bpp Namespace Reference

Defines the basic types of data flow nodes. More...

Namespaces
	BrentOneDimension
	Graph
	IntegerTools
	NewtonBacktrackOneDimension
	numeric
	PowellMultiDimensions
	StatTools
	TextTools
	VectorTools

Classes
class	DownhillSimplexMethod
class	AssociationGraphObserver
class	AssociationGraphImplObserver
class	GoldenSectionSearch
class	AbstractDiscreteDistribution
class	AllelicAlphabet
class	Fasta
class	AbstractColorSet
class	AbstractFontManager
class	AbstractGraphicDevice
class	AbstractHmmLikelihood
class	AbstractHmmTransitionMatrix
class	AbstractNumericalDerivative
class	AbstractOptimizationStopCondition
class	AbstractOptimizer
class	AbstractOutputStream
class	AbstractParameterAliasable
class	AbstractParametrizable
class	AdaptiveKernelDensityEstimation
class	AliasParameterListener
class	ApplicationTools
class	AssociationDAGraphImplObserver
class	AssociationDAGraphObserver
class	AssociationTreeGraphImplObserver
class	AssociationTreeGraphObserver
class	AttributesTools
class	AutoCorrelationTransitionMatrix
class	AutoParameter
class	BackupListener
class	BadIntegerException
class	BadNumberException
class	BadSizeException
class	BetaDiscreteDistribution
class	BfgsMultiDimensions
class	BinaryOperator
class	BppApplication
class	BppBoolean
class	BppDouble
class	BppInteger
class	BppNotANumber
class	BppNumberI
class	BppODiscreteDistributionFormat
class	BppOParametrizableFormat
class	BppString
class	BppUnsignedInteger
class	BppVector
class	Bracket
class	BracketPoint
class	BrentOneDimension
class	Clonable
class	ColMatrix
class	ColorManager
class	ColorSet
class	ColorTools
class	ComputationTree
class	ConjugateGradientMultiDimensions
class	ConstantDistribution
class	ConstantOperator
class	ConstraintException
class	ConstraintInterface
class	ContingencyTableGenerator
class	ContingencyTableTest
class	CoordsTools
class	CorrespondenceAnalysis
class	DAGraph
class	DAGraphImpl
class	DataTable
class	DefaultColorSet
class	DimensionException
class	DirectionFunction
class	DirichletDiscreteDistribution
class	DiscreteDistributionInterface
class	DualityDiagram
class	DuplicatedTableColumnNameException
class	DuplicatedTableRowNameException
class	DvipsColorSet
class	EdgesIteratorClass
class	EdgesIteratorClass< Graph::ALLGRAPHITER, is_const >
class	EdgesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const >
class	EdgesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const >
class	EigenValue
class	ElementNotFoundException
class	EmptyVectorException
class	Exception
class	ExponentialDiscreteDistribution
class	FileTools
class	FirstOrderDerivable
class	FirstOrderDerivableWrapper
class	FivePointsNumericalDerivative
class	Font
class	FontManager
class	FullHmmTransitionMatrix
class	FunctionInterface
class	FunctionOperator
class	FunctionStopCondition
class	FunctionTools
class	FunctionWrapper
class	GammaDiscreteDistribution
class	GaussianDiscreteDistribution
class	GlobalGraph
class	Graph
class	GraphicDevice
class	GraphObserver
class	HmmBadStateException
class	HmmEmissionProbabilities
class	HmmLikelihood
class	HmmStateAlphabet
class	HmmTransitionMatrix
class	HmmUnvalidAlphabetException
class	IDiscreteDistribution
class	IndexOutOfBoundsException
class	InfinityDerivableFirstOrderWrapper
class	InfinityDerivableSecondOrderWrapper
class	InfinityFunctionWrapper
class	IntervalConstraint
class	IntervalTransformedParameter
class	InvariantMixedDiscreteDistribution
class	IoDiscreteDistribution
class	IoDiscreteDistributionFactory
class	IOException
class	IOFormat
class	IOParametrizable
class	KeyvalException
class	KeyvalTools
class	LinearMatrix
class	LogsumHmmLikelihood
class	LowMemoryRescaledHmmLikelihood
class	LUDecomposition
class	MapTools
class	MathOperator
class	Matrix
class	MatrixTools
class	MetaOptimizer
class	MetaOptimizerInfos
class	MixtureOfDiscreteDistributions
class	MolscriptColorSet
class	MultipleDiscreteDistribution
class	MultiRange
class	NegativeOperator
class	NeighborIteratorClass
class	NestedStringTokenizer
class	NewtonBacktrackOneDimension
class	NewtonOneDimension
class	NodesIteratorClass
class	NodesIteratorClass< Graph::ALLGRAPHITER, is_const >
class	NodesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const >
class	NodesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const >
class	NoTableColumnNamesException
class	NoTableRowNamesException
class	NotImplementedException
class	NullOutputStream
class	NullPointerException
class	Number
class	NumberFormatException
class	NumCalcApplicationTools
class	NumConstants
class	NumTools
class	ODiscreteDistribution
class	OneDimensionOptimizationTools
class	OParametrizable
class	Operator
class	OptimizationEvent
class	OptimizationListener
class	OptimizationStopCondition
class	OptimizerInterface
class	OrderedSimplex
class	OutOfRangeException
class	OutputStream
class	Parameter
class	ParameterAliasable
class	ParameterAliasableAdapter
class	ParameterEvent
class	ParameterException
class	ParameterGrid
class	ParameterList
class	ParameterListener
class	ParameterNotFoundException
class	ParametersStopCondition
class	Parametrizable
class	ParametrizableAdapter
class	ParametrizableCollection
class	PgfGraphicDevice
class	PlaceboTransformedParameter
class	Point2D
class	PowellMultiDimensions
class	PrincipalComponentAnalysis
class	RandomTools
class	Range
class	RangeCollection
class	rangeComp_
class	RangeSet
class	RColorSet
class	ReparametrizationDerivableFirstOrderWrapper
class	ReparametrizationDerivableSecondOrderWrapper
class	ReparametrizationFunctionWrapper
class	RescaledHmmLikelihood
class	RGBColor
class	RowMatrix
class	RTransformedParameter
class	SecondOrderDerivable
class	SecondOrderDerivableWrapper
class	SimpleDiscreteDistribution
class	SimpleMultiDimensions
class	SimpleNewtonMultiDimensions
class	Simplex
class	StateChangedEvent
class	StateListener
class	StatTest
class	StatTools
class	StdErr
class	StdOut
class	StdStr
class	StlOutputStream
class	StlOutputStreamWrapper
class	StringTokenizer
class	SvgGraphicDevice
class	Table
class	TableColumnNameNotFoundException
class	TableColumnNamesException
class	TableNameNotFoundException
class	TableRowNameNotFoundException
class	TableRowNamesException
class	TestFunction
class	ThreePointsNumericalDerivative
class	TransformedParameter
class	TreeGraph
class	TreeGraphImpl
class	TruncatedExponentialDiscreteDistribution
class	TwoPointsNumericalDerivative
class	UniformDiscreteDistribution
class	UnvalidFlagException
class	VectorException
class	VectorTools
class	XFigColorManager
class	XFigGraphicDevice
class	XFigLaTeXFontManager
class	XFigPostscriptFontManager
class	ZeroDivisionException
class	AAChargeIndex
class	AAChenGuHuangHydrophobicityIndex
class	AAChouFasmanAHelixIndex
class	AAChouFasmanBSheetIndex
class	AAChouFasmanTurnIndex
class	AAIndex1Entry
class	AAIndex2Entry
class	AAMassIndex
class	AASEA1030Index
class	AASEAInf10Index
class	AASEASup30Index
class	AASurfaceIndex
class	AAVolumeIndex
class	AbstractAlphabet
class	AbstractCoreSequence
class	AbstractCoreSite
class	AbstractIAlignment
class	AbstractIAlignment2
class	AbstractIDistanceMatrix
class	AbstractIProbabilisticAlignment
class	AbstractIProbabilisticAlignment2
class	AbstractIProbabilisticSequence
class	AbstractISequence
class	AbstractOAlignment
class	AbstractODistanceMatrix
class	AbstractOProbabilisticAlignment
class	AbstractOProbabilisticSequence
class	AbstractOProbabilisticSequence2
class	AbstractOSequence
class	AbstractOSequence2
class	AbstractReverseTransliterator
class	AbstractSequencePositionIterator
class	AbstractTemplateEventDrivenSymbolList
class	AbstractTemplateSequenceContainer
class	AbstractTemplateSiteContainerIterator
class	AbstractTemplateSymbolList
class	AbstractTransliterator
class	Alphabet
class	AlphabetException
class	AlphabetIndex1
class	AlphabetIndex2
class	AlphabetMismatchException
class	AlphabetNumericState
class	AlphabetState
class	AlphabetTools
class	AscidianMitochondrialGeneticCode
class	BadCharException
class	BadIntException
class	BinaryAlphabet
class	BLOSUM50
class	BowkerTest
class	BppOAlignmentReaderFormat
class	BppOAlignmentWriterFormat
class	BppOAlphabetIndex1Format
class	BppOAlphabetIndex2Format
class	BppOSequenceReaderFormat
class	BppOSequenceStreamReaderFormat
class	BppOSequenceWriterFormat
class	BppSequenceApplication
class	CaseMaskedAlphabet
class	CharStateNotSupportedException
class	CiliateNuclearGeneticCode
class	Clustal
class	CodonAlphabet
class	CodonFromProteicAlphabetIndex1
class	CodonFromProteicAlphabetIndex2
class	CodonSiteTools
class	Commentable
class	CompleteTemplateSiteContainerIterator
class	CompressedVectorSiteContainer
class	CoreSequenceInterface
class	CoreSiteInterface
class	CoreSymbolListDeletionEvent
class	CoreSymbolListEditionEvent
class	CoreSymbolListInsertionEvent
class	CoreSymbolListListener
class	CoreSymbolListSubstitutionEvent
class	CoreWordAlphabet
class	CruxSymbolListInterface
class	DCSE
class	DefaultAlphabet
class	DefaultNucleotideScore
class	DistanceMatrix
class	DNA
class	DNAToRNA
class	EchinodermMitochondrialGeneticCode
class	EmptyContainerException
class	EmptySequenceException
class	EmptySiteException
class	EventDrivenIntSymbolList
class	GenBank
class	GeneticCode
class	GranthamAAChemicalDistance
class	GranthamAAPolarityIndex
class	GranthamAAVolumeIndex
class	IAlignment
class	IDistanceMatrix
class	IntegerAlphabet
class	IntSymbolList
class	IntSymbolListInterface
class	InvertebrateMitochondrialGeneticCode
class	IODistanceMatrix
class	IODistanceMatrixFactory
class	IOProbabilisticSequence
class	IOSequence
class	IoSequenceFactory
class	IOSequenceStream
class	IProbabilisticAlignment
class	IProbabilisticSequence
class	ISequence
class	KD_AAHydropathyIndex
class	KleinAANetChargeIndex
class	LetterAlphabet
class	LexicalAlphabet
class	MappedNamedContainer
class	Mase
class	MaseHeader
class	MaseTools
class	MiyataAAChemicalDistance
class	MoldMitochondrialGeneticCode
class	NamedContainerInterface
class	NexusIOSequence
class	NexusTools
class	NoGapTemplateSiteContainerIterator
class	NucleicAcidsReplication
class	NucleicAlphabet
class	NucleicAlphabetState
class	NumericAlphabet
class	OAlignment
class	ODistanceMatrix
class	OProbabilisticAlignment
class	OProbabilisticSequence
class	OSequence
class	Pasta
class	PhredPhd
class	PhredPoly
class	Phylip
class	PhylipDistanceMatrixFormat
class	PositionedContainerInterface
class	PositionedNamedContainerInterface
class	ProbabilisticSequence
class	ProbabilisticSequenceInterface
class	ProbabilisticSite
class	ProbabilisticSiteInterface
class	ProbabilisticSymbolList
class	ProbabilisticSymbolListInterface
class	ProteicAlphabet
class	ProteicAlphabetIndex1
class	ProteicAlphabetIndex2
class	ProteicAlphabetState
class	ReverseTransliteratorInterface
class	RNA
class	RNY
class	Sequence
class	SequenceAnnotation
class	SequenceApplicationTools
class	SequenceContainerTools
class	SequencedValuesContainer
class	SequenceException
class	SequenceFileIndex
class	SequenceInterface
class	SequenceMask
class	SequenceNotAlignedException
class	SequenceNotFoundException
class	SequencePositionIterator
class	SequenceQuality
class	SequenceTools
class	SequenceWalker
class	SequenceWithAnnotation
class	SequenceWithAnnotationTools
class	SequenceWithGapException
class	SequenceWithQuality
class	SequenceWithQualityTools
class	SimpleCommentable
class	SimpleIndexDistance
class	SimpleScore
class	SimpleSequencePositionIterator
class	SimpleTemplateSiteContainerIterator
class	Site
class	SiteContainerTools
class	SiteException
class	SiteInterface
class	SiteNotFoundException
class	SiteTools
class	SiteWithGapException
class	StandardGeneticCode
class	Stockholm
class	StopCodonException
class	StringSequenceTools
class	SwitchDeleter
class	SymbolListTools
class	TemplateAlignedSequenceContainer
class	TemplateAlignmentDataInterface
class	TemplateCoreSymbolListInterface
class	TemplateEventDrivenCoreSymbolListInterface
class	TemplateISequenceStream
class	TemplateOSequenceStream
class	TemplateSequenceContainerInterface
class	TemplateSequenceDataInterface
class	TemplateSequenceIteratorInterface
class	TemplateSiteContainerInterface
class	TemplateSiteIteratorInterface
class	TemplateStreamSequenceIterator
class	TemplateVectorSequenceContainer
class	TemplateVectorSiteContainer
class	TransliteratorInterface
class	UserAlphabetIndex1
class	UserAlphabetIndex2
class	VectorMappedContainer
class	VectorPositionedContainer
class	VertebrateMitochondrialGeneticCode
class	WordAlphabet
class	YeastMitochondrialGeneticCode
class	AncestralStateReconstruction
	Interface for ancestral states reconstruction methods. More...
class	BppPhylogeneticsApplication
class	PhylogeneticsApplicationTools
	This class provides some common tools for applications. More...
class	AbstractAgglomerativeDistanceMethod
	Partial implementation of the AgglomerativeDistanceMethod interface. More...
class	BioNJ
	The BioNJ distance method. More...
class	DistanceEstimation
class	DistanceMethodInterface
	General interface for distance-based phylogenetic reconstruction methods. More...
class	AgglomerativeDistanceMethodInterface
	Interface for agglomerative distance methods. More...
class	ClusterInfos
class	HierarchicalClustering
	Hierarchical clustering. More...
class	NeighborJoining
	The neighbor joining distance method. More...
struct	PGMAInfos
	Inner data structure for WPGMA and UPGMA distance methods. More...
class	PGMA
	Compute WPGMA and UPGMA trees from a distance matrix. More...
class	AbstractDendrogramPlot
	Basic implementation of dendrogram plots. More...
class	TreeDrawingNodeInfo
class	DrawINodeEvent
	Event class that uses INode object (more efficient than relying on nodes id, but less generic). More...
class	DrawIBranchEvent
	Event class that uses INode object (more efficient than relying on nodes id, but less generic). More...
class	AbstractTreeDrawing
	Partial implementation of the TreeDrawing interface. More...
class	CladogramDrawBranchEvent
class	CladogramPlot
	Cladogram representation of trees. More...
class	PhylogramDrawBranchEvent
class	PhylogramPlot
	Phylogram representation of trees. More...
class	TreeDrawingSettings
	A set of options to tune the display of a TreeDrawing object. More...
class	Cursor
	Data structure describing a plotting direction. More...
class	DrawNodeEvent
	Event class used by TreeDrawing classes. More...
class	DrawBranchEvent
	Event class used by TreeDrawing classes. More...
class	DrawTreeEvent
	Event class used by TreeDrawing classes. More...
class	TreeDrawing
	Basal interface for tree drawing classes. More...
class	TreeDrawingDisplayControler
	Easy tune of tree drawings display. More...
class	BasicTreeDrawingDisplayControler
	Easy tune of tree drawings display, a basic implementation: More...
class	TreeDrawingListener
	Interface allowing to capture drawing events. More...
class	TreeDrawingListenerAdapter
	An empty implementation of the TreeDrawingListener interface. More...
class	NodesIdTreeDrawingListener
	A TreeDrawingListener implementation that writes nodes id. More...
class	LeafNamesTreeDrawingListener
	A TreeDrawingListener implementation that write leaf names. More...
class	BranchLengthsTreeDrawingListener
	A TreeDrawingListener implementation that write the branch lengths of inner nodes. More...
class	BootstrapValuesTreeDrawingListener
	A TreeDrawingListener implementation that write the bootstrap values of inner nodes. More...
class	LabelInnerNodesTreeDrawingListener
	A TreeDrawingListener implementation that write the names of inner nodes. More...
class	LabelCollapsedNodesTreeDrawingListener
	A TreeDrawingListener implementation that label the collapsed nodes. More...
class	BppOBranchModelFormat
	Branch model I/O in BppO format. More...
class	BppOFrequencySetFormat
	Frequencies set I/O in BppO format. More...
class	BppOMultiTreeReaderFormat
	Tree I/O in BppO format. More...
class	BppOMultiTreeWriterFormat
	Tree I/O in BppO format. More...
class	BppORateDistributionFormat
	Rate Distribution I/O in BppO format. More...
class	BppOSubstitutionModelFormat
	Substitution model I/O in BppO format. More...
class	BppOTransitionModelFormat
	Transition model I/O in BppO format. More...
class	BppOTreeReaderFormat
	Tree I/O in BppO format. More...
class	BppOTreeWriterFormat
	Tree I/O in BppO format. More...
class	ExtendedNewick
	The so-called 'ExtendedNewick' parenthetic format for phylogenetic networks, where hybridization nodes are mandatory tagged and appear several times. More...
class	IODAG
	General interface for DAG I/O. More...
class	IPhyloDAG
	General interface for DAG readers. More...
class	OPhyloDAG
	General interface for DAG writers. More...
class	AbstractIPhyloDAG
	Partial implementation of the IDAG interface. More...
class	AbstractOPhyloDAG
	Partial implementation of the ODAG interface. More...
class	IMultiPhyloDAG
	General interface for multiple trees readers. More...
class	OMultiPhyloDAG
	General interface for tree writers. More...
class	AbstractIMultiPhyloDAG
	Partial implementation of the IMultiDAG interface. More...
class	AbstractOMultiPhyloDAG
	Partial implementation of the ODAG interface. More...
class	IoFrequencySet
	General interface for model I/O. More...
class	IFrequencySet
	General interface for distance matrix readers. More...
class	OFrequencySet
	General interface for distance matrix writers. More...
class	IOFrequencySetFactory
	Utilitary class for creating frequencies set readers and writers. More...
class	IoSubstitutionModel
	General interface for model I/O. More...
class	ISubstitutionModel
	General interface for model readers. More...
class	OSubstitutionModel
	General interface for distance matrix writers. More...
class	IOSubstitutionModelFactory
	Utilitary class for creating substitution model readers and writers. More...
class	IOTree
	General interface for tree I/O. More...
class	ITree
	General interface for tree readers. More...
class	IPhyloTree
	General interface for tree readers. More...
class	OTree
	General interface for tree writers. More...
class	OPhyloTree
	General interface for tree writers. More...
class	AbstractITree
	Partial implementation of the ITree interface. More...
class	AbstractIPhyloTree
class	AbstractOTree
	Partial implementation of the OTree interface. More...
class	AbstractOPhyloTree
	Partial implementation of the OTree interface. More...
class	IMultiTree
	General interface for multiple trees readers. More...
class	IMultiPhyloTree
class	OMultiTree
	General interface for tree writers. More...
class	OMultiPhyloTree
	General interface for tree writers. More...
class	AbstractIMultiTree
	Partial implementation of the IMultiTree interface. More...
class	AbstractIMultiPhyloTree
	Partial implementation of the IMultiTree interface. More...
class	AbstractOMultiTree
	Partial implementation of the OTree interface. More...
class	AbstractOMultiPhyloTree
	Partial implementation of the OTree interface. More...
class	IOTreeFactory
	Utilitary class for creating tree readers and writers. More...
class	Newick
	The so-called 'newick' parenthetic format. More...
class	NexusIOTree
	a simple parser for reading trees from a Nexus file. More...
class	Nhx
	The so-called 'Nhx - New Hampshire eXtended' parenthetic format. More...
class	LegacyAncestralStateReconstruction
	Interface for ancestral states reconstruction methods. More...
class	LegacyPhylogeneticsApplicationTools
	This class provides some common tools for applications. More...
class	IOPairedSiteLikelihoods
	Base class for I/O on paired-site likelihoods. More...
class	IOTreepuzzlePairedSiteLikelihoods
	This class provides I/O for the Tree-Puzzle/RAxML (phylip-like) paired-site likelihoods format. More...
class	IOPhymlPairedSiteLikelihoods
	This class provides input for the Phyml paired-site likelihoods format. More...
class	AbstractDiscreteRatesAcrossSitesTreeLikelihood
	Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface. More...
class	AbstractHomogeneousTreeLikelihood
	Partial implementation for homogeneous model of the TreeLikelihood interface. More...
class	AbstractNonHomogeneousTreeLikelihood
	Partial implementation for branch non-homogeneous models of the TreeLikelihood interface. More...
class	AbstractTreeLikelihood
	Partial implementation of the TreeLikelihood interface. More...
class	AbstractTreeLikelihoodData
	Partial implementation of the TreeLikelihoodData interface. More...
class	DiscreteRatesAcrossSitesTreeLikelihoodInterface
	Interface for rate across sites (RAS) implementation. More...
class	DRASDRTreeLikelihoodLeafData
	Likelihood data structure for a leaf. More...
class	DRASDRTreeLikelihoodNodeData
	Likelihood data structure for a node. More...
class	DRASDRTreeLikelihoodData
	Likelihood data structure for rate across sites models, using a double-recursive algorithm. More...
class	DRASRTreeLikelihoodNodeData
	Likelihood data structure for a node. More...
class	DRASRTreeLikelihoodData
	discrete Rate Across Sites, (simple) Recursive likelihood data structure. More...
class	DRHomogeneousMixedTreeLikelihood
	A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model. More...
class	DRHomogeneousTreeLikelihood
	This class implements the likelihood computation for a tree using the double-recursive algorithm. More...
class	DRNonHomogeneousTreeLikelihood
	This class implements the likelihood computation for a tree using the double-recursive algorithm, allowing for non-homogeneous models of substitutions. More...
class	DRTreeLikelihoodInterface
	Interface for double-recursive (DR) implementation of the likelihood computation. More...
class	DRTreeLikelihoodTools
	Utilitary methods dealing with objects implementing the DRTreeLikelihood interface. More...
class	GlobalClockTreeLikelihoodFunctionWrapper
class	HomogeneousTreeLikelihood
	Specialization of the TreeLikelihood interface for the Homogeneous case. More...
class	LegacyMarginalAncestralStateReconstruction
	Likelihood ancestral states reconstruction: marginal method. More...
