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

Example 41 with AnnotatedFunction

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

the class FunctionFileGenerator method writefunctionFile.

/**
 * Insert the method's description here.
 * Creation date: (1/12/2004 2:18:45 PM)
 */
public void writefunctionFile(PrintWriter out) {
    out.println("##---------------------------------------------");
    out.println("##  " + basefileName);
    out.println("##---------------------------------------------");
    out.println("");
    if (annotatedFunctionList != null) {
        for (AnnotatedFunction f : annotatedFunctionList) {
            out.print(f.getQualifiedName() + "; " + f.getExpression().infix() + "; " + f.getErrorString() + "; " + f.getFunctionType().toString() + "; " + f.isOldUserDefined());
            out.println();
        }
    }
    out.println("");
}

Example 42 with AnnotatedFunction

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

the class XmlReader method getOutputFunction.

private AnnotatedFunction getOutputFunction(Element param) throws XmlParseException {
    // get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String temp = param.getText();
    Expression exp = unMangleExpression(temp);
    String errStr = unMangle(param.getAttributeValue(XMLTags.ErrorStringTag));
    VariableType funcType = VariableType.UNKNOWN;
    String funcTypeAttr = param.getAttributeValue(XMLTags.FunctionTypeTag);
    if (funcTypeAttr != null) {
        String funcTypeStr = unMangle(funcTypeAttr);
        funcType = VariableType.getVariableTypeFromVariableTypeName(funcTypeStr);
    }
    // -- create new AnnotatedFunction --
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    AnnotatedFunction function = new AnnotatedFunction(name, exp, domain, errStr, funcType, FunctionCategory.OUTPUTFUNCTION);
    return function;
}

Example 43 with AnnotatedFunction

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

the class Xmlproducer method getXML.

/**
 * This method returns the XML representation of a MathModel.
 * Creation date: (3/28/2001 12:27:28 PM)
 * @return Element
 * @param param cbit.vcell.mathmodel.MathModel
 */
public Element getXML(MathModel param) throws XmlParseException {
    Element mathmodel = new Element(XMLTags.MathModelTag);
    // Add Attributes
    String name = param.getName();
    mathmodel.setAttribute(XMLTags.NameAttrTag, mangle(name));
    // add Annotation
    if (param.getDescription() != null && param.getDescription().length() > 0) {
        Element annotationElem = new Element(XMLTags.AnnotationTag);
        annotationElem.setText(mangle(param.getDescription()));
        mathmodel.addContent(annotationElem);
    }
    // Add Geometry
    try {
        mathmodel.addContent(getXML(param.getMathDescription().getGeometry()));
    } catch (XmlParseException e) {
        e.printStackTrace();
        throw new XmlParseException("A problem occurred when trying to process the geometry!", e);
    }
    // Add Mathdescription
    mathmodel.addContent(getXML(param.getMathDescription()));
    // Add output functions
    if (param.getOutputFunctionContext() != null) {
        ArrayList<AnnotatedFunction> outputFunctions = param.getOutputFunctionContext().getOutputFunctionsList();
        if (outputFunctions != null && outputFunctions.size() > 0) {
            // get output functions
            mathmodel.addContent(getXML(outputFunctions));
        }
    }
    // Add Simulations
    cbit.vcell.solver.Simulation[] arraysim = param.getSimulations();
    if (arraysim != null) {
        for (int i = 0; i < arraysim.length; i++) {
            mathmodel.addContent(getXML(arraysim[i]));
        }
    }
    // Add Metadata (if there is)
    if (param.getVersion() != null) {
        mathmodel.addContent(getXML(param.getVersion(), param.getName(), param.getDescription()));
    }
    // MIRIAMHelper.addToSBMLAnnotation(mathmodel, param.getMIRIAMAnnotation(), true);
    return mathmodel;
}

Example 44 with AnnotatedFunction

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

the class RuleBasedTest method checkNonspatialStochasticSimContext.

