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: 1447 $

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 java.util.Map<java.lang.String,java.lang.String>`	`annotationNamespaces` contains all the name spaces of the matching XML annotation node
`private java.util.Map<java.lang.String,Annotation>`	`extensions` contains all the annotation extension objects with the name space of their package.
`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 java.lang.StringBuilder`	`nonRDFannotation` contains all the annotation information which are not RDF.
`private java.util.Map<java.lang.String,java.lang.String>`	`rdfAnnotationNamespaces` contains all the name spaces of the matching XML RDF annotation node
`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

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.util.Map<java.lang.String,java.lang.String> annotations)` Creates an `Annotation` instance from a given `Map` of annotations.
`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
`void`	`addAnnotationNamespace(java.lang.String namespaceName, java.lang.String prefix, java.lang.String URI)` Adds a namespace to the map annotationNamespace of this object.
`boolean`	`addCVTerm(CVTerm cvTerm)` Adds a `CVTerm` and checks whether the required name spaces have already been added to the `rdfAnnotationNamespaces`.
`void`	`addExtension(java.lang.String namespace, Annotation annotation)` Adds an Annotation extension object to the extensions map of this object.
`void`	`addRDFAnnotationNamespace(java.lang.String namespaceName, java.lang.String prefix, java.lang.String URI)` Adds a name space to the rdfAnnotationNamespaces `Map` of this object.
`void`	`appendNoRDFAnnotation(java.lang.String annotation)` Appends some'annotation' to the non RDF annotation StringBuilder of this object.
`Annotation`	`clone()`
`private static void`	`copy(java.util.Map<java.lang.String,java.lang.String> origin, java.util.Map<java.lang.String,java.lang.String> target)` Copies one `Map` instance into another.
`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()`
`java.lang.StringBuilder`	`getAnnotationBuilder()` Returns the StringBuilder representing non RDF annotations.
`java.util.Map<java.lang.String,java.lang.String>`	`getAnnotationNamespaces()` Returns the annotationNamespace map of this object.
`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.
`static java.lang.String`	`getElementNameEquivalentToQualifier(CVTerm.Qualifier qualifier)` Returns a `String` which represents the given `CVTerm.Qualifier`.
`Annotation`	`getExtension(java.lang.String namespace)` Returns the Annotation extension object matching 'namespace'.
`History`	`getHistory()` Returns the `History` of the Annotation.
`java.util.List<CVTerm>`	`getListOfCVTerms()` Returns the list of CVTerms.
`java.util.Set<java.lang.String>`	`getNamespaces()` Returns the list of all the namespaces of all the packages which extend this object.
`java.lang.String`	`getNonRDFannotation()` Returns the String containing annotations other than RDF annotation.
`int`	`getNumCVTerms()` Gives the number of `CVTerm`s in this `Annotation`.
`java.util.Map<java.lang.String,java.lang.String>`	`getRDFAnnotationNamespaces()` Returns the rdfAnnotationNamespaces `Map` of this object.
`int`	`hashCode()`
`void`	`insertNoRDFAnnotation(java.lang.String annotation, int offset)` Inserts 'annotation' to the non RDF annotation StringBuilder at position 'offset'.
`boolean`	`isEmpty()`
`boolean`	`isSetAbout()` Checks whether the 'about' element has been initialized.