class	BranchLikelihood
	Compute likelihood for a 4-tree. More...
class	NNIHomogeneousTreeLikelihood
	This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class. More...
class	NonHomogeneousTreeLikelihood
	Specialization of the TreeLikelihood interface for the branch non-homogeneous and non-stationary models. More...
class	PairedSiteLikelihoods
	A container for paired-site likelihoods (likelihoods over the same sites for different models, especially topologies). An instance of this class is, roughly, a list of models, each of them having a name (stored in the modelNames attribute) and a set of site likelihoods (stored in the logLikelihoods attribute). More...
class	RASTools
	Tools to deal with Rates Across Sites (RAS) models. More...
class	RHomogeneousMixedTreeLikelihood
class	RHomogeneousTreeLikelihood
	This class implement the 'traditional' way of computing likelihood for a tree. More...
class	RNonHomogeneousMixedTreeLikelihood
class	RNonHomogeneousTreeLikelihood
	This class implement the 'traditional' way of computing likelihood for a tree, allowing for non-homogeneous models of substitutions. More...
class	SitePartitionHomogeneousTreeLikelihood
	Specialization of the TreeLikelihood interface for partition models, homogeneous case. More...
class	TreeLikelihoodInterface
	The TreeLikelihood interface. More...
class	TreeLikelihoodNodeData
	TreeLikelihood partial data structure. More...
class	TreeLikelihoodData
	TreeLikelihood data structure. More...
class	TreeLikelihoodTools
	Utilitary methods that work with TreeLikelihood objects. More...
class	LegacyMappingInterface
	General interface for storing mapping data. More...
class	LegacyAbstractMapping
	Partial implementation of the mapping interface. More...
class	LegacyProbabilisticRewardMapping
	Legacy data storage class for probabilistic rewards mappings. More...
class	LegacyProbabilisticSubstitutionMapping
	Legacy data storage class for probabilistic substitution mappings. More...
class	LegacyRewardMappingInterface
	Legacy interface for storing reward mapping data. More...
class	LegacyAbstractRewardMapping
	Partial implementation of the reward mapping interface. More...
class	LegacyRewardMappingTools
	Provide methods to compute reward mappings. More...
class	LegacySubstitutionMappingInterface
	Legacy interface for storing mapping data. More...
class	LegacyAbstractSubstitutionMapping
	Partial implementation of the substitution mapping interface. More...
class	LegacySubstitutionMappingTools
	Provide methods to compute substitution mappings. More...
class	MixedSubstitutionModelSet
	Substitution models manager for Mixed Substitution Models. This class inherits from SubstitutionModelSet. More...
class	SubstitutionModelSet
	Substitution models manager for non-homogeneous / non-reversible models of evolution. More...
class	SubstitutionModelSetTools
	Tools for automatically creating SubstitutionModelSet objects. More...
class	NNITopologyListener
	Listener used internally by the optimizeTreeNNI method. More...
class	NNITopologyListener2
	Listener used internally by the optimizeTreeNNI2 method. More...
class	LegacyOptimizationTools
	Optimization methods for phylogenetic inference. More...
class	SimData
class	NonHomogeneousSequenceSimulator
	(Legacy) Site and sequences simulation under non-homogeneous models. More...
class	AwareNode
	A node class aware of its neighbours. More...
class	NNITopologySearch
	NNI topology search method. More...
class	TreeIterator
class	PostOrderTreeIterator
class	PreOrderTreeIterator
class	InOrderTreeIterator
class	AbstractAutonomousSubstitutionProcess
	A partial implementation of the SubstitutionProcess interface. More...
class	AbstractSubstitutionProcess
	A partial implementation of the SubstitutionProcess interface. More...
class	AutoCorrelationSequenceEvolution
	Sequence evolution framework based on an auto-correlation of substitution processes. More...
class	AutonomousSubstitutionProcessInterface
	Interface for SubstitutionProcess objects that own their own ParametrizablePhyloTree & Scenario. More...
class	BackwardLikelihoodTree
class	CollectionNodes
class	Value
	Abstract Node storing a value of type T. More...
class	Node_DF
	Base dataflow Node class. More...
class	Context
	Context for dataflow node construction. More...
class	CWiseFill
class	CWiseMatching
class	CWiseCompound
class	CWisePattern
class	CWiseMatching< R, ReductionOf< T > >
class	CWiseCompound< R, ReductionOf< T > >
class	CWiseAdd
class	CWiseMean
class	CWiseSub
class	CWiseMul
class	CWiseDiv
class	MatrixProduct
class	CWiseNegate
class	CWiseInverse
class	CWiseLog
class	CWiseExp
class	CWiseConstantPow
class	ScalarProduct
class	LogSumExp
class	SumOfLogarithms
class	ShiftDelta
class	CombineDeltaShifted
class	CWiseApply
class	CWiseAdd< R, std::tuple< T0, T1 > >
class	CWiseSub< R, std::tuple< T0, T1 > >
class	CWiseAdd< R, ReductionOf< T > >
class	CWiseMean< R, ReductionOf< T >, ReductionOf< P > >
class	CWiseMean< R, ReductionOf< T >, P >
class	CWiseMul< R, std::tuple< T0, T1 > >
class	CWiseMul< R, ReductionOf< T > >
class	CWiseDiv< R, std::tuple< T0, T1 > >
struct	NumericalDerivativeConfiguration
	Configuration for a numerical derivation: what delta to use, and type of derivation. More...
class	ConstantTransitionFunction
struct	NoDimension
	Empty type representing no dimensions. More...
struct	MatrixDimension
	Basic matrix dimension type. More...
struct	VectorDimension
struct	RowVectorDimension
struct	Dimension
	Store a dimension for type T. More...
struct	Dimension< double >
	Specialisation of Dimension<T> for floating point types. More...
struct	Dimension< uint >
struct	Dimension< char >
struct	Dimension< std::string >
struct	Dimension< size_t >
struct	Dimension< float >
struct	Dimension< ExtendedFloat >
struct	Dimension< Parameter >
struct	Dimension< Eigen::Matrix< T, Rows, Cols > >
	Specialisation of Dimension<T> for eigen matrix types. More...
struct	Dimension< ExtendedFloatEigen< R, C, EigenType > >
struct	Dimension< TransitionFunction >
struct	ReductionOf
class	ConstantZero
	r = 0 for each component. More...
class	ConstantOne
	r = 1 for each component. More...
class	NumericConstant
	r = constant_value. More...
class	NumericMutable
	r = variable_value. More...
class	Convert
	r = convert(f). More...
struct	NumericalDependencyTransform
	Template struct used to describe a dependency transformation before compute(). More...
struct	Transposed
	The T dependency should be transposed before computation. More...
struct	NumericalDependencyTransform< Transposed< T > >
	Implementation for a dependency transposition. More...
class	Identity
	r = id(f) More...
class	ConfiguredDistribution
	Data flow node representing a DiscreteDistribution configured with parameter values. More...
class	ProbabilitiesFromDiscreteDistribution
class	ProbabilityFromDiscreteDistribution
class	CategoryFromDiscreteDistribution
class	ExtendedFloat
struct	ExtendedFloatEigenCore
class	ExtendedFloatEigenBase
class	ExtendedFloatEigen
class	ExtendedFloatArrayWrapper
class	ExtendedFloatVectorwiseOp
class	ExtendedFloatNoAlias
class	ExtendedFloatRow
class	ExtendedFloatCol
class	ForwardLikelihoodTree
class	ProbabilityDAG
class	ConfiguredFrequencySet
	Data flow node representing a Frequencies Set configured with parameter values. More...
class	FrequenciesFromFrequencySet
class	LikelihoodCalculation
class	AlignedLikelihoodCalculation
class	LikelihoodCalculationOnABranch
class	LikelihoodCalculationSingleProcess
class	ConfiguredModel
	Likelihood transition model. More...
class	EquilibriumFrequenciesFromModel
class	TransitionMatrixFromModel
class	TransitionFunctionFromModel
class	ProbabilitiesFromMixedModel
class	ProbabilityFromMixedModel
class	ConfiguredParameter
	Data flow node representing a parameter. More...
class	ShiftParameter
	shift param value = n * delta + x. More...
class	ValueFromConfiguredParameter
class	ConfiguredParametrizable
class	ProcessEdge
class	ProcessTree
class	Sequence_DF
	Data flow node representing a Sequence as a Value<Eigen::MatrixXd> with a name. More...
class	ConfiguredSimplex
	Data flow node representing a Frequencies Set configured with parameter values. More...
class	FrequenciesFromSimplex
class	ConfiguredTransitionMatrix
	Data flow node representing a TransitionMatrix configured with parameter values. More...
class	EquilibriumFrequenciesFromTransitionMatrix
class	TransitionMatrixFromTransitionMatrix
class	HmmEmissionProbabilities_Eigen
	Interface for computing emission probabilities in a Hidden Markov Model. More...
class	HmmProcessAlphabet
	Hidden states alphabet. More...
class	HmmSequenceEvolution
	Sequence evolution framework based on a hmm. More...
class	MarginalAncestralReconstruction
	Likelihood ancestral states reconstruction: marginal method. More...
class	MixtureSequenceEvolution
	Sequence evolution framework based on a mixture of substitution processes. More...
class	ModelPath
	Organization of submodels in mixed substitution models in a path. See class ModelScenario for a thorough description. More...
class	ModelScenario
	Organization of submodels in mixed substitution models as paths. More...
class	MultiProcessSequenceEvolution
	Partial implementation of multiple processes of sequences. More...
class	NonHomogeneousSubstitutionProcess
	Substitution process manager for non-homogeneous / non-reversible models of evolution. More...
class	OneProcessSequenceEvolution
	Evolution of a sequence performed by a unique SubstitutionProcess all along the sequence. More...
class	ParametrizablePhyloTree
	PhyloTree with Parametrizable Phylo Branches. They SHARE their branch length parameters. More...
class	PartitionSequenceEvolution
	Sequence evolution framework based on a mixture of substitution processes. More...
class	AbstractPhyloLikelihood
class	AlignedPhyloLikelihoodInterface
	The AlignedPhyloLikelihood interface, for phylogenetic likelihood. More...
class	AbstractAlignedPhyloLikelihood
class	AlignedPhyloLikelihoodAutoCorrelation
	Likelihood framework based on a hmm of simple likelihoods. More...
class	AlignedPhyloLikelihoodHmm
	Likelihood framework based on a hmm of simple likelihoods. More...
class	AlignedPhyloLikelihoodMixture
	Likelihood framework based on a mixture of aligned likelihoods. More...
class	AlignedPhyloLikelihoodProduct
	The AlignedPhyloLikelihoodProduct class, for phylogenetic likelihood on several independent data. More...
class	AlignedPhyloLikelihoodSetInterface
	Joint interface SetOf+Aligned PhylLikelihood. More...
class	AbstractAlignedPhyloLikelihoodSet
	The AlignedPhyloLikelihoodSet abstract class. More...
class	AutoCorrelationProcessPhyloLikelihood
	Likelihood framework based on an auto-correlation of simple likelihoods. More...
class	HmmLikelihood_DF
	A simple implementation of hidden Markov models recursion, in DataFlow implementation. More...
class	CondLikelihood
class	ForwardHmmLikelihood_DF
class	ForwardHmmDLikelihood_DF
class	ForwardHmmD2Likelihood_DF
class	BackwardHmmLikelihood_DF
class	HmmPhyloAlphabet
	Hidden states alphabet. More...
class	HmmPhyloEmissionProbabilities
	Emission probabilities in the context of DF phylolikeihoods. More...
class	HmmProcessPhyloLikelihood
	Likelihood framework based on a hmm of simple likelihoods. More...
class	MixtureProcessPhyloLikelihood
	Likelihood framework based on a mixture of simple likelihoods. More...
class	MultiProcessSequencePhyloLikelihood
	Partial implementation of the Likelihood interface for multiple processes. More...
class	OnABranchPhyloLikelihood
	Wraps a dataflow graph as a function: resultNode = f(variableNodes). More...
class	OneProcessSequencePhyloLikelihood
	The OneProcessSequencePhyloLikelihood class: phylogenetic likelihood computation with a single process. More...
struct	ProcPos
	Likelihood framework based on a partition of a sequence in simple likelihoods. More...
class	PartitionProcessPhyloLikelihood
class	PhyloLikelihoodInterface
	The PhyloLikelihood interface, for phylogenetic likelihood. More...
class	PhyloLikelihoodContainer
	The PhyloLikelihoodContainer, owns and assigns numbers to Phylolikelihoods. More...
class	PhyloLikelihoodFormula
	The PhyloLikelihoodFormula class, for phylogenetic likelihood on several independent data. More...
class	PhyloLikelihoodSetInterface
	The PhyloLikelihoodSet interface, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodContainer. More...
class	AbstractPhyloLikelihoodSet
	The PhyloLikelihoodSet class, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodContainer. More...
class	SequencePhyloLikelihoodInterface
	PhyloLikelihoods based on Sequence Evolution class, ie for which there is a (set of) processes able to build a sequence. More...
class	AbstractSequencePhyloLikelihood
class	AbstractParametrizableSequencePhyloLikelihood
class	SingleDataPhyloLikelihoodInterface
	The SingleDataPhyloLikelihood interface, for phylogenetic likelihood. More...
class	AbstractSingleDataPhyloLikelihood
class	SingleProcessPhyloLikelihood
	Wraps a dataflow graph as a function: resultNode = f(variableNodes). More...
class	ProcessComputationNode
	Tree Organization of Computing Nodes. More...
class	ProcessComputationEdge
class	ProcessComputationTree
class	RateAcrossSitesSubstitutionProcess
class	SequenceEvolution
	This interface describes the evolution process of a sequence. More...
class	SimpleSubstitutionProcess
	Space and time homogeneous substitution process, without mixture. More...
class	SitePartition
	This is the interface for classes describing a site partition, each partition being intended to have its own substitution model. More...
class	TrivialSitePartition
	Trivial site partition: all sites belong to the same, unique partition. More...
class	SubstitutionProcessInterface
	This interface describes the substitution process along the tree and sites of the alignment. More...
class	SubstitutionProcessCollection
	Collection of Substitution Process, which owns all the necessary objects: Substitution models, frequencies sets, rate distributions and trees. More...
class	SubstitutionProcessCollectionMember
class	BranchedModelSet
class	CategorySubstitutionRegister
	The CategorySubstitutionRegisters. More...
class	ComprehensiveSubstitutionRegister
	Distinguishes all types of substitutions. More...
class	GCSubstitutionRegister
	Distinguishes AT<->GC from GC<->AT. More...
class	GCSynonymousSubstitutionRegister
	Distinguishes AT->GC vs GC->AT inside synonymous substitutions on third codon position. More...
class	GCPositionSubstitutionRegister
	Distinguishes AT->GC vs GC->AT on given codon position (0, 1, or 2) More...
class	DecompositionMethods
	Methods useful for analytical substitution count and rewards using the eigen decomposition method. More...
class	DecompositionReward
	Analytical reward using the eigen decomposition method. More...
class	DecompositionSubstitutionCount
	Analytical substitution count using the eigen decomposition method. More...
class	LaplaceSubstitutionCount
	Laplace estimate of the substitution count. More...
class	MappingInterface
	General interface for storing mapping data. More...
class	AbstractMapping
	Partial implementation of the mapping interface. More...
class	NaiveSubstitutionCount
	Naive substitution count. More...
class	LabelSubstitutionCount
	Labelling substitution count. More...
class	OneJumpSubstitutionCount
	Computes the probability that at least one jump occurred on a branch, given the initial and final state. More...
class	PhyloBranchMapping
class	PhyloBranchReward
struct	ModelBranch
class	AbstractSinglePhyloSubstitutionMapping
	The AbstractSinglePhyloSubstitutionMapping class: substitution mapping linked with a Single Process PhyloLikelihood. More...
class	OneProcessSequenceSubstitutionMapping
	The OneProcessSequenceSubstitutionMapping class: substitution mapping linked with a OneProcessSequencePhyloLikelihood. More...
class	PhyloSubstitutionMapping
class	SingleProcessSubstitutionMapping
	The SingleProcessSubstitutionMapping class: substitution mapping linked with a SingleProcessPhyloLikelihood. More...
class	ProbabilisticRewardMapping
	Data storage class for probabilistic rewards mappings. More...
class	ProbabilisticSubstitutionMapping
	Data storage class for probabilistic substitution mappings. More...
class	Reward
	The Reward interface. More...
class	AbstractReward
	Basic implementation of the the Reward interface. More...
class	RewardMappingInterface
	General interface for storing reward mapping data. More...
class	AbstractRewardMapping
	Partial implementation of the substitution mapping interface. More...
class	RewardMappingTools
	Provide methods to compute reward mappings. More...
class	StochasticMapping
class	SubstitutionCountInterface
	The SubstitutionsCount interface. More...
class	AbstractSubstitutionCount
	Partial implementation of the SubstitutionCount interface. More...
class	SubstitutionDistance
	Interface allowing for using distances between states in substitution counts. More...
class	AbstractSubstitutionDistance
	Partial implementation of the SubstitutionDistance interface. More...
class	SubstitutionMapping
	General interface for storing mapping data. More...
class	AbstractSubstitutionMapping
	Partial implementation of the substitution mapping interface. More...
class	SubstitutionMappingTools
	Provide methods to compute substitution mappings. More...
class	SubstitutionRegisterInterface
	The SubstitutionRegister interface. More...
class	AbstractSubstitutionRegister
class	TotalSubstitutionRegister
	Count all substitutions. More...
class	CompleteSubstitutionRegister
	Completion of a given substitution register to consider all substitutions. The new substitutions are considered in an additional type. More...
class	VectorOfSubstitutionRegisters
	Sets a Register based on a vector of Registers. The categories are intersection of categories of those Registers. More...
class	GeneralSubstitutionRegister
	Sets a Register based on a matrix of integers. If M is the matrix, M[i,j] is the number of the substitution type from i to j, or 0 if there is no substitution type from i to j. More...
class	SelectedSubstitutionRegister
	Class inheriting from GeneralSubstitutionRegister, this one uses a special constructor which allows it to build a substitution matrix from string input specifying a desired substitutions. More...
class	AAInteriorSubstitutionRegister
	Indexes only intra amino-acid substitutions. Every group represents a substitutions for the same amino acid. Met and Trp are not taken into account due their non-degenerescence. More...
class	AAExteriorSubstitutionRegister
	Indexes only substitutions between amino-acids. Groups are distinguished by their direction. More...
class	TsTvSubstitutionRegister
	Distinguishes transitions from transversions. More...
class	SWSubstitutionRegister
	Distinguishes substitutions given the link between the changed nucleotides : S for strong (GC) and W for weak (AT). More...
class	DnDsSubstitutionRegister
	Distinguishes synonymous from non-synonymous substitutions. More...
class	KrKcSubstitutionRegister
	Count conservative and radical amino-acid substitutions. More...
class	UniformizationSubstitutionCount
	Analytical (weighted) substitution count using the uniformization method. More...
class	WeightedSubstitutionCount
	Interface allowing for weighting of substitution counts according to state properties. More...
class	AbstractWeightedSubstitutionCount
	Partial implementation of the WeightedSubstitutionCount interface. More...
class	AbstractBiblioMixedTransitionModel
	Abstract class for mixture models based on the bibliography. More...
class	AbstractBiblioTransitionModel
	Partial implementation of the SubstitutionModel interface for models that are set for matching the bibliography, and are only defined through a link to a "real" model. More...
class	AbstractBiblioSubstitutionModel
class	AbstractFromSubstitutionModelTransitionModel
	Virtual class of a Transition Model related to a given SubstitutionModel. More...
class	AbstractKroneckerWordSubstitutionModel
	Abstract Kronecker Word Model. More...
class	AbstractMixedTransitionModel
	Partial implementation for Mixed Transition models, defined as a mixture of "simple" substitution models. Each model has a specific probability and rate, with the constraint that the expectation (on the distribution of the models) of the rate of all the models equals one. More...
class	AbstractLkTransitionModel
	Partial implementation of the TransitionModel interface, with function for likelihood computations. More...
class	AbstractTransitionModel
	Partial implementation of the TransitionModel interface. More...
class	AbstractSubstitutionModel
class	AbstractReversibleSubstitutionModel
	Partial implementation of the ReversibleSubstitutionModel interface. More...
class	ModelList
	A list of models, for building a WordSubstitutionModel. More...
class	AbstractWordSubstitutionModel
	Abstract Basal class for words of substitution models. More...
class	AbstractWrappedModel
	Abstract class of Wrapping model class, where all methods are redirected from model(). More...
class	AbstractWrappedTransitionModel
class	AbstractTotallyWrappedTransitionModel
class	AbstractWrappedSubstitutionModel
class	AbstractTotallyWrappedSubstitutionModel
class	AnonymousSubstitutionModel
class	BinarySubstitutionModel
	The Model on two states. More...
class	AbstractCodonAAFitnessSubstitutionModel
	Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not. More...
class	AbstractCodonAARateSubstitutionModel
	Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, given an amino acid rate matrix (from a shared_ptr model). More...
class	AbstractCodonBGCSubstitutionModel
	Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, with gBGC. More...
class	AbstractCodonClusterAASubstitutionModel
	Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, with AA clustered. More...
class	AbstractCodonCpGSubstitutionModel
	Abstract class for modelling of CpG -> CpA or TpG (symmetric) hypermutability substitution rate inside codons. Note that the neihbouring effects between codons are not considered. More...
class	AbstractCodonDistanceSubstitutionModel
	Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models. More...
class	AbstractCodonFitnessSubstitutionModel
	Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not. More...
class	AbstractCodonFrequenciesSubstitutionModel
	Abstract Class for substitution models on codons parametrized by frequencies. More...
class	AbstractCodonPhaseFrequenciesSubstitutionModel
	Abstract Class for substitution models on codons parametrized by a frequency. More...
class	AbstractCodonSubstitutionModel
	Abstract class for substitution models on codons. More...
class	AbstractDFPSubstitutionModel
	Class for neutral substitution models on triplets, following the mutation process proposed in Doron-Fagenboim & Pupko, 2006, but without equilibrium frequencies. This model is an extension of Kimura 2-rates substitution model to codons. More...
class	AbstractKroneckerCodonSubstitutionModel
	Abstract class for substitution models on codons allowing multiple substitutions. More...
class	CodonAdHocSubstitutionModel
	Class for substitution models of codons with several layers of codon models. More...
class	CodonDistanceFrequenciesSubstitutionModel
	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models. More...
class	CodonDistancePhaseFrequenciesSubstitutionModel
	Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models. More...
class	CodonDistanceSubstitutionModel
	Class for substitution models of codons with non-synonymous/synonymous ratios of substitution rates defined through a distance between amino-acids. More...
class	CodonSameAARateSubstitutionModel
	Class for modelling of non-synonymous rates in codon models, such that the substitution rates between amino acids are similar to the ones in an amino acid rate matrix (from a shared_ptr model). More...
class	CoreCodonSubstitutionModelInterface
	Interface for codon models. More...
class	CodonSubstitutionModelInterface
class	CodonReversibleSubstitutionModelInterface
	Interface for reversible codon models. More...
class	DFP07
	Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions as parameterized in DFP model, with correction to mimic AA substitution rates from a given protein substitution model. More...
class	DFPDistanceFrequenciesSubstitutionModel
	Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions as parameterized in DFP model. More...
class	GY94
	The Goldman and Yang (1994) substitution model for codons. More...
class	KCM
	The general multiple substitution model for codons, from Zaheri & al, 2014. More...
class	KroneckerCodonDistanceFrequenciesSubstitutionModel
	Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions. More...
class	KroneckerCodonDistanceSubstitutionModel
	Class for non-synonymous substitution models on codons with parameterized nucleotidic models, with allowed multiple substitutions. More...
class	MG94
	The Muse and Gaut (1994) substitution model for codons. More...
class	RELAX
	The RELAX (2014) branch-site model for codons. More...
class	SENCA
	Class for non-synonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models. More...
class	TripletSubstitutionModel
	Class for neutral substitution models on triplets, which correspond to codons that do not have any significance (whether they are STOP or functional). More...
class	YN98
	The Yang and Nielsen (1998) substitution model for codons. More...
class	YNGP_M
	Abstract generic class for The Yang et al (2000) M substitution models for codons. al (2004). More...
class	YNGP_M1
	The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004). More...
class	YNGP_M10
	The Yang et al (2000) M10 substitution model for codons. More...
class	YNGP_M2
	The Yang et al (2000) M2 substitution model for codons, with the more realistic modification in Wong & al (2004). More...
class	YNGP_M3
	The Yang et al (2000) M3 substitution model for codons. More...
class	YNGP_M7
	The Yang et al (2000) M7 substitution model for codons. More...
class	YNGP_M8
	The Yang et al (2000) M8 substitution model for codons. More...
class	YNGP_M9
	The Yang et al (2000) M9 substitution model for codons. More...
class	D1WalkSubstitutionModel
	The D1Walk substitution model for Integer alphabet [0;N-1]. In this model, substitutions are possible between adjacent states only. The model is defined through an equilibrium distribution, and rates towards a state are proportional to its frequency at equilibrium. More...
class	EquiprobableSubstitutionModel
	The EquiprobableSubstitutionModel substitution model for any kind of alphabet. Jukes-Cantor models are specific case of this model, applied to nucleotides or proteins. More...
class	CodonFrequencySetInterface
	Parametrize a set of state frequencies for codons. More...
class	FullCodonFrequencySet
	A generic FrequencySet for Full Codon alphabets. More...
class	FixedCodonFrequencySet
	FrequencySet useful for homogeneous and stationary models, codon implementation. More...
class	UserCodonFrequencySet
class	FullPerAACodonFrequencySet
	FrequencySet integrating ProteinFrequencySet inside CodonFrequencySet. In this case, FrequencieSet defined inside each amino acid is parametrized as a FullFrequencySet. Hence there are 61-20=41 parameters in addition of the parameters of the ProteinFrequencySet. More...
class	CodonFromIndependentFrequencySet
	the Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero. More...
class	CodonFromUniqueFrequencySet
	the Frequencies in codons are the product of the frequencies for a unique FrequencySet in letters, with the frequencies of stop codons set to zero. More...
class	FrequencySetInterface
	Parametrize a set of state frequencies. More...
class	AbstractFrequencySet
	Basic implementation of the FrequencySet interface. More...
class	FullFrequencySet
	A generic FrequencySet allowing for the estimation of all frequencies. More...
class	FromModelFrequencySet
	FrequencySet defined from the equilibrium distribution of a given model. More...
class	MarkovModulatedFrequencySet
	FrequencySet to be used with a Markov-modulated substitution model. More...
class	FixedFrequencySet
	FrequencySet useful for homogeneous and stationary models. More...
class	UserFrequencySet
	FrequencySet to be read in a file. More specifically, a frequency set is read in a column of a given file, which column number is given in argument (default: 1). More...
class	MvaFrequencySet
	A frequencies set used to estimate frequencies at the root with the COaLA model. Frequencies at the root are optimized in the same way than the equlibrium frequencies on branches. Hyperparameters are used, which represent positions along the principal axes obtained from a preliminary Correspondence Analysis. From the optimized positions, the 20 frequencies are calculated. More...
class	NucleotideFrequencySetInterface
	Parametrize a set of state frequencies for nucleotides. More...
class	GCFrequencySet
	Nucleotide FrequencySet using only one parameter, the GC content. More...
class	FullNucleotideFrequencySet
	Nucleotide FrequencySet using three independent parameters (theta, theta1, theta2) to modelize the four frequencies: More...
class	FixedNucleotideFrequencySet
	FrequencySet useful for homogeneous and stationary models, nucleotide implementation. More...
class	UserNucleotideFrequencySet
	FrequencySet useful for homogeneous and stationary models, nucleotide implementation. More...
class	ProteinFrequencySetInterface
	Parametrize a set of state frequencies for proteins. More...
class	FullProteinFrequencySet
	Protein FrequencySet using 19 independent parameters to model the 20 frequencies. More...
class	FixedProteinFrequencySet
	FrequencySet useful for homogeneous and stationary models, protein implementation. More...
class	UserProteinFrequencySet
	FrequencySet from file. More...
class	WordFrequencySetInterface
	Frequencies in words computed from the frequencies on letters. The parameters are the parameters of the Frequencies on letters. The WordFrequencySet owns the std::shared_ptr<FrequencySet> it is built on. Interface class. More...
class	AbstractWordFrequencySet
class	WordFromIndependentFrequencySet
	the Frequencies in words are the product of Independent Frequencies in letters More...
class	WordFromUniqueFrequencySet
class	FromMixtureSubstitutionModel
	Model taken from a SubModel of a Mixture of SubstitutionModels. More...
class	G2001
	Galtier's 2001 covarion model. More...
class	InMixedSubstitutionModel
	SubModel taken from a MixedTransitionModel, kept in the context of the MixedTransitionModel (see FromMixtureSubstitutionModel for an out of context subModel). So "rate" and "scale" are set for the MixedTransitionModel. More...
class	KroneckerWordSubstitutionModel
	Basal class for words of substitution models with multiple substitutions. More...
class	MarkovModulatedSubstitutionModel
	Partial implementation of the Markov-modulated class of substitution models. More...
class	MixedTransitionModelInterface
	Interface for Transition models, defined as a mixture of "simple" transition models. More...
class	MixtureOfASubstitutionModel
class	MixtureOfATransitionModel
	Transition models defined as a mixture of nested substitution models. More...
class	MixtureOfSubstitutionModels
class	MixtureOfTransitionModels
	Transition models defined as a mixture of several substitution models. More...
class	MultinomialFromTransitionModel
	From a model, compute the likelihood of counts given an ancestral state. More...
class	F81
	The Felsenstein (1981) substitution model for nucleotides. More...
class	F84
	The Felsenstein (1984) substitution model for nucleotides. More...
class	gBGC
	gBGC model. More...
class	GTR
	The General Time-Reversible substitution model for nucleotides. More...
class	HKY85
	The Hasegawa M, Kishino H and Yano T (1985) substitution model for nucleotides. More...
class	JCnuc
	The Jukes-Cantor substitution model for nucleotides. More...
class	K80
	The Kimura 2-rates substitution model for nucleotides. More...
class	L95
	The no-strand bias substitution model for nucleotides, from Lobry 1995. The point of this model is that the substitution rate from a nucleotide N towards another M is the same as the rate from the complement of N towards the complement of M. Note that this model is not reversible. More...
class	NucleotideSubstitutionModelInterface
	Specialisation interface for nucleotide substitution model. More...
class	NucleotideReversibleSubstitutionModelInterface
	Specialisation interface for rversible nucleotide substitution model. More...
class	AbstractNucleotideSubstitutionModel
	Specialisation abstract class for nucleotide substitution model. More...
class	AbstractReversibleNucleotideSubstitutionModel
	Specialisation abstract class for reversible nucleotide substitution model. More...
class	RN95
	The model described by Rhetsky & Nei, where the only hypothesis is that the transversion rates are only dependent of the target nucleotide. This model is not reversible. More...
class	RN95s
	Intersection of models RN95 and L95. More...
class	SSR
	The Strand Symmetric Reversible substitution model for nucleotides. More...
class	T92
	The Tamura (1992) substitution model for nucleotides. More...
class	TN93
	The Tamura and Nei (1993) substitution model for nucleotides. More...
class	YpR
	YpR model. More...
class	YpR_Sym
	symmetrical YpR model. More...
class	YpR_Gen
	General YpR model. More...
class	OneChangeRegisterTransitionModel
	From a model, compute transition probabilities given there is at least a change of a category (ie a non null number in a register) in the branch. More...
class	OneChangeTransitionModel
	From a model, compute transition probabilities given there is at least a change in the branch. More...
class	POMO
class	Coala
	The Coala branch-heterogeneous amino-acid substitution model. More...
class	CoalaCore
	This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid substitution model. More...
class	DSO78
	The Dayhoff, Schwartz and Orcutt substitution model for proteins. More...
class	JCprot
	The Jukes-Cantor substitution model for proteins. More...
class	JTT92
	The Jones, Taylor and Thornton substitution model for proteins. More...
class	LG08
	The Le and Gascuel substitution model for proteins. More...
class	LG10_EX_EHO
	The Le and Gascuel (2010) EX_EHO substitution model for proteins. More...
class	LGL08_CAT
	The Le et al (2008) CAT substitution model for proteins. More...
class	LLG08_EHO
	The Le et al (2008) EH0 substitution model for proteins. More...
class	LLG08_EX2
	The Le et al (2008) EX2 substitution model for proteins. More...
class	LLG08_EX3
	The Le et al (2008) EX3 substitution model for proteins. More...
class	LLG08_UL2
	The Le et al (2008) UL2 substitution model for proteins. More...
class	LLG08_UL3
	The Le et al (2008) UL3 substitution model for proteins. More...
class	ProteinSubstitutionModelInterface
	Specialized interface for protein substitution model. More...
class	ProteinReversibleSubstitutionModelInterface
	Specialized interface for protein reversible substitution model. More...
class	AbstractProteinSubstitutionModel
	Specialisation abstract class for protein substitution model. More...
class	AbstractReversibleProteinSubstitutionModel
	Specialisation abstract class for reversible protein substitution model. More...
class	UserProteinSubstitutionModel
	Build an empirical protein substitution model from a file. More...
class	WAG01
	The Whelan and Goldman substitution model for proteins. More...
class	ConstantRateDistribution
class	ExponentialDiscreteRateDistribution
class	GammaDiscreteRateDistribution
class	GaussianDiscreteRateDistribution
class	RE08
	The Rivas-Eddy substitution model with gap characters. More...
class	RE08Nucleotide
	This is a wrapper class of RE08 for nucleotide substitution models. More...
class	RE08Protein
	This is a wrapper class of RE08 for protein substitution models. More...
class	RE08Codon
	This is a wrapper class of RE08 for codon substitution models. More...
class	RegisterRatesSubstitutionModel
	From a model, substitution rates are set into categories following a given register. Each substitution of a category is then multiplied by a rate parameter specific to this category. More...
class	StateMapInterface
	Map the states of a given alphabet which have a model state. More...
class	AbstractStateMap
	A convenience partial implementation of the StateMap interface. More...
class	CanonicalStateMap
	This class implements a state map where all resolved states are modeled. More...
class	MarkovModulatedStateMap
	This class implements a state map for Markov modulated models. More...
class	BranchModelInterface
	Interface for all Branch models. More...
class	TransitionModelInterface
	Interface for all transition models. More...
class	SubstitutionModelInterface
	Interface for all substitution models. More...
class	ReversibleSubstitutionModelInterface
	Interface for reversible substitution models. More...
class	TransitionFromTransitionModel
	From a transition model, compute the transition function probabilities. More...
class	TS98
	Tuffley and Steel's 1998 covarion model. More...
class	TwoParameterBinarySubstitutionModel
	The Model on two states. More...
class	WordSubstitutionModel
	Basal class for words of substitution models. More...
class	WrappedModelInterface
	Wrapping model interface. More...
class	WrappedTransitionModelInterface
class	WrappedSubstitutionModelInterface
class	NaNListener
	A listener which capture NaN function values and throw an exception in case this happens. More...
class	OptimizationTools
	Optimization methods for phylogenetic inference. More...
class	AbstractTreeParsimonyData
	Partial implementation of the TreeParsimonyData interface. More...
class	AbstractTreeParsimonyScore
	Partial implementation of the TreeParsimonyScore interface. More...
class	DRTreeParsimonyNodeData
	Parsimony data structure for a node. More...
class	DRTreeParsimonyLeafData
	Parsimony data structure for a leaf. More...
class	DRTreeParsimonyData
	Parsimony data structure for double-recursive (DR) algorithm. More...
class	DRTreeParsimonyScore
	Double recursive implementation of interface TreeParsimonyScore. More...
class	TreeParsimonyNodeDataInterface
	TreeParsimonyScore node data structure. More...
class	TreeParsimonyDataInterface
	TreeParsimonyScore data structure. More...
class	TreeParsimonyScoreInterface
	Compute a parsimony score. More...
class	PatternTools
	Utilitary methods to compute site patterns. More...
class	PhyloStatistics
	Compute several quantities on a tree simulateously, optimizing the recursions on the tree. More...
class	PseudoNewtonOptimizer
	This Optimizer implements Newton's algorithm for finding a minimum of a function. This is in fact a modified version of the algorithm, as suggested by Nicolas Galtier, for the purpose of optimizing phylogenetic likelihoods. More...
class	SiteSimulationResult
	Data structure to store the result of a DetailedSiteSimulator. More...
class	RASiteSimulationResult
	Data structure to store the result of a DetailedSiteSimulator. More...
class	DetailedSiteSimulatorInterface
	This interface adds the dSimulate method to the SiteSimulator interface. More...
class	EvolutionSequenceSimulator
class	GivenDataSubstitutionProcessSequenceSimulator
	Sequences simulation under a unique substitution process, but with site specific posterior probabilities. More...
class	GivenDataSubstitutionProcessSiteSimulator
	Site simulation under a unique substitution process, given data. More...
class	MutationPath
	This class is used by MutationProcess to store detailed results of simulations. More...
class	MutationProcess
	Interface for simulations. More...
class	AbstractMutationProcess
	Partial implementation of the MutationProcess interface. More...
class	SimpleMutationProcess
	Generally used mutation process model. More...
class	SelfMutationProcess
	This class is mainly for testing purpose. It allow "self" mutation of the kind i->i;. More...
class	SequenceSimulationTools
	Tools for sites and sequences simulation. More...
class	SequenceSimulatorInterface
	The SequenceSimulator interface. SequenceSimulator classes can simulate whole datasets. More...
class	SimpleSubstitutionProcessSequenceSimulator
	Sequences simulation under a unique substitution process. More...
class	SimProcessNode
class	SimProcessEdge
class	SimpleSubstitutionProcessSiteSimulator
	Site simulation under a unique substitution process. More...
class	SiteSimulatorInterface
	The SiteSimulator interface. SiteSimulator classes can simulate single sites. More...
class	SubstitutionProcessSequenceSimulator
	Sequences simulation under position specific substitution process. More...
class	SitePatterns
	Data structure for site patterns. More...
class	TreeTemplate
	The phylogenetic tree class. More...
class	BipartitionList
	This class deals with the bipartitions defined by trees. More...
class	BipartitionTools
	This class provides tools related to the BipartitionList class. More...
class	NNISearchable
	Interface for Nearest Neighbor Interchanges algorithms. More...
class	Node
	The phylogenetic node class. More...
class	NodeTemplate
	The NodeTemplate class. More...
class	PhyloBranch
class	PhyloBranchParam
class	NodeEvent
class	PhyloNode
class	PhyloTree
class	PhyloNodeException
	General exception thrown when something is wrong with a particular node. More...
class	PhyloNodePException
	General exception thrown when something is wrong with a particular node. More...
class	PhyloNodePropertyNotFoundException
	General exception thrown if a property could not be found. More...
class	PhyloNodeNotFoundException
	Exception thrown when something is wrong with a particular node. More...
class	PhyloBranchException
	General exception thrown when something is wrong with a particular branch. More...
class	PhyloBranchPException
	General exception thrown when something is wrong with a particular branch. More...
class	PhyloBranchPropertyNotFoundException
	General exception thrown if a property could not be found. More...
class	PhyloBranchNotFoundException
	Exception thrown when something is wrong with a particular branch. More...
class	PhyloTreeException
	General exception thrown when something wrong happened in a tree. More...
class	UnrootedPhyloTreeException
	Exception thrown when a tree is expected to be rooted. More...
class	PhyloTreeTools
	Generic utilitary methods dealing with trees. More...
class	TopologyChangeEvent
	Class for notifying new toplogy change events. More...
class	TopologyListener
	Implement this interface to be notified when the topology of a tree has changed during topology search. More...
class	TopologySearch
	Interface for topology search methods. More...
class	Tree
	Interface for phylogenetic tree objects. More...
class	NodeException
	General exception thrown when something is wrong with a particular node. More...
class	NodePException
	General exception thrown when something is wrong with a particular node. More...
class	PropertyNotFoundException
	General exception thrown if a property could not be found. More...
class	NodeNotFoundException
	Exception thrown when something is wrong with a particular node. More...
class	TreeException
	General exception thrown when something wrong happened in a tree. More...
class	UnrootedTreeException
	Exception thrown when a tree is expected to be rooted. More...
class	TreeTemplateTools
	Utilitary methods working with TreeTemplate and Node objects. More...
class	TreeTools
	Generic utilitary methods dealing with trees. More...

