org.sbml.jsbml.ext.multi

Class CompartmentReference

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.multi.CompartmentReference

All Implemented Interfaces:

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

public class CompartmentReference
extends AbstractNamedSBase
implements CompartmentalizedSBase, UniqueNamedSBase

Since:

1.0

Author:

Nicolas Rodriguez

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
CompartmentReference() Creates a new CompartmentReference instance.
CompartmentReference(CompartmentReference obj) Creates a new CompartmentReference instance, cloned from the given object.
CompartmentReference(int level, int version) Creates a CompartmentReference instance with a level and version.
CompartmentReference(String id) Creates a CompartmentReference instance with an id.
CompartmentReference(String id, int level, int version) Creates a CompartmentReference instance with an id, level, and version.
CompartmentReference(String id, String name, int level, int version) Creates a CompartmentReference instance with an id, name, level, and version.

Method Summary

Modifier and Type	Method and Description
CompartmentReference	clone()
boolean	equals(Object obj)
String	getCompartment()
Compartment	getCompartmentInstance()
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isCompartmentMandatory()
boolean	isIdMandatory()
boolean	isSetCompartment() Returns whether compartment is set.
boolean	isSetCompartmentInstance()
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	setCompartment(Compartment compartment)
boolean	setCompartment(String compartment)
boolean	unsetCompartment()
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, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, 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, 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, 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, removeTreeNodeChangeListener, 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

CompartmentReference

public CompartmentReference()

Creates a new CompartmentReference instance.

CompartmentReference

public CompartmentReference(CompartmentReference obj)

Creates a new CompartmentReference instance, cloned from the given object.

Parameters:

obj - the CompartmentReference to clone

CompartmentReference

public CompartmentReference(int level,
                            int version)

Creates a CompartmentReference instance with a level and version.

Parameters:

level - SBML Level

version - SBML Version

CompartmentReference

public CompartmentReference(String id)

Creates a CompartmentReference instance with an id.

Parameters:

id - the identifier for the new element.

CompartmentReference

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

Creates a CompartmentReference instance with an id, level, and version.

Parameters:

id - the identifier for this element.

level - the SBML Level

version - the SBML Version

CompartmentReference

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

Creates a CompartmentReference instance with an id, name, level, and version.

Parameters:

id - the identifier for this element.

name - a human-readable name for this element that can be used for display purposes.

level - the SBML Level

version - the SBML Version

Method Detail

clone

public CompartmentReference clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

getCompartment

public String getCompartment()

Specified by:

getCompartment in interface CompartmentalizedSBase

getCompartmentInstance

public Compartment getCompartmentInstance()

Specified by:

getCompartmentInstance in interface CompartmentalizedSBase

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

isCompartmentMandatory

public boolean isCompartmentMandatory()

Specified by:

isCompartmentMandatory in interface CompartmentalizedSBase

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

isSetCompartment

public boolean isSetCompartment()

Returns whether compartment is set.

Specified by:

isSetCompartment in interface CompartmentalizedSBase

Returns:

whether compartment is set.

isSetCompartmentInstance

public boolean isSetCompartmentInstance()

Specified by:

isSetCompartmentInstance in interface CompartmentalizedSBase

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

setCompartment

public boolean setCompartment(Compartment compartment)

Specified by:

setCompartment in interface CompartmentalizedSBase

setCompartment

public boolean setCompartment(String compartment)

Specified by:

setCompartment in interface CompartmentalizedSBase

unsetCompartment

public boolean unsetCompartment()

Specified by:

unsetCompartment in interface CompartmentalizedSBase

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase