applications/dynamicProps/DynamicPropsCmd.c

/*
  File autogenerated by gengetopt version 2.15
  generated with the following command:
  gengetopt -u -i DynamicProps.ggo -F DynamicPropsCmd 

  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 "DynamicPropsCmd.h"

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

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

static int
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);

static char *
gengetopt_strdup (const char *s);

static
void clear_given (struct gengetopt_args_info *args_info)
{
  args_info->help_given = 0 ;
  args_info->version_given = 0 ;
  args_info->input_given = 0 ;
  args_info->output_given = 0 ;
  args_info->sele1_given = 0 ;
  args_info->sele2_given = 0 ;
  args_info->order_given = 0 ;
  args_info->rcorr_given = 0 ;
  args_info->vcorr_given = 0 ;
  args_info->dcorr_given = 0 ;
  args_info->lcorr_given = 0 ;
  args_info->r_rcorr_given = 0 ;
  args_info->thetacorr_given = 0 ;
  args_info->dynamicProps_group_counter = 0 ;
}

static
void clear_args (struct gengetopt_args_info *args_info)
{
  args_info->input_arg = NULL;
  args_info->input_orig = NULL;
  args_info->output_arg = NULL;
  args_info->output_orig = NULL;
  args_info->sele1_arg = NULL;
  args_info->sele1_orig = NULL;
  args_info->sele2_arg = NULL;
  args_info->sele2_orig = NULL;
  args_info->order_orig = NULL;
  
}

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

void
cmdline_parser_print_help (void)
{
  cmdline_parser_print_version ();
  printf("\nUsage: DynamicProps [OPTIONS]... [FILES]...\n\n");
  printf("%s\n","  -h, --help                    Print help and exit");
  printf("%s\n","  -V, --version                 Print version and exit");
  printf("%s\n","  -i, --input=filename          input dump file");
  printf("%s\n","  -o, --output=filename         output file name");
  printf("%s\n","      --sele1=selection script  select first stuntdouble set");
  printf("%s\n","      --sele2=selection script  select second stuntdouble set (if sele2 is not \n                                  set, use script from sele1)");
  printf("%s\n","      --order=INT               Lengendre Polynomial Order");
  printf("%s\n","\n Group: dynamicProps\n   an option of this group is required");
  printf("%s\n","  -r, --rcorr                   rmsd");
  printf("%s\n","  -v, --vcorr                   velocity correlation function");
  printf("%s\n","  -d, --dcorr                   dipole correlation function");
  printf("%s\n","  -l, --lcorr                   Lengendre correlation function");
  printf("%s\n","      --r_rcorr                 Radial rmsd");
  printf("%s\n","      --thetacorr               Angular rmsd");
  
}

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

  args_info->inputs = NULL;
  args_info->inputs_num = 0;
}

static void
cmdline_parser_release (struct gengetopt_args_info *args_info)
{
  
  unsigned int i;
  if (args_info->input_arg)
    {
      free (args_info->input_arg); /* free previous argument */
      args_info->input_arg = 0;
    }
  if (args_info->input_orig)
    {
      free (args_info->input_orig); /* free previous argument */
      args_info->input_orig = 0;
    }
  if (args_info->output_arg)
    {
      free (args_info->output_arg); /* free previous argument */
      args_info->output_arg = 0;
    }
  if (args_info->output_orig)
    {
      free (args_info->output_orig); /* free previous argument */
      args_info->output_orig = 0;
    }
  if (args_info->sele1_arg)
    {
      free (args_info->sele1_arg); /* free previous argument */
      args_info->sele1_arg = 0;
    }
  if (args_info->sele1_orig)
    {
      free (args_info->sele1_orig); /* free previous argument */
      args_info->sele1_orig = 0;
    }
  if (args_info->sele2_arg)
    {
      free (args_info->sele2_arg); /* free previous argument */
      args_info->sele2_arg = 0;
    }
  if (args_info->sele2_orig)
    {
      free (args_info->sele2_orig); /* free previous argument */
      args_info->sele2_orig = 0;
    }
  if (args_info->order_orig)
    {
      free (args_info->order_orig); /* free previous argument */
      args_info->order_orig = 0;
    }
  
