cmdline_hmmsearch.c

马尔科夫模型的java版本实现

/*
  File autogenerated by gengetopt version 2.12.2
  generated with the following command:
  /home/ae/hakanv/gengetopt/bin/gengetopt --file-name=cmdline_hmmsearch 

  The developers of gengetopt consider the fixed text that goes in all
  gengetopt output files to be in the public domain:
  we make no copyright claims on it.
*/

/* If we use autoconf.  */
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include "getopt.h"

#include "cmdline_hmmsearch.h"

static
void clear_given (struct gengetopt_args_info *args_info);
static
void clear_args (struct gengetopt_args_info *args_info);

static int
cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error);

static char *
gengetopt_strdup (const char *s);

static
void clear_given (struct gengetopt_args_info *args_info)
{
  args_info->help_given = 0 ;
  args_info->version_given = 0 ;
  args_info->hmmnamefile_given = 0 ;
  args_info->seqnamefile_given = 0 ;
  args_info->seqformat_given = 0 ;
  args_info->outpath_given = 0 ;
  args_info->freqfile_given = 0 ;
  args_info->smxfile_given = 0 ;
  args_info->replfile_given = 0 ;
  args_info->priorfile_given = 0 ;
  args_info->nullfile_given = 0 ;
  args_info->anchor_given = 0 ;
  args_info->labeloutput_given = 0 ;
  args_info->alignmentoutput_given = 0 ;
  args_info->msascoring_given = 0 ;
  args_info->usecolumns_given = 0 ;
  args_info->nolabels_given = 0 ;
  args_info->verbose_given = 0 ;
  args_info->viterbi_given = 0 ;
  args_info->nbest_given = 0 ;
  args_info->forward_given = 0 ;
  args_info->max_d_given = 0 ;
  args_info->path_given = 0 ;
  args_info->nopostout_given = 0 ;
  args_info->nolabelout_given = 0 ;
  args_info->nollout_given = 0 ;
  args_info->nooddsout_given = 0 ;
  args_info->norevout_given = 0 ;
  args_info->alignpostout_given = 0 ;
  args_info->alignlabelout_given = 0 ;
  args_info->labelllout_given = 0 ;
  args_info->labeloddsout_given = 0 ;
  args_info->labelrevout_given = 0 ;
  args_info->score_algs_group_counter = 0 ;
}

static
void clear_args (struct gengetopt_args_info *args_info)
{
  args_info->hmmnamefile_arg = NULL;
  args_info->seqnamefile_arg = NULL;
  args_info->seqformat_arg = NULL;
  args_info->outpath_arg = NULL;
  args_info->freqfile_arg = NULL;
  args_info->smxfile_arg = NULL;
  args_info->replfile_arg = NULL;
  args_info->priorfile_arg = NULL;
  args_info->nullfile_arg = NULL;
  args_info->anchor_arg = NULL;
  args_info->labeloutput_flag = 0;
  args_info->alignmentoutput_flag = 0;
  args_info->msascoring_arg = NULL;
  args_info->usecolumns_arg = NULL;
  args_info->nolabels_flag = 0;
  args_info->verbose_flag = 0;
  args_info->max_d_flag = 0;
  args_info->path_flag = 0;
  args_info->nopostout_flag = 0;
  args_info->nolabelout_flag = 0;
  args_info->nollout_flag = 0;
  args_info->nooddsout_flag = 0;
  args_info->norevout_flag = 0;
  args_info->alignpostout_flag = 0;
  args_info->alignlabelout_flag = 0;
  args_info->labelllout_flag = 0;
  args_info->labeloddsout_flag = 0;
  args_info->labelrevout_flag = 0;
}

void
cmdline_parser_print_version (void)
{
  printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
}

