[med-svn] [libbpp-core] 02/04: Update upstream source from tag 'upstream/2.3.2'
Julien Dutheil
jdutheil-guest at moszumanska.debian.org
Mon Feb 5 12:32:05 UTC 2018
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jdutheil-guest pushed a commit to branch master
in repository libbpp-core.
commit 813798fb3d7416842240ae1aa5d26f242e854671
Merge: 7a94d80 30596ab
Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
Date: Mon Feb 5 13:13:08 2018 +0100
Update upstream source from tag 'upstream/2.3.2'
Update to upstream version '2.3.2'
with Debian dir a499817428f3ffafab2ff6e93e155a5ed6f984bb
.clang-format | 8 +
.gitignore | 1 +
Doxyfile | 479 +--
bpp_format.py | 546 +++
src/Bpp/App/ApplicationTools.cpp | 59 +-
src/Bpp/App/ApplicationTools.h | 24 +-
src/Bpp/App/BppApplication.h | 2 +-
src/Bpp/App/NumCalcApplicationTools.cpp | 4 +-
src/Bpp/App/NumCalcApplicationTools.h | 4 +-
src/Bpp/BppBoolean.h | 121 +-
src/Bpp/BppString.cpp | 104 +-
src/Bpp/BppString.h | 138 +-
src/Bpp/BppVector.h | 147 +-
src/Bpp/Clonable.h | 118 +-
src/Bpp/Exceptions.cpp | 216 +-
src/Bpp/Exceptions.h | 492 +--
src/Bpp/Graph/AssociationDAGraphImplObserver.h | 14 +-
src/Bpp/Graph/AssociationDAGraphObserver.h | 4 +
src/Bpp/Graph/AssociationGraphImplObserver.h | 128 +-
src/Bpp/Graph/AssociationGraphObserver.h | 2 +
src/Bpp/Graph/AssociationTreeGraphImplObserver.h | 14 +-
src/Bpp/Graph/AssociationTreeGraphObserver.h | 6 +-
src/Bpp/Graph/GlobalGraph.cpp | 83 +-
src/Bpp/Graph/TreeGraph.h | 4 +
src/Bpp/Graph/TreeGraphImpl.h | 894 ++---
src/Bpp/Graphics/AbstractGraphicDevice.h | 2 +-
src/Bpp/Graphics/ColorManager.h | 4 +-
src/Bpp/Graphics/ColorSet.h | 8 +-
src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp | 2 +-
src/Bpp/Graphics/Fig/XFigGraphicDevice.h | 4 +-
src/Bpp/Graphics/Font/FontManager.h | 8 +-
src/Bpp/Graphics/GraphicDevice.h | 2 +-
src/Bpp/Graphics/Latex/PgfGraphicDevice.cpp | 4 +-
src/Bpp/Graphics/Latex/PgfGraphicDevice.h | 4 +-
src/Bpp/Graphics/Svg/SvgGraphicDevice.cpp | 2 +-
src/Bpp/Graphics/Svg/SvgGraphicDevice.h | 2 +-
src/Bpp/Io/BppODiscreteDistributionFormat.cpp | 2 +-
src/Bpp/Io/BppODiscreteDistributionFormat.h | 2 +-
src/Bpp/Io/FileTools.cpp | 4 +-
src/Bpp/Io/IoDiscreteDistributionFactory.cpp | 4 +-
src/Bpp/Io/IoDiscreteDistributionFactory.h | 4 +-
src/Bpp/Numeric/AbstractParameterAliasable.cpp | 2 -
src/Bpp/Numeric/AbstractParameterAliasable.h | 12 +-
src/Bpp/Numeric/AbstractParametrizable.h | 25 +-
src/Bpp/Numeric/AutoParameter.cpp | 4 +-
src/Bpp/Numeric/AutoParameter.h | 4 +-
src/Bpp/Numeric/DataTable.cpp | 37 +-
src/Bpp/Numeric/DataTable.h | 67 +-
.../Numeric/Function/AbstractNumericalDerivative.h | 10 +-
src/Bpp/Numeric/Function/AbstractOptimizer.cpp | 6 +-
src/Bpp/Numeric/Function/AbstractOptimizer.h | 12 +-
src/Bpp/Numeric/Function/BfgsMultiDimensions.cpp | 4 +-
src/Bpp/Numeric/Function/BfgsMultiDimensions.h | 4 +-
src/Bpp/Numeric/Function/BrentOneDimension.cpp | 6 +-
src/Bpp/Numeric/Function/BrentOneDimension.h | 6 +-
.../Function/ConjugateGradientMultiDimensions.cpp | 4 +-
.../Function/ConjugateGradientMultiDimensions.h | 4 +-
src/Bpp/Numeric/Function/DirectionFunction.cpp | 5 +-
src/Bpp/Numeric/Function/DirectionFunction.h | 7 +-
src/Bpp/Numeric/Function/DownhillSimplexMethod.cpp | 6 +-
src/Bpp/Numeric/Function/DownhillSimplexMethod.h | 6 +-
.../Function/FivePointsNumericalDerivative.cpp | 1 -
.../Function/FivePointsNumericalDerivative.h | 6 +-
src/Bpp/Numeric/Function/FunctionTools.cpp | 8 +-
src/Bpp/Numeric/Function/FunctionTools.h | 10 +-
src/Bpp/Numeric/Function/Functions.h | 64 +-
src/Bpp/Numeric/Function/GoldenSectionSearch.cpp | 6 +-
src/Bpp/Numeric/Function/GoldenSectionSearch.h | 6 +-
src/Bpp/Numeric/Function/MetaOptimizer.cpp | 3 +-
src/Bpp/Numeric/Function/MetaOptimizer.h | 4 +-
.../Function/NewtonBacktrackOneDimension.cpp | 4 +-
.../Numeric/Function/NewtonBacktrackOneDimension.h | 4 +-
