SBase

All Superinterfaces:

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

All Known Subinterfaces:

Assignment, CallableSBase, MathContainer, NamedSBase, NamedSBaseWithDerivedUnit, Quantity, SBaseWithDerivedUnit, SBaseWithUnit, SpatialNamedSBase, UniqueNamedSBase, Variable

All Known Implementing Classes:

AbstractMathContainer, AbstractNamedSBase, AbstractNamedSBaseRef, AbstractNamedSBaseWithUnit, AbstractReferenceGlyph, AbstractSBase, AbstractSpatialNamedSBase, AdjacentDomains, AdvectionCoefficient, AlgebraicRule, AnalyticGeometry, AnalyticVolume, AssignmentRule, BindingSiteReference, Bond, Boundary, BoundaryCondition, BoundingBox, ChangedMath, ColorDefinition, Compartment, CompartmentGlyph, CompartmentMapping, CompartmentType, Constraint, ContainedSpeciesType, CoordinateComponent, CoordinateReference, CSGeometry, CSGHomogeneousTransformation, CSGNode, CSGObject, CSGPrimitive, CSGPseudoPrimitive, CSGRotation, CSGScale, CSGSetOperator, CSGTransformation, CSGTranslation, CubicBezier, Curve, CurveSegment, Delay, Deletion, DiffusionCoefficient, Dimension, Dimensions, Domain, DomainType, Ellipse, Event, EventAssignment, ExplicitRule, ExternalModelDefinition, FluxBound, FluxObjective, FunctionDefinition, FunctionTerm, GeneralGlyph, Geometry, GeometryDefinition, GlobalRenderInformation, GradientBase, GradientStop, GraphicalObject, GraphicalPrimitive1D, GraphicalPrimitive2D, Group, Image, ImageData, Index, InitialAssignment, InitialSpeciesInstance, Input, InteriorPoint, KineticLaw, Layout, LinearGradient, LineEnding, LineSegment, ListOf, ListOfMemberConstraint, ListOfObjectives, ListOfWithName, LocalParameter, LocalRenderInformation, LocalStyle, Member, MemberConstraint, MixedGeometry, Model, ModelDefinition, ModifierSpeciesReference, Objective, OrdinalMapping, Output, Parameter, ParameterType, ParametricGeometry, ParametricObject, Point, Polygon, PolygonObject, Port, PossibleValue, Priority, ProductSpeciesReference, QualitativeSpecies, QuantityWithUnit, RadialGradient, RateRule, Reaction, ReactionGlyph, ReactionRule, Rectangle, ReferenceGlyph, RenderCubicBezier, RenderCurve, RenderGroup, RenderInformationBase, RenderPoint, ReplacedBy, ReplacedElement, Rule, SampledField, SampledFieldGeometry, SampledVolume, SBaseRef, SBMLDocument, SBMLLevel1Rule, Selector, SelectorReference, SimpleSpeciesReference, SpatialPoint, SpatialSymbolReference, Species, SpeciesGlyph, SpeciesReference, SpeciesReferenceGlyph, SpeciesType, SpeciesType, SpeciesTypeInstance, SpeciesTypeInstanceChange, SpeciesTypeRestriction, SpeciesTypeRestrictionReference, SpeciesTypeState, StateFeature, StateFeatureInstance, StateFeatureValue, StoichiometryMath, Style, Submodel, Symbol, Text, TextGlyph, Transformation, Transformation2D, TransformationComponent, Transition, Trigger, Unit, UnitDefinition
```
public interface SBase
extends TreeNodeWithChangeSupport
```
The interface to implement for each SBML element.
In addition to serving as the parent class for most other classes of objects in SBML, this base type is designed to allow a modeler or a software package to attach arbitrary information to each major element in an SBML model.
SBase has an optional subelement called 'notes'. It is intended to serve as a place for storing optional information intended to be seen by humans. An example use of the 'notes' element would be to contain formatted user comments about the model element in which the 'notes' element is enclosed. There are certain conditions on the XHTML content permitted inside the 'notes' element; please consult the SBML specification document corresponding to the SBML Level and Version of your model for more information about the requirements for 'notes' content.
SBase has another optional subelement called 'annotation'. Whereas the 'notes' element described above 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. The element's content type is XML type 'any', allowing essentially arbitrary data content. SBML places only a few restrictions on the organization of the content; these are intended to help software tools read and write the data as well as help reduce conflicts between annotations added by different tools. As is the case with 'notes', it is important to refer to the SBML specification document corresponding to the SBML Level and Version of your model for more information about the requirements for 'annotation' content.
It is worth pointing out that the 'annotation' element in the definition of SBase exists in order that software developers may attach optional application-specific data to the elements in an SBML model. However, it is important that this facility not be misused. In particular, it is critical that data essential to a model definition or that can be encoded in existing SBML elements is not stored in 'annotation'. Parameter values, functional dependencies between model elements, etc., should not be recorded as annotations. It is crucial to keep in mind the fact that data placed in annotations can be freely ignored by software applications. If such data affects the interpretation of a model, then software interoperability is greatly impeded.
SBML Level 2 introduced an optional SBase attribute named 'metaid' for supporting metadata annotations using RDF (Resource Description Format). The attribute value has the data type XML ID, the XML identifier type, which means each 'metaid' value must be globally unique within an SBML file. (Importantly, this uniqueness criterion applies across any attribute with type XML ID, not just the 'metaid' attribute used by SBML—something to be aware of if your application-specific XML content inside the 'annotation' subelement happens to use XML ID.) The 'metaid' value serves to identify a model component for purposes such as referencing that component from metadata placed within 'annotation' subelements.
Beginning with SBML Level 2 Version 3, SBase also has 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; libSBML simplifies the representation by only storing the 'NNNNNNN' integer portion. Thus, in libSBML, the 'sboTerm' attribute on SBase has data type int, and SBO identifiers are stored simply as integers. (For convenience, SBase offers methods for returning both the integer form and a text-string form of the SBO identifier.) 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.

