addingEvidenceCodes_1.cs

Adds controlled vocabulary terms to a reaction in a model.

/**
 * \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) 2013-2018 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.
 *
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 * copy of this software and associated documentation files (the "Software"),
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 * the rights to use, copy, modify, merge, publish, distribute, sublicense,
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 * of the European Bioinformatics Institute (EMBL-EBI), nor of the University
 * of Heidelberg, nor the names of any contributors, may be used to endorse
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using System;
using libsbmlcs;

public class AddingEvidenceCodes1
{
    public static int Main(string[] args)
    {

        SBMLDocument d;

        long errors, n;
        Reaction r;

        if (args.Length != 2)
        {
            Console.Write(Environment.NewLine
                                      + "  usage: addingEvidenceCodes_1 <input-filename> <output-filename>" + Environment.NewLine
                                      + "  Adds controlled vocabulary term to a reaction" + Environment.NewLine
                                      + Environment.NewLine);
            return 2;
        }


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

        if (errors > 0)
        {
            Console.Write("Read Error(s):" + Environment.NewLine);
            d.printErrors();

            Console.Write("Correct the above and re-run." + Environment.NewLine);
        }
        else
        {

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

            if (n <= 0)
            {
                Console.Write("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]);
            }
        }

        return (int)errors;
    }
}