AbstractSBase (JSBML 1.5 API Specification)

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:

AbstractDistribSBase, AbstractMathContainer, AbstractNamedSBase, AbstractSpatialNamedSBase, CoordinateReference, Curve, CurveSegment, DefaultValues, GradientStop, InteriorPoint, ListOf, LogicalOperator, OrdinalMapping, OutwardBindingSite, ParameterType, PolygonObject, RenderCurveSegment, SBaseRef, SBMLDocument, SpeciesFeatureValue, SpeciesTypeComponentMapInProduct, Transformation, TransformationComponent, Unit
```
public abstract class AbstractSBase
extends AbstractTreeNode
implements SBase
```
The base class for each SBase component.

Since:

0.8

Author:

Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field and Description

static java.lang.String JSBML_WRONG_SBO_TERM

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`JSBML_WRONG_SBO_TERM`

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`.
`AbstractSBase(java.lang.String id)` Creates an `AbstractSBase` with the given identifier.
`AbstractSBase(java.lang.String id, int level, int version)` Creates an `AbstractSBase` from an id, level and version.
`AbstractSBase(java.lang.String id, java.lang.String name, int level, int version)` Creates an `AbstractSBase` from an id, name, level and version.

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Deprecated 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`	`appendAnnotation(java.lang.String annotation)` Appends the given annotation to the 'annotation' subelement of this object.
`void`	`appendAnnotation(XMLNode annotation)` Appends the given annotation to the 'annotation' subelement of this object.
`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.
`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`.
`static java.util.HashMap<java.lang.String,java.lang.String>`	`getAllDeclaredNamespaces(SBase sb)` Returns a map of all the declared namespaces in the SBML tree, visible to the given `SBase`.
`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.
`SBase`	`getElementByMetaId(java.lang.String id)` Returns the first child element found that has the given metaid.
`SBase`	`getElementBySId(java.lang.String id)` Returns the first child element found that has the given id.
`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`.
`static 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.
`java.lang.String`	`getId()` Returns the id of the element if it is set, an empty string otherwise.
`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`	`getName()` Returns the name of the element if it is set, an empty string otherwise.
`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`.
`java.lang.String`	`getPackageName()` Returns the name of the SBML Level 3 package in which this element is defined, as defined in the sbml.org community wiki.
`int`	`getPackageVersion()` Returns the version of the SBML Level 3 package to which this element belongs.
`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`.
`java.lang.String`	`getURI()` Returns the namespace to which this `SBase` belong to.
`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`	`isIdMandatory()` Returns `true` if the identifier of this `SBase` is required to be defined (i.e., not `null`) in the definition of SBML.
`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`	`isSetId()` Returns `true` if the id is not `null`.
`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`	`isSetName()` Returns `true` if the name is not `null`.
`boolean`	`isSetNotes()` Returns `true` or `false` depending on whether this object's 'notes' sub-element exists and has content.
`boolean`	`isSetPackageVErsion()` Returns `true` if the package version is not equals to '-1'.
`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)` Deprecated. use `SyntaxChecker.isValidMetaId(String)`
`boolean`	`readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)` Sets the given attribute in this `SBase`.
`boolean`	`registerChild(SBase sbase)` Sets this object as SBML parent of 'sbase'.
`boolean`	`removeCVTerm(CVTerm cvTerm)` Removes the given `CVTerm`.
`CVTerm`	`removeCVTerm(int index)` Removes the `CVTerm` at the given index.
`void`	`removeDeclaredNamespaceByNamespace(java.lang.String namespace)` Removes a namespace from the set of declared namespaces of this `SBase`.
`void`	`removeDeclaredNamespaceByPrefix(java.lang.String prefix)` Removes a namespace from the set of declared namespaces of this `SBase`.
`boolean`	`removeTopLevelAnnotationElement(java.lang.String name)` Removes the top-level element within the 'annotation' subelement of this SBML object with the given name.
`boolean`	`removeTopLevelAnnotationElement(java.lang.String name, java.lang.String elementURI)` Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and URI.
`boolean`	`removeTopLevelAnnotationElement(java.lang.String name, java.lang.String elementURI, boolean removeEmpty)` Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and URI.
`boolean`	`replaceTopLevelAnnotationElement(java.lang.String annotation)` Replaces the top-level element of this SBML object with same name as given annotation subelement by the given one.
`boolean`	`replaceTopLevelAnnotationElement(XMLNode annotation)` Replaces the top-level element of this SBML object with same name as given annotation subelement by the given one.
`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`	`setAnnotation(java.lang.String nonRDFAnnotation)` Sets the non RDF part of the annotation.
`void`	`setAnnotation(XMLNode nonRDFAnnotation)` Sets the non RDF part of the annotation.
`void`	`setHistory(History history)` Sets the history.
`void`	`setId(java.lang.String id)` Sets the id value with 'id'
`void`	`setLevel(int level)` Sets the level of this object with 'level'.
`void`	`setMetaId(java.lang.String metaId)` Sets the metaid value with 'metaid'.
`void`	`setName(java.lang.String name)` Sets the name value with 'name'.
`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.
`void`	`setPackageVersion(int packageVersion)` Sets the version of the SBML Level 3 package to which this element belongs.
`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'.
`java.lang.String`	`toString()` Returns a String representing this SBase with all the attributes that are defined.
`void`	`unregisterChild(SBase sbase)` Unregisters recursively the given SBase 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`	`unsetId()` Sets the id value to `null`.
`void`	`unsetMetaId()` Unsets the value of the 'metaid' attribute of this SBML object.
`void`	`unsetName()` Sets the name value to `null`.
`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
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
  - JSBML_WRONG_SBO_TERM
```
public static final transient java.lang.String JSBML_WRONG_SBO_TERM
```
    See Also:
    
