/**
* @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");
}
}