org.sbml.jsbml.xml.parsers

Class RDFAnnotationParser

java.lang.Object

org.sbml.jsbml.xml.parsers.RDFAnnotationParser

All Implemented Interfaces:

ReadingParser

public class RDFAnnotationParser
extends java.lang.Object
implements ReadingParser

A RDFAnnotationParser is used to parser the subNodes of an annotation which have the namespace URI : "http://www.w3.org/1999/02/22-rdf-syntax-ns#". This parser can only read the RDF annotations.

Since:

0.8

Version:

$Rev: 1447 $

Author:

Marine Dumousseau

Field Summary

Fields

Modifier and Type	Field and Description
private org.apache.log4j.Logger	logger
private static java.lang.String	namespaceURI The namespaceURI of this parser.
private java.util.HashMap<java.lang.String,java.lang.String>	previousElements A map containing the history of the previous element within a RDF node this parser has been read.

Constructor Summary

Constructors

Constructor and Description
RDFAnnotationParser()

Method Summary

Methods

Modifier and Type	Method and Description
static java.lang.String	getNamespaceURI()
void	processAttribute(java.lang.String elementName, java.lang.String attributeName, java.lang.String value, java.lang.String prefix, boolean isLastAttribute, java.lang.Object contextObject) Process the XML attribute and modify 'contextObject' in consequence.
void	processCharactersOf(java.lang.String elementName, java.lang.String characters, java.lang.Object contextObject) Process the text of a XML element and modify 'contextObject' in consequence.
void	processEndDocument(SBMLDocument sbmlDocument) Checks if the sbmlDocument and all the SBML components have a valid rdf:about value.
boolean	processEndElement(java.lang.String elementName, java.lang.String prefix, boolean isNested, java.lang.Object contextObject) Process the end of the element 'elementName'.
void	processNamespace(java.lang.String elementName, java.lang.String URI, java.lang.String prefix, java.lang.String localName, boolean hasAttributes, boolean isLastNamespace, java.lang.Object contextObject) Process the namespace and modify the contextObject in consequence.
java.lang.Object	processStartElement(java.lang.String elementName, java.lang.String prefix, boolean hasAttributes, boolean hasNamespaces, java.lang.Object contextObject) Process the XML element and modify 'contextObject' in consequence.
private void	setRDFAbout(SBase sbase)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logger

private transient org.apache.log4j.Logger logger

namespaceURI

private static final java.lang.String namespaceURI

The namespaceURI of this parser.

See Also:

Constant Field Values

previousElements

private java.util.HashMap<java.lang.String,java.lang.String> previousElements

A map containing the history of the previous element within a RDF node this parser has been read.

Constructor Detail

RDFAnnotationParser

public RDFAnnotationParser()

Method Detail

getNamespaceURI

public static java.lang.String getNamespaceURI()

Returns:

the namespaceURI

processAttribute

public void processAttribute(java.lang.String elementName,
                    java.lang.String attributeName,
                    java.lang.String value,
                    java.lang.String prefix,
                    boolean isLastAttribute,
                    java.lang.Object contextObject)

Description copied from interface: ReadingParser

Process the XML attribute and modify 'contextObject' in consequence. For example, if the contextObject is an instance of Reaction and the attributeName is 'fast', this method will set the 'fast' variable of the 'contextObject' to 'value'. Then it will return the modified Reaction instance.

Specified by:

processAttribute in interface ReadingParser

Parameters:

elementName - : the localName of the XML element.

attributeName - : the attribute localName of the XML element.

value - : the value of the XML attribute.

prefix - : the attribute prefix

isLastAttribute - : boolean value to know if this attribute is the last attribute of the XML element.

contextObject - : the object to set or modify depending on the identity of the current attribute. This object represents the context of the XML attribute in the SBMLDocument.

processCharactersOf

public void processCharactersOf(java.lang.String elementName,
                       java.lang.String characters,
                       java.lang.Object contextObject)

Description copied from interface: ReadingParser

Process the text of a XML element and modify 'contextObject' in consequence. For example, if the contextObject is an instance of ModelCreator and the elementName is 'Family', this method will set the familyName of the 'contextObject' to the text value. Then it will return the changed ModelCreator instance.

Specified by:

processCharactersOf in interface ReadingParser

Parameters:

elementName - : the localName of the XML element.

characters - : the text of this XML element.

contextObject - : the object to set or modify depending on the identity of the current element. This object represents the context of the XML element in the SBMLDocument.

setRDFAbout

private void setRDFAbout(SBase sbase)

Parameters:

sbase -

processEndDocument

public void processEndDocument(SBMLDocument sbmlDocument)

Checks if the sbmlDocument and all the SBML components have a valid rdf:about value.

Specified by:

processEndDocument in interface ReadingParser

Parameters:

sbmlDocument - : the final initialised SBMLDocument instance.

See Also:

org.sbml.jsbml.xml.ReadingParser#processEndDocument(SBMLDocument sbmlDocument)

processEndElement

public boolean processEndElement(java.lang.String elementName,
                        java.lang.String prefix,
                        boolean isNested,
                        java.lang.Object contextObject)

Description copied from interface: ReadingParser

Process the end of the element 'elementName'. Modify or not the contextObject.

Specified by:

processEndElement in interface ReadingParser

Parameters:

elementName - : the localName of the XML element.

prefix - : the prefix of the XML element.

isNested - : boolean value to know if the XML element is a nested element.

contextObject - : the object to set or modify depending on the identity of the current element. This object represents the context of the XML element in the SBMLDocument.

Returns:

true to remove the contextObject from the stack, if false is returned the contextObject will stay on top of the stack

processNamespace

public void processNamespace(java.lang.String elementName,
                    java.lang.String URI,
                    java.lang.String prefix,
                    java.lang.String localName,
                    boolean hasAttributes,
                    boolean isLastNamespace,
                    java.lang.Object contextObject)

Description copied from interface: ReadingParser

Process the namespace and modify the contextObject in consequence. For example, if the contextObject is an instance of SBMLDocument, the namespaces will be stored in the SBMLNamespaces HashMap of this SBMLDocument.

Specified by:

processNamespace in interface ReadingParser

Parameters:

elementName - : the localName of the XML element.

URI - : the URI of the namespace

prefix - : the prefix of the namespace.

localName - : the localName of the namespace.

hasAttributes - : boolean value to know if there are attributes after the namespace declarations.

isLastNamespace - : boolean value to know if this namespace is the last namespace of this element.

contextObject - : the object to set or modify depending on the identity of the current element. This object represents the context of the XML element in the SBMLDocument.

processStartElement

public java.lang.Object processStartElement(java.lang.String elementName,
                                   java.lang.String prefix,
                                   boolean hasAttributes,
                                   boolean hasNamespaces,
                                   java.lang.Object contextObject)

Description copied from interface: ReadingParser

Process the XML element and modify 'contextObject' in consequence. For example, if the contextObject is an instance of Event and the elementName is 'trigger', this method will create a new Trigger instance and will set the trigger instance of the 'contextObject' to the new Trigger. Then the method will return the new Trigger instance which is the new environment.

Specified by:

processStartElement in interface ReadingParser

Parameters:

elementName - : the localName of the XML element to process

prefix - : the prefix of the XML element to process

hasAttributes - : boolean value to know if this XML element has attributes.

hasNamespaces - : boolean value to know if this XML element contains namespace declarations.

contextObject - : the object to set or modify depending on the identity of the current XML element. This object represents the context of the XML element in the SBMLDocument.

Returns:

a new contextObject which represents the environment of the next node/subnode in the SBMLDocument. If null is returned, the contextObject will not change.