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

@@ -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

@@ -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@univ-montp2.fr> 2.4.1-1
+- Compatibility gcc8.
 * Mon Feb 26 2018 Julien Dutheil <julien.dutheil@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@univ-montp2.fr> 2.3.1-1
 - Increased interface number

debian/changelog

+libbpp-raa (2.4.1-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Wed, 22 Aug 2018 09:04:28 +0200
+
 libbpp-raa (2.4.0-2) unstable; urgency=medium
 
   [ Julien Dutheil ]

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

 libbpp-raa.so.4 libbpp-raa4 #MINVER#
- _ZN3bpp14RaaSpeciesTree10firstChildEi@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree11nextSynonymEi@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree5countEi@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree5labelB5cxx11Ei@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree6getTidEi@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree6parentEi@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree7getNameB5cxx11Ei@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree7isChildEii@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree8findNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree8findNodeEi@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree8getMajorEi@Base 2.4.0
- _ZN3bpp14RaaSpeciesTree9nextChildEii@Base 2.4.0
- _ZN3bpp16BadCharExceptionC1ERKS0_@Base 2.4.0
- _ZN3bpp16BadCharExceptionC2ERKS0_@Base 2.4.0
- _ZN3bpp16BadCharExceptionD0Ev@Base 2.4.0
- _ZN3bpp16BadCharExceptionD1Ev@Base 2.4.0
- _ZN3bpp16BadCharExceptionD2Ev@Base 2.4.0
- _ZN3bpp17AlphabetExceptionD0Ev@Base 2.4.0
- _ZN3bpp17AlphabetExceptionD1Ev@Base 2.4.0
- _ZN3bpp17AlphabetExceptionD2Ev@Base 2.4.0
- _ZN3bpp3RAA10deleteListEPNS_7RaaListE@Base 2.4.0
- _ZN3bpp3RAA10getSeqFragERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiRS6_@Base 2.4.0
- _ZN3bpp3RAA10getSeqFragEiiiRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
- _ZN3bpp3RAA11getSeq_bothERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEii@Base 2.4.0
- _ZN3bpp3RAA12openDatabaseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFPcPvESA_@Base 2.4.0
- _ZN3bpp3RAA12processQueryERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.0
- _ZN3bpp3RAA12translateCDSERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
- _ZN3bpp3RAA12translateCDSEi@Base 2.4.0
- _ZN3bpp3RAA13closeDatabaseEv@Base 2.4.0
- _ZN3bpp3RAA13getAttributesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
- _ZN3bpp3RAA13getAttributesEi@Base 2.4.0
- _ZN3bpp3RAA14getNextFeatureEPv@Base 2.4.0
- _ZN3bpp3RAA14keywordPatternERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
- _ZN3bpp3RAA14knownDatabasesERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EESA_@Base 2.4.0
- _ZN3bpp3RAA15createEmptyListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.0
- _ZN3bpp3RAA15freeSpeciesTreeEPNS_14RaaSpeciesTreeE@Base 2.4.0
- _ZN3bpp3RAA15loadSpeciesTreeEb@Base 2.4.0
- _ZN3bpp3RAA16getDirectFeatureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_S8_S8_@Base 2.4.0
- _ZN3bpp3RAA16getNextAnnotLineB5cxx11Ev@Base 2.4.0
