Program: 9426
Project: 9426
Buggy source:
@Override public void init() throws ComponentInitException {
  atomicConcepts=new TreeSet<OWLClass>();
  atomicRoles=new TreeSet<OWLObjectProperty>();
  datatypeProperties=new TreeSet<OWLDataProperty>();
  individuals=new TreeSet<OWLIndividual>();
  df=new OWLDataFactoryImpl();
  manager=OWLManager.createOWLOntologyManager();
  prefixes=new TreeMap<String,String>();
  for (  KnowledgeSource source : sources) {
    if (source instanceof OWLOntologyKnowledgeSource) {
      ontology=((OWLOntologyKnowledgeSource)source).createOWLOntology(manager);
      owlAPIOntologies.add(ontology);
    }
 else {
      throw new ComponentInitException("String_Node_Str" + source.getClass().getName());
    }
    atomicConcepts.addAll(ontology.getClassesInSignature(Imports.INCLUDED));
    atomicRoles.addAll(ontology.getObjectPropertiesInSignature(Imports.INCLUDED));
    datatypeProperties.addAll(ontology.getDataPropertiesInSignature(Imports.INCLUDED));
    individuals.addAll(ontology.getIndividualsInSignature(Imports.INCLUDED));
    OWLDocumentFormat format=manager.getOntologyFormat(ontology);
    if (format instanceof PrefixDocumentFormat) {
      prefixes.putAll(((PrefixDocumentFormat)format).getPrefixName2PrefixMap());
      baseURI=((PrefixDocumentFormat)format).getDefaultPrefix();
      prefixes.remove("String_Node_Str");
    }
  }
  try {
    ontology=manager.createOntology(IRI.create("String_Node_Str"),new HashSet<OWLOntology>(owlAPIOntologies));
    List<OWLOntologyChange> addImports=new ArrayList<OWLOntologyChange>();
    for (    OWLOntology ont : owlAPIOntologies) {
      for (      OWLImportsDeclaration importDeclaration : ont.getImportsDeclarations()) {
        addImports.add(new AddImport(ontology,importDeclaration));
      }
    }
    manager.applyChanges(addImports);
  }
 catch (  OWLOntologyCreationException e1) {
    e1.printStackTrace();
  }
  initBaseReasoner();
  boolean inconsistentOntology=!reasoner.isConsistent();
  if (!inconsistentOntology) {
    reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY,InferenceType.CLASS_ASSERTIONS);
  }
 else {
    PelletExplanation expGen=new PelletExplanation(ontology);
    System.out.println(expGen.getInconsistencyExplanation());
    reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
    throw new ComponentInitException("String_Node_Str");
  }
  df=manager.getOWLDataFactory();
  Set<OWLDataProperty> numericDataProperties=new HashSet<OWLDataProperty>();
  for (  OWLDataProperty dataProperty : datatypeProperties) {
    Collection<OWLDataRange> ranges=EntitySearcher.getRanges(dataProperty,owlAPIOntologies);
    Iterator<OWLDataRange> it=ranges.iterator();
    if (it.hasNext()) {
      OWLDataRange range=it.next();
      if (range.isDatatype() && range.asOWLDatatype().isBuiltIn()) {
        datatype2Properties.put(range.asOWLDatatype().getBuiltInDatatype(),dataProperty);
        if (isNumericDatatype(range.asOWLDatatype())) {
          numericDataProperties.add(dataProperty);
        }
      }
    }
 else {
      datatype2Properties.put(OWL2Datatype.XSD_STRING,dataProperty);
    }
  }
  Iterator<OWLClass> it=atomicConcepts.iterator();
  while (it.hasNext()) {
    OWLClass cls=(OWLClass)it.next();
    if (cls.getIRI().isReservedVocabulary()) {
      it.remove();
    }
  }
}

Fixed version (ground truth):
@Override public void init() throws ComponentInitException {
  atomicConcepts=new TreeSet<OWLClass>();
  atomicRoles=new TreeSet<OWLObjectProperty>();
  datatypeProperties=new TreeSet<OWLDataProperty>();
  individuals=new TreeSet<OWLIndividual>();
  df=new OWLDataFactoryImpl();
  manager=OWLManager.createOWLOntologyManager();
  prefixes=new TreeMap<String,String>();
  for (  KnowledgeSource source : sources) {
    if (source instanceof OWLOntologyKnowledgeSource) {
      ontology=((OWLOntologyKnowledgeSource)source).createOWLOntology(manager);
      owlAPIOntologies.add(ontology);
    }
 else {
      throw new ComponentInitException("String_Node_Str" + source.getClass().getName());
    }
    atomicConcepts.addAll(ontology.getClassesInSignature(Imports.INCLUDED));
    atomicRoles.addAll(ontology.getObjectPropertiesInSignature(Imports.INCLUDED));
    datatypeProperties.addAll(ontology.getDataPropertiesInSignature(Imports.INCLUDED));
    individuals.addAll(ontology.getIndividualsInSignature(Imports.INCLUDED));
    OWLDocumentFormat format=manager.getOntologyFormat(ontology);
    if (format instanceof PrefixDocumentFormat) {
      prefixes.putAll(((PrefixDocumentFormat)format).getPrefixName2PrefixMap());
      baseURI=((PrefixDocumentFormat)format).getDefaultPrefix();
      prefixes.remove("String_Node_Str");
    }
  }
  try {
    ontology=manager.createOntology(IRI.create("String_Node_Str"),new HashSet<OWLOntology>(owlAPIOntologies));
    List<OWLOntologyChange> addImports=new ArrayList<OWLOntologyChange>();
    for (    OWLOntology ont : owlAPIOntologies) {
      for (      OWLImportsDeclaration importDeclaration : ont.getImportsDeclarations()) {
        addImports.add(new AddImport(ontology,importDeclaration));
      }
    }
    manager.applyChanges(addImports);
  }
 catch (  OWLOntologyCreationException e1) {
    e1.printStackTrace();
  }
  initBaseReasoner();
  boolean inconsistentOntology=!reasoner.isConsistent();
  if (!inconsistentOntology) {
    reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY,InferenceType.CLASS_ASSERTIONS);
  }
 else {
    PelletExplanation expGen=new PelletExplanation(ontology);
    System.out.println(expGen.getInconsistencyExplanation());
    reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
    throw new ComponentInitException("String_Node_Str");
  }
  df=manager.getOWLDataFactory();
  Set<OWLDataProperty> numericDataProperties=new HashSet<OWLDataProperty>();
  for (  OWLDataProperty dataProperty : datatypeProperties) {
    Collection<OWLDataRange> ranges=EntitySearcher.getRanges(dataProperty,owlAPIOntologies);
    Iterator<OWLDataRange> it=ranges.iterator();
    if (it.hasNext()) {
      OWLDataRange range=it.next();
      if (range.isDatatype() && range.asOWLDatatype().isBuiltIn()) {
        datatype2Properties.put(range.asOWLDatatype().getBuiltInDatatype(),dataProperty);
        if (isNumericDatatype(range.asOWLDatatype())) {
          numericDataProperties.add(dataProperty);
        }
      }
    }
 else {
      datatype2Properties.put(OWL2Datatype.XSD_STRING,dataProperty);
    }
  }
  Iterator<OWLClass> it=atomicConcepts.iterator();
  while (it.hasNext()) {
    OWLClass cls=(OWLClass)it.next();
    if (cls.getIRI().isReservedVocabulary()) {
      it.remove();
    }
  }
  minimizer=new OWLClassExpressionMinimizer(df,this);
}