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

- o -

• offset_ : bpp::AbstractTreeLikelihood::SimpleSiteIterator
• OFrequencySet() : bpp::OFrequencySet
• omegaC_ : bpp::AbstractCodonClusterAASubstitutionModel
• omegaR_ : bpp::AbstractCodonClusterAASubstitutionModel
• OMultiPhyloDAG() : bpp::OMultiPhyloDAG
• OMultiPhyloTree() : bpp::OMultiPhyloTree
• OMultiTree() : bpp::OMultiTree
• OnABranchPhyloLikelihood() : bpp::OnABranchPhyloLikelihood
• onBranch : bpp::Nhx::Property
• OneChangeRegisterTransitionModel : bpp::AbstractSubstitutionModel , bpp::OneChangeRegisterTransitionModel
• OneChangeTransitionModel() : bpp::OneChangeTransitionModel
• OneJumpSubstitutionCount() : bpp::OneJumpSubstitutionCount
• oneModel_ : bpp::KCM
• OneProcessSequenceEvolution() : bpp::OneProcessSequenceEvolution
• OneProcessSequencePhyloLikelihood() : bpp::OneProcessSequencePhyloLikelihood
• OneProcessSequenceSubstitutionMapping() : bpp::OneProcessSequenceSubstitutionMapping
• Ones() : bpp::ExtendedFloatEigen< R, C, EigenType >
• operator double() : bpp::ExtendedFloat
• operator!=() : bpp::AbstractStateMap , bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::StateMapInterface
• operator()() : bpp::AbstractPhyloLikelihood::StringPairHash , bpp::ConstantTransitionFunction , bpp::Context::CachedNodeRefHash , bpp::CWiseCompound< R, ReductionOf< T > >::compound_functor , bpp::CWiseMatching< R, ReductionOf< T > >::matching_functor , bpp::CWisePattern< R >::pattern_functor , bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::HmmEmissionProbabilities_Eigen , bpp::HmmPhyloEmissionProbabilities , bpp::LegacyProbabilisticRewardMapping , bpp::LegacyProbabilisticSubstitutionMapping , bpp::LegacyRewardMappingInterface , bpp::LegacySubstitutionMappingInterface , bpp::PhyloBranchMapping , bpp::PhyloBranchReward , bpp::ProbabilisticRewardMapping , bpp::ProbabilisticSubstitutionMapping , bpp::RewardMappingInterface , bpp::SubstitutionMapping , bpp::SubstitutionProcessCollectionMember::Deleter
• operator*() : bpp::ExtendedFloat , bpp::ExtendedFloatArrayWrapper< R, C > , bpp::ExtendedFloatEigen< R, C, EigenType >
• operator*=() : bpp::ExtendedFloat , bpp::ExtendedFloatArrayWrapper< R, C > , bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::PhyloTree
• operator+() : bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType >
• operator++() : bpp::TreeIterator
• operator+=() : bpp::ExtendedFloat , bpp::ExtendedFloatArrayWrapper< R, C > , bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::ExtendedFloatNoAlias< DerivedEF > , bpp::MixedSubstitutionModelSet::HyperNode::Node , bpp::MixedSubstitutionModelSet::HyperNode , bpp::ModelPath , bpp::ModelPath::PathNode , bpp::PhyloTree
• operator-() : bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType >
• operator-=() : bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::ExtendedFloatNoAlias< DerivedEF > , bpp::ModelPath , bpp::ModelPath::PathNode , bpp::PhyloTree
• operator/() : bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType >
• operator/=() : bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::PhyloTree
• operator<() : bpp::ExtendedFloat , bpp::Nhx::Property , bpp::SitePatterns::SortableSite
• operator<< : bpp::ExtendedFloatEigen< R, C, EigenType >
• operator<=() : bpp::ExtendedFloat , bpp::MixedSubstitutionModelSet::HyperNode::Node , bpp::MixedSubstitutionModelSet::HyperNode , bpp::ModelPath , bpp::ModelPath::PathNode
