nus-yam/ex-repair huggingface dataset:
Program: 57060
Project: 57060
Buggy source:
@ListenTo(sendToMe=true) private void onUpdateNumerical(UpdateNumericalPreviewEvent event){
  if (wizard != null)   wizard.onUpdate(event);
 else {
    BrickColumn selected=stratomex.getBrickColumnManager().getActiveBrickColumn();
    if (selected == null) {
    }
 else {
      replaceClinicalTemplate(selected.getTablePerspective().getRecordPerspective(),event.getTablePerspective());
    }
  }
}

Fixed version (ground truth):
@ListenTo(sendToMe=true) private void onUpdateNumerical(UpdateNumericalPreviewEvent event){
  if (wizard != null)   wizard.onUpdate(event);
 else {
    BrickColumn selected=stratomex.getBrickColumnManager().getActiveBrickColumn();
    if (selected == null) {
    }
 else {
      createWizard(selected.getTablePerspective());
      replaceClinicalTemplate(selected.getTablePerspective().getRecordPerspective(),event.getTablePerspective());
    }
  }
}
Program: 57061
Project: 57061
Buggy source:
@Override public void fillStateMachine(IStateMachine stateMachine,List<TablePerspective> existing,TablePerspective dependee){
  IState source=stateMachine.get(IStateMachine.ADD_OTHER);
  BrowseOtherState browse=(BrowseOtherState)stateMachine.get(IStateMachine.BROWSE_OTHER);
  if (!existing.isEmpty() && dependee == null) {
  }
 else   if (dependee != null) {
  }
}

Fixed version (ground truth):
@Override public void fillStateMachine(IStateMachine stateMachine,List<TablePerspective> existing,TablePerspective dependee){
  if (dependee != null)   return;
  IState source=stateMachine.get(IStateMachine.ADD_STRATIFICATIONS);
  IState browseStratification=stateMachine.get(IStateMachine.BROWSE_STRATIFICATIONS);
  if (hasClinicialData(existing)) {
    IState browse=stateMachine.addState("String_Node_Str",new UpdateAndBrowseLogRank());
    IState target=stateMachine.addState("String_Node_Str",new CreateLogRankState(browse));
    stateMachine.addTransition(source,new SimpleTransition(target,"String_Node_Str"));
  }
}
Program: 57062
Project: 57062
Buggy source:
@Override protected boolean permitsWrappingDisplayLists(){
  return false;
}

Fixed version (ground truth):
@Override protected boolean permitsWrappingDisplayLists(){
  return true;
}
Program: 57063
Project: 57063
Buggy source:
@Override public void renderContent(GL2 gl){
  float xoffset=x * 0.04f;
  float yoffset=y * 0.04f;
  gl.glColor4f(color[0],color[1],color[2],0.75f);
  gl.glPushAttrib(GL2.GL_LINE_BIT);
  gl.glLineWidth(3);
  gl.glEnable(GL.GL_LINE_SMOOTH);
  gl.glBegin(GL.GL_LINE_LOOP);
{
    gl.glVertex3f(-xoffset,-yoffset,0);
    gl.glVertex3f(x + xoffset,-yoffset,0);
    gl.glVertex3f(x + xoffset,y + yoffset,0);
    gl.glVertex3f(-xoffset,y + yoffset,0);
  }
  gl.glEnd();
  gl.glPopAttrib();
}

Fixed version (ground truth):
@Override public void renderContent(GL2 gl){
  PixelGLConverter pixelGLConverter=layoutManager.getPixelGLConverter();
  float xoffset=pixelGLConverter.getGLWidthForPixelWidth(OFFSET);
  float yoffset=pixelGLConverter.getGLHeightForPixelHeight(OFFSET);
  gl.glPushAttrib(GL2.GL_LINE_BIT);
  gl.glLineWidth(3);
  gl.glEnable(GL.GL_LINE_SMOOTH);
  gl.glColor4f(color[0],color[1],color[2],0.75f);
  gl.glBegin(GL.GL_LINE_LOOP);
{
    gl.glVertex3f(-xoffset,-yoffset,0);
    gl.glVertex3f(x + xoffset,-yoffset,0);
    gl.glVertex3f(x + xoffset,y + yoffset,0);
    gl.glVertex3f(-xoffset,y + yoffset,0);
  }
  gl.glEnd();
  gl.glPopAttrib();
}
Program: 57064
Project: 57064
Buggy source:
public BrickHighlightRenderer(float[] color){
  super(color);
}

Fixed version (ground truth):
public BrickHighlightRenderer(float[] color){
  this.color=color;
}
Program: 57065
Project: 57065
Buggy source:
@ListenTo(sendToMe=true) private void onHighlight(HighlightBrickEvent event){
  BrickColumnManager manager=stratomex.getBrickColumnManager();
  BrickColumn brickColumn=manager.getBrickColumn(event.getStratification());
  if (brickColumn == null)   return;
  ElementLayout layout=null;
  if (event.getGroup() == null) {
    layout=brickColumn.getLayout();
  }
 else {
    Group g=event.getGroup();
    for (    GLBrick brick : brickColumn.getSegmentBricks()) {
      if (g.equals(brick.getTablePerspective().getRecordGroup())) {
        layout=brick.getLayout();
        break;
      }
    }
  }
  if (layout == null)   return;
  if (!event.isHighlight()) {
    layout.clearBackgroundRenderers();
  }
 else {
    layout.addBackgroundRenderer(new BrickHighlightRenderer(event.getColor().getRGBA()));
  }
  if (layout.getLayoutManager() != null)   layout.updateSubLayout();
}

Fixed version (ground truth):
@ListenTo(sendToMe=true) private void onHighlight(HighlightBrickEvent event){
  BrickColumnManager manager=stratomex.getBrickColumnManager();
  BrickColumn brickColumn=manager.getBrickColumn(event.getStratification());
  if (brickColumn == null)   return;
  ElementLayout layout=null;
  if (event.getGroup() == null) {
    layout=brickColumn.getLayout();
  }
 else {
    Group g=event.getGroup();
    for (    GLBrick brick : brickColumn.getSegmentBricks()) {
      if (g.equals(brick.getTablePerspective().getRecordGroup())) {
        layout=brick.getLayout();
        break;
      }
    }
  }
  if (layout == null)   return;
  if (!event.isHighlight()) {
    layout.clearBackgroundRenderers();
  }
 else {
    layout.addBackgroundRenderer(new BrickHighlightRenderer(event.getColor().getColorComponents(null)));
  }
  if (layout.getLayoutManager() != null)   layout.updateSubLayout();
}
Program: 57066
Project: 57066
Buggy source:
private void updateTableBased(ITablePerspectiveScoreRow old,ITablePerspectiveScoreRow new_,Collection<IScore> visibleColumns,IScore sortedBy){
  TablePerspective strat=new_ == null ? null : new_.asTablePerspective();
  Group group=new_ == null ? null : MaxGroupCombiner.getMax(old,sortedBy);
  if (currentPreview != null && strat != null) {
    if (currentPreview.equals(strat)) {
      if (!Objects.equal(currentPreviewGroup,group)) {
        unhighlightBrick(currentPreview,currentPreviewGroup);
        hightlightBrick(currentPreview,group,true);
        currentPreviewGroup=group;
      }
    }
 else {
      if (contains(strat)) {
        unhighlightBrick(currentPreview,currentPreviewGroup);
        hightlightBrick(strat,group,true);
      }
 else {
        updatePreview(strat,group);
      }
    }
  }
 else   if (currentPreview != null) {
    removePreview();
  }
 else   if (strat != null) {
    updatePreview(strat,group);
  }
  if (strat != null)   hightlightRows(new_,visibleColumns,group);
 else   if (old != null) {
    clearHighlightRows(old.getIdType(),old.getDataDomain());
  }
}

Fixed version (ground truth):
private void updateTableBased(ITablePerspectiveScoreRow old,ITablePerspectiveScoreRow new_,Collection<IScore> visibleColumns,IScore sortedBy){
  TablePerspective strat=new_ == null ? null : new_.asTablePerspective();
  Group group=new_ == null ? null : MaxGroupCombiner.getMax(new_,sortedBy);
  if (currentPreview != null && strat != null) {
    if (currentPreview.equals(strat)) {
      if (!Objects.equal(currentPreviewGroup,group)) {
        unhighlightBrick(currentPreview,currentPreviewGroup);
        hightlightBrick(currentPreview,group,true);
        currentPreviewGroup=group;
      }
    }
 else {
      if (contains(strat)) {
        unhighlightBrick(currentPreview,currentPreviewGroup);
        hightlightBrick(strat,group,true);
      }
 else {
        updatePreview(strat,group);
      }
    }
  }
 else   if (currentPreview != null) {
    removePreview();
  }
 else   if (strat != null) {
    updatePreview(strat,group);
  }
  if (strat != null)   hightlightRows(new_,visibleColumns,group);
 else   if (old != null) {
    clearHighlightRows(old.getIdType(),old.getDataDomain());
  }
}
Program: 57067
Project: 57067
Buggy source:
private void unhighlightBrick(TablePerspective strat,Group g){
  if (g == null)   return;
  triggerEvent(new HighlightBrickEvent(strat,g,receiver,this,null));
}

Fixed version (ground truth):
private void unhighlightBrick(TablePerspective strat,Group g){
  if (g == null)   return;
  triggerEvent(new HighlightBrickEvent(strat,g,null).to(receiver.getTourguide()));
}
Program: 57068
Project: 57068
Buggy source:
private void hightlightBrick(TablePerspective strat,Group g,boolean now){
  if (g == null)   return;
  AEvent event=new HighlightBrickEvent(strat,g,receiver,this,TourGuideRenderStyle.STRATOMEX_FOUND_GROUP);
  if (now)   triggerEvent(event);
 else   triggerDelayedEvent(event);
}

Fixed version (ground truth):
private void hightlightBrick(TablePerspective strat,Group g,boolean now){
  if (g == null)   return;
  AEvent event=new HighlightBrickEvent(strat,g,TourGuideRenderStyle.STRATOMEX_FOUND_GROUP).to(receiver.getTourguide());
  if (now)   triggerEvent(event);
 else   triggerDelayedEvent(event);
}
Program: 57070
Project: 57070
Buggy source:
/** 
 * see   {@link #register(Object,String)} but with an additional speedup criteria to support early stopping ofscanning
 * @param listener
 * @param eventSpace
 * @param stopAtClass
 */
public final <T>T register(T listener,String eventSpace,Predicate<? super Class<?>> scanWhile){
  Class<?> clazz=listener.getClass();
  if (nothingFounds.contains(clazz.getCanonicalName()))   return listener;
  boolean hasOne=scan(listener,listener,eventSpace,scanWhile);
  if (!hasOne)   nothingFounds.add(clazz.getCanonicalName());
  return listener;
}

Fixed version (ground truth):
/** 
 * see   {@link #register(Object,String)} but with an additional speedup criteria to support early stopping ofscanning
 * @param listener
 * @param eventSpace
 * @param stopAtClass
 */
public final <T>T register(T listener,String eventSpace,Predicate<? super Class<?>> scanWhile){
  scan(listener,listener,eventSpace,scanWhile);
  return listener;
}
Program: 57071
Project: 57071
Buggy source:
public PreviewTable(Composite parent,MatrixDefinition spec,IPreviewCallback previewCallback){
  this.spec=spec;
  this.previewCallback=previewCallback;
  delimeter=new DelimiterWidget(parent,new ICallback<String>(){
    @Override public void on(    String delimiter){
      onDelimiterChanged(delimiter);
    }
  }
);
  delimeter.setDelimeter(spec.getDelimiter());
  selectAllNone=new SelectAllNoneWidget(parent,new BooleanCallback(){
    @Override public void on(    boolean selectAll){
      onSelectAllNone(selectAll);
    }
  }
);
  this.selectAllNone.setEnabled(false);
  previewTable=new PreviewTableWidget(parent,new BooleanCallback(){
    @Override public void on(    boolean data){
      onShowAllColumns(data);
    }
  }
);
}

Fixed version (ground truth):
public PreviewTable(Composite parent,MatrixDefinition spec,IPreviewCallback previewCallback){
  this.spec=spec;
  this.previewCallback=previewCallback;
  delimeter=new DelimiterWidget(parent,new ICallback<String>(){
    @Override public void on(    String delimiter){
      onDelimiterChanged(delimiter);
    }
  }
);
  delimeter.setDelimeter(spec.getDelimiter());
  selectAllNone=new SelectAllNoneWidget(parent,new BooleanCallback(){
    @Override public void on(    boolean selectAll){
      onSelectAllNone(selectAll);
    }
  }
);
  this.selectAllNone.setEnabled(false);
  previewTable=new PreviewTableWidget(parent);
}
Program: 57072
Project: 57072
Buggy source:
/** 
 * Creates the preview table from the file specified by   {@link #groupingParseSpecification}. Widgets of the  {@link #dialog} are updated accordingly.
 */
public void createDataPreviewTableFromFile(){
  parser.parse(spec.getDataSourcePath(),spec.getDelimiter(),false,PreviewTableWidget.MAX_PREVIEW_TABLE_ROWS);
  dataMatrix=parser.getDataMatrix();
  totalNumberOfColumns=parser.getTotalNumberOfColumns();
  this.previewTable.createDataPreviewTableFromDataMatrix(dataMatrix);
  previewCallback.on(totalNumberOfColumns,parser.getTotalNumberOfRows(),dataMatrix);
  this.previewTable.updateTableColors(spec.getNumberOfHeaderLines(),-1,spec.getColumnOfRowIds());
}

