#include <Bpp/Phyl/Likelihood/DataFlow/ForwardLikelihoodTree.h>

Inheritance diagram for bpp::ForwardLikelihoodTree:

Collaboration diagram for bpp::ForwardLikelihoodTree:

Public Types
typedef AssociationGraphObserver< N, E >::NodeIndex	NodeIndex

typedef AssociationGraphObserver< N, E >::EdgeIndex	EdgeIndex

typedef Graph::NodeId	NodeGraphid

typedef Graph::EdgeId	EdgeGraphid

typedef AssociationGraphObserver< N, E >::NodeIterator	NodeIterator

typedef AssociationGraphObserver< N, E >::EdgeIterator	EdgeIterator

typedef std::shared_ptr< E >	Eref

typedef std::shared_ptr< N >	Nref

Public Member Functions
	ForwardLikelihoodTree (Context &c, std::shared_ptr< ProcessTree > tree, const StateMapInterface &statemap)

void	initialize (const AlignmentDataInterface &sites)

std::shared_ptr< const ProcessTree >	getProcessTree () const

const DAGindexes &	getDAGNodesIndexes (const Speciesindex speciesIndex) const

const DAGindexes &	getDAGEdgesIndexes (const Speciesindex speciesIndex) const

const ValueRef< MatrixLik >	getForwardLikelihoodArray (uint nodeId) const

const ValueRef< MatrixLik >	getForwardLikelihoodArrayAtRoot () const

AssociationDAGraphImplObserver< N, E, DAGraphImpl > *	clone () const

bool	isValid () const

bool	isRooted () const

std::vector< std::shared_ptr< N > >	getFathers (const std::shared_ptr< N > node) const

std::vector< NodeIndex >	getFathers (const NodeIndex node) const

virtual std::vector< NodeIndex >	getFathers (const NodeIndex node) const=0

virtual std::vector< NodeIndex >	getFathers (const NodeIndex node) const=0

void	rootAt (const std::shared_ptr< N > root)

bool	hasFather (const std::shared_ptr< N > nodeObject) const

bool	hasFather (const NodeIndex node) const

virtual bool	hasFather (const NodeIndex node) const=0

virtual bool	hasFather (const NodeIndex node) const=0

std::vector< std::shared_ptr< N > >	getSons (const std::shared_ptr< N > node) const

std::vector< NodeIndex >	getSons (const NodeIndex node) const

virtual std::vector< NodeIndex >	getSons (const NodeIndex node) const=0

virtual std::vector< NodeIndex >	getSons (const NodeIndex node) const=0

std::shared_ptr< N >	getSon (const std::shared_ptr< E > edge) const

NodeIndex	getSon (const EdgeIndex edgeId) const

virtual NodeIndex	getSon (const EdgeIndex edge) const=0

virtual NodeIndex	getSon (const EdgeIndex edge) const=0

std::shared_ptr< N >	getFatherOfEdge (const std::shared_ptr< E > edge) const

NodeIndex	getFatherOfEdge (const EdgeIndex edge) const

virtual NodeIndex	getFatherOfEdge (const EdgeIndex edge) const=0

virtual NodeIndex	getFatherOfEdge (const EdgeIndex edge) const=0

size_t	getNumberOfFathers (const std::shared_ptr< N > node) const

size_t	getNumberOfSons (const std::shared_ptr< N > node) const

std::vector< std::shared_ptr< N > >	getLeavesUnderNode (std::shared_ptr< N > node) const

std::vector< std::shared_ptr< N > >	removeFathers (const std::shared_ptr< N > node)

void	removeFather (const std::shared_ptr< N > node, const std::shared_ptr< N > father)

std::vector< std::shared_ptr< N > >	removeSons (const std::shared_ptr< N > node)

void	removeSon (const std::shared_ptr< N > node, const std::shared_ptr< N > son)

void	addFather (const std::shared_ptr< N > nodeObject, const std::shared_ptr< N > fatherNodeObject, const std::shared_ptr< E > edgeObject=0)

void	addSon (const std::shared_ptr< N > nodeObject, const std::shared_ptr< N > sonNodeObject, const std::shared_ptr< E > edgeObject=0)

std::unique_ptr< typename AssociationDAGraphObserver< N, E >::NodeIterator >	fathersIterator (std::shared_ptr< N > node)

std::unique_ptr< typename AssociationDAGraphObserver< N, E >::NodeIterator >	fathersIterator (std::shared_ptr< N > node) const

std::unique_ptr< typename AssociationDAGraphObserver< N, E >::NodeIterator >	sonsIterator (std::shared_ptr< N > node)

std::unique_ptr< typename AssociationDAGraphObserver< N, E >::NodeIterator >	sonsIterator (std::shared_ptr< N > node) const

std::vector< std::shared_ptr< N > >	getBelowNodes (const std::shared_ptr< N > localRoot)

std::vector< std::shared_ptr< E > >	getBelowEdges (const std::shared_ptr< N > localRoot)

virtual void	createNode (std::shared_ptr< N > newNodeObject)=0

virtual void	createNode (std::shared_ptr< N > objectOriginNode, std::shared_ptr< N > newNodeObject, std::shared_ptr< E > newEdgeObject=00)=0

void	createNode (Nref nodeObject)

void	createNode (Nref objectOriginNode, Nref newNodeObject, Eref newEdgeObject=00)

virtual void	createNode (std::shared_ptr< N > newNodeObject)=0

virtual void	createNode (std::shared_ptr< N > objectOriginNode, std::shared_ptr< N > newNodeObject, std::shared_ptr< E > newEdgeObject=00)=0

void	createNode (Nref nodeObject)

