nus-yam/ex-repair huggingface dataset:
Program: 9853
Project: 9853
Buggy source:
@Override public void mouseMoved(MouseEvent e){
  ResultTable result=((ResultTable)e.getSource());
  int column=result.columnAtPoint(e.getPoint());
  int row=result.rowAtPoint(e.getPoint());
  EvaluatedDescriptionClass ec=result.getValueAtRow(row);
  if (column == 0) {
    graphPanel2.clear();
    graphPanel2.setNewClassDescription(ec);
    showCoveragePanel(true);
  }
 else {
    showCoveragePanel(false);
  }
}

Fixed version (ground truth):
@Override public void mouseMoved(MouseEvent e){
  if (e.getSource() instanceof ResultTable) {
    ResultTable result=((ResultTable)e.getSource());
    int column=result.columnAtPoint(e.getPoint());
    int row=result.rowAtPoint(e.getPoint());
    if (column == 0 && row >= 0 && row <= 9) {
      EvaluatedDescriptionClass ec=result.getValueAtRow(row);
      graphPanel2.clear();
      graphPanel2.setNewClassDescription(ec);
      showCoveragePanel(true);
    }
 else {
      showCoveragePanel(false);
    }
  }
 else {
    showCoveragePanel(false);
  }
}
Program: 9855
Project: 9855
Buggy source:
public HyperLinkHandler(){
  try {
    launcher=new BrowserLauncher();
  }
 catch (  BrowserLaunchingInitializingException e) {
    e.printStackTrace();
  }
catch (  UnsupportedOperatingSystemException e) {
    e.printStackTrace();
  }
}

Fixed version (ground truth):
/** 
 * This is the constructor that instantiate the BrowserLauncher.
 */
public HyperLinkHandler(){
  try {
    launcher=new BrowserLauncher();
  }
 catch (  BrowserLaunchingInitializingException e) {
    e.printStackTrace();
  }
catch (  UnsupportedOperatingSystemException e) {
    e.printStackTrace();
  }
}
Program: 9858
Project: 9858
Buggy source:
/** 
 * Checks the URI if a "#" is in it.
 */
private void checkURI(){
  ontologieURI=new HashSet<String>();
  Set<OWLOntology> ont=editor.getModelManager().getActiveOntologies();
  Set<Individual> indi=reasoner.getIndividuals();
  for (  OWLOntology onto : ont) {
    String ontURI=onto.getURI().toString();
    for (    Individual ind : indi) {
      if (ind.toString().contains(ontURI)) {
        if (ind.toString().contains("String_Node_Str")) {
          ontologieURI.add(onto.getURI().toString() + "String_Node_Str");
          break;
        }
 else {
          ontologieURI.add(onto.getURI().toString());
          break;
        }
      }
    }
  }
  model.setOntologyURIString(ontologieURI);
}

Fixed version (ground truth):
/** 
 * Puts every base uri in a HashSet.
 */
private void checkURI(){
  ontologieURI=new HashSet<String>();
  Set<Individual> indi=reasoner.getIndividuals();
  for (  Individual ind : indi) {
    int ontURI=ind.toString().lastIndexOf("String_Node_Str");
    int ontURI2=ind.toString().lastIndexOf("String_Node_Str");
    String uriNeu="String_Node_Str";
    String uriAlt="String_Node_Str";
    if (ontURI2 != -1) {
      uriNeu=ind.toString().substring(0,ontURI2 + 1);
      if (uriNeu != uriAlt) {
        ontologieURI.add(uriNeu);
        uriAlt=uriNeu;
        uriNeu="String_Node_Str";
        String uriTest=indi.toString().replace(uriAlt,"String_Node_Str");
        if (!uriTest.contains("String_Node_Str") && !uriTest.contains("String_Node_Str")) {
          break;
        }
      }
    }
 else {
      uriNeu=ind.toString().substring(0,ontURI + 1);
      if (uriNeu != uriAlt) {
        ontologieURI.add(uriNeu);
        uriAlt=uriNeu;
        uriNeu="String_Node_Str";
        String uriTest=indi.toString().replace(uriAlt,"String_Node_Str");
        if (!uriTest.contains("String_Node_Str") && !uriTest.contains("String_Node_Str")) {
          break;
        }
      }
    }
  }
  model.setOntologyURIString(ontologieURI);
}
Program: 9861
Project: 9861
Buggy source:
/** 
 * This is the constructor for the SuggestClassPanelHandler.
 * @param v DLLearnerView
 * @param m DLLearnerModel
 */
public SuggestClassPanelHandler(DLLearnerView v,DLLearnerModel m){
  this.view=v;
  this.model=m;
}

Fixed version (ground truth):
/** 
 * This is the constructor for the SuggestClassPanelHandler.
 * @param v DLLearnerView
 * @param m DLLearnerModel
 */
public SuggestClassPanelHandler(DLLearnerView v,DLLearnerModel m,ActionHandler a){
  this.view=v;
  this.model=m;
  this.action=a;
}
Program: 9862
Project: 9862
Buggy source:
@Override public void mouseClicked(MouseEvent e){
  if (view.getSuggestClassPanel().getSuggestList().getSelectedValue() != null) {
    SuggestListItem item=(SuggestListItem)view.getSuggestClassPanel().getSuggestList().getSelectedValue();
    String desc=item.getValue();
    if (model.getEvaluatedDescriptionList() != null) {
      List<? extends EvaluatedDescription> evalList=model.getEvaluatedDescriptionList();
      Set<String> onto=model.getOntologyURIString();
      for (      EvaluatedDescription eDescription : evalList) {
        for (        String ont : onto) {
          if (desc.equals(eDescription.getDescription().toManchesterSyntaxString(ont,null))) {
            evaluatedDescription=eDescription;
            break;
          }
        }
      }
    }
    view.getMoreDetailForSuggestedConceptsPanel().renderDetailPanel(evaluatedDescription);
    view.setGraphicalPanel();
  }
}

Fixed version (ground truth):
@Override public void mouseClicked(MouseEvent e){
  if (view.getSuggestClassPanel().getSuggestList().getSelectedValue() != null) {
    SuggestListItem item=(SuggestListItem)view.getSuggestClassPanel().getSuggestList().getSelectedValue();
    String desc=item.getValue();
    if (model.getEvaluatedDescriptionList() != null) {
      List<? extends EvaluatedDescription> evalList=model.getEvaluatedDescriptionList();
      Set<String> onto=model.getOntologyURIString();
      for (      EvaluatedDescription eDescription : evalList) {
        for (        String ont : onto) {
          if (desc.equals(eDescription.getDescription().toManchesterSyntaxString(ont,null))) {
            evaluatedDescription=eDescription;
            action.setEvaluatedClassExpression(eDescription);
            break;
          }
        }
      }
    }
    view.getMoreDetailForSuggestedConceptsPanel().renderDetailPanel(evaluatedDescription);
    view.setGraphicalPanel();
  }
}
Program: 9864
Project: 9864
Buggy source:
@Override public void activeOntologyChanged(){
  ontology=OREManager.getInstance().getReasoner().getOWLAPIOntologies();
  reasoner=OREManager.getInstance().getReasoner().getReasoner();
  gen=new CachedExplanationGenerator(ontology,reasoner);
  orderingMap.clear();
}

