org.ginsim.core.graph.hierarchicaltransitiongraph

Class HierarchicalTransitionGraphImpl

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<HierarchicalNode,DecisionOnEdge>

org.ginsim.core.graph.hierarchicaltransitiongraph.HierarchicalTransitionGraphImpl

All Implemented Interfaces:

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

public class HierarchicalTransitionGraphImpl
extends TransitionGraphImpl<HierarchicalNode,DecisionOnEdge>
implements HierarchicalTransitionGraph

Implementation of the HTG interface

Author:

Duncan Berenguier

Field Summary

Fields

Modifier and Type	Field and Description
static String	GRAPH_ZIP_NAME

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
HierarchicalTransitionGraphImpl() create a new empty DynamicalHierarchicalGraph.
HierarchicalTransitionGraphImpl(List<org.colomoto.biolqm.NodeInfo> nodeOrder, boolean transientCompaction) create a new DynamicalHierarchicalGraph with a nodeOrder.

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()
protected List	doMerge(Graph otherGraph) not used for this kind of graph: it has no meaning
byte[]	getChildsCount() return an array indicating for each node in the nodeOrder their count of childs.
protected GINMLWriter	getGINMLWriter()
String	getGraphZipName() Return the zip extension for the graph type
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
int	getNodeOrderSize() Return the size of the node order
Graph	getSubgraph(Collection<HierarchicalNode> vertex, Collection<DecisionOnEdge> edges) Not used for this kind of graph: it's not interactively editable
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
List<HierarchicalNode>	searchNodes(String regexp) Search the vertices with ID matching the given regular expression.
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 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, removeEdge, removeNode, repaint, save, save, 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, removeEdge, removeNode, 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

Constructor Detail

HierarchicalTransitionGraphImpl

public HierarchicalTransitionGraphImpl()

create a new empty DynamicalHierarchicalGraph.

HierarchicalTransitionGraphImpl

public HierarchicalTransitionGraphImpl(List<org.colomoto.biolqm.NodeInfo> nodeOrder,
                                       boolean transientCompaction)

create a new DynamicalHierarchicalGraph with a nodeOrder.

Parameters:

nodeOrder - the node order

transientCompaction - flag to enable further compaction

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 NodeInfo

Specified by:

getNodeOrder in interface HierarchicalTransitionGraph

Returns:

the node order as a List of NodeInfo

getNodeOrderSize

public int getNodeOrderSize()

Return the size of the node order

Specified by:

getNodeOrderSize in interface GraphModel<HierarchicalNode,DecisionOnEdge>

Specified by:

getNodeOrderSize in class AbstractGraph<HierarchicalNode,DecisionOnEdge>

Returns:

the size of the node order

setNodeOrder

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

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

Specified by:

setNodeOrder in interface HierarchicalTransitionGraph

Parameters:

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

addEdge

public DecisionOnEdge addEdge(HierarchicalNode source,
                              HierarchicalNode target)

add an edge between source and target

Specified by:

addEdge in interface HierarchicalTransitionGraph

Parameters:

source - a HierarchicalNode

target - a HierarchicalNode

Returns:

the new edge

getGraphZipName

public String getGraphZipName()

Description copied from class: AbstractGraph

Return the zip extension for the graph type

Overrides:

getGraphZipName in class AbstractGraph<HierarchicalNode,DecisionOnEdge>

Returns:

the zip extension for the graph type

getGINMLWriter

protected GINMLWriter getGINMLWriter()

Overrides:

getGINMLWriter in class AbstractGraph<HierarchicalNode,DecisionOnEdge>

searchNodes

public List<HierarchicalNode> searchNodes(String regexp)

Description copied from class: AbstractGraph

Search the vertices with ID matching the given regular expression. Other kind of graph could overwrite this method.

Specified by:

searchNodes in interface GraphModel<HierarchicalNode,DecisionOnEdge>

Overrides:

searchNodes in class AbstractGraph<HierarchicalNode,DecisionOnEdge>

Parameters:

regexp - the regular expression node ID must match to be selected

Returns:

a List of vertices

getNodeForState

public HierarchicalNode getNodeForState(byte[] state)

Description copied from interface: HierarchicalTransitionGraph

Return the Node with the given state

Specified by:

getNodeForState in interface HierarchicalTransitionGraph

Returns:

the Node with the given state

getChildsCount

public byte[] getChildsCount()

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

Specified by:

getChildsCount in interface HierarchicalTransitionGraph

Returns:

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

setChildsCount

public void setChildsCount(byte[] cc)

Description copied from interface: HierarchicalTransitionGraph

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

Specified by:

setChildsCount in interface HierarchicalTransitionGraph

Parameters:

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

areTransientCompacted

public boolean areTransientCompacted()

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

Specified by:

areTransientCompacted in interface HierarchicalTransitionGraph

Returns:

setMode

public void setMode(boolean compacted)

Description copied from interface: HierarchicalTransitionGraph

Set the mode

Specified by:

setMode in interface HierarchicalTransitionGraph

isAssociationValid

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

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

Specified by:

isAssociationValid in class AbstractDerivedGraph<HierarchicalNode,DecisionOnEdge,RegulatoryGraph,RegulatoryNode,RegulatoryMultiEdge>

Parameters:

graph - the graph to associate to the current one

Returns:

true is association is possible, false if not

getSubgraph

public Graph getSubgraph(Collection<HierarchicalNode> vertex,
                         Collection<DecisionOnEdge> edges)

Not used for this kind of graph: it's not interactively editable

Specified by:

getSubgraph in interface GraphModel<HierarchicalNode,DecisionOnEdge>

Specified by:

getSubgraph in class AbstractGraph<HierarchicalNode,DecisionOnEdge>

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

doMerge

protected List doMerge(Graph otherGraph)

not used for this kind of graph: it has no meaning

Specified by:

doMerge in class AbstractGraph<HierarchicalNode,DecisionOnEdge>

Returns:

createStateSet

public StatesSet createStateSet()

Specified by:

createStateSet in interface HierarchicalTransitionGraph