[med-svn] [libbpp-core] 04/05: Updated version 2.3.0 from 'upstream/2.3.0'
Andreas Tille
tille at debian.org
Thu Jun 1 14:03:21 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libbpp-core.
commit ed3f2518c7df22d1736df72d8e1e1873a59fb322
Merge: 68716b5 d1b9141
Author: Andreas Tille <tille at debian.org>
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
More information about the debian-med-commit
mailing list