org.sbml.jsbml.ext.layout

Class SpeciesGlyph

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.SpeciesGlyph

All Implemented Interfaces:

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

public class SpeciesGlyph
extends AbstractReferenceGlyph

The SpeciesGlyph class has an optional species attribute, in addition to to the attributes from GraphicalObject.

Since:

1.0

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger, Clemens Wrzodek

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
SpeciesGlyph()
SpeciesGlyph(int level, int version)
SpeciesGlyph(SpeciesGlyph speciesGlyph)
SpeciesGlyph(String id)
SpeciesGlyph(String id, int level, int version)

Method Summary

Modifier and Type	Method and Description
SpeciesGlyph	clone()
String	getSpecies()
NamedSBase	getSpeciesInstance() 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.
void	initDefaults() Initializes the default values using the namespace.
boolean	isSetSpecies()
boolean	readAttribute(String attributeName, String prefix, String value)
void	setSpecies(Species species)
void	setSpecies(String species) The species attribute allows modelers to link the SpeciesGlyph to the id of the corresponding Species object in the Model.
void	unsetSpecies()
Map<String,String>	writeXMLAttributes()

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

equals, getNamedSBaseInstance, getReference, getReferenceInstance, getSBaseInstance, hashCode, isSetReference, setNamedSBase, setReference, setSBase, unsetReference

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

createBoundingBox, createBoundingBox, createBoundingBox, createBoundingBox, getAllowsChildren, getBoundingBox, getChildAt, getChildCount, 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

SpeciesGlyph

public SpeciesGlyph()

SpeciesGlyph

public SpeciesGlyph(int level,
                    int version)

Parameters:

level -

version -

SpeciesGlyph

public SpeciesGlyph(SpeciesGlyph speciesGlyph)

Parameters:

speciesGlyph -

SpeciesGlyph

public SpeciesGlyph(String id)

Parameters:

id -

SpeciesGlyph

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

Parameters:

id -

level -

version -

Method Detail

clone

public SpeciesGlyph 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

getSpecies

public String getSpecies()

Returns:

getSpeciesInstance

public NamedSBase getSpeciesInstance()

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:

isSetSpecies

public boolean isSetSpecies()

Returns:

the true if a species id is set, false otherwise.

See Also:

AbstractReferenceGlyph.isSetReference()

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class GraphicalObject

setSpecies

public void setSpecies(Species species)

Parameters:

species -

setSpecies

public void setSpecies(String species)

The species attribute allows modelers to link the SpeciesGlyph to the id of the corresponding Species object in the Model. The species attribute is optional to allow the program to specify species representations that do not have a direct correspondence in the Model. This might be useful if some pathway has been collapsed, but is still treated by layout programs.

Parameters:

species -

unsetSpecies

public void unsetSpecies()

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class GraphicalObject