Examples with ExpressionBindingException cbit.vcell.parser.ExpressionBindingException used on opensource projects

Example 26 with ExpressionBindingException

use of cbit.vcell.parser.ExpressionBindingException in project vcell by virtualcell.

the class BioModelEditorModelPanel method duplicateReactionRule.

private ReactionRule duplicateReactionRule(ReactionRule oldRule, Structure structure) {
    try {
        ReactionRule newRule = ReactionRule.duplicate(oldRule, structure);
        Model m = oldRule.getModel();
        m.getRbmModelContainer().addReactionRule(newRule);
        return newRule;
    } catch (PropertyVetoException | ExpressionBindingException e) {
        e.printStackTrace();
        throw new RuntimeException("Problem duplicating " + ReactionRule.typeName + " " + oldRule.getDisplayName());
    }
}

Example 27 with ExpressionBindingException

use of cbit.vcell.parser.ExpressionBindingException in project vcell by virtualcell.

the class XmlReader method getMathDescription.

/**
 * This method returns a MathDescription from a XML element.
 * Creation date: (4/26/2001 12:11:14 PM)
 * @return cbit.vcell.math.MathDescription
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
MathDescription getMathDescription(Element param, Geometry geometry) throws XmlParseException {
    MathDescription mathdes = null;
    Element tempelement;
    // Retrieve Metadata(Version)
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // Retrieve attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // Create new MathDescription
    if (version != null) {
        mathdes = new MathDescription(version);
    } else {
        mathdes = new MathDescription(name);
    }
    try {
        // this step is needed!
        mathdes.setGeometry(geometry);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("a PropertyVetoException was fired when setting the Geometry to the Mathdescription in the simContext " + name, e);
    }
    // set attributes
    try {
        mathdes.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // mathdes.setDescription(unMangle(annotation));
        // }
        // add Annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            mathdes.setDescription(unMangle(annotationText));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the name " + name + ", to a new MathDescription!", e);
    }
    VariableHash varHash = new VariableHash();
    // Retrieve Constant
    Iterator<Element> iterator = param.getChildren(XMLTags.ConstantTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getConstant(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve FilamentRegionVariables
    iterator = param.getChildren(XMLTags.FilamentRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFilamentRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve FilamentVariables
    iterator = param.getChildren(XMLTags.FilamentVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFilamentVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // retrieve InsideVariables
    // **** This variables are for internal USE ******
    // Retrieve MembraneRegionVariable
    iterator = param.getChildren(XMLTags.MembraneRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMembraneRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve MembraneVariable
    iterator = param.getChildren(XMLTags.MembraneVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMemVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve PointVariable
    iterator = param.getChildren(XMLTags.PointVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getPointVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // retrieve OutsideVariables
    // **** This variables are for internal USE ******
    // Retrieve Volume Region variable
    iterator = param.getChildren(XMLTags.VolumeRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve VolumeVariable
    iterator = param.getChildren(XMLTags.VolumeVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve StochVolVariable
    iterator = param.getChildren(XMLTags.StochVolVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getStochVolVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve all the Functions //This needs to be processed before all the variables are read!
    iterator = param.getChildren(XMLTags.FunctionTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFunction(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.VolumeRandomVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getRandomVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.MembraneRandomVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getRandomVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.VolumeParticleVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticalVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.MembraneParticleVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMembraneParticalVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // ParticleMolecularTypeTag       getParticleMolecularTypes
    // has to be done before VolumeParticleSpeciesPattern and VolumeParticleObservable
    iterator = param.getChildren(XMLTags.ParticleMolecularTypeTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        mathdes.addParticleMolecularType(getParticleMolecularType(tempelement));
    }
    // VolumeParticleSpeciesPatternTag
    iterator = param.getChildren(XMLTags.VolumeParticleSpeciesPatternTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticleSpeciesPattern(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // VolumeParticleObservableTag    getParticleObservables
    iterator = param.getChildren(XMLTags.VolumeParticleObservableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticleObservable(tempelement, varHash));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // 
    try {
        mathdes.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    } catch (MathException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding the Function variables to the MathDescription " + name, e);
    } catch (ExpressionBindingException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding the Function variables to the MathDescription " + name, e);
    }
    // Retrieve CompartmentsSubdomains
    iterator = param.getChildren(XMLTags.CompartmentSubDomainTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            mathdes.addSubDomain(getCompartmentSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new CompartmentSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve MembraneSubdomains
    iterator = param.getChildren(XMLTags.MembraneSubDomainTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            mathdes.addSubDomain(getMembraneSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new MembraneSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve the FilamentSubdomain (if any)
    tempelement = param.getChild(XMLTags.FilamentSubDomainTag, vcNamespace);
    if (tempelement != null) {
        try {
            mathdes.addSubDomain(getFilamentSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new FilamentSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve the PointSubdomain (if any)
    tempelement = param.getChild(XMLTags.PointSubDomainTag, vcNamespace);
    if (tempelement != null) {
        try {
            mathdes.addSubDomain(getPointSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new PointSubDomain to the MathDescription " + name, e);
        }
    }
    iterator = param.getChildren(XMLTags.EventTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        Event event = getEvent(mathdes, tempelement);
        try {
            mathdes.addEvent(event);
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.PostProcessingBlock, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        getPostProcessingBlock(mathdes, tempelement);
    }
    return mathdes;
}

Example 28 with ExpressionBindingException

use of cbit.vcell.parser.ExpressionBindingException in project vcell by virtualcell.

the class XmlReader method getModel.

/**
 * This method creates a Model object from a XML element.
 * Creation date: (3/14/2001 6:14:37 PM)
 * @return cbit.vcell.model.Model
 * @param param org.jdom.Element
 */
private Model getModel(Element param) throws XmlParseException {
    if (param == null) {
        throw new XmlParseException("Invalid 'NULL' XML 'model' element arrived!");
    }
    // Get version, if any
    Model newmodel = null;
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // if forcedModelUnitSystem has been set, ues that (could be overriding unit system for SBML export)
    if (forcedModelUnitSystem != null) {
        newmodel = new Model(version, forcedModelUnitSystem);
    } else {
        Element unitSystemNode = param.getChild(XMLTags.ModelUnitSystemTag, vcNamespace);
        if (unitSystemNode != null) {
            ModelUnitSystem modelUnitSystem = getUnitSystem(unitSystemNode);
            newmodel = new Model(version, modelUnitSystem);
        } else {
            newmodel = new Model(version);
        }
    }
    try {
        // Set attributes
        newmodel.setName(unMangle(param.getAttributeValue(XMLTags.NameAttrTag)));
        // Add annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            newmodel.setDescription(unMangle(annotationText));
        }
        // Add global parameters
        Element globalParamsElement = param.getChild(XMLTags.ModelParametersTag, vcNamespace);
        if (globalParamsElement != null) {
            ModelParameter[] modelParams = getModelParams(globalParamsElement, newmodel);
            // add global/model param to model - done inside getModelParam by passing newModel
            newmodel.setModelParameters(modelParams);
        }
        // Add Species (Compounds)
        Iterator<Element> iterator = param.getChildren(XMLTags.SpeciesTag, vcNamespace).iterator();
        ArrayList<Species> speciesList = new ArrayList<Species>();
        while (iterator.hasNext()) {
            org.jdom.Element temp = (Element) iterator.next();
            speciesList.add(getSpecies(temp));
        }
        newmodel.setSpecies(speciesList.toArray(new Species[speciesList.size()]));
        // Add Structures
        LinkedList<Structure> newstructures = new LinkedList<Structure>();
        // (features)
        List<Element> children = param.getChildren(XMLTags.FeatureTag, vcNamespace);
        for (Element featureElement : children) {
            newstructures.add(getFeature(featureElement));
        }
        // (Membrane)
        children = param.getChildren(XMLTags.MembraneTag, vcNamespace);
        for (Element memElement : children) {
            newstructures.add(getMembrane(newmodel, memElement, newstructures));
        }
        if (newstructures.size() > 0) {
            Structure[] structarray = new Structure[newstructures.size()];
            newstructures.toArray(structarray);
            // Add all the retrieved structures
            newmodel.setStructures(structarray);
        }
        // retrieve the RbmModelContainer, if present - must be done before we retrieve species context!
        Element element = param.getChild(XMLTags.RbmModelContainerTag, vcNamespace);
        if (element != null) {
            getRbmModelContainer(element, newmodel);
        } else {
            lg.info("RbmModelContainer is missing.");
        }
        // Add SpeciesContexts
        children = param.getChildren(XMLTags.SpeciesContextTag, vcNamespace);
        SpeciesContext[] newspeccon = new SpeciesContext[children.size()];
        int scCounter = 0;
        for (Element scElement : children) {
