org.sbml.jsbml.xml.stax

Class SBMLWriter

java.lang.Object

org.sbml.jsbml.xml.stax.SBMLWriter

public class SBMLWriter
extends java.lang.Object

A SBMLWriter provides the methods to write a SBML file.

Since:

0.8

Author:

Marine Dumousseau, Nicolas Rodriguez, Andreas Dräger

Field Summary

Fields

Modifier and Type	Field and Description
private char	indentChar The symbol for indentation.
private short	indentCount The number of indentation symbols.
private java.util.Map<java.lang.String,WritingParser>	instantiatedSBMLParsers contains the WritingParser instances of this class.
private java.util.List<java.lang.String>	issuedWarnings Remember already issued warnings to avoid having multiple lines, saying the same thing (Warning: Skipping detailed parsing of name space 'XYZ'.
private static org.apache.log4j.Logger	logger A Logger for this class.

Constructor Summary

Constructors

Constructor and Description
SBMLWriter() Creates a new SBMLWriter with default configuration for indentChar and indentCount.
SBMLWriter(char indentChar, short indentCount) Creates a new SBMLWriter with the given configuration for the indentChar and indentCount, i.e., the symbol to be used to indent elements in the XML representation of SBML data objects and the number of these symbols to be concatenated at the beginning of each new line for a new element.

Method Summary

Modifier and Type	Method and Description
private void	addWritingParser(java.util.List<WritingParser> sbmlParsers, WritingParser sbmlParser, java.lang.String namespace) Adds a WritingParser to the given list of WritingParser
private java.lang.String	createIndentationString(int indent) Creates the necessary number of white spaces at the beginning of an entry in the SBML file.
static char	getDefaultIndentChar() Returns the default symbol to be used to indent new elements in the XML representation of SBML data structures.
static short	getDefaultIndentCount() Returns the default number of indent symbols to be concatenated at the beginning of a new block in an XML representation of SBML data structures.
char	getIndentationChar() Gives the symbol that is used to indent the SBML output for a better structure and to improve human-readability.
short	getIndentationCount() Gives the number of indent symbols that are inserted in a line to better structure the SBML output.
private java.util.List<WritingParser>	getWritingParsers(java.lang.Object object, java.lang.String parentNamespace) Gets all the writing parsers necessary to write the given object.
private java.util.Map<java.lang.String,WritingParser>	initializePackageParsers() Creates the ReadingParser instances and stores them in a HashMap.
private boolean	isEmptyListOf(java.lang.Object object) Returns true if the given Object is an empty ListOf, false otherwise.
static void	main(java.lang.String[] args) Tests this class
void	setIndentationChar(char indentSymbol) Sets other blank character(s) for indentation.
void	setIndentationCount(int indentCount) Sets the indent for this SBMLWriter.
void	setIndentationCount(short indentCount) Sets the indent for this SBMLWriter.
void	write(SBMLDocument document, java.io.File file) Writes the SBMLDocument into a File.
void	write(SBMLDocument document, java.io.File file, java.lang.String programName, java.lang.String programVersion) Writes the SBMLDocument into a File.
void	write(SBMLDocument sbmlDocument, java.io.OutputStream stream) Writes the SBMLDocument into an OutputStream.
void	write(SBMLDocument sbmlDocument, java.io.OutputStream stream, java.lang.String programName, java.lang.String programVersion) Writes the XML representation of an SBMLDocument into an OutputStream.
void	write(SBMLDocument sbmlDocument, java.lang.String fileName) Writes the XML representation of an SBMLDocument in a SBML file.
void	write(SBMLDocument sbmlDocument, java.lang.String fileName, java.lang.String programName, java.lang.String programVersion) Writes the XML representation of an SBMLDocument in a SBML file.
java.lang.String	writeAnnotation(SBase sbase) Writes the Annotation of an SBase element to an XML String.
private void	writeAnnotation(SBase sbase, SMOutputContainer element, javax.xml.stream.XMLStreamWriter writer, int indent, boolean xmlFragment) Writes the Annotation of an SBase element.
private void	writeMathML(MathContainer m, SMOutputElement element, javax.xml.stream.XMLStreamWriter writer, int indent) Writes the MathML expression of a MathContainer element.
private void	writeMessage(Constraint sbase, SMOutputElement element, javax.xml.stream.XMLStreamWriter writer, java.lang.String sbmlNamespace, int indent) Writes the message of a Constraint to the given XMLStreamWriter.
private void	writeNotes(SBase sbase, SMOutputElement element, javax.xml.stream.XMLStreamWriter writer, java.lang.String sbmlNamespace, int indent) Writes the notes of this SBase element to the given XMLStreamWriter.
private void	writeSBMLElements(SBMLObjectForXML parentXmlObject, SMOutputElement smOutputParentElement, javax.xml.stream.XMLStreamWriter streamWriter, java.lang.Object parentObject, int indent) Writes the SBML elements to an XMLStreamWriter.
java.lang.String	writeSBMLToString(SBMLDocument doc) Writes the given SBMLDocument to an in-memory XML String.
java.lang.String	writeSBMLToString(SBMLDocument d, java.lang.String programName, java.lang.String programVersion) Writes the given SBMLDocument to an in-memory XML String.
private void	writeXMLNode(XMLNode xmlNode, SMOutputElement smOutputParentElement, javax.xml.stream.XMLStreamWriter writer, int indent)

