Data storage class for probabilistic substitution mappings. More...

#include <Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h>

Inheritance diagram for bpp::ProbabilisticSubstitutionMapping:

Collaboration diagram for bpp::ProbabilisticSubstitutionMapping:

Public Types
typedef AssociationTreeGlobalGraphObserver< PhyloNode, PhyloBranchMapping >	mapTree

typedef mapTree::EdgeIterator	EdgeIterator

typedef mapTree::NodeIterator	NodeIterator

typedef AssociationGraphObserver< N, E >::NodeIndex	NodeIndex

typedef AssociationGraphObserver< N, E >::EdgeIndex	EdgeIndex

typedef Graph::NodeId	NodeGraphid

typedef Graph::EdgeId	EdgeGraphid

typedef std::shared_ptr< E >	Eref

typedef std::shared_ptr< N >	Nref

Public Member Functions
	ProbabilisticSubstitutionMapping (const PhyloTree &tree, size_t nbTypes, size_t numberOfSites)
	Build a new ProbabilisticSubstitutionMapping object. More...

	ProbabilisticSubstitutionMapping (const PhyloTree &tree, size_t nbTypes, const PatternType &rootpatterns, size_t nbDistinctSites)
	the same with rootPatternLinks More...

	ProbabilisticSubstitutionMapping (const PhyloTree &tree)
	Build a new ProbabilisticSubstitutionMapping object. More...

ProbabilisticSubstitutionMapping *	clone () const override

	ProbabilisticSubstitutionMapping (const ProbabilisticSubstitutionMapping &psm)

ProbabilisticSubstitutionMapping &	operator= (const ProbabilisticSubstitutionMapping &psm)

virtual	~ProbabilisticSubstitutionMapping ()

const PhyloBranchMapping &	getBranch (unsigned int branchIndex) const override

PhyloBranchMapping &	getBranch (unsigned int branchIndex) override

size_t	getNumberOfBranches () const override

size_t	getNumberOfDistinctSites () const

double	getCount (unsigned int branchId, size_t site, size_t type) const
	Retrieve the counts, with REAL site positions. More...

const std::vector< double > &	getCounts (unsigned int branchId, size_t site) const

void	setNumberOfSitesAndTypes (size_t numberOfSites, size_t numberOfTypes)

void	setNumberOfSites (size_t numberOfSites) override

void	setNumberOfSubstitutionTypes (size_t numberOfTypes) override

double &	operator() (unsigned int branchId, size_t siteIndex, size_t type) override
	Direct access to substitution numbers, with COMPRESSED site positions (ie site indexes) More...

void	fillMappingVectorForSite (size_t siteIndex, VVdouble &counts) const
	Fill a VVdouble with the counts at a given site. The 1st coordinate of this VVdouble correspond to edges, ordered through their ids, & the second coordinate corresponds to the type numbers. More...

virtual const double &	operator() (unsigned int branchId, size_t siteIndex, size_t type) const override
	Direct access to substitution numbers, with COMPRESSED site positions (ie site indexes) More...

bool	usePatterns () const
	Does it use site patterns? More...

const PatternType	getPatterns () const
	returns the vector of site patterns More...

const size_t	getSiteIndex (size_t site) const

size_t	getNumberOfSubstitutionTypes () const

virtual size_t	getNumberOfSites () const =0

size_t	getNumberOfSites () const

virtual int	getSitePosition (size_t index) const =0

int	getSitePosition (size_t index) const

virtual void	setSitePosition (size_t index, int position)=0
	Set the position of a given site. More...

void	setSitePosition (size_t index, int position)
	Set the position of a given site. More...

bool	isValid () const

std::shared_ptr< E >	getEdgeToFather (const std::shared_ptr< N > nodeObject) const

std::shared_ptr< E >	getEdgeToFather (const NodeIndex index) const

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

bool	isRooted () const

std::shared_ptr< N >	getFatherOfNode (const std::shared_ptr< N > nodeObject) const

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

bool	hasFather (const NodeIndex index) const

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

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

std::vector< std::shared_ptr< E > >	getBranches (const std::shared_ptr< N > node) const

