- g -

G2001() : bpp::G2001
GammaDiscreteRateDistribution() : bpp::GammaDiscreteRateDistribution
GaussianDiscreteRateDistribution() : bpp::GaussianDiscreteRateDistribution
gBGC() : bpp::gBGC
GCFrequencySet() : bpp::GCFrequencySet
GCPositionSubstitutionRegister() : bpp::GCPositionSubstitutionRegister
GCSubstitutionRegister() : bpp::GCSubstitutionRegister
GCSynonymousSubstitutionRegister() : bpp::GCSynonymousSubstitutionRegister
GeneralSubstitutionRegister() : bpp::GeneralSubstitutionRegister
generateAnalyticExpectedMapping() : bpp::StochasticMapping
generateDerivativeSumDepsForComputations() : bpp::ConfiguredParametrizable
generateExpectedMapping() : bpp::StochasticMapping
generateStochasticMapping() : bpp::StochasticMapping
generator() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
getAAFitness() : bpp::AbstractCodonAAFitnessSubstitutionModel
getAAModel() : bpp::AbstractCodonAARateSubstitutionModel
getAlignedLikelihoodCalculation() : bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodInterface, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodProduct, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood
getAlignedPhyloLikelihood() : bpp::AbstractAlignedPhyloLikelihoodSet, bpp::AlignedPhyloLikelihoodSetInterface, bpp::HmmPhyloAlphabet
getAllAncestralStates() : bpp::AncestralStateReconstruction, bpp::LegacyAncestralStateReconstruction, bpp::LegacyMarginalAncestralStateReconstruction, bpp::MarginalAncestralReconstruction
getAllelicAlphabet() : bpp::POMO
getAllLeavesNames() : bpp::ParametrizablePhyloTree, bpp::PhyloDAG, bpp::PhyloTree
getAllNodes() : bpp::Context
getAllNumbersOfSubstitutions() : bpp::DecompositionSubstitutionCount, bpp::LabelSubstitutionCount, bpp::LaplaceSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::SubstitutionCountInterface, bpp::UniformizationSubstitutionCount
getAllRewards() : bpp::DecompositionReward, bpp::Reward
getAlphabet() : bpp::AbstractFrequencySet, bpp::AbstractSequencePhyloLikelihood, bpp::AbstractStateMap, bpp::AbstractSubstitutionProcess, bpp::AbstractSubstitutionRegister, bpp::AbstractTransitionModel, bpp::AbstractTreeLikelihood, bpp::AbstractTreeLikelihoodData, bpp::AbstractWrappedModel, bpp::BranchModelInterface, bpp::FrequencySetInterface, bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::LikelihoodCalculationOnABranch, bpp::MarginalAncestralReconstruction, bpp::MarkovModulatedSubstitutionModel, bpp::MultiProcessSequencePhyloLikelihood, bpp::MutationPath, bpp::NonHomogeneousSequenceSimulator, bpp::OneProcessSequencePhyloLikelihood, bpp::RegisterRatesSubstitutionModel, bpp::Reward, bpp::SequenceSimulatorInterface, bpp::SimpleSubstitutionProcessSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SingleDataPhyloLikelihoodInterface, bpp::SingleProcessPhyloLikelihood, bpp::SiteSimulationResult, bpp::SiteSimulatorInterface, bpp::StateMapInterface, bpp::SubstitutionCountInterface, bpp::SubstitutionModelSet, bpp::SubstitutionProcessSequenceSimulator, bpp::SubstitutionRegisterInterface, bpp::TreeLikelihoodData, bpp::TreeLikelihoodInterface
getAlphabetIndex() : bpp::AbstractReward, bpp::Reward
getAlphabetStateAsChar() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractStateMap, bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::BranchModelInterface, bpp::MarkovModulatedSubstitutionModel, bpp::RegisterRatesSubstitutionModel, bpp::StateMapInterface, bpp::SubstitutionModelSet, bpp::TreeLikelihoodInterface
getAlphabetStateAsInt() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractStateMap, bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::BranchModelInterface, bpp::MarkovModulatedSubstitutionModel, bpp::RegisterRatesSubstitutionModel, bpp::StateMapInterface, bpp::SubstitutionModelSet, bpp::TreeLikelihoodInterface
getAlphabetStates() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractStateMap, bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::BranchModelInterface, bpp::MarkovModulatedSubstitutionModel, bpp::RegisterRatesSubstitutionModel, bpp::StateMapInterface, bpp::SubstitutionModelSet, bpp::TreeLikelihoodInterface
getAlphabetStatesFrequencies() : bpp::AbstractFrequencySet, bpp::FrequencySetInterface
getAncestors() : bpp::TreeTools
getAncestorsId() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools
getAncestralFrequencies() : bpp::TreeLikelihoodTools
getAncestralFrequencies_() : bpp::TreeLikelihoodTools
getAncestralSequenceForNode() : bpp::AncestralStateReconstruction, bpp::LegacyAncestralStateReconstruction, bpp::LegacyMarginalAncestralStateReconstruction, bpp::MarginalAncestralReconstruction
getAncestralSequences() : bpp::AncestralStateReconstruction, bpp::LegacyAncestralStateReconstruction, bpp::LegacyMarginalAncestralStateReconstruction, bpp::MarginalAncestralReconstruction
getAncestralState() : bpp::SiteSimulationResult
getAncestralStatesForNode() : bpp::AncestralStateReconstruction, bpp::LegacyAncestralStateReconstruction, bpp::LegacyMarginalAncestralStateReconstruction, bpp::MarginalAncestralReconstruction
getAngle() : bpp::Cursor
getArrayPosition() : bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::DRTreeParsimonyData, bpp::TreeLikelihoodData, bpp::TreeParsimonyDataInterface
getArrayPositions() : bpp::DRASRTreeLikelihoodData
getAssign() : bpp::AbstractCodonClusterAASubstitutionModel
getBackwardLikelihoodArray() : bpp::BackwardLikelihoodTree
getBackwardLikelihoodsAtEdgeForClass() : bpp::LikelihoodCalculationSingleProcess
getBackwardLikelihoodsAtNodeForClass() : bpp::LikelihoodCalculationSingleProcess
getBackwardLikelihoodTree() : bpp::LikelihoodCalculationSingleProcess
getBestPair() : bpp::AbstractAgglomerativeDistanceMethod, bpp::HierarchicalClustering, bpp::NeighborJoining, bpp::PGMA
getBestRootInSubtree_() : bpp::TreeTemplateTools
getBipartition() : bpp::BipartitionList
getBitBipartition() : bpp::BipartitionList
getBitBipartitionList() : bpp::BipartitionList
getBitsetsArray() : bpp::DRTreeParsimonyData, bpp::DRTreeParsimonyLeafData
getBitsetsArrayForNeighbor() : bpp::DRTreeParsimonyNodeData
getBootstrapValue() : bpp::Node, bpp::PhyloBranch
getBranch() : bpp::MappingInterface, bpp::PhyloBranchPException, bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping
getBranchCursor() : bpp::CladogramDrawBranchEvent, bpp::DrawBranchEvent, bpp::PhylogramDrawBranchEvent
getBranchesId() : bpp::Tree, bpp::TreeTemplate< N >
getBranchesWithModel() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::BranchedModelSet
getBranchId() : bpp::PhyloBranchException, bpp::PhyloBranchPException
getBranchLengthParameters() : bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::MultiProcessSequenceEvolution, bpp::NonHomogeneousSubstitutionProcess, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequenceEvolution, bpp::PhyloLikelihoodInterface, bpp::RateAcrossSitesSubstitutionProcess, bpp::SequenceEvolution, bpp::SimpleSubstitutionProcess, bpp::SingleProcessPhyloLikelihood, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getBranchLengths() : bpp::LegacyAbstractMapping, bpp::LegacyMappingInterface, bpp::ParametrizablePhyloTree, bpp::PhyloDAG, bpp::PhyloStatistics, bpp::PhyloTree, bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools, bpp::TreeTools
getBranchLengthsParameters() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::TreeLikelihoodInterface
