LibSBML addCustomValidator.java

/**
 * @file    addCustomValidator.cpp
 * @brief   Example creating a custom validator to be called during validation
 * @author  Frank T. Bergmann
 *
 * 
 */

import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.SBMLError;
import org.sbml.libsbml.SBMLValidator;
import org.sbml.libsbml.libsbml;

/**
 * Declares a custom validator to be called. This allows you to validate any
 * aspect of an SBML Model that you want to be notified about. You could use
 * this to notify your application that a model contains an unsupported feature
 * of SBML (either as warning).
 * 
 * In this example the validator will go through the model and test for the
 * presence of 'fast' reactions and algebraic rules. If either is used a warning
 * will be added to the error log.
 */
public class addCustomValidator extends SBMLValidator {
    public addCustomValidator() {
        super();
    }

    public addCustomValidator(addCustomValidator orig) {
        super(orig);
    }

    public @Override
    SBMLValidator clone() {
        return new addCustomValidator(this);
    }

    public @Override
    long validate() {
        // if we don't have a model we don't apply this validator.
        if (getDocument() == null || getModel() == null)
            return 0;

        // if we have no rules and reactions we don't apply this validator
        // either
        if (getModel().getNumReactions() == 0 && getModel().getNumRules() == 0)
            return 0;

        int numErrors = 0;
        // test for algebraic rules
        for (int i = 0; i < getModel().getNumRules(); i++) {
            if (getModel().getRule(i).getTypeCode() == libsbml.SBML_ALGEBRAIC_RULE) {

                getErrorLog()
                        .add(new SBMLError(
                                99999,
                                3,
                                1,
                                "This model uses algebraic rules, however this application does not support them.",
                                0, 0, libsbml.LIBSBML_SEV_WARNING, // or
                                                                    // LIBSBML_SEV_ERROR
                                                                    // if you
                                                                    // want to
                                                                    // stop
                                libsbml.LIBSBML_CAT_SBML // or whatever category
                                                            // you prefer
                        ));

                numErrors++;
            }
        }

        // test for fast reactions
        for (int i = 0; i < getModel().getNumReactions(); i++) {
            // test whether value is set, and true
            if (getModel().getReaction(i).isSetFast()
                    && getModel().getReaction(i).getFast()) {

                getErrorLog()
                        .add(new SBMLError(
                                99999,
                                3,
                                1,
                                "This model uses fast reactions, however this application does not support them.",
                                0, 0, libsbml.LIBSBML_SEV_WARNING, // or
                                                                    // LIBSBML_SEV_ERROR
                                                                    // if you
                                                                    // want to
                                                                    // stop
                                libsbml.LIBSBML_CAT_SBML // or whatever category
                                                            // you prefer
                        ));

                numErrors++;

            }
        }

        return numErrors;
    }

    public static void main(String[] args) {
        if (args.length != 1) {
            System.out.println("Usage: addCustomValidator filename");
            System.exit(1);
        }

        System.loadLibrary("sbmlj");

        // read the file name
        SBMLDocument document = libsbml.readSBML(args[0]);

        // add a custom validator
        document.addValidator(new addCustomValidator());

        // check consistency like before
        int numErrors = (int) document.checkConsistency();

        // print errors and warnings
        document.printErrors();

        // return number of errors
        System.exit(numErrors);

    }

};

LibSBML, an application programming interface (API) library for SBML.

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