#include <Bpp/Graph/AssociationTreeGraphImplObserver.h>

Inheritance diagram for bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >:

Collaboration diagram for bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >:

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
	AssociationTreeGraphImplObserver (bool rooted=false)

	AssociationTreeGraphImplObserver (std::shared_ptr< TreeGraphImpl > subjectTreeGraph)

	AssociationTreeGraphImplObserver (bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > const &treeGraphObserver)

template<class N2 , class E2 >
	AssociationTreeGraphImplObserver (bpp::AssociationTreeGraphImplObserver< N2, E2, TreeGraphImpl > const &treeGraphObserver)

AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > &	operator= (bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > const &treeGraphObserver)

	~AssociationTreeGraphImplObserver ()

AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > *	clone () const

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

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

std::vector< NodeIndex >	getSubtreeNodes (const NodeIndex 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

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 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

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

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

Object Indexation
Get or set indexes to nodes and edges
bool	hasNode (NodeIndex node) const

bool	hasEdge (EdgeIndex edge) const

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)

NodeIndex	addNodeIndex (const Nref nodeObject)

EdgeIndex	addEdgeIndex (const Eref edgeObject)

Nref	getNode (NodeIndex node) const

Eref	getEdge (EdgeIndex edge) const

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
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

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

Nref	getRoot () const

NodeIndex	getRootIndex () const

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

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::vector< EdgeIndex >	getAllEdgesIndexes () 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

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

Eref	getEdgeLinking (Nref nodeA, Nref nodeB) const

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

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)

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_

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

std::shared_ptr< TreeGraphImpl >	getGraph ()

bool	hasNode (Nref nodeObject) const

bool	hasEdge (Eref edgeObject) const

std::string	nodeToString (const Nref nodeObject) const

std::string	edgeToString (const Eref edgeObject) const

enum	neighborType

std::vector< Nref >	graphidToN_

std::vector< Eref >	graphidToE_

std::map< Nref, NodeGraphid >	NToGraphid_

std::map< Eref, EdgeGraphid >	EToGraphid_

std::vector< Nref >	indexToN_

std::vector< Eref >	indexToE_

std::map< Nref, NodeIndex >	NToIndex_

std::map< Eref, EdgeIndex >	EToIndex_

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

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

Detailed Description

template<class N, class E, class TreeGraphImpl>
class bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >

Definition at line 57 of file AssociationTreeGraphImplObserver.h.

Member Typedef Documentation

◆ EdgeGraphid

template<class N , class E , class TreeGraphImpl >

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

Definition at line 67 of file AssociationTreeGraphImplObserver.h.

◆ EdgeIndex

template<class N , class E , class TreeGraphImpl >

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

Definition at line 63 of file AssociationTreeGraphImplObserver.h.

◆ EdgeIterator

template<class N , class E >

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

inherited

Definition at line 219 of file AssociationTreeGraphObserver.h.

◆ Eref

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

inherited

Definition at line 71 of file AssociationGraphImplObserver.h.

◆ NodeGraphid

template<class N , class E , class TreeGraphImpl >

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

Definition at line 65 of file AssociationTreeGraphImplObserver.h.

◆ NodeIndex

template<class N , class E , class TreeGraphImpl >

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

Definition at line 62 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 218 of file AssociationTreeGraphObserver.h.

◆ Nref

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

inherited

Definition at line 72 of file AssociationGraphImplObserver.h.

Member Enumeration Documentation

◆ neighborType

enum bpp::AssociationGraphImplObserver::neighborType

privateinherited

defines a type of neighbors : incoming and/or outgoing

Definition at line 415 of file AssociationGraphImplObserver.h.

Constructor & Destructor Documentation

◆ AssociationTreeGraphImplObserver() [1/4]

template<class N , class E , class TreeGraphImpl >

bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::AssociationTreeGraphImplObserver ( bool rooted = false )

inline

Constructor

Parameters

rooted if the graph rooted

Definition at line 74 of file AssociationTreeGraphImplObserver.h.

◆ AssociationTreeGraphImplObserver() [2/4]

template<class N , class E , class TreeGraphImpl >

bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::AssociationTreeGraphImplObserver ( std::shared_ptr< TreeGraphImpl > subjectTreeGraph )

inline

Constructor

Parameters

subjectTreeGraph the graph which is observed

Definition at line 83 of file AssociationTreeGraphImplObserver.h.

◆ AssociationTreeGraphImplObserver() [3/4]

template<class N , class E , class TreeGraphImpl >

bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::AssociationTreeGraphImplObserver ( bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > const & treeGraphObserver )

inline

Copy Constructor

Parameters

treeGraphObserver the treeGraphObserver to be copied

Definition at line 92 of file AssociationTreeGraphImplObserver.h.

