org.simulator
Class SBMLTestSuiteRunner

java.lang.Object
  org.simulator.SBMLTestSuiteRunner

public class SBMLTestSuiteRunner
extends Object

This class can test the simulation of all models from the SBML test suite.

Since:

1.0

Version:

$$Rev: 396 $$

Author:

Andreas Dräger

Nested Class Summary

static class

SBMLTestSuiteRunner.Options Commannd-line options for this test program.

Constructor Summary

SBMLTestSuiteRunner()

Method Summary

static String	convertAbsoluteFilePathToURI(String path) Converts spaces to %20 Converts \ to /
static void	main(String[] args) Input: directory with models (containing the SBML test suite), first model to be simulated, last model to be simulated, SBMLTestSuiteRunner.Options.all (for testing the models of the test suite with all given integrators) or SBMLTestSuiteRunner.Options.sedml (for testing the models of the test suite using the given SED-ML files) or nothing (for testing the models of the test suite with the RosenbrockSolver solver, should produce only successful tests)
static void	statisticForSolvers(String file, int from, int to) Computes a statistic for the SBML test suite testing all provided integrators
static MultiTable	testModel(AbstractDESSolver solver, Model model, double[] timePoints, double stepSize, Map<String,Boolean> amountHash) Tests one specific model
void	testModels() Tests the models of the SBML test suite using Rosenbrock as integrator TEST_CASES must be set to the address of the folder "semantic" in the SBML test suite.
static void	testRosenbrockSolver(String file, int from, int to) Computes a statistic for the SBML test suite using the Rosenbrock solver as integrator
static void	testRosenbrockSolverWithSEDML(String file, int from, int to) Computes a statistic for the SBML test suite using the Rosenbrock solver as integrator and the SED-ML files

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLTestSuiteRunner

public SBMLTestSuiteRunner()

Method Detail

main

public static void main(String[] args)
                 throws IOException,
                        URISyntaxException

Input:

1. directory with models (containing the SBML test suite),
2. first model to be simulated,
3. last model to be simulated,
4. SBMLTestSuiteRunner.Options.all (for testing the models of the test suite with all given integrators) or SBMLTestSuiteRunner.Options.sedml (for testing the models of the test suite using the given SED-ML files) or nothing (for testing the models of the test suite with the RosenbrockSolver solver, should produce only successful tests)

Parameters:

args -

Throws:

IOException

URISyntaxException

statisticForSolvers

public static void statisticForSolvers(String file,
                                       int from,
                                       int to)
                                throws FileNotFoundException,
                                       IOException

Computes a statistic for the SBML test suite testing all provided integrators

Parameters:

file -

from -

to -

Throws:

FileNotFoundException

IOException

testRosenbrockSolver

public static void testRosenbrockSolver(String file,
                                        int from,
                                        int to)
                                 throws FileNotFoundException,
                                        IOException,
                                        URISyntaxException

Computes a statistic for the SBML test suite using the Rosenbrock solver as integrator

Parameters:

file -

from -

to -

Throws:

FileNotFoundException

IOException

URISyntaxException

testRosenbrockSolverWithSEDML

public static void testRosenbrockSolverWithSEDML(String file,
                                                 int from,
                                                 int to)
                                          throws FileNotFoundException,
                                                 IOException,
                                                 URISyntaxException

Computes a statistic for the SBML test suite using the Rosenbrock solver as integrator and the SED-ML files

Parameters:

file -

from -

to -

Throws:

FileNotFoundException

IOException

URISyntaxException

testModel

public static MultiTable testModel(AbstractDESSolver solver,
                                   Model model,
                                   double[] timePoints,
                                   double stepSize,
                                   Map<String,Boolean> amountHash)
                            throws SBMLException,
                                   ModelOverdeterminedException,
                                   DerivativeException

Tests one specific model

Parameters:

solver -

model -

timePoints -

stepSize -

amountHash -

Returns:

result

Throws:

SBMLException

ModelOverdeterminedException

DerivativeException

testModels

public void testModels()
                throws FileNotFoundException,
                       IOException

Tests the models of the SBML test suite using Rosenbrock as integrator TEST_CASES must be set to the address of the folder "semantic" in the SBML test suite.

Throws:

FileNotFoundException

IOException

convertAbsoluteFilePathToURI

public static String convertAbsoluteFilePathToURI(String path)

• Converts spaces to %20
• Converts \ to /

  Parameters:

  path - A Windows absolute filepath

  Returns:

  A String of the filepath suitable for inclusion as a URI object.