Annotation

java.lang.Object
- org.sbml.jsbml.AbstractTreeNode
- - org.sbml.jsbml.AnnotationElement
  - - org.sbml.jsbml.Annotation

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, TreeNodeWithChangeSupport
```
public class Annotation
extends AnnotationElement
```
An Annotation represents the annotations of an SBase element. It contains the list of CVTerm objects, a Map containing an XML name space and a String containing all the annotation elements of this name space.

Since:

0.8

Version:

$Rev: 1650 $

Author:

Marine Dumousseau, Andreas Dräger

See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`private java.lang.String`	`about` matches the about XML attribute of an annotation element in a SBML file.
`private History`	`history` The ModelHistory which represents the history section of a RDF annotation
`private java.util.List<CVTerm>`	`listOfCVTerms` contains all the CVTerm of the RDF annotation
`private XMLNode`	`nonRDFannotation` contains all the remaining annotation not mapped to Objects.
`private static long`	`serialVersionUID` Generated serial version identifier.
`static java.lang.String`	`URI_RDF_SYNTAX_NS` The RDF syntax name space definition URI.

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

Constructor Summary

Constructors
Constructor and Description
`Annotation()` Creates an Annotation instance.
`Annotation(Annotation annotation)` Creates a new Annotation instance by cloning the given Annotation.
`Annotation(java.util.List<CVTerm> cvTerms)` Creates an `Annotation` instance from a list of `CVTerm` objects.
`Annotation(java.lang.String annotation)` Creates an `Annotation` instance from a `String` containing non RDF annotation.
`Annotation(java.lang.String annotation, java.util.List<CVTerm> cvTerms)` Creates an `Annotation` instance from a `String` containing non RDF annotation and a list of `CVTerm`.

Method Summary

Methods
Modifier and Type	Method and Description
`boolean`	`addCVTerm(CVTerm cvTerm)` Adds a `CVTerm`.
`void`	`addDeclaredNamespace(java.lang.String prefix, java.lang.String uri)` Adds an additional namespace to the set of declared namespaces of this `SBase`.
`void`	`appendNoRDFAnnotation(java.lang.String annotation)` Appends some 'annotation' to the non RDF annotation `XMLNode` of this object.
`Annotation`	`clone()`
`private History`	`createHistory()`
`boolean`	`equals(java.lang.Object object)`
`java.util.List<CVTerm>`	`filterCVTerms(CVTerm.Qualifier qualifier)` Returns a list of CVTerm having the given qualifier.
`java.util.List<java.lang.String>`	`filterCVTerms(CVTerm.Qualifier qualifier, java.lang.String pattern)` Returns a list of CVTerm having the given qualifier and where the URI contains the given pattern.
`java.lang.String`	`getAbout()` Returns the about String of this object.
`boolean`	`getAllowsChildren()`
`XMLNode`	`getAnnotationBuilder()` Deprecated.
`javax.swing.tree.TreeNode`	`getChildAt(int childIndex)`
`int`	`getChildCount()`
`CVTerm`	`getCVTerm(int i)` Returns the CVTerm at the ith position in the list of CVTerms.
`int`	`getCVTermCount()` Gives the number of `CVTerm`s in this `Annotation`.
`XMLNamespaces`	`getDeclaredNamespaces()`
`static java.lang.String`	`getElementNameEquivalentToQualifier(CVTerm.Qualifier qualifier)` Returns a `String` which represents the given `CVTerm.Qualifier`.
`XMLNode`	`getFullAnnotation()`
`java.lang.String`	`getFullAnnotationString()`
`History`	`getHistory()` Returns the `History` of the Annotation.
`java.util.List<CVTerm>`	`getListOfCVTerms()` Returns the list of CVTerms.
`XMLNode`	`getNonRDFannotation()` Returns the `XMLNode` containing annotations other than the official RDF annotation, as defined in the SBML specifications.
`java.lang.String`	`getNonRDFannotationAsString()` Returns the String containing annotations other than RDF annotation.
`int`	`getNumCVTerms()` Gives the number of `CVTerm`s in this `Annotation`.
`int`	`hashCode()`
`boolean`	`isEmpty()`
`boolean`	`isSetAbout()` Checks whether the 'about' element has been initialized.
`boolean`	`isSetAnnotation()` Checks if the `Annotation` is initialized.
`boolean`	`isSetHistory()` Checks if the `History` is initialized
`boolean`	`isSetListOfCVTerms()` Checks if the list of `CVTerm` is not empty.
`boolean`	`isSetNonRDFannotation()` Checks if the non RDF part of the Annotation is initialized.
`boolean`	`isSetOtherAnnotationThanRDF()` Deprecated. please use `isSetNonRDFannotation()`
`boolean`	`isSetRDFannotation()` Checks if the RDF part of the Annotation is initialized.
`boolean`	`readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)` Sets the about instance of this object if the attributeName is equal to 'about'.
`void`	`setAbout(java.lang.String about)` Sets the value of the about String of this object.
`void`	`setHistory(History history)` Changes the `History` instance to 'history'
`void`	`setNonRDFAnnotation(java.lang.String nonRDFAnnotationStr)` Sets the value of the non RDF annotations
`void`	`setNonRDFAnnotation(XMLNode nonRDFAnnotation)` Sets the value of the non RDF annotations
`void`	`unsetCVTerms()` Clears the `List` of `CVTerm`s and removes unnecessary entries from the `#rdfAnnotationNamespaces`.
`void`	`unsetHistory()` Sets the `History` instance of this object to `null`.
`void`	`unsetNonRDFannotation()` Sets the non RDF annotation String to `null`.

