org.sbml.jsbml

Class SBMLReader

java.lang.Object

org.sbml.jsbml.SBMLReader

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

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

Provides methods for reading SBML from files, text strings or streams.

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

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 SBMLReader.

The SBMLReader class provides the main interface for reading SBML content from files and strings. The methods for reading SBML all return an SBMLDocument object representing the results.

In the case of failures (such as if the SBML contains errors), the errors will be recorded with the SBMLErrorLog object kept in the SBMLDocument returned by SBMLReader. Consequently, immediately after calling a method on SBMLReader, callers should always check for errors and warnings using the methods for this purpose provided by SBMLDocument.

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger, Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private static SBMLReader	reader The singleton actual reader.
private static long	serialVersionUID Generated serial version identifier.
static java.lang.String	UNKNOWN_XML_NODE String used when reading an SBML file, to store XMLNode as user object when the XMLNode does not represents something known from the 'core'.

Constructor Summary

Constructors

Constructor and Description
SBMLReader() Creates a new SBMLReader.
SBMLReader(SBMLReader sbmlReader) Clone constructor.

Method Summary

Modifier and Type	Method and Description
SBMLReader	clone()
boolean	equals(java.lang.Object o)
static SBMLDocument	read(java.io.File file) Factory method for reading SBML from a given File.
static SBMLDocument	read(java.io.File file, TreeNodeChangeListener listener) Factory method for reading SBML from a given File.
static SBMLDocument	read(java.io.InputStream stream) Factory method for reading SBML from a given InputStream.
static SBMLDocument	read(java.lang.String xml) Factory method for reading SBML from given XML code in its String representation.
SBMLDocument	readSBML(java.io.File file) Reads an SBML document from a File.
SBMLDocument	readSBML(java.io.File file, TreeNodeChangeListener listener)
SBMLDocument	readSBML(java.lang.String fileName) Reads an SBML document from a file.
SBMLDocument	readSBMLFromFile(java.lang.String filename) Reads an SBML document from a file.
SBMLDocument	readSBMLFromStream(java.io.InputStream stream) Reads an SBML document from a data stream.
SBMLDocument	readSBMLFromString(java.lang.String xml) Reads an SBML document from the given XML string.
java.lang.String	toString()

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

reader

private static final SBMLReader reader

The singleton actual reader. This should speed up loading required classes, because the initialization is done only once if using the static read methods.

UNKNOWN_XML_NODE

public static java.lang.String UNKNOWN_XML_NODE

String used when reading an SBML file, to store XMLNode as user object when the XMLNode does not represents something known from the 'core'. What SBML core know is Notes, Annotation and the Constraint message that are all encoded as XMLNode.

Constructor Detail

SBMLReader

public SBMLReader()

Creates a new SBMLReader.

SBMLReader

public SBMLReader(SBMLReader sbmlReader)

Clone constructor.

Parameters:

sbmlReader -

Method Detail

read

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

Factory method for reading SBML from a given File.

Parameters:

file -

Returns:

Throws:

javax.xml.stream.XMLStreamException

java.io.IOException - if the file does not exist or cannot be read.

read

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

Factory method for reading SBML from a given File.

Parameters:

file -

listener -

Returns:

Throws:

javax.xml.stream.XMLStreamException

java.io.IOException - if the file does not exist or cannot be read.

readSBML

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

Parameters:

file -

listener -

Returns:

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

read

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

Factory method for reading SBML from a given InputStream.

Parameters:

stream -

Returns:

Throws:

javax.xml.stream.XMLStreamException

read

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

Factory method for reading SBML from given XML code in its String representation.

Parameters:

xml -

Returns:

Throws:

javax.xml.stream.XMLStreamException

clone

public SBMLReader clone()

Overrides:

clone in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

readSBML

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

Reads an SBML document from a File.

This method is identical to readSBMLFromFile(String filename) or readSBML(String filename).

If the File named file does not exist or its content is not valid SBML, one Exception will be thrown.

This methods is not part of the libSBML SBMLReader API.

Parameters:

file - the file to be read.

Returns:

an SBMLDocument created from the SBML content.

Throws:

javax.xml.stream.XMLStreamException - if any other problems prevent to create a SBMLDocument

java.io.IOException - if the file does not exist or cannot be read.

readSBML

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

Reads an SBML document from a file.

This method is identical to readSBMLFromFile(String filename) or readSBML(File file).

If the file named filename does not exist or its content is not valid SBML, one Exception will be thrown.

Parameters:

fileName - the name or full pathname of the file to be read.

Returns:

an SBMLDocument created from the SBML content.

Throws:

javax.xml.stream.XMLStreamException - if any other problems prevent to create a SBMLDocument

java.io.IOException - if the file does not exist or cannot be read.

readSBMLFromFile

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

Reads an SBML document from a file.

This method is identical to readSBML(String filename) or readSBML(File file).

If the file named filename does not exist or its content is not valid SBML, one Exception will be thrown.

Parameters:

filename - the name or full pathname of the file to be read.

Returns:

an SBMLDocument created from the SBML content.

Throws:

javax.xml.stream.XMLStreamException - if any other problems prevent to create a SBMLDocument

java.io.IOException - if the file does not exist or cannot be read.

readSBMLFromStream

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

Reads an SBML document from a data stream.

This methods is not part of the libSBML SBMLReader API.

Parameters:

stream - the stream of data to be read.

Returns:

an SBMLDocument created from the SBML content.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to create a SBMLDocument

readSBMLFromString

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

Reads an SBML document from the given XML string.

Parameters:

xml - a string containing a full SBML model

Returns:

an SBMLDocument created from the SBML content.

Throws:

javax.xml.stream.XMLStreamException - if any problems prevent to create a SBMLDocument

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object