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

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

NodeIndex	getSon (const EdgeIndex edge) const

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

NodeIndex	getFatherOfEdge (const EdgeIndex edge) 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< NodeIndex >	getLeavesUnderNode (NodeIndex node) const

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	setFather (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 AssociationTreeGraphObserver< N, E >::NodeIterator >	sonsIterator (std::shared_ptr< N > node)

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

std::unique_ptr< typename AssociationTreeGraphObserver< N, E >::EdgeIterator >	branchesIterator (std::shared_ptr< N > node)

std::unique_ptr< typename AssociationTreeGraphObserver< N, E >::EdgeIterator >	branchesIterator (std::shared_ptr< N > node) const

std::vector< std::shared_ptr< N > >	getNodePathBetweenTwoNodes (const std::shared_ptr< N > nodeA, const std::shared_ptr< N > nodeB, bool includeAncestor=true) const

std::vector< NodeIndex >	getNodePathBetweenTwoNodes (const NodeIndex nodeA, const NodeIndex nodeB, bool includeAncestor=true) const

std::vector< std::shared_ptr< E > >	getEdgePathBetweenTwoNodes (const std::shared_ptr< N > nodeA, const std::shared_ptr< N > nodeB) const

std::vector< EdgeIndex >	getEdgePathBetweenTwoNodes (const NodeIndex nodeA, const NodeIndex nodeB, bool includeAncestor=true) const

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

std::vector< NodeIndex >	getSubtreeNodes (const NodeIndex localRoot) const

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

std::vector< EdgeIndex >	getSubtreeEdges (const NodeIndex localRoot) const

std::shared_ptr< N >	MRCA (const std::vector< std::shared_ptr< N >> vNodeObject) const

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)

void	associateNode (Nref nodeObject, NodeGraphid graphNode)

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)

void	associateEdge (Eref edgeObject, EdgeGraphid graphEdge)

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

Nref	getNodeFromGraphid (NodeGraphid node)

const Nref	getNodeFromGraphid (NodeGraphid node) 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

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

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

Eref	getEdgeFromGraphid (EdgeGraphid edge)

const Eref	getEdgeFromGraphid (EdgeGraphid edge) const

Eref	getEdgeFromGraphid (EdgeGraphid edge)

const Eref	getEdgeFromGraphid (EdgeGraphid edge) 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

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

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

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)

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)

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

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

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

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

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

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

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

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

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

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

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< TreeGraphImpl >	getGraph () const

std::shared_ptr< TreeGraphImpl >	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 Attributes
std::vector< int >	sitesPositions_

size_t	nbSites_

std::shared_ptr< TreeGraphImpl >	subjectGraph_

Private Types
enum	neighborType

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

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

Private Attributes
PatternType	rootPatternLinks_
	Links between sites and patterns. More...

bool	usePatterns_

size_t	numberOfDistinctSites_

size_t	numberOfTypes_

	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_

Detailed Description

Data storage class for probabilistic substitution mappings.

A 'probabilistic' mapping contains an single value for each branch and each site. This number can be an average number of substitutions, optionally waited, or a probability of observing a certain number of substitutions. Probabilistic was coined there by opposition to the'stochastic' mapping, where a path (number of susbstitutions + there position along the branch) is available for each branch and site. The probabilistic mapping can however be extended to contain a matrix will all types of substitutions, instead of their total number.

Definition at line 31 of file ProbabilisticSubstitutionMapping.h.

Member Typedef Documentation

◆ EdgeIterator

typedef mapTree::EdgeIterator bpp::ProbabilisticSubstitutionMapping::EdgeIterator

Definition at line 57 of file ProbabilisticSubstitutionMapping.h.

◆ mapTree

typedef AssociationTreeGlobalGraphObserver<PhyloNode, PhyloBranchMapping> bpp::ProbabilisticSubstitutionMapping::mapTree

Definition at line 36 of file ProbabilisticSubstitutionMapping.h.

◆ NodeIterator

typedef mapTree::NodeIterator bpp::ProbabilisticSubstitutionMapping::NodeIterator

Definition at line 58 of file ProbabilisticSubstitutionMapping.h.

Constructor & Destructor Documentation

◆ ProbabilisticSubstitutionMapping() [1/4]

bpp::ProbabilisticSubstitutionMapping::ProbabilisticSubstitutionMapping	(	const PhyloTree &	tree,
		size_t	nbTypes,
		size_t	numberOfSites
	)

inline

Build a new ProbabilisticSubstitutionMapping object.

Parameters

tree	The PhyloTree object to use.
nbTypes	the number of types
numberOfSites	The number of sites to map.

Definition at line 68 of file ProbabilisticSubstitutionMapping.h.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::allEdgesIterator(), numberOfDistinctSites_, and setNumberOfSubstitutionTypes().

Referenced by clone().

◆ ProbabilisticSubstitutionMapping() [2/4]

bpp::ProbabilisticSubstitutionMapping::ProbabilisticSubstitutionMapping	(	const PhyloTree &	tree,
		size_t	nbTypes,
		const PatternType &	rootpatterns,
		size_t	nbDistinctSites
	)

inline

the same with rootPatternLinks

Definition at line 83 of file ProbabilisticSubstitutionMapping.h.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::allEdgesIterator(), numberOfDistinctSites_, and setNumberOfSubstitutionTypes().

◆ ProbabilisticSubstitutionMapping() [3/4]

bpp::ProbabilisticSubstitutionMapping::ProbabilisticSubstitutionMapping ( const PhyloTree & tree )

inline

Build a new ProbabilisticSubstitutionMapping object.

Parameters

tree	The tree object to use. It will be cloned for internal use.

Definition at line 99 of file ProbabilisticSubstitutionMapping.h.

◆ ProbabilisticSubstitutionMapping() [4/4]

bpp::ProbabilisticSubstitutionMapping::ProbabilisticSubstitutionMapping ( const ProbabilisticSubstitutionMapping & psm )

inline

Definition at line 108 of file ProbabilisticSubstitutionMapping.h.

◆ ~ProbabilisticSubstitutionMapping()

virtual bpp::ProbabilisticSubstitutionMapping::~ProbabilisticSubstitutionMapping ( )

inlinevirtual

Definition at line 124 of file ProbabilisticSubstitutionMapping.h.

Member Function Documentation

◆ clone()

ProbabilisticSubstitutionMapping* bpp::ProbabilisticSubstitutionMapping::clone ( ) const

inlineoverridevirtual

Reimplemented from bpp::AssociationTreeGraphImplObserver< class, class, class >.

Definition at line 103 of file ProbabilisticSubstitutionMapping.h.

References ProbabilisticSubstitutionMapping().

Referenced by bpp::SubstitutionMappingTools::computeNormalizedCounts().

◆ fillMappingVectorForSite()

void ProbabilisticSubstitutionMapping::fillMappingVectorForSite	(	size_t	siteIndex,
		VVdouble &	counts
	)		const

Fill a VVdouble with the counts at a given site. The 1st coordinate of this VVdouble correspond to edges, ordered through their ids, & the second coordinate corresponds to the type numbers.

Branches are read in the same order as returned by getAllEdgesIndexes() function.

Definition at line 59 of file ProbabilisticSubstitutionMapping.cpp.

References bpp::VectorTools::resize2().

◆ getBranch() [1/2]

const PhyloBranchMapping& bpp::ProbabilisticSubstitutionMapping::getBranch ( unsigned int branchId ) const

inlineoverridevirtual

Returns: The PhyloBranchMapping to a given index

Implements bpp::MappingInterface.

Definition at line 127 of file ProbabilisticSubstitutionMapping.h.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdge().

◆ getBranch() [2/2]

PhyloBranchMapping& bpp::ProbabilisticSubstitutionMapping::getBranch ( unsigned int branchIndex )

inlineoverridevirtual

Implements bpp::MappingInterface.

Definition at line 132 of file ProbabilisticSubstitutionMapping.h.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdge().

◆ getCount()

double bpp::ProbabilisticSubstitutionMapping::getCount	(	unsigned int	branchId,
		size_t	site,
		size_t	type
	)		const

inline

Retrieve the counts, with REAL site positions.