- _ZN3bpp3RAA17getFirstAnnotLineB5cxx11Ei@Base 2.4.0
- _ZN3bpp3RAA18listAllFeatureKeysB5cxx11Ev@Base 2.4.0
- _ZN3bpp3RAA18translateInitCodonEi@Base 2.4.0
- _ZN3bpp3RAA19nextMatchingKeywordERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
- _ZN3bpp3RAA20prepareGetAnyFeatureEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
- _ZN3bpp3RAA21getAnnotLineAtAddressB5cxx11ENS_10RaaAddressE@Base 2.4.0
- _ZN3bpp3RAA21listDirectFeatureKeysB5cxx11Ev@Base 2.4.0
- _ZN3bpp3RAA22getCurrentAnnotAddressEv@Base 2.4.0
- _ZN3bpp3RAA22interruptGetAnyFeatureEPv@Base 2.4.0
- _ZN3bpp3RAA6getSeqERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi@Base 2.4.0
- _ZN3bpp3RAA6getSeqEii@Base 2.4.0
- _ZN3bpp3RAAC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiS8_@Base 2.4.0
- _ZN3bpp3RAAC1EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
- _ZN3bpp3RAAC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiS8_@Base 2.4.0
- _ZN3bpp3RAAC2EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
- _ZN3bpp3RAAD1Ev@Base 2.4.0
- _ZN3bpp3RAAD2Ev@Base 2.4.0
- _ZN3bpp7RaaList10addElementEi@Base 2.4.0
- _ZN3bpp7RaaList11nextElementEv@Base 2.4.0
- _ZN3bpp7RaaList11parentsOnlyEv@Base 2.4.0
- _ZN3bpp7RaaList12LIST_SPECIESB5cxx11E@Base 2.4.0
- _ZN3bpp7RaaList12firstElementEv@Base 2.4.0
- _ZN3bpp7RaaList12modifyByDateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.0
- _ZN3bpp7RaaList12residueCountB5cxx11Ev@Base 2.4.0
- _ZN3bpp7RaaList13LIST_KEYWORDSB5cxx11E@Base 2.4.0
- _ZN3bpp7RaaList13removeElementEi@Base 2.4.0
- _ZN3bpp7RaaList14LIST_SEQUENCESB5cxx11E@Base 2.4.0
- _ZN3bpp7RaaList14modifyByLengthERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.0
- _ZN3bpp7RaaList7setFromEi@Base 2.4.0
- _ZN3bpp7RaaList8getCountEv@Base 2.4.0
- _ZN3bpp7RaaList8isInListEi@Base 2.4.0
- _ZN3bpp7RaaList8zeroListEv@Base 2.4.0
- _ZN3bpp7RaaListC1Ev@Base 2.4.0
- _ZN3bpp7RaaListC2Ev@Base 2.4.0
- _ZNK3bpp17AlphabetException11getAlphabetEv@Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_@Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm@Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base 2.4.0
- _ZTINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
- _ZTSNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.0
- ajout_reponse@Base 2.4.0
- aminoacids@Base 2.4.0
- atoi_u@Base 2.4.0
- calc_codon_number@Base 2.4.0
- chg_acnuc@Base 2.4.0
- clear_reponse@Base 2.4.0
- close_sock_gz_r@Base 2.4.0
- codaa@Base 2.4.0
- compact@Base 2.4.0
- compch@Base 2.4.0
- complementer_base@Base 2.4.0
- complementer_seq@Base 2.4.0
- genetic_code@Base 2.4.0
- get_acnuc_gc_number@Base 2.4.0
- get_code_descr@Base 2.4.0
- get_ncbi_gc_number@Base 2.4.0
- gets_no_echo@Base 2.4.0
- init_codon_to_aa@Base 2.4.0
- initreponse@Base 2.4.0
- majuscules@Base 2.4.0
- mycalloc@Base 2.4.0
- notrail2@Base 2.4.0
- padtosize@Base 2.4.0
- parse@Base 2.4.0
- prepare_sock_gz_r@Base 2.4.0
- prepch@Base 2.4.0
- print_raa_long@Base 2.4.0
- raa_1_coordinate_set@Base 2.4.0
- raa_MD5String@Base 2.4.0
- raa_acnucclose@Base 2.4.0
- raa_acnucopen@Base 2.4.0
- raa_acnucopen_alt@Base 2.4.0
- raa_alllistranks@Base 2.4.0
- raa_bcount@Base 2.4.0
- raa_bit0@Base 2.4.0
- raa_bit1@Base 2.4.0
