AbstractSBase

java.lang.Object
- org.sbml.jsbml.AbstractTreeNode
- - org.sbml.jsbml.AbstractSBase

All Implemented Interfaces:

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

Direct Known Subclasses:

AbstractMathContainer, AbstractNamedSBase, AbstractSpatialNamedSBase, BindingSiteReference, Bond, ContainedSpeciesType, CoordinateReference, CurveSegment, GradientStop, ImageData, InteriorPoint, ListOf, OrdinalMapping, ParameterType, PolygonObject, RenderPoint, SBaseRef, SBMLDocument, SelectorReference, SpeciesTypeRestrictionReference, StateFeatureValue, Transformation, TransformationComponent, Unit
```
public abstract class AbstractSBase
extends AbstractTreeNode
implements SBase
```
The base class for each SBase component.

Since:

0.8

Version:

$Rev: 1968 $

Author:

Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau

See Also:
Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

private static class AbstractSBase.NOTES_TYPE

Nested Classes
Modifier and Type	Class and Description
`private static class`	`AbstractSBase.NOTES_TYPE`

Field Summary

Fields
Modifier and Type	Field and Description
`private Annotation`	`annotation` Annotations of the SBML component.
`private java.util.Map<java.lang.String,java.lang.String>`	`declaredNamespaces` Contains all the namespaces declared on the XML node with their prefixes.
`private java.lang.String`	`elementNamespace` the namespace which this SBase element belong to.
`private java.util.SortedMap<java.lang.String,SBasePlugin>`	`extensions` `Map` containing the SBML extension object of additional packages with the appropriate name space of the package.
`private static java.util.regex.Pattern`	`idPattern` Pattern to recognize valid meta-identifier strings for SBML elements.
`protected java.util.SortedMap<java.lang.String,XMLNode>`	`ignoredExtensions` `Map` containing the ignored package objects.
`protected XMLNode`	`ignoredXMLElements` Contains the unknown XML attributes or elements.
`private static org.apache.log4j.Logger`	`logger` A logger for this class.
`(package private) ValuePair<java.lang.Integer,java.lang.Integer>`	`lv` Level and version of the SBML component.
`private java.lang.String`	`metaId` metaid of the SBML component.
`private XMLNode`	`notesXMLNode` notes of the SBML component.
`private int`	`sboTerm` sbo term of the SBML component.
`private static long`	`serialVersionUID` Generated serial version identifier.
`private static java.util.regex.Pattern`	`simpleIdPattern` Pattern to recognize valid meta-identifier strings for SBML elements.

Fields inherited from class org.sbml.jsbml.AbstractTreeNode
listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors
Constructor and Description
`AbstractSBase()` Creates an AbstractSBase instance.
`AbstractSBase(int level, int version)` Creates an `AbstractSBase` instance with the given SBML Level and Version.
`AbstractSBase(SBase sb)` Creates an `AbstractSBase` instance from a given `AbstractSBase`.

