org.sbml.jsbml.ext.comp

Class SBaseRef

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.comp.SBaseRef

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBase, TreeNodeWithChangeSupport

Direct Known Subclasses:

AbstractNamedSBaseRef, ReplacedBy, ReplacedElement

public class SBaseRef
extends AbstractSBase

Contains the machinery for constructing references to specific components within enclosed models or even within external models located in other files.

The four different attributes on SBaseRef are mutually exclusive: only one of the attributes can have a value at any given time, and exactly one must have a value in a given SBaseRef object instance.

Since:

1.0

Author:

Nicolas Rodriguez

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
SBaseRef() Creates a SBaseRef instance.
SBaseRef(int level, int version) Creates a SBaseRef instance with a level and version.
SBaseRef(SBaseRef obj) Clone constructor

Method Summary

Modifier and Type	Method and Description
SBaseRef	clone()
SBaseRef	createSBaseRef() Creates a new SBaseRef instance and add it to this SBaseRef
boolean	equals(Object obj)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
String	getIdRef() Returns the value of idRef
String	getMetaIdRef() Returns the value of metaIdRef
String	getPortRef() Returns the value of portRef
SBaseRef	getSBaseRef() Returns the value of sBaseRef
String	getUnitRef() Returns the value of unitRef
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isSetIdRef() Returns whether idRef is set
boolean	isSetMetaIdRef() Returns whether metaIdRef is set
boolean	isSetPortRef() Returns whether portRef is set
boolean	isSetSBaseRef() Returns whether sBaseRef is set
boolean	isSetUnitRef() Returns whether unitRef is set
boolean	readAttribute(String attributeName, String prefix, String value)
void	setIdRef(String idRef) Sets the value of the optional idRef attribute.
void	setMetaIdRef(String metaIdRef) Sets the value of the optional metaIdRef attribute.
void	setPortRef(String portRef) Sets the value of the optional portRef attribute.
void	setSBaseRef(SBaseRef sBaseRef) Sets the value of the optional sBaseRef element.
void	setUnitRef(String unitRef) Sets the value of the optional unitRef attribute This attribute is used to refer to the identifier of a UnitDefinition object.
boolean	unsetIdRef() Unsets the variable idRef
boolean	unsetMetaIdRef() Unsets the variable metaIdRef
boolean	unsetPortRef() Unsets the variable portRef
boolean	unsetSBaseRef() Unsets the variable sBaseRef
boolean	unsetUnitRef() Unsets the variable unitRef
Map<String,String>	writeXMLAttributes()

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, isIdMandatory, 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.SBase

removeTreeNodeChangeListener

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, isLeaf

Constructor Detail

SBaseRef

public SBaseRef()

Creates a SBaseRef instance.

SBaseRef

public SBaseRef(int level,
                int version)

Creates a SBaseRef instance with a level and version.

Parameters:

level -

version -

SBaseRef

public SBaseRef(SBaseRef obj)

Clone constructor

Parameters:

obj -

Method Detail

clone

public SBaseRef clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

getPortRef

public String getPortRef()

Returns the value of portRef

Returns:

the value of portRef

isSetPortRef

public boolean isSetPortRef()

Returns whether portRef is set

Returns:

whether portRef is set

setPortRef

public void setPortRef(String portRef)

Sets the value of the optional portRef attribute. As its name implies, this attribute is used to refer to a port identifier, in the case when the reference being constructed with the SBaseRef is intended to refer to a port on a submodel.

Parameters:

portRef -

unsetPortRef

public boolean unsetPortRef()

Unsets the variable portRef

Returns:

true, if portRef was set before, otherwise false

getIdRef

public String getIdRef()

Returns the value of idRef

Returns:

the value of idRef

isSetIdRef

public boolean isSetIdRef()

Returns whether idRef is set

Returns:

whether idRef is set

setIdRef

public void setIdRef(String idRef)

Sets the value of the optional idRef attribute. As its name implies, this attribute is used to refer to a regular identifier (i.e., the value of an id attribute on some other object), in the case when the reference being constructed with the SBaseRef is intended to refer to an object that does not have a port identifier.

Parameters:

idRef -

unsetIdRef

public boolean unsetIdRef()

Unsets the variable idRef

Returns:

true, if idRef was set before, otherwise false

getUnitRef

public String getUnitRef()

Returns the value of unitRef

Returns:

the value of unitRef

isSetUnitRef

public boolean isSetUnitRef()

Returns whether unitRef is set

Returns:

whether unitRef is set

setUnitRef

public void setUnitRef(String unitRef)

Sets the value of the optional unitRef attribute This attribute is used to refer to the identifier of a UnitDefinition object. The namespace of the UnitSIdRef value is the set of unit identifiers defined in the submodel, not the parent model. Note that even though this attribute is of type UnitSIdRef, the reserved unit identifiers that are defined by SBML Level 3 are not permitted as values of unitRef. Reserved unit identifiers may not be replaced or deleted.

Parameters:

unitRef -

unsetUnitRef

public boolean unsetUnitRef()

Unsets the variable unitRef

Returns:

true, if unitRef was set before, otherwise false

getMetaIdRef

public String getMetaIdRef()

Returns the value of metaIdRef

Returns:

the value of metaIdRef

isSetMetaIdRef

public boolean isSetMetaIdRef()

Returns whether metaIdRef is set

Returns:

whether metaIdRef is set

setMetaIdRef

public void setMetaIdRef(String metaIdRef)

Sets the value of the optional metaIdRef attribute. This attribute is used to refer to a metaid attribute value on some other object, in the case when the reference being constructed with the SBaseRef is intended to refer to an object that does not have a port identifier. The namespace of the metaIdRef value is the entire document in which the referenced model resides, but must refer to a subelement of the referenced model. Since meta identifiers are optional attributes of SBase, all SBML objects have the potential to have a meta identifier value.

Parameters:

metaIdRef -

unsetMetaIdRef

public boolean unsetMetaIdRef()

Unsets the variable metaIdRef

Returns:

true, if metaIdRef was set before, otherwise false

createSBaseRef

public SBaseRef createSBaseRef()

Creates a new SBaseRef instance and add it to this SBaseRef

Returns:

a new SBaseRef instance (added to this SBaseRef)

getSBaseRef

public SBaseRef getSBaseRef()

Returns the value of sBaseRef

Returns:

the value of sBaseRef

isSetSBaseRef

public boolean isSetSBaseRef()

Returns whether sBaseRef is set

Returns:

whether sBaseRef is set

setSBaseRef

public void setSBaseRef(SBaseRef sBaseRef)

Sets the value of the optional sBaseRef element. An SBaseRef object may have up to one subcomponent named sBaseRef, of type SBaseRef. This permits recursive structures to be constructed so that objects inside submodels can be referenced.

Parameters:

sBaseRef -

unsetSBaseRef

public boolean unsetSBaseRef()

Unsets the variable sBaseRef

Returns:

true, if sBaseRef was set before, otherwise false

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSBase

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSBase

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase