Defines a Computation Tree based on Operators. More...

#include <Bpp/Numeric/Function/Operators/ComputationTree.h>

Inheritance diagram for bpp::ComputationTree:

Collaboration diagram for bpp::ComputationTree:

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

typedef AssociationGraphObserver< N, E >::EdgeIndex	EdgeIndex

typedef Graph::NodeId	NodeGraphid

typedef Graph::EdgeId	EdgeGraphid

typedef AssociationGraphObserver< N, E >::NodeIterator	NodeIterator

typedef AssociationGraphObserver< N, E >::EdgeIterator	EdgeIterator

using	Eref = std::shared_ptr< E >

using	Nref = std::shared_ptr< N >

Public Member Functions
	ComputationTree (const std::string &formula, const std::map< std::string, std::shared_ptr< FunctionInterface >> &functionNames)

ComputationTree *	clone () const

double	getValue () const

double	getFirstOrderDerivative (const std::string &variable) const

double	getSecondOrderDerivative (const std::string &variable) const

void	readFormula (const std::string &formula, const std::map< std::string, std::shared_ptr< FunctionInterface >> &functionNames)

std::string	output () const

bool	isAllSum ()

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)
	Sets the root and make the tree directed from root to leaves. More...

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
	Get a vector of ancestor nodes between to nodes. More...

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

Graph Relations Management
Modificating the structure of the graph.
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

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

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

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

Graph Relations Management
Modificating the structure of the graph.
void	createNode (Nref nodeObject)

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

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

void	unlink (Nref nodeObjectA, Nref nodeObjectB)

void	deleteNode (Nref nodeObject)

Object Association
Associate or dissociate N and E objects to pre-existing Graph Nodes and Graph Edges
virtual void	associateNode (std::shared_ptr< N > nodeObject, NodeGraphid node)=0

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

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

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

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

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

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

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

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

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

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

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

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

virtual NodeIndex	getRootIndex () const =0

Object Association
Associate or dissociate N and E objects to pre-existing Graph Nodes and Graph Edges
void	associateNode (Nref nodeObject, NodeGraphid graphNode)

void	associateEdge (Eref edgeObject, EdgeGraphid graphEdge)

void	dissociateNode (Nref nodeObject)

void	dissociateEdge (Eref edgeObject)

NodeGraphid	getNodeGraphid (const Nref nodeObject) const

EdgeGraphid	getEdgeGraphid (const Eref edgeObject) const

Nref	getNodeFromGraphid (NodeGraphid node)

const Nref	getNodeFromGraphid (NodeGraphid node) const

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

Eref	getEdgeFromGraphid (EdgeGraphid edge)

const Eref	getEdgeFromGraphid (EdgeGraphid edge) const

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

Nref	getRoot () const

NodeIndex	getRootIndex () const

void	setRoot (const Nref newRoot)
	set the root (but no checking, to be used at first construction) More...

Object Indexation
Get or set indexes to nodes and edges
virtual bool	hasNodeIndex (const std::shared_ptr< N > nodeObject) const =0
	return if the object has an index. More...

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

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

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

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

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

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

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

virtual bool	hasNode (NodeIndex nodeIndex) const =0

virtual bool	hasEdge (EdgeIndex edgeIndex) const =0

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

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

Object Indexation
Get or set indexes to nodes and edges
bool	hasNodeIndex (const Nref nodeObject) const
	return if the object has an index. More...

bool	hasEdgeIndex (const Eref edgeObject) const

NodeIndex	getNodeIndex (const Nref nodeObject) const

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

EdgeIndex	getEdgeIndex (const Eref edgeObject) const

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

NodeIndex	setNodeIndex (const Nref nodeObject, NodeIndex index)

EdgeIndex	setEdgeIndex (const Eref edgeObject, EdgeIndex index)

bool	hasNode (NodeIndex node) const

bool	hasEdge (EdgeIndex edge) const

Nref	getNode (NodeIndex node) const

Eref	getEdge (EdgeIndex edge) const

NodeIndex	addNodeIndex (const Nref nodeObject)

EdgeIndex	addEdgeIndex (const Eref edgeObject)


bool	hasNode (Nref nodeObject) const

bool	hasEdge (Eref edgeObject) 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

Iterator interface on Nodes
virtual std::unique_ptr< NodeIterator >	allNodesIterator ()=0

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

std::vector< Nref >	getAllLeaves () const

std::vector< NodeIndex >	getAllLeavesIndexes () const

std::vector< Nref >	getAllInnerNodes () const

std::vector< NodeIndex >	getAllInnerNodesIndexes () const

std::vector< Nref >	getAllNodes () const

std::vector< NodeIndex >	getAllNodesIndexes () const

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

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

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

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

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

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

std::vector< Eref >	getAllEdges () const

std::vector< EdgeIndex >	getAllEdgesIndexes () const

Eref	getEdgeLinking (Nref nodeA, Nref nodeB) const

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

bool	isLeaf (const Nref node) const
	Is the node a leaf? More...

bool	isLeaf (const NodeIndex nodeid) const

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

Iterator interface on Edges
virtual std::unique_ptr< EdgeIterator >	allEdgesIterator ()=0

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

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

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

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

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

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

Function called by the subjectGraph
Methods called by the subject graph to make this observer so fit the subject graph
virtual void	deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete)=0

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

Function called by the subjectGraph
These methodes are called by the subject graph to make this observer so fit the subject graph
void	deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete)

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

Topology exploration
These methodes of the graph concern the topology exploration.
void	outputToDot (const std::string &fname, const std::string &name) const

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

General Info
General information about the graph
size_t	getNumberOfNodes () const

size_t	getNumberOfEdges () const

size_t	getNumberOfLeaves () const

size_t	getDegree (const Nref node) const

Static Public Member Functions
template<class A , class B >
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)

template<class A , class B >
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)

template<class A , class B >
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)

template<class A , class B >
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)

template<class A , class B >
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::shared_ptr< TreeGraphImpl >	subjectGraph_

Private Member Functions
std::shared_ptr< Operator >	readFormula_ (const std::string &formula, const std::map< std::string, std::shared_ptr< FunctionInterface >> &functionNames)

Detailed Description

Defines a Computation Tree based on Operators.

Definition at line 21 of file ComputationTree.h.

Member Typedef Documentation

◆ EdgeGraphid

template<class N, class E, class TreeGraphImpl>

typedef Graph::EdgeId bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::EdgeGraphid

inherited

Definition at line 31 of file AssociationTreeGraphImplObserver.h.

◆ EdgeIndex

template<class N, class E, class TreeGraphImpl>

typedef AssociationGraphObserver<N, E>::EdgeIndex bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::EdgeIndex

inherited

Definition at line 27 of file AssociationTreeGraphImplObserver.h.

◆ EdgeIterator

template<class N, class E>

typedef AssociationGraphObserver<N, E>::EdgeIterator bpp::AssociationTreeGraphObserver< N, E >::EdgeIterator

inherited

Definition at line 183 of file AssociationTreeGraphObserver.h.

◆ Eref

using bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::Eref = std::shared_ptr<E>

inherited

Definition at line 35 of file AssociationGraphImplObserver.h.

◆ NodeGraphid

template<class N, class E, class TreeGraphImpl>

typedef Graph::NodeId bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::NodeGraphid

inherited

Definition at line 29 of file AssociationTreeGraphImplObserver.h.

◆ NodeIndex

template<class N, class E, class TreeGraphImpl>

typedef AssociationGraphObserver<N, E>::NodeIndex bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::NodeIndex

inherited

Definition at line 26 of file AssociationTreeGraphImplObserver.h.

◆ NodeIterator

template<class N, class E>

typedef AssociationGraphObserver<N, E>::NodeIterator bpp::AssociationTreeGraphObserver< N, E >::NodeIterator

inherited

Iterators

Definition at line 182 of file AssociationTreeGraphObserver.h.

◆ Nref

using bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::Nref = std::shared_ptr<N>

inherited

Definition at line 36 of file AssociationGraphImplObserver.h.

Constructor & Destructor Documentation

◆ ComputationTree()

ComputationTree::ComputationTree	(	const std::string &	formula,
		const std::map< std::string, std::shared_ptr< FunctionInterface >> &	functionNames
	)

Definition at line 17 of file ComputationTree.cpp.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), readFormula_(), bpp::TextTools::removeWhiteSpaces(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::setRoot().

Referenced by clone().

Member Function Documentation

◆ addEdgeIndex()

EdgeIndex bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::addEdgeIndex ( const Eref edgeObject )

inlineinherited

Add an index associated to an edge

Parameters

edgeObject object to which one want to set the index

Returns: the given index

Definition at line 852 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::edgeToString().

◆ addNodeIndex()

NodeIndex bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::addNodeIndex ( const Nref nodeObject )

inlineinherited

Set an new index associated to a node

Parameters

nodeObject object to which one want to set the index

Returns: the given index

Definition at line 821 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::nodeToString().

◆ addSon()

template<class N, class E, class TreeGraphImpl>

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

inlinevirtualinherited

Add a son to a node

Parameters

nodeObject	the concerned node
sonNodeObject	the node to be added as a son to the father
edgeObject	the optional edge between the nodes (default = 00)

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 288 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

◆ allEdgesIterator() [1/3]

template<class N, class E>

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

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::EdgeIterator::~EdgeIterator().

◆ allEdgesIterator() [2/3]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1363 of file AssociationGraphImplObserver.h.

◆ allEdgesIterator() [3/3]

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

inlineinherited

Definition at line 1368 of file AssociationGraphImplObserver.h.

◆ allNodesIterator() [1/4]

template<class N, class E>

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

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ allNodesIterator() [2/4]

template<class N, class E>

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

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ allNodesIterator() [3/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1025 of file AssociationGraphImplObserver.h.

Referenced by isAllSum().

◆ allNodesIterator() [4/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1030 of file AssociationGraphImplObserver.h.

◆ associateEdge() [1/2]

template<class N, class E>

virtual void bpp::AssociationGraphObserver< N, E >::associateEdge	(	std::shared_ptr< E >	edgeObject,
		EdgeGraphid	edge
	)

pure virtualinherited

Associate a E object to an edge in the graph.

Parameters

edgeObject	object to associate
edge	existing edge to be associated

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ associateEdge() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::associateEdge	(	Eref	edgeObject,
		EdgeGraphid	graphEdge
	)

inlinevirtualinherited

Associate a E object to an edge in the graph.

Parameters

edgeObject	object to associate
graphEdge	existing edge to be associated

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 554 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::edgeToString(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasEdge().

◆ associateNode() [1/2]

template<class N, class E>

virtual void bpp::AssociationGraphObserver< N, E >::associateNode	(	std::shared_ptr< N >	nodeObject,
		NodeGraphid	node
	)

pure virtualinherited

Associate a N object to a node in the graph.

Parameters

nodeObject	object to associate
node	existing node to be associated

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ associateNode() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::associateNode	(	Nref	nodeObject,
		NodeGraphid	graphNode
	)

inlinevirtualinherited

Associate a N object to a node in the graph.

Parameters

nodeObject	object to associate
graphNode	existing node to be associated

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 534 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasNode(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::nodeToString().

◆ branchesIterator() [1/2]

template<class N, class E, class TreeGraphImpl>

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

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 319 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::outgoingEdgesIterator().

◆ branchesIterator() [2/2]

template<class N, class E, class TreeGraphImpl>

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

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 324 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::outgoingEdgesIterator().

◆ clone()

ComputationTree* bpp::ComputationTree::clone ( ) const

inlinevirtual

clone function

Reimplemented from bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.

Definition at line 37 of file ComputationTree.h.

References ComputationTree().

◆ copy() [1/5]

template<class N, class E>

template<class A , class B >

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

inlinestaticinherited

Specific copy of A and B objects, if clonable or not.

Definition at line 45 of file AssociationGraphObserver.h.

◆ copy() [2/5]

template<class N, class E>

template<class A , class B >

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

inlinestaticinherited

Definition at line 51 of file AssociationGraphObserver.h.

◆ copy() [3/5]

template<class N, class E>

template<class A , class B >

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

inlinestaticinherited

Definition at line 58 of file AssociationGraphObserver.h.

◆ copy() [4/5]

template<class N, class E>

template<class A , class B >

static B* bpp::AssociationGraphObserver< N, E >::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`
	)

inlinestaticinherited

Definition at line 64 of file AssociationGraphObserver.h.

◆ copy() [5/5]

template<class N, class E>

template<class A , class B >

static B* bpp::AssociationGraphObserver< N, E >::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`
	)

inlinestaticinherited

Definition at line 70 of file AssociationGraphObserver.h.

◆ createNode() [1/4]

template<class N, class E>

virtual void bpp::AssociationGraphObserver< N, E >::createNode ( std::shared_ptr< N > newNodeObject )

pure virtualinherited

Creates an orphaned node from a NodeClass object.

Parameters

newNodeObject the N object associated to the node in the graph.

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ createNode() [2/4]

template<class N, class E>

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

pure virtualinherited

Creates an node linked to an existing node. Order of parameters match the link method.

Parameters

newNodeObject	the N object associated to the node in the graph.
objectOriginNode	existing node. In a directed graph: origin -> newNode.
newEdgeObject	optional edge between nodes (default = 00)

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ createNode() [3/4]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::createNode ( Nref nodeObject )

inlinevirtualinherited

Creates an orphaned node from a NodeClass object.

Parameters

nodeObject the N object associated to the node in the graph.

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 438 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::associateNode(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasNode(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::nodeToString().

Referenced by readFormula_().

◆ createNode() [4/4]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::createNode	(	Nref	objectOriginNode,
		Nref	newNodeObject,
		Eref	newEdgeObject = `00`
	)

inlinevirtualinherited

Creates an node linked to an existing node. Order of parameters match the link method.

Parameters

objectOriginNode	existing node. In a directed graph: origin -> newNode.
newNodeObject	the N object associated to the node in the graph.
newEdgeObject	the optional edge between the nodes (default = 00)

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 455 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::createNode(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::link().

◆ deletedEdgesUpdate() [1/2]

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

pure virtualinherited

Delete unused object edges, since they have been deleted in the graph

Parameters

edgesToDelete a vector of Edges to delete

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ deletedEdgesUpdate() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::deletedEdgesUpdate ( const std::vector< unsigned int > & edgesToDelete )

inlinevirtualinherited

Delete unused object edges, since they have been deleted in the graph

Parameters

edgesToDelete a vector of Edges to delete

Implements bpp::GraphObserver.

Definition at line 1477 of file AssociationGraphImplObserver.h.

◆ deletedNodesUpdate() [1/2]

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

pure virtualinherited

Delete unused object nodes, since they have been deleted in the graph

Parameters

nodesToDelete a vector of N to delete

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ deletedNodesUpdate() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::deletedNodesUpdate ( const std::vector< unsigned int > & nodesToDelete )

inlinevirtualinherited

Delete unused object nodes, since they have been deleted in the graph

Parameters

nodesToDelete a vector of N to delete

Implements bpp::GraphObserver.

Definition at line 1495 of file AssociationGraphImplObserver.h.

◆ deleteNode() [1/2]

template<class N, class E>

virtual void bpp::AssociationGraphObserver< N, E >::deleteNode ( std::shared_ptr< N > nodeObject )

pure virtualinherited

Deletes a node

Parameters

nodeObject node to be deleted

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ deleteNode() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::deleteNode ( Nref nodeObject )

inlinevirtualinherited

Deletes a node

Parameters

nodeObject node to be deleted. The N node object given in argument is not deleted.

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 513 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::dissociateNode(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid().

◆ dissociateEdge() [1/2]

template<class N, class E>

virtual void bpp::AssociationGraphObserver< N, E >::dissociateEdge ( std::shared_ptr< E > edgeObject )

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ dissociateEdge() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::dissociateEdge ( Eref edgeObject )

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 581 of file AssociationGraphImplObserver.h.

◆ dissociateNode() [1/2]

template<class N, class E>

virtual void bpp::AssociationGraphObserver< N, E >::dissociateNode ( std::shared_ptr< N > nodeObject )

pure virtualinherited

Dissociate a N or E object to a node or an edge in the graph. Graph is not changed.

Parameters

nodeObject object to dissociate

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ dissociateNode() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::dissociateNode ( Nref nodeObject )

inlinevirtualinherited

Dissociate a N or E object to a node or an edge in the graph.

