org.sbml.jsbml.xml.stax

Class SBMLReader

java.lang.Object

org.sbml.jsbml.xml.stax.SBMLReader

public class SBMLReader
extends java.lang.Object

Provides all the methods to read a SBML file.

Since:

0.8

Author:

Marine Dumousseau, Andreas Dräger, Nicolas Rodriguez, Clemens Wrzodek

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.List<AnnotationReader>	annotationParsers
private MathContainer	astNodeParent The parent of the mathML we are parsing through the readMathML methods.
private java.util.Map<java.lang.String,ReadingParser>	initializedParsers Contains all the initialized parsers.
private static org.apache.log4j.Logger	logger A Logger for this class.
private static SBMLCoreParser	sbmlCoreParser Initialize a static instance of the core parser.

Constructor Summary

Constructors

Constructor and Description
SBMLReader()

Method Summary

Modifier and Type	Method and Description
private void	addAnnotationParsers(javax.xml.stream.events.StartElement startElement) Associates any unknown namespaces with the AnnotationReader.
private void	cleanTreeNode(AbstractTreeNode treeNode) Cleans the given node by removing user object(s) set during reading/parsing.
void	initializeAnnotationParsers() Initializes the packageParser HashMap of this class.
private java.util.Map<java.lang.String,ReadingParser>	initializePackageParsers() Creates the ReadingParser instances and stores them in a HashMap.
static void	main(java.lang.String[] args) Reads the file that is passed as argument and write it to the console, using the method SBMLWriter.write(SBMLDocument, java.io.OutputStream).
private void	processAttributes(java.util.Iterator<javax.xml.stream.events.Attribute> att, javax.xml.namespace.QName currentNode, java.util.Stack<java.lang.Object> sbmlElements, ReadingParser parser, boolean hasAttributes, boolean isInsideAnnotation) Process Attributes of the current element on the stack.
private SBMLDocument	processEndElement(javax.xml.namespace.QName currentNode, java.lang.Boolean isNested, java.lang.Boolean isText, java.lang.Boolean isHTML, int level, int version, ReadingParser parser, java.util.Stack<java.lang.Object> sbmlElements, boolean isInsideAnnotation) Process the end of an element.
private void	processNamespaces(java.util.Iterator<javax.xml.stream.events.Namespace> nam, javax.xml.namespace.QName currentNode, java.util.Stack<java.lang.Object> sbmlElements, ReadingParser parser, boolean hasAttributes) Process Namespaces of the current element on the stack.
private ReadingParser	processStartElement(javax.xml.stream.events.StartElement startElement, javax.xml.namespace.QName currentNode, java.lang.Boolean isHTML, java.util.Stack<java.lang.Object> sbmlElements, boolean isInsideAnnotation) Process a StartElement event.
ASTNode	readMathML(java.lang.String mathML)
ASTNode	readMathML(java.lang.String mathML, TreeNodeChangeListener listener) Reads a mathML String into an ASTNode.
ASTNode	readMathML(java.lang.String mathML, TreeNodeChangeListener listener, MathContainer parent) Reads a mathML String into an ASTNode.
XMLNode	readNotes(java.lang.String notesXHTML)
XMLNode	readNotes(java.lang.String notesXHTML, TreeNodeChangeListener listener) Reads a notes XML String into an XMLNode.
SBMLDocument	readSBML(java.io.File file)
SBMLDocument	readSBML(java.io.File file, TreeNodeChangeListener listener) Reads a SBML String from the given file.
SBMLDocument	readSBML(java.lang.String file) Reads SBML from a given file.
SBMLDocument	readSBML(javax.xml.stream.XMLEventReader xmlEventReader)
SBMLDocument	readSBML(javax.xml.stream.XMLEventReader xmlEventReader, TreeNodeChangeListener listener) Reads an SBMLDocument from the given XMLEventReader
SBMLDocument	readSBMLFile(java.lang.String fileName) Reads the SBML file 'fileName' and creates/initialises a SBMLDocument instance.
SBMLDocument	readSBMLFromStream(java.io.InputStream stream)
SBMLDocument	readSBMLFromStream(java.io.InputStream stream, TreeNodeChangeListener listener) Reads a SBML document from the given stream.
SBMLDocument	readSBMLFromString(java.lang.String xml)
SBMLDocument	readSBMLFromString(java.lang.String xml, TreeNodeChangeListener listener) Reads a SBML model from the given XML String.
private java.lang.Object	readXMLFromStream(java.io.InputStream stream, TreeNodeChangeListener listener) Reads a XML document from the given stream.
private java.lang.Object	readXMLFromString(java.lang.String xml, TreeNodeChangeListener listener) Reads an XML String that should the part of a SBML model.
private java.lang.Object	readXMLFromXMLEventReader(javax.xml.stream.XMLEventReader xmlEventReader, TreeNodeChangeListener listener) Reads an XML document from the given XMLEventReader.

