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

Example 31 with Expression

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

the class XmlReader method getMembraneRegionEquation.

/**
 * This method returns a MembraneRegionEquation from a XML Element.
 * Creation date: (5/17/2001 3:52:40 PM)
 * @return cbit.vcell.math.MembraneRegionEquation
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private MembraneRegionEquation getMembraneRegionEquation(Element param, MathDescription mathDesc) throws XmlParseException {
    // get attributes
    String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // find reference in the dictionnary
    // try a MembraneRegionVariable
    MembraneRegionVariable varref = (MembraneRegionVariable) mathDesc.getVariable(varname);
    if (varref == null) {
        throw new XmlParseException("The reference to the MembraneRegion variable " + varname + " could not be resolved!");
    }
    // get Initial condition
    String temp = param.getChildText(XMLTags.InitialTag, vcNamespace);
    Expression exp;
    exp = unMangleExpression(temp);
    // ** Create the Equation **
    MembraneRegionEquation memRegEq = new MembraneRegionEquation(varref, exp);
    // set the Uniform Rate
    temp = param.getChildText(XMLTags.UniformRateTag, vcNamespace);
    exp = unMangleExpression(temp);
    memRegEq.setUniformRateExpression(exp);
    // set the Membrane Rate
    temp = param.getChildText(XMLTags.MembraneRateTag, vcNamespace);
    exp = unMangleExpression(temp);
    memRegEq.setMembraneRateExpression(exp);
    return memRegEq;
}

Example 32 with Expression

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

the class XmlReader method readParameters.

private void readParameters(List<Element> parameterElements, ParameterContext parameterContext, HashMap<String, ParameterRoleEnum> roleHash, ParameterRoleEnum userDefinedRole, HashSet<String> xmlRolesTagsToIgnore, Model model) throws XmlParseException {
    String contextName = parameterContext.getNameScope().getName();
    try {
        // 
        // prepopulate varHash with reserved symbols
        // 
        VariableHash varHash = new VariableHash();
        addResevedSymbols(varHash, model);
        // 
        for (Element xmlParam : parameterElements) {
            String parsedParamName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
            String parsedRoleString = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
            String parsedExpressionString = xmlParam.getText();
            // 
            if (xmlRolesTagsToIgnore.contains(parsedRoleString)) {
                varHash.removeVariable(parsedParamName);
                continue;
            }
            Expression paramExp = null;
            if (parsedExpressionString.trim().length() > 0) {
                paramExp = unMangleExpression(parsedExpressionString);
            }
            if (varHash.getVariable(parsedParamName) == null) {
                Domain domain = null;
                varHash.addVariable(new Function(parsedParamName, paramExp, domain));
            } else {
                if (model.getReservedSymbolByName(parsedParamName) != null) {
                    varHash.removeVariable(parsedParamName);
                    Domain domain = null;
                    varHash.addVariable(new Function(parsedParamName, paramExp, domain));
                }
            }
            // 
            // get the parameter for this xml role string
            // 
            ParameterRoleEnum paramRole = roleHash.get(parsedRoleString);
            if (paramRole == null) {
                throw new XmlParseException("parameter '" + parsedParamName + "' has unexpected role '" + parsedRoleString + "' in '" + contextName + "'");
            }
            // 
            if (paramRole != userDefinedRole) {
                LocalParameter paramWithSameRole = parameterContext.getLocalParameterFromRole(paramRole);
                if (paramWithSameRole == null) {
                    throw new XmlParseException("can't find parameter with role '" + parsedRoleString + "' in '" + contextName + "'");
                }
                // 
                if (!paramWithSameRole.getName().equals(parsedParamName)) {
                    // 
                    // first rename other parameters with same name
                    // 
                    LocalParameter paramWithSameNameButDifferentRole = parameterContext.getLocalParameterFromName(parsedParamName);
                    if (paramWithSameNameButDifferentRole != null) {
                        // 
                        // find available name
                        // 
                        int n = 0;
                        String newName = parsedParamName + "_" + n++;
                        while (parameterContext.getEntry(newName) != null) {
                            newName = parsedParamName + "_" + n++;
                        }
                        parameterContext.renameLocalParameter(parsedParamName, newName);
                    }
                    // 
                    // then rename parameter with correct role
                    // 
                    parameterContext.renameLocalParameter(paramWithSameRole.getName(), parsedParamName);
                }
            }
        }
        // 
        // create unresolved parameters for all unresolved symbols
        // 
        String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        while (unresolvedSymbol != null) {
            try {
                Domain domain = null;
                // will turn into an UnresolvedParameter.
                varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), domain));
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e.getMessage());
            }
            parameterContext.addUnresolvedParameter(unresolvedSymbol);
            unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        }
        // 
        // in topological order, add parameters to model (getting units also).
        // note that all pre-defined parameters already have the correct names
        // here we set expressions on pre-defined parameters and add user-defined parameters
        // 
        Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
        ModelUnitSystem modelUnitSystem = model.getUnitSystem();
        for (int i = sortedVariables.length - 1; i >= 0; i--) {
            if (sortedVariables[i] instanceof Function) {
                Function paramFunction = (Function) sortedVariables[i];
                Element xmlParam = null;
                for (int j = 0; j < parameterElements.size(); j++) {
                    Element tempParam = (Element) parameterElements.get(j);
                    if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
                        xmlParam = tempParam;
                        break;
                    }
                }
                if (xmlParam == null) {
                    // must have been an unresolved parameter
                    continue;
                }
                String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                VCUnitDefinition unit = null;
                if (symbol != null) {
                    unit = modelUnitSystem.getInstance(symbol);
                }
                LocalParameter tempParam = parameterContext.getLocalParameterFromName(paramFunction.getName());
                if (tempParam == null) {
                    tempParam = parameterContext.addLocalParameter(paramFunction.getName(), new Expression(0.0), userDefinedRole, unit, userDefinedRole.getDescription());
                    parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true);
                } else {
                    if (tempParam.getExpression() != null) {
                        // if the expression is null, it should remain null.
                        parameterContext.setParameterValue(tempParam, paramFunction.getExpression(), true);
                    }
                    tempParam.setUnitDefinition(unit);
                }
            }
        }
    } catch (PropertyVetoException | ExpressionException | MathException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while setting parameters for '" + contextName + "': " + e.getMessage(), e);
    }
}

