[med-svn] [libbpp-seq] 07/07: Updated version 2.3.0 from 'upstream/2.3.0'
Andreas Tille
tille at debian.org
Sat Jun 3 12:48:08 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libbpp-seq.
commit 99cf6312960a119a27d3f83d3b9f187abc0bf085
Merge: 9ae6332 21f80ae
Author: Andreas Tille <tille at debian.org>
Date: Sat Jun 3 14:40:20 2017 +0200
Updated version 2.3.0 from 'upstream/2.3.0'
with Debian dir 8e7b5cecd11c2b80f46775b6540b1cec080d60f2
.gitignore | 15 -
AUTHORS.txt | 15 +-
CMakeLists.txt | 36 +-
CTestConfig.cmake | 4 +-
ChangeLog | 464 +++-
Doxyfile | 12 +-
bpp-core.spec | 102 -
bpp-seq.spec | 118 +
cmake/doc-cmake-for-developpers.cmake | 240 --
cmake/project-template-for-users.cmake | 106 -
package.cmake.in | 5 +-
src/Bpp/App/ApplicationTools.cpp | 374 ---
src/Bpp/App/ApplicationTools.h | 640 -----
src/Bpp/App/NumCalcApplicationTools.cpp | 141 --
src/Bpp/App/NumCalcApplicationTools.h | 134 -
src/Bpp/Clonable.h | 120 -
src/Bpp/Exceptions.h | 425 ----
src/Bpp/Graph/AssociationDAGraphImplObserver.h | 406 ---
src/Bpp/Graph/AssociationDAGraphObserver.h | 256 --
src/Bpp/Graph/AssociationGraphImplObserver.h | 1332 ----------
src/Bpp/Graph/AssociationGraphObserver.h | 483 ----
src/Bpp/Graph/AssociationTreeGraphImplObserver.h | 397 ---
src/Bpp/Graph/AssociationTreeGraphObserver.h | 255 --
src/Bpp/Graph/DAGraph.h | 174 --
src/Bpp/Graph/DAGraphImpl.h | 525 ----
src/Bpp/Graph/GlobalGraph.cpp | 990 --------
src/Bpp/Graph/GlobalGraph.h | 956 -------
src/Bpp/Graph/Graph.h | 582 -----
src/Bpp/Graph/TreeGraph.h | 201 --
src/Bpp/Graph/TreeGraphImpl.h | 593 -----
src/Bpp/Graphics/AbstractGraphicDevice.h | 112 -
src/Bpp/Graphics/ColorManager.h | 191 --
src/Bpp/Graphics/ColorSet.h | 132 -
src/Bpp/Graphics/ColorTools.cpp | 101 -
src/Bpp/Graphics/ColorTools.h | 133 -
src/Bpp/Graphics/DefaultColorSet.h | 74 -
src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp | 194 --
src/Bpp/Graphics/Fig/XFigGraphicDevice.h | 133 -
src/Bpp/Graphics/Fig/XFigLaTeXFontManager.cpp | 55 -
src/Bpp/Graphics/Fig/XFigLaTeXFontManager.h | 66 -
src/Bpp/Graphics/Fig/XFigPostscriptFontManager.cpp | 85 -
src/Bpp/Graphics/Fig/XFigPostscriptFontManager.h | 66 -
src/Bpp/Graphics/Font/Font.cpp | 56 -
src/Bpp/Graphics/Font/Font.h | 174 --
src/Bpp/Graphics/Font/FontManager.h | 150 --
src/Bpp/Graphics/GraphicDevice.cpp | 58 -
src/Bpp/Graphics/GraphicDevice.h | 199 --
src/Bpp/Graphics/Latex/DvipsColorSet.cpp | 115 -
src/Bpp/Graphics/Latex/DvipsColorSet.h | 65 -
src/Bpp/Graphics/Latex/PgfGraphicDevice.cpp | 299 ---
src/Bpp/Graphics/Latex/PgfGraphicDevice.h | 117 -
src/Bpp/Graphics/Molscript/MolscriptColorSet.cpp | 210 --
src/Bpp/Graphics/Point2D.h | 146 --
src/Bpp/Graphics/R/RColorSet.cpp | 704 ------
src/Bpp/Graphics/R/RColorSet.h | 78 -
src/Bpp/Graphics/RgbColor.h | 152 --
src/Bpp/Graphics/Svg/SvgGraphicDevice.cpp | 171 --