Since:

0.8

Version:

$Rev: 1968 $

Author:

Andreas Dräger, Marine Dumousseau, Nicolas Rodriguez

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 notes of this object.
`SBase`	`clone()` Creates a deep copy of this object, i.e., a new `SBase` with the same properties like this one.
`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 sbase)` 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.
`Annotation`	`getAnnotation()` Returns the content of the 'annotation' sub-element of this object as an `Annotation` instance.
`java.lang.String`	`getAnnotationString()` Returns the content of the 'annotation' sub-element of this object as a String.
`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`.
`History`	`getHistory()` Returns the `History` instance of this object.
`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 the `XMLNode` containing the notes sub-element of this object.
`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`	`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. use `isPackageEnabled(String)`
`boolean`	`isPkgURIEnabled(java.lang.String packageURIOrName)` Deprecated. use `isPackageEnabled(String)`
`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`.
`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'.
`boolean`	`removeCVTerm(CVTerm cvTerm)` Removes the given `CVTerm`.
`CVTerm`	`removeCVTerm(int index)` Removes the `CVTerm` at the given index.
`void`	`removeTreeNodeChangeListener(TreeNodeChangeListener listener)` Removes the given `TreeNodeChangeListener` from this element.
`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'.
`void`	`setMetaId(java.lang.String metaid)` Sets the metaid value with 'metaid'.
`void`	`setNotes(java.lang.String notes)` Sets the notes with 'notes'.
`void`	`setNotes(XMLNode notesXMLNode)` Sets the `XMLNode` containing the notes sub-element of this object.
`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. use `registerChild(SBase)`
`void`	`setVersion(int version)` Sets the version of this object with 'version'.
`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`	`unsetMetaId()` Unsets the value of the 'metaid' attribute of this SBML object.
`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 interface javax.swing.tree.TreeNode
children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

- Method Detail
  - addCVTerm
```
boolean addCVTerm(CVTerm term)
```
    Adds a CVTerm.
    
    Parameters:
    term - the CVTerm to add.
    
    Returns:
    true if a CVTerm instance has been added to the list of CVTerm of this object.
  - addDeclaredNamespace
```
void addDeclaredNamespace(java.lang.String prefix,
                        java.lang.String namespace)
```
    Adds an additional name space to the set of declared namespaces of this SBase.
    
    Parameters:
    prefix - the prefix of the namespace to add
    namespace - the namespace to add
  - addExtension
```
void addExtension(java.lang.String nameOrUri,
                SBasePlugin sbasePlugin)
```
    Adds a SBasePlugin extension object to this SBase.
    If a previous SBasePlugin associated with the same package was present before, it will be replaced.
    
    Parameters:
    nameOrUri - the name or URI of the package extension.
    sbasePlugin - the SBasePlugin to add.
  - addPlugin
```
void addPlugin(java.lang.String nameOrUri,
             SBasePlugin sbasePlugin)
```
    Adds a SBasePlugin extension object to this SBase.
    If a previous SBasePlugin associated with the same package was present before, it will be replaced.
    
