Program: 91872
Project: 91872
Buggy source:
/** 
 * Transforms the coordinates read from the given stream. This method ignores empty and comment lines.
 * @param in        the stream from where to read coordinates.
 * @param filename  the filename, for error reporting only.
 * @return the errors that occurred during transformation.
 */
private void transform(final LineNumberReader in,final String filename) throws IOException {
  final int dimension=operation.getSourceCRS().getCoordinateSystem().getDimension();
  final MathTransform mt=operation.getMathTransform();
  final double[] result=new double[mt.getTargetDimensions()];
  final double[] domainCoordinate;
  final DirectPositionView positionInDomain;
  if (toDomainOfValidityCRS != null) {
    domainCoordinate=new double[toDomainOfValidityCRS.getTargetDimensions()];
    positionInDomain=new DirectPositionView(domainCoordinate,0,domainCoordinate.length);
  }
 else {
    domainCoordinate=null;
    positionInDomain=null;
  }
  try {
    String line;
    while ((line=in.readLine()) != null) {
      final int start=CharSequences.skipLeadingWhitespaces(line,0,line.length());
      if (start < line.length() && line.charAt(start) != '#') {
        final double[] coordinates=CharSequences.parseDoubles(line,',');
        if (coordinates.length != dimension) {
          throw new MismatchedDimensionException(Errors.format(Errors.Keys.MismatchedDimensionForCRS_3,operation.getSourceCRS().getName().getCode(),dimension,coordinates.length));
        }
        mt.transform(coordinates,0,result,0,1);
        for (int i=0; i < result.length; i++) {
          if (i != 0) {
            out.print(',');
          }
          final double value=result[i];
          final String s;
          if (Math.abs(value) >= thresholdForScientificNotation[i]) {
            s=Double.toString(value);
          }
 else {
            coordinateFormat.setMinimumFractionDigits(numFractionDigits[i]);
            coordinateFormat.setMaximumFractionDigits(numFractionDigits[i]);
            s=coordinateFormat.format(value);
          }
          out.print(CharSequences.spaces(ordinateWidth - s.length()));
          out.print(s);
        }
        if (domainCoordinate != null) {
          boolean inside;
          try {
            toDomainOfValidityCRS.transform(coordinates,0,domainCoordinate,0,1);
            inside=domainOfValidity.contains(positionInDomain);
          }
 catch (          TransformException e) {
            inside=false;
            warning(e);
          }
          if (!inside) {
            out.print("String_Node_Str");
            printQuotedText(Errors.getResources(locale).getString(Errors.Keys.OutsideDomainOfValidity),0,X364.FOREGROUND_RED);
          }
        }
        out.println();
      }
    }
  }
 catch (  Exception e) {
    error(Errors.format(Errors.Keys.ErrorInFileAtLine_2,filename,in.getLineNumber()),e);
  }
}

Fixed version (ground truth):
/** 
 * Transforms the given coordinates.
 */
private void transform(final List<double[]> points) throws TransformException {
  final int dimension=operation.getSourceCRS().getCoordinateSystem().getDimension();
  final MathTransform mt=operation.getMathTransform();
  final double[] result=new double[mt.getTargetDimensions()];
  final double[] domainCoordinate;
  final DirectPositionView positionInDomain;
  final ImmutableEnvelope domainOfValidity;
  final GeographicBoundingBox bbox;
  if (toDomainOfValidity != null && (bbox=CRS.getGeographicBoundingBox(operation)) != null) {
    domainOfValidity=new ImmutableEnvelope(bbox);
    domainCoordinate=new double[toDomainOfValidity.getTargetDimensions()];
    positionInDomain=new DirectPositionView(domainCoordinate,0,domainCoordinate.length);
  }
 else {
    domainOfValidity=null;
    domainCoordinate=null;
    positionInDomain=null;
  }
  for (  final double[] coordinates : points) {
    if (coordinates.length != dimension) {
      throw new MismatchedDimensionException(Errors.format(Errors.Keys.MismatchedDimensionForCRS_3,operation.getSourceCRS().getName().getCode(),dimension,coordinates.length));
    }
    mt.transform(coordinates,0,result,0,1);
    for (int i=0; i < result.length; i++) {
      if (i != 0) {
        out.print(',');
      }
      final double value=result[i];
      final String s;
      if (Math.abs(value) >= thresholdForScientificNotation[i]) {
        s=Double.toString(value);
      }
 else {
        coordinateFormat.setMinimumFractionDigits(numFractionDigits[i]);
        coordinateFormat.setMaximumFractionDigits(numFractionDigits[i]);
        s=coordinateFormat.format(value);
      }
      out.print(CharSequences.spaces(ordinateWidth - s.length()));
      out.print(s);
    }
    if (domainOfValidity != null) {
      boolean inside;
      try {
        toDomainOfValidity.transform(coordinates,0,domainCoordinate,0,1);
        inside=domainOfValidity.contains(positionInDomain);
      }
 catch (      TransformException e) {
        inside=false;
        warning(e);
      }
      if (!inside) {
        out.print("String_Node_Str");
        printQuotedText(Errors.getResources(locale).getString(Errors.Keys.OutsideDomainOfValidity),0,X364.FOREGROUND_RED);
      }
    }
    out.println();
  }
}