This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository libbpp-phyl.
commit ba3ee2924119536bdad315d348836ce4c2498208 Merge: 802e328 f5b5b84 Author: Andreas Tille <[email protected]> Date: Tue Jun 13 16:03:05 2017 +0200 Updated version 2.3.1 from 'upstream/2.3.1' with Debian dir 51cbc2d848c8b12acdeb256739ac2c86512311e9 AUTHORS.txt | 3 + CMakeLists.txt | 176 +- CTestConfig.cmake | 13 + ChangeLog | 24 + Doxyfile | 2662 ++++++++++++-------- INSTALL.txt | 19 +- bpp-phyl.spec | 133 +- genIncludes.sh | 35 - package.cmake.in | 27 + src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp | 413 +-- src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h | 1197 ++++----- src/Bpp/Phyl/BipartitionList.h | 7 +- .../Distance/AbstractAgglomerativeDistanceMethod.h | 8 +- src/Bpp/Phyl/Distance/DistanceEstimation.cpp | 2 +- src/Bpp/Phyl/Distance/DistanceEstimation.h | 40 +- src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h | 11 +- src/Bpp/Phyl/Graphics/CladogramPlot.cpp | 6 +- src/Bpp/Phyl/Graphics/PhylogramPlot.cpp | 6 +- src/Bpp/Phyl/Graphics/TreeDrawing.h | 4 +- src/Bpp/Phyl/Graphics/TreeDrawingListener.h | 8 +- src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp | 354 ++- src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h | 1 + .../BppOMultiTreeReaderFormat.cpp} | 68 +- .../BppOMultiTreeReaderFormat.h} | 66 +- .../BppOMultiTreeWriterFormat.cpp} | 68 +- .../BppOMultiTreeWriterFormat.h} | 66 +- src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp | 6 +- src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp | 845 +++++-- src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h | 337 +-- src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp | 114 + src/Bpp/Phyl/Io/BppOTransitionModelFormat.h | 94 + .../BppOTreeReaderFormat.cpp} | 68 +- .../BppOTreeReaderFormat.h} | 66 +- .../BppOTreeWriterFormat.cpp} | 68 +- .../BppOTreeWriterFormat.h} | 66 +- src/Bpp/Phyl/Io/IoFrequenciesSet.h | 3 + src/Bpp/Phyl/Io/IoSubstitutionModel.h | 5 +- src/Bpp/Phyl/Io/IoTree.h | 172 +- src/Bpp/Phyl/Io/Newick.cpp | 11 +- src/Bpp/Phyl/Io/Newick.h | 161 +- src/Bpp/Phyl/Io/NexusIoTree.cpp | 9 +- src/Bpp/Phyl/Io/NexusIoTree.h | 142 +- src/Bpp/Phyl/Io/Nhx.cpp | 11 +- src/Bpp/Phyl/Io/Nhx.h | 140 +- .../AbstractHomogeneousTreeLikelihood.cpp | 25 +- .../Likelihood/AbstractHomogeneousTreeLikelihood.h | 466 ++-- .../AbstractNonHomogeneousTreeLikelihood.cpp | 51 +- .../AbstractNonHomogeneousTreeLikelihood.h | 8 +- src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h | 276 +- src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h | 4 - .../Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp | 7 +- src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h | 18 +- .../Phyl/Likelihood/DRASRTreeLikelihoodData.cpp | 15 +- src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h | 13 +- .../DRHomogeneousMixedTreeLikelihood.cpp | 6 +- .../Likelihood/DRHomogeneousMixedTreeLikelihood.h | 4 +- .../Likelihood/DRHomogeneousTreeLikelihood.cpp | 4 +- .../Phyl/Likelihood/DRHomogeneousTreeLikelihood.h | 4 +- src/Bpp/Phyl/Likelihood/DRTreeLikelihood.h | 2 - src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp | 12 +- .../Phyl/Likelihood/HomogeneousTreeLikelihood.h | 13 +- .../MarginalAncestralStateReconstruction.cpp | 12 +- .../MarginalAncestralStateReconstruction.h | 15 +- .../Likelihood/NNIHomogeneousTreeLikelihood.cpp | 6 +- .../Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h | 15 +- .../Phyl/Likelihood/NonHomogeneousTreeLikelihood.h | 11 +- .../Likelihood/RHomogeneousClockTreeLikelihood.cpp | 12 +- .../Likelihood/RHomogeneousClockTreeLikelihood.h | 6 +- .../Likelihood/RHomogeneousMixedTreeLikelihood.cpp | 6 +- .../Likelihood/RHomogeneousMixedTreeLikelihood.h | 14 +- .../Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp | 7 +- .../Phyl/Likelihood/RHomogeneousTreeLikelihood.h | 4 +- .../RNonHomogeneousMixedTreeLikelihood.cpp | 8 +- .../Phyl/Likelihood/SitePartitionTreeLikelihood.h | 11 +- src/Bpp/Phyl/Likelihood/TreeLikelihood.h | 166 +- src/Bpp/Phyl/Likelihood/TreeLikelihoodData.h | 9 +- .../Phyl/Mapping/CategorySubstitutionRegister.h | 405 +++ src/Bpp/Phyl/Mapping/DecompositionReward.cpp | 6 +- .../Mapping/DecompositionSubstitutionCount.cpp | 118 +- .../Phyl/Mapping/DecompositionSubstitutionCount.h | 20 +- src/Bpp/Phyl/Mapping/Mapping.h | 6 +- src/Bpp/Phyl/Mapping/RewardMapping.h | 4 - src/Bpp/Phyl/Mapping/RewardMappingTools.cpp | 14 +- src/Bpp/Phyl/Mapping/SubstitutionCount.h | 3 +- src/Bpp/Phyl/Mapping/SubstitutionMapping.h | 4 - src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp | 199 +- src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h | 45 +- src/Bpp/Phyl/Mapping/SubstitutionRegister.h | 1599 ++++++------ .../Mapping/UniformizationSubstitutionCount.cpp | 10 +- .../Phyl/Mapping/UniformizationSubstitutionCount.h | 20 +- .../Model/AbstractBiblioMixedSubstitutionModel.h | 14 +- .../Phyl/Model/AbstractBiblioSubstitutionModel.cpp | 41 +- .../Phyl/Model/AbstractBiblioSubstitutionModel.h | 279 +- ...stractFromSubstitutionModelTransitionModel.cpp} | 71 +- .../AbstractFromSubstitutionModelTransitionModel.h | 201 ++ .../AbstractKroneckerWordSubstitutionModel.cpp | 253 ++ .../Model/AbstractKroneckerWordSubstitutionModel.h | 218 ++ src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp | 52 +- src/Bpp/Phyl/Model/AbstractSubstitutionModel.h | 78 +- .../Phyl/Model/AbstractWordSubstitutionModel.cpp | 284 ++- src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h | 95 +- src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp | 12 +- ...l.cpp => AbstractCodonCpGSubstitutionModel.cpp} | 43 +- ...Model.h => AbstractCodonCpGSubstitutionModel.h} | 70 +- .../Codon/AbstractCodonDistanceSubstitutionModel.h | 2 +- .../AbstractCodonFrequenciesSubstitutionModel.h | 2 +- ...bstractCodonPhaseFrequenciesSubstitutionModel.h | 2 +- .../Model/Codon/AbstractCodonSubstitutionModel.cpp | 2 +- .../Model/Codon/AbstractCodonSubstitutionModel.h | 233 +- ...