src/Bpp/Numeric/Function/NewtonOneDimension.cpp | 4 +-
src/Bpp/Numeric/Function/NewtonOneDimension.h | 4 +-
src/Bpp/Numeric/Function/Optimizer.h | 8 +-
src/Bpp/Numeric/Function/PowellMultiDimensions.cpp | 6 +-
src/Bpp/Numeric/Function/PowellMultiDimensions.h | 6 +-
.../Function/ReparametrizationFunctionWrapper.h | 9 +-
src/Bpp/Numeric/Function/SimpleMultiDimensions.cpp | 4 +-
src/Bpp/Numeric/Function/SimpleMultiDimensions.h | 4 +-
.../Function/SimpleNewtonMultiDimensions.cpp | 4 +-
.../Numeric/Function/SimpleNewtonMultiDimensions.h | 4 +-
.../Function/ThreePointsNumericalDerivative.cpp | 1 -
.../Function/ThreePointsNumericalDerivative.h | 5 +-
.../Function/TwoPointsNumericalDerivative.cpp | 1 -
.../Function/TwoPointsNumericalDerivative.h | 7 +-
.../Numeric/Hmm/AbstractHmmTransitionMatrix.cpp | 2 +-
src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h | 2 +-
src/Bpp/Numeric/Hmm/HmmEmissionProbabilities.h | 2 +-
src/Bpp/Numeric/Hmm/HmmLikelihood.cpp | 4 +-
src/Bpp/Numeric/Hmm/HmmLikelihood.h | 8 +-
src/Bpp/Numeric/Hmm/HmmStateAlphabet.h | 2 +-
src/Bpp/Numeric/Hmm/HmmTransitionMatrix.h | 2 +-
src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp | 4 +-
src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h | 8 +-
.../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp | 2 +-
.../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h | 8 +-
src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp | 4 +-
src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h | 8 +-
src/Bpp/Numeric/IntegerTools.h | 86 +
src/Bpp/Numeric/Matrix/LUDecomposition.h | 4 +-
src/Bpp/Numeric/Matrix/Matrix.h | 9 +-
src/Bpp/Numeric/Matrix/MatrixTools.h | 194 +-
src/Bpp/Numeric/NumTools.cpp | 2 +-
src/Bpp/Numeric/NumTools.h | 2 +-
src/Bpp/Numeric/Parameter.cpp | 8 +-
src/Bpp/Numeric/Parameter.h | 8 +-
src/Bpp/Numeric/ParameterAliasable.h | 8 +-
src/Bpp/Numeric/ParameterExceptions.h | 6 +-
src/Bpp/Numeric/ParameterList.cpp | 39 +-
src/Bpp/Numeric/ParameterList.h | 53 +-
src/Bpp/Numeric/Parametrizable.h | 35 +-
.../Numeric/Prob/AbstractDiscreteDistribution.h | 4 +-
src/Bpp/Numeric/Prob/BetaDiscreteDistribution.h | 2 +-
src/Bpp/Numeric/Prob/ConstantDistribution.h | 2 +-
src/Bpp/Numeric/Prob/DiscreteDistribution.h | 2 +-
.../Numeric/Prob/ExponentialDiscreteDistribution.h | 2 +-
src/Bpp/Numeric/Prob/GammaDiscreteDistribution.h | 2 +-
.../Numeric/Prob/GaussianDiscreteDistribution.h | 2 +-
src/Bpp/Numeric/Prob/Simplex.cpp | 11 +-
.../TruncatedExponentialDiscreteDistribution.h | 2 +-
src/Bpp/Numeric/Prob/UniformDiscreteDistribution.h | 2 +-
src/Bpp/Numeric/Random/RandomTools.h | 12 +-
.../Numeric/Stat/Mva/CorrespondenceAnalysis.cpp | 2 +-
src/Bpp/Numeric/Stat/Mva/CorrespondenceAnalysis.h | 5 +-
src/Bpp/Numeric/Stat/Mva/DualityDiagram.cpp | 6 +-
src/Bpp/Numeric/Stat/Mva/DualityDiagram.h | 24 +-
.../Stat/Mva/PrincipalComponentAnalysis.cpp | 8 +-
.../Numeric/Stat/Mva/PrincipalComponentAnalysis.h | 14 +-
src/Bpp/Numeric/Table.h | 76 +-
src/Bpp/Numeric/TableExceptions.h | 18 +-
src/Bpp/Numeric/TransformedParameter.h | 24 +-
src/Bpp/Numeric/VectorExceptions.h | 238 +-
src/Bpp/Numeric/VectorTools.h | 3526 ++++++++++----------
src/Bpp/Text/KeyvalTools.cpp | 8 +-
src/Bpp/Text/KeyvalTools.h | 8 +-
src/Bpp/Text/NestedStringTokenizer.cpp | 5 +-
src/Bpp/Text/NestedStringTokenizer.h | 4 +-
src/Bpp/Text/StringTokenizer.h | 2 +-
src/Bpp/Text/TextTools.cpp | 828 +++--
src/Bpp/Text/TextTools.h | 287 +-
src/Bpp/Utils/AttributesTools.cpp | 3 +-
src/Bpp/Utils/AttributesTools.h | 4 +-
test/PolynomialFunction.h | 10 +-
test/doctest.h | 3488 +++++++++++++++++++
test/test_distributions.cpp | 4 +-
test/test_graphObs.cpp | 33 +-
test/test_reparametrization.cpp | 5 +-
test/test_text_tools.cpp | 295 +-
149 files changed, 8740 insertions(+), 4822 deletions(-)
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