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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, UniqueNamedSBase, TreeNodeWithChangeSupport

Direct Known Subclasses:

AbstractReferenceGlyph

public class GraphicalObject
extends AbstractNamedSBase
implements UniqueNamedSBase

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

Version:

$Rev: 1885 $

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger, Clemens Wrzodek

See Also:

Serialized Form

Field Summary

Fields

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.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

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)

Method Summary

Methods

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) Creates and sets a BoundingBox for this object, with the given parameters for Dimensions and Point.
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
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.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

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

Methods inherited from class org.sbml.jsbml.AbstractSBase

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

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, isLeaf, 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, 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

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

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

logger

private static final org.apache.log4j.Logger logger

A Logger for this class.

boundingBox

private BoundingBox boundingBox

metaidRef

private java.lang.String metaidRef

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(java.lang.String id)

Parameters:

id -

GraphicalObject

public GraphicalObject(java.lang.String id,
               int level,
               int version)

Parameters:

id -

level -

version -

Method Detail

clone

public GraphicalObject clone()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

createBoundingBox

public BoundingBox createBoundingBox()

Creates and sets a BoundingBox for this object.

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(java.lang.Object object)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractNamedSBase

Parameters:

object - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getBoundingBox

public BoundingBox getBoundingBox()

Returns:

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractSBase

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractNamedSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: NamedSBase

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.

Specified by:

isIdMandatory in interface NamedSBase

Returns:

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.

isSetBoundingBox

public boolean isSetBoundingBox()

Returns:

setBoundingBox

public void setBoundingBox(BoundingBox boundingBox)

This is the only required element (besides the SId) of the GraphicalObject. Because this class is not an abstract class and can be instantiated, Annotation objects are encouraged to be added.

Parameters:

boundingBox -

unsetBoundingBox

public void unsetBoundingBox()

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this 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.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractNamedSBase

Returns:

a Map containing the XML attributes of this object.

getMetaidRef

public java.lang.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(java.lang.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(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractNamedSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.