    Constant Field Values
- 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
  - AbstractSBase
```
public AbstractSBase(java.lang.String id)
```
    Creates an AbstractSBase with the given identifier.
    Note that with this constructor the level and version of the element are not specified. But when adding the SBase inside a Model, it will inherit the level and version from his parent.
    
    Parameters:
    
    id - the id of this AbstractSBase
  - AbstractSBase
```
public AbstractSBase(java.lang.String id,
                     int level,
                     int version)
```
    Creates an AbstractSBase from an id, level and version.
    
    Parameters:
    
    id - the id of this AbstractSBase
    
    level - the SBML level
    
    version - the SBML version
  - AbstractSBase
```
public AbstractSBase(java.lang.String id,
                     java.lang.String name,
                     int level,
                     int version)
```
    Creates an AbstractSBase from an id, name, level and version.
    
    Parameters:
    
    id - the id of this AbstractSBase
    
    name - the name of this AbstractSBase
    
    level - the SBML level
    
    version - the SBML version
- 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
```
@Deprecated
public static final boolean isValidMetaId(java.lang.String idCandidate)
```
    Deprecated. use SyntaxChecker.isValidMetaId(String)
    
    Checks if the given identifier candidate satisfies the requirements for a valid meta identifier (see SBML L2V4 p. 12 for details).
    
    Parameters:
    
    idCandidate - the id to check
    
    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)
  - appendAnnotation
```
public void appendAnnotation(java.lang.String annotation)
                      throws javax.xml.stream.XMLStreamException
```
    Description copied from interface: SBase
    
    Appends the given annotation to the 'annotation' subelement of this object. Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content. SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details. Unlike SBase.setAnnotation(XMLNode) or SBase.setAnnotation(String), this method allows other annotations to be preserved when an application adds its own data.
    
    Specified by:
    
    appendAnnotation in interface SBase
    
    Parameters:
    
    annotation - an XML string that is to be copied and appended to the content of the 'annotation' subelement of this object
    
    Throws:
    
    javax.xml.stream.XMLStreamException - thrown if the given annotation String cannot be parsed into XMLNode objects.
    
    See Also:
    
    SBase.appendAnnotation(XMLNode)
  - appendAnnotation
```
public void appendAnnotation(XMLNode annotation)
```
    Description copied from interface: SBase
    
    Appends the given annotation to the 'annotation' subelement of this object. Whereas the SBase 'notes' subelement is a container for content to be shown directly to humans, the 'annotation' element is a container for optional software-generated content not meant to be shown to humans. Every object derived from SBase can have its own value for 'annotation'. The element's content type is XML type 'any', allowing essentially arbitrary well-formed XML data content. SBML places a few restrictions on the organization of the content of annotations; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. Please see the SBML specifications for more details. Unlike SBase.setAnnotation(XMLNode) or SBase.setAnnotation(String), this method allows other annotations to be preserved when an application adds its own data.
    
    Specified by:
    
    appendAnnotation in interface SBase
    
    Parameters:
    
    annotation - an XML structure that is to be copied and appended to the content of the 'annotation' subelement of this object
  - 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 - the notes to append.
  - 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,
                                                      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...)
  - 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
  - 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
  - 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..
  - 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 - if there is a problem writing the annotation to XML.
  - 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.
  - getElementBySId
```
public SBase getElementBySId(java.lang.String id)
```
    Description copied from interface: SBase
    
    Returns the first child element found that has the given id.
    This operation searches the model-wide SId identifier type namespace. So it will not find for example LocalParameter or UnitDefinition.
    