Fixed version (ground truth):
@Override public void activeOntologyChanged(){
  ontology=OREManager.getInstance().getReasoner().getOWLAPIOntologies();
  reasoner=OREManager.getInstance().getReasoner().getReasoner();
  gen=new CachedExplanationGenerator(ontology,reasoner);
  orderingMap.clear();
  usageChecker=new AxiomUsageChecker(ontology);
}
Program: 9865
Project: 9865
Buggy source:
public LearningManager(){
  listeners=new ArrayList<LearningManagerListener>();
}

Fixed version (ground truth):
public LearningManager(){
  listeners=new ArrayList<LearningManagerListener>();
  newDescriptions=new ArrayList<EvaluatedDescriptionClass>();
}
Program: 9866
Project: 9866
Buggy source:
public void setNewDescriptions(List<EvaluatedDescriptionClass> newDescriptions){
  this.newDescriptions=newDescriptions;
  currentDescriptionIndex=0;
  fireNewDescriptionsAdded(newDescriptions);
  setNextDescription();
}

Fixed version (ground truth):
public void setNewDescriptions(List<List<EvaluatedDescriptionClass>> descriptions){
  newDescriptions.clear();
  newDescriptions.addAll(descriptions.get(0));
  newDescriptions.addAll(descriptions.get(1));
  equivalentDescriptions=descriptions.get(0);
  superDescriptions=descriptions.get(1);
  currentDescriptionIndex=0;
  fireNewDescriptionsAdded(newDescriptions);
  setNextDescription();
}
Program: 9867
Project: 9867
Buggy source:
public boolean consistentOntology() throws InconsistentOntologyException {
  return reasoner.isConsistent();
}

Fixed version (ground truth):
public boolean consistentOntology() throws InconsistentOntologyException {
  return consistentOntology;
}
Program: 9868
Project: 9868
Buggy source:
public void initPelletReasoner() throws URISyntaxException, OWLOntologyCreationException {
  reasoner=cm.reasoner(PelletReasoner.class,ks);
  try {
    reasoner.init();
  }
 catch (  ComponentInitException e) {
    e.printStackTrace();
  }
  reasoner.loadOntologies();
  reasoner.addProgressMonitor(TaskManager.getInstance().getStatusBar());
  baseURI=reasoner.getBaseURI();
  prefixes=reasoner.getPrefixes();
  modifier=new OntologyModifier(reasoner);
  fireActiveOntologyChanged();
}

Fixed version (ground truth):
public void initPelletReasoner() throws URISyntaxException, OWLOntologyCreationException {
  reasoner=cm.reasoner(PelletReasoner.class,ks);
  try {
    reasoner.init();
  }
 catch (  ComponentInitException e) {
    e.printStackTrace();
  }
  reasoner.loadOntologies();
  reasoner.addProgressMonitor(TaskManager.getInstance().getStatusBar());
  baseURI=reasoner.getBaseURI();
  prefixes=reasoner.getPrefixes();
  modifier=new OntologyModifier(reasoner);
  fireActiveOntologyChanged();
  consistentOntology=reasoner.isConsistent();
}
Program: 9870
Project: 9870
Buggy source:
public void addURI(URI uri){
  if (!uriList.contains(uri)) {
    uriList.add(uri);
  }
}

Fixed version (ground truth):
public void addURI(URI uri){
  if (uri != null && !uriList.contains(uri)) {
    uriList.add(uri);
  }
}
Program: 9872
Project: 9872
Buggy source:
public static void miniEconomyTest(){
  String file="String_Node_Str";
  try {
    OWLOntologyManager manager=OWLManager.createOWLOntologyManager();
    ManchesterSyntaxExplanationRenderer renderer=new ManchesterSyntaxExplanationRenderer();
    PrintWriter pw=new PrintWriter(System.out);
    renderer.startRendering(pw);
    OWLOntology ontology=manager.loadOntologyFromPhysicalURI(URI.create(file));
    Set<OWLOntology> ontologies=new HashSet<OWLOntology>();
    ontologies.add(ontology);
    PelletReasonerFactory resonerFact=new PelletReasonerFactory();
    OWLDataFactory dataFactory=manager.getOWLDataFactory();
    Reasoner reasoner=resonerFact.createReasoner(manager);
    reasoner.loadOntologies(ontologies);
    SwingProgressMonitor monitor=new SwingProgressMonitor();
    reasoner.getKB().getTaxonomyBuilder().setProgressMonitor(monitor);
    reasoner.classify();
    System.out.println(reasoner.getInconsistentClasses());
    LaconicExplanationGenerator expGen=new LaconicExplanationGenerator(manager,resonerFact,ontologies);
    Set<OWLClass> unsatClasses=reasoner.getInconsistentClasses();
    OWLSubClassAxiom unsatAxiom;
    unsatAxiom=dataFactory.getOWLSubClassAxiom(dataFactory.getOWLClass(URI.create("String_Node_Str")),dataFactory.getOWLNothing());
    Set<Explanation> preciseJusts=expGen.getExplanations(unsatAxiom);
    renderer.endRendering();
  }
 catch (  OWLOntologyCreationException e) {
    e.printStackTrace();
  }
catch (  OWLException e) {
    e.printStackTrace();
  }
catch (  UnsupportedOperationException e) {
    e.printStackTrace();
  }
}