            newspeccon[scCounter] = getSpeciesContext(scElement, newmodel);
            scCounter++;
        }
        newmodel.setSpeciesContexts(newspeccon);
        // Retrieve rateRules and add to model
        // Element rateRuleVarsElement = param.getChild(XMLTags.RateRuleVariablesTag, vcNamespace);
        // if(rateRuleVarsElement != null){
        // RateRuleVariable[] rateRuleVars = getRateRuleVariables(rateRuleVarsElement, newmodel);
        // newmodel.setRateRuleVariables(rateRuleVars);
        // }
        // Add Reaction steps (if available)
        // (Simplereaction)
        // Create a varHash with reserved symbols and global parameters, if any, to pass on to Kinetics
        // must create new hash for each reaction and flux, since each kinetics uses new variables hash
        iterator = param.getChildren(XMLTags.SimpleReactionTag, vcNamespace).iterator();
        ArrayList<ReactionStep> reactionStepList = new ArrayList<ReactionStep>();
        while (iterator.hasNext()) {
            org.jdom.Element temp = iterator.next();
            reactionStepList.add(getSimpleReaction(temp, newmodel));
        }
        // (fluxStep)
        iterator = param.getChildren(XMLTags.FluxStepTag, vcNamespace).iterator();
        while (iterator.hasNext()) {
            org.jdom.Element temp = iterator.next();
            reactionStepList.add(getFluxReaction(temp, newmodel));
        }
        newmodel.setReactionSteps(reactionStepList.toArray(new ReactionStep[reactionStepList.size()]));
        // Add Diagrams
        children = param.getChildren(XMLTags.DiagramTag, vcNamespace);
        if (children.size() > 0) {
            Diagram[] newdiagrams = new Diagram[children.size()];
            int diagramCounter = 0;
            for (Element diagramElement : children) {
                newdiagrams[diagramCounter] = getDiagram(diagramElement, newmodel);
                diagramCounter++;
            }
            reorderDiagramsInPlace_UponRead(docVCellSoftwareVersion, newdiagrams, newmodel.getStructureTopology());
            // if(docVCellSoftwareVersion != null && !docVCellSoftwareVersion.isValid() && docVCellSoftwareVersion.getMajorVersion()<=5 && docVCellSoftwareVersion.getMinorVersion() <=2){
            // //In Vcell 5.2 and previous we need to order diagrams topologically, in 5.3 and later the diagrams are displayed as they are ordered when read from document
            // final StructureTopology structureTopology = newmodel.getStructureTopology();
            // Arrays.sort(newdiagrams, new Comparator<Diagram>() {
            // @Override
            // public int compare(Diagram o1, Diagram o2) {
            // return getStructureLevel(o1.getStructure(), structureTopology) - getStructureLevel(o2.getStructure(), structureTopology);
            // }
            // });
            // }
            newmodel.setDiagrams(newdiagrams);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException(e);
    } catch (ModelException e) {
        e.printStackTrace();
    }
    // model param expresions are not bound when they are read in, since they could be functions of each other or structures/speciesContexts.
    // Hence bind the model param exprs at the end, after reading all model level quantities.
    ModelParameter[] modelParameters = newmodel.getModelParameters();
    for (int i = 0; modelParameters != null && i < modelParameters.length; i++) {
        try {
            modelParameters[i].getExpression().bindExpression(newmodel);
        } catch (ExpressionBindingException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error binding global parameter '" + modelParameters[i].getName() + "' to model." + e.getMessage());
        }
    }
    return newmodel;
}

