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Diffstat (limited to 'gcc/testsuite/go.test/test/bench/regex-dna.c')
| -rw-r--r-- | gcc/testsuite/go.test/test/bench/regex-dna.c | 154 |
1 files changed, 154 insertions, 0 deletions
diff --git a/gcc/testsuite/go.test/test/bench/regex-dna.c b/gcc/testsuite/go.test/test/bench/regex-dna.c new file mode 100644 index 00000000000..134f8215c7f --- /dev/null +++ b/gcc/testsuite/go.test/test/bench/regex-dna.c @@ -0,0 +1,154 @@ +/* +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * 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 +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +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 Shootout +** http://shootout.alioth.debian.org/ +** contributed by Mike Pall +** +** regex-dna benchmark using PCRE +** +** compile with: +** gcc -O3 -fomit-frame-pointer -o regexdna regexdna.c -lpcre +*/ + +#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, PCRE_CASELESS, &re_e, &re_eo, NULL))) exit(1); + re_ex = pcre_study(re, 0, &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, PCRE_CASELESS, &re_e, &re_eo, NULL))) exit(1); + re_ex = pcre_study(re, 0, &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[] = { + "B", "(c|g|t)", "D", "(a|g|t)", "H", "(a|c|t)", "K", "(g|t)", + "M", "(a|c)", "N", "(a|c|g|t)", "R", "(a|g)", "S", "(c|g)", + "V", "(a|c|g)", "W", "(a|t)", "Y", "(c|t)", 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; +} |