org.sbml.jsbml

Class SBMLWriter

java.lang.Object

org.sbml.jsbml.SBMLWriter

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public class SBMLWriter
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable

Provides methods for writing SBML to files, text strings or streams.

This SBMLWriter is just a wrapper for the actual implementation in SBMLWriter.

This class is provided for compatibility with libSBML and to avoid problems if the internal of jsbml change, so it is preferable to use it instead of directly using SBMLWriter. The SBMLWriter class is the converse of SBMLReader, and provides the main interface for serializing SBML models into XML and writing the result to files and text strings. The methods for writing SBML all take an SBMLDocument object and a destination.

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger, Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
(package private) java.lang.String	programName The name of the program that has been used to create an SBML String representation (possibly in a File) with the help of JSBML.
(package private) java.lang.String	programVersion The version of the program using JSBML to serialize a model in an SBML String or File.
protected SBMLWriter	sbmlWriter The actual writer.
private static long	serialVersionUID Generated serial version identifier.

Constructor Summary

Constructors

Constructor and Description
SBMLWriter() Creates a new SBMLWriter.
SBMLWriter(char indentChar, short indentCount) Creates a new SBMLWriter that uses the given character for indentation of the XML representation of SBML data structures (with the given number of such symbols).
SBMLWriter(SBMLWriter sbmlWriter) Clone constructor.
SBMLWriter(java.lang.String programName, java.lang.String programVersion) Creates a new SBMLWriter for the program with the given name and version.
SBMLWriter(java.lang.String programName, java.lang.String programVersion, char indentChar, short indentCount) Creates a new SBMLWriter for the program with the given name and version that uses the given character for indentation of the XML representation of SBML data structures (with the given number of such symbols).

Method Summary

Modifier and Type	Method and Description
SBMLWriter	clone()
boolean	equals(java.lang.Object o)
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.
java.lang.String	getProgramName()
java.lang.String	getProgramVersion()
boolean	isSetProgramName() Check if a program name has been defined for this SBMLWriter.
boolean	isSetProgramVersion() Check if a program version has been defined for this SBMLWriter.
void	setIndentationChar(char indentChar) Influences the way how SBML data structures are represented in XML.
void	setIndentationCount(short indentCount) Influences the way how SBML data structures are represented in XML.
int	setProgramName(java.lang.String name) Sets the name of this program, i.e., the program that is about to write out the SBMLDocument.
int	setProgramVersion(java.lang.String version) Sets the version of this program, i.e., the program that is about to write out the SBMLDocument.
java.lang.String	toString()
void	unsetProgramName()
void	unsetProgramVersion()
void	write(SBMLDocument sbmlDocument, java.io.File file) Writes the given SBML document to a File.
static void	write(SBMLDocument sbmlDocument, java.io.File file, char indentChar, short indentCount) Writes the given SBML document to a File.
static void	write(SBMLDocument sbmlDocument, java.io.File file, java.lang.String programName, java.lang.String programVersion) Writes the given SBML document to a File.
static void	write(SBMLDocument sbmlDocument, java.io.File file, java.lang.String programName, java.lang.String programVersion, char indentChar, short indentCount) Writes the given SBML document to a File.
void	write(SBMLDocument sbmlDocument, java.io.OutputStream stream) Writes the given SBML document to the OutputStream.
static void	write(SBMLDocument sbmlDocument, java.io.OutputStream stream, char indentChar, short indentCount) Writes the given SBMLDocument to the OutputStream.
static void	write(SBMLDocument sbmlDocument, java.io.OutputStream stream, java.lang.String programName, java.lang.String programVersion) Writes the given SBMLDocument to the OutputStream.
static void	write(SBMLDocument sbmlDocument, java.io.OutputStream stream, java.lang.String programName, java.lang.String programVersion, char indentChar, short indentCount) Writes the given SBMLDocument to the OutputStream.
void	write(SBMLDocument sbmlDocument, java.lang.String fileName) Writes the given SBMLDocument to file name.
static void	write(SBMLDocument sbmlDocument, java.lang.String fileName, char indentChar, short indentCount) Writes the given SBMLDocument to file name.
static void	write(SBMLDocument sbmlDocument, java.lang.String fileName, java.lang.String programName, java.lang.String programVersion) Writes the given SBMLDocument to file name.
static void	write(SBMLDocument sbmlDocument, java.lang.String fileName, java.lang.String programName, java.lang.String programVersion, char indentChar, short indentCount) Writes the given SBMLDocument to file name.
void	writeSBML(SBMLDocument sbmlDocument, java.io.File file) Writes the given SBML document to a File.
void	writeSBMLToFile(SBMLDocument sbmlDocument, java.lang.String fileName) Writes the given SBML document to file name.
java.lang.String	writeSBMLToString(SBMLDocument sbmlDocument) Writes the given SBML document to an in-memory String and returns it.