◆ AssociationTreeGraphImplObserver() [4/4]

template<class N , class E , class TreeGraphImpl >

template<class N2 , class E2 >

bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::AssociationTreeGraphImplObserver ( bpp::AssociationTreeGraphImplObserver< N2, E2, TreeGraphImpl > const & treeGraphObserver )

inline

Copy Constructor

Parameters

treeGraphObserver the treeGraphObserver to be copied

Definition at line 102 of file AssociationTreeGraphImplObserver.h.

◆ ~AssociationTreeGraphImplObserver()

template<class N , class E , class TreeGraphImpl >

bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::~AssociationTreeGraphImplObserver ( )

inline

Destructor

Definition at line 121 of file AssociationTreeGraphImplObserver.h.

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 888 of file AssociationGraphImplObserver.h.

◆ 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 857 of file AssociationGraphImplObserver.h.

◆ 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`
	)

inlinevirtual

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 324 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]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1399 of file AssociationGraphImplObserver.h.

◆ allEdgesIterator() [2/3]

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

inlineinherited

Definition at line 1404 of file AssociationGraphImplObserver.h.

◆ allEdgesIterator() [3/3]

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 >.

◆ allNodesIterator() [1/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1061 of file AssociationGraphImplObserver.h.

◆ allNodesIterator() [2/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1066 of file AssociationGraphImplObserver.h.

◆ allNodesIterator() [3/4]

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() [4/4]

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 >.

◆ associateEdge() [1/2]

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 590 of file AssociationGraphImplObserver.h.

◆ associateEdge() [2/2]

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 >.

◆ associateNode() [1/2]

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 570 of file AssociationGraphImplObserver.h.

◆ associateNode() [2/2]

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 >.

◆ 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 )

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 355 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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 360 of file AssociationTreeGraphImplObserver.h.

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

◆ clone()

template<class N , class E , class TreeGraphImpl >

AssociationTreeGraphImplObserver<N, E, TreeGraphImpl>* bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::clone ( ) const

inlinevirtual

clone function

Implements bpp::Clonable.

Reimplemented in bpp::ComputationTree.

Definition at line 128 of file AssociationTreeGraphImplObserver.h.

◆ 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 82 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 88 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 95 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 107 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 101 of file AssociationGraphObserver.h.

◆ createNode() [1/4]

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 474 of file AssociationGraphImplObserver.h.

◆ createNode() [2/4]

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 491 of file AssociationGraphImplObserver.h.

◆ createNode() [3/4]

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 >.

◆ createNode() [4/4]

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 >.

◆ deletedEdgesUpdate() [1/2]

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 1513 of file AssociationGraphImplObserver.h.

◆ deletedEdgesUpdate() [2/2]

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 >.

◆ deletedNodesUpdate() [1/2]

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 1531 of file AssociationGraphImplObserver.h.

◆ deletedNodesUpdate() [2/2]

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 >.

◆ deleteNode() [1/2]

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 549 of file AssociationGraphImplObserver.h.

◆ deleteNode() [2/2]

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 >.

◆ dissociateEdge() [1/2]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 617 of file AssociationGraphImplObserver.h.

◆ dissociateEdge() [2/2]

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 >.

◆ dissociateNode() [1/2]

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 609 of file AssociationGraphImplObserver.h.

◆ dissociateNode() [2/2]

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 >.

◆ edgeToString()

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

inlineinherited

Definition at line 397 of file AssociationGraphImplObserver.h.

◆ getAllEdges() [1/2]

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 1441 of file AssociationGraphImplObserver.h.

◆ getAllEdges() [2/2]

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 >.

◆ getAllEdgesIndexes() [1/2]

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 1352 of file AssociationGraphImplObserver.h.

◆ getAllEdgesIndexes() [2/2]

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 >.

◆ getAllInnerNodes() [1/2]

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 1272 of file AssociationGraphImplObserver.h.

◆ getAllInnerNodes() [2/2]

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 >.

◆ getAllInnerNodesIndexes() [1/2]

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 1293 of file AssociationGraphImplObserver.h.

◆ getAllInnerNodesIndexes() [2/2]

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 >.

◆ getAllLeaves() [1/2]

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 1229 of file AssociationGraphImplObserver.h.

◆ getAllLeaves() [2/2]

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 >.

◆ getAllLeavesIndexes() [1/2]

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 1250 of file AssociationGraphImplObserver.h.

◆ getAllLeavesIndexes() [2/2]

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 >.

◆ getAllNodes() [1/2]

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 1314 of file AssociationGraphImplObserver.h.

◆ getAllNodes() [2/2]

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 >.

◆ getAllNodesIndexes() [1/2]

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 1333 of file AssociationGraphImplObserver.h.

◆ getAllNodesIndexes() [2/2]

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 >.

◆ getBranches() [1/2]

template<class N , class E , class TreeGraphImpl >

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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 222 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().

◆ getBranches() [2/2]

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

inlinevirtual

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 217 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().

◆ 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 1595 of file AssociationGraphImplObserver.h.

◆ getEdge() [1/2]

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 947 of file AssociationGraphImplObserver.h.

◆ getEdge() [2/2]

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 >.

◆ getEdgeFromGraphid() [1/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 685 of file AssociationGraphImplObserver.h.

◆ getEdgeFromGraphid() [2/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 693 of file AssociationGraphImplObserver.h.

◆ getEdgeFromGraphid() [3/4]

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() [4/4]

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 >.

◆ getEdgeGraphid() [1/2]

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 644 of file AssociationGraphImplObserver.h.

◆ getEdgeGraphid() [2/2]

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 >.

◆ getEdgeIndex() [1/2]

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 787 of file AssociationGraphImplObserver.h.

◆ getEdgeIndex() [2/2]

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 >.

◆ getEdgeIndexes() [1/2]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 795 of file AssociationGraphImplObserver.h.

◆ getEdgeIndexes() [2/2]

template<class N , class E >

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

pure virtualinherited

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

◆ getEdgeLinking() [1/2]

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 1485 of file AssociationGraphImplObserver.h.

◆ getEdgeLinking() [2/2]

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 >.

◆ getEdgePathBetweenTwoNodes() [1/2]

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

inline

Definition at line 389 of file AssociationTreeGraphImplObserver.h.

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

◆ getEdgePathBetweenTwoNodes() [2/2]

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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 379 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().

◆ getEdges() [1/4]

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 1132 of file AssociationGraphImplObserver.h.

◆ getEdges() [2/4]

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 >.

◆ getEdges() [3/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1137 of file AssociationGraphImplObserver.h.

◆ getEdges() [4/4]

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_()

std::vector<Eref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdges_	(	const Nref	nodeObject,
		neighborType	type
	)		const

inlineprivateinherited

Get incoming / outgoing edges according to the enum type

Definition at line 443 of file AssociationGraphImplObserver.h.

◆ getEdgesFromGraphid() [1/2]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 701 of file AssociationGraphImplObserver.h.

◆ getEdgesFromGraphid() [2/2]

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 >.

◆ getEdgeToFather() [1/2]

template<class N , class E , class TreeGraphImpl >

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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 150 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().

◆ getEdgeToFather() [2/2]

template<class N , class E , class TreeGraphImpl >

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

inlinevirtual

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 145 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().

◆ getFatherOfEdge() [1/2]

template<class N , class E , class TreeGraphImpl >

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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 252 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().

◆ getFatherOfEdge() [2/2]

template<class N , class E , class TreeGraphImpl >

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

inlinevirtual

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 247 of file AssociationTreeGraphImplObserver.h.

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

◆ 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

inlinevirtual

Return, in a rooted tree, the father node

Parameters

nodeObject the concerned node

Returns: the father

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 179 of file AssociationTreeGraphImplObserver.h.

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

◆ getGraph() [1/2]

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

inlineinherited

Definition at line 356 of file AssociationGraphImplObserver.h.

◆ getGraph() [2/2]

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

inlineinherited

Definition at line 351 of file AssociationGraphImplObserver.h.

◆ getIncomingEdges() [1/4]

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 1198 of file AssociationGraphImplObserver.h.

◆ getIncomingEdges() [2/4]

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 >.

◆ getIncomingEdges() [3/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1203 of file AssociationGraphImplObserver.h.

◆ getIncomingEdges() [4/4]

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 >.

◆ getIncomingNeighbors() [1/4]

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 1181 of file AssociationGraphImplObserver.h.

◆ getIncomingNeighbors() [2/4]

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 >.

◆ getIncomingNeighbors() [3/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1186 of file AssociationGraphImplObserver.h.

◆ getIncomingNeighbors() [4/4]

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 >.

◆ getLeavesFromNode() [1/2]

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 1218 of file AssociationGraphImplObserver.h.

◆ getLeavesFromNode() [2/2]

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 >.

◆ getLeavesUnderNode() [1/2]

template<class N , class E , class TreeGraphImpl >

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

inline

Definition at line 279 of file AssociationTreeGraphImplObserver.h.

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

◆ getLeavesUnderNode() [2/2]

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

inlinevirtual

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 274 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().

