org.ginsim.core.graph.regulatorygraph

Class RegulatoryMultiEdge

java.lang.Object

org.ginsim.core.graph.Edge<RegulatoryNode>

org.ginsim.core.graph.regulatorygraph.RegulatoryMultiEdge

All Implemented Interfaces:

ToolTipsable

public class RegulatoryMultiEdge
extends Edge<RegulatoryNode>
implements ToolTipsable

Edges of the regulatory graph: provide a list of interactions.

Author:

Aurelien Naldi

Field Summary

Fields inherited from class org.ginsim.core.graph.Edge

source, target

Constructor Summary

Constructors

Constructor and Description
RegulatoryMultiEdge(RegulatoryGraph g, RegulatoryNode source, RegulatoryNode target)
RegulatoryMultiEdge(RegulatoryGraph g, RegulatoryNode source, RegulatoryNode target, RegulatoryEdgeSign param)
RegulatoryMultiEdge(RegulatoryGraph g, RegulatoryNode source, RegulatoryNode target, RegulatoryEdgeSign param, byte threshold)

Method Summary

Modifier and Type	Method and Description
void	addEdge(Graph graph)
void	addEdge(RegulatoryEdgeSign sign, Graph graph)
int	addEdge(RegulatoryEdgeSign sign, int threshold, Graph graph)
void	applyNewMaxValue(byte max)
void	canApplyNewMaxValue(byte max, List l_fixable, List l_conflict)
void	copyFrom(boolean[] t_required)
void	copyFrom(RegulatoryMultiEdge edgeOri)
Annotation	getAnnotation()
RegulatoryEdge	getEdge(int index)
int	getEdgeCount()
RegulatoryEdge	getEdgeForThreshold(int threshold)
String	getEdgeName(int index)
int[]	getFreeValues()
String	getId(int index) get the id of the corresponding subedge.
int	getIndexof(String id) get the index of the subedge having a given id
byte	getMax(int index)
byte	getMin(int index)
RegulatoryEdgeSign	getSign()
RegulatoryEdgeSign	getSign(int index)
boolean	isActive(int index, int sourceStatus)
void	markRemoved()
void	removeEdge(int index, RegulatoryGraph graph) remove an edge from this multiEdge
void	rescanSign(Graph graph)
void	setMin(int index, byte min, RegulatoryGraph graph) change a sub edge's min value.
void	setSign(int index, RegulatoryEdgeSign sign, Graph graph) change the sign of a sub edge.
String	toToolTip() retrieve the tooltip text
void	toXML(XMLWriter out)

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

getSource, getTarget, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

RegulatoryMultiEdge

public RegulatoryMultiEdge(RegulatoryGraph g,
                           RegulatoryNode source,
                           RegulatoryNode target,
                           RegulatoryEdgeSign param)

Parameters:

source -

target -

param -

RegulatoryMultiEdge

public RegulatoryMultiEdge(RegulatoryGraph g,
                           RegulatoryNode source,
                           RegulatoryNode target,
                           RegulatoryEdgeSign param,
                           byte threshold)

RegulatoryMultiEdge

public RegulatoryMultiEdge(RegulatoryGraph g,
                           RegulatoryNode source,
                           RegulatoryNode target)

Parameters:

source -

target -

Method Detail

addEdge

public void addEdge(Graph graph)

addEdge

public void addEdge(RegulatoryEdgeSign sign,
                    Graph graph)

addEdge

public int addEdge(RegulatoryEdgeSign sign,
                   int threshold,
                   Graph graph)

removeEdge

public void removeEdge(int index,
                       RegulatoryGraph graph)

remove an edge from this multiEdge

Parameters:

index - index of the edge to remove.

graph -

getEdgeCount

public int getEdgeCount()

Returns:

the number of edges in this multiEdge

getId

public String getId(int index)

get the id of the corresponding subedge. warning: this will return a byteened ID to put in the table, to get the real (full) id, use getFullId instead.

Parameters:

index - index of an edge of this multiEdge

Returns:

the id of the given sub edge.

toXML

public void toXML(XMLWriter out)
           throws IOException

Throws:

IOException

toToolTip

public String toToolTip()

Description copied from interface: ToolTipsable

retrieve the tooltip text

Specified by:

toToolTip in interface ToolTipsable

Overrides:

toToolTip in class Edge<RegulatoryNode>

Returns:

the string to be displayed in the tooltip

getSign

public RegulatoryEdgeSign getSign()

Returns:

Returns the sign.

getSign

public RegulatoryEdgeSign getSign(int index)

Parameters:

index -

Returns:

the sign of this subedge

setSign

public void setSign(int index,
                    RegulatoryEdgeSign sign,
                    Graph graph)

change the sign of a sub edge.

Parameters:

index - index of the sub edge

sign - the new sign

graph -

getAnnotation

public Annotation getAnnotation()

getEdgeName

public String getEdgeName(int index)

Parameters:

index - index of a subedge.

Returns:

name of this sub edge.

applyNewMaxValue

public void applyNewMaxValue(byte max)

canApplyNewMaxValue

public void canApplyNewMaxValue(byte max,
                                List l_fixable,
                                List l_conflict)

getMin

public byte getMin(int index)

Parameters:

index - index of a sub edge.

Returns:

the min value of the source node for which this sub edge is active

getMax

public byte getMax(int index)

Parameters:

index - index of a sub edge.

Returns:

the max value of the source node for which this sub edge is active

setMin

public void setMin(int index,
                   byte min,
                   RegulatoryGraph graph)

change a sub edge's min value.

Parameters:

index - index of a sub edge.

min - the new min value.

rescanSign

public void rescanSign(Graph graph)

isActive

public boolean isActive(int index,
                        int sourceStatus)

Parameters:

index -

sourceStatus -

Returns:

true if active

getIndexof

public int getIndexof(String id)

get the index of the subedge having a given id

Parameters:

id -

Returns:

index of the corresponding subedge or -1 if not avaible here

copyFrom

public void copyFrom(RegulatoryMultiEdge edgeOri)

Parameters:

edgeOri -

copyFrom

public void copyFrom(boolean[] t_required)

Parameters:

t_required -

getEdge

public RegulatoryEdge getEdge(int index)

markRemoved

public void markRemoved()

getFreeValues

public int[] getFreeValues()

getEdgeForThreshold

public RegulatoryEdge getEdgeForThreshold(int threshold)