Examples with ParameterRoleEnum cbit.vcell.mapping.ParameterContext.ParameterRoleEnum used on opensource projects

Example 1 with ParameterRoleEnum

use of cbit.vcell.mapping.ParameterContext.ParameterRoleEnum 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 2 with ParameterRoleEnum

use of cbit.vcell.mapping.ParameterContext.ParameterRoleEnum in project vcell by virtualcell.

the class XmlReader method getRbmReactionRule.

private ReactionRule getRbmReactionRule(Element reactionRuleElement, Model newModel) throws XmlParseException {
    String n = reactionRuleElement.getAttributeValue(XMLTags.NameAttrTag);
    if (n == null || n.isEmpty()) {
        System.out.println("XMLReader: getRbmReactionRule: name is missing.");
        return null;
    }
    try {
        boolean reversible = Boolean.valueOf(reactionRuleElement.getAttributeValue(XMLTags.RbmReactionRuleReversibleTag));
        // get 1st structure if attribute missing
        String structureName = reactionRuleElement.getAttributeValue(XMLTags.StructureAttrTag, newModel.getStructures()[0].getName());
        Structure structure = newModel.getStructure(structureName);
        ReactionRule reactionRule = new ReactionRule(newModel, n, structure, reversible);
        // we ignore this, name and label are the same thing for now
        String reactionRuleLabel = reactionRuleElement.getAttributeValue(XMLTags.RbmReactionRuleLabelTag);
        // 
        // old style kinetics placed parameter values as attributes
        // look for attributes named ("MassActionKf","MassActionKr","MichaelisMentenKcat","MichaelisMentenKm","SaturableKs","SaturableVmax")
        String[] oldKineticsAttributes = new String[] { XMLTags.RbmMassActionKfAttrTag_DEPRECATED, XMLTags.RbmMassActionKrAttrTag_DEPRECATED, XMLTags.RbmMichaelisMentenKcatAttrTag_DEPRECATED, XMLTags.RbmMichaelisMentenKmAttrTag_DEPRECATED, XMLTags.RbmSaturableKsAttrTag_DEPRECATED, XMLTags.RbmSaturableVmaxAttrTag_DEPRECATED };
        boolean bOldKineticsFound = false;
        for (String oldKineticsAttribute : oldKineticsAttributes) {
            if (reactionRuleElement.getAttribute(oldKineticsAttribute) != null) {
                bOldKineticsFound = true;
            }
        }
        if (bOldKineticsFound) {
            readOldRbmKineticsAttributes(reactionRuleElement, reactionRule);
        } else {
            Element kineticsElement = reactionRuleElement.getChild(XMLTags.KineticsTag, vcNamespace);
            if (kineticsElement != null) {
                String kineticLawTypeString = kineticsElement.getAttributeValue(XMLTags.KineticsTypeAttrTag);
                RbmKineticLaw.RateLawType rateLawType = null;
                if (XMLTags.RbmKineticTypeMassAction.equals(kineticLawTypeString)) {
                    rateLawType = RateLawType.MassAction;
                } else if (XMLTags.RbmKineticTypeMichaelisMenten.equals(kineticLawTypeString)) {
                    rateLawType = RateLawType.MichaelisMenten;
                } else if (XMLTags.RbmKineticTypeSaturable.equals(kineticLawTypeString)) {
                    rateLawType = RateLawType.Saturable;
                } else {
                    throw new RuntimeException("unexpected rate law type " + kineticLawTypeString);
                }
                reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, rateLawType));
                List<Element> parameterElements = kineticsElement.getChildren(XMLTags.ParameterTag, vcNamespace);
                HashMap<String, ParameterRoleEnum> roleHash = new HashMap<String, ParameterContext.ParameterRoleEnum>();
                roleHash.put(XMLTags.RbmMassActionKfRole, RbmKineticLawParameterType.MassActionForwardRate);
                roleHash.put(XMLTags.RbmMassActionKrRole, RbmKineticLawParameterType.MassActionReverseRate);
                roleHash.put(XMLTags.RbmMichaelisMentenKcatRole, RbmKineticLawParameterType.MichaelisMentenKcat);
                roleHash.put(XMLTags.RbmMichaelisMentenKmRole, RbmKineticLawParameterType.MichaelisMentenKm);
                roleHash.put(XMLTags.RbmSaturableVmaxRole, RbmKineticLawParameterType.SaturableVmax);
                roleHash.put(XMLTags.RbmSaturableKsRole, RbmKineticLawParameterType.SaturableKs);
                roleHash.put(XMLTags.RbmUserDefinedRole, RbmKineticLawParameterType.UserDefined);
                HashSet<String> xmlRolesToIgnore = new HashSet<String>();
                xmlRolesToIgnore.add(XMLTags.RbmRuleRateRole);
                ParameterContext parameterContext = reactionRule.getKineticLaw().getParameterContext();
                readParameters(parameterElements, parameterContext, roleHash, RbmKineticLawParameterType.UserDefined, xmlRolesToIgnore, newModel);
            }
        }
        Element e1 = reactionRuleElement.getChild(XMLTags.RbmReactantPatternsListTag, vcNamespace);
        getRbmReactantPatternsList(e1, reactionRule, newModel);
        Element e2 = reactionRuleElement.getChild(XMLTags.RbmProductPatternsListTag, vcNamespace);
        getRbmProductPatternsList(e2, reactionRule, newModel);
        reactionRule.checkMatchConsistency();
        return reactionRule;
    } catch (PropertyVetoException | ExpressionException ex) {
        ex.printStackTrace(System.out);
        throw new RuntimeException("failed to parse kinetics for reaction rule '" + n + "': " + ex.getMessage(), ex);
    }
}

Example 3 with ParameterRoleEnum

use of cbit.vcell.mapping.ParameterContext.ParameterRoleEnum 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;
}