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 library.
- Since:
- 1.1
- Version:
- $Rev: 203 $
- Author:
- Richard Adams
Fields inherited from class org.jlibsedml.execution.AbstractSedmlExecutor |
sedml |
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 |
SedMLSBMLSimulatorExecutor
public SedMLSBMLSimulatorExecutor(org.jlibsedml.SedML sedml,
org.jlibsedml.Output output)
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 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)