java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, IBoundingBox
, NamedSBase
, SBase
, UniqueNamedSBase
, UniqueSId
, TreeNodeWithChangeSupport
AbstractReferenceGlyph
public class GraphicalObject extends AbstractNamedSBase implements UniqueNamedSBase, IBoundingBox
CompartmentGlyph
, GeneralGlyph
,
SpeciesGlyph
, ReactionGlyph
, ReferenceGlyph
, TextGlyph
,
and SpeciesReferenceGlyph
) are derived from the class GraphicalObject
.
Each object of class GraphicalObject
has a mandatory BoundingBox
, which
specifies the position and the size of the object. While GraphicalObject
is the
base class for most elements in the Layout
package, it is not an abstract class.
It can be instantiated when used in the listOfAdditionalGraphicalObjects to describe
additional elements and relationships. Since it only describes a BoundingBox
,
programs are encouraged to add Annotation
objects that describe program-specific
graphical information.JSBML_WRONG_SBO_TERM
Constructor | Description |
---|---|
GraphicalObject() |
|
GraphicalObject(int level,
int version) |
|
GraphicalObject(java.lang.String id) |
|
GraphicalObject(java.lang.String id,
int level,
int version) |
|
GraphicalObject(GraphicalObject graphicalObject) |
Modifier and Type | Method | Description |
---|---|---|
GraphicalObject |
clone() |
Creates a deep copy of this object, i.e., a new
SBase with the same
properties
like this one. |
BoundingBox |
createBoundingBox() |
Creates and sets a
BoundingBox for this object. |
BoundingBox |
createBoundingBox(double width,
double height,
double depth) |
Creates and sets a
BoundingBox for this object, with the
given parameters for Dimensions . |
BoundingBox |
createBoundingBox(double width,
double height,
double depth,
double x,
double y,
double z) |
|
BoundingBox |
createBoundingBox(Dimensions dimensions) |
|
boolean |
equals(java.lang.Object object) |
|
boolean |
getAllowsChildren() |
|
BoundingBox |
getBoundingBox() |
Returns the
BoundingBox . |
javax.swing.tree.TreeNode |
getChildAt(int index) |
|
int |
getChildCount() |
|
java.lang.String |
getMetaidRef() |
Returns the value of metaidRef
|
int |
hashCode() |
Returns a hash code value for this
SBase instance. |
void |
initDefaults() |
Initializes the default values using the namespace.
|
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 |
isSetBoundingBox() |
Returns
true is the BoundingBox is set. |
boolean |
isSetMetaidRef() |
Returns whether metaidRef is set
|
boolean |
readAttribute(java.lang.String attributeName,
java.lang.String prefix,
java.lang.String value) |
Sets the given attribute in this
SBase . |
void |
setBoundingBox(BoundingBox boundingBox) |
Sets the
BoundingBox . |
void |
setMetaidRef(java.lang.String metaidRef) |
Sets the value of metaidRef which uniquely references elements in the model.
|
void |
unsetBoundingBox() |
Unsets the
BoundingBox . |
boolean |
unsetMetaidRef() |
Unsets the variable metaidRef
|
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, getAnnotation, getAnnotationString, 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
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 GraphicalObject()
public GraphicalObject(GraphicalObject graphicalObject)
graphicalObject
- public GraphicalObject(int level, int version)
level
- version
- public GraphicalObject(java.lang.String id)
id
- public GraphicalObject(java.lang.String id, int level, int version)
id
- level
- version
- public GraphicalObject clone()
SBase
SBase
with the same
properties
like this one.clone
in interface SBase
clone
in class AbstractSBase
public void initDefaults()
public BoundingBox createBoundingBox()
IBoundingBox
BoundingBox
for this object.createBoundingBox
in interface IBoundingBox
BoundingBox
.public BoundingBox createBoundingBox(Dimensions dimensions)
dimensions
- public BoundingBox createBoundingBox(double width, double height, double depth)
BoundingBox
for this object, with the
given parameters for Dimensions
.width
- height
- depth
- BoundingBox
.public BoundingBox createBoundingBox(double width, double height, double depth, double x, double y, double z)
width
- height
- depth
- x
- y
- z
- BoundingBox
.public boolean equals(java.lang.Object object)
SBase
public boolean getAllowsChildren()
getAllowsChildren
in interface javax.swing.tree.TreeNode
getAllowsChildren
in class AbstractSBase
public BoundingBox getBoundingBox()
IBoundingBox
BoundingBox
.getBoundingBox
in interface IBoundingBox
BoundingBox
.public javax.swing.tree.TreeNode getChildAt(int index)
getChildAt
in interface javax.swing.tree.TreeNode
getChildAt
in class AbstractSBase
public int getChildCount()
getChildCount
in interface javax.swing.tree.TreeNode
getChildCount
in class AbstractSBase
public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractSBase
SBase
instance.Object.hashCode()
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 isSetBoundingBox()
IBoundingBox
true
is the BoundingBox
is set.isSetBoundingBox
in interface IBoundingBox
BoundingBox
is set.public void setBoundingBox(BoundingBox boundingBox)
IBoundingBox
BoundingBox
.setBoundingBox
in interface IBoundingBox
boundingBox
- the BoundingBox
to set.public void unsetBoundingBox()
IBoundingBox
BoundingBox
.unsetBoundingBox
in interface IBoundingBox
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 java.lang.String getMetaidRef()
public boolean isSetMetaidRef()
public void setMetaidRef(java.lang.String metaidRef)
metaidRef
- public boolean unsetMetaidRef()
true
, if metaidRef was set before,
otherwise false
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.