- raa_btest@Base 2.4.0
- raa_copylist@Base 2.4.0
- raa_countfilles@Base 2.4.0
- raa_decode_address@Base 2.4.0
- raa_error_mess_proc@Base 2.4.0
- raa_fcode@Base 2.4.0
- raa_followshrt2@Base 2.4.0
- raa_get_taxon_info@Base 2.4.0
- raa_getattributes@Base 2.4.0
- raa_getemptylist@Base 2.4.0
- raa_getlistrank@Base 2.4.0
- raa_getliststate@Base 2.4.0
- raa_gfrag@Base 2.4.0
- raa_ghelp@Base 2.4.0
- raa_iknum@Base 2.4.0
- raa_isenum@Base 2.4.0
- raa_knowndbs@Base 2.4.0
- raa_loadtaxonomy@Base 2.4.0
- raa_modifylist@Base 2.4.0
- raa_next_annots@Base 2.4.0
- raa_nexteltinlist@Base 2.4.0
- raa_nexteltinlist_annots@Base 2.4.0
- raa_nextmatchkey@Base 2.4.0
- raa_open_socket@Base 2.4.0
- raa_opendb@Base 2.4.0
- raa_opendb_pw@Base 2.4.0
- raa_prep_acnuc_query@Base 2.4.0
- raa_prep_coordinates@Base 2.4.0
- raa_proc_query@Base 2.4.0
- raa_read_annots@Base 2.4.0
- raa_read_first_rec@Base 2.4.0
- raa_readacc@Base 2.4.0
- raa_readext@Base 2.4.0
- raa_readkey@Base 2.4.0
- raa_readlng@Base 2.4.0
- raa_readloc@Base 2.4.0
- raa_readshrt@Base 2.4.0
- raa_readsmj@Base 2.4.0
- raa_readspec@Base 2.4.0
- raa_readsub@Base 2.4.0
- raa_readsub_pannots@Base 2.4.0
- raa_releaselist@Base 2.4.0
- raa_residuecount@Base 2.4.0
- raa_savelist@Base 2.4.0
- raa_seq_to_annots@Base 2.4.0
- raa_seqrank_attributes@Base 2.4.0
- raa_setlistname@Base 2.4.0
- raa_setliststate@Base 2.4.0
- raa_short_descr@Base 2.4.0
- raa_translate_cds@Base 2.4.0
- raa_translate_init_codon@Base 2.4.0
- raa_zerolist@Base 2.4.0
- read_sock@Base 2.4.0
- read_sock_timeout@Base 2.4.0
- scan_raa_long@Base 2.4.0
- sock_flush@Base 2.4.0
- sock_fputs@Base 2.4.0
- sock_printf@Base 2.4.0
- strcmptrail@Base 2.4.0
- totcodes@Base 2.4.0
- trim_key@Base 2.4.0
- unprotect_quotes@Base 2.4.0
- val@Base 2.4.0
- z_getc@Base 2.4.0
- z_gets@Base 2.4.0
- z_read_sock@Base 2.4.0
+ _ZN3bpp14RaaSpeciesTree10firstChildEi@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree11nextSynonymEi@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree5countEi@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree5labelB5cxx11Ei@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree6getTidEi@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree6parentEi@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree7getNameB5cxx11Ei@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree7isChildEii@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree8findNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree8findNodeEi@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree8getMajorEi@Base 2.4.1
+ _ZN3bpp14RaaSpeciesTree9nextChildEii@Base 2.4.1
+ _ZN3bpp16BadCharExceptionD0Ev@Base 2.4.1
+ _ZN3bpp16BadCharExceptionD1Ev@Base 2.4.1
+ _ZN3bpp16BadCharExceptionD2Ev@Base 2.4.1
+ _ZN3bpp17AlphabetExceptionD0Ev@Base 2.4.1
+ _ZN3bpp17AlphabetExceptionD1Ev@Base 2.4.1
+ _ZN3bpp17AlphabetExceptionD2Ev@Base 2.4.1
+ _ZN3bpp3RAA10deleteListEPNS_7RaaListE@Base 2.4.1
+ _ZN3bpp3RAA10getSeqFragERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiRS6_@Base 2.4.1
+ _ZN3bpp3RAA10getSeqFragEiiiRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ _ZN3bpp3RAA11getSeq_bothERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEii@Base 2.4.1