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Generated serial version identifier.
    
    See Also:
    Constant Field Values
  - URI_RDF_SYNTAX_NS
```
public static final transient java.lang.String URI_RDF_SYNTAX_NS
```
    The RDF syntax name space definition URI.
    
    See Also:
    Constant Field Values
  - about
```
private java.lang.String about
```
    matches the about XML attribute of an annotation element in a SBML file.
  - history
```
private History history
```
    The ModelHistory which represents the history section of a RDF annotation
  - listOfCVTerms
```
private java.util.List<CVTerm> listOfCVTerms
```
    contains all the CVTerm of the RDF annotation
  - nonRDFannotation
```
private XMLNode nonRDFannotation
```
    contains all the remaining annotation not mapped to Objects.
- Constructor Detail
  - Annotation
```
public Annotation()
```
    Creates an Annotation instance.
    By default, the History and otherAnnotation Strings are null. The list of CVTerms and extensions are empty.
  - Annotation
```
public Annotation(Annotation annotation)
```
    Creates a new Annotation instance by cloning the given Annotation.
    
    Parameters:
    annotation - the annotation to be cloned.
  - Annotation
```
public Annotation(java.util.List<CVTerm> cvTerms)
```
    Creates an Annotation instance from a list of CVTerm objects. By default, the History and otherAnnotation Strings are null. The Map extensions is empty.
    
    Parameters:
    cvTerms - the list of CVTerm.
  - Annotation
```
public Annotation(java.lang.String annotation)
           throws javax.xml.stream.XMLStreamException
```
    Creates an Annotation instance from a String containing non RDF annotation. By default, the History is null, the list of CVTerms is empty. The Map extensions is empty.
    
    Parameters:
    annotation - a String containing non RDF annotation, it will be parsed to create a Map containing an XML name space associated with a String representing all the annotation elements of this name space.
    
    Throws:
    
    javax.xml.stream.XMLStreamException
  - Annotation
```
public Annotation(java.lang.String annotation,
          java.util.List<CVTerm> cvTerms)
           throws javax.xml.stream.XMLStreamException
```
    Creates an Annotation instance from a String containing non RDF annotation and a list of CVTerm. By default, the History is null. The Map extensions is empty.
    
    Parameters:
    annotation - a String containing non RDF annotation, it will be parsed to create a Map containing an XML name space associated with a String representing all the annotation elements of this name space.
    cvTerms - the List of CVTerm.
    
    Throws:
    
    javax.xml.stream.XMLStreamException
- Method Detail
  - getElementNameEquivalentToQualifier
```
public static java.lang.String getElementNameEquivalentToQualifier(CVTerm.Qualifier qualifier)
```
    Returns a String which represents the given CVTerm.Qualifier.
    
    Parameters:
    qualifier - a Qualifier
    
    Returns:
    a String which represents the given CVTerm.Qualifier.
  - addCVTerm
```
public boolean addCVTerm(CVTerm cvTerm)
```
    Adds a CVTerm.
    
    Parameters:
    cvTerm - the CVTerm to add.
    
    Returns:
    true if the 'cvTerm' element has been added to the List of CVTerm.Qualifiers.
  - appendNoRDFAnnotation
```
public void appendNoRDFAnnotation(java.lang.String annotation)
                           throws javax.xml.stream.XMLStreamException
```
    Appends some 'annotation' to the non RDF annotation XMLNode of this object.
    
    Parameters:
    annotation - some non RDF annotations.
    
    Throws:
    
    javax.xml.stream.XMLStreamException
  - clone
```
public Annotation clone()
```
    Specified by:
    
    clone in class AbstractTreeNode
  - equals
```
public boolean equals(java.lang.Object object)
```
    Overrides:
    
    equals in class AbstractTreeNode
  - filterCVTerms
```
public java.util.List<CVTerm> filterCVTerms(CVTerm.Qualifier qualifier)
```
    Returns a list of CVTerm having the given qualifier.
    
    Parameters:
    qualifier - the qualifier
    
    Returns:
    a list of CVTerm having the given qualifier, an empty list is returned if no CVTerm are found.
  - filterCVTerms
```
public java.util.List<java.lang.String> filterCVTerms(CVTerm.Qualifier qualifier,
                                             java.lang.String pattern)
```
    Returns a list of CVTerm having the given qualifier and where the URI contains the given pattern. The pattern can only be plain text.
    
    Parameters:
    qualifier - the qualifier.
    pattern - a plain text pattern.
    
    Returns:
    a list of CVTerm having the given qualifier and where the URI matches the given pattern.
  - getAbout
```
public java.lang.String getAbout()
```
    Returns the about String of this object.
    
