The SingleProcessSubstitutionMapping class: substitution mapping linked with a SingleProcessPhyloLikelihood. More...

#include <Bpp/Phyl/Mapping/PhyloMappings/SingleProcessSubstitutionMapping.h>

Inheritance diagram for bpp::SingleProcessSubstitutionMapping:

Collaboration diagram for bpp::SingleProcessSubstitutionMapping:

Public Types
typedef AssociationTreeGlobalGraphObserver< uint, ModelBranch >	modelTree

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
	SingleProcessSubstitutionMapping (std::shared_ptr< SingleProcessPhyloLikelihood > spp, std::shared_ptr< SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights, std::shared_ptr< const AlphabetIndex2 > distances, double threshold=-1, bool verbose=true)

	SingleProcessSubstitutionMapping (const SingleProcessSubstitutionMapping &sppm)

SingleProcessSubstitutionMapping &	operator= (const SingleProcessSubstitutionMapping &sppm)

virtual	~SingleProcessSubstitutionMapping ()

SingleProcessSubstitutionMapping *	clone () const

void	computeCounts (short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, double threshold=-1, bool verbose=true)
	ComputeCounts. More...

void	computeNormalizations (const ParameterList &nullParams, short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, bool verbose=true)
	compute Normalizations More...

size_t	getNumberOfModels () const

std::vector< size_t >	getModelNumbers () const

LikelihoodCalculationSingleProcess &	getLikelihoodCalculationSingleProcess ()

const LikelihoodCalculationSingleProcess &	getLikelihoodCalculationSingleProcess () const

virtual std::shared_ptr< const TransitionModelInterface >	getModelForBranch (unsigned int branchId) const =0
	Get the model associated to a particular branch id. More...

virtual std::shared_ptr< TransitionModelInterface >	getModelForBranch (unsigned int branchId)=0

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)

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	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 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::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::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::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


std::shared_ptr< TransitionModelInterface >	getModelForBranch (uint branchId) override
	From BranchedModelSet. More...

std::shared_ptr< const TransitionModelInterface >	getModelForBranch (uint branchId) const override

std::shared_ptr< const TransitionModelInterface >	getModel (unsigned int branchId, size_t classIndex) const override
	Get the substitution model corresponding to a certain branch and model class. More...

std::shared_ptr< TransitionModelInterface >	getModel (size_t index)

std::shared_ptr< const TransitionModelInterface >	getModel (size_t index) const override
	Get the model with a ginev index. More...

std::vector< uint >	getBranchesWithModel (size_t index) const override
	Get a list of branches id for which the given model is associated. More...


bool	normalizationsPerformed () const override
	From PhyloSubstitutionMapping. More...

ProbabilisticSubstitutionMapping &	normalizations () override
	Return the tree of factors. More...

const ProbabilisticSubstitutionMapping &	normalizations () const override

bool	countsPerformed () const override
	return if counts have been performed. More...

ProbabilisticSubstitutionMapping &	counts () override
	Return the tree of counts. More...

const ProbabilisticSubstitutionMapping &	counts () const override

void	setSubstitutionRegister (std::shared_ptr< const SubstitutionRegisterInterface > reg)
	For registers. More...

const SubstitutionRegisterInterface &	substitutionRegister () const

std::shared_ptr< const SubstitutionRegisterInterface >	getSubstitutionRegister () const

bool	matchParametersValues (const ParameterList &nullParams) override
	Checks and sets the models with given parameters. More...

const ParameterList &	getParameters () const override
	Gets the parameters. More...

std::shared_ptr< const AlphabetIndex2 >	getWeights () const

std::shared_ptr< const AlphabetIndex2 >	getDistances () const

void	addModel (size_t index, const TransitionModelInterface &model, Vuint brIds)
	add a Substitution Model in the map, and on all branches with given Ids. More...

void	setDistances (const AlphabetIndex2 &ndist) override
	change Distances More...

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::unique_ptr< ProbabilisticSubstitutionMapping >	counts_

std::unique_ptr< ProbabilisticSubstitutionMapping >	factors_

std::shared_ptr< TreeGraphImpl >	subjectGraph_

Private Types
enum	neighborType

Private Member Functions
void	setBranchedModelSet_ ()
	Set the models of the BranchedModelSet to the adhoc branches, for normalization. More...

