/* Converts a fasta file into a compressed code for DNA.
 * Note that the output is not printable.
 */

/* Copyright (c) 1999 Blossom Associates West */
/* All rights reserved.                       */

#include <stdio.h>

/* BUG: invalid codes become 'A' */
void putResidue( int r ) {
  static unsigned char b;
  unsigned char b1;
  char c;
  static int p = 0;

  c = toupper( r );
  switch ( c ) {
  case 'A': b1 = 0; break;
  case 'C': b1 = 1; break;
  case 'G': b1 = 2; break;
  case 'T': case 'U': b1 = 3; break;
  case '<': /* end of input */
    if ( 0 < p ) {
      printf( "%x) ", b );
    }
    return;
  default: return;
  }
  b1 = b1 << p;
  b |= b1;
  p += 2;
  p %= 8;
printf( "p%d ", p );
  putchar( '.' );
  printf( "%x ", b );
  if ( 0 == p ) {
    printf( "(%x) ", b );
    b = 0;
  }
}

int main( int argc, char* argv[] ) {

  int c;
  enum { BOL, HEAD, SEQ };
  int state = BOL;

  printf( "hello\n" );

  while ( EOF != ( c = getchar() ) ) {
    switch ( state ) {
    case SEQ:
      putResidue( c );
      break;
    case BOL:
      if ( '>' == c  || ';' == c ) {
        state = HEAD;
        putchar( c );
      }
      else {
        state = SEQ;
        putResidue( c );
      }
      break;
    case HEAD:
      putchar( c );
      if ( '\n' == c ) {
        state = BOL;
      }
      break;
    }
  }

}