[med-svn] [libbpp-seq] 02/06: Merge tag 'upstream/2.2.0'
Andreas Tille
tille at debian.org
Sat Apr 9 06:28:59 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libbpp-seq.
commit 158e044d8d66ebc9b8952feb8d7374262acddc39
Merge: a60cfd8 8490991
Author: Andreas Tille <tille at debian.org>
Date: Sat Apr 9 08:17:12 2016 +0200
Merge tag 'upstream/2.2.0'
Upstream version 2.2.0
CMakeLists.txt | 13 +-
COPYING.txt | 845 +++++++++-------
ChangeLog | 11 +
Doxyfile | 6 +-
Doxyfile => Doxyfile-build | 7 +-
bpp-seq.spec | 5 +-
debian/control | 11 +-
debian/copyright | 6 +-
debian/postinst | 22 +-
debian/postrm | 26 +-
debian/prerm | 22 +-
debian/rules | 4 +-
debian/postinst => genIncludes.sh | 10 +-
src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp | 63 +-
src/Bpp/Seq/Alphabet/AbstractAlphabet.h | 110 +-
src/Bpp/Seq/Alphabet/Alphabet.h | 75 +-
.../AlphabetNumericState.h} | 100 +-
src/Bpp/Seq/Alphabet/AlphabetTools.cpp | 2 +-
src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp | 11 +-
src/Bpp/Seq/Alphabet/BinaryAlphabet.h | 22 +-
src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp | 6 +-
src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h | 79 +-
src/Bpp/Seq/Alphabet/CodonAlphabet.cpp | 12 +-
src/Bpp/Seq/Alphabet/CodonAlphabet.h | 99 +-
src/Bpp/Seq/Alphabet/DNA.cpp | 47 +-
src/Bpp/Seq/Alphabet/DNA.h | 90 +-
src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp | 13 +-
src/Bpp/Seq/Alphabet/DefaultAlphabet.h | 108 +-
.../EchinodermMitochondrialCodonAlphabet.cpp | 75 --
.../EchinodermMitochondrialCodonAlphabet.h | 72 --
.../{BinaryAlphabet.cpp => IntegerAlphabet.cpp} | 16 +-
.../{BinaryAlphabet.h => IntegerAlphabet.h} | 54 +-
.../InvertebrateMitochondrialCodonAlphabet.cpp | 74 --
.../InvertebrateMitochondrialCodonAlphabet.h | 75 --
...{StandardCodonAlphabet.h => LetterAlphabet.cpp} | 44 +-
src/Bpp/Seq/Alphabet/LetterAlphabet.h | 157 +--
src/Bpp/Seq/Alphabet/NucleicAlphabet.h | 164 +--
src/Bpp/Seq/Alphabet/NumericAlphabet.cpp | 189 ++++
src/Bpp/Seq/Alphabet/NumericAlphabet.h | 131 +++
src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp | 271 ++---
src/Bpp/Seq/Alphabet/ProteicAlphabet.h | 185 ++--
src/Bpp/Seq/Alphabet/RNA.cpp | 47 +-
src/Bpp/Seq/Alphabet/RNA.h | 90 +-
src/Bpp/Seq/Alphabet/RNY.cpp | 1048 ++++++++++----------
src/Bpp/Seq/Alphabet/RNY.h | 15 +
src/Bpp/Seq/Alphabet/StandardCodonAlphabet.cpp | 75 --
.../VertebrateMitochondrialCodonAlphabet.cpp | 76 --
.../VertebrateMitochondrialCodonAlphabet.h | 71 --
src/Bpp/Seq/Alphabet/WordAlphabet.cpp | 60 +-
src/Bpp/Seq/Alphabet/WordAlphabet.h | 21 +-
.../Alphabet/YeastMitochondrialCodonAlphabet.cpp | 72 --
.../Seq/Alphabet/YeastMitochondrialCodonAlphabet.h | 75 --
src/Bpp/Seq/AlphabetIndex/AAChargeIndex.h | 4 +-
.../AAChenGuHuangHydrophobicityIndex.h | 4 +-
.../Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h | 4 +-
.../Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h | 4 +-
src/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h | 4 +-
src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp | 2 +-
src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h | 6 +-
src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp | 13 +-
src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h | 21 +-
src/Bpp/Seq/AlphabetIndex/AAMassIndex.h | 6 +-
src/Bpp/Seq/AlphabetIndex/AASEA1030Index.h | 6 +-
src/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h | 6 +-
src/Bpp/Seq/AlphabetIndex/AASEASup30Index.h | 6 +-
src/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h | 6 +-
src/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h | 4 +-