getBranchModel() : bpp::PhylogeneticsApplicationTools
getBranchModels() : bpp::PhylogeneticsApplicationTools
getBranchProperties() : bpp::TreeTemplateTools
getBranchProperty() : bpp::Node, bpp::Tree, bpp::TreeTemplate< N >
getBranchPropertyNames() : bpp::Node, bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools
getBrLen() : bpp::ProcessEdge
getCategory() : bpp::CategorySubstitutionRegister
getCategoryFrom() : bpp::CategorySubstitutionRegister
getCategoryName() : bpp::CategorySubstitutionRegister
getCategoryTo() : bpp::CategorySubstitutionRegister
getClassProbabilities() : bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getClassWithMaxPostProbPerSite() : bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood
getCodonAlphabet() : bpp::CodonFrequencySetInterface, bpp::CodonFromIndependentFrequencySet, bpp::CodonFromUniqueFrequencySet, bpp::FixedCodonFrequencySet, bpp::FullCodonFrequencySet, bpp::FullPerAACodonFrequencySet, bpp::UserCodonFrequencySet
getCodonsMulRate() : bpp::AbstractCodonAAFitnessSubstitutionModel, bpp::AbstractCodonAARateSubstitutionModel, bpp::AbstractCodonBGCSubstitutionModel, bpp::AbstractCodonClusterAASubstitutionModel, bpp::AbstractCodonCpGSubstitutionModel, bpp::AbstractCodonDistanceSubstitutionModel, bpp::AbstractCodonFitnessSubstitutionModel, bpp::AbstractCodonFrequenciesSubstitutionModel, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::CoreCodonSubstitutionModelInterface, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::GY94, bpp::KCM, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::MG94, bpp::RE08Codon, bpp::SENCA, bpp::YN98
getCoeffs() : bpp::CombineDeltaShifted< T >
getCollection() : bpp::BppPhylogeneticsApplication, bpp::CollectionNodes, bpp::MultiProcessSequenceEvolution, bpp::SubstitutionProcessCollectionMember
getCollectionNodes() : bpp::PhyloLikelihoodContainer
getColumnNumber() : bpp::UserFrequencySet
getColumnRightEigenVectors() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
getColumnWeights() : bpp::CoalaCore
getConditionalLikelihoodsAtNodeForClass() : bpp::LikelihoodCalculationSingleProcess
getCondLikelihood() : bpp::CondLikelihood
getConfiguredParameter() : bpp::ConfiguredDistribution, bpp::ConfiguredFrequencySet, bpp::ConfiguredModel, bpp::ConfiguredSimplex, bpp::ConfiguredTransitionMatrix
getContext() : bpp::ForwardLikelihoodTree, bpp::HmmPhyloAlphabet, bpp::LikelihoodCalculation
getContext_() : bpp::LikelihoodCalculation
getCount() : bpp::ProbabilisticSubstitutionMapping
getCounts() : bpp::PhyloBranchMapping, bpp::ProbabilisticSubstitutionMapping
getCountsForBranchPerType() : bpp::SubstitutionMappingTools
getCountsForSitePerBranch() : bpp::SubstitutionMappingTools
getCountsForSitePerType() : bpp::SubstitutionMappingTools
getCountsPerBranch() : bpp::LegacySubstitutionMappingTools
getCountsPerBranchPerType() : bpp::SubstitutionMappingTools
getCountsPerSitePerBranch() : bpp::SubstitutionMappingTools
getCountsPerSitePerBranchPerType() : bpp::SubstitutionMappingTools
getCountsPerSitePerType() : bpp::SubstitutionMappingTools
getCountsPerTypePerBranch() : bpp::SubstitutionMappingTools
getCurrentTolerance() : bpp::PseudoNewtonOptimizer::PNStopCondition
getCursor() : bpp::DrawBranchEvent, bpp::DrawNodeEvent
getD2LikelihoodArray() : bpp::DRASDRTreeLikelihoodData, bpp::DRASDRTreeLikelihoodNodeData, bpp::DRASRTreeLikelihoodData, bpp::DRASRTreeLikelihoodNodeData
getD2LikelihoodArrayForNeighbor() : bpp::DRASDRTreeLikelihoodNodeData
getD2LikelihoodForASite() : bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getD2LikelihoodForASiteForARateClass() : bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getD2LogLikelihood() : bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getD2LogLikelihoodForASite() : bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getd2Pij_dt2() : bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::BinarySubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::F84, bpp::HKY85, bpp::InMixedSubstitutionModel, bpp::JCnuc, bpp::JCprot, bpp::K80, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RE08, bpp::T92, bpp::TN93, bpp::TransitionModelInterface, bpp::TwoParameterBinarySubstitutionModel, bpp::WordSubstitutionModel
getDAGEdgesIndexes() : bpp::ForwardLikelihoodTree, bpp::ProcessTree
getDAGNodesIndexes() : bpp::ForwardLikelihoodTree
getData() : bpp::DistanceEstimation, bpp::LikelihoodCalculationSingleProcess, bpp::MultiProcessSequencePhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::PhyloLikelihoodContainer, bpp::SingleDataPhyloLikelihoodInterface, bpp::SingleProcessPhyloLikelihood
getDataType() : bpp::BppOMultiTreeReaderFormat, bpp::BppOMultiTreeWriterFormat, bpp::BppOTreeReaderFormat, bpp::BppOTreeWriterFormat, bpp::IODAG, bpp::IoFrequencySet, bpp::IoSubstitutionModel, bpp::IOTree
getDepth() : bpp::TreeTemplateTools, bpp::TreeTools
getDepths() : bpp::TreeTemplateTools, bpp::TreeTools
getDerivableParameters() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::OnABranchPhyloLikelihood, bpp::PhyloLikelihoodInterface, bpp::SingleProcessPhyloLikelihood, bpp::TreeLikelihoodInterface
getDescription() : bpp::WordFromIndependentFrequencySet, bpp::WordFromUniqueFrequencySet
getDistanceBetweenAnyTwoNodes() : bpp::TreeTemplateTools, bpp::TreeTools
getDistanceMatrix() : bpp::TreeTemplateTools, bpp::TreeTools
getDistances() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::AbstractSubstitutionDistance, bpp::SubstitutionDistance
getDistanceToFather() : bpp::AwareNode, bpp::Node, bpp::Tree, bpp::TreeTemplate< N >
getDLikelihoodArray() : bpp::DRASDRTreeLikelihoodData, bpp::DRASDRTreeLikelihoodNodeData, bpp::DRASRTreeLikelihoodData, bpp::DRASRTreeLikelihoodNodeData
getDLikelihoodForASite() : bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getDLikelihoodForASiteForARateClass() : bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getDLogLikelihood() : bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getDLogLikelihoodForASite() : bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getdPij_dt() : bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::BinarySubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::F84, bpp::HKY85, bpp::InMixedSubstitutionModel, bpp::JCnuc, bpp::JCprot, bpp::K80, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RE08, bpp::T92, bpp::TN93, bpp::TransitionModelInterface, bpp::TwoParameterBinarySubstitutionModel, bpp::WordSubstitutionModel
getEdgesIds() : bpp::LikelihoodCalculationSingleProcess
getEigenValues() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
getElement() : bpp::AbstractIPhyloDAG, bpp::AbstractIPhyloTree, bpp::AbstractITree, bpp::ExtendedNewick, bpp::Newick, bpp::Nhx, bpp::TreeTemplateTools
getElementNames() : bpp::BipartitionList
getEmissionProbabilities() : bpp::HmmPhyloEmissionProbabilities
getEmpiricalMatrixFile() : bpp::Coala
getEventCounts() : bpp::MutationPath
getExch() : bpp::Coala
getFact_() : bpp::MultinomialFromTransitionModel
getFather() : bpp::AwareNode, bpp::Node, bpp::NodeTemplate< NodeInfos >
getFatherId() : bpp::Node, bpp::Tree, bpp::TreeTemplate< N >
getFinalState() : bpp::MutationPath
getFinalStates() : bpp::SiteSimulationResult
getFirstOrderDerivative() : bpp::AbstractPhyloLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::GlobalClockTreeLikelihoodFunctionWrapper, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getFirstOrderDerivativeVector() : bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood
getFormatDescription() : bpp::BppOFrequencySetFormat, bpp::BppOMultiTreeReaderFormat, bpp::BppOMultiTreeWriterFormat, bpp::BppOSubstitutionModelFormat, bpp::BppOTreeReaderFormat, bpp::BppOTreeWriterFormat, bpp::ExtendedNewick, bpp::Newick, bpp::NexusIOTree, bpp::Nhx
getFormatName() : bpp::BppOFrequencySetFormat, bpp::BppOMultiTreeReaderFormat, bpp::BppOMultiTreeWriterFormat, bpp::BppOSubstitutionModelFormat, bpp::BppOTreeReaderFormat, bpp::BppOTreeWriterFormat, bpp::ExtendedNewick, bpp::Newick, bpp::NexusIOTree, bpp::Nhx
getForwardCondLikelihood() : bpp::ForwardHmmLikelihood_DF
getForwardDCondLikelihood() : bpp::ForwardHmmDLikelihood_DF
getForwardLikelihoodArray() : bpp::ForwardLikelihoodTree
getForwardLikelihoodArrayAtRoot() : bpp::ForwardLikelihoodTree
getForwardLikelihoodsAtNodeForClass() : bpp::LikelihoodCalculationSingleProcess
getForwardLikelihoodTree() : bpp::LikelihoodCalculationSingleProcess
getFreq_() : bpp::AbstractFrequencySet
getFrequencies() : bpp::AbstractFrequencySet, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::CollectionNodes, bpp::FrequencySetInterface, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::TransitionModelInterface
getFrequencies_() : bpp::AbstractFrequencySet, bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::TransitionModelInterface
getFrequenciesNumbers() : bpp::SubstitutionProcessCollection
getFrequencySet() : bpp::PhylogeneticsApplicationTools, bpp::SubstitutionProcessCollection
getFrequencySetForCodons() : bpp::CodonFrequencySetInterface
getFunctionValue() : bpp::PseudoNewtonOptimizer
getGeneticCode() : bpp::AbstractCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::CodonFrequencySetInterface, bpp::CodonFromIndependentFrequencySet, bpp::CodonFromUniqueFrequencySet, bpp::CodonSameAARateSubstitutionModel, bpp::CodonSubstitutionModelInterface, bpp::FixedCodonFrequencySet, bpp::FullCodonFrequencySet, bpp::FullPerAACodonFrequencySet, bpp::GY94, bpp::KCM, bpp::MG94, bpp::RE08Codon, bpp::UserCodonFrequencySet, bpp::YN98
getGraphicDevice() : bpp::DrawBranchEvent, bpp::DrawNodeEvent, bpp::DrawTreeEvent
getHeight() : bpp::CladogramPlot, bpp::PhylogramPlot, bpp::PhyloTreeTools, bpp::TreeDrawing, bpp::TreeTemplateTools, bpp::TreeTools
getHeightParameters() : bpp::GlobalClockTreeLikelihoodFunctionWrapper
getHeights() : bpp::TreeTemplateTools, bpp::TreeTools
getHiddenStatesPosteriorProbabilities() : bpp::HmmLikelihood_DF
getHiddenStatesPosteriorProbabilitiesForASite() : bpp::HmmLikelihood_DF
getHmmEmissionProbabilities() : bpp::HmmLikelihood_DF
getHmmProcessAlphabet() : bpp::AutoCorrelationSequenceEvolution, bpp::HmmSequenceEvolution
getHmmStateAlphabet() : bpp::AlignedPhyloLikelihoodHmm, bpp::HmmEmissionProbabilities_Eigen, bpp::HmmPhyloEmissionProbabilities
getHmmTransitionMatrix() : bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodHmm, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AutoCorrelationSequenceEvolution, bpp::HmmLikelihood_DF, bpp::HmmProcessPhyloLikelihood, bpp::HmmSequenceEvolution
getHorizontalOrientation() : bpp::AbstractDendrogramPlot
getHPos() : bpp::Cursor
getHyperNode() : bpp::MixedSubstitutionModelSet, bpp::RNonHomogeneousMixedTreeLikelihood
getHyperNodeProbability() : bpp::MixedSubstitutionModelSet
getId() : bpp::AwareNode, bpp::Node, bpp::NodeNotFoundException, bpp::PhyloBranchNotFoundException, bpp::PhyloNodeNotFoundException
getIEigenValues() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
getIndependentParameters() : bpp::OneProcessSequenceEvolution
getIndexes() : bpp::PatternTools
getIndices() : bpp::SitePatterns
getInfos() : bpp::NodeTemplate< NodeInfos >
getInitialState() : bpp::MutationPath
getInitValue() : bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::BranchModelInterface, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RE08, bpp::TransitionFromTransitionModel
getInnerNodes() : bpp::TreeTemplate< N >, bpp::TreeTemplateTools
getInnerNodesId() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools
getINode() : bpp::DrawIBranchEvent, bpp::DrawINodeEvent
getLastCommonAncestor() : bpp::TreeTools
getLeadModel() : bpp::ModelPath
getLeafData() : bpp::DRASDRTreeLikelihoodData
getLeafId() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools, bpp::TreeTools
getLeafLikelihoods() : bpp::DRASDRTreeLikelihoodData
getLeafNode() : bpp::AbstractAgglomerativeDistanceMethod, bpp::HierarchicalClustering, bpp::PGMA
getLeaveNames() : bpp::SiteSimulationResult
getLeaves() : bpp::TreeTemplate< N >, bpp::TreeTemplateTools
getLeavesId() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools, bpp::TreeTools
getLeavesNames() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools
getLeftMostPredecessor() : bpp::PostOrderTreeIterator
getLength() : bpp::AbstractWordFrequencySet, bpp::PhyloBranch, bpp::PhyloBranchParam, bpp::WordFrequencySetInterface, bpp::WordFromIndependentFrequencySet, bpp::WordFromUniqueFrequencySet
getLikelihood() : bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::TreeLikelihoodInterface
getLikelihoodArray() : bpp::DRASDRTreeLikelihoodData, bpp::DRASDRTreeLikelihoodLeafData, bpp::DRASRTreeLikelihoodData, bpp::DRASRTreeLikelihoodNodeData
getLikelihoodArrayForNeighbor() : bpp::DRASDRTreeLikelihoodNodeData
getLikelihoodArrays() : bpp::DRASDRTreeLikelihoodData, bpp::DRASDRTreeLikelihoodNodeData
getLikelihoodCalculation() : bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodProduct, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::PhyloLikelihoodFormula, bpp::PhyloLikelihoodInterface, bpp::SingleProcessPhyloLikelihood
getLikelihoodCalculationForAProcess() : bpp::MultiProcessSequencePhyloLikelihood
getLikelihoodCalculationForASite() : bpp::PartitionProcessPhyloLikelihood
getLikelihoodCalculationOnABranch() : bpp::OnABranchPhyloLikelihood
getLikelihoodCalculationSingleProcess() : bpp::OneProcessSequencePhyloLikelihood, bpp::OneProcessSequenceSubstitutionMapping, bpp::SingleProcessPhyloLikelihood, bpp::SingleProcessSubstitutionMapping
getLikelihoodForASite() : bpp::AbstractAlignedPhyloLikelihood, bpp::AlignedLikelihoodCalculation, bpp::AlignedPhyloLikelihoodInterface, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::HmmLikelihood_DF, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::TreeLikelihoodInterface
getLikelihoodForASiteForAPhyloLikelihood() : bpp::AbstractAlignedPhyloLikelihoodSet, bpp::AlignedPhyloLikelihoodSetInterface
getLikelihoodForASiteForAProcess() : bpp::MultiProcessSequencePhyloLikelihood
getLikelihoodForASiteForARateClass() : bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getLikelihoodForASiteForARateClassForAState() : bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getLikelihoodForASiteForAState() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::TreeLikelihoodInterface
getLikelihoodNode() : bpp::AbstractPhyloLikelihood, bpp::LikelihoodCalculation, bpp::PhyloLikelihoodInterface
getLikelihoodNode_() : bpp::LikelihoodCalculation
getLikelihoodPerSite() : bpp::AbstractAlignedPhyloLikelihood, bpp::AbstractTreeLikelihood, bpp::AlignedLikelihoodCalculation, bpp::AlignedPhyloLikelihoodInterface, bpp::TreeLikelihoodInterface