Fixed version (ground truth):
public static void miniEconomyTest(){
  String file="String_Node_Str";
  try {
    OWLOntologyManager manager=OWLManager.createOWLOntologyManager();
    OWLOntology ontology=manager.loadOntologyFromPhysicalURI(URI.create(file));
    PelletReasonerFactory resonerFact=new PelletReasonerFactory();
    OWLDataFactory dataFactory=manager.getOWLDataFactory();
    Reasoner reasoner=resonerFact.createReasoner(manager);
    reasoner.loadOntology(ontology);
    reasoner.classify();
    System.out.println(reasoner.getInconsistentClasses());
    LaconicExplanationGenerator expGen=new LaconicExplanationGenerator(manager,resonerFact,Collections.singleton(ontology));
    Set<OWLClass> unsatClasses=reasoner.getInconsistentClasses();
    OWLSubClassAxiom unsatAxiom;
    for (    OWLClass unsat : unsatClasses) {
      unsatAxiom=dataFactory.getOWLSubClassAxiom(unsat,dataFactory.getOWLNothing());
      Set<Explanation> explanations=expGen.getExplanations(unsatAxiom);
      System.out.println(explanations);
    }
  }
 catch (  OWLOntologyCreationException e) {
    e.printStackTrace();
  }
catch (  OWLException e) {
    e.printStackTrace();
  }
catch (  UnsupportedOperationException e) {
    e.printStackTrace();
  }
}
Program: 9873
Project: 9873
Buggy source:
public static void test(){
  String file="String_Node_Str";
  try {
    OWLOntologyManager manager=OWLManager.createOWLOntologyManager();
    ManchesterSyntaxExplanationRenderer renderer=new ManchesterSyntaxExplanationRenderer();
    PrintWriter pw=new PrintWriter(System.out);
    renderer.startRendering(pw);
    OWLDataFactory dataFactory=manager.getOWLDataFactory();
    PelletReasonerFactory resonerFact=new PelletReasonerFactory();
    OWLOntology ontology=manager.loadOntologyFromPhysicalURI(URI.create(file));
    Reasoner reasoner=resonerFact.createReasoner(manager);
    reasoner.loadOntologies(Collections.singleton(ontology));
    System.out.println(reasoner.getInconsistentClasses());
    PelletExplanation exp=new PelletExplanation(manager,Collections.singleton(ontology));
    System.out.println(exp.getUnsatisfiableExplanations(dataFactory.getOWLClass(URI.create("String_Node_Str"))));
    renderer.endRendering();
  }
 catch (  OWLOntologyCreationException e) {
    e.printStackTrace();
  }
catch (  OWLException e) {
    e.printStackTrace();
  }
}

Fixed version (ground truth):
public static void test(){
  String file="String_Node_Str";
  try {
    OWLOntologyManager manager=OWLManager.createOWLOntologyManager();
    ManchesterSyntaxExplanationRenderer renderer=new ManchesterSyntaxExplanationRenderer();
    PrintWriter pw=new PrintWriter(System.out);
    renderer.startRendering(pw);
    OWLDataFactory dataFactory=manager.getOWLDataFactory();
    PelletReasonerFactory resonerFact=new PelletReasonerFactory();
    OWLOntology ontology=manager.loadOntologyFromPhysicalURI(URI.create(file));
    Reasoner reasoner=resonerFact.createReasoner(manager);
    reasoner.loadOntologies(Collections.singleton(ontology));
    System.out.println(reasoner.getInconsistentClasses());
    PelletExplanation exp=new PelletExplanation(manager,Collections.singleton(ontology));
    System.out.println(exp.getUnsatisfiableExplanations(dataFactory.getOWLClass(URI.create("String_Node_Str"))));
    renderer.endRendering();
  }
 catch (  OWLOntologyCreationException e) {
    e.printStackTrace();
  }
}
Program: 9874
Project: 9874
Buggy source:
public static void main(String[] args){
  test();
  miniTest();
  miniEconomyTest();
  universityTest();
}

Fixed version (ground truth):
public static void main(String[] args){
  miniEconomyTest();
}
Program: 9876
Project: 9876
Buggy source:
public OntologyExtractingTask(ProgressMonitor mon){
  this.mon=mon;
}

Fixed version (ground truth):
public OntologyExtractingTask(JDialog dialog,ProgressMonitor mon){
  this.mon=mon;
  this.dialog=dialog;
}
Program: 9877
Project: 9877
Buggy source:
@Override public void done(){
  if (!isCancelled() && ks != null) {
    okButton.setEnabled(true);
    message.setText("String_Node_Str");
  }
}

Fixed version (ground truth):
@Override public void done(){
  dialog.setCursor(null);
  if (!isCancelled() && ks != null) {
    okButton.setEnabled(true);
    message.setText("String_Node_Str");
  }
}
Program: 9878
Project: 9878
Buggy source:
private void extract(){
  if (urlIsConnectable()) {
    message.setText("String_Node_Str");
    mon=new ProgressMonitor(this,"String_Node_Str","String_Node_Str",0,100);
    extractTask=new OntologyExtractingTask(mon);
    extractTask.addPropertyChangeListener(this);
    extractTask.execute();
  }
 else {
    message.setText("String_Node_Str");
  }
}

Fixed version (ground truth):
private void extract(){
  message.setText("String_Node_Str");
  setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
  mon=new ProgressMonitor(this,"String_Node_Str","String_Node_Str",0,100);
  extractTask=new OntologyExtractingTask(this,mon);
  extractTask.addPropertyChangeListener(this);
  extractTask.execute();
}
Program: 9879
Project: 9879
Buggy source:
public List<URI> getURIs(){
  uriList.clear();
  deserialize();
  return uriList;
}

Fixed version (ground truth):
public List<URI> getURIs(){
  return uriList;
}
Program: 9880
Project: 9880
Buggy source:
@SuppressWarnings("String_Node_Str") private void deserialize(){
  try {
    FileInputStream fileStream=new FileInputStream(file);
    ObjectInputStream inputStream=new ObjectInputStream(new BufferedInputStream(fileStream));
    try {
      List<URI> list=(List<URI>)inputStream.readObject();
      if (list != null) {
        uriList.addAll(list);
      }
    }
  finally {
      inputStream.close();
    }
  }
 catch (  IOException e) {
    e.printStackTrace();
  }
catch (  ClassNotFoundException e) {
    e.printStackTrace();
  }
}

Fixed version (ground truth):
@SuppressWarnings("String_Node_Str") public void deserialize(){
  try {
    FileInputStream fileStream=new FileInputStream(file);
    ObjectInputStream inputStream=new ObjectInputStream(new BufferedInputStream(fileStream));
    try {
      List<URI> list=(List<URI>)inputStream.readObject();
      if (list != null) {
        uriList.addAll(list);
      }
    }
  finally {
      inputStream.close();
    }
  }
 catch (  IOException e) {
    System.err.println("String_Node_Str");
  }
catch (  ClassNotFoundException e) {
    e.printStackTrace();
  }
}
Program: 9881
Project: 9881
Buggy source:
public Set<Explanation> getExplanations(OWLAxiom entailment,int limit) throws ExplanationException {
  Set<Explanation> explanations;
  try {
    explanations=computePreciseJusts(entailment,limit);
  }
 catch (  OWLException e) {
    throw new ExplanationException(e);
  }
  return explanations;
}

Fixed version (ground truth):
public Set<Explanation> getExplanations(OWLAxiom entailment,int limit) throws ExplanationException {
  if (log.isLoggable(Level.CONFIG))   log.config("String_Node_Str" + (limit == Integer.MAX_VALUE ? "String_Node_Str" : limit) + "String_Node_Str"+ entailment);
  Set<Explanation> explanations;
  try {
    explanations=computePreciseJusts(entailment,limit);
  }
 catch (  OWLException e) {
    throw new ExplanationException(e);
  }
  return explanations;
}
Program: 9883
Project: 9883
Buggy source:
@Override public boolean equals(Object o){
  return (compareTo((Individual)o) == 0);
}

Fixed version (ground truth):
@Override public boolean equals(Object o){
  if (o == null) {
    return false;
  }
  return (compareTo((Individual)o) == 0);
}
Program: 9884
Project: 9884
Buggy source:
/** 
 * This convenience method can be used to store and exchange evaluated descriptions by transforming them to a JSON string.
 * @return A JSON representation of an evaluated description.
 */
@Override public String asJSON(){
  JSONObject object=new JSONObject();
  try {
    object.put("String_Node_Str",description.toManchesterSyntaxString(null,null));
    OWLDescription d=OWLAPIDescriptionConvertVisitor.getOWLDescription(description);
    object.put("String_Node_Str",OWLAPIRenderers.toOWLXMLSyntax(d));
    object.put("String_Node_Str",description.toKBSyntaxString());
    object.put("String_Node_Str",score.getAccuracy());
    object.put("String_Node_Str",getAdditionalInstances());
    object.put("String_Node_Str",getCoveredInstances());
    object.put("String_Node_Str",isConsistent());
    object.put("String_Node_Str",getCoverage());
    object.put("String_Node_Str",getAddition());
    return object.toString(3);
  }
 catch (  JSONException e) {
    e.printStackTrace();
    return null;
  }
}

Fixed version (ground truth):
/** 
 * This convenience method can be used to store and exchange evaluated descriptions by transforming them to a JSON string.
 * @return A JSON representation of an evaluated description.
 */
@Override public String asJSON(){
  JSONObject object=new JSONObject();
  try {
    object.put("String_Node_Str",description.toManchesterSyntaxString(null,null));
    OWLDescription d=OWLAPIDescriptionConvertVisitor.getOWLDescription(description);
    object.put("String_Node_Str",OWLAPIRenderers.toOWLXMLSyntax(d));
    object.put("String_Node_Str",description.toKBSyntaxString());
    object.put("String_Node_Str",score.getAccuracy());
    object.put("String_Node_Str",new JSONArray(getAdditionalInstances()));
    object.put("String_Node_Str",new JSONArray(getCoveredInstances()));
    object.put("String_Node_Str",isConsistent());
    object.put("String_Node_Str",getCoverage());
    object.put("String_Node_Str",getAddition());
    return object.toString(3);
  }
 catch (  JSONException e) {
    e.printStackTrace();
    return null;
  }
}
Program: 9887
Project: 9887
Buggy source:
@Override public void run(){
  int ret=wizard.showModalDialog();
  System.out.println("String_Node_Str" + ret);
  System.exit(0);
}

Fixed version (ground truth):
@Override public void run(){
  System.out.println("String_Node_Str");
  int ret=wizard.showModalDialog();
  System.out.println("String_Node_Str");
  System.exit(0);
}
Program: 9888
Project: 9888
Buggy source:
public void loadOntology(){
  reasoner.loadOntologies();
}

Fixed version (ground truth):
public void loadOntology() throws OWLOntologyCreationException, URISyntaxException {
  reasoner.loadOntologies();
}
Program: 9889
Project: 9889
Buggy source:
public void initPelletReasoner(){
  reasoner=cm.reasoner(PelletReasoner.class,ks);
  try {
    reasoner.init();
  }
 catch (  ComponentInitException e) {
    e.printStackTrace();
  }
  reasoner.loadOntologies();
  baseURI=reasoner.getBaseURI();
  prefixes=reasoner.getPrefixes();
  modifier=new OntologyModifier(reasoner);
  fireActiveOntologyChanged();
}

Fixed version (ground truth):
public void initPelletReasoner() throws URISyntaxException, OWLOntologyCreationException {
  reasoner=cm.reasoner(PelletReasoner.class,ks);
  try {
    reasoner.init();
  }
 catch (  ComponentInitException e) {
    e.printStackTrace();
  }
  reasoner.loadOntologies();
  baseURI=reasoner.getBaseURI();
  prefixes=reasoner.getPrefixes();
  modifier=new OntologyModifier(reasoner);
  fireActiveOntologyChanged();
}
Program: 9890
Project: 9890
Buggy source:
@SuppressWarnings("String_Node_Str") private void deserialize(){
  try {
    FileInputStream fileStream=new FileInputStream(file);
    ObjectInputStream inputStream=new ObjectInputStream(new BufferedInputStream(fileStream));
    try {
      List<URI> list=(List<URI>)inputStream.readObject();
      uriList.addAll(list);
    }
  finally {
      inputStream.close();
    }
  }
 catch (  IOException e) {
    e.printStackTrace();
  }
catch (  ClassNotFoundException e) {
    e.printStackTrace();
  }
}

Fixed version (ground truth):
@SuppressWarnings("String_Node_Str") private void deserialize(){
  try {
    FileInputStream fileStream=new FileInputStream(file);
    ObjectInputStream inputStream=new ObjectInputStream(new BufferedInputStream(fileStream));
    try {
      List<URI> list=(List<URI>)inputStream.readObject();
      if (list != null) {
        uriList.addAll(list);
      }
    }
  finally {
      inputStream.close();
    }
  }
 catch (  IOException e) {
    e.printStackTrace();
  }
catch (  ClassNotFoundException e) {
    e.printStackTrace();
  }
}
Program: 9891
Project: 9891
Buggy source:
public Set<OWLAxiom> getRemainingAxioms(OWLAxiom source,OWLAxiom part){
  Set<OWLAxiom> parts=computeOPlus(Collections.singleton(source));
  System.out.println("String_Node_Str" + parts);
  parts.remove(part);
  System.out.println("String_Node_Str" + part);
  for (  OWLAxiom pa : parts) {
    System.out.println("String_Node_Str" + pa + "String_Node_Str"+ oPlus.getAxiomsMap().get(pa));
    if (oPlus.getAxiomsMap().get(pa).size() == 1) {
      System.out.println("String_Node_Str" + pa);
    }
  }
  return rebuildAxioms(parts);
}

