Examples of RDFIndividual

edu.stanford.smi.protegex.owl.model.RDFIndividual

Examples of edu.stanford.smi.protegex.owl.model.RDFIndividual

      ResidentNode domainResidentNode;
      InputNode generativeInputNode;
      Argument argument;
      MultiEntityNode multiEntityNode;


      RDFIndividual individualOne;
      RDFIndividual individualTwo;
      OWLObjectProperty objectProperty;


      OWLNamedClass domainResidentNodePr = this.getOwlModel().getOWLNamedClass(DOMAIN_RESIDENT);
      Collection instances = domainResidentNodePr.getInstances(true);
      MFrag mFragOfNode = null;


      for (Iterator it = instances.iterator(); it.hasNext();) {


        individualOne = (RDFIndividual) it.next();
        domainResidentNode = getMapDomainResidentNode().get(individualOne
            .getBrowserText());
        if (domainResidentNode == null) {
          throw new IOMebnException(
              getResource().getString("DomainResidentNotExistsInMTheory"),
              individualOne.getBrowserText());
        }


        Debug.println("Domain Resident loaded: "
            + individualOne.getBrowserText());


        domainResidentNode.setDescription(getDescription(individualOne));


        /* -> isResidentNodeIn */
        objectProperty = (OWLObjectProperty) getOwlModel()
            .getOWLObjectProperty("isResidentNodeIn");
        instances = individualOne.getPropertyValues(objectProperty);
        Iterator itAux = instances.iterator();
        individualTwo = (RDFIndividual) itAux.next();
        domainMFrag = getMapDomainMFrag().get(individualTwo.getBrowserText());
        if (domainMFrag.containsDomainResidentNode(domainResidentNode) == false) {
          throw new IOMebnException(
              getResource().getString("DomainResidentNotExistsInDomainMFrag"));
        }
        mFragOfNode = domainMFrag;
        Debug.println("-> " + individualOne.getBrowserText() + ": "
            + objectProperty.getBrowserText() + " = "
            + individualTwo.getBrowserText());


        /* -> hasArgument */
        objectProperty = (OWLObjectProperty) getOwlModel()
            .getOWLObjectProperty("hasArgument");
        instances = individualOne.getPropertyValues(objectProperty);
        for (Iterator itIn = instances.iterator(); itIn.hasNext();) {
          individualTwo = (RDFIndividual) itIn.next();
          argument = new Argument(individualTwo.getBrowserText(),
              domainResidentNode);
          domainResidentNode.addArgument(argument);
          getMapArgument().put(individualTwo.getBrowserText(), argument);
          Debug.println("-> " + individualOne.getBrowserText() + ": "
              + objectProperty.getBrowserText() + " = "
              + individualTwo.getBrowserText());
        }


        /* -> hasParent */
        objectProperty = (OWLObjectProperty) getOwlModel()
            .getOWLObjectProperty("hasParent");
        instances = individualOne.getPropertyValues(objectProperty);
        for (Iterator itIn = instances.iterator(); itIn.hasNext();) {
          individualTwo = (RDFIndividual) itIn.next();
          if (getMapDomainResidentNode().containsKey(individualTwo
              .getBrowserText())) {
            ResidentNode aux = getMapDomainResidentNode().get(individualTwo
                .getBrowserText());


            Edge auxEdge = new Edge(aux, domainResidentNode);
            try {
              mFragOfNode.addEdge(auxEdge);
            } catch (Exception e) {
              Debug.println("Erro: arco invalido!!!");
            }
          } else {
            if (getMapGenerativeInputNode().containsKey(individualTwo
                .getBrowserText())) {
              InputNode aux = getMapGenerativeInputNode()
                  .get(individualTwo.getBrowserText());


              Edge auxEdge = new Edge(aux, domainResidentNode);
              try {
                mFragOfNode.addEdge(auxEdge);
              } catch (Exception e) {
                Debug.println("Erro: arco invalido!!!");
              }


            } else {
              throw new IOMebnException(
                  getResource().getString("NodeNotFound"),
                  individualTwo.getBrowserText());
            }
          }
          Debug.println("-> " + individualOne.getBrowserText() + ": "
              + objectProperty.getBrowserText() + " = "
              + individualTwo.getBrowserText());
        }


