text: /*
    File autogenerated by gengetopt version 2.22.5
    generated with the following command:
    gengetopt -i ct2db.ggo --file-name=ct2db_cmdl --unamed-opts --include-getopt --default-optional --func-name=ct2db_cmdline_parser --arg-struct-name=ct2db_args_info
  
    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>
  
  #ifndef FIX_UNUSED
  #define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
  #endif
  
  
  #include "ct2db_cmdl.h"
  
  const char *ct2db_args_info_purpose = "Produce dot bracket notation of an RNA secondary structure from Zuker's .ct \nfile";
  
  const char *ct2db_args_info_usage = "Usage: ct2db [OPTIONS]... [FILES]...";
  
  const char *ct2db_args_info_description = "Convert Zuker's .ct files to dot-bracket string\n";
  
  const char *ct2db_args_info_help[] = {
    "  -h, --help      Print help and exit",
    "  -V, --version   Print version and exit",
    "  -p, --removePK  Remove pseudoknots from structure\n                      (default=off)",
    "  -v, --verbose   Be verbose\n                      (default=off)",
      0
  };
  
  typedef enum {ARG_NO
    , ARG_FLAG
  } ct2db_cmdline_parser_arg_type;
  
  static
  void clear_given (struct ct2db_args_info *args_info);
  static
  void clear_args (struct ct2db_args_info *args_info);
  
  static int
  ct2db_cmdline_parser_internal (int argc, char **argv, struct ct2db_args_info *args_info,
                          struct ct2db_cmdline_parser_params *params, const char *additional_error);
  
  
  static char *
  gengetopt_strdup (const char *s);
  
  static
  void clear_given (struct ct2db_args_info *args_info)
  {
    args_info->help_given = 0 ;
    args_info->version_given = 0 ;
    args_info->removePK_given = 0 ;
    args_info->verbose_given = 0 ;
  }
  
  static
  void clear_args (struct ct2db_args_info *args_info)
  {
    FIX_UNUSED (args_info);
    args_info->removePK_flag = 0;
    args_info->verbose_flag = 0;
    
  }
  
  static
  void init_args_info(struct ct2db_args_info *args_info)
  {
  
  
    args_info->help_help = ct2db_args_info_help[0] ;
    args_info->version_help = ct2db_args_info_help[1] ;
    args_info->removePK_help = ct2db_args_info_help[2] ;
    args_info->verbose_help = ct2db_args_info_help[3] ;
    
  }
  
  void
  ct2db_cmdline_parser_print_version (void)
  {
    printf ("%s %s\n",
       (strlen(CT2DB_CMDLINE_PARSER_PACKAGE_NAME) ? CT2DB_CMDLINE_PARSER_PACKAGE_NAME : CT2DB_CMDLINE_PARSER_PACKAGE),
       CT2DB_CMDLINE_PARSER_VERSION);
  }
  
  static void print_help_common(void) {
    ct2db_cmdline_parser_print_version ();
  
    if (strlen(ct2db_args_info_purpose) > 0)
      printf("\n%s\n", ct2db_args_info_purpose);
  
    if (strlen(ct2db_args_info_usage) > 0)
      printf("\n%s\n", ct2db_args_info_usage);
  
    printf("\n");
  
    if (strlen(ct2db_args_info_description) > 0)
      printf("%s\n\n", ct2db_args_info_description);
  }
  
  void
  ct2db_cmdline_parser_print_help (void)
  {
    int i = 0;
    print_help_common();
    while (ct2db_args_info_help[i])
      printf("%s\n", ct2db_args_info_help[i++]);
  }
  
  void
  ct2db_cmdline_parser_init (struct ct2db_args_info *args_info)
  {
    clear_given (args_info);
    clear_args (args_info);
    init_args_info (args_info);
  
    args_info->inputs = 0;
    args_info->inputs_num = 0;
  }
  
  void
  ct2db_cmdline_parser_params_init(struct ct2db_cmdline_parser_params *params)
  {
    if (params)
      { 
        params->override = 0;
        params->initialize = 1;
        params->check_required = 1;
        params->check_ambiguity = 0;
        params->print_errors = 1;
      }
  }
  
  struct ct2db_cmdline_parser_params *
  ct2db_cmdline_parser_params_create(void)
  {
    struct ct2db_cmdline_parser_params *params = 
      (struct ct2db_cmdline_parser_params *)malloc(sizeof(struct ct2db_cmdline_parser_params));
    ct2db_cmdline_parser_params_init(params);  
    return params;
  }
  