Methods inherited from class java.lang.Object

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

Field Detail

indentChar

private char indentChar

The symbol for indentation.

indentCount

private short indentCount

The number of indentation symbols.

instantiatedSBMLParsers

private java.util.Map<java.lang.String,WritingParser> instantiatedSBMLParsers

contains the WritingParser instances of this class.

issuedWarnings

private transient java.util.List<java.lang.String> issuedWarnings

Remember already issued warnings to avoid having multiple lines, saying the same thing (Warning: Skipping detailed parsing of name space 'XYZ'. No parser available.)

logger

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

A Logger for this class.

Constructor Detail

SBMLWriter

public SBMLWriter()

Creates a new SBMLWriter with default configuration for indentChar and indentCount.

SBMLWriter

public SBMLWriter(char indentChar,
                  short indentCount)

Creates a new SBMLWriter with the given configuration for the indentChar and indentCount, i.e., the symbol to be used to indent elements in the XML representation of SBML data objects and the number of these symbols to be concatenated at the beginning of each new line for a new element.

Parameters:

indentChar - the symbol to be used to indent elements in the XML representation

indentCount - the number of these symbols to be concatenated

Method Detail

getDefaultIndentChar

public static char getDefaultIndentChar()

Returns the default symbol to be used to indent new elements in the XML representation of SBML data structures.

Returns:

the default symbol to be used to indent new elements in the XML representation of SBML data structures.

getDefaultIndentCount

public static short getDefaultIndentCount()

Returns the default number of indent symbols to be concatenated at the beginning of a new block in an XML representation of SBML data structures.

Returns:

The default number of indent symbols to be concatenated at the beginning of a new block in an XML representation of SBML data structures.

main

public static void main(java.lang.String[] args)
                 throws SBMLException

Tests this class

Parameters:

args -

Throws:

SBMLException

addWritingParser

private void addWritingParser(java.util.List<WritingParser> sbmlParsers,
                              WritingParser sbmlParser,
                              java.lang.String namespace)

Adds a WritingParser to the given list of WritingParser

Parameters:

sbmlParsers -

sbmlParser -

namespace -

createIndentationString

private java.lang.String createIndentationString(int indent)

Creates the necessary number of white spaces at the beginning of an entry in the SBML file.

Parameters:

indent -

Returns:

getIndentationChar

public char getIndentationChar()

Gives the symbol that is used to indent the SBML output for a better structure and to improve human-readability.

Returns:

the character to be used for indentation.

getIndentationCount

public short getIndentationCount()

Gives the number of indent symbols that are inserted in a line to better structure the SBML output.

Returns:

the indentCount

getWritingParsers

private java.util.List<WritingParser> getWritingParsers(java.lang.Object object,
                                                        java.lang.String parentNamespace)

Gets all the writing parsers necessary to write the given object.

Parameters:

object -

parentNamespace -

Returns:

all the writing parsers necessary to write this element.

initializePackageParsers

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

Creates the ReadingParser instances and stores them in a HashMap.

