Package 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

Field Summary

Fields inherited from class org.jlibsedml.execution.AbstractSedmlExecutor

sedml

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected boolean	canExecuteSimulation(org.jlibsedml.Simulation sim)
protected org.jlibsedml.execution.IRawSedmlSimulationResults	executeSimulation(String modelStr, org.jlibsedml.OneStep sim)
protected org.jlibsedml.execution.IRawSedmlSimulationResults	executeSimulation(String modelStr, org.jlibsedml.Simulation sim, Map<String,double[]> mapChangesToList, int element)
protected org.jlibsedml.execution.IRawSedmlSimulationResults	executeSimulation(String modelStr, org.jlibsedml.SteadyState sim)
protected org.jlibsedml.execution.IRawSedmlSimulationResults	executeSimulation(String modelStr, org.jlibsedml.UniformTimeCourse sim)	This method performs the actual simulation, using the model and simulation configuration that are passed in as arguments.It runs UniformTimeCourse simulation
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. This method must be called before AbstractSedmlExecutor.runSimulations() is called, if a SED-ML archive is to be used as a model source.
protected boolean	supportsLanguage(String language)
protected org.jlibsedml.Simulation	tryAlternateAlgo(org.jlibsedml.Simulation sim)

Methods inherited from class org.jlibsedml.execution.AbstractSedmlExecutor

addModelResolver, addStatus, getFailureMessages, getSimulatableTasks, isExecuted, runSimulations

Methods inherited from class java.lang.Object

clone, equals, finalize, 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.

canExecuteSimulation

protected boolean canExecuteSimulation(org.jlibsedml.Simulation sim)

Specified by:

canExecuteSimulation in class org.jlibsedml.execution.AbstractSedmlExecutor

tryAlternateAlgo

protected org.jlibsedml.Simulation tryAlternateAlgo(org.jlibsedml.Simulation sim)
                                             throws org.semanticweb.owlapi.model.OWLOntologyCreationException

Throws:

org.semanticweb.owlapi.model.OWLOntologyCreationException

executeSimulation

protected org.jlibsedml.execution.IRawSedmlSimulationResults executeSimulation(String modelStr,
                                                                               org.jlibsedml.UniformTimeCourse sim)

This method performs the actual simulation, using the model and simulation configuration that are passed in as arguments.It runs UniformTimeCourse simulation

Specified by:

executeSimulation in class org.jlibsedml.execution.AbstractSedmlExecutor

Returns:

An IRawSedmlSimulationResults object that is used for post-processing by the framework. The actual implementation class in this implementation will be a MultTableSEDMLWrapper which wraps a MultiTable of raw results.

executeSimulation

protected org.jlibsedml.execution.IRawSedmlSimulationResults executeSimulation(String modelStr,
                                                                               org.jlibsedml.OneStep sim)

executeSimulation

protected org.jlibsedml.execution.IRawSedmlSimulationResults executeSimulation(String modelStr,
                                                                               org.jlibsedml.SteadyState sim)

executeSimulation

protected org.jlibsedml.execution.IRawSedmlSimulationResults executeSimulation(String modelStr,
                                                                               org.jlibsedml.Simulation sim,
                                                                               Map<String,double[]> mapChangesToList,
                                                                               int element)

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

supportsLanguage

protected boolean supportsLanguage(String language)

Specified by:

supportsLanguage in class org.jlibsedml.execution.AbstractSedmlExecutor

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