#include "sc.h"
#include <stdio.h>
#include "sc2seq.h"   /* This also includes scconst.h, sc.h, interface.h */
#include "options.h"
#include "scconst.h"
#include "switches.h"

extern int WINDOW;
extern double SCALE0;


void initialize( int *num_dist0, int window_length[MAX_TABLE_NUMBER],  double scale0s[MAX_TABLE_NUMBER], double scale0p[MAX_TABLE_NUMBER], FILE *fpin0, char likelihoods[MAX_TABLE_NUMBER][MAXLINE], char *pir_name0, char *print,   char gauss_param[2][MAXLINE], int *mode,double init_class_prob[MAX_CLASS_NUMBER])
{
  
  int i;

  *mode |= PROLINE_FREE_MODE;  /* Default mode is Proline Free. */
  *mode |= PAIRCOIL_PAIRS;     /*  Always default to pairs for PairCoil */

  *mode |= USE_LIKE_LINE;
  *mode |= WEB_OUT_MODE;       /* Make the out file by default be the  */
                               /* list of the seq and registers and probs */
                               /* instead of the raw list of tuples of    */
                               /* scores needed for plotting and making   */
                               /* gaussians.                              */

  *num_dist0=0;
  for (i=0; i< MAX_TABLE_NUMBER; i++) {
    window_length[i]=WINDOW;
    scale0s[i] = SCALE0;   /** Set to default **/
    scale0p[i] = SCALE0;
    likelihoods[i][0]=',';  /** A hack to check if get it in get_defaults */
  }
  fpin0=NULL;
  *pir_name0=',';        /** A hack to check if get it in get_defaults */

  strcpy(print,"/dev/null");   

  gauss_param[0][0]= ',';   /* Used as flag in multivariate_like.c. */
  gauss_param[1][0]= ',';
  
  init_class_prob[0] = .015;   /* Dimer probability*/
  init_class_prob[1] = .009;   /* Trimer probablity*/
  init_class_prob[2] = .976;   /*  Non-coiled prob. */
}


void read_command_line(int argc, char *argv[], char **command_line_pointer,
			     int combine_dist[MAX_TABLE_NUMBER],
			     int *mode,
			     int num_dist[MAX_TABLE_NUMBER],
		             char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
		             char **command_line_config)
{
  int number=0;
  int max_libnum;

  if (argc>2)
    if (!strcmp(argv[argc-2],CONFIG_SWITCH)) {
      *command_line_config = argv[argc-1];
      printf("got command config %s\n", argv[argc-1]);
      argc = argc-2;
    }

  if ((argc >= 3) && (argc <=5)) { 
                  /* Ignore pos options and removal options in config file */
    *command_line_pointer = argv[2];   
          /** This could point to the table to remove from. **/
    if (argc >= 4) {
      combine_dist[0]=1;
      combine_dist[1]=1;
      *mode |= LIB_AT_COMMAND_LINE;

      num_dist[0]=strlen(argv[3]);
      max_libnum = num_dist[0];

      if (argc ==5) {
	num_dist[1]=strlen(argv[4]);
	if (num_dist[1] > max_libnum) max_libnum = num_dist[1];
      }
      else num_dist[1]=num_dist[0];
       while (number < max_libnum) {
	if (num_dist[0] > number) {
	  multi_lib[0][number]= argv[3][number] - '0';
	}
	if (argc == 4) multi_lib[1][number] =multi_lib[0][number];
	else if (num_dist[1] > number) 
	  multi_lib[1][number]= argv[4][number]- '0'; 
	number++;
      }
      
    }
  }
  else if (argc != 2){
    /*    fprintf(stderr,"Usage: xcoil <file-name>\n"); */
    usage(argv[0]);
    exit(-1);
  }
}



int old_num_dim(int number_multi_lib, int number_of_distances) {
  
  if ( (number_multi_lib > 1) || (number_of_distances == 1))
    return(7);
  else return(1);
}