org.ginsim.core.graph

Interface GraphModel<V,E extends Edge<V>>

Type Parameters:

V - type for vertices

E - type for edges

All Known Subinterfaces:

DynamicGraph, Graph<V,E>, HierarchicalTransitionGraph, ReducedGraph<AG,AV,AE>, RegulatoryGraph, TransitionGraph<V,E>, TrapSpaceInclusionDiagram, Tree

All Known Implementing Classes:

AbstractDerivedGraph, AbstractGraph, DynamicGraphImpl, HierarchicalTransitionGraphImpl, ReducedGraphImpl, RegulatoryGraphImpl, TransitionGraphImpl, TrapSpaceTreeImpl, TreeImpl

public interface GraphModel<V,E extends Edge<V>>

Handle the basic structure of a graph. This provides methods to:

• add and remove vertices and edges
• get the list of existing vertices and edges
• some simple graph operations (shortest path, connected components)
• Handle some basic metadata: graph name and annotation

Author:

Aurelien Naldi, Lionel Spinelli

Method Summary

Modifier and Type	Method and Description
boolean	addEdge(E edge) Add an edge to this graph structure.
boolean	addNode(V node) Add a node to this graph structure
boolean	containsEdge(V from, V to)
boolean	containsNode(V node)
Annotation	getAnnotation() Give access to the annotation associated with this graph.
E	getEdge(V source, V target)
Collection<E>	getEdges()
V	getExistingNode(V node)
String	getGraphName() Give access to the name of the graph
Collection<E>	getIncomingEdges(V node)
V	getNodeByName(String id) Give access to the node named with the given name
int	getNodeCount() Return the number of node in this graph
int	getNodeOrderSize() Return the size of the node order
Collection<V>	getNodes() Return the Collection of the graph nodes
Collection<E>	getOutgoingEdges(V node)
List<E>	getShortestPath(V source, V target) Find the shortest path between the two given vertices
List<Set<V>>	getStronglyConnectedComponents() Return a list of set of node, each set containing a strongly connected component of the graph
Graph<V,E>	getSubgraph(Collection<V> node, Collection<E> edges) Build a graph from the provided vertices and edges based on the current graph
List<?>	merge(Graph<V,E> graph) Merge the provided graph with the current one
boolean	removeEdge(E edge) Remove an edge from the graph.
boolean	removeNode(V node) Remove a node from the graph.
List<V>	searchNodes(String regexp) Search the vertices with ID matching the given regular expression.
void	setGraphName(String graphName) changes (if success) the name associated with this graph.

Method Detail

getGraphName

String getGraphName()

Give access to the name of the graph

Returns:

the name associated with this graph.

setGraphName

void setGraphName(String graphName)
           throws GsException

changes (if success) the name associated with this graph. By default only valid xmlid are accepted.

Parameters:

graphName - the new name.

Throws:

GsException - if the name is invalid.

getAnnotation

Annotation getAnnotation()

Give access to the annotation associated with this graph.

Returns:

the association associated with this graph

addNode

boolean addNode(V node)

Add a node to this graph structure

Parameters:

node -

Returns:

the created node

addEdge

boolean addEdge(E edge)

Add an edge to this graph structure.

Parameters:

edge -

Returns:

the created edge

removeNode

boolean removeNode(V node)

Remove a node from the graph.

Parameters:

node -

Returns:

true if the node was effectively removed

removeEdge

boolean removeEdge(E edge)

Remove an edge from the graph.

Parameters:

edge -

Returns:

true if the edge was effectively removed

getNodeCount

int getNodeCount()

Return the number of node in this graph

Returns:

the number of node in this graph.

getNodes

Collection<V> getNodes()

Return the Collection of the graph nodes

Returns:

a Collection of the graph nodes

getNodeByName

V getNodeByName(String id)

Give access to the node named with the given name

Parameters:

id - name of a node

Returns:

the node corresponding to this unique id or null if not found.

getNodeOrderSize

int getNodeOrderSize()

Return the size of the node order

Returns:

the size of the node order

searchNodes

List<V> searchNodes(String regexp)

Search the vertices with ID matching the given regular expression. Other kind of graph could overwrite this method.

Parameters:

regexp - the regular expression node ID must match to be selected

Returns:

a List of vertices

getEdge

E getEdge(V source,
          V target)

Parameters:

source -

target -

Returns:

the edge between source and target or null if not found.

getEdges

Collection<E> getEdges()

Returns:

a Collection of the graph edges.

containsNode

boolean containsNode(V node)

Parameters:

node -

Returns:

true if the node is in the graph, false if not.

getExistingNode

V getExistingNode(V node)

containsEdge

boolean containsEdge(V from,
                     V to)

Parameters:

from -

to -

Returns:

true if an edge between the two provided vertices exists in the graph, false if not.

getIncomingEdges

Collection<E> getIncomingEdges(V node)

Parameters:

node -

Returns:

incoming edges of the given node.

getOutgoingEdges

Collection<E> getOutgoingEdges(V node)

Parameters:

node -

Returns:

outgoing edges of the given node.

getShortestPath

List<E> getShortestPath(V source,
                        V target)

Find the shortest path between the two given vertices

Parameters:

source - the node at the beginning of the searched path

target - the node at the end of the searched path

Returns:

the list of edges composing the shortest path

getStronglyConnectedComponents

List<Set<V>> getStronglyConnectedComponents()

Return a list of set of node, each set containing a strongly connected component of the graph

Returns:

a list of set of node, each set containing a strongly connected component of the graph

getSubgraph

Graph<V,E> getSubgraph(Collection<V> node,
                       Collection<E> edges)

Build a graph from the provided vertices and edges based on the current graph

Parameters:

node - the collection of vertices used to create the subgraph

edges - the collection of edges used to create the subgraph

Returns:

a Graph composed of the provided vertices and edges and based on the current graph

merge

List<?> merge(Graph<V,E> graph)

Merge the provided graph with the current one

Parameters:

graph - The graph to merge with the current graph