1// +build ignore
2
3/*
4Redistribution and use in source and binary forms, with or without
5modification, are permitted provided that the following conditions are met:
6
7 * Redistributions of source code must retain the above copyright
8 notice, this list of conditions and the following disclaimer.
9
10 * Redistributions in binary form must reproduce the above copyright
11 notice, this list of conditions and the following disclaimer in the
12 documentation and/or other materials provided with the distribution.
13
14 * Neither the name of "The Computer Language Benchmarks Game" nor the
15 name of "The Computer Language Shootout Benchmarks" nor the names of
16 its contributors may be used to endorse or promote products derived
17 from this software without specific prior written permission.
18
19THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
20AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
23LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
24CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
25SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
26INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
27CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
28ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
29POSSIBILITY OF SUCH DAMAGE.
30*/
31
32/*
33** The Computer Language Shootout
34** http://shootout.alioth.debian.org/
35** contributed by Mike Pall
36**
37** regex-dna benchmark using PCRE
38**
39** compile with:
40** gcc -O3 -fomit-frame-pointer -o regexdna regexdna.c -lpcre
41*/
42
43#define __USE_STRING_INLINES
44#include <stdio.h>
45#include <string.h>
46#include <stdlib.h>
47#include <pcre.h>
48
49typedef struct fbuf {
50 char *buf;
51 size_t size, len;
52} fbuf_t;
53
54static void fb_init(fbuf_t *b)
55{
56 b->buf = NULL;
57 b->len = b->size = 0;
58}
59
60static char *fb_need(fbuf_t *b, size_t need)
61{
62 need += b->len;
63 if (need > b->size) {
64 if (b->size == 0) b->size = need;
65 else while (need > b->size) b->size += b->size;
66 if (!(b->buf = realloc(b->buf, b->size))) exit(1);
67 }
68 return b->buf+b->len;
69}
70
71#define FB_MINREAD (3<<16)
72
73/* Read all of a stdio stream into dst buffer. */
74static size_t fb_readall(fbuf_t *dst, FILE *fp)
75{
76 char *dp;
77 int n;
78 for (dp = fb_need(dst, FB_MINREAD);
79 (n = fread(dp, 1, dst->size-dst->len, fp)) > 0;
80 dp = fb_need(dst, FB_MINREAD)) dst->len += n;
81 if (ferror(fp)) exit(1);
82 return dst->len;
83}
84
85/* Substitute pattern p with replacement r, copying from src to dst buffer. */
86static size_t fb_subst(fbuf_t *dst, fbuf_t *src, const char *p, const char *r)
87{
88 pcre *re;
89 pcre_extra *re_ex;
90 const char *re_e;
91 char *dp;
92 int re_eo, m[3], pos, rlen, clen;
93 if (!(re = pcre_compile(p, PCRE_CASELESS, &re_e, &re_eo, NULL))) exit(1);
94 re_ex = pcre_study(re, 0, &re_e);
95 for (dst->len = 0, rlen = strlen(r), pos = 0;
96 pcre_exec(re, re_ex, src->buf, src->len, pos, 0, m, 3) >= 0;
97 pos = m[1]) {
98 clen = m[0]-pos;
99 dp = fb_need(dst, clen+rlen);
100 dst->len += clen+rlen;
101 memcpy(dp, src->buf+pos, clen);
102 memcpy(dp+clen, r, rlen);
103 }
104 clen = src->len-pos;
105 dp = fb_need(dst, clen);
106 dst->len += clen;
107 memcpy(dp, src->buf+pos, clen);
108 return dst->len;
109}
110
111/* Count all matches with pattern p in src buffer. */
112static int fb_countmatches(fbuf_t *src, const char *p)
113{
114 pcre *re;
115 pcre_extra *re_ex;
116 const char *re_e;
117 int re_eo, m[3], pos, count;
118 if (!(re = pcre_compile(p, PCRE_CASELESS, &re_e, &re_eo, NULL))) exit(1);
119 re_ex = pcre_study(re, 0, &re_e);
120 for (count = 0, pos = 0;
121 pcre_exec(re, re_ex, src->buf, src->len, pos, 0, m, 3) >= 0;
122 pos = m[1]) count++;
123 return count;
124}
125
126static const char *variants[] = {
127 "agggtaaa|tttaccct", "[cgt]gggtaaa|tttaccc[acg]",
128 "a[act]ggtaaa|tttacc[agt]t", "ag[act]gtaaa|tttac[agt]ct",
129 "agg[act]taaa|ttta[agt]cct", "aggg[acg]aaa|ttt[cgt]ccct",
130 "agggt[cgt]aa|tt[acg]accct", "agggta[cgt]a|t[acg]taccct",
131 "agggtaa[cgt]|[acg]ttaccct", NULL
132};
133
134static const char *subst[] = {
135 "B", "(c|g|t)", "D", "(a|g|t)", "H", "(a|c|t)", "K", "(g|t)",
136 "M", "(a|c)", "N", "(a|c|g|t)", "R", "(a|g)", "S", "(c|g)",
137 "V", "(a|c|g)", "W", "(a|t)", "Y", "(c|t)", NULL
138};
139
140int main(int argc, char **argv)
141{
142 fbuf_t seq[2];
143 const char **pp;
144 size_t ilen, clen, slen;
145 int flip;
146 fb_init(&seq[0]);
147 fb_init(&seq[1]);
148 ilen = fb_readall(&seq[0], stdin);
149 clen = fb_subst(&seq[1], &seq[0], ">.*|\n", "");
150 for (pp = variants; *pp; pp++)
151 printf("%s %d\n", *pp, fb_countmatches(&seq[1], *pp));
152 for (slen = 0, flip = 1, pp = subst; *pp; pp += 2, flip = 1-flip)
153 slen = fb_subst(&seq[1-flip], &seq[flip], *pp, pp[1]);
154 printf("\n%zu\n%zu\n%zu\n", ilen, clen, slen);
155 return 0;
156}
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