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

programName

java.lang.String programName

The name of the program that has been used to create an SBML String representation (possibly in a File) with the help of JSBML.

programVersion

java.lang.String programVersion

The version of the program using JSBML to serialize a model in an SBML String or File.

sbmlWriter

protected SBMLWriter sbmlWriter

The actual writer.

Constructor Detail

SBMLWriter

public SBMLWriter()

Creates a new SBMLWriter.

SBMLWriter

public SBMLWriter(char indentChar,
                  short indentCount)

Creates a new SBMLWriter that uses the given character for indentation of the XML representation of SBML data structures (with the given number of such symbols).

Parameters:

indentChar - The symbol to be used to indent new blocks within an XML representation of SBML data structures.

indentCount - The number of indentation characters.

SBMLWriter

public SBMLWriter(SBMLWriter sbmlWriter)

Clone constructor.

Parameters:

sbmlWriter -

SBMLWriter

public SBMLWriter(java.lang.String programName,
                  java.lang.String programVersion)

Creates a new SBMLWriter for the program with the given name and version.

Parameters:

programName - The name of the program that has been used to create an SBML String representation (possibly in a File) with the help of JSBML.

programVersion - The version of the program using JSBML to serialize a model in an SBML String or File.

SBMLWriter

public SBMLWriter(java.lang.String programName,
                  java.lang.String programVersion,
                  char indentChar,
                  short indentCount)

Creates a new SBMLWriter for the program with the given name and version that uses the given character for indentation of the XML representation of SBML data structures (with the given number of such symbols).

Parameters:

programName - The name of the program that has been used to create an SBML String representation (possibly in a File) with the help of JSBML.

programVersion - The version of the program using JSBML to serialize a model in an SBML String or File.

indentChar - The symbol to be used to indent new blocks within an XML representation of SBML data structures.

indentCount - The number of indentation characters.

Method Detail

write

public static void write(SBMLDocument sbmlDocument,
                         java.io.File file,
                         char indentChar,
                         short indentCount)
                  throws javax.xml.stream.XMLStreamException,
                         SBMLException,
                         java.io.IOException

Writes the given SBML document to a File.

Parameters:

sbmlDocument - the SBMLDocument to be written

file - the file where the SBML document is to be written.

indentChar - The symbol to be used to indent new blocks within an XML representation of SBML data structures.

indentCount - The number of indentation characters.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write 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 static void write(SBMLDocument sbmlDocument,
                         java.io.File file,
                         java.lang.String programName,
                         java.lang.String programVersion)
                  throws javax.xml.stream.XMLStreamException,
                         SBMLException,
                         java.io.IOException

Writes the given SBML document to a File.

Parameters:

sbmlDocument - the SBMLDocument to be written

file - the file where the SBML document is to be written.

programName - the name of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

programVersion - the version of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write 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 static void write(SBMLDocument sbmlDocument,
                         java.io.File file,
                         java.lang.String programName,
                         java.lang.String programVersion,
                         char indentChar,
                         short indentCount)
                  throws javax.xml.stream.XMLStreamException,
                         SBMLException,
                         java.io.IOException

Writes the given SBML document to a File.

Parameters:

sbmlDocument - the SBMLDocument to be written

file - the file where the SBML document is to be written.

programName - the name of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

programVersion - the version of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

indentChar - The symbol to be used to indent new blocks within an XML representation of SBML data structures.

indentCount - The number of indentation characters.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write 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.

See Also:

write(SBMLDocument, File, String, String)

write

public static void write(SBMLDocument sbmlDocument,
                         java.io.OutputStream stream,
                         char indentChar,
                         short indentCount)
                  throws javax.xml.stream.XMLStreamException,
                         SBMLException

Writes the given SBMLDocument to the OutputStream.

Parameters:

sbmlDocument - the SBML document to be written

stream - the stream object where the SBML is to be written.

indentChar - The symbol to be used to indent new blocks within an XML representation of SBML data structures.

indentCount - The number of indentation characters.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write the SBMLDocument.

write

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

Writes the given SBMLDocument to the OutputStream.

Parameters:

sbmlDocument - the SBML document to be written

stream - the stream object where the SBML is to be written.

programName - the name of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

programVersion - the version of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write the SBMLDocument.

write

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

Writes the given SBMLDocument to the OutputStream.

Parameters:

sbmlDocument - the SBML document to be written

stream - the stream object where the SBML is to be written.

programName - the name of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

programVersion - the version of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

indentChar - The symbol to be used to indent new blocks within an XML representation of SBML data structures.

indentCount - The number of indentation characters.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write the SBMLDocument.

See Also:

write(SBMLDocument, OutputStream, String, String)

write

public static void write(SBMLDocument sbmlDocument,
                         java.lang.String fileName,
                         char indentChar,
                         short indentCount)
                  throws javax.xml.stream.XMLStreamException,
                         java.io.FileNotFoundException,
                         SBMLException

Writes the given SBMLDocument to file name.

Parameters:

sbmlDocument - the SBMLDocument to be written

fileName - the name or full pathname of the file where the SBML document is to be written.

indentChar - The symbol to be used to indent new blocks within an XML representation of SBML data structures.

indentCount - The number of indentation characters.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

java.io.FileNotFoundException - if the file does not exist or cannot be created.

SBMLException - if any SBML problems prevent to write the SBMLDocument.

write

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

Writes the given SBMLDocument to file name.

Parameters:

sbmlDocument - the SBMLDocument to be written

fileName - the name or full pathname of the file where the SBML document is to be written.

programName - the name of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

programVersion - the version of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

Throws:

java.io.FileNotFoundException - if the file does not exist or cannot be created.

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write the SBMLDocument.

write

public static void write(SBMLDocument sbmlDocument,
                         java.lang.String fileName,
                         java.lang.String programName,
                         java.lang.String programVersion,
                         char indentChar,
                         short indentCount)
                  throws javax.xml.stream.XMLStreamException,
                         java.io.FileNotFoundException,
                         SBMLException

Writes the given SBMLDocument to file name.

Parameters:

sbmlDocument - the SBMLDocument to be written

fileName - the name or full pathname of the file where the SBML document is to be written.

programName - the name of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

programVersion - the version of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

indentChar - The symbol to be used to indent new blocks within an XML representation of SBML data structures.

indentCount - The number of indentation characters.

Throws:

java.io.FileNotFoundException - if the file does not exist or cannot be created.

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write the SBMLDocument.

See Also:

write(SBMLDocument, String, String, String)

clone

public SBMLWriter clone()

Overrides:

clone in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

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 number of characters used for indentation in SBML serializations.

getProgramName

public java.lang.String getProgramName()

Returns:

the name of the program that uses JSBML for writing SBML data objects.

See Also:

setProgramName(String)

getProgramVersion

public java.lang.String getProgramVersion()

Returns:

the version of the program that uses JSBML for writing SBML data objects.

See Also:

setProgramVersion(String)

isSetProgramName

public boolean isSetProgramName()

Check if a program name has been defined for this SBMLWriter.

