cmdline_hmmsearch.c

马尔科夫模型的java版本实现

  if (initialize)
    cmdline_parser_init (args_info);

  cmdline_parser_init (&local_args_info);

  optarg = 0;
  optind = 1;
  opterr = 1;
  optopt = '?';

  while (1)
    {
      int option_index = 0;
      char *stop_char;

      static struct option long_options[] = {
        { "help",	0, NULL, 'h' },
        { "version",	0, NULL, 'V' },
        { "hmmnamefile",	1, NULL, 'm' },
        { "seqnamefile",	1, NULL, 's' },
        { "seqformat",	1, NULL, 'f' },
        { "outpath",	1, NULL, 'o' },
        { "freqfile",	1, NULL, 'q' },
        { "smxfile",	1, NULL, 'x' },
        { "replfile",	1, NULL, 'r' },
        { "priorfile",	1, NULL, 'p' },
        { "nullfile",	1, NULL, 'n' },
        { "anchor",	1, NULL, 'a' },
        { "labeloutput",	0, NULL, 'L' },
        { "alignmentoutput",	0, NULL, 'A' },
        { "msascoring",	1, NULL, 'M' },
        { "usecolumns",	1, NULL, 'c' },
        { "nolabels",	0, NULL, 0 },
        { "verbose",	0, NULL, 'v' },
        { "viterbi",	0, NULL, 0 },
        { "nbest",	0, NULL, 0 },
        { "forward",	0, NULL, 0 },
        { "max_d",	0, NULL, 0 },
        { "path",	0, NULL, 0 },
        { "nopostout",	0, NULL, 0 },
        { "nolabelout",	0, NULL, 0 },
        { "nollout",	0, NULL, 0 },
        { "nooddsout",	0, NULL, 0 },
        { "norevout",	0, NULL, 0 },
        { "alignpostout",	0, NULL, 0 },
        { "alignlabelout",	0, NULL, 0 },
        { "labelllout",	0, NULL, 0 },
        { "labeloddsout",	0, NULL, 0 },
        { "labelrevout",	0, NULL, 0 },
        { NULL,	0, NULL, 0 }
      };

      stop_char = 0;
      c = getopt_long (argc, argv, "hVm:s:f:o:q:x:r:p:n:a:LAM:c:v", long_options, &option_index);

      if (c == -1) break;	/* Exit from `while (1)' loop.  */

      switch (c)
        {
        case 'h':	/* Print help and exit.  */
          cmdline_parser_print_help ();
          exit (EXIT_SUCCESS);

        case 'V':	/* Print version and exit.  */
          cmdline_parser_print_version ();
          exit (EXIT_SUCCESS);

        case 'm':	/* model namefile for models in hmg format.  */
          if (local_args_info.hmmnamefile_given)
            {
              fprintf (stderr, "%s: `--hmmnamefile' (`-m') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->hmmnamefile_given && ! override)
            continue;
          local_args_info.hmmnamefile_given = 1;
          args_info->hmmnamefile_given = 1;
          if (args_info->hmmnamefile_arg)
            free (args_info->hmmnamefile_arg); /* free previous string */
          args_info->hmmnamefile_arg = gengetopt_strdup (optarg);
          break;

        case 's':	/* sequence namefile (for seuences in fasta, smod, msamod or prfmod format).  */
          if (local_args_info.seqnamefile_given)
            {
              fprintf (stderr, "%s: `--seqnamefile' (`-s') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->seqnamefile_given && ! override)
            continue;
          local_args_info.seqnamefile_given = 1;
          args_info->seqnamefile_given = 1;
          if (args_info->seqnamefile_arg)
            free (args_info->seqnamefile_arg); /* free previous string */
          args_info->seqnamefile_arg = gengetopt_strdup (optarg);
          break;

        case 'f':	/* format of input sequences (fa=fasta, s=smod, msa=msamod, prf=prfmod).  */
          if (local_args_info.seqformat_given)
            {
              fprintf (stderr, "%s: `--seqformat' (`-f') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->seqformat_given && ! override)
            continue;
          local_args_info.seqformat_given = 1;
          args_info->seqformat_given = 1;
          if (args_info->seqformat_arg)
            free (args_info->seqformat_arg); /* free previous string */
          args_info->seqformat_arg = gengetopt_strdup (optarg);
          break;

        case 'o':	/* output directory.  */
          if (local_args_info.outpath_given)
            {
              fprintf (stderr, "%s: `--outpath' (`-o') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->outpath_given && ! override)
            continue;
          local_args_info.outpath_given = 1;
          args_info->outpath_given = 1;
          if (args_info->outpath_arg)
            free (args_info->outpath_arg); /* free previous string */
          args_info->outpath_arg = gengetopt_strdup (optarg);
          break;

        case 'q':	/* background frequency file.  */
          if (local_args_info.freqfile_given)
            {
              fprintf (stderr, "%s: `--freqfile' (`-q') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->freqfile_given && ! override)
            continue;
          local_args_info.freqfile_given = 1;
          args_info->freqfile_given = 1;
          if (args_info->freqfile_arg)
            free (args_info->freqfile_arg); /* free previous string */
          args_info->freqfile_arg = gengetopt_strdup (optarg);
          break;

