZN3bpp3RAA20prepareGetAnyFeatureEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZN3bpp3RAA21getAnnotLineAtAddressB5cxx11ENS_10RaaAddressE at Base 2.4.1
+ _ZN3bpp3RAA21listDirectFeatureKeysB5cxx11Ev at Base 2.4.1
+ _ZN3bpp3RAA22getCurrentAnnotAddressEv at Base 2.4.1
+ _ZN3bpp3RAA22interruptGetAnyFeatureEPv at Base 2.4.1
+ _ZN3bpp3RAA6getSeqERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi at Base 2.4.1
+ _ZN3bpp3RAA6getSeqEii at Base 2.4.1
+ _ZN3bpp3RAAC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiS8_ at Base 2.4.1
+ _ZN3bpp3RAAC1EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZN3bpp3RAAC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiS8_ at Base 2.4.1
+ _ZN3bpp3RAAC2EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZN3bpp3RAAD1Ev at Base 2.4.1
+ _ZN3bpp3RAAD2Ev at Base 2.4.1
+ _ZN3bpp7RaaList10addElementEi at Base 2.4.1
+ _ZN3bpp7RaaList11nextElementEv at Base 2.4.1
+ _ZN3bpp7RaaList11parentsOnlyEv at Base 2.4.1
+ _ZN3bpp7RaaList12LIST_SPECIESB5cxx11E at Base 2.4.1
+ _ZN3bpp7RaaList12firstElementEv at Base 2.4.1
+ _ZN3bpp7RaaList12modifyByDateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.1
+ _ZN3bpp7RaaList12residueCountB5cxx11Ev at Base 2.4.1
+ _ZN3bpp7RaaList13LIST_KEYWORDSB5cxx11E at Base 2.4.1
+ _ZN3bpp7RaaList13removeElementEi at Base 2.4.1
+ _ZN3bpp7RaaList14LIST_SEQUENCESB5cxx11E at Base 2.4.1
+ _ZN3bpp7RaaList14modifyByLengthERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.1
+ _ZN3bpp7RaaList7setFromEi at Base 2.4.1
+ _ZN3bpp7RaaList8getCountEv at Base 2.4.1
+ _ZN3bpp7RaaList8isInListEi at Base 2.4.1
+ _ZN3bpp7RaaList8zeroListEv at Base 2.4.1
+ _ZN3bpp7RaaListC1Ev at Base 2.4.1
+ _ZN3bpp7RaaListC2Ev at Base 2.4.1
+ _ZNK3bpp17AlphabetException11getAlphabetEv at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 2.4.1
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag at Base 2.4.1
+ _ZTINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZTSNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ ajout_reponse at Base 2.4.1
+ aminoacids at Base 2.4.1
+ atoi_u at Base 2.4.1
+ calc_codon_number at Base 2.4.1
+ chg_acnuc at Base 2.4.1
+ clear_reponse at Base 2.4.1
+ close_sock_gz_r at Base 2.4.1
+ codaa at Base 2.4.1
+ compact at Base 2.4.1
+ compch at Base 2.4.1
+ complementer_base at Base 2.4.1
+ complementer_seq at Base 2.4.1
+ genetic_code at Base 2.4.1
+ get_acnuc_gc_number at Base 2.4.1
+ get_code_descr at Base 2.4.1
+ get_ncbi_gc_number at Base 2.4.1
+ gets_no_echo at Base 2.4.1
+ init_codon_to_aa at Base 2.4.1
+ initreponse at Base 2.4.1
+ majuscules at Base 2.4.1
+ mycalloc at Base 2.4.1
+ notrail2 at Base 2.4.1
+ padtosize at Base 2.4.1
+ parse at Base 2.4.1
+ prepare_sock_gz_r at Base 2.4.1
+ prepch at Base 2.4.1
+ print_raa_long at Base 2.4.1
+ raa_1_coordinate_set at Base 2.4.1
+ raa_MD5String at Base 2.4.1
+ raa_acnucclose at Base 2.4.1
+ raa_acnucopen at Base 2.4.1
+ raa_acnucopen_alt at Base 2.4.1
+ raa_alllistranks at Base 2.4.1
+ raa_bcount at Base 2.4.1
+ raa_bit0 at Base 2.4.1
+ raa_bit1 at Base 2.4.1
+ raa_btest at Base 2.4.1
+ raa_copylist at Base 2.4.1
+ raa_countfilles at Base 2.4.1
+ raa_decode_address at Base 2.4.1
+ raa_error_mess_proc at Base 2.4.1
+ raa_fcode at Base 2.4.1
+ raa_followshrt2 at Base 2.4.1
+ raa_get_taxon_info at Base 2.4.1
+ raa_getattributes at Base 2.4.1
+ raa_getemptylist at Base 2.4.1
+ raa_getlistrank at Base 2.4.1
+ raa_getliststate at Base 2.4.1
+ raa_gfrag at Base 2.4.1
+ raa_ghelp at Base 2.4.1
+ raa_iknum at Base 2.4.1
+ raa_isenum at Base 2.4.1
+ raa_knowndbs at Base 2.4.1
+ raa_loadtaxonomy at Base 2.4.1
+ raa_modifylist at Base 2.4.1
+ raa_next_annots at Base 2.4.1
+ raa_nexteltinlist at Base 2.4.1
+ raa_nexteltinlist_annots at Base 2.4.1
+ raa_nextmatchkey at Base 2.4.1