Typedefs
typedef AssociationDAGraphImplObserver< N, E, DAGlobalGraph >	AssociationDAGlobalGraphObserver
typedef AssociationGraphImplObserver< N, E, GlobalGraph >	AssociationGlobalGraphObserver
typedef AssociationTreeGraphImplObserver< N, E, TreeGlobalGraph >	AssociationTreeGlobalGraphObserver
typedef DAGraphImpl< GlobalGraph >	DAGlobalGraph
typedef TreeGraphImpl< GlobalGraph >	TreeGlobalGraph
typedef std::vector< std::complex< double > >	Vcomplex
typedef std::vector< Vcomplex >	VVcomplex
typedef std::vector< VVcomplex >	VVVcomplex
typedef std::vector< std::complex< long double > >	Vlcomplex
typedef std::vector< Vlcomplex >	VVlcomplex
typedef std::vector< VVlcomplex >	VVVlcomplex
typedef std::vector< double >	Vdouble
typedef std::vector< Vdouble >	VVdouble
typedef std::vector< VVdouble >	VVVdouble
typedef std::vector< VVVdouble >	VVVVdouble
typedef std::vector< long double >	Vldouble
typedef std::vector< Vldouble >	VVldouble
typedef std::vector< VVldouble >	VVVldouble
typedef std::vector< VVVldouble >	VVVVldouble
typedef std::vector< int >	Vint
typedef std::vector< Vint >	VVint
typedef std::vector< VVint >	VVVint
typedef std::vector< VVVint >	VVVVint
typedef std::vector< unsigned int >	Vuint
typedef std::vector< Vuint >	VVuint
typedef std::vector< VVuint >	VVVuint
typedef std::vector< VVVuint >	VVVVuint
typedef std::vector< std::string >	Comments
typedef TemplateAlignedSequenceContainer< Sequence, Site >	AlignedSequenceContainer
typedef TemplateAlignedSequenceContainer< ProbabilisticSequence, ProbabilisticSite >	ProbabilisticAlignedSequenceContainer
typedef TemplateAlignmentDataInterface< std::string >	AlignmentDataInterface
typedef TemplateSequenceContainerInterface< Sequence >	SequenceContainerInterface
typedef TemplateSequenceContainerInterface< ProbabilisticSequence >	ProbabilisticSequenceContainerInterface
typedef std::vector< size_t >	SequenceSelection
typedef std::vector< size_t >	SiteSelection
typedef TemplateSequenceDataInterface< std::string >	SequenceDataInterface
typedef TemplateSiteContainerInterface< Site, Sequence, std::string >	SiteContainerInterface
typedef TemplateSiteContainerInterface< ProbabilisticSite, ProbabilisticSequence, std::string >	ProbabilisticSiteContainerInterface
typedef SimpleTemplateSiteContainerIterator< Site, Sequence, std::string >	SimpleSiteContainerIterator
typedef SimpleTemplateSiteContainerIterator< ProbabilisticSite, ProbabilisticSequence, std::string >	SimpleProbabilisticSiteContainerIterator
typedef TemplateVectorSequenceContainer< Sequence >	VectorSequenceContainer
typedef TemplateVectorSequenceContainer< ProbabilisticSequence >	ProbabilisticVectorSequenceContainer
typedef TemplateVectorSiteContainer< Site, Sequence >	VectorSiteContainer
typedef TemplateVectorSiteContainer< ProbabilisticSite, ProbabilisticSequence >	ProbabilisticVectorSiteContainer
typedef TemplateCoreSymbolListInterface< int >	IntCoreSymbolListInterface
typedef TemplateCoreSymbolListInterface< std::vector< double > >	ProbabilisticCoreSymbolListInterface
typedef TemplateEventDrivenCoreSymbolListInterface< int >	IntEventDrivenCoreSymbolListInterface
typedef TemplateEventDrivenCoreSymbolListInterface< std::vector< double > >	ProbabilisticEventDrivenCoreSymbolListInterface
typedef CoreSymbolListListener< int >	IntSymbolListListener
typedef CoreSymbolListEditionEvent< int >	IntSymbolListEditionEvent
typedef CoreSymbolListInsertionEvent< int >	IntSymbolListInsertionEvent
typedef CoreSymbolListDeletionEvent< int >	IntSymbolListDeletionEvent
typedef CoreSymbolListSubstitutionEvent< int >	IntSymbolListSubstitutionEvent
typedef TemplateISequenceStream< Sequence >	ISequenceStream
typedef TemplateISequenceStream< SequenceWithQuality >	ISequenceWithQualityStream
typedef TemplateISequenceStream< ProbabilisticSequence >	IProbabilisticSequenceStream
typedef TemplateOSequenceStream< Sequence >	OSequenceStream
typedef TemplateOSequenceStream< SequenceWithQuality >	OSequenceWithQualityStream
typedef TemplateOSequenceStream< ProbabilisticSequence >	OProbabilisticSequenceStream
typedef NodeTemplate< TreeDrawingNodeInfo >	INode
typedef NodeTemplate< SimData >	SNode
using	SpeciationBackward = CWiseMul< MatrixLik, ReductionOf< MatrixLik > >
	: At the top of each edge below a speciation node More...
using	MixtureBackward = CWiseAdd< MatrixLik, ReductionOf< MatrixLik > >
	: At the top of each edge below a mixture node More...
using	BackwardTransition = MatrixProduct< MatrixLik, Transposed< Eigen::MatrixXd >, MatrixLik >
	: Above each node : bottom of an edge in case of transition from upper More...
using	BackwardProportion = CWiseMul< MatrixLik, std::tuple< double, MatrixLik > >
	: Above each node : in case of mixture of above edges More...
using	ConditionalLikelihood = Value< MatrixLik >
using	ConditionalLikelihoodRef = ValueRef< MatrixLik >
using	BackwardLikelihoodAbove = Value< MatrixLik >
using	BackwardLikelihoodAboveRef = ValueRef< MatrixLik >
using	NodeRef = std::shared_ptr< Node_DF >
using	NodeRefVec = std::vector< NodeRef >
	Alias for a dependency vector (of NodeRef). More...
template<typename T >
using	ValueRef = std::shared_ptr< Value< T > >
	Shared pointer alias for Value<T>. More...
typedef Eigen::Matrix< size_t, -1, 1 >	PatternType
typedef Eigen::Matrix< size_t, -1, 2 >	MatchingType
template<typename eVector , typename bVector >
using	ForConvert = typename std::enable_if<((std::is_same< bVector, Vdouble >::value||std::is_same< bVector, std::vector< ExtendedFloat > >::value) &&(std::is_same< eVector, Eigen::RowVectorXd >::value||std::is_same< eVector, Eigen::VectorXd >::value)), bool >::type
template<typename eVector >
using	EFVector = typename std::enable_if<(std::is_same< eVector, ExtendedFloatRowVectorXd >::value||std::is_same< eVector, ExtendedFloatVectorXd >::value), bool >::type
template<typename eVector >
using	EFoutput = typename std::enable_if<(std::is_same< eVector, ExtendedFloatRowVectorXd >::value||std::is_same< eVector, ExtendedFloatVectorXd >::value), bool >::type
template<typename eVector , typename bVector >
using	ForConvert2 = typename std::enable_if<((std::is_same< bVector, Vdouble >::value||std::is_same< bVector, std::vector< ExtendedFloat > >::value) &&(std::is_same< eVector, Eigen::RowVectorXd >::value||std::is_same< eVector, Eigen::VectorXd >::value||std::is_same< eVector, ExtendedFloatVectorXd >::value||std::is_same< eVector, ExtendedFloatRowVectorXd >::value)), bool >::type
using	TransitionFunction = std::function< VectorLik(const VectorLik &)>
typedef ExtendedFloatMatrixXd	MatrixLik
typedef ExtendedFloatRowVectorXd	RowLik
typedef ExtendedFloatVectorXd	VectorLik
typedef ExtendedFloat	DataLik
typedef std::vector< DataLik >	VDataLik
typedef std::vector< VDataLik >	VVDataLik
template<int R, int C>
using	EFMatrix = Eigen::Matrix< double, R, C >
template<int R, int C>
using	EFArray = Eigen::Array< double, R, C >
template<int R, int C>
using	ExtendedFloatMatrix = ExtendedFloatEigen< R, C, EFMatrix >
template<int R, int C>
using	ExtendedFloatArray = ExtendedFloatEigen< R, C, EFArray >
template<int R>
using	ExtendedFloatVector = ExtendedFloatMatrix< R, 1 >
template<int C>
using	ExtendedFloatRowVector = ExtendedFloatMatrix< 1, C >
typedef ExtendedFloatMatrix< Eigen::Dynamic, Eigen::Dynamic >	ExtendedFloatMatrixXd
typedef ExtendedFloatRowVector< Eigen::Dynamic >	ExtendedFloatRowVectorXd
typedef ExtendedFloatVector< Eigen::Dynamic >	ExtendedFloatVectorXd
typedef ExtendedFloatArray< Eigen::Dynamic, 1 >	ExtendedFloatArrayXd
using	SpeciationForward = CWiseMul< MatrixLik, ReductionOf< MatrixLik > >
using	MixtureForward = CWiseAdd< MatrixLik, ReductionOf< MatrixLik > >
using	ForwardTransition = MatrixProduct< MatrixLik, Eigen::MatrixXd, MatrixLik >
	forwardLikelihood = f(transitionMatrix, conditionalLikelihood). More...
using	ForwardTransitionFunction = CWiseApply< MatrixLik, MatrixLik, TransitionFunction >
using	ForwardProportion = CWiseMul< MatrixLik, std::tuple< double, MatrixLik > >
	forwardLikelihood = f(transitionMatrix, proportion). More...
using	ConditionalLikelihoodForward = Value< MatrixLik >
	Interface LikelihoodTree data structure. More...
using	ConditionalLikelihoodForwardRef = ValueRef< MatrixLik >
using	ForwardLikelihoodBelow = Value< MatrixLik >
using	ForwardLikelihoodBelowRef = ValueRef< MatrixLik >
using	DAGindexes = std::vector< uint >
	Helper: create a map with mutable dataflow nodes for each branch of the tree. The map is indexed by branch ids. More...
using	Speciesindex = uint
using	Proba = Value< double >
	DAG with the same shape as ForwardLikelihoodTree with computations of probabilities of nodes & branches. More...
using	ProbaRef = std::shared_ptr< Value< double > >
using	DAProb = AssociationDAGlobalGraphObserver< Proba, Proba >
using	ProbaMul = CWiseMul< double, std::tuple< double, double > >
using	ProbaSum = CWiseAdd< double, ReductionOf< double > >
using	SiteLikelihoods = Value< RowLik >
using	SiteLikelihoodsRef = ValueRef< RowLik >
using	LikelihoodFromRootConditionalAtRoot = MatrixProduct< RowLik, Eigen::RowVectorXd, MatrixLik >
using	TotalLogLikelihood = SumOfLogarithms< RowLik >
	totalLikelihood = product_site likelihood(site). More...
using	BuildConditionalLikelihood = CWiseMul< MatrixLik, std::tuple< MatrixLik, MatrixLik > >
	Conditionallikelihood = AboveConditionalLikelihood * BelowConditionalLikelihood. More...
using	AllRatesSiteLikelihoods = MatrixLik
using	SiteWeights = NumericConstant< Eigen::RowVectorXi >
using	LikelihoodFromRootConditional = MatrixProduct< RowLik, RowLik, MatrixLik >
	likelihood = f(equilibriumFrequencies, rootConditionalLikelihood). More...
using	ConditionalLikelihoodDAG = AssociationDAGlobalGraphObserver< ConditionalLikelihood, uint >
using	ConditionalLikelihoodTree = AssociationTreeGlobalGraphObserver< ConditionalLikelihood, uint >
using	SiteLikelihoodsDAG = AssociationDAGlobalGraphObserver< SiteLikelihoods, uint >
using	SiteLikelihoodsTree = AssociationTreeGlobalGraphObserver< SiteLikelihoods, uint >
typedef ProcessComputationNode	ProcessNode
using	ProcessEdgePtr = std::shared_ptr< ProcessEdge >
using	ProcessNodePtr = std::shared_ptr< ProcessNode >
using	EmissionLogk = CWiseCompound< MatrixLik, ReductionOf< RowLik > >
using	ProcessComputationNodeRef = std::shared_ptr< ProcessComputationNode >
using	BaseTree = AssociationTreeGlobalGraphObserver< ProcessComputationNode, ProcessComputationEdge >
typedef std::bitset< 21 >	Bitset
typedef AssociationTreeGlobalGraphObserver< SimProcessNode, SimProcessEdge >	SPTree

