Add missing binaty and statis library

[jabaws.git] / binaries / src / ViennaRNA / Progs / RNApdist_cmdl.c

/*
  File autogenerated by gengetopt version 2.22.5
  generated with the following command:
  gengetopt -i RNApdist.ggo --file-name=RNApdist_cmdl --include-getopt --default-optional --func-name=RNApdist_cmdline_parser --arg-struct-name=RNApdist_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 "RNApdist_cmdl.h"

const char *RNApdist_args_info_purpose = "Calculate distances between thermodynamic RNA secondary structures ensembles";

const char *RNApdist_args_info_usage = "Usage: RNApdist [OPTIONS]...";

const char *RNApdist_args_info_description = "This program reads RNA sequences from stdin and calculates structure distances \nbetween the thermodynamic ensembles of their secondary structures.\n";

const char *RNApdist_args_info_detailed_help[] = {
  "  -h, --help                    Print help and exit",
  "      --detailed-help           Print help, including all details and hidden \n                                  options, and exit",
  "      --full-help               Print help, including hidden options, and exit",
  "  -V, --version                 Print version and exit",
  "\nGeneral Options:",
  "      --noconv                  Do not automatically substitude nucleotide \n                                  \"T\" with \"U\"\n\n                                    (default=off)",
  "\nAlgorithms:",
  "  -X, --compare=p|m|f|c         Specify the comparison directive.\n                                    (default=`p')",
  "  Possible arguments for this option are: -Xp compare the structures pairwise \n  (p), i.e. first with 2nd, third with 4th etc.\n  -Xm calculate the distance matrix between all structures. The output is \n  formatted as a lower triangle matrix.\n  -Xf compare each structure to the first one.\n  -Xc compare continuously, that is i-th with (i+1)th structure.\n\n",
  "  -B, --backtrack[=<filename>]  Print an \"alignment\" with gaps of the \n                                  profiles. The aligned structures are written \n                                  to <filename>, if specified.\n                                    (default=`none')",
  "  Within the profile output, the following symbols will be used:\n\n   ()  essentially upstream (downstream) paired bases\n\n   {}  weakly upstream (downstream) paired bases\n\n   |    strongly paired bases without preference\n\n   ,    weakly paired bases without preference\n\n   .    essentially unpaired bases.\n\n   If <filename> is not specified, the output is written to stdout, unless the \n  \"-Xm\" option is set in which case \"backtrack.file\" is used.\n\n",
  "\nModel Details:",
  "  -T, --temp=DOUBLE             Rescale energy parameters to a temperature of \n                                  temp C. Default is 37C.\n\n",
  "  -4, --noTetra                 Do not include special tabulated stabilizing \n                                  energies for tri-, tetra- and hexaloop \n                                  hairpins. Mostly for testing.\n\n                                    (default=off)",
  "  -d, --dangles=INT             set energy model for treatment of dangling \n                                  bases\n\n                                    (possible values=\"0\", \"2\" default=`2')",
  "      --noLP                    Produce structures without lonely pairs \n                                  (helices of length 1).\n                                    (default=off)",
  "  For partition function folding this only disallows pairs that can only occur \n  isolated. Other pairs may still occasionally occur as helices of length 1.\n\n",
  "      --noGU                    Do not allow GU pairs\n\n                                    (default=off)",
  "      --noClosingGU             Do not allow GU pairs at the end of helices\n\n                                    (default=off)",
  "  -P, --paramFile=paramfile     Read energy parameters from paramfile, instead \n                                  of using the default parameter set.\n",
  "  A sample parameter file should accompany your distribution.\n  See the RNAlib documentation for details on the file format.\n\n",
  "      --nsp=STRING              Allow other pairs in addition to the usual \n                                  AU,GC,and GU pairs.\n",
  "  Its argument is a comma separated list of additionally allowed pairs. If the \n  first character is a \"-\" then AB will imply that AB and BA are allowed \n  pairs.\n  e.g. RNAfold -nsp -GA  will allow GA and AG pairs. Nonstandard pairs are \n  given 0 stacking energy.\n\n",
  "  -e, --energyModel=INT         Rarely used option to fold sequences from the \n                                  artificial ABCD... alphabet, where A pairs B, \n                                  C-D etc.  Use the energy parameters for GC \n                                  (-e 1) or AU (-e 2) pairs.\n\n",
  "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to rna@tbi.univie.ac.at.\n",
    0
};
static void
init_full_help_array(void)
{
  RNApdist_args_info_full_help[0] = RNApdist_args_info_detailed_help[0];
  RNApdist_args_info_full_help[1] = RNApdist_args_info_detailed_help[1];
  RNApdist_args_info_full_help[2] = RNApdist_args_info_detailed_help[2];
  RNApdist_args_info_full_help[3] = RNApdist_args_info_detailed_help[3];
  RNApdist_args_info_full_help[4] = RNApdist_args_info_detailed_help[4];
  RNApdist_args_info_full_help[5] = RNApdist_args_info_detailed_help[5];
  RNApdist_args_info_full_help[6] = RNApdist_args_info_detailed_help[6];
  RNApdist_args_info_full_help[7] = RNApdist_args_info_detailed_help[7];
  RNApdist_args_info_full_help[8] = RNApdist_args_info_detailed_help[9];
  RNApdist_args_info_full_help[9] = RNApdist_args_info_detailed_help[11];
  RNApdist_args_info_full_help[10] = RNApdist_args_info_detailed_help[12];
  RNApdist_args_info_full_help[11] = RNApdist_args_info_detailed_help[13];
  RNApdist_args_info_full_help[12] = RNApdist_args_info_detailed_help[14];
  RNApdist_args_info_full_help[13] = RNApdist_args_info_detailed_help[15];
  RNApdist_args_info_full_help[14] = RNApdist_args_info_detailed_help[17];
  RNApdist_args_info_full_help[15] = RNApdist_args_info_detailed_help[18];
  RNApdist_args_info_full_help[16] = RNApdist_args_info_detailed_help[19];
  RNApdist_args_info_full_help[17] = RNApdist_args_info_detailed_help[21];
  RNApdist_args_info_full_help[18] = RNApdist_args_info_detailed_help[23];
  RNApdist_args_info_full_help[19] = RNApdist_args_info_detailed_help[24];
  RNApdist_args_info_full_help[20] = 0; 
  
