org.sbml.jsbml.ext.layout

Class GeneralGlyph

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

org.sbml.jsbml.ext.layout.GeneralGlyph

All Implemented Interfaces:

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

public class GeneralGlyph
extends AbstractReferenceGlyph

The GeneralGlyph is used to facilitate the representation of elements other than Compartment, Species and Reaction and thus can be used for the display of relationships of Rule or elements defined by other SBML packages. It closely follows the structure of the ReactionGlyph. GeneralGlyph is defined to have an optional attribute reference as well as the elements curve, listOfReferenceGlyphs and listOfSubGlyphs.

Since:

1.0

Version:

$Rev$

Author:

Nicolas Rodriguez, Sebastian Frölich, 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 and Description
GeneralGlyph()
GeneralGlyph(GeneralGlyph generalGlyph)
GeneralGlyph(int level, int version)
GeneralGlyph(String id)
GeneralGlyph(String id, int level, int version)

Method Summary

Modifier and Type	Method and Description
boolean	addReferenceGlyph(ReferenceGlyph glyph) Appends the specified element to the end of the listOfReferenceGlyphs.
boolean	addSubGlyph(GraphicalObject subGlyph) Adds a new GraphicalObject to the listOfSubGlyphs.
GeneralGlyph	clone()
CompartmentGlyph	createCompartmentGlyph() Creates a new CompartmentGlyph element and adds it to the ListOfSubGlyphs list
CompartmentGlyph	createCompartmentGlyph(String id) Creates a new CompartmentGlyph element and adds it to the ListOfSubGlyphs list
GeneralGlyph	createGeneralGlyph() Creates a new GeneralGlyph element and adds it to the ListOfSubGlyphs list
GeneralGlyph	createGeneralGlyph(String id) Creates a new GeneralGlyph element and adds it to the ListOfSubGlyphs list
GraphicalObject	createGraphicalObject() Creates a new GraphicalObject element and adds it to the ListOfSubGlyphs list
GraphicalObject	createGraphicalObject(String id) Creates a new GraphicalObject element and adds it to the ListOfSubGlyphs list
ReactionGlyph	createReactionGlyph() Creates a new ReactionGlyph element and adds it to the ListOfSubGlyphs list
ReactionGlyph	createReactionGlyph(String id) Creates a new ReactionGlyph element and adds it to the ListOfSubGlyphs list
ReferenceGlyph	createReferenceGlyph() Creates a new ReferenceGlyph element and adds it to the ListOfSubGlyphs list
ReferenceGlyph	createReferenceGlyph(String id) Creates and adds a new ReferenceGlyph
ReferenceGlyph	createReferenceGlyphForList() Creates a new ReferenceGlyph element and adds it to the ListOfSubGlyphs list
ReferenceGlyph	createReferenceGlyphForList(String id) Creates a new ReferenceGlyph element and adds it to the ListOfSubGlyphs list
SpeciesGlyph	createSpeciesGlyph() Creates a new SpeciesGlyph element and adds it to the ListOfSubGlyphs list
SpeciesGlyph	createSpeciesGlyph(String id) Creates a new SpeciesGlyph element and adds it to the ListOfSubGlyphs list
SpeciesReferenceGlyph	createSpeciesReferenceGlyph() Creates a new SpeciesReferenceGlyph element and adds it to the ListOfSubGlyphs list
SpeciesReferenceGlyph	createSpeciesReferenceGlyph(String id) Creates a new SpeciesReferenceGlyph element and adds it to the ListOfSubGlyphs list
TextGlyph	createTextGlyph() Creates a new TextGlyph element and adds it to the ListOfSubGlyphs list
TextGlyph	createTextGlyph(String id) Creates a new TextGlyph element and adds it to the ListOfSubGlyphs list
boolean	equals(Object object)
TreeNode	getChildAt(int index)
int	getChildCount()
Curve	getCurve()
ListOf<ReferenceGlyph>	getListOfReferenceGlyphs() If the listOfReferenceGlyphs has not yet been initialized, this will be done by this method.
ListOf<GraphicalObject>	getListOfSubGlyphs() Returns the listOfSubGlyphs.
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isSetCurve()
boolean	isSetListOfReferenceGlyphs()
boolean	isSetListOfSubGlyphs() Returns true, if listOfSubGlyphs contains at least one element.
boolean	readAttribute(String attributeName, String prefix, String value)
void	removeGeneralGlyph(GraphicalObject subGlyph)
void	removeGeneralGlyph(int i)
boolean	removeSubGlyph(GraphicalObject subGlyph) Removes an element from the listOfSubGlyphs.
void	removeSubGlyph(int i) Removes an element from the listOfSubGlyphs at the given index.
void	setCurve(Curve curve) This is an optional attribute of type Curve.
void	setListOfReferenceGlyph(ListOf<ReferenceGlyph> listOfReferenceGlyph) The listOfReferenceGlyphs is optional, since conceivable the GeneralGlyph could just contain a number of subglyphs.
void	setListOfSubGlyphs(ListOf<GraphicalObject> listOfSubGlyphs) The listOfSubGlyphs is an optional list that can contain sub-glyphs of the GeneralGlyph.
boolean	unsetListOfSubGlyphs() Returns true, if listOfSubGlyphs contain at least one element, otherwise false
void	unsetReaction()
Map<String,String>	writeXMLAttributes()

