[med-svn] [libbpp-phyl] branch master updated (813cb14 -> 62da4ac)

Andreas Tille tille at debian.org
Wed Apr 13 13:38:59 UTC 2016


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tille pushed a change to branch master
in repository libbpp-phyl.

      from  813cb14   Add watch file
       new  1c804a7   Imported Upstream version 2.2.0
       new  62da4ac   Merge tag 'upstream/2.2.0'

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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 +-
 ...nMapping.cpp => ProbabilisticRewardMapping.cpp} |   25 +-
 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, 14707 insertions(+), 8335 deletions(-)
 copy debian/postinst => genIncludes.sh (80%)
 create mode 100644 src/Bpp/Phyl/Mapping/DecompositionReward.cpp
 create mode 100644 src/Bpp/Phyl/Mapping/DecompositionReward.h
 copy src/Bpp/Phyl/Mapping/{SubstitutionMapping.h => Mapping.h} (52%)
 copy src/Bpp/Phyl/Mapping/{ProbabilisticSubstitutionMapping.cpp => ProbabilisticRewardMapping.cpp} (72%)
 create mode 100644 src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h
 create mode 100644 src/Bpp/Phyl/Mapping/Reward.h
 copy src/Bpp/Phyl/{Simulation/SequenceSimulator.h => Mapping/RewardMapping.h} (52%)
 mode change 100755 => 100644
 create mode 100644 src/Bpp/Phyl/Mapping/RewardMappingTools.cpp
 create mode 100644 src/Bpp/Phyl/Mapping/RewardMappingTools.h
 copy src/Bpp/Phyl/{Model/StateMap.cpp => Mapping/SubstitutionRegister.cpp} (78%)
 create mode 100644 src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp
 create mode 100644 src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h
 create mode 100644 src/Bpp/Phyl/Model/Protein/__LG10_EX_EHOExchangeabilityCode
 create mode 100644 src/Bpp/Phyl/Model/Protein/__LG10_EX_EHOFrequenciesCode
 create mode 100644 src/Bpp/Phyl/Model/Protein/__LG10_EX_EHORatesProps

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