    Parameters:
    nameOrUri - the name or URI of the package extension.
    sbasePlugin - the SBasePlugin to add.
    See Also:
    addExtension(String, SBasePlugin)
  - appendNotes
```
void appendNotes(java.lang.String notes)
                 throws javax.xml.stream.XMLStreamException
```
    Appends 'notes' to the notes String of this object.
    
    Parameters:
    notes - the notes to be added.
    
    Throws:
    
    javax.xml.stream.XMLStreamException - if an error occurs while parsing the notes String.
  - appendNotes
```
void appendNotes(XMLNode notes)
```
    Appends 'notes' to the notes of this object.
    
    Parameters:
    notes - the notes to be added.
  - clone
```
SBase clone()
```
    Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
    
    Returns:
    a copy of this object
  - createPlugin
```
SBasePlugin createPlugin(java.lang.String nameOrUri)
```
    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.
    
    Parameters:
    nameOrUri - the package name or URI
    
    Returns:
    a new SBasePlugin for the given package name or URI
  - disablePackage
```
void disablePackage(java.lang.String packageURIOrName)
```
    Disables the given SBML Level 3 package on this SBMLDocument.
    
    Parameters:
    packageURIOrName - a package namespace URI or package name
  - enablePackage
```
void enablePackage(java.lang.String packageURIOrName)
```
    Enables the given SBML Level 3 package on this SBMLDocument.
    
    Parameters:
    packageURIOrName - a package namespace URI or package name
  - enablePackage
```
void enablePackage(java.lang.String packageURIOrName,
                 boolean enabled)
```
    Enables or disables the given SBML Level 3 package on this SBMLDocument.
    
    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
```
boolean equals(java.lang.Object sbase)
```
    Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
    
    Overrides:
    
    equals in class java.lang.Object
    
    Parameters:
    sbase - 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
```
java.util.List<CVTerm> filterCVTerms(CVTerm.Qualifier qualifier)
```
    Returns a list of all the CVTerm with the given CVTerm.Qualifier.
    
    Parameters:
    qualifier - CVTerm.Qualifier used to filter the CVTerms.
    
    Returns:
    a list of all the CVTerm with the given CVTerm.Qualifier.
  - filterCVTerms
```
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.
    
    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
```
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.
    This is a recursive implementation of #filterCVTerms(Qualifier, String) that considers all child elements of the current instance of SBase as well.
    
