public static void main(String[] args) { if (args.length == 0) { printDocs(); System.exit(0); } new Sgr2Bar(args); }
/** This method will process each argument and assign new varibles */ public void processArgs(String[] args) { Pattern pat = Pattern.compile("-[a-z]"); File dir = null; for (int i = 0; i < args.length; i++) { String lcArg = args[i].toLowerCase(); Matcher mat = pat.matcher(lcArg); if (mat.matches()) { char test = args[i].charAt(1); try { switch (test) { case 'f': dir = new File(args[i + 1]); i++; break; case 'v': genomeVersion = args[i + 1]; i++; break; case 's': strand = args[++i]; break; case 't': stairStep = true; break; case 'h': printDocs(); System.exit(0); default: Misc.printExit("\nError: unknown option! " + mat.group()); } } catch (Exception e) { Misc.printExit( "\nSorry, something doesn't look right with this parameter: -" + test + "\n"); } } } if (dir == null || dir.canRead() == false) Misc.printExit("\nError: cannot find or read your sgr file/ directory.\n"); File[][] tot = new File[3][]; tot[0] = IO.extractFiles(dir, ".sgr"); tot[1] = IO.extractFiles(dir, ".sgr.zip"); tot[2] = IO.extractFiles(dir, ".sgr.gz"); sgrFiles = IO.collapseFileArray(tot); if (sgrFiles == null || sgrFiles.length == 0) Misc.printExit("\nError: cannot find your xxx.sgr.zip file(s)"); if (genomeVersion == null) Misc.printExit( "\nError: you must supply a genome version. Goto http://genome.ucsc.edu/cgi-" + "bin/hgGateway load your organism to find the associated genome version.\n"); }