+ _ZN3bpp3RAA12openDatabaseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFPcPvESA_@Base 2.4.1
+ _ZN3bpp3RAA12processQueryERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.1
+ _ZN3bpp3RAA12translateCDSERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ _ZN3bpp3RAA12translateCDSEi@Base 2.4.1
+ _ZN3bpp3RAA13closeDatabaseEv@Base 2.4.1
+ _ZN3bpp3RAA13getAttributesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ _ZN3bpp3RAA13getAttributesEi@Base 2.4.1
+ _ZN3bpp3RAA14getNextFeatureEPv@Base 2.4.1
+ _ZN3bpp3RAA14keywordPatternERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ _ZN3bpp3RAA14knownDatabasesERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EESA_@Base 2.4.1
+ _ZN3bpp3RAA15createEmptyListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.1
+ _ZN3bpp3RAA15freeSpeciesTreeEPNS_14RaaSpeciesTreeE@Base 2.4.1
+ _ZN3bpp3RAA15loadSpeciesTreeEb@Base 2.4.1
+ _ZN3bpp3RAA16getDirectFeatureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_S8_S8_@Base 2.4.1
+ _ZN3bpp3RAA16getNextAnnotLineB5cxx11Ev@Base 2.4.1
+ _ZN3bpp3RAA17getFirstAnnotLineB5cxx11Ei@Base 2.4.1
+ _ZN3bpp3RAA18listAllFeatureKeysB5cxx11Ev@Base 2.4.1
+ _ZN3bpp3RAA18translateInitCodonEi@Base 2.4.1
+ _ZN3bpp3RAA19nextMatchingKeywordERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ _ZN3bpp3RAA20prepareGetAnyFeatureEiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ _ZN3bpp3RAA21getAnnotLineAtAddressB5cxx11ENS_10RaaAddressE@Base 2.4.1
+ _ZN3bpp3RAA21listDirectFeatureKeysB5cxx11Ev@Base 2.4.1
+ _ZN3bpp3RAA22getCurrentAnnotAddressEv@Base 2.4.1
+ _ZN3bpp3RAA22interruptGetAnyFeatureEPv@Base 2.4.1
+ _ZN3bpp3RAA6getSeqERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi@Base 2.4.1
+ _ZN3bpp3RAA6getSeqEii@Base 2.4.1
+ _ZN3bpp3RAAC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiS8_@Base 2.4.1
+ _ZN3bpp3RAAC1EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ _ZN3bpp3RAAC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiS8_@Base 2.4.1
+ _ZN3bpp3RAAC2EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ _ZN3bpp3RAAD1Ev@Base 2.4.1
+ _ZN3bpp3RAAD2Ev@Base 2.4.1
+ _ZN3bpp7RaaList10addElementEi@Base 2.4.1
+ _ZN3bpp7RaaList11nextElementEv@Base 2.4.1
+ _ZN3bpp7RaaList11parentsOnlyEv@Base 2.4.1
+ _ZN3bpp7RaaList12LIST_SPECIESB5cxx11E@Base 2.4.1
+ _ZN3bpp7RaaList12firstElementEv@Base 2.4.1
+ _ZN3bpp7RaaList12modifyByDateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.1
+ _ZN3bpp7RaaList12residueCountB5cxx11Ev@Base 2.4.1
+ _ZN3bpp7RaaList13LIST_KEYWORDSB5cxx11E@Base 2.4.1
+ _ZN3bpp7RaaList13removeElementEi@Base 2.4.1
+ _ZN3bpp7RaaList14LIST_SEQUENCESB5cxx11E@Base 2.4.1
+ _ZN3bpp7RaaList14modifyByLengthERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_@Base 2.4.1
+ _ZN3bpp7RaaList7setFromEi@Base 2.4.1
+ _ZN3bpp7RaaList8getCountEv@Base 2.4.1
+ _ZN3bpp7RaaList8isInListEi@Base 2.4.1
+ _ZN3bpp7RaaList8zeroListEv@Base 2.4.1
+ _ZN3bpp7RaaListC1Ev@Base 2.4.1
+ _ZN3bpp7RaaListC2Ev@Base 2.4.1
+ _ZNK3bpp17AlphabetException11getAlphabetEv@Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_@Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm@Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base 2.4.1