Definition at line 150 of file ProbabilisticSubstitutionMapping.h.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdge(), and getSiteIndex().

◆ getCounts()

const std::vector<double>& bpp::ProbabilisticSubstitutionMapping::getCounts	(	unsigned int	branchId,
		size_t	site
	)		const

inline

Definition at line 155 of file ProbabilisticSubstitutionMapping.h.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdge(), and getSiteIndex().

◆ getNumberOfBranches()

size_t bpp::ProbabilisticSubstitutionMapping::getNumberOfBranches ( ) const

inlineoverridevirtual

Returns: The number of branches mapped.

Implements bpp::MappingInterface.

Definition at line 137 of file ProbabilisticSubstitutionMapping.h.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getNumberOfEdges().

Referenced by bpp::SubstitutionMappingTools::getCountsForSitePerBranch().

◆ getNumberOfDistinctSites()

size_t bpp::ProbabilisticSubstitutionMapping::getNumberOfDistinctSites ( ) const

inline

Definition at line 142 of file ProbabilisticSubstitutionMapping.h.

References numberOfDistinctSites_.

Referenced by bpp::SubstitutionMappingTools::computeNormalizedCounts().

◆ getNumberOfSites() [1/2]

size_t bpp::AbstractMapping::getNumberOfSites ( ) const

inlinevirtualinherited

Returns: The number of sites mapped.

Implements bpp::MappingInterface.

Definition at line 111 of file Mapping.h.

References bpp::AbstractMapping::nbSites_.

Referenced by bpp::RewardMappingTools::computeSumForBranch(), bpp::SubstitutionMappingTools::getCountsForBranchPerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerBranch(), bpp::SubstitutionMappingTools::getCountsPerSitePerBranchPerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerType(), bpp::SubstitutionMappingTools::getTreeForType(), bpp::RewardMappingTools::writeToStream(), and bpp::SubstitutionMappingTools::writeToStream().

◆ getNumberOfSites() [2/2]

virtual size_t bpp::MappingInterface::getNumberOfSites ( ) const

pure virtualinherited

Returns: The number of sites mapped.

Implemented in bpp::AbstractMapping.

◆ getNumberOfSubstitutionTypes()

size_t bpp::AbstractSubstitutionMapping::getNumberOfSubstitutionTypes ( ) const

inlinevirtualinherited

Returns: The number of distinct types of substitutions mapped.

Implements bpp::SubstitutionMapping.

Definition at line 80 of file SubstitutionMapping.h.

References bpp::AbstractSubstitutionMapping::numberOfTypes_.

Referenced by bpp::SubstitutionMappingTools::computeNormalizedCounts(), bpp::SubstitutionMappingTools::getCountsForBranchPerType(), bpp::SubstitutionMappingTools::getCountsForSitePerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerBranchPerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerType(), bpp::SubstitutionMappingTools::getCountsPerTypePerBranch(), and bpp::SubstitutionMappingTools::getNormForSite().

◆ getPatterns()

const PatternType bpp::ProbabilisticSubstitutionMapping::getPatterns ( ) const

inline

returns the vector of site patterns

Definition at line 213 of file ProbabilisticSubstitutionMapping.h.

References rootPatternLinks_.

◆ getSiteIndex()

const size_t bpp::ProbabilisticSubstitutionMapping::getSiteIndex ( size_t site ) const

inline

Definition at line 218 of file ProbabilisticSubstitutionMapping.h.

References rootPatternLinks_, and usePatterns_.

Referenced by getCount(), getCounts(), bpp::SubstitutionMappingTools::getCountsForBranchPerType(), bpp::SubstitutionMappingTools::getCountsForSitePerBranch(), bpp::SubstitutionMappingTools::getCountsForSitePerType(), bpp::SubstitutionMappingTools::getCountsPerSitePerBranchPerType(), bpp::SubstitutionMappingTools::getNormForSite(), bpp::SubstitutionMappingTools::getTreeForType(), and bpp::SubstitutionMappingTools::writeToStream().

