org.ginsim.core.graph.dynamicgraph

Class DynamicGraphImpl

java.lang.Object

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

org.ginsim.core.graph.AbstractDerivedGraph<V,E,RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>

org.ginsim.core.graph.dynamicgraph.TransitionGraphImpl<DynamicNode,DynamicEdge>

org.ginsim.core.graph.dynamicgraph.DynamicGraphImpl

All Implemented Interfaces:

DynamicGraph, TransitionGraph<DynamicNode,DynamicEdge>, Graph<DynamicNode,DynamicEdge>, GraphAssociation<RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>, GraphListener<RegulatoryGraph>, GraphModel<DynamicNode,DynamicEdge>, GraphViewListener

public final class DynamicGraphImpl
extends TransitionGraphImpl<DynamicNode,DynamicEdge>
implements DynamicGraph

Implementation of dynamical graphs. This class should not be used directly: instances are created by the associated factory.

Author:

Aurelien Naldi, Lionel Spinelli

Field Summary

Fields

Modifier and Type	Field and Description
static String	GRAPH_ZIP_NAME
protected List	v_stables

Fields inherited from class org.ginsim.core.graph.dynamicgraph.TransitionGraphImpl

nodeOrder

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

Fields inherited from interface org.ginsim.core.graph.dynamicgraph.DynamicGraph

MAXLEVEL, STARLEVEL

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	DynamicGraphImpl()
protected	DynamicGraphImpl(List<org.colomoto.biolqm.NodeInfo> nodeOrder) create a new DynamicGraph.

Method Summary

Modifier and Type	Method and Description
DynamicEdge	addEdge(DynamicNode source, DynamicNode target, boolean multiple) add an edge between source and target
protected List	doMerge(Graph otherGraph) Specialized method that execute the merging of the given graph with the current one Must be override at specialized graph level
protected GINMLWriter	getGINMLWriter()
protected String	getGraphZipName() Return the zip extension for the graph type
List<org.colomoto.biolqm.NodeInfo>	getNodeOrder() Return the node order as a list of String
int	getNodeOrderSize() Return the size of the node order
Graph	getSubgraph(Collection vertex, Collection 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) Indicates if the given graph can be associated to the current one
boolean	removeEdge(DynamicEdge obj) Remove an edge from the graph.
void	setNodeOrder(List<org.colomoto.biolqm.NodeInfo> node_order) Set a list of String representing the order of node as defined by the model
List	shortestPath(byte[] source, byte[] target) look for the shortest path between two states.

Methods inherited from class org.ginsim.core.graph.dynamicgraph.TransitionGraphImpl

fillExtraValues, getExtraNames, setLogicalModel

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, getGraphName, getIncomingEdges, getNodeAttributeReader, getNodeByName, getNodeCount, getNodes, getOutgoingEdges, getShortestPath, getStronglyConnectedComponents, getStyleManager, isEmpty, merge, refresh, 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.dynamicgraph.TransitionGraph

fillExtraValues, getExtraNames, setLogicalModel

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, removeNode, searchNodes, setGraphName

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

getAssociatedGraph, getAssociatedGraphID, setAssociatedGraph, setAssociatedGraphID

Field Detail

GRAPH_ZIP_NAME

public static final String GRAPH_ZIP_NAME

See Also:

Constant Field Values

v_stables

protected List v_stables

Constructor Detail

DynamicGraphImpl

protected DynamicGraphImpl(List<org.colomoto.biolqm.NodeInfo> nodeOrder)

create a new DynamicGraph.

Parameters:

nodeOrder -

DynamicGraphImpl

protected DynamicGraphImpl()

Method Detail

graphChanged

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

Specified by:

graphChanged in interface GraphListener<RegulatoryGraph>

getNodeOrder

public List<org.colomoto.biolqm.NodeInfo> getNodeOrder()

Return the node order as a list of String

Specified by:

getNodeOrder in interface DynamicGraph

Returns:

the node order as a list of String

getNodeOrderSize

public int getNodeOrderSize()

Return the size of the node order

Specified by:

getNodeOrderSize in interface GraphModel<DynamicNode,DynamicEdge>

Specified by:

getNodeOrderSize in class AbstractGraph<DynamicNode,DynamicEdge>

Returns:

the size of the node order

setNodeOrder

public void setNodeOrder(List<org.colomoto.biolqm.NodeInfo> node_order)

Set a list of String representing the order of node as defined by the model

Specified by:

setNodeOrder in interface DynamicGraph

Parameters:

node_order - the list of String representing the order of node as defined by the model

getGraphZipName

protected String getGraphZipName()

Return the zip extension for the graph type

Overrides:

getGraphZipName in class AbstractGraph<DynamicNode,DynamicEdge>

Returns:

the zip extension for the graph type

getGINMLWriter

protected GINMLWriter getGINMLWriter()

Overrides:

getGINMLWriter in class AbstractGraph<DynamicNode,DynamicEdge>

removeEdge

public boolean removeEdge(DynamicEdge obj)

Description copied from class: AbstractGraph

Remove an edge from the graph.

Specified by:

removeEdge in interface GraphModel<DynamicNode,DynamicEdge>

Overrides:

removeEdge in class AbstractGraph<DynamicNode,DynamicEdge>

Returns:

true if the edge was effectively removed

addEdge

public DynamicEdge addEdge(DynamicNode source,
                           DynamicNode target,
                           boolean multiple)

Description copied from interface: DynamicGraph

add an edge between source and target

Specified by:

addEdge in interface DynamicGraph

Returns:

the new edge

doMerge

protected List doMerge(Graph otherGraph)

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<DynamicNode,DynamicEdge>

Returns:

getSubgraph

public Graph getSubgraph(Collection vertex,
                         Collection 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<DynamicNode,DynamicEdge>

Specified by:

getSubgraph in class AbstractGraph<DynamicNode,DynamicEdge>

Parameters:

vertex - 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

shortestPath

public List shortestPath(byte[] source,
                         byte[] target)

look for the shortest path between two states.

Specified by:

shortestPath in interface DynamicGraph

Parameters:

source -

target -

Returns:

the List describing the path or null if none is found

isAssociationValid

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

Indicates if the given graph can be associated to the current one

Specified by:

isAssociationValid in class AbstractDerivedGraph<DynamicNode,DynamicEdge,RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>

Parameters:

graph - the graph to associate to the current one

Returns:

true is association is possible, false if not