Enumerations
enum class	DotOptions { None = 0 , DetailedNodeInfo = 1 << 0 , FollowUpwardLinks = 1 << 1 , ShowDependencyIndex = 1 << 2 }
enum class	NumericalProperty { Constant , ConstantZero , ConstantOne , ConstantIdentity }
	Numerical properties for DF Node. More...
enum class	NumericalDerivativeType { Disabled , ThreePoints , FivePoints }

Functions
std::ostream &	operator<< (std::ostream &out, const BppBoolean &s)
std::ostream &	operator<< (std::ostream &out, const BppString &s)
bool	operator== (const Matrix< Scalar > &m1, const Matrix< Scalar > &m2)
std::vector< T >	operator+ (const std::vector< T > &v1, const std::vector< T > &v2)
std::vector< T >	operator- (const std::vector< T > &v1, const std::vector< T > &v2)
std::vector< T >	operator* (const std::vector< T > &v1, const std::vector< T > &v2)
std::vector< T >	operator/ (const std::vector< T > &v1, const std::vector< T > &v2)
std::vector< T >	operator+ (const std::vector< T > &v1, const C &c)
std::vector< T >	operator+ (const C &c, const std::vector< T > &v1)
std::vector< T >	operator- (const std::vector< T > &v1, const C &c)
std::vector< T >	operator- (const C &c, const std::vector< T > &v1)
std::vector< T >	operator* (const std::vector< T > &v1, const C &c)
std::vector< T >	operator* (const C &c, const std::vector< T > &v1)
std::vector< T >	operator/ (const std::vector< T > &v1, const C &c)
std::vector< T >	operator/ (const C &c, const std::vector< T > &v1)
void	operator+= (std::vector< T > &v1, const std::vector< T > &v2)
void	operator-= (std::vector< T > &v1, const std::vector< T > &v2)
void	operator*= (std::vector< T > &v1, const std::vector< T > &v2)
void	operator/= (std::vector< T > &v1, const std::vector< T > &v2)
void	operator&= (std::vector< T > &v1, const C &c)
void	operator+= (std::vector< T > &v1, const C &c)
void	operator-= (std::vector< T > &v1, const C &c)
void	operator*= (std::vector< T > &v1, const C &c)
void	operator/= (std::vector< T > &v1, const C &c)
std::string	prettyTypeName (const std::type_info &type_info)
	Debug: return a readable name for a C++ type descriptor (from typeid operator). More...
bool	isTransitivelyDependentOn (const Node_DF &searchedDependency, const Node_DF &node)
	Check if searchedDependency if a transitive dependency of node. More...
NodeRef	recreateWithSubstitution (Context &c, const NodeRef &node, const std::unordered_map< const Node_DF *, NodeRef > &substitutions)
	Recreate node by transitively replacing dependencies according to substitutions mapping. More...
DotOptions	operator| (DotOptions a, DotOptions b)
bool	operator& (DotOptions a, DotOptions b)
static std::string	dotLabelEscape (const std::string &s)
static std::string	dotIdentifier (const Node_DF &node)
static void	writeDotNode (std::ostream &os, const Node_DF &node, DotOptions opt)
static void	writeDotEdge (std::ostream &os, const Node_DF &from, std::size_t depIndex, DotOptions opt)
static void	writeGraphStructure (std::ostream &os, const std::vector< const Node_DF * > &entryPoints, DotOptions opt)
void	writeGraphToDot (std::ostream &os, const std::vector< const Node_DF * > &nodes, DotOptions opt=DotOptions::None)
	Write dataflow graph starting at nodes to output stream. More...
void	writeGraphToDot (const std::string &filename, const std::vector< const Node_DF * > &nodes, DotOptions opt=DotOptions::None)
	Write dataflow graph starting at nodes to file at filename, overwriting it. More...
template<typename T >
void	combineHash (std::size_t &seed, const T &t)
	Combine hashable value to a hash, from Boost library. More...
template<typename T >
std::string	to_string_with_precision (const T a_value, const int n=6)
	Output with given precision. More...
template<typename T , typename U >
std::shared_ptr< T >	convertRef (const std::shared_ptr< U > &from)
	Convert a node ref with runtime type check. More...
template<typename T >
const T &	accessValueConstCast (const Node_DF &node)
template<typename T >
std::shared_ptr< T >	cachedAs (Context &c, std::shared_ptr< T > &&newNode)
	Helper: Same as Context::cached but with a shared_ptr<T> node. More...
template<typename T >
std::shared_ptr< T >	cachedAs (Context &c, std::shared_ptr< T > &newNode)
void	failureDeltaNotDerivable (const std::type_info &contextNodeType)
void	failureNumericalDerivationNotConfigured ()
template<typename NodeT , typename DepT , typename B >
ValueRef< NodeT >	generateNumericalDerivative (Context &c, const NumericalDerivativeConfiguration &config, NodeRef dep, const Dimension< DepT > &depDim, Dimension< NodeT > &nodeDim, B buildNodeWithDep)
	Helper used to generate data flow expressions computing a numerical derivative. More...
template<typename NodeT , typename B >
ValueRef< NodeT >	generateNumericalDerivative (Context &c, const NumericalDerivativeConfiguration &config, NodeRef dep, const Dimension< NodeT > &nodeDim, B buildNodeWithDep)
template void	copyBppToEigen (const std::vector< ExtendedFloat > &bppVector, Eigen::RowVectorXd &eigenVector)
template void	copyBppToEigen (const std::vector< ExtendedFloat > &bppVector, Eigen::VectorXd &eigenVector)
template void	copyBppToEigen (const std::vector< ExtendedFloat > &bppVector, ExtendedFloatRowVectorXd &eigenVector)
template void	copyBppToEigen (const bpp::Vdouble &bppVector, Eigen::RowVectorXd &eigenVector)
template void	copyBppToEigen (const bpp::Vdouble &bppVector, Eigen::VectorXd &eigenVector)
template void	copyBppToEigen (const bpp::Vdouble &bppVector, ExtendedFloatRowVectorXd &eigenVector)
void	copyBppToEigen (const std::vector< ExtendedFloatVectorXd > &bppVector, ExtendedFloatMatrixXd &eigenVector)
void	copyBppToEigen (const std::vector< Eigen::VectorXd > &bppVector, Eigen::MatrixXd &eigenMatrix)
void	copyBppToEigen (const bpp::Matrix< double > &bppMatrix, ExtendedFloatMatrixXd &eigenMatrix)
void	copyBppToEigen (const bpp::Matrix< double > &bppMatrix, Eigen::MatrixXd &eigenMatrix)
template void	copyEigenToBpp (const ExtendedFloatMatrixXd &eigenMatrix, std::vector< std::vector< double >> &bppMatrix)
template void	copyEigenToBpp (const ExtendedFloatMatrixXd &eigenMatrix, std::vector< std::vector< bpp::ExtendedFloat >> &bppMatrix)
template void	copyEigenToBpp (const Eigen::MatrixXd &eigenMatrix, std::vector< std::vector< double >> &bppMatrix)
template void	copyEigenToBpp (const Eigen::MatrixXd &eigenMatrix, std::vector< std::vector< bpp::ExtendedFloat >> &bppMatrix)
void	copyEigenToBpp (const MatrixLik &eigenMatrix, bpp::Matrix< double > &bppMatrix)
template void	copyEigenToBpp (const RowLik &eigenVector, Vdouble &bppVector)
template void	copyEigenToBpp (const RowLik &eigenVector, std::vector< ExtendedFloat > &bppVector)
std::string	to_string (const NoDimension &)
std::string	to_string (const MatrixDimension &dim)
std::size_t	hash (const MatrixDimension &dim)
void	checkRecreateWithoutDependencies (const std::type_info &contextNodeType, const NodeRefVec &deps)
template<typename eVector , typename bVector , ForConvert< eVector, bVector > = true>
void	copyBppToEigen (const bVector &bppVector, eVector &eigenVector)
template<typename eVector , EFVector< eVector > = true>
void	copyBppToEigen (const std::vector< ExtendedFloat > &bppVector, eVector &eigenVector)
template<typename eVector , EFoutput< eVector > = true>
void	copyBppToEigen (const Vdouble &bppVector, eVector &eigenVector)
template<typename eType , typename = typename std::enable_if<(std::is_same<eType, double>::value || std::is_same<eType, ExtendedFloat>::value)>::type>
void	copyEigenToBpp (const ExtendedFloatMatrixXd &eigenMatrix, std::vector< std::vector< eType >> &bppMatrix)
template<typename eType , typename = typename std::enable_if<(std::is_same<eType, double>::value || std::is_same<eType, ExtendedFloat>::value)>::type>
void	copyEigenToBpp (const Eigen::MatrixXd &eigenMatrix, std::vector< std::vector< eType >> &bppMatrix)
template<typename eVector , typename bVector , ForConvert2< bVector, eVector > = true>
void	copyEigenToBpp (const bVector &eigenVector, eVector &bppVector)
std::size_t	hash (const NoDimension &)
bool	operator== (const NoDimension &, const NoDimension &)
bool	operator!= (const NoDimension &, const NoDimension &)
bool	operator== (const MatrixDimension &lhs, const MatrixDimension &rhs)
bool	operator!= (const MatrixDimension &lhs, const MatrixDimension &rhs)
template<typename Predicate >
void	removeDependenciesIf (NodeRefVec &deps, Predicate p)
template<typename T >
constexpr T	constexpr_power (T d, int n)
int	powi (int base, unsigned int exp)
std::ostream &	operator<< (std::ostream &os, const ExtendedFloat &ef)
std::string	to_string (const ExtendedFloat &ef)
double	log (const ExtendedFloat &ef)
ExtendedFloat	operator* (const double &lhs, const ExtendedFloat &rhs)
ExtendedFloat	operator- (const double &lhs, const ExtendedFloat &rhs)
ExtendedFloat	operator+ (const double &lhs, const ExtendedFloat &rhs)
ExtendedFloat	operator/ (const double &lhs, const ExtendedFloat &rhs)
ExtendedFloat	pow (const ExtendedFloat &ef, double exp)
ExtendedFloat	exp (const ExtendedFloat &ef)
ExtendedFloat	abs (const ExtendedFloat &ef)
double	convert (const bpp::ExtendedFloat &ef)
template<int R, int C>
ExtendedFloatArray< R, C >	log (const ExtendedFloatArray< R, C > &arr)
template<int R, int C, template< int R2=R, int C2=C > class MatType>
ExtendedFloatEigen< R, C, MatType >	exp (const ExtendedFloatEigen< R, C, MatType > &arr)
template<int R, int C>
ExtendedFloatArray< R, C >	pow (const ExtendedFloatArray< R, C > &obj, double exp)
template<int R, int C>
ExtendedFloatArray< R, C >	pow (const ExtendedFloatArray< R, C > &obj, int exp)
template<int R, int C, template< int R2=R, int C2=C > class MatType, typename T >
std::enable_if< std::is_same< T, ExtendedFloat >::value||std::is_floating_point< T >::value||std::is_integral< T >::value, ExtendedFloatEigen< R, C, MatType > >::type	operator+ (const T &d, const ExtendedFloatEigen< R, C, MatType > rhs)
template<int R, int C, template< int R2=R, int C2=C > class MatType, typename T >
std::enable_if< std::is_same< T, ExtendedFloat >::value||std::is_floating_point< T >::value||std::is_integral< T >::value, ExtendedFloatEigen< R, C, MatType > >::type	operator- (const T &d, const ExtendedFloatEigen< R, C, MatType > rhs)
template<int R, int C, template< int R2=R, int C2=C > class MatType, typename T >
std::enable_if< std::is_same< T, ExtendedFloat >::value||std::is_floating_point< T >::value||std::is_integral< T >::value, ExtendedFloatEigen< R, C, MatType > >::type	operator* (const T &fact, const ExtendedFloatEigen< R, C, MatType > mat)
template<typename Derived , typename EFType >
EFType	operator* (const Eigen::EigenBase< Derived > &lhs, const ExtendedFloatEigenBase< EFType > &rhs)
template<int R, int C>
ExtendedFloatArray< R, C >	operator* (const ExtendedFloatArray< R, C > &lhs, const ExtendedFloatArrayWrapper< R, C > &rhs)
Dimension< TransitionFunction >	transitionFunctionDimension (Eigen::Index nbState)
MatrixDimension	conditionalLikelihoodDimension (Eigen::Index nbState, Eigen::Index nbSite)
MatrixDimension	transitionMatrixDimension (std::size_t nbState)
RowVectorDimension	equilibriumFrequenciesDimension (std::size_t nbState)
std::unordered_map< std::string, std::shared_ptr< ConfiguredParameter > >	createParameterMap (Context &c, const ParameterAliasable &parametrizable)
std::unordered_map< std::string, std::shared_ptr< ConfiguredParameter > >	createParameterMap (Context &c, const Parametrizable &parametrizable)
NodeRefVec	createDependencyVector (const Parametrizable &parametrizable, const std::function< NodeRef(const std::string &)> &parameter)
NodeRefVec	createDependencyVector (const ParameterAliasable &parametrizable, const std::function< NodeRef(const std::string &)> &parameter)
NodeRefVec	createDependencyVector (const Parametrizable &parametrizable, const std::function< NodeRef(const std::string &)> &getParameter)
	Create a dependency vector suitable for a parametrizable class constructor. The vector is built from parameter names, and an opaque accessor function. For each named parameter, parameter(name) should return a valid node. If no node is found (NodeRef was null), an exception is thrown. Returned nodes must be Value<double> nodes. More...
NodeRefVec	createDependencyVector (const ParameterAliasable &parametrizable, const std::function< NodeRef(const std::string &)> &getParameter)
ParametrizableCollection< ConfiguredModel >	makeConfiguredModelCollection (Context &context, const SubstitutionProcessInterface &process, ParameterList &parList)
	Make a Collection of ConfiguredModel, from the models described in the SubstitutionProcess, and sharing ConfiguredParameters from a ParameterList. More...
Error functions (generate a message and throw exceptions).
void	failureComputeWasCalled (const std::type_info &nodeType)
void	failureNodeConversion (const std::type_info &handleType, const Node_DF &node)
void	failureDependencyNumberMismatch (const std::type_info &contextNodeType, std::size_t expectedSize, std::size_t givenSize)
void	failureEmptyDependency (const std::type_info &contextNodeType, std::size_t depIndex)
void	failureDependencyTypeMismatch (const std::type_info &contextNodeType, std::size_t depIndex, const std::type_info &expectedType, const std::type_info &givenNodeType)
Basic dependency check primitives
Checks the size of a dependency vector, throws if mismatch.
void	checkDependencyVectorSize (const std::type_info &contextNodeType, const NodeRefVec &deps, std::size_t expectedSize)
void	checkDependencyVectorMinSize (const std::type_info &contextNodeType, const NodeRefVec &deps, std::size_t expectedMinSize)
	Checks the minimum size of a dependency vector, throws if mismatch. More...
void	checkDependenciesNotNull (const std::type_info &contextNodeType, const NodeRefVec &deps)
	Checks that all dependencies are not null, throws if not. More...
void	checkNthDependencyNotNull (const std::type_info &contextNodeType, const NodeRefVec &deps, std::size_t index)
template<typename T >
void	checkNthDependencyIs (const std::type_info &contextNodeType, const NodeRefVec &deps, std::size_t index)
	Checks that deps[index] is a T node, throws if not. More...
template<typename T1 , typename T2 >
void	checkNthDependencyIs (const std::type_info &contextNodeType, const NodeRefVec &deps, std::size_t index)
	Checks that deps[index] is a T1 or a T2 node, throws if not. More...
template<typename T >
void	checkDependencyRangeIs (const std::type_info &contextNodeType, const NodeRefVec &deps, std::size_t start, std::size_t end)
	Check that deps[start, end[ contains T, throws if not. More...
template<typename T >
void	checkNthDependencyIsValue (const std::type_info &contextNodeType, const NodeRefVec &deps, std::size_t index)
	Checks that deps[index] is a Value<T> node, throws if not. More...
template<typename T >
void	checkDependencyRangeIsValue (const std::type_info &contextNodeType, const NodeRefVec &deps, std::size_t start, std::size_t end)
	Check that deps[start, end[ contains Value<T> nodes, throws if not. More...

Variables
NumericConstant< char >	NodeX ('X')

Detailed Description

Defines the basic types of data flow nodes.

POMO-like Model, based on AllelicAlphabet.

In the alphabet from which the AllelicAlphabet is built, this model needs a given mutation model with generator (aka SubstitutionModel in Bio++), and allele selection coefficients from a finesse vector (aka FrequencySet in Bio++).

If we denote this fitness, the drift term towards the fixation of allele is proportional , and follows the Moran law.

We set the generator of the model on set of states ,\ with the reversible mutation rates, with the equilibrium distribution of this mutation model, and , and the fitnesses of the states:

(with )

The equilibrium distribution is:

with

The generator should be normalized to ensure one substitution per unit of time. See document online:

https://www.overleaf.com/project/639760f5aacdcfbde3ced551

See:

De Maio, N., Schrempf, D., and Kosiol, C. (2015). PoMo: An allele frequency-based approach for 279 species tree estimation. Systematic Biology, 64(6):1018–1031.

Borges R, Szöllősi GJ, Kosiol C. Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models. Genetics. 2019 Aug;212(4):1321-1336.

Borges, R. and Kosiol, C. (2020). Consistency and identifiability of the polymorphism-aware phylo-genetic models. Journal of Theoretical Biology, 486:110074.

Typedef Documentation

AllRatesSiteLikelihoods

typedef MatrixLik bpp::AllRatesSiteLikelihoods

Definition at line 55 of file LikelihoodCalculationOnABranch.h.

BackwardLikelihoodAbove

typedef Value< MatrixLik > bpp::BackwardLikelihoodAbove

Definition at line 74 of file BackwardLikelihoodTree.h.

BackwardLikelihoodAboveRef

typedef ValueRef< MatrixLik > bpp::BackwardLikelihoodAboveRef

Definition at line 75 of file BackwardLikelihoodTree.h.

BackwardProportion

using bpp::BackwardProportion = typedef CWiseMul<MatrixLik, std::tuple<double, MatrixLik> >

: Above each node : in case of mixture of above edges

• backwardlikelihood: Matrix(state, site).
• proportion: Double
• conditionalLikelihood: Matrix(state, site).

f(State, site) = c(fromState, site) * prop

Definition at line 67 of file BackwardLikelihoodTree.h.

BackwardTransition

using bpp::BackwardTransition = typedef MatrixProduct<MatrixLik, Transposed<Eigen::MatrixXd>, MatrixLik>

: Above each node : bottom of an edge in case of transition from upper

backwardLikelihood = f(transitionMatrix, conditionalLikelihood).

• backwardLikelihood: Matrix(state, site).
• transitionMatrix: Matrix (FromState, toState)
• conditionalLikelihood: Matrix(state, site).

f(fromState, site) = sum_toState P(fromState, toState) * c(toState, site). Using matrix multiply: f = transposed(transitionMatrix) * c.

Definition at line 55 of file BackwardLikelihoodTree.h.

BaseTree

using bpp::BaseTree = typedef AssociationTreeGlobalGraphObserver<ProcessComputationNode, ProcessComputationEdge>

Definition at line 156 of file ProcessComputationTree.h.

Bitset

typedef std::bitset<21> bpp::Bitset

Definition at line 20 of file DRTreeParsimonyData.h.

BuildConditionalLikelihood

typedef CWiseMul< MatrixLik, std::tuple< MatrixLik, MatrixLik > > bpp::BuildConditionalLikelihood

Conditionallikelihood = AboveConditionalLikelihood * BelowConditionalLikelihood.

lik(state, site) = above(state, site) * below(state,site) Using member wise multiply

Definition at line 41 of file LikelihoodCalculationOnABranch.h.

ConditionalLikelihood

typedef Value< MatrixLik > bpp::ConditionalLikelihood

Definition at line 70 of file BackwardLikelihoodTree.h.

ConditionalLikelihoodDAG

using bpp::ConditionalLikelihoodDAG = typedef AssociationDAGlobalGraphObserver<ConditionalLikelihood, uint>

Definition at line 102 of file LikelihoodCalculationSingleProcess.h.

ConditionalLikelihoodForward

using bpp::ConditionalLikelihoodForward = typedef Value<MatrixLik>

Interface LikelihoodTree data structure.

Stores all the inner computations:

• conditional likelihoods for each node,
• correspondence between sites in the dataset and array indices.

The structure is initiated according to a tree topology, and data can be retrieved through node ids.

See also

LikelihoodNode

Definition at line 89 of file ForwardLikelihoodTree.h.

ConditionalLikelihoodForwardRef

using bpp::ConditionalLikelihoodForwardRef = typedef ValueRef<MatrixLik>

Definition at line 90 of file ForwardLikelihoodTree.h.

ConditionalLikelihoodRef

typedef ValueRef< MatrixLik > bpp::ConditionalLikelihoodRef

Definition at line 71 of file BackwardLikelihoodTree.h.

ConditionalLikelihoodTree

using bpp::ConditionalLikelihoodTree = typedef AssociationTreeGlobalGraphObserver<ConditionalLikelihood, uint>

Definition at line 104 of file LikelihoodCalculationSingleProcess.h.

DAGindexes

typedef std::vector< uint > bpp::DAGindexes

Helper: create a map with mutable dataflow nodes for each branch of the tree. The map is indexed by branch ids.

Definition at line 96 of file ForwardLikelihoodTree.h.

DAProb

using bpp::DAProb = typedef AssociationDAGlobalGraphObserver<Proba, Proba>

Definition at line 240 of file ForwardLikelihoodTree.h.

DataLik

typedef ExtendedFloat bpp::DataLik

Definition at line 16 of file Definitions.h.

EFArray

template<int R, int C>

using bpp::EFArray = typedef Eigen::Array<double, R, C>

Definition at line 58 of file ExtendedFloatEigen.h.

EFMatrix

template<int R, int C>

using bpp::EFMatrix = typedef Eigen::Matrix<double, R, C>

Definition at line 55 of file ExtendedFloatEigen.h.

EFoutput

template<typename eVector >

using bpp::EFoutput = typedef typename std::enable_if<(std::is_same<eVector, ExtendedFloatRowVectorXd>::value || std::is_same<eVector, ExtendedFloatVectorXd>::value), bool>::type

Definition at line 86 of file DataFlowNumeric.h.

EFVector

template<typename eVector >

using bpp::EFVector = typedef typename std::enable_if<(std::is_same<eVector, ExtendedFloatRowVectorXd>::value || std::is_same<eVector, ExtendedFloatVectorXd>::value), bool>::type

Definition at line 60 of file DataFlowNumeric.h.

EmissionLogk

using bpp::EmissionLogk = typedef CWiseCompound<MatrixLik, ReductionOf<RowLik> >

Definition at line 16 of file HmmPhyloEmissionProbabilities.h.

ExtendedFloatArray

template<int R, int C>

using bpp::ExtendedFloatArray = typedef ExtendedFloatEigen<R, C, EFArray>

Definition at line 882 of file ExtendedFloatEigen.h.

ExtendedFloatArrayXd

typedef ExtendedFloatArray<Eigen::Dynamic, 1> bpp::ExtendedFloatArrayXd

Definition at line 896 of file ExtendedFloatEigen.h.

ExtendedFloatMatrix

template<int R, int C>

using bpp::ExtendedFloatMatrix = typedef ExtendedFloatEigen<R, C, EFMatrix>

Definition at line 879 of file ExtendedFloatEigen.h.

ExtendedFloatMatrixXd

typedef ExtendedFloatMatrix<Eigen::Dynamic, Eigen::Dynamic> bpp::ExtendedFloatMatrixXd

Definition at line 890 of file ExtendedFloatEigen.h.

ExtendedFloatRowVector

template<int C>

using bpp::ExtendedFloatRowVector = typedef ExtendedFloatMatrix<1, C>

Definition at line 888 of file ExtendedFloatEigen.h.

ExtendedFloatRowVectorXd

typedef ExtendedFloatRowVector<Eigen::Dynamic> bpp::ExtendedFloatRowVectorXd

Definition at line 892 of file ExtendedFloatEigen.h.

ExtendedFloatVector

template<int R>

using bpp::ExtendedFloatVector = typedef ExtendedFloatMatrix<R, 1>

Definition at line 885 of file ExtendedFloatEigen.h.

ExtendedFloatVectorXd

typedef ExtendedFloatVector<Eigen::Dynamic> bpp::ExtendedFloatVectorXd

Definition at line 894 of file ExtendedFloatEigen.h.

ForConvert

template<typename eVector , typename bVector >

using bpp::ForConvert = typedef typename std::enable_if< ((std::is_same<bVector, Vdouble>::value || std::is_same<bVector, std::vector<ExtendedFloat> >::value) && (std::is_same<eVector, Eigen::RowVectorXd>::value || std::is_same<eVector, Eigen::VectorXd>::value)), bool>::type

Definition at line 33 of file DataFlowNumeric.h.