void	createNode (Nref objectOriginNode, Nref newNodeObject, Eref newEdgeObject=00)

virtual void	link (std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB, std::shared_ptr< E > edgeObject=00)=0

void	link (Nref nodeObjectA, Nref nodeObjectB, Eref edgeObject=00)

virtual void	link (std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB, std::shared_ptr< E > edgeObject=00)=0

void	link (Nref nodeObjectA, Nref nodeObjectB, Eref edgeObject=00)

virtual void	unlink (std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB)=0

void	unlink (Nref nodeObjectA, Nref nodeObjectB)

virtual void	unlink (std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB)=0

void	unlink (Nref nodeObjectA, Nref nodeObjectB)

virtual void	deleteNode (std::shared_ptr< N > nodeObject)=0

void	deleteNode (Nref nodeObject)

virtual void	deleteNode (std::shared_ptr< N > nodeObject)=0

void	deleteNode (Nref nodeObject)

virtual void	associateNode (std::shared_ptr< N > nodeObject, NodeGraphid node)=0

void	associateNode (Nref nodeObject, NodeGraphid graphNode)

virtual void	associateNode (std::shared_ptr< N > nodeObject, NodeGraphid node)=0

void	associateNode (Nref nodeObject, NodeGraphid graphNode)

virtual void	associateNode (std::shared_ptr< N > nodeObject, NodeGraphid node)=0

virtual void	associateEdge (std::shared_ptr< E > edgeObject, EdgeGraphid edge)=0

void	associateEdge (Eref edgeObject, EdgeGraphid graphEdge)

virtual void	associateEdge (std::shared_ptr< E > edgeObject, EdgeGraphid edge)=0

void	associateEdge (Eref edgeObject, EdgeGraphid graphEdge)

virtual void	associateEdge (std::shared_ptr< E > edgeObject, EdgeGraphid edge)=0

virtual void	dissociateNode (std::shared_ptr< N > nodeObject)=0

void	dissociateNode (Nref nodeObject)

virtual void	dissociateNode (std::shared_ptr< N > nodeObject)=0

void	dissociateNode (Nref nodeObject)

virtual void	dissociateEdge (std::shared_ptr< E > edgeObject)=0

void	dissociateEdge (Eref edgeObject)

virtual void	dissociateEdge (std::shared_ptr< E > edgeObject)=0

void	dissociateEdge (Eref edgeObject)

virtual NodeGraphid	getNodeGraphid (const std::shared_ptr< N > nodeObject) const=0

NodeGraphid	getNodeGraphid (const Nref nodeObject) const

virtual NodeGraphid	getNodeGraphid (const std::shared_ptr< N > nodeObject) const=0

NodeGraphid	getNodeGraphid (const Nref nodeObject) const

virtual EdgeGraphid	getEdgeGraphid (const std::shared_ptr< E > edgeObject) const=0

EdgeGraphid	getEdgeGraphid (const Eref edgeObject) const

virtual EdgeGraphid	getEdgeGraphid (const std::shared_ptr< E > edgeObject) const=0

EdgeGraphid	getEdgeGraphid (const Eref edgeObject) const

virtual const std::shared_ptr< N >	getNodeFromGraphid (NodeGraphid) const=0

virtual std::shared_ptr< N >	getNodeFromGraphid (NodeGraphid)=0

Nref	getNodeFromGraphid (NodeGraphid node)

const Nref	getNodeFromGraphid (NodeGraphid node) const

virtual const std::shared_ptr< N >	getNodeFromGraphid (NodeGraphid) const=0

virtual std::shared_ptr< N >	getNodeFromGraphid (NodeGraphid)=0

Nref	getNodeFromGraphid (NodeGraphid node)

const Nref	getNodeFromGraphid (NodeGraphid node) const

virtual const std::shared_ptr< N >	getNodeFromGraphid (NodeGraphid) const=0

virtual std::shared_ptr< N >	getNodeFromGraphid (NodeGraphid)=0

virtual std::vector< std::shared_ptr< N > >	getNodesFromGraphid (std::vector< NodeGraphid >) const=0

std::vector< Nref >	getNodesFromGraphid (std::vector< NodeGraphid > nodes) const

virtual std::vector< std::shared_ptr< N > >	getNodesFromGraphid (std::vector< NodeGraphid >) const=0

std::vector< Nref >	getNodesFromGraphid (std::vector< NodeGraphid > nodes) const

virtual std::vector< std::shared_ptr< N > >	getNodesFromGraphid (std::vector< NodeGraphid >) const=0

virtual std::shared_ptr< E >	getEdgeFromGraphid (EdgeGraphid)=0

virtual const std::shared_ptr< E >	getEdgeFromGraphid (EdgeGraphid) const=0

Eref	getEdgeFromGraphid (EdgeGraphid edge)

const Eref	getEdgeFromGraphid (EdgeGraphid edge) const

virtual std::shared_ptr< E >	getEdgeFromGraphid (EdgeGraphid)=0

virtual const std::shared_ptr< E >	getEdgeFromGraphid (EdgeGraphid) const=0

Eref	getEdgeFromGraphid (EdgeGraphid edge)

const Eref	getEdgeFromGraphid (EdgeGraphid edge) const

virtual std::shared_ptr< E >	getEdgeFromGraphid (EdgeGraphid)=0

virtual const std::shared_ptr< E >	getEdgeFromGraphid (EdgeGraphid) const=0

virtual std::vector< std::shared_ptr< E > >	getEdgesFromGraphid (std::vector< EdgeGraphid >) const=0