Parameters

nodeObject object to dissociate

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 573 of file AssociationGraphImplObserver.h.

◆ edgeToString()

std::string bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::edgeToString ( const Eref edgeObject ) const

inlineinherited

Definition at line 361 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgeIndex(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasEdge(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasEdgeIndex(), and bpp::TextTools::toString().

◆ getAllEdges() [1/2]

template<class N, class E>

virtual std::vector<std::shared_ptr<E> > bpp::AssociationGraphObserver< N, E >::getAllEdges ( ) const

pure virtualinherited

Get all the defined edges of a graphO,

Returns: a vector containing the branchesObjects

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::EdgeIterator::~EdgeIterator().

◆ getAllEdges() [2/2]

std::vector<Eref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getAllEdges ( ) const

inlinevirtualinherited

Get all the defined branches of a graph,

Returns: a vector containing the branchesObjects

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1405 of file AssociationGraphImplObserver.h.

◆ getAllEdgesIndexes() [1/2]

template<class N, class E>

virtual std::vector<EdgeIndex> bpp::AssociationGraphObserver< N, E >::getAllEdgesIndexes ( ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::EdgeIterator::~EdgeIterator().

◆ getAllEdgesIndexes() [2/2]

std::vector<EdgeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getAllEdgesIndexes ( ) const

inlinevirtualinherited

Get indexes of all defined edges of a graph,

Returns: a vector containing the edgesObjects

They are in the same order as the graphIds (and not necessary Indexes).

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1316 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgeIndex().

◆ getAllInnerNodes() [1/2]

template<class N, class E>

virtual std::vector<std::shared_ptr<N> > bpp::AssociationGraphObserver< N, E >::getAllInnerNodes ( ) const

pure virtualinherited

Get all the inner nodes of a graph, ie, nodes with degree >= 2.

Returns: a vector containing the inner nodes.

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getAllInnerNodes() [2/2]

std::vector<Nref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getAllInnerNodes ( ) const

inlinevirtualinherited

Get all the inner nodes of a graph, ie, nodes with degree >= 2.

Returns: a vector containing the inner nodes.

They are in the same order as the graphIds (and not necessary Indexes).

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1236 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph().

◆ getAllInnerNodesIndexes() [1/2]

template<class N, class E>

virtual std::vector<NodeIndex> bpp::AssociationGraphObserver< N, E >::getAllInnerNodesIndexes ( ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getAllInnerNodesIndexes() [2/2]

std::vector<NodeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getAllInnerNodesIndexes ( ) const

inlinevirtualinherited

Get the indexes of all inner nodes of a graph, ie, nodes with degree >= 2.

Returns: a vector containing the inner nodes.

They are in the same order as the graphIds (and not necessary Indexes).

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1257 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeIndex().

◆ getAllLeaves() [1/2]

template<class N, class E>

virtual std::vector<std::shared_ptr<N> > bpp::AssociationGraphObserver< N, E >::getAllLeaves ( ) const

pure virtualinherited

Get all the leaves objects of a graph, ie, nodes with only one neighbor,

Returns: a vector containing the leaves

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getAllLeaves() [2/2]

std::vector<Nref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getAllLeaves ( ) const

inlinevirtualinherited

Get all the leaves objects of a graph, ie, nodes with only one neighbor,

Returns: a vector containing the leaves

They are in the same order as the graphIds (and not necessary Indexes).

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1193 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph().

◆ getAllLeavesIndexes() [1/2]

template<class N, class E>

virtual std::vector<NodeIndex> bpp::AssociationGraphObserver< N, E >::getAllLeavesIndexes ( ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getAllLeavesIndexes() [2/2]

std::vector<NodeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getAllLeavesIndexes ( ) const

inlinevirtualinherited

Get index of the leaves objects of a graph, ie, nodes with only one neighbor,

Returns: a vector containing the leaves

They are in the same order as the graphIds (and not necessary Indexes).

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1214 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeIndex().

◆ getAllNodes() [1/2]

template<class N, class E>

virtual std::vector<std::shared_ptr<N> > bpp::AssociationGraphObserver< N, E >::getAllNodes ( ) const

pure virtualinherited

Get all the defined nodes of a graphO,

Returns: a vector containing the nodesObjects

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getAllNodes() [2/2]

std::vector<Nref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getAllNodes ( ) const

inlinevirtualinherited

Get all the defined nodes of a graph,

Returns: a vector containing the nodesObjects

They are in the same order as the graphIds (and not necessary Indexes).

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1278 of file AssociationGraphImplObserver.h.

◆ getAllNodesIndexes() [1/2]

template<class N, class E>

virtual std::vector<NodeIndex> bpp::AssociationGraphObserver< N, E >::getAllNodesIndexes ( ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getAllNodesIndexes() [2/2]

std::vector<NodeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getAllNodesIndexes ( ) const

inlinevirtualinherited

Get indexes of all defined nodes of a graph,

Returns: a vector containing the nodesObjects

They are in the same order as the graphIds (and not necessary Indexes).

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1297 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeIndex().

◆ getBranches() [1/2]

template<class N, class E, class TreeGraphImpl>

std::vector<std::shared_ptr<E> > bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getBranches ( const std::shared_ptr< N > node ) const

inlinevirtualinherited

Return, in a rooted tree, the branches to the sons of a node

Parameters

node	the concerned node

Returns: a vector of branch Nodes

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 181 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgesFromGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getBranches().

◆ getBranches() [2/2]

template<class N, class E, class TreeGraphImpl>

std::vector<EdgeIndex> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getBranches ( const NodeIndex node ) const

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 186 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getBranches(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeIndexes(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgesFromGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

◆ getDegree()

size_t bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getDegree ( const Nref node ) const

inlineinherited

Return the number of neighbors of a node

Parameters

node	the concerned node

Returns: the number of neighbors

Definition at line 1559 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid().

◆ getEdge() [1/2]

template<class N, class E>

virtual std::shared_ptr<E> bpp::AssociationGraphObserver< N, E >::getEdge ( EdgeIndex edgeIndex ) const

pure virtualinherited

Return the associated Node index

Parameters

edgeIndex the index of the wanted edge

Returns: E, an edge object

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getEdge() [2/2]

Eref bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdge ( EdgeIndex edge ) const

inlinevirtualinherited

Return the associated Node index

Parameters

edge	object which to return the node index

Returns: a node index

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 911 of file AssociationGraphImplObserver.h.

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getFatherOfEdge(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSon().

◆ getEdgeFromGraphid() [1/4]

template<class N, class E>

virtual std::shared_ptr<E> bpp::AssociationGraphObserver< N, E >::getEdgeFromGraphid ( EdgeGraphid )

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getEdgeFromGraphid() [2/4]

template<class N, class E>

virtual const std::shared_ptr<E> bpp::AssociationGraphObserver< N, E >::getEdgeFromGraphid ( EdgeGraphid ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ getEdgeFromGraphid() [3/4]

Eref bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeFromGraphid ( EdgeGraphid edge )

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 649 of file AssociationGraphImplObserver.h.

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getEdgeToFather().

◆ getEdgeFromGraphid() [4/4]

const Eref bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeFromGraphid ( EdgeGraphid edge ) const

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 657 of file AssociationGraphImplObserver.h.

◆ getEdgeGraphid() [1/2]

template<class N, class E>

virtual EdgeGraphid bpp::AssociationGraphObserver< N, E >::getEdgeGraphid ( const std::shared_ptr< E > edgeObject ) const

pure virtualinherited

Return the associated Node ID

Parameters

edgeObject object which to return the node ID

Returns: a node ID

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getEdgeGraphid() [2/2]

EdgeGraphid bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeGraphid ( const Eref edgeObject ) const

inlinevirtualinherited

Return the associated Edge ID

Parameters

edgeObject object which to return the node ID

Returns: a edge ID

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 608 of file AssociationGraphImplObserver.h.

References bpp::TextTools::toString().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::addSon(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getFatherOfEdge(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSon(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::setFather().

