jp.sbi.celldesigner.plugin

Class PluginSBase

java.lang.Object

jp.sbi.celldesigner.plugin.PluginSBase

Direct Known Subclasses:

PluginAntiSenseRNA, PluginBindingRegion, PluginCompartment, PluginCompartmentType, PluginConstraint, PluginEvent, PluginEventAssignment, PluginFunctionDefinition, PluginGene, PluginGLogicGate, PluginInformationBox, PluginInitialAssignment, PluginKineticLaw, PluginListOf, PluginModel, PluginModification, PluginModificationRegion, PluginModificationResidue, PluginParameter, PluginProtein, PluginReaction, PluginRNA, PluginRule, PluginSimpleSpeciesReference, PluginSpecies, PluginSpeciesAlias, PluginSpeciesType, PluginStructuralState, PluginUnit, PluginUnitDefinition

public class PluginSBase
extends java.lang.Object

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

Author:

The Systems Biology Institute

Field Summary

Fields

Modifier and Type	Field and Description
protected org.sbml.libsbml.SBase	sbase sbase

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	PluginSBase() Constructor

Method Summary

Modifier and Type	Method and Description
void	addCVTerm(org.sbml.libsbml.CVTerm term)
protected java.util.Vector	ChangeCVTermToMiriamDefinition(java.util.List CVTermT)
org.sbml.libsbml.XMLNode	getAnnotation() Get the annotation of this PluginSBase.
java.lang.String	getAnnotationString() Get the annotation of this PluginSBase.
org.sbml.libsbml.CVTerm	getCVTerm(int index)
org.sbml.libsbml.XMLNode	getNotes()
java.lang.String	getNotesString()
int	getNumCVTerms()
protected PluginSBase	getParentSBase()
static java.lang.String	getRelationFromCVTerm(org.sbml.libsbml.CVTerm term)
void	setAnnotation(org.sbml.libsbml.XMLNode annotations) Set the annotation of this PluginSBase.
void	setAnnotationString(java.lang.String annotations) Set the annotation of this PluginSBase.
protected void	setCVTerm(org.sbml.libsbml.XMLNode node)
void	setNotes(java.lang.String notes) Sets the Notes of this PluginSBase.
void	setNotes(org.sbml.libsbml.XMLNode notes)
protected void	setParentSBase(PluginSBase parentSBase) Sets the ParentSBase of this PluginSBase.
java.lang.String	toSBML() toSBML

Methods inherited from class java.lang.Object

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

Field Detail

sbase

protected org.sbml.libsbml.SBase sbase

sbase

Constructor Detail

PluginSBase

protected PluginSBase()

Constructor

Method Detail

setNotes

public void setNotes(java.lang.String notes)

Sets the Notes of this PluginSBase.

Parameters:

notes - String

setNotes

public void setNotes(org.sbml.libsbml.XMLNode notes)

getNotesString

public java.lang.String getNotesString()

Returns:

the notes of this PluginSBase.

getNotes

public org.sbml.libsbml.XMLNode getNotes()

getParentSBase

protected PluginSBase getParentSBase()

Returns:

the parentSBase of this PluginSBase.

setParentSBase

protected void setParentSBase(PluginSBase parentSBase)

Sets the ParentSBase of this PluginSBase.

Parameters:

parentSBase - PluginSBase

toSBML

public java.lang.String toSBML()

toSBML

Returns:

the string of SBML

getAnnotationString

public java.lang.String getAnnotationString()

Get the annotation of this PluginSBase.

Returns:

annotationString

setAnnotationString

public void setAnnotationString(java.lang.String annotations)

Set the annotation of this PluginSBase.

Parameters:

annotations - String

getAnnotation

public org.sbml.libsbml.XMLNode getAnnotation()

Get the annotation of this PluginSBase.

Returns:

annotation

setAnnotation

public void setAnnotation(org.sbml.libsbml.XMLNode annotations)

Set the annotation of this PluginSBase.

Parameters:

annotations - XMLNode

setCVTerm

protected void setCVTerm(org.sbml.libsbml.XMLNode node)

getCVTerm

public org.sbml.libsbml.CVTerm getCVTerm(int index)

getNumCVTerms

public int getNumCVTerms()

addCVTerm

public void addCVTerm(org.sbml.libsbml.CVTerm term)

ChangeCVTermToMiriamDefinition

protected java.util.Vector ChangeCVTermToMiriamDefinition(java.util.List CVTermT)

getRelationFromCVTerm

public static java.lang.String getRelationFromCVTerm(org.sbml.libsbml.CVTerm term)