src/Bpp/Graphics/Svg/SvgGraphicDevice.h | 107 -
src/Bpp/Io/BppODiscreteDistributionFormat.cpp | 455 ----
src/Bpp/Io/BppODiscreteDistributionFormat.h | 96 -
src/Bpp/Io/BppOParametrizableFormat.cpp | 120 -
src/Bpp/Io/BppOParametrizableFormat.h | 110 -
src/Bpp/Io/FileTools.cpp | 153 --
src/Bpp/Io/FileTools.h | 162 --
src/Bpp/Io/IoDiscreteDistribution.h | 125 -
src/Bpp/Io/IoDiscreteDistributionFactory.h | 99 -
src/Bpp/Io/IoParametrizable.h | 117 -
src/Bpp/Io/OutputStream.h | 350 ---
src/Bpp/Numeric/AbstractParameterAliasable.cpp | 397 ---
src/Bpp/Numeric/AbstractParameterAliasable.h | 281 ---
src/Bpp/Numeric/AbstractParametrizable.h | 259 --
.../Numeric/AdaptiveKernelDensityEstimation.cpp | 141 --
src/Bpp/Numeric/AdaptiveKernelDensityEstimation.h | 122 -
src/Bpp/Numeric/AutoParameter.cpp | 120 -
src/Bpp/Numeric/AutoParameter.h | 146 --
src/Bpp/Numeric/Constraints.h | 438 ----
src/Bpp/Numeric/DataTable.cpp | 716 ------
src/Bpp/Numeric/DataTable.h | 437 ----
.../Numeric/Function/AbstractNumericalDerivative.h | 276 ---
src/Bpp/Numeric/Function/AbstractOptimizer.cpp | 344 ---
src/Bpp/Numeric/Function/AbstractOptimizer.h | 391 ---
src/Bpp/Numeric/Function/BfgsMultiDimensions.cpp | 300 ---
src/Bpp/Numeric/Function/BfgsMultiDimensions.h | 123 -
src/Bpp/Numeric/Function/BrentOneDimension.cpp | 216 --
src/Bpp/Numeric/Function/BrentOneDimension.h | 150 --
.../Function/ConjugateGradientMultiDimensions.cpp | 134 -
.../Function/ConjugateGradientMultiDimensions.h | 110 -
src/Bpp/Numeric/Function/DirectionFunction.cpp | 109 -
src/Bpp/Numeric/Function/DirectionFunction.h | 116 -
src/Bpp/Numeric/Function/DownhillSimplexMethod.cpp | 243 --
src/Bpp/Numeric/Function/DownhillSimplexMethod.h | 166 --
.../Function/FivePointsNumericalDerivative.cpp | 147 --
.../Function/FivePointsNumericalDerivative.h | 136 -
src/Bpp/Numeric/Function/FunctionTools.cpp | 140 --
src/Bpp/Numeric/Function/FunctionTools.h | 122 -
src/Bpp/Numeric/Function/Functions.h | 639 -----
src/Bpp/Numeric/Function/GoldenSectionSearch.cpp | 174 --
src/Bpp/Numeric/Function/GoldenSectionSearch.h | 145 --
src/Bpp/Numeric/Function/MetaOptimizer.cpp | 208 --
src/Bpp/Numeric/Function/MetaOptimizer.h | 246 --
.../Function/NewtonBacktrackOneDimension.cpp | 124 -
.../Numeric/Function/NewtonBacktrackOneDimension.h | 124 -
src/Bpp/Numeric/Function/NewtonOneDimension.cpp | 122 -
.../Function/OneDimensionOptimizationTools.cpp | 267 --
.../Function/OneDimensionOptimizationTools.h | 138 --
.../Numeric/Function/Operators/BinaryOperator.h | 168 --
.../Numeric/Function/Operators/ComputationTree.cpp | 213 --
.../Numeric/Function/Operators/ComputationTree.h | 113 -
.../Numeric/Function/Operators/FunctionOperator.h | 133 -
src/Bpp/Numeric/Function/Operators/MathOperator.h | 138 --
.../Numeric/Function/OptimizationStopCondition.cpp | 241 --