getLikelihoodPerSitePerClass() : bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood
getLikelihoodPerSitePerProcess() : bpp::MultiProcessSequencePhyloLikelihood
getLikelihoodPerSitePerRateClass() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface
getLikelihoodPerSitePerRateClassPerState() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface
getLikelihoodPerSitePerState() : bpp::AbstractTreeLikelihood, bpp::TreeLikelihoodInterface
getLikelihoods() : bpp::PairedSiteLikelihoods
getLikelihoodsAtNode() : bpp::LikelihoodCalculationSingleProcess
getLikelihoodsAtNodeForClass() : bpp::LikelihoodCalculationSingleProcess
getLogLikelihood() : bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::PhyloLikelihoodInterface, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::TreeLikelihoodInterface
getLogLikelihoodForASite() : bpp::AbstractAlignedPhyloLikelihood, bpp::AlignedLikelihoodCalculation, bpp::AlignedPhyloLikelihoodInterface, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::TreeLikelihoodInterface
getLogLikelihoodForASiteForAPhyloLikelihood() : bpp::AbstractAlignedPhyloLikelihoodSet, bpp::AlignedPhyloLikelihoodSetInterface
getLogLikelihoodForASiteForARateClass() : bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getLogLikelihoodForASiteForARateClassForAState() : bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getLogLikelihoodForASiteForAState() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::TreeLikelihoodInterface
getLogLikelihoodPerSite() : bpp::AbstractTreeLikelihood, bpp::TreeLikelihoodInterface
getLogLikelihoodPerSitePerRateClass() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface
getLogLikelihoodPerSitePerRateClassPerState() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface
getLogLikelihoodPerSitePerState() : bpp::AbstractTreeLikelihood, bpp::TreeLikelihoodInterface
getMatrix() : bpp::DistanceEstimation
getMaxId() : bpp::TreeTools
getMaximumBranchLength() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::ParametrizablePhyloTree
getMessage() : bpp::TopologyChangeEvent
getMethod() : bpp::FullCodonFrequencySet, bpp::FullFrequencySet, bpp::FullPerAACodonFrequencySet
getMgmtStopCodon() : bpp::CodonFromIndependentFrequencySet, bpp::CodonFromUniqueFrequencySet
getMinimumBranchLength() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::ParametrizablePhyloTree
getModel() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractSinglePhyloSubstitutionMapping, bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription, bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription, bpp::BranchedModelSet, bpp::CollectionNodes, bpp::FromModelFrequencySet, bpp::HomogeneousTreeLikelihood, bpp::LikelihoodCalculationOnABranch, bpp::ModelList, bpp::NonHomogeneousSubstitutionProcess, bpp::PhyloSubstitutionMapping, bpp::ProcessComputationEdge, bpp::ProcessEdge, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SitePartitionHomogeneousTreeLikelihood, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface, bpp::TreeLikelihoodInterface::ConstBranchModelDescription, bpp::TreeLikelihoodInterface::ConstSiteModelDescription
getModelCollection() : bpp::CollectionNodes
getModelForBranch() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::BranchedModelSet
getModelForNode() : bpp::AbstractNonHomogeneousTreeLikelihood, bpp::NonHomogeneousSubstitutionProcess, bpp::NonHomogeneousTreeLikelihood, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getModelForSite() : bpp::HomogeneousTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, bpp::SitePartitionHomogeneousTreeLikelihood, bpp::TreeLikelihoodInterface
getModelIndex() : bpp::SubstitutionProcessCollection
getModelIndexForNode() : bpp::SubstitutionModelSet
getModelNames() : bpp::PairedSiteLikelihoods
getModelNumber() : bpp::ProcessComputationEdge
getModelNumberForNode() : bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getModelNumbers() : bpp::BranchedModelSet, bpp::NonHomogeneousSubstitutionProcess, bpp::OneProcessSequenceSubstitutionMapping, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SingleProcessSubstitutionMapping, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getModelParameters() : bpp::SubstitutionModelSet
getModelPath() : bpp::ModelScenario
getModelPaths() : bpp::PhylogeneticsApplicationTools
getModels() : bpp::ModelPath, bpp::ModelScenario
getModelScenario() : bpp::AbstractAutonomousSubstitutionProcess, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getModelScenarioNumber() : bpp::SubstitutionProcessCollectionMember
getModelScenarios() : bpp::PhylogeneticsApplicationTools
getModelStates() : bpp::AbstractStateMap, bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::BranchModelInterface, bpp::MarkovModulatedSubstitutionModel, bpp::RegisterRatesSubstitutionModel, bpp::StateMapInterface, bpp::SubstitutionModelSet
getMPNUId() : bpp::TreeTools
getMultipleDistributionDefaultInstance() : bpp::PhylogeneticsApplicationTools
getMutationPath() : bpp::SiteSimulationResult
getN() : bpp::CombineDeltaShifted< T >, bpp::ShiftDelta< T >, bpp::ShiftParameter
getName() : bpp::AbstractFrequencySet, bpp::AbstractSubstitutionRegister, bpp::AbstractWrappedModel, bpp::AnonymousSubstitutionModel, bpp::BinarySubstitutionModel, bpp::BioNJ, bpp::BranchModelInterface, bpp::CladogramPlot, bpp::Coala, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::D1WalkSubstitutionModel, bpp::DFP07, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::DistanceMethodInterface, bpp::DSO78, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::F84, bpp::FrequencySetInterface, bpp::FromMixtureSubstitutionModel, bpp::G2001, bpp::gBGC, bpp::GTR, bpp::GY94, bpp::HierarchicalClustering, bpp::HKY85, bpp::InMixedSubstitutionModel, bpp::JCnuc, bpp::JCprot, bpp::JTT92, bpp::K80, bpp::KCM, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerWordSubstitutionModel, bpp::L95, bpp::LG08, bpp::LG10_EX_EHO::EmbeddedModel, bpp::LG10_EX_EHO, bpp::LGL08_CAT::EmbeddedModel, bpp::LGL08_CAT, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_EHO, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EX2, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EX3, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_UL2, bpp::LLG08_UL3::EmbeddedModel, bpp::LLG08_UL3, bpp::MG94, bpp::MixtureOfATransitionModel, bpp::MixtureOfTransitionModels, bpp::MultinomialFromTransitionModel, bpp::NeighborJoining, bpp::Node, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::PGMA, bpp::PhyloDAG, bpp::PhylogramPlot, bpp::PhyloNode, bpp::PhyloTree, bpp::POMO, bpp::RE08, bpp::RegisterRatesSubstitutionModel, bpp::RELAX, bpp::RN95, bpp::RN95s, bpp::SENCA, bpp::Sequence_DF, bpp::SSR, bpp::SubstitutionRegisterInterface, bpp::T92, bpp::TN93, bpp::TransitionFromTransitionModel, bpp::Tree, bpp::TreeDrawing, bpp::TreeTemplate< N >, bpp::TripletSubstitutionModel, bpp::TS98, bpp::TwoParameterBinarySubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::WordSubstitutionModel, bpp::YN98, bpp::YNGP_M10, bpp::YNGP_M1, bpp::YNGP_M2, bpp::YNGP_M3, bpp::YNGP_M7, bpp::YNGP_M8, bpp::YNGP_M9, bpp::YpR_Gen, bpp::YpR_Sym
getNbAlleles() : bpp::POMO
getNBeta() : bpp::YNGP_M10, bpp::YNGP_M9
getNbrOfAxes() : bpp::CoalaCore
getNData() : bpp::AbstractSingleDataPhyloLikelihood, bpp::SingleDataPhyloLikelihoodInterface
getNeighbors() : bpp::Node, bpp::NodeTemplate< NodeInfos >
getNestedPrefix() : bpp::YpR
getNewBranchIterator() : bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription, bpp::TreeLikelihoodInterface::ConstSiteModelDescription
getNewBranchModelIterator() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::TreeLikelihoodInterface
getNewSiteIterator() : bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription, bpp::TreeLikelihoodInterface::ConstBranchModelDescription
getNewSiteModelIterator() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::TreeLikelihoodInterface
getNextId() : bpp::Tree, bpp::TreeTemplate< N >
getNGamma() : bpp::YNGP_M10, bpp::YNGP_M9
getNMod() : bpp::ProcessEdge
getNModel() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::MixedTransitionModelInterface
getNode() : bpp::DRASDRTreeLikelihoodLeafData, bpp::DRASDRTreeLikelihoodNodeData, bpp::DRASRTreeLikelihoodNodeData, bpp::DRTreeParsimonyLeafData, bpp::DRTreeParsimonyNodeData, bpp::LegacyAbstractMapping, bpp::MixedSubstitutionModelSet::HyperNode, bpp::NodePException, bpp::PhyloNodePException, bpp::TreeLikelihoodNodeData, bpp::TreeParsimonyNodeDataInterface, bpp::TreeTemplate< N >
getNodeAt() : bpp::AbstractTreeDrawing, bpp::TreeDrawing
getNodeData() : bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::TreeLikelihoodData
getNodeDepths() : bpp::PhyloStatistics
getNodeHeights() : bpp::PhyloStatistics
getNodeId() : bpp::DrawBranchEvent, bpp::DrawNodeEvent, bpp::NodeException, bpp::NodePException, bpp::PhyloNodeException, bpp::PhyloNodePException
getNodeIds() : bpp::PhyloStatistics
getNodeIndex() : bpp::LegacyAbstractMapping, bpp::LegacyMappingInterface
getNodeName() : bpp::Tree, bpp::TreeTemplate< N >
getNodeNumberOfSons() : bpp::PhyloStatistics
getNodeParameters() : bpp::SubstitutionModelSet
getNodePosition() : bpp::AbstractTreeDrawing, bpp::TreeDrawing
getNodeProperties() : bpp::TreeTemplateTools
getNodeProperty() : bpp::Node, bpp::Tree, bpp::TreeTemplate< N >
getNodePropertyNames() : bpp::Node, bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools
getNodes() : bpp::TreeTemplate< N >, bpp::TreeTemplateTools
getNodesId() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools, bpp::TreeTools
getNodesIds() : bpp::LikelihoodCalculationSingleProcess
getNodeState() : bpp::DRTreeParsimonyScore, bpp::StochasticMapping
getNodesWithModel() : bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getNodesWithParameter() : bpp::SubstitutionModelSet
getNonDerivableParameters() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::AbstractSubstitutionProcess, bpp::AutoCorrelationSequenceEvolution, bpp::MixtureSequenceEvolution, bpp::MultiProcessSequenceEvolution, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequenceEvolution, bpp::PhyloLikelihoodInterface, bpp::SequenceEvolution, bpp::SingleProcessPhyloLikelihood, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface, bpp::TreeLikelihoodInterface
getNormalizationsPerBranch() : bpp::LegacySubstitutionMappingTools
getNormalizedCountsPerBranch() : bpp::LegacySubstitutionMappingTools
getNormForSite() : bpp::SubstitutionMappingTools
getNProbability() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::MixedTransitionModelInterface
getNRate() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::MixedTransitionModelInterface
getNucleicAlphabet() : bpp::AbstractNucleotideSubstitutionModel, bpp::AbstractReversibleNucleotideSubstitutionModel, bpp::FixedNucleotideFrequencySet, bpp::FullNucleotideFrequencySet, bpp::GCFrequencySet, bpp::NucleotideFrequencySetInterface, bpp::NucleotideSubstitutionModelInterface, bpp::RE08Nucleotide, bpp::UserNucleotideFrequencySet
getNumberOfAncestors() : bpp::PhyloStatistics
getNumberOfBipartitions() : bpp::BipartitionList
getNumberOfBranches() : bpp::LegacyAbstractMapping, bpp::LegacyMappingInterface, bpp::MappingInterface, bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping, bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools
getNumberOfCategories() : bpp::CategorySubstitutionRegister, bpp::LGL08_CAT
getNumberOfClasses() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::AbstractSubstitutionProcess, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface, bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::LikelihoodCalculationSingleProcess, bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::SubstitutionProcessInterface
getNumberOfDistinctSites() : bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::DRTreeParsimonyData, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess, bpp::OnABranchPhyloLikelihood, bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping, bpp::SingleProcessPhyloLikelihood, bpp::TreeLikelihoodData
getNumberOfElements() : bpp::BipartitionList
getNumberOfEvents() : bpp::MutationPath
getNumberOfFrequencies() : bpp::AbstractFrequencySet, bpp::FrequencySetInterface
getNumberOfHyperNodes() : bpp::MixedSubstitutionModelSet
getNumberOfIndependentParameters() : bpp::LegacyOptimizationTools::ScaleFunction
getNumberOfLeaves() : bpp::PhyloStatistics, bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools, bpp::TreeTools
getNumberOfModelPaths() : bpp::ModelScenario
getNumberOfModels() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractWordSubstitutionModel, bpp::BranchedModelSet, bpp::CodonAdHocSubstitutionModel, bpp::MixedTransitionModelInterface, bpp::NonHomogeneousSubstitutionProcess, bpp::OneProcessSequenceSubstitutionMapping, bpp::PairedSiteLikelihoods, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SingleProcessSubstitutionMapping, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getNumberOfModelStates() : bpp::AbstractStateMap, bpp::StateMapInterface
getNumberOfNodes() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools
getNumberOfParameters() : bpp::LegacyOptimizationTools::ScaleFunction
getNumberOfPartitions() : bpp::SitePartition, bpp::TrivialSitePartition
getNumberOfPatternsForPartition() : bpp::SitePartition, bpp::TrivialSitePartition
getNumberOfPositions() : bpp::HmmEmissionProbabilities_Eigen, bpp::HmmPhyloEmissionProbabilities
getNumberOfProcesses() : bpp::SubstitutionProcessCollectionMember
getNumberOfSites() : bpp::AbstractAlignedPhyloLikelihood, bpp::AbstractMapping, bpp::AbstractTreeLikelihood, bpp::AlignedPhyloLikelihoodInterface, bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::DRTreeParsimonyData, bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::HmmPhyloAlphabet, bpp::HmmPhyloEmissionProbabilities, bpp::LegacyAbstractMapping, bpp::LegacyMappingInterface, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess, bpp::MappingInterface, bpp::OnABranchPhyloLikelihood, bpp::PairedSiteLikelihoods, bpp::PartitionProcessPhyloLikelihood, bpp::PartitionSequenceEvolution, bpp::PhyloBranchMapping, bpp::PhyloBranchReward, bpp::SingleProcessPhyloLikelihood, bpp::SubstitutionProcessSequenceSimulator, bpp::TreeLikelihoodData, bpp::TreeLikelihoodInterface
getNumberOfSons() : bpp::AwareNode, bpp::Node