src/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h | 2 +
src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h | 11 +-
src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp | 14 +-
src/Bpp/Seq/AlphabetIndex/BLOSUM50.h | 1 +
.../Seq/AlphabetIndex/DefaultNucleotideScore.cpp | 10 +-
src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h | 1 +
.../AlphabetIndex/GranthamAAChemicalDistance.cpp | 20 +-
.../Seq/AlphabetIndex/GranthamAAChemicalDistance.h | 2 +-
.../Seq/AlphabetIndex/GranthamAAPolarityIndex.h | 6 +-
src/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h | 6 +-
src/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h | 6 +-
.../Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp | 14 +-
.../Seq/AlphabetIndex/MiyataAAChemicalDistance.h | 6 +-
src/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h | 8 +-
src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp | 20 +-
src/Bpp/Seq/AlphabetIndex/SimpleScore.h | 1 +
.../{AAIndex1Entry.h => UserAlphabetIndex1.h} | 87 +-
src/Bpp/Seq/App/SequenceApplicationTools.cpp | 176 ++--
src/Bpp/Seq/App/SequenceApplicationTools.h | 439 ++++----
src/Bpp/Seq/CodonSiteTools.cpp | 239 +++--
src/Bpp/Seq/CodonSiteTools.h | 54 +-
src/Bpp/Seq/Container/AlignedSequenceContainer.cpp | 22 +-
src/Bpp/Seq/Container/AlignedSequenceContainer.h | 1 +
.../Container/CompressedVectorSiteContainer.cpp | 10 +-
src/Bpp/Seq/Container/MapSequenceContainer.cpp | 4 +-
src/Bpp/Seq/Container/OrderedSequenceContainer.h | 4 +
.../Seq/Container/SequenceContainerIterator.cpp | 2 +-
src/Bpp/Seq/Container/SequenceContainerIterator.h | 2 +-
src/Bpp/Seq/Container/SequenceContainerTools.cpp | 5 +-
src/Bpp/Seq/Container/SequenceContainerTools.h | 4 +-
src/Bpp/Seq/Container/SiteContainerIterator.cpp | 22 +-
src/Bpp/Seq/Container/SiteContainerTools.cpp | 42 +-
src/Bpp/Seq/Container/SiteContainerTools.h | 269 ++---
src/Bpp/Seq/Container/VectorSequenceContainer.cpp | 8 +-
src/Bpp/Seq/Container/VectorSequenceContainer.h | 350 +++----
src/Bpp/Seq/Container/VectorSiteContainer.cpp | 30 +-
src/Bpp/Seq/DistanceMatrix.h | 45 +-
.../AscidianMitochondrialGeneticCode.cpp | 117 +++
.../GeneticCode/AscidianMitochondrialGeneticCode.h | 113 +++
.../EchinodermMitochondrialGeneticCode.cpp | 187 ++--
.../EchinodermMitochondrialGeneticCode.h | 62 +-
src/Bpp/Seq/GeneticCode/GeneticCode.cpp | 53 +-
src/Bpp/Seq/GeneticCode/GeneticCode.h | 136 ++-
.../InvertebrateMitochondrialGeneticCode.cpp | 189 ++--
.../InvertebrateMitochondrialGeneticCode.h | 60 +-
.../GeneticCode/MoldMitochondrialGeneticCode.cpp | 117 +++
.../Seq/GeneticCode/MoldMitochondrialGeneticCode.h | 111 +++
src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp | 189 ++--
src/Bpp/Seq/GeneticCode/StandardGeneticCode.h | 62 +-
.../VertebrateMitochondrialGeneticCode.cpp | 191 ++--
.../VertebrateMitochondrialGeneticCode.h | 64 +-
.../GeneticCode/YeastMitochondrialGeneticCode.cpp | 189 ++--
.../GeneticCode/YeastMitochondrialGeneticCode.h | 59 +-
src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp | 57 +-
src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h | 7 +-
src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp | 57 +-
src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h | 9 +-
src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp | 1 -
src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp | 9 +-
src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp | 59 +-
src/Bpp/Seq/Io/BppOSequenceReaderFormat.h | 8 +-
src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h | 5 +-
src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp | 2 +-
