/**
  * Refills the section with rows. This method will be called by the system and should be directly
  * called.
  */
 protected void refill(OWLOntology ontology) {
   added.clear();
   for (OWLObjectPropertyAssertionAxiom ax :
       ontology.getObjectPropertyAssertionAxioms(getRootObject())) {
     addRow(
         new OWLObjectPropertyAssertionAxiomFrameSectionRow(
             getOWLEditorKit(), this, ontology, getRootObject(), ax));
     added.add(ax);
   }
 }
  public Set<OWLAxiom> write(OWLIndividual individual) {
    Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
    axioms.addAll(writeEntityStart(INDIVIDUAL, individual));
    if (!isFiltered(AxiomType.CLASS_ASSERTION)) {
      for (OWLOntology ontology : getOntologies()) {
        SectionMap expressions = new SectionMap();
        for (OWLClassAssertionAxiom ax : ontology.getClassAssertionAxioms(individual)) {
          if (isDisplayed(ax)) {
            expressions.add(ax.getClassExpression(), ax);
            axioms.add(ax);
          }
        }
        writeSection(TYPES, expressions, ",", true, ontology);
      }
    }
    for (OWLOntology ontology : getOntologies()) {

      List<OWLPropertyAssertionAxiom<?, ?>> assertions =
          new ArrayList<OWLPropertyAssertionAxiom<?, ?>>();
      assertions.addAll(ontology.getObjectPropertyAssertionAxioms(individual));
      assertions.addAll(ontology.getNegativeObjectPropertyAssertionAxioms(individual));
      assertions.addAll(ontology.getDataPropertyAssertionAxioms(individual));
      assertions.addAll(ontology.getNegativeDataPropertyAssertionAxioms(individual));

      if (!assertions.isEmpty()) {
        fireSectionRenderingPrepared(FACTS.toString());
        writeSection(FACTS);
        writeSpace();
        writeOntologiesList(ontology);
        incrementTab(1);
        writeNewLine();
        fireSectionRenderingStarted(FACTS.toString());

        for (Iterator<OWLPropertyAssertionAxiom<?, ?>> it = assertions.iterator(); it.hasNext(); ) {
          OWLPropertyAssertionAxiom<?, ?> ax = it.next();
          fireSectionItemPrepared(FACTS.toString());
          Set<OWLAnnotation> annos = ax.getAnnotations();
          if (!annos.isEmpty()) {
            writeAnnotations(annos);
            pushTab(getIndent() + 1);
          }

          if (ax instanceof OWLNegativeDataPropertyAssertionAxiom
              || ax instanceof OWLNegativeObjectPropertyAssertionAxiom) {
            write(NOT);
            writeSpace();
          }
          ax.getProperty().accept(this);
          writeSpace();
          writeSpace();
          ax.getObject().accept(this);
          if (!annos.isEmpty()) {
            popTab();
          }
          fireSectionItemFinished(FACTS.toString());
          if (it.hasNext()) {
            write(",");
            writeNewLine();
          }
        }
        popTab();
        writeNewLine();
        writeNewLine();
      }
    }

    if (!isFiltered(AxiomType.SAME_INDIVIDUAL)) {
      for (OWLOntology ontology : getOntologies()) {
        Set<OWLIndividual> inds = new TreeSet<OWLIndividual>();
        for (OWLSameIndividualAxiom ax : ontology.getSameIndividualAxioms(individual)) {
          if (isDisplayed(ax)) {
            inds.addAll(ax.getIndividuals());
            axioms.add(ax);
          }
        }
        inds.remove(individual);
        writeSection(SAME_AS, inds, ",", true, ontology);
      }
    }
    if (!isFiltered(AxiomType.DIFFERENT_INDIVIDUALS)) {
      for (OWLOntology ontology : getOntologies()) {
        Set<OWLIndividual> inds = new TreeSet<OWLIndividual>();
        Set<OWLDifferentIndividualsAxiom> nary = new TreeSet<OWLDifferentIndividualsAxiom>();
        for (OWLDifferentIndividualsAxiom ax : ontology.getDifferentIndividualAxioms(individual)) {
          if (ax.getIndividuals().size() == 2 && isDisplayed(ax)) {
            inds.addAll(ax.getIndividuals());
            axioms.add(ax);
          } else {
            nary.add(ax);
          }
        }
        inds.remove(individual);
        writeSection(DIFFERENT_FROM, inds, ",", true, ontology);
        if (renderExtensions) {
          for (OWLDifferentIndividualsAxiom ax : nary) {
            writeSection(DIFFERENT_INDIVIDUALS, ax.getIndividuals(), ", ", false, ontology);
          }
        }
      }
    }
    writeEntitySectionEnd(INDIVIDUAL.toString());
    return axioms;
  }
  public boolean retrieveSolutions(String siteNameHash) {
    // use the siteNameHash to access a certain Site individual in the ontology
    // retrieve each Solution individual of this site and use it to re-initialise the Solutions List
    OwlSolution tempSolution;
    OwlSolvedHouse tempSolvedHouse;
    OwlSolvedRoom tempSolvedRoom;

    // first clear the Solution List contents...
    this.solutionsList.clear();

    OWLIndividual tempSiteIndividual =
        OWLFactory.getOWLNamedIndividual(":" + siteNameHash, topIxPrefixManager);
    OWLClassExpression tempSolutionClassExpression =
        OWLFactory.getOWLClass(":Solution", topIxPrefixManager);
    Set<OWLObjectPropertyAssertionAxiom> tempSitePropertyAxioms =
        topIxOnt.getObjectPropertyAssertionAxioms(tempSiteIndividual);

    Set<OWLIndividual> tempSolutionIndividuals =
        new HashSet<>(); // Solution individuals for this particular site. will be filled below...
    Set<OWLIndividual> tempSolvedHouseIndividuals = new HashSet<>();
    Set<OWLIndividual> tempSolvedRoomIndividuals = new HashSet<>();

    // populate the tempSolutionIndividuals Set<OWLIndividual>
    // with the Solution individuals that are solutions of the current Site
    // this block runs through the set of all the object property axioms
    // that have this site as their subject
    // and filters out the ones that are of type "hasSolution"
    for (OWLObjectPropertyAssertionAxiom tempObjPropAssAx : tempSitePropertyAxioms) {
      OWLObjectProperty tempHasSolutionObjectProperty =
          OWLFactory.getOWLObjectProperty(
              IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasSolution"));
      if (tempObjPropAssAx.getProperty() == tempHasSolutionObjectProperty) {
        tempSolutionIndividuals.add(tempObjPropAssAx.getObject());
      }
    }
    // retrieving the site dimensions for this solution set
    // (the site remains the same throughout the plethos of solutions).
    int tempSiteLength = 0;
    int tempSiteWidth = 0;
    OWLDataProperty siteHasLengthProp = OWLFactory.getOWLDataProperty(":hasX", topIxPrefixManager);
    OWLDataProperty siteHasWidthProp = OWLFactory.getOWLDataProperty(":hasY", topIxPrefixManager);
    Set<OWLDataPropertyAssertionAxiom> tempSiteDataProperties = new HashSet<>();

    tempSiteDataProperties = topIxOnt.getDataPropertyAssertionAxioms(tempSiteIndividual);

    for (OWLDataPropertyAssertionAxiom tempSiteDataProperty : tempSiteDataProperties) {
      if (tempSiteDataProperty.getProperty() == siteHasLengthProp) {
        tempSiteLength = tempSiteDataProperty.getObject().parseInteger();
      }
      if (tempSiteDataProperty.getProperty() == siteHasWidthProp) {
        tempSiteWidth = tempSiteDataProperty.getObject().parseInteger();
      }
    }

    logger.info(tempSolutionIndividuals.size());

    // running every solution individual for/of that particular site in order
    // to extract the solvedHouse's and the solvedRoom's
    // via the hasSolvedHouse and hasSolvedRoom properties.
    int solutionCounter = 0;
    for (OWLIndividual tempSolutionIndividual : tempSolutionIndividuals) {
      tempSolution = new OwlSolution();
      tempSolution.setSolutionID(new Integer(++solutionCounter));

      tempSolution.setSiteLength(new Integer(tempSiteLength));
      tempSolution.setSiteWidth(new Integer(tempSiteWidth));