Example 29 with ExpressionBindingException

use of cbit.vcell.parser.ExpressionBindingException in project vcell by virtualcell.

the class FunctionFileGenerator method readFunctionsFile.

/**
 * This method was created in VisualAge.
 * @param logFile java.io.File
 */
public static synchronized Vector<AnnotatedFunction> readFunctionsFile(File functionsFile, String simJobID) throws java.io.FileNotFoundException, java.io.IOException {
    // Check if file exists
    if (!functionsFile.exists()) {
        throw new java.io.FileNotFoundException("functions file " + functionsFile.getPath() + " not found");
    }
    // 
    // Read characters from functionFile into character array and transfer into string buffer.
    // 
    Vector<AnnotatedFunction> annotatedFunctionsVector = new Vector<AnnotatedFunction>();
    long fnFileLength = functionsFile.length();
    StringBuffer stringBuffer = new StringBuffer();
    FileInputStream is = null;
    try {
        is = new FileInputStream(functionsFile);
        InputStreamReader reader = new InputStreamReader(is);
        BufferedReader br = new BufferedReader(reader);
        char[] charArray = new char[10000];
        while (true) {
            int numRead = br.read(charArray, 0, charArray.length);
            if (numRead > 0) {
                stringBuffer.append(charArray, 0, numRead);
            } else if (numRead == -1) {
                break;
            }
        }
    } finally {
        if (is != null) {
            is.close();
        }
    }
    if (stringBuffer.length() != fnFileLength) {
        System.out.println("<<<SYSOUT ALERT>>>SimulationData.readFunctionFile(), read " + stringBuffer.length() + " of " + fnFileLength + " bytes of input file");
    }
    String newLineDelimiters = "\n\r";
    StringTokenizer lineTokenizer = new StringTokenizer(stringBuffer.toString(), newLineDelimiters);
    String token1 = new String("");
    int j = 0;
    // 
    // Each token is a line representing a function name and function expression,
    // separated by a semicolon
    // 
    HashSet<String> allSymbols = new HashSet<String>();
    while (lineTokenizer.hasMoreTokens()) {
        token1 = lineTokenizer.nextToken();
        FunctionFileGenerator.FuncFileLineInfo funcFileLineInfo = readFunctionLine(token1);
        if (funcFileLineInfo != null && funcFileLineInfo.functionName != null && funcFileLineInfo.functionExpr != null && funcFileLineInfo.funcVarType != null) {
            Expression functionExpr = null;
            try {
                functionExpr = new Expression(funcFileLineInfo.functionExpr);
                functionExpr = MathFunctionDefinitions.fixFunctionSyntax(functionExpr);
            } catch (cbit.vcell.parser.ExpressionException e) {
                throw new RuntimeException("Error in reading expression '" + funcFileLineInfo.functionExpr + "' for function \"" + funcFileLineInfo.functionName + "\"");
            }
            Domain domain = Variable.getDomainFromCombinedIdentifier(funcFileLineInfo.functionName);
            String funcName = Variable.getNameFromCombinedIdentifier(funcFileLineInfo.functionName);
            AnnotatedFunction annotatedFunc = new AnnotatedFunction(funcName, functionExpr, domain, funcFileLineInfo.errorString, funcFileLineInfo.funcVarType, funcFileLineInfo.funcIsUserDefined ? FunctionCategory.OLDUSERDEFINED : FunctionCategory.PREDEFINED);
            allSymbols.add(annotatedFunc.getName());
            String[] symbols = annotatedFunc.getExpression().getSymbols();
            if (symbols != null) {
                allSymbols.addAll(Arrays.asList(symbols));
            }
            annotatedFunctionsVector.addElement(annotatedFunc);
        }
        j++;
    }
    if (simJobID != null && simJobID.trim().length() > 0) {
        SimpleSymbolTable simpleSymbolTable = new SimpleSymbolTable(allSymbols.toArray(new String[0]));
        // bind
        for (AnnotatedFunction func : annotatedFunctionsVector) {
            if (func.isOldUserDefined()) {
                try {
                    func.bind(simpleSymbolTable);
                } catch (ExpressionBindingException e) {
                    e.printStackTrace();
                }
            }
        }
        // rename symbol table entries
        for (int i = 0; i < annotatedFunctionsVector.size(); i++) {
            AnnotatedFunction func = annotatedFunctionsVector.get(i);
            if (func.isOldUserDefined()) {
                SimpleSymbolTableEntry ste = (SimpleSymbolTableEntry) simpleSymbolTable.getEntry(func.getName());
                ste.setName(simJobID + "_" + func.getName());
            }
        }
        // rename in the expressions
        for (int i = 0; i < annotatedFunctionsVector.size(); i++) {
            AnnotatedFunction func = annotatedFunctionsVector.get(i);
            if (func.isOldUserDefined()) {
                try {
                    Expression exp = func.getExpression().renameBoundSymbols(simpleSymbolTable.getNameScope());
                    AnnotatedFunction newfunc = new AnnotatedFunction(simJobID + "_" + func.getName(), exp, func.getDomain(), func.getName(), func.getErrorString(), func.getFunctionType(), FunctionCategory.OLDUSERDEFINED);
                    annotatedFunctionsVector.set(i, newfunc);
                } catch (ExpressionBindingException e) {
                    e.printStackTrace();
                }
            }
        }
    }
    return annotatedFunctionsVector;
}

Example 30 with ExpressionBindingException

use of cbit.vcell.parser.ExpressionBindingException in project vcell by virtualcell.

the class XmlReader method getRateRules.

public RateRule[] getRateRules(SimulationContext simContext, Element rateRulesElement) throws XmlParseException {
    Iterator<Element> rateRulesIterator = rateRulesElement.getChildren(XMLTags.RateRuleTag, vcNamespace).iterator();
    Vector<RateRule> rateRulesVector = new Vector<RateRule>();
    while (rateRulesIterator.hasNext()) {
        Element rrElement = (Element) rateRulesIterator.next();
        RateRule newRateRule = null;
        try {
            String rrName = unMangle(rrElement.getAttributeValue(XMLTags.NameAttrTag));
            String varname = rrElement.getAttributeValue(XMLTags.RateRuleVariableAttrTag);
            SymbolTableEntry rrVar = simContext.getEntry(varname);
            Expression rrExp = unMangleExpression(rrElement.getText());
            newRateRule = new RateRule(rrName, rrVar, rrExp, simContext);
            newRateRule.bind();
        } catch (ExpressionBindingException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e.getMessage());
        }
        if (newRateRule != null) {
            rateRulesVector.add(newRateRule);
        }
    }
    return ((RateRule[]) BeanUtils.getArray(rateRulesVector, RateRule.class));
}