void
cmdline_parser_print_help (void)
{
  cmdline_parser_print_version ();
  printf("\n"
  "Purpose:\n"
"  score sequences on hidden markov models\n"
  "\n"
  "Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
  printf("\n");
  printf("%s\n","  -h, --help                  Print help and exit");
  printf("%s\n","  -V, --version               Print version and exit");
  printf("%s\n","  -m, --hmmnamefile=filename  model namefile for models in hmg format");
  printf("%s\n","  -s, --seqnamefile=filename  sequence namefile (for seuences in fasta, smod, \n                                msamod or prfmod format)");
  printf("%s\n","  -f, --seqformat=STRING      format of input sequences (fa=fasta, s=smod, \n                                msa=msamod, prf=prfmod)");
  printf("%s\n","  -o, --outpath=dir           output directory");
  printf("%s\n","  -q, --freqfile=filename     background frequency file");
  printf("%s\n","  -x, --smxfile=filename      substitution matrix file");
  printf("%s\n","  -r, --replfile=filename     replacement letter file");
  printf("%s\n","  -p, --priorfile=filename    sequence prior file (for msa input files)");
  printf("%s\n","  -n, --nullfile=filename     null model file");
  printf("%s\n","  -a, --anchor=STRING         hmm=results are hmm-ancored (default), \n                                seq=results are sequence anchored");
  printf("%s\n","  -L, --labeloutput           output will print predicted labeling and \n                                posterior label probabilities  (default=off)");
  printf("%s\n","  -A, --alignmentoutput       output will print log likelihood, log odds and \n                                reversi scores  (default=off)");
  printf("%s\n","  -M, --msascoring=STRING     scoring method for alignment and profile data \n                                options = DP/DPPI/GM/GMR/DPPI/PI/PIS default=GM");
  printf("%s\n","  -c, --usecolumns=STRING     specify which columns to use for alignment input \n                                data, options = all/nr, where all means use all \n                                columns\n                                and nr specifies a sequence in the alignment \n                                and the columns where this sequence have \n                                non-gap symbls are used\n                                default = all");
  printf("%s\n","      --nolabels              do not use labels even though the input sequences \n                                are labeled  (default=off)");
  printf("%s\n","  -v, --verbose               print some information about what is going on  \n                                (default=off)");
  printf("%s\n","\n Group: score_algs");
  printf("%s\n","      --viterbi               Use viterbi algorithm for alignment and/or label \n                                scoring (default no)");
  printf("%s\n","      --nbest                 Use n-best (=1-best) algorithm for label scoring \n                                (default yes)");
  printf("%s\n","      --forward               Use forward algorithm for alignment scoring \n                                (default yes)");
  printf("%s\n","      --max_d                 Retrain model on each sequence using Baum-Welch \n                                before scoring  (default=off)");
  printf("%s\n","\noptions for specific output control:");
  printf("%s\n","      --path                  Print most likely statepath  (default=off)");
  printf("%s\n","      --nopostout             no posterior probability information for label \n                                scoring  (default=off)");
  printf("%s\n","      --nolabelout            no predicted labeling for label scoring  \n                                (default=off)");
  printf("%s\n","      --nollout               no log likelihood score for alignment scoring  \n                                (default=off)");
  printf("%s\n","      --nooddsout             no log odds score for alignment scoring  \n                                (default=off)");
  printf("%s\n","      --norevout              no reversi score for alignment scoring  \n                                (default=off)");
  printf("%s\n","      --alignpostout          print posterior probability information for \n                                alignment scoring  (default=off)");
  printf("%s\n","      --alignlabelout         print predicted labeling for alignment scoring  \n                                (default=off)");
  printf("%s\n","      --labelllout            print log likelihood score for label scoring  \n                                (default=off)");
  printf("%s\n","      --labeloddsout          print log odds score for label scoring  \n                                (default=off)");
  printf("%s\n","      --labelrevout           print reversi score for label scoring  \n                                (default=off)");
}

void
cmdline_parser_init (struct gengetopt_args_info *args_info)
{
  clear_given (args_info);
  clear_args (args_info);
}

void
cmdline_parser_free (struct gengetopt_args_info *args_info)
{
  
  if (args_info->hmmnamefile_arg)
    {
      free (args_info->hmmnamefile_arg); /* free previous argument */
      args_info->hmmnamefile_arg = 0;
    }
  if (args_info->seqnamefile_arg)
    {
      free (args_info->seqnamefile_arg); /* free previous argument */
      args_info->seqnamefile_arg = 0;
    }
  if (args_info->seqformat_arg)
    {
      free (args_info->seqformat_arg); /* free previous argument */
      args_info->seqformat_arg = 0;
    }
  if (args_info->outpath_arg)
    {
      free (args_info->outpath_arg); /* free previous argument */
      args_info->outpath_arg = 0;
    }
  if (args_info->freqfile_arg)
    {
      free (args_info->freqfile_arg); /* free previous argument */
      args_info->freqfile_arg = 0;
    }
  if (args_info->smxfile_arg)
    {
      free (args_info->smxfile_arg); /* free previous argument */
      args_info->smxfile_arg = 0;
    }
  if (args_info->replfile_arg)
    {
      free (args_info->replfile_arg); /* free previous argument */
      args_info->replfile_arg = 0;
    }
  if (args_info->priorfile_arg)
    {
      free (args_info->priorfile_arg); /* free previous argument */
      args_info->priorfile_arg = 0;
    }
  if (args_info->nullfile_arg)
    {
      free (args_info->nullfile_arg); /* free previous argument */
      args_info->nullfile_arg = 0;
    }
  if (args_info->anchor_arg)
    {
      free (args_info->anchor_arg); /* free previous argument */
      args_info->anchor_arg = 0;
    }
  if (args_info->msascoring_arg)
    {
      free (args_info->msascoring_arg); /* free previous argument */
      args_info->msascoring_arg = 0;
    }
  if (args_info->usecolumns_arg)
    {
      free (args_info->usecolumns_arg); /* free previous argument */
      args_info->usecolumns_arg = 0;
    }
  
  clear_given (args_info);
}

/* gengetopt_strdup() */
/* strdup.c replacement of strdup, which is not standard */
char *
gengetopt_strdup (const char *s)
{
  char *result = NULL;
  if (!s)
    return result;

  result = (char*)malloc(strlen(s) + 1);
  if (result == (char*)0)
    return (char*)0;
  strcpy(result, s);
  return result;
}

static void
reset_group_score_algs(struct gengetopt_args_info *args_info);

static void
reset_group_score_algs(struct gengetopt_args_info *args_info)
{
  if (! args_info->score_algs_group_counter)
    return;
  
  args_info->viterbi_given = 0 ;
  args_info->nbest_given = 0 ;
  args_info->forward_given = 0 ;

  args_info->score_algs_group_counter = 0;
}

int
cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
{
  return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
}

int
cmdline_parser2 (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
{
  int result;

  result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);

  if (result == EXIT_FAILURE)
    {
      cmdline_parser_free (args_info);
      exit (EXIT_FAILURE);
    }
  
  return result;
}

int
cmdline_parser_internal (int argc, char * const *argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required, const char *additional_error)
{
  int c;	/* Character of the parsed option.  */

  int error = 0;
  struct gengetopt_args_info local_args_info;