This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository libbpp-seq.
commit 0da99de7cb994445af4402dcc07ada790eace742 Merge: a4394dc bb4a617 Author: Andreas Tille <[email protected]> Date: Sat Jun 3 07:25:16 2017 +0200 Updated version 2.3.0 from 'upstream/2.3.0' with Debian dir 70e6441d18662f8c9123a182048222b9e3b14e41 .gitignore | 15 + AUTHORS.txt | 15 +- CMakeLists.txt | 184 +- CTestConfig.cmake | 13 + ChangeLog | 450 +--- Doxyfile | 2674 ++++++++++++-------- Doxyfile-build | 1889 -------------- INSTALL.txt | 19 +- bpp-core.spec | 102 + bpp-seq.spec | 203 -- cmake/doc-cmake-for-developpers.cmake | 240 ++ cmake/project-template-for-users.cmake | 106 + genIncludes.sh | 35 - package.cmake.in | 25 + src/Bpp/App/ApplicationTools.cpp | 374 +++ src/Bpp/App/ApplicationTools.h | 640 +++++ .../BppApplication.cpp} | 56 +- .../AbstractOAlignment.h => App/BppApplication.h} | 79 +- src/Bpp/App/NumCalcApplicationTools.cpp | 141 ++ src/Bpp/App/NumCalcApplicationTools.h | 134 + .../{Seq/Io/AbstractOAlignment.h => BppBoolean.h} | 61 +- .../Alphabet/DefaultAlphabet.cpp => BppString.cpp} | 31 +- src/Bpp/{Seq/Io/GenBank.h => BppString.h} | 86 +- src/Bpp/{Seq/Io/NexusTools.h => BppVector.h} | 72 +- src/Bpp/Clonable.h | 120 + .../Alphabet/CodonAlphabet.cpp => Exceptions.cpp} | 105 +- 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 +++++ .../AlphabetIndex1.h => Graph/GraphObserver.h} | 85 +- 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 + .../SiteIterator.h => Graphics/DefaultColorSet.h} | 60 +- src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp | 194 ++ src/Bpp/Graphics/Fig/XFigGraphicDevice.h | 133 + .../Bpp/Graphics/Fig/XFigLaTeXFontManager.cpp | 44 +- .../Fig/XFigLaTeXFontManager.h} | 40 +- src/Bpp/Graphics/Fig/XFigPostscriptFontManager.cpp | 85 + .../Fig/XFigPostscriptFontManager.h} | 40 +- .../DistanceMatrix.cpp => Graphics/Font/Font.cpp} | 33 +- src/Bpp/Graphics/Font/Font.h | 174 ++ src/Bpp/Graphics/Font/FontManager.h | 150 ++ .../Bpp/Graphics/GraphicDevice.cpp | 45 +- src/Bpp/Graphics/GraphicDevice.h | 199 ++ src/Bpp/Graphics/Latex/DvipsColorSet.cpp | 115 + .../Latex/DvipsColorSet.h} | 37 +- src/Bpp/Graphics/Latex/PgfGraphicDevice.cpp | 299 +++ src/Bpp/Graphics/Latex/PgfGraphicDevice.h | 117 + src/Bpp/Graphics/Molscript/MolscriptColorSet.cpp | 210 ++ .../Molscript/MolscriptColorSet.h} | 37 +- src/Bpp/Graphics/Point2D.h | 146 ++ .../Point2DTools.h} | 73 +- src/Bpp/Graphics/R/RColorSet.cpp | 704 ++++++ .../{Seq/SiteIterator.h => Graphics/R/RColorSet.h} | 64 +- 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 + .../CodonAlphabet.cpp => Io/FileTools.cpp} | 114 +- src/Bpp/Io/FileTools.h | 162 ++ src/Bpp/Io/IoDiscreteDistribution.h | 125 + .../IoDiscreteDistributionFactory.cpp} | 39 +- src/Bpp/Io/IoDiscreteDistributionFactory.h | 99 + .../AlphabetNumericState.h => Io/IoFormat.h} | 187 +- src/Bpp/Io/IoParametrizable.h | 117 + src/Bpp/Io/OutputStream.h | 350 +++ src/Bpp/Numeric/AbstractParameterAliasable.cpp | 397 +++ src/Bpp/Numeric/AbstractParameterAliasable.h | 281 ++ .../Bpp/Numeric/AbstractParametrizable.cpp | 51 +- 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/NewtonOneDimension.h} | 78 +- .../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 + .../Function/Operators/ConstantOperator.h} | 72 +- .../Numeric/Function/Operators/FunctionOperator.h | 133 + src/Bpp/Numeric/Function/Operators/MathOperator.h | 138 + .../Function/Operators/Operator.h} | 57 +- .../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 + .../Function/SimpleMultiDimensions.h} | 73 +- .../Function/SimpleNewtonMultiDimensions.cpp} | 96 +- .../Function/SimpleNewtonMultiDimensions.h} | 72 +- .../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 + .../SiteIterator.h => Numeric/Hmm/HmmExceptions.h} | 75 +- .../Hmm/HmmLikelihood.cpp} | 74 +- 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 + .../{Seq/Io/GenBank.cpp => Numeric/NumTools.cpp} | 83 +- 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 ++ .../ParameterExceptions.cpp} | 45 +- 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 + .../Prob/ConstantDistribution.cpp} | 70 +- .../Dcse.h => Numeric/Prob/ConstantDistribution.h} | 113 +- .../Numeric/Prob/DirichletDiscreteDistribution.cpp | 282 +++ .../Numeric/Prob/DirichletDiscreteDistribution.h | 178 ++ src/Bpp/Numeric/Prob/DiscreteDistribution.h | 320 +++ .../Prob/ExponentialDiscreteDistribution.cpp} | 56 +- .../Numeric/Prob/ExponentialDiscreteDistribution.h | 122 + src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp | 135 + src/Bpp/Numeric/Prob/GammaDiscreteDistribution.h | 125 + .../Numeric/Prob/GaussianDiscreteDistribution.cpp | 109 + .../Prob/GaussianDiscreteDistribution.h} | 88 +- .../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.cpp} | 76 +- .../TruncatedExponentialDiscreteDistribution.h | 154 ++ .../Prob/UniformDiscreteDistribution.cpp} | 70 +- src/Bpp/Numeric/Prob/UniformDiscreteDistribution.h | 113 + .../Numeric/Random/ContingencyTableGenerator.cpp | 199 ++ .../Random/ContingencyTableGenerator.h} | 92 +- .../Random/RandomFactory.h} | 50 +- src/Bpp/Numeric/Random/RandomTools.cpp | 1034 ++++++++ src/Bpp/Numeric/Random/RandomTools.h | 554 ++++ src/Bpp/Numeric/Random/Uniform01K.cpp | 106 + .../Random/Uniform01K.h} | 79 +- .../Random/Uniform01QD.cpp} | 27 +- .../Random/Uniform01QD.h} | 69 +- .../Random/Uniform01WH.cpp} | 34 +- .../Random/Uniform01WH.h} | 77 +- src/Bpp/Numeric/Range.h | 543 ++++ src/Bpp/Numeric/Stat/ContingencyTableTest.cpp | 129 + .../Stat/ContingencyTableTest.h} | 101 +- .../Numeric/Stat/Mva/CorrespondenceAnalysis.cpp | 114 + .../Stat/Mva/CorrespondenceAnalysis.h} | 87 +- 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 + .../Io/IoSequence.h => Numeric/Stat/StatTest.h} | 41 +- .../Stat/StatTools.cpp} | 38 +- .../Stat/StatTools.h} | 88 +- src/Bpp/Numeric/Table.h | 1222 +++++++++ src/Bpp/Numeric/TableExceptions.h | 175 ++ src/Bpp/Numeric/TransformedParameter.h | 312 +++ src/Bpp/Numeric/VectorExceptions.h | 155 ++ .../VectorTools.cpp} | 97 +- src/Bpp/Numeric/VectorTools.h | 2007 +++++++++++++++ src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp | 317 --- src/Bpp/Seq/Alphabet/AbstractAlphabet.h | 276 -- src/Bpp/Seq/Alphabet/Alphabet.h | 459 ---- src/Bpp/Seq/Alphabet/AlphabetExceptions.h | 213 -- src/Bpp/Seq/Alphabet/AlphabetState.h | 132 - src/Bpp/Seq/Alphabet/AlphabetTools.cpp | 126 - src/Bpp/Seq/Alphabet/AlphabetTools.h | 231 -- src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp | 59 - src/Bpp/Seq/Alphabet/BinaryAlphabet.h | 86 - src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp | 97 - src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h | 124 - src/Bpp/Seq/Alphabet/CodonAlphabet.h | 190 -- src/Bpp/Seq/Alphabet/DNA.cpp | 147 -- src/Bpp/Seq/Alphabet/DNA.h | 96 - src/Bpp/Seq/Alphabet/IntegerAlphabet.h | 94 - src/Bpp/Seq/Alphabet/LetterAlphabet.h | 123 - src/Bpp/Seq/Alphabet/NucleicAlphabet.h | 281 -- 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 -- src/Bpp/Seq/Alphabet/ProteicAlphabetState.h | 82 - src/Bpp/Seq/Alphabet/RNA.cpp | 145 -- src/Bpp/Seq/Alphabet/RNA.h | 93 - src/Bpp/Seq/Alphabet/RNY.cpp | 533 ---- src/Bpp/Seq/Alphabet/RNY.h | 126 - src/Bpp/Seq/Alphabet/WordAlphabet.cpp | 351 --- src/Bpp/Seq/Alphabet/WordAlphabet.h | 345 --- 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 - src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp | 85 - src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h | 102 - src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp | 104 - 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 - src/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h | 104 - .../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 | 123 - src/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h | 126 - src/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h | 124 - .../Seq/AlphabetIndex/MiyataAAChemicalDistance.h | 116 - src/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h | 134 - src/Bpp/Seq/AlphabetIndex/SimpleScore.h | 106 - src/Bpp/Seq/AlphabetIndex/UserAlphabetIndex1.h | 111 - src/Bpp/Seq/AlphabetIndex/__BLOSUM50MatrixCode | 400 --- src/Bpp/Seq/AlphabetIndex/__GranthamMatrixCode | 827 ------ src/Bpp/Seq/AlphabetIndex/__MiyataMatrixCode | 400 --- src/Bpp/Seq/App/SequenceApplicationTools.cpp | 599 ----- src/Bpp/Seq/App/SequenceApplicationTools.h | 288 --- src/Bpp/Seq/CodonSiteTools.cpp | 837 ------ src/Bpp/Seq/CodonSiteTools.h | 333 --- src/Bpp/Seq/Container/AbstractSequenceContainer.h | 190 -- src/Bpp/Seq/Container/AlignedSequenceContainer.cpp | 523 ---- 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 | 246 -- src/Bpp/Seq/Container/SequenceContainer.h | 316 --- .../Seq/Container/SequenceContainerExceptions.h | 149 -- src/Bpp/Seq/Container/SequenceContainerTools.cpp | 226 -- src/Bpp/Seq/Container/SequenceContainerTools.h | 299 --- src/Bpp/Seq/Container/SiteContainer.h | 183 -- src/Bpp/Seq/Container/SiteContainerIterator.cpp | 144 -- src/Bpp/Seq/Container/SiteContainerIterator.h | 128 - src/Bpp/Seq/Container/SiteContainerTools.cpp | 1082 -------- src/Bpp/Seq/Container/SiteContainerTools.h | 497 ---- src/Bpp/Seq/Container/VectorSequenceContainer.cpp | 399 --- src/Bpp/Seq/Container/VectorSequenceContainer.h | 306 --- src/Bpp/Seq/Container/VectorSiteContainer.cpp | 862 ------- src/Bpp/Seq/Container/VectorSiteContainer.h | 240 -- src/Bpp/Seq/DNAToRNA.h | 100 - 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 | 260 -- .../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 | 185 -- src/Bpp/Seq/Io/AbstractISequence.h | 182 -- src/Bpp/Seq/Io/AbstractOSequence.h | 107 - src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp | 123 - src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h | 94 - src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp | 116 - src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h | 96 - 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 - src/Bpp/Seq/Io/BppOSequenceReaderFormat.h | 95 - src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp | 70 - src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h | 93 - src/Bpp/Seq/Io/BppOSequenceWriterFormat.h | 94 - src/Bpp/Seq/Io/Clustal.cpp | 138 - src/Bpp/Seq/Io/Clustal.h | 146 -- src/Bpp/Seq/Io/Dcse.cpp | 97 - src/Bpp/Seq/Io/Fasta.cpp | 292 --- src/Bpp/Seq/Io/Fasta.h | 214 -- src/Bpp/Seq/Io/ISequence.h | 132 - src/Bpp/Seq/Io/ISequenceStream.h | 82 - src/Bpp/Seq/Io/IoSequenceFactory.cpp | 109 - src/Bpp/Seq/Io/IoSequenceFactory.h | 124 - src/Bpp/Seq/Io/Mase.cpp | 313 --- src/Bpp/Seq/Io/Mase.h | 256 -- src/Bpp/Seq/Io/MaseTools.cpp | 306 --- 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/Seq/Io/OSequence.h | 128 - src/Bpp/Seq/Io/OSequenceStream.h | 81 - src/Bpp/Seq/Io/PhredPhd.cpp | 138 - src/Bpp/Seq/Io/PhredPhd.h | 156 -- src/Bpp/Seq/Io/PhredPoly.cpp | 97 - src/Bpp/Seq/Io/PhredPoly.h | 91 - src/Bpp/Seq/Io/Phylip.cpp | 304 --- src/Bpp/Seq/Io/Phylip.h | 196 -- src/Bpp/Seq/Io/SequenceFileIndex.h | 75 - src/Bpp/Seq/Io/Stockholm.cpp | 83 - src/Bpp/Seq/Io/Stockholm.h | 120 - src/Bpp/Seq/Io/StreamSequenceIterator.cpp | 97 - src/Bpp/Seq/Io/StreamSequenceIterator.h | 138 - src/Bpp/Seq/NucleicAcidsReplication.cpp | 120 - src/Bpp/Seq/NucleicAcidsReplication.h | 105 - src/Bpp/Seq/Sequence.cpp | 222 -- src/Bpp/Seq/Sequence.h | 465 ---- src/Bpp/Seq/SequenceExceptions.h | 161 -- src/Bpp/Seq/SequencePositionIterators.cpp | 151 -- src/Bpp/Seq/SequencePositionIterators.h | 210 -- src/Bpp/Seq/SequenceTools.cpp | 727 ------ src/Bpp/Seq/SequenceTools.h | 435 ---- src/Bpp/Seq/SequenceWalker.cpp | 107 - src/Bpp/Seq/SequenceWithAnnotation.cpp | 303 --- src/Bpp/Seq/SequenceWithAnnotation.h | 443 ---- src/Bpp/Seq/SequenceWithAnnotationTools.cpp | 91 - src/Bpp/Seq/SequenceWithAnnotationTools.h | 207 -- src/Bpp/Seq/SequenceWithQuality.h | 786 ------ src/Bpp/Seq/SequenceWithQualityTools.cpp | 194 -- src/Bpp/Seq/SequenceWithQualityTools.h | 175 -- src/Bpp/Seq/Site.cpp | 101 - src/Bpp/Seq/Site.h | 179 -- src/Bpp/Seq/SiteExceptions.h | 124 - src/Bpp/Seq/SiteTools.cpp | 410 --- src/Bpp/Seq/SiteTools.h | 254 -- src/Bpp/Seq/StringSequenceTools.cpp | 344 --- src/Bpp/Seq/StringSequenceTools.h | 204 -- src/Bpp/Seq/SymbolList.cpp | 442 ---- src/Bpp/Seq/SymbolList.h | 745 ------ src/Bpp/Seq/SymbolListTools.cpp | 197 -- src/Bpp/Seq/SymbolListTools.h | 207 -- src/Bpp/Seq/Transliterator.cpp | 72 - src/Bpp/Seq/Transliterator.h | 187 -- 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 + .../{Seq/Alphabet/LetterAlphabet.cpp => Version.h} | 23 +- src/CMakeLists.txt | 360 +-- test/CMakeLists.txt | 90 +- 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_containers.cpp => test_bfgs.cpp} | 45 +- test/test_bowker.cpp | 101 - test/test_dAGraphObs.cpp | 159 ++ test/test_derivative1.cpp | 117 + test/test_distributions.cpp | 155 ++ test/{test_alphabets.cpp => test_downhill.cpp} | 42 +- test/{test_alphabets.cpp => test_eigen.cpp} | 52 +- .../test_gradient.cpp | 58 +- test/test_graphObs.cpp | 144 ++ test/test_io.cpp | 96 - test/{test_alphabets.cpp => test_matrices.cpp} | 44 +- test/test_mva.cpp | 175 ++ .../Seq/DNAToRNA.cpp => test/test_numconstants.cpp | 56 +- test/{test_alphabets.cpp => test_powell.cpp} | 42 +- 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_alphabets.cpp => test_stats.cpp} | 62 +- test/test_text_tools.cpp | 112 + test/test_treeGraphObs.cpp | 178 ++ test/test_walker.cpp | 119 - 459 files changed, 56533 insertions(+), 54125 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
