Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 1 | /* |
| 2 | Redistribution and use in source and binary forms, with or without |
| 3 | modification, are permitted provided that the following conditions are met: |
| 4 | |
| 5 | * Redistributions of source code must retain the above copyright |
| 6 | notice, this list of conditions and the following disclaimer. |
| 7 | |
| 8 | * Redistributions in binary form must reproduce the above copyright |
| 9 | notice, this list of conditions and the following disclaimer in the |
| 10 | documentation and/or other materials provided with the distribution. |
| 11 | |
| 12 | * Neither the name of "The Computer Language Benchmarks Game" nor the |
| 13 | name of "The Computer Language Shootout Benchmarks" nor the names of |
| 14 | its contributors may be used to endorse or promote products derived |
| 15 | from this software without specific prior written permission. |
| 16 | |
| 17 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" |
| 18 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE |
| 19 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE |
| 20 | ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE |
| 21 | LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR |
| 22 | CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF |
| 23 | SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS |
| 24 | INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN |
| 25 | CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) |
| 26 | ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE |
| 27 | POSSIBILITY OF SUCH DAMAGE. |
| 28 | */ |
| 29 | |
| 30 | /* |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 31 | * http://shootout.alioth.debian.org/u32/program.php?test=fasta&lang=gcc&id=3 |
| 32 | */ |
| 33 | |
| 34 | /* The Computer Language Benchmarks Game |
| 35 | * http://shootout.alioth.debian.org/ |
| 36 | * |
| 37 | * contributed by Petr Prokhorenkov |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 38 | */ |
| 39 | |
| 40 | #include <stdio.h> |
| 41 | #include <stdlib.h> |
| 42 | #include <string.h> |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 43 | |
Rob Pike | f57f8b6 | 2010-10-20 17:43:57 -0700 | [diff] [blame] | 44 | #ifndef fwrite_unlocked |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 45 | // not available on OS X |
| 46 | #define fwrite_unlocked fwrite |
| 47 | #define fputc_unlocked fputc |
| 48 | #define fputs_unlocked fputs |
Rob Pike | f57f8b6 | 2010-10-20 17:43:57 -0700 | [diff] [blame] | 49 | #endif |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 50 | |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 51 | #define ARRAY_SIZE(a) (sizeof(a)/sizeof(a[0])) |
| 52 | #define unlikely(x) __builtin_expect((x), 0) |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 53 | |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 54 | #define IM 139968 |
| 55 | #define IA 3877 |
| 56 | #define IC 29573 |
| 57 | |
| 58 | #define LINE_LEN 60 |
| 59 | #define LOOKUP_SIZE 4096 |
| 60 | #define LOOKUP_SCALE ((float)(LOOKUP_SIZE - 1)) |
| 61 | |
| 62 | typedef unsigned random_t; |
| 63 | |
| 64 | void |
| 65 | random_init(random_t *random) { |
| 66 | *random = 42; |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 67 | } |
| 68 | |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 69 | // Special version with result rescaled to LOOKUP_SCALE. |
| 70 | static inline |
| 71 | float |
| 72 | random_next_lookup(random_t *random) { |
| 73 | *random = (*random*IA + IC)%IM; |
| 74 | |
| 75 | return (*random)*(LOOKUP_SCALE/IM); |
| 76 | } |
| 77 | |
| 78 | struct amino_acid { |
| 79 | char sym; |
| 80 | float prob; |
| 81 | float cprob_lookup; |
| 82 | }; |
| 83 | |
| 84 | void |
| 85 | repeat(const char *alu, const char *title, int n) { |
| 86 | int len = strlen(alu); |
| 87 | char buffer[len + LINE_LEN]; |
| 88 | int pos = 0; |
| 89 | |
| 90 | memcpy(buffer, alu, len); |
| 91 | memcpy(buffer + len, alu, LINE_LEN); |
| 92 | |
| 93 | fputs_unlocked(title, stdout); |
| 94 | while (n > 0) { |
| 95 | int bytes = n > LINE_LEN ? LINE_LEN : n; |
| 96 | |
| 97 | fwrite_unlocked(buffer + pos, bytes, 1, stdout); |
| 98 | pos += bytes; |
| 99 | if (pos > len) { |
| 100 | pos -= len; |
| 101 | } |
| 102 | fputc_unlocked('\n', stdout); |
| 103 | n -= bytes; |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 104 | } |
| 105 | } |
| 106 | |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 107 | /* |
