[med-svn] [libbpp-seq] 02/07: Updated version 2.3.0 from 'upstream/2.3.0'
Andreas Tille
tille at debian.org
Sat Jun 3 12:48:05 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 0da99de7cb994445af4402dcc07ada790eace742
Merge: a4394dc bb4a617
Author: Andreas Tille <tille at debian.org>
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(-)
--
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