Program: 58510
Project: 58510
Buggy source:
public static void startCaleydoCore(){
  caleydoCoreBootloader.setXmlFileName(sCaleydoXMLfile);
  caleydoCoreBootloader.start();
  Shell shell=new Shell();
  if (applicationMode == EApplicationMode.COLLABORATION_CLIENT || applicationMode == EApplicationMode.PLEX_CLIENT) {
    AUseCase useCase=initData.getUseCase();
    LoadDataParameters loadDataParameters=useCase.getLoadDataParameters();
    SetUtils.saveSetFile(loadDataParameters,initData.getSetFileContent());
    if (initData.getGeneClusterTree() != null) {
      SetUtils.saveGeneTreeFile(loadDataParameters,initData.getGeneClusterTree());
    }
    if (initData.getGeneClusterTree() != null) {
      SetUtils.saveExperimentsTreeFile(loadDataParameters,initData.getGeneClusterTree());
    }
    GeneralManager.get().addUseCase(useCase);
    if (useCase instanceof GeneticUseCase)     triggerPathwayLoading();
    SetUtils.createStorages(loadDataParameters);
    SetUtils.createData(useCase);
    HashMap<EVAType,VirtualArray> virtualArrayMap=initData.getVirtualArrayMap();
    for (    Entry<EVAType,VirtualArray> entry : virtualArrayMap.entrySet()) {
      useCase.setVirtualArray(entry.getKey(),entry.getValue());
    }
    Application.initData=null;
  }
 else   if (applicationMode == EApplicationMode.LOAD_PROJECT) {
    AUseCase useCase=initData.getUseCase();
    GeneralManager.get().addUseCase(useCase);
    LoadDataParameters loadDataParameters=useCase.getLoadDataParameters();
    SetUtils.createStorages(loadDataParameters);
    SetUtils.createData(useCase);
    HashMap<EVAType,VirtualArray> virtualArrayMap=initData.getVirtualArrayMap();
    for (    Entry<EVAType,VirtualArray> entry : virtualArrayMap.entrySet()) {
      useCase.setVirtualArray(entry.getKey(),entry.getValue());
    }
    if (useCase instanceof GeneticUseCase)     triggerPathwayLoading();
    Application.initData=null;
  }
 else   if (applicationMode == EApplicationMode.GENE_EXPRESSION_SAMPLE_DATA) {
    triggerPathwayLoading();
    WizardDialog dataImportWizard=new WizardDialog(shell,new DataImportWizard(shell,REAL_DATA_SAMPLE_FILE));
    if (Window.CANCEL == dataImportWizard.open()) {
      shutdown();
      System.exit(0);
    }
  }
 else   if ((applicationMode == EApplicationMode.GENE_EXPRESSION_NEW_DATA || applicationMode == EApplicationMode.UNSPECIFIED_NEW_DATA) && (sCaleydoXMLfile.equals(BOOTSTRAP_FILE_GENE_EXPRESSION_MODE) || sCaleydoXMLfile.equals("String_Node_Str"))) {
    WizardDialog dataImportWizard=new WizardDialog(shell,new DataImportWizard(shell));
    if (Window.CANCEL == dataImportWizard.open()) {
      shutdown();
      System.exit(0);
    }
  }
  if (isStartedFromXML) {
    for (    IUseCase useCase : GeneralManager.get().getAllUseCases()) {
      useCase.updateSetInViews();
    }
  }
  initializeColorMapping();
  if (initializedStartViews == null) {
    initializeDefaultStartViews(applicationMode.getDataDomain());
  }
}

Fixed version (ground truth):
public static void startCaleydoCore(){
  caleydoCoreBootloader.setXmlFileName(sCaleydoXMLfile);
  caleydoCoreBootloader.start();
  Shell shell=new Shell();
  if (applicationMode == EApplicationMode.COLLABORATION_CLIENT || applicationMode == EApplicationMode.PLEX_CLIENT) {
    AUseCase useCase=initData.getUseCase();
    LoadDataParameters loadDataParameters=useCase.getLoadDataParameters();
    SetUtils.saveSetFile(loadDataParameters,initData.getSetFileContent());
    if (initData.getGeneClusterTree() != null) {
      SetUtils.saveGeneTreeFile(loadDataParameters,initData.getGeneClusterTree());
    }
    if (initData.getGeneClusterTree() != null) {
      SetUtils.saveExperimentsTreeFile(loadDataParameters,initData.getGeneClusterTree());
    }
    GeneralManager.get().addUseCase(useCase);
    if (useCase instanceof GeneticUseCase)     triggerPathwayLoading();
    SetUtils.createStorages(loadDataParameters);
    SetUtils.createData(useCase);
    HashMap<EVAType,VirtualArray> virtualArrayMap=initData.getVirtualArrayMap();
    for (    Entry<EVAType,VirtualArray> entry : virtualArrayMap.entrySet()) {
      useCase.setVirtualArray(entry.getKey(),entry.getValue());
    }
    Application.initData=null;
  }
 else   if (applicationMode == EApplicationMode.LOAD_PROJECT || applicationMode == EApplicationMode.SAMPLE_PROJECT) {
    AUseCase useCase=initData.getUseCase();
    GeneralManager.get().addUseCase(useCase);
    LoadDataParameters loadDataParameters=useCase.getLoadDataParameters();
    SetUtils.createStorages(loadDataParameters);
    SetUtils.createData(useCase);
    HashMap<EVAType,VirtualArray> virtualArrayMap=initData.getVirtualArrayMap();
    for (    Entry<EVAType,VirtualArray> entry : virtualArrayMap.entrySet()) {
      useCase.setVirtualArray(entry.getKey(),entry.getValue());
    }
    if (useCase instanceof GeneticUseCase)     triggerPathwayLoading();
    Application.initData=null;
  }
 else   if (applicationMode == EApplicationMode.GENE_EXPRESSION_SAMPLE_DATA) {
    triggerPathwayLoading();
    WizardDialog dataImportWizard=new WizardDialog(shell,new DataImportWizard(shell,REAL_DATA_SAMPLE_FILE));
    if (Window.CANCEL == dataImportWizard.open()) {
      shutdown();
      System.exit(0);
    }
  }
 else   if ((applicationMode == EApplicationMode.GENE_EXPRESSION_NEW_DATA || applicationMode == EApplicationMode.UNSPECIFIED_NEW_DATA) && (sCaleydoXMLfile.equals(BOOTSTRAP_FILE_GENE_EXPRESSION_MODE) || sCaleydoXMLfile.equals("String_Node_Str"))) {
    WizardDialog dataImportWizard=new WizardDialog(shell,new DataImportWizard(shell));
    if (Window.CANCEL == dataImportWizard.open()) {
      shutdown();
      System.exit(0);
    }
  }
  if (isStartedFromXML) {
    for (    IUseCase useCase : GeneralManager.get().getAllUseCases()) {
      useCase.updateSetInViews();
    }
  }
  initializeColorMapping();
  if (initializedStartViews == null) {
    initializeDefaultStartViews(applicationMode.getDataDomain());
  }
}