[med-svn] [libbpp-core] branch master updated (a70e498 -> e4ac0cb)
Andreas Tille
tille at debian.org
Fri Apr 8 20:01:36 UTC 2016
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tille pushed a change to branch master
in repository libbpp-core.
from a70e498 Fix cut-n-pasto
new cfd17d4 Wrote watch file
new 39df58f Imported Upstream version 2.2.0
new eb5156a Merge tag 'upstream/2.2.0'
new 8428f21 New upstream version
new 2a5f6bd Remove changelog entries not related to Debian packaging
new e4ac0cb DEP5
The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
CMakeLists.txt | 5 +-
ChangeLog | 13 +
Doxyfile | 2531 ++++++++++++--------
bpp-core.spec | 7 +-
debian/changelog | 4 +-
debian/copyright | 104 +-
debian/postinst | 22 +-
debian/postrm | 26 +-
debian/prerm | 22 +-
debian/rules | 4 +-
debian/watch | 4 +
debian/postinst => genIncludes.sh | 10 +-
src/Bpp/App/ApplicationTools.cpp | 126 +-
src/Bpp/App/ApplicationTools.h | 185 +-
src/Bpp/App/BppApplication.cpp | 11 +-
src/Bpp/App/BppApplication.h | 3 +-
src/Bpp/Exceptions.h | 1 +
src/Bpp/Graph/BasicONode.cpp | 4 +-
src/Bpp/Graph/BasicONode.h | 4 +-
src/Bpp/Graph/BasicTNode.cpp | 22 +-
src/Bpp/Graphics/AbstractGraphicDevice.h | 2 +-
src/Bpp/Graphics/ColorTools.cpp | 33 +-
src/Bpp/Graphics/Fig/XFigGraphicDevice.cpp | 2 +-
src/Bpp/Graphics/Fig/XFigGraphicDevice.h | 2 +-
src/Bpp/Graphics/RgbColor.h | 8 +-
src/Bpp/Io/BppOParametrizableFormat.cpp | 76 +-
src/Bpp/Io/FileTools.cpp | 12 +-
src/Bpp/Io/OutputStream.h | 18 +-
src/Bpp/Numeric/AbstractParameterAliasable.cpp | 128 +-
src/Bpp/Numeric/AbstractParameterAliasable.h | 318 ++-
src/Bpp/Numeric/AbstractParametrizable.h | 17 +-
.../Numeric/AdaptiveKernelDensityEstimation.cpp | 2 +-
src/Bpp/Numeric/Constraints.h | 108 +-
src/Bpp/Numeric/DataTable.cpp | 504 ++--
src/Bpp/Numeric/DataTable.h | 809 ++++---
.../Function/ConjugateGradientMultiDimensions.cpp | 10 +-
.../Function/FivePointsNumericalDerivative.cpp | 35 +-
.../Function/FivePointsNumericalDerivative.h | 149 +-
src/Bpp/Numeric/Function/GoldenSectionSearch.cpp | 8 +-
src/Bpp/Numeric/Function/MetaOptimizer.h | 22 +-
.../Function/OneDimensionOptimizationTools.cpp | 284 +--
.../Function/OneDimensionOptimizationTools.h | 230 +-
.../Function/ReparametrizationFunctionWrapper.cpp | 4 +-
.../Function/ReparametrizationFunctionWrapper.h | 2 +-
.../Function/ThreePointsNumericalDerivative.cpp | 180 +-
.../Function/ThreePointsNumericalDerivative.h | 143 +-
.../Function/TwoPointsNumericalDerivative.cpp | 32 +-
.../Function/TwoPointsNumericalDerivative.h | 150 +-
.../AbstractHmmTransitionMatrix.cpp} | 74 +-
...mExceptions.h => AbstractHmmTransitionMatrix.h} | 89 +-
.../Hmm/AutoCorrelationTransitionMatrix.cpp | 113 +
.../Numeric/Hmm/AutoCorrelationTransitionMatrix.h | 118 +
src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp | 155 ++
src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.h | 130 +
src/Bpp/Numeric/Hmm/HmmEmissionProbabilities.h | 133 +-
.../IoFormat.h => Numeric/Hmm/HmmLikelihood.cpp} | 179 +-
src/Bpp/Numeric/Hmm/HmmLikelihood.h | 224 +-
src/Bpp/Numeric/Hmm/HmmStateAlphabet.h | 140 +-
src/Bpp/Numeric/Hmm/HmmTransitionMatrix.h | 73 +-
src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.cpp | 325 ++-
src/Bpp/Numeric/Hmm/LogsumHmmLikelihood.h | 325 ++-
.../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp | 7 +-
.../Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h | 41 +-
src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp | 298 ++-
src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.h | 324 ++-
src/Bpp/Numeric/Matrix/EigenValue.h | 364 +--
src/Bpp/Numeric/Matrix/Matrix.h | 114 +-
src/Bpp/Numeric/Matrix/MatrixTools.h | 2032 ++++++++--------
src/Bpp/Numeric/NumConstants.h | 2 +-
src/Bpp/Numeric/Number.h | 144 +-
src/Bpp/Numeric/Parameter.h | 1 -
src/Bpp/Numeric/ParameterAliasable.h | 118 +-
src/Bpp/Numeric/ParameterList.cpp | 66 +-
src/Bpp/Numeric/ParameterList.h | 21 +-
src/Bpp/Numeric/ParametrizableCollection.h | 356 +++
.../Numeric/Prob/AbstractDiscreteDistribution.cpp | 4 +-
src/Bpp/Numeric/Prob/ConstantDistribution.cpp | 12 +-
src/Bpp/Numeric/Prob/ConstantDistribution.h | 3 +-
.../Prob/InvariantMixedDiscreteDistribution.h | 256 +-
.../Numeric/Prob/SimpleDiscreteDistribution.cpp | 4 +-
src/Bpp/Numeric/Prob/Simplex.cpp | 165 +-
src/Bpp/Numeric/Prob/Simplex.h | 140 +-
src/Bpp/Numeric/Random/RandomTools.cpp | 9 +-
src/Bpp/Numeric/Random/RandomTools.h | 21 +-
src/Bpp/Numeric/Range.h | 4 +-
src/Bpp/Numeric/TransformedParameter.h | 12 +-
src/Bpp/Numeric/VectorTools.h | 1 +
src/Bpp/Text/KeyvalTools.cpp | 2 +
src/Bpp/Text/NestedStringTokenizer.cpp | 110 +-
src/Bpp/Text/NestedStringTokenizer.h | 116 +-
src/Bpp/Text/StringTokenizer.cpp | 2 +-
src/Bpp/Text/StringTokenizer.h | 160 +-
src/Bpp/Text/TextTools.cpp | 29 +-
src/Bpp/Text/TextTools.h | 7 +-
src/Bpp/Utils/AttributesTools.cpp | 229 +-
src/Bpp/Utils/AttributesTools.h | 304 ++-
src/CMakeLists.txt | 8 +
test/CMakeLists.txt | 12 +-
test/test_derivative1.cpp | 12 +-
...{test_powell.cpp => test_reparametrization.cpp} | 55 +-
test/test_simplex.cpp | 117 +
101 files changed, 8885 insertions(+), 5271 deletions(-)
create mode 100644 debian/watch
copy debian/postinst => genIncludes.sh (80%)
copy src/Bpp/Numeric/{Prob/UniformDiscreteDistribution.cpp => Hmm/AbstractHmmTransitionMatrix.cpp} (53%)
copy src/Bpp/Numeric/Hmm/{HmmExceptions.h => AbstractHmmTransitionMatrix.h} (50%)
create mode 100644 src/Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.cpp
create mode 100644 src/Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.h
create mode 100644 src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.cpp
create mode 100644 src/Bpp/Numeric/Hmm/FullHmmTransitionMatrix.h
copy src/Bpp/{Io/IoFormat.h => Numeric/Hmm/HmmLikelihood.cpp} (51%)
create mode 100644 src/Bpp/Numeric/ParametrizableCollection.h
copy test/{test_powell.cpp => test_reparametrization.cpp} (58%)
create mode 100644 test/test_simplex.cpp
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