Method Summary

Methods
Modifier and Type	Method and Description
`boolean`	`addCVTerm(CVTerm term)` Adds a `CVTerm`.
`void`	`addDeclaredNamespace(java.lang.String prefix, java.lang.String namespace)` Adds an additional name space to the set of declared namespaces of this `SBase`.
`void`	`addExtension(java.lang.String nameOrUri, SBasePlugin sbasePlugin)` Adds a `SBasePlugin` extension object to this `SBase`.
`void`	`addPlugin(java.lang.String nameOrUri, SBasePlugin sbasePlugin)` Adds a `SBasePlugin` extension object to this `SBase`.
`void`	`appendNotes(java.lang.String notes)` Appends 'notes' to the notes String of this object.
`void`	`appendNotes(XMLNode notes)` Appends notes to the existing notes.
`protected boolean`	`checkLevelAndVersionCompatibility(SBase sbase)` Checks whether or not the given `SBase` has the same level and version configuration than this element.
`abstract AbstractSBase`	`clone()` Creates a deep copy of this object, i.e., a new `SBase` with the same properties like this one.
`History`	`createHistory()` Creates a new `History` and associates it with the annotation of this element.
`SBasePlugin`	`createPlugin(java.lang.String nameOrUri)` Creates a new `SBasePlugin` for the given package name or URI and adds it to this `SBase`.
`void`	`disablePackage(java.lang.String packageURIOrName)` Disables the given SBML Level 3 package on this `SBMLDocument`.
`void`	`enablePackage(java.lang.String packageURIOrName)` Enables the given SBML Level 3 package on this `SBMLDocument`.
`void`	`enablePackage(java.lang.String packageURIOrName, boolean enabled)` Enables or disables the given SBML Level 3 package on this `SBMLDocument`.
`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.util.List<CVTerm>`	`filterCVTerms(CVTerm.Qualifier qualifier)` Returns a list of all the `CVTerm` with the given `CVTerm.Qualifier`.
`java.util.List<java.lang.String>`	`filterCVTerms(CVTerm.Qualifier qualifier, boolean recursive, java.lang.String... patterns)` Returns a list of resource URIs for the given `CVTerm.Qualifier` that match the given patterns.
`java.util.List<java.lang.String>`	`filterCVTerms(CVTerm.Qualifier qualifier, java.lang.String pattern)` Queries the list of controlled vocabulary terms (`CVTerm`) for those terms whose `CVTerm.Qualifier` is of the given type and selects only those resources from these terms that contain the given pattern.
`java.util.List<java.lang.String>`	`filterCVTerms(CVTerm.Qualifier qualifier, java.lang.String pattern, boolean recursive)` Returns a list of resource URIs for the given `CVTerm.Qualifier` that match the given pattern.
`void`	`fireNodeRemovedEvent()` All `TreeNodeChangeListener` instances linked to this `TreeNode` are informed about the deletion of this `TreeNode` from a parent `Object`.
`void`	`firePropertyChange(java.lang.String propertyName, java.lang.Object oldValue, java.lang.Object newValue)` All `TreeNodeChangeListener`s are informed about the change in this `TreeNodeWithChangeSupport`.
`boolean`	`getAllowsChildren()`
`Annotation`	`getAnnotation()` Returns the content of the 'annotation' sub-element of this object as an `Annotation` instance.
`java.lang.String`	`getAnnotationString()` Returns the `Annotation` of this SBML object as a `String`.
`javax.swing.tree.TreeNode`	`getChildAt(int childIndex)`
`int`	`getChildCount()`
`CVTerm`	`getCVTerm(int index)` Returns the `CVTerm` instance at the position 'index' in the list of `CVTerm`s of this object.
`int`	`getCVTermCount()` Returns the number of `CVTerm`s of this `SBase`.
`java.util.List<CVTerm>`	`getCVTerms()` Returns the list of `CVTerm`s of this object.
`java.util.Map<java.lang.String,java.lang.String>`	`getDeclaredNamespaces()` Returns all the namespaces declared on this object.
`java.lang.String`	`getElementName()` Returns the XML element name of this object.
`SBasePlugin`	`getExtension(java.lang.String nameOrUri)` Returns the `SBasePlugin` extension object which matches this package name or URI.
`int`	`getExtensionCount()` Returns the number of `SBasePlugin`s of this `SBase`.
`java.util.Map<java.lang.String,SBasePlugin>`	`getExtensionPackages()` Returns the map containing all the `SBasePlugin` extension objects of this `SBase`.
`private int`	`getFirstElementIndex(XMLNode curNotes)` Return the index of the first child of type 'Element' for the given `XMLNode`.
`History`	`getHistory()` Returns the `History` instance of this object.
`protected IdManager`	`getIdManager(SBase sbase)` Returns an `IdManager` that can register the given `SBase`.
`int`	`getLevel()` Returns the SBML Level of the overall SBML document.
`ValuePair<java.lang.Integer,java.lang.Integer>`	`getLevelAndVersion()` Returns the Level and Version combination of this `SBase`.
`java.lang.String`	`getMetaId()` Returns the metaid of this element.
`Model`	`getModel()` Returns the `Model` object in which the current `SBase` is located.
`java.lang.String`	`getNamespace()` Returns the namespace to which this `SBase` belong to.
`XMLNode`	`getNotes()` Returns an `XMLNode` object that represent the notes of this element.
`java.lang.String`	`getNotesString()` Returns the notes sub-element of this object as a `String`.
`int`	`getNumCVTerms()` Returns the number of `CVTerm`s of this `SBase`.
`int`	`getNumPlugins()` Returns the number of `SBasePlugin`s of this `SBase`.
`SBase`	`getParent()` This is equivalent to calling `getParentSBMLObject()`, but this method is needed for `TreeNode`.
`SBase`	`getParentSBMLObject()` Returns the parent of this `SBase`.
`SBasePlugin`	`getPlugin(java.lang.String nameOrUri)` Returns an `SBasePlugin` for an SBML Level 3 package extension with the given package name or URI.
`SBMLDocument`	`getSBMLDocument()` Returns the parent `SBMLDocument` object.
`int`	`getSBOTerm()` Grants access to the Systems Biology Ontology (SBO) term associated with this `SBase`.
`java.lang.String`	`getSBOTermID()` Grants access to the Systems Biology Ontology (SBO) term associated with this `SBase`.
`int`	`getVersion()` Returns the Version within the SBML Level of the overall SBML document.
`int`	`hashCode()` Returns a hash code value for this `SBase` instance.
`boolean`	`hasValidAnnotation()` Returns `true` if the `Annotation` RDF 'about' attribute matches the metaid of this object.
`boolean`	`hasValidLevelVersionNamespaceCombination()` Returns `true` or `false` depending on whether this object's level/version and namespace values correspond to a valid SBML specification.
`boolean`	`isExtendedByOtherPackages()` Returns `true` if this object is extended by other packages.
`boolean`	`isPackageEnabled(java.lang.String packageURIOrName)` Returns `true` if the given SBML Level 3 package is enabled within the containing `SBMLDocument`.
`boolean`	`isPackageURIEnabled(java.lang.String packageURIOrName)` Returns `true` if the given SBML Level 3 package is enabled within the containing `SBMLDocument`.
`boolean`	`isPkgEnabled(java.lang.String packageURIOrName)` Deprecated.
`boolean`	`isPkgURIEnabled(java.lang.String packageURIOrName)` Deprecated.
`boolean`	`isSetAnnotation()` Returns `true` or `false` depending on whether this object's 'annotation' sub-elements exists and have some content.
`boolean`	`isSetHistory()` Returns `true` if the `History` instance of this object is set.
`boolean`	`isSetLevel()` Returns `true` if the level is set.
`boolean`	`isSetLevelAndVersion()` Returns `true` if both, Level and Version are set for this `SBase`.
`boolean`	`isSetMetaId()` Returns `true` or `false` depending on whether this object's 'metaid' attribute has been set.
`boolean`	`isSetNotes()` Returns `true` or `false` depending on whether this object's 'notes' sub-element exists and has content.
`boolean`	`isSetParentSBMLObject()` Check whether this `SBase` has been linked to a parent within the hierarchical SBML data structure.
`boolean`	`isSetPlugin(java.lang.String nameOrUri)` Returns `true` if an `SBasePlugin` is defined for the given package.
`boolean`	`isSetSBOTerm()` Returns `true` if the SBOTerm is set.
`boolean`	`isSetVersion()` Returns `true` if the version is not `null`.
`static boolean`	`isValidLevelAndVersionCombination(int level, int version)` Returns `true` if the level and version combination is a valid one, `false` otherwise.
`static boolean`	`isValidMetaId(java.lang.String idCandidate)` Checks if the given identifier candidate satisfies the requirements for a valid meta identifier (see SBML L2V4 p.
`protected void`	`notifyChildChange(javax.swing.tree.TreeNode oldChild, javax.swing.tree.TreeNode newChild)` This method is called when one child has been swapped with another one and can be used to check certain properties of the resulting changed tree.
`boolean`	`readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)` Sets the given attribute in this `SBase`.
`void`	`registerChild(SBase sbase)` Sets this object as SBML parent of 'sbase'.
`private void`	`registerChild(SBasePlugin sbasePlugin)` Registers recursively the given `SBasePlugin` from the `Model` and `SBMLDocument`.
`boolean`	`removeCVTerm(CVTerm cvTerm)` Removes the given `CVTerm`.
`CVTerm`	`removeCVTerm(int index)` Removes the `CVTerm` at the given index.
`void`	`setAnnotation(Annotation annotation)` Sets the value of the 'annotation' sub-element of this SBML object to a copy of annotation given as an `Annotation` instance.
`void`	`setHistory(History history)` Sets the history.
`void`	`setLevel(int level)` Sets the level of this object with 'level'.
`(package private) boolean`	`setLevelAndVersion(int level, int version, boolean strict)` Sets recursively the level and version attribute for this element and all sub-elements.
`void`	`setMetaId(java.lang.String metaId)` Sets the metaid value with 'metaid'.
`void`	`setNamespace(java.lang.String namespace)` Sets the XML namespace to which this `SBase` belong.
`void`	`setNotes(java.lang.String notes)` Sets the notes with 'notes'.
`void`	`setNotes(XMLNode notes)` Sets the `XMLNode` containing the notes sub-element of this object.
`protected void`	`setParentSBML(SBase parent)`
`protected void`	`setParentSBMLObject(SBase sbase)` Checks the Level/Version configuration of the new parent (if it is compliant to the one of this `SBase`), adds all changeListeners from the parent to this `SBase`, fires a `TreeNodeChangeListener.nodeAdded(TreeNode)` event, and and finally, it will forward the new parent to `setParentSBML(SBase)`.
`void`	`setSBOTerm(int term)` Sets the value of the 'sboTerm' attribute.
`void`	`setSBOTerm(java.lang.String sboid)` Sets the value of the 'sboTerm' attribute.
`void`	`setThisAsParentSBMLObject(SBase sbase)` Deprecated.
`void`	`setVersion(int version)` Sets the version of this object with 'version'.
`abstract java.lang.String`	`toString()`
`void`	`unregisterChild(SBase sbase)` Unregisters recursively the given SBase from the `Model` and `SBMLDocument`.
`private void`	`unregisterChild(SBasePlugin sbasePlugin)` Unregisters recursively the given `SBasePlugin` from the `Model` and `SBMLDocument`.
`void`	`unsetAnnotation()` Unsets the value of the 'annotation' sub-element of this SBML object.
`void`	`unsetCVTerms()` Unsets the list of `CVTerm` of this object.
`void`	`unsetExtension(java.lang.String nameOrUri)` Unsets the `SBasePlugin` extension object which matches this package name or URI.
`void`	`unsetHistory()` Unsets the `History` of this object.
`void`	`unsetMetaId()` Unsets the value of the 'metaid' attribute of this SBML object.
`void`	`unsetNamespace()` Unsets the namespace that is associated to this `SBase`.
`void`	`unsetNotes()` Unsets the value of the 'notes' sub-element of this SBML object.
`void`	`unsetPlugin(java.lang.String nameOrUri)` Unsets the `SBasePlugin` extension object which matches this package name or URI.
`void`	`unsetSBOTerm()` Unsets the value of the 'sboTerm' attribute of this SBML object.
`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 java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.SBase
removeTreeNodeChangeListener

