org.ginsim.core.graph.dynamicgraph

Class TransitionGraphImpl<V,E extends Edge<V>>

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<V,E>

All Implemented Interfaces:

TransitionGraph<V,E>, Graph<V,E>, GraphAssociation<RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>, GraphListener<RegulatoryGraph>, GraphModel<V,E>, GraphViewListener

Direct Known Subclasses:

DynamicGraphImpl, HierarchicalTransitionGraphImpl

public abstract class TransitionGraphImpl<V,E extends Edge<V>>
extends AbstractDerivedGraph<V,E,RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>
implements TransitionGraph<V,E>

Field Summary

Fields

Modifier and Type	Field and Description
protected List<org.colomoto.biolqm.NodeInfo>	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

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	TransitionGraphImpl(GraphFactory factory)

Method Summary

Modifier and Type	Method and Description
byte[]	fillExtraValues(byte[] state, byte[] extraValues) Retrieve the values for all extra components for a given state.
String[]	getExtraNames() Get the list of known extra components names.
void	setLogicalModel(org.colomoto.biolqm.LogicalModel model) Associate a logicalModel with this STG, notably to retrieve extra values.

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

getAssociatedGraph, getAssociatedGraphID, graphChanged, isAssociationValid, setAssociatedGraph, setAssociatedGraphID

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

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

Field Detail

nodeOrder

protected List<org.colomoto.biolqm.NodeInfo> nodeOrder

Constructor Detail

TransitionGraphImpl

protected TransitionGraphImpl(GraphFactory factory)

Method Detail

getExtraNames

public String[] getExtraNames()

Description copied from interface: TransitionGraph

Get the list of known extra components names. These components have no explicitly assigned value in the STG, but their values can be retrieved based on a given state.

Specified by:

getExtraNames in interface TransitionGraph<V,E extends Edge<V>>

Returns:

the list of names, or null if none

fillExtraValues

public byte[] fillExtraValues(byte[] state,
                              byte[] extraValues)

Description copied from interface: TransitionGraph

Retrieve the values for all extra components for a given state. If the provided array to fill is null or of the wrong size, a new array will be created and returned. Otherwise, extraValues will be filled and returned.

Specified by:

fillExtraValues in interface TransitionGraph<V,E extends Edge<V>>

extraValues - array in which to put the values.

Returns:

extraValues properly filled or a new array

setLogicalModel

public void setLogicalModel(org.colomoto.biolqm.LogicalModel model)

Description copied from interface: TransitionGraph

Associate a logicalModel with this STG, notably to retrieve extra values.

Specified by:

setLogicalModel in interface TransitionGraph<V,E extends Edge<V>>