Examples with TimeStep cbit.vcell.solver.TimeStep used on opensource projects

Example 6 with TimeStep

use of cbit.vcell.solver.TimeStep in project vcell by virtualcell.

the class TimeStepPanel method setNewTimeStep.

public void setNewTimeStep() {
    try {
        TimeStep oldTimeStep = solverTaskDescription.getTimeStep();
        double defaultTimeStep = !getDefaultTimeStepTextField().isEnabled() ? oldTimeStep.getDefaultTimeStep() : new Double(getDefaultTimeStepTextField().getText()).doubleValue();
        double minTimeStep = !getMinimumTimeStepTextField().isEnabled() ? oldTimeStep.getMinimumTimeStep() : new Double(getMinimumTimeStepTextField().getText()).doubleValue();
        double maxTimeStep = !getMaximumTimeStepTextField().isEnabled() ? oldTimeStep.getMaximumTimeStep() : new Double(getMaximumTimeStepTextField().getText()).doubleValue();
        TimeStep newTimeStep = new TimeStep(minTimeStep, defaultTimeStep, maxTimeStep);
        solverTaskDescription.setTimeStep(newTimeStep);
    } catch (java.lang.Throwable ivjExc) {
        // user code begin {3}
        // user code end
        handleException(ivjExc);
    }
}

Example 7 with TimeStep

use of cbit.vcell.solver.TimeStep in project vcell by virtualcell.

the class TimeStepPanel method refresh.

private void refresh() {
    if (solverTaskDescription == null) {
        return;
    }
    SolverDescription solverDescription = solverTaskDescription.getSolverDescription();
    if (solverDescription.compareEqual(SolverDescription.StochGibson)) {
        // stochastic time
        enableDefaultTimeStep(false);
        enableMinTimeStep(false);
        enableMaxTimeStep(false);
    } else if (solverDescription.compareEqual(SolverDescription.NFSim)) {
        ivjTimeStepLabel.setEnabled(false);
        enableDefaultTimeStep(false);
        enableMinTimeStep(false);
        enableMaxTimeStep(false);
    } else {
        setEnabled(true);
        TimeStep ts = solverTaskDescription.getTimeStep();
        getDefaultTimeStepTextField().setText(ts.getDefaultTimeStep() + "");
        getMinimumTimeStepTextField().setText(ts.getMinimumTimeStep() + "");
        getMaximumTimeStepTextField().setText(ts.getMaximumTimeStep() + "");
        // fixed time step solvers and non spatial stochastic solvers only show default time step.
        if (!solverDescription.hasVariableTimestep() || solverDescription.isNonSpatialStochasticSolver()) {
            enableDefaultTimeStep(true);
            enableMinTimeStep(false);
            enableMaxTimeStep(false);
        } else {
            // variable time step solvers shows min and max, but sundials solvers don't show min
            enableDefaultTimeStep(false);
            if (solverDescription.hasSundialsTimeStepping()) {
                enableMinTimeStep(false);
            }
            enableMaxTimeStep(true);
        }
    }
}

Example 8 with TimeStep

use of cbit.vcell.solver.TimeStep in project vcell by virtualcell.

the class XmlHelper method sedmlToBioModel.

public static VCDocument sedmlToBioModel(VCLogger transLogger, ExternalDocInfo externalDocInfo, SedML sedml, AbstractTask selectedTask) throws Exception {
    if (sedml.getModels().isEmpty()) {
        return null;
    }
    VCDocument doc = null;
    try {
        // extract the path only from the sedml file
        String fullPath = FileUtils.getFullPath(externalDocInfo.getFile().getAbsolutePath());
        // Namespace namespace = sedml.getNamespace();
        // iterate through all the elements and show them at the console
        List<org.jlibsedml.Model> mmm = sedml.getModels();
        for (Model mm : mmm) {
            System.out.println(mm.toString());
        }
        List<org.jlibsedml.Simulation> sss = sedml.getSimulations();
        for (org.jlibsedml.Simulation ss : sss) {
            System.out.println(ss.toString());
        }
        List<AbstractTask> ttt = sedml.getTasks();
        for (AbstractTask tt : ttt) {
            System.out.println(tt.toString());
        }
        List<DataGenerator> ddd = sedml.getDataGenerators();
        for (DataGenerator dd : ddd) {
            System.out.println(dd.toString());
        }
        List<Output> ooo = sedml.getOutputs();
        for (Output oo : ooo) {
            System.out.println(oo.toString());
        }
        KisaoTerm sedmlKisao = null;
        // this will become the vCell simulation
        org.jlibsedml.Simulation sedmlSimulation = null;
        // the "original" model referred to by the task
        org.jlibsedml.Model sedmlOriginalModel = null;
        String sedmlOriginalModelName = null;
        if (selectedTask == null) {
            // no task, just pick the Model and find its sbml file
            sedmlOriginalModelName = SEDMLUtil.getName(mmm.get(0));
        } else {
            if (selectedTask instanceof Task) {
                sedmlOriginalModel = sedml.getModelWithId(selectedTask.getModelReference());
                sedmlSimulation = sedml.getSimulation(selectedTask.getSimulationReference());
            } else if (selectedTask instanceof RepeatedTask) {
                RepeatedTask rt = (RepeatedTask) selectedTask;
                assert (rt.getSubTasks().size() == 1);
                // first (and only) subtask
                SubTask st = rt.getSubTasks().entrySet().iterator().next().getValue();
                String taskId = st.getTaskId();
                AbstractTask t = sedml.getTaskWithId(taskId);
                // get model and simulation from subtask
                sedmlOriginalModel = sedml.getModelWithId(t.getModelReference());
                sedmlSimulation = sedml.getSimulation(t.getSimulationReference());
            } else {
                throw new RuntimeException("Unexpected task " + selectedTask);
            }
            sedmlOriginalModelName = sedmlOriginalModel.getId();
            sedmlKisao = KisaoOntology.getInstance().getTermById(sedmlSimulation.getAlgorithm().getKisaoID());
        }
        // UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0,
        // Algorithm [kisaoID=KISAO:0000019], getId()=SimSlow]
        // identify the vCell solvers that would match best the sedml solver kisao id
        List<SolverDescription> solverDescriptions = new ArrayList<>();
        for (SolverDescription sd : SolverDescription.values()) {
            KisaoTerm solverKisaoTerm = KisaoOntology.getInstance().getTermById(sd.getKisao());
            if (solverKisaoTerm == null) {
                break;
            }
            boolean isExactlySame = solverKisaoTerm.equals(sedmlKisao);
            if (isExactlySame && !solverKisaoTerm.isObsolete()) {
                // we make a list with all the solvers that match the kisao
                solverDescriptions.add(sd);
            }
        }
        // from the list of vcell solvers that match the sedml kisao we select the ones that have a matching time step
        SolverDescription solverDescription = null;
        for (SolverDescription sd : solverDescriptions) {
            if (true) {
                solverDescription = sd;
                break;
            }
        }
        // find out everything else we need about the application we're going to use,
        // some of the info will be needed when we parse the sbml file
        boolean bSpatial = false;
        Application appType = Application.NETWORK_DETERMINISTIC;
        Set<SolverDescription.SolverFeature> sfList = solverDescription.getSupportedFeatures();
        for (SolverDescription.SolverFeature sf : sfList) {
            switch(sf) {
                case Feature_Rulebased:
                    appType = Application.RULE_BASED_STOCHASTIC;
                    break;
                case Feature_Stochastic:
                    appType = Application.NETWORK_STOCHASTIC;
                    break;
                case Feature_Deterministic:
                    appType = Application.NETWORK_DETERMINISTIC;
                    break;
                case Feature_Spatial:
                    bSpatial = true;
                    break;
                default:
                    break;
            }
        }
        // -------------------------------------------------------------------------------------------
        // extract bioModel name from sedx (or sedml) file
        String bioModelName = FileUtils.getBaseName(externalDocInfo.getFile().getAbsolutePath());
        // if we have repeated task, we ignore them, we just use the normal resolvers for archive and changes
        // once the application and simulation are built, we iterate through the repeated tasks and
        // add math overrides to the simulation for each repeated task
        ArchiveComponents ac = null;
