org.ginsim.core.graph.hierarchicaltransitiongraph

Interface HierarchicalTransitionGraph

All Superinterfaces:

Graph<HierarchicalNode,DecisionOnEdge>, GraphAssociation<RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>, GraphModel<HierarchicalNode,DecisionOnEdge>, TransitionGraph<HierarchicalNode,DecisionOnEdge>

All Known Implementing Classes:

HierarchicalTransitionGraphImpl

public interface HierarchicalTransitionGraph
extends TransitionGraph<HierarchicalNode,DecisionOnEdge>, GraphAssociation<RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>

Hierarchical Transition Graphs provide a compact representation of the dynamical behaviour. Each node in this graph represent a set of states with a similar fate in the STG (cycle, linear path...)

Author:

Duncan Berenguier

Method Summary

Modifier and Type	Method and Description
DecisionOnEdge	addEdge(HierarchicalNode source, HierarchicalNode target) add an edge between source and target
boolean	areTransientCompacted() Return true if the transients are compacted into component by their atteignability of attractors.
StatesSet	createStateSet()
byte[]	getChildsCount()
HierarchicalNode	getNodeForState(byte[] state) Return the Node with the given state
List<org.colomoto.biolqm.NodeInfo>	getNodeOrder() Return the node order as a List of NodeInfo
void	setChildsCount(byte[] cc) Set the array indicating for each node in the nodeOrder their count of childs.
void	setMode(boolean compacted) Set the mode
void	setNodeOrder(List<org.colomoto.biolqm.NodeInfo> node_order) Set a list of NodeInfo representing the order of node as defined by the model

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

Method Detail

addEdge

DecisionOnEdge addEdge(HierarchicalNode source,
                       HierarchicalNode target)

add an edge between source and target

Parameters:

source - a HierarchicalNode

target - a HierarchicalNode

Returns:

the new edge

getNodeForState

HierarchicalNode getNodeForState(byte[] state)

Return the Node with the given state

Parameters:

state -

Returns:

the Node with the given state

setNodeOrder

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

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

Parameters:

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

getNodeOrder

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

Return the node order as a List of NodeInfo

Returns:

the node order as a List of NodeInfo

getChildsCount

byte[] getChildsCount()

Returns:

an array indicating for each node in the nodeOrder their count of childs. (ie. their max value)

setChildsCount

void setChildsCount(byte[] cc)

Set the array indicating for each node in the nodeOrder their count of childs. (ie. their max value)

Parameters:

cc - the array indicating for each node in the nodeOrder their count of childs. (ie. their max value)

setMode

void setMode(boolean compacted)

Set the mode

Parameters:

compacted -

areTransientCompacted

boolean areTransientCompacted()

Return true if the transients are compacted into component by their atteignability of attractors.

Returns:

true if the transients are compacted into component by their atteignability of attractors.

createStateSet

StatesSet createStateSet()