}

const char *RNApdist_args_info_full_help[21];

static void
init_help_array(void)
{
  RNApdist_args_info_help[0] = RNApdist_args_info_detailed_help[0];
  RNApdist_args_info_help[1] = RNApdist_args_info_detailed_help[1];
  RNApdist_args_info_help[2] = RNApdist_args_info_detailed_help[2];
  RNApdist_args_info_help[3] = RNApdist_args_info_detailed_help[3];
  RNApdist_args_info_help[4] = RNApdist_args_info_detailed_help[4];
  RNApdist_args_info_help[5] = RNApdist_args_info_detailed_help[5];
  RNApdist_args_info_help[6] = RNApdist_args_info_detailed_help[6];
  RNApdist_args_info_help[7] = RNApdist_args_info_detailed_help[7];
  RNApdist_args_info_help[8] = RNApdist_args_info_detailed_help[9];
  RNApdist_args_info_help[9] = RNApdist_args_info_detailed_help[11];
  RNApdist_args_info_help[10] = RNApdist_args_info_detailed_help[12];
  RNApdist_args_info_help[11] = RNApdist_args_info_detailed_help[13];
  RNApdist_args_info_help[12] = RNApdist_args_info_detailed_help[14];
  RNApdist_args_info_help[13] = RNApdist_args_info_detailed_help[15];
  RNApdist_args_info_help[14] = RNApdist_args_info_detailed_help[17];
  RNApdist_args_info_help[15] = RNApdist_args_info_detailed_help[18];
  RNApdist_args_info_help[16] = RNApdist_args_info_detailed_help[19];
  RNApdist_args_info_help[17] = RNApdist_args_info_detailed_help[24];
  RNApdist_args_info_help[18] = 0; 
  
}

const char *RNApdist_args_info_help[19];

typedef enum {ARG_NO
  , ARG_FLAG
  , ARG_STRING
  , ARG_INT
  , ARG_DOUBLE
} RNApdist_cmdline_parser_arg_type;

