LibSBML addingEvidenceCodes_1.java

/**
 * \file    addingEvidenceCodes_1.cpp
 * \brief   adds controlled vocabulary terms to a reaction in a model
 * \author  Sarah Keating
 *
 * 
 */

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  "
                            + "\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);
    }
}

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

SBML Team http://www.sbml.org/ sbml-team@googlegroups.com