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• 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
• 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
• 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
• HierarchicalClustering() : bpp::HierarchicalClustering
• HKY85() : bpp::HKY85
• 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
• hmmTransitionMatrix() : bpp::AutoCorrelationSequenceEvolution, bpp::HmmSequenceEvolution
• HyperNode() : bpp::MixedSubstitutionModelSet::HyperNode