  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);
}

int
cmdline_parser_file_save(const char *filename, struct gengetopt_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", CMDLINE_PARSER_PACKAGE, filename);
      return EXIT_FAILURE;
    }

  if (args_info->help_given) {
    fprintf(outfile, "%s\n", "help");
  }
  if (args_info->version_given) {
    fprintf(outfile, "%s\n", "version");
  }
  if (args_info->input_given) {
    if (args_info->input_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
    } else {
      fprintf(outfile, "%s\n", "input");
    }
  }
  if (args_info->output_given) {
    if (args_info->output_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
    } else {
      fprintf(outfile, "%s\n", "output");
    }
  }
  if (args_info->sele1_given) {
    if (args_info->sele1_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
    } else {
      fprintf(outfile, "%s\n", "sele1");
    }
  }
  if (args_info->sele2_given) {
    if (args_info->sele2_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
    } else {
      fprintf(outfile, "%s\n", "sele2");
    }
  }
  if (args_info->order_given) {
    if (args_info->order_orig) {
      fprintf(outfile, "%s=\"%s\"\n", "order", args_info->order_orig);
    } else {
      fprintf(outfile, "%s\n", "order");
    }
  }
  if (args_info->rcorr_given) {
    fprintf(outfile, "%s\n", "rcorr");
  }
  if (args_info->vcorr_given) {
    fprintf(outfile, "%s\n", "vcorr");
  }
  if (args_info->dcorr_given) {
    fprintf(outfile, "%s\n", "dcorr");
  }
  if (args_info->lcorr_given) {
    fprintf(outfile, "%s\n", "lcorr");
  }
  if (args_info->r_rcorr_given) {
    fprintf(outfile, "%s\n", "r_rcorr");
  }
  if (args_info->thetacorr_given) {
    fprintf(outfile, "%s\n", "thetacorr");
  }
  
  fclose (outfile);

  i = EXIT_SUCCESS;
  return i;
}

void
cmdline_parser_free (struct gengetopt_args_info *args_info)
{
  cmdline_parser_release (args_info);
}


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

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

static void
reset_group_dynamicProps(struct gengetopt_args_info *args_info);

static void
reset_group_dynamicProps(struct gengetopt_args_info *args_info)
{
  if (! args_info->dynamicProps_group_counter)
    return;
  
  args_info->rcorr_given = 0 ;
  args_info->vcorr_given = 0 ;
  args_info->dcorr_given = 0 ;
  args_info->lcorr_given = 0 ;
  args_info->r_rcorr_given = 0 ;
  args_info->thetacorr_given = 0 ;

  args_info->dynamicProps_group_counter = 0;
}

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

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

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

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

int
cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
{
  int result = EXIT_SUCCESS;

  if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
    result = EXIT_FAILURE;

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

int
cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
{
  int error = 0;

  if (! args_info->input_given)
    {
      fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
      error = 1;
    }
  if (args_info->dynamicProps_group_counter == 0)
    {
      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", prog_name, args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
      error = 1;
    }
  

  return error;
}

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

  int error = 0;
  struct gengetopt_args_info local_args_info;

  if (initialize)
    cmdline_parser_init (args_info);

  cmdline_parser_init (&local_args_info);

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

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

      static struct option long_options[] = {
        { "help",       0, NULL, 'h' },
        { "version",    0, NULL, 'V' },
        { "input",      1, NULL, 'i' },
        { "output",     1, NULL, 'o' },
        { "sele1",      1, NULL, 0 },
        { "sele2",      1, NULL, 0 },
        { "order",      1, NULL, 0 },
        { "rcorr",      0, NULL, 'r' },
        { "vcorr",      0, NULL, 'v' },
        { "dcorr",      0, NULL, 'd' },
        { "lcorr",      0, NULL, 'l' },
        { "r_rcorr",    0, NULL, 0 },
        { "thetacorr",  0, NULL, 0 },
        { NULL, 0, NULL, 0 }
      };

      stop_char = 0;
      c = getopt_long (argc, argv, "hVi:o:rvdl", long_options, &option_index);

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

      switch (c)
        {
        case 'h':       /* Print help and exit.  */
          cmdline_parser_print_help ();
          cmdline_parser_free (&local_args_info);
          exit (EXIT_SUCCESS);

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

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

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

        case 'r':       /* rmsd.  */
          if (local_args_info.rcorr_given)
            {
              fprintf (stderr, "%s: `--rcorr' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->rcorr_given && ! override)
            continue;
          local_args_info.rcorr_given = 1;
          args_info->rcorr_given = 1;
          if (args_info->dynamicProps_group_counter && override)
            reset_group_dynamicProps (args_info);
          args_info->dynamicProps_group_counter += 1;
          break;

        case 'v':       /* velocity correlation function.  */
          if (local_args_info.vcorr_given)
            {
              fprintf (stderr, "%s: `--vcorr' (`-v') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->vcorr_given && ! override)
            continue;
          local_args_info.vcorr_given = 1;
          args_info->vcorr_given = 1;
          if (args_info->dynamicProps_group_counter && override)
            reset_group_dynamicProps (args_info);
          args_info->dynamicProps_group_counter += 1;
          break;

