[med-svn] [libbpp-seq] branch master updated (e0c4b38 -> 99cf631)
Andreas Tille
tille at debian.org
Sat Jun 3 12:48:04 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository libbpp-seq.
from e0c4b38 Add Bio++ Development Team
new a4394dc d/watch: point to github
new bb4a617 New upstream version 2.3.0
new 0da99de Updated version 2.3.0 from 'upstream/2.3.0'
new 48ccaf8 New upstream version
new 9ae6332 Update versioned dependencies
new 21f80ae New upstream version 2.3.0
new 99cf631 Updated version 2.3.0 from 'upstream/2.3.0'
The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
AUTHORS.txt | 2 +
CMakeLists.txt | 168 +-
CTestConfig.cmake | 13 +
ChangeLog | 16 +
Doxyfile | 2662 ++++++++++++--------
Doxyfile-build | 1889 --------------
INSTALL.txt | 19 +-
bpp-seq.spec | 105 +-
debian/changelog | 7 +
debian/control | 6 +-
debian/watch | 5 +-
genIncludes.sh | 35 -
package.cmake.in | 26 +
src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp | 16 +-
src/Bpp/Seq/Alphabet/AbstractAlphabet.h | 3 +-
src/Bpp/Seq/Alphabet/Alphabet.h | 14 +-
src/Bpp/Seq/Alphabet/AlphabetNumericState.h | 8 +-
src/Bpp/Seq/Alphabet/AlphabetState.h | 8 +-
src/Bpp/Seq/Alphabet/AlphabetTools.cpp | 3 -
src/Bpp/Seq/Alphabet/AlphabetTools.h | 6 +-
src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp | 45 +
src/Bpp/Seq/Alphabet/BinaryAlphabet.h | 120 +-
src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h | 2 +-
src/Bpp/Seq/Alphabet/CodonAlphabet.h | 2 +-
src/Bpp/Seq/Alphabet/DNA.cpp | 4 +-
src/Bpp/Seq/Alphabet/DNA.h | 2 +-
src/Bpp/Seq/Alphabet/DefaultAlphabet.h | 2 +-
src/Bpp/Seq/Alphabet/IntegerAlphabet.h | 2 +-
src/Bpp/Seq/Alphabet/LetterAlphabet.h | 2 -
.../LexicalAlphabet.cpp} | 99 +-
src/Bpp/Seq/Alphabet/LexicalAlphabet.h | 118 +
src/Bpp/Seq/Alphabet/NucleicAlphabet.h | 2 -
src/Bpp/Seq/Alphabet/NumericAlphabet.h | 2 +-
src/Bpp/Seq/Alphabet/ProteicAlphabet.h | 2 +-
src/Bpp/Seq/Alphabet/RNA.h | 2 +-
src/Bpp/Seq/Alphabet/RNY.h | 6 +-
src/Bpp/Seq/Alphabet/WordAlphabet.cpp | 39 +-
src/Bpp/Seq/Alphabet/WordAlphabet.h | 14 +-
.../Seq/AlphabetIndex/GranthamAAPolarityIndex.h | 1 +
src/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h | 1 +
src/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h | 2 +-
src/Bpp/Seq/App/SequenceApplicationTools.cpp | 234 +-
src/Bpp/Seq/App/SequenceApplicationTools.h | 9 +
src/Bpp/Seq/CodonSiteTools.cpp | 30 +-
src/Bpp/Seq/CodonSiteTools.h | 445 ++--
src/Bpp/Seq/Container/AbstractSequenceContainer.h | 9 -
src/Bpp/Seq/Container/AlignedSequenceContainer.cpp | 39 +-
.../Container/CompressedVectorSiteContainer.cpp | 2 +-
src/Bpp/Seq/Container/OrderedSequenceContainer.h | 9 -
src/Bpp/Seq/Container/SequenceContainer.h | 9 -
src/Bpp/Seq/Container/SequenceContainerTools.cpp | 6 +-
src/Bpp/Seq/Container/SequenceContainerTools.h | 8 +-
src/Bpp/Seq/Container/SiteContainerTools.cpp | 56 +-
