Program: 9993
Project: 9993
Buggy source:
/** 
 * This method sets the individuals that belong to the concept which is chosen in protege.
 */
private void setPositiveConcept(){
  current=editor.getOWLWorkspace().getOWLSelectionModel().getLastSelectedClass();
  if (current != null) {
    SortedSet<Individual> individuals=null;
    hasIndividuals=false;
    if (!(current.toString().equals("String_Node_Str"))) {
      List<NamedClass> classList=reasoner.getAtomicConceptsList();
      for (      NamedClass concept : classList) {
        if (individuals == null) {
          for (          String onto : ontologieURI) {
            if (concept.toString().contains(onto)) {
              if (concept.toString().equals(onto + current.toString())) {
                currentConcept=concept;
                if (reasoner.getIndividuals(concept) != null) {
                  if (reasoner.getIndividuals(concept).size() > 0) {
                    model.setInstancesCount(reasoner.getIndividuals(concept).size());
                    hasIndividuals=true;
                  }
                  individual=reasoner.getIndividuals(concept);
                  model.setIndividuals(individual);
                  model.setHasIndividuals(hasIndividuals);
                  System.out.println("String_Node_Str" + currentConcept);
                  model.setCurrentConcept(currentConcept);
                  view.getRunButton().setEnabled(true);
                  break;
                }
              }
            }
          }
        }
      }
    }
 else {
      System.out.println("String_Node_Str");
      if (reasoner.getIndividuals().size() > 0) {
        hasIndividuals=true;
      }
      individual=reasoner.getIndividuals();
      model.setIndividuals(individual);
      model.setHasIndividuals(hasIndividuals);
    }
  }
}

Fixed version (ground truth):
/** 
 * This method sets the individuals that belong to the concept which is chosen in protege.
 */
private void setPositiveConcept(){
  current=editor.getOWLWorkspace().getOWLSelectionModel().getLastSelectedClass();
  if (current != null) {
    SortedSet<Individual> individuals=null;
    hasIndividuals=false;
    if (!(current.toString().equals("String_Node_Str"))) {
      List<NamedClass> classList=reasoner.getAtomicConceptsList();
      for (      NamedClass concept : classList) {
        if (individuals == null) {
          for (          String onto : ontologieURI) {
            if (concept.toString().contains(onto)) {
              if (concept.toString().equals(onto + current.toString())) {
                currentConcept=concept;
                if (reasoner.getIndividuals(concept) != null) {
                  if (reasoner.getIndividuals(concept).size() > 0) {
                    model.setInstancesCount(reasoner.getIndividuals(concept).size());
                    hasIndividuals=true;
                  }
                  individual=reasoner.getIndividuals(concept);
                  model.setIndividuals(individual);
                  model.setHasIndividuals(hasIndividuals);
                  System.out.println("String_Node_Str" + currentConcept);
                  model.setCurrentConcept(currentConcept);
                  view.getRunButton().setEnabled(true);
                  break;
                }
              }
            }
          }
        }
      }
    }
 else {
      if (reasoner.getIndividuals().size() > 0) {
        hasIndividuals=true;
      }
      individual=reasoner.getIndividuals();
      model.setIndividuals(individual);
      model.setHasIndividuals(hasIndividuals);
    }
  }
}