jp.sbi.celldesigner.plugin
Class PluginReaction

java.lang.Object
  jp.sbi.celldesigner.plugin.PluginSBase
      jp.sbi.celldesigner.plugin.PluginReaction

public class PluginReaction
extends PluginSBase

This class wraps org.sbml.libsbml.Reaction for the plug-in.

Author:

Field Summary

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

sbase

Constructor Summary

	PluginReaction() Constructor
protected	PluginReaction(java.lang.String id) Constructor

Method Summary

void	addGLogicGate(PluginGLogicGate pgg)
void	addModifier(PluginModifierSpeciesReference ref) Adds a PluginModifierSpeciesReference to this PluginReaction.
void	addProduct(PluginSpeciesReference ref) Adds Product (PluginSpeciesReference) to this PluginReaction.
void	addReactant(PluginSpeciesReference ref) Adds the given Reactant (PluginSpeciesReference) to this PluginReaction.
PluginRealLineInformationDataObjOfReactionLink	getAllMyPostionInfomations()
PluginRealLineInformationDataObjOfReactionLink	getAllMyPostionInfomations(boolean bPrintDebugInfo)
boolean	getFast()
java.lang.String	getId()
PluginKineticLaw	getKineticLaw()
java.awt.Color	getLineColor()
double	getLineWidth()
PluginListOf	getListOfGLogicGates()
PluginListOf	getListOfModifiers()
PluginListOf	getListOfProducts()
PluginListOf	getListOfReactants()
PluginModifierSpeciesReference	getModifier(int index) Gets the PluginModifierSpeciesReference with the given index of this PluginReaction.
java.lang.String	getName()
int	getNumGLogicGates()
int	getNumModifiers()
int	getNumProducts()
int	getNumReactants()
PluginSpeciesReference	getProduct(int index) Gets the Product (PluginSpeciesReference) of this PluginReaction with the given index.
PluginSpeciesReference	getReactant(int index) Gets the Reactant (PluginSpeciesReference) with the given index from this PluginReaction.
java.lang.String	getReactionType()
boolean	getReversible()
void	removeGLogicGate(int index)
void	removeGLogicGate(PluginGLogicGate pgg)
void	removeModifier(int index) Removes the PluginModifierSpeciesReference from this PluginReaction.
void	removeModifier(PluginModifierSpeciesReference ref) Removes a PluginModifierSpeciesReference from this PluginReaction.
void	removeProduct(int index) Removes the Product (PluginSpeciesReference) with the given index from this PluginReaction.
void	removeProduct(PluginSpeciesReference ref) Removes the given Product (PluginSpeciesReference) from this PluginReaction.
void	removeReactant(int index) Removes the Reactant with the given index from this PluginReaction.
void	removeReactant(PluginSpeciesReference ref) Removes the given Reactant (PluginSpeciesReference) from this PluginReaction.
void	setFast(boolean fast) Sets the fast status of this PluginReaction to the given value (boolean)
void	setKineticLaw(PluginKineticLaw ki) Sets the PluginKineticLaw of this PluginReaction.
void	setLineColor(java.awt.Color lineColor) Sets the lineColor of this PluginReaction.
void	setLineWidth(double lineWidth) Sets the line width of this PluginReaction.
void	setListOfGLogicGates(PluginListOf listOfGLogicGates)
void	setListOfModifiers(PluginListOf listOfModifiers) Sets the list of PluginModifierSpeciesReference of this PluginReaction.
void	setListOfProducts(PluginListOf listOfProducts) Sets the list of Products (PluginSpeciesReference) of this PluginReaction.
void	setListOfReactants(PluginListOf listOfReactants) Sets the list of Reactants (PluginSpeciesReference) of this PluginReaction.
void	setName(java.lang.String name) Sets the name of this PluginReaction.
void	setReactionType(java.lang.String type) Sets the type of this PluginReaction.
void	setReversible(boolean reversible) Sets the reversible status of this PluginReaction to the given value (boolean).
void	update(PluginReaction reaction) Update all properties of this PluginReaction to the same as the given PluginReaction.

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

getNotes, getNotesString, getParentSBase, setNotes, setParentSBase, toSBML

Methods inherited from class java.lang.Object

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

Constructor Detail

PluginReaction

public PluginReaction()

Constructor

PluginReaction

protected PluginReaction(java.lang.String id)

Constructor

Parameters:

id -

Method Detail

update

public void update(PluginReaction reaction)

Update all properties of this PluginReaction to the same as the given PluginReaction.

Parameters:

reaction -

getId

public java.lang.String getId()

Returns:

the id of this PluginReaction.

getFast

public boolean getFast()

Returns:

the fast status of this Reaction.

setFast

public void setFast(boolean fast)

Sets the fast status of this PluginReaction to the given value (boolean)

Parameters:

fast -

getReversible

public boolean getReversible()

Returns:

the reversible status of this PluginReaction.

setReversible

public void setReversible(boolean reversible)

Sets the reversible status of this PluginReaction to the given value (boolean).

Parameters:

reversible -

getName

public java.lang.String getName()

Returns:

the name of this PluginReaction.

setName

public void setName(java.lang.String name)

Sets the name of this PluginReaction.

