Example #1
0
  @CLNames(
      names = {"-msms"},
      required = true)
  @CLDescription(
      "The msms comand line for contex. Need the number of demes and sampling stratagy and -s to be correct. Of course this includes the stats collectors used. Dont forget that each indivd is 2 samples")
  public void msmsCmdLine(String[] msmsArgs) {
    msmsparser = new CommandLineMarshal();
    try {
      CmdLineParser<CommandLineMarshal> marshel = CommandLineMarshal.getCacheParser(); // new
      // CmdLineParser<CommandLineMarshal>(msmsparser);
      marshel.processArguments(msmsArgs, msmsparser);
      sampleConfig = msmsparser.getSampleConfig();

      collectors = msmsparser.getStatsCollectors();
      if (collectors == null || collectors.size() == 0) {
        throw new RuntimeException("Need at least one -stat option");
      }
      for (StatsCollector sc : collectors) {
        sc.init();
      }

    } catch (Exception e) {
      System.err.println(
          "Error Parsing MSMS comand line. Note that all non msms options must come before the -msms switch.");
      throw new RuntimeException(e);
    }
  }
Example #2
0
  public static void main(String[] args) {
    MStoStats rse = new MStoStats();
    CmdLineParser<MStoStats> parser = null;
    try {
      parser = new CmdLineParser<MStoStats>(MStoStats.class);
    } catch (Exception e1) {
      e1.printStackTrace();
      return;
    }

    try {
      parser.processArguments(args, rse);
      if (rse.help) {
        System.err.println(parser.longUsage());
        System.exit(0);
      }
      rse.run();
    } catch (Exception e) {
      System.err.println(parser.longUsage());
      if (!rse.help) e.printStackTrace();
    }
  }