C++ (Cpp) CVTerm::setBiologicalQualifierType Examples

Example #1

File: TestValidation.cpp Project: TotteKarlsson/roadrunner

END_TEST


START_TEST (test_Validation_CVTerm2)
{
  CVTerm * cv = new CVTerm();
  fail_unless(cv != NULL);

  fail_unless (!(cv->hasRequiredAttributes()));

  cv->setQualifierType(BIOLOGICAL_QUALIFIER);

  fail_unless (!(cv->hasRequiredAttributes()));

  cv->setBiologicalQualifierType(BQB_IS);

  fail_unless (!(cv->hasRequiredAttributes()));

  cv->addResource("ggg");

  fail_unless ((cv->hasRequiredAttributes()));
  
  delete cv;
}

Example #2

File: TestRDFAnnotation2.cpp Project: alexholehouse/SBMLIntegrator

END_TEST


START_TEST (test_RDFAnnotation2_modelWithHistoryAndCVTerms)
{
  ModelHistory * h = new ModelHistory();

  ModelCreator *c = new ModelCreator();
  c->setFamilyName("Keating");
  c->setGivenName("Sarah");

  h->addCreator(c);

  Date *d = new Date(2008, 11, 17, 18, 37, 0, 0, 0, 0);
  h->setCreatedDate(d);
  h->setModifiedDate(d);

  m2->unsetModelHistory();

  m2->setModelHistory(h);

  CVTerm *cv = new CVTerm();
  cv->setQualifierType(BIOLOGICAL_QUALIFIER);
  cv->setBiologicalQualifierType(BQB_IS_VERSION_OF);
  cv->addResource("http://www.geneontology.org/#GO:0005892");

  m2->addCVTerm(cv);
  XMLNode *ann = RDFAnnotationParser::parseModelHistory(m2);

  const char * expected =
    "<annotation>\n"
		"  <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
		"    <rdf:Description rdf:about=\"#_000001\">\n"
		"      <dc:creator rdf:parseType=\"Resource\">\n"
		"        <rdf:Bag>\n"
		"          <rdf:li rdf:parseType=\"Resource\">\n"
		"            <vCard:N rdf:parseType=\"Resource\">\n"
		"              <vCard:Family>Keating</vCard:Family>\n"
		"              <vCard:Given>Sarah</vCard:Given>\n"
		"            </vCard:N>\n"
		"          </rdf:li>\n"
		"        </rdf:Bag>\n"
		"      </dc:creator>\n"
    "      <dcterms:created rdf:parseType=\"Resource\">\n"
    "        <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n"
    "      </dcterms:created>\n"
    "      <dcterms:modified rdf:parseType=\"Resource\">\n"
    "        <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n"
    "      </dcterms:modified>\n"
		"      <bqbiol:isVersionOf>\n"
		"        <rdf:Bag>\n"
		"          <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005892\"/>\n"
		"        </rdf:Bag>\n"
		"      </bqbiol:isVersionOf>\n"
		"    </rdf:Description>\n"
		"  </rdf:RDF>\n"
    "</annotation>";

  if (ann != NULL) 
  {
    fail_unless( equals(expected, ann->toXMLString().c_str()) );
  }
  else
  {
    fail("parseModelHistory failed");
  }
}

Example #3

File: addCVTerms.cpp Project: copasi/copasi-dependencies

LIBSBML_CPP_NAMESPACE_USE

int
main (int argc, char *argv[])
{

  SBMLDocument* d;
  unsigned int  errors, n;
  Species *s;

  if (argc != 3)
  {
    cout << endl
         << "  usage: addCVTerms <input-filename> <output-filename>" << endl
         << "  Adds controlled vocabulary term to a species"          << endl
         << endl;
    return 2;
  }


  d      = readSBML(argv[1]);
  errors = d->getNumErrors();

  if (errors > 0)
  {
    cout << "Read Error(s):" << endl;
	  d->printErrors(cout);

    cout << "Correct the above and re-run." << endl;
  }
  else
  {
  
    n = d->getModel()->getNumSpecies();
    
    if (n <= 0)
    {
      cout << "Model has no species.\n Cannot add CV terms\n";
    }
    else
    {
      s = d->getModel()->getSpecies(0);

      CVTerm *cv = new CVTerm();
      cv->setQualifierType(BIOLOGICAL_QUALIFIER);
      cv->setBiologicalQualifierType(BQB_IS_VERSION_OF);
      cv->addResource("http://www.geneontology.org/#GO:0005892");

      CVTerm *cv2 = new CVTerm();
      cv2->setQualifierType(BIOLOGICAL_QUALIFIER);
      cv2->setBiologicalQualifierType(BQB_IS);
      cv2->addResource("http://www.geneontology.org/#GO:0005895");

      CVTerm *cv1 = new CVTerm();
      cv1->setQualifierType(BIOLOGICAL_QUALIFIER);
      cv1->setBiologicalQualifierType(BQB_IS_VERSION_OF);
      cv1->addResource("http://www.ebi.ac.uk/interpro/#IPR002394");
      
      s->addCVTerm(cv);
      s->addCVTerm(cv2);
      s->addCVTerm(cv1);

      writeSBML(d, argv[2]);
    }
  }

  delete d;
  return errors;
}