        case 'd':       /* dipole correlation function.  */
          if (local_args_info.dcorr_given)
            {
              fprintf (stderr, "%s: `--dcorr' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->dcorr_given && ! override)
            continue;
          local_args_info.dcorr_given = 1;
          args_info->dcorr_given = 1;
          if (args_info->dynamicProps_group_counter && override)
            reset_group_dynamicProps (args_info);
          args_info->dynamicProps_group_counter += 1;
          break;

        case 'l':       /* Lengendre correlation function.  */
          if (local_args_info.lcorr_given)
            {
              fprintf (stderr, "%s: `--lcorr' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
              goto failure;
            }
          if (args_info->lcorr_given && ! override)
            continue;
          local_args_info.lcorr_given = 1;
          args_info->lcorr_given = 1;
          if (args_info->dynamicProps_group_counter && override)
            reset_group_dynamicProps (args_info);
          args_info->dynamicProps_group_counter += 1;
          break;


        case 0: /* Long option with no short option */
          /* select first stuntdouble set.  */
          if (strcmp (long_options[option_index].name, "sele1") == 0)
          {
            if (local_args_info.sele1_given)
              {
                fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->sele1_given && ! override)
              continue;
            local_args_info.sele1_given = 1;
            args_info->sele1_given = 1;
            if (args_info->sele1_arg)
              free (args_info->sele1_arg); /* free previous string */
            args_info->sele1_arg = gengetopt_strdup (optarg);
            if (args_info->sele1_orig)
              free (args_info->sele1_orig); /* free previous string */
            args_info->sele1_orig = gengetopt_strdup (optarg);
          }
          /* select second stuntdouble set (if sele2 is not set, use script from sele1).  */
          else if (strcmp (long_options[option_index].name, "sele2") == 0)
          {
            if (local_args_info.sele2_given)
              {
                fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->sele2_given && ! override)
              continue;
            local_args_info.sele2_given = 1;
            args_info->sele2_given = 1;
            if (args_info->sele2_arg)
              free (args_info->sele2_arg); /* free previous string */
            args_info->sele2_arg = gengetopt_strdup (optarg);
            if (args_info->sele2_orig)
              free (args_info->sele2_orig); /* free previous string */
            args_info->sele2_orig = gengetopt_strdup (optarg);
          }
          /* Lengendre Polynomial Order.  */
          else if (strcmp (long_options[option_index].name, "order") == 0)
          {
            if (local_args_info.order_given)
              {
                fprintf (stderr, "%s: `--order' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->order_given && ! override)
              continue;
            local_args_info.order_given = 1;
            args_info->order_given = 1;
            args_info->order_arg = strtol (optarg, &stop_char, 0);
            if (!(stop_char && *stop_char == '\0')) {
              fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
              goto failure;
            }
            if (args_info->order_orig)
              free (args_info->order_orig); /* free previous string */
            args_info->order_orig = gengetopt_strdup (optarg);
          }
          /* Radial rmsd.  */
          else if (strcmp (long_options[option_index].name, "r_rcorr") == 0)
          {
            if (local_args_info.r_rcorr_given)
              {
                fprintf (stderr, "%s: `--r_rcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->r_rcorr_given && ! override)
              continue;
            local_args_info.r_rcorr_given = 1;
            args_info->r_rcorr_given = 1;
            if (args_info->dynamicProps_group_counter && override)
              reset_group_dynamicProps (args_info);
            args_info->dynamicProps_group_counter += 1;
            break;
          }
          /* Angular rmsd.  */
          else if (strcmp (long_options[option_index].name, "thetacorr") == 0)
          {
            if (local_args_info.thetacorr_given)
              {
                fprintf (stderr, "%s: `--thetacorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
                goto failure;
              }
            if (args_info->thetacorr_given && ! override)
              continue;
            local_args_info.thetacorr_given = 1;
            args_info->thetacorr_given = 1;
            if (args_info->dynamicProps_group_counter && override)
              reset_group_dynamicProps (args_info);
            args_info->dynamicProps_group_counter += 1;
            break;
          }
          
          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", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
          abort ();
        } /* switch */
    } /* while */

  if (args_info->dynamicProps_group_counter > 1)
    {
      fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", argv[0], args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
      error = 1;
    }
  

  if (check_required)
    {
      error += cmdline_parser_required2 (args_info, argv[0], additional_error);
    }

  cmdline_parser_release (&local_args_info);

  if ( error )
    return (EXIT_FAILURE);

  if (optind < argc)
    {
      int i = 0 ;

      args_info->inputs_num = argc - optind ;
      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:
  