Fixed version (ground truth):
/** 
 * Creates the preview table from the file specified by   {@link #groupingParseSpecification}. Widgets of the  {@link #dialog} are updated accordingly.
 */
public void createDataPreviewTableFromFile(){
  parser.parse(spec.getDataSourcePath(),spec.getDelimiter(),false,PreviewTableWidget.MAX_PREVIEW_TABLE_ROWS);
  dataMatrix=parser.getDataMatrix();
  totalNumberOfColumns=parser.getTotalNumberOfColumns();
  this.previewTable.createDataPreviewTableFromDataMatrix(dataMatrix,totalNumberOfColumns);
  previewCallback.on(totalNumberOfColumns,parser.getTotalNumberOfRows(),dataMatrix);
  this.previewTable.updateTableColors(spec.getNumberOfHeaderLines(),-1,spec.getColumnOfRowIds());
}
Program: 57073
Project: 57073
Buggy source:
public PreviewTableWidget(Composite parent,final BooleanCallback onSelectAllColumnsCallback){
  this.parent=parent;
  bodyDataProvider=new BodyDataProvider(null,1);
  buildTable(bodyDataProvider,new ColumnHeaderDataProvider(1),new RowHeaderDataProvider(1));
}

Fixed version (ground truth):
public PreviewTableWidget(Composite parent){
  this.parent=parent;
  bodyDataProvider=new BodyDataProvider(null,1);
  buildTable(bodyDataProvider,new ColumnHeaderDataProvider(1),new RowHeaderDataProvider(1));
}
Program: 57074
Project: 57074
Buggy source:
/** 
 * Creates the   {@link #previewTable} according to the {@link #dataMatrix}.
 */
public void createDataPreviewTableFromDataMatrix(List<? extends List<String>> dataMatrix){
  if (dataMatrix == null || dataMatrix.isEmpty())   return;
  int numTableColumns=dataMatrix.get(0).size();
  columnSelectionStatus=new ArrayList<>(numTableColumns);
  for (int i=0; i < numTableColumns; i++) {
    columnSelectionStatus.add(true);
  }
  bodyDataProvider=new BodyDataProvider(dataMatrix,numTableColumns);
  buildTable(bodyDataProvider,new ColumnHeaderDataProvider(numTableColumns),new RowHeaderDataProvider(dataMatrix.size()));
}

Fixed version (ground truth):
/** 
 * Creates the   {@link #previewTable} according to the {@link #dataMatrix}.
 */
public void createDataPreviewTableFromDataMatrix(List<? extends List<String>> dataMatrix,int numColumns){
  if (dataMatrix == null || dataMatrix.isEmpty())   return;
  columnSelectionStatus=new ArrayList<>(numColumns);
  for (int i=0; i < numColumns; i++) {
    columnSelectionStatus.add(true);
  }
  bodyDataProvider=new BodyDataProvider(dataMatrix,numColumns);
  buildTable(bodyDataProvider,new ColumnHeaderDataProvider(numColumns),new RowHeaderDataProvider(dataMatrix.size()));
}
Program: 57075
Project: 57075
Buggy source:
@Override public void createControl(Composite parent){
  int numGridCols=2;
  parentComposite=new Composite(parent,SWT.NONE);
  GridLayout layout=new GridLayout(numGridCols,true);
  parentComposite.setLayout(layout);
  loadFile=new LoadFileWidget(parentComposite,"String_Node_Str",new ICallback<String>(){
    @Override public void on(    String data){
      mediator.onSelectFile(data);
    }
  }
);
  label=new LabelWidget(parentComposite,"String_Node_Str");
  createRowConfigPart(parentComposite);
  createColumnConfigPart(parentComposite);
  delimiterRadioGroup=new DelimiterWidget(parentComposite,new ICallback<String>(){
    @Override public void on(    String data){
      mediator.onDelimiterChanged(data);
    }
  }
);
  selectAllNone=new SelectAllNoneWidget(parentComposite,new BooleanCallback(){
    @Override public void on(    boolean selectAll){
      mediator.onSelectAllNone(selectAll);
    }
  }
);
  previewTable=new PreviewTableWidget(parentComposite,new BooleanCallback(){
    @Override public void on(    boolean showAllColumns){
      mediator.onShowAllColumns(showAllColumns);
    }
  }
);
  mediator.guiCreated();
  setControl(parentComposite);
}

Fixed version (ground truth):
@Override public void createControl(Composite parent){
  int numGridCols=2;
  parentComposite=new Composite(parent,SWT.NONE);
  GridLayout layout=new GridLayout(numGridCols,true);
  parentComposite.setLayout(layout);
  loadFile=new LoadFileWidget(parentComposite,"String_Node_Str",new ICallback<String>(){
    @Override public void on(    String data){
      mediator.onSelectFile(data);
    }
  }
);
  label=new LabelWidget(parentComposite,"String_Node_Str");
  createRowConfigPart(parentComposite);
  createColumnConfigPart(parentComposite);
  delimiterRadioGroup=new DelimiterWidget(parentComposite,new ICallback<String>(){
    @Override public void on(    String data){
      mediator.onDelimiterChanged(data);
    }
  }
);
  selectAllNone=new SelectAllNoneWidget(parentComposite,new BooleanCallback(){
    @Override public void on(    boolean selectAll){
      mediator.onSelectAllNone(selectAll);
    }
  }
);
  previewTable=new PreviewTableWidget(parentComposite);
  mediator.guiCreated();
  setControl(parentComposite);
}
Program: 57076
Project: 57076
Buggy source:
@Override public void on(boolean showAllColumns){
  mediator.onShowAllColumns(showAllColumns);
}

Fixed version (ground truth):
@Override public void on(boolean selectAll){
  mediator.onSelectAllNone(selectAll);
}
Program: 57077
Project: 57077
Buggy source:
public void createDataPreviewTableFromFile(){
  parser.parse(dataSetDescription.getDataSourcePath(),dataSetDescription.getDelimiter(),false,MAX_PREVIEW_TABLE_ROWS);
  dataMatrix=parser.getDataMatrix();
  totalNumberOfColumns=parser.getTotalNumberOfColumns();
  totalNumberOfRows=parser.getTotalNumberOfRows();
  DataImportWizard wizard=(DataImportWizard)page.getWizard();
  wizard.setTotalNumberOfColumns(totalNumberOfColumns);
  wizard.setTotalNumberOfRows(totalNumberOfRows);
  page.previewTable.createDataPreviewTableFromDataMatrix(dataMatrix);
  updateWidgetsAccordingToTableChanges();
  determineIDTypes();
  guessNumberOfHeaderRows();
  page.previewTable.updateTableColors(dataSetDescription.getNumberOfHeaderLines(),dataSetDescription.getRowOfColumnIDs(),dataSetDescription.getColumnOfRowIds());
  page.parentComposite.pack();
}

