Executable Code

/* These numbers are designed so base k always pairs with base (k+2)%4.
   The order corresponds to that in bases.h.
 */
 
char *base_names = "ACTG";
 
/* Given a string including ACTG's, turn it into an array of up to n
ints 0-3 in the given place. */
 
void read_bases (s, n, out, nout)
     char *s;
     int n;
     int *out;
     int *nout;
{
  int k=0;
  while (*s && k<n) {
    int i;
    for(i=0;i<4;i++){
      if (base_names[i] == *s) {
        out[k++] = i;
        break;
      }
    }
    s++;
  }
  *nout = k;
}
 
/* Print all the 1-letter codes for the bases in the given strand
   of length n. */
 
void print_bases (strand, n)
     int *strand;
     int n;
{
  int i;
  for(i=0;i<n;i++){
    putchar(base_names[strand[i]]);
  }
}
 
/* Print all the 1-letter codes for the bases in the given strand
   of length n. */
 
void print_reverse (strand, n)
     int *strand;
     int n;
{
  int i;
  for(i=n-1;i>=0;i--){
    putchar(base_names[strand[i]]);
  }
}
 
/* Reverse the order of bases in the given strand and write
   to the output strand. */
 
void reverse_strand (s_in, n, s_out)
     int *s_in;
     int n;
     int *s_out;
{
  int i;
  for(i=0;i<n;i++){
    s_out[n-1-i] = s_in[i];
  }
}