[med-svn] [libbpp-phyl] 02/02: Merge tag 'upstream/2.2.0'
Andreas Tille
tille at debian.org
Wed Apr 13 13:39:00 UTC 2016
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 <tille at debian.org>
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
More information about the debian-med-commit
mailing list