jp.sbi.celldesigner.plugin
Class PluginSBase

java.lang.Object
  extended by 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:

Field Summary
protected  SBase sbase
          sbase
 
Constructor Summary
protected PluginSBase()
          Constructor
 
Method Summary
 void addCVTerm(CVTerm term)
           
protected  java.util.Vector ChangeCVTermToMiriamDefinition(java.util.List CVTermT)
           
 XMLNode getAnnotation()
           
 java.lang.String getAnnotationString()
           
 CVTerm getCVTerm(int index)
           
 XMLNode getNotes()
           
 java.lang.String getNotesString()
           
 int getNumCVTerms()
           
protected  PluginSBase getParentSBase()
           
static java.lang.String getRelationFromCVTerm(CVTerm term)
           
 void setAnnotation(XMLNode annotations)
           
 void setAnnotationString(java.lang.String annotations)
           
protected  void setCVTerm(XMLNode node)
           
 void setNotes(java.lang.String notes)
          Sets the Notes of this PluginSBase.
 void setNotes(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 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 -

setNotes

public void setNotes(XMLNode notes)

getNotesString

public java.lang.String getNotesString()
Returns:
the notes of this PluginSBase.

getNotes

public 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 -

toSBML

public java.lang.String toSBML()
toSBML

Returns:
the string of SBML

getAnnotationString

public java.lang.String getAnnotationString()
Returns:
get the annotation of this PluginSBase.

setAnnotationString

public void setAnnotationString(java.lang.String annotations)

getAnnotation

public XMLNode getAnnotation()
Returns:
get the annotation of this PluginSBase.

setAnnotation

public void setAnnotation(XMLNode annotations)

setCVTerm

protected void setCVTerm(XMLNode node)

getCVTerm

public CVTerm getCVTerm(int index)

getNumCVTerms

public int getNumCVTerms()

addCVTerm

public void addCVTerm(CVTerm term)

ChangeCVTermToMiriamDefinition

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

getRelationFromCVTerm

public static java.lang.String getRelationFromCVTerm(CVTerm term)