org.sbml.jsbml

Interface CompartmentalizedSBase

All Superinterfaces:

java.lang.Cloneable, NamedSBase, SBase, java.io.Serializable, javax.swing.tree.TreeNode, TreeNodeWithChangeSupport

All Known Implementing Classes:

Reaction, Species

public interface CompartmentalizedSBase
extends NamedSBase

Since:

1.1

Version:

$Rev$

Author:

Andreas Dräger

Method Summary

Modifier and Type	Method and Description
java.lang.String	getCompartment() Returns the value of the referenced compartment.
NamedSBase	getCompartmentInstance() Returns the Compartment that is referenced by this SBase.
boolean	isCompartmentMandatory()
boolean	isSetCompartment()
boolean	isSetCompartmentInstance()
boolean	setCompartment(Compartment compartment) Sets the compartment identifiers of this CompartmentalizedSBase to the id of the Compartment 'compartment'.
boolean	setCompartment(java.lang.String compartmentId) Sets the compartment attribute.
boolean	unsetCompartment() Remove the reference to a compartment, i.e., unset the value of the variable 'compartment'.

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, clone, createPlugin, disablePackage, enablePackage, enablePackage, equals, 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, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, readAttribute, 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, writeXMLAttributes

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

Method Detail

getCompartment

java.lang.String getCompartment()

Returns the value of the referenced compartment.

Returns:

the value of the referenced compartment or an empty String if it is not set.

getCompartmentInstance

NamedSBase getCompartmentInstance()

Returns the Compartment that is referenced by this SBase. Note that the return type of this method is NamedSBase because it could be possible that some subclasses link other elements than Compartment.

Returns:

the object in the Model that represents the linked Compartment or null if it does not exist or cannot be retrieved (e.g., if this component has not yet been linked to a Model).

isCompartmentMandatory

boolean isCompartmentMandatory()

Returns:

true if for this object the compartment attribute is mandatory, false otherwise.

isSetCompartment

boolean isSetCompartment()

Returns:

true if compartment attribute is set, i.e., not null, false otherwise.

isSetCompartmentInstance

boolean isSetCompartmentInstance()

Returns:

true if the Compartment which has the compartment identifier stored in this CompartmentalizedSBase as id is not null and this Compartment can be retrieved from the Model that contains this CompartmentalizedSBase. In other words, this method also returns false if the this object is not linked to any model.

setCompartment

boolean setCompartment(Compartment compartment)

Sets the compartment identifiers of this CompartmentalizedSBase to the id of the Compartment 'compartment'.

The compartment attribute is used to add a reference to the id of the corresponding Compartment in the Model. In some situations, the compartment might be optional, so that the user can even specify Compartments that are not part of the Model.

Parameters:

compartment - the Compartment whose identifier should be referenced.

Returns:

true if this operation caused any change.

See Also:

setCompartment(String), isCompartmentMandatory()

setCompartment

boolean setCompartment(java.lang.String compartmentId)

Sets the compartment attribute.

The required attribute compartment is used to identify the Compartment in which the CompartmentalizedSBase is located. The attribute's value should be the identifier of an existing Compartment object in the model.

Parameters:

compartmentId - the identifier of the compartment to be set.

Returns:

true if this operation caused any change.

See Also:

setCompartment(Compartment), isCompartmentMandatory()

unsetCompartment

boolean unsetCompartment()

Remove the reference to a compartment, i.e., unset the value of the variable 'compartment'.

Returns:

true if compartment was set before, otherwise false.