Fixed version (ground truth):
public Set<OWLAxiom> getRemainingAxioms(OWLAxiom source,OWLAxiom part){
  Set<OWLAxiom> parts=computeOPlus(Collections.singleton(source));
  for (  OWLAxiom par : parts) {
    System.out.println("String_Node_Str" + par);
  }
  for (  OWLAxiom pa : parts) {
    System.out.println("String_Node_Str" + pa);
    for (    OWLAxiom ax : oPlus.getAxiomsMap().get(pa)) {
      System.out.println("String_Node_Str" + ax);
    }
  }
  return rebuildAxioms(parts);
}
Program: 9894
Project: 9894
Buggy source:
@Override public void run(){
  System.out.println("String_Node_Str");
  int ret=wizard.showModalDialog();
  System.out.println("String_Node_Str");
  System.exit(0);
}

Fixed version (ground truth):
@Override public void run(){
  System.out.println("String_Node_Str");
  wizard.showModalDialog();
  System.out.println("String_Node_Str");
  System.exit(0);
}
Program: 9895
Project: 9895
Buggy source:
public static void main(String[] args) throws OWLOntologyCreationException {
  String file="String_Node_Str";
  String NS="String_Node_Str";
  OWLOntologyManager manager=OWLManager.createOWLOntologyManager();
  OWLDataFactory factory=manager.getOWLDataFactory();
  OWLOntology ontology=manager.loadOntology(URI.create(file));
  Reasoner reasoner=new PelletReasonerFactory().createReasoner(manager);
  reasoner.loadOntology(ontology);
  OWLDataProperty property=factory.getOWLDataProperty(URI.create(NS + "String_Node_Str"));
  OWLClass domain=factory.getOWLClass(URI.create(NS + "String_Node_Str"));
  OWLDataPropertyDomainAxiom axiom=factory.getOWLDataPropertyDomainAxiom(property,domain);
  PelletExplanation expGen=new PelletExplanation(manager,Collections.singleton(ontology));
  System.out.println(reasoner.isEntailed(axiom));
}

Fixed version (ground truth):
public static void main(String[] args) throws OWLOntologyCreationException {
  String file="String_Node_Str";
  String NS="String_Node_Str";
  OWLOntologyManager manager=OWLManager.createOWLOntologyManager();
  OWLDataFactory factory=manager.getOWLDataFactory();
  OWLOntology ontology=manager.loadOntology(URI.create(file));
  Reasoner reasoner=new PelletReasonerFactory().createReasoner(manager);
  reasoner.loadOntology(ontology);
  OWLDataProperty property=factory.getOWLDataProperty(URI.create(NS + "String_Node_Str"));
  OWLClass domain=factory.getOWLClass(URI.create(NS + "String_Node_Str"));
  OWLDataPropertyDomainAxiom axiom=factory.getOWLDataPropertyDomainAxiom(property,domain);
  PelletExplanation expGen=new PelletExplanation(manager,Collections.singleton(ontology));
  System.out.println(reasoner.isEntailed(axiom));
  System.out.println(expGen.getEntailmentExplanations(axiom));
  OWLDataRange range=factory.getTopDataType();
  OWLDataSomeRestriction dataSome=factory.getOWLDataSomeRestriction(property,range);
  OWLSubClassAxiom subClass=factory.getOWLSubClassAxiom(dataSome,domain);
  System.out.println(reasoner.isEntailed(subClass));
  System.out.println(expGen.getEntailmentExplanations(subClass));
}
Program: 9896
Project: 9896
Buggy source:
public void removeFromRepairPlan(OWLOntologyChange change){
  repairPlan.remove(change);
  fireRepairPlanChanged();
}

Fixed version (ground truth):
public void removeFromRepairPlan(List<OWLOntologyChange> changes){
  repairPlan.removeAll(changes);
  fireRepairPlanChanged();
}
Program: 9897
Project: 9897
Buggy source:
public void addToRepairPlan(OWLOntologyChange change){
  repairPlan.add(change);
  fireRepairPlanChanged();
}

Fixed version (ground truth):
public void addToRepairPlan(List<OWLOntologyChange> changes){
  repairPlan.addAll(changes);
  fireRepairPlanChanged();
}
Program: 9898
Project: 9898
Buggy source:
private Set<Explanation> computeLaconicExplanations(OWLAxiom entailment,int limit) throws ExplanationException {
  Set<Explanation> explanations=laconicExplanationCache.get(entailment);
  Integer lastRequestedSize=lastRequestedLaconicSize.get(entailment);
  if (lastRequestedSize == null) {
    lastRequestedSize=Integer.valueOf(0);
  }
  if (explanations == null || lastRequestedSize.intValue() != -1 && lastRequestedSize.intValue() < limit) {
    OWLOntology module=axiom2Module.get(entailment);
    if (module == null) {
      module=OntologyUtils.getOntologyFromAxioms(ModularityUtils.extractModule(Collections.singleton(ontology),entailment.getSignature(),ModuleType.TOP_OF_BOT));
    }
    axiom2Module.put(entailment,module);
    laconicExpGen=new LaconicExplanationGenerator(manager,new PelletReasonerFactory(),Collections.singleton(module));
    if (limit == -1) {
      explanations=laconicExpGen.getExplanations(entailment);
    }
 else {
      explanations=laconicExpGen.getExplanations(entailment,limit);
    }
    laconicExplanationCache.put(entailment,explanations);
    lastRequestedLaconicSize.put(entailment,Integer.valueOf(limit));
  }
  return explanations;
}

Fixed version (ground truth):
private Set<Explanation> computeLaconicExplanations(OWLAxiom entailment,int limit) throws ExplanationException {
  Set<Explanation> explanations=laconicExplanationCache.get(entailment);
  Integer lastRequestedSize=lastRequestedLaconicSize.get(entailment);
  if (lastRequestedSize == null) {
    lastRequestedSize=Integer.valueOf(0);
  }
  if (explanations == null || lastRequestedSize.intValue() != -1 && lastRequestedSize.intValue() < limit) {
    OWLOntology module=axiom2Module.get(entailment);
    if (module == null) {
      module=OntologyUtils.getOntologyFromAxioms(ModularityUtils.extractModule(Collections.singleton(ontology),entailment.getSignature(),ModuleType.TOP_OF_BOT));
    }
    axiom2Module.put(entailment,module);
    laconicExpGen=new LaconicExplanationGenerator(manager,new PelletReasonerFactory(),Collections.singleton(module));
    laconicExpGen.setProgressMonitor(TaskManager.getInstance().getStatusBar());
    if (limit == -1) {
      explanations=laconicExpGen.getExplanations(entailment);
    }
 else {
      explanations=laconicExpGen.getExplanations(entailment,limit);
    }
    laconicExplanationCache.put(entailment,explanations);
    lastRequestedLaconicSize.put(entailment,Integer.valueOf(limit));
  }
  return explanations;
}
Program: 9899
Project: 9899
Buggy source:
public Set<Set<OWLAxiom>> getExplanations(OWLDescription unsatClass,int maxExplanations){
  if (maxExplanations < 0)   throw new IllegalArgumentException();
  if (log.isLoggable(Level.CONFIG))   log.config("String_Node_Str" + (maxExplanations == 0 ? "String_Node_Str" : maxExplanations) + "String_Node_Str"+ unsatClass);
  try {
    Set<OWLAxiom> firstMups=getExplanation(unsatClass);
    if (firstMups.isEmpty()) {
      return Collections.emptySet();
    }
    Set<Set<OWLAxiom>> allMups=new LinkedHashSet<Set<OWLAxiom>>();
    progressMonitor.foundExplanation(firstMups);
    allMups.add(firstMups);
    Set<Set<OWLAxiom>> satPaths=new HashSet<Set<OWLAxiom>>();
    Set<OWLAxiom> currentPathContents=new HashSet<OWLAxiom>();
    singleExplanationGenerator.beginTransaction();
    try {
      constructHittingSetTree(unsatClass,firstMups,allMups,satPaths,currentPathContents,maxExplanations);
    }
  finally {
      singleExplanationGenerator.endTransaction();
    }
    progressMonitor.foundAllExplanations();
    return allMups;
  }
 catch (  OWLException e) {
    throw new OWLRuntimeException(e);
  }
}

