cmdline_modseqalign.c

马尔科夫模型的java版本实现

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

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

        case 't':	/* sequence namefile (for seuences in fasta, smod, msamod or prfmod format).  */
          if (local_args_info.template_given)
            {
              fprintf (stderr, "%s: `--template' (`-t') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->template_given && ! override)
            continue;
          local_args_info.template_given = 1;
          args_info->template_given = 1;
          if (args_info->template_arg)
            free (args_info->template_arg); /* free previous string */
          args_info->template_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':	/* model outfile.  */
          if (local_args_info.outfile_given)
            {
              fprintf (stderr, "%s: `--outfile' (`-o') option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->outfile_given && ! override)
            continue;
          local_args_info.outfile_given = 1;
          args_info->outfile_given = 1;
          if (args_info->outfile_arg)
            free (args_info->outfile_arg); /* free previous string */
          args_info->outfile_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 '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 : ""));
                goto failure;
              }
            if (args_info->nolabels_given && ! override)
              continue;
            local_args_info.nolabels_given = 1;
            args_info->nolabels_given = 1;
            args_info->nolabels_flag = !(args_info->nolabels_flag);
          }
          

          break;
        case '?':	/* Invalid option.  */
          /* `getopt_long' already printed an error message.  */
          goto failure;

        default:	/* bug: option not considered.  */
          fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
          abort ();
        } /* switch */
    } /* while */



  if (check_required)
    {
      if (! args_info->hmmfile_given)
        {
          fprintf (stderr, "%s: '--hmmfile' ('-m') option required%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
          error = 1;
        }
      if (! args_info->target_given)
        {
          fprintf (stderr, "%s: '--target' ('-s') option required%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
          error = 1;
        }
      if (! args_info->template_given)
        {
          fprintf (stderr, "%s: '--template' ('-t') option required%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
          error = 1;
        }
      if (! args_info->seqformat_given)
        {
          fprintf (stderr, "%s: '--seqformat' ('-f') option required%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
          error = 1;
        }
      if (! args_info->outfile_given)
        {
          fprintf (stderr, "%s: '--outfile' ('-o') option required%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
          error = 1;
        }
    }

  if ( error )
    return (EXIT_FAILURE);

  return 0;

failure:
  return (EXIT_FAILURE);
}