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Viewing changes to src/Bpp/Phyl/Model/JCprot.h

Committer: Package Import Robot
Author(s): Julien Dutheil
Date: 2013-02-09 16:00:00 UTC
mfrom: (1.1.1)
Revision ID: package-import@ubuntu.com-20130209160000-5v65ba68z8032nzj

Tags: 2.0.3-1

* Reorganized model hierarchy
* New pairwise models
* Several bugs fixed

files added:
src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp

src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h

src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractCodonDistanceSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractCodonDistanceSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractCodonFrequenciesSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractCodonFrequenciesSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractCodonPhaseFrequenciesSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractCodonSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractCodonSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h

src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp

src/Bpp/Phyl/Model/BinarySubstitutionModel.h

src/Bpp/Phyl/Model/CodonDistanceFrequenciesSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonDistanceFrequenciesSubstitutionModel.h

src/Bpp/Phyl/Model/CodonDistancePhaseFrequenciesSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonDistancePhaseFrequenciesSubstitutionModel.h

src/Bpp/Phyl/Model/CodonDistanceSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonDistanceSubstitutionModel.h

src/Bpp/Phyl/Model/CodonRateFrequenciesSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonRateFrequenciesSubstitutionModel.h

src/Bpp/Phyl/Model/CodonRateSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonRateSubstitutionModel.h

src/Bpp/Phyl/Model/CodonSubstitutionModel.h

src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp

src/Bpp/Phyl/Model/MixedSubstitutionModelSet.h

src/Bpp/Phyl/Model/TripletSubstitutionModel.cpp

src/Bpp/Phyl/Model/TripletSubstitutionModel.h

src/Bpp/Phyl/Model/WordSubstitutionModel.cpp

src/Bpp/Phyl/Model/WordSubstitutionModel.h

src/Bpp/Phyl/Model/YpR.cpp

src/Bpp/Phyl/Model/YpR.h

test/test_likelihood_clock.cpp

test/test_likelihood_nh.cpp

files removed:
src/Bpp/Phyl.all

src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractCodonFrequenciesReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractCodonReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractCodonReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractWordReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractWordReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonAsynonymousFrequenciesReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonAsynonymousFrequenciesReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonAsynonymousReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonAsynonymousReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonNeutralFrequenciesReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonNeutralFrequenciesReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/CodonNeutralReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/CodonNeutralReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/TripletReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/TripletReversibleSubstitutionModel.h