  
  
  static void
  ct2db_cmdline_parser_release (struct ct2db_args_info *args_info)
  {
    unsigned int i;
    
    
    for (i = 0; i < args_info->inputs_num; ++i)
      free (args_info->inputs [i]);
  
    if (args_info->inputs_num)
      free (args_info->inputs);
  
    clear_given (args_info);
  }
  
  
  static void
  write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
  {
    FIX_UNUSED (values);
    if (arg) {
      fprintf(outfile, "%s=\"%s\"\n", opt, arg);
    } else {
      fprintf(outfile, "%s\n", opt);
    }
  }
  
  
  int
  ct2db_cmdline_parser_dump(FILE *outfile, struct ct2db_args_info *args_info)
  {
    int i = 0;
  
    if (!outfile)
      {
        fprintf (stderr, "%s: cannot dump options to stream\n", CT2DB_CMDLINE_PARSER_PACKAGE);
        return EXIT_FAILURE;
      }
  
    if (args_info->help_given)
      write_into_file(outfile, "help", 0, 0 );
    if (args_info->version_given)
      write_into_file(outfile, "version", 0, 0 );
    if (args_info->removePK_given)
      write_into_file(outfile, "removePK", 0, 0 );
    if (args_info->verbose_given)
      write_into_file(outfile, "verbose", 0, 0 );
    
  
    i = EXIT_SUCCESS;
    return i;
  }
  
  int
  ct2db_cmdline_parser_file_save(const char *filename, struct ct2db_args_info *args_info)
  {
    FILE *outfile;
    int i = 0;
  
    outfile = fopen(filename, "w");
  
    if (!outfile)
      {
        fprintf (stderr, "%s: cannot open file for writing: %s\n", CT2DB_CMDLINE_PARSER_PACKAGE, filename);
        return EXIT_FAILURE;
      }
  
    i = ct2db_cmdline_parser_dump(outfile, args_info);
    fclose (outfile);
  
    return i;
  }
  
  void
  ct2db_cmdline_parser_free (struct ct2db_args_info *args_info)
  {
    ct2db_cmdline_parser_release (args_info);
  }
  
  /** @brief replacement of strdup, which is not standard */
  char *
  gengetopt_strdup (const char *s)
  {
    char *result = 0;
    if (!s)
      return result;
  
    result = (char*)malloc(strlen(s) + 1);
    if (result == (char*)0)
      return (char*)0;
    strcpy(result, s);
    return result;
  }
  
  int
  ct2db_cmdline_parser (int argc, char **argv, struct ct2db_args_info *args_info)
  {
    return ct2db_cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
  }
  
  int
  ct2db_cmdline_parser_ext (int argc, char **argv, struct ct2db_args_info *args_info,
                     struct ct2db_cmdline_parser_params *params)
  {
    int result;
    result = ct2db_cmdline_parser_internal (argc, argv, args_info, params, 0);
  
    if (result == EXIT_FAILURE)
      {
        ct2db_cmdline_parser_free (args_info);
        exit (EXIT_FAILURE);
      }
    
    return result;
  }
  
  int
  ct2db_cmdline_parser2 (int argc, char **argv, struct ct2db_args_info *args_info, int override, int initialize, int check_required)
  {
    int result;
    struct ct2db_cmdline_parser_params params;
    
    params.override = override;
    params.initialize = initialize;
    params.check_required = check_required;
    params.check_ambiguity = 0;
    params.print_errors = 1;
  
    result = ct2db_cmdline_parser_internal (argc, argv, args_info, &params, 0);
  
    if (result == EXIT_FAILURE)
      {
        ct2db_cmdline_parser_free (args_info);
        exit (EXIT_FAILURE);
      }
    
    return result;
  }
  
  int
  ct2db_cmdline_parser_required (struct ct2db_args_info *args_info, const char *prog_name)
  {
    FIX_UNUSED (args_info);
    FIX_UNUSED (prog_name);
    return EXIT_SUCCESS;
  }
  
  /*
   * Extracted from the glibc source tree, version 2.3.6
   *
   * Licensed under the GPL as per the whole glibc source tree.
   *
   * This file was modified so that getopt_long can be called
   * many times without risking previous memory to be spoiled.
   *
   * Modified by Andre Noll and Lorenzo Bettini for use in
   * GNU gengetopt generated files.
   *
   */
  
  /* 
   * we must include anything we need since this file is not thought to be
   * inserted in a file already using getopt.h
   *
   * Lorenzo
   */
  
  struct option
  {
    const char *name;
    /* has_arg can't be an enum because some compilers complain about
       type mismatches in all the code that assumes it is an int.  */
    int has_arg;
    int *flag;
    int val;
  };
  
  /* This version of `getopt' appears to the caller like standard Unix `getopt'
     but it behaves differently for the user, since it allows the user
     to intersperse the options with the other arguments.
  
     As `getopt' works, it permutes the elements of ARGV so that,
     when it is done, all the options precede everything else.  Thus
     all application programs are extended to handle flexible argument order.
  */
  /*
     If the field `flag' is not NULL, it points to a variable that is set
     to the value given in the field `val' when the option is found, but
     left unchanged if the option is not found.
  
     To have a long-named option do something other than set an `int' to
     a compiled-in constant, such as set a value from `custom_optarg', set the
     option's `flag' field to zero and its `val' field to a nonzero
     value (the equivalent single-letter option character, if there is
     one).  For long options that have a zero `flag' field, `getopt'
     returns the contents of the `val' field.  */
  
  /* Names for the values of the `has_arg' field of `struct option'.  */
  #ifndef no_argument
  #define no_argument		0
  #endif
  
  #ifndef required_argument
  #define required_argument	1
  #endif
  
  #ifndef optional_argument
  #define optional_argument	2
  #endif
  
  struct custom_getopt_data {
  	/*
  	 * These have exactly the same meaning as the corresponding global variables,
  	 * except that they are used for the reentrant versions of getopt.
  	 */
  	int custom_optind;
  	int custom_opterr;
  	int custom_optopt;
  	char *custom_optarg;
  
  	/* True if the internal members have been initialized.  */
  	int initialized;
  
  	/*
  	 * The next char to be scanned in the option-element in which the last option
  	 * character we returned was found.  This allows us to pick up the scan where
  	 * we left off.  If this is zero, or a null string, it means resume the scan by
  	 * advancing to the next ARGV-element.
  	 */
  	char *nextchar;
  
  	/*
  	 * Describe the part of ARGV that contains non-options that have been skipped.
  	 * `first_nonopt' is the index in ARGV of the first of them; `last_nonopt' is
  	 * the index after the last of them.
  	 */
  	int first_nonopt;
  	int last_nonopt;
  };
  
  /*
   * the variables optarg, optind, opterr and optopt are renamed with
   * the custom_ prefix so that they don't interfere with getopt ones.
   *
   * Moreover they're static so they are visible only from within the
   * file where this very file will be included.
   */
  
  /*
   * For communication from `custom_getopt' to the caller.  When `custom_getopt' finds an
   * option that takes an argument, the argument value is returned here.
   */
  static char *custom_optarg;
  
  /*
   * Index in ARGV of the next element to be scanned.  This is used for
   * communication to and from the caller and for communication between
   * successive calls to `custom_getopt'.
   *
   * On entry to `custom_getopt', 1 means this is the first call; initialize.
   *
   * When `custom_getopt' returns -1, this is the index of the first of the non-option
   * elements that the caller should itself scan.
   *
   * Otherwise, `custom_optind' communicates from one call to the next how much of ARGV
   * has been scanned so far.
   *
   * 1003.2 says this must be 1 before any call.
   */
  static int custom_optind = 1;
  
  /*
   * Callers store zero here to inhibit the error message for unrecognized
   * options.
   */
  static int custom_opterr = 1;
  
  /*
   * Set to an option character which was unrecognized.  This must be initialized
   * on some systems to avoid linking in the system's own getopt implementation.
   */
  static int custom_optopt = '?';
  
  /*
   * Exchange two adjacent subsequences of ARGV.  One subsequence is elements
   * [first_nonopt,last_nonopt) which contains all the non-options that have been
   * skipped so far.  The other is elements [last_nonopt,custom_optind), which contains
   * all the options processed since those non-options were skipped.
   * `first_nonopt' and `last_nonopt' are relocated so that they describe the new
   * indices of the non-options in ARGV after they are moved.
   */
  static void exchange(char **argv, struct custom_getopt_data *d)
  {
  	int bottom = d->first_nonopt;
  	int middle = d->last_nonopt;
  	int top = d->custom_optind;
  	char *tem;
  