        if (externalDocInfo.getFile().getPath().toLowerCase().endsWith("sedx") || externalDocInfo.getFile().getPath().toLowerCase().endsWith("omex")) {
            ac = Libsedml.readSEDMLArchive(new FileInputStream(externalDocInfo.getFile().getPath()));
        }
        ModelResolver resolver = new ModelResolver(sedml);
        if (ac != null) {
            resolver.add(new ArchiveModelResolver(ac));
        }
        resolver.add(new FileModelResolver());
        resolver.add(new RelativeFileModelResolver(fullPath));
        String newMdl = resolver.getModelString(sedmlOriginalModel);
        // sbmlSource with all the changes applied
        XMLSource sbmlSource = new XMLSource(newMdl);
        doc = XmlHelper.importSBML(transLogger, sbmlSource, bSpatial);
        BioModel bioModel = (BioModel) doc;
        bioModel.setName(bioModelName);
        // we already have an application loaded from the sbml file, with initial conditions and stuff
        // which may be not be suitable because the sedml kisao may need a different app type
        // so we do a "copy as" to the right type and then delete the original we loaded from the sbml file
        // the new application we're making from the old one
        SimulationContext newSimulationContext = null;
        if (bioModel.getSimulationContexts().length == 1) {
            SimulationContext oldSimulationContext = bioModel.getSimulationContext(0);
            newSimulationContext = SimulationContext.copySimulationContext(oldSimulationContext, sedmlOriginalModelName, bSpatial, appType);
            bioModel.removeSimulationContext(oldSimulationContext);
            bioModel.addSimulationContext(newSimulationContext);
        } else {
            // length == 0
            newSimulationContext = bioModel.addNewSimulationContext(sedmlOriginalModelName, appType);
        }
        // making the new vCell simulation based on the sedml simulation
        newSimulationContext.refreshDependencies();
        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(null);
        newSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
        Simulation newSimulation = new Simulation(newSimulationContext.getMathDescription());
        newSimulation.setName(SEDMLUtil.getName(sedmlSimulation));
        // TODO: make sure that everything has proper names
        // we check the repeated tasks, if any, and add to the list of math overrides
        // if(selectedTask instanceof RepeatedTask) {
        // for(Change change : ((RepeatedTask) selectedTask).getChanges()) {
        // if(!(change instanceof SetValue)) {
        // throw new RuntimeException("Only 'SetValue' changes are supported for repeated tasks.");
        // }
        // SetValue setValue = (SetValue)change;
        // // TODO: extract target from XPath
        // // ......
        // //
        // String target = "s0";	// for now we just use a hardcoded thing
        // ConstantArraySpec cas;
        // Range range = ((RepeatedTask) selectedTask).getRange(setValue.getRangeReference());
        // if(range instanceof UniformRange) {
        // cas = ConstantArraySpec.createIntervalSpec(target, ((UniformRange) range).getStart(), ((UniformRange) range).getEnd(),
        // range.getNumElements(), ((UniformRange) range).getType() == UniformRange.UniformType.LOG ? true : false);
        // } else if(range instanceof VectorRange) {
        // //    				List<String> constants = new ArrayList<> ();
        // //    				for(int i=0; i<range.getNumElements(); i++) {
        // //    					constants.add(new Constant(i+"", new Expression(range.getElementAt(i))));
        // //    				}
        // //    				cas = ConstantArraySpec.createListSpec(target, constants);
        // 
        // } else {
        // throw new RuntimeException("Only 'Uniform Range' and 'Vector Range' are supported at this time.");
        // }
        // 
        // }
        // }
        // we identify the type of sedml simulation (uniform time course, etc)
        // and set the vCell simulation parameters accordingly
        SolverTaskDescription simTaskDesc = newSimulation.getSolverTaskDescription();
        TimeBounds timeBounds = new TimeBounds();
        TimeStep timeStep = new TimeStep();
        double outputTimeStep = 0.1;
        if (sedmlSimulation instanceof UniformTimeCourse) {
            // we translate initial time to zero, we provide output for the duration of the simulation
            // because we can't select just an interval the way the SEDML simulation can
            double initialTime = ((UniformTimeCourse) sedmlSimulation).getInitialTime();
            double outputStartTime = ((UniformTimeCourse) sedmlSimulation).getOutputStartTime();
            double outputEndTime = ((UniformTimeCourse) sedmlSimulation).getOutputEndTime();
            double outputNumberOfPoints = ((UniformTimeCourse) sedmlSimulation).getNumberOfPoints();
            outputTimeStep = (outputEndTime - outputStartTime) / outputNumberOfPoints;
            timeBounds = new TimeBounds(0, outputEndTime - initialTime);
        } else if (sedmlSimulation instanceof OneStep) {
        // for anything other than UniformTimeCourse we just ignore
        } else if (sedmlSimulation instanceof SteadyState) {
        } else {
        }
        OutputTimeSpec outputTimeSpec = new UniformOutputTimeSpec(outputTimeStep);
        simTaskDesc.setTimeBounds(timeBounds);
        simTaskDesc.setTimeStep(timeStep);
        simTaskDesc.setOutputTimeSpec(outputTimeSpec);
        newSimulation.setSolverTaskDescription(simTaskDesc);
        bioModel.addSimulation(newSimulation);
        newSimulation.refreshDependencies();
    } catch (Exception e) {
        e.printStackTrace();
        throw new RuntimeException("Unable to initialize bioModel for the given selection.");
    }
    return doc;
}