  cmdline_parser_release (&local_args_info);
  return (EXIT_FAILURE);
}
Revision:	1112
Committed:	Wed Jan 3 20:47:00 2007 UTC (18 years, 4 months ago) by chuckv
Content type:	text/plain
File size:	20661 byte(s)
Log Message:	Changes to add thetacorr to dynamic props and fixes to radial rcorr.
#	User	Rev	Content
1	tim	320	/*
2	chuckv	1098	File autogenerated by gengetopt version 2.15
3	tim	320	generated with the following command:
4	chuckv	1112	gengetopt -u -i DynamicProps.ggo -F DynamicPropsCmd
5	tim	320
6			The developers of gengetopt consider the fixed text that goes in all
7			gengetopt output files to be in the public domain:
8			we make no copyright claims on it.
9			*/
10
11	chuckv	1098	/* If we use autoconf. */
12			#ifdef HAVE_CONFIG_H
13			#include "config.h"
14			#endif
15	tim	320
16			#include <stdio.h>
17			#include <stdlib.h>
18			#include <string.h>
19
20			#include "getopt.h"
21
22			#include "DynamicPropsCmd.h"
23
24	chuckv	1098	static
25			void clear_given (struct gengetopt_args_info *args_info);
26			static
27			void clear_args (struct gengetopt_args_info *args_info);
28
29			static int
30			cmdline_parser_internal (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required, const char *additional_error);
31
32			static int
33			cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error);
34
35			static char *
36			gengetopt_strdup (const char *s);
37
38			static
39			void clear_given (struct gengetopt_args_info *args_info)
40			{
41			args_info->help_given = 0 ;
42			args_info->version_given = 0 ;
43			args_info->input_given = 0 ;
44			args_info->output_given = 0 ;
45			args_info->sele1_given = 0 ;
46			args_info->sele2_given = 0 ;
47			args_info->order_given = 0 ;
48			args_info->rcorr_given = 0 ;
49			args_info->vcorr_given = 0 ;
50			args_info->dcorr_given = 0 ;
51			args_info->lcorr_given = 0 ;
52			args_info->r_rcorr_given = 0 ;
53	chuckv	1112	args_info->thetacorr_given = 0 ;
54	chuckv	1098	args_info->dynamicProps_group_counter = 0 ;
55			}
56
57			static
58			void clear_args (struct gengetopt_args_info *args_info)
59			{
60			args_info->input_arg = NULL;
61			args_info->input_orig = NULL;
62			args_info->output_arg = NULL;
63			args_info->output_orig = NULL;
64			args_info->sele1_arg = NULL;
65			args_info->sele1_orig = NULL;
66			args_info->sele2_arg = NULL;
67			args_info->sele2_orig = NULL;
68			args_info->order_orig = NULL;
69
70			}
71
72	tim	320	void
73			cmdline_parser_print_version (void)
74			{
75			printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
76			}
77
78			void
79			cmdline_parser_print_help (void)
80			{
81			cmdline_parser_print_version ();
82	chuckv	1112	printf("\nUsage: DynamicProps [OPTIONS]... [FILES]...\n\n");
83	chuckv	1098	printf("%s\n"," -h, --help Print help and exit");
84			printf("%s\n"," -V, --version Print version and exit");
85			printf("%s\n"," -i, --input=filename input dump file");
86			printf("%s\n"," -o, --output=filename output file name");
87			printf("%s\n"," --sele1=selection script select first stuntdouble set");
88			printf("%s\n"," --sele2=selection script select second stuntdouble set (if sele2 is not \n set, use script from sele1)");
89			printf("%s\n"," --order=INT Lengendre Polynomial Order");
90			printf("%s\n","\n Group: dynamicProps\n an option of this group is required");
91			printf("%s\n"," -r, --rcorr rmsd");
92			printf("%s\n"," -v, --vcorr velocity correlation function");
93			printf("%s\n"," -d, --dcorr dipole correlation function");
94			printf("%s\n"," -l, --lcorr Lengendre correlation function");
95			printf("%s\n"," --r_rcorr Radial rmsd");
96	chuckv	1112	printf("%s\n"," --thetacorr Angular rmsd");
97	chuckv	1098
98	tim	320	}
99
100	chuckv	1098	void
101			cmdline_parser_init (struct gengetopt_args_info *args_info)
102			{
103			clear_given (args_info);
104			clear_args (args_info);
105	chuckv	1112
106			args_info->inputs = NULL;
107			args_info->inputs_num = 0;
108	chuckv	1098	}
109	tim	320
110	chuckv	1098	static void
111			cmdline_parser_release (struct gengetopt_args_info *args_info)
112			{
113
114	chuckv	1112	unsigned int i;
115	chuckv	1098	if (args_info->input_arg)
116			{
117			free (args_info->input_arg); /* free previous argument */
118			args_info->input_arg = 0;
119			}
120			if (args_info->input_orig)
121			{