Fixed version (ground truth):
public void createDataPreviewTableFromFile(){
  parser.parse(dataSetDescription.getDataSourcePath(),dataSetDescription.getDelimiter(),false,MAX_PREVIEW_TABLE_ROWS);
  dataMatrix=parser.getDataMatrix();
  totalNumberOfColumns=parser.getTotalNumberOfColumns();
  totalNumberOfRows=parser.getTotalNumberOfRows();
  DataImportWizard wizard=(DataImportWizard)page.getWizard();
  wizard.setTotalNumberOfColumns(totalNumberOfColumns);
  wizard.setTotalNumberOfRows(totalNumberOfRows);
  page.previewTable.createDataPreviewTableFromDataMatrix(dataMatrix,totalNumberOfColumns);
  updateWidgetsAccordingToTableChanges();
  determineIDTypes();
  guessNumberOfHeaderRows();
  page.previewTable.updateTableColors(dataSetDescription.getNumberOfHeaderLines(),dataSetDescription.getRowOfColumnIDs(),dataSetDescription.getColumnOfRowIds());
  page.parentComposite.pack();
}
Program: 57078
Project: 57078
Buggy source:
private void hightlightRows(ITablePerspectiveScoreRow new_,Collection<IScore> visibleColumns,Group new_g){
  Pair<Collection<Integer>,IDType> intersection=new_.getIntersection(visibleColumns,new_g);
  AEvent event=new SelectElementsEvent(intersection.getFirst(),intersection.getSecond(),this.previewSelectionType).to(receiver.getTourguide());
  event.setEventSpace(new_.getDataDomain().getDataDomainID());
  triggerEvent(event);
}

Fixed version (ground truth):
private void hightlightRows(ITablePerspectiveScoreRow new_,Collection<IScore> visibleColumns,Group new_g){
  Pair<Collection<Integer>,IDType> intersection=new_.getIntersection(visibleColumns,new_g);
  AEvent event=new SelectElementsEvent(intersection.getFirst(),intersection.getSecond(),this.previewSelectionType).to(receiver);
  event.setEventSpace(new_.getDataDomain().getDataDomainID());
  triggerEvent(event);
}
Program: 57079
Project: 57079
Buggy source:
private void clearHighlightRows(IDType idType,IDataDomain dataDomain){
  AEvent event=new SelectElementsEvent(Collections.<Integer>emptyList(),idType,this.previewSelectionType).to(receiver.getTourguide());
  event.setEventSpace(dataDomain.getDataDomainID());
  triggerEvent(event);
}

Fixed version (ground truth):
private void clearHighlightRows(IDType idType,IDataDomain dataDomain){
  AEvent event=new SelectElementsEvent(Collections.<Integer>emptyList(),idType,this.previewSelectionType).to(receiver);
  event.setEventSpace(dataDomain.getDataDomainID());
  triggerEvent(event);
}
Program: 57080
Project: 57080
Buggy source:
private void scheduleAllOf(Collection<IScore> toCompute,boolean removeLeadingScoreColumns){
  ComputeForScoreJob job=new ComputeForScoreJob(toCompute,table.getData(),table.getDefaultFilter().getFilter(),this,removeLeadingScoreColumns);
  if (job.hasThingsToDo()) {
    waiting.resetJob(job);
    job.addJobChangeListener(jobListener);
    getPopupLayer().show(waiting,null,0);
    job.schedule();
  }
 else {
    addColumns(toCompute,removeLeadingScoreColumns);
  }
}

Fixed version (ground truth):
private void scheduleAllOf(Collection<IScore> toCompute,boolean removeLeadingScoreColumns){
  ComputeForScoreJob job=new ComputeForScoreJob(toCompute,table.getData(),table.getMyRanker(null).getFilter(),this,removeLeadingScoreColumns);
  if (job.hasThingsToDo()) {
    waiting.resetJob(job);
    job.addJobChangeListener(jobListener);
    getPopupLayer().show(waiting,null,0);
    job.schedule();
  }
 else {
    addColumns(toCompute,removeLeadingScoreColumns);
  }
}
Program: 57081
Project: 57081
Buggy source:
public RankTableModel(RankTableModel copy){
  this.config=copy.config;
  this.selectedRow=copy.selectedRow;
  this.dataMask=copy.dataMask;
  this.data.addAll(copy.data);
  this.defaultRanker=copy.defaultRanker.clone(this);
  this.defaultFilter=copy.defaultFilter.clone(this);
  for (  ARankColumnModel c : copy.pool)   this.pool.add(c.clone());
  for (  ARankColumnModel c : copy.columns)   this.columns.add(c.clone());
}

Fixed version (ground truth):
public RankTableModel(RankTableModel copy){
  this.config=copy.config;
  this.selectedRow=copy.selectedRow;
  this.dataMask=copy.dataMask;
  this.data.addAll(copy.data);
  this.defaultRanker=copy.defaultRanker.clone(this);
  for (  ARankColumnModel c : copy.pool)   this.pool.add(c.clone());
  for (  ARankColumnModel c : copy.columns)   this.columns.add(c.clone());
}
Program: 57082
Project: 57082
Buggy source:
/** 
 * removes all columns and clears the data
 */
public void reset(){
  for (  ARankColumnModel c : this.columns)   takeDown(c);
  this.columns.clear();
  for (  ARankColumnModel c : this.pool)   takeDown(c);
  this.pool.clear();
  this.dataMask=null;
  this.data.clear();
  this.selectedRow=null;
  this.defaultFilter.reset();
}

Fixed version (ground truth):
/** 
 * removes all columns and clears the data
 */
public void reset(){
  for (  ARankColumnModel c : this.columns)   takeDown(c);
  this.columns.clear();
  for (  ARankColumnModel c : this.pool)   takeDown(c);
  this.pool.clear();
  this.dataMask=null;
  this.data.clear();
  this.selectedRow=null;
}
Program: 57083
Project: 57083
Buggy source:
@Override public void display(GL2 gl){
  checkForHits(gl);
  processEvents();
  handleBrickResize(gl);
  if (isBaseDisplayListDirty)   buildBaseDisplayList(gl);
  GLStratomex stratomex=getBrickColumn().getStratomexView();
  gl.glPushName(stratomex.getPickingManager().getPickingID(stratomex.getID(),EPickingType.BRICK.name(),getID()));
  gl.glPushName(getPickingManager().getPickingID(getID(),EPickingType.BRICK.name(),getID()));
  gl.glColor4f(1.0f,0.0f,0.0f,0.5f);
  gl.glTranslatef(0,0,0.1f);
  gl.glBegin(GL2.GL_QUADS);
  float zpos=0f;
  gl.glVertex3f(0,0,zpos);
  gl.glVertex3f(wrappingLayout.getSizeScaledX(),0,zpos);
  gl.glVertex3f(wrappingLayout.getSizeScaledX(),wrappingLayout.getSizeScaledY(),zpos);
  gl.glVertex3f(0,wrappingLayout.getSizeScaledY(),zpos);
  gl.glEnd();
  gl.glPopName();
  gl.glPopName();
  if (brickColumn.getDetailLevel() != EDetailLevel.LOW || isHeaderBrick)   layoutManager.render(gl);
  gl.glCallList(baseDisplayListIndex);
}