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

getNamedSBaseInstance, getReference, getReferenceInstance, isSetReference, setNamedSBase, setReference, unsetReference

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

createBoundingBox, createBoundingBox, createBoundingBox, createBoundingBox, getAllowsChildren, getBoundingBox, getMetaidRef, isIdMandatory, isSetBoundingBox, isSetMetaidRef, setBoundingBox, setMetaidRef, unsetBoundingBox, unsetMetaidRef

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, 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, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, toString, 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

GeneralGlyph

public GeneralGlyph()

GeneralGlyph

public GeneralGlyph(int level,
                    int version)

Parameters:

level -

version -

GeneralGlyph

public GeneralGlyph(GeneralGlyph generalGlyph)

Parameters:

generalGlyph -

GeneralGlyph

public GeneralGlyph(String id)

Parameters:

id -

GeneralGlyph

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

Parameters:

id -

level -

version -

Method Detail

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

Overrides:

initDefaults in class GraphicalObject

isSetListOfSubGlyphs

public boolean isSetListOfSubGlyphs()

Returns true, if listOfSubGlyphs contains at least one element.

Returns:

true, if listOfSubGlyphs contains at least one element, otherwise false

getListOfSubGlyphs

public ListOf<GraphicalObject> getListOfSubGlyphs()

Returns the listOfSubGlyphs. Creates it if it is not already existing.

Returns:

the listOfSubGlyphs

setListOfSubGlyphs

public void setListOfSubGlyphs(ListOf<GraphicalObject> listOfSubGlyphs)

The listOfSubGlyphs is an optional list that can contain sub-glyphs of the GeneralGlyph. One example of its use could be a sub-module containing SpeciesGlyphs and ReactionGlyphs that are not necessarily part of the enclosing Model. Another example is an Event, visualized with its Trigger and additional GeneralGlyphs for its EventAssignment. The listOfSubGlyphs consists of GraphicalObjects or derived classes. Thus, unlike the listOfAdditionalGraphicalObjects (which may only contain GraphicalObject or GeneralGlyphs), the listOfSubGlyphs may contain any derived class, such as for example TextGlyph elements. Sets the given ListOf<GraphicalObject>. If listOfSubGlyphs was defined before and contains some elements, they are all unset.

Parameters:

listOfSubGlyphs -

unsetListOfSubGlyphs

public boolean unsetListOfSubGlyphs()

Returns true, if listOfSubGlyphs contain at least one element, otherwise false

Returns:

true, if listOfSubGlyphs contain at least one element, otherwise false

addSubGlyph

public boolean addSubGlyph(GraphicalObject subGlyph)

Adds a new GraphicalObject to the listOfSubGlyphs.

The listOfSubGlyphs is initialized if necessary.

Parameters:

subGlyph - the element to add to the list

Returns:

true (as specified by Collection#add)

removeSubGlyph

public boolean removeSubGlyph(GraphicalObject subGlyph)

Removes an element from the listOfSubGlyphs.

Parameters:

subGlyph - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List#remove(Object)

removeSubGlyph

public void removeSubGlyph(int i)

Removes an element from the listOfSubGlyphs at the given index.

Parameters:

i - the index where to remove the GraphicalObject

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size)

removeGeneralGlyph

public void removeGeneralGlyph(int i)

Parameters:

i -

removeGeneralGlyph

public void removeGeneralGlyph(GraphicalObject subGlyph)

Parameters:

subGlyph -

createReferenceGlyph

public ReferenceGlyph createReferenceGlyph()

Creates a new ReferenceGlyph element and adds it to the ListOfSubGlyphs list

Returns:

createTextGlyph

public TextGlyph createTextGlyph()

Creates a new TextGlyph element and adds it to the ListOfSubGlyphs list

Returns:

createTextGlyph

public TextGlyph createTextGlyph(String id)

Creates a new TextGlyph element and adds it to the ListOfSubGlyphs list

Parameters:

id -

Returns:

a new TextGlyph element

createReferenceGlyphForList

public ReferenceGlyph createReferenceGlyphForList()