.../Numeric/Function/OptimizationStopCondition.h | 303 ---
src/Bpp/Numeric/Function/Optimizer.h | 398 ---
src/Bpp/Numeric/Function/PowellMultiDimensions.cpp | 170 --
src/Bpp/Numeric/Function/PowellMultiDimensions.h | 115 -
.../Function/ReparametrizationFunctionWrapper.cpp | 194 --
.../Function/ReparametrizationFunctionWrapper.h | 262 --
src/Bpp/Numeric/Function/SimpleMultiDimensions.cpp | 114 -
src/Bpp/Numeric/Function/SimpleMultiDimensions.h | 99 -
.../Numeric/Function/SimpleNewtonMultiDimensions.h | 98 -
.../Function/ThreePointsNumericalDerivative.cpp | 263 --
.../Function/ThreePointsNumericalDerivative.h | 135 -
.../Function/TwoPointsNumericalDerivative.cpp | 127 -
.../Function/TwoPointsNumericalDerivative.h | 121 -
.../Numeric/Hmm/AbstractHmmTransitionMatrix.cpp | 129 -
src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h | 120 -
.../Hmm/AutoCorrelationTransitionMatrix.cpp | 113 -
.../Numeric/Hmm/AutoCorrelationTransitionMatrix.h | 118 -
src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp | 142 --
src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.h | 130 -
src/Bpp/Numeric/Hmm/HmmEmissionProbabilities.h | 131 -
src/Bpp/Numeric/Hmm/HmmLikelihood.h | 213 --
src/Bpp/Numeric/Hmm/HmmStateAlphabet.h | 122 -
src/Bpp/Numeric/Hmm/HmmTransitionMatrix.h | 108 -
src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp | 579 -----
src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h | 306 ---
.../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp | 256 --
.../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h | 240 --
src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp | 597 -----
src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h | 259 --
src/Bpp/Numeric/Matrix/EigenValue.h | 1248 ----------
src/Bpp/Numeric/Matrix/LUDecomposition.h | 465 ----
src/Bpp/Numeric/Matrix/Matrix.h | 547 ----
src/Bpp/Numeric/Matrix/MatrixTools.h | 1361 ----------
src/Bpp/Numeric/NumConstants.h | 102 -
src/Bpp/Numeric/NumTools.h | 205 --
src/Bpp/Numeric/Number.h | 231 --
src/Bpp/Numeric/Parameter.cpp | 210 --
src/Bpp/Numeric/Parameter.h | 328 ---
src/Bpp/Numeric/ParameterAliasable.h | 194 --
src/Bpp/Numeric/ParameterExceptions.h | 164 --
src/Bpp/Numeric/ParameterList.cpp | 593 -----
src/Bpp/Numeric/ParameterList.h | 439 ----
src/Bpp/Numeric/Parametrizable.h | 230 --
src/Bpp/Numeric/ParametrizableCollection.h | 382 ---
.../Numeric/Prob/AbstractDiscreteDistribution.cpp | 466 ----
.../Numeric/Prob/AbstractDiscreteDistribution.h | 246 --
src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp | 122 -
src/Bpp/Numeric/Prob/BetaDiscreteDistribution.h | 117 -
src/Bpp/Numeric/Prob/ConstantDistribution.cpp | 103 -
src/Bpp/Numeric/Prob/ConstantDistribution.h | 108 -
.../Numeric/Prob/DirichletDiscreteDistribution.cpp | 282 ---
.../Numeric/Prob/DirichletDiscreteDistribution.h | 178 --