  	/*
  	 * Exchange the shorter segment with the far end of the longer segment.
  	 * That puts the shorter segment into the right place.  It leaves the
  	 * longer segment in the right place overall, but it consists of two
  	 * parts that need to be swapped next.
  	 */
  	while (top > middle && middle > bottom) {
  		if (top - middle > middle - bottom) {
  			/* Bottom segment is the short one.  */
  			int len = middle - bottom;
  			int i;
  
  			/* Swap it with the top part of the top segment.  */
  			for (i = 0; i < len; i++) {
  				tem = argv[bottom + i];
  				argv[bottom + i] =
  					argv[top - (middle - bottom) + i];
  				argv[top - (middle - bottom) + i] = tem;
  			}
  			/* Exclude the moved bottom segment from further swapping.  */
  			top -= len;
  		} else {
  			/* Top segment is the short one.  */
  			int len = top - middle;
  			int i;
  
  			/* Swap it with the bottom part of the bottom segment.  */
  			for (i = 0; i < len; i++) {
  				tem = argv[bottom + i];
  				argv[bottom + i] = argv[middle + i];
  				argv[middle + i] = tem;
  			}
  			/* Exclude the moved top segment from further swapping.  */
  			bottom += len;
  		}
  	}
  	/* Update records for the slots the non-options now occupy.  */
  	d->first_nonopt += (d->custom_optind - d->last_nonopt);
  	d->last_nonopt = d->custom_optind;
  }
  
  /* Initialize the internal data when the first call is made.  */
  static void custom_getopt_initialize(struct custom_getopt_data *d)
  {
  	/*
  	 * Start processing options with ARGV-element 1 (since ARGV-element 0
  	 * is the program name); the sequence of previously skipped non-option
  	 * ARGV-elements is empty.
  	 */
  	d->first_nonopt = d->last_nonopt = d->custom_optind;
  	d->nextchar = NULL;
  	d->initialized = 1;
  }
  
  #define NONOPTION_P (argv[d->custom_optind][0] != '-' || argv[d->custom_optind][1] == '\0')
  
  /* return: zero: continue, nonzero: return given value to user */
  static int shuffle_argv(int argc, char *const *argv,const struct option *longopts,
  	struct custom_getopt_data *d)
  {
  	/*
  	 * Give FIRST_NONOPT & LAST_NONOPT rational values if CUSTOM_OPTIND has been
  	 * moved back by the user (who may also have changed the arguments).
  	 */
  	if (d->last_nonopt > d->custom_optind)
  		d->last_nonopt = d->custom_optind;
  	if (d->first_nonopt > d->custom_optind)
  		d->first_nonopt = d->custom_optind;
  	/*
  	 * If we have just processed some options following some
  	 * non-options, exchange them so that the options come first.
  	 */
  	if (d->first_nonopt != d->last_nonopt &&
  			d->last_nonopt != d->custom_optind)
  		exchange((char **) argv, d);
  	else if (d->last_nonopt != d->custom_optind)
  		d->first_nonopt = d->custom_optind;
  	/*
  	 * Skip any additional non-options and extend the range of
  	 * non-options previously skipped.
  	 */
  	while (d->custom_optind < argc && NONOPTION_P)
  		d->custom_optind++;
  	d->last_nonopt = d->custom_optind;
  	/*
  	 * The special ARGV-element `--' means premature end of options.  Skip
  	 * it like a null option, then exchange with previous non-options as if
  	 * it were an option, then skip everything else like a non-option.
  	 */
  	if (d->custom_optind != argc && !strcmp(argv[d->custom_optind], "--")) {
  		d->custom_optind++;
  		if (d->first_nonopt != d->last_nonopt
  				&& d->last_nonopt != d->custom_optind)
  			exchange((char **) argv, d);
  		else if (d->first_nonopt == d->last_nonopt)
  			d->first_nonopt = d->custom_optind;
  		d->last_nonopt = argc;
  		d->custom_optind = argc;
  	}
  	/*
  	 * If we have done all the ARGV-elements, stop the scan and back over
  	 * any non-options that we skipped and permuted.
  	 */
  	if (d->custom_optind == argc) {
  		/*
  		 * Set the next-arg-index to point at the non-options that we
  		 * previously skipped, so the caller will digest them.
  		 */
  		if (d->first_nonopt != d->last_nonopt)
  			d->custom_optind = d->first_nonopt;
  		return -1;
  	}
  	/*
  	 * If we have come to a non-option and did not permute it, either stop
  	 * the scan or describe it to the caller and pass it by.
  	 */
  	if (NONOPTION_P) {
  		d->custom_optarg = argv[d->custom_optind++];
  		return 1;
  	}
  	/*
  	 * We have found another option-ARGV-element. Skip the initial
  	 * punctuation.
  	 */
  	d->nextchar = (argv[d->custom_optind] + 1 + (longopts != NULL && argv[d->custom_optind][1] == '-'));
  	return 0;
  }
  