◆ getNeighbors() [1/4]

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 1109 of file AssociationGraphImplObserver.h.

◆ getNeighbors() [2/4]

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 >.

◆ getNeighbors() [3/4]

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 1121 of file AssociationGraphImplObserver.h.

◆ getNeighbors() [4/4]

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_()

std::vector<Nref > bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNeighbors_	(	const Nref	nodeObject,
		neighborType	type
	)		const

inlineprivateinherited

Get incoming / outgoing neighbors according to the enum type

Definition at line 420 of file AssociationGraphImplObserver.h.

◆ getNode() [1/2]

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 937 of file AssociationGraphImplObserver.h.

◆ getNode() [2/2]

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 >.

◆ getNodeFromGraphid() [1/4]

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 656 of file AssociationGraphImplObserver.h.

◆ getNodeFromGraphid() [2/4]

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 663 of file AssociationGraphImplObserver.h.

◆ getNodeFromGraphid() [3/4]

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 >.

◆ getNodeFromGraphid() [4/4]

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 >.

◆ getNodeGraphid() [1/2]

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 630 of file AssociationGraphImplObserver.h.

◆ getNodeGraphid() [2/2]

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 >.

◆ getNodeIndex() [1/2]

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 764 of file AssociationGraphImplObserver.h.

◆ getNodeIndex() [2/2]

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 >.

◆ getNodeIndexes() [1/2]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 773 of file AssociationGraphImplObserver.h.

◆ getNodeIndexes() [2/2]

template<class N , class E >

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

pure virtualinherited

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

◆ getNodePathBetweenTwoNodes() [1/2]

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

inline

Definition at line 384 of file AssociationTreeGraphImplObserver.h.

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

◆ getNodePathBetweenTwoNodes() [2/2]

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

inlinevirtual

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 374 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().

◆ 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 1473 of file AssociationGraphImplObserver.h.

◆ getNodesFromGraphid() [1/2]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 670 of file AssociationGraphImplObserver.h.

◆ getNodesFromGraphid() [2/2]

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 >.

◆ 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 1567 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 1578 of file AssociationGraphImplObserver.h.

◆ 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 1557 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

inlinevirtual

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 263 of file AssociationTreeGraphImplObserver.h.

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

◆ getOutgoingEdges() [1/4]

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 1165 of file AssociationGraphImplObserver.h.

◆ getOutgoingEdges() [2/4]

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 >.

◆ getOutgoingEdges() [3/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1170 of file AssociationGraphImplObserver.h.

◆ getOutgoingEdges() [4/4]

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 >.

◆ getOutgoingNeighbors() [1/4]

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 1149 of file AssociationGraphImplObserver.h.

◆ getOutgoingNeighbors() [2/4]

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 >.

◆ getOutgoingNeighbors() [3/4]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 1154 of file AssociationGraphImplObserver.h.

◆ getOutgoingNeighbors() [4/4]

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 >.

◆ getRoot() [1/2]

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

inlinevirtualinherited

Returns: the root

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 728 of file AssociationGraphImplObserver.h.

◆ getRoot() [2/2]

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 >.

◆ getRootIndex() [1/2]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 733 of file AssociationGraphImplObserver.h.

◆ getRootIndex() [2/2]

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 >.

◆ getSon() [1/2]

template<class N , class E , class TreeGraphImpl >

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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 237 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().

◆ getSon() [2/2]

template<class N , class E , class TreeGraphImpl >

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

inlinevirtual

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 232 of file AssociationTreeGraphImplObserver.h.

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

◆ getSons() [1/2]

template<class N , class E , class TreeGraphImpl >

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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 207 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().

◆ getSons() [2/2]

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

inlinevirtual

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 202 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().

◆ getSubtreeEdges() [1/2]

template<class N , class E , class TreeGraphImpl >

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

inline

Definition at line 409 of file AssociationTreeGraphImplObserver.h.

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

◆ getSubtreeEdges() [2/2]

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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 399 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().

◆ getSubtreeNodes() [1/2]

template<class N , class E , class TreeGraphImpl >

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

inline

Definition at line 404 of file AssociationTreeGraphImplObserver.h.

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

◆ getSubtreeNodes() [2/2]

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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 394 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().

◆ hasEdge() [1/3]

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 927 of file AssociationGraphImplObserver.h.

◆ hasEdge() [2/3]

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 >.

◆ hasEdge() [3/3]

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

inlineinherited

Definition at line 373 of file AssociationGraphImplObserver.h.

◆ hasEdgeIndex() [1/2]

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

inlinevirtualinherited

Implements bpp::AssociationGraphObserver< N, E >.