        /* -> hasInputInstance */
        objectProperty = (OWLObjectProperty) getOwlModel()
            .getOWLObjectProperty("hasInputInstance");
        instances = individualOne.getPropertyValues(objectProperty);


        for (Iterator itIn = instances.iterator(); itIn.hasNext();) {
          individualTwo = (RDFIndividual) itIn.next();
          generativeInputNode = getMapGenerativeInputNode().get(individualTwo
              .getBrowserText());
          try {
            generativeInputNode.setInputInstanceOf(domainResidentNode);
          } catch (Exception e) {
            e.printStackTrace();
          }
          Debug.println("-> " + individualOne.getBrowserText() + ": "
              + objectProperty.getBrowserText() + " = "
              + individualTwo.getBrowserText());
        }


        /* -> isInnerTermOf */
        objectProperty = (OWLObjectProperty) getOwlModel()
            .getOWLObjectProperty("isInnerTermOf");
        instances = individualOne.getPropertyValues(objectProperty);
        itAux = instances.iterator();
        for (Iterator itIn = instances.iterator(); itIn.hasNext();) {
          individualTwo = (RDFIndividual) itIn.next();
          multiEntityNode = getMapMultiEntityNode().get(individualTwo
              .getBrowserText());
          domainResidentNode.addInnerTermFromList(multiEntityNode);
          multiEntityNode.addInnerTermOfList(domainResidentNode);
          Debug.println("-> " + individualOne.getBrowserText() + ": "
              + objectProperty.getBrowserText() + " = "
              + individualTwo.getBrowserText());
        }


        /* -> hasPossibleValues */
        {
          CategoricalStateEntity state = null;
          objectProperty = (OWLObjectProperty) getOwlModel()
              .getOWLObjectProperty("hasPossibleValues");
          instances = individualOne.getPropertyValues(objectProperty);
          itAux = instances.iterator();
          for (Object instance : instances) {
            individualTwo = (RDFIndividual) instance;
            String stateName = individualTwo.getBrowserText();
            /* case 1: booleans states */
            if (stateName.equals("true")) {
              StateLink link = domainResidentNode
                  .addPossibleValueLink(getMebn()
                      .getBooleanStatesEntityContainer()
                      .getTrueStateEntity());
              List<String> globallyObjects = getMapBooleanStateGloballyObjects()
                  .get("true");
              if (globallyObjects.contains(domainResidentNode
                  .getName())) {
                link.setGloballyExclusive(true);
              } else {
                link.setGloballyExclusive(false);
              }
              domainResidentNode
                  .setTypeOfStates(IResidentNode.BOOLEAN_RV_STATES);
            } else {
              if (stateName.equals("false")) {
                StateLink link = domainResidentNode
                    .addPossibleValueLink(getMebn()
                        .getBooleanStatesEntityContainer()
                        .getFalseStateEntity());
                List<String> globallyObjects = getMapBooleanStateGloballyObjects()
                    .get("false");
                if (globallyObjects.contains(domainResidentNode
                    .getName())) {
                  link.setGloballyExclusive(true);
                } else {
                  link.setGloballyExclusive(false);
                }
                domainResidentNode
                    .setTypeOfStates(IResidentNode.BOOLEAN_RV_STATES);
              } else {
                if (stateName.equals("absurd")) {
                  StateLink link = domainResidentNode
                      .addPossibleValueLink(getMebn()
                          .getBooleanStatesEntityContainer()
                          .getAbsurdStateEntity());
                  List<String> globallyObjects = getMapBooleanStateGloballyObjects()
                      .get("absurd");
                  if (globallyObjects.contains(domainResidentNode
                      .getName())) {
                    link.setGloballyExclusive(true);
                  } else {
                    link.setGloballyExclusive(false);
                  }
                  domainResidentNode
                      .setTypeOfStates(IResidentNode.BOOLEAN_RV_STATES);
                } else {
                  if (getMapTypes().get(stateName) != null) {


                    /* case 2:object entities */


                    StateLink link = domainResidentNode
                        .addPossibleValueLink(getMapTypes()
                            .get(stateName));
                    domainResidentNode
                        .setTypeOfStates(IResidentNode.OBJECT_ENTITY);


                  } else {
                    /* case 3: categorical states */
                    try {
                      state = getMebn()
                          .getCategoricalStatesEntityContainer()
                          .getCategoricalState(
                              individualTwo
                                  .getBrowserText());
                      StateLink link = domainResidentNode
                          .addPossibleValueLink(state);


                      List<String> globallyObjects = getMapCategoricalStateGloballyObjects()
                          .get(state.getName());
                      if (globallyObjects
                          .contains(domainResidentNode
                              .getName())) {
                        link.setGloballyExclusive(true);
                      } else {
                        link.setGloballyExclusive(false);
                      }
                      domainResidentNode
                          .setTypeOfStates(IResidentNode.CATEGORY_RV_STATES);
                    } catch (CategoricalStateDoesNotExistException e) {
                      // TODO Auto-generated catch block
                      e.printStackTrace();
                    }
                  }