Parameters:

name -

addReactant

public void addReactant(PluginSpeciesReference ref)

Adds the given Reactant (PluginSpeciesReference) to this PluginReaction.

Parameters:

ref - PluginSpeciesReference

removeReactant

public void removeReactant(PluginSpeciesReference ref)

Removes the given Reactant (PluginSpeciesReference) from this PluginReaction.

Parameters:

ref -

removeReactant

public void removeReactant(int index)

Removes the Reactant with the given index from this PluginReaction.

Parameters:

index -

getReactant

public PluginSpeciesReference getReactant(int index)

Gets the Reactant (PluginSpeciesReference) with the given index from this PluginReaction.

Parameters:

index -

Returns:

PluginSpeciesReference

addProduct

public void addProduct(PluginSpeciesReference ref)

Adds Product (PluginSpeciesReference) to this PluginReaction.

Parameters:

ref - Product

removeProduct

public void removeProduct(PluginSpeciesReference ref)

Removes the given Product (PluginSpeciesReference) from this PluginReaction.

Parameters:

ref -

removeProduct

public void removeProduct(int index)

Removes the Product (PluginSpeciesReference) with the given index from this PluginReaction.

Parameters:

index -

getProduct

public PluginSpeciesReference getProduct(int index)

Gets the Product (PluginSpeciesReference) of this PluginReaction with the given index.

Parameters:

index -

Returns:

PluginSpeciesReference

addModifier

public void addModifier(PluginModifierSpeciesReference ref)

Adds a PluginModifierSpeciesReference to this PluginReaction.

Parameters:

ref - PluginModifierSpeciesReference

removeModifier

public void removeModifier(PluginModifierSpeciesReference ref)

Removes a PluginModifierSpeciesReference from this PluginReaction.

Parameters:

ref -

removeModifier

public void removeModifier(int index)

Removes the PluginModifierSpeciesReference from this PluginReaction.

Parameters:

index -

getModifier

public PluginModifierSpeciesReference getModifier(int index)

Gets the PluginModifierSpeciesReference with the given index of this PluginReaction.

Parameters:

index -

Returns:

PluginModifierSpeciesReference

getKineticLaw

public PluginKineticLaw getKineticLaw()

Returns:

the PluginKineticLaw of this PluginReaction.

setKineticLaw

public void setKineticLaw(PluginKineticLaw ki)

Sets the PluginKineticLaw of this PluginReaction.

Parameters:

ki -

getLineColor

public java.awt.Color getLineColor()

Returns:

the lineColor of this PluginReaction.

setLineColor

public void setLineColor(java.awt.Color lineColor)

Sets the lineColor of this PluginReaction.

Parameters:

lineColor - 設定する lineColor。

getLineWidth

public double getLineWidth()

Returns:

the line width of this PluginReaction.

setLineWidth

public void setLineWidth(double lineWidth)

Sets the line width of this PluginReaction.

Parameters:

lineWidth -

getListOfModifiers

public PluginListOf getListOfModifiers()

Returns:

the list of PluginModifierSpeciesReference of this PluginReaction.

setListOfModifiers

public void setListOfModifiers(PluginListOf listOfModifiers)

Sets the list of PluginModifierSpeciesReference of this PluginReaction.

Parameters:

listOfModifiers -

getListOfProducts

public PluginListOf getListOfProducts()

Returns:

the list of Products (PluginSpeciesReference) of this PluginReaction.

setListOfProducts

public void setListOfProducts(PluginListOf listOfProducts)

Sets the list of Products (PluginSpeciesReference) of this PluginReaction.

Parameters:

listOfProducts -

getListOfReactants

public PluginListOf getListOfReactants()

Returns:

the list of Reactants (PluginSpeciesReference) of this PluginReaction.

setListOfReactants

public void setListOfReactants(PluginListOf listOfReactants)

Sets the list of Reactants (PluginSpeciesReference) of this PluginReaction.

Parameters:

listOfReactants -

getReactionType

public java.lang.String getReactionType()

Returns:

the type of this PluginReaction.

setReactionType

public void setReactionType(java.lang.String type)

Sets the type of this PluginReaction.

Parameters:

type -

getNumReactants

public int getNumReactants()

Returns:

the number of Reactants of this PluginReaction.

getNumProducts

public int getNumProducts()

Returns:

the number of Products of this PluginReaction.

getNumModifiers

public int getNumModifiers()

Returns:

the number of Modifiers of this PluginReaction.

getNumGLogicGates

public int getNumGLogicGates()

Returns:

the number of GLogicGates of this PluginReaction.

addGLogicGate

public void addGLogicGate(PluginGLogicGate pgg)

Parameters:

pgg -

removeGLogicGate

public void removeGLogicGate(int index)

removeGLogicGate

public void removeGLogicGate(PluginGLogicGate pgg)

getListOfGLogicGates

public PluginListOf getListOfGLogicGates()

setListOfGLogicGates

public void setListOfGLogicGates(PluginListOf listOfGLogicGates)

getAllMyPostionInfomations

public PluginRealLineInformationDataObjOfReactionLink getAllMyPostionInfomations()

getAllMyPostionInfomations

public PluginRealLineInformationDataObjOfReactionLink getAllMyPostionInfomations(boolean bPrintDebugInfo)