src/Bpp/Phyl/Model/WordReversibleSubstitutionModel.cpp

src/Bpp/Phyl/Model/WordReversibleSubstitutionModel.h

files modified:
AUTHORS.txt

CMakeLists.txt

ChangeLog

Doxyfile

Phyl.spec

debian/changelog

debian/control

src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp

src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h

src/Bpp/Phyl/Io/Newick.cpp

src/Bpp/Phyl/Io/Nhx.cpp

src/Bpp/Phyl/Io/Nhx.h

src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp

src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h

src/Bpp/Phyl/Likelihood.all

src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h

src/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h

src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp

src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h

src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h

src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp

src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h

src/Bpp/Phyl/Likelihood/TreeLikelihood.h

src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp

src/Bpp/Phyl/Model.all

src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h

src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp

src/Bpp/Phyl/Model/AbstractSubstitutionModel.h

src/Bpp/Phyl/Model/DSO78.cpp

src/Bpp/Phyl/Model/DSO78.h

src/Bpp/Phyl/Model/F84.cpp

src/Bpp/Phyl/Model/FrequenciesSet.cpp

src/Bpp/Phyl/Model/FrequenciesSet.h

src/Bpp/Phyl/Model/G2001.h

src/Bpp/Phyl/Model/GTR.cpp

src/Bpp/Phyl/Model/GY94.cpp

src/Bpp/Phyl/Model/GY94.h

src/Bpp/Phyl/Model/HKY85.cpp

src/Bpp/Phyl/Model/JCnuc.cpp

src/Bpp/Phyl/Model/JCprot.cpp

src/Bpp/Phyl/Model/JCprot.h

src/Bpp/Phyl/Model/JTT92.cpp

src/Bpp/Phyl/Model/JTT92.h

src/Bpp/Phyl/Model/K80.cpp

src/Bpp/Phyl/Model/L95.cpp

src/Bpp/Phyl/Model/L95.h

src/Bpp/Phyl/Model/LG08.cpp

src/Bpp/Phyl/Model/LG08.h

src/Bpp/Phyl/Model/LLG08_EHO.cpp

src/Bpp/Phyl/Model/LLG08_EHO.h

src/Bpp/Phyl/Model/LLG08_EX2.cpp

src/Bpp/Phyl/Model/LLG08_EX2.h

src/Bpp/Phyl/Model/LLG08_EX3.cpp

src/Bpp/Phyl/Model/LLG08_EX3.h

src/Bpp/Phyl/Model/LLG08_UL2.cpp

src/Bpp/Phyl/Model/LLG08_UL2.h

src/Bpp/Phyl/Model/LLG08_UL3.cpp

src/Bpp/Phyl/Model/LLG08_UL3.h

src/Bpp/Phyl/Model/MG94.cpp

src/Bpp/Phyl/Model/MG94.h

src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp

src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h

src/Bpp/Phyl/Model/MixedSubstitutionModel.h

src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp

src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h

src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp

src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h

src/Bpp/Phyl/Model/RE08.cpp

src/Bpp/Phyl/Model/RE08.h

src/Bpp/Phyl/Model/RN95.cpp

src/Bpp/Phyl/Model/RN95s.cpp

src/Bpp/Phyl/Model/RN95s.h

src/Bpp/Phyl/Model/SSR.cpp

src/Bpp/Phyl/Model/SubstitutionModel.h

src/Bpp/Phyl/Model/SubstitutionModelSet.cpp

src/Bpp/Phyl/Model/SubstitutionModelSet.h

src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp

src/Bpp/Phyl/Model/T92.cpp

src/Bpp/Phyl/Model/TN93.cpp

src/Bpp/Phyl/Model/UserProteinSubstitutionModel.cpp

src/Bpp/Phyl/Model/UserProteinSubstitutionModel.h

src/Bpp/Phyl/Model/WAG01.cpp

src/Bpp/Phyl/Model/WAG01.h

src/Bpp/Phyl/Model/YN98.cpp

src/Bpp/Phyl/Model/YN98.h

src/Bpp/Phyl/Model/YNGKP_M1.cpp

src/Bpp/Phyl/Model/YNGKP_M1.h

src/Bpp/Phyl/Model/YNGKP_M2.cpp

src/Bpp/Phyl/Model/YNGKP_M2.h

src/Bpp/Phyl/Model/YNGKP_M3.cpp

src/Bpp/Phyl/Model/YNGKP_M3.h

src/Bpp/Phyl/Model/YNGKP_M7.cpp

src/Bpp/Phyl/Model/YNGKP_M7.h

src/Bpp/Phyl/Model/YNGKP_M8.cpp

src/Bpp/Phyl/Model/YNGKP_M8.h

src/Bpp/Phyl/Model/__LLG08_EHOExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_EHOFrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EHORatesProps

src/Bpp/Phyl/Model/__LLG08_EX2ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_EX2FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EX2RatesProps

src/Bpp/Phyl/Model/__LLG08_EX3ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_EX3FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_EX3RatesProps

src/Bpp/Phyl/Model/__LLG08_UL2ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_UL2FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_UL2RatesProps

src/Bpp/Phyl/Model/__LLG08_UL3ExchangeabilityCode

src/Bpp/Phyl/Model/__LLG08_UL3FrequenciesCode

src/Bpp/Phyl/Model/__LLG08_UL3RatesProps

src/Bpp/Phyl/Node.h *

src/Bpp/Phyl/NodeTemplate.h

src/Bpp/Phyl/OptimizationTools.cpp *

src/Bpp/Phyl/OptimizationTools.h *

src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h

src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp

src/Bpp/Phyl/Tree.h

src/Bpp/Phyl/TreeTemplate.h *

src/Bpp/Phyl/TreeTemplateTools.cpp

src/Bpp/Phyl/TreeTemplateTools.h

src/Bpp/Phyl/TreeTools.cpp

src/Bpp/Phyl/TreeTools.h

src/CMakeLists.txt

test/CMakeLists.txt

test/test_likelihood.cpp

test/test_mapping_codon.cpp

test/test_simulations.cpp

test/test_tree.cpp

Show diffs side-by-side

added added

removed removed

src/Bpp/Phyl/Model/JCprot.h

159

JCprot(const ProteicAlphabet* alpha, ProteinFrequenciesSet* freqSet, bool initFreqs = false);

160

161

JCprot(const JCprot& model) :

162

AbstractParameterAliasable(model),

163

AbstractSubstitutionModel(model),

162

164

AbstractReversibleSubstitutionModel(model),

163

165

exp_(model.exp_),

164

166

p_(model.p_),

167

169

168

170

JCprot& operator=(const JCprot& model)

169

171

{

172

AbstractParameterAliasable::operator=(model);

173

AbstractSubstitutionModel::operator=(model);

170

174

AbstractReversibleSubstitutionModel::operator=(model);

171

175

exp_ = model.exp_;

172

176

p_ = model.p_;

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