                }
              }
            }
          } /* for */


        }


        /* hasProbDist */


        OWLObjectProperty hasProbDist = (OWLObjectProperty) getOwlModel()
            .getOWLObjectProperty("hasProbDist");
        OWLDatatypeProperty hasDeclaration = getOwlModel()
            .getOWLDatatypeProperty("hasDeclaration");
        String cpt = null;
        for (Iterator iter = individualOne.getPropertyValues(hasProbDist)
            .iterator(); iter.hasNext();) {
          RDFIndividual element = (RDFIndividual) iter.next();
          try {
            cpt = (String) element.getPropertyValue(hasDeclaration);
          } catch (Exception e) {
            cpt = "";
          }
          domainResidentNode.setTableFunction(cpt);
        }

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Examples of edu.stanford.smi.protegex.owl.model.RDFIndividual

      ContextNode contextNode;
      ResidentNode domainResidentNode;
      InputNode generativeInputNode;
      BuiltInRV builtInRV;


      RDFIndividual individualOne;
      RDFIndividual individualTwo;
      OWLNamedClass owlNamedClass;
      OWLObjectProperty objectProperty;


      owlNamedClass = getOwlModel().getOWLNamedClass(DOMAIN_MFRAG);
      Collection instances = owlNamedClass.getInstances(false);


      for (Iterator it = instances.iterator(); it.hasNext();) {
        individualOne = (RDFIndividual) it.next();
        domainMFrag = getMapDomainMFrag().get(individualOne.getBrowserText());
        if (domainMFrag == null) {
          throw new IOMebnException(
              getResource().getString("DomainMFragNotExistsInMTheory"),
              individualOne.getBrowserText());
        }


        Debug.println("DomainMFrag loaded: "
            + individualOne.getBrowserText());


        domainMFrag.setDescription(getDescription(individualOne));


        /* -> hasResidentNode */
        objectProperty = (OWLObjectProperty) getOwlModel()
            .getOWLObjectProperty("hasResidentNode");
        instances = individualOne.getPropertyValues(objectProperty);
        for (Iterator itIn = instances.iterator(); itIn.hasNext();) {
          Object itInNext = itIn.next();
          if (!(itInNext instanceof RDFIndividual)) {
            try {
              System.err.println(itInNext + " != RDFIndividual");
            } catch (Throwable t) {
              t.printStackTrace();
            }
            continue;
          }
          individualTwo = (RDFIndividual) itInNext;


          // remove prefixes from the name
          String name = individualTwo.getBrowserText();
          if (name.startsWith(SaverPrOwlIO.RESIDENT_NAME_PREFIX)) {
            try {
              name = name.substring(SaverPrOwlIO.RESIDENT_NAME_PREFIX
                  .length());
            } catch (Exception e) {
              // ignore, because we can still try the original name
              e.printStackTrace();
            }
          }


          // instanciate a continuous resident node instead of resident node, if individual is assignable to a continuous node
          if (individualTwo.hasRDFType(getOwlModel().getOWLNamedClass(CONTINUOUS_RESIDENT_NODE), true)) {
            domainResidentNode = new ContinuousResidentNode(name, domainMFrag);
//            try {
//              ((ContinuousResidentNode)domainResidentNode).onAddToMFrag(domainMFrag);
//            } catch (MFragDoesNotExistException e) {
//              e.printStackTrace();
//            }
          } else {
            domainResidentNode = new ResidentNode(name, domainMFrag);
          }
          getMebn().getNamesUsed().add(name);


          domainMFrag.addResidentNode(domainResidentNode);


          // the mappings uses the original names (no prefix removal)
          getMapDomainResidentNode().put(individualTwo.getBrowserText(),
              domainResidentNode);
          getMapMultiEntityNode().put(individualTwo.getBrowserText(),
              domainResidentNode);
          Debug.println("-> " + individualOne.getBrowserText() + ": "
              + objectProperty.getBrowserText() + " = "
              + individualTwo.getBrowserText());
        }