src/Bpp/Numeric/Prob/DiscreteDistribution.h | 320 ---
.../Numeric/Prob/ExponentialDiscreteDistribution.h | 122 -
src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp | 135 -
src/Bpp/Numeric/Prob/GammaDiscreteDistribution.h | 125 -
.../Numeric/Prob/GaussianDiscreteDistribution.cpp | 109 -
.../Numeric/Prob/GaussianDiscreteDistribution.h | 104 -
.../Prob/InvariantMixedDiscreteDistribution.cpp | 157 --
.../Prob/InvariantMixedDiscreteDistribution.h | 162 --
.../Prob/MixtureOfDiscreteDistributions.cpp | 319 ---
.../Numeric/Prob/MixtureOfDiscreteDistributions.h | 163 --
.../Numeric/Prob/MultipleDiscreteDistribution.h | 149 --
.../Numeric/Prob/SimpleDiscreteDistribution.cpp | 350 ---
src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.h | 158 --
src/Bpp/Numeric/Prob/Simplex.cpp | 299 ---
src/Bpp/Numeric/Prob/Simplex.h | 183 --
.../TruncatedExponentialDiscreteDistribution.h | 154 --
src/Bpp/Numeric/Prob/UniformDiscreteDistribution.h | 113 -
.../Numeric/Random/ContingencyTableGenerator.cpp | 199 --
src/Bpp/Numeric/Random/RandomTools.cpp | 1034 --------
src/Bpp/Numeric/Random/RandomTools.h | 554 -----
src/Bpp/Numeric/Random/Uniform01K.cpp | 106 -
src/Bpp/Numeric/Random/Uniform01K.h | 97 -
src/Bpp/Numeric/Range.h | 543 ----
src/Bpp/Numeric/Stat/ContingencyTableTest.cpp | 129 -
.../Numeric/Stat/Mva/CorrespondenceAnalysis.cpp | 114 -
src/Bpp/Numeric/Stat/Mva/DualityDiagram.cpp | 291 ---
src/Bpp/Numeric/Stat/Mva/DualityDiagram.h | 155 --
.../Stat/Mva/PrincipalComponentAnalysis.cpp | 182 --
.../Numeric/Stat/Mva/PrincipalComponentAnalysis.h | 138 --
src/Bpp/Numeric/Stat/StatTools.h | 89 -
src/Bpp/Numeric/Table.h | 1222 ---------
src/Bpp/Numeric/TableExceptions.h | 175 --
src/Bpp/Numeric/TransformedParameter.h | 312 ---
src/Bpp/Numeric/VectorExceptions.h | 155 --
src/Bpp/Numeric/VectorTools.h | 2007 ---------------
src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp | 327 +++
src/Bpp/Seq/Alphabet/AbstractAlphabet.h | 275 +++
src/Bpp/Seq/Alphabet/Alphabet.h | 465 ++++
.../Alphabet/AlphabetExceptions.cpp} | 96 +-
src/Bpp/Seq/Alphabet/AlphabetExceptions.h | 213 ++
.../Alphabet/AlphabetNumericState.h} | 183 +-
src/Bpp/Seq/Alphabet/AlphabetState.h | 128 +
src/Bpp/Seq/Alphabet/AlphabetTools.cpp | 123 +
src/Bpp/Seq/Alphabet/AlphabetTools.h | 235 ++
.../Alphabet/BinaryAlphabet.cpp} | 92 +-
src/Bpp/Seq/Alphabet/BinaryAlphabet.h | 90 +
src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp | 97 +
src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h | 124 +
.../Alphabet/CodonAlphabet.cpp} | 105 +-
src/Bpp/Seq/Alphabet/CodonAlphabet.h | 190 ++
src/Bpp/Seq/Alphabet/DNA.cpp | 147 ++
src/Bpp/{Io/IoFormat.h => Seq/Alphabet/DNA.h} | 185 +-
.../Alphabet/DefaultAlphabet.cpp} | 31 +-
.../Alphabet/DefaultAlphabet.h} | 92 +-
.../Alphabet/IntegerAlphabet.cpp} | 73 +-
.../Alphabet/IntegerAlphabet.h} | 92 +-
.../{Version.h => Seq/Alphabet/LetterAlphabet.cpp} | 23 +-
src/Bpp/Seq/Alphabet/LetterAlphabet.h | 121 +
.../Alphabet/LexicalAlphabet.cpp} | 105 +-
src/Bpp/Seq/Alphabet/LexicalAlphabet.h | 118 +
src/Bpp/Seq/Alphabet/NucleicAlphabet.h | 279 +++
src/Bpp/Seq/Alphabet/NucleicAlphabetState.h | 116 +
src/Bpp/Seq/Alphabet/NumericAlphabet.cpp | 189 ++
src/Bpp/Seq/Alphabet/NumericAlphabet.h | 131 +
src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp | 251 ++
src/Bpp/Seq/Alphabet/ProteicAlphabet.h | 162 ++
.../Alphabet/ProteicAlphabetState.h} | 77 +-
src/Bpp/Seq/Alphabet/RNA.cpp | 145 ++
src/Bpp/{Io/IoFormat.h => Seq/Alphabet/RNA.h} | 182 +-
src/Bpp/Seq/Alphabet/RNY.cpp | 533 ++++
src/Bpp/Seq/Alphabet/RNY.h | 126 +
src/Bpp/Seq/Alphabet/WordAlphabet.cpp | 370 +++
src/Bpp/Seq/Alphabet/WordAlphabet.h | 357 +++
src/Bpp/Seq/AlphabetIndex/AAChargeIndex.h | 151 ++
.../AAChenGuHuangHydrophobicityIndex.h | 122 +
.../Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h | 111 +
.../Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h | 111 +
src/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h | 111 +
.../AlphabetIndex/AAIndex1Entry.cpp} | 73 +-
.../AlphabetIndex/AAIndex1Entry.h} | 92 +-
.../AlphabetIndex/AAIndex2Entry.cpp} | 113 +-
src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h | 117 +
src/Bpp/Seq/AlphabetIndex/AAMassIndex.h | 108 +
src/Bpp/Seq/AlphabetIndex/AASEA1030Index.h | 109 +
src/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h | 109 +
src/Bpp/Seq/AlphabetIndex/AASEASup30Index.h | 109 +
src/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h | 109 +
src/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h | 111 +
.../AlphabetIndex/AlphabetIndex1.h} | 85 +-
.../AlphabetIndex/AlphabetIndex2.h} | 96 +-
.../AlphabetIndex/BLOSUM50.cpp} | 56 +-
.../AlphabetIndex/BLOSUM50.h} | 87 +-
.../Seq/AlphabetIndex/DefaultNucleotideScore.cpp | 113 +
src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h | 109 +
.../AlphabetIndex/GranthamAAChemicalDistance.cpp | 108 +
.../Seq/AlphabetIndex/GranthamAAChemicalDistance.h | 158 ++
.../Seq/AlphabetIndex/GranthamAAPolarityIndex.h | 124 +
src/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h | 127 +
src/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h | 124 +
.../AlphabetIndex/MiyataAAChemicalDistance.cpp} | 70 +-
.../Seq/AlphabetIndex/MiyataAAChemicalDistance.h | 116 +
src/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h | 134 +
.../AlphabetIndex/SimpleScore.cpp} | 62 +-
.../AlphabetIndex/SimpleScore.h} | 96 +-
.../AlphabetIndex/UserAlphabetIndex1.h} | 103 +-
src/Bpp/Seq/AlphabetIndex/__BLOSUM50MatrixCode | 400 +++
src/Bpp/Seq/AlphabetIndex/__GranthamMatrixCode | 827 +++++++
src/Bpp/Seq/AlphabetIndex/__MiyataMatrixCode | 400 +++
src/Bpp/Seq/App/SequenceApplicationTools.cpp | 717 ++++++