src/Bpp/Seq/Io/BppOSequenceWriterFormat.h | 7 +-
src/Bpp/Seq/Io/Dcse.cpp | 4 +-
src/Bpp/Seq/Io/Fasta.cpp | 9 +-
src/Bpp/Seq/Io/Mase.cpp | 2 +-
src/Bpp/Seq/Io/MaseTools.cpp | 68 +-
src/Bpp/Seq/Io/MaseTools.h | 98 +-
src/Bpp/Seq/Io/Phylip.cpp | 26 +-
src/Bpp/Seq/Io/Phylip.h | 4 +-
src/Bpp/Seq/Sequence.cpp | 2 +-
src/Bpp/Seq/SequencePositionIterators.cpp | 35 +-
src/Bpp/Seq/SequenceTools.cpp | 64 +-
src/Bpp/Seq/SequenceTools.h | 33 +-
src/Bpp/Seq/SequenceWithAnnotation.cpp | 2 +-
src/Bpp/Seq/SequenceWithAnnotationTools.cpp | 6 +-
src/Bpp/Seq/SequenceWithAnnotationTools.h | 6 +-
src/Bpp/Seq/SequenceWithQuality.cpp | 8 +-
src/Bpp/Seq/SequenceWithQuality.h | 9 +-
src/Bpp/Seq/SiteTools.cpp | 18 +-
src/Bpp/Seq/SiteTools.h | 5 -
src/Bpp/Seq/StringSequenceTools.cpp | 16 +-
src/Bpp/Seq/StringSequenceTools.h | 6 +-
src/Bpp/Seq/SymbolList.cpp | 16 +-
src/CMakeLists.txt | 19 +-
test/test_alphabets.cpp | 18 +-
test/test_bowker.cpp | 2 +-
test/test_walker.cpp | 4 +-
156 files changed, 5243 insertions(+), 4378 deletions(-)
diff --cc debian/control
index dc137cb,02efa76..0666ea5
--- a/debian/control
+++ b/debian/control
@@@ -1,43 -1,25 +1,48 @@@
Source: libbpp-seq
-Section: libs
-Priority: optional
-Maintainer: Loic Dachary <loic at dachary.org>
-Uploaders: Julien Dutheil <julien.dutheil at univ-montp2.fr>
-Build-Depends: debhelper (>= 5), cmake (>= 2.6),
- libbpp-core-dev (>= 2.2.0)
-Standards-Version: 3.9.4
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Julien Dutheil <julien.dutheil at univ-montp2.fr>,
+ Andreas Tille <tille at debian.org>
+Section: science
- Build-Depends: debhelper (>= 5),
++Build-Depends: debhelper (>= 9),
+ cmake,
- libbpp-core-dev (>= 2.1.0)
++ libbpp-core-dev (>= 2.2.0)
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-seq.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-seq.git
+Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Package: libbpp-seq-dev
-Section: libdevel
Architecture: any
-Depends: libbpp-seq9 (= ${binary:Version}), ${misc:Depends},
- libbpp-core-dev (>= 2.2.0)
+Section: libdevel
+Depends: libbpp-seq9 (= ${binary:Version}),
+ ${misc:Depends},
- libbpp-core-dev (>= 2.1.0)
++ libbpp-core-dev (>= 2.2.0)
Description: Bio++ Sequence library development files.
- Contains the Bio++ classes for sequence analysis.
+ Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ analysis, phylogenetics, molecular evolution and population genetics.
+ Bio++ is Object Oriented and is designed to be both easy to use and
+ computer efficient. Bio++ intends to help programmers to write computer
+ expensive programs, by providing them a set of re-usable tools.
+ .
+ This package contains the static library and the header files of Bio++
+ classes for sequence analysis classes.
Package: libbpp-seq9
-Section: libs
Architecture: any
++<<<<<<< HEAD
+Section: libs
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libbpp-core2 (>= 2.1.0)
++=======
+ Depends: ${shlibs:Depends}, ${misc:Depends},
+ libbpp-core2 (>= 2.2.0)
++>>>>>>> upstream/2.2.0
Description: Bio++ Sequence library.
- Contains the Bio++ classes for sequence analysis.
-
+ Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+ analysis, phylogenetics, molecular evolution and population genetics.
+ Bio++ is Object Oriented and is designed to be both easy to use and
+ computer efficient. Bio++ intends to help programmers to write computer
+ expensive programs, by providing them a set of re-usable tools.
+ .
+ This package contains the Bio++ classes for sequence analysis.
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-seq.git
More information about the debian-med-commit
mailing list