    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
```
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.
    
    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...)
  - getAnnotation
```
Annotation getAnnotation()
```
    Returns the content of the 'annotation' sub-element of this object as an Annotation instance.
    
    Returns:
    the content of the 'annotation' sub-element of this object as an Annotation instance.
  - getAnnotationString
```
java.lang.String getAnnotationString()
                                     throws javax.xml.stream.XMLStreamException
```
    Returns the content of the 'annotation' sub-element of this object as a String.
    
    Returns:
    the content of the 'annotation' sub-element of this object as a String.
    
    Throws:
    
    javax.xml.stream.XMLStreamException - if an error occurs while writing the XMLNode to a String
  - getCVTerm
```
CVTerm getCVTerm(int index)
```
    Returns the CVTerm instance at the position 'index' in the list of CVTerms of this object.
    
    Parameters:
    index - index of the element to return
    
    Returns:
    the CVTerm instance at the position 'index' in the list of CVTerms of this object.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the index is out of range (index < 0 || index >= size()) or if the list of CVTerm is not set.
  - getCVTerms
```
java.util.List<CVTerm> getCVTerms()
```
    Returns the list of CVTerms of this object.
    
    Returns:
    the list of CVTerms of this object. If not yet set, this method initializes the annotation and returns an empty list.
  - getDeclaredNamespaces
```
java.util.Map<java.lang.String,java.lang.String> getDeclaredNamespaces()
```
    Returns all the namespaces declared on this object. These will be written on the resulting XML element.
    
    Returns:
    all the namespaces declared on this object. These will be written on the resulting XML element.
  - getElementName
```
java.lang.String getElementName()
```
    Returns the XML element name of this object.
    
    Returns:
    the XML element name of this object.
  - getExtension
```
SBasePlugin getExtension(java.lang.String nameOrUri)
```
    Returns the SBasePlugin extension object which matches this package name or URI.
    
    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
```
int getExtensionCount()
```
    Returns the number of SBasePlugins of this SBase.
    
    Returns:
    the number of SBasePlugins of this SBase.
  - getExtensionPackages
```
java.util.Map<java.lang.String,SBasePlugin> getExtensionPackages()
```
    Returns the map containing all the SBasePlugin extension objects of this SBase.
    
    Returns:
    the map containing all the SBasePlugin extension objects of this SBase.
  - getHistory
```
History getHistory()
```
    Returns the History instance of this object.
    
    Returns:
    the History instance of this object.
  - getLevel
```
int getLevel()
```
    Returns the SBML Level of the overall SBML document. Returns -1 if it is not set.
    
    Returns:
    the SBML level of this SBML object.
    See Also:
    getVersion()
  - getLevelAndVersion
```
ValuePair<java.lang.Integer,java.lang.Integer> getLevelAndVersion()
```
    Returns the Level and Version combination of this 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
```
java.lang.String getMetaId()
```
    Returns the metaid of this element.
    
    Returns:
    the metaid of this element.
  - getModel
```
Model getModel()
```
    Returns the Model object in which the current SBase is located.
    
    Returns:
    the Model object in which the current SBase is located.
  - getNamespace
```
java.lang.String getNamespace()
```
    Returns the namespace to which this SBase belong to.
    
    Returns:
    the namespace to which this SBase belong to.
  - getNotes
```
XMLNode getNotes()
```
    Returns the XMLNode containing the notes sub-element of this object.
    
    Returns:
    the XMLNode containing the notes sub-element of this object.
  - getNotesString
```
java.lang.String getNotesString()
                                throws javax.xml.stream.XMLStreamException
```
    Returns the notes sub-element of this object as a String.
    If no notes are set, an empty String will be returned.
    
    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
```
int getNumCVTerms()
```
    Returns the number of CVTerms of this SBase.
    
    Returns:
    the number of CVTerms of this SBase.
  - getNumPlugins
```
int getNumPlugins()
```
    Returns the number of SBasePlugins of this SBase.
    
    Returns:
    the number of SBasePlugins of this SBase.
  - getCVTermCount
```
int getCVTermCount()
```
    Returns the number of CVTerms of this SBase.
    
    Returns:
    the number of CVTerms of this SBase.
  - getParentSBMLObject
```
SBase getParentSBMLObject()
```
    Returns the parent of this SBase.
    
    Returns:
    the parent SBML object.
    See Also:
    TreeNode.getParent()
  - getPlugin
```
SBasePlugin getPlugin(java.lang.String nameOrUri)
```
    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.
    
    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
```
SBMLDocument getSBMLDocument()
```
    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.
    
    Returns:
    the parent SBMLDocument object of this SBML object.
  - getSBOTerm
```
int getSBOTerm()
```
    Grants access to the Systems Biology Ontology (SBO) term associated with this SBase.
    
    Returns:
    the SBOTerm attribute of this element.
    See Also:
    SBO
  - getSBOTermID
```
java.lang.String getSBOTermID()
```
    Grants access to the Systems Biology Ontology (SBO) term associated with this SBase.
    
    Returns:
    the SBO term ID of this element.
    See Also:
    SBO
  - getVersion
```
int getVersion()
```
    Returns the Version within the SBML Level of the overall SBML document. Return -1 if it is not set.
    
    Returns:
    the SBML version of this SBML object.
    See Also:
    getLevel()
  - hashCode
```
int hashCode()
```
    Returns a hash code value for this SBase instance.
    
    Overrides:
    
    hashCode in class java.lang.Object
    
    Returns:
    a hash code value for this SBase instance.
    See Also:
    Object.hashCode()
  - hasValidAnnotation
```
boolean hasValidAnnotation()
```
    Returns true if the Annotation RDF 'about' attribute matches the metaid of this object.
    
    Returns:
    true if the Annotation 'about' String of this object matches the metaid of this object.
  - hasValidLevelVersionNamespaceCombination
```
boolean hasValidLevelVersionNamespaceCombination()
```
    Returns true or false depending on whether this object's level/version and namespace values correspond to a valid SBML specification.
    
    Returns:
    true if this object's level, version and namespace values correspond to a valid SBML specification.
  - isExtendedByOtherPackages
```
boolean isExtendedByOtherPackages()
```
    Returns true if this object is extended by other packages.
    
    Returns:
    true if this object is extended by other packages.
  - isPackageEnabled
```
boolean isPackageEnabled(java.lang.String packageURIOrName)
```
    Returns true if the given SBML Level 3 package is enabled within the containing SBMLDocument.
    
    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
```
boolean isPackageURIEnabled(java.lang.String packageURIOrName)
```
    Returns true if the given SBML Level 3 package is enabled within the containing SBMLDocument.
    
    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
boolean isPkgEnabled(java.lang.String packageURIOrName)
```
    Deprecated. use isPackageEnabled(String)
    
    Returns true if the given SBML Level 3 package is enabled within the containing SBMLDocument.
    
