java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, CompartmentalizedSBase
, NamedSBase
, SBase
, UniqueNamedSBase
, UniqueSId
, TreeNodeWithChangeSupport
public class CompartmentReference extends AbstractNamedSBase implements CompartmentalizedSBase, UniqueNamedSBase
JSBML_WRONG_SBO_TERM
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. |
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) |
|
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. |
isValidId
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
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
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName
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
children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf
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
public CompartmentReference()
CompartmentReference
instance.public CompartmentReference(CompartmentReference obj)
CompartmentReference
instance, cloned from the given object.obj
- the CompartmentReference
to clonepublic CompartmentReference(int level, int version)
level
- SBML Levelversion
- SBML Versionpublic CompartmentReference(java.lang.String id)
id
- the identifier for the new element.public CompartmentReference(java.lang.String id, int level, int version)
id
- the identifier for this element.level
- the SBML Levelversion
- the SBML Versionpublic CompartmentReference(java.lang.String id, java.lang.String name, int level, int version)
id
- the identifier for this element.name
- a human-readable name for this element that can be used for display purposes.level
- the SBML Levelversion
- the SBML Versionpublic CompartmentReference clone()
SBase
SBase
with the same
properties
like this one.clone
in interface SBase
clone
in class AbstractSBase
public java.lang.String getCompartment()
CompartmentalizedSBase
getCompartment
in interface CompartmentalizedSBase
String
if it is not set.public Compartment getCompartmentInstance()
CompartmentalizedSBase
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
.getCompartmentInstance
in interface CompartmentalizedSBase
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
).public void initDefaults()
public boolean isCompartmentMandatory()
isCompartmentMandatory
in interface CompartmentalizedSBase
true
if for this object the compartment attribute is
mandatory, false
otherwise.public boolean isIdMandatory()
SBase
true
if the identifier of this
SBase
is required to be defined (i.e., not null
)
in the definition of SBML.isIdMandatory
in interface NamedSBase
isIdMandatory
in interface SBase
isIdMandatory
in class AbstractSBase
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.public boolean isSetCompartment()
compartment
is set.isSetCompartment
in interface CompartmentalizedSBase
compartment
is set.public boolean isSetCompartmentInstance()
isSetCompartmentInstance
in interface CompartmentalizedSBase
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.public boolean readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
SBase
SBase
.
If the given attribute name is not recognized, nothing is done and
false
is returned.
readAttribute
in interface SBase
readAttribute
in class AbstractSBase
attributeName
- localName of the XML attributeprefix
- prefix of the XML attributevalue
- value of the XML attributetrue
if the attribute has been successfully read.public boolean setCompartment(Compartment compartment)
CompartmentalizedSBase
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 Compartment
s that are not part of the Model
.
setCompartment
in interface CompartmentalizedSBase
compartment
- the Compartment
whose identifier should be referenced.true
if this operation caused any change.CompartmentalizedSBase.setCompartment(String)
,
CompartmentalizedSBase.isCompartmentMandatory()
public boolean setCompartment(java.lang.String compartment)
CompartmentalizedSBase
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.
setCompartment
in interface CompartmentalizedSBase
compartment
- the identifier of the compartment to be set.true
if this operation caused any change.CompartmentalizedSBase.setCompartment(Compartment)
,
CompartmentalizedSBase.isCompartmentMandatory()
public boolean unsetCompartment()
CompartmentalizedSBase
unsetCompartment
in interface CompartmentalizedSBase
true
if compartment was set before, otherwise false
.public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
SBase
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.
writeXMLAttributes
in interface SBase
writeXMLAttributes
in class AbstractSBase
Map
containing the XML attributes of this object.public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractSBase
SBase
instance.Object.hashCode()
public boolean equals(java.lang.Object obj)
SBase