org.sbml.jsbml.ext.fbc

Class GeneProductRef

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.fbc.GeneProductRef

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, Association, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

public class GeneProductRef
extends AbstractNamedSBase
implements Association, UniqueNamedSBase

References a GeneProduct.

Introduced to FBC in version 2.

Since:

1.1

Author:

Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
GeneProductRef() Creates a new GeneProductRef instance.
GeneProductRef(GeneProductRef gpr) Creates a new GeneProductRef instance.
GeneProductRef(int level, int version) Creates a new GeneProductRef instance.
GeneProductRef(String id) Creates a new GeneProductRef instance.
GeneProductRef(String id, int level, int version) Creates a new GeneProductRef instance.
GeneProductRef(String id, String name, int level, int version) Creates a new GeneProductRef instance.

Method Summary

Modifier and Type	Method and Description
GeneProductRef	clone()
boolean	equals(Object obj)
String	getGeneProduct() Returns the value of geneProduct.
GeneProduct	getGeneProductInstance() Returns the GeneProduct referenced by this GeneProductRef.
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory()
boolean	isSetGeneProduct() Returns whether geneProduct is set.
boolean	isSetGeneProductInstance() Returns whether the gene product id is set and this id is a valid GeneProduct id in this model.
boolean	readAttribute(String attributeName, String prefix, String value)
void	setGeneProduct(String geneProduct) Sets the value of geneProduct
boolean	unsetGeneProduct() Unsets the variable geneProduct
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

Constructor Detail

GeneProductRef

public GeneProductRef()

Creates a new GeneProductRef instance.

GeneProductRef

public GeneProductRef(GeneProductRef gpr)

Creates a new GeneProductRef instance.

Parameters:

gpr - the instance to clone

GeneProductRef

public GeneProductRef(int level,
                      int version)

Creates a new GeneProductRef instance.

Parameters:

level - the SBML level

version - the SBML version

GeneProductRef

public GeneProductRef(String id)

Creates a new GeneProductRef instance.

Parameters:

id - the id

GeneProductRef

public GeneProductRef(String id,
                      int level,
                      int version)

Creates a new GeneProductRef instance.

Parameters:

id - the id

level - the SBML level

version - the SBML version

GeneProductRef

public GeneProductRef(String id,
                      String name,
                      int level,
                      int version)

Creates a new GeneProductRef instance.

Parameters:

id - the id

name - the name

level - the SBML level

version - the SBML version

Method Detail

clone

public GeneProductRef clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

getGeneProduct

public String getGeneProduct()

Returns the value of geneProduct.

Returns:

the value of geneProduct.

getGeneProductInstance

public GeneProduct getGeneProductInstance()

Returns the GeneProduct referenced by this GeneProductRef.

Returns:

the GeneProduct instance referenced by this GeneProductRef or null.

isSetGeneProductInstance

public boolean isSetGeneProductInstance()

Returns whether the gene product id is set and this id is a valid GeneProduct id in this model.

Returns:

true the gene product id is set and this id is a valid GeneProduct id in this model.

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

isSetGeneProduct

public boolean isSetGeneProduct()

Returns whether geneProduct is set.

Returns:

whether geneProduct is set.

readAttribute

public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

setGeneProduct

public void setGeneProduct(String geneProduct)

Sets the value of geneProduct

Parameters:

geneProduct - the GeneProduct id

unsetGeneProduct

public boolean unsetGeneProduct()

Unsets the variable geneProduct

Returns:

true, if geneProduct was set before, otherwise false

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase