[med-svn] [libbpp-phyl] branch upstream updated (1c804a7 -> f5b5b84)
Andreas Tille
tille at debian.org
Tue Jun 13 15:16:04 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository libbpp-phyl.
from 1c804a7 Imported Upstream version 2.2.0
new f5b5b84 New upstream version 2.3.1
The 1 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:
AUTHORS.txt | 3 +
CMakeLists.txt | 176 +-
CTestConfig.cmake | 13 +
ChangeLog | 24 +
Doxyfile | 2662 ++++++++++++--------
INSTALL.txt | 19 +-
bpp-phyl.spec | 133 +-
debian/changelog | 85 -
debian/compat | 1 -
debian/control | 25 -
debian/copyright | 66 -
debian/docs | 0
debian/libbpp-phyl-dev.install | 3 -
debian/libbpp-phyl9.install | 1 -
debian/postinst | 57 -
debian/postrm | 59 -
debian/prerm | 41 -
debian/rules | 122 -
debian/source/format | 1 -
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} | 65 +-
.../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 +-
.../Codon/AbstractCodonCpGSubstitutionModel.cpp} | 46 +-
.../Codon/AbstractCodonCpGSubstitutionModel.h} | 69 +-
.../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 ++
...l.cpp => CodonDistanceCpGSubstitutionModel.cpp} | 30 +-
...Model.h => CodonDistanceCpGSubstitutionModel.h} | 35 +-
.../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 +-
src/Bpp/Phyl/Model/Codon/{YN98.cpp => KCM.cpp} | 58 +-
src/Bpp/Phyl/Model/Codon/KCM.h | 119 +
...erCodonDistanceFrequenciesSubstitutionModel.cpp | 137 +
...kerCodonDistanceFrequenciesSubstitutionModel.h} | 120 +-
...=> KroneckerCodonDistanceSubstitutionModel.cpp} | 76 +-
.../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 +-
.../FromMixtureSubstitutionModel.cpp} | 69 +-
...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.cpp | 64 -
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_nhx.cpp => test_tree_getpath.cpp} | 60 +-
test/{test_nhx.cpp => test_tree_rootat.cpp} | 47 +-
288 files changed, 12913 insertions(+), 9464 deletions(-)
create mode 100644 CTestConfig.cmake
delete mode 100644 debian/changelog
delete mode 100644 debian/compat
delete mode 100644 debian/control
delete mode 100644 debian/copyright
delete mode 100644 debian/docs
delete mode 100644 debian/libbpp-phyl-dev.install
delete mode 100644 debian/libbpp-phyl9.install
delete mode 100755 debian/postinst
delete mode 100755 debian/postrm
delete mode 100755 debian/prerm
delete mode 100755 debian/rules
delete mode 100644 debian/source/format
delete mode 100755 genIncludes.sh
create mode 100644 package.cmake.in
copy src/Bpp/Phyl/{Model/Nucleotide/NucleotideSubstitutionModel.h => Io/BppOMultiTreeReaderFormat.cpp} (60%)
mode change 100755 => 100644
copy src/Bpp/Phyl/{Model/Nucleotide/NucleotideSubstitutionModel.h => Io/BppOMultiTreeReaderFormat.h} (51%)
mode change 100755 => 100644
copy src/Bpp/Phyl/{Model/Nucleotide/NucleotideSubstitutionModel.h => Io/BppOMultiTreeWriterFormat.cpp} (60%)
mode change 100755 => 100644
copy src/Bpp/Phyl/{Model/Nucleotide/NucleotideSubstitutionModel.h => Io/BppOMultiTreeWriterFormat.h} (51%)
mode change 100755 => 100644
create mode 100644 src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp
create mode 100644 src/Bpp/Phyl/Io/BppOTransitionModelFormat.h
copy src/Bpp/Phyl/{Model/Nucleotide/NucleotideSubstitutionModel.h => Io/BppOTreeReaderFormat.cpp} (61%)
mode change 100755 => 100644
copy src/Bpp/Phyl/{Model/Nucleotide/NucleotideSubstitutionModel.h => Io/BppOTreeReaderFormat.h} (51%)
mode change 100755 => 100644
copy src/Bpp/Phyl/{Model/Nucleotide/NucleotideSubstitutionModel.h => Io/BppOTreeWriterFormat.cpp} (61%)
mode change 100755 => 100644
copy src/Bpp/Phyl/{Model/Nucleotide/NucleotideSubstitutionModel.h => Io/BppOTreeWriterFormat.h} (51%)
mode change 100755 => 100644
mode change 100755 => 100644 src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h
