org.sbml.jsbml.ext.layout

Class SpeciesReferenceGlyph

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.SpeciesReferenceGlyph

All Implemented Interfaces:

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

public class SpeciesReferenceGlyph
extends AbstractReferenceGlyph

The SpeciesReferenceGlyph class describes the graphical connection between a SpeciesGlyph and a ReactionGlyph (which would be an arrow or some curve in most cases).

Since:

1.0

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
SpeciesReferenceGlyph()
SpeciesReferenceGlyph(int level, int version)
SpeciesReferenceGlyph(SpeciesReferenceGlyph speciesReferenceGlyph)
SpeciesReferenceGlyph(String id)
SpeciesReferenceGlyph(String id, int level, int version)

Method Summary

Modifier and Type	Method and Description
SpeciesReferenceGlyph	clone()
Curve	createCurve()
boolean	equals(Object object)
TreeNode	getChildAt(int index)
int	getChildCount()
Curve	getCurve()
ReactionGlyph	getReactionGlyph()
SpeciesReferenceRole	getRole()
String	getSpeciesGlyph()
SpeciesGlyph	getSpeciesGlyphInstance()
String	getSpeciesReference()
NamedSBase	getSpeciesReferenceInstance() Note that the return type of this method is NamedSBase because it could be possible to link some element from other packages to this glyph.
SpeciesReferenceRole	getSpeciesReferenceRole()
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isSetCurve()
boolean	isSetSpeciesGlyph()
boolean	isSetSpeciesReference()
boolean	isSetSpeciesReferenceRole()
boolean	readAttribute(String attributeName, String prefix, String value)
void	setCurve(Curve curve) The curve is an optional element of type Curve.
void	setRole(SpeciesReferenceRole role) The role attribute is of type SpeciesReferenceRole and is used to specify how the species reference should be displayed.
void	setSpeciesGlyph(String speciesGlyph) The speciesGlyph attribute contains a reference to the id of a SpeciesGlyph object that is to be connected to the ReactionGlyph.
void	setSpeciesReference(SimpleSpeciesReference speciesReference) See setSpeciesReference(String).
void	setSpeciesReference(String speciesReference) The speciesReference is an optional attribute that allows modelers to connect the SpeciesReferenceGlyph with a particular SpeciesReference of the containing Model.
void	setSpeciesReferenceRole(SpeciesReferenceRole role)
boolean	unsetCurve()
void	unsetSpeciesReference()
Map<String,String>	writeXMLAttributes()

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

getNamedSBaseInstance, getReference, getReferenceInstance, getSBaseInstance, isSetReference, setNamedSBase, setReference, setSBase, 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, 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, isLeaf, isReadingInProgress, 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, 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

SpeciesReferenceGlyph

public SpeciesReferenceGlyph()

SpeciesReferenceGlyph

public SpeciesReferenceGlyph(int level,
                             int version)

Parameters:

level -

version -

SpeciesReferenceGlyph

public SpeciesReferenceGlyph(SpeciesReferenceGlyph speciesReferenceGlyph)

Parameters:

speciesReferenceGlyph -

SpeciesReferenceGlyph

public SpeciesReferenceGlyph(String id)

Parameters:

id -

SpeciesReferenceGlyph

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

Parameters:

id -

level -

version -

Method Detail

getReactionGlyph

public ReactionGlyph getReactionGlyph()

Returns:

clone

public SpeciesReferenceGlyph clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractReferenceGlyph

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

Overrides:

initDefaults in class GraphicalObject

createCurve

public Curve createCurve()

Returns:

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:

getSpeciesGlyph

public String getSpeciesGlyph()

Returns:

String id of the speciesGlyph

getSpeciesGlyphInstance

public SpeciesGlyph getSpeciesGlyphInstance()

Returns:

getSpeciesReference

public String getSpeciesReference()

Returns:

getSpeciesReferenceInstance

public NamedSBase getSpeciesReferenceInstance()

Note that the return type of this method is NamedSBase because it could be possible to link some element from other packages to this glyph.

Returns:

getSpeciesReferenceRole

public SpeciesReferenceRole getSpeciesReferenceRole()

Returns:

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractReferenceGlyph

isSetCurve

public boolean isSetCurve()

Returns:

isSetSpeciesGlyph

public boolean isSetSpeciesGlyph()

Returns:

isSetSpeciesReference

public boolean isSetSpeciesReference()

Returns:

isSetSpeciesReferenceRole

public boolean isSetSpeciesReferenceRole()

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)

The curve is an optional element of type Curve. When present, the glyphs bounding box (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 SpeciesReferenceGlyph. If no role attribute is defined, the role to be assumed is taken from the role that the SpeciesReference referenced via the attribute speciesReference has, otherwise it is undefined.

Parameters:

curve -

setRole

public void setRole(SpeciesReferenceRole role)

The role attribute is of type SpeciesReferenceRole and is used to specify how the species reference should be displayed. This attribute is optional and should only be necessary if the optional speciesReference attribute is not given or if the respective information from the model needs to be overridden. To define more specific interactions, the recommended practice is to use the sboTerm attribute on the SpeciesReference. If both role and sboTerm are specified and they conflict, it is the role that takes precedence.

Parameters:

role -

setSpeciesReferenceRole

public void setSpeciesReferenceRole(SpeciesReferenceRole role)

Parameters:

role -

See Also:

setRole(SpeciesReferenceRole)

getRole

public SpeciesReferenceRole getRole()

Returns:

See Also:

getSpeciesReferenceRole()

setSpeciesGlyph

public void setSpeciesGlyph(String speciesGlyph)

The speciesGlyph attribute contains a reference to the id of a SpeciesGlyph object that is to be connected to the ReactionGlyph. This attribute is mandatory so as to ensure unambiguity about which SpeciesGlyph has to be connected with this ReactionGlyph.

Parameters:

speciesGlyph -

setSpeciesReference

public void setSpeciesReference(SimpleSpeciesReference speciesReference)

See setSpeciesReference(String).

Parameters:

speciesReference -

setSpeciesReference

public void setSpeciesReference(String speciesReference)

The speciesReference is an optional attribute that allows modelers to connect the SpeciesReferenceGlyph with a particular SpeciesReference of the containing Model.

Parameters:

speciesReference -

unsetCurve

public boolean unsetCurve()

Returns:

unsetSpeciesReference

public void unsetSpeciesReference()

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class GraphicalObject