[med-svn] [libbpp-phyl] 03/04: Updated version 2.3.1 from 'upstream/2.3.1'
Andreas Tille
tille at debian.org
Tue Jun 13 15:16:03 UTC 2017
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 <tille at debian.org>
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 deletions(-)
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