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

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

Private Attributes
std::shared_ptr< SingleProcessPhyloLikelihood >	pSPP_

std::shared_ptr< const SubstitutionRegisterInterface >	pReg_

std::shared_ptr< const AlphabetIndex2 >	weights_
	weights of the substitutions. If null, no weights are used. More...

std::shared_ptr< const AlphabetIndex2 >	distances_
	distances of the substitutions. If null, no distances are used. More...

ParametrizableCollection< TransitionModelInterface >	modelColl_
	A collection of Transition Models. More...

std::map< size_t, std::vector< uint > >	mModBrid_
	a map <model index, vector of branch ids> More...

	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

The SingleProcessSubstitutionMapping class: substitution mapping linked with a SingleProcessPhyloLikelihood.

Definition at line 25 of file SingleProcessSubstitutionMapping.h.

Member Typedef Documentation

◆ modelTree

typedef AssociationTreeGlobalGraphObserver<uint, ModelBranch> bpp::AbstractSinglePhyloSubstitutionMapping::modelTree

inherited

Definition at line 35 of file AbstractSinglePhyloSubstitutionMapping.h.

Constructor & Destructor Documentation

◆ SingleProcessSubstitutionMapping() [1/2]

SingleProcessSubstitutionMapping::SingleProcessSubstitutionMapping	(	std::shared_ptr< SingleProcessPhyloLikelihood >	spp,
		std::shared_ptr< SubstitutionRegisterInterface >	reg,
		std::shared_ptr< const AlphabetIndex2 >	weights,
		std::shared_ptr< const AlphabetIndex2 >	distances,
		double	threshold = `-1`,
		bool	verbose = `true`
	)

Definition at line 10 of file SingleProcessSubstitutionMapping.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::allEdgesIterator(), bpp::AssociationTreeGraphImplObserver< class, class, class >::allNodesIterator(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeGraphid(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNodeGraphid(), setBranchedModelSet_(), bpp::AssociationTreeGraphImplObserver< class, class, class >::setEdgeIndex(), and bpp::AssociationTreeGraphImplObserver< class, class, class >::setNodeIndex().

Referenced by clone().

◆ SingleProcessSubstitutionMapping() [2/2]

bpp::SingleProcessSubstitutionMapping::SingleProcessSubstitutionMapping ( const SingleProcessSubstitutionMapping & sppm )

inline

Definition at line 47 of file SingleProcessSubstitutionMapping.h.

◆ ~SingleProcessSubstitutionMapping()

virtual bpp::SingleProcessSubstitutionMapping::~SingleProcessSubstitutionMapping ( )

inlinevirtual

Definition at line 59 of file SingleProcessSubstitutionMapping.h.

Member Function Documentation

◆ addModel()

void AbstractSinglePhyloSubstitutionMapping::addModel	(	size_t	index,
		const TransitionModelInterface &	model,
		Vuint	brIds
	)

inherited

add a Substitution Model in the map, and on all branches with given Ids.

Parameters

index	the index of the model
model	the model that will be COPIED.
brIds	the Ids of the branches that will carry this model.

Definition at line 95 of file AbstractSinglePhyloSubstitutionMapping.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::associateEdge(), bpp::TransitionModelInterface::clone(), bpp::AbstractSinglePhyloSubstitutionMapping::mModBrid_, and bpp::AbstractSinglePhyloSubstitutionMapping::modelColl_.

Referenced by bpp::OneProcessSequenceSubstitutionMapping::setBranchedModelSet_(), and setBranchedModelSet_().

◆ clone()

SingleProcessSubstitutionMapping * bpp::SingleProcessSubstitutionMapping::clone ( ) const

inlinevirtual

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

Definition at line 61 of file SingleProcessSubstitutionMapping.h.

References SingleProcessSubstitutionMapping().

◆ computeCounts()

void bpp::SingleProcessSubstitutionMapping::computeCounts	(	short	unresolvedOption = `SubstitutionMappingTools::UNRESOLVED_ZERO`,
		double	threshold = `-1`,
		bool	verbose = `true`
	)

inlinevirtual

ComputeCounts.

Parameters

unresolvedOption	mgmt of gaps in the counts (default: counted as zeros)
threshold
verbose

Implements bpp::PhyloSubstitutionMapping.

Definition at line 70 of file SingleProcessSubstitutionMapping.h.