Fixed version (ground truth):
@Override public void display(GL2 gl){
  checkForHits(gl);
  processEvents();
  handleBrickResize(gl);
  if (isBaseDisplayListDirty)   buildBaseDisplayList(gl);
  GLStratomex stratomex=getBrickColumn().getStratomexView();
  gl.glPushName(stratomex.getPickingManager().getPickingID(stratomex.getID(),EPickingType.BRICK.name(),getID()));
  gl.glPushName(getPickingManager().getPickingID(getID(),EPickingType.BRICK.name(),getID()));
  gl.glColor4f(1.0f,0.0f,0.0f,0.5f);
  gl.glTranslatef(0,0,0.1f);
  gl.glBegin(GL2.GL_QUADS);
  float zpos=0f;
  gl.glVertex3f(0,0,zpos);
  gl.glVertex3f(wrappingLayout.getSizeScaledX(),0,zpos);
  gl.glVertex3f(wrappingLayout.getSizeScaledX(),wrappingLayout.getSizeScaledY(),zpos);
  gl.glVertex3f(0,wrappingLayout.getSizeScaledY(),zpos);
  gl.glEnd();
  gl.glPopName();
  gl.glPopName();
  if (brickColumn.getDetailLevel() != EDetailLevel.LOW || isHeaderBrick)   layoutManager.render(gl);
  gl.glCallList(baseDisplayListIndex);
  gl.glTranslatef(0,0,-0.1f);
}
Program: 57084
Project: 57084
Buggy source:
private void renderBackground(GL2 gl){
  int pickingID=stratomex.getPickingManager().getPickingID(stratomex.getID(),EPickingType.DIMENSION_GROUP_SPACER.name(),ID);
  gl.glPushName(pickingID);
  gl.glColor4f(1f,1f,1f,0);
  gl.glBegin(GL2.GL_POLYGON);
  gl.glVertex3f(0,0,-0.2f);
  gl.glVertex3f(x,0,-0.2f);
  gl.glVertex3f(x,y,-0.2f);
  gl.glVertex3f(0,y,-0.2f);
  gl.glEnd();
  gl.glPopName();
}

Fixed version (ground truth):
private void renderBackground(GL2 gl){
  int pickingID=stratomex.getPickingManager().getPickingID(stratomex.getID(),EPickingType.DIMENSION_GROUP_SPACER.name(),ID);
  gl.glPushName(pickingID);
  gl.glColor4f(1f,1f,1f,0);
  gl.glBegin(GL2.GL_POLYGON);
  gl.glVertex3f(0,0,0.f);
  gl.glVertex3f(x,0,0.f);
  gl.glVertex3f(x,y,0.f);
  gl.glVertex3f(0,y,0.f);
  gl.glEnd();
  gl.glPopName();
}
Program: 57086
Project: 57086
Buggy source:
@ListenTo(sendToMe=true) private void onAddEmptyColumn(AddNewColumnEvent event){
  if (preview != null || templateColumn != null)   return;
  int index;
  if (event.getObjectId() <= 0) {
    index=-1;
  }
 else {
    BrickColumnManager brickColumnManager=stratomex.getBrickColumnManager();
    BrickColumn col=brickColumnManager.getBrickColumnSpacers().get(event.getObjectId()).getLeftDimGroup();
    index=col == null ? 0 : brickColumnManager.getBrickColumns().indexOf(col);
  }
  templateIndex=index;
  templateColumn=createTemplateElement(index + 1);
  stratomex.relayout();
}

Fixed version (ground truth):
@ListenTo(sendToMe=true) private void onAddEmptyColumn(AddNewColumnEvent event){
  if (preview != null || templateColumn != null)   return;
  int index;
  if (event.getObjectId() <= 0) {
    index=-1;
  }
 else {
    BrickColumnManager brickColumnManager=stratomex.getBrickColumnManager();
    BrickColumn col=brickColumnManager.getBrickColumnSpacers().get(event.getObjectId()).getLeftDimGroup();
    index=col == null ? -1 : brickColumnManager.getBrickColumns().indexOf(col);
  }
  templateIndex=index;
  templateColumn=createTemplateElement(index + 1);
  stratomex.relayout();
}
Program: 57087
Project: 57087
Buggy source:
/** 
 * @param pick
 */
protected void onBrickPick(Pick pick){
  if (pick.getPickingMode() != PickingMode.CLICKED || selectionMode == null)   return;
  GLBrick brick=findBick(pick.getObjectID());
  if (brick == null)   return;
  boolean isHeader=brick.isHeaderBrick();
  if (isHeader != (selectionMode == ESelectionMode.STRATIFICATION))   return;
  for (  BrickColumnGlowRenderer glow : Iterables.filter(brick.getLayout().getBackgroundRenderer(),BrickColumnGlowRenderer.class)) {
    glow.setColor(Colors.YELLOW.getRGBA());
  }
  stratomex.setDisplayListDirty();
  TablePerspective tablePerspective=brick.getBrickColumn().getTablePerspective();
  if (selectionMode == ESelectionMode.GROUP) {
    Group group=brick.getTablePerspective().getRecordGroup();
    EventPublisher.trigger(new SelectGroupReplyEvent(tablePerspective,group).to(selectionReceiver).from(this));
  }
 else {
    EventPublisher.trigger(new SelectStratificationReplyEvent(tablePerspective).to(selectionReceiver).from(this));
  }
}

Fixed version (ground truth):
/** 
 * if we pick an brick
 * @param pick
 */
protected void onBrickPick(Pick pick){
  if (pick.getPickingMode() != PickingMode.CLICKED || selectionMode == null)   return;
  GLBrick brick=findBick(pick.getObjectID());
  if (brick == null)   return;
  boolean isHeader=brick.isHeaderBrick();
  if (isHeader != (selectionMode == ESelectionMode.STRATIFICATION))   return;
  if (this.selectionCurrent != null) {
    changeHighlight(this.selectionCurrent,Colors.GREEN);
  }
  changeHighlight(brick,Colors.YELLOW);
  this.selectionCurrent=brick;
  stratomex.setDisplayListDirty();
  TablePerspective tablePerspective=brick.getBrickColumn().getTablePerspective();
  if (selectionMode == ESelectionMode.GROUP) {
    Group group=brick.getTablePerspective().getRecordGroup();
    EventPublisher.trigger(new SelectGroupReplyEvent(tablePerspective,group).to(selectionReceiver).from(this));
  }
 else {
    EventPublisher.trigger(new SelectStratificationReplyEvent(tablePerspective).to(selectionReceiver).from(this));
  }
}
Program: 57088
Project: 57088
Buggy source:
@ListenTo(sendToMe=true) private void onUpdatePreview(UpdatePreviewEvent event){
  if (templateColumn == null)   return;
  List<Pair<Integer,BrickColumn>> added;
  if (preview == null) {
    int index=destroyTemplate();
    BrickColumnManager bcm=stratomex.getBrickColumnManager();
    BrickColumn left=index < 0 ? null : bcm.getBrickColumns().get(bcm.getCenterColumnStartIndex() + index);
    added=stratomex.addTablePerspectives(Collections.singletonList(event.getTablePerspective()),null,left,true);
  }
 else {
    added=stratomex.addTablePerspectives(Collections.singletonList(event.getTablePerspective()),null,preview,true);
    stratomex.removeTablePerspective(preview.getTablePerspective());
  }
  preview=added.get(0).getSecond();
  preview.getLayout().addBackgroundRenderer(new ConfirmCancelLayoutRenderer(stratomex,templateIndex,this));
}

