jigcell.xpp
Class StochKitLauncher

java.lang.Object
  jigcell.xpp.SBMLToStochKitTranslator
      jigcell.xpp.StochKitLauncher

public class StochKitLauncher
extends SBMLToStochKitTranslator

Runs StochKit on an SBML file. This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Author:

Pengyuan Wang

Field Summary

private boolean	displayConcentration
private int	volumeColumn

Fields inherited from class jigcell.xpp.SBMLToStochKitTranslator

DEFAULT_LOWER_BOUND, DEFAULT_MODEL_NAME, DEFAULT_NML_FILENAME, DEFAULT_UPPER_BOUND, EST_TASK, INDENT, PRE_RUN, reactionIndex, RUN_PE, SIM_TASK, speciesIndex, STATUS, targetFile, TRANSFORM_TASK

Constructor Summary

StochKitLauncher(jigcell.simulation.Simulator simulator, jigcell.sbml2.Model model)
Runs StochKit on an SBML file.

StochKitLauncher(jigcell.simulation.Simulator simulator, jigcell.sbml2.Model model, boolean displayConcentration, int volumeColumn)

Method Summary

protected jigcell.compare.IDataElement	readSimulationData(jigcell.simulation.Simulator simulator, java.lang.Process process, java.io.File outputFile) Reads simulation data that a running process will write to disk.
protected jigcell.compare.IDataElement	simulate(jigcell.simulation.Simulator simulator, java.io.File targetFile, java.io.File outputFile) Performs a simulation using the current model and settings.

Methods inherited from class jigcell.xpp.SBMLToStochKitTranslator

computeSelectionList, estimatorStatus, extractParameters, getAvailableSelections, getProgramDirectory, getSettableNames, main, setCWD, simulate, writeCppCode

Methods inherited from class java.lang.Object

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

Field Detail

displayConcentration

private boolean displayConcentration

volumeColumn

private int volumeColumn

Constructor Detail

StochKitLauncher

public StochKitLauncher(jigcell.simulation.Simulator simulator,
                        jigcell.sbml2.Model model)
                 throws java.lang.Exception

Runs StochKit on an SBML file.

Parameters:

simulator - Simulator

model - SBML model

Throws:

java.lang.Exception

StochKitLauncher

public StochKitLauncher(jigcell.simulation.Simulator simulator,
                        jigcell.sbml2.Model model,
                        boolean displayConcentration,
                        int volumeColumn)
                 throws java.lang.Exception

Throws:

java.lang.Exception

Method Detail

readSimulationData

protected jigcell.compare.IDataElement readSimulationData(jigcell.simulation.Simulator simulator,
                                                          java.lang.Process process,
                                                          java.io.File outputFile)
                                                   throws java.lang.Exception

Reads simulation data that a running process will write to disk.

Parameters:

simulator - Simulator

process - Simulation program

outputFile - Location where the output will be written

Throws:

java.lang.Exception

simulate

protected jigcell.compare.IDataElement simulate(jigcell.simulation.Simulator simulator,
                                                java.io.File targetFile,
                                                java.io.File outputFile)
                                         throws java.lang.Exception

Performs a simulation using the current model and settings.

Overrides:

simulate in class SBMLToStochKitTranslator

Parameters:

simulator - Simulator

targetFile - SBML file

outputFile - File that will contain the simulator output

Throws:

java.lang.Exception