nus-yam/ex-repair huggingface dataset:
Program: 140980
Project: 140980
Buggy source:
private void updateGeneralizationGUIEnabledState(){
  boolean f=model == null ? false : model.isGeneralizing();
  boolean isSharpening=generalizationLICSharpeningSlider.getValue() > 0;
  generalizationMaxLevelsSpinner.setEnabled(f);
  generalizationDetailSlider.setEnabled(f);
  generalizationDetaiIsLabel.setEnabled(f);
  generalizationLICSizeSlider.setEnabled(f);
  generalizationLICIterationsSlider.setEnabled(f);
  generalizationLICSharpeningSlider.setEnabled(f);
  generalizationLICSharpeningLimitSlider.setEnabled(f && isSharpening);
  generalizationLICMinimumSlopeSlider.setEnabled(f);
  generalizationFilterSizeLabel.setEnabled(f);
  generalizationIterationsLabel.setEnabled(f);
  generalizationSharpeningLabel.setEnabled(f);
  generalizationSharpeningLimitLabel.setEnabled(f && isSharpening);
  generalizationMinSlopeLabel.setEnabled(f);
  generalizationLargeLandformRemovalLabel.setEnabled(f);
  generalizationSmallDetailsRemovalLabel.setEnabled(f);
  updateSharpeningSliderLabels();
}

Fixed version (ground truth):
private void updateGeneralizationGUIEnabledState(){
  boolean f=generalizationCheckBox.isSelected();
  boolean isSharpening=generalizationLICSharpeningSlider.getValue() > 0;
  generalizationMaxLevelsSpinner.setEnabled(f);
  generalizationDetailSlider.setEnabled(f);
  generalizationDetaiIsLabel.setEnabled(f);
  generalizationLICSizeSlider.setEnabled(f);
  generalizationLICIterationsSlider.setEnabled(f);
  generalizationLICSharpeningSlider.setEnabled(f);
  generalizationLICSharpeningLimitSlider.setEnabled(f && isSharpening);
  generalizationLICMinimumSlopeSlider.setEnabled(f);
  generalizationFilterSizeLabel.setEnabled(f);
  generalizationIterationsLabel.setEnabled(f);
  generalizationSharpeningLabel.setEnabled(f);
  generalizationSharpeningLimitLabel.setEnabled(f && isSharpening);
  generalizationMinSlopeLabel.setEnabled(f);
  generalizationLargeLandformRemovalLabel.setEnabled(f);
  generalizationSmallDetailsRemovalLabel.setEnabled(f);
  updateSharpeningSliderLabels();
}
Program: 140981
Project: 140981
Buggy source:
private void readGeneralizationGUI(final JSlider slider){
  SwingUtilities.invokeLater(new Runnable(){
    @Override public void run(){
      if (generalizer != null) {
        generalizer.cancel();
      }
      if (slider == null || slider.getValueIsAdjusting() == false) {
        model.setGeneralizing(generalizationCheckBox.isSelected());
        model.setGeneralizationLICSize(generalizationLICSizeSlider.getValue() / 10d);
        model.setGeneralizationLICSharpening(generalizationLICSharpeningSlider.getValue() / 100d);
        model.setGeneralizationLICMinSlopeDeg(generalizationLICMinimumSlopeSlider.getValue());
        model.setGeneralizationLICIterations(generalizationLICIterationsSlider.getValue());
        model.setGeneralizationLICSharpeningLimit(generalizationLICSharpeningLimitSlider.getValue() / 100d);
        generalizeAndRender();
      }
      updateGeneralizationGUIEnabledState();
    }
  }
);
}

Fixed version (ground truth):
private void readGeneralizationGUI(JSlider slider){
  updateGeneralizationGUIEnabledState();
  model.setGeneralizing(generalizationCheckBox.isSelected());
  if (slider != null && slider.getValueIsAdjusting() == false) {
    model.setGeneralizationLICSize(generalizationLICSizeSlider.getValue() / 10d);
    model.setGeneralizationLICSharpening(generalizationLICSharpeningSlider.getValue() / 100d);
    model.setGeneralizationLICMinSlopeDeg(generalizationLICMinimumSlopeSlider.getValue());
    model.setGeneralizationLICIterations(generalizationLICIterationsSlider.getValue());
    model.setGeneralizationLICSharpeningLimit(generalizationLICSharpeningLimitSlider.getValue() / 100d);
    generalizeAndRender();
  }
}
Program: 140982
Project: 140982
Buggy source:
public void modelChanged(){
  settingsPanel.updateImage(SettingsPanel.RenderSpeed.REGULAR);
  settingsPanel.updateGUI();
}

Fixed version (ground truth):
/** 
 * Updates the generalization, visualization and the GUI after the grid values have been changed.
 */
public void modelChanged(){
  settingsPanel.getModel().updateGeneralizedGrid();
  settingsPanel.updateImage(SettingsPanel.RenderSpeed.REGULAR);
  settingsPanel.updateGUI();
}
Program: 140983
Project: 140983
Buggy source:
/** 
 * @param illuminated
 * @param shadowWidthLow
 * @param shadowWidthHigh
 * @param illuminatedWidthLow
 * @param minWidth
 * @param illuminatedWidthHigh
 * @param azimuth
 * @param interval
 * @param gradientAngle
 * @param illluminatedGray
 * @param aspectGaussBlur
 * @param transitionAngle
 * @param gridMinMax
 */
public IlluminatedContoursOperator(boolean illuminated,double shadowWidthLow,double shadowWidthHigh,double illuminatedWidthLow,double illuminatedWidthHigh,double minWidth,double azimuth,double interval,int gradientAngle,int illluminatedGray,double aspectGaussBlur,int transitionAngle,float[] gridMinMax){
  this.illuminated=illuminated;
  this.shadowWidthLow=shadowWidthLow;
  this.shadowWidthHigh=shadowWidthHigh;
  this.illuminatedWidthLow=illuminatedWidthLow;
  this.illuminatedWidthHigh=illuminatedWidthHigh;
  this.minWidth=minWidth;
  this.azimuth=azimuth;
  this.interval=interval;
  this.gradientAngle=gradientAngle;
  this.illluminatedGray=illluminatedGray;
  this.aspectGaussBlur=aspectGaussBlur;
  this.transitionAngle=transitionAngle;
  this.gridMin=gridMinMax[0];
  this.gridMax=gridMinMax[1];
}

Fixed version (ground truth):
/** 
 * @param illuminated
 * @param shadowWidthLow
 * @param shadowWidthHigh
 * @param illuminatedWidthLow
 * @param minWidth
 * @param illuminatedWidthHigh
 * @param azimuth
 * @param interval
 * @param gradientAngle
 * @param illluminatedGray
 * @param aspectGaussBlur
 * @param transitionAngle
 * @param gridMinMax
 */
public IlluminatedContoursOperator(boolean illuminated,double shadowWidthLow,double shadowWidthHigh,double illuminatedWidthLow,double illuminatedWidthHigh,double minWidth,double azimuth,double interval,int gradientAngle,int illluminatedGray,double aspectGaussBlur,int transitionAngle,float[] gridMinMax){
  this.illuminated=illuminated;
  this.shadowWidthLow=shadowWidthLow;
  this.shadowWidthHigh=shadowWidthHigh;
  this.illuminatedWidthLow=illuminatedWidthLow;
  this.illuminatedWidthHigh=illuminatedWidthHigh;
  this.minWidth=minWidth;
  this.azimuth=azimuth;
  this.interval=Math.abs(interval);
  this.gradientAngle=gradientAngle;
  this.illluminatedGray=illluminatedGray;
  this.aspectGaussBlur=aspectGaussBlur;
  this.transitionAngle=transitionAngle;
  this.gridMin=gridMinMax[0];
  this.gridMax=gridMinMax[1];
}
Program: 140985
Project: 140985
Buggy source:
/** 
 * Compute the gray value for the illuminated contour line image
 * @param elevation Elevation of the point.
 * @param aspect Aspect of the point.
 * @param slope Slope of the point.
 * @param cellSize
 * @return Gray value between 0 and 255.
 */
public int computeGray(double elevation,double aspect,double slope,double cellSize){
  double angleDiff=getAngleDifference(azimuth,aspect);
  double a;
  if (angleDiff > 90) {
    a=shadowWidth * slope * cellSize;
  }
 else {
    a=illuminatedWidth * slope * cellSize;
  }
  if (tanaka) {
    a*=Math.abs(Math.cos(angleDiff / 180 * Math.PI));
  }
  a=Math.max(minWidth * slope * cellSize,a);
  double dist=elevation % interval;
  if (dist > a) {
    dist=interval - dist;
  }
  if (a > dist) {
    if (angleDiff >= (90 + gradientAngle)) {
      return 0;
    }
 else     if (angleDiff <= (90 - gradientAngle)) {
      return illuminated ? illluminatedGray : 0;
    }
 else     if (angleDiff > (90 - gradientAngle) && angleDiff < (90 + gradientAngle)) {
      return (int)((angleDiff - (90 - gradientAngle)) / ((90 + gradientAngle) - (90 - gradientAngle)) * (-255) + 255);
    }
  }
  return CONTOURS_TRANSPARENT;
}

Fixed version (ground truth):
/** 
 * Compute the gray value for the illuminated contour line image
 * @param elevation Elevation of the point.
 * @param aspect Aspect of the point.
 * @param slope Slope of the point.
 * @param cellSize
 * @return Gray value between 0 and 255.
 */
public int computeGray(double elevation,double aspect,double slope,double cellSize){
  double angleDiff=getAngleDifference(azimuth,aspect);
  double a;
  if (angleDiff > 90) {
    a=shadowWidth * slope * cellSize;
  }
 else {
    a=illuminatedWidth * slope * cellSize;
  }
  if (tanaka) {
    a*=Math.abs(Math.cos(angleDiff / 180 * Math.PI));
  }
  a=Math.max(minWidth * slope * cellSize,a);
  double dist=Math.abs(elevation) % interval;
  if (dist > a) {
    dist=interval - dist;
  }
  if (a > dist) {
    if (angleDiff >= (90 + gradientAngle)) {
      return 0;
    }
 else     if (angleDiff <= (90 - gradientAngle)) {
      return illuminated ? illluminatedGray : 0;
    }
 else     if (angleDiff > (90 - gradientAngle) && angleDiff < (90 + gradientAngle)) {
      return (int)((angleDiff - (90 - gradientAngle)) / ((90 + gradientAngle) - (90 - gradientAngle)) * (-255) + 255);
    }
  }
  return CONTOURS_TRANSPARENT;
}
Program: 140986
Project: 140986
Buggy source:
@Override protected void operate(Grid src,Grid dst,int startRow,int endRow){
  for (int row=startRow; row < endRow; ++row) {
    float[] srcArray=src.getGrid()[row];
    float[] dstArray=src.getGrid()[row];
    System.arraycopy(srcArray,0,dstArray,0,srcArray.length);
  }
}

Fixed version (ground truth):
@Override protected void operate(Grid src,Grid dst,int startRow,int endRow){
  for (int row=startRow; row < endRow; ++row) {
    float[] srcArray=src.getGrid()[row];
    float[] dstArray=dst.getGrid()[row];
    System.arraycopy(srcArray,0,dstArray,0,srcArray.length);
  }
}
Program: 140987
Project: 140987
Buggy source:
/** 
 * Create the MultiQC report using docker.
 * @param dockerImage docker image to use
 * @param inputDirectory input directory
 * @param multiQCReportFile output report
 * @param projectName project name
 * @throws IOException if an error occurs while creating the report
 * @throws EoulsanException if MultiQC execution fails
 */
private static void createMultiQCReportWithDocker(final String dockerImage,final File inputDirectory,final File multiQCReportFile,final String projectName,final File temporaryDirectory) throws IOException, EoulsanException {
  SimpleProcess process=DockerManager.getInstance().createImageInstance(dockerImage);
  File executionDirectory=multiQCReportFile.getParentFile();
  File stdoutFile=new File(executionDirectory,"String_Node_Str");
  File stderrFile=new File(executionDirectory,"String_Node_Str");
  List<File> filesUsed=new ArrayList<>();
  filesUsed.add(executionDirectory);
  filesUsed.add(temporaryDirectory);
  filesUsed.add(multiQCReportFile);
  for (  File f : inputDirectory.listFiles()) {
    if (!f.getName().startsWith("String_Node_Str") && Files.isSymbolicLink(f.toPath())) {
      filesUsed.add(f.toPath().toRealPath().toFile());
    }
  }
  final int exitValue=process.execute(createMultiQCOptions(inputDirectory,multiQCReportFile,projectName),executionDirectory,temporaryDirectory,stdoutFile,stderrFile,filesUsed.toArray(new File[filesUsed.size()]));
  if (exitValue > 0) {
    throw new EoulsanException("String_Node_Str" + exitValue);
  }
}