122			free (args_info->input_orig); /* free previous argument */
123			args_info->input_orig = 0;
124			}
125			if (args_info->output_arg)
126			{
127			free (args_info->output_arg); /* free previous argument */
128			args_info->output_arg = 0;
129			}
130			if (args_info->output_orig)
131			{
132			free (args_info->output_orig); /* free previous argument */
133			args_info->output_orig = 0;
134			}
135			if (args_info->sele1_arg)
136			{
137			free (args_info->sele1_arg); /* free previous argument */
138			args_info->sele1_arg = 0;
139			}
140			if (args_info->sele1_orig)
141			{
142			free (args_info->sele1_orig); /* free previous argument */
143			args_info->sele1_orig = 0;
144			}
145			if (args_info->sele2_arg)
146			{
147			free (args_info->sele2_arg); /* free previous argument */
148			args_info->sele2_arg = 0;
149			}
150			if (args_info->sele2_orig)
151			{
152			free (args_info->sele2_orig); /* free previous argument */
153			args_info->sele2_orig = 0;
154			}
155			if (args_info->order_orig)
156			{
157			free (args_info->order_orig); /* free previous argument */
158			args_info->order_orig = 0;
159			}
160
161	chuckv	1112	for (i = 0; i < args_info->inputs_num; ++i)
162			free (args_info->inputs [i]);
163
164			if (args_info->inputs_num)
165			free (args_info->inputs);
166
167	chuckv	1098	clear_given (args_info);
168			}
169	tim	320
170	chuckv	1098	int
171			cmdline_parser_file_save(const char filename, struct gengetopt_args_info args_info)
172			{
173			FILE *outfile;
174			int i = 0;
175
176			outfile = fopen(filename, "w");
177
178			if (!outfile)
179			{
180			fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
181			return EXIT_FAILURE;
182			}
183
184			if (args_info->help_given) {
185			fprintf(outfile, "%s\n", "help");
186			}
187			if (args_info->version_given) {
188			fprintf(outfile, "%s\n", "version");
189			}
190			if (args_info->input_given) {
191			if (args_info->input_orig) {
192			fprintf(outfile, "%s=\"%s\"\n", "input", args_info->input_orig);
193			} else {
194			fprintf(outfile, "%s\n", "input");
195			}
196			}
197			if (args_info->output_given) {
198			if (args_info->output_orig) {
199			fprintf(outfile, "%s=\"%s\"\n", "output", args_info->output_orig);
200			} else {
201			fprintf(outfile, "%s\n", "output");
202			}
203			}
204			if (args_info->sele1_given) {
205			if (args_info->sele1_orig) {
206			fprintf(outfile, "%s=\"%s\"\n", "sele1", args_info->sele1_orig);
207			} else {
208			fprintf(outfile, "%s\n", "sele1");
209			}
210			}
211			if (args_info->sele2_given) {
212			if (args_info->sele2_orig) {
213			fprintf(outfile, "%s=\"%s\"\n", "sele2", args_info->sele2_orig);
214			} else {
215			fprintf(outfile, "%s\n", "sele2");
216			}
217			}
218			if (args_info->order_given) {
219			if (args_info->order_orig) {
220			fprintf(outfile, "%s=\"%s\"\n", "order", args_info->order_orig);
221			} else {
222			fprintf(outfile, "%s\n", "order");
223			}
224			}
225			if (args_info->rcorr_given) {
226			fprintf(outfile, "%s\n", "rcorr");
227			}
228			if (args_info->vcorr_given) {
229			fprintf(outfile, "%s\n", "vcorr");
230			}
231			if (args_info->dcorr_given) {
232			fprintf(outfile, "%s\n", "dcorr");
233			}
234			if (args_info->lcorr_given) {
235			fprintf(outfile, "%s\n", "lcorr");
236			}
237			if (args_info->r_rcorr_given) {
238			fprintf(outfile, "%s\n", "r_rcorr");
239			}
240	chuckv	1112	if (args_info->thetacorr_given) {
241			fprintf(outfile, "%s\n", "thetacorr");
242			}
243	chuckv	1098
244			fclose (outfile);
245
246			i = EXIT_SUCCESS;
247			return i;
248			}
249
250			void
251			cmdline_parser_free (struct gengetopt_args_info *args_info)
252			{
253			cmdline_parser_release (args_info);
254			}
255
256
257	tim	320	/* gengetopt_strdup() */
258			/* strdup.c replacement of strdup, which is not standard */
259			char *
260			gengetopt_strdup (const char *s)
261			{
262	chuckv	1098	char *result = NULL;
263			if (!s)
264			return result;
265
266			result = (char*)malloc(strlen(s) + 1);
267	tim	320	if (result == (char*)0)
268			return (char*)0;
269			strcpy(result, s);
270			return result;
271			}
272
273	chuckv	1098	static void
274			reset_group_dynamicProps(struct gengetopt_args_info *args_info);
275
276			static void
277			reset_group_dynamicProps(struct gengetopt_args_info *args_info)
278	tim	320	{
279	chuckv	1098	if (! args_info->dynamicProps_group_counter)
280			return;
281	tim	320
282			args_info->rcorr_given = 0 ;
283			args_info->vcorr_given = 0 ;
284			args_info->dcorr_given = 0 ;
285	tim	876	args_info->lcorr_given = 0 ;
286	chuckv	1098	args_info->r_rcorr_given = 0 ;
287	chuckv	1112	args_info->thetacorr_given = 0 ;
288	chuckv	1098
289			args_info->dynamicProps_group_counter = 0;
290	tim	876	}
291	tim	320
292	chuckv	1098	int
293			cmdline_parser (int argc, char * const argv, struct gengetopt_args_info args_info)
294			{
295			return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
296			}
297	tim	320
298	chuckv	1098	int
299			cmdline_parser2 (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required)
300			{
301			int result;
302
303			result = cmdline_parser_internal (argc, argv, args_info, override, initialize, check_required, NULL);
304
305			if (result == EXIT_FAILURE)
306			{
307			cmdline_parser_free (args_info);
308			exit (EXIT_FAILURE);
309			}
310
311			return result;
312			}
313
314			int
315			cmdline_parser_required (struct gengetopt_args_info args_info, const char prog_name)
316			{
317			int result = EXIT_SUCCESS;
318
319			if (cmdline_parser_required2(args_info, prog_name, NULL) > 0)
320			result = EXIT_FAILURE;
321
322			if (result == EXIT_FAILURE)
323			{
324			cmdline_parser_free (args_info);
325			exit (EXIT_FAILURE);
326			}
327
328			return result;
329			}
330
331			int
332			cmdline_parser_required2 (struct gengetopt_args_info args_info, const char prog_name, const char *additional_error)
333			{
334			int error = 0;
335
336			if (! args_info->input_given)
337			{
338			fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
339			error = 1;
340			}
341			if (args_info->dynamicProps_group_counter == 0)
342			{
343			fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", prog_name, args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
344			error = 1;
345			}
346
347
348			return error;
349			}
350
351			int
352			cmdline_parser_internal (int argc, char * const argv, struct gengetopt_args_info args_info, int override, int initialize, int check_required, const char *additional_error)
353			{
354			int c; /* Character of the parsed option. */
355
356			int error = 0;
357			struct gengetopt_args_info local_args_info;
358
359			if (initialize)
360			cmdline_parser_init (args_info);
361
362			cmdline_parser_init (&local_args_info);
363
364	tim	320	optarg = 0;
365			optind = 1;
366			opterr = 1;
367			optopt = '?';
368
369			while (1)
370			{
371			int option_index = 0;
372			char *stop_char;
373
374			static struct option long_options[] = {
375			{ "help", 0, NULL, 'h' },
376			{ "version", 0, NULL, 'V' },
377			{ "input", 1, NULL, 'i' },
378			{ "output", 1, NULL, 'o' },
379			{ "sele1", 1, NULL, 0 },
380			{ "sele2", 1, NULL, 0 },
381	tim	876	{ "order", 1, NULL, 0 },
382	tim	320	{ "rcorr", 0, NULL, 'r' },
383			{ "vcorr", 0, NULL, 'v' },
384			{ "dcorr", 0, NULL, 'd' },
385	tim	876	{ "lcorr", 0, NULL, 'l' },
386	chuckv	1098	{ "r_rcorr", 0, NULL, 0 },
387	chuckv	1112	{ "thetacorr", 0, NULL, 0 },
388	tim	320	{ NULL, 0, NULL, 0 }
389			};
390
391			stop_char = 0;
392	tim	917	c = getopt_long (argc, argv, "hVi:o:rvdl", long_options, &option_index);
393	tim	320
394			if (c == -1) break; /* Exit from `while (1)' loop. */
395
396			switch (c)
397			{
398			case 'h': /* Print help and exit. */
399			cmdline_parser_print_help ();
400	chuckv	1098	cmdline_parser_free (&local_args_info);
401	tim	320	exit (EXIT_SUCCESS);
402
403			case 'V': /* Print version and exit. */
404			cmdline_parser_print_version ();
405	chuckv	1098	cmdline_parser_free (&local_args_info);
406	tim	320	exit (EXIT_SUCCESS);
407
408			case 'i': /* input dump file. */
409	chuckv	1098	if (local_args_info.input_given)
410	tim	320	{
411	chuckv	1098	fprintf (stderr, "%s: `--input' (`-i') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
412			goto failure;
413	tim	320	}
414	chuckv	1098	if (args_info->input_given && ! override)
415			continue;
416			local_args_info.input_given = 1;
417	tim	320	args_info->input_given = 1;
418	chuckv	1098	if (args_info->input_arg)
419			free (args_info->input_arg); /* free previous string */
420	tim	320	args_info->input_arg = gengetopt_strdup (optarg);
