@Override
public int compare(String o1, String o2) {
if (Extractors.isHeaderLine(o1)) {
return -1;
} else if (Extractors.isHeaderLine(o2)) {
return 1;
}
String[] splitLine1 = Utils.splitWithTab(o1);
String[] splitLine2 = Utils.splitWithTab(o2);
int cmp;
try {
cmp =
chromosomeComparator.compareChromosomeName(
splitLine1[chromoFieldIndex], splitLine2[chromoFieldIndex]);
} catch (Exception e) {
// if the chromosome comparator doesn't work we use a string cpmparator
cmp =
new StringComparator()
.compare(splitLine1[chromoFieldIndex], splitLine2[chromoFieldIndex]);
}
// if the chromosomes are equals we compare the positions
if (cmp == 0) {
try {
ChromosomeWindow cw1 =
new SimpleChromosomeWindow(splitLine1[startFieldIndex], splitLine1[stopFieldIndex]);
ChromosomeWindow cw2 =
new SimpleChromosomeWindow(splitLine2[startFieldIndex], splitLine2[stopFieldIndex]);
cmp = cw1.compareTo(cw2);
} catch (Exception e) {
new StringComparator().compare(splitLine1[startFieldIndex], splitLine2[startFieldIndex]);
}
}
return cmp;
}
/**
* @param inputFile input file
* @return a new File with prefix ".sorted" added before the extension
*/
public static File generateOutputFile(File inputFile) {
String extension = Utils.getExtension(inputFile);
String nameWithoutExtension = Utils.getFileNameWithoutExtension(inputFile);
String newFileName = nameWithoutExtension + ".sorted." + extension;
File parentDirectory = inputFile.getParentFile();
return new File(parentDirectory, newFileName);
}
/**
* @param inputFile
* @return a string comparator adapted that compares the lines of the input file
* @throws InvalidParameterException
*/
private static Comparator<String> generateComparator(File inputFile)
throws InvalidParameterException {
String fileExtension = Utils.getExtension(inputFile);
if (fileExtension == null) {
throw new InvalidParameterException(
"Cannot sort the specified file: "
+ inputFile.getName()
+ "\n"
+ "Files without extension are not recognized by the sorting function");
} else if (fileExtension.equalsIgnoreCase("gff")) {
return new GenomicFileLineComparator(0, 3, 4);
} else if (fileExtension.equalsIgnoreCase("gr")) {
return new GenomicFileLineComparator(0, 1, 2);
} else if (fileExtension.equalsIgnoreCase("bed")) {
return new GenomicFileLineComparator(0, 1, 2);
} else if (fileExtension.equalsIgnoreCase("bgr")) {
return new GenomicFileLineComparator(0, 1, 2);
} else if (fileExtension.equalsIgnoreCase("pair")) {
return new GenomicFileLineComparator(0, 4, 4);
} else if (fileExtension.equalsIgnoreCase("psl")) {
return new GenomicFileLineComparator(13, 15, 16);
} else if (fileExtension.equalsIgnoreCase("sam")) {
return new GenomicFileLineComparator(0, 3, 3);
} else {
throw new InvalidParameterException(
"Cannot sort the specified file: "
+ inputFile.getName()
+ "\n"
+ "Files with "
+ fileExtension
+ " extension are not recognized by the sorting function");
}
}
/**
* Sorts a genomic file per chromosome, start and then stop position
*
* @param inputFile
* @throws IOException
*/
public static void externalSortGenomicFile(File inputFile) throws IOException {
Comparator<String> comparator = generateComparator(inputFile);
int maxTmpFiles = ExternalSort.DEFAULTMAXTEMPFILES;
Charset charset = Charset.defaultCharset();
File tmpDir = new File(Utils.getTmpDirectoryPath());
File outputFile = generateOutputFile(inputFile);
List<File> l =
ExternalSort.sortInBatch(
inputFile, comparator, maxTmpFiles, charset, tmpDir, false, 0, false);
ExternalSort.mergeSortedFiles(l, outputFile, comparator, charset, false, false, false);
}
private void setTrackLock(boolean lock) {
// Update tracks
LayerType[] filter = {LayerType.VARIANT_LAYER};
List<Layer<?>> allLayers =
MainFrame.getInstance().getTrackListPanel().getModel().getAllLayers();
List<Layer<?>> layers = Utils.getLayers(allLayers, filter);
for (Layer<?> layer : layers) {
if (lock) {
((VariantLayer) layer).getGenomeDrawer().lockPainting();
} else {
((VariantLayer) layer).getGenomeDrawer().unlockPainting();
}
}
}
@Override
public void run() {
// Lock the painting
setTrackLock(true);
// Create and start the filter thread
FilterThread filterThread = new FilterThread();
filterThread.setPreviousFilterList(previousFilterList);
if (filterThread.hasToBeStarted()) {
CountDownLatch filterLatch = new CountDownLatch(1);
filterThread.setLatch(filterLatch);
filterThread.start();
// The current thread is waiting for the filter thread to finish
try {
filterLatch.await();
} catch (InterruptedException e) {
ExceptionManager.getInstance().caughtException(e);
}
}
// Update tracks
TrackThread trackThread = new TrackThread();
CountDownLatch trackLatch = new CountDownLatch(1); // one for the track update action
trackThread.setLatch(trackLatch);
trackThread.start();
// The current thread is waiting for the filter thread to finish
try {
trackLatch.await();
} catch (InterruptedException e) {
ExceptionManager.getInstance().caughtException(e);
}
// Many data has been loaded, removed, garbage collecting free some memory
Utils.garbageCollect();
// Unlock the painting and force the repaint
setTrackLock(false);
repaintTrack();
}