Fixed version (ground truth):
/** 
 * Create the MultiQC report using docker.
 * @param dockerImage docker image to use
 * @param inputDirectory input directory
 * @param multiQCReportFile output report
 * @param projectName project name
 * @throws IOException if an error occurs while creating the report
 * @throws EoulsanException if MultiQC execution fails
 */
private static void createMultiQCReportWithDocker(final String dockerImage,final File inputDirectory,final File multiQCReportFile,final String projectName,final File temporaryDirectory) throws IOException, EoulsanException {
  SimpleProcess process=DockerManager.getInstance().createImageInstance(dockerImage);
  File executionDirectory=multiQCReportFile.getParentFile();
  File stdoutFile=new File(executionDirectory,"String_Node_Str");
  File stderrFile=new File(executionDirectory,"String_Node_Str");
  List<File> filesUsed=new ArrayList<>();
  filesUsed.add(executionDirectory);
  filesUsed.add(temporaryDirectory);
  filesUsed.add(multiQCReportFile);
  for (  File f : inputDirectory.listFiles()) {
    if (!f.getName().startsWith("String_Node_Str")) {
      filesUsed.add(f);
    }
  }
  final int exitValue=process.execute(createMultiQCOptions(inputDirectory,multiQCReportFile,projectName),executionDirectory,temporaryDirectory,stdoutFile,stderrFile,filesUsed.toArray(new File[filesUsed.size()]));
  if (exitValue > 0) {
    throw new EoulsanException("String_Node_Str" + exitValue);
  }
}
Program: 140988
Project: 140988
Buggy source:
/** 
 * Save genome description.
 * @param file output file
 */
public void save(final File file) throws FileNotFoundException, IOException {
  checkNotNull(file,"String_Node_Str");
  save(FileUtils.createOutputStream(file));
}

Fixed version (ground truth):
/** 
 * Save genome description.
 * @param file output file
 */
public void save(final File file) throws IOException {
  checkNotNull(file,"String_Node_Str");
  save(FileUtils.createOutputStream(file));
}
Program: 140989
Project: 140989
Buggy source:
/** 
 * Save the annotation.
 * @param outputFile Output file
 */
public void save(final File outputFile) throws FileNotFoundException, IOException {
  if (outputFile == null) {
    throw new NullPointerException("String_Node_Str");
  }
  save(FileUtils.createOutputStream(outputFile));
}

Fixed version (ground truth):
/** 
 * Save the annotation.
 * @param outputFile Output file
 */
public void save(final File outputFile) throws IOException {
  if (outputFile == null) {
    throw new NullPointerException("String_Node_Str");
  }
  save(FileUtils.createOutputStream(outputFile));
}
Program: 140990
Project: 140990
Buggy source:
/** 
 * Load the annotation.
 * @param inputFile input file
 */
public void load(final File inputFile) throws FileNotFoundException, IOException {
  if (inputFile == null) {
    throw new NullPointerException("String_Node_Str");
  }
  load(FileUtils.createInputStream(inputFile));
}

Fixed version (ground truth):
/** 
 * Load the annotation.
 * @param inputFile input file
 */
public void load(final File inputFile) throws IOException {
  if (inputFile == null) {
    throw new NullPointerException("String_Node_Str");
  }
  load(FileUtils.createInputStream(inputFile));
}
Program: 140991
Project: 140991
Buggy source:
@Override public int compareTo(final GenomicInterval e){
  if (e == null) {
    return -1;
  }
  if (!getChromosome().equals(e.getChromosome())) {
    return getChromosome().compareTo(e.getChromosome());
  }
  final int startComp=Integer.compare(this.start,e.getStart());
  if (startComp != 0) {
    return startComp;
  }
  return ((Integer)this.end).compareTo(e.getEnd());
}

Fixed version (ground truth):
@Override public int compareTo(final GenomicInterval e){
  if (e == null) {
    return -1;
  }
  if (!getChromosome().equals(e.getChromosome())) {
    return getChromosome().compareTo(e.getChromosome());
  }
  final int startComp=Integer.compare(this.start,e.getStart());
  if (startComp != 0) {
    return startComp;
  }
  return Integer.compare(this.end,e.getEnd());
}
Program: 140992
Project: 140992
Buggy source:
@Override public boolean hasNext(){
  if (this.end) {
    return false;
  }
  this.nextCallDone=false;
  if (!this.reuse) {
    this.result=new ReadSequence();
  }
  String line=null;
  try {
    while ((line=this.reader.readLine()) != null) {
      final String trim=line.trim();
      if ("String_Node_Str".equals(trim)) {
        continue;
      }
      this.result.parse(trim);
      this.result.setId(++this.count);
      return true;
    }
    this.sb.setLength(0);
    this.end=true;
    return false;
  }
 catch (  IOException e) {
    this.ioException=e;
    this.end=true;
    return false;
  }
}

Fixed version (ground truth):
@Override public boolean hasNext(){
  if (this.end) {
    return false;
  }
  this.nextCallDone=false;
  if (!this.reuse) {
    this.result=new ReadSequence();
  }
  String line=null;
  try {
    while ((line=this.reader.readLine()) != null) {
      final String trim=line.trim();
      if ("String_Node_Str".equals(trim)) {
        continue;
      }
      this.result.parse(trim);
      this.result.setId(++this.count);
      return true;
    }
    this.end=true;
    return false;
  }
 catch (  IOException e) {
    this.ioException=e;
    this.end=true;
    return false;
  }
}
Program: 140993
Project: 140993
Buggy source:
public void initialize(InputSplit genericSplit,TaskAttemptContext context) throws IOException {
  FileSplit split=(FileSplit)genericSplit;
  Configuration job=context.getConfiguration();
  this.maxLineLength=job.getInt(MAX_LINE_LENGTH,Integer.MAX_VALUE);
  start=split.getStart();
  end=start + split.getLength();
  final Path file=split.getPath();
  final FileSystem fs=file.getFileSystem(job);
  fileIn=fs.open(file);
  CompressionCodec codec=new CompressionCodecFactory(job).getCodec(file);
  if (null != codec) {
    isCompressedInput=true;
    decompressor=CodecPool.getDecompressor(codec);
    if (codec instanceof SplittableCompressionCodec) {
      final SplitCompressionInputStream cIn=((SplittableCompressionCodec)codec).createInputStream(fileIn,decompressor,start,end,SplittableCompressionCodec.READ_MODE.BYBLOCK);
      in=new CompressedSplitFastqLineReader(cIn,job,this.recordDelimiterBytes);
      start=cIn.getAdjustedStart();
      end=cIn.getAdjustedEnd();
      filePosition=cIn;
    }
 else {
      in=new SplitLineReader(codec.createInputStream(fileIn,decompressor),job,this.recordDelimiterBytes);
      filePosition=fileIn;
    }
  }
 else {
    fileIn.seek(start);
    in=new SplitLineReader(fileIn,job,this.recordDelimiterBytes);
    filePosition=fileIn;
  }
  if (start != 0) {
    start+=in.readLine(new Text(),0,maxBytesToConsume(start));
  }
  this.pos=start;
}