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

static int
RNApdist_cmdline_parser_internal (int argc, char **argv, struct RNApdist_args_info *args_info,
                        struct RNApdist_cmdline_parser_params *params, const char *additional_error);


const char *RNApdist_cmdline_parser_dangles_values[] = {"0", "2", 0}; /*< Possible values for dangles. */

static char *
gengetopt_strdup (const char *s);

static
void clear_given (struct RNApdist_args_info *args_info)
{
  args_info->help_given = 0 ;
  args_info->detailed_help_given = 0 ;
  args_info->full_help_given = 0 ;
  args_info->version_given = 0 ;
  args_info->noconv_given = 0 ;
  args_info->compare_given = 0 ;
  args_info->backtrack_given = 0 ;
  args_info->temp_given = 0 ;
  args_info->noTetra_given = 0 ;
  args_info->dangles_given = 0 ;
  args_info->noLP_given = 0 ;
  args_info->noGU_given = 0 ;
  args_info->noClosingGU_given = 0 ;
  args_info->paramFile_given = 0 ;
  args_info->nsp_given = 0 ;
  args_info->energyModel_given = 0 ;
}

static
void clear_args (struct RNApdist_args_info *args_info)
{
  FIX_UNUSED (args_info);
  args_info->noconv_flag = 0;
  args_info->compare_arg = gengetopt_strdup ("p");
  args_info->compare_orig = NULL;
  args_info->backtrack_arg = gengetopt_strdup ("none");
  args_info->backtrack_orig = NULL;
  args_info->temp_orig = NULL;
  args_info->noTetra_flag = 0;
  args_info->dangles_arg = 2;
  args_info->dangles_orig = NULL;
  args_info->noLP_flag = 0;
  args_info->noGU_flag = 0;
  args_info->noClosingGU_flag = 0;
  args_info->paramFile_arg = NULL;
  args_info->paramFile_orig = NULL;
  args_info->nsp_arg = NULL;
  args_info->nsp_orig = NULL;
  args_info->energyModel_orig = NULL;
  
}

static
void init_args_info(struct RNApdist_args_info *args_info)
{
  init_full_help_array(); 
  init_help_array(); 
  args_info->help_help = RNApdist_args_info_detailed_help[0] ;
  args_info->detailed_help_help = RNApdist_args_info_detailed_help[1] ;
  args_info->full_help_help = RNApdist_args_info_detailed_help[2] ;
  args_info->version_help = RNApdist_args_info_detailed_help[3] ;
  args_info->noconv_help = RNApdist_args_info_detailed_help[5] ;
  args_info->compare_help = RNApdist_args_info_detailed_help[7] ;
  args_info->backtrack_help = RNApdist_args_info_detailed_help[9] ;
  args_info->temp_help = RNApdist_args_info_detailed_help[12] ;
  args_info->noTetra_help = RNApdist_args_info_detailed_help[13] ;
  args_info->dangles_help = RNApdist_args_info_detailed_help[14] ;
  args_info->noLP_help = RNApdist_args_info_detailed_help[15] ;
  args_info->noGU_help = RNApdist_args_info_detailed_help[17] ;
  args_info->noClosingGU_help = RNApdist_args_info_detailed_help[18] ;
  args_info->paramFile_help = RNApdist_args_info_detailed_help[19] ;
  args_info->nsp_help = RNApdist_args_info_detailed_help[21] ;
  args_info->energyModel_help = RNApdist_args_info_detailed_help[23] ;
  
}

void
RNApdist_cmdline_parser_print_version (void)
{
  printf ("%s %s\n",
     (strlen(RNAPDIST_CMDLINE_PARSER_PACKAGE_NAME) ? RNAPDIST_CMDLINE_PARSER_PACKAGE_NAME : RNAPDIST_CMDLINE_PARSER_PACKAGE),
     RNAPDIST_CMDLINE_PARSER_VERSION);
}

static void print_help_common(void) {
  RNApdist_cmdline_parser_print_version ();

  if (strlen(RNApdist_args_info_purpose) > 0)
    printf("\n%s\n", RNApdist_args_info_purpose);

  if (strlen(RNApdist_args_info_usage) > 0)
    printf("\n%s\n", RNApdist_args_info_usage);