| 108 | * Lookup table contains mapping from real values to cumulative |
| 109 | * probabilities. Careful selection of table size allows lookup |
| 110 | * virtually in constant time. |
| 111 | * |
| 112 | * All cumulative probabilities are rescaled to LOOKUP_SCALE, |
| 113 | * this allows to save one multiplication operation on each iteration |
| 114 | * in randomize(). |
| 115 | */ |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 116 | |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 117 | void * |
| 118 | fill_lookup(struct amino_acid **lookup, struct amino_acid *amino_acid, int amino_acid_size) { |
| 119 | float p = 0; |
| 120 | int i, j; |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 121 | |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 122 | for (i = 0; i < amino_acid_size; i++) { |
| 123 | p += amino_acid[i].prob; |
| 124 | amino_acid[i].cprob_lookup = p*LOOKUP_SCALE; |
| 125 | } |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 126 | |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 127 | // Prevent rounding error. |
| 128 | amino_acid[amino_acid_size - 1].cprob_lookup = LOOKUP_SIZE - 1; |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 129 | |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 130 | for (i = 0, j = 0; i < LOOKUP_SIZE; i++) { |
| 131 | while (amino_acid[j].cprob_lookup < i) { |
| 132 | j++; |
| 133 | } |
| 134 | lookup[i] = &amino_acid[j]; |
| 135 | } |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 136 | |
Rob Pike | 9155bb3 | 2009-08-03 21:03:58 -0700 | [diff] [blame] | 137 | return 0; |
| 138 | } |
Russ Cox | f8f83e8 | 2010-05-03 17:47:59 -0700 | [diff] [blame] | 139 | |
| 140 | void |
| 141 | randomize(struct amino_acid *amino_acid, int amino_acid_size, |
| 142 | const char *title, int n, random_t *rand) { |
| 143 | struct amino_acid *lookup[LOOKUP_SIZE]; |
| 144 | char line_buffer[LINE_LEN + 1]; |
| 145 | int i, j; |
| 146 | |
| 147 | line_buffer[LINE_LEN] = '\n'; |
| 148 | |
| 149 | fill_lookup(lookup, amino_acid, amino_acid_size); |
| 150 | |
| 151 | fputs_unlocked(title, stdout); |
| 152 | |
| 153 | for (i = 0, j = 0; i < n; i++, j++) { |
| 154 | if (j == LINE_LEN) { |
| 155 | fwrite_unlocked(line_buffer, LINE_LEN + 1, 1, stdout); |
| 156 | j = 0; |
| 157 | } |
| 158 | |
| 159 | float r = random_next_lookup(rand); |
| 160 | struct amino_acid *u = lookup[(short)r]; |
| 161 | while (unlikely(u->cprob_lookup < r)) { |
| 162 | ++u; |
| 163 | } |
| 164 | line_buffer[j] = u->sym; |
| 165 | } |
| 166 | line_buffer[j] = '\n'; |
| 167 | fwrite_unlocked(line_buffer, j + 1, 1, stdout); |
| 168 | } |
| 169 | |
| 170 | struct amino_acid amino_acid[] = { |
| 171 | { 'a', 0.27 }, |
| 172 | { 'c', 0.12 }, |
| 173 | { 'g', 0.12 }, |
| 174 | { 't', 0.27 }, |
| 175 | |
| 176 | { 'B', 0.02 }, |
| 177 | { 'D', 0.02 }, |
| 178 | { 'H', 0.02 }, |
| 179 | { 'K', 0.02 }, |
| 180 | { 'M', 0.02 }, |
| 181 | { 'N', 0.02 }, |
| 182 | { 'R', 0.02 }, |
| 183 | { 'S', 0.02 }, |
| 184 | { 'V', 0.02 }, |
| 185 | { 'W', 0.02 }, |
| 186 | { 'Y', 0.02 }, |
| 187 | }; |
| 188 | |
| 189 | struct amino_acid homo_sapiens[] = { |
| 190 | { 'a', 0.3029549426680 }, |
| 191 | { 'c', 0.1979883004921 }, |
| 192 | { 'g', 0.1975473066391 }, |
| 193 | { 't', 0.3015094502008 }, |
| 194 | }; |
| 195 | |
| 196 | static const char alu[] = |
| 197 | "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTG" |
| 198 | "GGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGA" |
| 199 | "GACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAA" |
| 200 | "AATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAAT" |
| 201 | "CCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAAC" |
| 202 | "CCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTG" |
| 203 | "CACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"; |
| 204 | |
| 205 | int |
| 206 | main(int argc, const char **argv) { |
| 207 | int n = argc > 1 ? atoi( argv[1] ) : 512; |
| 208 | random_t rand; |
| 209 | |
| 210 | random_init(&rand); |
| 211 | |
| 212 | repeat(alu, ">ONE Homo sapiens alu\n", n*2); |
| 213 | randomize(amino_acid, ARRAY_SIZE(amino_acid), |
| 214 | ">TWO IUB ambiguity codes\n", n*3, &rand); |
| 215 | randomize(homo_sapiens, ARRAY_SIZE(homo_sapiens), |
| 216 | ">THREE Homo sapiens frequency\n", n*5, &rand); |
| 217 | |
| 218 | return 0; |
Rob Pike | f57f8b6 | 2010-10-20 17:43:57 -0700 | [diff] [blame] | 219 | } |