[med-svn] [libbpp-phyl] branch master updated (c8a90af -> d6dea21)
Julien Dutheil
jdutheil-guest at moszumanska.debian.org
Tue Feb 6 12:41:09 UTC 2018
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jdutheil-guest pushed a change to branch master
in repository libbpp-phyl.
from c8a90af DEP3
new 7e00775 New upstream version 2.3.2
new 6f35a10 Update upstream source from tag 'upstream/2.3.2'
new d6dea21 Version 2.3.2.
The 3 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:
CTestConfig.cmake | 1 +
Doxyfile | 477 +++-----
debian/changelog | 7 +
debian/control | 6 +-
...-unit-tests-compilation-on-some-platforms.patch | 19 -
.../patches/correct_constructors_inheritance.patch | 48 +
debian/patches/relax_test_timeout.patch | 13 -
debian/patches/remove_deprecated_warnings.patch | 98 --
debian/patches/series | 6 +-
debian/patches/test_likelihood_clock.patch | 67 --
debian/patches/test_mapping.patch | 132 ---
debian/patches/unforce-cxxflags.patch | 2 +-
src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp | 146 ++-
src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h | 12 +
src/Bpp/Phyl/Distance/DistanceEstimation.h | 119 +-
src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp | 12 +-
src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp | 416 +++++--
src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h | 6 +-
src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp | 48 +-
.../AbstractHomogeneousTreeLikelihood.cpp | 4 +-
.../Likelihood/AbstractHomogeneousTreeLikelihood.h | 29 +-
.../AbstractNonHomogeneousTreeLikelihood.h | 4 +-
src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h | 13 +-
.../Phyl/Likelihood/DRHomogeneousTreeLikelihood.h | 2 +-
.../DiscreteRatesAcrossSitesTreeLikelihood.h | 324 +++---
.../Phyl/Likelihood/HomogeneousTreeLikelihood.h | 104 +-
.../MarginalAncestralStateReconstruction.cpp | 4 +-
.../Phyl/Likelihood/NonHomogeneousTreeLikelihood.h | 85 +-
.../Phyl/Likelihood/SitePartitionTreeLikelihood.h | 12 +-
src/Bpp/Phyl/Likelihood/TreeLikelihood.h | 5 +-
.../Phyl/Mapping/CategorySubstitutionRegister.h | 27 +-
src/Bpp/Phyl/Mapping/DecompositionMethods.cpp | 300 +++++
src/Bpp/Phyl/Mapping/DecompositionMethods.h | 174 +++
src/Bpp/Phyl/Mapping/DecompositionReward.cpp | 112 +-
src/Bpp/Phyl/Mapping/DecompositionReward.h | 178 ++-
.../Mapping/DecompositionSubstitutionCount.cpp | 163 +--
.../Phyl/Mapping/DecompositionSubstitutionCount.h | 47 +-
src/Bpp/Phyl/Mapping/RewardMappingTools.cpp | 3 +-
src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp | 718 ++++++++++--
src/Bpp/Phyl/Mapping/SubstitutionMappingTools.h | 1217 +++++++++++++-------
src/Bpp/Phyl/Mapping/SubstitutionRegister.h | 411 +++++--
.../Mapping/UniformizationSubstitutionCount.cpp | 2 +-
.../Model/AbstractBiblioMixedSubstitutionModel.cpp | 13 +-
.../Model/AbstractBiblioMixedSubstitutionModel.h | 309 ++---
.../Phyl/Model/AbstractBiblioSubstitutionModel.cpp | 18 +-
.../Phyl/Model/AbstractBiblioSubstitutionModel.h | 95 +-
...bstractFromSubstitutionModelTransitionModel.cpp | 6 +-
.../AbstractFromSubstitutionModelTransitionModel.h | 113 +-
.../AbstractKroneckerWordSubstitutionModel.cpp | 33 +-