  printf("\n");

  if (strlen(RNApdist_args_info_description) > 0)
    printf("%s\n\n", RNApdist_args_info_description);
}

void
RNApdist_cmdline_parser_print_help (void)
{
  int i = 0;
  print_help_common();
  while (RNApdist_args_info_help[i])
    printf("%s\n", RNApdist_args_info_help[i++]);
}

void
RNApdist_cmdline_parser_print_full_help (void)
{
  int i = 0;
  print_help_common();
  while (RNApdist_args_info_full_help[i])
    printf("%s\n", RNApdist_args_info_full_help[i++]);
}

void
RNApdist_cmdline_parser_print_detailed_help (void)
{
  int i = 0;
  print_help_common();
  while (RNApdist_args_info_detailed_help[i])
    printf("%s\n", RNApdist_args_info_detailed_help[i++]);
}

void
RNApdist_cmdline_parser_init (struct RNApdist_args_info *args_info)
{
  clear_given (args_info);
  clear_args (args_info);
  init_args_info (args_info);
}

void
RNApdist_cmdline_parser_params_init(struct RNApdist_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 RNApdist_cmdline_parser_params *
RNApdist_cmdline_parser_params_create(void)
{
  struct RNApdist_cmdline_parser_params *params = 
    (struct RNApdist_cmdline_parser_params *)malloc(sizeof(struct RNApdist_cmdline_parser_params));
  RNApdist_cmdline_parser_params_init(params);  
  return params;
}

static void
free_string_field (char **s)
{
  if (*s)
    {
      free (*s);
      *s = 0;
    }
}


static void
RNApdist_cmdline_parser_release (struct RNApdist_args_info *args_info)
{

  free_string_field (&(args_info->compare_arg));
  free_string_field (&(args_info->compare_orig));
  free_string_field (&(args_info->backtrack_arg));
  free_string_field (&(args_info->backtrack_orig));
  free_string_field (&(args_info->temp_orig));
  free_string_field (&(args_info->dangles_orig));
  free_string_field (&(args_info->paramFile_arg));
  free_string_field (&(args_info->paramFile_orig));
  free_string_field (&(args_info->nsp_arg));
  free_string_field (&(args_info->nsp_orig));
  free_string_field (&(args_info->energyModel_orig));
  
  

  clear_given (args_info);
}

/**
 * @param val the value to check
 * @param values the possible values
 * @return the index of the matched value:
 * -1 if no value matched,
 * -2 if more than one value has matched
 */
static int
check_possible_values(const char *val, const char *values[])
{
  int i, found, last;
  size_t len;

  if (!val)   /* otherwise strlen() crashes below */
    return -1; /* -1 means no argument for the option */

  found = last = 0;

  for (i = 0, len = strlen(val); values[i]; ++i)
    {
      if (strncmp(val, values[i], len) == 0)
        {
          ++found;
          last = i;
          if (strlen(values[i]) == len)
            return i; /* exact macth no need to check more */
        }
    }

  if (found == 1) /* one match: OK */
    return last;

  return (found ? -2 : -1); /* return many values or none matched */
}


static void
write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
{
  int found = -1;
  if (arg) {
    if (values) {
      found = check_possible_values(arg, values);      
    }
    if (found >= 0)
      fprintf(outfile, "%s=\"%s\" # %s\n", opt, arg, values[found]);
    else
      fprintf(outfile, "%s=\"%s\"\n", opt, arg);
  } else {
    fprintf(outfile, "%s\n", opt);
  }
}


int
RNApdist_cmdline_parser_dump(FILE *outfile, struct RNApdist_args_info *args_info)
{
  int i = 0;

  if (!outfile)
    {
      fprintf (stderr, "%s: cannot dump options to stream\n", RNAPDIST_CMDLINE_PARSER_PACKAGE);
      return EXIT_FAILURE;
    }

