Here is a list of all class members with links to the classes they belong to:

- g -

• G2001() : bpp::G2001
• gacd_ : bpp::GY94
• gamma_ : bpp::AbstractCodonAARateSubstitutionModel , bpp::AbstractCodonDistanceSubstitutionModel , bpp::L95 , bpp::RN95 , bpp::RN95s , bpp::SSR
• GammaDiscreteRateDistribution() : bpp::GammaDiscreteRateDistribution
• GaussianDiscreteRateDistribution() : bpp::GaussianDiscreteRateDistribution
• gBGC() : bpp::gBGC
• GCFrequencySet() : bpp::GCFrequencySet
• gCode_ : bpp::AbstractCodonSubstitutionModel , bpp::AbstractDFPSubstitutionModel , bpp::AbstractKroneckerCodonSubstitutionModel
• GCPositionSubstitutionRegister() : bpp::GCPositionSubstitutionRegister
• GCSubstitutionRegister() : bpp::GCSubstitutionRegister
• GCSynonymousSubstitutionRegister() : bpp::GCSynonymousSubstitutionRegister
• gd_ : bpp::DrawBranchEvent , bpp::DrawNodeEvent , bpp::DrawTreeEvent
• genCode_ : bpp::AAExteriorSubstitutionRegister , bpp::AAInteriorSubstitutionRegister , bpp::DnDsSubstitutionRegister , bpp::GCPositionSubstitutionRegister , bpp::GCSynonymousSubstitutionRegister , bpp::KrKcSubstitutionRegister , bpp::SWSubstitutionRegister , bpp::TsTvSubstitutionRegister
• 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
• generator_ : bpp::AbstractSubstitutionModel , bpp::MarkovModulatedSubstitutionModel
• geneticCode_ : bpp::BppOFrequencySetFormat , bpp::BppOSubstitutionModelFormat
• 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::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::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
• getDisplaySettings() : bpp::AbstractTreeDrawing , bpp::TreeDrawing
• 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::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::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::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::AbstractTreeDrawing , bpp::AbstractTreeLikelihoodData , bpp::AbstractTreeParsimonyData , bpp::NonHomogeneousSequenceSimulator , bpp::PhylogeneticsApplicationTools , bpp::PhyloTreeException , bpp::SimpleSubstitutionProcessSiteSimulator , bpp::SubstitutionProcessCollection , bpp::TreeDrawing , bpp::TreeException , bpp::TreeLikelihoodData , bpp::TreeParsimonyDataInterface
• getTree_() : bpp::AbstractTreeDrawing
• 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 , bpp::SimProcessEdge , bpp::SimProcessNode
• GlobalClockTreeLikelihoodFunctionWrapper() : bpp::GlobalClockTreeLikelihoodFunctionWrapper
• GTR() : bpp::GTR
• GY94() : bpp::GY94