src/Bpp/Seq/App/SequenceApplicationTools.h | 297 +++
src/Bpp/Seq/CodonSiteTools.cpp | 833 +++++++
src/Bpp/Seq/CodonSiteTools.h | 296 +++
.../Container/AbstractSequenceContainer.cpp} | 38 +-
src/Bpp/Seq/Container/AbstractSequenceContainer.h | 181 ++
src/Bpp/Seq/Container/AlignedSequenceContainer.cpp | 510 ++++
src/Bpp/Seq/Container/AlignedSequenceContainer.h | 202 ++
.../Container/CompressedVectorSiteContainer.cpp | 597 +++++
.../Seq/Container/CompressedVectorSiteContainer.h | 290 +++
src/Bpp/Seq/Container/MapSequenceContainer.cpp | 466 ++++
src/Bpp/Seq/Container/MapSequenceContainer.h | 240 ++
src/Bpp/Seq/Container/OrderedSequenceContainer.h | 237 ++
src/Bpp/Seq/Container/SequenceContainer.h | 307 +++
.../Seq/Container/SequenceContainerExceptions.h | 149 ++
.../Seq/Container/SequenceContainerIterator.cpp | 58 +-
.../Container/SequenceContainerIterator.h} | 81 +-
src/Bpp/Seq/Container/SequenceContainerTools.cpp | 226 ++
src/Bpp/Seq/Container/SequenceContainerTools.h | 301 +++
src/Bpp/Seq/Container/SiteContainer.h | 183 ++
.../Container/SiteContainerExceptions.cpp} | 39 +-
.../Container/SiteContainerExceptions.h} | 77 +-
src/Bpp/Seq/Container/SiteContainerIterator.cpp | 144 ++
src/Bpp/Seq/Container/SiteContainerIterator.h | 128 +
src/Bpp/Seq/Container/SiteContainerTools.cpp | 1098 +++++++++
src/Bpp/Seq/Container/SiteContainerTools.h | 505 ++++
.../Container/VectorProbabilisticSiteContainer.cpp | 187 ++
.../Container/VectorProbabilisticSiteContainer.h | 123 +
src/Bpp/Seq/Container/VectorSequenceContainer.cpp | 399 +++
src/Bpp/Seq/Container/VectorSequenceContainer.h | 306 +++
src/Bpp/Seq/Container/VectorSiteContainer.cpp | 874 +++++++
src/Bpp/Seq/Container/VectorSiteContainer.h | 241 ++
src/Bpp/Seq/CoreSequence.h | 257 ++
src/Bpp/Seq/CoreSite.h | 191 ++
test/test_bfgs.cpp => src/Bpp/Seq/DNAToRNA.cpp | 61 +-
.../NewtonOneDimension.h => Seq/DNAToRNA.h} | 76 +-
.../Uniform01WH.cpp => Seq/DistanceMatrix.cpp} | 29 +-
src/Bpp/Seq/DistanceMatrix.h | 256 ++
.../AscidianMitochondrialGeneticCode.cpp | 117 +
.../GeneticCode/AscidianMitochondrialGeneticCode.h | 113 +
.../EchinodermMitochondrialGeneticCode.cpp | 116 +
.../EchinodermMitochondrialGeneticCode.h | 110 +
src/Bpp/Seq/GeneticCode/GeneticCode.cpp | 213 ++
src/Bpp/Seq/GeneticCode/GeneticCode.h | 252 ++
.../InvertebrateMitochondrialGeneticCode.cpp | 117 +
.../InvertebrateMitochondrialGeneticCode.h | 111 +
.../GeneticCode/MoldMitochondrialGeneticCode.cpp | 117 +
.../Seq/GeneticCode/MoldMitochondrialGeneticCode.h | 111 +
src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp | 117 +
src/Bpp/Seq/GeneticCode/StandardGeneticCode.h | 111 +
.../VertebrateMitochondrialGeneticCode.cpp | 117 +
.../VertebrateMitochondrialGeneticCode.h | 113 +
.../GeneticCode/YeastMitochondrialGeneticCode.cpp | 117 +
.../GeneticCode/YeastMitochondrialGeneticCode.h | 112 +