    This method is here for compatibility with libSBML, it is less efficient than the methods that are located in the Model and SBMLDocument classes.
    
    If you want to get an SBase that is not in the SId namespace, you can use the filter methods (for example: TreeNodeWithChangeSupport.filter(Filter)) using the IdFilter filter.
    
    Specified by:
    
    getElementBySId in interface SBase
    
    Parameters:
    
    id - string representing the id of the SBase to find.
    
    Returns:
    
    the first child element found that has the given id.
    
    See Also:
    
    Model.getSBaseById(String)
  - getElementByMetaId
```
public SBase getElementByMetaId(java.lang.String id)
```
    Description copied from interface: SBase
    
    Returns the first child element found that has the given metaid.
    This method is here for compatibility with libSBML, it is less efficient than the methods that are located in the Model and SBMLDocument classes.
    
    Specified by:
    
    getElementByMetaId in interface SBase
    
    Parameters:
    
    id - string representing the metaid of the SBase to find.
    
    Returns:
    
    the first child element found that has the given metaid.
    
    See Also:
    
    SBMLDocument.findSBase(String)
  - 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
```
public static int getFirstElementIndex(XMLNode curNotes)
```
    Return the index of the first child of type 'Element' for the given XMLNode.
    
    Parameters:
    
    curNotes - the XMLNode
    
    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.
  - 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.
  - getPackageName
```
public java.lang.String getPackageName()
```
    Description copied from interface: SBase
    
    Returns the name of the SBML Level 3 package in which this element is defined, as defined in the sbml.org community wiki.
    For example, the string "core" will be returned if this element is defined in SBML Level 3 Core.
    
    Specified by:
    
    getPackageName in interface SBase
    
    Returns:
    
    the name of the SBML Level 3 package in which this element is defined.
  - getPackageVersion
```
public int getPackageVersion()
```
    Description copied from interface: SBase
    
    Returns the version of the SBML Level 3 package to which this element belongs.
    The value 0 will be returned if this element belongs to the SBML Level 3 Core package. The value -1 will be returned if this element does not belong to the SBML Level core and the value has not been set properly.
    
    Specified by:
    
    getPackageVersion in interface SBase
    
    Returns:
    
    the version of the SBML Level 3 package to which this element belongs.
  - 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
  - getURI
```
public java.lang.String getURI()
```
    Description copied from interface: SBase
    
    Returns the namespace to which this SBase belong to. Same as SBase.getNamespace().
    For example, all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1'.
    The elements that belong to SBML core might return null.
    
    Specified by:
    
    getURI in interface SBase
    
    Returns:
    
    the namespace to which this SBase belong to.
    
    See Also:
    
    SBase.getNamespace()
  - 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.
  - isIdMandatory
```
public boolean isIdMandatory()
```
    Description copied from interface: SBase
    
    Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.
    
    Specified by:
    
    isIdMandatory in interface SBase
    
    Returns:
    
    true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.
  - 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.
  - isSetPackageVErsion
```
public boolean isSetPackageVErsion()
```
    Description copied from interface: SBase
    
    Returns true if the package version is not equals to '-1'.
    
    Specified by:
    
    isSetPackageVErsion in interface SBase
    
    Returns:
    
    true if the package version is not equals to '-1'.
  - 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.
  - 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 boolean 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.
    
    Returns:
    
    true if the element could successfully be registered, false otherwise, e.g., if the element has already been registered.
    
    Throws:
    
    LevelVersionError - In case the given SBase has a different, but defined Level/Version combination than this current SBase, an LevelVersionError is thrown.
  - 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())
  - removeDeclaredNamespaceByPrefix
```
public void removeDeclaredNamespaceByPrefix(java.lang.String prefix)
```
    Removes a namespace from the set of declared namespaces of this SBase.
    
    Specified by:
    
    removeDeclaredNamespaceByPrefix in interface SBase
    
    Parameters:
    
    prefix - the prefix of the namespace to remove
  - removeDeclaredNamespaceByNamespace
```
public void removeDeclaredNamespaceByNamespace(java.lang.String namespace)
```
    Removes a namespace from the set of declared namespaces of this SBase.
    