  /*
   * Check whether the ARGV-element is a long option.
   *
   * If there's a long option "fubar" and the ARGV-element is "-fu", consider
   * that an abbreviation of the long option, just like "--fu", and not "-f" with
   * arg "u".
   *
   * This distinction seems to be the most useful approach.
   *
   */
  static int check_long_opt(int argc, char *const *argv, const char *optstring,
  		const struct option *longopts, int *longind,
  		int print_errors, struct custom_getopt_data *d)
  {
  	char *nameend;
  	const struct option *p;
  	const struct option *pfound = NULL;
  	int exact = 0;
  	int ambig = 0;
  	int indfound = -1;
  	int option_index;
  
  	for (nameend = d->nextchar; *nameend && *nameend != '='; nameend++)
  		/* Do nothing.  */ ;
  
  	/* Test all long options for either exact match or abbreviated matches */
  	for (p = longopts, option_index = 0; p->name; p++, option_index++)
  		if (!strncmp(p->name, d->nextchar, nameend - d->nextchar)) {
  			if ((unsigned int) (nameend - d->nextchar)
  					== (unsigned int) strlen(p->name)) {
  				/* Exact match found.  */
  				pfound = p;
  				indfound = option_index;
  				exact = 1;
  				break;
  			} else if (pfound == NULL) {
  				/* First nonexact match found.  */
  				pfound = p;
  				indfound = option_index;
  			} else if (pfound->has_arg != p->has_arg
  					|| pfound->flag != p->flag
  					|| pfound->val != p->val)
  				/* Second or later nonexact match found.  */
  				ambig = 1;
  		}
  	if (ambig && !exact) {
  		if (print_errors) {
  			fprintf(stderr,
  				"%s: option `%s' is ambiguous\n",
  				argv[0], argv[d->custom_optind]);
  		}
  		d->nextchar += strlen(d->nextchar);
  		d->custom_optind++;
  		d->custom_optopt = 0;
  		return '?';
  	}
  	if (pfound) {
  		option_index = indfound;
  		d->custom_optind++;
  		if (*nameend) {
  			if (pfound->has_arg != no_argument)
  				d->custom_optarg = nameend + 1;
  			else {
  				if (print_errors) {
  					if (argv[d->custom_optind - 1][1] == '-') {
  						/* --option */
  						fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n",
  							argv[0], pfound->name);
  					} else {
  						/* +option or -option */
  						fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n",
  							argv[0], argv[d->custom_optind - 1][0], pfound->name);
  					}
  
  				}
  				d->nextchar += strlen(d->nextchar);
  				d->custom_optopt = pfound->val;
  				return '?';
  			}
  		} else if (pfound->has_arg == required_argument) {
  			if (d->custom_optind < argc)
  				d->custom_optarg = argv[d->custom_optind++];
  			else {
  				if (print_errors) {
  					fprintf(stderr,
  						"%s: option `%s' requires an argument\n",
  						argv[0],
  						argv[d->custom_optind - 1]);
  				}
  				d->nextchar += strlen(d->nextchar);
  				d->custom_optopt = pfound->val;
  				return optstring[0] == ':' ? ':' : '?';
  			}
  		}
  		d->nextchar += strlen(d->nextchar);
  		if (longind != NULL)
  			*longind = option_index;
  		if (pfound->flag) {
  			*(pfound->flag) = pfound->val;
  			return 0;
  		}
  		return pfound->val;
  	}
  	/*
  	 * Can't find it as a long option.  If this is not getopt_long_only, or
  	 * the option starts with '--' or is not a valid short option, then
  	 * it's an error.  Otherwise interpret it as a short option.
  	 */
  	if (print_errors) {
  		if (argv[d->custom_optind][1] == '-') {
  			/* --option */
  			fprintf(stderr,
  				"%s: unrecognized option `--%s'\n",
  				argv[0], d->nextchar);
  		} else {
  			/* +option or -option */
  			fprintf(stderr,
  				"%s: unrecognized option `%c%s'\n",
  				argv[0], argv[d->custom_optind][0],
  				d->nextchar);
  		}
  	}
  	d->nextchar = (char *) "";
  	d->custom_optind++;
  	d->custom_optopt = 0;
  	return '?';
  }
  
  static int check_short_opt(int argc, char *const *argv, const char *optstring,
  		int print_errors, struct custom_getopt_data *d)
  {
  	char c = *d->nextchar++;
  	const char *temp = strchr(optstring, c);
  
