LibSBML addingEvidenceCodes_2.java

/**
 * \file    addingEvidenceCodes_2.cpp
 * \brief   adds evidence codes to a species in a model
 * \author  Sarah Keating
 *
 * 
 */

import org.sbml.libsbml.CVTerm;
import org.sbml.libsbml.SBMLDocument;
import org.sbml.libsbml.Species;
import org.sbml.libsbml.XMLAttributes;
import org.sbml.libsbml.XMLNamespaces;
import org.sbml.libsbml.XMLNode;
import org.sbml.libsbml.XMLToken;
import org.sbml.libsbml.XMLTriple;
import org.sbml.libsbml.libsbml;

public class addingEvidenceCodes_2 {
    public static void main(String[] args) {
        System.loadLibrary("sbmlj");

        if (args.length != 2) {
            System.out
                    .println("  usage: addingEvidenceCodes_2  ");
            System.out
                    .println("  Adds controlled vocabulary term to a species");
            System.out.println();
            System.exit( 2);
        }

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

        if (errors > 0) {
            System.out.println("Read Error(s):");
            d.printErrors();

            System.out.println("Correct the above and re-run.");
        } else {
            long n = d.getModel().getNumSpecies();

            if (n <= 0) {
                System.out
                        .println("Model has no species.\n Cannot add CV terms\n");
            } else {
                Species s = d.getModel().getSpecies(0);

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

                CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
                cv1.setBiologicalQualifierType(libsbml.BQB_OCCURS_IN);
                cv1.addResource("urn:miriam:obo.go:GO%3A0005764");

                s.addCVTerm(cv1);

                // now create the additional annotation

                // 
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                // 

                /* attributes */
                XMLAttributes blank_att = new XMLAttributes();

                XMLAttributes resource_att = new XMLAttributes();

                /* create the outer statement node */
                XMLTriple statement_triple = new XMLTriple("Statement",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                XMLToken statement_token = new XMLToken(statement_triple,
                        blank_att);

                XMLNode statement = new XMLNode(statement_token);

                /* create the subject node */
                XMLTriple subject_triple = new XMLTriple("subject",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                resource_att.clear();
                resource_att.add("rdf:resource", "#" + s.getMetaId());

                XMLToken subject_token = new XMLToken(subject_triple,
                        resource_att);

                XMLNode subject = new XMLNode(subject_token);

                /* create the predicate node */
                XMLTriple predicate_triple = new XMLTriple("predicate",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                resource_att.clear();
                resource_att.add("rdf:resource",
                        "http://biomodels.net/biology-qualifiers/occursIn");

                XMLToken predicate_token = new XMLToken(predicate_triple,
                        resource_att);

                XMLNode predicate = new XMLNode(predicate_token);

                /* create the object node */
                XMLTriple object_triple = new XMLTriple("object",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                resource_att.clear();
                resource_att.add("rdf:resource",
                        "urn:miriam:obo.go:GO%3A0005764");

                XMLToken object_token = new XMLToken(object_triple,
                        resource_att);

                XMLNode object_ = new XMLNode(object_token);

                /* create the bqbiol node */
                XMLTriple bqbiol_triple = new XMLTriple("isDescribedBy",
                        "http://biomodels.net/biology-qualifiers/", "bqbiol");

                XMLToken bqbiol_token = new XMLToken(bqbiol_triple, blank_att);

                XMLNode bqbiol = new XMLNode(bqbiol_token);

                /* create the bag node */
                XMLTriple bag_triple = new XMLTriple("Bag",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                XMLToken bag_token = new XMLToken(bag_triple, blank_att);

                XMLNode bag = new XMLNode(bag_token);

                /* create each li node and add to the bag */
                XMLTriple li_triple = new XMLTriple("li",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                resource_att.clear();
                resource_att.add("rdf:resource",
                        "urn:miriam:obo.eco:ECO%3A0000004");

                XMLToken li_token = new XMLToken(li_triple, resource_att);
                li_token.setEnd();

                XMLNode li = new XMLNode(li_token);

                bag.addChild(li);

                resource_att.clear();
                resource_att.add("rdf:resource", "urn:miriam:pubmed:7017716");
                li_token = new XMLToken(li_triple, resource_att);
                li_token.setEnd();
                li = new XMLNode(li_token);

                bag.addChild(li);

                /* add the bag to bqbiol */
                bqbiol.addChild(bag);

                /* add subject, predicate, object and bqbiol to statement */
                statement.addChild(subject);
                statement.addChild(predicate);
                statement.addChild(object_);
                statement.addChild(bqbiol);

                /*
                 * create a top-level RDF element this will ensure correct
                 * merging
                 */

                XMLNamespaces xmlns = new XMLNamespaces();
                xmlns.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
                xmlns.add("http://purl.org/dc/elements/1.1/", "dc");
                xmlns.add("http://purl.org/dc/terms/", "dcterms");
                xmlns.add("http://www.w3.org/2001/vcard-rdf/3.0#", "vCard");
                xmlns.add("http://biomodels.net/biology-qualifiers/", "bqbiol");
                xmlns.add("http://biomodels.net/model-qualifiers/", "bqmodel");

                XMLTriple RDF_triple = new XMLTriple("RDF",
                        "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");

                XMLToken RDF_token = new XMLToken(RDF_triple, blank_att, xmlns);

                XMLNode annotation = new XMLNode(RDF_token);

                /* add the staement node to the RDF node */
                annotation.addChild(statement);

                s.appendAnnotation(annotation);

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

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

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

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