• operator=() : bpp::AAExteriorSubstitutionRegister , bpp::AAInteriorSubstitutionRegister , bpp::AbstractAgglomerativeDistanceMethod , bpp::AbstractAlignedPhyloLikelihood , bpp::AbstractAlignedPhyloLikelihoodSet , bpp::AbstractAutonomousSubstitutionProcess , bpp::AbstractBiblioMixedTransitionModel , bpp::AbstractBiblioSubstitutionModel , bpp::AbstractBiblioTransitionModel , bpp::AbstractCodonAAFitnessSubstitutionModel , bpp::AbstractCodonAARateSubstitutionModel , bpp::AbstractCodonBGCSubstitutionModel , bpp::AbstractCodonClusterAASubstitutionModel , bpp::AbstractCodonCpGSubstitutionModel , bpp::AbstractCodonDistanceSubstitutionModel , bpp::AbstractCodonFitnessSubstitutionModel , bpp::AbstractCodonFrequenciesSubstitutionModel , bpp::AbstractCodonPhaseFrequenciesSubstitutionModel , bpp::AbstractCodonSubstitutionModel , bpp::AbstractDFPSubstitutionModel , bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::AbstractFrequencySet , bpp::AbstractFromSubstitutionModelTransitionModel , bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractKroneckerCodonSubstitutionModel , bpp::AbstractKroneckerWordSubstitutionModel , bpp::AbstractMapping , bpp::AbstractMixedTransitionModel , bpp::AbstractNonHomogeneousTreeLikelihood , bpp::AbstractParametrizableSequencePhyloLikelihood , bpp::AbstractPhyloLikelihood , bpp::AbstractPhyloLikelihoodSet , bpp::AbstractReward , bpp::AbstractRewardMapping , bpp::AbstractSequencePhyloLikelihood , bpp::AbstractSingleDataPhyloLikelihood , bpp::AbstractSinglePhyloSubstitutionMapping , bpp::AbstractStateMap , bpp::AbstractSubstitutionDistance , bpp::AbstractSubstitutionMapping , bpp::AbstractSubstitutionModel , bpp::AbstractSubstitutionRegister , bpp::AbstractTransitionModel , bpp::AbstractTreeDrawing , bpp::AbstractTreeLikelihood::ConstNoPartitionBranchModelDescription , bpp::AbstractTreeLikelihood::ConstNoPartitionSiteModelDescription , bpp::AbstractTreeLikelihood , bpp::AbstractTreeLikelihoodData , bpp::AbstractTreeParsimonyData , bpp::AbstractWeightedSubstitutionCount , bpp::AbstractWordFrequencySet , bpp::AbstractWordSubstitutionModel , bpp::AlignedPhyloLikelihoodAutoCorrelation , bpp::AlignedPhyloLikelihoodHmm , bpp::AlignedPhyloLikelihoodMixture , bpp::AlignedPhyloLikelihoodProduct , bpp::AutoCorrelationProcessPhyloLikelihood , bpp::AutoCorrelationSequenceEvolution , bpp::AwareNode , bpp::BasicTreeDrawingDisplayControler , bpp::BipartitionList , bpp::BootstrapValuesTreeDrawingListener , bpp::BppOBranchModelFormat , bpp::BppOFrequencySetFormat , bpp::BppOSubstitutionModelFormat , bpp::BppOTransitionModelFormat , bpp::BranchLengthsTreeDrawingListener , bpp::BranchLikelihood , bpp::CodonAdHocSubstitutionModel , bpp::CodonFromIndependentFrequencySet , bpp::CodonFromUniqueFrequencySet , bpp::CodonSameAARateSubstitutionModel , bpp::CompleteSubstitutionRegister , bpp::D1WalkSubstitutionModel , bpp::DecompositionMethods , bpp::DecompositionReward , bpp::DecompositionSubstitutionCount , bpp::DFP07 , bpp::DistanceEstimation , bpp::DnDsSubstitutionRegister , bpp::DRASDRTreeLikelihoodData , bpp::DRASDRTreeLikelihoodLeafData , bpp::DRASDRTreeLikelihoodNodeData , bpp::DRASRTreeLikelihoodData , bpp::DRASRTreeLikelihoodNodeData , bpp::DrawBranchEvent , bpp::DrawIBranchEvent , bpp::DrawINodeEvent , bpp::DrawNodeEvent , bpp::DrawTreeEvent , bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood , bpp::DRTreeParsimonyData , bpp::DRTreeParsimonyLeafData , bpp::DRTreeParsimonyNodeData , bpp::DRTreeParsimonyScore , bpp::DSO78 , bpp::EquiprobableSubstitutionModel , bpp::EvolutionSequenceSimulator , bpp::ExtendedFloat , bpp::ExtendedFloatArrayWrapper< R, C > , bpp::ExtendedFloatCol< R, C, EigenType > , bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::ExtendedFloatNoAlias< DerivedEF > , bpp::ExtendedFloatRow< R, C, EigenType > , bpp::ExtendedFloatVectorwiseOp< DerivedEF, MatType, Direction > , bpp::FixedCodonFrequencySet , bpp::FromMixtureSubstitutionModel , bpp::FromModelFrequencySet , bpp::FullCodonFrequencySet , bpp::FullPerAACodonFrequencySet , bpp::G2001 , bpp::gBGC , bpp::GCPositionSubstitutionRegister , bpp::GCSynonymousSubstitutionRegister , bpp::GeneralSubstitutionRegister , bpp::GivenDataSubstitutionProcessSiteSimulator , bpp::GlobalClockTreeLikelihoodFunctionWrapper , bpp::GY94 , bpp::HmmProcessAlphabet , bpp::HmmSequenceEvolution , bpp::InMixedSubstitutionModel , bpp::JCprot , bpp::JTT92 , bpp::KCM , bpp::KrKcSubstitutionRegister , bpp::LaplaceSubstitutionCount , bpp::LeafNamesTreeDrawingListener , bpp::LegacyAbstractMapping , bpp::LegacyAbstractRewardMapping , bpp::LegacyAbstractSubstitutionMapping , bpp::LegacyMarginalAncestralStateReconstruction , bpp::LegacyOptimizationTools::ScaleFunction , bpp::LegacyProbabilisticRewardMapping , bpp::LegacyProbabilisticSubstitutionMapping , bpp::LG08 , bpp::LGL08_CAT , bpp::MarginalAncestralReconstruction , bpp::MarkovModulatedFrequencySet , bpp::MarkovModulatedSubstitutionModel , bpp::MG94 , bpp::MixedSubstitutionModelSet::HyperNode::Node , bpp::MixedSubstitutionModelSet::HyperNode , bpp::MixedSubstitutionModelSet , bpp::MixtureOfASubstitutionModel , bpp::MixtureOfATransitionModel , bpp::MixtureOfSubstitutionModels , bpp::MixtureOfTransitionModels , bpp::MixtureProcessPhyloLikelihood , bpp::MixtureSequenceEvolution , bpp::ModelList , bpp::ModelPath , bpp::ModelPath::PathNode , bpp::ModelScenario , bpp::MultinomialFromTransitionModel , bpp::MultiProcessSequenceEvolution , bpp::MultiProcessSequencePhyloLikelihood , bpp::MutationPath , bpp::NaNListener , bpp::NNIHomogeneousTreeLikelihood , bpp::NNITopologyListener2 , bpp::NNITopologyListener , bpp::NNITopologySearch , bpp::Node , bpp::Node_DF , bpp::NodePException , bpp::NodesIdTreeDrawingListener , bpp::NodeTemplate< NodeInfos > , bpp::NonHomogeneousSequenceSimulator , bpp::NonHomogeneousSubstitutionProcess , bpp::OneChangeRegisterTransitionModel , bpp::OneChangeTransitionModel , bpp::OneJumpSubstitutionCount , bpp::OneProcessSequenceEvolution , bpp::OneProcessSequencePhyloLikelihood , bpp::OneProcessSequenceSubstitutionMapping , bpp::ParametrizablePhyloTree , bpp::PartitionProcessPhyloLikelihood , bpp::PartitionSequenceEvolution , bpp::PhyloBranch , bpp::PhyloBranchMapping , bpp::PhyloBranchParam , bpp::PhyloBranchPException , bpp::PhyloBranchReward , bpp::PhyloLikelihoodFormula , bpp::PhyloNode , bpp::PhyloNodePException , bpp::PhyloTreeException , bpp::POMO , bpp::ProbabilisticRewardMapping , bpp::ProbabilisticSubstitutionMapping , bpp::ProcessTree , bpp::RateAcrossSitesSubstitutionProcess , bpp::RE08 , bpp::RegisterRatesSubstitutionModel , bpp::RHomogeneousMixedTreeLikelihood , bpp::RHomogeneousTreeLikelihood , bpp::RNonHomogeneousMixedTreeLikelihood , bpp::RNonHomogeneousTreeLikelihood , bpp::SimData , bpp::SimpleSubstitutionProcess , bpp::SimpleSubstitutionProcessSiteSimulator , bpp::SingleProcessSubstitutionMapping , bpp::SitePatterns::SortableSite , bpp::SiteSimulationResult , bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollection , bpp::SubstitutionProcessCollectionMember , bpp::SubstitutionProcessSequenceSimulator , bpp::SWSubstitutionRegister , bpp::TransitionFromTransitionModel , bpp::TreeDrawingDisplayControler , bpp::TreeException , bpp::TreeIterator , bpp::TreeTemplate< N > , bpp::TsTvSubstitutionRegister , bpp::UniformizationSubstitutionCount , bpp::UserCodonFrequencySet , bpp::UserFrequencySet , bpp::UserProteinSubstitutionModel , bpp::WAG01 , bpp::WordFromIndependentFrequencySet , bpp::WordFromUniqueFrequencySet , bpp::YN98 , bpp::YNGP_M10 , bpp::YNGP_M7 , bpp::YNGP_M8 , bpp::YNGP_M9 , bpp::YNGP_M , bpp::YpR
