#include <begin.h>

typedef
struct {
  int x[1000000], length;
} String;

String dna[10];

void translate(int type)
{
  char original[1000000], filename[100];
  FILE *fp;
  int i=0;

  printf("Enter the location of the string\n");
  scanf("%s", filename);

  fp=fopen(filename, "r");
  if (fp == NULL) {printf("Can't open file\n"); exit(1);}
  fscanf(fp, "%s", original);

  while ((original[i]) =='g' || (original[i]) =='a' || (original[i]) =='c' || (original[i]) =='t')
    { 
      if((original[i])=='a') { dna[type].x[i]=1;}
      else if((original[i])=='c') { dna[type].x[i]=2;}
      else if((original[i])=='g') { dna[type].x[i]=3;}
      else {dna[type].x[i]=4;}
      i++;
    }
  dna[type].length=i;
}

int main()
{
  int i, j, true, match=0;

  printf("for the full dna string:\n");
  translate(0);

  printf("for the substring we are searching for:\n");
  translate(1);

  for(i=0; i < dna[0].length-dna[1].length; i++)
    {
      j=i;
      true=0;
      while (j < i+dna[1].length)
	{
	  if(dna[0].x[j] == dna[1].x[j-i]) {true++;}
	  j++;
	}
      if(true == dna[1].length) {match++;}
    }
  printf("this substring has appeared %d times\n\n",match);
}