org.sbml.jsbml.ext.comp

Class AbstractNamedSBaseRef

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.comp.SBaseRef

org.sbml.jsbml.ext.comp.AbstractNamedSBaseRef

All Implemented Interfaces:

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

Direct Known Subclasses:

Deletion, Port

public abstract class AbstractNamedSBaseRef
extends SBaseRef
implements NamedSBase

This abstract class is used by Deletion and Port classes.

Since:

1.0

Version:

$Rev: 1808 $

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	id id of the SBML component (can be optional depending on the level and version).
private java.lang.String	name name of the SBML component (can be optional depending on the level and version).
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
AbstractNamedSBaseRef() Creates an AbstractNamedSBase.
AbstractNamedSBaseRef(AbstractNamedSBaseRef nsb) Creates an AbstractNamedSBase from a given AbstractNamedSBase.
AbstractNamedSBaseRef(int level, int version) Creates an AbstractNamedSBase from a level and version.
AbstractNamedSBaseRef(java.lang.String id) Creates an AbstractNamedSBase with the given identifier.
AbstractNamedSBaseRef(java.lang.String id, int level, int version) Creates an AbctractNamedSBase from an id, level and version.
AbstractNamedSBaseRef(java.lang.String id, java.lang.String name, int level, int version) Creates an AbctractNamedSBase from an id, name, level and version.

Method Summary

Methods

Modifier and Type	Method and Description
(package private) boolean	checkIdentifier(java.lang.String sID) Checks if the sID is a valid identifier.
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
java.lang.String	getId()
java.lang.String	getName()
int	hashCode() Returns a hash code value for this SBase instance.
boolean	isSetId()
boolean	isSetName()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setId(java.lang.String id) sets the id value with 'id'
void	setName(java.lang.String name) sets the name value with 'name'.
java.lang.String	toString() Returns the name of the component, if it is available.
void	unsetId() sets the id value to null.
void	unsetName() sets the name value to null.
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.comp.SBaseRef

clone, createSBaseRef, getAllowsChildren, getChildAt, getChildCount, getIdRef, getMetaIdRef, getPortRef, getSBaseRef, getUnitRef, isSetIdRef, isSetMetaIdRef, isSetPortRef, isSetSBaseRef, isSetUnitRef, setIdRef, setMetaIdRef, setPortRef, setSBaseRef, setUnitRef, unsetIdRef, unsetMetaIdRef, unsetPortRef, unsetSBaseRef, unsetUnitRef

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

isIdMandatory

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, clone, 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, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

id

private java.lang.String id

id of the SBML component (can be optional depending on the level and version). Matches the id attribute of an element in a SBML file.

name

private java.lang.String name

name of the SBML component (can be optional depending on the level and version). Matches the name attribute of an element in a SBML file.

Constructor Detail

AbstractNamedSBaseRef

public AbstractNamedSBaseRef()

Creates an AbstractNamedSBase. By default, id and name are null.

AbstractNamedSBaseRef

public AbstractNamedSBaseRef(AbstractNamedSBaseRef nsb)

Creates an AbstractNamedSBase from a given AbstractNamedSBase.

Parameters:

nsb - an AbstractNamedSBase object to clone

AbstractNamedSBaseRef

public AbstractNamedSBaseRef(int level,
                     int version)

Creates an AbstractNamedSBase from a level and version. By default, id and name are null.

Parameters:

level - the SBML level

version - the SBML version

AbstractNamedSBaseRef

public AbstractNamedSBaseRef(java.lang.String id)

Creates an AbstractNamedSBase with the given identifier. Note that with this constructor the level and version of the element are not specified. These elements are however required to ensure the validity of the SBML data structure. Without level and version, it may not be possible to serialize this class to SBML.

Parameters:

id - the id of this AbstractNamedSBase

AbstractNamedSBaseRef

public AbstractNamedSBaseRef(java.lang.String id,
                     int level,
                     int version)

Creates an AbctractNamedSBase from an id, level and version.

Parameters:

id - the id of this AbstractNamedSBase

level - the SBML level

version - the SBML version

AbstractNamedSBaseRef

public AbstractNamedSBaseRef(java.lang.String id,
                     java.lang.String name,
                     int level,
                     int version)

Creates an AbctractNamedSBase from an id, name, level and version.

Parameters:

id - the id of this AbstractNamedSBase

name - the name of this AbstractNamedSBase

level - the SBML level

version - the SBML version

Method Detail

checkIdentifier

boolean checkIdentifier(java.lang.String sID)

Checks if the sID is a valid identifier.

Parameters:

sID - the identifier to be checked. If null or an invalid identifier, an exception will be thrown.

Returns:

true only if the sID is a valid identifier. Otherwise this method throws an IllegalArgumentException. This is an intended behavior.

Throws:

java.lang.IllegalArgumentException - if the given id is not valid in this model.

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 SBaseRef

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.

getId

public java.lang.String getId()

Specified by:

getId in interface NamedSBase

Returns:

the id of the element if it is set, an empty string otherwise.

getName

public java.lang.String getName()

Specified by:

getName in interface NamedSBase

Returns:

the name of the element if it is set, an empty string otherwise.

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 SBaseRef

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isSetId

public boolean isSetId()

Specified by:

isSetId in interface NamedSBase

Returns:

true if the id is not null.

isSetName

public boolean isSetName()

Specified by:

isSetName in interface NamedSBase

Returns:

true if the name is not null.

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 SBaseRef

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.

setId

public void setId(java.lang.String id)

Description copied from interface: NamedSBase

sets the id value with 'id'

Specified by:

setId in interface NamedSBase

setName

public void setName(java.lang.String name)

Description copied from interface: NamedSBase

sets the name value with 'name'. If level is 1, sets automatically the id to 'name'

Specified by:

setName in interface NamedSBase

toString

public java.lang.String toString()

Returns the name of the component, if it is available. Otherwise, the identifier is returned. If both is not possible, the class name of this element is returned.

Overrides:

toString in class SBaseRef

unsetId

public void unsetId()

Description copied from interface: NamedSBase

sets the id value to null.

Specified by:

unsetId in interface NamedSBase

unsetName

public void unsetName()

Description copied from interface: NamedSBase

sets the name value to null.

Specified by:

unsetName in interface NamedSBase

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 SBaseRef

Returns:

a Map containing the XML attributes of this object.