Example 33 with Expression

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

the class XmlReader method getJumpCondition.

/**
 * This method returns a JumpCondition object from a XML Element.
 * Creation date: (5/18/2001 5:10:10 PM)
 * @return cbit.vcell.math.JumpCondition
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private JumpCondition getJumpCondition(Element param, MathDescription mathDesc) throws XmlParseException {
    // get VolVariable ref
    String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Variable var = mathDesc.getVariable(varname);
    if (var == null) {
        throw new XmlParseException("The reference to the Variable " + varname + ", could not be resolved!");
    }
    JumpCondition jumpCondition = null;
    if (var instanceof VolVariable) {
        jumpCondition = new JumpCondition((VolVariable) var);
    } else if (var instanceof VolumeRegionVariable) {
        jumpCondition = new JumpCondition((VolumeRegionVariable) var);
    } else {
        throw new XmlParseException("unexpected variable type for jump condition");
    }
    // process InFlux
    String temp = param.getChildText(XMLTags.InFluxTag, vcNamespace);
    Expression exp = unMangleExpression(temp);
    jumpCondition.setInFlux(exp);
    // process OutFlux
    temp = param.getChildText(XMLTags.OutFluxTag, vcNamespace);
    exp = unMangleExpression(temp);
    jumpCondition.setOutFlux(exp);
    return jumpCondition;
}

Example 34 with Expression

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

the class XmlReader method getParticleJumpProcess.

private ParticleJumpProcess getParticleJumpProcess(Element param, MathDescription md) throws XmlParseException {
    // name
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    ProcessSymmetryFactor processSymmetryFactor = null;
    Attribute symmetryFactorAttr = param.getAttribute(XMLTags.ProcessSymmetryFactorAttrTag);
    if (symmetryFactorAttr != null) {
        processSymmetryFactor = new ProcessSymmetryFactor(Double.parseDouble(symmetryFactorAttr.getValue()));
    }
    // selected particle
    List<ParticleVariable> varList = new ArrayList<ParticleVariable>();
    Iterator<Element> iterator = param.getChildren(XMLTags.SelectedParticleTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        String varname = unMangle(tempelement.getAttributeValue(XMLTags.NameAttrTag));
        Variable var = md.getVariable(varname);
        if (!(var instanceof ParticleVariable)) {
            throw new XmlParseException("Not a ParticleVariable in ParticleJumpProcess.");
        }
        varList.add((ParticleVariable) var);
    }
    // probability rate
    JumpProcessRateDefinition jprd = null;
    // for old models
    Element pb = param.getChild(XMLTags.ParticleProbabilityRateTag, vcNamespace);
    if (pb != null) {
        Expression exp = unMangleExpression(pb.getText());
        jprd = new MacroscopicRateConstant(exp);
    } else // for new models
    {
        pb = param.getChild(XMLTags.MacroscopicRateConstantTag, vcNamespace);
        if (// jump process rate defined by macroscopic rate constant
        pb != null) {
            Expression exp = unMangleExpression(pb.getText());
            jprd = new MacroscopicRateConstant(exp);
        } else // jump process rate defined by binding radius
        {
            pb = param.getChild(XMLTags.InteractionRadiusTag, vcNamespace);
            if (pb != null) {
                Expression exp = unMangleExpression(pb.getText());
                jprd = new InteractionRadius(exp);
            }
        }
    }
    // add actions
    List<Action> actionList = new ArrayList<Action>();
    iterator = param.getChildren(XMLTags.ActionTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            actionList.add(getAction(tempelement, md));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        } catch (ExpressionException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    ParticleJumpProcess jump = new ParticleJumpProcess(name, varList, jprd, actionList, processSymmetryFactor);
    return jump;
}

Example 35 with Expression

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

the class XmlReader method getAction.

/**
 * This method returns a Action object from a XML element.
 * Creation date: (7/24/2006 5:56:36 PM)
 * @return cbit.vcell.math.Action
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private Action getAction(Element param, MathDescription md) throws XmlParseException, MathException, ExpressionException {
    // retrieve values
    String operation = unMangle(param.getAttributeValue(XMLTags.OperationAttrTag));
    String operand = param.getText();
    Expression exp = null;
    if (operand != null && operand.length() != 0) {
        exp = unMangleExpression(operand);
    }
    String name = unMangle(param.getAttributeValue(XMLTags.VarNameAttrTag));
    Variable var = md.getVariable(name);
    if (var == null) {
        throw new MathFormatException("variable " + name + " not defined");
    }
    if (!(var instanceof StochVolVariable) && !(var instanceof ParticleVariable)) {
        throw new MathFormatException("variable " + name + " not a Stochastic Volume Variable");
    }
    try {
        Action action = new Action(var, operation, exp);
        return action;
    } catch (Exception e) {
        e.printStackTrace();
    }
    return null;
}