    Returns:
    the about String of this object.
  - getAllowsChildren
```
public boolean getAllowsChildren()
```
  - getAnnotationBuilder
```
public XMLNode getAnnotationBuilder()
```
    Deprecated.
    
    Returns the XMLNode representing non RDF annotations.
    
    Returns:
    the XMLNode representing non RDF annotations.
  - getFullAnnotation
```
public XMLNode getFullAnnotation()
```
    Returns:
  - getFullAnnotationString
```
public java.lang.String getFullAnnotationString()
```
    Returns:
  - getChildAt
```
public javax.swing.tree.TreeNode getChildAt(int childIndex)
```
  - getChildCount
```
public int getChildCount()
```
  - getCVTerm
```
public CVTerm getCVTerm(int i)
```
    Returns the CVTerm at the ith position in the list of CVTerms.
    
    Parameters:
    i - the index of the CVTerm to retrieve.
    
    Returns:
    the CVTerm at the ith position in the list of CVTerms.
  - getHistory
```
public History getHistory()
```
    Returns the History of the Annotation.
    
    Returns:
    the History of the Annotation.
  - createHistory
```
private History createHistory()
```
  - getListOfCVTerms
```
public java.util.List<CVTerm> getListOfCVTerms()
```
    Returns the list of CVTerms. If they are no CVTerm, an empty list is returned.
    
    Returns:
    the list of CVTerms.
  - getNonRDFannotationAsString
```
public java.lang.String getNonRDFannotationAsString()
```
    Returns the String containing annotations other than RDF annotation.
    
    Returns:
    the String containing annotations other than RDF annotation. Return null if there are none.
  - getNonRDFannotation
```
public XMLNode getNonRDFannotation()
```
    Returns the XMLNode containing annotations other than the official RDF annotation, as defined in the SBML specifications.
    
    Returns:
    the XMLNode containing annotations other than RDF annotation. Return null if there are none.
  - getNumCVTerms
```
public int getNumCVTerms()
```
    Gives the number of CVTerms in this Annotation.
    
    Returns:
    the number of controlled vocabulary terms in this Annotation.
  - getCVTermCount
```
public int getCVTermCount()
```
    Gives the number of CVTerms in this Annotation.
    
    Returns:
    the number of controlled vocabulary terms in this Annotation.
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class AbstractTreeNode
  - isEmpty
```
public boolean isEmpty()
```
    Returns:
  - isSetAbout
```
public boolean isSetAbout()
```
    Checks whether the 'about' element has been initialized.
    
    Returns:
    true if the 'about' element has been initialized.
  - isSetAnnotation
```
public boolean isSetAnnotation()
```
    Checks if the Annotation is initialized.
    An Annotation is initialized if at least one of the following is true:
  - there is some non RDF annotation
  - one or more CVTerm are defined
  - there is an history defined.

Returns:: true if the Annotation is initialized

isSetHistory
```
public boolean isSetHistory()
```
Checks if the History is initialized

Returns:
true if the History is initialized

isSetListOfCVTerms
```
public boolean isSetListOfCVTerms()
```
Checks if the list of CVTerm is not empty.

Returns:
true if there is one or more CVTerm defined.

isSetNonRDFannotation
```
public boolean isSetNonRDFannotation()
```
Checks if the non RDF part of the Annotation is initialized.
An Annotation is initialized if there is some non RDF annotation

Returns:
true if the non RDF part of the Annotation is initialized.

isSetOtherAnnotationThanRDF
```
@Deprecated
public boolean isSetOtherAnnotationThanRDF()
```
Deprecated. please use isSetNonRDFannotation()

Returns true if there is some non RDF annotation.
Same as isSetNonRDFannotation()

Returns:
true if there is some non RDF annotation.
See Also:
isSetNonRDFannotation()

isSetRDFannotation
```
public boolean isSetRDFannotation()
```
Checks if the RDF part of the Annotation is initialized.
An Annotation is initialized if at least one of the following is true:
one or more CVTerm are defined
there is an history defined.

Class Annotation

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

URI_RDF_SYNTAX_NS

about

history

listOfCVTerms

nonRDFannotation

Constructor Detail

Annotation

Annotation

Annotation

Annotation

Annotation

Method Detail

getElementNameEquivalentToQualifier

addCVTerm

appendNoRDFAnnotation

clone

equals

filterCVTerms

filterCVTerms

getAbout

getAllowsChildren

getAnnotationBuilder

getFullAnnotation

getFullAnnotationString

getChildAt

getChildCount

getCVTerm

getHistory

createHistory

getListOfCVTerms

getNonRDFannotationAsString

getNonRDFannotation

getNumCVTerms

getCVTermCount

hashCode

isEmpty

isSetAbout

isSetAnnotation

isSetHistory

isSetListOfCVTerms

isSetNonRDFannotation

isSetOtherAnnotationThanRDF

isSetRDFannotation

readAttribute

setAbout

setHistory

setNonRDFAnnotation

setNonRDFAnnotation

unsetCVTerms

unsetHistory

unsetNonRDFannotation

addDeclaredNamespace

getDeclaredNamespaces