Methods inherited from class java.lang.Object

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

Field Detail

initializedParsers

private java.util.Map<java.lang.String,ReadingParser> initializedParsers

Contains all the initialized parsers.

astNodeParent

private MathContainer astNodeParent

The parent of the mathML we are parsing through the readMathML methods. It allow to parse properly the FunctionDefinition contained in the mathML.

annotationParsers

private java.util.List<AnnotationReader> annotationParsers

sbmlCoreParser

private static SBMLCoreParser sbmlCoreParser

Initialize a static instance of the core parser.

logger

private static final transient org.apache.log4j.Logger logger

A Logger for this class.

Constructor Detail

SBMLReader

public SBMLReader()

Method Detail

initializePackageParsers

private java.util.Map<java.lang.String,ReadingParser> initializePackageParsers()

Creates the ReadingParser instances and stores them in a HashMap.

Returns:

the map containing the ReadingParser instances.

addAnnotationParsers

private void addAnnotationParsers(javax.xml.stream.events.StartElement startElement)

Associates any unknown namespaces with the AnnotationReader.

Parameters:

startElement -

initializeAnnotationParsers

public void initializeAnnotationParsers()

Initializes the packageParser HashMap of this class.

main

public static void main(java.lang.String[] args)
                 throws java.io.IOException,
                        javax.xml.stream.XMLStreamException,
                        SBMLException

Reads the file that is passed as argument and write it to the console, using the method SBMLWriter.write(SBMLDocument, java.io.OutputStream).

Parameters:

args - the command line arguments, we are taking the first one as the file name to read.

Throws:

java.io.IOException - if the file name is not valid.

SBMLException - if there are any problems reading or writing the SBML model.

javax.xml.stream.XMLStreamException - if there are any problems reading or writing the XML file.

readSBML

public SBMLDocument readSBML(java.io.File file)
                      throws java.io.IOException,
                             javax.xml.stream.XMLStreamException

Parameters:

file -

Returns:

Throws:

javax.xml.stream.XMLStreamException

java.io.IOException

readSBML

public SBMLDocument readSBML(java.io.File file,
                             TreeNodeChangeListener listener)
                      throws java.io.IOException,
                             javax.xml.stream.XMLStreamException

Reads a SBML String from the given file.

Parameters:

file - A file containing SBML content.

listener -

Returns:

the matching SBMLDocument instance.

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

readSBML

public SBMLDocument readSBML(java.lang.String file)
                      throws javax.xml.stream.XMLStreamException,
                             java.io.IOException

Reads SBML from a given file.

Parameters:

file - The path to an SBML file.

Returns:

the matching SBMLDocument instance.

Throws:

javax.xml.stream.XMLStreamException

java.io.IOException

readSBMLFile

public SBMLDocument readSBMLFile(java.lang.String fileName)
                          throws javax.xml.stream.XMLStreamException,
                                 java.io.IOException

Reads the SBML file 'fileName' and creates/initialises a SBMLDocument instance.

Parameters:

fileName - name of the SBML file to read.

Returns:

the initialised SBMLDocument.

Throws:

javax.xml.stream.XMLStreamException

java.io.IOException

readSBML

public SBMLDocument readSBML(javax.xml.stream.XMLEventReader xmlEventReader,
                             TreeNodeChangeListener listener)
                      throws javax.xml.stream.XMLStreamException

Reads an SBMLDocument from the given XMLEventReader

Parameters:

xmlEventReader -

listener -

Returns:

Throws:

javax.xml.stream.XMLStreamException

readSBML

public SBMLDocument readSBML(javax.xml.stream.XMLEventReader xmlEventReader)
                      throws javax.xml.stream.XMLStreamException

Parameters:

xmlEventReader -

Returns:

Throws:

javax.xml.stream.XMLStreamException

readMathML

public ASTNode readMathML(java.lang.String mathML,
                          TreeNodeChangeListener listener)
                   throws javax.xml.stream.XMLStreamException

Reads a mathML String into an ASTNode.

Parameters:

mathML -

listener -

Returns:

an ASTNode representing the given mathML String.

Throws:

javax.xml.stream.XMLStreamException

cleanTreeNode

private void cleanTreeNode(AbstractTreeNode treeNode)

Cleans the given node by removing user object(s) set during reading/parsing.

Parameters:

treeNode - the node to be cleaned

readMathML

public ASTNode readMathML(java.lang.String mathML,
                          TreeNodeChangeListener listener,
                          MathContainer parent)
                   throws javax.xml.stream.XMLStreamException

Reads a mathML String into an ASTNode.

Parameters:

mathML -

listener -

parent - the parent MathContainer of the mathML to parse

Returns:

an ASTNode representing the given mathML String.

Throws:

javax.xml.stream.XMLStreamException

readMathML

public ASTNode readMathML(java.lang.String mathML)
                   throws javax.xml.stream.XMLStreamException

Parameters:

mathML -

Returns:

Throws:

javax.xml.stream.XMLStreamException

readNotes

public XMLNode readNotes(java.lang.String notesXHTML,
                         TreeNodeChangeListener listener)
                  throws javax.xml.stream.XMLStreamException

Reads a notes XML String into an XMLNode.

