This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository libbpp-phyl.
commit 62da4acae94c85573876f22985467b17bf681c51 Merge: 813cb14 1c804a7 Author: Andreas Tille <[email protected]> Date: Wed Apr 13 15:37:57 2016 +0200 Merge tag 'upstream/2.2.0' Upstream version 2.2.0 CMakeLists.txt | 13 +- ChangeLog | 15 + Doxyfile | 8 +- bpp-phyl.spec | 5 +- debian/copyright | 6 +- debian/postinst | 22 +- debian/postrm | 26 +- debian/prerm | 22 +- debian/rules | 4 +- debian/postinst => genIncludes.sh | 10 +- src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp | 513 +++-- src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h | 319 ++- src/Bpp/Phyl/BipartitionList.cpp | 20 +- src/Bpp/Phyl/BipartitionTools.cpp | 93 +- src/Bpp/Phyl/BipartitionTools.h | 12 +- .../AbstractAgglomerativeDistanceMethod.cpp | 4 +- .../Distance/AbstractAgglomerativeDistanceMethod.h | 2 +- src/Bpp/Phyl/Distance/BioNJ.h | 2 +- src/Bpp/Phyl/Distance/DistanceEstimation.cpp | 12 +- src/Bpp/Phyl/Distance/DistanceEstimation.h | 10 +- src/Bpp/Phyl/Distance/DistanceMethod.h | 4 +- src/Bpp/Phyl/Distance/NeighborJoining.h | 2 +- src/Bpp/Phyl/Distance/PGMA.h | 2 +- .../Phyl/Graphics/TreeDrawingDisplayControler.h | 8 +- src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp | 235 +- src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h | 63 +- src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp | 214 +- src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h | 47 +- src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp | 8 +- src/Bpp/Phyl/Io/IoDistanceMatrixFactory.h | 12 +- src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp | 4 +- src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp | 2 +- src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp | 6 +- ...bstractDiscreteRatesAcrossSitesTreeLikelihood.h | 94 +- .../AbstractHomogeneousTreeLikelihood.cpp | 5 +- .../Likelihood/AbstractHomogeneousTreeLikelihood.h | 150 +- .../AbstractNonHomogeneousTreeLikelihood.cpp | 401 ++-- .../AbstractNonHomogeneousTreeLikelihood.h | 16 +- src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h | 89 +- .../DRHomogeneousMixedTreeLikelihood.cpp | 36 +- .../Likelihood/DRHomogeneousMixedTreeLikelihood.h | 14 +- .../Likelihood/DRHomogeneousTreeLikelihood.cpp | 92 +- .../Phyl/Likelihood/DRHomogeneousTreeLikelihood.h | 2 +- .../Likelihood/DRNonHomogeneousTreeLikelihood.cpp | 6 +- .../MarginalAncestralStateReconstruction.cpp | 10 +- .../MarginalAncestralStateReconstruction.h | 2 +- src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp | 2 +- .../Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp | 4 +- .../RNonHomogeneousMixedTreeLikelihood.cpp | 26 +- .../Likelihood/RNonHomogeneousTreeLikelihood.cpp | 6 +- .../Likelihood/RNonHomogeneousTreeLikelihood.h | 2 +- .../Phyl/Likelihood/SitePartitionTreeLikelihood.h | 18 +- src/Bpp/Phyl/Likelihood/TreeLikelihood.h | 19 +- src/Bpp/Phyl/Mapping/DecompositionReward.cpp | 214 ++ src/Bpp/Phyl/Mapping/DecompositionReward.h | 144 ++ .../Mapping/DecompositionSubstitutionCount.cpp | 29 +- .../Phyl/Mapping/DecompositionSubstitutionCount.h | 6 +- src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp | 8 +- src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h | 10 +- .../Mapping/{SubstitutionMapping.h => Mapping.h} | 155 +- src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp | 21 +- src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h | 36 +- src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h | 30 +- .../ProbabilisticRewardMapping.cpp} | 54 +- src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h | 177 ++ .../Mapping/ProbabilisticSubstitutionMapping.h | 6 +- src/Bpp/Phyl/Mapping/Reward.h | 205 ++ .../RewardMapping.h} | 82 +- src/Bpp/Phyl/Mapping/RewardMappingTools.cpp | 447 ++++ src/Bpp/Phyl/Mapping/RewardMappingTools.h | 136 ++ src/Bpp/Phyl/Mapping/SubstitutionCount.h | 35 +- src/Bpp/Phyl/Mapping/SubstitutionMapping.h | 167 +- src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp | 1539 ++++++++++--- src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h | 619 +++-- .../SubstitutionRegister.cpp} | 28 +- src/Bpp/Phyl/Mapping/SubstitutionRegister.h | 543 ++++- .../Mapping/UniformizationSubstitutionCount.cpp | 75 +- .../Phyl/Mapping/UniformizationSubstitutionCount.h | 6 +- src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h | 21 +- .../Model/AbstractBiblioMixedSubstitutionModel.h | 3 +- .../Phyl/Model/AbstractBiblioSubstitutionModel.h | 12 +- .../Phyl/Model/AbstractMixedSubstitutionModel.cpp | 247 +- .../Phyl/Model/AbstractMixedSubstitutionModel.h | 394 ++-- src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp | 19 +- src/Bpp/Phyl/Model/AbstractSubstitutionModel.h | 52 +- .../Phyl/Model/AbstractWordSubstitutionModel.cpp | 108 +- src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h | 20 +- src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp | 4 +- .../AbstractCodonDistanceSubstitutionModel.cpp | 8 +- .../Codon/AbstractCodonDistanceSubstitutionModel.h | 29 +- .../AbstractCodonFitnessSubstitutionModel.cpp | 4 +- .../Codon/AbstractCodonFitnessSubstitutionModel.h | 2 +- .../AbstractCodonFrequenciesSubstitutionModel.cpp | 2 +- ...tractCodonPhaseFrequenciesSubstitutionModel.cpp | 30 +- ...bstractCodonPhaseFrequenciesSubstitutionModel.h | 18 +- .../Model/Codon/AbstractCodonSubstitutionModel.cpp | 53 +- .../Model/Codon/AbstractCodonSubstitutionModel.h | 53 +- ...nceFitnessPhaseFrequenciesSubstitutionModel.cpp | 56 +- ...tanceFitnessPhaseFrequenciesSubstitutionModel.h | 68 +- .../CodonDistanceFrequenciesSubstitutionModel.cpp | 40 +- .../CodonDistanceFrequenciesSubstitutionModel.h | 57 +- ...onDistancePhaseFrequenciesSubstitutionModel.cpp | 36 +- ...odonDistancePhaseFrequenciesSubstitutionModel.h | 51 +- .../Model/Codon/CodonDistanceSubstitutionModel.cpp | 38 +- .../Model/Codon/CodonDistanceSubstitutionModel.h | 45 +- .../CodonRateFrequenciesSubstitutionModel.cpp | 28 +- .../Codon/CodonRateFrequenciesSubstitutionModel.h | 44 +- .../Model/Codon/CodonRateSubstitutionModel.cpp | 24 +- .../Phyl/Model/Codon/CodonRateSubstitutionModel.h | 37 +- src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h | 10 +- .../Phyl/Model/Codon/TripletSubstitutionModel.cpp | 6 +- src/Bpp/Phyl/Model/Codon/YN98.cpp | 2 +- src/Bpp/Phyl/Model/Codon/YN98.h | 7 +- src/Bpp/Phyl/Model/Codon/YNGKP_M1.cpp | 20 +- src/Bpp/Phyl/Model/Codon/YNGKP_M1.h | 9 +- src/Bpp/Phyl/Model/Codon/YNGKP_M2.cpp | 18 +- src/Bpp/Phyl/Model/Codon/YNGKP_M2.h | 11 +- src/Bpp/Phyl/Model/Codon/YNGKP_M3.cpp | 26 +- src/Bpp/Phyl/Model/Codon/YNGKP_M3.h | 10 +- src/Bpp/Phyl/Model/Codon/YNGKP_M7.cpp | 16 +- src/Bpp/Phyl/Model/Codon/YNGKP_M7.h | 9 +- src/Bpp/Phyl/Model/Codon/YNGKP_M8.cpp | 14 +- src/Bpp/Phyl/Model/Codon/YNGKP_M8.h | 9 +- .../Model/FrequenciesSet/CodonFrequenciesSet.cpp | 564 ++--- .../Model/FrequenciesSet/CodonFrequenciesSet.h | 680 +++--- .../Phyl/Model/FrequenciesSet/FrequenciesSet.cpp | 133 +- src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h | 114 +- .../Model/FrequenciesSet/MvaFrequenciesSet.cpp | 10 +- .../FrequenciesSet/NucleotideFrequenciesSet.cpp | 4 +- .../FrequenciesSet/NucleotideFrequenciesSet.h | 10 +- .../Model/FrequenciesSet/ProteinFrequenciesSet.h | 23 +- .../Model/FrequenciesSet/WordFrequenciesSet.cpp | 37 +- .../Phyl/Model/FrequenciesSet/WordFrequenciesSet.h | 2 +- src/Bpp/Phyl/Model/G2001.h | 5 +- .../Model/MarkovModulatedSubstitutionModel.cpp | 9 +- .../Phyl/Model/MarkovModulatedSubstitutionModel.h | 47 +- src/Bpp/Phyl/Model/MixedSubstitutionModel.h | 2 +- src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp | 26 +- src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h | 622 +++-- src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp | 20 +- src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h | 38 +- src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp | 52 +- src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h | 329 ++- src/Bpp/Phyl/Model/Nucleotide/F84.cpp | 9 +- src/Bpp/Phyl/Model/Nucleotide/F84.h | 14 +- src/Bpp/Phyl/Model/Nucleotide/GTR.cpp | 3 +- src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp | 721 +++--- src/Bpp/Phyl/Model/Nucleotide/HKY85.h | 8 +- src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp | 7 +- src/Bpp/Phyl/Model/Nucleotide/JCnuc.h | 5 +- src/Bpp/Phyl/Model/Nucleotide/K80.cpp | 641 +++--- src/Bpp/Phyl/Model/Nucleotide/K80.h | 21 +- src/Bpp/Phyl/Model/Nucleotide/L95.cpp | 4 +- src/Bpp/Phyl/Model/Nucleotide/L95.h | 4 +- .../Model/Nucleotide/NucleotideSubstitutionModel.h | 72 +- src/Bpp/Phyl/Model/Nucleotide/RN95.cpp | 52 +- src/Bpp/Phyl/Model/Nucleotide/RN95.h | 6 +- src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp | 52 +- src/Bpp/Phyl/Model/Nucleotide/RN95s.h | 6 +- src/Bpp/Phyl/Model/Nucleotide/SSR.cpp | 85 +- src/Bpp/Phyl/Model/Nucleotide/SSR.h | 98 +- src/Bpp/Phyl/Model/Nucleotide/T92.cpp | 9 +- src/Bpp/Phyl/Model/Nucleotide/T92.h | 6 +- src/Bpp/Phyl/Model/Nucleotide/TN93.cpp | 13 +- src/Bpp/Phyl/Model/Nucleotide/TN93.h | 10 +- src/Bpp/Phyl/Model/Nucleotide/YpR.cpp | 375 +-- src/Bpp/Phyl/Model/Nucleotide/YpR.h | 14 +- src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp | 241 +- src/Bpp/Phyl/Model/Nucleotide/gBGC.h | 129 +- src/Bpp/Phyl/Model/Protein/Coala.cpp | 412 ++-- src/Bpp/Phyl/Model/Protein/Coala.h | 224 +- src/Bpp/Phyl/Model/Protein/CoalaCore.cpp | 20 +- src/Bpp/Phyl/Model/Protein/CoalaCore.h | 17 +- src/Bpp/Phyl/Model/Protein/DSO78.cpp | 27 +- src/Bpp/Phyl/Model/Protein/DSO78.h | 6 +- src/Bpp/Phyl/Model/Protein/JCprot.cpp | 30 +- src/Bpp/Phyl/Model/Protein/JCprot.h | 12 +- src/Bpp/Phyl/Model/Protein/JTT92.cpp | 26 +- src/Bpp/Phyl/Model/Protein/JTT92.h | 6 +- src/Bpp/Phyl/Model/Protein/LG08.cpp | 26 +- src/Bpp/Phyl/Model/Protein/LG08.h | 4 +- src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp | 119 + src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h | 131 ++ src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp | 3 +- src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp | 3 +- src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp | 3 +- src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp | 3 +- src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp | 3 +- src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp | 3 +- .../Model/Protein/UserProteinSubstitutionModel.cpp | 23 +- .../Model/Protein/UserProteinSubstitutionModel.h | 4 +- src/Bpp/Phyl/Model/Protein/WAG01.cpp | 21 +- src/Bpp/Phyl/Model/Protein/WAG01.h | 4 +- .../Model/Protein/__LG10_EX_EHOExchangeabilityCode | 2423 ++++++++++++++++++++ .../Model/Protein/__LG10_EX_EHOFrequenciesCode | 142 ++ src/Bpp/Phyl/Model/Protein/__LG10_EX_EHORatesProps | 34 + src/Bpp/Phyl/Model/RE08.cpp | 10 +- src/Bpp/Phyl/Model/RE08.h | 102 +- src/Bpp/Phyl/Model/StateMap.cpp | 22 +- src/Bpp/Phyl/Model/StateMap.h | 73 +- src/Bpp/Phyl/Model/SubstitutionModel.h | 64 +- src/Bpp/Phyl/Model/SubstitutionModelSet.cpp | 295 +-- src/Bpp/Phyl/Model/SubstitutionModelSet.h | 220 +- src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp | 16 +- src/Bpp/Phyl/Model/TS98.h | 10 +- src/Bpp/Phyl/Model/WordSubstitutionModel.cpp | 32 +- src/Bpp/Phyl/Model/WordSubstitutionModel.h | 14 +- src/Bpp/Phyl/NNITopologySearch.cpp | 28 +- src/Bpp/Phyl/Node.h | 13 +- src/Bpp/Phyl/OptimizationTools.cpp | 10 +- src/Bpp/Phyl/OptimizationTools.h | 8 +- .../Phyl/Parsimony/AbstractTreeParsimonyScore.cpp | 4 +- src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp | 6 +- src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h | 33 +- src/Bpp/Phyl/Simulation/MutationProcess.cpp | 42 +- src/Bpp/Phyl/Simulation/MutationProcess.h | 350 +-- .../Simulation/NonHomogeneousSequenceSimulator.cpp | 158 +- .../Simulation/NonHomogeneousSequenceSimulator.h | 249 +- .../Phyl/Simulation/SequenceSimulationTools.cpp | 34 +- src/Bpp/Phyl/Simulation/SequenceSimulationTools.h | 92 +- src/Bpp/Phyl/Simulation/SequenceSimulator.h | 9 +- src/Bpp/Phyl/Simulation/SiteSimulator.h | 12 +- src/Bpp/Phyl/TreeTemplate.h | 2 +- src/Bpp/Phyl/TreeTemplateTools.cpp | 321 ++- src/Bpp/Phyl/TreeTemplateTools.h | 2227 +++++++++--------- src/Bpp/Phyl/TreeTools.cpp | 63 +- src/Bpp/Phyl/TreeTools.h | 36 +- src/CMakeLists.txt | 12 + test/test_detailed_simulations.cpp | 2 +- test/test_likelihood.cpp | 57 +- test/test_likelihood_clock.cpp | 5 +- test/test_likelihood_nh.cpp | 5 +- test/test_mapping.cpp | 30 +- test/test_mapping_codon.cpp | 38 +- test/test_models.cpp | 6 +- test/test_simulations.cpp | 16 +- test/test_tree.cpp | 23 + 237 files changed, 14717 insertions(+), 8354 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-phyl.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