`boolean`	`isSetAnnotation()` Checks if the Annotation is initialised.
`boolean`	`isSetHistory()` Checks if the `History` is initialised
`boolean`	`isSetListOfCVTerms()` Checks if the list of `CVTerm` is not empty.
`boolean`	`isSetNonRDFannotation()` Checks if the non RDF part of the Annotation is initialised.
`boolean`	`isSetOtherAnnotationThanRDF()` Deprecated. please use `isSetNonRDFannotation()`
`boolean`	`isSetRDFannotation()` Checks if the RDF part of the Annotation is initialised.
`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`	`setAnnotationAttributes(org.w3c.dom.NamedNodeMap annotationNamespaces)` Sets the annotationNamespaces.
`void`	`setAnnotationNamespaces(java.util.Map<java.lang.String,java.lang.String> annotationNamespaces)` Sets the annotationNamespaces.
`void`	`setHistory(History history)` Changes the `History` instance to 'history'
`void`	`setNonRDFAnnotation(java.lang.String nonRDFAnnotation)` Sets the value of the non RDF annotations
`void`	`setRdfAnnotationNamespaces(java.util.Map<java.lang.String,java.lang.String> rdfAnnotationNamespaces)` Sets the rdfAnnotationNamespace map to 'rdfAnnotationNamespaces'.
`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.
  - annotationNamespaces
```
private java.util.Map<java.lang.String,java.lang.String> annotationNamespaces
```
    contains all the name spaces of the matching XML annotation node
  - extensions
```
private java.util.Map<java.lang.String,Annotation> extensions
```
    contains all the annotation extension objects with the name space of their package.
  - 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 java.lang.StringBuilder nonRDFannotation
```
    contains all the annotation information which are not RDF.
  - rdfAnnotationNamespaces
```
private java.util.Map<java.lang.String,java.lang.String> rdfAnnotationNamespaces
```
    contains all the name spaces of the matching XML RDF annotation node
- Constructor Detail
  - Annotation
```
public Annotation()
```
    Creates an Annotation instance. By default, the History and otherAnnotation Strings are null. The list of CVTerms, annotationNamespaces, rdfAnnotationNamespaces 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 Maps annotationNamespaces, rdfAnnotationNamespaces and extensions are empty.
    
    Parameters:
    cvTerms - the list of CVTerm.
  - Annotation
```
public Annotation(java.util.Map<java.lang.String,java.lang.String> annotations)
```
    Creates an Annotation instance from a given Map of annotations. By default, the History and otherAnnotation Strings are null. The list of CVTerms, rdfAnnotationNamespaces and extensions are empty.
    
    Parameters:
    annotations - a map containing an XML name space and a String containing all the annotation elements of this name space.
  - Annotation
```
public Annotation(java.lang.String annotation)
```
    Creates an Annotation instance from a String containing non RDF annotation. By default, the History is null, the list of CVTerms is empty. The Maps annotationNamespaces, rdfAnnotationNamespaces and extensions are 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.
  - Annotation
```
public 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. By default, the History is null. The Maps annotationNamespaces, rdfAnnotationNamespaces and extensions are 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.
- Method Detail
  - copy
```
private static final void copy(java.util.Map<java.lang.String,java.lang.String> origin,
        java.util.Map<java.lang.String,java.lang.String> target)
```
    Copies one Map instance into another.
    