Creates a new ReferenceGlyph element and adds it to the ListOfSubGlyphs list

Returns:

createReferenceGlyphForList

public ReferenceGlyph createReferenceGlyphForList(String id)

Creates a new ReferenceGlyph element and adds it to the ListOfSubGlyphs list

Parameters:

id -

Returns:

a new ReferenceGlyph element

createSpeciesGlyph

public SpeciesGlyph createSpeciesGlyph()

Creates a new SpeciesGlyph element and adds it to the ListOfSubGlyphs list

Returns:

createSpeciesGlyph

public SpeciesGlyph createSpeciesGlyph(String id)

Creates a new SpeciesGlyph element and adds it to the ListOfSubGlyphs list

Parameters:

id -

Returns:

a new SpeciesGlyph element

createSpeciesReferenceGlyph

public SpeciesReferenceGlyph createSpeciesReferenceGlyph()

Creates a new SpeciesReferenceGlyph element and adds it to the ListOfSubGlyphs list

Returns:

createSpeciesReferenceGlyph

public SpeciesReferenceGlyph createSpeciesReferenceGlyph(String id)

Creates a new SpeciesReferenceGlyph element and adds it to the ListOfSubGlyphs list

Parameters:

id -

Returns:

a new SpeciesReferenceGlyph element

createCompartmentGlyph

public CompartmentGlyph createCompartmentGlyph()

Creates a new CompartmentGlyph element and adds it to the ListOfSubGlyphs list

Returns:

createCompartmentGlyph

public CompartmentGlyph createCompartmentGlyph(String id)

Creates a new CompartmentGlyph element and adds it to the ListOfSubGlyphs list

Parameters:

id -

Returns:

a new CompartmentGlyph element

createGeneralGlyph

public GeneralGlyph createGeneralGlyph()

Creates a new GeneralGlyph element and adds it to the ListOfSubGlyphs list

Returns:

createGeneralGlyph

public GeneralGlyph createGeneralGlyph(String id)

Creates a new GeneralGlyph element and adds it to the ListOfSubGlyphs list

Parameters:

id -

Returns:

a new GeneralGlyph element

createReactionGlyph

public ReactionGlyph createReactionGlyph()

Creates a new ReactionGlyph element and adds it to the ListOfSubGlyphs list

Returns:

createReactionGlyph

public ReactionGlyph createReactionGlyph(String id)

Creates a new ReactionGlyph element and adds it to the ListOfSubGlyphs list

Parameters:

id -

Returns:

a new ReactionGlyph element

createGraphicalObject

public GraphicalObject createGraphicalObject()

Creates a new GraphicalObject element and adds it to the ListOfSubGlyphs list

Returns:

createGraphicalObject

public GraphicalObject createGraphicalObject(String id)

Creates a new GraphicalObject element and adds it to the ListOfSubGlyphs list

Parameters:

id -

Returns:

a new GraphicalObject element

addReferenceGlyph

public boolean addReferenceGlyph(ReferenceGlyph glyph)

Appends the specified element to the end of the listOfReferenceGlyphs.

Parameters:

glyph -

Returns:

true (as specified by Collection#add)

Throws:

NullPointerException - if the specified element is null and this list does not permit null elements

IllegalArgumentException - if some property of this element prevents it from being added to this list

clone

public GeneralGlyph clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractReferenceGlyph

createReferenceGlyph

public ReferenceGlyph createReferenceGlyph(String id)

Creates and adds a new ReferenceGlyph

Parameters:

id - the identifier for the ReferenceGlyph to be created.

Returns:

a new ReferenceGlyph.

equals

public boolean equals(Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractReferenceGlyph

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class GraphicalObject

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class GraphicalObject

getCurve

public Curve getCurve()

Returns:

getListOfReferenceGlyphs

public ListOf<ReferenceGlyph> getListOfReferenceGlyphs()

If the listOfReferenceGlyphs has not yet been initialized, this will be done by this method.

Returns:

the listOfReferenceGlyphs

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractReferenceGlyph

isSetCurve

public boolean isSetCurve()

Returns:

isSetListOfReferenceGlyphs

public boolean isSetListOfReferenceGlyphs()

Returns:

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class GraphicalObject

setCurve

public void setCurve(Curve curve)

This is an optional attribute of type Curve. If this is defined, then the BoundingBox is to be ignored.

Parameters:

curve -

setListOfReferenceGlyph

public void setListOfReferenceGlyph(ListOf<ReferenceGlyph> listOfReferenceGlyph)

The listOfReferenceGlyphs is optional, since conceivable the GeneralGlyph could just contain a number of subglyphs. When present, it must include at least one ReferenceGlyph.

Parameters:

listOfReferenceGlyph -

unsetReaction

public void unsetReaction()

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class GraphicalObject