Fixed version (ground truth):
public void initialize(InputSplit genericSplit,TaskAttemptContext context) throws IOException {
  FileSplit split=(FileSplit)genericSplit;
  Configuration job=context.getConfiguration();
  this.maxLineLength=job.getInt(MAX_LINE_LENGTH,Integer.MAX_VALUE);
  start=split.getStart();
  end=start + split.getLength();
  final Path file=split.getPath();
  final FileSystem fs=file.getFileSystem(job);
  final FSDataInputStream fileIn=fs.open(file);
  CompressionCodec codec=new CompressionCodecFactory(job).getCodec(file);
  if (null != codec) {
    isCompressedInput=true;
    decompressor=CodecPool.getDecompressor(codec);
    if (codec instanceof SplittableCompressionCodec) {
      final SplitCompressionInputStream cIn=((SplittableCompressionCodec)codec).createInputStream(fileIn,decompressor,start,end,SplittableCompressionCodec.READ_MODE.BYBLOCK);
      in=new CompressedSplitFastqLineReader(cIn,job,this.recordDelimiterBytes);
      start=cIn.getAdjustedStart();
      end=cIn.getAdjustedEnd();
      filePosition=cIn;
    }
 else {
      in=new SplitLineReader(codec.createInputStream(fileIn,decompressor),job,this.recordDelimiterBytes);
      filePosition=fileIn;
    }
  }
 else {
    fileIn.seek(start);
    in=new SplitLineReader(fileIn,job,this.recordDelimiterBytes);
    filePosition=fileIn;
  }
  if (start != 0) {
    start+=in.readLine(new Text(),0,maxBytesToConsume(start));
  }
  this.pos=start;
}
Program: 140994
Project: 140994
Buggy source:
/** 
 * Constructor.
 * @param mapperName mapper name
 * @param executor executor
 * @param temporaryDirectory temporary directory
 * @param pairedEnd paired-end mode
 * @throws IOException if en error occurs
 */
protected MapperProcess(final String mapperName,MapperExecutor executor,final File temporaryDirectory,final boolean pairedEnd,final boolean threadForRead1) throws IOException {
  requireNonNull(mapperName,"String_Node_Str");
  requireNonNull(executor,"String_Node_Str");
  requireNonNull(temporaryDirectory,"String_Node_Str");
  try {
    this.mapperName=mapperName;
    this.uuid=UUID.randomUUID().toString();
    this.executor=executor;
    this.pairedEnd=pairedEnd;
    final File tmpDir=temporaryDirectory;
    this.pipeFile1=new File(tmpDir,"String_Node_Str" + uuid + "String_Node_Str");
    this.pipeFile2=new File(tmpDir,"String_Node_Str" + uuid + "String_Node_Str");
    this.writer1=threadForRead1 ? new FastqWriterThread(this.pipeFile1,"String_Node_Str") : new FastqWriterNoThread(this.pipeFile1);
    this.writer2=pairedEnd ? new FastqWriterThread(this.pipeFile2,"String_Node_Str") : null;
    addFilesToRemove(this.pipeFile1,this.pipeFile2);
    additionalInit();
    startProcess(tmpDir);
  }
 catch (  InterruptedException e) {
    throw new IOException(e);
  }
}

Fixed version (ground truth):
/** 
 * Constructor.
 * @param mapperName mapper name
 * @param executor executor
 * @param temporaryDirectory temporary directory
 * @param pairedEnd paired-end mode
 * @throws IOException if en error occurs
 */
protected MapperProcess(final String mapperName,MapperExecutor executor,final File temporaryDirectory,final boolean pairedEnd,final boolean threadForRead1) throws IOException {
  requireNonNull(mapperName,"String_Node_Str");
  requireNonNull(executor,"String_Node_Str");
  requireNonNull(temporaryDirectory,"String_Node_Str");
  try {
    this.mapperName=mapperName;
    this.uuid=UUID.randomUUID().toString();
    this.executor=executor;
    this.pairedEnd=pairedEnd;
    this.pipeFile1=new File(temporaryDirectory,"String_Node_Str" + uuid + "String_Node_Str");
    this.pipeFile2=new File(temporaryDirectory,"String_Node_Str" + uuid + "String_Node_Str");
    this.writer1=threadForRead1 ? new FastqWriterThread(this.pipeFile1,"String_Node_Str") : new FastqWriterNoThread(this.pipeFile1);
    this.writer2=pairedEnd ? new FastqWriterThread(this.pipeFile2,"String_Node_Str") : null;
    addFilesToRemove(this.pipeFile1,this.pipeFile2);
    additionalInit();
    startProcess(temporaryDirectory);
  }
 catch (  InterruptedException e) {
    throw new IOException(e);
  }
}
Program: 140995
Project: 140995
Buggy source:
/** 
 * Format a GFFEntry in GFF3 or GTF format.
 * @param e the entry
 * @param gtfFormat true if the entry is in GTF format
 * @return the entry in the correct format
 */
private static final String formatEntry(final GFFEntry e,final boolean gtfFormat){
  if (gtfFormat) {
    return e.toGTF();
  }
  return e.toGFF3();
}

Fixed version (ground truth):
/** 
 * Format a GFFEntry in GFF3 or GTF format.
 * @param e the entry
 * @param gtfFormat true if the entry is in GTF format
 * @return the entry in the correct format
 */
private static String formatEntry(final GFFEntry e,final boolean gtfFormat){
  if (gtfFormat) {
    return e.toGTF();
  }
  return e.toGFF3();
}
Program: 140996
Project: 140996
Buggy source:
/** 
 * Compare 2 Version object.
 * @param version Version to compare.
 * @return a negative integer, zero, or a positive integer as this object isless than, equal to, or greater than the specified object.
 */
@Override public int compareTo(final Version version){
  if (version == null) {
    return 1;
  }
  final int compMajor=Integer.compare(getMajor(),version.getMajor());
  if (compMajor != 0) {
    return compMajor;
  }
  final int compMinor=Integer.valueOf(getMinor()).compareTo(version.getMinor());
  if (compMinor != 0) {
    return compMinor;
  }
  final int compRevision=Integer.valueOf(getRevision()).compareTo(version.getRevision());
  if (compRevision != 0) {
    return compRevision;
  }
  return getType().compareTo(version.getType());
}