Example 9 with TimeStep

use of cbit.vcell.solver.TimeStep in project vcell by virtualcell.

the class OptXmlWriter method getModelXML.

public static Element getModelXML(PdeObjectiveFunction pdeObjectiveFunction, String[] parameterNames) {
    Element modelElement = new Element(OptXmlTags.Model_Tag);
    try {
        SpatialReferenceData refData = pdeObjectiveFunction.getReferenceData();
        double refDataEndTime = refData.getDataByRow(refData.getNumDataRows() - 1)[0];
        // 
        // post the problem either as an IDA or CVODE model
        // 
        org.vcell.util.document.SimulationVersion simVersion = new org.vcell.util.document.SimulationVersion(new KeyValue("12345"), "name", new org.vcell.util.document.User("user", new KeyValue("123")), new org.vcell.util.document.GroupAccessNone(), // versionBranchPointRef
        null, // branchID
        new java.math.BigDecimal(1.0), new java.util.Date(), org.vcell.util.document.VersionFlag.Archived, "", null);
        Simulation simulation = new Simulation(simVersion, pdeObjectiveFunction.getMathDescription());
        simulation.getMeshSpecification().setSamplingSize(refData.getDataISize());
        double[] times = refData.getDataByColumn(0);
        double minDt = Double.POSITIVE_INFINITY;
        for (int i = 1; i < times.length; i++) {
            minDt = Math.min(minDt, times[i] - times[i - 1]);
        }
        simulation.getSolverTaskDescription().setTimeBounds(new cbit.vcell.solver.TimeBounds(0.0, refDataEndTime));
        simulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolume);
        simulation.getSolverTaskDescription().setTimeStep(new TimeStep(minDt / 5, minDt / 5, minDt / 5));
        // clone and resample geometry
        Geometry resampledGeometry = null;
        try {
            resampledGeometry = (Geometry) BeanUtils.cloneSerializable(simulation.getMathDescription().getGeometry());
            GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
            ISize newSize = simulation.getMeshSpecification().getSamplingSize();
            geoSurfaceDesc.setVolumeSampleSize(newSize);
            geoSurfaceDesc.updateAll();
        } catch (Exception e) {
            e.printStackTrace();
            throw new SolverException(e.getMessage());
        }
        SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, pdeObjectiveFunction.getFieldDataIDSs()), 0);
        StringWriter simulationInputStringWriter = new StringWriter();
        FiniteVolumeFileWriter fvFileWriter = new FiniteVolumeFileWriter(new PrintWriter(simulationInputStringWriter, true), simTask, resampledGeometry, pdeObjectiveFunction.getWorkingDirectory());
        fvFileWriter.write(parameterNames);
        simulationInputStringWriter.close();
        modelElement.setAttribute(OptXmlTags.ModelType_Attr, OptXmlTags.ModelType_Attr_FVSOLVER);
        CDATA simulationInputText = new CDATA(simulationInputStringWriter.getBuffer().toString());
        modelElement.addContent(simulationInputText);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new OptimizationException("failed to create fv input file: " + e.getMessage());
    }
    return modelElement;
}

Example 10 with TimeStep

use of cbit.vcell.solver.TimeStep in project vcell by virtualcell.

the class SbmlVcmlConverter method main.

/**
 * @param args -import or -export
 */
public static void main(String[] args) {
    Logging.init();
    ResourceUtil.setNativeLibraryDirectory();
    if (args.length < 2 || args.length > 3) {
        System.out.println("Usage:\n\t -export path_of_input_file\n\tOR\n\t -import path_of_input_file [-simulate]");
        System.exit(1);
    }
    if (args.length > 2 && args[0].equals("-export")) {
        System.out.println("Export cannot have arguments other than input file.");
        System.out.println("Usage:\n\t -export path_of_input_file\n\tOR\n\t-import path_of_input_file [-simulate]");
        System.exit(1);
    }
    try {
        String pathName = args[1];
        // Read xml file (Sbml or Vcml) into stringbuffer, pass the string into VCell's importer/exporter
        String xmlString = getXMLString(pathName);
        if (args[0].equals("-import")) {
            if (args.length > 3 || (args.length == 3 && !args[2].equals("-simulate"))) {
                System.out.println(args[2] + " : Unknown arguments for import; please check and re-run import command");
                System.out.println("Usage:\n\t -import path_of_input_file [-simulate]");
                System.exit(1);
            }
            boolean bSimulate = false;
            if (args.length == 3 && args[2].equals("-simulate")) {
                bSimulate = true;
            }
            // Create a default VCLogger - SBMLImporter needs it
            cbit.util.xml.VCLogger logger = new cbit.util.xml.VCLogger() {