Fixed version (ground truth):
@ListenTo(sendToMe=true) private void onUpdatePreview(UpdatePreviewEvent event){
  if (templateColumn == null)   return;
  List<Pair<Integer,BrickColumn>> added;
  if (preview == null) {
    int index=destroyTemplate();
    BrickColumnManager bcm=stratomex.getBrickColumnManager();
    BrickColumn left=index < 0 ? null : bcm.getBrickColumns().get(bcm.getCenterColumnStartIndex() + index);
    added=stratomex.addTablePerspectives(Collections.singletonList(event.getTablePerspective()),null,left,false);
  }
 else {
    added=stratomex.addTablePerspectives(Collections.singletonList(event.getTablePerspective()),null,preview,true);
    stratomex.removeTablePerspective(preview.getTablePerspective());
  }
  preview=added.get(0).getSecond();
  preview.getLayout().addBackgroundRenderer(new ConfirmCancelLayoutRenderer(stratomex,templateIndex,this));
}
Program: 57089
Project: 57089
Buggy source:
@ListenTo(sendToMe=true) private void onConfirmCancelColumn(ConfirmCancelNewColumnEvent event){
  boolean confirm=event.isConfirm();
  if (templateColumn == null && preview == null)   return;
  reset();
  if (preview == null && confirm)   return;
  if (confirm) {
    preview.getLayout().clearBackgroundRenderers();
  }
 else {
    destroyTemplate();
    if (preview != null)     stratomex.removeTablePerspective(preview.getTablePerspective());
  }
  preview=null;
  stratomex.relayout();
}

Fixed version (ground truth):
@ListenTo(sendToMe=true) private void onConfirmCancelColumn(ConfirmCancelNewColumnEvent event){
  boolean confirm=event.isConfirm();
  if (templateColumn == null && preview == null)   return;
  reset();
  if (confirm) {
    if (preview != null)     preview.getLayout().clearBackgroundRenderers();
  }
 else {
    destroyTemplate();
    if (preview != null)     stratomex.removeTablePerspective(preview.getTablePerspective());
  }
  preview=null;
  stratomex.relayout();
  EventPublisher.trigger(new ConfirmedCancelNewColumnEvent().from(this));
}
Program: 57090
Project: 57090
Buggy source:
public ASelectGroupState(String label,IState target,Object receiver){
  this.label=label;
  this.receiver=receiver;
  this.target=target;
}

Fixed version (ground truth):
public ASelectGroupState(IState target,Object receiver){
  super(target);
  this.receiver=receiver;
}
Program: 57091
Project: 57091
Buggy source:
@ListenTo(sendToMe=true) private void onEvent(SelectGroupReplyEvent event){
  handleSelection(event.getTablePerspective(),event.getGroup());
  this.onAutomaticSwitch.on(target);
}

Fixed version (ground truth):
@ListenTo(sendToMe=true) private void onEvent(SelectGroupReplyEvent event){
  handleSelection(event.getTablePerspective(),event.getGroup());
  switchToTarget();
}
Program: 57092
Project: 57092
Buggy source:
public LayoutRendererAdapter(AGLView view,IResourceLocator locator,GLElement root,String eventSpace){
  this.view=view;
  this.root=new WindowGLElement(root);
  this.eventListeners=EventListenerManagers.wrap(view);
  this.eventSpace=eventSpace;
  this.local=new GLContextLocal(view.getTextRenderer(),view.getTextureManager(),locator);
  this.root.init(this);
}

Fixed version (ground truth):
public LayoutRendererAdapter(AGLView view,IResourceLocator locator,GLElement root,String eventSpace){
  this.view=view;
  this.root=new WindowGLElement(root);
  this.eventListeners=EventListenerManagers.createQueued();
  this.eventSpace=eventSpace;
  this.local=new GLContextLocal(view.getTextRenderer(),view.getTextureManager(),locator);
  this.root.init(this);
}
Program: 57095
Project: 57095
Buggy source:
@Override public AGLView createRemoteView(AGLView remoteRenderingView,List<TablePerspective> tablePerspectives,String embeddingEventSpace){
  GLPathway pathwayView=(GLPathway)GeneralManager.get().getViewManager().createGLView(GLPathway.class,remoteRenderingView.getParentGLCanvas(),remoteRenderingView.getParentComposite(),new ViewFrustum(CameraProjectionMode.ORTHOGRAPHIC,0,1,0,1,-1,1));
  if (tablePerspectives.size() > 0) {
    TablePerspective tablePerspective=tablePerspectives.get(0);
    if (!(tablePerspective instanceof PathwayTablePerspective)) {
      throw new IllegalArgumentException("String_Node_Str");
    }
    pathwayView.setRemoteRenderingGLView((IGLRemoteRenderingView)remoteRenderingView);
    pathwayView.addTablePerspective(tablePerspective);
  }
  pathwayView.setPathwayPathEventSpace(embeddingEventSpace);
  pathwayView.setMinHeightPixels(120);
  pathwayView.setMinWidthPixels(120);
  pathwayView.setDynamicDetail(true);
  pathwayView.initialize();
  return pathwayView;
}

Fixed version (ground truth):
@Override public AGLView createRemoteView(AGLView remoteRenderingView,List<TablePerspective> tablePerspectives,String embeddingEventSpace){
  GLPathway pathwayView=(GLPathway)GeneralManager.get().getViewManager().createGLView(GLPathway.class,remoteRenderingView.getParentGLCanvas(),remoteRenderingView.getParentComposite(),new ViewFrustum(CameraProjectionMode.ORTHOGRAPHIC,0,1,0,1,-1,1));
  TablePerspective tablePerspective=null;
  if (tablePerspectives.size() > 0) {
    tablePerspective=tablePerspectives.get(0);
    if (!(tablePerspective instanceof PathwayTablePerspective)) {
      throw new IllegalArgumentException("String_Node_Str");
    }
    pathwayView.setRemoteRenderingGLView((IGLRemoteRenderingView)remoteRenderingView);
    pathwayView.addTablePerspective(tablePerspective);
  }
  pathwayView.setPathwayPathEventSpace(embeddingEventSpace);
  pathwayView.setMinHeightPixels(120);
  pathwayView.setMinWidthPixels(120);
  pathwayView.setDynamicDetail(true);
  pathwayView.initialize();
  PathwayMappingEvent event=new PathwayMappingEvent(tablePerspective);
  event.to(pathwayView);
  pathwayView.onMapTablePerspective(event);
  return pathwayView;
}
Program: 57096
Project: 57096
Buggy source:
@Override public void addToolBarContent(){
  SelectPathAction selectPathAction=new SelectPathAction(false,GLPathway.DEFAULT_PATHWAY_PATH_EVENT_SPACE);
  if (view instanceof GLPathway)   ((GLPathway)view).setSelectPathAction(selectPathAction);
  toolBarManager.add(selectPathAction);
  toolBarManager.add(new ClearPathAction(GLPathway.DEFAULT_PATHWAY_PATH_EVENT_SPACE));
  SampleSelectionMode sampleSelectionMode=new SampleSelectionMode(((SerializedPathwayView)serializedView).getMappingMode());
  toolBarManager.add(sampleSelectionMode);
  DatasetSelectionBox dataSelectionBox=new DatasetSelectionBox(DataDomainManager.get().getDataDomainByID(((SerializedPathwayView)serializedView).getDataDomainID()));
  toolBarManager.add(dataSelectionBox);
  PathwaySearchBox pathwaySearchBox=new PathwaySearchBox((GLPathway)view);
  toolBarManager.add(pathwaySearchBox);
  toolBarManager.add(new OpenOnlineHelpAction("String_Node_Str",false));
}