Returns:

isSetProgramVersion

public boolean isSetProgramVersion()

Check if a program version has been defined for this SBMLWriter.

Returns:

setIndentationChar

public void setIndentationChar(char indentChar)

Influences the way how SBML data structures are represented in XML.

Parameters:

indentChar - The symbol to be used to indent new blocks within an XML representation of SBML data structures.

setIndentationCount

public void setIndentationCount(short indentCount)

Influences the way how SBML data structures are represented in XML.

Parameters:

indentCount - The number of indentation characters in the XML representation of SBML data structures.

setProgramName

public int setProgramName(java.lang.String name)

Sets the name of this program, i.e., the program that is about to write out the SBMLDocument.

If the program name and version are set (see setProgramVersion(String version)), the following XML comment, intended for human consumption, will be written at the beginning of the document:

 <!-- Created by <program name> version <program version> on yyyy-MM-dd HH:mm with JSBML version <JSBML version>. -->
 

Parameters:

name - the name of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

• JSBML.OPERATION_SUCCESS

See Also:

setProgramVersion(String version)

setProgramVersion

public int setProgramVersion(java.lang.String version)

Sets the version of this program, i.e., the program that is about to write out the SBMLDocument.

If the program version and name are set (see setProgramName(String name)), the following XML comment, intended for human consumption, will be written at the beginning of the document:

 <!-- Created by <program name> version <program version> on yyyy-MM-dd HH:mm with JSBML version <JSBML version>. -->
 

Parameters:

version - the version of this program (where 'this program' refers to the program in which JSBML is embedded, not JSBML itself!)

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

• JSBML.OPERATION_SUCCESS

See Also:

setProgramName(String name)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

unsetProgramName

public void unsetProgramName()

unsetProgramVersion

public void unsetProgramVersion()

write

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

Writes the given SBML document to a File. If specified in the constructor of this SBMLWriter, the programName and programVersion of the calling program will be made persistent in the resulting SBML File.

Parameters:

sbmlDocument - the SBMLDocument to be written

file - the file where the SBML document is to be written.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write 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 given SBML document to the OutputStream. If specified in the constructor of this SBMLWriter, the programName and programVersion of the calling program will be made persistent in the resulting SBML representation.

Parameters:

sbmlDocument - the SBML document to be written

stream - the stream object where the SBML is to be written.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write the SBMLDocument.

write

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

Writes the given SBMLDocument to file name. If specified in the constructor of this SBMLWriter, the programName and programVersion of the calling program will be made persistent in the resulting SBML File.

Parameters:

sbmlDocument - the SBMLDocument to be written

fileName - the name or full pathname of the file where the SBML document is to be written.

Throws:

java.io.FileNotFoundException - if the file does not exist or cannot be created.

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write the SBMLDocument.

writeSBML

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

Writes the given SBML document to a File. If specified in the constructor of this SBMLWriter, the programName and programVersion of the calling program will be made persistent in the resulting SBML File.

Parameters:

sbmlDocument - the SBML document to be written

file - the file where the SBML document is to be written.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write 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.

writeSBMLToFile

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

Writes the given SBML document to file name. If specified in the constructor of this SBMLWriter, the programName and programVersion of the calling program will be made persistent in the resulting SBML File.

Parameters:

sbmlDocument - the SBML document to be written

fileName - the name or full pathname of the file where the SBML document is to be written.

Throws:

java.io.FileNotFoundException - if the file does not exist or cannot be created.

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write the SBMLDocument.

writeSBMLToString

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

Writes the given SBML document to an in-memory String and returns it. If specified in the constructor of this SBMLWriter, the programName and programVersion of the calling program will be made persistent in the resulting SBML String.

Parameters:

sbmlDocument - the SBML document to be written

Returns:

the string representing the SBML document as XML.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to write the SBMLDocument as XML.

SBMLException - if any SBML problems prevent to write the SBMLDocument.