org.ginsim.core.graph.trapspacetree

Class TrapSpaceTreeImpl

java.lang.Object

org.ginsim.core.graph.AbstractGraph<V,E>

org.ginsim.core.graph.AbstractDerivedGraph<TrapSpaceNode,TrapSpaceInclusion,RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>

org.ginsim.core.graph.trapspacetree.TrapSpaceTreeImpl

All Implemented Interfaces:

Graph<TrapSpaceNode,TrapSpaceInclusion>, GraphAssociation<RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>, GraphListener<RegulatoryGraph>, GraphModel<TrapSpaceNode,TrapSpaceInclusion>, GraphViewListener, TrapSpaceInclusionDiagram

public class TrapSpaceTreeImpl
extends AbstractDerivedGraph<TrapSpaceNode,TrapSpaceInclusion,RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>
implements TrapSpaceInclusionDiagram

Author:

Aurelien Naldi

Field Summary

Fields inherited from class org.ginsim.core.graph.AbstractDerivedGraph

associatedGraph, associatedID

Fields inherited from class org.ginsim.core.graph.AbstractGraph

attributes, graphAnnotation, graphName, ZIP_PREFIX

Constructor Summary

Constructors

Constructor and Description
TrapSpaceTreeImpl(GraphFactory factory)

Method Summary

Modifier and Type	Method and Description
protected List<?>	doMerge(Graph<TrapSpaceNode,TrapSpaceInclusion> graph) Specialized method that execute the merging of the given graph with the current one Must be override at specialized graph level
int	getNodeOrderSize() Return the size of the node order
Graph<TrapSpaceNode,TrapSpaceInclusion>	getSubgraph(Collection<TrapSpaceNode> node, Collection<TrapSpaceInclusion> edges) Specialized method that build the sub-graph corresponding to the given lists of vertices and edges The returned graph contains clones of the given graph objects structured as they are in the current graph
GraphEventCascade	graphChanged(RegulatoryGraph g, GraphChangeType type, Object data)
protected boolean	isAssociationValid(Graph<?,?> graph) test if a graph can be associated with this one.

Methods inherited from class org.ginsim.core.graph.AbstractDerivedGraph

getAssociatedGraph, getAssociatedGraphID, graphChanged, setAssociatedGraph, setAssociatedGraphID

Methods inherited from class org.ginsim.core.graph.AbstractGraph

addEdge, addNode, addViewListener, containsEdge, containsNode, copyView, damage, doSave, fireGraphChange, fireMetaChange, getAnnotation, getAttributes, getCachedEdgeAttributeReader, getCachedNodeAttributeReader, getDimension, getDisplayName, getEdge, getEdgeAttributeReader, getEdges, getExistingNode, getGINMLWriter, getGraphName, getGraphZipName, getIncomingEdges, getNodeAttributeReader, getNodeByName, getNodeCount, getNodes, getOutgoingEdges, getShortestPath, getStronglyConnectedComponents, getStyleManager, isEmpty, merge, refresh, removeEdge, removeNode, repaint, save, save, searchNodes, setAttribute, setGraphName

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.ginsim.core.graph.Graph

addViewListener, copyView, fireGraphChange, getAttributes, getDimension, getDisplayName, getEdgeAttributeReader, getNodeAttributeReader, getStyleManager, save, save, setAttribute

Methods inherited from interface org.ginsim.core.graph.GraphModel

addEdge, addNode, containsEdge, containsNode, getAnnotation, getEdge, getEdges, getExistingNode, getGraphName, getIncomingEdges, getNodeByName, getNodeCount, getNodes, getOutgoingEdges, getShortestPath, getStronglyConnectedComponents, merge, removeEdge, removeNode, searchNodes, setGraphName

Methods inherited from interface org.ginsim.core.graph.GraphAssociation

getAssociatedGraph, getAssociatedGraphID, setAssociatedGraph, setAssociatedGraphID

Constructor Detail

TrapSpaceTreeImpl

public TrapSpaceTreeImpl(GraphFactory factory)

Method Detail

getNodeOrderSize

public int getNodeOrderSize()

Description copied from class: AbstractGraph

Return the size of the node order

Specified by:

getNodeOrderSize in interface GraphModel<TrapSpaceNode,TrapSpaceInclusion>

Specified by:

getNodeOrderSize in class AbstractGraph<TrapSpaceNode,TrapSpaceInclusion>

Returns:

the size of the node order

getSubgraph

public Graph<TrapSpaceNode,TrapSpaceInclusion> getSubgraph(Collection<TrapSpaceNode> node,
                                                           Collection<TrapSpaceInclusion> edges)

Description copied from class: AbstractGraph

Specialized method that build the sub-graph corresponding to the given lists of vertices and edges The returned graph contains clones of the given graph objects structured as they are in the current graph

Specified by:

getSubgraph in interface GraphModel<TrapSpaceNode,TrapSpaceInclusion>

Specified by:

getSubgraph in class AbstractGraph<TrapSpaceNode,TrapSpaceInclusion>

Parameters:

node - the list of node to include in the desired sub-graph

edges - the list of edges to include in the sub-graph

Returns:

a Graph containing clones of initial vertices and edges structured as they are in the current graph

graphChanged

public GraphEventCascade graphChanged(RegulatoryGraph g,
                                      GraphChangeType type,
                                      Object data)

Specified by:

graphChanged in interface GraphListener<RegulatoryGraph>

isAssociationValid

protected boolean isAssociationValid(Graph<?,?> graph)

Description copied from class: AbstractDerivedGraph

test if a graph can be associated with this one. this is a default implementation and will always return false, override to do something useful.

Specified by:

isAssociationValid in class AbstractDerivedGraph<TrapSpaceNode,TrapSpaceInclusion,RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>

Returns:

true if this is a valid associated graph.

doMerge

protected List<?> doMerge(Graph<TrapSpaceNode,TrapSpaceInclusion> graph)

Description copied from class: AbstractGraph

Specialized method that execute the merging of the given graph with the current one Must be override at specialized graph level

Specified by:

doMerge in class AbstractGraph<TrapSpaceNode,TrapSpaceInclusion>

Returns: