Here is a list of all class members with links to the classes they belong to:
- i -
- id_ : bpp::AwareNode, bpp::DrawBranchEvent, bpp::DrawNodeEvent, bpp::Identity< R >, bpp::Node, bpp::NodeNotFoundException, bpp::PhyloBranchNotFoundException, bpp::PhyloNodeNotFoundException
- Identity() : bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::Identity< R >
- idToNode_ : bpp::AbstractNonHomogeneousTreeLikelihood
- iEigenValues_ : bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel
- IFrequencySet() : bpp::IFrequencySet
- IMultiPhyloDAG() : bpp::IMultiPhyloDAG
- IMultiPhyloTree() : bpp::IMultiPhyloTree
- IMultiTree() : bpp::IMultiTree
- incrementAllIds() : bpp::TreeTemplateTools
- ind : IntAndInt, StringAndInt
- index_ : bpp::AbstractHomogeneousTreeLikelihood::ConstHomogeneousSiteModelIterator, bpp::AbstractNonHomogeneousTreeLikelihood::ConstNonHomogeneousSiteModelIterator, bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelIterator, bpp::AbstractTreeLikelihood::SimpleBranchIterator, bpp::AbstractTreeLikelihood::SimpleSiteIterator, bpp::CategorySubstitutionRegister
- indexes_ : bpp::SiteSimulationResult
- indices_ : bpp::SitePatterns
- IndicesType : bpp::SitePatterns
- infos_ : bpp::NodeTemplate< NodeInfos >
- init() : bpp::DRTreeParsimonyData, bpp::GivenDataSubstitutionProcessSiteSimulator, bpp::KrKcSubstitutionRegister, bpp::NonHomogeneousSequenceSimulator, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::SimpleSubstitutionProcessSiteSimulator, bpp::TreeIterator
- init_() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractTreeParsimonyScore, bpp::Coala, bpp::CoalaCore, bpp::DistanceEstimation, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRTreeParsimonyData, bpp::DRTreeParsimonyScore, bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::SitePatterns
- initBMatrices_() : bpp::DecompositionMethods, bpp::UniformizationSubstitutionCount
- initBranchLengthsGrafen() : bpp::PhyloTreeTools, bpp::TreeTools
- initBranchLengthsParameters() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood
- initCounts_() : bpp::DecompositionSubstitutionCount
- initGenerators_() : bpp::AbstractKroneckerWordSubstitutionModel
- initialize() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, bpp::ForwardLikelihoodTree, bpp::RHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::TreeLikelihoodInterface
- initialize_() : bpp::BppOFrequencySetFormat, bpp::BppOSubstitutionModelFormat
- initialized_ : bpp::AbstractTreeLikelihood
- initialState_ : bpp::MutationPath
- initLikelihoods() : bpp::BranchLikelihood, bpp::DRASDRTreeLikelihoodData, bpp::DRASRTreeLikelihoodData
- initLikelihoodsWithPatterns() : bpp::DRASRTreeLikelihoodData
- initModel() : bpp::BranchLikelihood
- initParameters() : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood
- initParameters_() : bpp::GlobalClockTreeLikelihoodFunctionWrapper
- initRewards_() : bpp::DecompositionReward
- initSet() : bpp::MvaFrequencySet
- initStates_() : bpp::DecompositionMethods
- InMixedSubstitutionModel : bpp::AbstractLkTransitionModel, bpp::InMixedSubstitutionModel, bpp::MixedTransitionModelInterface, bpp::TransitionModelInterface
- InOrderTreeIterator() : bpp::InOrderTreeIterator
- insertN() : bpp::MixedSubstitutionModelSet::HyperNode::Node, bpp::ModelPath::PathNode
- insideIProducts_ : bpp::DecompositionMethods
- insideProducts_ : bpp::DecompositionMethods