  if (args_info->help_given)
    write_into_file(outfile, "help", 0, 0 );
  if (args_info->detailed_help_given)
    write_into_file(outfile, "detailed-help", 0, 0 );
  if (args_info->full_help_given)
    write_into_file(outfile, "full-help", 0, 0 );
  if (args_info->version_given)
    write_into_file(outfile, "version", 0, 0 );
  if (args_info->noconv_given)
    write_into_file(outfile, "noconv", 0, 0 );
  if (args_info->compare_given)
    write_into_file(outfile, "compare", args_info->compare_orig, 0);
  if (args_info->backtrack_given)
    write_into_file(outfile, "backtrack", args_info->backtrack_orig, 0);
  if (args_info->temp_given)
    write_into_file(outfile, "temp", args_info->temp_orig, 0);
  if (args_info->noTetra_given)
    write_into_file(outfile, "noTetra", 0, 0 );
  if (args_info->dangles_given)
    write_into_file(outfile, "dangles", args_info->dangles_orig, RNApdist_cmdline_parser_dangles_values);
  if (args_info->noLP_given)
    write_into_file(outfile, "noLP", 0, 0 );
  if (args_info->noGU_given)
    write_into_file(outfile, "noGU", 0, 0 );
  if (args_info->noClosingGU_given)
    write_into_file(outfile, "noClosingGU", 0, 0 );
  if (args_info->paramFile_given)
    write_into_file(outfile, "paramFile", args_info->paramFile_orig, 0);
  if (args_info->nsp_given)
    write_into_file(outfile, "nsp", args_info->nsp_orig, 0);
  if (args_info->energyModel_given)
    write_into_file(outfile, "energyModel", args_info->energyModel_orig, 0);
  

  i = EXIT_SUCCESS;
  return i;
}

int
RNApdist_cmdline_parser_file_save(const char *filename, struct RNApdist_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", RNAPDIST_CMDLINE_PARSER_PACKAGE, filename);
      return EXIT_FAILURE;
    }

  i = RNApdist_cmdline_parser_dump(outfile, args_info);
  fclose (outfile);

  return i;
}

void
RNApdist_cmdline_parser_free (struct RNApdist_args_info *args_info)
{
  RNApdist_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
RNApdist_cmdline_parser (int argc, char **argv, struct RNApdist_args_info *args_info)
{
  return RNApdist_cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
}

int
RNApdist_cmdline_parser_ext (int argc, char **argv, struct RNApdist_args_info *args_info,
                   struct RNApdist_cmdline_parser_params *params)
{
  int result;
  result = RNApdist_cmdline_parser_internal (argc, argv, args_info, params, 0);

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

int
RNApdist_cmdline_parser2 (int argc, char **argv, struct RNApdist_args_info *args_info, int override, int initialize, int check_required)
{
  int result;
  struct RNApdist_cmdline_parser_params params;
  
  params.override = override;
  params.initialize = initialize;
  params.check_required = check_required;
  params.check_ambiguity = 0;
  params.print_errors = 1;

  result = RNApdist_cmdline_parser_internal (argc, argv, args_info, &params, 0);

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

int
RNApdist_cmdline_parser_required (struct RNApdist_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 RNApdist_cmdline_parser_params.check_ambiguity
 * @param override @see RNApdist_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,
               RNApdist_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;
  char **string_field;
  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 */
    }

  if (possible_values && (found = check_possible_values((value ? value : default_value), possible_values)) < 0)
    {
      if (short_opt != '-')
        fprintf (stderr, "%s: %s argument, \"%s\", for option `--%s' (`-%c')%s\n", 
          package_name, (found == -2) ? "ambiguous" : "invalid", value, long_opt, short_opt,
          (additional_error ? additional_error : ""));
      else
        fprintf (stderr, "%s: %s argument, \"%s\", for option `--%s'%s\n", 
          package_name, (found == -2) ? "ambiguous" : "invalid", value, long_opt,
          (additional_error ? additional_error : ""));
      return 1; /* failure */
    }
    
  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;
  case ARG_INT:
    if (val) *((int *)field) = strtol (val, &stop_char, 0);
    break;
  case ARG_DOUBLE:
    if (val) *((double *)field) = strtod (val, &stop_char);
    break;
  case ARG_STRING:
    if (val) {
      string_field = (char **)field;
      if (!no_free && *string_field)
        free (*string_field); /* free previous string */
      *string_field = gengetopt_strdup (val);
    }
    break;
  default:
    break;
  };