◆ getEdgeIndex() [1/2]

template<class N, class E>

virtual EdgeIndex bpp::AssociationGraphObserver< N, E >::getEdgeIndex ( const std::shared_ptr< E > edgeObject ) const

pure virtualinherited

Return the associated Node index

Parameters

edgeObject object which to return the node index

Returns: a node index

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getEdgeIndex() [2/2]

EdgeIndex bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeIndex ( const Eref edgeObject ) const

inlinevirtualinherited

Return the associated Node index

Parameters

edgeObject object which to return the node index

Returns: a node index

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 751 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::edgeToString().

◆ getEdgeIndexes() [1/2]

template<class N, class E>

virtual std::vector<EdgeIndex> bpp::AssociationGraphObserver< N, E >::getEdgeIndexes ( std::vector< std::shared_ptr< E >> edgeObjects ) const

pure virtualinherited

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getEdgeIndexes() [2/2]

std::vector<EdgeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeIndexes ( std::vector< Eref > edges ) const

inlineinherited

Definition at line 759 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgeIndex().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getBranches(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getEdgePathBetweenTwoNodes(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeEdges().

◆ getEdgeLinking() [1/2]

template<class N, class E>

virtual std::shared_ptr<E> bpp::AssociationGraphObserver< N, E >::getEdgeLinking	(	std::shared_ptr< N >	nodeA,
		std::shared_ptr< N >	nodeB
	)		const

pure virtualinherited

Returns the Edge between two nodes nodeA -> nodeB

Parameters

nodeA	source node (if directed)
nodeB	destination node (if directed)

Returns: the edge between these two nodes

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::EdgeIterator::~EdgeIterator().

◆ getEdgeLinking() [2/2]

Eref bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeLinking	(	Nref	nodeA,
		Nref	nodeB
	)		const

inlinevirtualinherited

Returns the Edge between two nodes nodeA -> nodeB

Parameters

nodeA	source node (if directed)
nodeB	destination node (if directed)

Returns: the edge between these two nodes, or 0 if edge does not exist

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1449 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdge(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgeFromGraphid(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid().

◆ getEdgePathBetweenTwoNodes() [1/2]

template<class N, class E, class TreeGraphImpl>

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

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 343 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgesFromGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getEdgePathBetweenTwoNodes().

◆ getEdgePathBetweenTwoNodes() [2/2]

template<class N, class E, class TreeGraphImpl>

std::vector<EdgeIndex> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getEdgePathBetweenTwoNodes	(	const NodeIndex	nodeA,
		const NodeIndex	nodeB,
		bool	includeAncestor = `true`
	)		const

inlineinherited

Definition at line 353 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeIndexes(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getEdgePathBetweenTwoNodes(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode().

◆ getEdges() [1/4]

template<class N, class E>

virtual std::vector<std::shared_ptr<E> > bpp::AssociationGraphObserver< N, E >::getEdges ( const std::shared_ptr< N > node ) const

pure virtualinherited

Get all the edges from/to a node in the graph.

Parameters

node	the node one wants to get its neighbor edges

Returns: a vector containing the edges

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getEdges() [2/4]

template<class N, class E>

virtual std::vector<EdgeIndex> bpp::AssociationGraphObserver< N, E >::getEdges ( NodeIndex node ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ getEdges() [3/4]

std::vector<Eref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdges ( const Nref node ) const

inlinevirtualinherited

Get all the edges of a node in the graph.

Parameters

node	the node one wants to get its edges

Returns: a vector containing the edges

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1096 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdges(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgesFromGraphid(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid().

◆ getEdges() [4/4]

std::vector<EdgeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdges ( NodeIndex node ) const

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1101 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgeIndexes(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdges(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNode().

◆ getEdgesFromGraphid() [1/2]

template<class N, class E>

virtual std::vector<std::shared_ptr<E> > bpp::AssociationGraphObserver< N, E >::getEdgesFromGraphid ( std::vector< EdgeGraphid > ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getEdgesFromGraphid() [2/2]

std::vector<Eref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgesFromGraphid ( std::vector< EdgeGraphid > edges ) const

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 665 of file AssociationGraphImplObserver.h.

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getBranches(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getEdgePathBetweenTwoNodes().

◆ getEdgeToFather() [1/2]

template<class N, class E, class TreeGraphImpl>

std::shared_ptr<E> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getEdgeToFather ( const std::shared_ptr< N > nodeObject ) const

inlinevirtualinherited

Return, in a rooted tree, the branch leading to the father

Parameters

nodeObject the concerned node

Returns: an Edge which is the branch to the father

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 109 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeFromGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getEdgeToFather().

◆ getEdgeToFather() [2/2]

template<class N, class E, class TreeGraphImpl>

std::shared_ptr<E> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getEdgeToFather ( const NodeIndex index ) const

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 114 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeFromGraphid(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getEdgeToFather(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

◆ getFatherOfEdge() [1/2]

template<class N, class E, class TreeGraphImpl>

std::shared_ptr<N> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getFatherOfEdge ( const std::shared_ptr< E > edge ) const

inlinevirtualinherited

Return, in a rooted tree, the father of an edge

Parameters

edge	the concerned edge

Returns: the father Node

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 211 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeFromGraphid().

◆ getFatherOfEdge() [2/2]

template<class N, class E, class TreeGraphImpl>

NodeIndex bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getFatherOfEdge ( const EdgeIndex edge ) const

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 216 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdge(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeFromGraphid(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeIndex().

◆ getFatherOfNode()

template<class N, class E, class TreeGraphImpl>

std::shared_ptr<N> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getFatherOfNode ( const std::shared_ptr< N > nodeObject ) const

inlinevirtualinherited

Return, in a rooted tree, the father node

Parameters

nodeObject the concerned node

Returns: the father

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 143 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeFromGraphid(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

◆ getFirstOrderDerivative()

double bpp::ComputationTree::getFirstOrderDerivative ( const std::string & variable ) const

inline

Definition at line 47 of file ComputationTree.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getRoot().

◆ getGraph() [1/2]

const std::shared_ptr<TreeGraphImpl > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph ( ) const

inlineinherited

Definition at line 315 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::subjectGraph_.

◆ getGraph() [2/2]

std::shared_ptr<TreeGraphImpl > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph ( )

inlineinherited

Definition at line 320 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::subjectGraph_.

◆ getIncomingEdges() [1/4]

template<class N, class E>

virtual std::vector<std::shared_ptr<E> > bpp::AssociationGraphObserver< N, E >::getIncomingEdges ( const std::shared_ptr< N > node ) const

pure virtualinherited

In an directed graph, get all the edges which are coming to a node in the graph.

Parameters

node	the node one wants to get its edges

Returns: a vector containing the incoming edges

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getIncomingEdges() [2/4]

template<class N, class E>

virtual std::vector<EdgeIndex> bpp::AssociationGraphObserver< N, E >::getIncomingEdges ( NodeIndex node ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ getIncomingEdges() [3/4]

std::vector<Eref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getIncomingEdges ( const Nref node ) const

inlinevirtualinherited

In an directed graph, get all the edges which are coming to a node in the graph.

Parameters

node	the node one wants to get its edges

Returns: a vector containing the incoming edges

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1162 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgesFromGraphid(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getIncomingEdges(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid().

◆ getIncomingEdges() [4/4]

std::vector<EdgeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getIncomingEdges ( NodeIndex node ) const

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1167 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgeIndexes(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getIncomingEdges(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNode().

◆ getIncomingNeighbors() [1/4]

template<class N, class E>

virtual std::vector<std::shared_ptr<N> > bpp::AssociationGraphObserver< N, E >::getIncomingNeighbors ( const std::shared_ptr< N > node ) const

pure virtualinherited

In an directed graph, get all the neighbors which are coming to a node in the graph.

Parameters

node	the node one wants to get its neighbors

Returns: a vector containing the incoming neighbors

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getIncomingNeighbors() [2/4]

template<class N, class E>

virtual std::vector<NodeIndex> bpp::AssociationGraphObserver< N, E >::getIncomingNeighbors ( NodeIndex node ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ getIncomingNeighbors() [3/4]

std::vector<Nref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getIncomingNeighbors ( const Nref node ) const

inlinevirtualinherited

In an directed graph, get all the neighbors which are coming to a node in the graph.

Parameters

node	the node one wants to get its neighbors

Returns: a vector containing the incoming neighbors

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1145 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getIncomingNeighbors(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodesFromGraphid().