- INTEGER : bpp::BppOSubstitutionModelFormat
- intersects() : bpp::MixedSubstitutionModelSet::HyperNode, bpp::MixedSubstitutionModelSet::HyperNode::Node, bpp::ModelPath, bpp::ModelPath::PathNode
- invalidateRecursively() : bpp::Node_DF
- IODAG() : bpp::IODAG
- IoFrequencySet() : bpp::IoFrequencySet
- IOFrequencySetFactory() : bpp::IOFrequencySetFactory
- IoSubstitutionModel() : bpp::IoSubstitutionModel
- IOSubstitutionModelFactory() : bpp::IOSubstitutionModelFactory
- IOTree() : bpp::IOTree
- IOTreeFactory() : bpp::IOTreeFactory
- IPhyloDAG() : bpp::IPhyloDAG
- IPhyloTree() : bpp::IPhyloTree
- isAutonomous() : bpp::TreeDrawingListener, bpp::TreeDrawingListenerAdapter
- isCollapsed() : bpp::TreeDrawingNodeInfo
- isCompatibleWith() : bpp::AbstractSubstitutionProcess, bpp::MultiProcessSequenceEvolution, bpp::OneProcessSequenceEvolution, bpp::SequenceEvolution, bpp::SubstitutionProcessInterface
- isComplete() : bpp::MixedSubstitutionModelSet::HyperNode
- IsComplex : Eigen::NumTraits< bpp::ExtendedFloat >
- isDiagonalizable() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
- isDiagonalizable_ : bpp::AbstractSubstitutionModel
- isEmpty() : bpp::LegacyAbstractMapping, bpp::LegacyMappingInterface
- isEnabled() : bpp::TreeDrawingListener, bpp::TreeDrawingListenerAdapter
- isFullySetUp() : bpp::NonHomogeneousSubstitutionProcess, bpp::SubstitutionProcessCollectionMember
- isFullySetUpFor() : bpp::SubstitutionModelSet
- isHybridization() : bpp::NodeEvent
- isInitialized() : bpp::AbstractPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::AbstractTreeLikelihood, bpp::LikelihoodCalculation, bpp::MultiProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::PhyloLikelihoodInterface, bpp::SingleProcessPhyloLikelihood, bpp::TreeLikelihoodInterface
- IsInteger : Eigen::NumTraits< bpp::ExtendedFloat >
- isLeaf() : bpp::AwareNode, bpp::IODAG::Element, bpp::IOTree::Element, bpp::Node, bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools::Element
- isLengthDefined_ : bpp::PhyloBranch
- isListenerEnabled() : bpp::TreeDrawingDisplayControler
- isMixture() : bpp::NodeEvent, bpp::ProcessComputationNode
- isMultifurcating() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools
- isNeighbor() : bpp::DRASDRTreeLikelihoodNodeData, bpp::DRTreeParsimonyNodeData
- isNodeCollapsed() : bpp::AbstractTreeDrawing, bpp::TreeDrawing
- isNonSingular() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
- isNonSingular_ : bpp::AbstractSubstitutionModel
- isRegComplete_ : bpp::CompleteSubstitutionRegister
- isRoot() : bpp::Tree, bpp::TreeTemplate< N >, bpp::TreeTemplateTools
- isRooted() : bpp::Tree, bpp::TreeTemplate< N >
- isScalable() : bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::SubstitutionModelInterface
- isScalable_ : bpp::AbstractSubstitutionModel
- IsSigned : Eigen::NumTraits< bpp::ExtendedFloat >
- isSorted() : bpp::BipartitionList
- isSpeciation() : bpp::NodeEvent, bpp::ProcessComputationNode
- isStationary() : bpp::CategorySubstitutionRegister, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember
- isToleranceReached() : bpp::PseudoNewtonOptimizer::PNStopCondition
- ISubstitutionModel() : bpp::ISubstitutionModel
- isValid() : bpp::Node_DF
- isValid_ : bpp::Node_DF
- isVerbose() : bpp::AbstractAgglomerativeDistanceMethod, bpp::DistanceMethodInterface
- isWeighted() : bpp::PGMA
- ITree() : bpp::ITree