Methods inherited from interface javax.swing.tree.TreeNode
children, getIndex, isLeaf

- Field Detail
  - idPattern
```
private static final java.util.regex.Pattern idPattern
```
    Pattern to recognize valid meta-identifier strings for SBML elements.
  - simpleIdPattern
```
private static final java.util.regex.Pattern simpleIdPattern
```
    Pattern to recognize valid meta-identifier strings for SBML elements.
  - logger
```
private static final org.apache.log4j.Logger logger
```
    A logger for this class.
  - serialVersionUID
```
private static final long serialVersionUID
```
    Generated serial version identifier.
    
    See Also:
    Constant Field Values
  - annotation
```
private Annotation annotation
```
    Annotations of the SBML component. Matches the annotation XML node in a SBML file.
  - declaredNamespaces
```
private final java.util.Map<java.lang.String,java.lang.String> declaredNamespaces
```
    Contains all the namespaces declared on the XML node with their prefixes.
  - extensions
```
private final java.util.SortedMap<java.lang.String,SBasePlugin> extensions
```
    Map containing the SBML extension object of additional packages with the appropriate name space of the package.
  - ignoredExtensions
```
protected java.util.SortedMap<java.lang.String,XMLNode> ignoredExtensions
```
    Map containing the ignored package objects.
    Package are considered ignored if JSBML does not support this package or support the package but not the associated namespace.
  - ignoredXMLElements
```
protected XMLNode ignoredXMLElements
```
    Contains the unknown XML attributes or elements.
  - lv
```
ValuePair<java.lang.Integer,java.lang.Integer> lv
```
    Level and version of the SBML component. Matches the level XML attribute of an SBML node.
  - metaId
```
private java.lang.String metaId
```
    metaid of the SBML component. Matches the metaid XML attribute of an element in a SBML file.
  - notesXMLNode
```
private XMLNode notesXMLNode
```
    notes of the SBML component. Matches the notes XML node in a SBML file.
  - sboTerm
```
private int sboTerm
```
    sbo term of the SBML component. Matches the sboTerm XML attribute of an element in a SBML file.
  - elementNamespace
```
private java.lang.String elementNamespace
```
    the namespace which this SBase element belong to.
- Constructor Detail
  - AbstractSBase
```
public AbstractSBase()
```
    Creates an AbstractSBase instance.
    By default, the sboTerm is -1, the metaid, notes, parentSBMLObject, annotation, and notes are null. The level and version are set to -1. The setOfListeners list and the extensions hash map are empty.
  - AbstractSBase
```
public AbstractSBase(int level,
             int version)
```
    Creates an AbstractSBase instance with the given SBML Level and Version.
    By default, the sboTerm is -1, the metaid, notes, AbstractTreeNode.parent, annotation, and notes are null. The declaredNamespaces list and the extensions Map are empty.
    
    Parameters:
    level - the SBML level
    version - the SBML version
  - AbstractSBase
```
public AbstractSBase(SBase sb)
```
    Creates an AbstractSBase instance from a given AbstractSBase.
    
    Parameters:
    sb - an AbstractSBase object to clone
- Method Detail
  - isValidLevelAndVersionCombination
```
public static boolean isValidLevelAndVersionCombination(int level,
                                        int version)
```
    Returns true if the level and version combination is a valid one, false otherwise.
    
    Parameters:
    level - the SBML level
    version - the SBML version
    
    Returns:
    true if the level and version combination is a valid one, false otherwise.
  - isValidMetaId
```
public static final boolean isValidMetaId(java.lang.String idCandidate)
```
    Checks if the given identifier candidate satisfies the requirements for a valid meta identifier (see SBML L2V4 p. 12 for details).
    
    Parameters:
    idCandidate -
    
    Returns:
    true if the given argument is a valid meta identifier String, false otherwise.
  - addCVTerm
```
public boolean addCVTerm(CVTerm term)
```
    Description copied from interface: SBase
    
    Adds a CVTerm.
    
    Specified by:
    
    addCVTerm in interface SBase
    
    Parameters:
    term - the CVTerm to add.
    
    Returns:
    true if a CVTerm instance has been added to the list of CVTerm of this object.
  - addDeclaredNamespace
```
public void addDeclaredNamespace(java.lang.String prefix,
                        java.lang.String namespace)
```
    Adds an additional name space to the set of declared namespaces of this SBase.
    
    Specified by:
    
    addDeclaredNamespace in interface SBase
    
    Parameters:
    prefix - the prefix of the namespace to add
    namespace - the namespace to add
  - addExtension
```
public void addExtension(java.lang.String nameOrUri,
                SBasePlugin sbasePlugin)
```
    Description copied from interface: SBase
    
    Adds a SBasePlugin extension object to this SBase.
    If a previous SBasePlugin associated with the same package was present before, it will be replaced.
    
    Specified by:
    
    addExtension in interface SBase
    
    Parameters:
    nameOrUri - the name or URI of the package extension.
    sbasePlugin - the SBasePlugin to add.
  - addPlugin
```
public void addPlugin(java.lang.String nameOrUri,
             SBasePlugin sbasePlugin)
```
    Description copied from interface: SBase
    
    Adds a SBasePlugin extension object to this SBase.
    If a previous SBasePlugin associated with the same package was present before, it will be replaced.
    
    Specified by:
    
    addPlugin in interface SBase
    
    Parameters:
    nameOrUri - the name or URI of the package extension.
    sbasePlugin - the SBasePlugin to add.
    See Also:
    SBase.addExtension(String, SBasePlugin)
  - setNamespace
```
public void setNamespace(java.lang.String namespace)
```
    Sets the XML namespace to which this SBase belong.
    This an internal method that should not be used outside of the main jsbml code (core + packages). One class should always belong to the same namespace, although the namespaces can have different level and version (and package version). You have to know what you are doing when using this method.
    
    Parameters:
    namespace - the XML namespace to which this SBase belong.
  - appendNotes
```
public void appendNotes(java.lang.String notes)
                 throws javax.xml.stream.XMLStreamException
```
    Description copied from interface: SBase
    
    Appends 'notes' to the notes String of this object.
    
    Specified by:
    
    appendNotes in interface SBase
    
    Parameters:
    notes - the notes to be added.
    