src/Bpp/Seq/Io/AbstractIAlignment.h | 175 ++
src/Bpp/Seq/Io/AbstractISequence.h | 172 ++
.../{BppBoolean.h => Seq/Io/AbstractOAlignment.h} | 61 +-
.../{BppString.h => Seq/Io/AbstractOSequence.h} | 81 +-
src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp | 123 +
.../Io/BppOAlignmentReaderFormat.h} | 183 +-
src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp | 116 +
.../Io/BppOAlignmentWriterFormat.h} | 185 +-
src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp | 154 ++
src/Bpp/Seq/Io/BppOAlphabetIndex1Format.h | 114 +
src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp | 124 +
src/Bpp/Seq/Io/BppOAlphabetIndex2Format.h | 114 +
src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp | 128 +
.../Io/BppOSequenceReaderFormat.h} | 184 +-
.../Io/BppOSequenceStreamReaderFormat.cpp} | 70 +-
src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h | 93 +
.../Io/BppOSequenceWriterFormat.cpp} | 163 +-
.../Io/BppOSequenceWriterFormat.h} | 183 +-
src/Bpp/Seq/Io/Clustal.cpp | 138 ++
src/Bpp/Seq/Io/Clustal.h | 146 ++
src/Bpp/Seq/Io/Dcse.cpp | 97 +
.../Stat/ContingencyTableTest.h => Seq/Io/Dcse.h} | 90 +-
src/Bpp/Seq/Io/Fasta.cpp | 300 +++
src/Bpp/Seq/Io/Fasta.h | 224 ++
.../{Numeric/NumTools.cpp => Seq/Io/GenBank.cpp} | 83 +-
src/Bpp/{BppString.h => Seq/Io/GenBank.h} | 86 +-
src/Bpp/Seq/Io/ISequence.h | 132 +
.../Io/ISequenceStream.h} | 86 +-
.../Stat/StatTest.h => Seq/Io/IoSequence.h} | 41 +-
src/Bpp/Seq/Io/IoSequenceFactory.cpp | 109 +
src/Bpp/Seq/Io/IoSequenceFactory.h | 124 +
.../Io/IoSequenceStream.h} | 37 +-
src/Bpp/Seq/Io/Mase.cpp | 314 +++
src/Bpp/Seq/Io/Mase.h | 256 ++
src/Bpp/Seq/Io/MaseTools.cpp | 283 +++
src/Bpp/Seq/Io/MaseTools.h | 146 ++
src/Bpp/Seq/Io/NexusIoSequence.cpp | 209 ++
src/Bpp/Seq/Io/NexusIoSequence.h | 150 ++
src/Bpp/Seq/Io/NexusTools.cpp | 119 +
src/Bpp/{BppVector.h => Seq/Io/NexusTools.h} | 72 +-
src/Bpp/Seq/Io/OSequence.h | 128 +
.../RandomFactory.h => Seq/Io/OSequenceStream.h} | 57 +-
src/Bpp/Seq/Io/PhredPhd.cpp | 138 ++
src/Bpp/Seq/Io/PhredPhd.h | 156 ++
.../{Numeric/NumTools.cpp => Seq/Io/PhredPoly.cpp} | 104 +-
.../Hmm/HmmExceptions.h => Seq/Io/PhredPoly.h} | 80 +-
src/Bpp/Seq/Io/Phylip.cpp | 304 +++
src/Bpp/Seq/Io/Phylip.h | 196 ++
.../Stat/StatTest.h => Seq/Io/SequenceFileIndex.h} | 78 +-
.../Io/Stockholm.cpp} | 63 +-
src/Bpp/Seq/Io/Stockholm.h | 120 +
.../Io/StreamSequenceIterator.cpp} | 78 +-
src/Bpp/Seq/Io/StreamSequenceIterator.h | 138 ++
src/Bpp/Seq/NucleicAcidsReplication.cpp | 120 +
src/Bpp/Seq/NucleicAcidsReplication.h | 105 +
src/Bpp/Seq/Sequence.cpp | 243 ++
src/Bpp/Seq/Sequence.h | 331 +++
.../SequenceExceptions.cpp} | 45 +-
src/Bpp/Seq/SequenceExceptions.h | 161 ++
.../Uniform01QD.h => Seq/SequenceIterator.h} | 99 +-
src/Bpp/Seq/SequencePositionIterators.cpp | 151 ++
src/Bpp/Seq/SequencePositionIterators.h | 210 ++
