Package 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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.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

JSBML_WRONG_SBO_TERM

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
CompartmentReference	clone()	Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	equals(java.lang.Object obj)	Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
java.lang.String	getCompartment()	Returns the value of the referenced compartment.
Compartment	getCompartmentInstance()	Returns the Compartment that is referenced by this SBase.
int	hashCode()	Returns a hash code value for this SBase instance.
void	initDefaults()	Initializes the default values using the namespace.
boolean	isCompartmentMandatory()
boolean	isIdMandatory()	Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isSetCompartment()	Returns whether compartment is set.
boolean	isSetCompartmentInstance()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)	Sets the given attribute in this SBase.
boolean	setCompartment(java.lang.String compartment)	Sets the compartment attribute.
boolean	setCompartment(Compartment compartment)	Sets the compartment identifiers of this CompartmentalizedSBase to the id of the Compartment 'compartment'.
boolean	unsetCompartment()	Remove the reference to a compartment, i.e., unset the value of the variable 'compartment'.
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()	Returns a map with all the attributes of this SBase that need to be written out in XML.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, 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, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, 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, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

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, hasExtension, 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 javax.swing.tree.TreeNode

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

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

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(java.lang.String id)

Creates a CompartmentReference instance with an id.

Parameters:

id - the identifier for the new element.

CompartmentReference

public CompartmentReference(java.lang.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(java.lang.String id,
                            java.lang.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()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

getCompartment

public java.lang.String getCompartment()

Description copied from interface: CompartmentalizedSBase

Returns the value of the referenced compartment.

Specified by:

getCompartment in interface CompartmentalizedSBase

Returns:

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

getCompartmentInstance

public Compartment getCompartmentInstance()

Description copied from interface: CompartmentalizedSBase

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.

Specified by:

getCompartmentInstance in interface CompartmentalizedSBase

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).

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

isCompartmentMandatory

public boolean isCompartmentMandatory()

Specified by:

isCompartmentMandatory in interface CompartmentalizedSBase

Returns:

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

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: SBase

Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

Returns:

true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.

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

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.

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                             java.lang.String prefix,
                             java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

setCompartment

public boolean setCompartment(Compartment compartment)

Description copied from interface: CompartmentalizedSBase

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.

Specified by:

setCompartment in interface CompartmentalizedSBase

Parameters:

compartment - the Compartment whose identifier should be referenced.

Returns:

true if this operation caused any change.

See Also:

CompartmentalizedSBase.setCompartment(String), CompartmentalizedSBase.isCompartmentMandatory()

setCompartment

public boolean setCompartment(java.lang.String compartment)

Description copied from interface: CompartmentalizedSBase

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.

Specified by:

setCompartment in interface CompartmentalizedSBase

Parameters:

compartment - the identifier of the compartment to be set.

Returns:

true if this operation caused any change.

See Also:

CompartmentalizedSBase.setCompartment(Compartment), CompartmentalizedSBase.isCompartmentMandatory()

unsetCompartment

public boolean unsetCompartment()

Description copied from interface: CompartmentalizedSBase

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

Specified by:

unsetCompartment in interface CompartmentalizedSBase

Returns:

true if compartment was set before, otherwise false.

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this SBase that need to be written out in XML.

The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

Returns:

a Map containing the XML attributes of this object.

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

equals

public boolean equals(java.lang.Object obj)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

Parameters:

obj - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.