[med-svn] [libbpp-seq] branch master updated (a60cfd8 -> d9886b4)
Andreas Tille
tille at debian.org
Sat Apr 9 06:28:58 UTC 2016
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tille pushed a change to branch master
in repository libbpp-seq.
from a60cfd8 Add watch file
new 8490991 Imported Upstream version 2.2.0
new 158e044 Merge tag 'upstream/2.2.0'
new 15d5bac New upstream version
new 60620ef DEP 5
new c61840e short dh rules file using d-shlibs
new d9886b4 Library transition dealing with bug #791099
The 6 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 | 8 +-
debian/compat | 2 +-
debian/control | 17 +-
debian/copyright | 94 +-
debian/libbpp-seq-dev.install | 3 -
debian/libbpp-seq9.install | 1 -
debian/postinst | 22 +-
debian/postrm | 26 +-
debian/prerm | 22 +-
debian/rules | 127 +--
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 +-
161 files changed, 5316 insertions(+), 4589 deletions(-)
copy Doxyfile => Doxyfile-build (99%)
delete mode 100644 debian/libbpp-seq-dev.install
delete mode 100644 debian/libbpp-seq9.install
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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