org.sbml.jsbml

Class 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:

$Rev$

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, resourceBundle

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.
Annotation(XMLNode annotation)

Method Summary

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	appendNonRDFAnnotation(java.lang.String annotation) Appends some 'annotation' to the non RDF annotation XMLNode of this object.
void	appendNonRDFAnnotation(XMLNode annotationToAppend)
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 CVTerms 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 CVTerms in this Annotation.
XMLNode	getXMLNode()
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'.
boolean	removeCVTerm(CVTerm cvTerm) Removes the given CVTerm.
CVTerm	removeCVTerm(int index) Removes the CVTerm at the given index.
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	setXMLNode(XMLNode nonRDFannotation)
void	unsetCVTerms() Clears the List of CVTerms.
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 org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getParent, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, notifyChildChange, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, toString, userObjectKeySet

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

Annotation

public Annotation(XMLNode annotation)

Parameters:

annotation -

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.

addDeclaredNamespace

public void addDeclaredNamespace(java.lang.String prefix,
                                 java.lang.String uri)

Adds an additional namespace to the set of declared namespaces of this SBase.

Parameters:

prefix - the prefix of the namespace to add

uri - the namespace uri

appendNonRDFAnnotation

public void appendNonRDFAnnotation(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

appendNonRDFAnnotation

public void appendNonRDFAnnotation(XMLNode annotationToAppend)

Parameters:

annotationToAppend -

clone

public Annotation clone()

Specified by:

clone in class AbstractTreeNode

createHistory

private History createHistory()

Returns:

See Also:

SBase.getHistory()

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

@Deprecated
public XMLNode getAnnotationBuilder()

Deprecated.

Returns the XMLNode representing non RDF annotations.

Returns:

the XMLNode representing non RDF annotations.

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.

getCVTermCount

public int getCVTermCount()

Gives the number of CVTerms in this Annotation.

Returns:

the number of controlled vocabulary terms in this Annotation.

getDeclaredNamespaces

public XMLNamespaces getDeclaredNamespaces()

Returns:

getFullAnnotation

public XMLNode getFullAnnotation()

Returns:

getFullAnnotationString

public java.lang.String getFullAnnotationString()

Returns:

getHistory

public History getHistory()

Returns the History of the Annotation.

Returns:

the History of the Annotation.

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.

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.

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.

getNumCVTerms

public int getNumCVTerms()

Gives the number of CVTerms in this Annotation.

Returns:

the number of controlled vocabulary terms in this Annotation.

getXMLNode

public XMLNode getXMLNode()

Returns:

setXMLNode

public void setXMLNode(XMLNode nonRDFannotation)

Parameters:

nonRDFannotation -

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.

Returns:

true if the RDF part of the Annotation is initialized

readAttribute

public 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'.

Parameters:

attributeName - the attribute name.

prefix - the attribute prefix.

value - the attribute value.

Returns:

true if an about XML attribute has been read

removeCVTerm

public boolean removeCVTerm(CVTerm cvTerm)

Removes the given CVTerm.

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.

Parameters:

index - the index

Returns:

the removed CVTerm.

Throws:

java.lang.IndexOutOfBoundsException - if the index is out of range (index < 0 || index >= size())

setAbout

public void setAbout(java.lang.String about)

Sets the value of the about String of this object.

Parameters:

about - the about String to set.

setHistory

public void setHistory(History history)

Changes the History instance to 'history'

Parameters:

history - the history to set.

setNonRDFAnnotation

public void setNonRDFAnnotation(java.lang.String nonRDFAnnotationStr)
                         throws javax.xml.stream.XMLStreamException

Sets the value of the non RDF annotations

Parameters:

nonRDFAnnotationStr -

Throws:

javax.xml.stream.XMLStreamException

setNonRDFAnnotation

public void setNonRDFAnnotation(XMLNode nonRDFAnnotation)

Sets the value of the non RDF annotations

Parameters:

nonRDFAnnotation -

unsetCVTerms

public void unsetCVTerms()

Clears the List of CVTerms.

unsetHistory

public void unsetHistory()

Sets the History instance of this object to null.

unsetNonRDFannotation

public void unsetNonRDFannotation()

Sets the non RDF annotation String to null.