cmdline_modseqalign.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_modseqalign 

  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_modseqalign.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->hmmfile_given = 0 ;
  args_info->target_given = 0 ;
  args_info->template_given = 0 ;
  args_info->seqformat_given = 0 ;
  args_info->outfile_given = 0 ;
  args_info->freqfile_given = 0 ;
  args_info->smxfile_given = 0 ;
  args_info->replfile_given = 0 ;
  args_info->priorfile_given = 0 ;
  args_info->msascoring_given = 0 ;
  args_info->usecolumns_given = 0 ;
  args_info->nolabels_given = 0 ;
  args_info->verbose_given = 0 ;
}

static
void clear_args (struct gengetopt_args_info *args_info)
{
  args_info->hmmfile_arg = NULL;
  args_info->target_arg = NULL;
  args_info->template_arg = NULL;
  args_info->seqformat_arg = NULL;
  args_info->outfile_arg = NULL;
  args_info->freqfile_arg = NULL;
  args_info->smxfile_arg = NULL;
  args_info->replfile_arg = NULL;
  args_info->priorfile_arg = NULL;
  args_info->msascoring_arg = NULL;
  args_info->usecolumns_arg = NULL;
  args_info->nolabels_flag = 0;
  args_info->verbose_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"
"  align 2 sequences to each other using their most likely state path through a \n  given HMM\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, --hmmfile=filename    model namefile for models in hmg format");
  printf("%s\n","  -s, --target=filename     sequence namefile (for seuences in fasta, smod, \n                              msamod or prfmod format)");
  printf("%s\n","  -t, --template=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, --outfile=filename    model outfile");
  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","  -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 and \n                              the columns where this sequence have non-gap \n                              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)");
}

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->hmmfile_arg)
    {
      free (args_info->hmmfile_arg); /* free previous argument */
      args_info->hmmfile_arg = 0;
    }
  if (args_info->target_arg)
    {
      free (args_info->target_arg); /* free previous argument */
      args_info->target_arg = 0;
    }
  if (args_info->template_arg)
    {
      free (args_info->template_arg); /* free previous argument */
      args_info->template_arg = 0;
    }
  if (args_info->seqformat_arg)
    {
      free (args_info->seqformat_arg); /* free previous argument */
      args_info->seqformat_arg = 0;
    }
  if (args_info->outfile_arg)
    {
      free (args_info->outfile_arg); /* free previous argument */
      args_info->outfile_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->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;
}

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;

  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' },
        { "hmmfile",	1, NULL, 'm' },
        { "target",	1, NULL, 's' },
        { "template",	1, NULL, 't' },
        { "seqformat",	1, NULL, 'f' },
        { "outfile",	1, NULL, 'o' },
        { "freqfile",	1, NULL, 'q' },
        { "smxfile",	1, NULL, 'x' },
        { "replfile",	1, NULL, 'r' },
        { "priorfile",	1, NULL, 'p' },
        { "msascoring",	1, NULL, 'M' },
        { "usecolumns",	1, NULL, 'c' },
        { "nolabels",	0, NULL, 0 },
        { "verbose",	0, NULL, 'v' },
        { NULL,	0, NULL, 0 }
      };

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

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