    Throws:
    
    javax.xml.stream.XMLStreamException - if an error occurs while parsing the notes String.
  - appendNotes
```
public void appendNotes(XMLNode notes)
```
    Appends notes to the existing notes.
    This allows other notes to be preserved whilst adding additional information.
    
    Specified by:
    
    appendNotes in interface SBase
    
    Parameters:
    notes -
  - checkLevelAndVersionCompatibility
```
protected boolean checkLevelAndVersionCompatibility(SBase sbase)
```
    Checks whether or not the given SBase has the same level and version configuration than this element. If the L/V combination for the given sbase is not yet defined, this method sets it to the identical values as it is for the current object.
    
    Parameters:
    sbase - the element to be checked.
    
    Returns:
    true if the given sbase and this object have the same L/V configuration.
    
    Throws:
    
    LevelVersionError - In case the given SBase has a different, but defined Level/Version combination than this current SBase, an LevelVersionError is thrown. This method is only package-wide visible because it is not intended to be a "real" check, rather than to indicate potential errors.
  - clone
```
public abstract AbstractSBase clone()
```
    Description copied from interface: SBase
    
    Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
    
    Specified by:
    
    clone in interface SBase
    
    Specified by:
    
    clone in class AbstractTreeNode
    
    Returns:
    a copy of this object
  - createHistory
```
public History createHistory()
```
    Creates a new History and associates it with the annotation of this element. If no Annotation exists, a new such element is created as well.
    
    Returns:
    A new History instance that is directly associated with this element.
    See Also:
    getHistory()
  - createPlugin
```
public SBasePlugin createPlugin(java.lang.String nameOrUri)
```
    Description copied from interface: SBase
    
    Creates a new SBasePlugin for the given package name or URI and adds it to this SBase.
    If an SBasePlugin was already present in this SBase it will be replaced.
    
    Specified by:
    
    createPlugin in interface SBase
    
    Parameters:
    nameOrUri - the package name or URI
    
    Returns:
    a new SBasePlugin for the given package name or URI
  - disablePackage
```
public void disablePackage(java.lang.String packageURIOrName)
```
    Disables the given SBML Level 3 package on this SBMLDocument.
    
    Specified by:
    
    disablePackage in interface SBase
    
    Parameters:
    packageURIOrName - a package namespace URI or package name
  - enablePackage
```
public void enablePackage(java.lang.String packageURIOrName)
```
    Enables the given SBML Level 3 package on this SBMLDocument.
    
    Specified by:
    
    enablePackage in interface SBase
    
    Parameters:
    packageURIOrName - a package namespace URI or package name
  - enablePackage
```
public void enablePackage(java.lang.String packageURIOrName,
                 boolean enabled)
```
    Enables or disables the given SBML Level 3 package on this SBMLDocument.
    
    Specified by:
    
    enablePackage in interface SBase
    
    Parameters:
    packageURIOrName - a package namespace URI or package name
    enabled - a boolean to tell if the package need to be enabled or disabled. It true the package will be enabled, otherwise it will be disabled.
  - 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 AbstractTreeNode
    
    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.
  - filterCVTerms
```
public java.util.List<CVTerm> filterCVTerms(CVTerm.Qualifier qualifier)
```
    Description copied from interface: SBase
    
    Returns a list of all the CVTerm with the given CVTerm.Qualifier.
    
    Specified by:
    
    filterCVTerms in interface SBase
    
    Parameters:
    qualifier - CVTerm.Qualifier used to filter the CVTerms.
    
    Returns:
    a list of all the CVTerm with the given CVTerm.Qualifier.
  - filterCVTerms
```
public java.util.List<java.lang.String> filterCVTerms(CVTerm.Qualifier qualifier,
                                             java.lang.String pattern)
```
    Description copied from interface: SBase
    
    Queries the list of controlled vocabulary terms (CVTerm) for those terms whose CVTerm.Qualifier is of the given type and selects only those resources from these terms that contain the given pattern.
    
    Specified by:
    
    filterCVTerms in interface SBase
    
    Parameters:
    qualifier - CVTerm.Qualifier used to filter the CVTerms.
    pattern - a regexp pattern, for instance, '.*kegg.*' or '.*chebi.*'.
    
    Returns:
    a list of resource URIs that matches the pattern.
    See Also:
    Pattern
  - filterCVTerms
```
public java.util.List<java.lang.String> filterCVTerms(CVTerm.Qualifier qualifier,
                                             java.lang.String pattern,
                                             boolean recursive)
```
    Description copied from interface: SBase
    
    Returns a list of resource URIs for the given CVTerm.Qualifier that match the given pattern.
    This is a recursive implementation of #filterCVTerms(Qualifier, String) that considers all child elements of the current instance of SBase as well.
    
    Specified by:
    
    filterCVTerms in interface SBase
    
    Parameters:
    qualifier - CVTerm.Qualifier used to filter the CVTerms.
    pattern - a regexp pattern, for instance, '.*kegg.*' or '.*chebi.*'.
    recursive - decides whether or not to consider all child elements of this SBase and collecting the matching CVTerms of all children recursively. If this argument is false, the behavior of the method will be equivalent to calling #filterCVTerms(Qualifier, String).
    
    Returns:
    a list of resources for the given CVTerm.Qualifier that match the given pattern.
    See Also:
    #filterCVTerms(Qualifier, String), Pattern
  - filterCVTerms
```
public java.util.List<java.lang.String> filterCVTerms(CVTerm.Qualifier qualifier,
                                             boolean recursive,
                                             java.lang.String... patterns)
```
    Description copied from interface: SBase
    
    Returns a list of resource URIs for the given CVTerm.Qualifier that match the given patterns.
    
    Specified by:
    
    filterCVTerms in interface SBase
    
    Parameters:
    qualifier - CVTerm.Qualifier used to filter the CVTerms.
    recursive - boolean used to decides whether or not to consider all child elements of this SBase and collecting the matching CVTerms of all children recursively.
    patterns - an arbitrary list of patterns to be matched to the resources of each CVTerm.
    
    Returns:
    a list of resources for the given CVTerm.Qualifier that match the given pattern.
    See Also:
    #filterCVTerms(Qualifier, String, boolean), CVTerm.filterResources(String...)
  - firePropertyChange
```
public void firePropertyChange(java.lang.String propertyName,
                      java.lang.Object oldValue,
                      java.lang.Object newValue)
```
    Description copied from interface: TreeNodeWithChangeSupport
    
    All TreeNodeChangeListeners are informed about the change in this TreeNodeWithChangeSupport.
    
    Specified by:
    
    firePropertyChange in interface TreeNodeWithChangeSupport
    
    Overrides:
    
    firePropertyChange in class AbstractTreeNode
    
    Parameters:
    propertyName - Tells the TreeNodeChangeListener the name of the property whose value has been changed.
    oldValue - This is the value before the change.
    newValue - This gives the new value that is now the new value for the given property..
  - fireNodeRemovedEvent
```
public void fireNodeRemovedEvent()
```
    Description copied from interface: TreeNodeWithChangeSupport
    
    All TreeNodeChangeListener instances linked to this TreeNode are informed about the deletion of this TreeNode from a parent Object.
    
