public static void main(String[] args) throws IOException, ParseException {
		Options opt = new Options();
		opt.addOption("", "db", true, "The File used for Training");
		opt.addOption("", "method", true, "The method used for Training");
		opt.addOption("", "probabilities", false, "Print Probabilities?");
		opt.addOption("", "seq", true, "Sequence input");
		CommandLineParser parser = new GnuParser();
		CommandLine cmd = parser.parse(opt, args);
		String database = "";
		String topred = "";
		String reality = "";
		String probabilities = "";
		String probabilitiesHtml = "";
		boolean probs = false;

		int type = 1;
		if (cmd.hasOption("db")) {
			database = cmd.getOptionValue("db");
		} else {
			System.out.println("Select Database");
		}
		if (cmd.hasOption("method")) {
			if (cmd.getOptionValue("method").equals("gor1")) {
				type = 1;
			} else if (cmd.getOptionValue("method").equals("gor3")) {
				type = 3;
			}
		} else {
			System.out.println("Default Method Gor1 selected");
		}
		if (cmd.hasOption("probabilities")) {
			probs = true;
		} else {
			System.out.println("What's this?");
		}
		if (cmd.hasOption("seq")) {
			topred = cmd.getOptionValue("seq");
		} else {
			System.out.println("U stupid?");
		}
		Sequence[] prim = Useful.filetosequence(topred);
		Sequence[] p = new Sequence[prim.length];
		// String p =
		// "/home/proj/biocluster/praktikum/bioprakt/Data/GOR/CB513DSSP.db";
		// String filename =
		// "/home/proj/biocluster/praktikum/bioprakt/progprakt6/Solution4/test.txt";
		// TODO Auto-generated method stub
		String content = "";
		String content2 = "";
		if (type == 3) {
			Gor3Model g = new Gor3Model();
			g.train(database);
			for (int i = 0; i < prim.length; i++) {
				String prediction = g.predictString(prim[i].getps());
				reality = prim[i].getss();
				p[i] = new Sequence(prim[i].getid(), prim[i].getps(),
						prediction);
			}
		} else {
			Gor1Model g = new Gor1Model();
			g.train(database);
			for (int i = 0; i < prim.length; i++) {
				String prediction = g.predictString(prim[i].getps());
				reality = prim[i].getss();
				p[i] = new Sequence(prim[i].getid(), prim[i].getps(),
						prediction);
			}
		}
	}