[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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