                @Override
                public void sendMessage(Priority p, ErrorType et, String message) {
                    System.err.println("LOGGER: msgLevel=" + p + ", msgType=" + et + ", " + message);
                    if (p == VCLogger.Priority.HighPriority) {
                        throw new RuntimeException("Import failed : " + message);
                    }
                }

                public void sendAllMessages() {
                }

                public boolean hasMessages() {
                    return false;
                }
            };
            // invoke SBMLImporter, which returns a Biomodel, convert that to VCML using XMLHelper
            try {
                // import SBML model into VCML, store VCML string in 'fileName.vcml'
                // Instantiate an SBMLImporter to get the speciesUnitsHash - to compute the conversion factor from VC->SB species units.
                // and import SBML  (sbml->bioModel)
                org.vcell.sbml.vcell.SBMLImporter sbmlImporter = new org.vcell.sbml.vcell.SBMLImporter(pathName, logger, false);
                BioModel bioModel = sbmlImporter.getBioModel();
                // Hashtable<String, SBMLImporter.SBVCConcentrationUnits> speciesUnitsHash = sbmlImporter.getSpeciesUnitsHash();
                // double timeFactor = sbmlImporter.getSBMLTimeUnitsFactor();
                // convert biomodel to vcml and save to file.
                String vcmlString = XmlHelper.bioModelToXML(bioModel);
                String fileExtensionStr;
                if (pathName.endsWith(".xml")) {
                    fileExtensionStr = ".xml";
                } else if (pathName.endsWith(".sbml")) {
                    fileExtensionStr = ".sbml";
                } else {
                    throw new RuntimeException("Unknown file extension for SBML file name; Exiting SbmlConverter.");
                }
                String vcmlFileName = pathName.replace(fileExtensionStr, ".vcml");
                File vcmlFile = new File(vcmlFileName);
                XmlUtil.writeXMLStringToFile(vcmlString, vcmlFile.getAbsolutePath(), true);
                // If user doesn't choose to simulate, you are done.
                if (!bSimulate) {
                    return;
                }
                // Generate math for lone simContext
                SimulationContext simContext = (SimulationContext) bioModel.getSimulationContext(0);
                MathDescription mathDesc = simContext.createNewMathMapping().getMathDescription();
                simContext.setMathDescription(mathDesc);
                // Create basic simulation, with IDA solver (set in solve method) and other defaults, and end time 'Te'
                org.vcell.util.document.SimulationVersion simVersion = new org.vcell.util.document.SimulationVersion(new KeyValue("12345"), "name", new org.vcell.util.document.User("user", new KeyValue("123")), new org.vcell.util.document.GroupAccessNone(), // versionBranchPointRef
                null, // branchID
                new java.math.BigDecimal(1.0), new java.util.Date(), org.vcell.util.document.VersionFlag.Archived, "", null);
                Simulation sim1 = new Simulation(simVersion, simContext.getMathDescription());
                simContext.addSimulation(sim1);
                sim1.setName("sim1");
                // using a default end time of 10.0 secs, and a forcing default output time step of 0.01.
                // If user wants anything different, user can modify the .idaInput file and re-run simulation separately.
                // double newEndTime = endTime * timeFactor;
                double newEndTime = endTime;
                sim1.getSolverTaskDescription().setTimeBounds(new cbit.vcell.solver.TimeBounds(0, newEndTime));
                TimeStep timeStep_1 = new TimeStep();
                sim1.getSolverTaskDescription().setTimeStep(new TimeStep(timeStep_1.getMinimumTimeStep(), timeStep_1.getDefaultTimeStep(), newEndTime / 10000));
                sim1.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec((newEndTime - 0) / numTimeSteps));
                sim1.getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(1e-10, 1e-12));
                // save the new vcml with generated math and new sim in file named : fileName_IDA_simulation.vcml
                String newVcmlString = XmlHelper.bioModelToXML(bioModel);
                String newVcmlFileName = vcmlFile.getPath().replace(".vcml", "_IDA_simulation.vcml");
                File newVcmlFile = new File(newVcmlFileName);
                XmlUtil.writeXMLStringToFile(newVcmlString, newVcmlFile.getAbsolutePath(), true);
                // Solve simulation, which also generates and saves the .idainput file and .csv