create mode 100644 src/Bpp/Phyl/Mapping/CategorySubstitutionRegister.h
copy src/Bpp/Phyl/{TreeExceptions.cpp => Model/AbstractFromSubstitutionModelTransitionModel.cpp} (56%)
mode change 100755 => 100644
create mode 100644 src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h
create mode 100644 src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp
create mode 100644 src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h
copy src/Bpp/Phyl/{Mapping/SubstitutionRegister.cpp => Model/Codon/AbstractCodonCpGSubstitutionModel.cpp} (63%)
copy src/Bpp/Phyl/{Io/BppORateDistributionFormat.h => Model/Codon/AbstractCodonCpGSubstitutionModel.h} (52%)
copy src/Bpp/Phyl/Model/Codon/{AbstractCodonSubstitutionModel.cpp => AbstractKroneckerCodonSubstitutionModel.cpp} (55%)
create mode 100644 src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h
copy src/Bpp/Phyl/Model/Codon/{CodonDistanceSubstitutionModel.cpp => CodonDistanceCpGSubstitutionModel.cpp} (72%)
copy src/Bpp/Phyl/Model/Codon/{CodonDistanceSubstitutionModel.h => CodonDistanceCpGSubstitutionModel.h} (82%)
copy src/Bpp/Phyl/Model/Codon/{YN98.cpp => KCM.cpp} (60%)
create mode 100644 src/Bpp/Phyl/Model/Codon/KCM.h
create mode 100644 src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp
copy src/Bpp/Phyl/Model/Codon/{CodonDistanceFrequenciesSubstitutionModel.h => KroneckerCodonDistanceFrequenciesSubstitutionModel.h} (54%)
copy src/Bpp/Phyl/Model/Codon/{CodonDistancePhaseFrequenciesSubstitutionModel.cpp => KroneckerCodonDistanceSubstitutionModel.cpp} (51%)
create mode 100644 src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h
rename src/Bpp/Phyl/Model/Codon/{CodonDistanceFitnessPhaseFrequenciesSubstitutionModel.cpp => SENCA.cpp} (53%)
rename src/Bpp/Phyl/Model/Codon/{CodonDistanceFitnessPhaseFrequenciesSubstitutionModel.h => SENCA.h} (66%)
rename src/Bpp/Phyl/Model/Codon/{YNGKP_M1.cpp => YNGP_M1.cpp} (85%)
rename src/Bpp/Phyl/Model/Codon/{YNGKP_M1.h => YNGP_M1.h} (89%)
copy src/Bpp/Phyl/Model/Codon/{YNGKP_M8.cpp => YNGP_M10.cpp} (69%)
copy src/Bpp/Phyl/Model/Codon/{YNGKP_M8.h => YNGP_M10.h} (71%)
rename src/Bpp/Phyl/Model/Codon/{YNGKP_M2.cpp => YNGP_M2.cpp} (85%)
rename src/Bpp/Phyl/Model/Codon/{YNGKP_M2.h => YNGP_M2.h} (89%)
rename src/Bpp/Phyl/Model/Codon/{YNGKP_M3.cpp => YNGP_M3.cpp} (87%)
rename src/Bpp/Phyl/Model/Codon/{YNGKP_M3.h => YNGP_M3.h} (88%)
rename src/Bpp/Phyl/Model/Codon/{YNGKP_M7.cpp => YNGP_M7.cpp} (86%)
rename src/Bpp/Phyl/Model/Codon/{YNGKP_M7.h => YNGP_M7.h} (88%)
copy src/Bpp/Phyl/Model/Codon/{YNGKP_M8.cpp => YNGP_M8.cpp} (86%)
copy src/Bpp/Phyl/Model/Codon/{YNGKP_M8.h => YNGP_M8.h} (83%)
rename src/Bpp/Phyl/Model/Codon/{YNGKP_M8.cpp => YNGP_M9.cpp} (69%)
rename src/Bpp/Phyl/Model/Codon/{YNGKP_M8.h => YNGP_M9.h} (74%)
copy src/Bpp/Phyl/{TreeExceptions.cpp => Model/FromMixtureSubstitutionModel.cpp} (53%)
mode change 100755 => 100644
copy src/Bpp/Phyl/Model/{AbstractBiblioSubstitutionModel.h => FromMixtureSubstitutionModel.h} (63%)
create mode 100644 src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp
create mode 100644 src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h
create mode 100644 src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp
copy src/Bpp/Phyl/Model/{Nucleotide/gBGC.h => OneChangeTransitionModel.h} (50%)
delete mode 100644 src/Bpp/Phyl/Model/RateDistributionFactory.cpp
delete mode 100644 src/Bpp/Phyl/Model/RateDistributionFactory.h
delete mode 100644 src/Bpp/Phyl/Model/SubstitutionModelFactory.cpp
delete mode 100644 src/Bpp/Phyl/Model/SubstitutionModelFactory.h
copy test/{test_nhx.cpp => test_tree_getpath.cpp} (58%)
copy test/{test_nhx.cpp => test_tree_rootat.cpp} (63%)
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