References bpp::SubstitutionMappingTools::computeCounts(), bpp::AbstractSinglePhyloSubstitutionMapping::counts_, bpp::AbstractSinglePhyloSubstitutionMapping::getDistances(), getLikelihoodCalculationSingleProcess(), bpp::AbstractSinglePhyloSubstitutionMapping::getSubstitutionRegister(), and bpp::AbstractSinglePhyloSubstitutionMapping::getWeights().

◆ computeNormalizations()

void SingleProcessSubstitutionMapping::computeNormalizations	(	const ParameterList &	nullParams,
		short	unresolvedOption = `SubstitutionMappingTools::UNRESOLVED_ZERO`,
		bool	verbose = `true`
	)

virtual

compute Normalizations

Parameters

nullParams	a list of null parameters
unresolvedOption	mgmt of gaps in the counts (default: counted as zeros)
verbose

Implements bpp::PhyloSubstitutionMapping.

Definition at line 46 of file SingleProcessSubstitutionMapping.cpp.

References bpp::SubstitutionMappingTools::computeNormalizations(), bpp::AbstractSinglePhyloSubstitutionMapping::factors_, bpp::AbstractSinglePhyloSubstitutionMapping::getDistances(), getLikelihoodCalculationSingleProcess(), bpp::AbstractSinglePhyloSubstitutionMapping::getSubstitutionRegister(), and bpp::AbstractSinglePhyloSubstitutionMapping::matchParametersValues().

◆ counts() [1/2]

const ProbabilisticSubstitutionMapping & bpp::AbstractSinglePhyloSubstitutionMapping::counts ( ) const

inlineoverridevirtualinherited

Implements bpp::PhyloSubstitutionMapping.

Definition at line 157 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::counts_.

◆ counts() [2/2]

ProbabilisticSubstitutionMapping & bpp::AbstractSinglePhyloSubstitutionMapping::counts ( )

inlineoverridevirtualinherited

Return the tree of counts.

Implements bpp::PhyloSubstitutionMapping.

Definition at line 152 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::counts_.

◆ countsPerformed()

bool bpp::AbstractSinglePhyloSubstitutionMapping::countsPerformed ( ) const

inlineoverridevirtualinherited

return if counts have been performed.

Implements bpp::PhyloSubstitutionMapping.

Definition at line 147 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::counts_.

◆ getBranchesWithModel()

std::vector< uint > bpp::AbstractSinglePhyloSubstitutionMapping::getBranchesWithModel ( size_t index ) const

inlineoverridevirtualinherited

Get a list of branches id for which the given model is associated.

Parameters

index The index of the model.

Returns: A vector with the ids of the branch associated to this model.

Implements bpp::BranchedModelSet.

Definition at line 114 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::mModBrid_.

◆ getDistances()

std::shared_ptr< const AlphabetIndex2 > bpp::AbstractSinglePhyloSubstitutionMapping::getDistances ( ) const

inlineinherited

Definition at line 196 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::distances_.

Referenced by computeCounts(), bpp::OneProcessSequenceSubstitutionMapping::computeCounts(), computeNormalizations(), and bpp::OneProcessSequenceSubstitutionMapping::computeNormalizations().

◆ getLikelihoodCalculationSingleProcess() [1/2]

LikelihoodCalculationSingleProcess & bpp::SingleProcessSubstitutionMapping::getLikelihoodCalculationSingleProcess ( )

inline

Definition at line 108 of file SingleProcessSubstitutionMapping.h.

References pSPP_.

Referenced by computeCounts(), and computeNormalizations().

◆ getLikelihoodCalculationSingleProcess() [2/2]

const LikelihoodCalculationSingleProcess & bpp::SingleProcessSubstitutionMapping::getLikelihoodCalculationSingleProcess ( ) const

inline

Definition at line 113 of file SingleProcessSubstitutionMapping.h.

References pSPP_.

◆ getModel() [1/3]

std::shared_ptr< TransitionModelInterface > bpp::AbstractSinglePhyloSubstitutionMapping::getModel ( size_t index )

inlineinherited

Definition at line 104 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::modelColl_.

◆ getModel() [2/3]

std::shared_ptr< const TransitionModelInterface > bpp::AbstractSinglePhyloSubstitutionMapping::getModel ( size_t index ) const

inlineoverridevirtualinherited

Get the model with a ginev index.

Parameters

index The index of the query model.

Returns: A pointer toward the corresponding model.

Implements bpp::BranchedModelSet.

Definition at line 109 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::modelColl_.

