Package 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, IBoundingBox, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, 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

Author:

Andreas Dräger

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	Description
AbstractReferenceGlyph()	Creates a new instance of AbstractReferenceGlyph.
AbstractReferenceGlyph(int level, int version)	Creates a new instance of AbstractReferenceGlyph.
AbstractReferenceGlyph(java.lang.String id)	Creates a new instance of AbstractReferenceGlyph.
AbstractReferenceGlyph(java.lang.String id, int level, int version)	Creates a new instance of AbstractReferenceGlyph.
AbstractReferenceGlyph(AbstractReferenceGlyph glyph)	Creates a new instance of AbstractReferenceGlyph from the given glyph.

Method Summary

Modifier and Type	Method	Description
abstract AbstractReferenceGlyph	clone()
boolean	equals(java.lang.Object object)
NamedSBase	getNamedSBaseInstance()	Gets the NamedSBase instance corresponding to the reference id.
java.lang.String	getReference()	Gets the reference.
NamedSBase	getReferenceInstance()	Gets the NamedSBase instance corresponding to the reference id.
SBase	getSBaseInstance()	Gets the SBase instance corresponding to the reference id.
int	hashCode()
boolean	isSetReference()	Returns true if the reference attribute is not null and not empty.
void	setNamedSBase(NamedSBase namedSBase)	Sets the reference based on the id of the given NamedSBase.
boolean	setReference(java.lang.String sbase)	Sets the reference.
void	setSBase(SBase sbase)	Sets the reference based on the id of the given SBase.
boolean	unsetReference()	Unsets the reference.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, 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, getIdManager, 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, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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 org.sbml.jsbml.ext.layout.GraphicalObject

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

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Methods inherited from class java.lang.Object

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

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, 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

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

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

Constructor Detail

AbstractReferenceGlyph

public AbstractReferenceGlyph()

Creates a new instance of AbstractReferenceGlyph.

AbstractReferenceGlyph

public AbstractReferenceGlyph(int level,
                              int version)

Creates a new instance of AbstractReferenceGlyph.

Parameters:

level - the SBML level

version - the SBML version

AbstractReferenceGlyph

public AbstractReferenceGlyph(AbstractReferenceGlyph glyph)

Creates a new instance of AbstractReferenceGlyph from the given glyph.

Parameters:

glyph - the glyph to clone.

AbstractReferenceGlyph

public AbstractReferenceGlyph(java.lang.String id)

Creates a new instance of AbstractReferenceGlyph.

Parameters:

id - the id

AbstractReferenceGlyph

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

Creates a new instance of AbstractReferenceGlyph.

Parameters:

id - the id

level - the SBML level

version - the SBML version

Method Detail

clone

public abstract AbstractReferenceGlyph clone()

Specified by:

clone in interface SBase

Overrides:

clone in class GraphicalObject

equals

public boolean equals(java.lang.Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class GraphicalObject

getReference

public java.lang.String getReference()

Gets the reference.

This attribute is used to store all the references from the different glyphs, meaning the 'compartment' for CompartmentGlyph, the 'species' for SpeciesGlyph, the 'reaction' for ReactionGlyph amd the 'reference' for GeneralGlyph.

The optional reference attribute of type SIdRef that can be used to specify the id of the corresponding element in the model that is represented.
If the reference attribute is used together with the metaidRef, they need to refer to the same object in the Model.

Returns:

the reference.

getReferenceInstance

public NamedSBase getReferenceInstance()

Gets the NamedSBase instance corresponding to the reference id.

Careful if you want to support SBML L3V2, you should use getSBaseInstance(). This method might be deprecated in future JSBML releases.

Returns:

the NamedSBase instance corresponding to the reference id.

getSBaseInstance

public SBase getSBaseInstance()

Gets the SBase instance corresponding to the reference id.

Returns:

the SBase instance corresponding to the reference id.

getNamedSBaseInstance

public NamedSBase getNamedSBaseInstance()

Gets the NamedSBase instance corresponding to the reference id.

Careful if you want to support SBML L3V2, you should use getSBaseInstance(). This method might be deprecated in future JSBML releases.

Returns:

the NamedSBase instance corresponding to the reference id.

See Also:

getSBaseInstance()

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class GraphicalObject

isSetReference

public boolean isSetReference()

Returns true if the reference attribute is not null and not empty.

Returns:

true if the reference attribute is set.

setNamedSBase

public void setNamedSBase(NamedSBase namedSBase)

Sets the reference based on the id of the given NamedSBase.

Parameters:

namedSBase - the NamedSBase to set as reference for this glyph.

See Also:

setReference(String)

setSBase

public void setSBase(SBase sbase)

Sets the reference based on the id of the given SBase.

Parameters:

sbase - the SBase to set as reference for this glyph.

See Also:

setReference(String)

setReference

public boolean setReference(java.lang.String sbase)

Sets the reference.

Parameters:

sbase - the id of an SBase.

Returns:

true if this operation caused any change.

unsetReference

public boolean unsetReference()

Unsets the reference. (This method corresponds to setReference(java.lang.String), setNamedSBase(org.sbml.jsbml.NamedSBase) and setSBase(org.sbml.jsbml.SBase))

Returns:

true if this operation caused any change.