getNumberOfStates() : bpp::AbstractDFPSubstitutionModel, bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractSingleDataPhyloLikelihood, bpp::AbstractSubstitutionProcess, bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::BinarySubstitutionModel, bpp::BranchModelInterface, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData, bpp::DRTreeParsimonyData, bpp::gBGC, bpp::HmmPhyloAlphabet, bpp::HmmPhyloEmissionProbabilities, bpp::HmmProcessAlphabet, bpp::MarkovModulatedSubstitutionModel, bpp::RE08Codon, bpp::RE08Nucleotide, bpp::RE08Protein, bpp::RegisterRatesSubstitutionModel, bpp::Reward, bpp::SingleDataPhyloLikelihoodInterface, bpp::SubstitutionCountInterface, bpp::SubstitutionModelSet, bpp::SubstitutionProcessInterface, bpp::TreeLikelihoodData, bpp::TreeLikelihoodInterface, bpp::TwoParameterBinarySubstitutionModel, bpp::YpR
getNumberOfSubstitutionProcess() : bpp::MultiProcessSequenceEvolution, bpp::MultiProcessSequencePhyloLikelihood, bpp::SubstitutionProcessCollection
getNumberOfSubstitutions() : bpp::DecompositionSubstitutionCount, bpp::LabelSubstitutionCount, bpp::LaplaceSubstitutionCount, bpp::LegacyProbabilisticSubstitutionMapping, bpp::NaiveSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::SubstitutionCountInterface, bpp::UniformizationSubstitutionCount
getNumberOfSubstitutionsPerType() : bpp::DecompositionSubstitutionCount, bpp::LabelSubstitutionCount, bpp::LaplaceSubstitutionCount, bpp::NaiveSubstitutionCount, bpp::OneJumpSubstitutionCount, bpp::SubstitutionCountInterface, bpp::UniformizationSubstitutionCount
getNumberOfSubstitutionTypes() : bpp::AbstractSubstitutionMapping, bpp::CategorySubstitutionRegister, bpp::CompleteSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::GeneralSubstitutionRegister, bpp::KrKcSubstitutionRegister, bpp::LegacyProbabilisticSubstitutionMapping, bpp::LegacySubstitutionMappingInterface, bpp::SubstitutionCountInterface, bpp::SubstitutionMapping, bpp::SubstitutionRegisterInterface, bpp::SWSubstitutionRegister, bpp::TotalSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::VectorOfSubstitutionRegisters
getNumberOfTypes() : bpp::PhyloBranchMapping
getNumbersOfPhyloLikelihoods() : bpp::AbstractPhyloLikelihoodSet, bpp::PhyloLikelihoodContainer, bpp::PhyloLikelihoodSetInterface
getOptimizer() : bpp::DistanceEstimation
getParameters() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::LegacyOptimizationTools::ScaleFunction, bpp::OneProcessSequenceEvolution, bpp::PhyloSubstitutionMapping, bpp::ProcessTree
getParameters_() : bpp::LegacyOptimizationTools::ScaleFunction
getParameterValue() : bpp::LegacyOptimizationTools::ScaleFunction
getParametrizablePhyloTree() : bpp::AbstractAutonomousSubstitutionProcess, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getParCondLik() : bpp::ForwardHmmLikelihood_DF
getParDCondLik() : bpp::ForwardHmmDLikelihood_DF
getParentNode() : bpp::AbstractAgglomerativeDistanceMethod, bpp::HierarchicalClustering, bpp::PGMA
getParNameFromPmodel() : bpp::AbstractBiblioTransitionModel
getPartitionSequenceEvolution() : bpp::PartitionProcessPhyloLikelihood
getPartitionSize() : bpp::BipartitionList
getPath() : bpp::UserFrequencySet, bpp::UserProteinSubstitutionModel
getPathBetweenAnyTwoNodes() : bpp::TreeTemplateTools, bpp::TreeTools
getPathNode() : bpp::ModelPath
getPatterns() : bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping
getPhyloContainer() : bpp::AbstractPhyloLikelihoodSet, bpp::PhyloLikelihoodSetInterface
getPhyloLikelihood() : bpp::AbstractPhyloLikelihoodSet, bpp::PhyloLikelihoodContainer, bpp::PhyloLikelihoodSetInterface
getPhyloLikelihoodContainer() : bpp::PhylogeneticsApplicationTools
getPhyloLikelihoodForASite() : bpp::PartitionProcessPhyloLikelihood
getPhyloLikelihoods() : bpp::BppPhylogeneticsApplication
getPhyloNode() : bpp::PhyloDAG, bpp::PhyloTree
getPhyloProb() : bpp::AlignedPhyloLikelihoodMixture
getPhyloProbabilities() : bpp::AlignedPhyloLikelihoodMixture
getPhyloTrees() : bpp::PhylogeneticsApplicationTools
getPhyloTreesMap() : bpp::BppPhylogeneticsApplication
getPij_t() : bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::BinarySubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::F84, bpp::HKY85, bpp::InMixedSubstitutionModel, bpp::JCnuc, bpp::JCprot, bpp::K80, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RE08, bpp::T92, bpp::TN93, bpp::TransitionModelInterface, bpp::TwoParameterBinarySubstitutionModel, bpp::WordSubstitutionModel
getPmodelParName() : bpp::AbstractBiblioTransitionModel
getPosition() : bpp::TreeDrawingNodeInfo
getPosteriorProbabilitiesForASitePerAligned() : bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodHmm
getPosteriorProbabilitiesForSitePerClass() : bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood
getPosteriorProbabilitiesPerRate() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface
getPosteriorProbabilitiesPerSitePerAligned() : bpp::AlignedPhyloLikelihoodAutoCorrelation, bpp::AlignedPhyloLikelihoodHmm
getPosteriorProbabilitiesPerSitePerClass() : bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood
getPosteriorProbabilitiesPerSitePerProcess() : bpp::AutoCorrelationProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::MultiProcessSequencePhyloLikelihood
getPosteriorProbabilitiesPerStatePerRate() : bpp::DRTreeLikelihoodTools
getPosteriorRateDistribution() : bpp::RASTools
getPosteriorRatePerSite() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface, bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood
getPosteriorStateFrequencies() : bpp::DRTreeLikelihoodTools, bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood
getProba() : bpp::ProcessEdge
getProbaAtEdge() : bpp::ProbabilityDAG
getProbaAtNode() : bpp::ProbabilityDAG
getProbabilities() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::MixedTransitionModelInterface
getProbability() : bpp::MixedSubstitutionModelSet::HyperNode, bpp::ModelPath, bpp::RNonHomogeneousMixedTreeLikelihood
getProbabilityForModel() : bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getProcess() : bpp::DistanceEstimation
getProcesses() : bpp::BppPhylogeneticsApplication
getProcessNumbersPerSite() : bpp::PartitionSequenceEvolution
getProcessSiteRelations() : bpp::PartitionProcessPhyloLikelihood
getProcessTree() : bpp::CollectionNodes, bpp::ForwardLikelihoodTree
getProperty() : bpp::PhyloBranch, bpp::PhyloNode
getPropertyName() : bpp::PhyloBranchPropertyNotFoundException, bpp::PhyloNodePropertyNotFoundException, bpp::PropertyNotFoundException
getPropertyNames() : bpp::PhyloBranch, bpp::PhyloNode
getProportion() : bpp::LG10_EX_EHO::EmbeddedModel, bpp::LGL08_CAT::EmbeddedModel, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_UL3::EmbeddedModel
getProteicAlphabet() : bpp::AbstractProteinSubstitutionModel, bpp::AbstractReversibleProteinSubstitutionModel, bpp::FixedProteinFrequencySet, bpp::FullProteinFrequencySet, bpp::MvaFrequencySet, bpp::ProteinFrequencySetInterface, bpp::ProteinSubstitutionModelInterface, bpp::RE08Protein, bpp::UserProteinFrequencySet
getRadius() : bpp::TreeTemplateTools
getRandomTree() : bpp::TreeTemplateTools
getRate() : bpp::AbstractTotallyWrappedTransitionModel, bpp::AbstractTransitionModel, bpp::BranchModelInterface, bpp::G2001, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RASiteSimulationResult, bpp::RegisterRatesSubstitutionModel, bpp::TransitionFromTransitionModel, bpp::TS98
getRateClassWithMaxPostProbPerSite() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface
getRateDistribution() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::CollectionNodes, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface, bpp::NonHomogeneousSequenceSimulator, bpp::NonHomogeneousSubstitutionProcess, bpp::PhylogeneticsApplicationTools, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getRateDistributionNumber() : bpp::SubstitutionProcessCollectionMember
getRateDistributionNumbers() : bpp::SubstitutionProcessCollection
getRateDistributionParameters() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface, bpp::MultiProcessSequenceEvolution, bpp::NonHomogeneousSubstitutionProcess, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequenceEvolution, bpp::PhyloLikelihoodInterface, bpp::RateAcrossSitesSubstitutionProcess, bpp::SequenceEvolution, bpp::SimpleSubstitutionProcess, bpp::SingleProcessPhyloLikelihood, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getRateDistributions() : bpp::PhylogeneticsApplicationTools
getRateForModel() : bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getRateWithMaxPostProbPerSite() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface
getRegisterName() : bpp::OneChangeRegisterTransitionModel, bpp::RegisterRatesSubstitutionModel
getRegisterNumbers() : bpp::OneChangeRegisterTransitionModel
getRelativeCountsPerBranch() : bpp::LegacySubstitutionMappingTools
getRemainingNeighbors() : bpp::TreeTemplateTools
getReward() : bpp::DecompositionReward, bpp::LegacyProbabilisticRewardMapping, bpp::ProbabilisticRewardMapping, bpp::Reward
getRewards() : bpp::PhyloBranchReward
getRootArrayPosition() : bpp::AbstractTreeLikelihoodData, bpp::AbstractTreeParsimonyData, bpp::DRASRTreeLikelihoodData, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess, bpp::TreeLikelihoodData, bpp::TreeParsimonyDataInterface
getRootArrayPositions() : bpp::AbstractTreeLikelihoodData, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess
getRootBitset() : bpp::DRTreeParsimonyData
getRootBitsets() : bpp::DRTreeParsimonyData
getRootFreqs() : bpp::LikelihoodCalculationSingleProcess
getRootFrequencies() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::SimpleSubstitutionProcess, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface, bpp::TreeLikelihoodInterface
getRootFrequenciesNumber() : bpp::SubstitutionProcessCollectionMember
getRootFrequenciesParameters() : bpp::AbstractAutonomousSubstitutionProcess, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::MultiProcessSequenceEvolution, bpp::NonHomogeneousTreeLikelihood, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequenceEvolution, bpp::PhyloLikelihoodInterface, bpp::SequenceEvolution, bpp::SingleProcessPhyloLikelihood, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getRootFrequencySet() : bpp::AbstractAutonomousSubstitutionProcess, bpp::PhylogeneticsApplicationTools, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
getRootFrequencySets() : bpp::PhylogeneticsApplicationTools
getRootId() : bpp::Tree, bpp::TreeTemplate< N >
getRootLikelihoodArray() : bpp::DRASDRTreeLikelihoodData
getRootNode() : bpp::TreeTemplate< N >
getRootPatternLinks() : bpp::LikelihoodCalculationSingleProcess
getRootRateSiteLikelihoodArray() : bpp::DRASDRTreeLikelihoodData
getRootScore() : bpp::DRTreeParsimonyData
getRootScores() : bpp::DRTreeParsimonyData
getRootSiteLikelihoodArray() : bpp::DRASDRTreeLikelihoodData
getRootWeights() : bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess
getRowCoordinates() : bpp::CoalaCore
getRowLeftEigenVectors() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
getScale() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
getScenarioNumbers() : bpp::SubstitutionProcessCollection
getScore() : bpp::DRTreeParsimonyScore, bpp::TreeParsimonyScoreInterface
getScoreForSite() : bpp::DRTreeParsimonyScore, bpp::TreeParsimonyScoreInterface
getScorePerSite() : bpp::AbstractTreeParsimonyScore, bpp::TreeParsimonyScoreInterface
getScoresArray() : bpp::DRTreeParsimonyData
getScoresArrayForNeighbor() : bpp::DRTreeParsimonyNodeData
getSearchableObject() : bpp::NNITopologySearch
getSecondOrderDerivableFunction() : bpp::PseudoNewtonOptimizer
getSecondOrderDerivative() : bpp::AbstractPhyloLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::GlobalClockTreeLikelihoodFunctionWrapper, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
getSecondOrderDerivativeVector() : bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::SingleProcessPhyloLikelihood
getSequenceEvolution() : bpp::AbstractSequencePhyloLikelihood, bpp::SequencePhyloLikelihoodInterface
getSequenceEvolutionNumber() : bpp::AbstractSequencePhyloLikelihood, bpp::SequencePhyloLikelihoodInterface
getSequenceEvolutions() : bpp::PhylogeneticsApplicationTools
getSequenceNames() : bpp::GivenDataSubstitutionProcessSequenceSimulator, bpp::NonHomogeneousSequenceSimulator, bpp::SequenceSimulatorInterface, bpp::SimpleSubstitutionProcessSequenceSimulator, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SiteSimulatorInterface, bpp::SubstitutionProcessSequenceSimulator
getSequenceSubset() : bpp::PatternTools
getShrunkData() : bpp::DRASDRTreeLikelihoodData, bpp::LikelihoodCalculationSingleProcess, bpp::SingleProcessPhyloLikelihood
getSite() : bpp::SiteSimulationResult
getSiteCount() : bpp::PhyloBranchMapping
getSiteIndex() : bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::TreeLikelihoodInterface
getSiteLikelihoods() : bpp::AlignedLikelihoodCalculation
getSiteLikelihoods_() : bpp::LikelihoodCalculationOnABranch
getSiteLikelihoodsForAClass() : bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess
getSiteLikelihoodsForAllClasses() : bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess
getSiteLikelihoodsTree_() : bpp::LikelihoodCalculationSingleProcess
getSitePosition() : bpp::AbstractMapping, bpp::LegacyAbstractMapping, bpp::LegacyMappingInterface, bpp::MappingInterface
getSiteReward() : bpp::PhyloBranchReward
getSites() : bpp::SitePatterns
getSiteTypeCount() : bpp::PhyloBranchMapping
getSize() : bpp::PhyloLikelihoodContainer
getSizeFromVector() : bpp::AbstractWordFrequencySet, bpp::WordFrequencySetInterface
getSon() : bpp::AwareNode, bpp::Node, bpp::NodeTemplate< NodeInfos >
getSonPosition() : bpp::AwareNode, bpp::Node
getSons() : bpp::AwareNode, bpp::Node
getSonsId() : bpp::AwareNode, bpp::Node, bpp::Tree, bpp::TreeTemplate< N >
getSpeciesIndex() : bpp::ProcessComputationEdge, bpp::ProcessComputationNode, bpp::ProcessEdge
getState() : bpp::HmmPhyloAlphabet, bpp::HmmProcessAlphabet
getStateDescription() : bpp::CanonicalStateMap, bpp::MarkovModulatedStateMap, bpp::StateMapInterface
getStateMap() : bpp::AbstractFrequencySet, bpp::AbstractSubstitutionRegister, bpp::AbstractTransitionModel, bpp::AbstractTreeParsimonyScore, bpp::AbstractWrappedModel, bpp::BranchModelInterface, bpp::FrequencySetInterface, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess, bpp::MarkovModulatedSubstitutionModel, bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess, bpp::RegisterRatesSubstitutionModel, bpp::SequenceEvolution, bpp::SimpleSubstitutionProcess, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface, bpp::SubstitutionRegisterInterface, bpp::TreeParsimonyScoreInterface
getStatesFrequencySet() : bpp::MarkovModulatedFrequencySet