◆ getIncomingNeighbors() [4/4]

std::vector<NodeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getIncomingNeighbors ( NodeIndex node ) const

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1150 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getIncomingNeighbors(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNode(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeIndexes().

◆ getLeavesFromNode() [1/2]

template<class N, class E>

virtual std::vector<std::shared_ptr<N> > bpp::AssociationGraphObserver< N, E >::getLeavesFromNode	(	std::shared_ptr< N >	node,
		unsigned int	maxDepth
	)		const

pure virtualinherited

Get the leaves of a graph, ie, nodes with only one neighbor, starting from a peculiar node, up to a specific depth.

Parameters

node	the starting node
maxDepth	the max recursion depth

Returns: a vector containing the leaves

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getLeavesFromNode() [2/2]

std::vector<Nref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getLeavesFromNode	(	Nref	node,
		unsigned int	maxDepth
	)		const

inlinevirtualinherited

Get the leaves of a graph, ie, nodes with only one neighbor, starting from a peculiar node, with maxDepth recursion depths.

Parameters

node	the starting node
maxDepth	the max recursion depth

Returns: a vector containing the leaves

They are in the same order as the graphIds (and not necessary Indexes).

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1182 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getLeavesFromNode(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodesFromGraphid().

◆ getLeavesUnderNode() [1/2]

template<class N, class E, class TreeGraphImpl>

std::vector<std::shared_ptr<N> > bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getLeavesUnderNode ( std::shared_ptr< N > node ) const

inlinevirtualinherited

Get the leaves of a tree under a peculiar node.

Parameters

node	the starting node

Returns: a vector containing the leaves

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 238 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodesFromGraphid().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getLeavesUnderNode().

◆ getLeavesUnderNode() [2/2]

template<class N, class E, class TreeGraphImpl>

std::vector<NodeIndex> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getLeavesUnderNode ( NodeIndex node ) const

inlineinherited

Definition at line 243 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getLeavesUnderNode(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeIndexes().

◆ getNeighbors() [1/4]

template<class N, class E>

virtual std::vector<std::shared_ptr<N> > bpp::AssociationGraphObserver< N, E >::getNeighbors ( const std::shared_ptr< N > node ) const

pure virtualinherited

Get all the neighbors of a node in the graph.

Parameters

node	the node one wants to get its neighbors

Returns: a vector containing the neighbors

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getNeighbors() [2/4]

template<class N, class E>

virtual std::vector<NodeIndex> bpp::AssociationGraphObserver< N, E >::getNeighbors ( NodeIndex node ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ getNeighbors() [3/4]

std::vector<Nref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNeighbors ( const Nref node ) const

inlinevirtualinherited

Get all the neighbors of a node in the graph.

Parameters

node	the node one wants to get its neighbors

Returns: a vector containing the neighbors

They are in the same order as the graphIds (and not necessary Indexes).

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1073 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNeighbors(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodesFromGraphid().

◆ getNeighbors() [4/4]

std::vector<NodeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNeighbors ( NodeIndex node ) const

inlinevirtualinherited

Get the index of all neighbors of a node in the graph.

Parameters

node	the node one wants to get its neighbors

Returns: a vector containing the neighbors

They are in the same order as the graphIds (and not necessary Indexes).

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1085 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNeighbors(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNode(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeIndexes().

◆ getNode() [1/2]

template<class N, class E>

virtual std::shared_ptr<N> bpp::AssociationGraphObserver< N, E >::getNode ( NodeIndex nodeIndex ) const

pure virtualinherited

Return the associated Node, querying with an index

Parameters

nodeIndex the index of the wanted node

Returns: N, a node object

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getNode() [2/2]

Nref bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode ( NodeIndex node ) const

inlinevirtualinherited

Return the associated Node index

Parameters

node	object which to return the node index

Returns: a node index

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 901 of file AssociationGraphImplObserver.h.

◆ getNodeFromGraphid() [1/4]

template<class N, class E>

virtual const std::shared_ptr<N> bpp::AssociationGraphObserver< N, E >::getNodeFromGraphid ( NodeGraphid ) const

pure virtualinherited

Transforms an (a list of) id(s) into an (a list of) object(s)

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getNodeFromGraphid() [2/4]

template<class N, class E>

virtual std::shared_ptr<N> bpp::AssociationGraphObserver< N, E >::getNodeFromGraphid ( NodeGraphid )

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ getNodeFromGraphid() [3/4]

Nref bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeFromGraphid ( NodeGraphid node )

inlinevirtualinherited

Transforms an (a list of) id(s) into an (a list of) object(s)

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 620 of file AssociationGraphImplObserver.h.

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getFatherOfEdge(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getFatherOfNode(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSon(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::MRCA().

◆ getNodeFromGraphid() [4/4]

const Nref bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeFromGraphid ( NodeGraphid node ) const

inlinevirtualinherited

Transforms an (a list of) id(s) into an (a list of) object(s)

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 627 of file AssociationGraphImplObserver.h.

◆ getNodeGraphid() [1/2]

template<class N, class E>

virtual NodeGraphid bpp::AssociationGraphObserver< N, E >::getNodeGraphid ( const std::shared_ptr< N > nodeObject ) const

pure virtualinherited

Return the associated Node ID

Parameters

nodeObject object which to return the node ID

Returns: a node ID

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getNodeGraphid() [2/2]

NodeGraphid bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid ( const Nref nodeObject ) const

inlinevirtualinherited

Return the associated Node ID

Parameters

nodeObject object which to return the node ID

Returns: a node ID

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 594 of file AssociationGraphImplObserver.h.

References bpp::TextTools::toString().

◆ getNodeIndex() [1/2]

template<class N, class E>

virtual NodeIndex bpp::AssociationGraphObserver< N, E >::getNodeIndex ( const std::shared_ptr< N > nodeObject ) const

pure virtualinherited

Return the associated Node index

Parameters

nodeObject object which to return the node index

Returns: a node index

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getNodeIndex() [2/2]

NodeIndex bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeIndex ( const Nref nodeObject ) const

inlinevirtualinherited

Return the associated Node index

Parameters

nodeObject object which to return the node index

Returns: a node index

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 728 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::nodeToString().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getFatherOfEdge(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSon().

◆ getNodeIndexes() [1/2]

template<class N, class E>

virtual std::vector<NodeIndex> bpp::AssociationGraphObserver< N, E >::getNodeIndexes ( std::vector< std::shared_ptr< N >> nodeObjects ) const

pure virtualinherited

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getNodeIndexes() [2/2]

std::vector<NodeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeIndexes ( std::vector< Nref > nodes ) const

inlineinherited

Definition at line 737 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeIndex().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getLeavesUnderNode(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getNodePathBetweenTwoNodes(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSons(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeNodes().

◆ getNodePathBetweenTwoNodes() [1/2]

template<class N, class E, class TreeGraphImpl>

std::vector<std::shared_ptr<N> > bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getNodePathBetweenTwoNodes	(	const std::shared_ptr< N >	nodeA,
		const std::shared_ptr< N >	nodeB,
		bool	includeAncestor = `true`
	)		const

inlinevirtualinherited

Get a vector of ancestor nodes between to nodes.

Parameters

nodeA	first node.
nodeB	second node.
includeAncestor	Tell if the common ancestor must be included in the vector.

Returns: A vector of ancestor nodes ids.

Exceptions

PhyloNodeNotFoundException If a node is not found.

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 338 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodesFromGraphid().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getNodePathBetweenTwoNodes().

◆ getNodePathBetweenTwoNodes() [2/2]

template<class N, class E, class TreeGraphImpl>

std::vector<NodeIndex> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getNodePathBetweenTwoNodes	(	const NodeIndex	nodeA,
		const NodeIndex	nodeB,
		bool	includeAncestor = `true`
	)		const

inlineinherited

Definition at line 348 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeIndexes(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getNodePathBetweenTwoNodes().

◆ getNodes()

std::pair<Nref, Nref> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodes ( Eref edge ) const

inlineinherited

Get nodes located at the extremities of an edge

Parameters

edge an edge

Returns: a pair of the Nodes at each extremity of the edge example : N1–E1–>N2; getNodes(E1) will return (N1,N2);

Definition at line 1437 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgeGraphid(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeFromGraphid().

