/**
 * \file    addingEvidenceCodes_1.cpp
 * \brief   adds controlled vocabulary terms to a reaction in a model
 * \author  Sarah Keating
 *
 * <!--------------------------------------------------------------------------
 * This sample program is distributed under a different license than the rest
 * of libSBML.  This program uses the open-source MIT license, as follows:
 *
 * Copyright (c) 2013-2017 by the California Institute of Technology
 * (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
 * and the University of Heidelberg (Germany), with support from the National
 * Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
 *
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the "Software"),
 * to deal in the Software without restriction, including without limitation
 * the rights to use, copy, modify, merge, publish, distribute, sublicense,
 * and/or sell copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
 * THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 * DEALINGS IN THE SOFTWARE.
 *
 * Neither the name of the California Institute of Technology (Caltech), nor
 * of the European Bioinformatics Institute (EMBL-EBI), nor of the University
 * of Heidelberg, nor the names of any contributors, may be used to endorse
 * or promote products derived from this software without specific prior
 * written permission.
 * ------------------------------------------------------------------------ -->
 */

import org.sbml.libsbml.CVTerm;
import org.sbml.libsbml.Reaction;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.libsbml;

public class addingEvidenceCodes_1 {
    public static void main(String[] args) {

        System.loadLibrary("sbmlj");

        SBMLDocument d;

        long errors, n;
        Reaction r;

        if (args.length != 2) {
            System.out
                    .print("\n"
                            + "  usage: addingEvidenceCodes_1 <input-filename> <output-filename>"
                            + "\n"
                            + "  Adds controlled vocabulary term to a reaction"
                            + "\n" + "\n");
            System.exit(2);
        }

        d = libsbml.readSBML(args[0]);
        errors = d.getNumErrors();

        if (errors > 0) {
            System.out.print("Read Error(s):" + "\n");
            d.printErrors();

            System.out.print("Correct the above and re-run." + "\n");
        } else {

            n = d.getModel().getNumReactions();

            if (n <= 0) {
                System.out
                        .print("Model has no reactions.\n Cannot add CV terms\n");
            } else {
                r = d.getModel().getReaction(0);

                /*
                 * check that the reaction has a metaid no CVTerms will be added
                 * if there is no metaid to reference
                 */
                if (!r.isSetMetaId())
                    r.setMetaId("metaid_0000052");

                CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
                cv1.setBiologicalQualifierType(libsbml.BQB_IS_DESCRIBED_BY);
                cv1.addResource("urn:miriam:obo.eco:ECO%3A0000183");

                r.addCVTerm(cv1);

                CVTerm cv2 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
                cv2.setBiologicalQualifierType(libsbml.BQB_IS);
                cv2.addResource("urn:miriam:kegg.reaction:R00756");
                cv2.addResource("urn:miriam:reactome:REACT_736");

                r.addCVTerm(cv2);

                libsbml.writeSBML(d, args[1]);
            }
        }

        System.exit( (int) errors);
    }
}