◆ getSitePosition() [1/2]

int bpp::AbstractMapping::getSitePosition ( size_t index ) const

inlinevirtualinherited

Parameters

index The site index.

Returns: The site position corresponding to the index.

Implements bpp::MappingInterface.

Definition at line 98 of file Mapping.h.

References bpp::AbstractMapping::sitesPositions_.

◆ getSitePosition() [2/2]

virtual int bpp::MappingInterface::getSitePosition ( size_t index ) const

pure virtualinherited

Parameters

index The site index.

Returns: The site position corresponding to the index.

Implemented in bpp::AbstractMapping.

◆ operator()() [1/2]

virtual const double& bpp::ProbabilisticSubstitutionMapping::operator()	(	unsigned int	branchId,
		size_t	siteIndex,
		size_t	type
	)		const

inlineoverridevirtual

Direct access to substitution numbers, with COMPRESSED site positions (ie site indexes)

Warning: No index checking is performed, use with care!

Implements bpp::SubstitutionMapping.

Definition at line 195 of file ProbabilisticSubstitutionMapping.h.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdge().

◆ operator()() [2/2]

double& bpp::ProbabilisticSubstitutionMapping::operator()	(	unsigned int	branchId,
		size_t	siteIndex,
		size_t	type
	)

inlineoverridevirtual

Direct access to substitution numbers, with COMPRESSED site positions (ie site indexes)

Warning: No index checking is performed, use with care!

Implements bpp::SubstitutionMapping.

Definition at line 172 of file ProbabilisticSubstitutionMapping.h.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdge().

◆ operator=()

ProbabilisticSubstitutionMapping& bpp::ProbabilisticSubstitutionMapping::operator= ( const ProbabilisticSubstitutionMapping & psm )

inline

Definition at line 112 of file ProbabilisticSubstitutionMapping.h.

References numberOfDistinctSites_, bpp::AssociationTreeGraphImplObserver< class, class, class >::operator=(), bpp::AbstractSubstitutionMapping::operator=(), rootPatternLinks_, and usePatterns_.

◆ setNumberOfSites()

void ProbabilisticSubstitutionMapping::setNumberOfSites ( size_t numberOfSites )

overridevirtual

Reimplemented from bpp::AbstractMapping.

Definition at line 10 of file ProbabilisticSubstitutionMapping.cpp.

References bpp::AbstractMapping::setNumberOfSites().

Referenced by bpp::SubstitutionMappingTools::readFromStream().

◆ setNumberOfSitesAndTypes()

void ProbabilisticSubstitutionMapping::setNumberOfSitesAndTypes	(	size_t	numberOfSites,
		size_t	numberOfTypes
	)

Definition at line 28 of file ProbabilisticSubstitutionMapping.cpp.

References bpp::AbstractMapping::setNumberOfSites(), and bpp::AbstractSubstitutionMapping::setNumberOfSubstitutionTypes().

◆ setNumberOfSubstitutionTypes()

void ProbabilisticSubstitutionMapping::setNumberOfSubstitutionTypes ( size_t numberOfTypes )

overridevirtual

Reimplemented from bpp::AbstractSubstitutionMapping.

Definition at line 47 of file ProbabilisticSubstitutionMapping.cpp.

References bpp::AbstractSubstitutionMapping::setNumberOfSubstitutionTypes().

Referenced by ProbabilisticSubstitutionMapping().

◆ setSitePosition() [1/2]

void bpp::AbstractMapping::setSitePosition	(	size_t	index,
		int	position
	)

inlinevirtualinherited

Set the position of a given site.

Warning: No index checking is performed, use with care!

Parameters

index	The site index.
position	The position of the site.

Implements bpp::MappingInterface.

Definition at line 103 of file Mapping.h.

References bpp::AbstractMapping::nbSites_, and bpp::AbstractMapping::sitesPositions_.

Referenced by bpp::RewardMappingTools::readFromStream(), and bpp::SubstitutionMappingTools::readFromStream().

◆ setSitePosition() [2/2]

virtual void bpp::MappingInterface::setSitePosition	(	size_t	index,
		int	position
	)

pure virtualinherited

Set the position of a given site.