    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
boolean isPkgURIEnabled(java.lang.String packageURIOrName)
```
    Deprecated. use isPackageEnabled(String)
    
    Returns true if the given SBML Level 3 package is enabled within the containing SBMLDocument.
    
    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
```
boolean isSetAnnotation()
```
    Returns true or false depending on whether this object's 'annotation' sub-elements exists and have some content.
    
    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
```
boolean isSetHistory()
```
    Returns true if the History instance of this object is set.
    
    Returns:
    true if the History instance of this object is set.
  - isSetLevel
```
boolean isSetLevel()
```
    Returns true if the level is set.
    
    Returns:
    true if the level is set.
  - isSetLevelAndVersion
```
boolean isSetLevelAndVersion()
```
    Returns true if both, Level and Version are set for this SBase.
    
    Returns:
    true if isSetLevel() and isSetVersion().
  - isSetMetaId
```
boolean isSetMetaId()
```
    Returns true or false depending on whether this object's 'metaid' attribute has been set.
    
    Returns:
    true if the metaid is not null.
  - isSetNotes
```
boolean isSetNotes()
```
    Returns true or false depending on whether this object's 'notes' sub-element exists and has content.
    
    Returns:
    true if the notes String is not null.
  - isSetParentSBMLObject
```
boolean isSetParentSBMLObject()
```
    Check whether this SBase has been linked to a parent within the hierarchical SBML data structure.
    
    Returns:
    true if this SBase has a parent SBML object, false otherwise.
    See Also:
    getParentSBMLObject()
  - isSetPlugin
```
boolean isSetPlugin(java.lang.String nameOrUri)
```
    Returns true if an SBasePlugin is defined for the given package.
    
    Parameters:
    nameOrUri - the package name or URI
    
    Returns:
    true if an SBasePlugin is defined for the given package.
  - isSetSBOTerm
```
boolean isSetSBOTerm()
```
    Returns true if the SBOTerm is set.
    
    Returns:
    true if the SBOTerm is set.
    See Also:
    SBO
  - isSetVersion
```
boolean isSetVersion()
```
    Returns true if the version is not null.
    
    Returns:
    true if the version is not null.
  - readAttribute
```
boolean readAttribute(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)
```
    Sets the given attribute in this SBase.
    If the given attribute name is not recognized, nothing is done and false is returned.
    
    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
```
void registerChild(SBase sbase)
                   throws LevelVersionError
```
    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.
    
    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.
  - unregisterChild
```
void unregisterChild(SBase sbase)
```
    Unregisters recursively the given SBase from the Model and SBMLDocument.
    
    Parameters:
    sbase - the SBase to be unregistered.
  - removeCVTerm
```
boolean removeCVTerm(CVTerm cvTerm)
```
    Removes the given CVTerm.
    
    Parameters:
    cvTerm - the CVTerm to remove
    
    Returns:
    true if the CVTerm was successfully removed.
  - removeCVTerm
```
CVTerm removeCVTerm(int index)
```
    Removes the CVTerm at the given index.
    
    Parameters:
    index - the index
    
    Returns:
    the removed CVTerm.
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the index is out of range (index < 0 || index >= size())
  - removeTreeNodeChangeListener
```
void removeTreeNodeChangeListener(TreeNodeChangeListener listener)
```
    Removes the given TreeNodeChangeListener from this element.
    
    Specified by:
    
    removeTreeNodeChangeListener in interface TreeNodeWithChangeSupport
    
    Parameters:
    listener - the listener to be removed.
    See Also:
    TreeNodeWithChangeSupport.removeTreeNodeChangeListener(TreeNodeChangeListener, boolean)
  - setAnnotation
```
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.
    
    Parameters:
    annotation - the annotation of this SBase
  - setHistory
```
void setHistory(History history)
```
    Sets the history.
    
    Parameters:
    history - the history of this SBase
  - setLevel
```
void setLevel(int level)
```
    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.
    
    Parameters:
    level - the SBML level.
  - setMetaId
```
void setMetaId(java.lang.String metaid)
```
    Sets the metaid value with 'metaid'.
    
