org.ginsim.core.graph.dynamicgraph

Interface DynamicGraph

All Superinterfaces:

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

All Known Implementing Classes:

DynamicGraphImpl

public interface DynamicGraph
extends TransitionGraph<DynamicNode,DynamicEdge>, GraphAssociation<RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>

the dynamic (state transition) graph.

Author:

Aurelien Naldi

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAXLEVEL
static int	STARLEVEL

Method Summary

Modifier and Type	Method and Description
DynamicEdge	addEdge(DynamicNode source, DynamicNode target, boolean multiple) add an edge between source and target
List<org.colomoto.biolqm.NodeInfo>	getNodeOrder() Return the node order as a list of String
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<Edge>	shortestPath(byte[] source, byte[] target) look for the shortest path between two states.

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, getNodeOrderSize, getNodes, getOutgoingEdges, getShortestPath, getStronglyConnectedComponents, getSubgraph, merge, removeEdge, removeNode, searchNodes, setGraphName

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

getAssociatedGraph, getAssociatedGraphID, setAssociatedGraph, setAssociatedGraphID

Field Detail

MAXLEVEL

static final int MAXLEVEL

See Also:

Constant Field Values

STARLEVEL

static final int STARLEVEL

See Also:

Constant Field Values

Method Detail

addEdge

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

add an edge between source and target

Parameters:

source -

target -

multiple -

Returns:

the new edge

getNodeOrder

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

Return the node order as a list of String

Returns:

the node order as a list of String

setNodeOrder

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

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

Parameters:

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

shortestPath

List<Edge> shortestPath(byte[] source,
                        byte[] target)

look for the shortest path between two states.

Parameters:

source -

target -

Returns:

the List describing the path or null if none is found