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: 391 $

Author:

Richard Adams

Field Summary

Fields inherited from class org.jlibsedml.execution.AbstractSedmlExecutor

sedml

Constructor Summary

SedMLSBMLSimulatorExecutor(org.jlibsedml.SedML sedml, org.jlibsedml.Output output)

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

Method Summary

protected boolean	canExecuteSimulation(org.jlibsedml.Simulation sim)
MultiTable	createMultiTableFromProcessedResults(org.jlibsedml.Output wanted, org.jlibsedml.execution.IProcessedSedMLSimulationResults prRes)
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.
MultiTable	processSimulationResults(org.jlibsedml.Output wanted, Map<org.jlibsedml.Task,org.jlibsedml.execution.IRawSedmlSimulationResults> res)
void	setIsArchive(org.jlibsedml.ArchiveComponents ac) Enables models to be retrieved from a SED-ML archive format.
protected boolean	supportsLanguage(String language)

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)

SedMLSBMLSimulatorExecutor

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

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

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.

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.

supportsLanguage

protected boolean supportsLanguage(String language)

Specified by:

supportsLanguage in class org.jlibsedml.execution.AbstractSedmlExecutor

processSimulationResults

public MultiTable processSimulationResults(org.jlibsedml.Output wanted,
                                           Map<org.jlibsedml.Task,org.jlibsedml.execution.IRawSedmlSimulationResults> res)

createMultiTableFromProcessedResults

public MultiTable createMultiTableFromProcessedResults(org.jlibsedml.Output wanted,
                                                       org.jlibsedml.execution.IProcessedSedMLSimulationResults prRes)