std::vector< Eref >	getEdgesFromGraphid (std::vector< EdgeGraphid > edges) const

virtual std::vector< std::shared_ptr< E > >	getEdgesFromGraphid (std::vector< EdgeGraphid >) const=0

std::vector< Eref >	getEdgesFromGraphid (std::vector< EdgeGraphid > edges) const

virtual std::vector< std::shared_ptr< E > >	getEdgesFromGraphid (std::vector< EdgeGraphid >) const=0

virtual std::shared_ptr< N >	getRoot () const=0

Nref	getRoot () const

virtual std::shared_ptr< N >	getRoot () const=0

Nref	getRoot () const

virtual NodeIndex	getRootIndex () const=0

NodeIndex	getRootIndex () const

virtual NodeIndex	getRootIndex () const=0

NodeIndex	getRootIndex () const

virtual bool	hasNodeIndex (const std::shared_ptr< N > nodeObject) const=0

bool	hasNodeIndex (const Nref nodeObject) const

virtual bool	hasNodeIndex (const std::shared_ptr< N > nodeObject) const=0

bool	hasNodeIndex (const Nref nodeObject) const

virtual bool	hasEdgeIndex (const std::shared_ptr< E > edgeObject) const=0

bool	hasEdgeIndex (const Eref edgeObject) const

virtual bool	hasEdgeIndex (const std::shared_ptr< E > edgeObject) const=0

bool	hasEdgeIndex (const Eref edgeObject) const

virtual NodeIndex	getNodeIndex (const std::shared_ptr< N > nodeObject) const=0

NodeIndex	getNodeIndex (const Nref nodeObject) const

virtual NodeIndex	getNodeIndex (const std::shared_ptr< N > nodeObject) const=0

NodeIndex	getNodeIndex (const Nref nodeObject) const

virtual std::vector< NodeIndex >	getNodeIndexes (std::vector< std::shared_ptr< N > > nodeObjects) const=0

std::vector< NodeIndex >	getNodeIndexes (std::vector< Nref > nodes) const

virtual std::vector< NodeIndex >	getNodeIndexes (std::vector< std::shared_ptr< N > > nodeObjects) const=0

std::vector< NodeIndex >	getNodeIndexes (std::vector< Nref > nodes) const

virtual EdgeIndex	getEdgeIndex (const std::shared_ptr< E > edgeObject) const=0

EdgeIndex	getEdgeIndex (const Eref edgeObject) const

virtual EdgeIndex	getEdgeIndex (const std::shared_ptr< E > edgeObject) const=0

EdgeIndex	getEdgeIndex (const Eref edgeObject) const

virtual std::vector< EdgeIndex >	getEdgeIndexes (std::vector< std::shared_ptr< E > > edgeObjects) const=0

std::vector< EdgeIndex >	getEdgeIndexes (std::vector< Eref > edges) const

virtual std::vector< EdgeIndex >	getEdgeIndexes (std::vector< std::shared_ptr< E > > edgeObjects) const=0

std::vector< EdgeIndex >	getEdgeIndexes (std::vector< Eref > edges) const

virtual NodeIndex	setNodeIndex (const std::shared_ptr< N > nodeObject, NodeIndex index)=0

NodeIndex	setNodeIndex (const Nref nodeObject, NodeIndex index)

virtual NodeIndex	setNodeIndex (const std::shared_ptr< N > nodeObject, NodeIndex index)=0

NodeIndex	setNodeIndex (const Nref nodeObject, NodeIndex index)

virtual NodeIndex	setNodeIndex (const std::shared_ptr< N > nodeObject, NodeIndex index)=0

NodeIndex	setNodeIndex (const Nref nodeObject, NodeIndex index)

virtual EdgeIndex	setEdgeIndex (const std::shared_ptr< E > edgeObject, EdgeIndex index)=0

EdgeIndex	setEdgeIndex (const Eref edgeObject, EdgeIndex index)

virtual EdgeIndex	setEdgeIndex (const std::shared_ptr< E > edgeObject, EdgeIndex index)=0

EdgeIndex	setEdgeIndex (const Eref edgeObject, EdgeIndex index)

virtual EdgeIndex	setEdgeIndex (const std::shared_ptr< E > edgeObject, EdgeIndex index)=0

EdgeIndex	setEdgeIndex (const Eref edgeObject, EdgeIndex index)

virtual bool	hasNode (NodeIndex nodeIndex) const=0

bool	hasNode (NodeIndex node) const

virtual bool	hasNode (NodeIndex nodeIndex) const=0

bool	hasNode (Nref nodeObject) const

bool	hasNode (NodeIndex node) const

virtual bool	hasNode (NodeIndex nodeIndex) const=0

bool	hasNode (NodeIndex node) const

virtual bool	hasEdge (EdgeIndex edgeIndex) const=0

bool	hasEdge (EdgeIndex edge) const

virtual bool	hasEdge (EdgeIndex edgeIndex) const=0

bool	hasEdge (Eref edgeObject) const

bool	hasEdge (EdgeIndex edge) const

virtual bool	hasEdge (EdgeIndex edgeIndex) const=0

bool	hasEdge (EdgeIndex edge) const

virtual std::shared_ptr< N >	getNode (NodeIndex nodeIndex) const=0

Nref	getNode (NodeIndex node) const

virtual std::shared_ptr< N >	getNode (NodeIndex nodeIndex) const=0

Nref	getNode (NodeIndex node) const

virtual std::shared_ptr< N >	getNode (NodeIndex nodeIndex) const=0

Nref	getNode (NodeIndex node) const

virtual std::shared_ptr< E >	getEdge (EdgeIndex edgeIndex) const=0

Eref	getEdge (EdgeIndex edge) const

virtual std::shared_ptr< E >	getEdge (EdgeIndex edgeIndex) const=0

Eref	getEdge (EdgeIndex edge) const

virtual std::shared_ptr< E >	getEdge (EdgeIndex edgeIndex) const=0

Eref	getEdge (EdgeIndex edge) const

virtual std::unique_ptr< NodeIterator >	allNodesIterator ()=0

virtual std::unique_ptr< NodeIterator >	allNodesIterator () const=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	allNodesIterator ()

