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

Example 26 with ExpressionException

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

the class XmlReader method getVarIniCount.

/**
 * This method return a VarIniCondition object from a XML element.
 * Creation date: (7/24/2006 5:26:05 PM)
 * @return cbit.vcell.math.VarIniCondition
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private VarIniCondition getVarIniCount(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException {
    // retrieve values
    Expression exp = unMangleExpression(param.getText());
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Variable var = md.getVariable(name);
    if (var == null) {
        throw new MathFormatException("variable " + name + " not defined");
    }
    if (!(var instanceof StochVolVariable)) {
        throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable");
    }
    try {
        VarIniCondition varIni = new VarIniCount(var, exp);
        return varIni;
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}

Example 27 with ExpressionException

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

the class CellQuanVCTranslator method addFunction.

private Function addFunction(Element temp, Element comp, String mangledName) {
    String expStr = null;
    Expression exp = null;
    Element parent = (Element) temp.getParent();
    Element sibling = parent.getChild(MathMLTags.APPLY, mathns);
    if (sibling == null) {
        // check if its value is assigned to another variable (i.e. A = B)
        @SuppressWarnings("unchecked") ArrayList<Element> list = new ArrayList<Element>(parent.getChildren(MathMLTags.IDENTIFIER, mathns));
        if (list.size() == 2) {
            expStr = (list.get(1)).getTextTrim();
        }
        if (expStr == null || expStr.length() == 0) {
            expStr = parent.getChildText(MathMLTags.CONSTANT, mathns);
        }
        if (expStr == null || expStr.length() == 0) {
            // check if 'piecewise'
            sibling = parent.getChild(MathMLTags.PIECEWISE, mathns);
        }
        if (expStr != null) {
            try {
                exp = new Expression(expStr);
                exp = processMathExp(comp, exp);
                nl.mangleString(expStr);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException(e.getMessage());
            }
        }
    }
    if (sibling != null) {
        Element trimmedMath = new Element(CELLMLTags.MATH, mathns).addContent(sibling.detach());
        fixMathMLBug(trimmedMath);
        try {
            exp = (new ExpressionMathMLParser(null)).fromMathML(trimmedMath);
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException(e.getMessage());
        }
        exp = processMathExp(comp, exp);
        expStr = exp.infix();
        nl.mangleString(expStr);
    }
    Domain domain = null;
    return new Function(mangledName, exp, domain);
}

Example 28 with ExpressionException

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

the class SBPAXHMMIrrevLawBuilder method addKinetics.

public void addKinetics(KineticContext context) {
    try {
        ReactionStep reaction = context.getReaction();
        HMM_IRRKinetics kinetics = new HMM_IRRKinetics((SimpleReaction) reaction);
        NameScope modelScope = reaction.getModel().getNameScope();
        ModelParameter kMichaelis = context.getParameter(SBOList.MICHAELIS_CONST_FORW);
        if (kMichaelis != null) {
            KineticsParameter kmParameter = kinetics.getKmParameter();
            kmParameter.setExpression(new Expression(kMichaelis, modelScope));
            kmParameter.setUnitDefinition(kMichaelis.getUnitDefinition());
        }
        ModelParameter kcat = context.getParameter(SBOList.CATALYTIC_RATE_CONST_FORW);
        if (kcat != null && context.getCatalysts().size() == 1) {
            KineticsParameter vmaxParameter = kinetics.getVmaxParameter();
            Catalyst catalyst = context.getCatalysts().iterator().next();
            vmaxParameter.setExpression(Expression.mult(new Expression(kcat, modelScope), new Expression(catalyst.getSpeciesContext(), modelScope)));
        // vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
        } else {
            ModelParameter vMax = context.getParameter(SBOList.MAXIMAL_VELOCITY_FORW);
            if (vMax != null) {
                KineticsParameter vmaxParameter = kinetics.getVmaxParameter();
                vmaxParameter.setExpression(new Expression(vMax, modelScope));
                vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
            }
        }
    } catch (ExpressionException e) {
        e.printStackTrace();
    }
}

Example 29 with ExpressionException

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

the class RefinementRoi method readVCML.

private void readVCML(CommentStringTokenizer tokens) throws DataAccessException {
    try {
        String token = tokens.nextToken();
        if (token.equalsIgnoreCase(VCML.RefinementRoi)) {
            token = tokens.nextToken();
            if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
                throw new DataAccessException("unexpected token " + token + " expecting " + VCML.BeginBlock);
            }
        }
        while (tokens.hasMoreTokens()) {
            token = tokens.nextToken();
            if (token.equalsIgnoreCase(VCML.EndBlock)) {
                break;
            } else if (token.equalsIgnoreCase(VCML.RefinementRoiType)) {
                token = tokens.nextToken();
                type = RoiType.valueOf(token);
            } else if (token.equalsIgnoreCase(VCML.Level)) {
                token = tokens.nextToken();
                level = Integer.parseInt(token);
            } else if (token.equalsIgnoreCase(VCML.TagsGrow)) {
            // backward compatible
            } else if (token.equalsIgnoreCase(VCML.ROIExpression)) {
                token = tokens.readToSemicolon();
                try {
                    setRoiExpression(token);
                } catch (ExpressionException e) {
                    System.err.println("Invalid " + VCML.ROIExpression + ": " + token);
                }
            } else {
                throw new DataAccessException("unexpected identifier " + token);
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("line #" + (tokens.lineIndex() + 1) + " Exception: " + e.getMessage());
    }
}

Example 30 with ExpressionException

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

the class SpeciesContextSpec method convertParticlesToConcentration.

public Expression convertParticlesToConcentration(Expression iniParticles) throws ExpressionException, MappingException {
    Expression iniConcentrationExpr = null;
    Structure structure = getSpeciesContext().getStructure();
    double structSize = computeStructureSize();
    if (structure instanceof Membrane) {
        // iniConcentration(molecules/um2) = particles/size(um2)
        try {
            iniConcentrationExpr = new Expression((iniParticles.evaluateConstant() * 1.0) / structSize);
        } catch (ExpressionException e) {
            iniConcentrationExpr = Expression.div(iniParticles, new Expression(structSize)).flatten();
        }
    } else {
        // convert concentration(particles/volume) to number of particles
        // particles = [iniParticles(uM)/size(um3)]*KMOLE
        // @Note : 'kMole' variable here is used only as a var name, it does not represent the previously known ReservedSymbol KMOLE.
        ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
        VCUnitDefinition stochasticToVolSubstance = modelUnitSystem.getVolumeSubstanceUnit().divideBy(modelUnitSystem.getStochasticSubstanceUnit());
        double stochasticToVolSubstanceScale = stochasticToVolSubstance.getDimensionlessScale().doubleValue();
        try {
            iniConcentrationExpr = new Expression((iniParticles.evaluateConstant() * stochasticToVolSubstanceScale / structSize));
        } catch (ExpressionException e) {
            Expression numeratorExpr = Expression.mult(iniParticles, new Expression(stochasticToVolSubstanceScale));
            Expression denominatorExpr = new Expression(structSize);
            iniConcentrationExpr = Expression.div(numeratorExpr, denominatorExpr).flatten();
        }
    }
    return iniConcentrationExpr;
}