Definition at line 754 of file AssociationGraphImplObserver.h.

◆ hasEdgeIndex() [2/2]

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 >.

◆ hasFather() [1/2]

template<class N , class E , class TreeGraphImpl >

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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 192 of file AssociationTreeGraphImplObserver.h.

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

inlinevirtual

Has the node a father?

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 187 of file AssociationTreeGraphImplObserver.h.

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

◆ hasNode() [1/3]

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 918 of file AssociationGraphImplObserver.h.

◆ hasNode() [2/3]

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 >.

◆ hasNode() [3/3]

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

inlineinherited

Definition at line 366 of file AssociationGraphImplObserver.h.

◆ hasNodeIndex() [1/2]

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 749 of file AssociationGraphImplObserver.h.

◆ hasNodeIndex() [2/2]

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 >.

◆ incomingEdgesIterator() [1/3]

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 1427 of file AssociationGraphImplObserver.h.

◆ incomingEdgesIterator() [2/3]

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

inlineinherited

Definition at line 1432 of file AssociationGraphImplObserver.h.

◆ incomingEdgesIterator() [3/3]

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 >.

◆ incomingNeighborNodesIterator() [1/4]

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 1091 of file AssociationGraphImplObserver.h.

◆ incomingNeighborNodesIterator() [2/4]

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 1096 of file AssociationGraphImplObserver.h.

◆ incomingNeighborNodesIterator() [3/4]

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() [4/4]

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 >.

◆ isLeaf() [1/2]

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

inlineinherited

Definition at line 1462 of file AssociationGraphImplObserver.h.

◆ isLeaf() [2/2]

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

inlineinherited

Is the node a leaf?

Definition at line 1457 of file AssociationGraphImplObserver.h.

◆ isRooted()

template<class N , class E , class TreeGraphImpl >

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

inlinevirtual

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 169 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

inlinevirtual

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 135 of file AssociationTreeGraphImplObserver.h.

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

◆ link() [1/2]

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 506 of file AssociationGraphImplObserver.h.

◆ link() [2/2]

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 >.

◆ 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

inline

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 419 of file AssociationTreeGraphImplObserver.h.

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

◆ nodeToString()

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

inlineinherited

Definition at line 383 of file AssociationGraphImplObserver.h.

◆ operator=()

template<class N , class E , class TreeGraphImpl >

AssociationTreeGraphImplObserver<N, E, TreeGraphImpl>& bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >::operator= ( bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > const & treeGraphObserver )

inline

= Operator

Parameters

treeGraphObserver the treeGraphObserver we want to copy the values

Definition at line 111 of file AssociationTreeGraphImplObserver.h.

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

◆ outgoingEdgesIterator() [1/3]

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 1413 of file AssociationGraphImplObserver.h.

◆ outgoingEdgesIterator() [2/3]

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

inlineinherited

Definition at line 1418 of file AssociationGraphImplObserver.h.

◆ outgoingEdgesIterator() [3/3]

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 >.

◆ outgoingNeighborNodesIterator() [1/4]

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 1076 of file AssociationGraphImplObserver.h.

◆ outgoingNeighborNodesIterator() [2/4]

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 1081 of file AssociationGraphImplObserver.h.

◆ outgoingNeighborNodesIterator() [3/4]

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() [4/4]

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 >.

◆ outputToDot() [1/2]

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

inlineinherited

Definition at line 971 of file AssociationGraphImplObserver.h.

◆ outputToDot() [2/2]

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

inlineinherited

Definition at line 979 of file AssociationGraphImplObserver.h.

◆ 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
	)

inlinevirtual

Remove a son of a node

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 296 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 )

inlinevirtual

Remove the sons of a node

Returns: a vector containing the removed nodes

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 288 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 )

inlinevirtual

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

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 160 of file AssociationTreeGraphImplObserver.h.

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

◆ setEdgeIndex() [1/2]

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 834 of file AssociationGraphImplObserver.h.

◆ setEdgeIndex() [2/2]

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 >.

◆ setEdgeLinking() [1/2]

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 1496 of file AssociationGraphImplObserver.h.

◆ setEdgeLinking() [2/2]

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 >.

◆ 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`
	)

inlinevirtual

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 308 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 bpp::ComputationTree::readFormula_().

◆ setNodeIndex() [1/2]

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 810 of file AssociationGraphImplObserver.h.

◆ setNodeIndex() [2/2]

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 >.

◆ 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 720 of file AssociationGraphImplObserver.h.

◆ 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 )

inlinevirtual

Iterators

Implements bpp::AssociationTreeGraphObserver< N, E >.

Definition at line 341 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