org.sbml.jsbml.xml.parsers

Interface ReadingParser

All Known Implementing Classes:

AbstractReaderWriter, MathMLParser, MathMLStaxParser, SBMLCoreParser, XMLNodeReader

public interface ReadingParser

The interface to implement for the SBML parsers reading SBML files.

Since:

0.8

Version:

$Rev$

Author:

Marine Dumousseau, Nicolas Rodriguez

Method Summary

Modifier and Type	Method and Description
java.util.List<java.lang.String>	getNamespaces() Returns a List of all the namespaces that this parser is handling.
boolean	processAttribute(java.lang.String elementName, java.lang.String attributeName, java.lang.String value, java.lang.String URI, 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) Process the end of the document.
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 URI, java.lang.String prefix, boolean hasAttributes, boolean hasNamespaces, java.lang.Object contextObject) Process the XML element and modify 'contextObject' in consequence.

Method Detail

processAttribute

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

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.

Parameters:

elementName - the localName of the XML element.

attributeName - the attribute localName of the XML element.

value - the value of the XML attribute.

URI -

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.

Returns:

true if the attribute was recognized and stored in the contextObject, false otherwise.

processCharactersOf

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.

For example, if the contextObject is an instance of Creator and the elementName is 'Family', this method will set the familyName of the 'contextObject' to the text value. Then it will return the changed Creator instance.

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.

processEndDocument

void processEndDocument(SBMLDocument sbmlDocument)

Process the end of the document. Do the necessary changes in the SBMLDocument. For example, check if all the annotations are valid, etc.

Parameters:

sbmlDocument - the final initialized SBMLDocument instance.

processEndElement

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

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

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

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.

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

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

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

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.

Parameters:

elementName - the localName of the XML element to process

URI -

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.

getNamespaces

java.util.List<java.lang.String> getNamespaces()

Returns a List of all the namespaces that this parser is handling.

Returns:

a List of all the namespaces that this parser is handling