  /* check numeric conversion */
  switch(arg_type) {
  case ARG_INT:
  case ARG_DOUBLE:
    if (val && !(stop_char && *stop_char == '\0')) {
      fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
      return 1; /* failure */
    }
    break;
  default:
    ;
  };

  /* 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
RNApdist_cmdline_parser_internal (
  int argc, char **argv, struct RNApdist_args_info *args_info,
                        struct RNApdist_cmdline_parser_params *params, const char *additional_error)
{
  int c;        /* Character of the parsed option.  */

  int error = 0;
  struct RNApdist_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)
    RNApdist_cmdline_parser_init (args_info);

  RNApdist_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' },
        { "detailed-help",      0, NULL, 0 },
        { "full-help",  0, NULL, 0 },
        { "version",    0, NULL, 'V' },
        { "noconv",     0, NULL, 0 },
        { "compare",    1, NULL, 'X' },
        { "backtrack",  2, NULL, 'B' },
        { "temp",       1, NULL, 'T' },
        { "noTetra",    0, NULL, '4' },
        { "dangles",    1, NULL, 'd' },
        { "noLP",       0, NULL, 0 },
        { "noGU",       0, NULL, 0 },
        { "noClosingGU",        0, NULL, 0 },
        { "paramFile",  1, NULL, 'P' },
        { "nsp",        1, NULL, 0 },
        { "energyModel",        1, NULL, 'e' },
        { 0,  0, 0, 0 }
      };

      custom_optarg = optarg;
      custom_optind = optind;
      custom_opterr = opterr;
      custom_optopt = optopt;

      c = custom_getopt_long (argc, argv, "hVX:B::T:4d:P:e:", 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.  */
          RNApdist_cmdline_parser_print_help ();
          RNApdist_cmdline_parser_free (&local_args_info);
          exit (EXIT_SUCCESS);

        case 'V':       /* Print version and exit.  */
          RNApdist_cmdline_parser_print_version ();
          RNApdist_cmdline_parser_free (&local_args_info);
          exit (EXIT_SUCCESS);

        case 'X':       /* Specify the comparison directive.
.  */
        
        
          if (update_arg( (void *)&(args_info->compare_arg), 
               &(args_info->compare_orig), &(args_info->compare_given),
              &(local_args_info.compare_given), optarg, 0, "p", ARG_STRING,
              check_ambiguity, override, 0, 0,
              "compare", 'X',
              additional_error))
            goto failure;
        
          break;
        case 'B':       /* Print an \"alignment\" with gaps of the profiles. The aligned structures are written to <filename>, if specified.
.  */
        
        
          if (update_arg( (void *)&(args_info->backtrack_arg), 
               &(args_info->backtrack_orig), &(args_info->backtrack_given),
              &(local_args_info.backtrack_given), optarg, 0, "none", ARG_STRING,
              check_ambiguity, override, 0, 0,
              "backtrack", 'B',
              additional_error))
            goto failure;
        
          break;
        case 'T':       /* Rescale energy parameters to a temperature of temp C. Default is 37C.
        
.  */
        
        
          if (update_arg( (void *)&(args_info->temp_arg), 
               &(args_info->temp_orig), &(args_info->temp_given),
              &(local_args_info.temp_given), optarg, 0, 0, ARG_DOUBLE,
              check_ambiguity, override, 0, 0,
              "temp", 'T',
              additional_error))
            goto failure;
        
          break;
        case '4':       /* Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.
        
.  */
        
        
          if (update_arg((void *)&(args_info->noTetra_flag), 0, &(args_info->noTetra_given),
              &(local_args_info.noTetra_given), optarg, 0, 0, ARG_FLAG,
              check_ambiguity, override, 1, 0, "noTetra", '4',
              additional_error))
            goto failure;
        
          break;
        case 'd':       /* set energy model for treatment of dangling bases
        
.  */
        
        
          if (update_arg( (void *)&(args_info->dangles_arg), 
               &(args_info->dangles_orig), &(args_info->dangles_given),
              &(local_args_info.dangles_given), optarg, RNApdist_cmdline_parser_dangles_values, "2", ARG_INT,
              check_ambiguity, override, 0, 0,
              "dangles", 'd',
              additional_error))
            goto failure;
        
          break;
        case 'P':       /* Read energy parameters from paramfile, instead of using the default parameter set.
.  */
        
        
          if (update_arg( (void *)&(args_info->paramFile_arg), 
               &(args_info->paramFile_orig), &(args_info->paramFile_given),
              &(local_args_info.paramFile_given), optarg, 0, 0, ARG_STRING,
              check_ambiguity, override, 0, 0,
              "paramFile", 'P',
              additional_error))
            goto failure;
        
          break;
        case 'e':       /* Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc.  Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.
        
