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

Example 56 with Expression

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

the class XmlReader method getExplicitDataGenerator.

private ExplicitDataGenerator getExplicitDataGenerator(Element element) {
    String name = unMangle(element.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(element.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    String temp = element.getText();
    Expression exp = unMangleExpression(temp);
    ExplicitDataGenerator explicitDataGenerator = new ExplicitDataGenerator(name, domain, exp);
    return explicitDataGenerator;
}

Example 57 with Expression

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

the class XmlReader method getGaussianDistribution.

private GaussianDistribution getGaussianDistribution(Element distElement) {
    Element element = distElement.getChild(XMLTags.GaussianDistributionMeanTag, vcNamespace);
    Expression mu = unMangleExpression(element.getText());
    element = distElement.getChild(XMLTags.GaussianDistributionStandardDeviationTag, vcNamespace);
    Expression sigma = unMangleExpression(element.getText());
    return new GaussianDistribution(mu, sigma);
}

Example 58 with Expression

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

the class XmlReader method getFunction.

/**
 * This method returns a Function variable object from a XML Element.
 * Creation date: (5/16/2001 3:45:21 PM)
 * @return cbit.vcell.math.Function
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private Function getFunction(Element param) throws XmlParseException {
    // get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    /**
     * ---------------------------------------------------------------
     * ATTENTATION: this is a quick fix for a specific user to load his model
     * with a function name as "ATP/ADP".  This syntax is not allowed.
     *-----------------------------------------------------------------------
     */
    if (name.equals("ATP/ADP")) {
        name = "ATP_ADP_renamed";
        System.err.print("Applying species function name change ATP/ADP to ATP_ADP for a specific user (key=2288008)");
        Thread.dumpStack();
    }
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    String temp = param.getText();
    Expression exp = unMangleExpression(temp);
    // -- create new Function --
    Function function = new Function(name, exp, domain);
    transcribeComments(param, function);
    return function;
}

Example 59 with Expression

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

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a OdeEquation object.
 * Creation date: (3/2/2001 2:52:14 PM)
 * @return Element
 * @param param cbit.vcell.math.OdeEquation
 */
private Element getXML(OdeEquation param) throws XmlParseException {
    Element ode = new Element(XMLTags.OdeEquationTag);
    // Add atribute
    ode.setAttribute(XMLTags.NameAttrTag, mangle(param.getVariable().getName()));
    // Add Rate subelement
    Element rate = new Element(XMLTags.RateTag);
    if (param.getRateExpression() != null) {
        rate.addContent(mangleExpression(param.getRateExpression()));
    } else {
        rate.addContent("0.0");
    }
    ode.addContent(rate);
    // Add Initial
    Element initial = new Element(XMLTags.InitialTag);
    if (param.getInitialExpression() != null) {
        initial.addContent(mangleExpression(param.getInitialExpression()));
        ode.addContent(initial);
    }
    // add solution expression
    switch(param.getSolutionType()) {
        case Equation.UNKNOWN_SOLUTION:
            {
                ode.setAttribute(XMLTags.SolutionTypeTag, XMLTags.UnknownTypeTag);
                if (param.getInitialExpression() == null) {
                    initial.setText(mangleExpression(new cbit.vcell.parser.Expression(0.0)));
                    ode.addContent(initial);
                }
                break;
            }
        case Equation.EXACT_SOLUTION:
            {
                ode.setAttribute(XMLTags.SolutionTypeTag, XMLTags.ExactTypeTag);
                Element solution = new Element(XMLTags.SolutionExpressionTag);
                solution.setText(mangle(param.getExactSolution().infix()));
                ode.addContent(solution);
                break;
            }
        default:
            {
                throw new XmlParseException("Unknown solution type:" + param.getSolutionType());
            }
    }
    return ode;
}

Example 60 with Expression

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

the class Xmlproducer method getXML.

private Element getXML(RbmKineticLaw param) {
    Element kinetics = new Element(XMLTags.KineticsTag);
    switch(param.getRateLawType()) {
        case MassAction:
            {
                kinetics.setAttribute(XMLTags.KineticsTypeAttrTag, XMLTags.RbmKineticTypeMassAction);
                break;
            }
        case MichaelisMenten:
            {
                kinetics.setAttribute(XMLTags.KineticsTypeAttrTag, XMLTags.RbmKineticTypeMichaelisMenten);
                break;
            }
        case Saturable:
            {
                kinetics.setAttribute(XMLTags.KineticsTypeAttrTag, XMLTags.RbmKineticTypeSaturable);
                break;
            }
    }
    HashMap<ParameterRoleEnum, String> roleHash = new HashMap<ParameterRoleEnum, String>();
    roleHash.put(RbmKineticLawParameterType.MassActionForwardRate, XMLTags.RbmMassActionKfRole);
    roleHash.put(RbmKineticLawParameterType.MassActionReverseRate, XMLTags.RbmMassActionKrRole);
    roleHash.put(RbmKineticLawParameterType.MichaelisMentenKcat, XMLTags.RbmMichaelisMentenKcatRole);
    roleHash.put(RbmKineticLawParameterType.MichaelisMentenKm, XMLTags.RbmMichaelisMentenKmRole);
    roleHash.put(RbmKineticLawParameterType.SaturableVmax, XMLTags.RbmSaturableVmaxRole);
    roleHash.put(RbmKineticLawParameterType.SaturableKs, XMLTags.RbmSaturableKsRole);
    roleHash.put(RbmKineticLawParameterType.RuleRate, XMLTags.RbmRuleRateRole);
    roleHash.put(RbmKineticLawParameterType.UserDefined, XMLTags.RbmUserDefinedRole);
    // Add Kinetics Parameters
    LocalParameter[] parameters = param.getLocalParameters();
    for (int i = 0; i < parameters.length; i++) {
        LocalParameter parm = parameters[i];
        Element tempparameter = new Element(XMLTags.ParameterTag);
        // Get parameter attributes
        tempparameter.setAttribute(XMLTags.NameAttrTag, mangle(parm.getName()));
        tempparameter.setAttribute(XMLTags.ParamRoleAttrTag, roleHash.get(parm.getRole()));
        VCUnitDefinition unit = parm.getUnitDefinition();
        if (unit != null) {
            tempparameter.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
        }
        Expression expression = parm.getExpression();
        if (expression != null) {
            tempparameter.addContent(mangleExpression(expression));
        }
        // Add the parameter to the general kinetics object
        kinetics.addContent(tempparameter);
    }
    return kinetics;
}