    Specified by:
    
    removeDeclaredNamespaceByNamespace in interface SBase
    
    Parameters:
    
    namespace - the namespace to remove
  - removeTopLevelAnnotationElement
```
public boolean removeTopLevelAnnotationElement(java.lang.String name)
```
    Description copied from interface: SBase
    
    Removes the top-level element within the 'annotation' subelement of this SBML object with the given name. If the name is null, "" or "*", nothing will be removed (return=false). If the annotation is empty after removal, it will be removed/unset
    
    Specified by:
    
    removeTopLevelAnnotationElement in interface SBase
    
    Parameters:
    
    name - of the annotation element to be removed
    
    Returns:
    
    Whether the element was found and removed
  - removeTopLevelAnnotationElement
```
public boolean removeTopLevelAnnotationElement(java.lang.String name,
                                               java.lang.String elementURI)
```
    Description copied from interface: SBase
    
    Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and URI. If the name is null, "" or "*", nothing will be removed (return=false). If the annotation is empty after removal, it will be removed/unset
    
    Specified by:
    
    removeTopLevelAnnotationElement in interface SBase
    
    Parameters:
    
    name - of the annotation element to be removed
    
    elementURI - of the annotation element to be removed
    
    Returns:
    
    Whether the element was found and removed
  - removeTopLevelAnnotationElement
```
public boolean removeTopLevelAnnotationElement(java.lang.String name,
                                               java.lang.String elementURI,
                                               boolean removeEmpty)
```
    Description copied from interface: SBase
    
    Removes the top-level element within the 'annotation' subelement of this SBML object with the given name and URI. If the name is null, "" or "*", nothing will be removed (return=false).
    
    Specified by:
    
    removeTopLevelAnnotationElement in interface SBase
    
    Parameters:
    
    name - of the annotation element to be removed
    
    elementURI - of the annotation element to be removed (if null, "" or "*", will match any URI)
    
    removeEmpty - Whether to remove/unset the annotation, if it is empty after removing the specified element
    
    Returns:
    
    Whether the element was found and removed
  - replaceTopLevelAnnotationElement
```
public boolean replaceTopLevelAnnotationElement(java.lang.String annotation)
                                         throws javax.xml.stream.XMLStreamException,
                                                java.lang.IllegalArgumentException
```
    Description copied from interface: SBase
    
    Replaces the top-level element of this SBML object with same name as given annotation subelement by the given one. Ordering of annotation will remain the same. Name of element to be replaced is inferred from given annotation string.
    
    Specified by:
    
    replaceTopLevelAnnotationElement in interface SBase
    
    Parameters:
    
    annotation - XML-string representing the annotation subelement to replace the existing one of same name
    
    Returns:
    
    whether a corresponding element was found and replaced
    
    Throws:
    
    javax.xml.stream.XMLStreamException - if the annotation-string cannot be parsed into an XML
    
    java.lang.IllegalArgumentException - if the annotation-string encodes more than one annotation element
  - replaceTopLevelAnnotationElement
```
public boolean replaceTopLevelAnnotationElement(XMLNode annotation)
```
    Description copied from interface: SBase
    
    Replaces the top-level element of this SBML object with same name as given annotation subelement by the given one. Ordering of annotation will remain the same. Name of element to be replaced is inferred from given annotation XMLNode.
    
    Specified by:
    
    replaceTopLevelAnnotationElement in interface SBase
    
    Parameters:
    
    annotation - XMLNode representing the annotation subelement to replace the existing one of same name
    
    Returns:
    
    whether a corresponding element was found and replaced
  - 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
  - setAnnotation
```
public void setAnnotation(java.lang.String nonRDFAnnotation)
                   throws javax.xml.stream.XMLStreamException
```
    Description copied from interface: SBase
    
    Sets the non RDF part of the annotation.
    
    Specified by:
    
    setAnnotation in interface SBase
    
    Parameters:
    
    nonRDFAnnotation - a String representing a piece of XML.
    
    Throws:
    
    javax.xml.stream.XMLStreamException - - if any problem occurs while reading the XML.
  - setAnnotation
```
public void setAnnotation(XMLNode nonRDFAnnotation)
```
    Description copied from interface: SBase
    
    Sets the non RDF part of the annotation.
    
    Specified by:
    
    setAnnotation in interface SBase
    
    Parameters:
    
    nonRDFAnnotation - an XMLNode
  - 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.
  - setMetaId
```
public void setMetaId(java.lang.String metaId)
               throws java.lang.IllegalArgumentException
```
    Description copied from interface: SBase
    
    Sets the metaid value with 'metaid'.
    
    Specified by:
    
    setMetaId in interface SBase
    
    Parameters:
    
    metaId - the meatId to be set.
    
    Throws:
    
    java.lang.IllegalArgumentException - if the given metaid does not follow the pattern for valid metaids ore if it is already used in the SBMLDocument
  - 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.
  - 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.
  - setPackageVersion
```
public void setPackageVersion(int packageVersion)
```
    Description copied from interface: SBase
    
    Sets the version of the SBML Level 3 package to which this element belongs.
    Use with caution, only if you know what you are doing. This should be set automatically.
    