◆ getModel() [3/3]

std::shared_ptr< const TransitionModelInterface > bpp::AbstractSinglePhyloSubstitutionMapping::getModel	(	unsigned int	branchId,
		size_t	classIndex
	)		const

inlineoverridevirtualinherited

Get the substitution model corresponding to a certain branch and model class.

Parameters

branchId	The id of the branch.
classIndex	The model class index.

Implements bpp::PhyloSubstitutionMapping.

Definition at line 99 of file AbstractSinglePhyloSubstitutionMapping.h.

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

◆ getModelForBranch() [1/4]

std::shared_ptr< const TransitionModelInterface > bpp::AbstractSinglePhyloSubstitutionMapping::getModelForBranch ( uint branchId ) const

inlineoverrideinherited

Definition at line 94 of file AbstractSinglePhyloSubstitutionMapping.h.

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

◆ getModelForBranch() [2/4]

std::shared_ptr< TransitionModelInterface > bpp::AbstractSinglePhyloSubstitutionMapping::getModelForBranch ( uint branchId )

inlineoverrideinherited

From BranchedModelSet.

Definition at line 89 of file AbstractSinglePhyloSubstitutionMapping.h.

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

◆ getModelForBranch() [3/4]

virtual std::shared_ptr< const TransitionModelInterface > bpp::BranchedModelSet::getModelForBranch ( unsigned int branchId ) const

pure virtualinherited

Get the model associated to a particular branch id.

Parameters

branchId The id of the query branch.

Returns: A pointer toward the corresponding model.

Exceptions

Exception If no model is found for this branch.

◆ getModelForBranch() [4/4]

virtual std::shared_ptr< TransitionModelInterface > bpp::BranchedModelSet::getModelForBranch ( unsigned int branchId )

pure virtualinherited

◆ getModelNumbers()

std::vector< size_t > bpp::SingleProcessSubstitutionMapping::getModelNumbers ( ) const

inlinevirtual

Returns: The vector of model indexes.

Implements bpp::BranchedModelSet.

Definition at line 103 of file SingleProcessSubstitutionMapping.h.

References pSPP_.

◆ getNumberOfModels()

size_t bpp::SingleProcessSubstitutionMapping::getNumberOfModels ( ) const

inlinevirtual

Returns: The current number of distinct substitution models in this set.

Implements bpp::BranchedModelSet.

Definition at line 98 of file SingleProcessSubstitutionMapping.h.

References pSPP_.

◆ getParameters()

const ParameterList & bpp::AbstractSinglePhyloSubstitutionMapping::getParameters ( ) const

inlineoverridevirtualinherited

Gets the parameters.

Implements bpp::PhyloSubstitutionMapping.

Definition at line 186 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::modelColl_.

◆ getSubstitutionRegister()

std::shared_ptr< const SubstitutionRegisterInterface > bpp::AbstractSinglePhyloSubstitutionMapping::getSubstitutionRegister ( ) const

inlineinherited

Definition at line 176 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::pReg_.

Referenced by computeCounts(), bpp::OneProcessSequenceSubstitutionMapping::computeCounts(), computeNormalizations(), and bpp::OneProcessSequenceSubstitutionMapping::computeNormalizations().

◆ getWeights()

std::shared_ptr< const AlphabetIndex2 > bpp::AbstractSinglePhyloSubstitutionMapping::getWeights ( ) const

inlineinherited

Definition at line 191 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::weights_.

Referenced by computeCounts(), and bpp::OneProcessSequenceSubstitutionMapping::computeCounts().

◆ matchParametersValues()

bool bpp::AbstractSinglePhyloSubstitutionMapping::matchParametersValues ( const ParameterList & nullParams )

inlineoverridevirtualinherited

Checks and sets the models with given parameters.

Implements bpp::PhyloSubstitutionMapping.

Definition at line 181 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::modelColl_.

Referenced by computeNormalizations(), and bpp::OneProcessSequenceSubstitutionMapping::computeNormalizations().

◆ normalizations() [1/2]

const ProbabilisticSubstitutionMapping & bpp::AbstractSinglePhyloSubstitutionMapping::normalizations ( ) const

inlineoverridevirtualinherited

Implements bpp::PhyloSubstitutionMapping.

Definition at line 142 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::factors_.

