[med-svn] [libbpp-seq] branch upstream updated (c5e2fe5 -> 8490991)
Andreas Tille
tille at debian.org
Sat Apr 9 06:29:00 UTC 2016
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tille pushed a change to branch upstream
in repository libbpp-seq.
from c5e2fe5 Imported Upstream version 2.1.0
new 8490991 Imported Upstream version 2.2.0
The 1 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:
CMakeLists.txt | 13 +-
COPYING.txt | 845 +++++++++-------
ChangeLog | 11 +
Doxyfile | 6 +-
Doxyfile => Doxyfile-build | 7 +-
bpp-seq.spec | 5 +-
debian/changelog | 7 +
debian/control | 8 +-
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 --
.../LetterAlphabet.cpp} | 26 +-
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 --
src/Bpp/Seq/Alphabet/StandardCodonAlphabet.h | 71 --
.../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 +-
158 files changed, 5246 insertions(+), 4432 deletions(-)
copy Doxyfile => Doxyfile-build (99%)
copy debian/postinst => genIncludes.sh (80%)
copy src/Bpp/Seq/{Io/BppOSequenceWriterFormat.cpp => Alphabet/AlphabetNumericState.h} (54%)
delete mode 100644 src/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.cpp
delete mode 100644 src/Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.h
copy src/Bpp/Seq/Alphabet/{BinaryAlphabet.cpp => IntegerAlphabet.cpp} (81%)
copy src/Bpp/Seq/Alphabet/{BinaryAlphabet.h => IntegerAlphabet.h} (64%)
delete mode 100644 src/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.cpp
delete mode 100644 src/Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.h
copy src/Bpp/Seq/{DistanceMatrix.cpp => Alphabet/LetterAlphabet.cpp} (75%)
create mode 100644 src/Bpp/Seq/Alphabet/NumericAlphabet.cpp
create mode 100644 src/Bpp/Seq/Alphabet/NumericAlphabet.h
delete mode 100644 src/Bpp/Seq/Alphabet/StandardCodonAlphabet.cpp
delete mode 100644 src/Bpp/Seq/Alphabet/StandardCodonAlphabet.h
delete mode 100644 src/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.cpp
delete mode 100644 src/Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.h
delete mode 100644 src/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.cpp
delete mode 100644 src/Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.h
copy src/Bpp/Seq/AlphabetIndex/{AAIndex1Entry.h => UserAlphabetIndex1.h} (57%)
create mode 100644 src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp
create mode 100644 src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h
create mode 100644 src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp
create mode 100644 src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h
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