jp.sbi.celldesigner.plugin

Class PluginKineticLaw

java.lang.Object

jp.sbi.celldesigner.plugin.PluginSBase

jp.sbi.celldesigner.plugin.PluginKineticLaw

public class PluginKineticLaw
extends PluginSBase

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

Author:

The Systems Biology Institute

Field Summary

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

sbase

Constructor Summary

Constructors

Constructor and Description
PluginKineticLaw(PluginReaction parent) Constructor

Method Summary

Modifier and Type	Method and Description
void	addParameter(PluginParameter param) Adds a PluginParameter to the list of PluginParameter of this PluginKineticLaw.
void	clear() Clears all PluginParameter of this PluginKineticLaw.
java.lang.String	getFormula()
PluginListOf	getListOfParameters()
org.sbml.libsbml.ASTNode	getMath()
int	getNumParameters()
PluginParameter	getParameter(int index) Gets the PluginParameter with the given index from the list.
PluginReaction	getParentReaction()
java.lang.String	getParentReactionID()
java.lang.String	getSubstanceUnits()
java.lang.String	getTimeUnits()
void	removeParameter(int index) Remove the PluginParameter with the given index from the list.
void	removeParameter(PluginParameter param) Removes the PluginParameter from the list of PluginParameter of this PluginKineticLaw.
void	setFormula(java.lang.String fomula) Sets the formula of this PluginKineticLaw.
void	setFormulaFromMath() Deprecated. setFormulaFromMath is removed in libSBML 3.x
void	setListOfParameters(PluginListOf listOfParameters) Sets the list of PluginParameter of this PluginKineticLaw.
void	setMath(org.sbml.libsbml.ASTNode math) Sets the Math of this PluginKineticLaw to the given ASTNode.
void	setMathFromFormula() Deprecated. setFormulaFromMath is removed in libSBML 3.x
void	setSubstanceUnits(java.lang.String unit) Sets the substanceUnits of this PluginKineticLaw.
void	setTimeUnits(java.lang.String unit) Sets the timeUnits of this PluginKineticLaw.
void	update(PluginKineticLaw kineticLaw) Update all properties of this PluginKineticLaw same as the given PluginKineticLaw.

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

PluginKineticLaw

public PluginKineticLaw(PluginReaction parent)

Constructor

Parameters:

parent - PluginReaction as the parent of this PluginKineticLaw

Method Detail

update

public void update(PluginKineticLaw kineticLaw)

Update all properties of this PluginKineticLaw same as the given PluginKineticLaw.

Parameters:

kineticLaw - PluginKineticLaw

getListOfParameters

public PluginListOf getListOfParameters()

Returns:

the list of PluginParameter of this PluginKineticLaw.

setListOfParameters

public void setListOfParameters(PluginListOf listOfParameters)

Sets the list of PluginParameter of this PluginKineticLaw.

Parameters:

listOfParameters - PluginListOf

addParameter

public void addParameter(PluginParameter param)

Adds a PluginParameter to the list of PluginParameter of this PluginKineticLaw.

Parameters:

param - PluginParameter

removeParameter

public void removeParameter(PluginParameter param)

Removes the PluginParameter from the list of PluginParameter of this PluginKineticLaw.

Parameters:

param - the PluginParameter to remove

removeParameter

public void removeParameter(int index)

Remove the PluginParameter with the given index from the list.

Parameters:

index - int

getParameter

public PluginParameter getParameter(int index)

Gets the PluginParameter with the given index from the list.

Parameters:

index - int

Returns:

PluginParameter

clear

public void clear()

Clears all PluginParameter of this PluginKineticLaw.

getFormula

public java.lang.String getFormula()

Returns:

the formula of this PluginKineticLaw.

setFormula

public void setFormula(java.lang.String fomula)

Sets the formula of this PluginKineticLaw.

Parameters:

fomula - String

getMath

public org.sbml.libsbml.ASTNode getMath()

Returns:

the Math of this PluginKineticLaw

setMath

public void setMath(org.sbml.libsbml.ASTNode math)

Sets the Math of this PluginKineticLaw to the given ASTNode.

Parameters:

math - ASTNode

setFormulaFromMath

public void setFormulaFromMath()

Deprecated. setFormulaFromMath is removed in libSBML 3.x

See Also:

KineticLaw

setMathFromFormula

public void setMathFromFormula()

Deprecated. setFormulaFromMath is removed in libSBML 3.x

See Also:

KineticLaw

getSubstanceUnits

public java.lang.String getSubstanceUnits()

Returns:

the substanceUnits of this PluginKineticLaw.

setSubstanceUnits

public void setSubstanceUnits(java.lang.String unit)

Sets the substanceUnits of this PluginKineticLaw.

Parameters:

unit - a substanceUnits

getTimeUnits

public java.lang.String getTimeUnits()

Returns:

the timeUnits of this PluginKineticLaw.

setTimeUnits

public void setTimeUnits(java.lang.String unit)

Sets the timeUnits of this PluginKineticLaw.

Parameters:

unit - String

getParentReactionID

public java.lang.String getParentReactionID()

Returns:

the ParentReactionID of this PluginKineticLaw.

getParentReaction

public PluginReaction getParentReaction()

Returns:

the PluginReaction of this PluginKineticLaw, or null if the ParentSBase isn't PluginReaction.

getNumParameters

public int getNumParameters()

Returns:

the number of PluginParameter