Fixed version (ground truth):
public Set<Set<OWLAxiom>> getExplanations(OWLDescription unsatClass,int maxExplanations){
  if (maxExplanations < 0)   throw new IllegalArgumentException();
  logger.debug("String_Node_Str" + (maxExplanations == 0 ? "String_Node_Str" : maxExplanations) + "String_Node_Str"+ unsatClass);
  try {
    Set<OWLAxiom> firstMups=getExplanation(unsatClass);
    if (firstMups.isEmpty()) {
      return Collections.emptySet();
    }
    Set<Set<OWLAxiom>> allMups=new LinkedHashSet<Set<OWLAxiom>>();
    progressMonitor.foundExplanation(firstMups);
    allMups.add(firstMups);
    Set<Set<OWLAxiom>> satPaths=new HashSet<Set<OWLAxiom>>();
    Set<OWLAxiom> currentPathContents=new HashSet<OWLAxiom>();
    singleExplanationGenerator.beginTransaction();
    try {
      constructHittingSetTree(unsatClass,firstMups,allMups,satPaths,currentPathContents,maxExplanations);
    }
  finally {
      singleExplanationGenerator.endTransaction();
    }
    progressMonitor.foundAllExplanations();
    return allMups;
  }
 catch (  OWLException e) {
    throw new OWLRuntimeException(e);
  }
}
Program: 9901
Project: 9901
Buggy source:
public static void test(){
  String file="String_Node_Str";
  try {
    OWLOntologyManager manager=OWLManager.createOWLOntologyManager();
    ManchesterSyntaxExplanationRenderer renderer=new ManchesterSyntaxExplanationRenderer();
    PrintWriter pw=new PrintWriter(System.out);
    renderer.startRendering(pw);
    OWLDataFactory dataFactory=manager.getOWLDataFactory();
    PelletReasonerFactory resonerFact=new PelletReasonerFactory();
    OWLOntology ontology=manager.loadOntologyFromPhysicalURI(URI.create(file));
    Set<OWLOntology> ontologies=new HashSet<OWLOntology>();
    Reasoner reasoner=resonerFact.createReasoner(manager);
    reasoner.loadOntologies(Collections.singleton(ontology));
    System.out.println(reasoner.getInconsistentClasses());
    PelletExplanation exp=new PelletExplanation(manager,Collections.singleton(ontology));
    System.out.println(exp.getUnsatisfiableExplanations(dataFactory.getOWLClass(URI.create("String_Node_Str"))));
    renderer.endRendering();
  }
 catch (  OWLOntologyCreationException e) {
    e.printStackTrace();
  }
catch (  OWLException e) {
    e.printStackTrace();
  }
}

Fixed version (ground truth):
public static void test(){
  String file="String_Node_Str";
  try {
    OWLOntologyManager manager=OWLManager.createOWLOntologyManager();
    ManchesterSyntaxExplanationRenderer renderer=new ManchesterSyntaxExplanationRenderer();
    PrintWriter pw=new PrintWriter(System.out);
    renderer.startRendering(pw);
    OWLDataFactory dataFactory=manager.getOWLDataFactory();
    PelletReasonerFactory resonerFact=new PelletReasonerFactory();
    OWLOntology ontology=manager.loadOntologyFromPhysicalURI(URI.create(file));
    Reasoner reasoner=resonerFact.createReasoner(manager);
    reasoner.loadOntologies(Collections.singleton(ontology));
    System.out.println(reasoner.getInconsistentClasses());
    PelletExplanation exp=new PelletExplanation(manager,Collections.singleton(ontology));
    System.out.println(exp.getUnsatisfiableExplanations(dataFactory.getOWLClass(URI.create("String_Node_Str"))));
    renderer.endRendering();
  }
 catch (  OWLOntologyCreationException e) {
    e.printStackTrace();
  }
catch (  OWLException e) {
    e.printStackTrace();
  }
}
Program: 9902
Project: 9902
Buggy source:
public static void main(String[] args){
  miniTest();
}

Fixed version (ground truth):
public static void main(String[] args){
  test();
  miniTest();
  miniEconomyTest();
  universityTest();
}
Program: 9908
Project: 9908
Buggy source:
@Override public String toString(){
  String str=uri + "String_Node_Str" + label+ "String_Node_Str"+ geoLat+ "String_Node_Str"+ geoLong+ "String_Node_Str";
  for (  String clazz : classes) {
    str+=clazz + "String_Node_Str";
  }
  return str + "String_Node_Str";
}

Fixed version (ground truth):
@Override public String toString(){
  String str=uri + "String_Node_Str" + label+ "String_Node_Str"+ geoLat+ "String_Node_Str"+ geoLong+ "String_Node_Str"+ classes.length+ "String_Node_Str";
  for (  String clazz : classes) {
    str+=clazz + "String_Node_Str";
  }
  return str + "String_Node_Str";
}
Program: 9909
Project: 9909
Buggy source:
/** 
 * This is the constructor for DL-Learner model.
 * @param editorKit Editor Kit to get the currently loaded Ontology
 * @param view current view of the DL-Learner tab
 */
public DLLearnerModel(OWLEditorKit editorKit,DLLearnerView view){
  editor=editorKit;
  isReasonerSet=false;
  this.view=view;
  ontologyConsistent=true;
  owlDescription=new HashSet<OWLDescription>();
  ComponentManager.setComponentClasses(componenten);
  cm=ComponentManager.getInstance();
  ds=new HashSet<OWLDescription>();
  suggestModel=new DefaultListModel();
  ontologieURI=new HashSet<String>();
  sources=new HashSet<KnowledgeSource>();
}