private static void checkNonspatialStochasticSimContext(SimulationContext srcSimContext, File baseDirectory, int numTrials) throws Exception {
    if (!srcSimContext.getApplicationType().equals(Application.NETWORK_STOCHASTIC) || srcSimContext.getGeometry().getDimension() != 0) {
        throw new RuntimeException("simContext is of type " + srcSimContext.getApplicationType() + " and geometry dimension of " + srcSimContext.getGeometry().getDimension() + ", expecting nonspatial stochastic");
    }
    BioModel origBioModel = srcSimContext.getBioModel();
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(XmlHelper.bioModelToXML(origBioModel)));
    bioModel.refreshDependencies();
    // create ODE and RuleBased
    SimulationContext newODEApp = SimulationContext.copySimulationContext(srcSimContext, "aUniqueNewODEApp", false, Application.NETWORK_DETERMINISTIC);
    SimulationContext newRuleBasedApp = SimulationContext.copySimulationContext(srcSimContext, "aUniqueNewRuleBasedApp", false, Application.RULE_BASED_STOCHASTIC);
    newODEApp.setBioModel(bioModel);
    newRuleBasedApp.setBioModel(bioModel);
    ArrayList<AnnotatedFunction> outputFunctionsList = srcSimContext.getOutputFunctionContext().getOutputFunctionsList();
    // OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
    newODEApp.getOutputFunctionContext().setOutputFunctions(outputFunctionsList);
    newRuleBasedApp.getOutputFunctionContext().setOutputFunctions(outputFunctionsList);
    NetworkGenerationRequirements networkGenerationRequirements = NetworkGenerationRequirements.AllowTruncatedStandardTimeout;
    bioModel.addSimulationContext(newODEApp);
    newODEApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    bioModel.addSimulationContext(newRuleBasedApp);
    newRuleBasedApp.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    srcSimContext.refreshMathDescription(new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    // Create non-spatialStoch, ODE and RuleBased sims
    Simulation nonspatialStochAppNewSim = srcSimContext.addNewSimulation(STOCH_SIM_NAME, /*SimulationOwner.DEFAULT_SIM_NAME_PREFIX*/
    new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    Simulation newODEAppNewSim = newODEApp.addNewSimulation(ODE_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    Simulation newRuleBasedAppNewSim = newRuleBasedApp.addNewSimulation(NFS_SIM_NAME, new MathMappingCallbackTaskAdapter(null), networkGenerationRequirements);
    nonspatialStochAppNewSim.setSimulationOwner(srcSimContext);
    newODEAppNewSim.setSimulationOwner(newODEApp);
    newRuleBasedAppNewSim.setSimulationOwner(newRuleBasedApp);
    try {
        bioModel.getModel().getSpeciesContexts();
        ArrayList<String> varNameList = new ArrayList<String>();
        for (SpeciesContextSpec scs : srcSimContext.getReactionContext().getSpeciesContextSpecs()) {
            varNameList.add(scs.getSpeciesContext().getName());
        }
        String[] varNames = varNameList.toArray(new String[0]);
        OutputTimeSpec outputTimeSpec = nonspatialStochAppNewSim.getSolverTaskDescription().getOutputTimeSpec();
        ArrayList<Double> sampleTimeList = new ArrayList<Double>();
        if (outputTimeSpec instanceof UniformOutputTimeSpec) {
            double endingTime = nonspatialStochAppNewSim.getSolverTaskDescription().getTimeBounds().getEndingTime();
            double dT = ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep();
            int currTimeIndex = 0;
            while (currTimeIndex * dT <= (endingTime + 1e-8)) {
                sampleTimeList.add(currTimeIndex * dT);
                currTimeIndex++;
            }
        }
        double[] sampleTimes = new double[sampleTimeList.size()];
        for (int i = 0; i < sampleTimes.length; i++) {
            sampleTimes[i] = sampleTimeList.get(i);
        }
        TimeSeriesMultitrialData sampleDataStoch1 = new TimeSeriesMultitrialData("stochastic1", varNames, sampleTimes, numTrials);
        TimeSeriesMultitrialData sampleDataStoch2 = new TimeSeriesMultitrialData("stochastic2", varNames, sampleTimes, numTrials);
        TimeSeriesMultitrialData sampleDataDeterministic = new TimeSeriesMultitrialData("determinstic", varNames, sampleTimes, 1);
        runsolver(nonspatialStochAppNewSim, baseDirectory, numTrials, sampleDataStoch1);
        runsolver(newODEAppNewSim, baseDirectory, 1, sampleDataDeterministic);
        runsolver(newRuleBasedAppNewSim, baseDirectory, numTrials, sampleDataStoch2);
        writeVarDiffData(baseDirectory, sampleDataStoch1, sampleDataStoch2);
        writeKolmogorovSmirnovTest(baseDirectory, sampleDataStoch1, sampleDataStoch2);
        writeChiSquareTest(baseDirectory, sampleDataStoch1, sampleDataStoch2);
        writeData(baseDirectory, sampleDataStoch1);
        writeData(baseDirectory, sampleDataStoch2);
        writeData(baseDirectory, sampleDataDeterministic);
    } finally {
        srcSimContext.removeSimulation(nonspatialStochAppNewSim);
        newODEApp.removeSimulation(newODEAppNewSim);
        newRuleBasedApp.removeSimulation(newRuleBasedAppNewSim);
    }
}

Example 45 with AnnotatedFunction

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

the class OutputFunctionsListTableModel method setValueAt.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2004 2:01:23 PM)
 * @param aValue java.lang.Object
 * @param rowIndex int
 * @param columnIndex int
 */
public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    AnnotatedFunction outputFunction = getValueAt(rowIndex);
    switch(columnIndex) {
        case COLUMN_OUTPUTFN_EXPRESSION:
            {
                try {
                    Expression exp = new Expression((String) aValue);
                    if (exp.compareEqual(outputFunction.getExpression())) {
                        return;
                    }
                    exp.bindExpression(outputFunctionContext);
                    VariableType vt = outputFunctionContext.computeFunctionTypeWRTExpression(outputFunction, exp);
                    if (!vt.compareEqual(outputFunction.getFunctionType())) {
                    }
                    outputFunction.setExpression(exp);
                    fireTableRowsUpdated(rowIndex, rowIndex);
                    outputFunctionContext.firePropertyChange("outputFunctions", null, outputFunctionContext.getOutputFunctionsList());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Expression error:\n" + e.getMessage());
                } catch (InconsistentDomainException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "Expression error:\n" + e.getMessage());
                }
                break;
            }
    }
}