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

- h -

• hasAlphabetIndex() : bpp::AbstractReward , bpp::Reward
• hasBootstrapValue() : bpp::Node , bpp::PhyloBranch
• hasBranchProperty() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• hasCodonFrequencySet() : bpp::AbstractCodonAAFitnessSubstitutionModel , bpp::AbstractCodonAARateSubstitutionModel , bpp::AbstractCodonBGCSubstitutionModel , bpp::AbstractCodonClusterAASubstitutionModel , bpp::AbstractCodonCpGSubstitutionModel , bpp::AbstractCodonDistanceSubstitutionModel , bpp::AbstractCodonFitnessSubstitutionModel , bpp::AbstractCodonFrequenciesSubstitutionModel , bpp::AbstractCodonPhaseFrequenciesSubstitutionModel , bpp::CodonAdHocSubstitutionModel , bpp::CodonDistanceFrequenciesSubstitutionModel , bpp::CodonDistancePhaseFrequenciesSubstitutionModel , bpp::CodonSameAARateSubstitutionModel , bpp::CoreCodonSubstitutionModelInterface , bpp::DFPDistanceFrequenciesSubstitutionModel , bpp::KCM , bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel , bpp::MG94 , bpp::RE08Codon , bpp::SENCA , bpp::YN98
• hasDistances() : bpp::AbstractSubstitutionDistance , bpp::SubstitutionDistance
• hasDistanceToFather() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• hasDistribution() : bpp::MixtureOfATransitionModel
• hasDistributionNumber() : bpp::SubstitutionProcessCollection
• hasExclusivePaths() : bpp::MixedSubstitutionModelSet , bpp::ModelScenario
• hasFather() : bpp::AwareNode , bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• hasFitness() : bpp::POMO
• hasFrequenciesNumber() : bpp::SubstitutionProcessCollection
• hashAdditionalArguments() : bpp::CombineDeltaShifted< T > , bpp::ConfiguredDistribution , bpp::ConfiguredFrequencySet , bpp::ConfiguredModel , bpp::ConfiguredParameter , bpp::ConfiguredSimplex , bpp::ConfiguredTransitionMatrix , bpp::ConstantOne< T > , bpp::ConstantZero< T > , bpp::CWiseConstantPow< T > , bpp::Node_DF , bpp::NumericConstant< T > , bpp::Sequence_DF , bpp::ShiftDelta< T > , bpp::ShiftParameter
• hasIds_ : bpp::Nhx
• hasLength() : bpp::PhyloBranch
• hasLikelihoodData() : bpp::AbstractTreeLikelihood , bpp::TreeLikelihoodInterface
• hasListenerFor() : bpp::TreeDrawingDisplayControler
• hasMixedTransitionModel() : bpp::NonHomogeneousSubstitutionProcess , bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollectionMember
• hasModel() : bpp::ModelPath , bpp::SubstitutionProcessCollection
• hasModelNumber() : bpp::SubstitutionProcessCollection
• hasModelScenario() : bpp::SubstitutionProcessCollection
• hasName() : bpp::Node , bpp::PhyloNode
• hasNext() : bpp::AbstractHomogeneousTreeLikelihood::ConstHomogeneousSiteModelIterator , bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator , bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelIterator , bpp::AbstractTreeLikelihood::SimpleBranchIterator , bpp::AbstractTreeLikelihood::SimpleSiteIterator , bpp::TreeLikelihoodInterface::BranchIterator , bpp::TreeLikelihoodInterface::ConstBranchModelIterator , bpp::TreeLikelihoodInterface::ConstSiteModelIterator , bpp::TreeLikelihoodInterface::SiteIterator
• hasNode() : bpp::Tree , bpp::TreeTemplate< N >
• hasNodeName() : bpp::Tree , bpp::TreeTemplate< N >
• hasNodeProperty() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• hasNodeWithId() : bpp::TreeTemplateTools
• hasNodeWithName() : bpp::TreeTemplateTools
• hasNoSon() : bpp::AwareNode , bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• hasNumericalProperty() : bpp::ConstantOne< T > , bpp::ConstantZero< T > , bpp::Node_DF , bpp::NumericConstant< T >
• hasOnlySubstitutionModels() : bpp::SubstitutionModelSet
• hasParametrizedRates_ : bpp::AbstractCodonSubstitutionModel
• hasPhyloLikelihood() : bpp::AbstractPhyloLikelihoodSet , bpp::PhyloLikelihoodContainer , bpp::PhyloLikelihoodSetInterface
• hasProcess() : bpp::DistanceEstimation
• hasProperty() : bpp::PhyloBranch , bpp::PhyloNode
• hasProteinFrequencySet() : bpp::FullPerAACodonFrequencySet
• hasRootFrequencySet() : bpp::AbstractAutonomousSubstitutionProcess , bpp::SubstitutionProcessCollectionMember , bpp::SubstitutionProcessInterface
• hasSameTopologyAs() : bpp::TreeTemplate< N >
• hasSubstitutionProcessNumber() : bpp::SubstitutionProcessCollection
• hasSubstitutionRegister() : bpp::AbstractSubstitutionCount , bpp::SubstitutionCountInterface
• hasTree() : bpp::AbstractAgglomerativeDistanceMethod , bpp::AbstractTreeDrawing , bpp::DistanceMethodInterface , bpp::TreeDrawing
• hasTreeNumber() : bpp::SubstitutionProcessCollection
• hasWeights() : bpp::AbstractWeightedSubstitutionCount , bpp::WeightedSubstitutionCount
• haveSameElementsThan() : bpp::BipartitionList
• haveSameOrderedTopology() : bpp::TreeTemplateTools
• haveSameTopology() : bpp::TreeTools
• hiddenAlphabet_ : bpp::HmmLikelihood_DF
• hiddenPostProb_ : bpp::HmmLikelihood_DF
• HierarchicalClustering() : bpp::HierarchicalClustering
• HKY85() : bpp::HKY85
• hma_ : bpp::AlignedPhyloLikelihoodAutoCorrelation , bpp::AlignedPhyloLikelihoodHmm
• hmm_ : bpp::AlignedPhyloLikelihoodAutoCorrelation , bpp::AlignedPhyloLikelihoodHmm , bpp::AutoCorrelationProcessPhyloLikelihood , bpp::ConfiguredTransitionMatrix , bpp::HmmProcessPhyloLikelihood
• hmmAlph_ : bpp::AutoCorrelationSequenceEvolution , bpp::HmmSequenceEvolution
• hmmEmis_ : bpp::HmmLikelihood_DF
• hmmEq_ : bpp::HmmLikelihood_DF
• HmmLikelihood_DF() : bpp::HmmLikelihood_DF
• HmmPhyloAlphabet() : bpp::HmmPhyloAlphabet
• HmmPhyloEmissionProbabilities() : bpp::HmmPhyloEmissionProbabilities
• hmmProcessAlphabet() : bpp::AutoCorrelationSequenceEvolution
• HmmProcessAlphabet() : bpp::HmmProcessAlphabet
• hmmProcessAlphabet() : bpp::HmmSequenceEvolution
• HmmProcessPhyloLikelihood() : bpp::HmmProcessPhyloLikelihood
• HmmSequenceEvolution() : bpp::HmmSequenceEvolution
• hmmStateAlphabet() : bpp::AlignedPhyloLikelihoodHmm , bpp::HmmLikelihood_DF
• hmmTrans_ : bpp::HmmLikelihood_DF
• hmmTransitionMatrix() : bpp::AutoCorrelationSequenceEvolution , bpp::HmmSequenceEvolution
• hmmTransMat_ : bpp::HmmSequenceEvolution
• horOrientation_ : bpp::AbstractDendrogramPlot
• hpep_ : bpp::AlignedPhyloLikelihoodAutoCorrelation , bpp::AlignedPhyloLikelihoodHmm
• Hpep_ : bpp::AutoCorrelationProcessPhyloLikelihood , bpp::HmmProcessPhyloLikelihood
• hpos_ : bpp::Cursor
• htm_ : bpp::AlignedPhyloLikelihoodAutoCorrelation , bpp::AlignedPhyloLikelihoodHmm
• HyperNode() : bpp::MixedSubstitutionModelSet::HyperNode
• hyperNode_ : bpp::RNonHomogeneousMixedTreeLikelihood