    Specified by:
    
    setPackageVersion in interface SBase
    
    Parameters:
    
    packageVersion - the version of the SBML Level 3 package to which this element belongs.
  - 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 - - if the parent and the child have a different level and version.
  - 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 java.lang.String toString()
```
    Returns a String representing this SBase with all the attributes that are defined.
    
    Overrides:
    
    toString in class AbstractTreeNode
    
    Returns:
    
    a String representing this SBase with all its attributes
  - 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.
  - 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
  - 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
  - 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
  - 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.
  - getId
```
public java.lang.String getId()
```
    Description copied from interface: SBase
    
    Returns the id of the element if it is set, an empty string otherwise.
    
    Specified by:
    
    getId in interface SBase
    
    Returns:
    
    the id of the element if it is set, an empty string otherwise.
  - getName
```
public java.lang.String getName()
```
    Description copied from interface: SBase
    
    Returns the name of the element if it is set, an empty string otherwise.
    
    Specified by:
    
    getName in interface SBase
    
    Returns:
    
    the name of the element if it is set, an empty string otherwise.
  - isSetId
```
public boolean isSetId()
```
    Description copied from interface: SBase
    
    Returns true if the id is not null.
    
    Specified by:
    
    isSetId in interface SBase
    
    Returns:
    
    true if the id is not null.
  - isSetName
```
public boolean isSetName()
```
    Description copied from interface: SBase
    
    Returns true if the name is not null.
    
    Specified by:
    
    isSetName in interface SBase
    
    Returns:
    
    true if the name is not null.
  - setId
```
public void setId(java.lang.String id)
```
    Description copied from interface: SBase
    
    Sets the id value with 'id'
    
    Specified by:
    
    setId in interface SBase
    
    Parameters:
    
    id - the id to set
  - setName
```
public void setName(java.lang.String name)
```
    Description copied from interface: SBase
    
    Sets the name value with 'name'. If level is 1, sets automatically the id to 'name' as well.
    
    Specified by:
    
    setName in interface SBase
    
    Parameters:
    
    name - the name to set
  - unsetId
```
public void unsetId()
```
    Description copied from interface: SBase
    
    Sets the id value to null.
    
    Specified by:
    
    unsetId in interface SBase
  - unsetName
```
public void unsetName()
```
    Description copied from interface: SBase
    
    Sets the name value to null.
    
    Specified by:
    
    unsetName in interface SBase
  - getAllDeclaredNamespaces
```
public static java.util.HashMap<java.lang.String,java.lang.String> getAllDeclaredNamespaces(SBase sb)
```
    Returns a map of all the declared namespaces in the SBML tree, visible to the given SBase.
    Starting from the given SBase, we will use getDeclaredNamespaces() on it and all the parents until we reached the SBMLDocument or these is no more parent set. That will give us a complete set of all the declared namespace visible to this SBase. If a prefix if declared twice, we keep only the first occurrence encountered, meaning that we will have the declaration that is the deeper in the tree, the one that is active for XML code.
    
    Parameters:
    
    sb - the SBase
    
    Returns:
    
    a map of all the declared namespaces in the SBML tree, visible to the given SBase.

Class AbstractSBase

Field Summary

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

JSBML_WRONG_SBO_TERM

Constructor Detail

AbstractSBase

AbstractSBase

AbstractSBase

AbstractSBase

AbstractSBase

AbstractSBase

Method Detail

isValidLevelAndVersionCombination

isValidMetaId

addCVTerm

addDeclaredNamespace

addExtension

addPlugin

appendAnnotation

appendAnnotation

appendNotes

appendNotes

clone

createHistory

createPlugin

disablePackage

enablePackage

enablePackage

equals

filterCVTerms

filterCVTerms

filterCVTerms

filterCVTerms

fireNodeRemovedEvent

firePropertyChange

getAllowsChildren

getAnnotation

getAnnotationString

getChildAt

getChildCount

getCVTerm

getCVTermCount

getCVTerms

getDeclaredNamespaces

getElementBySId

getElementByMetaId

getElementName

getExtension

getExtensionCount

getExtensionPackages

getFirstElementIndex

getHistory

getLevel

getLevelAndVersion

getMetaId

getModel

getNamespace

getNotes

getNotesString

getNumCVTerms

getNumPlugins

getPackageName

getPackageVersion

getParent

getParentSBMLObject

getPlugin

getSBMLDocument

getSBOTerm

getSBOTermID

getURI

getVersion

hashCode

hasValidAnnotation