◆ normalizations() [2/2]

ProbabilisticSubstitutionMapping & bpp::AbstractSinglePhyloSubstitutionMapping::normalizations ( )

inlineoverridevirtualinherited

Return the tree of factors.

Implements bpp::PhyloSubstitutionMapping.

Definition at line 137 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::factors_.

◆ normalizationsPerformed()

bool bpp::AbstractSinglePhyloSubstitutionMapping::normalizationsPerformed ( ) const

inlineoverridevirtualinherited

From PhyloSubstitutionMapping.

Return the tree of factors

Implements bpp::PhyloSubstitutionMapping.

Definition at line 132 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::factors_.

◆ operator=()

SingleProcessSubstitutionMapping & bpp::SingleProcessSubstitutionMapping::operator= ( const SingleProcessSubstitutionMapping & sppm )

inline

Definition at line 52 of file SingleProcessSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::operator=(), and pSPP_.

◆ setBranchedModelSet_()

void SingleProcessSubstitutionMapping::setBranchedModelSet_ ( )

private

Set the models of the BranchedModelSet to the adhoc branches, for normalization.

Definition at line 61 of file SingleProcessSubstitutionMapping.cpp.

References bpp::AbstractSinglePhyloSubstitutionMapping::addModel(), bpp::SubstitutionProcessInterface::getModelNumbers(), bpp::SubstitutionProcessInterface::getNodesWithModel(), bpp::SubstitutionProcessInterface::model(), and pSPP_.

Referenced by SingleProcessSubstitutionMapping().

◆ setDistances()

void bpp::AbstractSinglePhyloSubstitutionMapping::setDistances ( const AlphabetIndex2 & ndist )

inlineoverridevirtualinherited

change Distances

Implements bpp::PhyloSubstitutionMapping.

Definition at line 216 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AlphabetIndex2::clone(), and bpp::AbstractSinglePhyloSubstitutionMapping::distances_.

◆ setSubstitutionRegister()

void bpp::AbstractSinglePhyloSubstitutionMapping::setSubstitutionRegister ( std::shared_ptr< const SubstitutionRegisterInterface > reg )

inlineinherited

For registers.

Definition at line 166 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::pReg_.

◆ substitutionRegister()

const SubstitutionRegisterInterface & bpp::AbstractSinglePhyloSubstitutionMapping::substitutionRegister ( ) const

inlineinherited

Definition at line 171 of file AbstractSinglePhyloSubstitutionMapping.h.

References bpp::AbstractSinglePhyloSubstitutionMapping::pReg_.

Member Data Documentation

◆ counts_

std::unique_ptr<ProbabilisticSubstitutionMapping> bpp::AbstractSinglePhyloSubstitutionMapping::counts_

protectedinherited

Definition at line 53 of file AbstractSinglePhyloSubstitutionMapping.h.

Referenced by computeCounts(), bpp::OneProcessSequenceSubstitutionMapping::computeCounts(), bpp::AbstractSinglePhyloSubstitutionMapping::counts(), bpp::AbstractSinglePhyloSubstitutionMapping::countsPerformed(), and bpp::AbstractSinglePhyloSubstitutionMapping::operator=().

◆ distances_

std::shared_ptr<const AlphabetIndex2> bpp::AbstractSinglePhyloSubstitutionMapping::distances_

privateinherited

distances of the substitutions. If null, no distances are used.

Definition at line 50 of file AbstractSinglePhyloSubstitutionMapping.h.

Referenced by bpp::AbstractSinglePhyloSubstitutionMapping::getDistances(), bpp::AbstractSinglePhyloSubstitutionMapping::operator=(), and bpp::AbstractSinglePhyloSubstitutionMapping::setDistances().

◆ factors_

std::unique_ptr<ProbabilisticSubstitutionMapping> bpp::AbstractSinglePhyloSubstitutionMapping::factors_

protectedinherited

Definition at line 54 of file AbstractSinglePhyloSubstitutionMapping.h.

Referenced by computeNormalizations(), bpp::OneProcessSequenceSubstitutionMapping::computeNormalizations(), bpp::AbstractSinglePhyloSubstitutionMapping::normalizations(), bpp::AbstractSinglePhyloSubstitutionMapping::normalizationsPerformed(), and bpp::AbstractSinglePhyloSubstitutionMapping::operator=().

◆ mModBrid_

std::map<size_t, std::vector<uint> > bpp::AbstractSinglePhyloSubstitutionMapping::mModBrid_

privateinherited

a map <model index, vector of branch ids>

Definition at line 67 of file AbstractSinglePhyloSubstitutionMapping.h.

