# include "pdb.h"

char **e_argv ;
int e_argc = -1;
int next_file_argument =1;


char *d_getopt( char *what, int with_arg)
{
   int ii ;

  for (ii = 1; ii < e_argc ; ii++)
     {
	char *arg = e_argv[ii] ; 
	

	if(*arg == '-')
	  {
		if (arg[1] == '-')
	          {
			next_file_argument = ii + 1;
			return NULL ;
                  }
	      if(!strncmp(arg+1, what,8) )
		{
		  if (with_arg)
		    {
			if (ii +2 > next_file_argument)
			    	next_file_argument = ii+2;
			return e_argv[ii +1] ;
		   }
		else
		   {
			if (ii +1 > next_file_argument)	
				next_file_argument = ii+1;
			return  arg;
          	   }
	        }
	  }
    }
   return NULL ;
}



void print_options_message() 
{
  printf("Standard options are : \n\
-a   atoms_types    :  atom_types is a file name contain definitions of atom types. \n\
-r   residues       :  residues is a file name contain residue definitions.\n\
-R      :  use the radii from the original Richards code ( as opposed to CHC values).\n\
-d  debug           : set the dbugging switch to debug\n\
-s    : set selection by atoms, directly or from a file. \n\
-resi : set selection by residue. \n\
-resf : set selection by residue from a file. \n\
-sscheck arg :  check ss bonds : 0)not check, 1)if no SSBOND records, 2)always\n\
-dicheck arg  : set the distance check used by volume \n\
-h    : print this message \n " ) ;

}

extern int deal_with_disorder ;
extern int handle_missing_atom_definition ;

extern char * selection_argument ;
extern char * residue_selection_argument ;
extern char * residue_selection_file ;
extern double distance_check ;
void initialize_selection ()
{
  residue_selection_argument = command_line_arg("residues") ;
  residue_selection_file = command_line_arg("resfile") ;
  
	selection_argument =   command_line_arg("s") ;	
}



extern int give_warning ;


extern int check_sulphur_bridges ; 
void do_initialization (int argc, char **argv)
{

   char *types_file     = NULL ;
   char *res_file       = NULL;
   int c ;
   int chc = 1 ; 


   e_argv = argv ;
   e_argc = argc ;

   if (argc >= 1)
     {
       if(d_getopt("h",0) != NULL)
	 {   print_options_message() ; call_exit(0) ;  }
       types_file = d_getopt("a",1) ;
       res_file = d_getopt("r",1) ;



       if(command_line_option("R"))   chc = 0 ;
       if(command_line_option("w")) give_warning = 1   ;
       { char * a =d_getopt("d",1)  ;
	 if (a != NULL)
	   debugging = atoi(a) ; }
     }
   SET_INT_FROM_OPTION(check_sulphur_bridges, "sscheck") ;
   SET_INT_FROM_OPTION(handle_missing_atom_definition, "missing") ;
   SET_DOUBLE_FROM_OPTION(distance_check, "dicheck") ;
   initialize_selection () ;
   initial_residues(types_file,res_file,chc) ;
}


file_records *read_next_file(format)
{
  int index = next_file_argument ;

  if (index >= e_argc) return NULL;
  next_file_argument++ ;

  while(1) 
    { file_records *ff =  open_and_read_pdb(e_argv[index],format) ;
      if (ff == NULL)
	switch(action_flag)
	  {
	  case ACTION_NMR : if (read_nmr_files == 0) continue ; break ;
	  }
      return ff ;
    }
}

file_records * read_next_file_checked(format)
{
  int cc = next_file_argument ;
  file_records * file = read_next_file (format) ;
  if (file == NULL)
    {
      if (cc == next_file_argument)
	return NULL ;
      else serious_error (ARG_TYPE_STRING, "Failed to open input", e_argv[cc]) ;
      return NULL;
    }
  else return file ;

}

file_records * read_next_file_and_check(format)
{
  int cc = next_file_argument ;
  file_records * file = read_next_file (format) ;
  if (file == NULL)
    serious_error (ARG_TYPE_STRING, "Failed to open input", 
		        (cc == next_file_argument) ? "No argument" :e_argv[cc]) ;
  return file ;
}

file_records *read_all_files (int format)
{
  file_records *file1 = read_next_file (format) ;
  file_records * file2 ; 

  if (file1 == NULL) return NULL ;
  
  while ((file2 =  read_next_file (format)) != NULL)
    file1 = merge_files_and_purge(file1 ,file2) ;
  
  return file1 ;
}


char * command_line_arg( char *cc)
{
  return d_getopt( cc, 1) ;
}

int  command_line_option( char *cc)
{
  return d_getopt(  cc, 0) == NULL ? 0 : 1 ;
}


double double_from_option(char * string, double the_default)    
{
  char * a = command_line_arg(string);
  if (a == NULL) 
    return the_default ;
  else 
    return atof(a) ;
}