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~ubuntu-branches/ubuntu/saucy/libbpp-core/saucy

Viewing all changes in revision 3.

Committer: Package Import Robot
Author(s): Julien Dutheil
Date: 2012-02-09 13:00:00 UTC
mfrom: (1.1.1)
Revision ID: package-import@ubuntu.com-20120209130000-je7bujslsp6ixsaw

Tags: 2.0.3-1

* New range classes
* Linear assigment method
* Improved string tokenizer and text tools.

files added:
src/Bpp/Graph

src/Bpp/Graph/BasicONode.cpp

src/Bpp/Graph/BasicONode.h

src/Bpp/Graph/BasicTNode.cpp

src/Bpp/Graph/BasicTNode.h

src/Bpp/Graph/ONode.h

src/Bpp/Graph/TNode.h

src/Bpp/Graph/UNode.h

src/Bpp/Numeric/Prob/Simplex.cpp

src/Bpp/Numeric/Prob/Simplex.h

src/Bpp/Numeric/Range.h

test/test_matrices.cpp

test/test_range.cpp

test/test_sample.cpp

test/test_text_tools.cpp

files modified:
AUTHORS.txt

CMakeLists.txt

ChangeLog

Core.spec

Doxyfile

debian/changelog

debian/control

src/Bpp/App/ApplicationTools.cpp

src/Bpp/App/ApplicationTools.h

src/Bpp/Exceptions.h

src/Bpp/Graphics/R/RColorSet.cpp

src/Bpp/Numeric.all

src/Bpp/Numeric/AbstractParameterAliasable.cpp

src/Bpp/Numeric/AbstractParametrizable.h

src/Bpp/Numeric/AutoParameter.cpp

src/Bpp/Numeric/AutoParameter.h

src/Bpp/Numeric/Constraints.h

src/Bpp/Numeric/Function/AbstractNumericalDerivative.h

src/Bpp/Numeric/Function/AbstractOptimizer.cpp

src/Bpp/Numeric/Function/BrentOneDimension.cpp

src/Bpp/Numeric/Function/BrentOneDimension.h

src/Bpp/Numeric/Function/DownhillSimplexMethod.cpp

src/Bpp/Numeric/Function/DownhillSimplexMethod.h

src/Bpp/Numeric/Function/FivePointsNumericalDerivative.cpp

src/Bpp/Numeric/Function/Functions.h

src/Bpp/Numeric/Function/GoldenSectionSearch.cpp

src/Bpp/Numeric/Function/GoldenSectionSearch.h

src/Bpp/Numeric/Function/MetaOptimizer.cpp

src/Bpp/Numeric/Function/NewtonBacktrackOneDimension.cpp

src/Bpp/Numeric/Function/NewtonBacktrackOneDimension.h

src/Bpp/Numeric/Function/NewtonOneDimension.cpp

src/Bpp/Numeric/Function/NewtonOneDimension.h

src/Bpp/Numeric/Function/OptimizationStopCondition.cpp

src/Bpp/Numeric/Function/OptimizationStopCondition.h

src/Bpp/Numeric/Function/PowellMultiDimensions.cpp

src/Bpp/Numeric/Function/PowellMultiDimensions.h

src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp

src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.cpp

src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp

src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h

src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp

src/Bpp/Numeric/Matrix/Matrix.h

src/Bpp/Numeric/Matrix/MatrixTools.h

src/Bpp/Numeric/NumConstants.cpp

src/Bpp/Numeric/NumConstants.h

src/Bpp/Numeric/NumTools.cpp

src/Bpp/Numeric/NumTools.h

src/Bpp/Numeric/Parameter.cpp

src/Bpp/Numeric/Parameter.h

src/Bpp/Numeric/ParameterAliasable.h

src/Bpp/Numeric/ParameterExceptions.cpp

src/Bpp/Numeric/ParameterExceptions.h

src/Bpp/Numeric/ParameterList.cpp

src/Bpp/Numeric/ParameterList.h

src/Bpp/Numeric/Prob.all

src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h

src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/ConstantDistribution.cpp

src/Bpp/Numeric/Prob/ConstantDistribution.h

src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.h

src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/GammaDiscreteDistribution.h

src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.h

src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h

src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.cpp

src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.h

src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.h

src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.h

src/Bpp/Numeric/Prob/UniformDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/UniformDiscreteDistribution.h