ForConvert2

template<typename eVector , typename bVector >

using bpp::ForConvert2 = typedef typename std::enable_if< ((std::is_same<bVector, Vdouble>::value || std::is_same<bVector, std::vector<ExtendedFloat> >::value) && (std::is_same<eVector, Eigen::RowVectorXd>::value || std::is_same<eVector, Eigen::VectorXd>::value || std::is_same<eVector, ExtendedFloatVectorXd>::value || std::is_same<eVector, ExtendedFloatRowVectorXd>::value)), bool>::type

Definition at line 170 of file DataFlowNumeric.h.

ForwardLikelihoodBelow

typedef Value< MatrixLik > bpp::ForwardLikelihoodBelow

Definition at line 93 of file ForwardLikelihoodTree.h.

ForwardLikelihoodBelowRef

typedef ValueRef< MatrixLik > bpp::ForwardLikelihoodBelowRef

Definition at line 94 of file ForwardLikelihoodTree.h.

ForwardProportion

using bpp::ForwardProportion = typedef CWiseMul<MatrixLik, std::tuple<double, MatrixLik> >

forwardLikelihood = f(transitionMatrix, proportion).

• forwardLikelihood: Matrix(state, site).
• proportion: Double
• conditionalLikelihood: Matrix(state, site).

f(State, site) = c(fromState, site) * prop

Definition at line 72 of file ForwardLikelihoodTree.h.

ForwardTransition

typedef MatrixProduct< MatrixLik, Eigen::MatrixXd, MatrixLik > bpp::ForwardTransition

forwardLikelihood = f(transitionMatrix, conditionalLikelihood).

• forwardLikelihood: Matrix(state, site).
• transitionMatrix: Matrix (fromState, toState)
• conditionalLikelihood: Matrix(state, site).

f(toState, site) = sum_fromState P(fromState, toState) * c(fromState, site).

Definition at line 58 of file ForwardLikelihoodTree.h.

ForwardTransitionFunction

using bpp::ForwardTransitionFunction = typedef CWiseApply<MatrixLik, MatrixLik, TransitionFunction>

Definition at line 61 of file ForwardLikelihoodTree.h.

INode

typedef NodeTemplate<TreeDrawingNodeInfo> bpp::INode

Definition at line 43 of file AbstractTreeDrawing.h.

LikelihoodFromRootConditional

using bpp::LikelihoodFromRootConditional = typedef MatrixProduct<RowLik, RowLik, MatrixLik>

likelihood = f(equilibriumFrequencies, rootConditionalLikelihood).

• likelihood: RowVector(site).
• equilibriumFrequencies: RowVector(state).
• rootConditionalLikelihood: Matrix(state, site).

likelihood(site) = sum_state equFreqs(state) * rootConditionalLikelihood(state, site). Using matrix multiply: likelihood = equilibriumFrequencies * rootConditionalLikelihood.

Definition at line 63 of file LikelihoodCalculationSingleProcess.h.

LikelihoodFromRootConditionalAtRoot

typedef MatrixProduct< RowLik, Eigen::RowVectorXd, MatrixLik > bpp::LikelihoodFromRootConditionalAtRoot

Likelihood computed on a branch. This likelihood is dependent on a LikelihoodCalculationSingleProcess, from which it will get the conditional likelihoods at both ends of the branch, a Branch Node (with the parameterized length), as well as a Model DF.

Definition at line 25 of file LikelihoodCalculationOnABranch.h.

MatchingType

typedef Eigen::Matrix<size_t, -1, 2> bpp::MatchingType

Definition at line 290 of file DataFlowCWise.h.

MatrixLik

typedef ExtendedFloatMatrixXd bpp::MatrixLik

Definition at line 13 of file Definitions.h.

MixtureBackward

using bpp::MixtureBackward = typedef CWiseAdd<MatrixLik, ReductionOf<MatrixLik> >

: At the top of each edge below a mixture node

backwardLikelihood = f(backwardLikelihood[father[i]] for i) backwardLikelihood: Matrix(state, site). backwardLikelihood[i]: Matrix(state, site).

c(state, site) = sum_i f_i(state, site) Using member wise addition: c = sum_member_i f_i Using member wise multiplication: c(state, site) = prod_i f_i(state, site).

Definition at line 41 of file BackwardLikelihoodTree.h.

MixtureForward

using bpp::MixtureForward = typedef CWiseAdd<MatrixLik, ReductionOf<MatrixLik> >

conditionalLikelihood = f(forwardLikelihood[children[i]] for i). conditionalLikelihood: Matrix(state, site). forwardLikelihood[i]: Matrix(state, site).

c(state, site) = sum_i f_i(state, site) Using member wise addition: c = sum_member_i f_i

Definition at line 48 of file ForwardLikelihoodTree.h.

NodeRef

using bpp::NodeRef = typedef std::shared_ptr<Node_DF>

Node instances are always manipulated as shared pointers: provide a short alias.

Definition at line 78 of file DataFlow.h.

NodeRefVec

using bpp::NodeRefVec = typedef std::vector<NodeRef>

Alias for a dependency vector (of NodeRef).

Definition at line 81 of file DataFlow.h.

PatternType

typedef Eigen::Matrix<size_t, -1, 1> bpp::PatternType

Definition at line 181 of file DataFlowCWise.h.

Proba

using bpp::Proba = typedef Value<double>

DAG with the same shape as ForwardLikelihoodTree with computations of probabilities of nodes & branches.

Definition at line 237 of file ForwardLikelihoodTree.h.

ProbaMul

using bpp::ProbaMul = typedef CWiseMul<double, std::tuple<double, double> >

Definition at line 242 of file ForwardLikelihoodTree.h.

ProbaRef

using bpp::ProbaRef = typedef std::shared_ptr<Value<double> >

Definition at line 238 of file ForwardLikelihoodTree.h.

ProbaSum

using bpp::ProbaSum = typedef CWiseAdd<double, ReductionOf<double> >

Definition at line 244 of file ForwardLikelihoodTree.h.

ProcessComputationNodeRef

using bpp::ProcessComputationNodeRef = typedef std::shared_ptr<ProcessComputationNode>

Definition at line 71 of file ProcessComputationTree.h.

ProcessEdgePtr

using bpp::ProcessEdgePtr = typedef std::shared_ptr<ProcessEdge>

Definition at line 147 of file ProcessTree.h.

ProcessNode

typedef ProcessComputationNode bpp::ProcessNode

Definition at line 145 of file ProcessTree.h.

ProcessNodePtr

using bpp::ProcessNodePtr = typedef std::shared_ptr<ProcessNode>

Definition at line 148 of file ProcessTree.h.

RowLik

typedef ExtendedFloatRowVectorXd bpp::RowLik

Definition at line 14 of file Definitions.h.

SiteLikelihoods

typedef Value< RowLik > bpp::SiteLikelihoods

Definition at line 121 of file LikelihoodCalculation.h.

SiteLikelihoodsDAG

using bpp::SiteLikelihoodsDAG = typedef AssociationDAGlobalGraphObserver<SiteLikelihoods, uint>

Definition at line 106 of file LikelihoodCalculationSingleProcess.h.

SiteLikelihoodsRef

typedef ValueRef< RowLik > bpp::SiteLikelihoodsRef

Definition at line 122 of file LikelihoodCalculation.h.

SiteLikelihoodsTree

using bpp::SiteLikelihoodsTree = typedef AssociationTreeGlobalGraphObserver<SiteLikelihoods, uint>

Definition at line 108 of file LikelihoodCalculationSingleProcess.h.

SiteWeights

typedef NumericConstant< Eigen::RowVectorXi > bpp::SiteWeights

Definition at line 57 of file LikelihoodCalculationOnABranch.h.

SNode

typedef NodeTemplate<SimData> bpp::SNode

Definition at line 52 of file NonHomogeneousSequenceSimulator.h.

SpeciationBackward

using bpp::SpeciationBackward = typedef CWiseMul<MatrixLik, ReductionOf<MatrixLik> >

: At the top of each edge below a speciation node

conditionalLikelihood = f(backwardLikelihood[father[i]], forwardlikelihood[brothers[i]]). conditionalLikelihood: Matrix(state, site). backwardLikelihood, forwardlikelihood: Matrix(state, site).

Using member wise multiplication: c(state, site) = prod_i f_i(state, site).

Definition at line 28 of file BackwardLikelihoodTree.h.

SpeciationForward

using bpp::SpeciationForward = typedef CWiseMul<MatrixLik, ReductionOf<MatrixLik> >

conditionalLikelihood = f(forwardLikelihood[children[i]] for i). conditionalLikelihood: Matrix(state, site). forwardLikelihood[i]: Matrix(state, site).

c(state, site) = prod_i f_i(state, site). Using member wise multiply: c = prod_member_i f_i.

Definition at line 38 of file ForwardLikelihoodTree.h.

Speciesindex

typedef uint bpp::Speciesindex

Definition at line 97 of file ForwardLikelihoodTree.h.

SPTree

typedef AssociationTreeGlobalGraphObserver<SimProcessNode, SimProcessEdge> bpp::SPTree

Definition at line 63 of file SimpleSubstitutionProcessSiteSimulator.h.

TotalLogLikelihood

typedef SumOfLogarithms< RowLik > bpp::TotalLogLikelihood

totalLikelihood = product_site likelihood(site).

• likelihood: RowVector (site).
• totalLikelihood: Extended float.

Definition at line 33 of file LikelihoodCalculationOnABranch.h.

TransitionFunction

using bpp::TransitionFunction = typedef std::function<VectorLik (const VectorLik&)>

Definition at line 198 of file DataFlowNumeric.h.

ValueRef

template<typename T >

using bpp::ValueRef = typedef std::shared_ptr<Value<T> >

Shared pointer alias for Value<T>.

Definition at line 84 of file DataFlow.h.

VDataLik

typedef std::vector<DataLik> bpp::VDataLik

Definition at line 23 of file Definitions.h.

VectorLik

typedef ExtendedFloatVectorXd bpp::VectorLik

Definition at line 15 of file Definitions.h.

VVDataLik

typedef std::vector<VDataLik> bpp::VVDataLik

Definition at line 24 of file Definitions.h.

Enumeration Type Documentation

DotOptions

enum bpp::DotOptions

strong

Dot output Flags to control dot output of dataflow graphs.

Enumerator
None
DetailedNodeInfo
FollowUpwardLinks
ShowDependencyIndex

Definition at line 46 of file DataFlow.h.

NumericalDerivativeType

enum bpp::NumericalDerivativeType

strong

Enumerator
Disabled
ThreePoints
FivePoints

Definition at line 2700 of file DataFlowCWiseComputing.h.

NumericalProperty

enum bpp::NumericalProperty

strong

Numerical properties for DF Node.

Enumerator
Constant
ConstantZero
ConstantOne
ConstantIdentity

Definition at line 87 of file DataFlow.h.

Function Documentation

abs()

ExtendedFloat bpp::abs ( const ExtendedFloat &  ef )

inline

Definition at line 479 of file ExtendedFloat.h.

References bpp::ExtendedFloat::abs().

Referenced by bpp::ExtendedFloat::abs(), bpp::HierarchicalClustering::computeDistancesFromPair(), bpp::AbstractDFPSubstitutionModel::getCodonsMulRate(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::TsTvSubstitutionRegister::getType(), bpp::DecompositionMethods::jFunction_(), bpp::ExtendedFloat::normalize_big(), bpp::ExtendedFloat::normalize_small(), bpp::OptimizationTools::OptimizationOptions::OptimizationOptions(), bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::POMO::updateMatrices_(), and bpp::YpR::updateMatrices_().

accessValueConstCast()

template<typename T >

const T& bpp::accessValueConstCast

(

const Node_DF &

node

)

Helper: access value of Node as a Value<T> with unchecked cast.

Definition at line 424 of file DataFlow.h.

cachedAs() [1/2]

template<typename T >

std::shared_ptr<T> bpp::cachedAs	(	Context &	c,
		std::shared_ptr< T > &&	newNode
	)

Helper: Same as Context::cached but with a shared_ptr<T> node.

Definition at line 611 of file DataFlow.h.

References bpp::Context::cached().

cachedAs() [2/2]

template<typename T >

std::shared_ptr<T> bpp::cachedAs	(	Context &	c,
		std::shared_ptr< T > &	newNode
	)

Definition at line 617 of file DataFlow.h.

References bpp::Context::cached().

checkDependenciesNotNull()

void bpp::checkDependenciesNotNull	(	const std::type_info &	contextNodeType,
		const NodeRefVec &	deps
	)

Checks that all dependencies are not null, throws if not.

Definition at line 103 of file DataFlow.cpp.

References failureEmptyDependency().

Referenced by bpp::ScalarProduct< R, T0, T1 >::create(), bpp::ProbabilitiesFromDiscreteDistribution::create(), bpp::ProbabilitiesFromMixedModel::create(), bpp::ValueFromConfiguredParameter::create(), bpp::CondLikelihood::create(), bpp::ForwardHmmLikelihood_DF::create(), bpp::ForwardHmmDLikelihood_DF::create(), bpp::ForwardHmmD2Likelihood_DF::create(), bpp::BackwardHmmLikelihood_DF::create(), bpp::SumOfLogarithms< F >::create(), bpp::CWiseFill< R, T >::create(), bpp::CWisePattern< R >::create(), bpp::CWiseMatching< R, ReductionOf< T > >::create(), bpp::CWiseCompound< R, ReductionOf< T > >::create(), bpp::CWiseApply< R, T, F >::create(), bpp::CWiseAdd< R, std::tuple< T0, T1 > >::create(), bpp::CWiseSub< R, std::tuple< T0, T1 > >::create(), bpp::CWiseAdd< R, ReductionOf< T > >::create(), bpp::CWiseAdd< R, T >::create(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::create(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::create(), bpp::CWiseMul< R, ReductionOf< T > >::create(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::create(), bpp::MatrixProduct< R, T0, T1 >::create(), bpp::Convert< R, F >::create(), bpp::Identity< R >::create(), bpp::CWiseNegate< T >::create(), bpp::CWiseInverse< T >::create(), bpp::CWiseLog< T >::create(), bpp::CWiseExp< T >::create(), bpp::TransitionFunctionFromModel::create(), bpp::LogSumExp< R, T0, T1 >::create(), bpp::ConfiguredParameter::create(), bpp::CWiseConstantPow< T >::create(), bpp::ShiftDelta< T >::create(), bpp::CombineDeltaShifted< T >::create(), bpp::ShiftParameter::create(), bpp::ProbabilityFromMixedModel::create(), bpp::ProbabilityFromDiscreteDistribution::create(), bpp::CategoryFromDiscreteDistribution::create(), bpp::ConfiguredParametrizable::createConfigured(), bpp::ConfiguredParametrizable::createDouble(), and bpp::ConfiguredParameter::resetDependencies().

checkDependencyRangeIs()

template<typename T >

void bpp::checkDependencyRangeIs	(	const std::type_info &	contextNodeType,
		const NodeRefVec &	deps,
		std::size_t	start,
		std::size_t	end
	)

Check that deps[start, end[ contains T, throws if not.

Definition at line 473 of file DataFlow.h.

checkDependencyRangeIsValue()

template<typename T >

void bpp::checkDependencyRangeIsValue	(	const std::type_info &	contextNodeType,
		const NodeRefVec &	deps,
		std::size_t	start,
		std::size_t	end
	)

Check that deps[start, end[ contains Value<T> nodes, throws if not.

Definition at line 492 of file DataFlow.h.

checkDependencyVectorMinSize()

void bpp::checkDependencyVectorMinSize	(	const std::type_info &	contextNodeType,
		const NodeRefVec &	deps,
		std::size_t	expectedMinSize
	)

Checks the minimum size of a dependency vector, throws if mismatch.

Definition at line 93 of file DataFlow.cpp.

References failureDependencyNumberMismatch().

Referenced by bpp::SumOfLogarithms< F >::create(), bpp::ConfiguredParametrizable::createMatrix(), bpp::ConfiguredParametrizable::createRowVector(), and bpp::ConfiguredParametrizable::createVector().

checkDependencyVectorSize()

void bpp::checkDependencyVectorSize	(	const std::type_info &	contextNodeType,
		const NodeRefVec &	deps,
		std::size_t	expectedSize
	)

Definition at line 83 of file DataFlow.cpp.

References failureDependencyNumberMismatch().

Referenced by bpp::ScalarProduct< R, T0, T1 >::create(), bpp::ProbabilitiesFromDiscreteDistribution::create(), bpp::ProbabilitiesFromMixedModel::create(), bpp::ValueFromConfiguredParameter::create(), bpp::CondLikelihood::create(), bpp::ForwardHmmLikelihood_DF::create(), bpp::ForwardHmmDLikelihood_DF::create(), bpp::ForwardHmmD2Likelihood_DF::create(), bpp::BackwardHmmLikelihood_DF::create(), bpp::CWiseFill< R, T >::create(), bpp::CWisePattern< R >::create(), bpp::CWiseApply< R, T, F >::create(), bpp::CWiseAdd< R, std::tuple< T0, T1 > >::create(), bpp::CWiseSub< R, std::tuple< T0, T1 > >::create(), bpp::CWiseAdd< R, T >::create(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::create(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::create(), bpp::MatrixProduct< R, T0, T1 >::create(), bpp::Convert< R, F >::create(), bpp::Identity< R >::create(), bpp::CWiseNegate< T >::create(), bpp::CWiseInverse< T >::create(), bpp::CWiseLog< T >::create(), bpp::CWiseExp< T >::create(), bpp::TransitionFunctionFromModel::create(), bpp::LogSumExp< R, T0, T1 >::create(), bpp::ConfiguredParameter::create(), bpp::CWiseConstantPow< T >::create(), bpp::ShiftDelta< T >::create(), bpp::CombineDeltaShifted< T >::create(), bpp::ShiftParameter::create(), bpp::ProbabilityFromMixedModel::create(), bpp::ProbabilityFromDiscreteDistribution::create(), bpp::CategoryFromDiscreteDistribution::create(), bpp::ConfiguredParametrizable::createConfigured(), bpp::ConfiguredParametrizable::createDouble(), and bpp::ConfiguredParameter::resetDependencies().

checkNthDependencyIs() [1/2]

template<typename T >

void bpp::checkNthDependencyIs	(	const std::type_info &	contextNodeType,
		const NodeRefVec &	deps,
		std::size_t	index
	)

Checks that deps[index] is a T node, throws if not.

Definition at line 447 of file DataFlow.h.

References failureDependencyTypeMismatch().

checkNthDependencyIs() [2/2]

template<typename T1 , typename T2 >

void bpp::checkNthDependencyIs	(	const std::type_info &	contextNodeType,
		const NodeRefVec &	deps,
		std::size_t	index
	)

Checks that deps[index] is a T1 or a T2 node, throws if not.

Definition at line 457 of file DataFlow.h.

References prettyTypeName(), and to_string().

checkNthDependencyIsValue()

template<typename T >

void bpp::checkNthDependencyIsValue	(	const std::type_info &	contextNodeType,
		const NodeRefVec &	deps,
		std::size_t	index
	)

Checks that deps[index] is a Value<T> node, throws if not.

Definition at line 484 of file DataFlow.h.

checkNthDependencyNotNull()

void bpp::checkNthDependencyNotNull	(	const std::type_info &	contextNodeType,
		const NodeRefVec &	deps,
		std::size_t	index
	)

Definition at line 114 of file DataFlow.cpp.

References failureEmptyDependency().

Referenced by bpp::ConfiguredParametrizable::createMatrix(), bpp::ConfiguredParametrizable::createRowVector(), and bpp::ConfiguredParametrizable::createVector().

checkRecreateWithoutDependencies()

void bpp::checkRecreateWithoutDependencies	(	const std::type_info &	contextNodeType,
		const NodeRefVec &	deps
	)

Definition at line 173 of file DataFlowNumeric.cpp.

References prettyTypeName().

Referenced by bpp::ConstantZero< T >::recreate(), bpp::ConstantOne< T >::recreate(), bpp::NumericMutable< T >::recreate(), bpp::NumericConstant< T >::recreate(), and bpp::Sequence_DF::recreate().

combineHash()

template<typename T >

void bpp::combineHash	(	std::size_t &	seed,
		const T &	t
	)

Combine hashable value to a hash, from Boost library.

Definition at line 33 of file DataFlow.h.

Referenced by bpp::numeric::hash(), hash(), bpp::CWiseConstantPow< T >::hashAdditionalArguments(), bpp::ShiftDelta< T >::hashAdditionalArguments(), bpp::CombineDeltaShifted< T >::hashAdditionalArguments(), bpp::ShiftParameter::hashAdditionalArguments(), and bpp::Context::CachedNodeRefHash::operator()().

conditionalLikelihoodDimension()

MatrixDimension bpp::conditionalLikelihoodDimension ( Eigen::Index  nbState, Eigen::Index  nbSite  )

inline

Definition at line 25 of file ForwardLikelihoodTree.h.

Referenced by bpp::ForwardLikelihoodTree::initialize(), bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtDAGNode_(), and bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtNode_().

constexpr_power()

template<typename T >

constexpr T bpp::constexpr_power ( T  d, int  n  )

constexpr

Definition at line 18 of file ExtendedFloat.h.

convert()

double bpp::convert ( const bpp::ExtendedFloat &  ef )

inline

Definition at line 486 of file ExtendedFloat.h.

References bpp::ExtendedFloat::exponent_part(), bpp::ExtendedFloat::float_part(), and bpp::ExtendedFloat::radix.

Referenced by bpp::CWiseFill< R, T >::compute(), bpp::Convert< R, F >::compute(), bpp::ForwardHmmLikelihood_DF::compute(), bpp::ForwardHmmDLikelihood_DF::compute(), bpp::ForwardHmmD2Likelihood_DF::compute(), bpp::BackwardHmmLikelihood_DF::compute(), copyBppToEigen(), copyEigenToBpp(), bpp::AbstractPhyloLikelihood::getFirstOrderDerivative(), bpp::MultiProcessSequencePhyloLikelihood::getLikelihoodPerSitePerProcess(), bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorProbabilitiesForSitePerClass(), bpp::SingleProcessPhyloLikelihood::getPosteriorProbabilitiesForSitePerClass(), bpp::MixtureProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorRatePerSite(), bpp::SingleProcessPhyloLikelihood::getPosteriorRatePerSite(), bpp::AbstractPhyloLikelihood::getSecondOrderDerivative(), bpp::AbstractPhyloLikelihood::getValue(), bpp::GivenDataSubstitutionProcessSiteSimulator::init(), bpp::OptimizationTools::OptimizationOptions::OptimizationOptions(), and bpp::LegacyPhylogeneticsApplicationTools::optimizeParameters().

convertRef()

template<typename T , typename U >

std::shared_ptr<T> bpp::convertRef

(

const std::shared_ptr< U > &

from

)

Convert a node ref with runtime type check.

Definition at line 320 of file DataFlow.h.

References failureNodeConversion().

copyBppToEigen() [1/13]

void bpp::copyBppToEigen	(	const bpp::Matrix< double > &	bppMatrix,
		Eigen::MatrixXd &	eigenMatrix
	)

Definition at line 87 of file DataFlowNumeric.cpp.

References bpp::Matrix< class >::getNumberOfColumns(), and bpp::Matrix< class >::getNumberOfRows().

copyBppToEigen() [2/13]

void bpp::copyBppToEigen	(	const bpp::Matrix< double > &	bppMatrix,
		ExtendedFloatMatrixXd &	eigenMatrix
	)

Definition at line 65 of file DataFlowNumeric.cpp.

References bpp::ExtendedFloatEigen< R, C, EigenType >::fill(), bpp::ExtendedFloatEigen< R, C, EigenType >::float_part(), bpp::Matrix< class >::getNumberOfColumns(), bpp::Matrix< class >::getNumberOfRows(), and bpp::ExtendedFloatEigen< R, C, EigenType >::resize().

copyBppToEigen() [3/13]

template void bpp::copyBppToEigen	(	const bpp::Vdouble &	bppVector,
		Eigen::RowVectorXd &	eigenVector
	)

copyBppToEigen() [4/13]

template void bpp::copyBppToEigen	(	const bpp::Vdouble &	bppVector,
		Eigen::VectorXd &	eigenVector
	)

copyBppToEigen() [5/13]

template void bpp::copyBppToEigen	(	const bpp::Vdouble &	bppVector,
		ExtendedFloatRowVectorXd &	eigenVector
	)

copyBppToEigen() [6/13]

template<typename eVector , typename bVector , ForConvert< eVector, bVector > = true>

void bpp::copyBppToEigen	(	const bVector &	bppVector,
		eVector &	eigenVector
	)

Definition at line 41 of file DataFlowNumeric.h.

References convert().

copyBppToEigen() [7/13]

void bpp::copyBppToEigen	(	const std::vector< Eigen::VectorXd > &	bppVector,
		Eigen::MatrixXd &	eigenMatrix
	)

Definition at line 47 of file DataFlowNumeric.cpp.

copyBppToEigen() [8/13]

template void bpp::copyBppToEigen	(	const std::vector< ExtendedFloat > &	bppVector,
		Eigen::RowVectorXd &	eigenVector
	)

Referenced by bpp::CWiseApply< R, T, F >::compute(), bpp::TransitionMatrixFromModel::compute(), bpp::TransitionMatrixFromTransitionMatrix::compute(), bpp::ForwardHmmLikelihood_DF::compute(), bpp::ForwardHmmDLikelihood_DF::compute(), bpp::ForwardHmmD2Likelihood_DF::compute(), bpp::BackwardHmmLikelihood_DF::compute(), copyBppToEigen(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorProbabilitiesPerSitePerClass(), and bpp::SingleProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerClass().

copyBppToEigen() [9/13]

template void bpp::copyBppToEigen	(	const std::vector< ExtendedFloat > &	bppVector,
		Eigen::VectorXd &	eigenVector
	)

copyBppToEigen() [10/13]

template<typename eVector , EFVector< eVector > = true>

void bpp::copyBppToEigen	(	const std::vector< ExtendedFloat > &	bppVector,
		eVector &	eigenVector
	)

Definition at line 64 of file DataFlowNumeric.h.

copyBppToEigen() [11/13]

template void bpp::copyBppToEigen	(	const std::vector< ExtendedFloat > &	bppVector,
		ExtendedFloatRowVectorXd &	eigenVector
	)

copyBppToEigen() [12/13]

void bpp::copyBppToEigen	(	const std::vector< ExtendedFloatVectorXd > &	bppVector,
		ExtendedFloatMatrixXd &	eigenVector
	)

Definition at line 31 of file DataFlowNumeric.cpp.

References bpp::ExtendedFloatEigen< R, C, EigenType >::exponent_part(), and bpp::ExtendedFloatEigen< R, C, EigenType >::float_part().

copyBppToEigen() [13/13]

template<typename eVector , EFoutput< eVector > = true>

void bpp::copyBppToEigen	(	const Vdouble &	bppVector,
		eVector &	eigenVector
	)

Definition at line 91 of file DataFlowNumeric.h.

References copyBppToEigen().

copyEigenToBpp() [1/10]

template<typename eVector , typename bVector , ForConvert2< bVector, eVector > = true>

void bpp::copyEigenToBpp	(	const bVector &	eigenVector,
		eVector &	bppVector
	)

Definition at line 181 of file DataFlowNumeric.h.

References convert().

copyEigenToBpp() [2/10]

template void bpp::copyEigenToBpp	(	const Eigen::MatrixXd &	eigenMatrix,
		std::vector< std::vector< bpp::ExtendedFloat >> &	bppMatrix
	)

copyEigenToBpp() [3/10]

template void bpp::copyEigenToBpp	(	const Eigen::MatrixXd &	eigenMatrix,
		std::vector< std::vector< double >> &	bppMatrix
	)

copyEigenToBpp() [4/10]

template<typename eType , typename = typename std::enable_if<(std::is_same<eType, double>::value || std::is_same<eType, ExtendedFloat>::value)>::type>

void bpp::copyEigenToBpp	(	const Eigen::MatrixXd &	eigenMatrix,
		std::vector< std::vector< eType >> &	bppMatrix
	)

Definition at line 144 of file DataFlowNumeric.h.

copyEigenToBpp() [5/10]

template void bpp::copyEigenToBpp	(	const ExtendedFloatMatrixXd &	eigenMatrix,
		std::vector< std::vector< bpp::ExtendedFloat >> &	bppMatrix
	)

copyEigenToBpp() [6/10]

template void bpp::copyEigenToBpp	(	const ExtendedFloatMatrixXd &	eigenMatrix,
		std::vector< std::vector< double >> &	bppMatrix
	)

Referenced by bpp::MarginalAncestralReconstruction::getAncestralStatesForNode(), bpp::AlignedLikelihoodCalculation::getLikelihoodPerSite(), bpp::OnABranchPhyloLikelihood::getLikelihoodPerSitePerClass(), bpp::OneProcessSequencePhyloLikelihood::getLikelihoodPerSitePerClass(), bpp::SingleProcessPhyloLikelihood::getLikelihoodPerSitePerClass(), bpp::AlignedPhyloLikelihoodAutoCorrelation::getPosteriorProbabilitiesForASitePerAligned(), bpp::AlignedPhyloLikelihoodHmm::getPosteriorProbabilitiesForASitePerAligned(), bpp::AlignedPhyloLikelihoodAutoCorrelation::getPosteriorProbabilitiesPerSitePerAligned(), bpp::AlignedPhyloLikelihoodHmm::getPosteriorProbabilitiesPerSitePerAligned(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorProbabilitiesPerSitePerClass(), bpp::SingleProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerClass(), bpp::AutoCorrelationProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess(), bpp::HmmProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorStateFrequencies(), bpp::SingleProcessPhyloLikelihood::getPosteriorStateFrequencies(), bpp::GivenDataSubstitutionProcessSiteSimulator::init(), and bpp::PhylogeneticsApplicationTools::printParameters().

copyEigenToBpp() [7/10]

template<typename eType , typename = typename std::enable_if<(std::is_same<eType, double>::value || std::is_same<eType, ExtendedFloat>::value)>::type>

void bpp::copyEigenToBpp	(	const ExtendedFloatMatrixXd &	eigenMatrix,
		std::vector< std::vector< eType >> &	bppMatrix
	)

Definition at line 120 of file DataFlowNumeric.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::cols(), convert(), and bpp::ExtendedFloatEigen< R, C, EigenType >::rows().

copyEigenToBpp() [8/10]

void bpp::copyEigenToBpp	(	const MatrixLik &	eigenMatrix,
		bpp::Matrix< double > &	bppMatrix
	)

Definition at line 118 of file DataFlowNumeric.cpp.

References bpp::ExtendedFloatEigen< R, C, EigenType >::cols(), bpp::numeric::convert(), bpp::Matrix< class >::resize(), and bpp::ExtendedFloatEigen< R, C, EigenType >::rows().

copyEigenToBpp() [9/10]

template void bpp::copyEigenToBpp	(	const RowLik &	eigenVector,
		std::vector< ExtendedFloat > &	bppVector
	)

copyEigenToBpp() [10/10]

template void bpp::copyEigenToBpp	(	const RowLik &	eigenVector,
		Vdouble &	bppVector
	)

createDependencyVector() [1/4]

NodeRefVec bpp::createDependencyVector	(	const ParameterAliasable &	parametrizable,
		const std::function< NodeRef(const std::string &)> &	getParameter
	)

createDependencyVector() [2/4]

NodeRefVec bpp::createDependencyVector	(	const ParameterAliasable &	parametrizable,
		const std::function< NodeRef(const std::string &)> &	parameter
	)

Definition at line 66 of file Parametrizable.cpp.

References bpp::ParameterAliasable::getIndependentParameters(), and bpp::ParameterList::size().

createDependencyVector() [3/4]

NodeRefVec bpp::createDependencyVector	(	const Parametrizable &	parametrizable,
		const std::function< NodeRef(const std::string &)> &	getParameter
	)

Create a dependency vector suitable for a parametrizable class constructor. The vector is built from parameter names, and an opaque accessor function. For each named parameter, parameter(name) should return a valid node. If no node is found (NodeRef was null), an exception is thrown. Returned nodes must be Value<double> nodes.

createDependencyVector() [4/4]

NodeRefVec bpp::createDependencyVector	(	const Parametrizable &	parametrizable,
		const std::function< NodeRef(const std::string &)> &	parameter
	)

Definition at line 48 of file Parametrizable.cpp.

References bpp::Parametrizable::getParameters(), and bpp::ParameterList::size().

Referenced by bpp::ConfiguredParametrizable::createConfigured().

createParameterMap() [1/2]

std::unordered_map< std::string, std::shared_ptr< ConfiguredParameter > > bpp::createParameterMap	(	Context &	c,
		const ParameterAliasable &	parametrizable
	)

Definition at line 17 of file Parametrizable.cpp.

References bpp::ParameterAliasable::getIndependentParameters(), and bpp::ParameterList::size().

Referenced by bpp::ConfiguredParametrizable::createConfigured().

createParameterMap() [2/2]

std::unordered_map< std::string, std::shared_ptr< ConfiguredParameter > > bpp::createParameterMap	(	Context &	c,
		const Parametrizable &	parametrizable
	)

Helper: create a map with mutable dataflow nodes for each parameter of the parametrizable. The map is indexed by parameter names.

Definition at line 33 of file Parametrizable.cpp.

References bpp::Parametrizable::getParameters(), and bpp::ParameterList::size().

dotIdentifier()

static std::string bpp::dotIdentifier ( const Node_DF &  node )

static

Definition at line 469 of file DataFlow.cpp.

References to_string().

Referenced by writeDotEdge(), and writeDotNode().

dotLabelEscape()

static std::string bpp::dotLabelEscape ( const std::string &  s )

static

Definition at line 449 of file DataFlow.cpp.

Referenced by writeDotNode().

equilibriumFrequenciesDimension()

RowVectorDimension bpp::equilibriumFrequenciesDimension ( std::size_t  nbState )

inline

Definition at line 24 of file Model.h.

exp() [1/2]

ExtendedFloat bpp::exp ( const ExtendedFloat &  ef )

inline

Definition at line 474 of file ExtendedFloat.h.

References bpp::ExtendedFloat::exp().

Referenced by bpp::CWiseExp< T >::compute(), bpp::LogSumExp< R, T0, T1 >::compute(), bpp::MultinomialFromTransitionModel::compute_d2Multinomial_dt2_(), bpp::MultinomialFromTransitionModel::compute_dMultinomial_dt_(), bpp::MultinomialFromTransitionModel::compute_Multinomial_(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::PairedSiteLikelihoods::computeExpectedLikelihoodWeights(), bpp::BinarySubstitutionModel::d2Pij_dt2(), bpp::F84::d2Pij_dt2(), bpp::HKY85::d2Pij_dt2(), bpp::TwoParameterBinarySubstitutionModel::d2Pij_dt2(), bpp::EquiprobableSubstitutionModel::d2Pij_dt2(), bpp::F81::d2Pij_dt2(), bpp::JCnuc::d2Pij_dt2(), bpp::K80::d2Pij_dt2(), bpp::T92::d2Pij_dt2(), bpp::TN93::d2Pij_dt2(), bpp::JCprot::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::OneChangeTransitionModel::d2Pij_dt2(), bpp::AbstractMutationProcess::detailedEvolve(), bpp::BinarySubstitutionModel::dPij_dt(), bpp::F84::dPij_dt(), bpp::HKY85::dPij_dt(), bpp::TwoParameterBinarySubstitutionModel::dPij_dt(), bpp::EquiprobableSubstitutionModel::dPij_dt(), bpp::F81::dPij_dt(), bpp::JCnuc::dPij_dt(), bpp::K80::dPij_dt(), bpp::T92::dPij_dt(), bpp::TN93::dPij_dt(), bpp::JCprot::dPij_dt(), bpp::RE08::dPij_dt(), bpp::OneChangeTransitionModel::dPij_dt(), bpp::AbstractCodonBGCSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonDistanceSubstitutionModel::getCodonsMulRate(), bpp::BinarySubstitutionModel::getd2Pij_dt2(), bpp::F84::getd2Pij_dt2(), bpp::HKY85::getd2Pij_dt2(), bpp::TwoParameterBinarySubstitutionModel::getd2Pij_dt2(), bpp::EquiprobableSubstitutionModel::getd2Pij_dt2(), bpp::F81::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::K80::getd2Pij_dt2(), bpp::T92::getd2Pij_dt2(), bpp::TN93::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::OneChangeTransitionModel::getd2Pij_dt2(), bpp::BinarySubstitutionModel::getdPij_dt(), bpp::F84::getdPij_dt(), bpp::HKY85::getdPij_dt(), bpp::TwoParameterBinarySubstitutionModel::getdPij_dt(), bpp::EquiprobableSubstitutionModel::getdPij_dt(), bpp::F81::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::K80::getdPij_dt(), bpp::T92::getdPij_dt(), bpp::TN93::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::OneChangeTransitionModel::getdPij_dt(), bpp::BinarySubstitutionModel::getPij_t(), bpp::F84::getPij_t(), bpp::HKY85::getPij_t(), bpp::TwoParameterBinarySubstitutionModel::getPij_t(), bpp::EquiprobableSubstitutionModel::getPij_t(), bpp::F81::getPij_t(), bpp::JCnuc::getPij_t(), bpp::K80::getPij_t(), bpp::T92::getPij_t(), bpp::TN93::getPij_t(), bpp::JCprot::getPij_t(), bpp::RE08::getPij_t(), bpp::OneChangeTransitionModel::getPij_t(), bpp::LegacyOptimizationTools::ScaleFunction::getValue(), bpp::LegacyOptimizationTools::optimizeTreeScale(), bpp::BinarySubstitutionModel::Pij_t(), bpp::F84::Pij_t(), bpp::HKY85::Pij_t(), bpp::TwoParameterBinarySubstitutionModel::Pij_t(), bpp::EquiprobableSubstitutionModel::Pij_t(), bpp::F81::Pij_t(), bpp::JCnuc::Pij_t(), bpp::K80::Pij_t(), bpp::T92::Pij_t(), bpp::TN93::Pij_t(), bpp::JCprot::Pij_t(), bpp::RE08::Pij_t(), bpp::OneChangeTransitionModel::Pij_t(), pow(), powi(), bpp::PhylogeneticsApplicationTools::printAnalysisInformation(), and bpp::gBGC::updateMatrices_().

exp() [2/2]

template<int R, int C, template< int R2=R, int C2=C > class MatType>

ExtendedFloatEigen<R, C, MatType> bpp::exp ( const ExtendedFloatEigen< R, C, MatType > &  arr )

inline

Definition at line 909 of file ExtendedFloatEigen.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::exp().

failureComputeWasCalled()

void bpp::failureComputeWasCalled

(

const std::type_info &

nodeType

)

Definition at line 51 of file DataFlow.cpp.

References prettyTypeName().

Referenced by bpp::NumericConstant< T >::compute(), bpp::NumericMutable< T >::compute(), and bpp::Sequence_DF::compute().

failureDeltaNotDerivable()

void bpp::failureDeltaNotDerivable

(

const std::type_info &

contextNodeType

)

Definition at line 11 of file DataFlowCWiseComputing.cpp.

References prettyTypeName().

Referenced by bpp::CombineDeltaShifted< T >::derive().

failureDependencyNumberMismatch()

void bpp::failureDependencyNumberMismatch	(	const std::type_info &	contextNodeType,
		std::size_t	expectedSize,
		std::size_t	givenSize
	)

Definition at line 61 of file DataFlow.cpp.

References prettyTypeName(), and to_string().

Referenced by checkDependencyVectorMinSize(), and checkDependencyVectorSize().

failureDependencyTypeMismatch()

void bpp::failureDependencyTypeMismatch	(	const std::type_info &	contextNodeType,
		std::size_t	depIndex,
		const std::type_info &	expectedType,
		const std::type_info &	givenNodeType
	)

Definition at line 74 of file DataFlow.cpp.

References prettyTypeName(), and to_string().