◆ getNodesFromGraphid() [1/2]

template<class N, class E>

virtual std::vector<std::shared_ptr<N> > bpp::AssociationGraphObserver< N, E >::getNodesFromGraphid ( std::vector< NodeGraphid > ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getNodesFromGraphid() [2/2]

std::vector<Nref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodesFromGraphid ( std::vector< NodeGraphid > nodes ) const

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 634 of file AssociationGraphImplObserver.h.

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getLeavesUnderNode(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getNodePathBetweenTwoNodes(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSons(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeNodes(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::removeSons().

◆ getNumberOfEdges()

size_t bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNumberOfEdges ( ) const

inlineinherited

Return the number of defined edges, ie edges that have a corresponding object in this GraphObserver

Returns: the number of edges

Definition at line 1531 of file AssociationGraphImplObserver.h.

◆ getNumberOfLeaves()

size_t bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNumberOfLeaves ( ) const

inlineinherited

Return the number of defined leaves, ie leaves that have a corresponding object in this GraphObserver

Returns: the number of leaves

Definition at line 1542 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::isLeaf().

◆ getNumberOfNodes()

size_t bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNumberOfNodes ( ) const

inlineinherited

Return the number of defined nodes, ie nodes that have a corresponding object in this GraphObserver

Returns: the number of nodes

Definition at line 1521 of file AssociationGraphImplObserver.h.

◆ getNumberOfSons()

template<class N, class E, class TreeGraphImpl>

size_t bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getNumberOfSons ( const std::shared_ptr< N > node ) const

inlinevirtualinherited

Return, in a rooted tree, the number of sons

Parameters

node	the concerned node

Returns: the number of sons

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 227 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

◆ getOutgoingEdges() [1/4]

template<class N, class E>

virtual std::vector<std::shared_ptr<E> > bpp::AssociationGraphObserver< N, E >::getOutgoingEdges ( const std::shared_ptr< N > node ) const

pure virtualinherited

In an directed graph, get all the edges which are leaving a node in the graph.

Parameters

node	the node one wants to get its edges

Returns: a vector containing the outgoing edges

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getOutgoingEdges() [2/4]

template<class N, class E>

virtual std::vector<EdgeIndex> bpp::AssociationGraphObserver< N, E >::getOutgoingEdges ( NodeIndex node ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ getOutgoingEdges() [3/4]

std::vector<Eref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getOutgoingEdges ( const Nref node ) const

inlinevirtualinherited

In an directed graph, get all the edges which are leaving a node in the graph.

Parameters

node	the node one wants to get its edges

Returns: a vector containing the outgoing edges

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1129 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgesFromGraphid(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getOutgoingEdges().

◆ getOutgoingEdges() [4/4]

std::vector<EdgeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getOutgoingEdges ( NodeIndex node ) const

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1134 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgeIndexes(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNode(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getOutgoingEdges().

◆ getOutgoingNeighbors() [1/4]

template<class N, class E>

virtual std::vector<std::shared_ptr<N> > bpp::AssociationGraphObserver< N, E >::getOutgoingNeighbors ( const std::shared_ptr< N > node ) const

pure virtualinherited

In an directed graph, get all the neighbors which are leaving a node in the graph.

Parameters

node	the node one wants to get its neighbors

Returns: a vector containing the outgoing neighbors

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ getOutgoingNeighbors() [2/4]

template<class N, class E>

virtual std::vector<NodeIndex> bpp::AssociationGraphObserver< N, E >::getOutgoingNeighbors ( NodeIndex node ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ getOutgoingNeighbors() [3/4]

std::vector<Nref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getOutgoingNeighbors ( const Nref node ) const

inlinevirtualinherited

In an directed graph, get all the neighbors which are leaving a node in the graph.

Parameters

node	the node one wants to get its neighbors

Returns: a vector containing the outgoing neighbors

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1113 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodesFromGraphid(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getOutgoingNeighbors().

◆ getOutgoingNeighbors() [4/4]

std::vector<NodeIndex> bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getOutgoingNeighbors ( NodeIndex node ) const

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1118 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNode(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeIndexes(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getOutgoingNeighbors().

◆ getRoot() [1/2]

template<class N, class E>

virtual std::shared_ptr<N> bpp::AssociationGraphObserver< N, E >::getRoot ( ) const

pure virtualinherited

Returns: the root

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getRoot() [2/2]

Nref bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getRoot ( ) const

inlinevirtualinherited

Returns: the root

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 692 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeFromGraphid(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getRoot().

Referenced by getFirstOrderDerivative(), getSecondOrderDerivative(), getValue(), and output().

◆ getRootIndex() [1/2]

template<class N, class E>

virtual NodeIndex bpp::AssociationGraphObserver< N, E >::getRootIndex ( ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ getRootIndex() [2/2]

NodeIndex bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getRootIndex ( ) const

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 697 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeFromGraphid(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeIndex(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getRoot().

◆ getSecondOrderDerivative()

double bpp::ComputationTree::getSecondOrderDerivative ( const std::string & variable ) const

inline

Definition at line 52 of file ComputationTree.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getRoot().

◆ getSon() [1/2]

template<class N, class E, class TreeGraphImpl>

std::shared_ptr<N> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSon ( const std::shared_ptr< E > edge ) const

inlinevirtualinherited

Return, in a rooted tree, the son of an edge

Parameters

edge	the concerned edge

Returns: the son Node

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 196 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeFromGraphid().

◆ getSon() [2/2]

template<class N, class E, class TreeGraphImpl>

NodeIndex bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSon ( const EdgeIndex edge ) const

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 201 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdge(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeFromGraphid(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeIndex().

◆ getSons() [1/2]

template<class N, class E, class TreeGraphImpl>

std::vector<std::shared_ptr<N> > bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSons ( const std::shared_ptr< N > node ) const

inlinevirtualinherited

Return, in a rooted tree, the sons of a node

Parameters

node	the concerned node

Returns: a vector of son Nodes

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 166 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodesFromGraphid().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSons().

◆ getSons() [2/2]

template<class N, class E, class TreeGraphImpl>

std::vector<NodeIndex> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSons ( const NodeIndex node ) const

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 171 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeIndexes(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodesFromGraphid(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSons().

◆ getSubtreeEdges() [1/2]

template<class N, class E, class TreeGraphImpl>

std::vector<std::shared_ptr<E> > bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeEdges ( const std::shared_ptr< N > localRoot ) const

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 363 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdgesFromGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeEdges().

◆ getSubtreeEdges() [2/2]

template<class N, class E, class TreeGraphImpl>

std::vector<EdgeIndex> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeEdges ( const NodeIndex localRoot ) const

inlineinherited

Definition at line 373 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeIndexes(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeEdges().

◆ getSubtreeNodes() [1/2]

template<class N, class E, class TreeGraphImpl>

std::vector<std::shared_ptr<N> > bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeNodes ( const std::shared_ptr< N > localRoot ) const

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 358 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodesFromGraphid().

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeNodes().

◆ getSubtreeNodes() [2/2]

template<class N, class E, class TreeGraphImpl>

std::vector<NodeIndex> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeNodes ( const NodeIndex localRoot ) const

inlineinherited

Definition at line 368 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeIndexes(), and bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::getSubtreeNodes().

◆ getValue()

double bpp::ComputationTree::getValue ( ) const

inline

Definition at line 42 of file ComputationTree.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getRoot().

◆ hasEdge() [1/3]

template<class N, class E>

virtual bool bpp::AssociationGraphObserver< N, E >::hasEdge ( EdgeIndex edgeIndex ) const

pure virtualinherited

Return if the Graph has an edge matching edgeIndex

Parameters

edgeIndex the index of the wanted edge

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ hasEdge() [2/3]

bool bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::hasEdge ( Eref edgeObject ) const

inlineinherited

Definition at line 337 of file AssociationGraphImplObserver.h.

◆ hasEdge() [3/3]

bool bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::hasEdge ( EdgeIndex edge ) const

inlinevirtualinherited

Return if has Edge matching EdgeIndex

Parameters

edge	EdgeIndex index

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 891 of file AssociationGraphImplObserver.h.

◆ hasEdgeIndex() [1/2]

template<class N, class E>

virtual bool bpp::AssociationGraphObserver< N, E >::hasEdgeIndex ( const std::shared_ptr< E > edgeObject ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ hasEdgeIndex() [2/2]

bool bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::hasEdgeIndex ( const Eref edgeObject ) const

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 718 of file AssociationGraphImplObserver.h.