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag@Base 2.4.1
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag@Base 2.4.1
+ _ZTINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ _ZTSNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ ajout_reponse@Base 2.4.1
+ aminoacids@Base 2.4.1
+ atoi_u@Base 2.4.1
+ calc_codon_number@Base 2.4.1
+ chg_acnuc@Base 2.4.1
+ clear_reponse@Base 2.4.1
+ close_sock_gz_r@Base 2.4.1
+ codaa@Base 2.4.1
+ compact@Base 2.4.1
+ compch@Base 2.4.1
+ complementer_base@Base 2.4.1
+ complementer_seq@Base 2.4.1
+ genetic_code@Base 2.4.1
+ get_acnuc_gc_number@Base 2.4.1
+ get_code_descr@Base 2.4.1
+ get_ncbi_gc_number@Base 2.4.1
+ gets_no_echo@Base 2.4.1
+ init_codon_to_aa@Base 2.4.1
+ initreponse@Base 2.4.1
+ majuscules@Base 2.4.1
+ mycalloc@Base 2.4.1
+ notrail2@Base 2.4.1
+ padtosize@Base 2.4.1
+ parse@Base 2.4.1
+ prepare_sock_gz_r@Base 2.4.1
+ prepch@Base 2.4.1
+ print_raa_long@Base 2.4.1
+ raa_1_coordinate_set@Base 2.4.1
+ raa_MD5String@Base 2.4.1
+ raa_acnucclose@Base 2.4.1
+ raa_acnucopen@Base 2.4.1
+ raa_acnucopen_alt@Base 2.4.1
+ raa_alllistranks@Base 2.4.1
+ raa_bcount@Base 2.4.1
+ raa_bit0@Base 2.4.1
+ raa_bit1@Base 2.4.1
+ raa_btest@Base 2.4.1
+ raa_copylist@Base 2.4.1
+ raa_countfilles@Base 2.4.1
+ raa_decode_address@Base 2.4.1
+ raa_error_mess_proc@Base 2.4.1
+ raa_fcode@Base 2.4.1
+ raa_followshrt2@Base 2.4.1
+ raa_get_taxon_info@Base 2.4.1
+ raa_getattributes@Base 2.4.1
+ raa_getemptylist@Base 2.4.1
+ raa_getlistrank@Base 2.4.1
+ raa_getliststate@Base 2.4.1
+ raa_gfrag@Base 2.4.1
+ raa_ghelp@Base 2.4.1
+ raa_iknum@Base 2.4.1
+ raa_isenum@Base 2.4.1
+ raa_knowndbs@Base 2.4.1
+ raa_loadtaxonomy@Base 2.4.1
+ raa_modifylist@Base 2.4.1
+ raa_next_annots@Base 2.4.1
+ raa_nexteltinlist@Base 2.4.1
+ raa_nexteltinlist_annots@Base 2.4.1
+ raa_nextmatchkey@Base 2.4.1
+ raa_open_socket@Base 2.4.1
+ raa_opendb@Base 2.4.1
+ raa_opendb_pw@Base 2.4.1
+ raa_prep_acnuc_query@Base 2.4.1
+ raa_prep_coordinates@Base 2.4.1
+ raa_proc_query@Base 2.4.1
+ raa_read_annots@Base 2.4.1
+ raa_read_first_rec@Base 2.4.1
+ raa_readacc@Base 2.4.1
+ raa_readext@Base 2.4.1
+ raa_readkey@Base 2.4.1
+ raa_readlng@Base 2.4.1
+ raa_readloc@Base 2.4.1
+ raa_readshrt@Base 2.4.1
+ raa_readsmj@Base 2.4.1
+ raa_readspec@Base 2.4.1
+ raa_readsub@Base 2.4.1
+ raa_readsub_pannots@Base 2.4.1
+ raa_releaselist@Base 2.4.1
+ raa_residuecount@Base 2.4.1
+ raa_savelist@Base 2.4.1
+ raa_seq_to_annots@Base 2.4.1
+ raa_seqrank_attributes@Base 2.4.1
+ raa_setlistname@Base 2.4.1
+ raa_setliststate@Base 2.4.1
+ raa_short_descr@Base 2.4.1
+ raa_translate_cds@Base 2.4.1
+ raa_translate_init_codon@Base 2.4.1
+ raa_zerolist@Base 2.4.1
+ read_sock@Base 2.4.1
+ read_sock_timeout@Base 2.4.1
+ scan_raa_long@Base 2.4.1
+ sock_flush@Base 2.4.1
+ sock_fputs@Base 2.4.1
+ sock_printf@Base 2.4.1
+ strcmptrail@Base 2.4.1
+ totcodes@Base 2.4.1
+ trim_key@Base 2.4.1
+ unprotect_quotes@Base 2.4.1
+ val@Base 2.4.1
+ z_getc@Base 2.4.1
+ z_gets@Base 2.4.1
+ z_read_sock@Base 2.4.1

header.html

-<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

@@ -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;
-  }
   return Sprot;
 }