Parameters:

notesXHTML -

listener -

Returns:

an XMLNode representing the given notes String.

Throws:

javax.xml.stream.XMLStreamException

readNotes

public XMLNode readNotes(java.lang.String notesXHTML)
                  throws javax.xml.stream.XMLStreamException

Parameters:

notesXHTML -

Returns:

Throws:

javax.xml.stream.XMLStreamException

readSBMLFromStream

public SBMLDocument readSBMLFromStream(java.io.InputStream stream,
                                       TreeNodeChangeListener listener)
                                throws javax.xml.stream.XMLStreamException

Reads a SBML document from the given stream.

Parameters:

stream -

listener -

Returns:

Throws:

javax.xml.stream.XMLStreamException

readSBMLFromStream

public SBMLDocument readSBMLFromStream(java.io.InputStream stream)
                                throws javax.xml.stream.XMLStreamException

Parameters:

stream -

Returns:

Throws:

javax.xml.stream.XMLStreamException

readXMLFromStream

private java.lang.Object readXMLFromStream(java.io.InputStream stream,
                                           TreeNodeChangeListener listener)
                                    throws javax.xml.stream.XMLStreamException

Reads a XML document from the given stream. It need to be a self contain part of an SBML document.

Parameters:

stream -

listener -

Returns:

Throws:

javax.xml.stream.XMLStreamException

readXMLFromXMLEventReader

private java.lang.Object readXMLFromXMLEventReader(javax.xml.stream.XMLEventReader xmlEventReader,
                                                   TreeNodeChangeListener listener)
                                            throws javax.xml.stream.XMLStreamException

Reads an XML document from the given XMLEventReader. It need to represent a self contain part of an SBML document. It can be either a math element, a notes element or the whole SBML model. If math or notes are given, a Rule containing the math or notes will be returned, otherwise an SBMLDocument is returned.

Parameters:

xmlEventReader -

listener -

Returns:

an Object representing the given XML.

Throws:

javax.xml.stream.XMLStreamException

readSBMLFromString

public SBMLDocument readSBMLFromString(java.lang.String xml,
                                       TreeNodeChangeListener listener)
                                throws javax.xml.stream.XMLStreamException

Reads a SBML model from the given XML String.

Parameters:

xml -

listener -

Returns:

Throws:

javax.xml.stream.XMLStreamException

readSBMLFromString

public SBMLDocument readSBMLFromString(java.lang.String xml)
                                throws javax.xml.stream.XMLStreamException

Parameters:

xml -

Returns:

Throws:

javax.xml.stream.XMLStreamException

readXMLFromString

private java.lang.Object readXMLFromString(java.lang.String xml,
                                           TreeNodeChangeListener listener)
                                    throws javax.xml.stream.XMLStreamException

Reads an XML String that should the part of a SBML model.

Parameters:

xml -

listener -

Returns:

Throws:

javax.xml.stream.XMLStreamException

processStartElement

private ReadingParser processStartElement(javax.xml.stream.events.StartElement startElement,
                                          javax.xml.namespace.QName currentNode,
                                          java.lang.Boolean isHTML,
                                          java.util.Stack<java.lang.Object> sbmlElements,
                                          boolean isInsideAnnotation)

Process a StartElement event.

Parameters:

startElement -

currentNode -

isHTML -

sbmlElements -

isInsideAnnotation -

Returns:

processNamespaces

private void processNamespaces(java.util.Iterator<javax.xml.stream.events.Namespace> nam,
                               javax.xml.namespace.QName currentNode,
                               java.util.Stack<java.lang.Object> sbmlElements,
                               ReadingParser parser,
                               boolean hasAttributes)

Process Namespaces of the current element on the stack.

Parameters:

nam -

currentNode -

sbmlElements -

parser -

hasAttributes -

processAttributes

private void processAttributes(java.util.Iterator<javax.xml.stream.events.Attribute> att,
                               javax.xml.namespace.QName currentNode,
                               java.util.Stack<java.lang.Object> sbmlElements,
                               ReadingParser parser,
                               boolean hasAttributes,
                               boolean isInsideAnnotation)

Process Attributes of the current element on the stack.

Parameters:

att -

currentNode -

sbmlElements -

parser -

hasAttributes -

isInsideAnnotation -

processEndElement

private SBMLDocument processEndElement(javax.xml.namespace.QName currentNode,
                                       java.lang.Boolean isNested,
                                       java.lang.Boolean isText,
                                       java.lang.Boolean isHTML,
                                       int level,
                                       int version,
                                       ReadingParser parser,
                                       java.util.Stack<java.lang.Object> sbmlElements,
                                       boolean isInsideAnnotation)

Process the end of an element.

Parameters:

currentNode -

isNested -

isText -

isHTML -

level -

version -

parser -

sbmlElements -

isInsideAnnotation -

Returns: