jigcell.xpp
Class Oscill8Launcher

java.lang.Object
  jigcell.xpp.SBMLToXPPTranslator
      jigcell.xpp.XPPLauncher
          jigcell.xpp.Oscill8Launcher

public class Oscill8Launcher
extends XPPLauncher

Runs Oscill8 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

Oscill8Launcher(jigcell.simulation.Simulator simulator, jigcell.sbml2.Model model)
Runs Oscill8 on an SBML file.

Method Summary

protected java.lang.String	getProgramDirectory() The location where Oscill8 is installed.
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.XPPLauncher

readSimulationData

Methods inherited from class jigcell.xpp.SBMLToXPPTranslator

calculateEquationsFromReactions, computeSelectionList, convertMathToInfix, generateODEFromModelBuilder, getAvailableSelections, getConcentration, getEquation, getOriginalValue, 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

Oscill8Launcher

public Oscill8Launcher(jigcell.simulation.Simulator simulator,
                       jigcell.sbml2.Model model)
                throws java.lang.Exception

Runs Oscill8 on an SBML file.

Parameters:

simulator - Simulator

model - SBML model

Throws:

java.lang.Exception

Method Detail

getProgramDirectory

protected java.lang.String getProgramDirectory()
                                        throws java.lang.Exception

The location where Oscill8 is installed.

Overrides:

getProgramDirectory in class SBMLToXPPTranslator

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 XPPLauncher

Parameters:

simulator - Simulator

targetFile - ODE file

outputFile - File that will contain the simulator output

Throws:

java.lang.Exception