#include "findpath.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "fold.h"
#include "fold_vars.h"
#include "utils.h"
#include <time.h>

typedef struct move {
  int i;  /* i,j>0 insert; i,j<0 delete */
  int j;
  int when;  /* 0 if still available, else resulting distance from start */
  int E;
} move_t;

int get_BP_dist(char *struc1, char *struc2);

int main(int argc, char *argv[]){
  char seq[1000], struc1[1000],struc2[1000];
  int maxkeep, dist, i;
  path_t *route;
  double myTime;

  if (argc!=5){
    printf("Usage: %s seq struc1 struc2 maxkeep\n", argv[0]);
    printf("\n\tProgram will then find potential low\n");
    printf("\tenergy path, changing one bp at a time,\n");
    printf("\tfrom struc1 to struc2, using findPath\n");
    printf("\talgorithm.\n");
    exit(1);
  }
  
  myTime=clock();
  maxkeep=10;
  strcpy(seq, argv[1]);
  strcpy(struc1, argv[2]);
  strcpy(struc2, argv[3]);
  maxkeep=atoi(argv[4]);
  route=get_path(seq, struc1, struc2, maxkeep);
  dist=get_BP_dist(struc1, struc2);
  for (i=0;i<dist+1;i++){
    printf("%d: %g %s\n", i, route[i].en, route[i].s);
  }
  myTime=clock()-myTime;
  // printf("time is %f\n", myTime/CLOCKS_PER_SEC);
  return 0;
}

int get_BP_dist(char *struc1, char *struc2) {
  short *pt1, *pt2;
  move_t *mlist;
  int i, len, dist=0;

  pt1 = make_pair_table(struc1);
  pt2 = make_pair_table(struc2);
  len = (int) strlen(struc1);

  mlist = (move_t *) space(sizeof(move_t)*len); /* bp_dist < n */

  for (i=1; i<=len; i++) {
    if (pt1[i] != pt2[i]) {
      if (i<pt1[i]) { /* need to delete this pair */
	mlist[dist].i = -i;
	mlist[dist].j = -pt1[i];
	mlist[dist++].when = 0;
      }
      if (i<pt2[i]) { /* need to insert this pair */
	mlist[dist].i = i;
	mlist[dist].j = pt2[i];
	mlist[dist++].when = 0;
      }
    }
  }
  free(pt1);
  free(pt2);
  free(mlist);
  return dist;//Modified to just get BP distance.
}