.  */
        
        
          if (update_arg( (void *)&(args_info->energyModel_arg), 
               &(args_info->energyModel_orig), &(args_info->energyModel_given),
              &(local_args_info.energyModel_given), optarg, 0, 0, ARG_INT,
              check_ambiguity, override, 0, 0,
              "energyModel", 'e',
              additional_error))
            goto failure;
        
          break;

        case 0: /* Long option with no short option */
          if (strcmp (long_options[option_index].name, "detailed-help") == 0) {
            RNApdist_cmdline_parser_print_detailed_help ();
            RNApdist_cmdline_parser_free (&local_args_info);
            exit (EXIT_SUCCESS);
          }

          if (strcmp (long_options[option_index].name, "full-help") == 0) {
            RNApdist_cmdline_parser_print_full_help ();
            RNApdist_cmdline_parser_free (&local_args_info);
            exit (EXIT_SUCCESS);
          }

          /* Do not automatically substitude nucleotide \"T\" with \"U\"
          
.  */
          if (strcmp (long_options[option_index].name, "noconv") == 0)
          {
          
          
            if (update_arg((void *)&(args_info->noconv_flag), 0, &(args_info->noconv_given),
                &(local_args_info.noconv_given), optarg, 0, 0, ARG_FLAG,
                check_ambiguity, override, 1, 0, "noconv", '-',
                additional_error))
              goto failure;
          
          }
          /* Produce structures without lonely pairs (helices of length 1).
.  */
          else if (strcmp (long_options[option_index].name, "noLP") == 0)
          {
          
          
            if (update_arg((void *)&(args_info->noLP_flag), 0, &(args_info->noLP_given),
                &(local_args_info.noLP_given), optarg, 0, 0, ARG_FLAG,
                check_ambiguity, override, 1, 0, "noLP", '-',
                additional_error))
              goto failure;
          
          }
          /* Do not allow GU pairs
          
.  */
          else if (strcmp (long_options[option_index].name, "noGU") == 0)
          {
          
          
            if (update_arg((void *)&(args_info->noGU_flag), 0, &(args_info->noGU_given),
                &(local_args_info.noGU_given), optarg, 0, 0, ARG_FLAG,
                check_ambiguity, override, 1, 0, "noGU", '-',
                additional_error))
              goto failure;
          
          }
          /* Do not allow GU pairs at the end of helices
          
.  */
          else if (strcmp (long_options[option_index].name, "noClosingGU") == 0)
          {
          
          
            if (update_arg((void *)&(args_info->noClosingGU_flag), 0, &(args_info->noClosingGU_given),
                &(local_args_info.noClosingGU_given), optarg, 0, 0, ARG_FLAG,
                check_ambiguity, override, 1, 0, "noClosingGU", '-',
                additional_error))
              goto failure;
          
          }
          /* Allow other pairs in addition to the usual AU,GC,and GU pairs.
.  */
          else if (strcmp (long_options[option_index].name, "nsp") == 0)
          {
          
          
            if (update_arg( (void *)&(args_info->nsp_arg), 
                 &(args_info->nsp_orig), &(args_info->nsp_given),
                &(local_args_info.nsp_given), optarg, 0, 0, ARG_STRING,
                check_ambiguity, override, 0, 0,
                "nsp", '-',
                additional_error))
              goto failure;
          
          }
          
          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", RNAPDIST_CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
          abort ();
        } /* switch */
    } /* while */




  RNApdist_cmdline_parser_release (&local_args_info);

  if ( error )
    return (EXIT_FAILURE);

  return 0;

failure:
  
  RNApdist_cmdline_parser_release (&local_args_info);
  return (EXIT_FAILURE);
}