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 <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-seq.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
