private void getPelletIncrementalClassifierRunTime(String baseOnt, String ontDir)
      throws Exception {
    System.out.println("Using Pellet Incremental Classifier...");
    GregorianCalendar start = new GregorianCalendar();
    File ontFile = new File(baseOnt);
    IRI documentIRI = IRI.create(ontFile);
    OWLOntology baseOntology = OWL.manager.loadOntology(documentIRI);
    IncrementalClassifier classifier = new IncrementalClassifier(baseOntology);
    classifier.classify();
    System.out.println("Logical axioms: " + baseOntology.getLogicalAxiomCount());
    System.out.println("Time taken for base ontology (millis): " + Util.getElapsedTime(start));
    File ontDirPath = new File(ontDir);
    File[] allFiles = ontDirPath.listFiles();
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    addTripsBaseOntologies(manager);
    int count = 1;
    for (File owlFile : allFiles) {
      IRI owlDocumentIRI = IRI.create(owlFile);
      OWLOntology ontology = manager.loadOntologyFromOntologyDocument(owlDocumentIRI);
      Set<OWLLogicalAxiom> axioms = ontology.getLogicalAxioms();
      for (OWLLogicalAxiom axiom : axioms)
        OWL.manager.applyChange(new AddAxiom(baseOntology, axiom));

      System.out.println("\nLogical axioms: " + baseOntology.getLogicalAxiomCount());
      System.out.println(count + "  file: " + owlFile.getName());
      //			System.out.println("" + count + "  file: " + owlFile.getName());
      //			GregorianCalendar start2 = new GregorianCalendar();
      classifier.classify();
      //	        System.out.println("Time taken (millis): " +
      //					Util.getElapsedTime(start2));
      manager.removeOntology(ontology);
      count++;
    }
    System.out.println("\nTotal time taken (millis): " + Util.getElapsedTime(start));
  }
    @Override
    public void prepare() throws TaskException {
      // load positive and negative deltas via the OWL API
      try {
        OWLOntology additions = loadFromDisk(ADDITION_SUFFIX);
        OWLOntology deletions = loadFromDisk(DELETION_SUFFIX);

        applyToReasoner(additions.getLogicalAxioms(), true);
        applyToReasoner(deletions.getLogicalAxioms(), false);

        measureTime = additions.getLogicalAxiomCount() > 0 && deletions.getLogicalAxiomCount() > 0;

      } catch (OWLOntologyCreationException e) {
        throw new TaskException(e);
      }
    }
  public void getELKIncrementalRuntime(String baseOnt, String ontDir) throws Exception {
    GregorianCalendar start = new GregorianCalendar();
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    IRI documentIRI = IRI.create(new File(baseOnt));
    OWLOntology baseOntology = manager.loadOntology(documentIRI);
    System.out.println("Logical axioms: " + baseOntology.getLogicalAxiomCount());
    //		findDataHasValueAxiom(baseOntology.getAxioms(AxiomType.SUBCLASS_OF));

    OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
    OWLReasoner reasoner = reasonerFactory.createReasoner(baseOntology);
    reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
    File[] files = new File(ontDir).listFiles();
    int count = 0;
    OWLOntologyManager manager2 = OWLManager.createOWLOntologyManager();
    addTripsBaseOntologies(manager2);
    for (File file : files) {
      System.out.println("File name: " + file.getName());
      documentIRI = IRI.create(file);
      OWLOntology ontology = manager2.loadOntology(documentIRI);
      Set<OWLLogicalAxiom> axioms = ontology.getLogicalAxioms();
      //	    	findDataHasValueAxiom(ontology.getAxioms(AxiomType.SUBCLASS_OF));
      manager.addAxioms(baseOntology, axioms);
      reasoner.flush();
      System.out.println("Logical axioms: " + baseOntology.getLogicalAxiomCount());

      // From the ELK wiki, it seems ABox reasoning will trigger TBox reasoning
      reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS);

      manager2.removeOntology(ontology);
      count++;
      System.out.println("Done with " + count);
      //	    	if(count == 5)
      //	    		break;
    }
    reasoner.dispose();
    System.out.println("Time taken (millis): " + Util.getElapsedTime(start));
  }
 @Test
 public void testNamedOntologyToString() throws Exception {
   OWLOntologyManager man = Factory.getManager();
   IRI ontIRI = IRI("http://owlapi.sourceforge.net/ont");
   OWLOntology ont = man.createOntology(ontIRI);
   String s = ont.toString();
   String expected =
       "Ontology("
           + ont.getOntologyID().toString()
           + ") [Axioms: "
           + ont.getAxiomCount()
           + " Logical Axioms: "
           + ont.getLogicalAxiomCount()
           + "]";
   assertEquals(expected, s);
 }