Fixed version (ground truth):
@Override public void addToolBarContent(){
  SelectPathAction selectPathAction=new SelectPathAction(false,GLPathway.DEFAULT_PATHWAY_PATH_EVENT_SPACE);
  if (view instanceof GLPathway)   ((GLPathway)view).setSelectPathAction(selectPathAction);
  toolBarManager.add(selectPathAction);
  toolBarManager.add(new ClearPathAction(GLPathway.DEFAULT_PATHWAY_PATH_EVENT_SPACE));
  SampleSelectionMode sampleSelectionMode=new SampleSelectionMode(((SerializedPathwayView)serializedView).getMappingMode());
  toolBarManager.add(sampleSelectionMode);
  DatasetSelectionBox dataSelectionBox=new DatasetSelectionBox(DataDomainManager.get().getDataDomainByID(((SerializedPathwayView)serializedView).getDataDomainID()),(GLPathway)view);
  toolBarManager.add(dataSelectionBox);
  PathwaySearchBox pathwaySearchBox=new PathwaySearchBox((GLPathway)view);
  toolBarManager.add(pathwaySearchBox);
  toolBarManager.add(new OpenOnlineHelpAction("String_Node_Str",false));
}
Program: 57097
Project: 57097
Buggy source:
@Override public void handleEvent(AEvent event){
  if (event instanceof PathwayMappingEvent) {
    PathwayMappingEvent pEvent=(PathwayMappingEvent)event;
    handler.mapTablePerspective(pEvent.getTablePerspective());
  }
}

Fixed version (ground truth):
@Override public void handleEvent(AEvent event){
  if (event instanceof PathwayMappingEvent) {
    PathwayMappingEvent pEvent=(PathwayMappingEvent)event;
  }
}
Program: 57098
Project: 57098
Buggy source:
@Override public void widgetSelected(SelectionEvent e){
  for (  AGLView view : ViewManager.get().getAllGLViews()) {
    if (view instanceof GLPathway) {
      GLPathway pwView=(GLPathway)view;
      AddTablePerspectivesEvent addTablePerspectivesEvent=new AddTablePerspectivesEvent();
      addTablePerspectivesEvent.setReceiver(pwView);
      TablePerspective tablePerspective=null;
      if (dataSetChooser.getSelectionIndex() != 0) {
        GeneticDataDomain dataDomain=candidateDataDomains.get(dataSetChooser.getSelectionIndex() - 1);
        addTablePerspectivesEvent.setEventSpace(dataDomain.getDataDomainID());
        tablePerspective=dataDomain.getDefaultTablePerspective();
        tablePerspective.setPrivate(false);
        addTablePerspectivesEvent.addTablePerspective(tablePerspective);
        GeneralManager.get().getEventPublisher().triggerEvent(addTablePerspectivesEvent);
        PathwayMappingEvent event=new PathwayMappingEvent(tablePerspective);
        event.setSender(this);
        GeneralManager.get().getEventPublisher().triggerEvent(event);
      }
 else {
        PathwayMappingEvent event=new PathwayMappingEvent();
        event.setSender(this);
        GeneralManager.get().getEventPublisher().triggerEvent(event);
      }
    }
  }
}

Fixed version (ground truth):
@Override public void widgetSelected(SelectionEvent e){
  AddTablePerspectivesEvent addTablePerspectivesEvent=new AddTablePerspectivesEvent();
  addTablePerspectivesEvent.setReceiver(pathwayView);
  TablePerspective tablePerspective=null;
  if (dataSetChooser.getSelectionIndex() != 0) {
    GeneticDataDomain dataDomain=candidateDataDomains.get(dataSetChooser.getSelectionIndex() - 1);
    addTablePerspectivesEvent.setEventSpace(dataDomain.getDataDomainID());
    tablePerspective=dataDomain.getDefaultTablePerspective();
    tablePerspective.setPrivate(false);
    addTablePerspectivesEvent.addTablePerspective(tablePerspective);
    GeneralManager.get().getEventPublisher().triggerEvent(addTablePerspectivesEvent);
    PathwayMappingEvent event=new PathwayMappingEvent(tablePerspective);
    event.setSender(this);
    event.to(pathwayView);
    GeneralManager.get().getEventPublisher().triggerEvent(event);
  }
 else {
    PathwayMappingEvent event=new PathwayMappingEvent();
    event.setSender(this);
    GeneralManager.get().getEventPublisher().triggerEvent(event);
  }
}
Program: 57099
Project: 57099
Buggy source:
/** 
 * constructor as requested by ControlContribution
 */
public DatasetSelectionBox(IDataDomain mappingDataDomain){
  super("String_Node_Str");
  this.mappingDataDomain=mappingDataDomain;
}

Fixed version (ground truth):
/** 
 * constructor as requested by ControlContribution
 */
public DatasetSelectionBox(IDataDomain mappingDataDomain,GLPathway pathwayView){
  super("String_Node_Str");
  this.mappingDataDomain=mappingDataDomain;
  this.pathwayView=pathwayView;
}
Program: 57101
Project: 57101
Buggy source:
/** 
 * Initializes the container.
 * @param size
 * @param dataType
 * @param unknownCategoryType The value used for the unknown value. Use  {@link #UNKNOWN_CATEGORY_INT} and{@link #UNKNOWN_CATEOGRY_STRING} unless there is a good reason not to do so.
 */
public CategoricalContainer(int size,EDataType dataType,CATEGORY_TYPE unknownCategoryType){
  container=new short[size];
  this.unknownCategoryType=unknownCategoryType;
  add(unknownCategoryType);
}

