This is an automated email from the git hooks/post-receive script. jdutheil-guest pushed a commit to branch master in repository libbpp-phyl.
commit 6f35a104db31d20caae674941602454f38ca6e9b Merge: c8a90af 7e00775 Author: Julien Y. Dutheil <[email protected]> Date: Mon Feb 5 20:55:43 2018 +0100 Update upstream source from tag 'upstream/2.3.2' Update to upstream version '2.3.2' with Debian dir 5591c51c6ce5765ad19b3ff75a7bb0418d7ca9e0 CTestConfig.cmake | 1 + Doxyfile | 477 +++----- src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp | 146 ++- src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h | 12 + src/Bpp/Phyl/Distance/DistanceEstimation.h | 119 +- src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp | 12 +- src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp | 416 +++++-- src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h | 6 +- src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp | 48 +- .../AbstractHomogeneousTreeLikelihood.cpp | 4 +- .../Likelihood/AbstractHomogeneousTreeLikelihood.h | 29 +- .../AbstractNonHomogeneousTreeLikelihood.h | 4 +- src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h | 13 +- .../Phyl/Likelihood/DRHomogeneousTreeLikelihood.h | 2 +- .../DiscreteRatesAcrossSitesTreeLikelihood.h | 324 +++--- .../Phyl/Likelihood/HomogeneousTreeLikelihood.h | 104 +- .../MarginalAncestralStateReconstruction.cpp | 4 +- .../Phyl/Likelihood/NonHomogeneousTreeLikelihood.h | 85 +- .../Phyl/Likelihood/SitePartitionTreeLikelihood.h | 12 +- src/Bpp/Phyl/Likelihood/TreeLikelihood.h | 5 +- .../Phyl/Mapping/CategorySubstitutionRegister.h | 27 +- src/Bpp/Phyl/Mapping/DecompositionMethods.cpp | 300 +++++ src/Bpp/Phyl/Mapping/DecompositionMethods.h | 174 +++ src/Bpp/Phyl/Mapping/DecompositionReward.cpp | 112 +- src/Bpp/Phyl/Mapping/DecompositionReward.h | 178 ++- .../Mapping/DecompositionSubstitutionCount.cpp | 163 +-- .../Phyl/Mapping/DecompositionSubstitutionCount.h | 47 +- src/Bpp/Phyl/Mapping/RewardMappingTools.cpp | 3 +- src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp | 718 ++++++++++-- src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h | 1217 +++++++++++++------- src/Bpp/Phyl/Mapping/SubstitutionRegister.h | 411 +++++-- .../Mapping/UniformizationSubstitutionCount.cpp | 2 +- .../Model/AbstractBiblioMixedSubstitutionModel.cpp | 13 +- .../Model/AbstractBiblioMixedSubstitutionModel.h | 309 ++--- .../Phyl/Model/AbstractBiblioSubstitutionModel.cpp | 18 +- .../Phyl/Model/AbstractBiblioSubstitutionModel.h | 95 +- ...bstractFromSubstitutionModelTransitionModel.cpp | 6 +- .../AbstractFromSubstitutionModelTransitionModel.h | 113 +- .../AbstractKroneckerWordSubstitutionModel.cpp | 33 +- src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp | 294 ++++- src/Bpp/Phyl/Model/AbstractSubstitutionModel.h | 733 ++++++------ .../Phyl/Model/AbstractWordSubstitutionModel.cpp | 272 +---- src/Bpp/Phyl/Model/AbstractWrappedModel.h | 289 +++++ ...itutionModel.h => AnonymousSubstitutionModel.h} | 78 +- ...