  	/* Increment `custom_optind' when we start to process its last character.  */
  	if (*d->nextchar == '\0')
  		++d->custom_optind;
  	if (!temp || c == ':') {
  		if (print_errors)
  			fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c);
  
  		d->custom_optopt = c;
  		return '?';
  	}
  	if (temp[1] == ':') {
  		if (temp[2] == ':') {
  			/* This is an option that accepts an argument optionally.  */
  			if (*d->nextchar != '\0') {
  				d->custom_optarg = d->nextchar;
  				d->custom_optind++;
  			} else
  				d->custom_optarg = NULL;
  			d->nextchar = NULL;
  		} else {
  			/* This is an option that requires an argument.  */
  			if (*d->nextchar != '\0') {
  				d->custom_optarg = d->nextchar;
  				/*
  				 * If we end this ARGV-element by taking the
  				 * rest as an arg, we must advance to the next
  				 * element now.
  				 */
  				d->custom_optind++;
  			} else if (d->custom_optind == argc) {
  				if (print_errors) {
  					fprintf(stderr,
  						"%s: option requires an argument -- %c\n",
  						argv[0], c);
  				}
  				d->custom_optopt = c;
  				if (optstring[0] == ':')
  					c = ':';
  				else
  					c = '?';
  			} else
  				/*
  				 * We already incremented `custom_optind' once;
  				 * increment it again when taking next ARGV-elt
  				 * as argument.
  				 */
  				d->custom_optarg = argv[d->custom_optind++];
  			d->nextchar = NULL;
  		}
  	}
  	return c;
  }
  
  /*
   * Scan elements of ARGV for option characters given in OPTSTRING.
   *
   * If an element of ARGV starts with '-', and is not exactly "-" or "--",
   * then it is an option element.  The characters of this element
   * (aside from the initial '-') are option characters.  If `getopt'
   * is called repeatedly, it returns successively each of the option characters
   * from each of the option elements.
   *
   * If `getopt' finds another option character, it returns that character,
   * updating `custom_optind' and `nextchar' so that the next call to `getopt' can
   * resume the scan with the following option character or ARGV-element.
   *
   * If there are no more option characters, `getopt' returns -1.
   * Then `custom_optind' is the index in ARGV of the first ARGV-element
   * that is not an option.  (The ARGV-elements have been permuted
   * so that those that are not options now come last.)
   *
   * OPTSTRING is a string containing the legitimate option characters.
   * If an option character is seen that is not listed in OPTSTRING,
   * return '?' after printing an error message.  If you set `custom_opterr' to
   * zero, the error message is suppressed but we still return '?'.
   *
   * If a char in OPTSTRING is followed by a colon, that means it wants an arg,
   * so the following text in the same ARGV-element, or the text of the following
   * ARGV-element, is returned in `custom_optarg'.  Two colons mean an option that
   * wants an optional arg; if there is text in the current ARGV-element,
   * it is returned in `custom_optarg', otherwise `custom_optarg' is set to zero.
   *
   * If OPTSTRING starts with `-' or `+', it requests different methods of
   * handling the non-option ARGV-elements.
   * See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above.
   *
   * Long-named options begin with `--' instead of `-'.
   * Their names may be abbreviated as long as the abbreviation is unique
   * or is an exact match for some defined option.  If they have an
   * argument, it follows the option name in the same ARGV-element, separated
   * from the option name by a `=', or else the in next ARGV-element.
   * When `getopt' finds a long-named option, it returns 0 if that option's
   * `flag' field is nonzero, the value of the option's `val' field
   * if the `flag' field is zero.
   *
   * The elements of ARGV aren't really const, because we permute them.
   * But we pretend they're const in the prototype to be compatible
   * with other systems.
   *
   * LONGOPTS is a vector of `struct option' terminated by an
   * element containing a name which is zero.
   *
   * LONGIND returns the index in LONGOPT of the long-named option found.
   * It is only valid when a long-named option has been found by the most
   * recent call.
   *
   * Return the option character from OPTS just read.  Return -1 when there are
   * no more options.  For unrecognized options, or options missing arguments,
   * `custom_optopt' is set to the option letter, and '?' is returned.
   *
   * The OPTS string is a list of characters which are recognized option letters,
   * optionally followed by colons, specifying that that letter takes an
   * argument, to be placed in `custom_optarg'.
   *
   * If a letter in OPTS is followed by two colons, its argument is optional.
   * This behavior is specific to the GNU `getopt'.
   *
   * The argument `--' causes premature termination of argument scanning,
   * explicitly telling `getopt' that there are no more options.  If OPTS begins
   * with `--', then non-option arguments are treated as arguments to the option
   * '\0'.  This behavior is specific to the GNU `getopt'.
   */
  