        /* -> hasInputNode */
        objectProperty = (OWLObjectProperty) getOwlModel()
            .getOWLObjectProperty("hasInputNode");
        instances = individualOne.getPropertyValues(objectProperty);
        for (Iterator itIn = instances.iterator(); itIn.hasNext();) {
          individualTwo = (RDFIndividual) itIn.next();
          generativeInputNode = new InputNode(
              individualTwo.getBrowserText(), domainMFrag);
          getMebn().getNamesUsed().add(individualTwo.getBrowserText());
          domainMFrag.addInputNode(generativeInputNode);
          getMapGenerativeInputNode().put(individualTwo.getBrowserText(),
              generativeInputNode);
          getMapMultiEntityNode().put(individualTwo.getBrowserText(),
              generativeInputNode);
          Debug.println("-> " + individualOne.getBrowserText() + ": "
              + objectProperty.getBrowserText() + " = "
              + individualTwo.getBrowserText());
        }


        /* -> hasContextNode */
        objectProperty = (OWLObjectProperty) getOwlModel()
            .getOWLObjectProperty("hasContextNode");
        instances = individualOne.getPropertyValues(objectProperty);
        for (Iterator itIn = instances.iterator(); itIn.hasNext();) {
          individualTwo = (RDFIndividual) itIn.next();
          contextNode = new ContextNode(individualTwo.getBrowserText(),
              domainMFrag);
          getMebn().getNamesUsed().add(individualTwo.getBrowserText());
          domainMFrag.addContextNode(contextNode);
          getMapContextNode().put(individualTwo.getBrowserText(), contextNode);
          getMapMultiEntityNode().put(individualTwo.getBrowserText(),
              contextNode);
          Debug.println("-> " + individualOne.getBrowserText() + ": "
              + objectProperty.getBrowserText() + " = "
              + individualTwo.getBrowserText());
        }


        /* -> hasOVariable */
        objectProperty = (OWLObjectProperty) getOwlModel()
            .getOWLObjectProperty("hasOVariable");
        instances = individualOne.getPropertyValues(objectProperty);
        String ovName = null;
        for (Iterator itIn = instances.iterator(); itIn.hasNext();) {
          individualTwo = (RDFIndividual) itIn.next();
          ovName = individualTwo.getBrowserText(); // Name of the OV
                                // individual
          // Remove MFrag name from ovName. MFrag name is a scope
          // identifier
          try {
            ovName = ovName.split(domainMFrag.getName()
                + this.getOrdinaryVarScopeSeparator())[1];
          } catch (java.lang.ArrayIndexOutOfBoundsException e) {
            // Use the original name...
            ovName = ovName; // If its impossible to split, then no
                      // Scope id was found
          }
          // Debug.println("> Internal OV name is : " + ovName);
          // Create instance of OV w/o scope identifier
          oVariable = new OrdinaryVariable(ovName, getMebn()
              .getTypeContainer().getDefaultType(), domainMFrag);
          domainMFrag.addOrdinaryVariable(oVariable);
          // let's map objects w/ scope identifier included
          getMapOVariable().put(individualTwo.getBrowserText(), oVariable);
          Debug.println("-> " + individualOne.getBrowserText() + ": "
              + objectProperty.getBrowserText() + " = "
              + individualTwo.getBrowserText());
        }
      }
    }

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Examples of edu.stanford.smi.protegex.owl.model.RDFIndividual

            node.addChild(cl.getURI(),childClass);


            if (instances.size() > 0) {
                for (Iterator<RDFIndividual> jt = instances.iterator(); jt.hasNext();) {
                  try{
                    RDFIndividual individual = (RDFIndividual)jt.next();
                    //OWLIndividual individual = (OWLIndividual) jt.next();    
                    TreeNode child = new TreeNodeImpl();
                      OntologyProperty ontologyProperty = new OntologyPropertyImpl(individual);
                      
                      boolean bMatchesFilter = true;

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Examples of edu.stanford.smi.protegex.owl.model.RDFIndividual

    public List<String> getIsSameAsNames(){
      if(lis_same_asNames==null){
        lis_same_asNames = new ArrayList<String>();
        Iterator<RDFIndividual> it = this.getIsSameAs().iterator();
        while(it.hasNext()){
        RDFIndividual sameAsIndividual = it.next();
        lis_same_asNames.add(sameAsIndividual.getLocalName());
      }
      }
        return lis_same_asNames;
    }

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Examples of edu.stanford.smi.protegex.owl.model.RDFIndividual

    public OntologyProperty getProperty(String uri){
      //FIXME There may be more models coming
      OWLNamedClass startClass = owlModel.getOWLNamedClass(OWLMODEL_ROOT_CLASS);
      
      //TB property uris correspond to OWLIndividuals
      RDFIndividual individual = this.getOWLModel().getRDFIndividual(uri);
      
      if(individual != null){
          //create ontology property for this individual
          OntologyProperty ontoprop = new OntologyPropertyImpl(individual);
          return ontoprop;

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