jp.sbi.celldesigner.plugin

Class PluginGLogicGate

java.lang.Object

jp.sbi.celldesigner.plugin.PluginSBase

jp.sbi.celldesigner.plugin.PluginGLogicGate

public class PluginGLogicGate
extends PluginSBase

Author:

The Systems Biology Institute

Field Summary

Fields inherited from class jp.sbi.celldesigner.plugin.PluginSBase

sbase

Constructor Summary

Constructors

Constructor and Description
PluginGLogicGate(PluginReaction parent, java.util.Vector vctSpecs)
PluginGLogicGate(PluginReaction parent, java.util.Vector vctSpecs, java.lang.String strGateType)
PluginGLogicGate(PluginReaction pParent, java.util.Vector vctSpecs, java.lang.String strGateType, java.lang.String sModType)

Method Summary

Modifier and Type	Method and Description
void	addModifiers(PluginModifierSpeciesReference pmsr1)
void	addSpecies(PluginSpecies species)
boolean	addSpecies(java.lang.String id)
void	addSpeciesAlias(PluginSpeciesAlias alias)
java.awt.Color	getColor()
jp.sbi.celldesigner.ReactionLink	getGateLink()
java.lang.String	getGLogicGateType()
double	getLineWidth()
java.lang.String	getModificationType()
java.util.ArrayList	getModifiers()
PluginReaction	getParentReaction()
PluginListOf	getRefsOfGateInReaction()
java.util.Vector	getSpeciesAliases()
void	removeSpecies(PluginSpecies species)
boolean	removeSpecies(java.lang.String id)
void	removeSpeciesAlias(int index)
void	setColor(java.awt.Color gateColor) Sets the color of this GLogicGate.
void	setGateLink(jp.sbi.celldesigner.ReactionLink link)
void	setGateSpeciesAliasesAndModificationType()
void	setGLogicGateType(java.lang.String gLogicGateType)
void	setLineWidth(double lineWidth) Sets the line width of this GLogicGate.
void	setModificationType(java.lang.String _modificationType)
void	setParentReaction(PluginReaction parent)
void	setPluginGLogicGateEventEnd() If setPluginGLogicGateEventStart() method has been called, called after last notifySBaseXXX method.
void	setPluginGLogicGateEventStart() Must be called before first notifySBaseXXX method.
void	setRefsOfGateInReaction(jp.sbi.celldesigner.SBModel sbml, PluginGLogicGate pGate) Sets the references of the GLogicGate.

Methods inherited from class jp.sbi.celldesigner.plugin.PluginSBase

addCVTerm, ChangeCVTermToMiriamDefinition, getAnnotation, getAnnotationString, getCVTerm, getNotes, getNotesString, getNumCVTerms, getParentSBase, getRelationFromCVTerm, setAnnotation, setAnnotationString, setCVTerm, setNotes, setNotes, setParentSBase, toSBML

Methods inherited from class java.lang.Object

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

Constructor Detail

PluginGLogicGate

public PluginGLogicGate(PluginReaction parent,
                        java.util.Vector vctSpecs)

PluginGLogicGate

public PluginGLogicGate(PluginReaction parent,
                        java.util.Vector vctSpecs,
                        java.lang.String strGateType)

PluginGLogicGate

public PluginGLogicGate(PluginReaction pParent,
                        java.util.Vector vctSpecs,
                        java.lang.String strGateType,
                        java.lang.String sModType)

Method Detail

setGLogicGateType

public void setGLogicGateType(java.lang.String gLogicGateType)

getGLogicGateType

public java.lang.String getGLogicGateType()

getColor

public java.awt.Color getColor()

Returns:

the color of this GLogicGate.

setColor

public void setColor(java.awt.Color gateColor)

Sets the color of this GLogicGate.

Parameters:

gateColor - the color of logic gate

getLineWidth

public double getLineWidth()

Returns:

the line width of this GLogicGate.

setLineWidth

public void setLineWidth(double lineWidth)

Sets the line width of this GLogicGate.

Parameters:

lineWidth - double

getParentReaction

public PluginReaction getParentReaction()

setParentReaction

public void setParentReaction(PluginReaction parent)

setGateLink

public void setGateLink(jp.sbi.celldesigner.ReactionLink link)

setGateSpeciesAliasesAndModificationType

public void setGateSpeciesAliasesAndModificationType()

setRefsOfGateInReaction

public void setRefsOfGateInReaction(jp.sbi.celldesigner.SBModel sbml,
                                    PluginGLogicGate pGate)

Sets the references of the GLogicGate. Only can be called after reaction created.

Parameters:

sbml - SBModel

pGate - PluginGLogicGate

getRefsOfGateInReaction

public PluginListOf getRefsOfGateInReaction()

getGateLink

public jp.sbi.celldesigner.ReactionLink getGateLink()

addSpecies

public void addSpecies(PluginSpecies species)

addSpeciesAlias

public void addSpeciesAlias(PluginSpeciesAlias alias)

addSpecies

public boolean addSpecies(java.lang.String id)

getSpeciesAliases

public java.util.Vector getSpeciesAliases()

removeSpeciesAlias

public void removeSpeciesAlias(int index)

removeSpecies

public boolean removeSpecies(java.lang.String id)

removeSpecies

public void removeSpecies(PluginSpecies species)

addModifiers

public void addModifiers(PluginModifierSpeciesReference pmsr1)

getModifiers

public java.util.ArrayList getModifiers()

setModificationType

public void setModificationType(java.lang.String _modificationType)

getModificationType

public java.lang.String getModificationType()

setPluginGLogicGateEventStart

public void setPluginGLogicGateEventStart()

Must be called before first notifySBaseXXX method.

setPluginGLogicGateEventEnd

public void setPluginGLogicGateEventEnd()

If setPluginGLogicGateEventStart() method has been called, called after last notifySBaseXXX method.