org.simulator.sedml

Class SedMLSBMLSimulatorExecutor

java.lang.Object

org.jlibsedml.execution.AbstractSedmlExecutor

org.simulator.sedml.SedMLSBMLSimulatorExecutor

public class SedMLSBMLSimulatorExecutor
extends org.jlibsedml.execution.AbstractSedmlExecutor

This class extends an abstract class from jlibsedml, which provides various support functions such as retrieving models, applying changes to models, working out what tasks need to be executed to achieve an Output, and post-processing of results.

Typical usage for this class is demonstrated in the JUnit test for this class.

Models can be resolved either from local files, URLs, or BioModels MIRIAM URNs.
TO resolve models from different sources, see the documentation for AbstractSedmlExecutor in the jlibsedml.jar library.

Since:

1.1

Version:

$Rev$

Author:

Richard Adams, Shalin Shah

Constructor Summary

Constructors

Constructor and Description
SedMLSBMLSimulatorExecutor(org.jlibsedml.SedML sedml, org.jlibsedml.Output wanted, Map<String,Boolean> amountHash, String sedmlDir)
SedMLSBMLSimulatorExecutor(org.jlibsedml.SedML sedml, org.jlibsedml.Output output, String sedmlDir)

Method Summary

Modifier and Type	Method and Description
org.jlibsedml.execution.IProcessedSedMLSimulationResults	processSimulationResults(org.jlibsedml.Output wanted, Map<org.jlibsedml.AbstractTask,List<org.jlibsedml.execution.IRawSedmlSimulationResults>> res) Process raw data from simulations and return a output MultiTable which contains wanted Output
Map<org.jlibsedml.AbstractTask,List<org.jlibsedml.execution.IRawSedmlSimulationResults>>	run() This method is a wrapper to the runSimulations method from AbstractSedmlExecutor to add additional support for repeatedTasks.
void	setIsArchive(org.jlibsedml.ArchiveComponents ac) Enables models to be retrieved from a SED-ML archive format.

Methods inherited from class org.jlibsedml.execution.AbstractSedmlExecutor

addModelResolver, getFailureMessages, getSimulatableTasks, isExecuted, runSimulations

Methods inherited from class java.lang.Object

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

Constructor Detail

SedMLSBMLSimulatorExecutor

public SedMLSBMLSimulatorExecutor(org.jlibsedml.SedML sedml,
                                  org.jlibsedml.Output output,
                                  String sedmlDir)

SedMLSBMLSimulatorExecutor

public SedMLSBMLSimulatorExecutor(org.jlibsedml.SedML sedml,
                                  org.jlibsedml.Output wanted,
                                  Map<String,Boolean> amountHash,
                                  String sedmlDir)

Parameters:

sedml -

wanted -

amountHash -

Method Detail

setIsArchive

public void setIsArchive(org.jlibsedml.ArchiveComponents ac)

Enables models to be retrieved from a SED-ML archive format.
This method must be called before AbstractSedmlExecutor.runSimulations() is called, if a SED-ML archive is to be used as a model source.

Parameters:

ac - A non-null ArchiveComponents object.

run

public Map<org.jlibsedml.AbstractTask,List<org.jlibsedml.execution.IRawSedmlSimulationResults>> run()
                                                                                             throws org.semanticweb.owlapi.model.OWLOntologyCreationException

This method is a wrapper to the runSimulations method from AbstractSedmlExecutor to add additional support for repeatedTasks. It identifies the type of task, before running the simulations.

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException

processSimulationResults

public org.jlibsedml.execution.IProcessedSedMLSimulationResults processSimulationResults(org.jlibsedml.Output wanted,
                                                                                         Map<org.jlibsedml.AbstractTask,List<org.jlibsedml.execution.IRawSedmlSimulationResults>> res)

Process raw data from simulations and return a output MultiTable which contains wanted Output

Parameters:

wanted -

res -

Returns:

MultiTable