Fixed version (ground truth):
/** 
 * Initializes the container.
 * @param size
 * @param dataType
 * @param unknownCategoryType The value used for the unknown value. Use  {@link #UNKNOWN_CATEGORY_INT} and{@link #UNKNOWN_CATEOGRY_STRING} unless there is a good reason not to do so.
 */
public CategoricalContainer(int size,EDataType dataType,CATEGORY_TYPE unknownCategoryType){
  container=new short[size];
  this.unknownCategoryType=unknownCategoryType;
  initCategory(unknownCategoryType);
}
Program: 57103
Project: 57103
Buggy source:
private DataSetDescription setUpMRNAData(){
  DataSetDescription mrnaData=new DataSetDescription(ECreateDefaultProperties.NUMERICAL);
  mrnaData.setDataSetName("String_Node_Str");
  mrnaData.setDataSourcePath(MRNA);
  mrnaData.setNumberOfHeaderLines(2);
  mrnaData.setRowOfColumnIDs(0);
  ParsingRule parsingRule=new ParsingRule();
  parsingRule.setFromColumn(1);
  parsingRule.setParseUntilEnd(true);
  parsingRule.setColumnDescripton(new ColumnDescription());
  mrnaData.addParsingRule(parsingRule);
  mrnaData.setTransposeMatrix(true);
  IDSpecification geneIDSpecification=new IDSpecification();
  geneIDSpecification.setIDTypeGene(true);
  geneIDSpecification.setIdType("String_Node_Str");
  mrnaData.setRowIDSpecification(geneIDSpecification);
  mrnaData.setColumnIDSpecification(sampleIDSpecification);
  GroupingParseSpecification firehoseClustering=new GroupingParseSpecification(MRNA_GROUPING);
  firehoseClustering.setContainsColumnIDs(false);
  firehoseClustering.setRowIDSpecification(sampleIDSpecification);
  mrnaData.addColumnGroupingSpecification(firehoseClustering);
  GroupingParseSpecification groundTruthGrouping=new GroupingParseSpecification();
  groundTruthGrouping.setDataSourcePath(GROUND_TRUTH_GROUPING);
  groundTruthGrouping.addColum(2);
  groundTruthGrouping.setRowIDSpecification(sampleIDSpecification);
  mrnaData.addColumnGroupingSpecification(groundTruthGrouping);
  return mrnaData;
}

Fixed version (ground truth):
private DataSetDescription setUpMRNAData(){
  DataSetDescription mrnaData=new DataSetDescription(ECreateDefaultProperties.NUMERICAL);
  mrnaData.setDataSetName("String_Node_Str");
  mrnaData.setDataSourcePath(MRNA);
  mrnaData.setNumberOfHeaderLines(3);
  mrnaData.setRowOfColumnIDs(2);
  ParsingRule parsingRule=new ParsingRule();
  parsingRule.setFromColumn(1);
  parsingRule.setParseUntilEnd(true);
  parsingRule.setColumnDescripton(new ColumnDescription());
  mrnaData.addParsingRule(parsingRule);
  mrnaData.setTransposeMatrix(true);
  IDSpecification geneIDSpecification=new IDSpecification();
  geneIDSpecification.setIDTypeGene(true);
  geneIDSpecification.setIdType("String_Node_Str");
  mrnaData.setRowIDSpecification(geneIDSpecification);
  mrnaData.setColumnIDSpecification(sampleIDSpecification);
  GroupingParseSpecification firehoseClustering=new GroupingParseSpecification(MRNA_GROUPING);
  firehoseClustering.setContainsColumnIDs(false);
  firehoseClustering.setRowIDSpecification(sampleIDSpecification);
  mrnaData.addColumnGroupingSpecification(firehoseClustering);
  GroupingParseSpecification groundTruthGrouping=new GroupingParseSpecification();
  groundTruthGrouping.setDataSourcePath(GROUND_TRUTH_GROUPING);
  groundTruthGrouping.addColum(2);
  groundTruthGrouping.setRowIDSpecification(sampleIDSpecification);
  mrnaData.addColumnGroupingSpecification(groundTruthGrouping);
  return mrnaData;
}
Program: 57104
Project: 57104
Buggy source:
private DataSetDescription setUpCopyNumberData(){
  DataSetDescription copyNumberData=new DataSetDescription(ECreateDefaultProperties.CATEGORICAL);
  copyNumberData.setDataSetName("String_Node_Str");
  copyNumberData.setDataSourcePath(COPY_NUMBER);
  copyNumberData.setNumberOfHeaderLines(1);
  ParsingRule parsingRule=new ParsingRule();
  parsingRule.setFromColumn(3);
  parsingRule.setParseUntilEnd(true);
  parsingRule.setColumnDescripton(new ColumnDescription());
  copyNumberData.addParsingRule(parsingRule);
  copyNumberData.setTransposeMatrix(true);
  IDSpecification geneIDSpecification=new IDSpecification();
  geneIDSpecification.setIDTypeGene(true);
  geneIDSpecification.setIdType("String_Node_Str");
  copyNumberData.setRowIDSpecification(geneIDSpecification);
  copyNumberData.setColumnIDSpecification(sampleIDSpecification);
  GroupingParseSpecification groundTruthGrouping=new GroupingParseSpecification();
  groundTruthGrouping.setDataSourcePath(GROUND_TRUTH_GROUPING);
  groundTruthGrouping.addColum(2);
  groundTruthGrouping.setRowIDSpecification(sampleIDSpecification);
  copyNumberData.addColumnGroupingSpecification(groundTruthGrouping);
  return copyNumberData;
}

Fixed version (ground truth):
private DataSetDescription setUpCopyNumberData(){
  DataSetDescription copyNumberData=new DataSetDescription(ECreateDefaultProperties.CATEGORICAL);
  copyNumberData.setDataSetName("String_Node_Str");
  copyNumberData.setDataSourcePath(COPY_NUMBER);
  copyNumberData.setNumberOfHeaderLines(1);
  @SuppressWarnings("String_Node_Str") CategoricalClassDescription<Integer> categoricalClassDescription=(CategoricalClassDescription<Integer>)copyNumberData.getDataDescription().getCategoricalClassDescription();
  categoricalClassDescription.setCategoryType(ECategoryType.ORDINAL);
  categoricalClassDescription.setRawDataType(EDataType.INTEGER);
  categoricalClassDescription.addCategoryProperty(-2,"String_Node_Str",new Color("String_Node_Str"));
  categoricalClassDescription.addCategoryProperty(-1,"String_Node_Str",new Color("String_Node_Str"));
  categoricalClassDescription.addCategoryProperty(0,"String_Node_Str",Colors.NEUTRAL_GREY);
  categoricalClassDescription.addCategoryProperty(1,"String_Node_Str",new Color("String_Node_Str"));
  categoricalClassDescription.addCategoryProperty(2,"String_Node_Str",new Color("String_Node_Str"));
  ParsingRule parsingRule=new ParsingRule();
  parsingRule.setFromColumn(3);
  parsingRule.setParseUntilEnd(true);
  parsingRule.setColumnDescripton(new ColumnDescription());
  copyNumberData.addParsingRule(parsingRule);
  copyNumberData.setTransposeMatrix(true);
  IDSpecification geneIDSpecification=new IDSpecification();
  geneIDSpecification.setIDTypeGene(true);
  geneIDSpecification.setIdType("String_Node_Str");
  copyNumberData.setRowIDSpecification(geneIDSpecification);
  copyNumberData.setColumnIDSpecification(sampleIDSpecification);
  return copyNumberData;
}