Program: 10252
Project: 10252
Buggy source:
@Override public void init(){
  OWLOntologyManager manager=OWLManager.createOWLOntologyManager();
  Comparator<OWLNamedObject> namedObjectComparator=new Comparator<OWLNamedObject>(){
    public int compare(    OWLNamedObject o1,    OWLNamedObject o2){
      return o1.getURI().compareTo(o2.getURI());
    }
  }
;
  Set<OWLClass> classes=new TreeSet<OWLClass>(namedObjectComparator);
  Set<OWLObjectProperty> properties=new TreeSet<OWLObjectProperty>(namedObjectComparator);
  Set<OWLIndividual> owlIndividuals=new TreeSet<OWLIndividual>(namedObjectComparator);
  Set<OWLOntology> allImports=new HashSet<OWLOntology>();
  for (  KnowledgeSource source : sources) {
    if (source instanceof OWLFile) {
      URL url=((OWLFile)source).getURL();
      try {
        OWLOntology ontology=manager.loadOntologyFromPhysicalURI(url.toURI());
        allImports.addAll(manager.getImportsClosure(ontology));
        classes.addAll(ontology.getReferencedClasses());
        properties.addAll(ontology.getReferencedObjectProperties());
        owlIndividuals.addAll(ontology.getReferencedIndividuals());
      }
 catch (      OWLOntologyCreationException e) {
        e.printStackTrace();
      }
catch (      URISyntaxException e) {
        e.printStackTrace();
      }
    }
 else {
      KB kb=source.toKB();
      URI ontologyURI=URI.create("String_Node_Str");
      OWLOntology ontology=null;
      try {
        ontology=manager.createOntology(ontologyURI);
      }
 catch (      OWLOntologyCreationException e) {
        e.printStackTrace();
      }
      OWLAPIAxiomConvertVisitor.fillOWLOntology(manager,ontology,kb);
    }
  }
  if (reasonerType.equals("String_Node_Str")) {
    try {
      reasoner=new uk.ac.manchester.cs.factplusplus.owlapi.Reasoner(manager);
    }
 catch (    Exception e) {
      e.printStackTrace();
    }
  }
 else {
    reasoner=new org.mindswap.pellet.owlapi.Reasoner(manager);
    Logger pelletLogger=Logger.getLogger("String_Node_Str");
    pelletLogger.setLevel(Level.WARN);
  }
  try {
    reasoner.loadOntologies(allImports);
    reasoner.classify();
    reasoner.realise();
  }
 catch (  OWLReasonerException e) {
    e.printStackTrace();
  }
  factory=manager.getOWLDataFactory();
  atomicConcepts=new TreeSet<NamedClass>(conceptComparator);
  for (  OWLClass owlClass : classes)   atomicConcepts.add(new NamedClass(owlClass.getURI().toString()));
  atomicRoles=new TreeSet<ObjectProperty>(roleComparator);
  for (  OWLObjectProperty owlProperty : properties)   atomicRoles.add(new ObjectProperty(owlProperty.getURI().toString()));
  individuals=new TreeSet<Individual>();
  for (  OWLIndividual owlIndividual : owlIndividuals)   individuals.add(new Individual(owlIndividual.getURI().toString()));
}

Fixed version (ground truth):
@Override public void init(){
  OWLOntologyManager manager=OWLManager.createOWLOntologyManager();
  Comparator<OWLNamedObject> namedObjectComparator=new Comparator<OWLNamedObject>(){
    public int compare(    OWLNamedObject o1,    OWLNamedObject o2){
      return o1.getURI().compareTo(o2.getURI());
    }
  }
;
  Set<OWLClass> classes=new TreeSet<OWLClass>(namedObjectComparator);
  Set<OWLObjectProperty> properties=new TreeSet<OWLObjectProperty>(namedObjectComparator);
  Set<OWLIndividual> owlIndividuals=new TreeSet<OWLIndividual>(namedObjectComparator);
  Set<OWLOntology> allImports=new HashSet<OWLOntology>();
  for (  KnowledgeSource source : sources) {
    if (source instanceof OWLFile) {
      URL url=((OWLFile)source).getURL();
      try {
        OWLOntology ontology=manager.loadOntologyFromPhysicalURI(url.toURI());
        allImports.addAll(manager.getImportsClosure(ontology));
        classes.addAll(ontology.getReferencedClasses());
        properties.addAll(ontology.getReferencedObjectProperties());
        owlIndividuals.addAll(ontology.getReferencedIndividuals());
      }
 catch (      OWLOntologyCreationException e) {
        e.printStackTrace();
      }
catch (      URISyntaxException e) {
        e.printStackTrace();
      }
    }
 else {
      KB kb=source.toKB();
      URI ontologyURI=URI.create("String_Node_Str");
      OWLOntology ontology=null;
      try {
        ontology=manager.createOntology(ontologyURI);
      }
 catch (      OWLOntologyCreationException e) {
        e.printStackTrace();
      }
      OWLAPIAxiomConvertVisitor.fillOWLOntology(manager,ontology,kb);
      allImports.add(ontology);
      atomicConcepts.addAll(kb.findAllAtomicConcepts());
      atomicRoles.addAll(kb.findAllAtomicRoles());
      individuals.addAll(kb.findAllIndividuals());
    }
  }
  if (reasonerType.equals("String_Node_Str")) {
    try {
      reasoner=new uk.ac.manchester.cs.factplusplus.owlapi.Reasoner(manager);
    }
 catch (    Exception e) {
      e.printStackTrace();
    }
  }
 else {
    reasoner=new org.mindswap.pellet.owlapi.Reasoner(manager);
    Logger pelletLogger=Logger.getLogger("String_Node_Str");
    pelletLogger.setLevel(Level.WARN);
  }
  try {
    reasoner.loadOntologies(allImports);
    reasoner.classify();
    reasoner.realise();
  }
 catch (  OWLReasonerException e) {
    e.printStackTrace();
  }
  factory=manager.getOWLDataFactory();
  for (  OWLClass owlClass : classes)   atomicConcepts.add(new NamedClass(owlClass.getURI().toString()));
  for (  OWLObjectProperty owlProperty : properties)   atomicRoles.add(new ObjectProperty(owlProperty.getURI().toString()));
  for (  OWLIndividual owlIndividual : owlIndividuals)   individuals.add(new Individual(owlIndividual.getURI().toString()));
}