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, NamedSBase, SBase, UniqueNamedSBase, 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

Version:

$Rev: 1464 $

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private Curve	curve
private java.lang.String	glyph
private java.lang.String	role
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
ReferenceGlyph()
ReferenceGlyph(int level, int version)
ReferenceGlyph(ReferenceGlyph speciesReferenceGlyph)
ReferenceGlyph(java.lang.String id)
ReferenceGlyph(java.lang.String id, int level, int version)

Method Summary

Methods

Modifier and Type	Method and Description
ReferenceGlyph	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
Curve	createCurve()
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
Curve	getCurve()
java.lang.String	getGlyph()
java.lang.String	getRole()
int	hashCode() Returns a hash code value for this SBase instance.
boolean	isSetCurve()
boolean	isSetGlyph()
boolean	isSetRole()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
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.
void	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()
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.ext.layout.AbstractReferenceGlyph

getNamedSBaseInstance, getReference, getReferenceInstance, isSetReference, setNamedSBase, setReference, toString, 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

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

curve

private Curve curve

role

private java.lang.String role

glyph

private java.lang.String glyph

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

clone

public ReferenceGlyph 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 AbstractReferenceGlyph

Returns:

a copy of this object

createCurve

public Curve createCurve()

Returns:

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 AbstractReferenceGlyph

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.

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()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractReferenceGlyph

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isSetCurve

public boolean isSetCurve()

Returns:

isSetGlyph

public boolean isSetGlyph()

Returns:

isSetRole

public boolean isSetRole()

Returns:

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 GraphicalObject

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.

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 void 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 -

unsetCurve

public boolean unsetCurve()

Returns:

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 GraphicalObject

Returns:

a Map containing the XML attributes of this object.