Examples with FunctionDefinition org.sbml.jsbml.FunctionDefinition used on opensource projects

Example 1 with FunctionDefinition

use of org.sbml.jsbml.FunctionDefinition in project vcell by virtualcell.

the class SBMLImporter method addFunctionDefinitions.

private void addFunctionDefinitions() {
    if (sbmlModel == null) {
        throw new SBMLImportException("SBML model is NULL");
    }
    ListOf<FunctionDefinition> listofFunctionDefinitions = sbmlModel.getListOfFunctionDefinitions();
    if (listofFunctionDefinitions == null) {
        System.out.println("No Function Definitions");
        return;
    }
    // The function definitions contain lambda function definition.
    // Each lambda function has a name, (list of) argument(s), function body
    // which is represented as a math element.
    lambdaFunctions = new LambdaFunction[(int) sbmlModel.getNumFunctionDefinitions()];
    try {
        for (int i = 0; i < sbmlModel.getNumFunctionDefinitions(); i++) {
            FunctionDefinition fnDefn = (FunctionDefinition) listofFunctionDefinitions.get(i);
            String functionName = new String(fnDefn.getId());
            ASTNode math = null;
            Vector<String> argsVector = new Vector<String>();
            Vector<String> secureArgsVector = new Vector<>();
            String[] functionArgs = null;
            if (fnDefn.isSetMath()) {
                math = fnDefn.getMath();
                // Function body.
                if (math.getNumChildren() == 0) {
                    System.out.println("(no function body defined)");
                    continue;
                }
                // Note that lambda function always should have at least 2 children
                for (int j = 0; j < math.getNumChildren() - 1; ++j) {
                    String baseName = new String(math.getChild(j).getName());
                    argsVector.addElement(baseName);
                    secureArgsVector.addElement(baseName + "_" + functionName + FormalArgumentSuffix);
                }
                functionArgs = secureArgsVector.toArray(new String[0]);
                math = math.getChild(math.getNumChildren() - 1);
                // formula = libsbml.formulaToString(math);
                Expression fnExpr = getExpressionFromFormula(math);
                for (int j = 0; j < argsVector.size(); j++) {
                    fnExpr.substituteInPlace(new Expression(argsVector.get(j)), new Expression(secureArgsVector.get(j)));
                }
                lambdaFunctions[i] = new LambdaFunction(functionName, fnExpr, functionArgs);
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Error adding Lambda function" + e.getMessage(), e);
    }
}