Referenced by bpp::AbstractSinglePhyloSubstitutionMapping::addModel(), bpp::AbstractSinglePhyloSubstitutionMapping::getBranchesWithModel(), and bpp::AbstractSinglePhyloSubstitutionMapping::operator=().

◆ modelColl_

ParametrizableCollection<TransitionModelInterface> bpp::AbstractSinglePhyloSubstitutionMapping::modelColl_

privateinherited

A collection of Transition Models.

Definition at line 60 of file AbstractSinglePhyloSubstitutionMapping.h.

Referenced by bpp::AbstractSinglePhyloSubstitutionMapping::AbstractSinglePhyloSubstitutionMapping(), bpp::AbstractSinglePhyloSubstitutionMapping::addModel(), bpp::AbstractSinglePhyloSubstitutionMapping::getModel(), bpp::AbstractSinglePhyloSubstitutionMapping::getParameters(), bpp::AbstractSinglePhyloSubstitutionMapping::matchParametersValues(), and bpp::AbstractSinglePhyloSubstitutionMapping::operator=().

◆ pReg_

std::shared_ptr<const SubstitutionRegisterInterface> bpp::AbstractSinglePhyloSubstitutionMapping::pReg_

privateinherited

Definition at line 38 of file AbstractSinglePhyloSubstitutionMapping.h.

Referenced by bpp::AbstractSinglePhyloSubstitutionMapping::getSubstitutionRegister(), bpp::AbstractSinglePhyloSubstitutionMapping::operator=(), bpp::AbstractSinglePhyloSubstitutionMapping::setSubstitutionRegister(), and bpp::AbstractSinglePhyloSubstitutionMapping::substitutionRegister().

◆ pSPP_

std::shared_ptr<SingleProcessPhyloLikelihood> bpp::SingleProcessSubstitutionMapping::pSPP_

private

Definition at line 30 of file SingleProcessSubstitutionMapping.h.

Referenced by getLikelihoodCalculationSingleProcess(), getModelNumbers(), getNumberOfModels(), operator=(), and setBranchedModelSet_().

◆ weights_

std::shared_ptr<const AlphabetIndex2> bpp::AbstractSinglePhyloSubstitutionMapping::weights_

privateinherited

weights of the substitutions. If null, no weights are used.

Definition at line 44 of file AbstractSinglePhyloSubstitutionMapping.h.

Referenced by bpp::AbstractSinglePhyloSubstitutionMapping::getWeights(), and bpp::AbstractSinglePhyloSubstitutionMapping::operator=().

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

Bpp/Phyl/Mapping/PhyloMappings/SingleProcessSubstitutionMapping.h
Bpp/Phyl/Mapping/PhyloMappings/SingleProcessSubstitutionMapping.cpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ modelTree

Constructor & Destructor Documentation

◆ SingleProcessSubstitutionMapping() [1/2]

◆ SingleProcessSubstitutionMapping() [2/2]

◆ ~SingleProcessSubstitutionMapping()

Member Function Documentation

◆ addModel()

◆ clone()

◆ computeCounts()

◆ computeNormalizations()

◆ counts() [1/2]

◆ counts() [2/2]

◆ countsPerformed()

◆ getBranchesWithModel()

◆ getDistances()

◆ getLikelihoodCalculationSingleProcess() [1/2]

◆ getLikelihoodCalculationSingleProcess() [2/2]

◆ getModel() [1/3]

◆ getModel() [2/3]

◆ getModel() [3/3]

◆ getModelForBranch() [1/4]

◆ getModelForBranch() [2/4]

◆ getModelForBranch() [3/4]

◆ getModelForBranch() [4/4]

◆ getModelNumbers()

◆ getNumberOfModels()

◆ getParameters()

◆ getSubstitutionRegister()

◆ getWeights()

◆ matchParametersValues()

◆ normalizations() [1/2]

◆ normalizations() [2/2]

◆ normalizationsPerformed()

◆ operator=()

◆ setBranchedModelSet_()

◆ setDistances()

◆ setSubstitutionRegister()

◆ substitutionRegister()

Member Data Documentation

◆ counts_

◆ distances_

◆ factors_

◆ mModBrid_

◆ modelColl_

◆ pReg_

◆ pSPP_

◆ weights_