=> AbstractKroneckerCodonSubstitutionModel.cpp} | 131 +- .../AbstractKroneckerCodonSubstitutionModel.h | 201 ++ .../Codon/CodonDistanceCpGSubstitutionModel.cpp | 93 + .../Codon/CodonDistanceCpGSubstitutionModel.h | 133 + .../CodonDistanceFrequenciesSubstitutionModel.h | 8 +- .../Codon/CodonRateFrequenciesSubstitutionModel.h | 7 +- .../Model/Codon/CodonRateSubstitutionModel.cpp | 9 - .../Phyl/Model/Codon/CodonRateSubstitutionModel.h | 3 - src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h | 20 +- src/Bpp/Phyl/Model/Codon/GY94.h | 2 +- .../{CodonRateSubstitutionModel.cpp => KCM.cpp} | 76 +- src/Bpp/Phyl/Model/Codon/KCM.h | 119 + ...erCodonDistanceFrequenciesSubstitutionModel.cpp | 137 + ...kerCodonDistanceFrequenciesSubstitutionModel.h} | 120 +- .../KroneckerCodonDistanceSubstitutionModel.cpp | 121 + .../KroneckerCodonDistanceSubstitutionModel.h | 190 ++ src/Bpp/Phyl/Model/Codon/MG94.h | 17 +- ...eFrequenciesSubstitutionModel.cpp => SENCA.cpp} | 76 +- ...PhaseFrequenciesSubstitutionModel.h => SENCA.h} | 55 +- .../Phyl/Model/Codon/TripletSubstitutionModel.h | 7 +- src/Bpp/Phyl/Model/Codon/YN98.h | 5 +- .../Phyl/Model/Codon/{YNGKP_M1.cpp => YNGP_M1.cpp} | 26 +- src/Bpp/Phyl/Model/Codon/{YNGKP_M1.h => YNGP_M1.h} | 24 +- .../Model/Codon/{YNGKP_M8.cpp => YNGP_M10.cpp} | 73 +- .../Phyl/Model/Codon/{YNGKP_M8.h => YNGP_M10.h} | 54 +- .../Phyl/Model/Codon/{YNGKP_M2.cpp => YNGP_M2.cpp} | 28 +- src/Bpp/Phyl/Model/Codon/{YNGKP_M2.h => YNGP_M2.h} | 24 +- .../Phyl/Model/Codon/{YNGKP_M3.cpp => YNGP_M3.cpp} | 28 +- src/Bpp/Phyl/Model/Codon/{YNGKP_M3.h => YNGP_M3.h} | 24 +- .../Phyl/Model/Codon/{YNGKP_M7.cpp => YNGP_M7.cpp} | 27 +- src/Bpp/Phyl/Model/Codon/{YNGKP_M7.h => YNGP_M7.h} | 24 +- .../Phyl/Model/Codon/{YNGKP_M8.cpp => YNGP_M8.cpp} | 30 +- src/Bpp/Phyl/Model/Codon/{YNGKP_M8.h => YNGP_M8.h} | 30 +- .../Phyl/Model/Codon/{YNGKP_M8.cpp => YNGP_M9.cpp} | 72 +- src/Bpp/Phyl/Model/Codon/{YNGKP_M8.h => YNGP_M9.h} | 52 +- .../Model/FrequenciesSet/CodonFrequenciesSet.cpp | 84 +- .../Model/FrequenciesSet/CodonFrequenciesSet.h | 93 +- .../Phyl/Model/FrequenciesSet/FrequenciesSet.cpp | 63 +- src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h | 564 +++-- .../Model/FrequenciesSet/MvaFrequenciesSet.cpp | 1 + .../Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h | 8 +- .../FrequenciesSet/NucleotideFrequenciesSet.cpp | 2 + .../FrequenciesSet/NucleotideFrequenciesSet.h | 33 +- .../Model/FrequenciesSet/ProteinFrequenciesSet.h | 21 +- .../Model/FrequenciesSet/WordFrequenciesSet.cpp | 2 + .../Phyl/Model/FrequenciesSet/WordFrequenciesSet.h | 22 +- .../Phyl/Model/FromMixtureSubstitutionModel.cpp | 93 + ...utionModel.h => FromMixtureSubstitutionModel.h} | 130 +- .../Phyl/Model/KroneckerWordSubstitutionModel.cpp | 125 + .../Phyl/Model/KroneckerWordSubstitutionModel.h | 148 ++ .../Model/MarkovModulatedSubstitutionModel.cpp | 9 +- .../Phyl/Model/MarkovModulatedSubstitutionModel.h | 30 +- src/Bpp/Phyl/Model/MixedSubstitutionModel.h | 9 + src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp | 14 +- src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h | 7 +- src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp | 13 +- src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h | 9 + src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp | 23 +- src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h | 9 + src/Bpp/Phyl/Model/Nucleotide/F84.cpp | 7 +- src/Bpp/Phyl/Model/Nucleotide/F84.h | 15 +- src/Bpp/Phyl/Model/Nucleotide/GTR.cpp | 6 +- src/Bpp/Phyl/Model/Nucleotide/GTR.h | 10 +- src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp | 7 +- src/Bpp/Phyl/Model/Nucleotide/HKY85.h | 52 +- src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp | 2 +- src/Bpp/Phyl/Model/Nucleotide/JCnuc.h | 10 +- src/Bpp/Phyl/Model/Nucleotide/K80.cpp | 6 +- src/Bpp/Phyl/Model/Nucleotide/K80.h | 10 +- src/Bpp/Phyl/Model/Nucleotide/L95.cpp | 5 +- src/Bpp/Phyl/Model/Nucleotide/L95.h | 10 +- .../Model/Nucleotide/NucleotideSubstitutionModel.h | 83 +- src/Bpp/Phyl/Model/Nucleotide/RN95.cpp | 8 +- src/Bpp/Phyl/Model/Nucleotide/RN95.h | 10 +- src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp | 8 +- src/Bpp/Phyl/Model/Nucleotide/RN95s.h | 10 +- src/Bpp/Phyl/Model/Nucleotide/SSR.cpp | 2 +- src/Bpp/Phyl/Model/Nucleotide/SSR.h | 18 +- src/Bpp/Phyl/Model/Nucleotide/T92.cpp | 7 +- src/Bpp/Phyl/Model/Nucleotide/T92.h | 10 +- src/Bpp/Phyl/Model/Nucleotide/TN93.cpp | 599 ++--- src/Bpp/Phyl/Model/Nucleotide/TN93.h | 52 +- src/Bpp/Phyl/Model/Nucleotide/YpR.cpp | 19 +- src/Bpp/Phyl/Model/Nucleotide/YpR.h | 4 +- src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp | 179 +- src/Bpp/Phyl/Model/Nucleotide/gBGC.h | 144 +- src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp | 303 +++ .../gBGC.h => OneChangeTransitionModel.h} | 114 +- src/Bpp/Phyl/Model/Protein/Coala.cpp | 3 +- src/Bpp/Phyl/Model/Protein/Coala.h | 14 +- src/Bpp/Phyl/Model/Protein/CoalaCore.cpp | 3 +- src/Bpp/Phyl/Model/Protein/CoalaCore.h | 8 +- src/Bpp/Phyl/Model/Protein/DSO78.cpp | 9 +- src/Bpp/Phyl/Model/Protein/DSO78.h | 16 +- src/Bpp/Phyl/Model/Protein/JCprot.cpp | 4 +- src/Bpp/Phyl/Model/Protein/JCprot.h | 16 +- src/Bpp/Phyl/Model/Protein/JTT92.cpp | 4 +- src/Bpp/Phyl/Model/Protein/JTT92.h | 30 +- src/Bpp/Phyl/Model/Protein/LG08.cpp | 12 +- src/Bpp/Phyl/Model/Protein/LG08.h | 16 +- src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp | 4 +- src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h | 8 +- src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp | 32 +- src/Bpp/Phyl/Model/Protein/LGL08_CAT.h | 7 +- src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp | 4 +- src/Bpp/Phyl/Model/Protein/LLG08_EHO.h | 7 +- src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp | 4 +- src/Bpp/Phyl/Model/Protein/LLG08_EX2.h | 9 +- src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp | 4 +- src/Bpp/Phyl/Model/Protein/LLG08_EX3.h | 5 +- src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp | 4 +- src/Bpp/Phyl/Model/Protein/LLG08_UL2.h | 7 +- src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp | 4 +- src/Bpp/Phyl/Model/Protein/LLG08_UL3.h | 7 +- .../Phyl/Model/Protein/ProteinSubstitutionModel.h | 89 +- .../Model/Protein/UserProteinSubstitutionModel.cpp | 8 +- .../Model/Protein/UserProteinSubstitutionModel.h | 16 +- src/Bpp/Phyl/Model/Protein/WAG01.cpp | 4 +- src/Bpp/Phyl/Model/Protein/WAG01.h | 17 +- src/Bpp/Phyl/Model/RE08.cpp | 2 +- src/Bpp/Phyl/Model/RE08.h | 135 +- .../RateDistribution/ConstantRateDistribution.h | 2 +- src/Bpp/Phyl/Model/RateDistributionFactory.h | 110 - src/Bpp/Phyl/Model/StateMap.cpp | 4 +- src/Bpp/Phyl/Model/StateMap.h | 259 +- src/Bpp/Phyl/Model/SubstitutionModel.h | 744 +++--- src/Bpp/Phyl/Model/SubstitutionModelFactory.cpp | 188 -- src/Bpp/Phyl/Model/SubstitutionModelFactory.h | 131 - src/Bpp/Phyl/Model/SubstitutionModelSet.cpp | 23 +- src/Bpp/Phyl/Model/SubstitutionModelSet.h | 120 +- src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp | 104 +- src/Bpp/Phyl/Model/SubstitutionModelSetTools.h | 6 +- src/Bpp/Phyl/Model/TS98.h | 7 +- src/Bpp/Phyl/Model/WordSubstitutionModel.cpp | 18 +- src/Bpp/Phyl/Model/WordSubstitutionModel.h | 8 +- src/Bpp/Phyl/NNISearchable.h | 2 - src/Bpp/Phyl/OptimizationTools.cpp | 28 +- src/Bpp/Phyl/OptimizationTools.h | 7 +- src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h | 7 +- src/Bpp/Phyl/Parsimony/TreeParsimonyData.h | 4 - src/Bpp/Phyl/Parsimony/TreeParsimonyScore.h | 4 - src/Bpp/Phyl/PhyloStatistics.h | 7 +- src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h | 2 +- .../Phyl/Simulation/HomogeneousSequenceSimulator.h | 78 +- .../Simulation/NonHomogeneousSequenceSimulator.cpp | 168 +- .../Simulation/NonHomogeneousSequenceSimulator.h | 81 +- src/Bpp/Phyl/Simulation/SequenceSimulator.h | 2 - src/Bpp/Phyl/SitePatterns.h | 7 +- src/Bpp/Phyl/TopologySearch.h | 2 - src/Bpp/Phyl/Tree.h | 2 +- src/Bpp/Phyl/TreeTemplate.h | 19 +- src/Bpp/Phyl/TreeTemplateTools.cpp | 43 +- src/Bpp/Phyl/TreeTemplateTools.h | 11 +- src/CMakeLists.txt | 397 +-- test/CMakeLists.txt | 104 +- test/test_bowker.cpp | 20 +- test/test_likelihood.cpp | 6 +- test/test_likelihood_clock.cpp | 8 +- test/test_likelihood_nh.cpp | 10 +- test/test_mapping.cpp | 20 +- test/test_mapping_codon.cpp | 2 +- test/test_parsimony.cpp | 4 +- test/test_simulations.cpp | 8 +- test/test_tree.cpp | 70 +- test/{test_parsimony.cpp => test_tree_getpath.cpp} | 55 +- .../test_tree_rootat.cpp | 59 +- 275 files changed, 13223 insertions(+), 8888 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