  static int getopt_internal_r(int argc, char *const *argv, const char *optstring,
  		const struct option *longopts, int *longind,
  		struct custom_getopt_data *d)
  {
  	int ret, print_errors = d->custom_opterr;
  
  	if (optstring[0] == ':')
  		print_errors = 0;
  	if (argc < 1)
  		return -1;
  	d->custom_optarg = NULL;
  
  	/* 
  	 * This is a big difference with GNU getopt, since optind == 0
  	 * means initialization while here 1 means first call.
  	 */
  	if (d->custom_optind == 0 || !d->initialized) {
  		if (d->custom_optind == 0)
  			d->custom_optind = 1;	/* Don't scan ARGV[0], the program name.  */
  		custom_getopt_initialize(d);
  	}
  	if (d->nextchar == NULL || *d->nextchar == '\0') {
  		ret = shuffle_argv(argc, argv, longopts, d);
  		if (ret)
  			return ret;
  	}
  	if (longopts && (argv[d->custom_optind][1] == '-' ))
  		return check_long_opt(argc, argv, optstring, longopts,
  			longind, print_errors, d);
  	return check_short_opt(argc, argv, optstring, print_errors, d);
  }
  
  static int custom_getopt_internal(int argc, char *const *argv, const char *optstring,
  	const struct option *longopts, int *longind)
  {
  	int result;
  	/* Keep a global copy of all internal members of d */
  	static struct custom_getopt_data d;
  
  	d.custom_optind = custom_optind;
  	d.custom_opterr = custom_opterr;
  	result = getopt_internal_r(argc, argv, optstring, longopts,
  		longind, &d);
  	custom_optind = d.custom_optind;
  	custom_optarg = d.custom_optarg;
  	custom_optopt = d.custom_optopt;
  	return result;
  }
  
  static int custom_getopt_long (int argc, char *const *argv, const char *options,
  	const struct option *long_options, int *opt_index)
  {
  	return custom_getopt_internal(argc, argv, options, long_options,
  		opt_index);
  }
  
  
  static char *package_name = 0;
  
  /**
   * @brief updates an option
   * @param field the generic pointer to the field to update
   * @param orig_field the pointer to the orig field
   * @param field_given the pointer to the number of occurrence of this option
   * @param prev_given the pointer to the number of occurrence already seen
   * @param value the argument for this option (if null no arg was specified)
   * @param possible_values the possible values for this option (if specified)
   * @param default_value the default value (in case the option only accepts fixed values)
   * @param arg_type the type of this option
   * @param check_ambiguity @see ct2db_cmdline_parser_params.check_ambiguity
   * @param override @see ct2db_cmdline_parser_params.override
   * @param no_free whether to free a possible previous value
   * @param multiple_option whether this is a multiple option
   * @param long_opt the corresponding long option
   * @param short_opt the corresponding short option (or '-' if none)
   * @param additional_error possible further error specification
   */
  static
  int update_arg(void *field, char **orig_field,
                 unsigned int *field_given, unsigned int *prev_given, 
                 char *value, const char *possible_values[],
                 const char *default_value,
                 ct2db_cmdline_parser_arg_type arg_type,
                 int check_ambiguity, int override,
                 int no_free, int multiple_option,
                 const char *long_opt, char short_opt,
                 const char *additional_error)
  {
    char *stop_char = 0;
    const char *val = value;
    int found;
    FIX_UNUSED (field);
  
    stop_char = 0;
    found = 0;
  
    if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
      {
        if (short_opt != '-')
          fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n", 
                 package_name, long_opt, short_opt,
                 (additional_error ? additional_error : ""));
        else
          fprintf (stderr, "%s: `--%s' option given more than once%s\n", 
                 package_name, long_opt,
                 (additional_error ? additional_error : ""));
        return 1; /* failure */
      }
  