=> AbstractCodonAAFitnessSubstitutionModel.cpp} | 37 +- ...h => AbstractCodonAAFitnessSubstitutionModel.h} | 75 +- ...pp => AbstractCodonAARateSubstitutionModel.cpp} | 41 +- .../Codon/AbstractCodonAARateSubstitutionModel.h | 162 +++ ...l.cpp => AbstractCodonBGCSubstitutionModel.cpp} | 54 +- .../Codon/AbstractCodonBGCSubstitutionModel.h | 138 +++ .../Codon/AbstractCodonCpGSubstitutionModel.cpp | 3 +- .../Codon/AbstractCodonCpGSubstitutionModel.h | 155 +-- .../AbstractCodonDistanceSubstitutionModel.cpp | 9 +- .../Codon/AbstractCodonDistanceSubstitutionModel.h | 180 +-- .../AbstractCodonFitnessSubstitutionModel.cpp | 10 +- .../Codon/AbstractCodonFitnessSubstitutionModel.h | 28 +- .../AbstractCodonFrequenciesSubstitutionModel.cpp | 3 +- .../AbstractCodonFrequenciesSubstitutionModel.h | 171 +-- ...tractCodonPhaseFrequenciesSubstitutionModel.cpp | 7 +- ...bstractCodonPhaseFrequenciesSubstitutionModel.h | 160 +-- .../Model/Codon/AbstractCodonSubstitutionModel.cpp | 1 + .../Model/Codon/AbstractCodonSubstitutionModel.h | 1 + .../Model/Codon/CodonAdHocSubstitutionModel.cpp | 172 +++ ...tutionModel.h => CodonAdHocSubstitutionModel.h} | 104 +- .../Codon/CodonDistanceCpGSubstitutionModel.cpp | 93 -- .../CodonDistanceFrequenciesSubstitutionModel.cpp | 10 +- .../CodonDistanceFrequenciesSubstitutionModel.h | 4 + ...onDistancePhaseFrequenciesSubstitutionModel.cpp | 12 +- ...odonDistancePhaseFrequenciesSubstitutionModel.h | 7 + .../Model/Codon/CodonDistanceSubstitutionModel.cpp | 6 +- .../Model/Codon/CodonDistanceSubstitutionModel.h | 2 +- .../CodonRateFrequenciesSubstitutionModel.cpp | 100 -- .../Codon/CodonRateFrequenciesSubstitutionModel.h | 124 -- .../Phyl/Model/Codon/CodonRateSubstitutionModel.h | 107 -- src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h | 34 +- src/Bpp/Phyl/Model/Codon/GY94.h | 101 +- src/Bpp/Phyl/Model/Codon/KCM.h | 11 +- ...erCodonDistanceFrequenciesSubstitutionModel.cpp | 12 +- ...ckerCodonDistanceFrequenciesSubstitutionModel.h | 5 + .../KroneckerCodonDistanceSubstitutionModel.cpp | 12 +- src/Bpp/Phyl/Model/Codon/MG94.h | 100 +- src/Bpp/Phyl/Model/Codon/SENCA.cpp | 30 +- src/Bpp/Phyl/Model/Codon/SENCA.h | 29 +- .../Phyl/Model/Codon/TripletSubstitutionModel.h | 10 +- src/Bpp/Phyl/Model/Codon/YN98.cpp | 2 + src/Bpp/Phyl/Model/Codon/YN98.h | 100 +- .../Codon/{CodonSubstitutionModel.h => YNGP_M.h} | 118 +- src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp | 26 +- src/Bpp/Phyl/Model/Codon/YNGP_M1.h | 136 +-- src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp | 31 +- src/Bpp/Phyl/Model/Codon/YNGP_M10.h | 160 ++- src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp | 25 +- src/Bpp/Phyl/Model/Codon/YNGP_M2.h | 119 +- src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp | 25 +- src/Bpp/Phyl/Model/Codon/YNGP_M3.h | 122 +- src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp | 25 +- src/Bpp/Phyl/Model/Codon/YNGP_M7.h | 132 +-- src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp | 25 +- src/Bpp/Phyl/Model/Codon/YNGP_M8.h | 133 +-- src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp | 31 +- src/Bpp/Phyl/Model/Codon/YNGP_M9.h | 166 ++- .../Model/FrequenciesSet/CodonFrequenciesSet.cpp | 36 +- .../Model/FrequenciesSet/CodonFrequenciesSet.h | 12 +- src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h | 4 +- .../Model/FrequenciesSet/WordFrequenciesSet.cpp | 63 +- .../Phyl/Model/FrequenciesSet/WordFrequenciesSet.h | 11 +- .../Phyl/Model/FromMixtureSubstitutionModel.cpp | 27 +- src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h | 308 ++--- ...utionModel.cpp => InMixedSubstitutionModel.cpp} | 54 +- src/Bpp/Phyl/Model/InMixedSubstitutionModel.h | 314 +++++ .../Model/MarkovModulatedSubstitutionModel.cpp | 18 + .../Phyl/Model/MarkovModulatedSubstitutionModel.h | 56 +- src/Bpp/Phyl/Model/MixedSubstitutionModel.h | 2 +- src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp | 12 +- src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h | 39 +- src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp | 2 +- src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h | 2 +- src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp | 2 +- src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h | 2 +- src/Bpp/Phyl/Model/Nucleotide/L95.cpp | 1 + src/Bpp/Phyl/Model/Nucleotide/RN95.cpp | 1 + src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp | 1 + src/Bpp/Phyl/Model/Nucleotide/YpR.cpp | 3 + src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp | 3 + src/Bpp/Phyl/Model/Nucleotide/gBGC.h | 4 +- .../Model/OneChangeRegisterTransitionModel.cpp | 422 +++++++ .../Phyl/Model/OneChangeRegisterTransitionModel.h | 215 ++++ src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp | 22 +- src/Bpp/Phyl/Model/OneChangeTransitionModel.h | 39 +- src/Bpp/Phyl/Model/Protein/DSO78.h | 6 + src/Bpp/Phyl/Model/Protein/JCprot.cpp | 213 ++-- src/Bpp/Phyl/Model/Protein/JCprot.h | 18 +- src/Bpp/Phyl/Model/Protein/JTT92.h | 75 +- src/Bpp/Phyl/Model/Protein/LG08.h | 6 + src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp | 20 +- src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h | 146 ++- src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp | 19 +- src/Bpp/Phyl/Model/Protein/LGL08_CAT.h | 152 ++- src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp | 18 +- src/Bpp/Phyl/Model/Protein/LLG08_EHO.h | 155 ++- src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp | 19 +- src/Bpp/Phyl/Model/Protein/LLG08_EX2.h | 152 ++- src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp | 19 +- src/Bpp/Phyl/Model/Protein/LLG08_EX3.h | 153 ++- src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp | 19 +- src/Bpp/Phyl/Model/Protein/LLG08_UL2.h | 154 ++- src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp | 18 +- src/Bpp/Phyl/Model/Protein/LLG08_UL3.h | 153 ++- .../Model/Protein/UserProteinSubstitutionModel.h | 7 + src/Bpp/Phyl/Model/Protein/WAG01.h | 6 + src/Bpp/Phyl/Model/RE08.h | 4 + .../Phyl/Model/RegisterRatesSubstitutionModel.cpp | 113 ++ .../Phyl/Model/RegisterRatesSubstitutionModel.h | 268 +++++ src/Bpp/Phyl/Model/SubstitutionModel.h | 47 +- src/Bpp/Phyl/Model/SubstitutionModelSet.cpp | 2 +- src/Bpp/Phyl/Model/SubstitutionModelSet.h | 51 +- src/Bpp/Phyl/Model/WordSubstitutionModel.cpp | 13 +- src/Bpp/Phyl/Model/WordSubstitutionModel.h | 1 + .../WrappedModel.h} | 74 +- src/Bpp/Phyl/OptimizationTools.cpp | 6 +- .../Phyl/Simulation/HomogeneousSequenceSimulator.h | 2 +- src/Bpp/Phyl/Simulation/MutationProcess.cpp | 33 +- src/CMakeLists.txt | 11 +- test/CMakeLists.txt | 3 + test/test_likelihood_clock.cpp | 20 +- test/test_mapping.cpp | 103 +- test/test_mapping_codon.cpp | 7 +- test/test_models.cpp | 1 + 168 files changed, 9197 insertions(+), 5889 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