Returns:

the map containing the ReadingParser instances.

setIndentationChar

public void setIndentationChar(char indentSymbol)

Sets other blank character(s) for indentation.

Allowed are only tabs and white spaces, i.e., '\t' and ' '.

Parameters:

indentSymbol - the character to be used for indentation

setIndentationCount

public void setIndentationCount(int indentCount)

Sets the indent for this SBMLWriter.

Parameters:

indentCount - the indent count to set

See Also:

setIndentationCount(short)

setIndentationCount

public void setIndentationCount(short indentCount)

Sets the indent for this SBMLWriter.

Parameters:

indentCount - the indent count to set

write

public void write(SBMLDocument document,
                  java.io.File file)
           throws javax.xml.stream.XMLStreamException,
                  SBMLException,
                  java.io.IOException

Writes the SBMLDocument into a File.

Parameters:

document - the SBMLDocument to write.

file - the File to write to.

Throws:

SBMLException - if any error is detected in the SBMLDocument.

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

java.io.IOException - if it is not possible to write to the given file, e.g., due to an invalid file name or missing permissions.

write

public void write(SBMLDocument document,
                  java.io.File file,
                  java.lang.String programName,
                  java.lang.String programVersion)
           throws javax.xml.stream.XMLStreamException,
                  SBMLException,
                  java.io.IOException

Writes the SBMLDocument into a File.

Parameters:

document - the SBMLDocument to write.

file - the File to write to.

programName - the program name.

programVersion - the program version.

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

SBMLException - if any error is detected in the SBMLDocument.

java.io.IOException - if it is not possible to write to the given file, e.g., due to an invalid file name or missing permissions.

write

public void write(SBMLDocument sbmlDocument,
                  java.io.OutputStream stream)
           throws javax.xml.stream.XMLStreamException,
                  SBMLException

Writes the SBMLDocument into an OutputStream.

Parameters:

sbmlDocument - the SBMLDocument to write.

stream - a OutputStream where to write the content of the model to.

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

SBMLException - if any error is detected in the SBMLDocument.

write

public void write(SBMLDocument sbmlDocument,
                  java.io.OutputStream stream,
                  java.lang.String programName,
                  java.lang.String programVersion)
           throws javax.xml.stream.XMLStreamException,
                  SBMLException

Writes the XML representation of an SBMLDocument into an OutputStream.

Parameters:

sbmlDocument - the SBMLDocument

stream - the OutputStream to write to.

programName - the program name (can be null).

programVersion - the program version (can be null).

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

SBMLException - if any error is detected in the SBMLDocument.

write

public void write(SBMLDocument sbmlDocument,
                  java.lang.String fileName)
           throws javax.xml.stream.XMLStreamException,
                  SBMLException,
                  java.io.IOException

Writes the XML representation of an SBMLDocument in a SBML file.

Parameters:

sbmlDocument - the SBMLDocument to write.

fileName - the name of the file where to write the SBMLDocument

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

SBMLException - if any error is detected in the SBMLDocument.

java.io.IOException - if an I/O error occurs.

write

public void write(SBMLDocument sbmlDocument,
                  java.lang.String fileName,
                  java.lang.String programName,
                  java.lang.String programVersion)
           throws javax.xml.stream.XMLStreamException,
                  SBMLException,
                  java.io.IOException

Writes the XML representation of an SBMLDocument in a SBML file.

Parameters:

sbmlDocument - the SBMLDocument to write.

fileName - the name of the file where to write the SBMLDocument

programName - the program name that created the SBMLDocument

programVersion - the program version that created the SBMLDocument

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

SBMLException - if any error is detected in the SBMLDocument.

java.io.IOException - if an I/O error occurs.

writeAnnotation

public java.lang.String writeAnnotation(SBase sbase)
                                 throws javax.xml.stream.XMLStreamException

Writes the Annotation of an SBase element to an XML String.

Parameters:

sbase - the SBase element.

Returns:

the Annotation of the given SBase element as an XML String.

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

writeAnnotation

private void writeAnnotation(SBase sbase,
                             SMOutputContainer element,
                             javax.xml.stream.XMLStreamWriter writer,
                             int indent,
                             boolean xmlFragment)
                      throws javax.xml.stream.XMLStreamException

Writes the Annotation of an SBase element.

Parameters:

sbase - the SBase element.

element - the matching SMOutputElement

writer - the XMLStreamWriter to write to.

indent - the number of indent white spaces of this annotation.

xmlFragment -

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

writeXMLNode

private void writeXMLNode(XMLNode xmlNode,
                          SMOutputElement smOutputParentElement,
                          javax.xml.stream.XMLStreamWriter writer,
                          int indent)
                   throws javax.xml.stream.XMLStreamException

Parameters:

xmlNode -

smOutputParentElement -

writer -

indent -

Throws:

javax.xml.stream.XMLStreamException

writeMathML

private void writeMathML(MathContainer m,
                         SMOutputElement element,
                         javax.xml.stream.XMLStreamWriter writer,
                         int indent)
                  throws javax.xml.stream.XMLStreamException

Writes the MathML expression of a MathContainer element.

Parameters:

m - the MathContainer element.

element - the matching SMOutputElement.

writer - the XMLStreamWriter to write to.

indent - the number of white spaces to indent this element.

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

writeMessage

private void writeMessage(Constraint sbase,
                          SMOutputElement element,
                          javax.xml.stream.XMLStreamWriter writer,
                          java.lang.String sbmlNamespace,
                          int indent)
                   throws javax.xml.stream.XMLStreamException

Writes the message of a Constraint to the given XMLStreamWriter.

Parameters:

sbase - the Constraint element.

element - the matching SMOutputElement.

writer - the XMLStreamWriter to write to.

sbmlNamespace - the SBML namespace.

indent - the number of white spaces to indent this element.

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

writeNotes

private void writeNotes(SBase sbase,
                        SMOutputElement element,
                        javax.xml.stream.XMLStreamWriter writer,
                        java.lang.String sbmlNamespace,
                        int indent)
                 throws javax.xml.stream.XMLStreamException

Writes the notes of this SBase element to the given XMLStreamWriter.

Parameters:

sbase - the SBase element.

element - the matching SMOutputElement

writer - the XMLStreamWriter to write to.

sbmlNamespace - the SBML namespace.

indent - the number of white spaces to indent this element.

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

writeSBMLElements

private void writeSBMLElements(SBMLObjectForXML parentXmlObject,
                               SMOutputElement smOutputParentElement,
                               javax.xml.stream.XMLStreamWriter streamWriter,
                               java.lang.Object parentObject,
                               int indent)
                        throws javax.xml.stream.XMLStreamException,
                               SBMLException

Writes the SBML elements to an XMLStreamWriter.

Parameters:

parentXmlObject - contains the XML information of the parentElement.

smOutputParentElement - SMOutputElement of the parentElement.

streamWriter - the XMLStreamWriter to write to.

parentObject - the Object to write.

indent - the number of white spaces to indent this element.

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

SBMLException - if any error is detected in the SBMLDocument.

isEmptyListOf

private boolean isEmptyListOf(java.lang.Object object)

Returns true if the given Object is an empty ListOf, false otherwise.

Parameters:

object - the Object to test

Returns:

true if the given Object is an empty ListOf, false otherwise.

writeSBMLToString

public java.lang.String writeSBMLToString(SBMLDocument doc)
                                   throws javax.xml.stream.XMLStreamException,
                                          SBMLException

Writes the given SBMLDocument to an in-memory XML String.

Parameters:

doc - the SBMLdocument

Returns:

the XML representation of the SBMLdocument as a String.

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

SBMLException - if any error is detected in the SBMLDocument.

writeSBMLToString

public java.lang.String writeSBMLToString(SBMLDocument d,
                                          java.lang.String programName,
                                          java.lang.String programVersion)
                                   throws javax.xml.stream.XMLStreamException,
                                          SBMLException

Writes the given SBMLDocument to an in-memory XML String.

Parameters:

d -

programName -

programVersion -

Returns:

the XML representation of the SBMLdocument as a String.

Throws:

javax.xml.stream.XMLStreamException - if any error occur while creating the XML document.

SBMLException - if any error is detected in the SBMLDocument.