    Specified by:
    
    fireNodeRemovedEvent in interface TreeNodeWithChangeSupport
    
    Overrides:
    
    fireNodeRemovedEvent in class AbstractTreeNode
  - getAllowsChildren
```
public boolean getAllowsChildren()
```
    Specified by:
    
    getAllowsChildren in interface javax.swing.tree.TreeNode
  - getAnnotation
```
public Annotation getAnnotation()
```
    Description copied from interface: SBase
    
    Returns the content of the 'annotation' sub-element of this object as an Annotation instance.
    
    Specified by:
    
    getAnnotation in interface SBase
    
    Returns:
    the content of the 'annotation' sub-element of this object as an Annotation instance.
  - getAnnotationString
```
public java.lang.String getAnnotationString()
                                     throws javax.xml.stream.XMLStreamException
```
    Returns the Annotation of this SBML object as a String.
    
    Specified by:
    
    getAnnotationString in interface SBase
    
    Returns:
    the Annotation of this SBML object as a String or an empty String if there are no Annotation.
    
    Throws:
    
    javax.xml.stream.XMLStreamException
  - getChildAt
```
public javax.swing.tree.TreeNode getChildAt(int childIndex)
```
    Specified by:
    
    getChildAt in interface javax.swing.tree.TreeNode
  - getChildCount
```
public int getChildCount()
```
    Specified by:
    
    getChildCount in interface javax.swing.tree.TreeNode
  - getCVTerm
```
public CVTerm getCVTerm(int index)
```
    Description copied from interface: SBase
    
    Returns the CVTerm instance at the position 'index' in the list of CVTerms of this object.
    
    Specified by:
    
    getCVTerm in interface SBase
    
    Parameters:
    index - index of the element to return
    
    Returns:
    the CVTerm instance at the position 'index' in the list of CVTerms of this object.
  - getCVTermCount
```
public int getCVTermCount()
```
    Description copied from interface: SBase
    
    Returns the number of CVTerms of this SBase.
    
    Specified by:
    
    getCVTermCount in interface SBase
    
    Returns:
    the number of CVTerms of this SBase.
  - getCVTerms
```
public java.util.List<CVTerm> getCVTerms()
```
    Description copied from interface: SBase
    
    Returns the list of CVTerms of this object.
    
    Specified by:
    
    getCVTerms in interface SBase
    
    Returns:
    the list of CVTerms of this object. If not yet set, this method initializes the annotation and returns an empty list.
  - getDeclaredNamespaces
```
public java.util.Map<java.lang.String,java.lang.String> getDeclaredNamespaces()
```
    Description copied from interface: SBase
    
    Returns all the namespaces declared on this object. These will be written on the resulting XML element.
    
    Specified by:
    
    getDeclaredNamespaces in interface SBase
    
    Returns:
    all the namespaces declared on this object. These will be written on the resulting XML element.
  - getElementName
```
public java.lang.String getElementName()
```
    Description copied from interface: SBase
    
    Returns the XML element name of this object.
    
    Specified by:
    
    getElementName in interface SBase
    
    Returns:
    the XML element name of this object.
  - getExtension
```
public SBasePlugin getExtension(java.lang.String nameOrUri)
```
    Description copied from interface: SBase
    
    Returns the SBasePlugin extension object which matches this package name or URI.
    
    Specified by:
    
    getExtension in interface SBase
    
    Parameters:
    nameOrUri - the package name or URI
    
    Returns:
    the SBasePlugin extension object which matches this package name or URI, null is returned if nothing matching the name or URI is found.
  - getExtensionCount
```
public int getExtensionCount()
```
    Description copied from interface: SBase
    
    Returns the number of SBasePlugins of this SBase.
    
    Specified by:
    
    getExtensionCount in interface SBase
    
    Returns:
    the number of SBasePlugins of this SBase.
  - getExtensionPackages
```
public java.util.Map<java.lang.String,SBasePlugin> getExtensionPackages()
```
    Description copied from interface: SBase
    
    Returns the map containing all the SBasePlugin extension objects of this SBase.
    
    Specified by:
    
    getExtensionPackages in interface SBase
    
    Returns:
    the map containing all the SBasePlugin extension objects of this SBase.
  - getFirstElementIndex
```
private int getFirstElementIndex(XMLNode curNotes)
```
    Return the index of the first child of type 'Element' for the given XMLNode.
    
    Parameters:
    curNotes -
    
    Returns:
    the index of the first child of type 'Element' for the given XMLNode, -1 otherwise.
  - getHistory
```
public History getHistory()
```
    Description copied from interface: SBase
    
    Returns the History instance of this object.
    
    Specified by:
    
    getHistory in interface SBase
    
    Returns:
    the History instance of this object.
  - getIdManager
```
protected IdManager getIdManager(SBase sbase)
```
    Returns an IdManager that can register the given SBase.
    It means that the method IdManager.accept(SBase) returned true.
    
    Parameters:
    sbase - the SBase that we try to register or unregister.
    
    Returns:
    an IdManager that can register the given SBase.
  - getLevel
```
public int getLevel()
```
    Description copied from interface: SBase
    
    Returns the SBML Level of the overall SBML document. Returns -1 if it is not set.
    
    Specified by:
    
    getLevel in interface SBase
    
    Returns:
    the SBML level of this SBML object.
    See Also:
    SBase.getVersion()
  - getLevelAndVersion
```
public ValuePair<java.lang.Integer,java.lang.Integer> getLevelAndVersion()
```
    Description copied from interface: SBase
    
    Returns the Level and Version combination of this SBase.
    
    Specified by:
    
    getLevelAndVersion in interface SBase
    
    Returns:
    A ValuePair with the Level and Version of this SBase. Note that the returned ValuePair is never null, but if undeclared it may contain elements set to -1.
  - getMetaId
```
public java.lang.String getMetaId()
```
    Description copied from interface: SBase
    
    Returns the metaid of this element.
    
    Specified by:
    
    getMetaId in interface SBase
    
    Returns:
    the metaid of this element.
  - getModel
```
public Model getModel()
```
    Description copied from interface: SBase
    
    Returns the Model object in which the current SBase is located.
    
    Specified by:
    
    getModel in interface SBase
    
    Returns:
    the Model object in which the current SBase is located.
  - getNamespace
```
public java.lang.String getNamespace()
```
    Description copied from interface: SBase
    
    Returns the namespace to which this SBase belong to.
    
    Specified by:
    
    getNamespace in interface SBase
    
    Returns:
    the namespace to which this SBase belong to.
  - getNotes
```
public XMLNode getNotes()
```
    Returns an XMLNode object that represent the notes of this element.
    
    Specified by:
    
    getNotes in interface SBase
    
    Returns:
    an XMLNode object that represent the notes of this element.
  - getNotesString
```
public java.lang.String getNotesString()
                                throws javax.xml.stream.XMLStreamException
```
    Description copied from interface: SBase
    
    Returns the notes sub-element of this object as a String.
    If no notes are set, an empty String will be returned.
    
    Specified by:
    
    getNotesString in interface SBase
    
    Returns:
    the notes sub-element of this object as a String. If no notes are set, an empty String will be returned.
    
    Throws:
    
    javax.xml.stream.XMLStreamException - if an error occurs while writing the XMLNode to a String.
  - getNumCVTerms
```
public int getNumCVTerms()
```
    Description copied from interface: SBase
    
    Returns the number of CVTerms of this SBase.
    
    Specified by:
    
    getNumCVTerms in interface SBase
    
    Returns:
    the number of CVTerms of this SBase.
  - getNumPlugins
```
public int getNumPlugins()
```
    Description copied from interface: SBase
    
    Returns the number of SBasePlugins of this SBase.
    
    Specified by:
    
    getNumPlugins in interface SBase
    
    Returns:
    the number of SBasePlugins of this SBase.
  - getParent
```
public SBase getParent()
```
    This is equivalent to calling getParentSBMLObject(), but this method is needed for TreeNode.
    
    Specified by:
    
    getParent in interface javax.swing.tree.TreeNode
    
    Overrides:
    
    getParent in class AbstractTreeNode
    
    Returns:
    the parent element of this element.
    See Also:
    getParentSBMLObject()
  - getParentSBMLObject
```
public SBase getParentSBMLObject()
```
    Description copied from interface: SBase
    
    Returns the parent of this SBase.
    
    Specified by:
    
    getParentSBMLObject in interface SBase
    
    Returns:
    the parent SBML object.
    See Also:
    TreeNode.getParent()
  - getPlugin
```
public SBasePlugin getPlugin(java.lang.String nameOrUri)
```
    Description copied from interface: SBase
    
    Returns an SBasePlugin for an SBML Level 3 package extension with the given package name or URI.
    If no SBasePlugin is found for this package, a new SBasePlugin is created, added to this SBase and returned.
    
    Specified by:
    
    getPlugin in interface SBase
    
    Parameters:
    nameOrUri - the name or URI of the package
    
    Returns:
    an SBasePlugin for an SBML Level 3 package extension with the given package name or URI.
  - getSBMLDocument
```
public SBMLDocument getSBMLDocument()
```
    Description copied from interface: SBase
    
    Returns the parent SBMLDocument object. LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class 'sbml' defined in the SBML Level 2 specification, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1 or Level 2.) This method allows the SBMLDocument for the current object to be retrieved.
    
    Specified by:
    
    getSBMLDocument in interface SBase
    
    Returns:
    the parent SBMLDocument object of this SBML object.
  - getSBOTerm
```
public int getSBOTerm()
```
    Description copied from interface: SBase
    
    Grants access to the Systems Biology Ontology (SBO) term associated with this SBase.
    
    Specified by:
    
    getSBOTerm in interface SBase
    
    Returns:
    the SBOTerm attribute of this element.
    See Also:
    SBO
  - getSBOTermID
```
public java.lang.String getSBOTermID()
```
    Description copied from interface: SBase
    
    Grants access to the Systems Biology Ontology (SBO) term associated with this SBase.
    
    Specified by:
    
    getSBOTermID in interface SBase
    
    Returns:
    the SBO term ID of this element.
    See Also:
    SBO
  - getVersion
```
public int getVersion()
```
    Description copied from interface: SBase
    
    Returns the Version within the SBML Level of the overall SBML document. Return -1 if it is not set.
    
    Specified by:
    
    getVersion in interface SBase
    
    Returns:
    the SBML version of this SBML object.
    See Also:
    SBase.getLevel()
  - 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 AbstractTreeNode
    
    Returns:
    a hash code value for this SBase instance.
    See Also:
    Object.hashCode()
  - hasValidAnnotation
```
public boolean hasValidAnnotation()
```
    Description copied from interface: SBase
    
    Returns true if the Annotation RDF 'about' attribute matches the metaid of this object.
    
    Specified by:
    
    hasValidAnnotation in interface SBase
    
    Returns:
    true if the Annotation 'about' String of this object matches the metaid of this object.
  - hasValidLevelVersionNamespaceCombination
```
public boolean hasValidLevelVersionNamespaceCombination()
```
    Description copied from interface: SBase
    
    Returns true or false depending on whether this object's level/version and namespace values correspond to a valid SBML specification.
    
    Specified by:
    
    hasValidLevelVersionNamespaceCombination in interface SBase
    
    Returns:
    true if this object's level, version and namespace values correspond to a valid SBML specification.
  - isExtendedByOtherPackages
```
public boolean isExtendedByOtherPackages()
```
    Description copied from interface: SBase
    
    Returns true if this object is extended by other packages.
    
    Specified by:
    
    isExtendedByOtherPackages in interface SBase
    
    Returns:
    true if this object is extended by other packages.
  - isPackageEnabled
```
public boolean isPackageEnabled(java.lang.String packageURIOrName)
```
    Description copied from interface: SBase
    
    Returns true if the given SBML Level 3 package is enabled within the containing SBMLDocument.
    
    Specified by:
    
    isPackageEnabled in interface SBase
    
    Parameters:
    packageURIOrName - the name or URI of the package extension.
    
    Returns:
    true if the given SBML Level 3 package is enabled within the containing SBMLDocument, false otherwise.
  - isPackageURIEnabled
```
public boolean isPackageURIEnabled(java.lang.String packageURIOrName)
```
    Description copied from interface: SBase
    
    Returns true if the given SBML Level 3 package is enabled within the containing SBMLDocument.
    
    Specified by:
    
    isPackageURIEnabled in interface SBase
    
    Parameters:
    packageURIOrName - the name or URI of the package extension.
    
    Returns:
    true if the given SBML Level 3 package is enabled within the containing SBMLDocument, false otherwise.
  - isPkgEnabled
```
@Deprecated
public boolean isPkgEnabled(java.lang.String packageURIOrName)
```
    Deprecated.
    
    Description copied from interface: SBase
    
    Returns true if the given SBML Level 3 package is enabled within the containing SBMLDocument.
    
    Specified by:
    
    isPkgEnabled in interface SBase
    
    Parameters:
    packageURIOrName - the name or URI of the package extension.
    
    Returns:
    true if the given SBML Level 3 package is enabled within the containing SBMLDocument, false otherwise.
  - isPkgURIEnabled
```
@Deprecated
public boolean isPkgURIEnabled(java.lang.String packageURIOrName)
```
    Deprecated.
    
    Description copied from interface: SBase
    
    Returns true if the given SBML Level 3 package is enabled within the containing SBMLDocument.
    
    Specified by:
    
    isPkgURIEnabled in interface SBase
    
    Parameters:
    packageURIOrName - the name or URI of the package extension.
    
    Returns:
    true if the given SBML Level 3 package is enabled within the containing SBMLDocument, false otherwise.
  - isSetAnnotation
```
public boolean isSetAnnotation()
```
    Description copied from interface: SBase
    
    Returns true or false depending on whether this object's 'annotation' sub-elements exists and have some content.
    
    Specified by:
    
    isSetAnnotation in interface SBase
    
    Returns:
    true if the Annotation instance of this object is not null and contains at least one CVTerm or one String containing other annotations than RDF or a History instance.
  - isSetHistory
```
public boolean isSetHistory()
```
    Description copied from interface: SBase
    
    Returns true if the History instance of this object is set.
    
    Specified by:
    
    isSetHistory in interface SBase
    
    Returns:
    true if the History instance of this object is set.
  - isSetLevel
```
public boolean isSetLevel()
```
    Description copied from interface: SBase
    
    Returns true if the level is set.
    
    Specified by:
    
    isSetLevel in interface SBase
    
    Returns:
    true if the level is set.
  - isSetLevelAndVersion
```
public boolean isSetLevelAndVersion()
```
    Description copied from interface: SBase
    
    Returns true if both, Level and Version are set for this SBase.
    
    Specified by:
    
    isSetLevelAndVersion in interface SBase
    
    Returns:
    true if SBase.isSetLevel() and SBase.isSetVersion().
  - isSetMetaId
```
public boolean isSetMetaId()
```
    Description copied from interface: SBase
    
    Returns true or false depending on whether this object's 'metaid' attribute has been set.
    
    Specified by:
    
    isSetMetaId in interface SBase
    
    Returns:
    true if the metaid is not null.
  - isSetNotes
```
public boolean isSetNotes()
```
    Description copied from interface: SBase
    
    Returns true or false depending on whether this object's 'notes' sub-element exists and has content.
    
    Specified by:
    
    isSetNotes in interface SBase
    
    Returns:
    true if the notes String is not null.
  - isSetParentSBMLObject
```
public boolean isSetParentSBMLObject()
```
    Description copied from interface: SBase
    
    Check whether this SBase has been linked to a parent within the hierarchical SBML data structure.
    
    Specified by:
    
    isSetParentSBMLObject in interface SBase
    
    Returns:
    true if this SBase has a parent SBML object, false otherwise.
    See Also:
    SBase.getParentSBMLObject()
  - isSetPlugin
```
public boolean isSetPlugin(java.lang.String nameOrUri)
```
    Description copied from interface: SBase
    
    Returns true if an SBasePlugin is defined for the given package.
    
    Specified by:
    
    isSetPlugin in interface SBase
    
    Parameters:
    nameOrUri - the package name or URI
    
    Returns:
    true if an SBasePlugin is defined for the given package.
  - isSetSBOTerm
```
public boolean isSetSBOTerm()
```
    Description copied from interface: SBase
    
    Returns true if the SBOTerm is set.
    
    Specified by:
    
    isSetSBOTerm in interface SBase
    
    Returns:
    true if the SBOTerm is set.
    See Also:
    SBO
  - isSetVersion
```
public boolean isSetVersion()
```
    Description copied from interface: SBase
    
    Returns true if the version is not null.
    
    Specified by:
    
    isSetVersion in interface SBase
    
    Returns:
    true if the version is not null.
  - notifyChildChange
```
protected void notifyChildChange(javax.swing.tree.TreeNode oldChild,
                     javax.swing.tree.TreeNode newChild)
```
    Description copied from class: AbstractTreeNode
    
    This method is called when one child has been swapped with another one and can be used to check certain properties of the resulting changed tree.
    
    Overrides:
    
    notifyChildChange in class AbstractTreeNode
    
    Parameters:
    oldChild - the element that was a child of this node before the change.
    newChild - the new child whose new parent is this node.
  - 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
    
    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.
  - registerChild
```
public void registerChild(SBase sbase)
                   throws LevelVersionError
```
    Description copied from interface: SBase
    
    Sets this object as SBML parent of 'sbase'. Check if the level and version of sbase are set, otherwise sets the level and version of 'sbase' with those of this object. This method should actually not be called by any tool as it is used internally within JSBML to maintain the hierarchical document structure. If the level and version of sbase are set but not valid, an Exception is thrown.
    
    Specified by:
    
    registerChild in interface SBase
    
    Parameters:
    sbase - the SBase to be registered.
    
    Throws:
    
    LevelVersionError - In case the given SBase has a different, but defined Level/Version combination than this current SBase, an LevelVersionError is thrown.
  - registerChild
```
private void registerChild(SBasePlugin sbasePlugin)
```
    Registers recursively the given SBasePlugin from the Model and SBMLDocument.
    
    Parameters:
    sbasePlugin - the SBasePlugin to register.
  - removeCVTerm
```
public boolean removeCVTerm(CVTerm cvTerm)
```
    Removes the given CVTerm.
    
    Specified by:
    
    removeCVTerm in interface SBase
    
    Parameters:
    cvTerm - the CVTerm to remove
    
    Returns:
    true if the CVTerm was successfully removed.
  - removeCVTerm
```
public CVTerm removeCVTerm(int index)
```
    Removes the CVTerm at the given index.
    
    Specified by:
    
    removeCVTerm in interface SBase
    
    Parameters:
    index - the index
    
    Returns:
    the removed CVTerm.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the index is out of range (index < 0 || index >= size())
  - setAnnotation
```
public void setAnnotation(Annotation annotation)
```
    Description copied from interface: SBase
    
    Sets the value of the 'annotation' sub-element of this SBML object to a copy of annotation given as an Annotation instance.
    
    Specified by:
    
    setAnnotation in interface SBase
    
    Parameters:
    annotation - the annotation of this SBase
  - setHistory
```
public void setHistory(History history)
```
    Description copied from interface: SBase
    
    Sets the history.
    
    Specified by:
    
    setHistory in interface SBase
    
    Parameters:
    history - the history of this SBase
  - setLevel
```
public void setLevel(int level)
```
    Description copied from interface: SBase
    
    Sets the level of this object with 'level'. If the SBML parent of this object is set and 'level' is different with the SBML parent level, an Exception is thrown.
    
    Specified by:
    
    setLevel in interface SBase
    
    Parameters:
    level - the SBML level.
  - setLevelAndVersion
```
boolean setLevelAndVersion(int level,
                         int version,
                         boolean strict)
```
    Sets recursively the level and version attribute for this element and all sub-elements.
    
    Parameters:
    level - the SBML level
    version - the SBML version
    strict - a boolean to say if the method need to be strict or not (not used at the moment)
    
    Returns:
    true if the operation as been successful.
  - setMetaId
```
public void setMetaId(java.lang.String metaId)
```
    Description copied from interface: SBase
    
    Sets the metaid value with 'metaid'.
    
    Specified by:
    
    setMetaId in interface SBase
    
    Parameters:
    metaId - the meatId to be set.
  - setNotes
```
public void setNotes(java.lang.String notes)
              throws javax.xml.stream.XMLStreamException
```
    Description copied from interface: SBase
    
    Sets the notes with 'notes'.
    
    Specified by:
    
    setNotes in interface SBase
    
    Parameters:
    notes - the notes for this SBase.
    
    Throws:
    
    javax.xml.stream.XMLStreamException - if an error occurs while parsing the notes.
  - setNotes
```
public void setNotes(XMLNode notes)
```
    Description copied from interface: SBase
    
    Sets the XMLNode containing the notes sub-element of this object.
    
    Specified by:
    
    setNotes in interface SBase
    
    Parameters:
    notes - the notes for this SBase.
  - setParentSBML
```
protected void setParentSBML(SBase parent)
```
  - setParentSBMLObject
```
protected void setParentSBMLObject(SBase sbase)
                            throws LevelVersionError
```
    Checks the Level/Version configuration of the new parent (if it is compliant to the one of this SBase), adds all changeListeners from the parent to this SBase, fires a TreeNodeChangeListener.nodeAdded(TreeNode) event, and and finally, it will forward the new parent to setParentSBML(SBase). Note that this will cause another event to be triggered: PropertyChangeListener.propertyChange(java.beans.PropertyChangeEvent) with the old and the new parent.
    