src/Bpp/Seq/Container/SiteContainerTools.h | 8 +
.../Container/VectorProbabilisticSiteContainer.cpp | 187 ++
.../Container/VectorProbabilisticSiteContainer.h | 123 +
src/Bpp/Seq/Container/VectorSiteContainer.cpp | 14 +-
src/Bpp/Seq/Container/VectorSiteContainer.h | 1 +
src/Bpp/Seq/CoreSequence.h | 257 ++
src/Bpp/Seq/CoreSite.h | 191 ++
src/Bpp/Seq/DistanceMatrix.h | 96 +-
.../GeneticCode/AscidianMitochondrialGeneticCode.h | 2 +-
.../EchinodermMitochondrialGeneticCode.h | 2 +-
src/Bpp/Seq/GeneticCode/GeneticCode.cpp | 10 +-
src/Bpp/Seq/GeneticCode/GeneticCode.h | 38 +-
.../InvertebrateMitochondrialGeneticCode.h | 2 +-
.../Seq/GeneticCode/MoldMitochondrialGeneticCode.h | 2 +-
src/Bpp/Seq/GeneticCode/StandardGeneticCode.h | 2 +-
.../VertebrateMitochondrialGeneticCode.h | 2 +-
.../GeneticCode/YeastMitochondrialGeneticCode.h | 2 +-
src/Bpp/Seq/Io/AbstractIAlignment.h | 14 +-
src/Bpp/Seq/Io/AbstractISequence.h | 14 +-
src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp | 2 +-
src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp | 2 +-
src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp | 2 +-
src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp | 2 +-
src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp | 2 +-
src/Bpp/Seq/Io/Fasta.cpp | 10 +-
src/Bpp/Seq/Io/Fasta.h | 14 +-
src/Bpp/Seq/Io/Mase.cpp | 13 +-
src/Bpp/Seq/Io/MaseTools.cpp | 23 -
src/Bpp/Seq/Sequence.cpp | 191 +-
src/Bpp/Seq/Sequence.h | 186 +-
src/Bpp/Seq/SequenceTools.cpp | 90 +-
src/Bpp/Seq/SequenceTools.h | 48 +-
src/Bpp/Seq/SequenceWithAnnotation.cpp | 22 +-
src/Bpp/Seq/SequenceWithAnnotation.h | 40 +-
src/Bpp/Seq/SequenceWithAnnotationTools.h | 7 +-
src/Bpp/Seq/SequenceWithQuality.h | 38 +-
src/Bpp/Seq/SequenceWithQualityTools.cpp | 53 +-
src/Bpp/Seq/SequenceWithQualityTools.h | 61 +-
src/Bpp/Seq/Site.cpp | 21 +-
src/Bpp/Seq/Site.h | 12 +-
src/Bpp/Seq/SiteTools.cpp | 130 +-
src/Bpp/Seq/SiteTools.h | 75 +-
src/Bpp/Seq/SymbolList.cpp | 30 +-
src/Bpp/Seq/SymbolList.h | 29 +-
src/Bpp/Seq/SymbolListTools.cpp | 14 +-
src/Bpp/Seq/SymbolListTools.h | 6 +-
src/Bpp/Seq/Transliterator.cpp | 32 +-
src/Bpp/Seq/Transliterator.h | 196 +-
src/CMakeLists.txt | 294 +--
test/CMakeLists.txt | 84 +-
test/test_bowker.cpp | 8 +-
104 files changed, 4233 insertions(+), 4807 deletions(-)
create mode 100644 CTestConfig.cmake
delete mode 100644 Doxyfile-build
delete mode 100755 genIncludes.sh
create mode 100644 package.cmake.in
copy src/Bpp/Seq/{AlphabetIndex/AAIndex1Entry.cpp => Alphabet/LexicalAlphabet.cpp} (55%)
create mode 100644 src/Bpp/Seq/Alphabet/LexicalAlphabet.h
create mode 100644 src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.cpp
create mode 100644 src/Bpp/Seq/Container/VectorProbabilisticSiteContainer.h
create mode 100644 src/Bpp/Seq/CoreSequence.h
create mode 100644 src/Bpp/Seq/CoreSite.h
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