◆ hasFather() [1/2]

template<class N, class E, class TreeGraphImpl>

bool bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::hasFather ( const std::shared_ptr< N > nodeObject ) const

inlinevirtualinherited

Has the node a father?

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 151 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

◆ hasFather() [2/2]

template<class N, class E, class TreeGraphImpl>

bool bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::hasFather ( const NodeIndex index ) const

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 156 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

◆ hasNode() [1/3]

template<class N, class E>

virtual bool bpp::AssociationGraphObserver< N, E >::hasNode ( NodeIndex nodeIndex ) const

pure virtualinherited

Return if the Graph has a node matching nodeIndex

Parameters

nodeIndex the index of the wanted node

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ hasNode() [2/3]

bool bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::hasNode ( Nref nodeObject ) const

inlineinherited

Definition at line 330 of file AssociationGraphImplObserver.h.

◆ hasNode() [3/3]

bool bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::hasNode ( NodeIndex node ) const

inlinevirtualinherited

Return if has Node matching NodeIndex

Parameters

node	NodeIndex index

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 882 of file AssociationGraphImplObserver.h.

◆ hasNodeIndex() [1/2]

template<class N, class E>

virtual bool bpp::AssociationGraphObserver< N, E >::hasNodeIndex ( const std::shared_ptr< N > nodeObject ) const

pure virtualinherited

return if the object has an index.

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ hasNodeIndex() [2/2]

bool bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::hasNodeIndex ( const Nref nodeObject ) const

inlinevirtualinherited

return if the object has an index.

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 713 of file AssociationGraphImplObserver.h.

◆ incomingEdgesIterator() [1/3]

template<class N, class E>

virtual std::unique_ptr<EdgeIterator> bpp::AssociationGraphObserver< N, E >::incomingEdgesIterator ( std::shared_ptr< N > node )

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::EdgeIterator::~EdgeIterator().

◆ incomingEdgesIterator() [2/3]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1391 of file AssociationGraphImplObserver.h.

◆ incomingEdgesIterator() [3/3]

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

inlineinherited

Definition at line 1396 of file AssociationGraphImplObserver.h.

◆ incomingNeighborNodesIterator() [1/4]

template<class N, class E>

virtual std::unique_ptr<NodeIterator> bpp::AssociationGraphObserver< N, E >::incomingNeighborNodesIterator ( std::shared_ptr< N > node )

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ incomingNeighborNodesIterator() [2/4]

template<class N, class E>

virtual std::unique_ptr<NodeIterator> bpp::AssociationGraphObserver< N, E >::incomingNeighborNodesIterator ( std::shared_ptr< N > node ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ incomingNeighborNodesIterator() [3/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1055 of file AssociationGraphImplObserver.h.

◆ incomingNeighborNodesIterator() [4/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1060 of file AssociationGraphImplObserver.h.

◆ isAllSum()

bool ComputationTree::isAllSum ( )

Definition at line 174 of file ComputationTree.cpp.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::allNodesIterator(), bpp::AssociationGraphObserver< N, E >::NodeIterator::end(), bpp::BinaryOperator::getSymbol(), and bpp::AssociationGraphObserver< N, E >::NodeIterator::next().

Referenced by readFormula().

◆ isLeaf() [1/2]

bool bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::isLeaf ( const Nref node ) const

inlineinherited

Is the node a leaf?

Definition at line 1421 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid().

◆ isLeaf() [2/2]

bool bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::isLeaf ( const NodeIndex nodeid ) const

inlineinherited

Definition at line 1426 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNode(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid().

◆ isRooted()

template<class N, class E, class TreeGraphImpl>

bool bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::isRooted ( ) const

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 133 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph().

◆ isValid()

template<class N, class E, class TreeGraphImpl>

bool bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::isValid ( ) const

inlinevirtualinherited

Is the graph a tree? A tree must be acyclic and with no isolated node.

Returns: true if valid tree

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 99 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph().

◆ link() [1/2]

template<class N, class E>

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

pure virtualinherited

Creates a link between two existing nodes. If directed graph: nodeA -> nodeB.

Parameters

nodeObjectA	source node (or first node if undirected)
nodeObjectB	target node (or second node if undirected)
edgeObject	the optional edge between the nodes (default = 00)

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ link() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::link	(	Nref	nodeObjectA,
		Nref	nodeObjectB,
		Eref	edgeObject = `00`
	)

inlinevirtualinherited

Creates a link between two existing nodes. If directed graph: nodeA -> nodeB.

Parameters

nodeObjectA	source node (or first node if undirected)
nodeObjectB	target node (or second node if undirected)
edgeObject	the optional edge between the nodes (default = 00)

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 470 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::edgeToString(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodes(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasEdge(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasNode(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::nodeToString().

◆ MRCA()

template<class N, class E, class TreeGraphImpl>

std::shared_ptr<N> bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::MRCA ( const std::vector< std::shared_ptr< N >> vNodeObject ) const

inlineinherited

Return, in a rooted tree, the MRCA node of a vector of nodes

Parameters

vNodeObject the vector of concerned nodes

Returns: the MRCA

Definition at line 383 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeFromGraphid(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

◆ nodeToString()

std::string bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::nodeToString ( const Nref nodeObject ) const

inlineinherited

Definition at line 347 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeIndex(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasNode(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasNodeIndex(), and bpp::TextTools::toString().

◆ outgoingEdgesIterator() [1/3]

template<class N, class E>

virtual std::unique_ptr<EdgeIterator> bpp::AssociationGraphObserver< N, E >::outgoingEdgesIterator ( std::shared_ptr< N > node )

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::EdgeIterator::~EdgeIterator().

◆ outgoingEdgesIterator() [2/3]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1377 of file AssociationGraphImplObserver.h.

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::branchesIterator().

◆ outgoingEdgesIterator() [3/3]

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

inlineinherited

Definition at line 1382 of file AssociationGraphImplObserver.h.

◆ outgoingNeighborNodesIterator() [1/4]

template<class N, class E>

virtual std::unique_ptr<NodeIterator> bpp::AssociationGraphObserver< N, E >::outgoingNeighborNodesIterator ( std::shared_ptr< N > node )

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().

◆ outgoingNeighborNodesIterator() [2/4]

template<class N, class E>

virtual std::unique_ptr<NodeIterator> bpp::AssociationGraphObserver< N, E >::outgoingNeighborNodesIterator ( std::shared_ptr< N > node ) const

pure virtualinherited

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

◆ outgoingNeighborNodesIterator() [3/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1040 of file AssociationGraphImplObserver.h.

Referenced by bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::sonsIterator().

◆ outgoingNeighborNodesIterator() [4/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1045 of file AssociationGraphImplObserver.h.

◆ output()

std::string ComputationTree::output ( ) const

Definition at line 188 of file ComputationTree.cpp.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getRoot().

Referenced by readFormula().

◆ outputToDot() [1/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::outputToDot	(	const std::string &	fname,
		const std::string &	name
	)		const

inlineinherited

Definition at line 935 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::outputToDot().

◆ outputToDot() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::outputToDot	(	std::ostream &	out,
		const std::string &	name
	)		const

inlineinherited

Definition at line 943 of file AssociationGraphImplObserver.h.

◆ readFormula()

void bpp::ComputationTree::readFormula	(	const std::string &	formula,
		const std::map< std::string, std::shared_ptr< FunctionInterface >> &	functionNames
	)

inline

Definition at line 57 of file ComputationTree.h.

References isAllSum(), output(), and readFormula_().

◆ readFormula_()

std::shared_ptr< Operator > ComputationTree::readFormula_	(	const std::string &	formula,
		const std::map< std::string, std::shared_ptr< FunctionInterface >> &	functionNames
	)

private

Definition at line 35 of file ComputationTree.cpp.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::createNode(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::setFather(), and bpp::TextTools::toDouble().

Referenced by ComputationTree(), and readFormula().

