org.sbml.jsbml.ext.layout
public class CompartmentGlyph extends AbstractReferenceGlyph implements CompartmentalizedSBase
CompartmentGlyph class is derived from GraphicalObject
and inherits its attributes. Additionally it has tow optional attributes:
compartment and order.UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS| Constructor and Description |
|---|
CompartmentGlyph() |
CompartmentGlyph(CompartmentGlyph compartmentGlyph) |
CompartmentGlyph(int level,
int version) |
CompartmentGlyph(String id) |
CompartmentGlyph(String id,
int level,
int version) |
| Modifier and Type | Method and Description |
|---|---|
CompartmentGlyph |
clone()
Creates a deep copy of this object, i.e., a new
SBase with the same
properties
like this one. |
String |
getCompartment()
Returns the value of the referenced compartment.
|
NamedSBase |
getCompartmentInstance()
Returns the
Compartment that is referenced by this SBase. |
double |
getOrder()
Returns the value of order
|
void |
initDefaults()
Initializes the default values using the namespace.
|
boolean |
isCompartmentMandatory() |
boolean |
isSetCompartment() |
boolean |
isSetCompartmentInstance() |
boolean |
isSetOrder()
Returns whether order is set
|
boolean |
readAttribute(String attributeName,
String prefix,
String value)
Sets the given attribute in this
SBase. |
boolean |
setCompartment(Compartment compartment)
Sets the compartment identifiers of this
CompartmentalizedSBase to
the id of the Compartment 'compartment'. |
boolean |
setCompartment(String compartment)
Sets the compartment attribute.
|
void |
setOrder(double order)
The order attribute is an optional attribute of type
Double. |
boolean |
unsetCompartment()
Remove the reference to a compartment, i.e., unset the value of the
variable 'compartment'.
|
boolean |
unsetOrder()
Unsets the variable order
|
Map<String,String> |
writeXMLAttributes()
Returns a map with all the attributes of this
SBase that
need to be written out in XML. |
equals, getNamedSBaseInstance, getReference, getReferenceInstance, hashCode, isSetReference, setNamedSBase, setReference, toString, unsetReferencecreateBoundingBox, createBoundingBox, createBoundingBox, createBoundingBox, getAllowsChildren, getBoundingBox, getChildAt, getChildCount, getMetaidRef, isIdMandatory, isSetBoundingBox, isSetMetaidRef, setBoundingBox, setMetaidRef, unsetBoundingBox, unsetMetaidRefgetId, getName, isSetId, isSetName, isValidId, setId, setName, unsetId, unsetNameaddCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, 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, isValidLevelAndVersionCombination, isValidMetaId, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTermaddAllChangeListeners, 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, userObjectKeySetgetId, getName, isIdMandatory, isSetId, isSetName, setId, setName, unsetId, unsetNameaddCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, equals, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, 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, 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, unsetSBOTermaddAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySetchildren, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeafpublic CompartmentGlyph()
public CompartmentGlyph(CompartmentGlyph compartmentGlyph)
compartmentGlyph - public CompartmentGlyph(int level,
int version)
level - version - public CompartmentGlyph(String id)
id - public CompartmentGlyph(String id, int level, int version)
id - level - version - public CompartmentGlyph clone()
SBaseSBase with the same
properties
like this one.clone in interface SBaseclone in class AbstractReferenceGlyphpublic void initDefaults()
initDefaults in class GraphicalObjectpublic String getCompartment()
CompartmentalizedSBasegetCompartment in interface CompartmentalizedSBaseString
if it is not set.public NamedSBase getCompartmentInstance()
CompartmentalizedSBaseCompartment 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 CompartmentalizedSBaseModel 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 double getOrder()
public boolean isCompartmentMandatory()
isCompartmentMandatory in interface CompartmentalizedSBasetrue if for this object the compartment attribute is
mandatory, false otherwise.public boolean isSetCompartment()
isSetCompartment in interface CompartmentalizedSBasetrue if compartment attribute is set, i.e., not
null, false otherwise.public boolean isSetCompartmentInstance()
isSetCompartmentInstance in interface CompartmentalizedSBasetrue 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 isSetOrder()
public boolean readAttribute(String attributeName, String prefix, String value)
SBaseSBase.
If the given attribute name is not recognized, nothing is done and
false is returned.
readAttribute in interface SBasereadAttribute in class GraphicalObjectattributeName - 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)
CompartmentalizedSBaseCompartmentalizedSBase 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.
setCompartment in interface CompartmentalizedSBasecompartment - the Compartment whose identifier should be referenced.true if this operation caused any change.CompartmentalizedSBase.setCompartment(String),
CompartmentalizedSBase.isCompartmentMandatory()public boolean setCompartment(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 CompartmentalizedSBasecompartment - the identifier of the compartment to be set.true if this operation caused any change.CompartmentalizedSBase.setCompartment(Compartment),
CompartmentalizedSBase.isCompartmentMandatory()public void setOrder(double order)
Double. It is there
to handle the case where compartments in a layout overlap, and tools want to
clearly disambiguate which CompartmentGlyph is on top of the other.
The order attribute follows the coordinate system. There are z dimension points
into a screen; thus, an element with a lower order value will be in front
of an elements with a higher value. If not specified, the order is undefined
and tools are free to display the compartment glyphs in the order that best fits their
needs.
Note: if z coordinates are used (and this order is seemingly redundant), the order
can still be used to disambiguate drawing order.order - public boolean unsetCompartment()
CompartmentalizedSBaseunsetCompartment in interface CompartmentalizedSBasetrue if compartment was set before, otherwise false.public boolean unsetOrder()
true, if order was set before,
otherwise falsepublic Map<String,String> writeXMLAttributes()
SBaseSBase 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 SBasewriteXMLAttributes in class GraphicalObjectMap containing the XML attributes of this object.