Fixed version (ground truth):
/** 
 * This is the constructor for DL-Learner model.
 * @param editorKit Editor Kit to get the currently loaded Ontology
 * @param view current view of the DL-Learner tab
 */
public DLLearnerModel(OWLEditorKit editorKit,DLLearnerView view){
  editor=editorKit;
  isReasonerSet=false;
  this.view=view;
  ontologyConsistent=true;
  knowledgeSourceIsUpdated=false;
  owlDescription=new HashSet<OWLDescription>();
  ComponentManager.setComponentClasses(componenten);
  cm=ComponentManager.getInstance();
  ds=new HashSet<OWLDescription>();
  suggestModel=new DefaultListModel();
  ontologieURI=new HashSet<String>();
  sources=new HashSet<KnowledgeSource>();
}
Program: 9912
Project: 9912
Buggy source:
@Override public void run(){
  String loading="String_Node_Str";
  view.getHintPanel().setForeground(Color.RED);
  view.setHintMessage(loading);
  if (!model.isReasonerSet()) {
    model.setKnowledgeSource();
    model.setReasoner();
  }
  reasoner=model.getReasoner();
  isInconsistent=view.getIsInconsistent();
  if (!isInconsistent) {
    this.checkURI();
    this.setPositiveConcept();
    if (this.hasIndividuals()) {
      view.getRunButton().setEnabled(true);
      view.getHintPanel().setForeground(Color.BLACK);
      view.setHintMessage("String_Node_Str");
    }
 else {
      view.getRunButton().setEnabled(false);
      view.getHintPanel().setVisible(true);
      String message="String_Node_Str" + current + "String_Node_Str";
      view.getHintPanel().setForeground(Color.RED);
      view.setHintMessage(message);
    }
  }
 else {
    view.getHintPanel().setForeground(Color.RED);
    view.getRunButton().setEnabled(false);
    view.setHintMessage("String_Node_Str");
  }
}

Fixed version (ground truth):
@Override public void run(){
  String loading="String_Node_Str";
  view.getHintPanel().setForeground(Color.RED);
  view.setHintMessage(loading);
  if (!model.isReasonerSet() || model.getIsKnowledgeSourceIsUpdated() == true) {
    model.setKnowledgeSource();
    model.setReasoner();
  }
  reasoner=model.getReasoner();
  isInconsistent=view.getIsInconsistent();
  if (!isInconsistent) {
    this.checkURI();
    this.setPositiveConcept();
    if (this.hasIndividuals()) {
      view.getRunButton().setEnabled(true);
      view.getHintPanel().setForeground(Color.BLACK);
      view.setHintMessage("String_Node_Str");
    }
 else {
      view.getRunButton().setEnabled(false);
      view.getHintPanel().setVisible(true);
      String message="String_Node_Str" + current + "String_Node_Str";
      view.getHintPanel().setForeground(Color.RED);
      view.setHintMessage(message);
    }
  }
 else {
    view.getHintPanel().setForeground(Color.RED);
    view.getRunButton().setEnabled(false);
    view.setHintMessage("String_Node_Str");
  }
}
Program: 9914
Project: 9914
Buggy source:
/** 
 * This method sets the reasoner. Only FastInstanceChecker is available.
 */
public void setReasoner(){
  this.reasoner=cm.reasoner(FastInstanceChecker.class,sources);
  try {
    reasoner.init();
    reasoner.isSatisfiable();
    view.setIsInconsistent(false);
    isReasonerSet=true;
  }
 catch (  ComponentInitException e) {
    System.out.println("String_Node_Str");
    e.printStackTrace();
  }
catch (  InconsistentOntologyException incon) {
    view.setIsInconsistent(true);
  }
}

Fixed version (ground truth):
/** 
 * This method sets the reasoner. Only FastInstanceChecker is available.
 */
public void setReasoner(){
  this.reasoner=cm.reasoner(FastInstanceChecker.class,sources);
  try {
    reasoner.init();
    reasoner.isSatisfiable();
    view.setIsInconsistent(false);
    isReasonerSet=true;
  }
 catch (  ComponentInitException e) {
    System.out.println("String_Node_Str");
    view.setIsInconsistent(true);
  }
catch (  InconsistentOntologyException incon) {
    System.out.println("String_Node_Str");
    view.setIsInconsistent(true);
  }
}
Program: 9916
Project: 9916
Buggy source:
@Override public void run(){
  String loading="String_Node_Str";
  view.getHintPanel().setForeground(Color.RED);
  view.setHintMessage(loading);
  if (!model.isReasonerSet()) {
    model.setKnowledgeSource();
    model.setReasoner();
  }
  reasoner=model.getReasoner();
  isInconsistent=false;
  if (!isInconsistent) {
    this.checkURI();
    this.setPositiveConcept();
    if (this.hasIndividuals()) {
      view.getRunButton().setEnabled(true);
      view.getHintPanel().setForeground(Color.BLACK);
      view.setHintMessage("String_Node_Str");
    }
 else {
      view.getRunButton().setEnabled(false);
      view.getHintPanel().setVisible(true);
      String message="String_Node_Str" + current + "String_Node_Str";
      view.getHintPanel().setForeground(Color.RED);
      view.setHintMessage(message);
    }
  }
 else {
    view.getHintPanel().setForeground(Color.RED);
    view.getRunButton().setEnabled(false);
    view.setHintMessage("String_Node_Str");
  }
}

Fixed version (ground truth):
@Override public void run(){
  String loading="String_Node_Str";
  view.getHintPanel().setForeground(Color.RED);
  view.setHintMessage(loading);
  if (!model.isReasonerSet()) {
    model.setKnowledgeSource();
    model.setReasoner();
  }
  reasoner=model.getReasoner();
  isInconsistent=view.getIsInconsistent();
  if (!isInconsistent) {
    this.checkURI();
    this.setPositiveConcept();
    if (this.hasIndividuals()) {
      view.getRunButton().setEnabled(true);
      view.getHintPanel().setForeground(Color.BLACK);
      view.setHintMessage("String_Node_Str");
    }
 else {
      view.getRunButton().setEnabled(false);
      view.getHintPanel().setVisible(true);
      String message="String_Node_Str" + current + "String_Node_Str";
      view.getHintPanel().setForeground(Color.RED);
      view.setHintMessage(message);
    }
  }
 else {
    view.getHintPanel().setForeground(Color.RED);
    view.getRunButton().setEnabled(false);
    view.setHintMessage("String_Node_Str");
  }
}
Program: 9917
Project: 9917
Buggy source:
/** 
 * This is the constructor for DL-Learner model.
 * @param editorKit Editor Kit to get the currently loaded Ontology
 * @param id String if it learns a subclass or a superclass.
 * @param view current view of the DL-Learner tab
 */
public DLLearnerModel(OWLEditorKit editorKit,DLLearnerView view){
  editor=editorKit;
  this.view=view;
  ontologyConsistent=true;
  owlDescription=new HashSet<OWLDescription>();
  ComponentManager.setComponentClasses(componenten);
  cm=ComponentManager.getInstance();
  ds=new HashSet<OWLDescription>();
  suggestModel=new DefaultListModel();
  ontologieURI=new HashSet<String>();
  sources=new HashSet<KnowledgeSource>();
}