                // SimSpec to get vars to solve and output in .csv
                SimSpec simSpec = SimSpec.fromSBML(xmlString);
                solveSimulation(new SimulationJob(sim1, 0, null), vcmlFile.getPath(), simSpec);
            } catch (Exception e) {
                e.printStackTrace(System.err);
                // and an annotation saying why it failed.
                try {
                    String fileExtensionStr;
                    if (pathName.endsWith(".xml")) {
                        fileExtensionStr = ".xml";
                    } else if (pathName.endsWith(".sbml")) {
                        fileExtensionStr = ".sbml";
                    } else {
                        throw new RuntimeException("Unknown file extension for SBML file name; Exiting SbmlConverter.");
                    }
                    String dummyVcmlFileName = pathName.replace(fileExtensionStr, ".vcml");
                    File dummyVcmlFile = new File(dummyVcmlFileName);
                    BioModel dummy_biomodel = new BioModel(null);
                    String dummyName = dummyVcmlFile.getName().substring(0, dummyVcmlFile.getName().indexOf(".vcml"));
                    dummy_biomodel.setName(dummyName);
                    dummy_biomodel.setDescription("SBML Model could not be automatically converted to VCML : " + e.getMessage());
                    String vcmlString = XmlHelper.bioModelToXML(dummy_biomodel);
                    XmlUtil.writeXMLStringToFile(vcmlString, dummyVcmlFile.getAbsolutePath(), true);
                } catch (Exception e1) {
                    e.printStackTrace(System.err);
                }
            }
        } else if (args[0].equals("-export")) {
            try {
                BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(xmlString));
                for (int i = 0; i < bioModel.getSimulationContexts().length; i++) {
                    SimulationContext simContext = bioModel.getSimulationContext(i);
                    if (simContext.getGeometry().getDimension() == 0 && !simContext.isStoch()) {
                        if (!simContext.getGeometryContext().isAllSizeSpecifiedPositive()) {
                            Structure structure = simContext.getModel().getStructure(0);
                            double structureSize = 1.0;
                            StructureMapping structMapping = simContext.getGeometryContext().getStructureMapping(structure);
                            StructureSizeSolver.updateAbsoluteStructureSizes(simContext, structure, structureSize, structMapping.getSizeParameter().getUnitDefinition());
                        }
                        // Export the application itself, with default overrides
                        String sbmlString = XmlHelper.exportSBML(bioModel, 2, 4, 0, false, simContext, null);
                        String filePath = pathName.substring(0, pathName.lastIndexOf("\\") + 1);
                        String sbmlFileName = TokenMangler.mangleToSName(bioModel.getName() + "_" + i);
                        File sbmlFile = new File(filePath + sbmlFileName + ".xml");
                        XmlUtil.writeXMLStringToFile(sbmlString, sbmlFile.getAbsolutePath(), true);
                        // Now export each simulation in the application that has overrides
                        Simulation[] simulations = bioModel.getSimulations(simContext);
                        for (int j = 0; j < simulations.length; j++) {
                            if (simulations[j].getMathOverrides().hasOverrides()) {
                                // Check for parameter scan and create simJob to pass into exporter
                                for (int k = 0; k < simulations[j].getScanCount(); k++) {
                                    SimulationJob simJob = new SimulationJob(simulations[j], k, null);
                                    sbmlString = XmlHelper.exportSBML(bioModel, 2, 4, 0, false, simContext, simJob);
                                    String fileName = TokenMangler.mangleToSName(sbmlFileName + "_" + j + "_" + k);
                                    sbmlFile = new File(filePath + fileName + ".xml");
                                    XmlUtil.writeXMLStringToFile(sbmlString, sbmlFile.getAbsolutePath(), true);
                                }
                            }
                        }
                    }
                }
                System.out.println("Successfully translated model : " + pathName);
            } catch (Exception e) {
                e.printStackTrace(System.err);
            }
        }
        System.exit(0);
    } catch (IOException e) {
        e.printStackTrace(System.err);
        System.exit(1);
    }
}