cmdline_hmmsearch.c

马尔科夫模型的java版本实现

                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);
          }
          
          /* Use viterbi algorithm for alignment and/or label scoring (default no).  */
          else if (strcmp (long_options[option_index].name, "viterbi") == 0)
          {
            if (local_args_info.viterbi_given)
              {
                fprintf (stderr, "%s: `--viterbi' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->viterbi_given && ! override)
              continue;
            local_args_info.viterbi_given = 1;
            args_info->viterbi_given = 1;
            if (args_info->score_algs_group_counter && override)
              reset_group_score_algs (args_info);
            args_info->score_algs_group_counter += 1;
            
            break;
          }
          
          /* Use n-best (=1-best) algorithm for label scoring (default yes).  */
          else if (strcmp (long_options[option_index].name, "nbest") == 0)
          {
            if (local_args_info.nbest_given)
              {
                fprintf (stderr, "%s: `--nbest' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->nbest_given && ! override)
              continue;
            local_args_info.nbest_given = 1;
            args_info->nbest_given = 1;
            if (args_info->score_algs_group_counter && override)
              reset_group_score_algs (args_info);
            args_info->score_algs_group_counter += 1;
            
            break;
          }
          
          /* Use forward algorithm for alignment scoring (default yes).  */
          else if (strcmp (long_options[option_index].name, "forward") == 0)
          {
            if (local_args_info.forward_given)
              {
                fprintf (stderr, "%s: `--forward' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->forward_given && ! override)
              continue;
            local_args_info.forward_given = 1;
            args_info->forward_given = 1;
            if (args_info->score_algs_group_counter && override)
              reset_group_score_algs (args_info);
            args_info->score_algs_group_counter += 1;
            
            break;
          }
          
          /* Retrain model on each sequence using Baum-Welch before scoring.  */
          else if (strcmp (long_options[option_index].name, "max_d") == 0)
          {
            if (local_args_info.max_d_given)
              {
                fprintf (stderr, "%s: `--max_d' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->max_d_given && ! override)
              continue;
            local_args_info.max_d_given = 1;
            args_info->max_d_given = 1;
            args_info->max_d_flag = !(args_info->max_d_flag);
          }
          
          /* Print most likely statepath.  */
          else if (strcmp (long_options[option_index].name, "path") == 0)
          {
            if (local_args_info.path_given)
              {
                fprintf (stderr, "%s: `--path' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->path_given && ! override)
              continue;
            local_args_info.path_given = 1;
            args_info->path_given = 1;
            args_info->path_flag = !(args_info->path_flag);
          }
          
          /* no posterior probability information for label scoring.  */
          else if (strcmp (long_options[option_index].name, "nopostout") == 0)
          {
            if (local_args_info.nopostout_given)
              {
                fprintf (stderr, "%s: `--nopostout' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->nopostout_given && ! override)
              continue;
            local_args_info.nopostout_given = 1;
            args_info->nopostout_given = 1;
            args_info->nopostout_flag = !(args_info->nopostout_flag);
          }
          
          /* no predicted labeling for label scoring.  */
          else if (strcmp (long_options[option_index].name, "nolabelout") == 0)
          {
            if (local_args_info.nolabelout_given)
              {
                fprintf (stderr, "%s: `--nolabelout' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->nolabelout_given && ! override)
              continue;
            local_args_info.nolabelout_given = 1;
            args_info->nolabelout_given = 1;
            args_info->nolabelout_flag = !(args_info->nolabelout_flag);
          }
          
          /* no log likelihood score for alignment scoring.  */
          else if (strcmp (long_options[option_index].name, "nollout") == 0)
          {
            if (local_args_info.nollout_given)
              {
                fprintf (stderr, "%s: `--nollout' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->nollout_given && ! override)
              continue;
            local_args_info.nollout_given = 1;
            args_info->nollout_given = 1;
            args_info->nollout_flag = !(args_info->nollout_flag);
          }
          