Referenced by checkNthDependencyIs(), bpp::ProbabilitiesFromMixedModel::create(), and bpp::ProbabilityFromMixedModel::create().

failureEmptyDependency()

void bpp::failureEmptyDependency	(	const std::type_info &	contextNodeType,
		std::size_t	depIndex
	)

Definition at line 68 of file DataFlow.cpp.

References prettyTypeName(), and to_string().

Referenced by checkDependenciesNotNull(), and checkNthDependencyNotNull().

failureNodeConversion()

void bpp::failureNodeConversion	(	const std::type_info &	handleType,
		const Node_DF &	node
	)

Definition at line 56 of file DataFlow.cpp.

References prettyTypeName().

Referenced by convertRef().

failureNumericalDerivationNotConfigured()

void bpp::failureNumericalDerivationNotConfigured

(

)

Definition at line 16 of file DataFlowCWiseComputing.cpp.

Referenced by generateNumericalDerivative().

generateNumericalDerivative() [1/2]

template<typename NodeT , typename DepT , typename B >

ValueRef<NodeT> bpp::generateNumericalDerivative	(	Context &	c,
		const NumericalDerivativeConfiguration &	config,
		NodeRef	dep,
		const Dimension< DepT > &	depDim,
		Dimension< NodeT > &	nodeDim,
		B	buildNodeWithDep
	)

Helper used to generate data flow expressions computing a numerical derivative.

For an expression e = f(x0,...,xn), which may be composed of multiple nodes. dep is one of the expression dependencies: exists i, dep is node xi. buildNodeWithDep(new_xi) should create the f(x0,...,new_xi,...,xn) node. It must duplicate the expression by replacing dep by new_xi. e must be a Value<NodeT>, and xi a Value<DepT>.

This function generates a new node de_ddep. de_ddep = g(delta,x0,...xn) = df/ddep value at x0,...,xn. delta is the shift between points of computation of f (numerical derivation). The pattern of computation points and delta are given by config. After creation, the pattern and node for delta cannot change, but delta value can.

Definition at line 2724 of file DataFlowCWiseComputing.h.

References bpp::ShiftDelta< T >::create(), bpp::CombineDeltaShifted< T >::create(), bpp::NumericalDerivativeConfiguration::delta, failureNumericalDerivationNotConfigured(), FivePoints, ThreePoints, and bpp::NumericalDerivativeConfiguration::type.

generateNumericalDerivative() [2/2]

template<typename NodeT , typename B >

ValueRef<NodeT> bpp::generateNumericalDerivative	(	Context &	c,
		const NumericalDerivativeConfiguration &	config,
		NodeRef	dep,
		const Dimension< NodeT > &	nodeDim,
		B	buildNodeWithDep
	)

Definition at line 2767 of file DataFlowCWiseComputing.h.

References bpp::CombineDeltaShifted< T >::create(), bpp::ShiftParameter::create(), bpp::NumericalDerivativeConfiguration::delta, failureNumericalDerivationNotConfigured(), FivePoints, ThreePoints, and bpp::NumericalDerivativeConfiguration::type.

hash() [1/2]

std::size_t bpp::hash

(

const MatrixDimension &

dim

)

Definition at line 153 of file DataFlowNumeric.cpp.

References bpp::MatrixDimension::cols, combineHash(), and bpp::MatrixDimension::rows.

Referenced by bpp::ConstantZero< T >::hashAdditionalArguments(), bpp::ConstantOne< T >::hashAdditionalArguments(), bpp::NumericConstant< T >::hashAdditionalArguments(), and bpp::Sequence_DF::hashAdditionalArguments().

hash() [2/2]

std::size_t bpp::hash ( const NoDimension &  )

inline

Definition at line 235 of file DataFlowNumeric.h.

isTransitivelyDependentOn()

bool bpp::isTransitivelyDependentOn	(	const Node_DF &	searchedDependency,
		const Node_DF &	node
	)

Check if searchedDependency if a transitive dependency of node.

Definition at line 254 of file DataFlow.cpp.

Referenced by bpp::CombineDeltaShifted< T >::derive().

log() [1/2]

double bpp::log ( const ExtendedFloat &  ef )

inline

Definition at line 443 of file ExtendedFloat.h.

References bpp::ExtendedFloat::log().

Referenced by bpp::CWiseLog< T >::compute(), bpp::LogSumExp< R, T0, T1 >::compute(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::PhyloStatistics::computeForSubtree_(), bpp::BranchLikelihood::computeLogLikelihood(), bpp::AbstractMutationProcess::detailedEvolve(), bpp::AbstractCodonAAFitnessSubstitutionModel::getCodonsMulRate(), bpp::AbstractCodonFitnessSubstitutionModel::getCodonsMulRate(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihood(), bpp::AlignedLikelihoodCalculation::getLogLikelihoodForASite(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihoodForASite(), bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RHomogeneousMixedTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::RHomogeneousMixedTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(), and bpp::ExtendedFloat::log().

log() [2/2]

template<int R, int C>

ExtendedFloatArray<R, C> bpp::log ( const ExtendedFloatArray< R, C > &  arr )

inline

Definition at line 902 of file ExtendedFloatEigen.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::log().

makeConfiguredModelCollection()

ParametrizableCollection<ConfiguredModel> bpp::makeConfiguredModelCollection ( Context &  context, const SubstitutionProcessInterface &  process, ParameterList &  parList  )

inline

Make a Collection of ConfiguredModel, from the models described in the SubstitutionProcess, and sharing ConfiguredParameters from a ParameterList.

Parameter names from the ParameterList may have "_suff" terminations, with suff matching the numbers of the models in the process.

Definition at line 262 of file ProcessTree.h.

References bpp::ParametrizableCollection< class >::addObject(), bpp::SubstitutionProcessInterface::getModel(), bpp::SubstitutionProcessInterface::getModelNumbers(), and bpp::TextTools::toString().

Referenced by bpp::ProcessTree::makeProcessTree().

operator!=() [1/2]

bool bpp::operator!= ( const MatrixDimension &  lhs, const MatrixDimension &  rhs  )

inline

Definition at line 298 of file DataFlowNumeric.h.

operator!=() [2/2]

bool bpp::operator!= ( const NoDimension &  , const NoDimension &    )

inline

Definition at line 237 of file DataFlowNumeric.h.

operator&()

bool bpp::operator&	(	DotOptions	a,
		DotOptions	b
	)

Definition at line 442 of file DataFlow.cpp.

operator*() [1/4]

ExtendedFloat bpp::operator* ( const double &  lhs, const ExtendedFloat &  rhs  )

inline

Definition at line 448 of file ExtendedFloat.h.

operator*() [2/4]

template<typename Derived , typename EFType >

EFType bpp::operator* ( const Eigen::EigenBase< Derived > &  lhs, const ExtendedFloatEigenBase< EFType > &  rhs  )

inline

Definition at line 961 of file ExtendedFloatEigen.h.

operator*() [3/4]

template<int R, int C>

ExtendedFloatArray<R, C> bpp::operator* ( const ExtendedFloatArray< R, C > &  lhs, const ExtendedFloatArrayWrapper< R, C > &  rhs  )

inline

Definition at line 1050 of file ExtendedFloatEigen.h.

operator*() [4/4]

template<int R, int C, template< int R2=R, int C2=C > class MatType, typename T >

std::enable_if<std::is_same<T, ExtendedFloat>::value || std::is_floating_point<T>::value || std::is_integral<T>::value, ExtendedFloatEigen<R, C, MatType> >::type bpp::operator* ( const T &  fact, const ExtendedFloatEigen< R, C, MatType >  mat  )

inline

Definition at line 953 of file ExtendedFloatEigen.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::denorm_mul().

operator+() [1/2]

ExtendedFloat bpp::operator+ ( const double &  lhs, const ExtendedFloat &  rhs  )

inline

Definition at line 458 of file ExtendedFloat.h.

operator+() [2/2]

template<int R, int C, template< int R2=R, int C2=C > class MatType, typename T >

std::enable_if<std::is_same<T, ExtendedFloat>::value || std::is_floating_point<T>::value || std::is_integral<T>::value, ExtendedFloatEigen<R, C, MatType> >::type bpp::operator+ ( const T &  d, const ExtendedFloatEigen< R, C, MatType >  rhs  )

inline

Definition at line 935 of file ExtendedFloatEigen.h.

operator-() [1/2]

ExtendedFloat bpp::operator- ( const double &  lhs, const ExtendedFloat &  rhs  )

inline

Definition at line 453 of file ExtendedFloat.h.

operator-() [2/2]

template<int R, int C, template< int R2=R, int C2=C > class MatType, typename T >

std::enable_if<std::is_same<T, ExtendedFloat>::value || std::is_floating_point<T>::value || std::is_integral<T>::value, ExtendedFloatEigen<R, C, MatType> >::type bpp::operator- ( const T &  d, const ExtendedFloatEigen< R, C, MatType >  rhs  )

inline

Definition at line 944 of file ExtendedFloatEigen.h.

operator/()

ExtendedFloat bpp::operator/ ( const double &  lhs, const ExtendedFloat &  rhs  )

inline

Definition at line 463 of file ExtendedFloat.h.

operator<<()

std::ostream& bpp::operator<< ( std::ostream &  os, const ExtendedFloat &  ef  )

inline

Definition at line 431 of file ExtendedFloat.h.

References bpp::ExtendedFloat::exponent_part(), and bpp::ExtendedFloat::float_part().

operator==() [1/2]

bool bpp::operator== ( const MatrixDimension &  lhs, const MatrixDimension &  rhs  )

inline

Definition at line 294 of file DataFlowNumeric.h.

References bpp::MatrixDimension::cols, and bpp::MatrixDimension::rows.

operator==() [2/2]

bool bpp::operator== ( const NoDimension &  , const NoDimension &    )

inline

Definition at line 236 of file DataFlowNumeric.h.

operator|()

DotOptions bpp::operator|	(	DotOptions	a,
		DotOptions	b
	)

Definition at line 437 of file DataFlow.cpp.

pow() [1/3]

ExtendedFloat bpp::pow ( const ExtendedFloat &  ef, double  exp  )

inline

Definition at line 469 of file ExtendedFloat.h.

References exp(), and bpp::ExtendedFloat::pow().

Referenced by bpp::CodonFromIndependentFrequencySet::CodonFromIndependentFrequencySet(), bpp::CodonFromUniqueFrequencySet::CodonFromUniqueFrequencySet(), bpp::CombineDeltaShifted< T >::compute(), bpp::CWiseConstantPow< T >::compute(), bpp::TreeTools::computeBootstrapValues(), bpp::PhyloTreeTools::computeBranchLengthsGrafen(), bpp::TreeTools::computeBranchLengthsGrafen(), bpp::LaplaceSubstitutionCount::computeCounts(), bpp::HierarchicalClustering::computeDistancesFromPair(), bpp::EquiprobableSubstitutionModel::d2Pij_dt2(), bpp::ExtendedFloat::denorm_pow(), bpp::ExtendedFloat::exp(), bpp::AbstractCodonAAFitnessSubstitutionModel::getCodonsMulRate(), bpp::RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), bpp::EquiprobableSubstitutionModel::getd2Pij_dt2(), bpp::DRHomogeneousMixedTreeLikelihood::getLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::CodonFromIndependentFrequencySet::updateFrequencies(), bpp::CodonFromUniqueFrequencySet::updateFrequencies(), bpp::RELAX::updateMatrices_(), and bpp::POMO::updateMatrices_().

pow() [2/3]

template<int R, int C>

ExtendedFloatArray<R, C> bpp::pow ( const ExtendedFloatArray< R, C > &  obj, double  exp  )

inline

Definition at line 915 of file ExtendedFloatEigen.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::denorm_pow(), and bpp::ExtendedFloatEigen< R, C, EigenType >::exp().

pow() [3/3]

template<int R, int C>

ExtendedFloatArray<R, C> bpp::pow ( const ExtendedFloatArray< R, C > &  obj, int  exp  )

inline

Definition at line 923 of file ExtendedFloatEigen.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::denorm_pow(), and bpp::ExtendedFloatEigen< R, C, EigenType >::exp().

Referenced by bpp::ExtendedFloatEigen< R, C, EigenType >::denorm_pow(), and bpp::ExtendedFloatEigen< R, C, EigenType >::exp().

powi()

int bpp::powi ( int  base, unsigned int  exp  )

inline

Definition at line 24 of file ExtendedFloat.h.

References exp().

Referenced by bpp::ExtendedFloat::lround().

prettyTypeName()

std::string bpp::prettyTypeName

(

const std::type_info &

ti

)

Debug: return a readable name for a C++ type descriptor (from typeid operator).

Definition at line 43 of file DataFlow.cpp.

References demangle().

Referenced by checkNthDependencyIs(), checkRecreateWithoutDependencies(), bpp::Node_DF::description(), failureComputeWasCalled(), failureDeltaNotDerivable(), failureDependencyNumberMismatch(), failureDependencyTypeMismatch(), failureEmptyDependency(), and failureNodeConversion().

recreateWithSubstitution()

NodeRef bpp::recreateWithSubstitution	(	Context &	c,
		const NodeRef &	node,
		const std::unordered_map< const Node_DF *, NodeRef > &	substitutions
	)

Recreate node by transitively replacing dependencies according to substitutions mapping.

Definition at line 272 of file DataFlow.cpp.

removeDependenciesIf()

template<typename Predicate >

void bpp::removeDependenciesIf	(	NodeRefVec &	deps,
		Predicate	p
	)

Definition at line 908 of file DataFlowNumeric.h.

Referenced by bpp::CWiseAdd< R, ReductionOf< T > >::create(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::create(), and bpp::CWiseMul< R, ReductionOf< T > >::create().

to_string() [1/3]

std::string bpp::to_string ( const ExtendedFloat &  ef )

inline

Definition at line 437 of file ExtendedFloat.h.

References bpp::ExtendedFloat::exponent_part(), bpp::ExtendedFloat::float_part(), and to_string().

to_string() [2/3]

std::string bpp::to_string

(

const MatrixDimension &

dim

)

Definition at line 148 of file DataFlowNumeric.cpp.

References bpp::MatrixDimension::cols, and bpp::MatrixDimension::rows.

Referenced by bpp::numeric::checkDimensionIsSquare().

to_string() [3/3]

std::string bpp::to_string

(

const NoDimension &

)

Definition at line 143 of file DataFlowNumeric.cpp.

Referenced by checkNthDependencyIs(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::create(), bpp::numeric::debug(), bpp::ConfiguredDistribution::debugInfo(), bpp::ProbabilitiesFromDiscreteDistribution::debugInfo(), bpp::ConfiguredFrequencySet::debugInfo(), bpp::FrequenciesFromFrequencySet::debugInfo(), bpp::ConfiguredModel::debugInfo(), bpp::EquilibriumFrequenciesFromModel::debugInfo(), bpp::TransitionMatrixFromModel::debugInfo(), bpp::TransitionFunctionFromModel::debugInfo(), bpp::ProbabilitiesFromMixedModel::debugInfo(), bpp::ConfiguredSimplex::debugInfo(), bpp::FrequenciesFromSimplex::debugInfo(), bpp::ConfiguredTransitionMatrix::debugInfo(), bpp::EquilibriumFrequenciesFromTransitionMatrix::debugInfo(), bpp::TransitionMatrixFromTransitionMatrix::debugInfo(), bpp::CWiseFill< R, T >::debugInfo(), bpp::CWisePattern< R >::debugInfo(), bpp::CWiseMatching< R, ReductionOf< T > >::debugInfo(), bpp::CWiseCompound< R, ReductionOf< T > >::debugInfo(), bpp::CWiseApply< R, T, F >::debugInfo(), bpp::CWiseAdd< R, std::tuple< T0, T1 > >::debugInfo(), bpp::CWiseSub< R, std::tuple< T0, T1 > >::debugInfo(), bpp::CWiseAdd< R, ReductionOf< T > >::debugInfo(), bpp::CWiseAdd< R, T >::debugInfo(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::debugInfo(), bpp::CWiseMean< R, ReductionOf< T >, P >::debugInfo(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::debugInfo(), bpp::CWiseMul< R, ReductionOf< T > >::debugInfo(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::debugInfo(), bpp::CWiseNegate< T >::debugInfo(), bpp::CWiseInverse< T >::debugInfo(), bpp::CWiseLog< T >::debugInfo(), bpp::CWiseExp< T >::debugInfo(), bpp::CWiseConstantPow< T >::debugInfo(), bpp::MatrixProduct< R, T0, T1 >::debugInfo(), bpp::ShiftDelta< T >::debugInfo(), bpp::CombineDeltaShifted< T >::debugInfo(), bpp::ConstantZero< T >::debugInfo(), bpp::ConstantOne< T >::debugInfo(), bpp::Convert< R, F >::debugInfo(), bpp::Identity< R >::debugInfo(), bpp::ShiftParameter::debugInfo(), bpp::CondLikelihood::debugInfo(), bpp::ForwardHmmLikelihood_DF::debugInfo(), bpp::ForwardHmmDLikelihood_DF::debugInfo(), bpp::ForwardHmmD2Likelihood_DF::debugInfo(), bpp::BackwardHmmLikelihood_DF::debugInfo(), bpp::CombineDeltaShifted< T >::description(), bpp::ConfiguredParameter::description(), dotIdentifier(), failureDependencyNumberMismatch(), failureDependencyTypeMismatch(), failureEmptyDependency(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::ModelPath::PathNode::to_string(), and to_string().

to_string_with_precision()

template<typename T >

std::string bpp::to_string_with_precision	(	const T	a_value,
		const int	n = 6
	)

Output with given precision.

Definition at line 66 of file DataFlow.h.

transitionFunctionDimension()

Dimension<TransitionFunction> bpp::transitionFunctionDimension ( Eigen::Index  nbState )

inline

Definition at line 20 of file ForwardLikelihoodTree.h.

Referenced by bpp::ForwardLikelihoodTree::makeForwardLikelihoodAtEdge().

transitionMatrixDimension()

MatrixDimension bpp::transitionMatrixDimension ( std::size_t  nbState )

inline

Definition at line 19 of file Model.h.

Referenced by bpp::ForwardLikelihoodTree::makeForwardLikelihoodAtEdge(), and bpp::LikelihoodCalculationOnABranch::makeLikelihoods().

writeDotEdge()

static void bpp::writeDotEdge ( std::ostream &  os, const Node_DF &  from, std::size_t  depIndex, DotOptions  opt  )

static

Definition at line 492 of file DataFlow.cpp.

References bpp::Node_DF::color(), bpp::Node_DF::dependency(), dotIdentifier(), ShowDependencyIndex, and to().

Referenced by writeGraphStructure().

writeDotNode()

static void bpp::writeDotNode ( std::ostream &  os, const Node_DF &  node, DotOptions  opt  )

static

Definition at line 475 of file DataFlow.cpp.

References bpp::Node_DF::color(), bpp::Node_DF::debugInfo(), bpp::Node_DF::description(), DetailedNodeInfo, dotIdentifier(), dotLabelEscape(), bpp::Node_DF::isValid(), and bpp::Node_DF::shape().

Referenced by writeGraphStructure().

writeGraphStructure()

static void bpp::writeGraphStructure ( std::ostream &  os, const std::vector< const Node_DF * > &  entryPoints, DotOptions  opt  )

static

Definition at line 517 of file DataFlow.cpp.

References FollowUpwardLinks, writeDotEdge(), and writeDotNode().

Referenced by writeGraphToDot().

writeGraphToDot() [1/2]

void bpp::writeGraphToDot	(	const std::string &	filename,
		const std::vector< const Node_DF * > &	nodes,
		DotOptions	opt
	)

Write dataflow graph starting at nodes to file at filename, overwriting it.

Definition at line 571 of file DataFlow.cpp.

References writeGraphToDot().

writeGraphToDot() [2/2]

void bpp::writeGraphToDot	(	std::ostream &	os,
		const std::vector< const Node_DF * > &	nodes,
		DotOptions	opt
	)

Write dataflow graph starting at nodes to output stream.

Definition at line 564 of file DataFlow.cpp.

References writeGraphStructure().

Referenced by bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_(), and writeGraphToDot().

Variable Documentation

NodeX

NumericConstant< char > bpp::NodeX

(

'X'

)

Definition at line 1475 of file DataFlowNumeric.h.

Referenced by bpp::CWiseApply< R, T, F >::derive(), and bpp::TransitionFunctionFromModel::derive().