• operator==() : bpp::AbstractStateMap , bpp::Context::CachedNodeRef , bpp::ExtendedFloat , bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::Node , bpp::StateMapInterface
• operator>() : bpp::ExtendedFloat
• operator>=() : bpp::ExtendedFloat , bpp::MixedSubstitutionModelSet::HyperNode::Node , bpp::MixedSubstitutionModelSet::HyperNode , bpp::ModelPath , bpp::ModelPath::PathNode
• operator[]() : bpp::AwareNode , bpp::ExtendedFloatEigen< R, C, EigenType > , bpp::LegacyProbabilisticRewardMapping , bpp::LegacyProbabilisticSubstitutionMapping , bpp::MixedSubstitutionModelSet::HyperNode::Node , bpp::Node , bpp::NodeTemplate< NodeInfos > , bpp::PhyloLikelihoodContainer
• OPhyloDAG() : bpp::OPhyloDAG
• OPhyloTree() : bpp::OPhyloTree
• OPTIMIZATION_BFGS : bpp::OptimizationTools
• OPTIMIZATION_BRENT : bpp::OptimizationTools
• OPTIMIZATION_GRADIENT : bpp::OptimizationTools
• OPTIMIZATION_NEWTON : bpp::OptimizationTools
• optimizationInitializationPerformed() : bpp::NaNListener
• OptimizationOptions() : bpp::OptimizationTools::OptimizationOptions
• optimizationStepPerformed() : bpp::NaNListener
• OptimizationTools() : bpp::OptimizationTools
• optimizeBranchLengthsParameters() : bpp::LegacyOptimizationTools
• optimizeCounter_ : bpp::NNITopologyListener2 , bpp::NNITopologyListener
• optimizeNumerical_ : bpp::NNITopologyListener2 , bpp::NNITopologyListener
• optimizeNumericalParameters() : bpp::LegacyOptimizationTools , bpp::OptimizationTools
• optimizeNumericalParameters2() : bpp::LegacyOptimizationTools , bpp::OptimizationTools
• optimizeParameters() : bpp::LegacyPhylogeneticsApplicationTools , bpp::PhylogeneticsApplicationTools
• optimizer() : bpp::DistanceEstimation
• optimizer_ : bpp::DistanceEstimation , bpp::NaNListener
• optimizeTreeNNI() : bpp::LegacyOptimizationTools
• optimizeTreeNNI2() : bpp::LegacyOptimizationTools
• optimizeTreeScale() : bpp::LegacyOptimizationTools
• optMethod_ : bpp::NNITopologyListener2 , bpp::NNITopologyListener
• optMethodDeriv : bpp::OptimizationTools::OptimizationOptions
• optMethodModel : bpp::OptimizationTools::OptimizationOptions
• orderTree() : bpp::TreeTemplateTools
• orderTree_() : bpp::TreeTemplateTools
• OrderTreeData_() : bpp::TreeTemplateTools::OrderTreeData_
• orientation_ : bpp::CladogramDrawBranchEvent , bpp::PhylogramDrawBranchEvent
• ORIENTATION_BOTTOM_TO_TOP : bpp::AbstractDendrogramPlot
• ORIENTATION_LEFT_TO_RIGHT : bpp::AbstractDendrogramPlot
• ORIENTATION_RIGHT_TO_LEFT : bpp::AbstractDendrogramPlot
• ORIENTATION_TOP_TO_BOTTOM : bpp::AbstractDendrogramPlot
• originalModel_ : bpp::RegisterRatesSubstitutionModel
• originalPosition : bpp::SitePatterns::SortableSite
• OSubstitutionModel() : bpp::OSubstitutionModel
• OTree() : bpp::OTree
• output() : bpp::PhyloLikelihoodFormula
• outputInternalSequences() : bpp::GivenDataSubstitutionProcessSequenceSimulator , bpp::NonHomogeneousSequenceSimulator , bpp::SequenceSimulatorInterface , bpp::SimpleSubstitutionProcessSequenceSimulator , bpp::SubstitutionProcessSequenceSimulator
• outputInternalSequences_ : bpp::NonHomogeneousSequenceSimulator
• outputInternalSites() : bpp::NonHomogeneousSequenceSimulator , bpp::SimpleSubstitutionProcessSiteSimulator , bpp::SiteSimulatorInterface
• outputInternalSites_ : bpp::SimpleSubstitutionProcessSiteSimulator
• outputPerSitePerBranch() : bpp::LegacySubstitutionMappingTools , bpp::SubstitutionMappingTools
• outputPerSitePerBranchPerType() : bpp::LegacySubstitutionMappingTools , bpp::SubstitutionMappingTools
• outputPerSitePerType() : bpp::LegacySubstitutionMappingTools , bpp::SubstitutionMappingTools
• outputPerType() : bpp::SubstitutionMappingTools
• outputPositiveLengths() : bpp::NeighborJoining
• OwnedExtendedFloat() : bpp::ExtendedFloatEigen< R, C, EigenType >::OwnedExtendedFloat