src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp | 294 ++++-
src/Bpp/Phyl/Model/AbstractSubstitutionModel.h | 733 ++++++------
.../Phyl/Model/AbstractWordSubstitutionModel.cpp | 272 +----
src/Bpp/Phyl/Model/AbstractWrappedModel.h | 289 +++++
...itutionModel.h => AnonymousSubstitutionModel.h} | 78 +-
...=> AbstractCodonAAFitnessSubstitutionModel.cpp} | 37 +-
...h => AbstractCodonAAFitnessSubstitutionModel.h} | 75 +-
...pp => AbstractCodonAARateSubstitutionModel.cpp} | 41 +-
.../Codon/AbstractCodonAARateSubstitutionModel.h | 162 +++
...l.cpp => AbstractCodonBGCSubstitutionModel.cpp} | 54 +-
.../Codon/AbstractCodonBGCSubstitutionModel.h | 138 +++
.../Codon/AbstractCodonCpGSubstitutionModel.cpp | 3 +-
.../Codon/AbstractCodonCpGSubstitutionModel.h | 155 +--
.../AbstractCodonDistanceSubstitutionModel.cpp | 9 +-
.../Codon/AbstractCodonDistanceSubstitutionModel.h | 180 +--
.../AbstractCodonFitnessSubstitutionModel.cpp | 10 +-
.../Codon/AbstractCodonFitnessSubstitutionModel.h | 28 +-
.../AbstractCodonFrequenciesSubstitutionModel.cpp | 3 +-
.../AbstractCodonFrequenciesSubstitutionModel.h | 171 +--
...tractCodonPhaseFrequenciesSubstitutionModel.cpp | 7 +-
...bstractCodonPhaseFrequenciesSubstitutionModel.h | 160 +--
.../Model/Codon/AbstractCodonSubstitutionModel.cpp | 1 +
.../Model/Codon/AbstractCodonSubstitutionModel.h | 1 +
.../Model/Codon/CodonAdHocSubstitutionModel.cpp | 172 +++
...tutionModel.h => CodonAdHocSubstitutionModel.h} | 104 +-
.../Codon/CodonDistanceCpGSubstitutionModel.cpp | 93 --
.../CodonDistanceFrequenciesSubstitutionModel.cpp | 10 +-
.../CodonDistanceFrequenciesSubstitutionModel.h | 4 +
...onDistancePhaseFrequenciesSubstitutionModel.cpp | 12 +-
...odonDistancePhaseFrequenciesSubstitutionModel.h | 7 +
.../Model/Codon/CodonDistanceSubstitutionModel.cpp | 6 +-
.../Model/Codon/CodonDistanceSubstitutionModel.h | 2 +-
.../CodonRateFrequenciesSubstitutionModel.cpp | 100 --
.../Codon/CodonRateFrequenciesSubstitutionModel.h | 124 --
.../Phyl/Model/Codon/CodonRateSubstitutionModel.h | 107 --
src/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h | 34 +-
src/Bpp/Phyl/Model/Codon/GY94.h | 101 +-
src/Bpp/Phyl/Model/Codon/KCM.h | 11 +-
...erCodonDistanceFrequenciesSubstitutionModel.cpp | 12 +-
...ckerCodonDistanceFrequenciesSubstitutionModel.h | 5 +
.../KroneckerCodonDistanceSubstitutionModel.cpp | 12 +-
src/Bpp/Phyl/Model/Codon/MG94.h | 100 +-
src/Bpp/Phyl/Model/Codon/SENCA.cpp | 30 +-
src/Bpp/Phyl/Model/Codon/SENCA.h | 29 +-
.../Phyl/Model/Codon/TripletSubstitutionModel.h | 10 +-
src/Bpp/Phyl/Model/Codon/YN98.cpp | 2 +
src/Bpp/Phyl/Model/Codon/YN98.h | 100 +-
.../Codon/{CodonSubstitutionModel.h => YNGP_M.h} | 118 +-
src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp | 26 +-
src/Bpp/Phyl/Model/Codon/YNGP_M1.h | 136 +--
src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp | 31 +-
src/Bpp/Phyl/Model/Codon/YNGP_M10.h | 160 ++-
src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp | 25 +-
src/Bpp/Phyl/Model/Codon/YNGP_M2.h | 119 +-
src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp | 25 +-
src/Bpp/Phyl/Model/Codon/YNGP_M3.h | 122 +-
src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp | 25 +-
src/Bpp/Phyl/Model/Codon/YNGP_M7.h | 132 +--