Fixed version (ground truth):
/** 
 * Compare 2 Version object.
 * @param version Version to compare.
 * @return a negative integer, zero, or a positive integer as this object isless than, equal to, or greater than the specified object.
 */
@Override public int compareTo(final Version version){
  if (version == null) {
    return 1;
  }
  final int compMajor=Integer.compare(getMajor(),version.getMajor());
  if (compMajor != 0) {
    return compMajor;
  }
  final int compMinor=Integer.compare(getMinor(),version.getMinor());
  if (compMinor != 0) {
    return compMinor;
  }
  final int compRevision=Integer.compare(getRevision(),version.getRevision());
  if (compRevision != 0) {
    return compRevision;
  }
  return getType().compareTo(version.getType());
}
Program: 140997
Project: 140997
Buggy source:
/** 
 * Constructor.
 * @param format format of the data
 */
protected AbstractData(final DataFormat format){
  checkNotNull(format,"String_Node_Str");
synchronized (this.getClass()) {
    this.id=++instanceCount;
  }
  this.name="String_Node_Str" + (++instanceCount);
  this.format=format;
}

Fixed version (ground truth):
/** 
 * Constructor.
 * @param format format of the data
 */
protected AbstractData(final DataFormat format){
  checkNotNull(format,"String_Node_Str");
synchronized (AbstractData.class) {
    this.id=++instanceCount;
  }
  this.name="String_Node_Str" + (++instanceCount);
  this.format=format;
}
Program: 140998
Project: 140998
Buggy source:
/** 
 * Initialize the settings of the Workflow.
 */
private void initializeSettings(){
  final CommandWorkflowModel c=this.workflowCommand;
  final Set<Parameter> globalParameters=c.getGlobalParameters();
  final Settings settings=EoulsanRuntime.getSettings();
  getLogger().info("String_Node_Str" + globalParameters);
  for (  Parameter p : globalParameters) {
    settings.setSetting(p.getName(),p.getStringValue());
  }
  DataFormatRegistry.getInstance().reload();
}

Fixed version (ground truth):
/** 
 * Initialize the settings of the Workflow.
 */
private void initializeSettings(){
  final Set<Parameter> globalParameters=this.workflowCommand.getGlobalParameters();
  final Settings settings=EoulsanRuntime.getSettings();
  getLogger().info("String_Node_Str" + globalParameters);
  for (  Parameter p : globalParameters) {
    settings.setSetting(p.getName(),p.getStringValue());
  }
  DataFormatRegistry.getInstance().reload();
}
Program: 140999
Project: 140999
Buggy source:
/** 
 * Create an OutputStream for the DataFile. The output stream will not automatically compress data.
 * @return an OutputStream object
 * @throws IOException if an error occurs while creating the DataFile
 */
public OutputStream rawCreate() throws IOException {
  return getProtocol().putData(this,this.md == null ? null : this.md);
}

Fixed version (ground truth):
/** 
 * Create an OutputStream for the DataFile. The output stream will not automatically compress data.
 * @return an OutputStream object
 * @throws IOException if an error occurs while creating the DataFile
 */
public OutputStream rawCreate() throws IOException {
  return getProtocol().putData(this,this.md);
}
Program: 141000
Project: 141000
Buggy source:
private Object loadClass(final String className,final Class<?> interf){
  if (className == null) {
    return null;
  }
  try {
    final Class<?> result=this.getClass().getClassLoader().loadClass(className);
    if (result == null) {
      return null;
    }
    final Object o=result.newInstance();
    if (interf.isInstance(o)) {
      return result.newInstance();
    }
    return null;
  }
 catch (  ClassNotFoundException e) {
    return null;
  }
catch (  InstantiationException e) {
    return null;
  }
catch (  IllegalAccessException e) {
    return null;
  }
}

Fixed version (ground truth):
private Object loadClass(final String className,final Class<?> interf){
  if (className == null) {
    return null;
  }
  try {
    final Class<?> result=this.getClass().getClassLoader().loadClass(className);
    if (result == null) {
      return null;
    }
    final Object o=result.newInstance();
    if (interf.isInstance(o)) {
      return result.newInstance();
    }
    return null;
  }
 catch (  ClassNotFoundException|InstantiationException|IllegalAccessException e) {
    return null;
  }
}
Program: 141001
Project: 141001
Buggy source:
@Override public boolean exists(final DataFile src,final boolean followLink){
  try {
    return new S3URL(src).getS3Object() != null;
  }
 catch (  AmazonS3Exception e) {
    return false;
  }
catch (  IOException e) {
    return false;
  }
}

Fixed version (ground truth):
@Override public boolean exists(final DataFile src,final boolean followLink){
  try {
    return new S3URL(src).getS3Object() != null;
  }
 catch (  AmazonS3Exception|IOException e) {
    return false;
  }
}
Program: 141002
Project: 141002
Buggy source:
/** 
 * Create a GenomeDescStorage
 * @param dir the path of the genome descriptions storage
 * @return a GenomeDescStorage object if the path contains an index storage ornull if no index storage is found
 */
public static final GenomeDescStorage getInstance(final DataFile dir){
  try {
    return new SimpleGenomeDescStorage(dir);
  }
 catch (  IOException e) {
    return null;
  }
catch (  NullPointerException e) {
    return null;
  }
}

Fixed version (ground truth):
/** 
 * Create a GenomeDescStorage
 * @param dir the path of the genome descriptions storage
 * @return a GenomeDescStorage object if the path contains an index storage ornull if no index storage is found
 */
public static final GenomeDescStorage getInstance(final DataFile dir){
  try {
    return new SimpleGenomeDescStorage(dir);
  }
 catch (  IOException|NullPointerException e) {
    return null;
  }
}
Program: 141003
Project: 141003
Buggy source:
/** 
 * Create a GenomeIndexStorage
 * @param dir the path of the index storage
 * @return a GenomeIndexStorage object if the path contains an index storageor null if no index storage is found
 */
public static final GenomeIndexStorage getInstance(final DataFile dir){
  try {
    return new SimpleGenomeIndexStorage(dir);
  }
 catch (  IOException e) {
    return null;
  }
catch (  NullPointerException e) {
    return null;
  }
}