421	chuckv	1098	if (args_info->input_orig)
422			free (args_info->input_orig); /* free previous string */
423			args_info->input_orig = gengetopt_strdup (optarg);
424	tim	320	break;
425
426			case 'o': /* output file name. */
427	chuckv	1098	if (local_args_info.output_given)
428	tim	320	{
429	chuckv	1098	fprintf (stderr, "%s: `--output' (`-o') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
430			goto failure;
431	tim	320	}
432	chuckv	1098	if (args_info->output_given && ! override)
433			continue;
434			local_args_info.output_given = 1;
435	tim	320	args_info->output_given = 1;
436	chuckv	1098	if (args_info->output_arg)
437			free (args_info->output_arg); /* free previous string */
438	tim	320	args_info->output_arg = gengetopt_strdup (optarg);
439	chuckv	1098	if (args_info->output_orig)
440			free (args_info->output_orig); /* free previous string */
441			args_info->output_orig = gengetopt_strdup (optarg);
442	tim	320	break;
443
444	tim	917	case 'r': /* rmsd. */
445	chuckv	1098	if (local_args_info.rcorr_given)
446	tim	320	{
447	chuckv	1098	fprintf (stderr, "%s: `--rcorr' (`-r') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
448			goto failure;
449	tim	320	}
450	chuckv	1098	if (args_info->rcorr_given && ! override)
451			continue;
452			local_args_info.rcorr_given = 1;
453	tim	320	args_info->rcorr_given = 1;
454	chuckv	1098	if (args_info->dynamicProps_group_counter && override)
455			reset_group_dynamicProps (args_info);
456			args_info->dynamicProps_group_counter += 1;
457			break;
458	tim	320
459			case 'v': /* velocity correlation function. */
460	chuckv	1098	if (local_args_info.vcorr_given)
461	tim	320	{
462	chuckv	1098	fprintf (stderr, "%s: `--vcorr' (`-v') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
463			goto failure;
464	tim	320	}
465	chuckv	1098	if (args_info->vcorr_given && ! override)
466			continue;
467			local_args_info.vcorr_given = 1;
468	tim	320	args_info->vcorr_given = 1;
469	chuckv	1098	if (args_info->dynamicProps_group_counter && override)
470			reset_group_dynamicProps (args_info);
471			args_info->dynamicProps_group_counter += 1;
472			break;
473	tim	320
474			case 'd': /* dipole correlation function. */
475	chuckv	1098	if (local_args_info.dcorr_given)
476	tim	320	{
477	chuckv	1098	fprintf (stderr, "%s: `--dcorr' (`-d') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
478			goto failure;
479	tim	320	}
480	chuckv	1098	if (args_info->dcorr_given && ! override)
481			continue;
482			local_args_info.dcorr_given = 1;
483	tim	320	args_info->dcorr_given = 1;
484	chuckv	1098	if (args_info->dynamicProps_group_counter && override)
485			reset_group_dynamicProps (args_info);
486			args_info->dynamicProps_group_counter += 1;
487			break;
488	tim	320
489	tim	876	case 'l': /* Lengendre correlation function. */
490	chuckv	1098	if (local_args_info.lcorr_given)
491	tim	876	{
492	chuckv	1098	fprintf (stderr, "%s: `--lcorr' (`-l') option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
493			goto failure;
494	tim	876	}
495	chuckv	1098	if (args_info->lcorr_given && ! override)
496			continue;
497			local_args_info.lcorr_given = 1;
498	tim	876	args_info->lcorr_given = 1;
499	chuckv	1098	if (args_info->dynamicProps_group_counter && override)
500			reset_group_dynamicProps (args_info);
501			args_info->dynamicProps_group_counter += 1;
502			break;
503	tim	320
504	tim	876
505	tim	320	case 0: /* Long option with no short option */
506			/* select first stuntdouble set. */
507			if (strcmp (long_options[option_index].name, "sele1") == 0)
508	tim	876	{
509	chuckv	1098	if (local_args_info.sele1_given)
510	tim	876	{
511	chuckv	1098	fprintf (stderr, "%s: `--sele1' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
512			goto failure;
513	tim	876	}
514	chuckv	1098	if (args_info->sele1_given && ! override)
515			continue;
516			local_args_info.sele1_given = 1;
517	tim	876	args_info->sele1_given = 1;
518	chuckv	1098	if (args_info->sele1_arg)
519			free (args_info->sele1_arg); /* free previous string */
520	tim	876	args_info->sele1_arg = gengetopt_strdup (optarg);
521	chuckv	1098	if (args_info->sele1_orig)
522			free (args_info->sele1_orig); /* free previous string */
523			args_info->sele1_orig = gengetopt_strdup (optarg);
524	tim	876	}
525	tim	320	/* select second stuntdouble set (if sele2 is not set, use script from sele1). */