    Parameters:
    origin - copy from here
    target - copy everything into this target Map.
  - 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.
  - addAnnotationNamespace
```
public void addAnnotationNamespace(java.lang.String namespaceName,
                          java.lang.String prefix,
                          java.lang.String URI)
```
    Adds a namespace to the map annotationNamespace of this object.
    
    Parameters:
    namespaceName - an XML namespace name.
    prefix - an optional prefix for the namespace.
    URI - the URI of the namespace
  - addCVTerm
```
public boolean addCVTerm(CVTerm cvTerm)
```
    Adds a CVTerm and checks whether the required name spaces have already been added to the rdfAnnotationNamespaces. If name spaces are missing, these are added automatically.
    
    Parameters:
    cvTerm - the CVTerm to add.
    
    Returns:
    true if the 'cvTerm' element has been added to the List of CVTerm.Qualifiers.
  - addExtension
```
public void addExtension(java.lang.String namespace,
                Annotation annotation)
```
    Adds an Annotation extension object to the extensions map of this object.
    
    Parameters:
    namespace - the name space.
    annotation - the annotation extension object.
  - addRDFAnnotationNamespace
```
public void addRDFAnnotationNamespace(java.lang.String namespaceName,
                             java.lang.String prefix,
                             java.lang.String URI)
```
    Adds a name space to the rdfAnnotationNamespaces Map of this object.
    
    Parameters:
    namespaceName - the name space name
    prefix - the name space prefix
    URI - the name space URI
  - appendNoRDFAnnotation
```
public void appendNoRDFAnnotation(java.lang.String annotation)
```
    Appends some'annotation' to the non RDF annotation StringBuilder of this object.
    
    Parameters:
    annotation - some non RDF annotations.
  - 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 java.lang.StringBuilder getAnnotationBuilder()
```
    Returns the StringBuilder representing non RDF annotations.
    
    Returns:
    the StringBuilder representing non RDF annotations.
  - getAnnotationNamespaces
```
public java.util.Map<java.lang.String,java.lang.String> getAnnotationNamespaces()
```
    Returns the annotationNamespace map of this object.
    
    Returns:
    the annotationNamespace map of this object.
  - 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.
  - getExtension
```
public Annotation getExtension(java.lang.String namespace)
```
    Returns the Annotation extension object matching 'namespace'. Return null if there is no matching object.
    
    Parameters:
    namespace - the namespace
    
    Returns:
    the Annotation extension object matching 'namespace'. Return null if there is no matching object.
  - 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.
  - getNamespaces
```
public java.util.Set<java.lang.String> getNamespaces()
```
    Returns the list of all the namespaces of all the packages which extend this object.
    
    Returns:
    the list of all the namespaces of all the packages which extend this object.
  - getNonRDFannotation
```
public java.lang.String getNonRDFannotation()
```
    Returns the String containing annotations other than RDF annotation.
    
    Returns:
    the String 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.
  - getRDFAnnotationNamespaces
```
public java.util.Map<java.lang.String,java.lang.String> getRDFAnnotationNamespaces()
```
    Returns the rdfAnnotationNamespaces Map of this object.
    
    Returns:
    the rdfAnnotationNamespaces Map of this object.
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class AbstractTreeNode
  - insertNoRDFAnnotation
```
public void insertNoRDFAnnotation(java.lang.String annotation,
                         int offset)
```
    Inserts 'annotation' to the non RDF annotation StringBuilder at position 'offset'.
    
    Parameters:
    annotation - the piece of annotation to add.
    offset - the position where to add it in the StringBuilder.
  - 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 initialised.
    An Annotation is initialised 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 initialised

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

Returns:
true if the History is initialised

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 initialised.
An Annotation is initialised if there is some non RDF annotation

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

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 initialised.
An Annotation is initialised 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

annotationNamespaces

extensions

history

listOfCVTerms

nonRDFannotation

rdfAnnotationNamespaces

Constructor Detail

Annotation

Annotation

Annotation

Annotation

Annotation

Annotation

Method Detail

copy

getElementNameEquivalentToQualifier

addAnnotationNamespace

addCVTerm

addExtension

addRDFAnnotationNamespace

appendNoRDFAnnotation

clone

equals

filterCVTerms

filterCVTerms

getAbout

getAllowsChildren

getAnnotationBuilder

getAnnotationNamespaces

getChildAt

getChildCount

getCVTerm

getExtension

getHistory

createHistory

getListOfCVTerms

getNamespaces

getNonRDFannotation

getNumCVTerms

getRDFAnnotationNamespaces

hashCode

insertNoRDFAnnotation

isEmpty

isSetAbout

isSetAnnotation

isSetHistory

isSetListOfCVTerms

isSetNonRDFannotation

isSetOtherAnnotationThanRDF

isSetRDFannotation

readAttribute

setAbout

setAnnotationAttributes

setAnnotationNamespaces

setHistory

setNonRDFAnnotation

setRdfAnnotationNamespaces

unsetCVTerms

unsetHistory

unsetNonRDFannotation