public void test_XMLNode_create() {
   XMLNode node = new XMLNode();
   assertTrue(node != null);
   assertTrue(node.getNumChildren() == 0);
   node = null;
   node = new XMLNode();
   assertTrue(node != null);
   XMLNode node2 = new XMLNode();
   assertTrue(node2 != null);
   node.addChild(node2);
   assertTrue(node.getNumChildren() == 1);
   XMLNode node3 = new XMLNode();
   assertTrue(node3 != null);
   node.addChild(node3);
   assertTrue(node.getNumChildren() == 2);
   node = null;
   node2 = null;
   node3 = null;
 }
  public static void main(String[] args) {
    System.loadLibrary("sbmlj");

    if (args.length != 2) {
      System.out.println("  usage: addingEvidenceCodes_2 <input-filename> <output-filename>");
      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

        // <rdf:Statement>
        // <rdf:subject rdf:resource="#metaid_0000052"/>
        // <rdf:predicate
        // rdf:resource="http://biomodels.net/biology-qualifiers/occursIn"/>
        // <rdf:object rdf:resource="urn:miriam:obo.go:GO%3A0005764"/>
        // <bqbiol:isDescribedBy>
        // <rdf:Bag>
        // <rdf:li rdf:resource="urn:miriam:obo.eco:ECO%3A0000004"/>
        // <rdf:li rdf:resource="urn:miriam:pubmed:7017716"/>
        // </rdf:Bag>
        // </bqbiol:isDescribedBy>
        // </rdf:Statement>

