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commit ed3f2518c7df22d1736df72d8e1e1873a59fb322 Merge: 68716b5 d1b9141 Author: Andreas Tille <[email protected]> Date: Thu Jun 1 15:58:49 2017 +0200 Updated version 2.3.0 from 'upstream/2.3.0' with Debian dir c684d57358f412fcf3af507155ae45bc15120b41 .gitignore | 15 + AUTHORS.txt | 3 + CMakeLists.txt | 137 +- CTestConfig.cmake | 13 + ChangeLog | 8 + Doxyfile | 420 +++--- INSTALL.txt | 19 +- bpp-core.spec | 104 +- 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 | 39 - src/Bpp/App/ApplicationTools.h | 41 +- src/Bpp/App/NumCalcApplicationTools.cpp | 1 + src/Bpp/BppBoolean.h | 7 +- src/Bpp/BppString.h | 7 +- src/Bpp/BppVector.h | 7 +- src/Bpp/Clonable.h | 32 +- src/Bpp/Exceptions.cpp | 6 - src/Bpp/Exceptions.h | 7 +- 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/BasicTNode.cpp | 208 --- src/Bpp/Graph/BasicTNode.h | 160 --- 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 +++++++++ .../GraphObserver.h} | 97 +- src/Bpp/Graph/ONode.h | 170 --- src/Bpp/Graph/TNode.h | 129 -- src/Bpp/Graph/TreeGraph.h | 201 +++ src/Bpp/Graph/TreeGraphImpl.h | 593 +++++++++ src/Bpp/Graph/UNode.h | 123 -- src/Bpp/Graphics/Font/Font.h | 7 +- src/Bpp/Graphics/Font/FontManager.h | 1 + src/Bpp/Graphics/RgbColor.h | 7 +- src/Bpp/Io/BppODiscreteDistributionFormat.cpp | 19 +- src/Bpp/Io/OutputStream.h | 10 +- src/Bpp/Numeric/AbstractParameterAliasable.cpp | 206 ++- src/Bpp/Numeric/AbstractParameterAliasable.h | 443 +++---- src/Bpp/Numeric/AbstractParametrizable.h | 95 +- src/Bpp/Numeric/AutoParameter.cpp | 134 +- src/Bpp/Numeric/DataTable.h | 3 +- src/Bpp/Numeric/DataTableExceptions.h | 175 --- .../Numeric/Function/AbstractNumericalDerivative.h | 51 +- src/Bpp/Numeric/Function/BrentOneDimension.cpp | 2 + .../Function/ConjugateGradientMultiDimensions.cpp | 6 + src/Bpp/Numeric/Function/DownhillSimplexMethod.h | 7 +- src/Bpp/Numeric/Function/Functions.h | 22 +- src/Bpp/Numeric/Function/MetaOptimizer.h | 4 - .../Function/OneDimensionOptimizationTools.cpp | 8 + .../Numeric/Function/Operators/BinaryOperator.h | 168 +++ .../Numeric/Function/Operators/ComputationTree.cpp | 213 ++++ .../Numeric/Function/Operators/ComputationTree.h | 113 ++ .../Function/Operators/ConstantOperator.h} | 92 +- .../Numeric/Function/Operators/FunctionOperator.h | 133 ++ src/Bpp/Numeric/Function/Operators/MathOperator.h | 138 ++ .../Function/Operators/Operator.h} | 68 +- .../Numeric/Function/OptimizationStopCondition.h | 14 +- src/Bpp/Numeric/Function/Optimizer.h | 4 - .../Function/ReparametrizationFunctionWrapper.h | 12 - .../Function/ThreePointsNumericalDerivative.cpp | 6 +- .../Numeric/Hmm/AbstractHmmTransitionMatrix.cpp | 45 + src/Bpp/Numeric/Hmm/AbstractHmmTransitionMatrix.h | 12 + .../Hmm/AutoCorrelationTransitionMatrix.cpp | 2 +- src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp | 19 +- src/Bpp/Numeric/Hmm/HmmLikelihood.h | 9 +- src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp | 165 ++- src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h | 139 +- .../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp | 9 + .../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h | 39 +- src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp | 68 +- src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h | 25 +- src/Bpp/Numeric/Matrix/Matrix.h | 9 +- src/Bpp/Numeric/Matrix/MatrixTools.h | 211 ++-- src/Bpp/Numeric/Number.h | 1 + src/Bpp/Numeric/Parameter.h | 21 +- src/Bpp/Numeric/ParameterAliasable.h | 10 +- src/Bpp/Numeric/ParameterList.cpp | 158 ++- src/Bpp/Numeric/ParameterList.h | 52 +- src/Bpp/Numeric/ParametrizableCollection.h | 26 + src/Bpp/Numeric/Prob/DiscreteDistribution.h | 2 - src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp | 18 +- src/Bpp/Numeric/Prob/GammaDiscreteDistribution.h | 17 +- .../Numeric/Prob/MixtureOfDiscreteDistributions.h | 4 - .../Numeric/Prob/MultipleDiscreteDistribution.h | 2 - src/Bpp/Numeric/Prob/Simplex.cpp | 6 +- src/Bpp/Numeric/Prob/Simplex.h | 7 +- src/Bpp/Numeric/Random/RandomTools.cpp | 19 - src/Bpp/Numeric/Random/RandomTools.h | 15 +- src/Bpp/Numeric/Range.h | 24 + src/Bpp/Numeric/Stat/ContingencyTableTest.h | 7 +- src/Bpp/Numeric/Stat/Mva/CorrespondenceAnalysis.h | 11 +- src/Bpp/Numeric/Stat/Mva/DualityDiagram.h | 7 +- src/Bpp/Numeric/Table.h | 1222 ++++++++++++++++++ src/Bpp/Numeric/TableExceptions.h | 175 +++ src/Bpp/Numeric/VectorTools.h | 95 +- src/Bpp/Text/KeyvalTools.cpp | 76 +- src/Bpp/Text/KeyvalTools.h | 23 +- src/Bpp/Text/StringTokenizer.cpp | 6 - src/Bpp/Text/StringTokenizer.h | 6 +- src/Bpp/Text/TextTools.cpp | 18 +- src/Bpp/Text/TextTools.h | 762 +++++------ src/Bpp/{Graph/BasicONode.cpp => Version.h} | 19 +- src/CMakeLists.txt | 257 +--- test/CMakeLists.txt | 120 +- test/test_dAGraphObs.cpp | 159 +++ test/test_graphObs.cpp | 144 +++ test/test_treeGraphObs.cpp | 178 +++ 116 files changed, 12728 insertions(+), 3161 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-core.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
