org.sbml.jsbml.validator

Class SBMLValidator

java.lang.Object

org.sbml.jsbml.validator.SBMLValidator

public class SBMLValidator
extends java.lang.Object

Validates the SBML document given by filename.xml or located at the http:// URL. Output-format will always be xml

usage: java org.sbml.jsbml.validator.SBMLValidator [-h] [-d opt1[,opt2,...]] filename.xml
usage: java validateSBML [-h] [-d opt1[,opt2,...]] http://...

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SBMLValidator.CHECK_CATEGORY Enumerates the different possible check categories when performing the validation of an SBML document.

Constructor Summary

Constructors

Constructor and Description
SBMLValidator()

Method Summary

Modifier and Type	Method and Description
static SBMLErrorLog	checkConsistency(java.lang.String xmlValidationString) Parses the XML String returned by the libSBML online validator or web services.
static SBMLErrorLog	checkConsistency(java.lang.String fileName, java.util.Map<java.lang.String,java.lang.String> parameters) Validates an SBML model using the SBML.org online validator (http://sbml.org/validator/).
static void	main(java.lang.String[] args)
(package private) static void	print(java.io.InputStream source, java.io.OutputStream destination)
(package private) static void	print(java.io.Reader source, java.io.Writer destination)
(package private) static void	usage()

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLValidator

public SBMLValidator()

Method Detail

usage

static void usage()

main

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

Parameters:

args -

print

static void print(java.io.InputStream source,
                  java.io.OutputStream destination)
           throws java.io.IOException

Parameters:

source -

destination -

Throws:

java.io.IOException

print

static void print(java.io.Reader source,
                  java.io.Writer destination)
           throws java.io.IOException

Parameters:

source -

destination -

Throws:

java.io.IOException

checkConsistency

public static SBMLErrorLog checkConsistency(java.lang.String fileName,
                                            java.util.Map<java.lang.String,java.lang.String> parameters)

Validates an SBML model using the SBML.org online validator (http://sbml.org/validator/).

You can control the consistency checks that are performed when checkConsistency(String) is called with the HashMap of parameters given. It will fill the SBMLErrorLog with SBMLErrors for each problem within this whole model.

If this method returns a non empty SBMLErrorLog, the failures may be due to warnings @em or errors. Callers should inspect the severity flag in the individual SBMLError objects to determine the nature of the failures.

This method is called from SBMLDocument.checkConsistency(). To know what to set in the parameters map, you can have a look at SBMLDocument#setConsistencyChecks(CHECK_CATEGORY, boolean). But the key should be one of the category in SBMLValidator.CHECK_CATEGORY and the value should be "true" or "false".

Parameters:

fileName - a file name

parameters - parameters for the libsbml checkConsistency()

Returns:

an SBMLErrorLog containing the list of errors.

See Also:

sbml.org Validator Web API

checkConsistency

public static SBMLErrorLog checkConsistency(java.lang.String xmlValidationString)

Parses the XML String returned by the libSBML online validator or web services.

It will fill the SBMLErrorLog with SBMLErrors for each problem within this whole model.

If this method returns a non empty SBMLErrorLog, the failures may be due to warnings @em or errors. Callers should inspect the severity flag in the individual SBMLError objects to determine the nature of the failures.

Parameters:

xmlValidationString - an XML String representing an SBML model.

Returns:

an SBMLErrorLog containing the list of errors.

See Also:

sbml.org Validator Web API