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::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, bpp::SimProcessEdge, bpp::SimProcessNode
• GlobalClockTreeLikelihoodFunctionWrapper() : bpp::GlobalClockTreeLikelihoodFunctionWrapper
• GTR() : bpp::GTR
• GY94() : bpp::GY94