org.sbml.jsbml

Class AbstractNamedSBase

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

All Implemented Interfaces:

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

Direct Known Subclasses:

AbstractNamedSBaseWithUnit, CompartmentType, Model, Reaction, SimpleSpeciesReference, SpeciesType, UnitDefinition

public abstract class AbstractNamedSBase
extends AbstractSBase
implements NamedSBase

Base abstract class for all the SBML components with an id and a name (optional or not) in SBML Level 3 Version 1 or lower. Since SBML Level 3 Version 2, every SBase have an id an a name. This class is kept for compatibility but it is more or less empty, all code dealing with id and name has been moved to AbstractSBase.

Since:

0.8

Author:

Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private static long	serialVersionUID Generated serial version identifier.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, lv, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
AbstractNamedSBase() Creates a new AbstractNamedSBase instance.
AbstractNamedSBase(AbstractNamedSBase nsb) Creates an AbstractNamedSBase from a given AbstractNamedSBase.
AbstractNamedSBase(int level, int version) Creates an AbstractNamedSBase from a level and version.
AbstractNamedSBase(java.lang.String id) Creates an AbstractNamedSBase with the given identifier.
AbstractNamedSBase(java.lang.String id, int level, int version) Creates an AbstractNamedSBase from an id, level and version.
AbstractNamedSBase(java.lang.String id, java.lang.String name, int level, int version) Creates an AbctractNamedSBase from an id, name, level and version.

Method Summary

Modifier and Type	Method and Description
static boolean	isValidId(java.lang.String idCandidate, int level, int version) Deprecated. use SyntaxChecker.isValidId(String, int, int)

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, clone, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, equals, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, 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, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, readAttribute, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setLevelAndVersion, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageNamespaceAndVersion, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm, writeXMLAttributes

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, isIdMandatory, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, clone, createPlugin, disablePackage, enablePackage, enablePackage, equals, 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, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, readAttribute, 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, writeXMLAttributes

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

Constructor Detail

AbstractNamedSBase

public AbstractNamedSBase()

Creates a new AbstractNamedSBase instance. By default, id and name are null.

AbstractNamedSBase

public AbstractNamedSBase(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

AbstractNamedSBase

public AbstractNamedSBase(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

AbstractNamedSBase

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

Creates an AbstractNamedSBase from an id, level and version.

Parameters:

id - the id of this AbstractNamedSBase

level - the SBML level

version - the SBML version

AbstractNamedSBase

public AbstractNamedSBase(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

AbstractNamedSBase

public AbstractNamedSBase(AbstractNamedSBase nsb)

Creates an AbstractNamedSBase from a given AbstractNamedSBase.

Parameters:

nsb - an AbstractNamedSBase object to clone

Method Detail

isValidId

@Deprecated
public static final boolean isValidId(java.lang.String idCandidate,
                                                  int level,
                                                  int version)

Deprecated. use SyntaxChecker.isValidId(String, int, int)

Checks whether the given idCandidate is a valid identifier according to the SBML specifications.

Parameters:

idCandidate - The String to be tested.

level - Level of the SBML to be used.

version - Version of the SBML to be used.

Returns:

True if the argument satisfies the specification of identifiers in the SBML specifications or false otherwise.