source code
/* The Computer Language Benchmarks Game
* https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
**
** regex-dna program contributed by Mike Pall
** converted from regex-dna program by Jeremy Zerfas
**
*/
#define __USE_STRING_INLINES
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <pcre.h>
typedef struct fbuf {
char *buf;
size_t size, len;
} fbuf_t;
static void fb_init(fbuf_t *b)
{
b->buf = NULL;
b->len = b->size = 0;
}
static char *fb_need(fbuf_t *b, size_t need)
{
need += b->len;
if (need > b->size) {
if (b->size == 0) b->size = need;
else while (need > b->size) b->size += b->size;
if (!(b->buf = realloc(b->buf, b->size))) exit(1);
}
return b->buf+b->len;
}
#define FB_MINREAD (3<<16)
/* Read all of a stdio stream into dst buffer. */
static size_t fb_readall(fbuf_t *dst, FILE *fp)
{
char *dp;
int n;
for (dp = fb_need(dst, FB_MINREAD);
(n = fread(dp, 1, dst->size-dst->len, fp)) > 0;
dp = fb_need(dst, FB_MINREAD)) dst->len += n;
if (ferror(fp)) exit(1);
return dst->len;
}
/* Substitute pattern p with replacement r, copying from src to dst buffer. */
static size_t fb_subst(fbuf_t *dst, fbuf_t *src, const char *p, const char *r)
{
pcre *re;
pcre_extra *re_ex;
const char *re_e;
char *dp;
int re_eo, m[3], pos, rlen, clen;
if (!(re = pcre_compile(p, 0, &re_e, &re_eo, NULL))) exit(1);
re_ex = pcre_study(re, PCRE_STUDY_JIT_COMPILE, &re_e);
for (dst->len = 0, rlen = strlen(r), pos = 0;
pcre_exec(re, re_ex, src->buf, src->len, pos, 0, m, 3) >= 0;
pos = m[1]) {
clen = m[0]-pos;
dp = fb_need(dst, clen+rlen);
dst->len += clen+rlen;
memcpy(dp, src->buf+pos, clen);
memcpy(dp+clen, r, rlen);
}
clen = src->len-pos;
dp = fb_need(dst, clen);
dst->len += clen;
memcpy(dp, src->buf+pos, clen);
return dst->len;
}
/* Count all matches with pattern p in src buffer. */
static int fb_countmatches(fbuf_t *src, const char *p)
{
pcre *re;
pcre_extra *re_ex;
const char *re_e;
int re_eo, m[3], pos, count;
if (!(re = pcre_compile(p, 0, &re_e, &re_eo, NULL))) exit(1);
re_ex = pcre_study(re, PCRE_STUDY_JIT_COMPILE, &re_e);
for (count = 0, pos = 0;
pcre_exec(re, re_ex, src->buf, src->len, pos, 0, m, 3) >= 0;
pos = m[1]) count++;
return count;
}
static const char *variants[] = {
"agggtaaa|tttaccct", "[cgt]gggtaaa|tttaccc[acg]",
"a[act]ggtaaa|tttacc[agt]t", "ag[act]gtaaa|tttac[agt]ct",
"agg[act]taaa|ttta[agt]cct", "aggg[acg]aaa|ttt[cgt]ccct",
"agggt[cgt]aa|tt[acg]accct", "agggta[cgt]a|t[acg]taccct",
"agggtaa[cgt]|[acg]ttaccct", NULL
};
static const char *subst[] = {
"tHa[Nt]", "<4>",
"aND|caN|Ha[DS]|WaS", "<3>",
"a[NSt]|BY", "<2>",
"<[^>]*>", "|",
"\\|[^|][^|]*\\|", "-",
NULL
};
int main(int argc, char **argv)
{
fbuf_t seq[2];
const char **pp;
size_t ilen, clen, slen;
int flip;
fb_init(&seq[0]);
fb_init(&seq[1]);
ilen = fb_readall(&seq[0], stdin);
clen = fb_subst(&seq[1], &seq[0], ">.*|\n", "");
for (pp = variants; *pp; pp++)
printf("%s %d\n", *pp, fb_countmatches(&seq[1], *pp));
for (slen = 0, flip = 1, pp = subst; *pp; pp += 2, flip = 1-flip)
slen = fb_subst(&seq[1-flip], &seq[flip], *pp, pp[1]);
printf("\n%zu\n%zu\n%zu\n", ilen, clen, slen);
return 0;
}