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	allNodesIterator () const

virtual std::unique_ptr< NodeIterator >	allNodesIterator ()=0

virtual std::unique_ptr< NodeIterator >	allNodesIterator () const=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	allNodesIterator ()

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	allNodesIterator () const

virtual std::unique_ptr< NodeIterator >	outgoingNeighborNodesIterator (std::shared_ptr< N > node)=0

virtual std::unique_ptr< NodeIterator >	outgoingNeighborNodesIterator (std::shared_ptr< N > node) const=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	outgoingNeighborNodesIterator (Nref node)

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	outgoingNeighborNodesIterator (Nref node) const

virtual std::unique_ptr< NodeIterator >	outgoingNeighborNodesIterator (std::shared_ptr< N > node)=0

virtual std::unique_ptr< NodeIterator >	outgoingNeighborNodesIterator (std::shared_ptr< N > node) const=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	outgoingNeighborNodesIterator (Nref node)

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	outgoingNeighborNodesIterator (Nref node) const

virtual std::unique_ptr< NodeIterator >	incomingNeighborNodesIterator (std::shared_ptr< N > node)=0

virtual std::unique_ptr< NodeIterator >	incomingNeighborNodesIterator (std::shared_ptr< N > node) const=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	incomingNeighborNodesIterator (Nref node)

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	incomingNeighborNodesIterator (Nref node) const

virtual std::unique_ptr< NodeIterator >	incomingNeighborNodesIterator (std::shared_ptr< N > node)=0

virtual std::unique_ptr< NodeIterator >	incomingNeighborNodesIterator (std::shared_ptr< N > node) const=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	incomingNeighborNodesIterator (Nref node)

std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator >	incomingNeighborNodesIterator (Nref node) const

virtual std::vector< std::shared_ptr< N > >	getNeighbors (const std::shared_ptr< N > node) const=0

virtual std::vector< NodeIndex >	getNeighbors (NodeIndex node) const=0

std::vector< Nref >	getNeighbors (const Nref node) const

std::vector< NodeIndex >	getNeighbors (NodeIndex node) const

virtual std::vector< std::shared_ptr< N > >	getNeighbors (const std::shared_ptr< N > node) const=0

virtual std::vector< NodeIndex >	getNeighbors (NodeIndex node) const=0

std::vector< Nref >	getNeighbors (const Nref node) const

std::vector< NodeIndex >	getNeighbors (NodeIndex node) const

virtual std::vector< NodeIndex >	getNeighbors (NodeIndex node) const=0

std::vector< NodeIndex >	getNeighbors (NodeIndex node) const

virtual std::vector< std::shared_ptr< E > >	getEdges (const std::shared_ptr< N > node) const=0

virtual std::vector< EdgeIndex >	getEdges (NodeIndex node) const=0

std::vector< Eref >	getEdges (const Nref node) const

std::vector< EdgeIndex >	getEdges (NodeIndex node) const

virtual std::vector< std::shared_ptr< E > >	getEdges (const std::shared_ptr< N > node) const=0

virtual std::vector< EdgeIndex >	getEdges (NodeIndex node) const=0

std::vector< Eref >	getEdges (const Nref node) const

std::vector< EdgeIndex >	getEdges (NodeIndex node) const

virtual std::vector< EdgeIndex >	getEdges (NodeIndex node) const=0

std::vector< EdgeIndex >	getEdges (NodeIndex node) const

virtual std::vector< std::shared_ptr< N > >	getOutgoingNeighbors (const std::shared_ptr< N > node) const=0

virtual std::vector< NodeIndex >	getOutgoingNeighbors (NodeIndex node) const=0

std::vector< Nref >	getOutgoingNeighbors (const Nref node) const

std::vector< NodeIndex >	getOutgoingNeighbors (NodeIndex node) const

virtual std::vector< std::shared_ptr< N > >	getOutgoingNeighbors (const std::shared_ptr< N > node) const=0

virtual std::vector< NodeIndex >	getOutgoingNeighbors (NodeIndex node) const=0

std::vector< Nref >	getOutgoingNeighbors (const Nref node) const

std::vector< NodeIndex >	getOutgoingNeighbors (NodeIndex node) const

virtual std::vector< NodeIndex >	getOutgoingNeighbors (NodeIndex node) const=0

std::vector< NodeIndex >	getOutgoingNeighbors (NodeIndex node) const

virtual std::vector< std::shared_ptr< E > >	getOutgoingEdges (const std::shared_ptr< N > node) const=0

virtual std::vector< EdgeIndex >	getOutgoingEdges (NodeIndex node) const=0

std::vector< Eref >	getOutgoingEdges (const Nref node) const

std::vector< EdgeIndex >	getOutgoingEdges (NodeIndex node) const

virtual std::vector< std::shared_ptr< E > >	getOutgoingEdges (const std::shared_ptr< N > node) const=0

virtual std::vector< EdgeIndex >	getOutgoingEdges (NodeIndex node) const=0

std::vector< Eref >	getOutgoingEdges (const Nref node) const

std::vector< EdgeIndex >	getOutgoingEdges (NodeIndex node) const

virtual std::vector< EdgeIndex >	getOutgoingEdges (NodeIndex node) const=0

std::vector< EdgeIndex >	getOutgoingEdges (NodeIndex node) const

virtual std::vector< std::shared_ptr< N > >	getIncomingNeighbors (const std::shared_ptr< N > node) const=0

