#include <begin.h>

int numdna[1000000], thestring[1000];
char finalstring[1000];

int translation()
{
  char dna[1000000], filename[100];
  FILE *fp;
  int i=0;

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

  fp=fopen(filename, "r");
  if (fp == NULL) {printf("Can't open file\n"); exit(1);}
  fscanf(fp, "%s", dna);
  while ((dna[i]) =='g' || (dna[i]) =='a' || (dna[i]) =='c' || (dna[i]) =='t')
    { 
      if((dna[i])=='a') { numdna[i]=1;}
      else if((dna[i])=='c') { numdna[i]=2;}
      else if((dna[i])=='g') { numdna[i]=3;}
      else { numdna[i]=4;}
      i++;
    }
  return i;
}

void decode()
{
  int i=0;
  while (thestring[i]>0 && thestring[i]<5)
    { 
      if(thestring[i]==1) { finalstring[i]='a';}
      else if(thestring[i]==2) { finalstring[i]='c';}
      else if(thestring[i]==3) { finalstring[i]='g';}
      else { finalstring[i]='t';}
      i++;
    }
}

int main()
{
  int length, substringlength, substring[1000], i, j, k, count, true, match, high=0;

  printf("Enter the length of substring\n");
  scanf("%d", &substringlength);

  length=translation();
  printf("the number is %d - %d = %d\n",length, substringlength, length-substringlength);
  for (count=0; count < length-substringlength; count++)
    {
      printf("in the first loop for the %ds time\n",count);
      for (i=count; i < count+substringlength; i++)
	{
	  substring[i-count]=numdna[i];
	}
      match=0;

 
      for (j=count+1; j <= length-substringlength; j++)
	{
	  k=j;
	  true=0;
	  while (k < j+substringlength)
	    {
	      if (numdna[k] == substring[k-j]) {true++;}
	      k++;
	    }
	  if (true == substringlength) {match++;}
	}
      if (match > high)
	{
	  high=match;
	  for(k=0; k < substringlength; k++)
	    {
	      thestring[k]=substring[k];
	    }
	}
    }

  decode();

  printf("the substring that appeared the most is %s, it appeared %d times\n",finalstring, high+1);
}