test/bench/reverse-complement.c

/*
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    * Redistributions of source code must retain the above copyright
    notice, this list of conditions and the following disclaimer.

    * Redistributions in binary form must reproduce the above copyright
    notice, this list of conditions and the following disclaimer in the
    documentation and/or other materials provided with the distribution.

    * Neither the name of "The Computer Language Benchmarks Game" nor the
    name of "The Computer Language Shootout Benchmarks" nor the names of
    its contributors may be used to endorse or promote products derived
    from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/

/*
 * The Computer Language Benchmarks Game
 * http://shootout.alioth.debian.org
 *
 * contributed by Bob W
 */

#include <stdio.h>
#include <stdlib.h>

#define JBFSIZE 82      // line input buffer size
#define QBFSIZE 5200     // output buffer initial size
#define Z16     "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0"
#define V32     "\0TVGH\0\0CD\0\0M\0KN\0\0\0YSA\0BW\0R\0\0\0\0\0\0"
#define VALL    Z16 Z16 Z16 Z16 V32 V32 Z16 Z16 Z16 Z16 Z16 Z16 Z16 Z16

int errex(char *s, int n) {      // error message+value, return 1
  fprintf(stderr,"\n*** Error: %s [%d]!\n", s, n);
  return 1;
}

int main () {                    // ***** main *****
  char *pj, *pq, *pr;            // buffer pointers: inp,out,/out
  char *jjj = malloc(JBFSIZE);   // allocate input line buffer
  char *qqq = malloc(QBFSIZE);   // output buffer (dyn. size)
  char *pqstop = qqq+QBFSIZE;    // end-of-buffer pointer
  char xtab[256] = VALL;         // char conversion table

  if (!jjj || !qqq)
    return errex("Buffer allocation", !jjj + !qqq);
  pj = fgets(jjj,JBFSIZE,stdin);         // fetch 1st line
  if (!pj)
    return errex("No input data",0);
  if (*jjj != '>')
    return errex("1st char not '>'", 0);

  while (pj) {                           // MAIN LOOP: process data
    fputs(jjj, stdout);                  // output ID line

    for (pq=qqq+1, pr=pqstop; ; pq++) {  // LOOP: fill output buffer
      pj = fgets(jjj, JBFSIZE, stdin);   // get line from stdin
      if (!pj || (*jjj=='>'))  break;    // EOF or new ID line
      if (pr <= (pq+61)) {               // need to resize buffer
        char *newstop = pqstop + 12777888;
        char *newptr  = realloc(qqq, newstop-qqq);
        if (!newptr)
          return errex("Out of memory", 0);
        if (newptr != qqq) {             // new base: adj. pointers
          size_t x = newptr-qqq;         // offset for pointer update
          pq+=x;  pr+=x;  qqq+=x;
          newstop+=x;  pqstop+=x;
        }
        pr = __builtin_memmove(newstop-(pqstop-pr), pr, pqstop-pr);
        pqstop = newstop;                // buffer resize complete
      }
      while (*pj) {                      // LOOP: conv. & revert line
        char c = xtab[(unsigned char)(*pj++)];
        if (c)                           // conversion valid
          *(--pr) = c;
      }
    }

    for (pq = qqq; pr<pqstop; ) {        // LOOP: format output
      size_t x = (pqstop-pr)<60 ? pqstop-pr : 60;
      __builtin_memmove(pq,pr,x);        // move line to free space
      pr+=x;  pq+=x;  *(pq++) = 0xA;     // adjust pointers, add LF
    }
    fwrite(qqq, 1, pq-qqq, stdout);      // output converted data
  }
  return 0;
}