        /* 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);
  }
 public void test_XMLNode_remove() {
   XMLAttributes attr = new XMLAttributes();
   XMLTriple trp_p = new XMLTriple("parent", "", "");
   XMLTriple trp_c1 = new XMLTriple("child1", "", "");
   XMLTriple trp_c2 = new XMLTriple("child2", "", "");
   XMLTriple trp_c3 = new XMLTriple("child3", "", "");
   XMLTriple trp_c4 = new XMLTriple("child4", "", "");
   XMLTriple trp_c5 = new XMLTriple("child5", "", "");
   XMLNode p = new XMLNode(trp_p, attr);
   XMLNode c1 = new XMLNode(trp_c1, attr);
   XMLNode c2 = new XMLNode(trp_c2, attr);
   XMLNode c3 = new XMLNode(trp_c3, attr);
   XMLNode c4 = new XMLNode(trp_c4, attr);
   XMLNode c5 = new XMLNode(trp_c5, attr);
   XMLNode r;
   p.addChild(c1);
   p.addChild(c2);
   p.addChild(c3);
   p.addChild(c4);
   p.addChild(c5);
   r = p.removeChild(5);
   assertTrue(r == null);
   r = p.removeChild(1);
   assertTrue(p.getNumChildren() == 4);
   assertTrue(!r.getName().equals("child2") == false);
   r = null;
   r = p.removeChild(3);
   assertTrue(p.getNumChildren() == 3);
   assertTrue(!r.getName().equals("child5") == false);
   r = null;
   r = p.removeChild(0);
   assertTrue(p.getNumChildren() == 2);
   assertTrue(!r.getName().equals("child1") == false);
   r = null;
   r = p.removeChild(1);
   assertTrue(p.getNumChildren() == 1);
   assertTrue(!r.getName().equals("child4") == false);
   r = null;
   r = p.removeChild(0);
   assertTrue(p.getNumChildren() == 0);
   assertTrue(!r.getName().equals("child3") == false);
   r = null;
   p.addChild(c1);
   p.addChild(c2);
   p.addChild(c3);
   p.addChild(c4);
   p.addChild(c5);
   r = p.removeChild(4);
   assertTrue(p.getNumChildren() == 4);
   assertTrue(!r.getName().equals("child5") == false);
   r = null;
   r = p.removeChild(3);
   assertTrue(p.getNumChildren() == 3);
   assertTrue(!r.getName().equals("child4") == false);
   r = null;
   r = p.removeChild(2);
   assertTrue(p.getNumChildren() == 2);
   assertTrue(!r.getName().equals("child3") == false);
   r = null;
   r = p.removeChild(1);
   assertTrue(p.getNumChildren() == 1);
   assertTrue(!r.getName().equals("child2") == false);
   r = null;
   r = p.removeChild(0);
   assertTrue(p.getNumChildren() == 0);
   assertTrue(!r.getName().equals("child1") == false);
   r = null;
   p.addChild(c1);
   p.addChild(c2);
   p.addChild(c3);
   p.addChild(c4);
   p.addChild(c5);
   r = p.removeChild(0);
   assertTrue(p.getNumChildren() == 4);
   assertTrue(!r.getName().equals("child1") == false);
   r = null;
   r = p.removeChild(0);
   assertTrue(p.getNumChildren() == 3);
   assertTrue(!r.getName().equals("child2") == false);
   r = null;
   r = p.removeChild(0);
   assertTrue(p.getNumChildren() == 2);
   assertTrue(!r.getName().equals("child3") == false);
   r = null;
   r = p.removeChild(0);
   assertTrue(p.getNumChildren() == 1);
   assertTrue(!r.getName().equals("child4") == false);
   r = null;
   r = p.removeChild(0);
   assertTrue(p.getNumChildren() == 0);
   assertTrue(!r.getName().equals("child5") == false);
   r = null;
   p.addChild(c1);
   p.addChild(c2);
   p.addChild(c3);
   p.addChild(c4);
   p.addChild(c5);
   r = p.removeChild(0);
   assertTrue(!r.getName().equals("child1") == false);
   p.insertChild(0, r);
   assertTrue(p.getNumChildren() == 5);
   assertTrue(!p.getChild(0).getName().equals("child1") == false);
   r = null;
   r = p.removeChild(1);
   assertTrue(!r.getName().equals("child2") == false);
   p.insertChild(1, r);
   assertTrue(p.getNumChildren() == 5);
   assertTrue(!p.getChild(1).getName().equals("child2") == false);
   r = null;
   r = p.removeChild(2);
   assertTrue(!r.getName().equals("child3") == false);
   p.insertChild(2, r);
   assertTrue(p.getNumChildren() == 5);
   assertTrue(!p.getChild(2).getName().equals("child3") == false);
   r = null;
   r = p.removeChild(3);
   assertTrue(!r.getName().equals("child4") == false);
   p.insertChild(3, r);
   assertTrue(p.getNumChildren() == 5);
   assertTrue(!p.getChild(3).getName().equals("child4") == false);
   r = null;
   r = p.removeChild(4);
   assertTrue(!r.getName().equals("child5") == false);
   p.insertChild(4, r);
   assertTrue(p.getNumChildren() == 5);
   assertTrue(!p.getChild(4).getName().equals("child5") == false);
   r = null;
   p = null;
   c1 = null;
   c2 = null;
   c3 = null;
   c4 = null;
   c5 = null;
   attr = null;
   trp_p = null;
   trp_c1 = null;
   trp_c2 = null;
   trp_c3 = null;
   trp_c4 = null;
   trp_c5 = null;
 }
 public void test_XMLNode_insert() {
   XMLAttributes attr = new XMLAttributes();
   XMLTriple trp_p = new XMLTriple("parent", "", "");
   XMLTriple trp_c1 = new XMLTriple("child1", "", "");
   XMLTriple trp_c2 = new XMLTriple("child2", "", "");
   XMLTriple trp_c3 = new XMLTriple("child3", "", "");
   XMLTriple trp_c4 = new XMLTriple("child4", "", "");
   XMLTriple trp_c5 = new XMLTriple("child5", "", "");
   XMLNode p = new XMLNode(trp_p, attr);
   XMLNode c1 = new XMLNode(trp_c1, attr);
   XMLNode c2 = new XMLNode(trp_c2, attr);
   XMLNode c3 = new XMLNode(trp_c3, attr);
   XMLNode c4 = new XMLNode(trp_c4, attr);
   XMLNode c5 = new XMLNode(trp_c5, attr);
   p.addChild(c2);
   p.addChild(c4);
   p.insertChild(0, c1);
   p.insertChild(2, c3);
   p.insertChild(4, c5);
   assertTrue(p.getNumChildren() == 5);
   assertTrue(!p.getChild(0).getName().equals("child1") == false);
   assertTrue(!p.getChild(1).getName().equals("child2") == false);
   assertTrue(!p.getChild(2).getName().equals("child3") == false);
   assertTrue(!p.getChild(3).getName().equals("child4") == false);
   assertTrue(!p.getChild(4).getName().equals("child5") == false);
   p.removeChildren();
   p.insertChild(0, c1);
   p.insertChild(0, c2);
   p.insertChild(0, c3);
   p.insertChild(0, c4);
   p.insertChild(0, c5);
   assertTrue(p.getNumChildren() == 5);
   assertTrue(!p.getChild(0).getName().equals("child5") == false);
   assertTrue(!p.getChild(1).getName().equals("child4") == false);
   assertTrue(!p.getChild(2).getName().equals("child3") == false);
   assertTrue(!p.getChild(3).getName().equals("child2") == false);
   assertTrue(!p.getChild(4).getName().equals("child1") == false);
   p.removeChildren();
   p.insertChild(1, c1);
   p.insertChild(2, c2);
   p.insertChild(3, c3);
   p.insertChild(4, c4);
   p.insertChild(5, c5);
   assertTrue(p.getNumChildren() == 5);
   assertTrue(!p.getChild(0).getName().equals("child1") == false);
   assertTrue(!p.getChild(1).getName().equals("child2") == false);
   assertTrue(!p.getChild(2).getName().equals("child3") == false);
   assertTrue(!p.getChild(3).getName().equals("child4") == false);
   assertTrue(!p.getChild(4).getName().equals("child5") == false);
   p.removeChildren();
   XMLNode tmp;
   tmp = p.insertChild(0, c1);
   assertTrue(!tmp.getName().equals("child1") == false);
   tmp = p.insertChild(0, c2);
   assertTrue(!tmp.getName().equals("child2") == false);
   tmp = p.insertChild(0, c3);
   assertTrue(!tmp.getName().equals("child3") == false);
   tmp = p.insertChild(0, c4);
   assertTrue(!tmp.getName().equals("child4") == false);
   tmp = p.insertChild(0, c5);
   assertTrue(!tmp.getName().equals("child5") == false);
   p.removeChildren();
   tmp = p.insertChild(1, c1);
   assertTrue(!tmp.getName().equals("child1") == false);
   tmp = p.insertChild(2, c2);
   assertTrue(!tmp.getName().equals("child2") == false);
   tmp = p.insertChild(3, c3);
   assertTrue(!tmp.getName().equals("child3") == false);
   tmp = p.insertChild(4, c4);
   assertTrue(!tmp.getName().equals("child4") == false);
   tmp = p.insertChild(5, c5);
   assertTrue(!tmp.getName().equals("child5") == false);
   p = null;
   c1 = null;
   c2 = null;
   c3 = null;
   c4 = null;
   c5 = null;
   attr = null;
   trp_p = null;
   trp_c1 = null;
   trp_c2 = null;
   trp_c3 = null;
   trp_c4 = null;
   trp_c5 = null;
 }