        case 'x':	/* substitution matrix file.  */
          if (local_args_info.smxfile_given)
            {
              fprintf (stderr, "%s: `--smxfile' (`-x') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->smxfile_given && ! override)
            continue;
          local_args_info.smxfile_given = 1;
          args_info->smxfile_given = 1;
          if (args_info->smxfile_arg)
            free (args_info->smxfile_arg); /* free previous string */
          args_info->smxfile_arg = gengetopt_strdup (optarg);
          break;

        case 'r':	/* replacement letter file.  */
          if (local_args_info.replfile_given)
            {
              fprintf (stderr, "%s: `--replfile' (`-r') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->replfile_given && ! override)
            continue;
          local_args_info.replfile_given = 1;
          args_info->replfile_given = 1;
          if (args_info->replfile_arg)
            free (args_info->replfile_arg); /* free previous string */
          args_info->replfile_arg = gengetopt_strdup (optarg);
          break;

        case 'p':	/* sequence prior file (for msa input files).  */
          if (local_args_info.priorfile_given)
            {
              fprintf (stderr, "%s: `--priorfile' (`-p') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->priorfile_given && ! override)
            continue;
          local_args_info.priorfile_given = 1;
          args_info->priorfile_given = 1;
          if (args_info->priorfile_arg)
            free (args_info->priorfile_arg); /* free previous string */
          args_info->priorfile_arg = gengetopt_strdup (optarg);
          break;

        case 'n':	/* null model file.  */
          if (local_args_info.nullfile_given)
            {
              fprintf (stderr, "%s: `--nullfile' (`-n') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->nullfile_given && ! override)
            continue;
          local_args_info.nullfile_given = 1;
          args_info->nullfile_given = 1;
          if (args_info->nullfile_arg)
            free (args_info->nullfile_arg); /* free previous string */
          args_info->nullfile_arg = gengetopt_strdup (optarg);
          break;

        case 'a':	/* hmm=results are hmm-ancored (default), seq=results are sequence anchored.  */
          if (local_args_info.anchor_given)
            {
              fprintf (stderr, "%s: `--anchor' (`-a') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->anchor_given && ! override)
            continue;
          local_args_info.anchor_given = 1;
          args_info->anchor_given = 1;
          if (args_info->anchor_arg)
            free (args_info->anchor_arg); /* free previous string */
          args_info->anchor_arg = gengetopt_strdup (optarg);
          break;

        case 'L':	/* output will print predicted labeling and posterior label probabilities.  */
          if (local_args_info.labeloutput_given)
            {
              fprintf (stderr, "%s: `--labeloutput' (`-L') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->labeloutput_given && ! override)
            continue;
          local_args_info.labeloutput_given = 1;
          args_info->labeloutput_given = 1;
          args_info->labeloutput_flag = !(args_info->labeloutput_flag);
          break;

        case 'A':	/* output will print log likelihood, log odds and reversi scores.  */
          if (local_args_info.alignmentoutput_given)
            {
              fprintf (stderr, "%s: `--alignmentoutput' (`-A') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->alignmentoutput_given && ! override)
            continue;
          local_args_info.alignmentoutput_given = 1;
          args_info->alignmentoutput_given = 1;
          args_info->alignmentoutput_flag = !(args_info->alignmentoutput_flag);
          break;

        case 'M':	/* scoring method for alignment and profile data options = DP/DPPI/GM/GMR/DPPI/PI/PIS default=GM.  */
          if (local_args_info.msascoring_given)
            {
              fprintf (stderr, "%s: `--msascoring' (`-M') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->msascoring_given && ! override)
            continue;
          local_args_info.msascoring_given = 1;
          args_info->msascoring_given = 1;
          if (args_info->msascoring_arg)
            free (args_info->msascoring_arg); /* free previous string */
          args_info->msascoring_arg = gengetopt_strdup (optarg);
          break;

        case 'c':	/* specify which columns to use for alignment input data, options = all/nr, where all means use all columns
        and nr specifies a sequence in the alignment and the columns where this sequence have non-gap symbls are used
        default = all.  */
          if (local_args_info.usecolumns_given)
            {
              fprintf (stderr, "%s: `--usecolumns' (`-c') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->usecolumns_given && ! override)
            continue;
          local_args_info.usecolumns_given = 1;
          args_info->usecolumns_given = 1;
          if (args_info->usecolumns_arg)
            free (args_info->usecolumns_arg); /* free previous string */
          args_info->usecolumns_arg = gengetopt_strdup (optarg);
          break;

        case 'v':	/* print some information about what is going on.  */
          if (local_args_info.verbose_given)
            {
              fprintf (stderr, "%s: `--verbose' (`-v') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->verbose_given && ! override)
            continue;
          local_args_info.verbose_given = 1;
          args_info->verbose_given = 1;
          args_info->verbose_flag = !(args_info->verbose_flag);
          break;


        case 0:	/* Long option with no short option */
          /* do not use labels even though the input sequences are labeled.  */
          if (strcmp (long_options[option_index].name, "nolabels") == 0)
          {
            if (local_args_info.nolabels_given)
              {
                fprintf (stderr, "%s: `--nolabels' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));