/*
  File autogenerated by gengetopt version 2.13
  generated with the following command:
  gengetopt -ibootstrap_prog.ggo -Fbootstrap_prog_cmdline -f bootstrap_prog_cmdline_parser --arg-struct-name=bootstrap_prog_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>

#include "getopt.h"

#include "bootstrap_prog_cmdline.h"

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

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

static int
bootstrap_prog_cmdline_parser_required2 (struct bootstrap_prog_args_info *args_info, const char *prog_name, const char *additional_error);

static char *
gengetopt_strdup (const char *s);

static
void clear_given (struct bootstrap_prog_args_info *args_info)
{
  args_info->help_given = 0 ;
  args_info->version_given = 0 ;
  args_info->treesList_given = 0 ;
  args_info->reftree_given = 0 ;
  args_info->outputfile_given = 0 ;
  args_info->Logfile_given = 0 ;
  args_info->verbose_given = 0 ;
  args_info->ConsensusLevel_given = 0 ;
  args_info->noBranchLen_given = 0 ;
}

static
void clear_args (struct bootstrap_prog_args_info *args_info)
{
  args_info->treesList_arg = NULL;
  args_info->reftree_arg = NULL;
  args_info->outputfile_arg = gengetopt_strdup ("-");
  args_info->Logfile_arg = gengetopt_strdup ("-");
  args_info->verbose_arg = 0 ;
  args_info->ConsensusLevel_arg = 0.5 ;
  args_info->noBranchLen_flag = 0;
}

void
bootstrap_prog_cmdline_parser_print_version (void)
{
  printf ("%s %s\n", BOOTSTRAP_PROG_CMDLINE_PARSER_PACKAGE, BOOTSTRAP_PROG_CMDLINE_PARSER_VERSION);
}

void
bootstrap_prog_cmdline_parser_print_help (void)
{
  bootstrap_prog_cmdline_parser_print_version ();
  printf("\n%s\n", "compute bootstrap values and consensus trees from a list of trees");
  printf("\nUsage: bootstrap [OPTIONS]...\n\n");
  printf("%s\n","  -h, --help                  Print help and exit");
  printf("%s\n","  -V, --version               Print version and exit");
  printf("%s\n","  -t, --treesList=STRING      filename of list of input trees");
  printf("%s\n","  -r, --reftree=STRING        Refremce Tree file name");
  printf("%s\n","  -o, --outputfile=STRING     Output tree file  (default=`-')");
  printf("%s\n","  -l, --Logfile=STRING        Log file output name  (default=`-')");
  printf("%s\n","  -v, --verbose=INT           Log report level (verbose)  (default=`0')");
  printf("%s\n","  -c, --ConsensusLevel=FLOAT  use only branches with sport above this  \n                                (default=`0.5')");
  printf("%s\n","  -b, --noBranchLen           Do not output branch lengths in output tree  \n                                (default=off)");
  
}

void
bootstrap_prog_cmdline_parser_init (struct bootstrap_prog_args_info *args_info)
{
  clear_given (args_info);
  clear_args (args_info);
}

void
bootstrap_prog_cmdline_parser_free (struct bootstrap_prog_args_info *args_info)
{
  
  if (args_info->treesList_arg)
    {
      free (args_info->treesList_arg); /* free previous argument */
      args_info->treesList_arg = 0;
    }
  if (args_info->reftree_arg)
    {
      free (args_info->reftree_arg); /* free previous argument */
      args_info->reftree_arg = 0;
    }
  if (args_info->outputfile_arg)
    {
      free (args_info->outputfile_arg); /* free previous argument */
      args_info->outputfile_arg = 0;
    }
  if (args_info->Logfile_arg)
    {
      free (args_info->Logfile_arg); /* free previous argument */
      args_info->Logfile_arg = 0;
    }
  
  clear_given (args_info);
}

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

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

int
bootstrap_prog_cmdline_parser (int argc, char * const *argv, struct bootstrap_prog_args_info *args_info)
{
  return bootstrap_prog_cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
}

int
bootstrap_prog_cmdline_parser2 (int argc, char * const *argv, struct bootstrap_prog_args_info *args_info, int override, int initialize, int check_required)
{
  int result;

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

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

int
bootstrap_prog_cmdline_parser_required (struct bootstrap_prog_args_info *args_info, const char *prog_name)
{
  int result = EXIT_SUCCESS;

  if (bootstrap_prog_cmdline_parser_required2(args_info, prog_name, NULL) > 0)
    result = EXIT_FAILURE;