Fixed version (ground truth):
/** 
 * Create a GenomeIndexStorage
 * @param dir the path of the index storage
 * @return a GenomeIndexStorage object if the path contains an index storageor null if no index storage is found
 */
public static final GenomeIndexStorage getInstance(final DataFile dir){
  try {
    return new SimpleGenomeIndexStorage(dir);
  }
 catch (  IOException|NullPointerException e) {
    return null;
  }
}
Program: 141004
Project: 141004
Buggy source:
/** 
 * Parse the sample name from its filename.
 * @param filename the filename to parse
 * @return the sample name
 */
private static String parseSampleNameFromFilename(final String filename){
  if (filename == null) {
    return null;
  }
  final List<String> list=new ArrayList<String>(Arrays.asList(filename.split("String_Node_Str")));
  final int size=list.size();
  if (size < 5) {
    return null;
  }
  StringBuilder sb=new StringBuilder();
  boolean first=true;
  for (  String field : list.subList(0,size - 4)) {
    if (first) {
      first=false;
    }
 else {
      sb.append('_');
    }
    sb.append(field);
  }
  return sb.toString();
}

Fixed version (ground truth):
/** 
 * Parse the sample name from its filename.
 * @param filename the filename to parse
 * @return the sample name
 */
private static String parseSampleNameFromFilename(final String filename){
  if (filename == null) {
    return null;
  }
  final List<String> list=new ArrayList<>(Arrays.asList(filename.split("String_Node_Str")));
  final int size=list.size();
  if (size < 5) {
    return null;
  }
  StringBuilder sb=new StringBuilder();
  boolean first=true;
  for (  String field : list.subList(0,size - 4)) {
    if (first) {
      first=false;
    }
 else {
      sb.append('_');
    }
    sb.append(field);
  }
  return sb.toString();
}
Program: 141005
Project: 141005
Buggy source:
@Override public List<ExperimentSample> getExperimentSamples(){
  List<ExperimentSample> samples=this.experiment.getExperimentSamples();
  List<ExperimentSample> result=new ArrayList<ExperimentSample>(samples.size());
  for (  ExperimentSample sample : samples) {
    result.add(new UnmodifiableExperimentSample(sample));
  }
  return Collections.unmodifiableList(result);
}

Fixed version (ground truth):
@Override public List<ExperimentSample> getExperimentSamples(){
  List<ExperimentSample> samples=this.experiment.getExperimentSamples();
  List<ExperimentSample> result=new ArrayList<>(samples.size());
  for (  ExperimentSample sample : samples) {
    result.add(new UnmodifiableExperimentSample(sample));
  }
  return Collections.unmodifiableList(result);
}
Program: 141006
Project: 141006
Buggy source:
@Override public List<Sample> getSamples(){
  List<Sample> samples=this.experiment.getSamples();
  List<Sample> result=new ArrayList<Sample>(samples.size());
  for (  Sample sample : samples) {
    result.add(new UnmodifiableSample(sample));
  }
  return Collections.unmodifiableList(result);
}

Fixed version (ground truth):
@Override public List<Sample> getSamples(){
  List<Sample> samples=this.experiment.getSamples();
  List<Sample> result=new ArrayList<>(samples.size());
  for (  Sample sample : samples) {
    result.add(new UnmodifiableSample(sample));
  }
  return Collections.unmodifiableList(result);
}
Program: 141007
Project: 141007
Buggy source:
/** 
 * Get the DesignReader for the data.
 * @return the DesignReader for the data
 * @throws IOException if an error occurs while reading data
 */
public DesignReader getDesignReader() throws IOException, IOException {
switch (getDesignFormatVersion()) {
case 1:
    return new Eoulsan1DesignReader(this);
case 2:
  return new Eoulsan2DesignReader(this);
default :
throw new IOException("String_Node_Str");
}
}

Fixed version (ground truth):
/** 
 * Get the DesignReader for the data.
 * @return the DesignReader for the data
 * @throws IOException if an error occurs while reading data
 */
public DesignReader getDesignReader() throws IOException {
switch (getDesignFormatVersion()) {
case 1:
    return new Eoulsan1DesignReader(this);
case 2:
  return new Eoulsan2DesignReader(this);
default :
throw new IOException("String_Node_Str");
}
}
Program: 141010
Project: 141010
Buggy source:
protected void additionalInit() throws IOException {
  final File tmpDir=EoulsanRuntime.getRuntime().getTempDirectory();
  final String uuid=getUUID();
  this.saiFile1=new File(tmpDir,PREFIX_FILES + "String_Node_Str" + uuid+ SAI_EXTENSION);
  this.saiFile2=new File(tmpDir,PREFIX_FILES + "String_Node_Str" + uuid+ SAI_EXTENSION);
  this.fastqFile1=new File(tmpDir,PREFIX_FILES + "String_Node_Str" + uuid+ FASTQ_EXTENSION);
  this.fastqFile2=new File(tmpDir,PREFIX_FILES + "String_Node_Str" + uuid+ FASTQ_EXTENSION);
  FileUtils.createNamedPipe(this.saiFile1);
  FileUtils.createNamedPipe(this.saiFile2);
  addFilesToRemove(this.saiFile1,this.saiFile2,this.fastqFile1,this.fastqFile2);
  this.writer1=new FastqWriterThread(this.fastqFile1,"String_Node_Str");
  this.writer2=new FastqWriterThread(this.fastqFile2,"String_Node_Str");
}

Fixed version (ground truth):
protected void additionalInit() throws IOException {
  final File tmpDir=EoulsanRuntime.getRuntime().getTempDirectory();
  final String uuid=getUUID();
  this.saiFile1=new File(tmpDir,PREFIX_FILES + "String_Node_Str" + uuid+ SAI_EXTENSION);
  this.saiFile2=new File(tmpDir,PREFIX_FILES + "String_Node_Str" + uuid+ SAI_EXTENSION);
  if (inputFile1 == null) {
    this.fastqFile1=new File(tmpDir,PREFIX_FILES + "String_Node_Str" + uuid+ FASTQ_EXTENSION);
    this.fastqFile2=new File(tmpDir,PREFIX_FILES + "String_Node_Str" + uuid+ FASTQ_EXTENSION);
    this.writer1=new FastqWriterThread(this.fastqFile1,"String_Node_Str");
    this.writer2=new FastqWriterThread(this.fastqFile2,"String_Node_Str");
  }
  FileUtils.createNamedPipe(this.saiFile1);
  FileUtils.createNamedPipe(this.saiFile2);
  addFilesToRemove(this.saiFile1,this.saiFile2,this.fastqFile1,this.fastqFile2);
}
Program: 141011
Project: 141011
Buggy source:
/** 
 * Remove a temporary file.
 * @param f f file to remove
 */
private void removeFile(final File f){
  if (f.exists()) {
    if (!f.delete()) {
      getLogger().warning("String_Node_Str" + f);
    }
  }
}

