public void classifyOntology(OWLOntology ontology, OWLReasonerFactory factory) {
   ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
   OWLReasoner reasoner = factory.createNonBufferingReasoner(ontology);
   // reasoner.precomputeInferences(InferenceType.values());
   long time = System.currentTimeMillis();
   boolean isConsistent = reasoner.isConsistent();
   int numOfUnsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size();
   time = System.currentTimeMillis() - time;
   DLExpressivityChecker checker = new DLExpressivityChecker(Collections.singleton(ontology));
   String e = checker.getDescriptionLogicName();
   String name = ontology.getOntologyID().getOntologyIRI().getFragment();
   logger.info(
       "ontology: "
           + name
           + ", reasoner: "
           + factory.getReasonerName()
           + ", expressivity: "
           + e
           + ", consistent: "
           + isConsistent
           + ", unsat classes: "
           + numOfUnsatClasses
           + ", time: "
           + time);
 }
 public void add(Set<O> clique) {
   resultCliques = null;
   final Set<O> unmodClique = Collections.unmodifiableSet(clique);
   originalCliques.add(unmodClique);
   List<O> orderedOperands = new ArrayList<O>(clique);
   for (int i = 0; i < orderedOperands.size(); i++) {
     O a = orderedOperands.get(i);
     for (int j = i + 1; j < orderedOperands.size(); j++) {
       O b = orderedOperands.get(j);
       addEdge(a, b);
       addEdge(b, a);
     }
   }
 }
  private AutocompleteResult exceptionToAutocomplete(
      final String expression,
      final ParserException e,
      final OWLEntityFinder finder,
      final ShortFormProvider sfp) {

    String lastToken;
    int pos;
    if (e.getCurrentToken().endsWith(ERROR_TOKEN)) {
      lastToken = e.getCurrentToken();
      lastToken =
          lastToken.substring(0, lastToken.length() - ERROR_TOKEN.length()); // remove the $$
      pos = e.getStartPos();
    } else {
      lastToken = e.getTokenSequence().get(e.getTokenSequence().size() - 1);
      if (lastToken.endsWith(ERROR_TOKEN)) {
        lastToken =
            lastToken.substring(0, lastToken.length() - ERROR_TOKEN.length()); // remove the $$
      } else if (lastToken.equals("<EOF>")) {
        lastToken = e.getTokenSequence().get(e.getTokenSequence().size() - 2); // EOF is last
        lastToken =
            lastToken.substring(0, lastToken.length() - ERROR_TOKEN.length()); // remove the $$
      } else if (!expression.endsWith(lastToken)) { // later invalid tokens are not in the list
        lastToken =
            expression.substring(
                expression.lastIndexOf(" ") + 1); // we just have to guess at the last word
      }
      pos = expression.length() - lastToken.length();
    }

    Map<String, List<String>> expected = new HashMap<String, List<String>>();

    String search = lastToken + ".*"; // starts with

    if (pos == e.getStartPos()) { // then the error is the last token and we can determine the type

      if (hasExpectedToken(e)) {
        final Set<String> keywords = e.getExpectedKeywords();
        if (!keywords.isEmpty()) {
          List<String> matchingKeywords = new ArrayList<String>();
          for (String keyword : keywords) {
            if (lastToken.length() == 0 || keyword.startsWith(lastToken)) {
              matchingKeywords.add(keyword);
            }
          }
          expected.put("keyword", matchingKeywords);
        }

        if (e.isClassNameExpected()) {
          addResults(expected, OWLClass.class, finder.getOWLClasses(search), sfp);
        }
        if (e.isObjectPropertyNameExpected()) {
          addResults(expected, OWLObjectProperty.class, finder.getOWLObjectProperties(search), sfp);
        }
        if (e.isDataPropertyNameExpected()) {
          addResults(expected, OWLDataProperty.class, finder.getOWLDataProperties(search), sfp);
        }
        if (e.isDatatypeNameExpected()) {
          addResults(expected, OWLDatatype.class, finder.getOWLDatatypes(search), sfp);
        }
        if (e.isAnnotationPropertyNameExpected()) {
          addResults(
              expected,
              OWLAnnotationProperty.class,
              finder.getOWLAnnotationProperties(search),
              sfp);
        }
        if (e.isIndividualNameExpected()) {
          addResults(expected, OWLNamedIndividual.class, finder.getOWLIndividuals(search), sfp);
        }
      } else {
        expected.put("literal", Collections.<String>emptyList());
      }
    } else {
      addKeywords(expected, lastToken);
      addResults(expected, OWLClass.class, finder.getOWLClasses(search), sfp);
      addResults(expected, OWLObjectProperty.class, finder.getOWLObjectProperties(search), sfp);
      addResults(expected, OWLDataProperty.class, finder.getOWLDataProperties(search), sfp);
      addResults(expected, OWLDatatype.class, finder.getOWLDatatypes(search), sfp);
      addResults(
          expected, OWLAnnotationProperty.class, finder.getOWLAnnotationProperties(search), sfp);
      addResults(expected, OWLNamedIndividual.class, finder.getOWLIndividuals(search), sfp);
    }

    return new AutocompleteResult(expression, pos, lastToken, expected);
  }
 @Test
 public void expressivityTest() {
   OWLOntology ontology = loadBigOntology("mouse");
   DLExpressivityChecker checker = new DLExpressivityChecker(Collections.singleton(ontology));
   logger.info(checker.getDescriptionLogicName());
 }
 public Iterator getRelatedObjectsToRemove(Object obj) {
   return Collections.emptySet().iterator();
 }