    FIX_UNUSED (default_value);
      
    if (field_given && *field_given && ! override)
      return 0;
    if (prev_given)
      (*prev_given)++;
    if (field_given)
      (*field_given)++;
    if (possible_values)
      val = possible_values[found];
  
    switch(arg_type) {
    case ARG_FLAG:
      *((int *)field) = !*((int *)field);
      break;
    default:
      break;
    };
  
  
    /* store the original value */
    switch(arg_type) {
    case ARG_NO:
    case ARG_FLAG:
      break;
    default:
      if (value && orig_field) {
        if (no_free) {
          *orig_field = value;
        } else {
          if (*orig_field)
            free (*orig_field); /* free previous string */
          *orig_field = gengetopt_strdup (value);
        }
      }
    };
  
    return 0; /* OK */
  }
  
  
  int
  ct2db_cmdline_parser_internal (
    int argc, char **argv, struct ct2db_args_info *args_info,
                          struct ct2db_cmdline_parser_params *params, const char *additional_error)
  {
    int c;	/* Character of the parsed option.  */
  
    int error = 0;
    struct ct2db_args_info local_args_info;
    
    int override;
    int initialize;
    int check_required;
    int check_ambiguity;
  
    char *optarg;
    int optind;
    int opterr;
    int optopt;
    
    package_name = argv[0];
    
    override = params->override;
    initialize = params->initialize;
    check_required = params->check_required;
    check_ambiguity = params->check_ambiguity;
  
    if (initialize)
      ct2db_cmdline_parser_init (args_info);
  
    ct2db_cmdline_parser_init (&local_args_info);
  
    optarg = 0;
    optind = 0;
    opterr = params->print_errors;
    optopt = '?';
  
    while (1)
      {
        int option_index = 0;
  
        static struct option long_options[] = {
          { "help",	0, NULL, 'h' },
          { "version",	0, NULL, 'V' },
          { "removePK",	0, NULL, 'p' },
          { "verbose",	0, NULL, 'v' },
          { 0,  0, 0, 0 }
        };
  
        custom_optarg = optarg;
        custom_optind = optind;
        custom_opterr = opterr;
        custom_optopt = optopt;
  
        c = custom_getopt_long (argc, argv, "hVpv", long_options, &option_index);
  
        optarg = custom_optarg;
        optind = custom_optind;
        opterr = custom_opterr;
        optopt = custom_optopt;
  
        if (c == -1) break;	/* Exit from `while (1)' loop.  */
  
        switch (c)
          {
          case 'h':	/* Print help and exit.  */
            ct2db_cmdline_parser_print_help ();
            ct2db_cmdline_parser_free (&local_args_info);
            exit (EXIT_SUCCESS);
  
          case 'V':	/* Print version and exit.  */
            ct2db_cmdline_parser_print_version ();
            ct2db_cmdline_parser_free (&local_args_info);
            exit (EXIT_SUCCESS);
  
          case 'p':	/* Remove pseudoknots from structure
  .  */
          
          
            if (update_arg((void *)&(args_info->removePK_flag), 0, &(args_info->removePK_given),
                &(local_args_info.removePK_given), optarg, 0, 0, ARG_FLAG,
                check_ambiguity, override, 1, 0, "removePK", 'p',
                additional_error))
              goto failure;
          
            break;
          case 'v':	/* Be verbose
  .  */
          
          
            if (update_arg((void *)&(args_info->verbose_flag), 0, &(args_info->verbose_given),
                &(local_args_info.verbose_given), optarg, 0, 0, ARG_FLAG,
                check_ambiguity, override, 1, 0, "verbose", 'v',
                additional_error))
              goto failure;
          
            break;
  
          case 0:	/* Long option with no short option */
          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", CT2DB_CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
            abort ();
          } /* switch */
      } /* while */
  
  
  
  
    ct2db_cmdline_parser_release (&local_args_info);
  
    if ( error )
      return (EXIT_FAILURE);
  
    if (optind < argc)
      {
        int i = 0 ;
        int found_prog_name = 0;
        /* whether program name, i.e., argv[0], is in the remaining args
           (this may happen with some implementations of getopt,
            but surely not with the one included by gengetopt) */
  
  
        args_info->inputs_num = argc - optind - found_prog_name;
        args_info->inputs =
          (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
        while (optind < argc)
          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
      }
  
    return 0;
  
  failure:
    
    ct2db_cmdline_parser_release (&local_args_info);
    return (EXIT_FAILURE);
  }
  