Fixed version (ground truth):
/** 
 * Remove a temporary file.
 * @param f f file to remove
 */
private void removeFile(final File f){
  if (f != null && f.exists()) {
    if (!f.delete()) {
      getLogger().warning("String_Node_Str" + f);
    }
  }
}
Program: 141012
Project: 141012
Buggy source:
/** 
 * Add an emergency task.
 * @param task the task to add
 */
public void add(final EmergencyStopTask task){
  checkNotNull(task,"String_Node_Str");
synchronized (this.tasks) {
    this.tasks.add(task);
  }
}

Fixed version (ground truth):
/** 
 * Add an emergency task.
 * @param task the task to add
 */
public void add(final EmergencyStopTask task){
  checkNotNull(task,"String_Node_Str");
  this.tasks.add(task);
}
Program: 141013
Project: 141013
Buggy source:
/** 
 * Remove an emergency task.
 * @param task the task to add
 */
public void remove(final EmergencyStopTask task){
  checkNotNull(task,"String_Node_Str");
synchronized (this.tasks) {
    this.tasks.remove(task);
  }
}

Fixed version (ground truth):
/** 
 * Remove an emergency task.
 * @param task the task to add
 */
public void remove(final EmergencyStopTask task){
  checkNotNull(task,"String_Node_Str");
  this.tasks.remove(task);
}
Program: 141014
Project: 141014
Buggy source:
@Override protected String internalGetMapperVersion(){
  try {
    final String bowtiePath;
synchronized (SYNC) {
      bowtiePath=install(getMapperExecutables());
    }
    final List<String> cmd=Lists.newArrayList(bowtiePath,"String_Node_Str");
    final String s=executeToString(cmd);
    final String[] lines=s.split("String_Node_Str");
    if (lines.length == 0) {
      return null;
    }
    final String[] tokens=lines[0].split("String_Node_Str");
    if (tokens.length > 1) {
      return tokens[1].trim();
    }
    return null;
  }
 catch (  IOException e) {
    return null;
  }
}

Fixed version (ground truth):
@Override protected String internalGetMapperVersion(){
  try {
    final String bowtiePath;
synchronized (SYNC) {
      bowtiePath=install(getMapperExecutableName());
    }
    final List<String> cmd=Lists.newArrayList(bowtiePath,"String_Node_Str");
    final String s=executeToString(cmd);
    final String[] lines=s.split("String_Node_Str");
    if (lines.length == 0) {
      return null;
    }
    final String[] tokens=lines[0].split("String_Node_Str");
    if (tokens.length > 1) {
      return tokens[1].trim();
    }
    return null;
  }
 catch (  IOException e) {
    return null;
  }
}
Program: 141015
Project: 141015
Buggy source:
@Override protected MapperProcess internalMapSE(final File archiveIndexDir) throws IOException {
  final String bowtiePath;
synchronized (SYNC) {
    bowtiePath=install(getMapperExecutables());
  }
  final String index=getIndexArgument(archiveIndexDir);
  return new MapperProcess(this,false){
    @Override protected List<List<String>> createCommandLines(){
      final List<String> cmd=new ArrayList<>();
      cmd.addAll(createCommonArgs(bowtiePath,index));
      if (isMultipleInstancesEnabled()) {
        cmd.add("String_Node_Str");
      }
      cmd.add(getNamedPipeFile1().getAbsolutePath());
      getLogger().info(cmd.toString());
      return Collections.singletonList(cmd);
    }
    @Override protected File executionDirectory(){
      return archiveIndexDir;
    }
  }
;
}

Fixed version (ground truth):
@Override protected MapperProcess internalMapSE(final File archiveIndexDir) throws IOException {
  final String bowtiePath;
synchronized (SYNC) {
    bowtiePath=install(getMapperExecutableName());
  }
  final String index=getIndexArgument(archiveIndexDir);
  return new MapperProcess(this,false){
    @Override protected List<List<String>> createCommandLines(){
      final List<String> cmd=new ArrayList<>();
      cmd.addAll(createCommonArgs(bowtiePath,index));
      if (isMultipleInstancesEnabled()) {
        cmd.add("String_Node_Str");
      }
      cmd.add(getNamedPipeFile1().getAbsolutePath());
      getLogger().info(cmd.toString());
      return Collections.singletonList(cmd);
    }
    @Override protected File executionDirectory(){
      return archiveIndexDir;
    }
  }
;
}
Program: 141016
Project: 141016
Buggy source:
@Override protected MapperProcess internalMapPE(final File archiveIndexDir) throws IOException {
  final String bowtiePath;
synchronized (SYNC) {
    bowtiePath=install(getMapperExecutables());
  }
  final String index=getIndexArgument(archiveIndexDir);
  return new MapperProcess(this,true){
    @Override protected List<List<String>> createCommandLines(){
      final List<String> cmd=new ArrayList<>();
      cmd.addAll(createCommonArgs(bowtiePath,index));
      if (isMultipleInstancesEnabled()) {
        cmd.add("String_Node_Str");
      }
      cmd.add("String_Node_Str");
      cmd.add(getNamedPipeFile1().getAbsolutePath());
      cmd.add("String_Node_Str");
      cmd.add(getNamedPipeFile2().getAbsolutePath());
      return Collections.singletonList(cmd);
    }
    @Override protected File executionDirectory(){
      return archiveIndexDir;
    }
  }
;
}