    Parameters:
    metaid - the meatId to be set.
    
    Throws:
    
    PropertyNotAvailableException - in SBML level 1, as this attribute was introduced only from SBML level 2.
  - setNotes
```
void setNotes(java.lang.String notes)
              throws javax.xml.stream.XMLStreamException
```
    Sets the notes with 'notes'.
    
    Parameters:
    notes - the notes for this SBase.
    
    Throws:
    
    javax.xml.stream.XMLStreamException - if an error occurs while parsing the notes.
  - setNotes
```
void setNotes(XMLNode notesXMLNode)
```
    Sets the XMLNode containing the notes sub-element of this object.
    
    Parameters:
    notesXMLNode - the notes for this SBase.
  - setSBOTerm
```
void setSBOTerm(int term)
```
    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.
    
    Parameters:
    term - the NNNNNNN integer portion of the SBO identifier
    
    Throws:
    
    PropertyNotAvailableException - in Level 1.
    See Also:
    SBO
  - setSBOTerm
```
void setSBOTerm(java.lang.String sboid)
```
    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.
    
    Parameters:
    sboid - the SBO identifier of the form 'SBO:NNNNNNN'
    See Also:
    SBO
  - setThisAsParentSBMLObject
```
@Deprecated
void setThisAsParentSBMLObject(SBase sbase)
                               throws LevelVersionError
```
    Deprecated. use registerChild(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.
    
    Parameters:
    sbase - the child SBase
    
    Throws:
    
    LevelVersionError
  - setVersion
```
void setVersion(int version)
```
    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.
    
    Parameters:
    version - the SBML version
  - unsetAnnotation
```
void unsetAnnotation()
```
    Unsets the value of the 'annotation' sub-element of this SBML object.
  - unsetCVTerms
```
void unsetCVTerms()
```
    Unsets the list of CVTerm of this object.
  - unsetExtension
```
void unsetExtension(java.lang.String nameOrUri)
```
    Unsets the SBasePlugin extension object which matches this package name or URI.
    
    Parameters:
    nameOrUri - the package name or URI
  - unsetHistory
```
void unsetHistory()
```
    Unsets the History of this object.
  - unsetMetaId
```
void unsetMetaId()
```
    Unsets the value of the 'metaid' attribute of this SBML object.
  - unsetNotes
```
void unsetNotes()
```
    Unsets the value of the 'notes' sub-element of this SBML object.
  - unsetPlugin
```
void unsetPlugin(java.lang.String nameOrUri)
```
    Unsets the SBasePlugin extension object which matches this package name or URI.
    
    Parameters:
    nameOrUri - the package name or URI
  - unsetSBOTerm
```
void unsetSBOTerm()
```
    Unsets the value of the 'sboTerm' attribute of this SBML object.
  - writeXMLAttributes
```
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.
    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.
    
    Returns:
    a Map containing the XML attributes of this object.

Interface SBase

Method Summary

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

Methods inherited from interface javax.swing.tree.TreeNode

Method Detail

addCVTerm

addDeclaredNamespace

addExtension

addPlugin

appendNotes

appendNotes

clone

createPlugin

disablePackage

enablePackage

enablePackage

equals

filterCVTerms

filterCVTerms

filterCVTerms

filterCVTerms

getAnnotation

getAnnotationString

getCVTerm

getCVTerms

getDeclaredNamespaces

getElementName

getExtension

getExtensionCount

getExtensionPackages

getHistory

getLevel

getLevelAndVersion

getMetaId

getModel

getNamespace

getNotes

getNotesString

getNumCVTerms

getNumPlugins

getCVTermCount

getParentSBMLObject

getPlugin

getSBMLDocument

getSBOTerm

getSBOTermID

getVersion

hashCode

hasValidAnnotation

hasValidLevelVersionNamespaceCombination

isExtendedByOtherPackages

isPackageEnabled

isPackageURIEnabled

isPkgEnabled

isPkgURIEnabled

isSetAnnotation

isSetHistory

isSetLevel

isSetLevelAndVersion

isSetMetaId

isSetNotes

isSetParentSBMLObject

isSetPlugin

isSetSBOTerm

isSetVersion

readAttribute

registerChild

unregisterChild

removeCVTerm

removeCVTerm

removeTreeNodeChangeListener

setAnnotation

setHistory

setLevel

setMetaId

setNotes

setNotes

setSBOTerm

setSBOTerm

setThisAsParentSBMLObject