Fixed version (ground truth):
/** 
 * This is the constructor for DL-Learner model.
 * @param editorKit Editor Kit to get the currently loaded Ontology
 * @param id String if it learns a subclass or a superclass.
 * @param view current view of the DL-Learner tab
 */
public DLLearnerModel(OWLEditorKit editorKit,DLLearnerView view){
  editor=editorKit;
  isReasonerSet=false;
  this.view=view;
  ontologyConsistent=true;
  owlDescription=new HashSet<OWLDescription>();
  ComponentManager.setComponentClasses(componenten);
  cm=ComponentManager.getInstance();
  ds=new HashSet<OWLDescription>();
  suggestModel=new DefaultListModel();
  ontologieURI=new HashSet<String>();
  sources=new HashSet<KnowledgeSource>();
}
Program: 9918
Project: 9918
Buggy source:
/** 
 * This method sets the reasoner. Only FastInstanceChecker is available.
 */
public void setReasoner(){
  this.reasoner=cm.reasoner(FastInstanceChecker.class,sources);
  try {
    reasoner.init();
    reasoner.isSatisfiable();
    view.setIsInconsistent(false);
  }
 catch (  ComponentInitException e) {
    System.out.println("String_Node_Str");
    e.printStackTrace();
  }
catch (  InconsistentOntologyException incon) {
    view.setIsInconsistent(true);
  }
}

Fixed version (ground truth):
/** 
 * This method sets the reasoner. Only FastInstanceChecker is available.
 */
public void setReasoner(){
  this.reasoner=cm.reasoner(FastInstanceChecker.class,sources);
  try {
    reasoner.init();
    reasoner.isSatisfiable();
    view.setIsInconsistent(false);
    isReasonerSet=true;
  }
 catch (  ComponentInitException e) {
    System.out.println("String_Node_Str");
    e.printStackTrace();
  }
catch (  InconsistentOntologyException incon) {
    view.setIsInconsistent(true);
  }
}
Program: 9921
Project: 9921
Buggy source:
@Override public void initialise() throws Exception {
  view=new DLLearnerView(super.getOWLEditorKit());
  if (this.getAxiomType().toString().equals(EQUIVALENT_CLASS_STRING)) {
    view.makeView("String_Node_Str");
  }
 else   if (this.getAxiomType().toString().equals(SUPERCLASS_STRING)) {
    view.makeView("String_Node_Str");
  }
}

Fixed version (ground truth):
@Override public void initialise() throws Exception {
  view=new DLLearnerView(super.getOWLEditorKit());
}
Program: 9922
Project: 9922
Buggy source:
@Override public void run(){
  model.getSuggestModel().removeAllElements();
  reasoner=model.getReasoner();
  isInconsistent=false;
  if (!isInconsistent) {
    this.checkURI();
    this.setPositiveConcept();
    if (this.hasIndividuals()) {
      view.getRunButton().setEnabled(true);
      view.getHintPanel().setForeground(Color.BLACK);
      view.setHintMessage("String_Node_Str");
    }
 else {
      view.getRunButton().setEnabled(false);
      view.getHintPanel().setVisible(true);
      String message="String_Node_Str" + current + "String_Node_Str";
      view.getHintPanel().setForeground(Color.RED);
      view.setHintMessage(message);
    }
  }
 else {
    view.getHintPanel().setForeground(Color.RED);
    view.getRunButton().setEnabled(false);
    view.setHintMessage("String_Node_Str");
  }
}

Fixed version (ground truth):
@Override public void run(){
  String loading="String_Node_Str";
  view.getHintPanel().setForeground(Color.RED);
  view.setHintMessage(loading);
  if (!model.isReasonerSet()) {
    model.setKnowledgeSource();
    model.setReasoner();
  }
  reasoner=model.getReasoner();
  isInconsistent=false;
  if (!isInconsistent) {
    this.checkURI();
    this.setPositiveConcept();
    if (this.hasIndividuals()) {
      view.getRunButton().setEnabled(true);
      view.getHintPanel().setForeground(Color.BLACK);
      view.setHintMessage("String_Node_Str");
    }
 else {
      view.getRunButton().setEnabled(false);
      view.getHintPanel().setVisible(true);
      String message="String_Node_Str" + current + "String_Node_Str";
      view.getHintPanel().setForeground(Color.RED);
      view.setHintMessage(message);
    }
  }
 else {
    view.getHintPanel().setForeground(Color.RED);
    view.getRunButton().setEnabled(false);
    view.setHintMessage("String_Node_Str");
  }
}
Program: 9923
Project: 9923
Buggy source:
/** 
 * Adds the wrong negative and positive examples to the lists.
 */
public void refreshExampleLists(){
  this.ore=getWizardModel().getOre();
  repairPanel.setCellRenderers(ore);
  DefaultListModel negModel=repairPanel.getNegFailureModel();
  negModel.clear();
  for (  Individual ind : ore.getNewClassDescription().getCoveredNegatives()) {
    negModel.addElement(ind);
  }
  DefaultListModel posModel=repairPanel.getPosFailureModel();
  posModel.clear();
  for (  Individual ind : ore.getNewClassDescription().getNotCoveredPositives()) {
    posModel.addElement(ind);
  }
}

Fixed version (ground truth):
/** 
 * Adds the wrong negative and positive examples to the lists.
 */
public void refreshExampleLists(){
  this.ore=getWizardModel().getOre();
  repairPanel.setCellRenderers(ore);
  DefaultListModel negModel=repairPanel.getNegFailureModel();
  negModel.clear();
  for (  Individual ind : ore.getNewClassDescription().getAdditionalInstances()) {
    negModel.addElement(ind);
  }
  DefaultListModel posModel=repairPanel.getPosFailureModel();
  posModel.clear();
  System.out.println(ore.getNewClassDescription().getCoveredInstances());
  Set<Individual> posNotCovered=ore.getOwlReasoner().getIndividuals(ore.getIgnoredConcept());
  posNotCovered.removeAll(ore.getNewClassDescription().getCoveredInstances());
  for (  Individual ind : posNotCovered) {
    posModel.addElement(ind);
  }
}