Fixed version (ground truth):
@Override protected MapperProcess internalMapPE(final File archiveIndexDir) throws IOException {
  final String bowtiePath;
synchronized (SYNC) {
    bowtiePath=install(getMapperExecutableName());
  }
  final String index=getIndexArgument(archiveIndexDir);
  return new MapperProcess(this,true){
    @Override protected List<List<String>> createCommandLines(){
      final List<String> cmd=new ArrayList<>();
      cmd.addAll(createCommonArgs(bowtiePath,index));
      if (isMultipleInstancesEnabled()) {
        cmd.add("String_Node_Str");
      }
      cmd.add("String_Node_Str");
      cmd.add(getNamedPipeFile1().getAbsolutePath());
      cmd.add("String_Node_Str");
      cmd.add(getNamedPipeFile2().getAbsolutePath());
      return Collections.singletonList(cmd);
    }
    @Override protected File executionDirectory(){
      return archiveIndexDir;
    }
  }
;
}
Program: 141017
Project: 141017
Buggy source:
/** 
 * Wait a free JVM.
 * @param context the Hadoop context
 */
private void waitFreeJVM(final Context context){
  final long waitStartTime=System.currentTimeMillis();
  ProcessUtils.waitUntilExecutableRunning(this.mapper.getMapperName().toLowerCase());
  getLogger().info("String_Node_Str" + StringUtils.toTimeHumanReadable(System.currentTimeMillis() - waitStartTime) + "String_Node_Str"+ this.mapper.getMapperName());
  context.setStatus("String_Node_Str" + this.mapper.getMapperName());
}

Fixed version (ground truth):
/** 
 * Wait a free JVM.
 * @param context the Hadoop context
 */
private void waitFreeJVM(final Context context){
  final long waitStartTime=System.currentTimeMillis();
  ProcessUtils.waitUntilExecutableRunning(this.mapper.getMapperExecutableName());
  getLogger().info("String_Node_Str" + StringUtils.toTimeHumanReadable(System.currentTimeMillis() - waitStartTime) + "String_Node_Str"+ this.mapper.getMapperName());
  context.setStatus("String_Node_Str" + this.mapper.getMapperName());
}
Program: 141019
Project: 141019
Buggy source:
/** 
 * This method runs the ExpressionCounter.
 * @param alignmentFile file containing SAM alignments
 * @param annotationFile file containing the reference genome annotation
 * @param gtfFormat true if the annotation is in GTF format
 * @param expressionFile output file for the expression step
 * @param genomeDescFile file containing the genome description
 * @param reporter the Reporter object of the Eoulsan run
 * @param counterGroup string with the counter name group for the expressionstep
 * @throws IOException
 */
protected abstract void internalCount(final DataFile alignmentFile,final DataFile annotationFile,final boolean gtfFormat,final DataFile expressionFile,final DataFile genomeDescFile,Reporter reporter,String counterGroup) throws IOException, EoulsanException, BadBioEntryException ;

Fixed version (ground truth):
/** 
 * This method runs the ExpressionCounter.
 * @param alignmentFile file containing SAM alignments
 * @param annotationFile file containing the reference genome annotation
 * @param gtfFormat true if the annotation is in GTF format
 * @param expressionFile output file for the expression step
 * @param genomeDescFile file containing the genome description
 * @param reporter the Reporter object of the Eoulsan run
 * @param counterGroup string with the counter name group for the expressionstep
 * @throws IOException if the methods fails
 */
protected abstract void internalCount(final DataFile alignmentFile,final DataFile annotationFile,final boolean gtfFormat,final DataFile expressionFile,final DataFile genomeDescFile,Reporter reporter,String counterGroup) throws IOException, EoulsanException, BadBioEntryException ;
Program: 141020
Project: 141020
Buggy source:
/** 
 * This method runs the ExpressionCounter.
 * @param alignmentFile file containing SAM alignments
 * @param annotationFile file containing the reference genome annotation
 * @param gtfFormat true if the annotation is in GTF format
 * @param expressionFile output file for the expression step
 * @param genomeDescFile file containing the genome description
 * @throws IOException
 */
void count(DataFile alignmentFile,DataFile annotationFile,final boolean gtfFormat,DataFile expressionFile,DataFile genomeDescFile) throws IOException, EoulsanException, BadBioEntryException ;

Fixed version (ground truth):
/** 
 * This method runs the ExpressionCounter.
 * @param alignmentFile file containing SAM alignments
 * @param annotationFile file containing the reference genome annotation
 * @param gtfFormat true if the annotation is in GTF format
 * @param expressionFile output file for the expression step
 * @param genomeDescFile file containing the genome description
 * @throws IOException if the counting fails
 */
void count(DataFile alignmentFile,DataFile annotationFile,final boolean gtfFormat,DataFile expressionFile,DataFile genomeDescFile) throws IOException, EoulsanException, BadBioEntryException ;
Program: 141021
Project: 141021
Buggy source:
/** 
 * Close the stream.
 * @throws IOException
 */
@Override public void close() throws IOException {
  this.reader.close();
}

Fixed version (ground truth):
/** 
 * Close the stream.
 * @throws IOException if an error occurs while closing the file
 */
@Override public void close() throws IOException {
  this.reader.close();
}
Program: 141022
Project: 141022
Buggy source:
/** 
 * @param trimmerArgs
 * @return new sequence after trimmomatic
 */
protected abstract AbstractSingleRecordTrimmer createTrimmer(String trimmerArgs);

Fixed version (ground truth):
/** 
 * Create a Trimmer object
 * @param trimmerArgs trimmer arguments
 * @return new sequence after trimmomatic
 */
protected abstract AbstractSingleRecordTrimmer createTrimmer(String trimmerArgs);
Program: 141023
Project: 141023
Buggy source:
/** 
 * Constructor.
 * @param dockerClient Docker client
 * @param dockerImage Docker image
 * @param temporaryDirectory temporary directory
 * @throws IOException if an error occurs while creating the connection
 */
DockerMapperExecutor(final String dockerImage,final File temporaryDirectory) throws IOException {
  checkNotNull(dockerImage,"String_Node_Str");
  checkNotNull(temporaryDirectory,"String_Node_Str");
  this.temporaryDirectory=temporaryDirectory;
  this.dockerConnection=DockerManager.getInstance().createImageInstance(dockerImage);
}

Fixed version (ground truth):
/** 
 * Constructor.
 * @param dockerImage Docker image
 * @param temporaryDirectory temporary directory
 * @throws IOException if an error occurs while creating the connection
 */
DockerMapperExecutor(final String dockerImage,final File temporaryDirectory) throws IOException {
  checkNotNull(dockerImage,"String_Node_Str");
  checkNotNull(temporaryDirectory,"String_Node_Str");
  this.temporaryDirectory=temporaryDirectory;
  this.dockerConnection=DockerManager.getInstance().createImageInstance(dockerImage);
}