virtual std::vector< NodeIndex >	getIncomingNeighbors (NodeIndex node) const=0

std::vector< Nref >	getIncomingNeighbors (const Nref node) const

std::vector< NodeIndex >	getIncomingNeighbors (NodeIndex node) const

virtual std::vector< std::shared_ptr< N > >	getIncomingNeighbors (const std::shared_ptr< N > node) const=0

virtual std::vector< NodeIndex >	getIncomingNeighbors (NodeIndex node) const=0

std::vector< Nref >	getIncomingNeighbors (const Nref node) const

std::vector< NodeIndex >	getIncomingNeighbors (NodeIndex node) const

virtual std::vector< NodeIndex >	getIncomingNeighbors (NodeIndex node) const=0

std::vector< NodeIndex >	getIncomingNeighbors (NodeIndex node) const

virtual std::vector< std::shared_ptr< E > >	getIncomingEdges (const std::shared_ptr< N > node) const=0

virtual std::vector< EdgeIndex >	getIncomingEdges (NodeIndex node) const=0

std::vector< Eref >	getIncomingEdges (const Nref node) const

std::vector< EdgeIndex >	getIncomingEdges (NodeIndex node) const

virtual std::vector< std::shared_ptr< E > >	getIncomingEdges (const std::shared_ptr< N > node) const=0

virtual std::vector< EdgeIndex >	getIncomingEdges (NodeIndex node) const=0

std::vector< Eref >	getIncomingEdges (const Nref node) const

std::vector< EdgeIndex >	getIncomingEdges (NodeIndex node) const

virtual std::vector< EdgeIndex >	getIncomingEdges (NodeIndex node) const=0

std::vector< EdgeIndex >	getIncomingEdges (NodeIndex node) const

virtual std::vector< std::shared_ptr< N > >	getLeavesFromNode (std::shared_ptr< N > node, unsigned int maxDepth) const=0

std::vector< Nref >	getLeavesFromNode (Nref node, unsigned int maxDepth) const

virtual std::vector< std::shared_ptr< N > >	getLeavesFromNode (std::shared_ptr< N > node, unsigned int maxDepth) const=0

std::vector< Nref >	getLeavesFromNode (Nref node, unsigned int maxDepth) const

virtual std::vector< std::shared_ptr< N > >	getAllLeaves () const=0

std::vector< Nref >	getAllLeaves () const

virtual std::vector< std::shared_ptr< N > >	getAllLeaves () const=0

std::vector< Nref >	getAllLeaves () const

virtual std::vector< NodeIndex >	getAllLeavesIndexes () const=0

std::vector< NodeIndex >	getAllLeavesIndexes () const

virtual std::vector< NodeIndex >	getAllLeavesIndexes () const=0

std::vector< NodeIndex >	getAllLeavesIndexes () const

virtual std::vector< std::shared_ptr< N > >	getAllInnerNodes () const=0

std::vector< Nref >	getAllInnerNodes () const

virtual std::vector< std::shared_ptr< N > >	getAllInnerNodes () const=0

std::vector< Nref >	getAllInnerNodes () const

virtual std::vector< NodeIndex >	getAllInnerNodesIndexes () const=0

std::vector< NodeIndex >	getAllInnerNodesIndexes () const

virtual std::vector< NodeIndex >	getAllInnerNodesIndexes () const=0

std::vector< NodeIndex >	getAllInnerNodesIndexes () const

virtual std::vector< std::shared_ptr< N > >	getAllNodes () const=0

std::vector< Nref >	getAllNodes () const

virtual std::vector< std::shared_ptr< N > >	getAllNodes () const=0

std::vector< Nref >	getAllNodes () const

virtual std::vector< NodeIndex >	getAllNodesIndexes () const=0

std::vector< NodeIndex >	getAllNodesIndexes () const

virtual std::vector< NodeIndex >	getAllNodesIndexes () const=0

std::vector< NodeIndex >	getAllNodesIndexes () const

virtual std::unique_ptr< EdgeIterator >	allEdgesIterator ()=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	allEdgesIterator ()

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	allEdgesIterator () const

virtual std::unique_ptr< EdgeIterator >	allEdgesIterator ()=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	allEdgesIterator ()

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	allEdgesIterator () const

virtual std::unique_ptr< EdgeIterator >	outgoingEdgesIterator (std::shared_ptr< N > node)=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	outgoingEdgesIterator (Nref node)

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	outgoingEdgesIterator (Nref node) const

virtual std::unique_ptr< EdgeIterator >	outgoingEdgesIterator (std::shared_ptr< N > node)=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	outgoingEdgesIterator (Nref node)

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	outgoingEdgesIterator (Nref node) const

virtual std::unique_ptr< EdgeIterator >	incomingEdgesIterator (std::shared_ptr< N > node)=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	incomingEdgesIterator (Nref node)

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	incomingEdgesIterator (Nref node) const

virtual std::unique_ptr< EdgeIterator >	incomingEdgesIterator (std::shared_ptr< N > node)=0

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	incomingEdgesIterator (Nref node)

std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator >	incomingEdgesIterator (Nref node) const

virtual std::vector< std::shared_ptr< E > >	getAllEdges () const=0

std::vector< Eref >	getAllEdges () const

virtual std::vector< std::shared_ptr< E > >	getAllEdges () const=0

std::vector< Eref >	getAllEdges () const

virtual std::vector< EdgeIndex >	getAllEdgesIndexes () const=0

std::vector< EdgeIndex >	getAllEdgesIndexes () const

virtual std::vector< EdgeIndex >	getAllEdgesIndexes () const=0

std::vector< EdgeIndex >	getAllEdgesIndexes () const

virtual std::shared_ptr< E >	getEdgeLinking (std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB) const=0

