org.sbml.jsbml.ext.layout

Class GraphicalObject

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.layout.GraphicalObject

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, IBoundingBox, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

Direct Known Subclasses:

AbstractReferenceGlyph

public class GraphicalObject
extends AbstractNamedSBase
implements UniqueNamedSBase, IBoundingBox

All the more specific layout elements (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.

Since:

1.0

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger, Clemens Wrzodek

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
GraphicalObject()
GraphicalObject(GraphicalObject graphicalObject)
GraphicalObject(int level, int version)
GraphicalObject(String id)
GraphicalObject(String id, int level, int version)

Method Summary

Modifier and Type	Method and Description
GraphicalObject	clone()
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) Creates and sets a BoundingBox for this object, with the given parameters for Dimensions and Point.
boolean	equals(Object object)
boolean	getAllowsChildren()
BoundingBox	getBoundingBox() Returns the BoundingBox.
TreeNode	getChildAt(int index)
int	getChildCount()
String	getMetaidRef() Returns the value of metaidRef
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory()
boolean	isSetBoundingBox() Returns true is the BoundingBox is set.
boolean	isSetMetaidRef() Returns whether metaidRef is set
boolean	readAttribute(String attributeName, String prefix, String value)
void	setBoundingBox(BoundingBox boundingBox) Sets the BoundingBox.
void	setMetaidRef(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
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, 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, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

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, 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, unsetSBOTerm

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

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

Constructor Detail

GraphicalObject

public GraphicalObject()

GraphicalObject

public GraphicalObject(GraphicalObject graphicalObject)

Parameters:

graphicalObject -

GraphicalObject

public GraphicalObject(int level,
                       int version)

Parameters:

level -

version -

GraphicalObject

public GraphicalObject(String id)

Parameters:

id -

GraphicalObject

public GraphicalObject(String id,
                       int level,
                       int version)

Parameters:

id -

level -

version -

Method Detail

clone

public GraphicalObject clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

createBoundingBox

public BoundingBox createBoundingBox()

Description copied from interface: IBoundingBox

Creates and sets a BoundingBox for this object.

Specified by:

createBoundingBox in interface IBoundingBox

Returns:

BoundingBox.

createBoundingBox

public BoundingBox createBoundingBox(Dimensions dimensions)

Parameters:

dimensions -

Returns:

createBoundingBox

public BoundingBox createBoundingBox(double width,
                                     double height,
                                     double depth)

Creates and sets a BoundingBox for this object, with the given parameters for Dimensions.

Parameters:

width -

height -

depth -

Returns:

BoundingBox.

createBoundingBox

public BoundingBox createBoundingBox(double width,
                                     double height,
                                     double depth,
                                     double x,
                                     double y,
                                     double z)

Creates and sets a BoundingBox for this object, with the given parameters for Dimensions and Point.

Parameters:

width -

height -

depth -

x -

y -

z -

Returns:

BoundingBox.

equals

public boolean equals(Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getBoundingBox

public BoundingBox getBoundingBox()

Description copied from interface: IBoundingBox

Returns the BoundingBox.

Specified by:

getBoundingBox in interface IBoundingBox

Returns:

the BoundingBox.

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSBase

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

isSetBoundingBox

public boolean isSetBoundingBox()

Description copied from interface: IBoundingBox

Returns true is the BoundingBox is set.

Specified by:

isSetBoundingBox in interface IBoundingBox

Returns:

if the BoundingBox is set.

setBoundingBox

public void setBoundingBox(BoundingBox boundingBox)

Description copied from interface: IBoundingBox

Sets the BoundingBox.

Specified by:

setBoundingBox in interface IBoundingBox

Parameters:

boundingBox - the BoundingBox to set.

unsetBoundingBox

public void unsetBoundingBox()

Description copied from interface: IBoundingBox

Unsets the BoundingBox.

Specified by:

unsetBoundingBox in interface IBoundingBox

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

getMetaidRef

public String getMetaidRef()

Returns the value of metaidRef

Returns:

the value of metaidRef

isSetMetaidRef

public boolean isSetMetaidRef()

Returns whether metaidRef is set

Returns:

whether metaidRef is set

setMetaidRef

public void setMetaidRef(String metaidRef)

Sets the value of metaidRef which uniquely references elements in the model.

Parameters:

metaidRef -

unsetMetaidRef

public boolean unsetMetaidRef()

Unsets the variable metaidRef

Returns:

true, if metaidRef was set before, otherwise false

readAttribute

public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase