org.ginsim.core.graph.regulatorygraph.logicalfunction

Class LogicalParameter

java.lang.Object

org.ginsim.core.graph.regulatorygraph.logicalfunction.LogicalParameter

All Implemented Interfaces:

XMLize

public class LogicalParameter
extends Object
implements XMLize

the Class in which we store biological data for logical parameters (in the vertex)

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	hasConflict
protected boolean	isDup

Constructor Summary

Constructors

Constructor and Description
LogicalParameter(int v) Constructs an empty vector and set the value
LogicalParameter(List newEI, int v)

Method Summary

Modifier and Type	Method and Description
boolean	activable(RegulatoryGraph regGraph, RegulatoryNode node)
void	addEdge(RegulatoryEdge edge) Adds the GsEdgeIndex to the interaction
void	applyNewGraph(RegulatoryNode clone, Map copyMap)
int	EdgeCount()
boolean	equals(Object obj)
RegulatoryEdge	getEdge(int index)
List	getEdges()
int	getMDD(RegulatoryGraph graph, RegulatoryNode node, org.colomoto.mddlib.MDDManager factory) Build a MDD corresponding to this parameter (using the new MDD toolkit)
int	getValue() get value of the interaction
boolean	hasConflict()
int	hashCode()
boolean	isDirty()
boolean	isDup()
void	setEdges(List list) Set the vector of GsEdgeIndex
void	setValue(int i, Graph graph) set value of the interaction
String	toString()
void	toXML(XMLWriter out) write the XML representation of this object to a file

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

isDup

protected boolean isDup

hasConflict

protected boolean hasConflict

Constructor Detail

LogicalParameter

public LogicalParameter(int v)

Constructs an empty vector and set the value

Parameters:

v - of the interaction

LogicalParameter

public LogicalParameter(List newEI,
                        int v)

Parameters:

newEI -

v -

Method Detail

isDup

public boolean isDup()

hasConflict

public boolean hasConflict()

getValue

public int getValue()

get value of the interaction

Returns:

int

setValue

public void setValue(int i,
                     Graph graph)

set value of the interaction

Parameters:

i -

addEdge

public void addEdge(RegulatoryEdge edge)

Adds the GsEdgeIndex to the interaction

Parameters:

edge -

isDirty

public boolean isDirty()

getEdge

public RegulatoryEdge getEdge(int index)

Parameters:

index -

Returns:

the GsEdgeIndex at the specified position index in the parameter.

EdgeCount

public int EdgeCount()

Returns:

the number of edges in this parameter.

getEdges

public List getEdges()

Returns:

all the GsEdgeIndex

setEdges

public void setEdges(List list)

Set the vector of GsEdgeIndex

Parameters:

list -

activable

public boolean activable(RegulatoryGraph regGraph,
                         RegulatoryNode node)

Parameters:

regGraph -

node -

Returns:

true if this logical parameter is activable

getMDD

public int getMDD(RegulatoryGraph graph,
                  RegulatoryNode node,
                  org.colomoto.mddlib.MDDManager factory)

Build a MDD corresponding to this parameter (using the new MDD toolkit)

Parameters:

factory -

Returns:

toXML

public void toXML(XMLWriter out)
           throws IOException

Description copied from interface: XMLize

write the XML representation of this object to a file

Specified by:

toXML in interface XMLize

Throws:

IOException

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

applyNewGraph

public void applyNewGraph(RegulatoryNode clone,
                          Map copyMap)

Parameters:

clone -

copyMap -

toString

public String toString()

Overrides:

toString in class Object