          /* no log odds score for alignment scoring.  */
          else if (strcmp (long_options[option_index].name, "nooddsout") == 0)
          {
            if (local_args_info.nooddsout_given)
              {
                fprintf (stderr, "%s: `--nooddsout' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->nooddsout_given && ! override)
              continue;
            local_args_info.nooddsout_given = 1;
            args_info->nooddsout_given = 1;
            args_info->nooddsout_flag = !(args_info->nooddsout_flag);
          }
          
          /* no reversi score for alignment scoring.  */
          else if (strcmp (long_options[option_index].name, "norevout") == 0)
          {
            if (local_args_info.norevout_given)
              {
                fprintf (stderr, "%s: `--norevout' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->norevout_given && ! override)
              continue;
            local_args_info.norevout_given = 1;
            args_info->norevout_given = 1;
            args_info->norevout_flag = !(args_info->norevout_flag);
          }
          
          /* print posterior probability information for alignment scoring.  */
          else if (strcmp (long_options[option_index].name, "alignpostout") == 0)
          {
            if (local_args_info.alignpostout_given)
              {
                fprintf (stderr, "%s: `--alignpostout' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->alignpostout_given && ! override)
              continue;
            local_args_info.alignpostout_given = 1;
            args_info->alignpostout_given = 1;
            args_info->alignpostout_flag = !(args_info->alignpostout_flag);
          }
          
          /* print predicted labeling for alignment scoring.  */
          else if (strcmp (long_options[option_index].name, "alignlabelout") == 0)
          {
            if (local_args_info.alignlabelout_given)
              {
                fprintf (stderr, "%s: `--alignlabelout' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->alignlabelout_given && ! override)
              continue;
            local_args_info.alignlabelout_given = 1;
            args_info->alignlabelout_given = 1;
            args_info->alignlabelout_flag = !(args_info->alignlabelout_flag);
          }
          
          /* print log likelihood score for label scoring.  */
          else if (strcmp (long_options[option_index].name, "labelllout") == 0)
          {
            if (local_args_info.labelllout_given)
              {
                fprintf (stderr, "%s: `--labelllout' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->labelllout_given && ! override)
              continue;
            local_args_info.labelllout_given = 1;
            args_info->labelllout_given = 1;
            args_info->labelllout_flag = !(args_info->labelllout_flag);
          }
          
          /* print log odds score for label scoring.  */
          else if (strcmp (long_options[option_index].name, "labeloddsout") == 0)
          {
            if (local_args_info.labeloddsout_given)
              {
                fprintf (stderr, "%s: `--labeloddsout' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->labeloddsout_given && ! override)
              continue;
            local_args_info.labeloddsout_given = 1;
            args_info->labeloddsout_given = 1;
            args_info->labeloddsout_flag = !(args_info->labeloddsout_flag);
          }
          
          /* print reversi score for label scoring.  */
          else if (strcmp (long_options[option_index].name, "labelrevout") == 0)
          {
            if (local_args_info.labelrevout_given)
              {
                fprintf (stderr, "%s: `--labelrevout' option given more than once%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->labelrevout_given && ! override)
              continue;
            local_args_info.labelrevout_given = 1;
            args_info->labelrevout_given = 1;
            args_info->labelrevout_flag = !(args_info->labelrevout_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 ( args_info->score_algs_group_counter > 1)
    {
      fprintf (stderr, "%s: %d options of group score_algs were given. At most one is required.%s\n", CMDLINE_PARSER_PACKAGE, args_info->score_algs_group_counter, (additional_error ? additional_error : ""));
      error = 1;
    }
  


  if (check_required)
    {
      if (! args_info->hmmnamefile_given)
        {
          fprintf (stderr, "%s: '--hmmnamefile' ('-m') option required%s\n", CMDLINE_PARSER_PACKAGE, (additional_error ? additional_error : ""));
          error = 1;
        }
      if (! args_info->seqnamefile_given)
        {
          fprintf (stderr, "%s: '--seqnamefile' ('-s') 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 ( error )
    return (EXIT_FAILURE);

  return 0;

failure:
  return (EXIT_FAILURE);
}