org.sbml.jsbml.ext.layout
public class GraphicalObject extends AbstractNamedSBase implements UniqueNamedSBase
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.Modifier and Type | Field and Description |
---|---|
private BoundingBox |
boundingBox |
private static org.apache.log4j.Logger |
logger
A
Logger for this class. |
private java.lang.String |
metaidRef |
private static long |
serialVersionUID
Generated serial version identifier.
|
ignoredExtensions, ignoredXMLElements
listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS
Constructor and Description |
---|
GraphicalObject() |
GraphicalObject(GraphicalObject graphicalObject) |
GraphicalObject(int level,
int version) |
GraphicalObject(java.lang.String id) |
GraphicalObject(java.lang.String id,
int level,
int version) |
Modifier and Type | Method and 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(Dimensions dimensions) |
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)
|
boolean |
equals(java.lang.Object object)
|
boolean |
getAllowsChildren() |
BoundingBox |
getBoundingBox() |
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. |
boolean |
isIdMandatory()
This method can be used to query if the identifier of this
NamedSBase is required to be defined (i.e., not null )
in the definition of SBML. |
boolean |
isSetBoundingBox() |
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)
This is the only required element (besides the SId) of the
GraphicalObject . |
void |
setMetaidRef(java.lang.String metaidRef)
Sets the value of metaidRef which uniquely references elements in the model.
|
void |
unsetBoundingBox() |
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. |
getId, getName, isSetId, isSetName, isValidId, setId, setName, toString, unsetId, unsetName
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, 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
finalize, getClass, notify, notifyAll, wait, wait, wait
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, 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
private static final long serialVersionUID
private static final org.apache.log4j.Logger logger
Logger
for this class.private BoundingBox boundingBox
private java.lang.String metaidRef
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 BoundingBox createBoundingBox()
BoundingBox
for this object.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()
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 AbstractNamedSBase
SBase
instance.Object.hashCode()
public boolean isIdMandatory()
NamedSBase
NamedSBase
is required to be defined (i.e., not null
)
in the definition of SBML.isIdMandatory
in interface NamedSBase
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()
public void setBoundingBox(BoundingBox boundingBox)
GraphicalObject
. Because
this class is not an abstract class and can be instantiated, Annotation
objects are
encouraged to be added.boundingBox
- public void unsetBoundingBox()
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 AbstractNamedSBase
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 AbstractNamedSBase
attributeName
- localName of the XML attributeprefix
- prefix of the XML attributevalue
- value of the XML attributetrue
if the attribute has been successfully read.