[med-svn] [libbpp-core] branch upstream updated (8a8f217 -> 39df58f)
Andreas Tille
tille at debian.org
Fri Apr 8 20:01:38 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository libbpp-core.
from 8a8f217 Imported Upstream version 2.1.0
new 39df58f Imported Upstream version 2.2.0
The 1 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 | 9 +
debian/control | 2 +-
debian/copyright | 6 +-
debian/postinst | 22 +-
debian/postrm | 26 +-
debian/prerm | 22 +-
debian/rules | 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, 8838 insertions(+), 5223 deletions(-)
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
--
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