Eref	getEdgeLinking (Nref nodeA, Nref nodeB) const

virtual std::shared_ptr< E >	getEdgeLinking (std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB) const=0

Eref	getEdgeLinking (Nref nodeA, Nref nodeB) const

virtual void	setEdgeLinking (std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB, std::shared_ptr< E > edge)=0

void	setEdgeLinking (Nref nodeA, Nref nodeB, Eref edge)

virtual void	setEdgeLinking (std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB, std::shared_ptr< E > edge)=0

void	setEdgeLinking (Nref nodeA, Nref nodeB, Eref edge)

virtual void	deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete)=0

void	deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete)

virtual void	deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete)=0

void	deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete)

virtual void	deletedNodesUpdate (const std::vector< unsigned int > &nodesToDelete)=0

void	deletedNodesUpdate (const std::vector< unsigned int > &nodesToDelete)

virtual void	deletedNodesUpdate (const std::vector< unsigned int > &nodesToDelete)=0

void	deletedNodesUpdate (const std::vector< unsigned int > &nodesToDelete)

NodeIndex	addNodeIndex (const Nref nodeObject)

NodeIndex	addNodeIndex (const Nref nodeObject)

EdgeIndex	addEdgeIndex (const Eref edgeObject)

EdgeIndex	addEdgeIndex (const Eref edgeObject)

void	setRoot (const Nref newRoot)

void	setRoot (const Nref newRoot)

void	outputToDot (const std::string &fname, const std::string &name) const

void	outputToDot (std::ostream &out, const std::string &name) const

void	outputToDot (const std::string &fname, const std::string &name) const

void	outputToDot (std::ostream &out, const std::string &name) const

bool	isLeaf (const Nref node) const

bool	isLeaf (const NodeIndex nodeid) const

bool	isLeaf (const Nref node) const

bool	isLeaf (const NodeIndex nodeid) const

bool	isLeaf (const NodeIndex nodeid) const

std::pair< Nref, Nref >	getNodes (Eref edge) const

std::pair< Nref, Nref >	getNodes (Eref edge) const

size_t	getNumberOfNodes () const

size_t	getNumberOfNodes () const

size_t	getNumberOfEdges () const

size_t	getNumberOfEdges () const

size_t	getNumberOfLeaves () const

size_t	getNumberOfLeaves () const

size_t	getDegree (const Nref node) const

size_t	getDegree (const Nref node) const

const std::shared_ptr< DAGraphImpl >	getGraph () const

std::shared_ptr< DAGraphImpl >	getGraph ()

std::string	nodeToString (const Nref nodeObject) const

std::string	edgeToString (const Eref edgeObject) const

Static Public Member Functions
static B *	copy (const A &a, typename std::enable_if< !std::is_base_of< B, A >::value &&!std::is_abstract< B >::value, B * >::type *=0)

static B *	copy (const A &a, typename std::enable_if< !std::is_base_of< B, A >::value &&std::is_abstract< B >::value, B * >::type *=0)

static B *	copy (const A &a, typename std::enable_if< std::is_base_of< B, A >::value &&!std::is_abstract< A >::value, B * >::type *=0)

static B *	copy (const A &a, typename std::enable_if< std::is_base_of< B, A >::value &&std::is_abstract< A >::value &&std::is_base_of< Clonable, A >::value, B * >::type *=0)

static B *	copy (const A &a, typename std::enable_if< std::is_base_of< B, A >::value &&std::is_abstract< A >::value &&!std::is_base_of< Clonable, A >::value, B * >::type *=0)

static B *	copy (const A &a, typename std::enable_if< std::is_base_of< B, A >::value &&std::is_abstract< A >::value &&std::is_base_of< Clonable, A >::value, B * >::type *=0)

static B *	copy (const A &a, typename std::enable_if< std::is_base_of< B, A >::value &&std::is_abstract< A >::value &&!std::is_base_of< Clonable, A >::value, B * >::type *=0)

Protected Member Functions
Context &	getContext ()

Protected Attributes
std::shared_ptr< DAGraphImpl >	subjectGraph_

Private Types
using	DAClass = AssociationDAGlobalGraphObserver< ConditionalLikelihoodForward, ForwardLikelihoodBelow >

enum	neighborType

Private Member Functions
ForwardLikelihoodBelowRef	makeForwardLikelihoodAtEdge (std::shared_ptr< ProcessEdge > edge, const AlignmentDataInterface &sites)
	Compute ConditionalLikelihood after reading edge on the forward process (ie at top of the edge). More...