src/Bpp/Numeric/Random/RandomTools.cpp

src/Bpp/Numeric/Random/RandomTools.h

src/Bpp/Numeric/VectorTools.h

src/Bpp/Text/KeyvalTools.cpp

src/Bpp/Text/KeyvalTools.h

src/Bpp/Text/NestedStringTokenizer.cpp

src/Bpp/Text/NestedStringTokenizer.h

src/Bpp/Text/StringTokenizer.cpp

src/Bpp/Text/StringTokenizer.h

src/Bpp/Text/TextTools.cpp

src/Bpp/Text/TextTools.h

src/CMakeLists.txt

test/CMakeLists.txt

Show diffs side-by-side

added added

removed removed

debian/changelog

src/Bpp/App/ApplicationTools.cpp

src/Bpp/App/ApplicationTools.h

src/Bpp/Exceptions.h

src/Bpp/Graph/BasicONode.cpp

src/Bpp/Graph/BasicONode.h

src/Bpp/Graph/BasicTNode.cpp

src/Bpp/Graph/BasicTNode.h

src/Bpp/Graph/ONode.h

src/Bpp/Graph/TNode.h

src/Bpp/Graph/UNode.h

src/Bpp/Graphics/R/RColorSet.cpp

src/Bpp/Numeric.all

src/Bpp/Numeric/AbstractParameterAliasable.cpp

src/Bpp/Numeric/AbstractParametrizable.h

src/Bpp/Numeric/AutoParameter.cpp

src/Bpp/Numeric/AutoParameter.h

src/Bpp/Numeric/Constraints.h

src/Bpp/Numeric/Function/AbstractNumericalDerivative.h

src/Bpp/Numeric/Function/AbstractOptimizer.cpp

src/Bpp/Numeric/Function/BrentOneDimension.cpp

src/Bpp/Numeric/Function/BrentOneDimension.h

src/Bpp/Numeric/Function/DownhillSimplexMethod.cpp

src/Bpp/Numeric/Function/DownhillSimplexMethod.h

src/Bpp/Numeric/Function/FivePointsNumericalDerivative.cpp

src/Bpp/Numeric/Function/Functions.h

src/Bpp/Numeric/Function/GoldenSectionSearch.cpp

src/Bpp/Numeric/Function/GoldenSectionSearch.h

src/Bpp/Numeric/Function/MetaOptimizer.cpp

src/Bpp/Numeric/Function/NewtonBacktrackOneDimension.cpp

src/Bpp/Numeric/Function/NewtonBacktrackOneDimension.h

src/Bpp/Numeric/Function/NewtonOneDimension.cpp

src/Bpp/Numeric/Function/NewtonOneDimension.h

src/Bpp/Numeric/Function/OptimizationStopCondition.cpp

src/Bpp/Numeric/Function/OptimizationStopCondition.h

src/Bpp/Numeric/Function/PowellMultiDimensions.cpp

src/Bpp/Numeric/Function/PowellMultiDimensions.h

src/Bpp/Numeric/Function/ThreePointsNumericalDerivative.cpp

src/Bpp/Numeric/Function/TwoPointsNumericalDerivative.cpp

src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.cpp

src/Bpp/Numeric/Hmm/LowMemoryRescaledHmmLikelihood.h

src/Bpp/Numeric/Hmm/RescaledHmmLikelihood.cpp

src/Bpp/Numeric/Matrix/Matrix.h

src/Bpp/Numeric/Matrix/MatrixTools.h

src/Bpp/Numeric/NumConstants.cpp

src/Bpp/Numeric/NumConstants.h

src/Bpp/Numeric/NumTools.cpp

src/Bpp/Numeric/NumTools.h

src/Bpp/Numeric/Parameter.cpp

src/Bpp/Numeric/Parameter.h

src/Bpp/Numeric/ParameterAliasable.h

src/Bpp/Numeric/ParameterExceptions.cpp

src/Bpp/Numeric/ParameterExceptions.h

src/Bpp/Numeric/ParameterList.cpp

src/Bpp/Numeric/ParameterList.h

src/Bpp/Numeric/Prob.all

src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h

src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/ConstantDistribution.cpp

src/Bpp/Numeric/Prob/ConstantDistribution.h

src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.h

src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/GammaDiscreteDistribution.h

src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.h

src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h

src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.cpp

src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.h

src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.h

src/Bpp/Numeric/Prob/Simplex.cpp

src/Bpp/Numeric/Prob/Simplex.h

src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.h

src/Bpp/Numeric/Prob/UniformDiscreteDistribution.cpp

src/Bpp/Numeric/Prob/UniformDiscreteDistribution.h

src/Bpp/Numeric/Random/RandomTools.cpp

src/Bpp/Numeric/Random/RandomTools.h

src/Bpp/Numeric/Range.h

src/Bpp/Numeric/VectorTools.h

src/Bpp/Text/KeyvalTools.cpp

src/Bpp/Text/KeyvalTools.h

src/Bpp/Text/NestedStringTokenizer.cpp

src/Bpp/Text/NestedStringTokenizer.h

src/Bpp/Text/StringTokenizer.cpp

src/Bpp/Text/StringTokenizer.h

src/Bpp/Text/TextTools.cpp

src/Bpp/Text/TextTools.h

src/CMakeLists.txt

test/CMakeLists.txt

test/test_matrices.cpp

test/test_range.cpp

test/test_sample.cpp

test/test_text_tools.cpp

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