getSubModelNumber() : bpp::InMixedSubstitutionModel
getSubmodelNumbers() : bpp::AbstractBiblioMixedTransitionModel, bpp::MixedTransitionModelInterface, bpp::MixtureOfATransitionModel, bpp::MixtureOfTransitionModels
getSubProcessProb() : bpp::MixtureProcessPhyloLikelihood, bpp::MixtureSequenceEvolution
getSubProcessProbabilities() : bpp::MixtureSequenceEvolution
getSubstitutionCount() : bpp::PhylogeneticsApplicationTools, bpp::SiteSimulationResult
getSubstitutionModel() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractMutationProcess, bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription, bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription, bpp::HomogeneousTreeLikelihood, bpp::MutationProcess, bpp::PhylogeneticsApplicationTools, bpp::SubstitutionModelSet, bpp::TreeLikelihoodInterface::ConstBranchModelDescription, bpp::TreeLikelihoodInterface::ConstSiteModelDescription
getSubstitutionModelForNode() : bpp::SubstitutionModelSet
getSubstitutionModelParameters() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::MultiProcessSequenceEvolution, bpp::NonHomogeneousSubstitutionProcess, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequenceEvolution, bpp::PhyloLikelihoodInterface, bpp::RateAcrossSitesSubstitutionProcess, bpp::SequenceEvolution, bpp::SimpleSubstitutionProcess, bpp::SingleProcessPhyloLikelihood, bpp::SubstitutionProcessCollection, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface, bpp::TreeLikelihoodInterface
getSubstitutionModelSet() : bpp::AbstractNonHomogeneousTreeLikelihood, bpp::LegacyPhylogeneticsApplicationTools, bpp::NonHomogeneousSequenceSimulator, bpp::NonHomogeneousTreeLikelihood
getSubstitutionProcess() : bpp::LikelihoodCalculationSingleProcess, bpp::MultiProcessSequenceEvolution, bpp::OneProcessSequenceEvolution, bpp::OneProcessSequencePhyloLikelihood, bpp::PhylogeneticsApplicationTools, bpp::SequenceEvolution, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SingleProcessPhyloLikelihood, bpp::SubstitutionProcessCollection
getSubstitutionProcessCollection() : bpp::PhylogeneticsApplicationTools
getSubstitutionProcessNumber() : bpp::OneProcessSequenceEvolution, bpp::PartitionSequenceEvolution, bpp::SingleProcessPhyloLikelihood
getSubstitutionProcessNumbers() : bpp::MultiProcessSequenceEvolution, bpp::OneProcessSequenceEvolution, bpp::SequenceEvolution, bpp::SubstitutionProcessCollection
getSubstitutionProcessParameters() : bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::MultiProcessSequenceEvolution, bpp::OneProcessSequenceEvolution, bpp::SequenceEvolution, bpp::SubstitutionProcessCollection
getSubstitutionRegister() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::AbstractSubstitutionCount, bpp::PhylogeneticsApplicationTools, bpp::SubstitutionCountInterface
getSubstitutionVector() : bpp::SiteSimulationResult
getSubtreeMoments_() : bpp::TreeTemplateTools
getTimeBeforeNextMutationEvent() : bpp::AbstractMutationProcess, bpp::MutationProcess
getTopologyValue() : bpp::DRTreeParsimonyScore, bpp::NNIHomogeneousTreeLikelihood, bpp::NNISearchable
getTotalLength() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools, bpp::TreeTools
getTotalTime() : bpp::MutationPath
getTppalAxesMatrix() : bpp::CoalaCore
getTransitionMatrix() : bpp::ProcessEdge
getTransitionProbabilities() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood, bpp::TreeLikelihoodInterface
getTransitionProbabilitiesPerRateClass() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface
getTranslation() : bpp::Cursor
getTree() : bpp::AbstractTreeLikelihoodData, bpp::AbstractTreeParsimonyData, bpp::NonHomogeneousSequenceSimulator, bpp::PhylogeneticsApplicationTools, bpp::PhyloTreeException, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::SubstitutionProcessCollection, bpp::TreeException, bpp::TreeLikelihoodData, bpp::TreeParsimonyDataInterface
getTreeDrawing() : bpp::DrawBranchEvent, bpp::DrawNodeEvent, bpp::DrawTreeEvent
getTreeForType() : bpp::SubstitutionMappingTools
getTreeNode() : bpp::LikelihoodCalculationSingleProcess
getTreeNumber() : bpp::SubstitutionProcessCollectionMember
getTreeNumbers() : bpp::SubstitutionProcessCollection
getTrees() : bpp::LegacyPhylogeneticsApplicationTools, bpp::PhylogeneticsApplicationTools
getTreeTemplate() : bpp::AbstractTreeParsimonyScore
getTreeTemplate_() : bpp::AbstractTreeParsimonyScore
getType() : bpp::CategorySubstitutionRegister, bpp::CompleteSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::GCPositionSubstitutionRegister, bpp::GCSynonymousSubstitutionRegister, bpp::GeneralSubstitutionRegister, bpp::KrKcSubstitutionRegister, bpp::SubstitutionRegisterInterface, bpp::SWSubstitutionRegister, bpp::TotalSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::VectorOfSubstitutionRegisters
getTypeName() : bpp::AAExteriorSubstitutionRegister, bpp::AAInteriorSubstitutionRegister, bpp::CategorySubstitutionRegister, bpp::CompleteSubstitutionRegister, bpp::DnDsSubstitutionRegister, bpp::GCPositionSubstitutionRegister, bpp::GCSynonymousSubstitutionRegister, bpp::GeneralSubstitutionRegister, bpp::KrKcSubstitutionRegister, bpp::SelectedSubstitutionRegister, bpp::SubstitutionRegisterInterface, bpp::SWSubstitutionRegister, bpp::TotalSubstitutionRegister, bpp::TsTvSubstitutionRegister, bpp::VectorOfSubstitutionRegisters
getUnparsedArguments() : bpp::BppOFrequencySetFormat, bpp::BppOMultiTreeReaderFormat, bpp::BppOMultiTreeWriterFormat, bpp::BppOSubstitutionModelFormat, bpp::BppOTreeReaderFormat, bpp::BppOTreeWriterFormat, bpp::IFrequencySet, bpp::ISubstitutionModel
getValue() : bpp::AbstractPhyloLikelihood, bpp::BranchLikelihood, bpp::ConfiguredParameter, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::GlobalClockTreeLikelihoodFunctionWrapper, bpp::LegacyOptimizationTools::ScaleFunction, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::ShiftParameter
getVerbose() : bpp::DistanceEstimation
getVerticalOrientation() : bpp::AbstractDendrogramPlot
getVPos() : bpp::Cursor
getVRates() : bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractMixedTransitionModel, bpp::MixedTransitionModelInterface
getWeight() : bpp::AbstractTreeLikelihoodData, bpp::AbstractTreeParsimonyData, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess, bpp::TreeLikelihoodData
getWeights() : bpp::AbstractSinglePhyloSubstitutionMapping, bpp::AbstractTreeLikelihoodData, bpp::AbstractWeightedSubstitutionCount, bpp::SitePatterns, bpp::TreeLikelihoodData, bpp::WeightedSubstitutionCount
getWidth() : bpp::CladogramPlot, bpp::PhylogramPlot, bpp::TreeDrawing
getWordAlphabet() : bpp::AbstractWordFrequencySet, bpp::ModelList, bpp::WordFrequencySetInterface
getX() : bpp::Cursor, bpp::TreeDrawingNodeInfo
getXUnit() : bpp::AbstractTreeDrawing, bpp::TreeDrawing
getY() : bpp::Cursor, bpp::TreeDrawingNodeInfo
getYUnit() : bpp::AbstractTreeDrawing, bpp::TreeDrawing
getZero() : bpp::Context
giveNamesToInternalNodes() : bpp::StochasticMapping
GivenDataSubstitutionProcessSequenceSimulator() : bpp::GivenDataSubstitutionProcessSequenceSimulator
GivenDataSubstitutionProcessSiteSimulator() : bpp::GivenDataSubstitutionProcessSiteSimulator
GlobalClockTreeLikelihoodFunctionWrapper() : bpp::GlobalClockTreeLikelihoodFunctionWrapper
GTR() : bpp::GTR
GY94() : bpp::GY94