Package org.sbml.jsbml.ext.layout

Class ReferenceGlyph

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.ReferenceGlyph

All Implemented Interfaces:

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

public class ReferenceGlyph
extends AbstractReferenceGlyph

The ReferenceGlyph element describes the graphical connection between an arbitrary GraphicalObject (or derived element) and a GeneralGlyph (which would be an arrow or some curve in most cases). A ReferenceGlyph inherits from GraphicalObject. Additionally, it has a mandatory attribute 'glyph' and two optional attributes 'reference' and 'role'. Optionally, the ReferenceGlyph also has an element 'curve'. The ReferenceGlyph should either contain a bounding box or a curve specification. If both are given, the bounding box should be ignored.

Since:

1.0

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger, David Vetter

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
ReferenceGlyph()
ReferenceGlyph(int level, int version)
ReferenceGlyph(java.lang.String id)
ReferenceGlyph(java.lang.String id, int level, int version)
ReferenceGlyph(ReferenceGlyph speciesReferenceGlyph)

Method Summary

Modifier and Type	Method	Description
ReferenceGlyph	clone()
Curve	createCurve()
boolean	equals(java.lang.Object object)
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
Curve	getCurve()
java.lang.String	getGlyph()
java.lang.String	getRole()
int	hashCode()
void	initDefaults()	Initializes the default values using the namespace.
boolean	isSetCurve()
boolean	isSetGlyph()
boolean	isSetReferenceInstance()
boolean	isSetRole()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
void	setCurve(Curve curve)	The curve is an optional element of type Curve.
void	setGlyph(java.lang.String glyph)	It contains a reference to the id of a GraphicalObject (or derived) object that is to be connected to the GeneralGlyph.
boolean	setReference(java.lang.String reference)	The reference is an optional attribute that is used to connect the ReferenceGlyph with an element of the containing Model.
void	setRole(java.lang.String role)	The role attribute is used to specify how the reference should be displayed.
boolean	unsetCurve()
void	unsetGlyph()	Unsets the glyph attribute
void	unsetRole()	Unsets the role attribute
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

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

getNamedSBaseInstance, getReference, getReferenceInstance, getSBaseInstance, isSetReference, setNamedSBase, setSBase, unsetReference

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, getMetaidRef, isIdMandatory, isSetBoundingBox, isSetMetaidRef, setBoundingBox, setMetaidRef, unsetBoundingBox, unsetMetaidRef

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

ReferenceGlyph

public ReferenceGlyph()

ReferenceGlyph

public ReferenceGlyph(int level,
                      int version)

Parameters:

level -

version -

ReferenceGlyph

public ReferenceGlyph(ReferenceGlyph speciesReferenceGlyph)

Parameters:

speciesReferenceGlyph -

ReferenceGlyph

public ReferenceGlyph(java.lang.String id)

Parameters:

id -

ReferenceGlyph

public ReferenceGlyph(java.lang.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

clone

public ReferenceGlyph clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractReferenceGlyph

createCurve

public Curve createCurve()

Returns:

equals

public boolean equals(java.lang.Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractReferenceGlyph

getChildAt

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

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class GraphicalObject

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class GraphicalObject

getCurve

public Curve getCurve()

Returns:

getGlyph

public java.lang.String getGlyph()

Returns:

getRole

public java.lang.String getRole()

Returns:

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractReferenceGlyph

isSetCurve

public boolean isSetCurve()

Returns:

isSetGlyph

public boolean isSetGlyph()

Returns:

isSetRole

public boolean isSetRole()

Returns:

isSetReferenceInstance

public boolean isSetReferenceInstance()

Returns:

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class GraphicalObject

setCurve

public void setCurve(Curve curve)

The curve is an optional element of type Curve. When present, the glyph’s BoundingBox (as inherited from the GraphicalObject) is to be disregarded. So as to make the drawing of these curves as easy as possible the line segments should be ordered depending on the role of the ReferenceGlyph. If the glyph represents a modification it should start at the glyph and end at the center of the GeneralGlyph. Otherwise it should begin at the center section of the GeneralGlyph and end at the reference glyph.

Parameters:

curve -

setRole

public void setRole(java.lang.String role)

The role attribute is used to specify how the reference should be displayed. While as a string, the value of the role attribute is unconstrained, current implementations use the same values as defined in SpeciesReferenceRole.

Parameters:

role -

setGlyph

public void setGlyph(java.lang.String glyph)

It contains a reference to the id of a GraphicalObject (or derived) object that is to be connected to the GeneralGlyph. This attribute is mandatory so as to ensure unambiguously which glyph has to be connected with this GeneralGlyph.

Parameters:

glyph -

setReference

public boolean setReference(java.lang.String reference)

The reference is an optional attribute that is used to connect the ReferenceGlyph with an element of the containing Model.

Overrides:

setReference in class AbstractReferenceGlyph

Parameters:

reference -

Returns:

true if this operation caused any change.

unsetCurve

public boolean unsetCurve()

Returns:

unsetGlyph

public void unsetGlyph()

Unsets the glyph attribute

unsetRole

public void unsetRole()

Unsets the role attribute

writeXMLAttributes

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

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class GraphicalObject