ConditionalLikelihoodForwardRef	makeForwardLikelihoodAtNode (std::shared_ptr< ProcessNode > node, const AlignmentDataInterface &sites)

ConditionalLikelihoodForwardRef	makeInitialConditionalLikelihood (const std::string &sequenceName, const AlignmentDataInterface &sites)
	Compute ConditionalLikelihood for leaf. More...

void	setSpeciesMapIndexes_ ()
	Map the species indexes and the likelihood DAG indexes. More...

std::vector< Nref >	getNeighbors_ (const Nref nodeObject, neighborType type) const

std::vector< Eref >	getEdges_ (const Nref nodeObject, neighborType type) const

Private Attributes
Context &	context_

std::shared_ptr< ProcessTree >	processTree_

MatrixDimension	likelihoodMatrixDim_

const StateMapInterface &	statemap_

Eigen::Index	nbState_

Eigen::Index	nbSites_

std::map< Speciesindex, DAGindexes >	mapNodesIndexes_

std::map< Speciesindex, DAGindexes >	mapEdgesIndexes_

	INCOMING

	OUTGOING

	BOTH

std::vector< Nref >	graphidToN_

std::vector< Eref >	graphidToE_

std::map< Nref, NodeGraphid >	NToGraphid_

std::map< Eref, EdgeGraphid >	EToGraphid_

std::vector< Nref >	indexToN_

std::vector< Eref >	indexToE_

std::map< Nref, NodeIndex >	NToIndex_

std::map< Eref, EdgeIndex >	EToIndex_

Friends
class	LikelihoodCalculationSingleProcess

class	ProbabilityDAG

Detailed Description

Definition at line 100 of file ForwardLikelihoodTree.h.

Member Typedef Documentation

◆ DAClass

using bpp::ForwardLikelihoodTree::DAClass = AssociationDAGlobalGraphObserver<ConditionalLikelihoodForward, ForwardLikelihoodBelow>

private

Definition at line 102 of file ForwardLikelihoodTree.h.

Constructor & Destructor Documentation

◆ ForwardLikelihoodTree()

bpp::ForwardLikelihoodTree::ForwardLikelihoodTree	(	Context &	c,
		std::shared_ptr< ProcessTree >	tree,
		const StateMapInterface &	statemap
	)

inline

Definition at line 122 of file ForwardLikelihoodTree.h.

Member Function Documentation

◆ getContext()

Context & bpp::ForwardLikelihoodTree::getContext ( )

inlineprotected

Definition at line 177 of file ForwardLikelihoodTree.h.

References context_.

◆ getDAGEdgesIndexes()

const DAGindexes & bpp::ForwardLikelihoodTree::getDAGEdgesIndexes ( const Speciesindex speciesIndex ) const

inline

Definition at line 205 of file ForwardLikelihoodTree.h.

References mapEdgesIndexes_.

◆ getDAGNodesIndexes()

const DAGindexes & bpp::ForwardLikelihoodTree::getDAGNodesIndexes ( const Speciesindex speciesIndex ) const

inline

Definition at line 196 of file ForwardLikelihoodTree.h.

References mapNodesIndexes_.

◆ getForwardLikelihoodArray()

const ValueRef< MatrixLik > bpp::ForwardLikelihoodTree::getForwardLikelihoodArray ( uint nodeId ) const

inline

Definition at line 216 of file ForwardLikelihoodTree.h.

References bpp::AssociationDAGraphImplObserver< class, class, class >::getNode().

◆ getForwardLikelihoodArrayAtRoot()

const ValueRef< MatrixLik > bpp::ForwardLikelihoodTree::getForwardLikelihoodArrayAtRoot ( ) const

inline

Definition at line 221 of file ForwardLikelihoodTree.h.

References bpp::AssociationDAGraphImplObserver< class, class, class >::getRoot().

◆ getProcessTree()

std::shared_ptr< const ProcessTree > bpp::ForwardLikelihoodTree::getProcessTree ( ) const

inline

Definition at line 187 of file ForwardLikelihoodTree.h.

References processTree_.

◆ initialize()

void bpp::ForwardLikelihoodTree::initialize ( const AlignmentDataInterface & sites )

inline

Definition at line 129 of file ForwardLikelihoodTree.h.

References bpp::conditionalLikelihoodDimension(), context_, bpp::ConstantZero< T >::create(), bpp::AssociationDAGraphImplObserver< class, class, class >::createNode(), bpp::AssociationDAGraphImplObserver< class, class, class >::deleteNode(), bpp::TemplateAlignmentDataInterface< class >::getNumberOfSites(), likelihoodMatrixDim_, makeForwardLikelihoodAtNode(), nbSites_, nbState_, processTree_, and bpp::AssociationDAGraphImplObserver< class, class, class >::rootAt().

◆ makeForwardLikelihoodAtEdge()

ForwardLikelihoodBelowRef ForwardLikelihoodTree::makeForwardLikelihoodAtEdge	(	std::shared_ptr< ProcessEdge >	edge,
		const AlignmentDataInterface &	sites
	)

private

Compute ConditionalLikelihood after reading edge on the forward process (ie at top of the edge).

Definition at line 38 of file ForwardLikelihoodTree.cpp.

References context_, bpp::CWiseApply< R, T, F >::create(), bpp::MatrixProduct< R, T0, T1 >::create(), bpp::TransitionFunctionFromModel::create(), bpp::AssociationDAGraphImplObserver< class, class, class >::getEdgeIndex(), bpp::AssociationDAGraphImplObserver< class, class, class >::getRoot(), bpp::Context::getZero(), bpp::AssociationDAGraphImplObserver< class, class, class >::hasEdgeIndex(), likelihoodMatrixDim_, bpp::AssociationDAGraphImplObserver< class, class, class >::link(), makeForwardLikelihoodAtNode(), mapEdgesIndexes_, nbState_, processTree_, bpp::AssociationDAGraphImplObserver< class, class, class >::setEdgeIndex(), bpp::transitionFunctionDimension(), bpp::transitionMatrixDimension(), and bpp::numeric::zero().

Referenced by makeForwardLikelihoodAtNode().

◆ makeForwardLikelihoodAtNode()

ConditionalLikelihoodForwardRef ForwardLikelihoodTree::makeForwardLikelihoodAtNode	(	std::shared_ptr< ProcessNode >	node,
		const AlignmentDataInterface &	sites
	)

private

Definition at line 108 of file ForwardLikelihoodTree.cpp.