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

int
bootstrap_prog_cmdline_parser_required2 (struct bootstrap_prog_args_info *args_info, const char *prog_name, const char *additional_error)
{
  int error = 0;

  if (! args_info->treesList_given)
    {
      fprintf (stderr, "%s: '--treesList' ('-t') option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }

  return error;
}

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

  int error = 0;
  struct bootstrap_prog_args_info local_args_info;

  if (initialize)
    bootstrap_prog_cmdline_parser_init (args_info);

  bootstrap_prog_cmdline_parser_init (&local_args_info);

  optarg = 0;
  optind = 1;
  opterr = 1;
  optopt = '?';

  while (1)
    {
      int option_index = 0;
      char *stop_char;

      static struct option long_options[] = {
        { "help",	0, NULL, 'h' },
        { "version",	0, NULL, 'V' },
        { "treesList",	1, NULL, 't' },
        { "reftree",	1, NULL, 'r' },
        { "outputfile",	1, NULL, 'o' },
        { "Logfile",	1, NULL, 'l' },
        { "verbose",	1, NULL, 'v' },
        { "ConsensusLevel",	1, NULL, 'c' },
        { "noBranchLen",	0, NULL, 'b' },
        { NULL,	0, NULL, 0 }
      };

      stop_char = 0;
      c = getopt_long (argc, argv, "hVt:r:o:l:v:c:b", long_options, &option_index);

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

      switch (c)
        {
        case 'h':	/* Print help and exit.  */
          bootstrap_prog_cmdline_parser_print_help ();
          exit (EXIT_SUCCESS);

        case 'V':	/* Print version and exit.  */
          bootstrap_prog_cmdline_parser_print_version ();
          exit (EXIT_SUCCESS);

        case 't':	/* filename of list of input trees.  */
          if (local_args_info.treesList_given)
            {
              fprintf (stderr, "%s: `--treesList' (`-t') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->treesList_given && ! override)
            continue;
          local_args_info.treesList_given = 1;
          args_info->treesList_given = 1;
          if (args_info->treesList_arg)
            free (args_info->treesList_arg); /* free previous string */
          args_info->treesList_arg = gengetopt_strdup (optarg);
          break;

        case 'r':	/* Refremce Tree file name.  */
          if (local_args_info.reftree_given)
            {
              fprintf (stderr, "%s: `--reftree' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->reftree_given && ! override)
            continue;
          local_args_info.reftree_given = 1;
          args_info->reftree_given = 1;
          if (args_info->reftree_arg)
            free (args_info->reftree_arg); /* free previous string */
          args_info->reftree_arg = gengetopt_strdup (optarg);
          break;

        case 'o':	/* Output tree file.  */
          if (local_args_info.outputfile_given)
            {
              fprintf (stderr, "%s: `--outputfile' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->outputfile_given && ! override)
            continue;
          local_args_info.outputfile_given = 1;
          args_info->outputfile_given = 1;
          if (args_info->outputfile_arg)
            free (args_info->outputfile_arg); /* free previous string */
          args_info->outputfile_arg = gengetopt_strdup (optarg);
          break;

        case 'l':	/* Log file output name.  */
          if (local_args_info.Logfile_given)
            {
              fprintf (stderr, "%s: `--Logfile' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->Logfile_given && ! override)
            continue;
          local_args_info.Logfile_given = 1;
          args_info->Logfile_given = 1;
          if (args_info->Logfile_arg)
            free (args_info->Logfile_arg); /* free previous string */
          args_info->Logfile_arg = gengetopt_strdup (optarg);
          break;

        case 'v':	/* Log report level (verbose).  */
          if (local_args_info.verbose_given)
            {
              fprintf (stderr, "%s: `--verbose' (`-v') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->verbose_given && ! override)
            continue;
          local_args_info.verbose_given = 1;
          args_info->verbose_given = 1;
          args_info->verbose_arg = strtol (optarg,&stop_char,0);
          break;

        case 'c':	/* use only branches with sport above this.  */
          if (local_args_info.ConsensusLevel_given)
            {
              fprintf (stderr, "%s: `--ConsensusLevel' (`-c') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->ConsensusLevel_given && ! override)
            continue;
          local_args_info.ConsensusLevel_given = 1;
          args_info->ConsensusLevel_given = 1;
          args_info->ConsensusLevel_arg = (float)strtod (optarg, NULL);
          break;

        case 'b':	/* Do not output branch lengths in output tree.  */
          if (local_args_info.noBranchLen_given)
            {
              fprintf (stderr, "%s: `--noBranchLen' (`-b') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->noBranchLen_given && ! override)
            continue;
          local_args_info.noBranchLen_given = 1;
          args_info->noBranchLen_given = 1;
          args_info->noBranchLen_flag = !(args_info->noBranchLen_flag);
          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", BOOTSTRAP_PROG_CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
          abort ();
        } /* switch */
    } /* while */



  if (check_required)
    {
      error += bootstrap_prog_cmdline_parser_required2 (args_info, argv[0], additional_error);
    }

  bootstrap_prog_cmdline_parser_free (&local_args_info);

  if ( error )
    return (EXIT_FAILURE);

  return 0;

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