    Parameters:
    sbase - the new parent element.
    
    Throws:
    
    LevelVersionError - if the SBML Level and Version configuration of the new parent differs from the one of this SBase.
    See Also:
    #setParentSBML(SBase)}
  - setSBOTerm
```
public void setSBOTerm(int term)
```
    Description copied from interface: SBase
    
    Sets the value of the 'sboTerm' attribute.
    Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; JSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in JSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
    SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
    
    Specified by:
    
    setSBOTerm in interface SBase
    
    Parameters:
    term - the NNNNNNN integer portion of the SBO identifier
    See Also:
    SBO
  - setSBOTerm
```
public void setSBOTerm(java.lang.String sboid)
```
    Description copied from interface: SBase
    
    Sets the value of the 'sboTerm' attribute.
    Beginning with SBML Level 2 Version 3, objects derived from SBase have an optional attribute named 'sboTerm' for supporting the use of the Systems Biology Ontology. In SBML proper, the data type of the attribute is a string of the form 'SBO:NNNNNNN', where 'NNNNNNN' is a seven digit integer number; JSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in JSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers.
    SBO terms are a type of optional annotation, and each different class of SBML object derived from SBase imposes its own requirements about the values permitted for 'sboTerm'. Please consult the SBML Level 2 Version 4 specification for more information about the use of SBO and the 'sboTerm' attribute.
    
    Specified by:
    
    setSBOTerm in interface SBase
    
    Parameters:
    sboid - the SBO identifier of the form 'SBO:NNNNNNN'
    See Also:
    SBO
  - setThisAsParentSBMLObject
```
@Deprecated
public void setThisAsParentSBMLObject(SBase sbase)
                               throws LevelVersionError
```
    Deprecated.
    
    Description copied from interface: SBase
    
    Sets this object as SBML parent of 'sbase'. Check if the level and version of sbase are set, otherwise sets the level and version of 'sbase' with those of this object. This method should actually not be called by any tool as it is used internally within JSBML to maintain the hierarchical document structure. If the level and version of sbase are set but not valid, an Exception is thrown.
    
    Specified by:
    
    setThisAsParentSBMLObject in interface SBase
    
    Parameters:
    sbase - the child SBase
    
    Throws:
    
    LevelVersionError
  - setVersion
```
public void setVersion(int version)
```
    Description copied from interface: SBase
    
    Sets the version of this object with 'version'. If the SBML parent of this object is set and 'version' is different with the SBMLparent version, an Exception is thrown.
    
    Specified by:
    
    setVersion in interface SBase
    
    Parameters:
    version - the SBML version
  - toString
```
public abstract java.lang.String toString()
```
    Overrides:
    
    toString in class AbstractTreeNode
  - unregisterChild
```
public void unregisterChild(SBase sbase)
```
    Description copied from interface: SBase
    
    Unregisters recursively the given SBase from the Model and SBMLDocument.
    
    Specified by:
    
    unregisterChild in interface SBase
    
    Parameters:
    sbase - the SBase to be unregistered.
  - unregisterChild
```
private void unregisterChild(SBasePlugin sbasePlugin)
```
    Unregisters recursively the given SBasePlugin from the Model and SBMLDocument.
    
    Parameters:
    sbasePlugin - the SBasePlugin to unregister.
  - unsetAnnotation
```
public void unsetAnnotation()
```
    Description copied from interface: SBase
    
    Unsets the value of the 'annotation' sub-element of this SBML object.
    
    Specified by:
    
    unsetAnnotation in interface SBase
  - unsetCVTerms
```
public void unsetCVTerms()
```
    Description copied from interface: SBase
    
    Unsets the list of CVTerm of this object.
    
    Specified by:
    
    unsetCVTerms in interface SBase
  - unsetHistory
```
public void unsetHistory()
```
    Description copied from interface: SBase
    
    Unsets the History of this object.
    
    Specified by:
    
    unsetHistory in interface SBase
  - unsetMetaId
```
public void unsetMetaId()
```
    Description copied from interface: SBase
    
    Unsets the value of the 'metaid' attribute of this SBML object.
    
    Specified by:
    
    unsetMetaId in interface SBase
  - unsetNamespace
```
public void unsetNamespace()
```
    Unsets the namespace that is associated to this SBase.
    This is an internal method of JSBML that should be used with caution.
  - unsetNotes
```
public void unsetNotes()
```
    Description copied from interface: SBase
    
    Unsets the value of the 'notes' sub-element of this SBML object.
    
    Specified by:
    
    unsetNotes in interface SBase
  - unsetExtension
```
public void unsetExtension(java.lang.String nameOrUri)
```
    Description copied from interface: SBase
    
    Unsets the SBasePlugin extension object which matches this package name or URI.
    
    Specified by:
    
    unsetExtension in interface SBase
    
    Parameters:
    nameOrUri - the package name or URI
  - unsetPlugin
```
public void unsetPlugin(java.lang.String nameOrUri)
```
    Description copied from interface: SBase
    
    Unsets the SBasePlugin extension object which matches this package name or URI.
    
    Specified by:
    
    unsetPlugin in interface SBase
    
    Parameters:
    nameOrUri - the package name or URI
  - unsetSBOTerm
```
public void unsetSBOTerm()
```
    Description copied from interface: SBase
    
    Unsets the value of the 'sboTerm' attribute of this SBML object.
    
    Specified by:
    
    unsetSBOTerm in interface SBase
  - 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
    
    Returns:
    a Map containing the XML attributes of this object.

Class AbstractSBase

Nested Class Summary

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from class java.lang.Object

Methods inherited from interface org.sbml.jsbml.SBase

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

Methods inherited from interface javax.swing.tree.TreeNode

Field Detail

idPattern

simpleIdPattern

logger

serialVersionUID

annotation

declaredNamespaces

extensions

ignoredExtensions

ignoredXMLElements

lv

metaId

notesXMLNode

sboTerm

elementNamespace

Constructor Detail

AbstractSBase

AbstractSBase

AbstractSBase

Method Detail

isValidLevelAndVersionCombination

isValidMetaId

addCVTerm

addDeclaredNamespace

addExtension

addPlugin

setNamespace

appendNotes

appendNotes

checkLevelAndVersionCompatibility

clone

createHistory

createPlugin

disablePackage

enablePackage

enablePackage

equals

filterCVTerms

filterCVTerms

filterCVTerms

filterCVTerms

firePropertyChange

fireNodeRemovedEvent

getAllowsChildren

getAnnotation

getAnnotationString

getChildAt

getChildCount

getCVTerm

getCVTermCount

getCVTerms

getDeclaredNamespaces

getElementName

getExtension

getExtensionCount

getExtensionPackages

getFirstElementIndex

getHistory

getIdManager

getLevel

getLevelAndVersion

getMetaId

getModel

getNamespace

getNotes

getNotesString

getNumCVTerms

getNumPlugins

getParent