References context_, bpp::CWiseAdd< R, T >::create(), bpp::AssociationDAGraphImplObserver< class, class, class >::createNode(), bpp::AssociationDAGraphImplObserver< class, class, class >::getNodeIndex(), bpp::AssociationDAGraphImplObserver< class, class, class >::getNodes(), bpp::AssociationDAGraphImplObserver< class, class, class >::hasNodeIndex(), likelihoodMatrixDim_, bpp::AssociationDAGraphImplObserver< class, class, class >::link(), makeForwardLikelihoodAtEdge(), makeInitialConditionalLikelihood(), mapNodesIndexes_, processTree_, bpp::AssociationDAGraphImplObserver< class, class, class >::setNodeIndex(), bpp::TextTools::toString(), and bpp::AssociationDAGraphImplObserver< class, class, class >::unlink().

Referenced by initialize(), and makeForwardLikelihoodAtEdge().

◆ makeInitialConditionalLikelihood()

ConditionalLikelihoodForwardRef ForwardLikelihoodTree::makeInitialConditionalLikelihood	(	const std::string &	sequenceName,
		const AlignmentDataInterface &	sites
	)

private

Compute ConditionalLikelihood for leaf.

Definition at line 17 of file ForwardLikelihoodTree.cpp.

References context_, bpp::Sequence_DF::create(), bpp::StateMapInterface::getAlphabetStateAsInt(), bpp::TemplateAlignmentDataInterface< class >::getNumberOfSites(), bpp::TemplateAlignmentDataInterface< class >::getSequencePosition(), nbState_, and statemap_.

Referenced by makeForwardLikelihoodAtNode().

◆ setSpeciesMapIndexes_()

void bpp::ForwardLikelihoodTree::setSpeciesMapIndexes_ ( )

private

Map the species indexes and the likelihood DAG indexes.

Friends And Related Function Documentation

◆ LikelihoodCalculationSingleProcess

friend class LikelihoodCalculationSingleProcess

friend

Definition at line 226 of file ForwardLikelihoodTree.h.

◆ ProbabilityDAG

friend class ProbabilityDAG

friend

Definition at line 227 of file ForwardLikelihoodTree.h.

Member Data Documentation

◆ context_

Context& bpp::ForwardLikelihoodTree::context_

private

Definition at line 105 of file ForwardLikelihoodTree.h.

Referenced by getContext(), initialize(), makeForwardLikelihoodAtEdge(), makeForwardLikelihoodAtNode(), and makeInitialConditionalLikelihood().

◆ likelihoodMatrixDim_

MatrixDimension bpp::ForwardLikelihoodTree::likelihoodMatrixDim_

private

Definition at line 107 of file ForwardLikelihoodTree.h.

Referenced by initialize(), makeForwardLikelihoodAtEdge(), and makeForwardLikelihoodAtNode().

◆ mapEdgesIndexes_

std::map<Speciesindex, DAGindexes> bpp::ForwardLikelihoodTree::mapEdgesIndexes_

private

Definition at line 118 of file ForwardLikelihoodTree.h.

Referenced by getDAGEdgesIndexes(), and makeForwardLikelihoodAtEdge().

◆ mapNodesIndexes_

std::map<Speciesindex, DAGindexes> bpp::ForwardLikelihoodTree::mapNodesIndexes_

private

Definition at line 115 of file ForwardLikelihoodTree.h.

Referenced by getDAGNodesIndexes(), and makeForwardLikelihoodAtNode().

◆ nbSites_

Eigen::Index bpp::ForwardLikelihoodTree::nbSites_

private

Definition at line 110 of file ForwardLikelihoodTree.h.

Referenced by initialize().

◆ nbState_

Eigen::Index bpp::ForwardLikelihoodTree::nbState_

private

Definition at line 109 of file ForwardLikelihoodTree.h.

Referenced by initialize(), makeForwardLikelihoodAtEdge(), and makeInitialConditionalLikelihood().

◆ processTree_

std::shared_ptr<ProcessTree> bpp::ForwardLikelihoodTree::processTree_

private

Definition at line 106 of file ForwardLikelihoodTree.h.

Referenced by getProcessTree(), initialize(), makeForwardLikelihoodAtEdge(), and makeForwardLikelihoodAtNode().

◆ statemap_

const StateMapInterface& bpp::ForwardLikelihoodTree::statemap_

private

Definition at line 108 of file ForwardLikelihoodTree.h.

Referenced by makeInitialConditionalLikelihood().

The documentation for this class was generated from the following files:

Bpp/Phyl/Likelihood/DataFlow/ForwardLikelihoodTree.h
Bpp/Phyl/Likelihood/DataFlow/ForwardLikelihoodTree.cpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ DAClass

Constructor & Destructor Documentation

◆ ForwardLikelihoodTree()

Member Function Documentation

◆ getContext()

◆ getDAGEdgesIndexes()

◆ getDAGNodesIndexes()

◆ getForwardLikelihoodArray()

◆ getForwardLikelihoodArrayAtRoot()

◆ getProcessTree()

◆ initialize()

◆ makeForwardLikelihoodAtEdge()

◆ makeForwardLikelihoodAtNode()

◆ makeInitialConditionalLikelihood()

◆ setSpeciesMapIndexes_()

Friends And Related Function Documentation

◆ LikelihoodCalculationSingleProcess

◆ ProbabilityDAG

Member Data Documentation

◆ context_

◆ likelihoodMatrixDim_

◆ mapEdgesIndexes_

◆ mapNodesIndexes_

◆ nbSites_

◆ nbState_

◆ processTree_

◆ statemap_