- o -

OFrequencySet() : bpp::OFrequencySet
OMultiPhyloDAG() : bpp::OMultiPhyloDAG
OMultiPhyloTree() : bpp::OMultiPhyloTree
OMultiTree() : bpp::OMultiTree
OnABranchPhyloLikelihood() : bpp::OnABranchPhyloLikelihood
OneChangeRegisterTransitionModel() : bpp::OneChangeRegisterTransitionModel
OneChangeTransitionModel() : bpp::OneChangeTransitionModel
OneJumpSubstitutionCount() : bpp::OneJumpSubstitutionCount
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::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
optimizationInitializationPerformed() : bpp::NaNListener
OptimizationOptions() : bpp::OptimizationTools::OptimizationOptions
optimizationStepPerformed() : bpp::NaNListener
OptimizationTools() : bpp::OptimizationTools
optimizeBranchLengthsParameters() : bpp::LegacyOptimizationTools
optimizeNumericalParameters() : bpp::LegacyOptimizationTools , bpp::OptimizationTools
optimizeNumericalParameters2() : bpp::LegacyOptimizationTools , bpp::OptimizationTools
optimizeParameters() : bpp::LegacyPhylogeneticsApplicationTools , bpp::PhylogeneticsApplicationTools
optimizer() : bpp::DistanceEstimation
optimizeTreeNNI() : bpp::LegacyOptimizationTools
optimizeTreeNNI2() : bpp::LegacyOptimizationTools
optimizeTreeScale() : bpp::LegacyOptimizationTools
orderTree() : bpp::TreeTemplateTools
orderTree_() : bpp::TreeTemplateTools
OrderTreeData_() : bpp::TreeTemplateTools::OrderTreeData_
OSubstitutionModel() : bpp::OSubstitutionModel
OTree() : bpp::OTree
output() : bpp::PhyloLikelihoodFormula
outputInternalSequences() : bpp::GivenDataSubstitutionProcessSequenceSimulator , bpp::NonHomogeneousSequenceSimulator , bpp::SequenceSimulatorInterface , bpp::SimpleSubstitutionProcessSequenceSimulator , bpp::SubstitutionProcessSequenceSimulator
outputInternalSites() : bpp::NonHomogeneousSequenceSimulator , bpp::SimpleSubstitutionProcessSiteSimulator , bpp::SiteSimulatorInterface
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