jigcell.xpp
Class XPPLauncher

java.lang.Object
  jigcell.xpp.SBMLToXPPTranslator
      jigcell.xpp.XPPLauncher

Direct Known Subclasses:

Oscill8Launcher

public class XPPLauncher
extends SBMLToXPPTranslator

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

Author:

Nicholas Allen

Constructor Summary

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

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.SBMLToXPPTranslator

calculateEquationsFromReactions, computeSelectionList, convertMathToInfix, generateODEFromModelBuilder, getAvailableSelections, getConcentration, getEquation, getOriginalValue, getProgramDirectory, getSettableNames, main, printParseTreeMassAction, printParseTreeMichaelisMenten, printParseTreeStochMassAction, printParseTreeStochMichaelisMenten, replaceIdWithName, setValue, simulate

Methods inherited from class java.lang.Object

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

Constructor Detail

XPPLauncher

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

Runs XPP on an SBML file.

Parameters:

simulator - Simulator

model - SBML model

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 SBMLToXPPTranslator

Parameters:

simulator - Simulator

targetFile - ODE file

outputFile - File that will contain the simulator output

Throws:

java.lang.Exception