src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp | 25 +-
src/Bpp/Phyl/Model/Codon/YNGP_M8.h | 133 +--
src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp | 31 +-
src/Bpp/Phyl/Model/Codon/YNGP_M9.h | 166 ++-
.../Model/FrequenciesSet/CodonFrequenciesSet.cpp | 36 +-
.../Model/FrequenciesSet/CodonFrequenciesSet.h | 12 +-
src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h | 4 +-
.../Model/FrequenciesSet/WordFrequenciesSet.cpp | 63 +-
.../Phyl/Model/FrequenciesSet/WordFrequenciesSet.h | 11 +-
.../Phyl/Model/FromMixtureSubstitutionModel.cpp | 27 +-
src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h | 308 ++---
...utionModel.cpp => InMixedSubstitutionModel.cpp} | 54 +-
src/Bpp/Phyl/Model/InMixedSubstitutionModel.h | 314 +++++
.../Model/MarkovModulatedSubstitutionModel.cpp | 18 +
.../Phyl/Model/MarkovModulatedSubstitutionModel.h | 56 +-
src/Bpp/Phyl/Model/MixedSubstitutionModel.h | 2 +-
src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp | 12 +-
src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h | 39 +-
src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp | 2 +-
src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h | 2 +-
src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp | 2 +-
src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h | 2 +-
src/Bpp/Phyl/Model/Nucleotide/L95.cpp | 1 +
src/Bpp/Phyl/Model/Nucleotide/RN95.cpp | 1 +
src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp | 1 +
src/Bpp/Phyl/Model/Nucleotide/YpR.cpp | 3 +
src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp | 3 +
src/Bpp/Phyl/Model/Nucleotide/gBGC.h | 4 +-
.../Model/OneChangeRegisterTransitionModel.cpp | 422 +++++++
.../Phyl/Model/OneChangeRegisterTransitionModel.h | 215 ++++
src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp | 22 +-
src/Bpp/Phyl/Model/OneChangeTransitionModel.h | 39 +-
src/Bpp/Phyl/Model/Protein/DSO78.h | 6 +
src/Bpp/Phyl/Model/Protein/JCprot.cpp | 213 ++--
src/Bpp/Phyl/Model/Protein/JCprot.h | 18 +-
src/Bpp/Phyl/Model/Protein/JTT92.h | 75 +-
src/Bpp/Phyl/Model/Protein/LG08.h | 6 +
src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp | 20 +-
src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h | 146 ++-
src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp | 19 +-
src/Bpp/Phyl/Model/Protein/LGL08_CAT.h | 152 ++-
src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp | 18 +-
src/Bpp/Phyl/Model/Protein/LLG08_EHO.h | 155 ++-
src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp | 19 +-
src/Bpp/Phyl/Model/Protein/LLG08_EX2.h | 152 ++-
src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp | 19 +-
src/Bpp/Phyl/Model/Protein/LLG08_EX3.h | 153 ++-
src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp | 19 +-
src/Bpp/Phyl/Model/Protein/LLG08_UL2.h | 154 ++-
src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp | 18 +-
src/Bpp/Phyl/Model/Protein/LLG08_UL3.h | 153 ++-
.../Model/Protein/UserProteinSubstitutionModel.h | 7 +
src/Bpp/Phyl/Model/Protein/WAG01.h | 6 +
src/Bpp/Phyl/Model/RE08.h | 4 +
.../Phyl/Model/RegisterRatesSubstitutionModel.cpp | 113 ++
.../Phyl/Model/RegisterRatesSubstitutionModel.h | 268 +++++
src/Bpp/Phyl/Model/SubstitutionModel.h | 47 +-
src/Bpp/Phyl/Model/SubstitutionModelSet.cpp | 2 +-
src/Bpp/Phyl/Model/SubstitutionModelSet.h | 51 +-
src/Bpp/Phyl/Model/WordSubstitutionModel.cpp | 13 +-
src/Bpp/Phyl/Model/WordSubstitutionModel.h | 1 +
.../WrappedModel.h} | 74 +-
src/Bpp/Phyl/OptimizationTools.cpp | 6 +-
.../Phyl/Simulation/HomogeneousSequenceSimulator.h | 2 +-
src/Bpp/Phyl/Simulation/MutationProcess.cpp | 33 +-
src/CMakeLists.txt | 11 +-
test/CMakeLists.txt | 3 +
test/test_likelihood_clock.cpp | 20 +-
test/test_mapping.cpp | 103 +-
test/test_mapping_codon.cpp | 7 +-
test/test_models.cpp | 1 +
178 files changed, 9257 insertions(+), 6227 deletions(-)
delete mode 100644 debian/patches/0002-Fixed-unit-tests-compilation-on-some-platforms.patch
create mode 100644 debian/patches/correct_constructors_inheritance.patch
delete mode 100644 debian/patches/relax_test_timeout.patch
delete mode 100644 debian/patches/remove_deprecated_warnings.patch
delete mode 100644 debian/patches/test_likelihood_clock.patch
delete mode 100644 debian/patches/test_mapping.patch
create mode 100644 src/Bpp/Phyl/Mapping/DecompositionMethods.cpp
create mode 100644 src/Bpp/Phyl/Mapping/DecompositionMethods.h
create mode 100644 src/Bpp/Phyl/Model/AbstractWrappedModel.h
copy src/Bpp/Phyl/Model/{Codon/CodonSubstitutionModel.h => AnonymousSubstitutionModel.h} (54%)
copy src/Bpp/Phyl/Model/Codon/{AbstractCodonFitnessSubstitutionModel.cpp => AbstractCodonAAFitnessSubstitutionModel.cpp} (64%)
copy src/Bpp/Phyl/Model/Codon/{AbstractCodonFitnessSubstitutionModel.h => AbstractCodonAAFitnessSubstitutionModel.h} (59%)
copy src/Bpp/Phyl/Model/Codon/{AbstractCodonDistanceSubstitutionModel.cpp => AbstractCodonAARateSubstitutionModel.cpp} (70%)
create mode 100644 src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h
rename src/Bpp/Phyl/Model/Codon/{CodonRateSubstitutionModel.cpp => AbstractCodonBGCSubstitutionModel.cpp} (57%)
create mode 100644 src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h
create mode 100644 src/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp
rename src/Bpp/Phyl/Model/Codon/{CodonDistanceCpGSubstitutionModel.h => CodonAdHocSubstitutionModel.h} (60%)
delete mode 100644 src/Bpp/Phyl/Model/Codon/CodonDistanceCpGSubstitutionModel.cpp
delete mode 100644 src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.cpp
delete mode 100644 src/Bpp/Phyl/Model/Codon/CodonRateFrequenciesSubstitutionModel.h
delete mode 100644 src/Bpp/Phyl/Model/Codon/CodonRateSubstitutionModel.h
copy src/Bpp/Phyl/Model/Codon/{CodonSubstitutionModel.h => YNGP_M.h} (50%)
copy src/Bpp/Phyl/Model/{FromMixtureSubstitutionModel.cpp => InMixedSubstitutionModel.cpp} (58%)
create mode 100644 src/Bpp/Phyl/Model/InMixedSubstitutionModel.h
create mode 100644 src/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp
create mode 100644 src/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.h
create mode 100644 src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp
create mode 100644 src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.h
copy src/Bpp/Phyl/{Simulation/HomogeneousSequenceSimulator.h => Model/WrappedModel.h} (59%)
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