Warning: No index checking is performed, use with care!

Parameters

index	The site index.
position	The position of the site.

Implemented in bpp::AbstractMapping.

◆ usePatterns()

bool bpp::ProbabilisticSubstitutionMapping::usePatterns ( ) const

inline

Does it use site patterns?

Definition at line 204 of file ProbabilisticSubstitutionMapping.h.

References usePatterns_.

Member Data Documentation

◆ nbSites_

size_t bpp::AbstractMapping::nbSites_

protectedinherited

Definition at line 82 of file Mapping.h.

Referenced by bpp::AbstractMapping::getNumberOfSites(), bpp::AbstractMapping::setNumberOfSites(), and bpp::AbstractMapping::setSitePosition().

◆ numberOfDistinctSites_

size_t bpp::ProbabilisticSubstitutionMapping::numberOfDistinctSites_

private

Definition at line 54 of file ProbabilisticSubstitutionMapping.h.

Referenced by getNumberOfDistinctSites(), operator=(), and ProbabilisticSubstitutionMapping().

◆ numberOfTypes_

size_t bpp::AbstractSubstitutionMapping::numberOfTypes_

privateinherited

Definition at line 60 of file SubstitutionMapping.h.

Referenced by bpp::AbstractSubstitutionMapping::getNumberOfSubstitutionTypes(), bpp::AbstractSubstitutionMapping::operator=(), and bpp::AbstractSubstitutionMapping::setNumberOfSubstitutionTypes().

◆ rootPatternLinks_

PatternType bpp::ProbabilisticSubstitutionMapping::rootPatternLinks_

private

Links between sites and patterns.

The size of this vector is equal to the number of sites in the container, each element corresponds to a site in the container and points to the corresponding column in the count array of the root node. If the container contains no repeated site, there will be a strict equivalence between each site and the likelihood array of the root node. However, if this is not the case, some pointers may point toward the same element in the likelihood array.

Definition at line 50 of file ProbabilisticSubstitutionMapping.h.

Referenced by getPatterns(), getSiteIndex(), and operator=().

◆ sitesPositions_

std::vector<int> bpp::AbstractMapping::sitesPositions_

protectedinherited

Definition at line 81 of file Mapping.h.

Referenced by bpp::AbstractMapping::getSitePosition(), bpp::AbstractMapping::setNumberOfSites(), and bpp::AbstractMapping::setSitePosition().

◆ usePatterns_

bool bpp::ProbabilisticSubstitutionMapping::usePatterns_

private

Definition at line 52 of file ProbabilisticSubstitutionMapping.h.

Referenced by getSiteIndex(), operator=(), and usePatterns().

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

Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h
Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ EdgeIterator

◆ mapTree

◆ NodeIterator

Constructor & Destructor Documentation

◆ ProbabilisticSubstitutionMapping() [1/4]

◆ ProbabilisticSubstitutionMapping() [2/4]

◆ ProbabilisticSubstitutionMapping() [3/4]

◆ ProbabilisticSubstitutionMapping() [4/4]

◆ ~ProbabilisticSubstitutionMapping()

Member Function Documentation

◆ clone()

◆ fillMappingVectorForSite()

◆ getBranch() [1/2]

◆ getBranch() [2/2]

◆ getCount()

◆ getCounts()

◆ getNumberOfBranches()

◆ getNumberOfDistinctSites()

◆ getNumberOfSites() [1/2]

◆ getNumberOfSites() [2/2]

◆ getNumberOfSubstitutionTypes()

◆ getPatterns()

◆ getSiteIndex()

◆ getSitePosition() [1/2]

◆ getSitePosition() [2/2]

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator=()

◆ setNumberOfSites()

◆ setNumberOfSitesAndTypes()

◆ setNumberOfSubstitutionTypes()

◆ setSitePosition() [1/2]

◆ setSitePosition() [2/2]

◆ usePatterns()

Member Data Documentation

◆ nbSites_

◆ numberOfDistinctSites_

◆ numberOfTypes_

◆ rootPatternLinks_

◆ sitesPositions_

◆ usePatterns_