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https://github.com/golang/go
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regex-dna
R=rsc DELTA=243 (242 added, 0 deleted, 1 changed) OCL=32786 CL=32791
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154
test/bench/regex-dna.c
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154
test/bench/regex-dna.c
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/*
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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* Neither the name of "The Computer Language Benchmarks Game" nor the
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name of "The Computer Language Shootout Benchmarks" nor the names of
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its contributors may be used to endorse or promote products derived
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from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
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LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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POSSIBILITY OF SUCH DAMAGE.
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*/
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/*
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** The Computer Language Shootout
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** http://shootout.alioth.debian.org/
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** contributed by Mike Pall
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**
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** regex-dna benchmark using PCRE
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**
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** compile with:
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** gcc -O3 -fomit-frame-pointer -o regexdna regexdna.c -lpcre
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*/
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#define __USE_STRING_INLINES
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#include <stdio.h>
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#include <string.h>
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#include <stdlib.h>
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#include <pcre.h>
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typedef struct fbuf {
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char *buf;
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size_t size, len;
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} fbuf_t;
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static void fb_init(fbuf_t *b)
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{
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b->buf = NULL;
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b->len = b->size = 0;
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}
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static char *fb_need(fbuf_t *b, size_t need)
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{
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need += b->len;
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if (need > b->size) {
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if (b->size == 0) b->size = need;
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else while (need > b->size) b->size += b->size;
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if (!(b->buf = realloc(b->buf, b->size))) exit(1);
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}
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return b->buf+b->len;
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}
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#define FB_MINREAD (3<<16)
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/* Read all of a stdio stream into dst buffer. */
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static size_t fb_readall(fbuf_t *dst, FILE *fp)
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{
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char *dp;
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int n;
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for (dp = fb_need(dst, FB_MINREAD);
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(n = fread(dp, 1, dst->size-dst->len, fp)) > 0;
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dp = fb_need(dst, FB_MINREAD)) dst->len += n;
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if (ferror(fp)) exit(1);
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return dst->len;
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}
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/* Substitute pattern p with replacement r, copying from src to dst buffer. */
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static size_t fb_subst(fbuf_t *dst, fbuf_t *src, const char *p, const char *r)
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{
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pcre *re;
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pcre_extra *re_ex;
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const char *re_e;
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char *dp;
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int re_eo, m[3], pos, rlen, clen;
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if (!(re = pcre_compile(p, PCRE_CASELESS, &re_e, &re_eo, NULL))) exit(1);
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re_ex = pcre_study(re, 0, &re_e);
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for (dst->len = 0, rlen = strlen(r), pos = 0;
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pcre_exec(re, re_ex, src->buf, src->len, pos, 0, m, 3) >= 0;
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pos = m[1]) {
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clen = m[0]-pos;
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dp = fb_need(dst, clen+rlen);
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dst->len += clen+rlen;
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memcpy(dp, src->buf+pos, clen);
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memcpy(dp+clen, r, rlen);
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}
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clen = src->len-pos;
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dp = fb_need(dst, clen);
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dst->len += clen;
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memcpy(dp, src->buf+pos, clen);
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return dst->len;
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}
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/* Count all matches with pattern p in src buffer. */
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static int fb_countmatches(fbuf_t *src, const char *p)
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{
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pcre *re;
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pcre_extra *re_ex;
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const char *re_e;
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int re_eo, m[3], pos, count;
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if (!(re = pcre_compile(p, PCRE_CASELESS, &re_e, &re_eo, NULL))) exit(1);
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re_ex = pcre_study(re, 0, &re_e);
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for (count = 0, pos = 0;
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pcre_exec(re, re_ex, src->buf, src->len, pos, 0, m, 3) >= 0;
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pos = m[1]) count++;
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return count;
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}
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static const char *variants[] = {
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"agggtaaa|tttaccct", "[cgt]gggtaaa|tttaccc[acg]",
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"a[act]ggtaaa|tttacc[agt]t", "ag[act]gtaaa|tttac[agt]ct",
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"agg[act]taaa|ttta[agt]cct", "aggg[acg]aaa|ttt[cgt]ccct",
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"agggt[cgt]aa|tt[acg]accct", "agggta[cgt]a|t[acg]taccct",
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"agggtaa[cgt]|[acg]ttaccct", NULL
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};
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static const char *subst[] = {
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"B", "(c|g|t)", "D", "(a|g|t)", "H", "(a|c|t)", "K", "(g|t)",
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"M", "(a|c)", "N", "(a|c|g|t)", "R", "(a|g)", "S", "(c|g)",
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"V", "(a|c|g)", "W", "(a|t)", "Y", "(c|t)", NULL
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};
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int main(int argc, char **argv)
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{
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fbuf_t seq[2];
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const char **pp;
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size_t ilen, clen, slen;
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int flip;
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fb_init(&seq[0]);
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fb_init(&seq[1]);
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ilen = fb_readall(&seq[0], stdin);
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clen = fb_subst(&seq[1], &seq[0], ">.*|\n", "");
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for (pp = variants; *pp; pp++)
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printf("%s %d\n", *pp, fb_countmatches(&seq[1], *pp));
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for (slen = 0, flip = 1, pp = subst; *pp; pp += 2, flip = 1-flip)
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slen = fb_subst(&seq[1-flip], &seq[flip], *pp, pp[1]);
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printf("\n%zu\n%zu\n%zu\n", ilen, clen, slen);
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return 0;
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}
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117
test/bench/regex-dna.go
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117
test/bench/regex-dna.go
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@ -0,0 +1,117 @@
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/*
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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* Neither the name of "The Computer Language Benchmarks Game" nor the
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name of "The Computer Language Shootout Benchmarks" nor the names of
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its contributors may be used to endorse or promote products derived
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from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
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LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
|
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CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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POSSIBILITY OF SUCH DAMAGE.
