org.sbml.jsbml.ext.layout

Class AbstractReferenceGlyph

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.layout.GraphicalObject

org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

All Implemented Interfaces:

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

Direct Known Subclasses:

CompartmentGlyph, GeneralGlyph, ReactionGlyph, ReferenceGlyph, SpeciesGlyph, SpeciesReferenceGlyph, TextGlyph

public abstract class AbstractReferenceGlyph
extends GraphicalObject

Abstract super class for all kinds of glyphs that graphically represent an instance of NamedSBase.

Since:

1.0

Version:

$Rev: 1445 $

Author:

Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	reference The identifier of the NamedSBase represented by this GraphicalObject.
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
AbstractReferenceGlyph()
AbstractReferenceGlyph(AbstractReferenceGlyph glyph)
AbstractReferenceGlyph(int level, int version)
AbstractReferenceGlyph(java.lang.String id)
AbstractReferenceGlyph(java.lang.String id, int level, int version)

Method Summary

Methods

Modifier and Type	Method and Description
abstract AbstractReferenceGlyph	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
NamedSBase	getNamedSBaseInstance()
java.lang.String	getReference()
NamedSBase	getReferenceInstance()
int	hashCode() Returns a hash code value for this SBase instance.
boolean	isSetReference()
void	setNamedSBase(NamedSBase namedSBase)
void	setReference(java.lang.String sbase)
(package private) void	setReference(java.lang.String sbase, java.lang.String type) Sets the reference object to which the id sbase refers to.
java.lang.String	toString() Returns the name of the component, if it is available.
void	unsetReference()

Methods inherited from class org.sbml.jsbml.ext.layout.GraphicalObject

createBoundingBox, createBoundingBox, createBoundingBox, createBoundingBox, getAllowsChildren, getBoundingBox, getChildAt, getChildCount, getMetaidRef, isIdMandatory, isSetBoundingBox, isSetMetaidRef, readAttribute, setBoundingBox, setMetaidRef, unsetBoundingBox, unsetMetaidRef, writeXMLAttributes

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

getId, getName, isSetId, isSetName, isValidId, setId, setName, 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

reference

private java.lang.String reference

The identifier of the NamedSBase represented by this GraphicalObject.

Constructor Detail

AbstractReferenceGlyph

public AbstractReferenceGlyph()

AbstractReferenceGlyph

public AbstractReferenceGlyph(int level,
                      int version)

Parameters:

level -

version -

AbstractReferenceGlyph

public AbstractReferenceGlyph(AbstractReferenceGlyph glyph)

Parameters:

glyp -

AbstractReferenceGlyph

public AbstractReferenceGlyph(java.lang.String id)

Parameters:

id -

AbstractReferenceGlyph

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

Parameters:

id -

level -

version -

Method Detail

clone

public abstract AbstractReferenceGlyph 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

Overrides:

clone in class GraphicalObject

Returns:

a copy of this object

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 GraphicalObject

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.

getReference

public java.lang.String getReference()

Returns:

getReferenceInstance

public NamedSBase getReferenceInstance()

Returns:

getNamedSBaseInstance

public NamedSBase getNamedSBaseInstance()

Returns:

See Also:

getReferenceInstance()

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 GraphicalObject

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isSetReference

public boolean isSetReference()

Returns:

setNamedSBase

public void setNamedSBase(NamedSBase namedSBase)

Parameters:

namedSBase -

setReference

public void setReference(java.lang.String sbase)

Parameters:

sbase -

setReference

void setReference(java.lang.String sbase,
                java.lang.String type)

Sets the reference object to which the id sbase refers to. The type defines the category that changed for the TreeNodeChangeEvent.

Parameters:

sbase -

type -

toString

public java.lang.String toString()

Description copied from class: AbstractNamedSBase

Returns the name of the component, if it is available. Otherwise, the identifier is returned. If both is not possible, the class name of this element is returned.

Overrides:

toString in class AbstractNamedSBase

unsetReference

public void unsetReference()