526			else if (strcmp (long_options[option_index].name, "sele2") == 0)
527	tim	876	{
528	chuckv	1098	if (local_args_info.sele2_given)
529	tim	876	{
530	chuckv	1098	fprintf (stderr, "%s: `--sele2' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
531			goto failure;
532	tim	876	}
533	chuckv	1098	if (args_info->sele2_given && ! override)
534			continue;
535			local_args_info.sele2_given = 1;
536	tim	876	args_info->sele2_given = 1;
537	chuckv	1098	if (args_info->sele2_arg)
538			free (args_info->sele2_arg); /* free previous string */
539	tim	876	args_info->sele2_arg = gengetopt_strdup (optarg);
540	chuckv	1098	if (args_info->sele2_orig)
541			free (args_info->sele2_orig); /* free previous string */
542			args_info->sele2_orig = gengetopt_strdup (optarg);
543	tim	876	}
544			/* Lengendre Polynomial Order. */
545			else if (strcmp (long_options[option_index].name, "order") == 0)
546			{
547	chuckv	1098	if (local_args_info.order_given)
548	tim	876	{
549	chuckv	1098	fprintf (stderr, "%s: `--order' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
550			goto failure;
551	tim	876	}
552	chuckv	1098	if (args_info->order_given && ! override)
553			continue;
554			local_args_info.order_given = 1;
555	tim	876	args_info->order_given = 1;
556	chuckv	1098	args_info->order_arg = strtol (optarg, &stop_char, 0);
557			if (!(stop_char && *stop_char == '\0')) {
558			fprintf(stderr, "%s: invalid numeric value: %s\n", argv[0], optarg);
559			goto failure;
560			}
561			if (args_info->order_orig)
562			free (args_info->order_orig); /* free previous string */
563			args_info->order_orig = gengetopt_strdup (optarg);
564			}
565			/* Radial rmsd. */
566			else if (strcmp (long_options[option_index].name, "r_rcorr") == 0)
567			{
568			if (local_args_info.r_rcorr_given)
569			{
570			fprintf (stderr, "%s: `--r_rcorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
571			goto failure;
572			}
573			if (args_info->r_rcorr_given && ! override)
574			continue;
575			local_args_info.r_rcorr_given = 1;
576			args_info->r_rcorr_given = 1;
577			if (args_info->dynamicProps_group_counter && override)
578			reset_group_dynamicProps (args_info);
579			args_info->dynamicProps_group_counter += 1;
580	tim	876	break;
581			}
582	chuckv	1112	/* Angular rmsd. */
583			else if (strcmp (long_options[option_index].name, "thetacorr") == 0)
584			{
585			if (local_args_info.thetacorr_given)
586			{
587			fprintf (stderr, "%s: `--thetacorr' option given more than once%s\n", argv[0], (additional_error ? additional_error : ""));
588			goto failure;
589			}
590			if (args_info->thetacorr_given && ! override)
591			continue;
592			local_args_info.thetacorr_given = 1;
593			args_info->thetacorr_given = 1;
594			if (args_info->dynamicProps_group_counter && override)
595			reset_group_dynamicProps (args_info);
596			args_info->dynamicProps_group_counter += 1;
597			break;
598			}
599	tim	876
600	chuckv	1098	break;
601	tim	320	case '?': /* Invalid option. */
602			/* `getopt_long' already printed an error message. */
603	chuckv	1098	goto failure;
604	tim	320
605			default: /* bug: option not considered. */
606	chuckv	1098	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
607	tim	320	abort ();
608			} /* switch */
609			} /* while */
610
611	chuckv	1098	if (args_info->dynamicProps_group_counter > 1)
612	tim	320	{
613	chuckv	1098	fprintf (stderr, "%s: %d options of group dynamicProps were given. One is required.%s\n", argv[0], args_info->dynamicProps_group_counter, (additional_error ? additional_error : ""));
614			error = 1;
615	tim	320	}
616
617
618	chuckv	1098
619			if (check_required)
620	tim	320	{
621	chuckv	1098	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
622	tim	320	}
623
624	chuckv	1098	cmdline_parser_release (&local_args_info);
625
626			if ( error )
627			return (EXIT_FAILURE);
628
629	chuckv	1112	if (optind < argc)
630			{
631			int i = 0 ;
632
633			args_info->inputs_num = argc - optind ;
634			args_info->inputs =
635			(char *)(malloc ((args_info->inputs_num)sizeof(char *))) ;
636			while (optind < argc)
637			args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind++]) ;
638			}
639
640	tim	320	return 0;
641	chuckv	1098
642			failure:
643
644			cmdline_parser_release (&local_args_info);
645			return (EXIT_FAILURE);
646	tim	320	}