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*/
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/* The Computer Language Benchmarks Game
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* http://shootout.alioth.debian.org/
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*
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* contributed by The Go Authors.
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*/
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package main
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import (
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"fmt";
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"io";
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"os";
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"regexp";
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)
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func compile(s string) *regexp.Regexp {
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r, err := regexp.Compile(s);
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if err != nil {
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fmt.Fprintf(os.Stderr, "can't compile pattern %q: %s\n", s, err);
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os.Exit(2);
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}
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return r;
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}
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var variants = []string {
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"agggtaaa|tttaccct",
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"[cgt]gggtaaa|tttaccc[acg]",
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"a[act]ggtaaa|tttacc[agt]t",
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"ag[act]gtaaa|tttac[agt]ct",
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"agg[act]taaa|ttta[agt]cct",
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"aggg[acg]aaa|ttt[cgt]ccct",
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"agggt[cgt]aa|tt[acg]accct",
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"agggta[cgt]a|t[acg]taccct",
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"agggtaa[cgt]|[acg]ttaccct",
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}
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type Subst struct {
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pat, repl string
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}
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var substs = [] Subst {
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Subst {"B", "(c|g|t)"},
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Subst {"D", "(a|g|t)"},
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Subst {"H", "(a|c|t)"},
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Subst {"K", "(g|t)"},
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Subst {"M", "(a|c)"},
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Subst {"N", "(a|c|g|t)"},
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Subst {"R", "(a|g)"},
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Subst {"S", "(c|g)"},
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Subst {"V", "(a|c|g)"},
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Subst {"W", "(a|t)"},
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Subst {"Y", "(c|t)"},
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}
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func countMatches(pat, str string) int {
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re := compile(pat);
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n := 0;
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pos := 0;
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for {
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e := re.Execute(str);
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if len(e) == 0 {
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break;
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}
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n++;
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str = str[e[1]:len(str)];
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}
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return n;
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}
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func main() {
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bytes, err := io.ReadFile("/dev/stdin");
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if err != nil {
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fmt.Fprintf(os.Stderr, "can't read input: %s\n", err);
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os.Exit(2);
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}
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str := string(bytes);
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ilen := len(str);
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// Delete the comment lines and newlines
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str = compile("(>[^\n]+)?\n").ReplaceAll(str, "");
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clen := len(str);
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for i, s := range variants {
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fmt.Printf("%s %d\n", s, countMatches(s, str));
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}
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for i, sub := range substs {
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str = compile(sub.pat).ReplaceAll(str, sub.repl);
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}
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fmt.Printf("\n%d\n%d\n%d\n", ilen, clen, len(str));
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}
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13
test/bench/regex-dna.txt
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13
test/bench/regex-dna.txt
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agggtaaa|tttaccct 0
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[cgt]gggtaaa|tttaccc[acg] 3
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a[act]ggtaaa|tttacc[agt]t 9
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ag[act]gtaaa|tttac[agt]ct 8
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agg[act]taaa|ttta[agt]cct 10
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aggg[acg]aaa|ttt[cgt]ccct 3
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agggt[cgt]aa|tt[acg]accct 4
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agggta[cgt]a|t[acg]taccct 3
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agggtaa[cgt]|[acg]ttaccct 5
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101745
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100000
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133640
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@ -53,3 +53,8 @@ fannkuch 12
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gccgo -O2 fannkuch.go 64.89u 0.00s 64.92r
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gc fannkuch 124.59u 0.00s 124.67r
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gc_B fannkuch 91.14u 0.00s 91.16r
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regex-dna 100000
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gcc -O2 regex-dna.c -lpcre 0.92u 0.00s 0.99r
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gc regexp-dna 26.94u 0.18s 28.75r
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gc_B regexp-dna 26.51u 0.09s 26.75r
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@ -65,9 +65,20 @@ fannkuch() {
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run 'gc_B fannkuch' $O.out -n 12
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}
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regexdna() {
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gcc -O2 fasta.c
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a.out 100000 > x
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echo 'regex-dna 100000'
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run 'gcc -O2 regex-dna.c -lpcre' a.out <x
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# run 'gccgo -O2 regex-dna.go' a.out <x # pages badly; don't run
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run 'gc regex-dna' $O.out <x
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run 'gc_B regex-dna' $O.out <x
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rm x
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}
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case $# in
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0)
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run="fasta revcom nbody binarytree fannkuch"
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run="fasta revcom nbody binarytree fannkuch regexdna"
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;;
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*)
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run=$*
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