      // clearing the contents of these two structuresin order to accommodate the solved entities of
      // the next solution.
      tempSolvedHouseIndividuals.clear();
      tempSolvedRoomIndividuals.clear();

      for (OWLObjectPropertyAssertionAxiom tempObjPropAssAx :
          topIxOnt.getObjectPropertyAssertionAxioms(tempSolutionIndividual)) {
        OWLObjectProperty tempHasSolvedHouseObjectProperty =
            OWLFactory.getOWLObjectProperty(
                IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasSolvedHouse"));
        OWLObjectProperty tempHasSolvedRoomObjectProperty =
            OWLFactory.getOWLObjectProperty(
                IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasSolvedRoom"));
        if (tempObjPropAssAx.getProperty() == tempHasSolvedHouseObjectProperty) {
          tempSolvedHouseIndividuals.add(tempObjPropAssAx.getObject());
        } else if (tempObjPropAssAx.getProperty() == tempHasSolvedRoomObjectProperty) {
          tempSolvedRoomIndividuals.add(tempObjPropAssAx.getObject());
        }
      }

      for (OWLIndividual tempSolvedHouseIndividual : tempSolvedHouseIndividuals) {
        tempSolvedHouse = new OwlSolvedHouse();
        for (OWLDataPropertyAssertionAxiom tempDatPropAssAx :
            topIxOnt.getDataPropertyAssertionAxioms(tempSolvedHouseIndividual)) {
          if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasL", topIxPrefixManager))) {
            // logger.info(tempDatPropAssAx.getObject().parseInteger());
            tempSolvedHouse.setSolvedHouseLength(tempDatPropAssAx.getObject().parseInteger());
          } else if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasW", topIxPrefixManager))) {
            tempSolvedHouse.setSolvedHouseWidth(tempDatPropAssAx.getObject().parseInteger());
          } else if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasX", topIxPrefixManager))) {
            tempSolvedHouse.setSolvedHouseX(tempDatPropAssAx.getObject().parseInteger());
          } else if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasY", topIxPrefixManager))) {
            tempSolvedHouse.setSolvedHouseY(tempDatPropAssAx.getObject().parseInteger());
          } else if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasLiteral", topIxPrefixManager))) {
            tempSolvedHouse.setSolvedHouseLiteral(tempDatPropAssAx.getObject().getLiteral());
          }
        }
        // logger.info(tempSolvedHouse.getSolvedHouseX()+" "+tempSolvedHouse.getSolvedHouseY());
        tempSolution.getSolvedHouses().add(tempSolvedHouse);
      }

      for (OWLIndividual tempSolvedRoomIndividual : tempSolvedRoomIndividuals) {
        tempSolvedRoom = new OwlSolvedRoom();
        for (OWLDataPropertyAssertionAxiom tempDatPropAssAx :
            topIxOnt.getDataPropertyAssertionAxioms(tempSolvedRoomIndividual)) {
          if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasL", topIxPrefixManager))) {
            tempSolvedRoom.setSolvedRoomLength(tempDatPropAssAx.getObject().parseInteger());
          } else if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasW", topIxPrefixManager))) {
            tempSolvedRoom.setSolvedRoomWidth(tempDatPropAssAx.getObject().parseInteger());
          } else if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasH", topIxPrefixManager))) {
            tempSolvedRoom.setSolvedRoomHeight(tempDatPropAssAx.getObject().parseInteger());
          } else if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasX", topIxPrefixManager))) {
            tempSolvedRoom.setSolvedRoomX(tempDatPropAssAx.getObject().parseInteger());
          } else if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasY", topIxPrefixManager))) {
            tempSolvedRoom.setSolvedRoomY(tempDatPropAssAx.getObject().parseInteger());
          } else if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasZ", topIxPrefixManager))) {
            tempSolvedRoom.setSolvedRoomZ(tempDatPropAssAx.getObject().parseInteger());
          } else if (tempDatPropAssAx.getProperty()
              == (OWLFactory.getOWLDataProperty(":hasLiteral", topIxPrefixManager))) {
            tempSolvedRoom.setSolvedRoomLiteral(tempDatPropAssAx.getObject().getLiteral());
          }
        }
        tempSolution.getSolvedRooms().add(tempSolvedRoom);
      }
      this.solutionsList.add(tempSolution);
    }

    return true;
  }