src/Bpp/Seq/SequenceTools.cpp | 729 ++++++
src/Bpp/Seq/SequenceTools.h | 467 ++++
src/Bpp/Seq/SequenceWalker.cpp | 107 +
.../NewtonOneDimension.h => Seq/SequenceWalker.h} | 78 +-
src/Bpp/Seq/SequenceWithAnnotation.cpp | 315 +++
src/Bpp/Seq/SequenceWithAnnotation.h | 417 ++++
.../SequenceWithAnnotationTools.cpp} | 68 +-
src/Bpp/Seq/SequenceWithAnnotationTools.h | 202 ++
.../SequenceWithQuality.cpp} | 70 +-
src/Bpp/Seq/SequenceWithQuality.h | 760 ++++++
src/Bpp/Seq/SequenceWithQualityTools.cpp | 173 ++
src/Bpp/Seq/SequenceWithQualityTools.h | 196 ++
src/Bpp/Seq/Site.cpp | 100 +
src/Bpp/Seq/Site.h | 175 ++
.../Uniform01QD.cpp => Seq/SiteExceptions.cpp} | 32 +-
.../Random/Uniform01QD.h => Seq/SiteExceptions.h} | 97 +-
.../Operators/Operator.h => Seq/SiteIterator.h} | 57 +-
src/Bpp/Seq/SiteTools.cpp | 512 ++++
src/Bpp/Seq/SiteTools.h | 285 +++
src/Bpp/Seq/StringSequenceTools.cpp | 344 +++
src/Bpp/Seq/StringSequenceTools.h | 204 ++
src/Bpp/Seq/SymbolList.cpp | 456 ++++
src/Bpp/Seq/SymbolList.h | 722 ++++++
src/Bpp/Seq/SymbolListTools.cpp | 193 ++
src/Bpp/Seq/SymbolListTools.h | 205 ++
.../BppApplication.cpp => Seq/Transliterator.cpp} | 59 +-
src/Bpp/Seq/Transliterator.h | 175 ++
src/Bpp/Text/KeyvalTools.cpp | 194 --
src/Bpp/Text/KeyvalTools.h | 138 --
src/Bpp/Text/NestedStringTokenizer.cpp | 153 --
src/Bpp/Text/NestedStringTokenizer.h | 99 -
src/Bpp/Text/StringTokenizer.cpp | 116 -
src/Bpp/Text/StringTokenizer.h | 146 --
src/Bpp/Text/TextTools.cpp | 522 ----
src/Bpp/Text/TextTools.h | 416 ----
src/Bpp/Utils/AttributesTools.cpp | 317 ---
src/Bpp/Utils/AttributesTools.h | 245 --
src/Bpp/Utils/MapTools.h | 129 -
src/CMakeLists.txt | 180 +-
test/CMakeLists.txt | 4 +-
test/PolynomialFunction.h | 127 -
test/example.aln | 2143 ++++++++++++++++
test/example.fasta | 1702 +++++++++++++
test/example.fastq | 12 +
test/example.gff | 25 +
test/example.mase | 1500 +++++++++++
test/example.ph | 2526 +++++++++++++++++++
test/example.ph3 | 2601 ++++++++++++++++++++
test/test_alignment_scores.cpp | 102 +
test/{test_matrices.cpp => test_alphabets.cpp} | 44 +-
test/test_bowker.cpp | 101 +
test/{test_downhill.cpp => test_containers.cpp} | 45 +-
test/test_dAGraphObs.cpp | 159 --
test/test_derivative1.cpp | 117 -
test/test_distributions.cpp | 155 --
test/test_eigen.cpp | 73 -
test/test_graphObs.cpp | 144 --
test/test_io.cpp | 96 +
test/test_mva.cpp | 175 --
test/test_numconstants.cpp | 62 -
test/test_powell.cpp | 65 -
test/test_range.cpp | 198 --
test/test_reparametrization.cpp | 98 -
test/test_sample.cpp | 131 -
test/test_sequences.cpp | 92 +
test/test_simplex.cpp | 117 -
test/test_stats.cpp | 87 -
test/test_text_tools.cpp | 112 -
test/test_treeGraphObs.cpp | 178 --
test/test_walker.cpp | 119 +
457 files changed, 50117 insertions(+), 56990 deletions(-)
--
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