+ raa_open_socket at Base 2.4.1
+ raa_opendb at Base 2.4.1
+ raa_opendb_pw at Base 2.4.1
+ raa_prep_acnuc_query at Base 2.4.1
+ raa_prep_coordinates at Base 2.4.1
+ raa_proc_query at Base 2.4.1
+ raa_read_annots at Base 2.4.1
+ raa_read_first_rec at Base 2.4.1
+ raa_readacc at Base 2.4.1
+ raa_readext at Base 2.4.1
+ raa_readkey at Base 2.4.1
+ raa_readlng at Base 2.4.1
+ raa_readloc at Base 2.4.1
+ raa_readshrt at Base 2.4.1
+ raa_readsmj at Base 2.4.1
+ raa_readspec at Base 2.4.1
+ raa_readsub at Base 2.4.1
+ raa_readsub_pannots at Base 2.4.1
+ raa_releaselist at Base 2.4.1
+ raa_residuecount at Base 2.4.1
+ raa_savelist at Base 2.4.1
+ raa_seq_to_annots at Base 2.4.1
+ raa_seqrank_attributes at Base 2.4.1
+ raa_setlistname at Base 2.4.1
+ raa_setliststate at Base 2.4.1
+ raa_short_descr at Base 2.4.1
+ raa_translate_cds at Base 2.4.1
+ raa_translate_init_codon at Base 2.4.1
+ raa_zerolist at Base 2.4.1
+ read_sock at Base 2.4.1
+ read_sock_timeout at Base 2.4.1
+ scan_raa_long at Base 2.4.1
+ sock_flush at Base 2.4.1
+ sock_fputs at Base 2.4.1
+ sock_printf at Base 2.4.1
+ strcmptrail at Base 2.4.1
+ totcodes at Base 2.4.1
+ trim_key at Base 2.4.1
+ unprotect_quotes at Base 2.4.1
+ val at Base 2.4.1
+ z_getc at Base 2.4.1
+ z_gets at Base 2.4.1
+ z_read_sock at Base 2.4.1
=====================================
header.html deleted
=====================================
--- a/header.html
+++ /dev/null
@@ -1,27 +0,0 @@
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
- <head>
- <meta http-equiv="Content-Type" content="text/xhtml;charset=utf-8" />
- <meta http-equiv="Content-Style-Type" content="text/css" />
- <meta http-equiv="Content-Language" content="en" />
- <link href="doxygen.css" rel="stylesheet" type="text/css">
- <link href="tabs.css" rel="stylesheet" type="text/css">
- </head>
-
- <body>
- <div id="banner">
- <h1><a href="http://kimura.univ-montp2.fr/BioPP/" accesskey="1" target="_top">Bio++</a> Class documentation</h1>
- </div>
-
- <div class="tabs">
- <ul>
- <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Utils/html/index.html" target="_top"><span>Utils</span></a></li>
- <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/NumCalc/html/index.html" target="_top"><span>NumCalc</span></a></li>
- <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Seq/html/index.html" target="_top"><span>SeqLib</span></a></li>
- <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Phyl/html/index.html" target="_top"><span>PhylLib</span></a></li>
- <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Pop/html/index.html" target="_top"><span>PopGenLib</span></a></li>
- <li><a href="http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Raa/html/index.html" target="_top"><span>Raa</span></a></li>
- </ul>
- </div>
-
- <br />
-
=====================================
src/Bpp/Raa/RAA.cpp
=====================================
--- a/src/Bpp/Raa/RAA.cpp
+++ b/src/Bpp/Raa/RAA.cpp
@@ -262,7 +262,7 @@ Sequence* RAA::translateCDS(int seqrank)
{
Sprot = new BasicSequence(*sname, *pstring, &AlphabetTools::PROTEIN_ALPHABET );
}
- catch (BadCharException e)
+ catch (BadCharException& e)
{
delete sname;
delete pstring;
@@ -283,14 +283,7 @@ Sequence* RAA::translateCDS(const string& name)
if (rank == 0)
return NULL;
Sequence* Sprot;
- try
- {
- Sprot = translateCDS(rank);
- }
- catch (BadCharException e)
- {
- throw e;
- }
+ Sprot = translateCDS(rank);
return Sprot;
}
View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/compare/d31369150300a5a337fdd8e7ee52ba7681dd22fc...49529bac83f23c9c9c1bd9cec459f27eb87404f3
--
View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/compare/d31369150300a5a337fdd8e7ee52ba7681dd22fc...49529bac83f23c9c9c1bd9cec459f27eb87404f3
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