◆ removeSon()

template<class N, class E, class TreeGraphImpl>

void bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::removeSon	(	const std::shared_ptr< N >	node,
		const std::shared_ptr< N >	son
	)

inlinevirtualinherited

Remove a son of a node

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 260 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

◆ removeSons()

template<class N, class E, class TreeGraphImpl>

std::vector<std::shared_ptr<N> > bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::removeSons ( const std::shared_ptr< N > node )

inlinevirtualinherited

Remove the sons of a node

Returns: a vector containing the removed nodes

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 252 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodesFromGraphid().

◆ rootAt()

template<class N, class E, class TreeGraphImpl>

void bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::rootAt ( const std::shared_ptr< N > root )

inlinevirtualinherited

Sets the root and make the tree directed from root to leaves.

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 124 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

◆ setEdgeIndex() [1/2]

template<class N, class E>

virtual EdgeIndex bpp::AssociationGraphObserver< N, E >::setEdgeIndex	(	const std::shared_ptr< E >	edgeObject,
		EdgeIndex	index
	)

pure virtualinherited

Set an index associated to an edge

Parameters

edgeObject	object to which one want to set the index
index	intex to be given, 0 to get the first free index

Returns: the given index

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ setEdgeIndex() [2/2]

EdgeIndex bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::setEdgeIndex	(	const Eref	edgeObject,
		EdgeIndex	index
	)

inlinevirtualinherited

Set an index associated to an edge

Parameters

edgeObject	object to which one want to set the index
index	intex to be given, 0 to get the first free index

Returns: the given index

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 798 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::edgeToString(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasEdge().

◆ setEdgeLinking() [1/2]

template<class N, class E>

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

pure virtualinherited

Sets the Edge between two nodes nodeA -> nodeB

Parameters

nodeA	source node (if directed)
nodeB	destination node (if directed)
edge	the edge between these two nodes

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::EdgeIterator::~EdgeIterator().

◆ setEdgeLinking() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::setEdgeLinking	(	Nref	nodeA,
		Nref	nodeB,
		Eref	edge
	)

inlinevirtualinherited

Sets the Edge between two nodes nodeA -> nodeB

Parameters

nodeA	source node (if directed)
nodeB	destination node (if directed)
edge	the edge between these two nodes

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1460 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::associateEdge(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getEdge(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid().

◆ setFather()

template<class N, class E, class TreeGraphImpl>

void bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::setFather	(	const std::shared_ptr< N >	nodeObject,
		const std::shared_ptr< N >	fatherNodeObject,
		const std::shared_ptr< E >	edgeObject = `0`
	)

inlinevirtualinherited

Change / set the father of a node

Parameters

nodeObject	the concerned node
fatherNodeObject	the node to be the father
edgeObject	the optional edge between the nodes (default = 00)

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 272 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeGraphid(), bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeGraphid().

Referenced by readFormula_().

◆ setNodeIndex() [1/2]

template<class N, class E>

virtual NodeIndex bpp::AssociationGraphObserver< N, E >::setNodeIndex	(	const std::shared_ptr< N >	nodeObject,
		NodeIndex	index
	)

pure virtualinherited

Set an index associated to a node

Parameters

nodeObject	object to which one want to set the index
index	intex to be given, 0 to get the first free index

Returns: the given index

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ setNodeIndex() [2/2]

NodeIndex bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::setNodeIndex	(	const Nref	nodeObject,
		NodeIndex	index
	)

inlinevirtualinherited

Set an index associated to a node

Parameters

nodeObject	object to which one want to set the index
index	index to be given

Returns: the given index

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 774 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasNode(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::nodeToString().

◆ setRoot()

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::setRoot ( const Nref newRoot )

inlineinherited

set the root (but no checking, to be used at first construction)

Definition at line 684 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getNodeGraphid().

Referenced by ComputationTree().

◆ sonsIterator() [1/2]

template<class N, class E, class TreeGraphImpl>

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

inlinevirtualinherited

Iterators

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 305 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::outgoingNeighborNodesIterator().

◆ sonsIterator() [2/2]

template<class N, class E, class TreeGraphImpl>

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

inlinevirtualinherited

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 310 of file AssociationTreeGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::outgoingNeighborNodesIterator().

◆ unlink() [1/2]

template<class N, class E>

virtual void bpp::AssociationGraphObserver< N, E >::unlink	(	std::shared_ptr< N >	nodeObjectA,
		std::shared_ptr< N >	nodeObjectB
	)

pure virtualinherited

Detroys a link between two existing nodes in the graph. If directed graph: nodeA -> nodeB.

Parameters

nodeObjectA	source node (or first node if undirected)
nodeObjectB	target node (or second node if undirected)

Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.

Referenced by bpp::AssociationGraphObserver< N, E >::copy().

◆ unlink() [2/2]

void bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::unlink	(	Nref	nodeObjectA,
		Nref	nodeObjectB
	)

inlinevirtualinherited

Deletes the link between two existing nodes in the graph.

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 497 of file AssociationGraphImplObserver.h.

References bpp::AssociationGraphImplObserver< N, E, GraphImpl >::getGraph(), bpp::AssociationGraphImplObserver< N, E, GraphImpl >::hasNode(), and bpp::AssociationGraphImplObserver< N, E, GraphImpl >::nodeToString().

Member Data Documentation

◆ subjectGraph_

std::shared_ptr<TreeGraphImpl > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::subjectGraph_

protectedinherited

The observed Graph. Anytime this graph is observed, the current object will be warned to take changes into account.

Definition at line 44 of file AssociationGraphImplObserver.h.

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

Bpp/Numeric/Function/Operators/ComputationTree.h
Bpp/Numeric/Function/Operators/ComputationTree.cpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Member Typedef Documentation

◆ EdgeGraphid

◆ EdgeIndex

◆ EdgeIterator

◆ Eref

◆ NodeGraphid

◆ NodeIndex

◆ NodeIterator

◆ Nref

Constructor & Destructor Documentation

◆ ComputationTree()

Member Function Documentation

◆ addEdgeIndex()

◆ addNodeIndex()

◆ addSon()

◆ allEdgesIterator() [1/3]

◆ allEdgesIterator() [2/3]

◆ allEdgesIterator() [3/3]

◆ allNodesIterator() [1/4]

◆ allNodesIterator() [2/4]

◆ allNodesIterator() [3/4]

◆ allNodesIterator() [4/4]

◆ associateEdge() [1/2]

◆ associateEdge() [2/2]

◆ associateNode() [1/2]

◆ associateNode() [2/2]

◆ branchesIterator() [1/2]

◆ branchesIterator() [2/2]

◆ clone()

◆ copy() [1/5]

◆ copy() [2/5]

◆ copy() [3/5]

◆ copy() [4/5]

◆ copy() [5/5]

◆ createNode() [1/4]

◆ createNode() [2/4]

◆ createNode() [3/4]

◆ createNode() [4/4]

◆ deletedEdgesUpdate() [1/2]

◆ deletedEdgesUpdate() [2/2]

◆ deletedNodesUpdate() [1/2]

◆ deletedNodesUpdate() [2/2]

◆ deleteNode() [1/2]

◆ deleteNode() [2/2]

◆ dissociateEdge() [1/2]

◆ dissociateEdge() [2/2]

◆ dissociateNode() [1/2]

◆ dissociateNode() [2/2]

◆ edgeToString()

◆ getAllEdges() [1/2]

◆ getAllEdges() [2/2]

◆ getAllEdgesIndexes() [1/2]

◆ getAllEdgesIndexes() [2/2]

◆ getAllInnerNodes() [1/2]

◆ getAllInnerNodes() [2/2]

◆ getAllInnerNodesIndexes() [1/2]

◆ getAllInnerNodesIndexes() [2/2]

◆ getAllLeaves() [1/2]

◆ getAllLeaves() [2/2]

◆ getAllLeavesIndexes() [1/2]

◆ getAllLeavesIndexes() [2/2]

◆ getAllNodes() [1/2]

◆ getAllNodes() [2/2]

◆ getAllNodesIndexes() [1/2]

◆ getAllNodesIndexes() [2/2]

◆ getBranches() [1/2]

◆ getBranches() [2/2]

◆ getDegree()

◆ getEdge() [1/2]

◆ getEdge() [2/2]

◆ getEdgeFromGraphid() [1/4]

◆ getEdgeFromGraphid() [2/4]

◆ getEdgeFromGraphid() [3/4]

◆ getEdgeFromGraphid() [4/4]