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comparison NGSrich_0.5.5/src/NGSrich.java @ 0:89ad0a9cca52 default tip

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author pfrommolt
date Mon, 21 Nov 2011 08:12:19 -0500
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-1:000000000000 0:89ad0a9cca52
1 import java.io.IOException;
2
3 import _main.NGSrichEvaluate;
4 import _main.NGSrichSummarize;
5 import exceptions.FileFormatException;
6
7 /**
8 * This is the main class.
9 *
10 * @author Peter Frommolt
11 * @author Ali Abdallah
12 */
13
14 public class NGSrich {
15
16 /**
17 * Self Explanatory.
18 *
19 * @param args an Array of argument. The first argument is command and the
20 * other arguments are its options.
21 *
22 * @throws FileFormatException if the used files have formally a bad format.
23 * @throws IOException
24 * @throws InterruptedException
25 */
26 public static void main(String[] args) throws FileFormatException,
27 IOException, InterruptedException {
28
29 String usagestr =
30 "\nThis is NGSrich, version 0.5.4.\n\n"
31 + "Usage: java NGSrich [command] [options]\n\n"
32 + "\tCommands:\n"
33 + "\tevaluate"
34 + "\tEvaluate target enrichment for a single sample.\n"
35 + "\tsummarize"
36 + "\tCreate a summary report for several evaluations.\n";
37
38 int alen = args.length;
39 if (alen == 0) {
40 System.out.println(usagestr);
41 System.exit(0);
42 } else {
43 String[] cparams = new String[alen - 1];
44 for (int i = 0; i < alen - 1; i = i + 1) {
45 cparams[i] = args[i + 1];
46 }
47 String eval = "evaluate", summ = "summarize";
48 if (eval.equals(args[0])) {
49 // Geändert von AA 27.07.2011.
50 new NGSrichEvaluate(cparams).evaluate();
51 }
52 if (summ.equals(args[0])) {
53 // Geändert von AA 27.07.2011.
54 new NGSrichSummarize(cparams).summarize();
55 }
56 }
57 }
58 }