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https://github.com/golang/go
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k-nucleotide
R=rsc DELTA=367 (366 added, 0 deleted, 1 changed) OCL=32832 CL=32836
This commit is contained in:
Rob Pike
parent
5876cb0e63
commit
ae3939cb78
228
test/bench/k-nucleotide.c
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228
test/bench/k-nucleotide.c
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@ -0,0 +1,228 @@
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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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#include <stdio.h>
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#include <string.h>
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#include <ctype.h>
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#include <stdlib.h>
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#include <glib.h>
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typedef struct stat_s stat_t;
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struct stat_s
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{
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const gchar *key;
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long stat;
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};
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#define MAX_ELM (8192 / sizeof (stat_t))
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static int
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generate_frequencies (int fl, char *buffer, long buflen,
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GHashTable *ht, GTrashStack **ts, GPtrArray *roots, GStringChunk *sc)
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{
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gchar *key;
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long i;
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if (fl > buflen) return 0;
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if (fl == 0) return 0;
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for (i = 0; i < buflen - fl + 1; ++i)
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{
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char nulled;
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stat_t *stat;
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nulled = buffer[i + fl];
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buffer[i + fl] = '\0';
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key = g_string_chunk_insert_const(sc, buffer + i);
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stat = g_hash_table_lookup(ht, key);
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if (!stat)
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{
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stat = g_trash_stack_pop(ts);
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if (!stat)
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{
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int j;
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stat = malloc(sizeof (stat_t) * MAX_ELM);
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g_ptr_array_add(roots, stat);
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for (j = 1; j < MAX_ELM; ++j)
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g_trash_stack_push(ts, stat + j);
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}
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stat->stat = 1;
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stat->key = key;
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g_hash_table_insert(ht, key, stat);
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}
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else
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stat->stat++;
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buffer[i + fl] = nulled;
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}
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return buflen - fl + 1;
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}
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static int
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cmp_func(gconstpointer a, gconstpointer b)
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{
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const stat_t *left = a;
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const stat_t *right = b;
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return right->stat - left->stat;
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}
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static void
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sorted_list(gpointer key, gpointer value, gpointer user_data)
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{
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stat_t *data = value;
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GList **lst = user_data;
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*lst = g_list_insert_sorted(*lst, data, cmp_func);
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}
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static void
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display_stat(gpointer data, gpointer user_data)
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{
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long *total = user_data;
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stat_t *st = data;
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printf("%s %.3f\n", st->key, 100 * (float) st->stat / *total);
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}
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void
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write_frequencies (int fl, char *buffer, long buflen, GTrashStack **ts, GPtrArray *roots)
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{
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GStringChunk *sc;
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GHashTable *ht;
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GList *lst;
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long total;
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ht = g_hash_table_new_full(g_str_hash, g_str_equal, NULL /* free key */, NULL /* free value */);
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sc = g_string_chunk_new(buflen);
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lst = NULL;
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total = generate_frequencies (fl, buffer, buflen, ht, ts, roots, sc);
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if (!total) goto on_error;
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g_hash_table_foreach(ht, sorted_list, &lst);
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g_list_foreach(lst, display_stat, &total);
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g_list_free(lst);
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on_error:
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g_hash_table_destroy(ht);
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g_string_chunk_free(sc);
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}
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void
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write_count (char *searchFor, char *buffer, long buflen, GTrashStack **ts, GPtrArray *roots)
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{
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GStringChunk *sc;
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GHashTable *ht;
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stat_t *result;
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GList *lst;
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long total;
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long fl;
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fl = strlen(searchFor);
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ht = g_hash_table_new_full(g_str_hash, g_str_equal, NULL /* free key */, NULL /* free value */);
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sc = g_string_chunk_new(buflen);
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lst = NULL;
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result = NULL;
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total = generate_frequencies (fl, buffer, buflen, ht, ts, roots, sc);
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if (!total) goto on_error;
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result = g_hash_table_lookup(ht, searchFor);
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on_error:
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printf("%ld\t%s\n", result ? result->stat : 0, searchFor);
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g_hash_table_destroy(ht);
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g_string_chunk_free(sc);
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}
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int
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main ()
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{
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char buffer[4096];
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GTrashStack *ts;
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GPtrArray *roots;
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GString *stuff;
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gchar *s;
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int len;
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roots = g_ptr_array_new();
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ts = NULL;
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while (fgets(buffer, sizeof (buffer), stdin))
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if (strncmp(buffer, ">THREE", 6) == 0)
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break;
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stuff = g_string_new(NULL);
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while (fgets(buffer, sizeof (buffer), stdin))
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{
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size_t sz;
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if (buffer[0] == '>')
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break;
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sz = strlen(buffer);
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if (buffer[sz - 1] == '\n')
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--sz;
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stuff = g_string_append_len(stuff, buffer, sz);
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}
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stuff = g_string_ascii_up(stuff);
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len = stuff->len;
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s = g_string_free(stuff, FALSE);
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write_frequencies(1, s, len, &ts, roots);
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printf("\n");
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write_frequencies(2, s, len, &ts, roots);
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printf("\n");
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write_count("GGT", s, len, &ts, roots);
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write_count("GGTA", s, len, &ts, roots);
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write_count("GGTATT", s, len, &ts, roots);
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write_count("GGTATTTTAATT", s, len, &ts, roots);
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write_count("GGTATTTTAATTTATAGT", s, len, &ts, roots);
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free(s);
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g_ptr_array_foreach(roots, free, NULL);
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g_ptr_array_free(roots, TRUE);
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return 0;
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}
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151
test/bench/k-nucleotide.go
Normal file
151
test/bench/k-nucleotide.go
Normal file
@ -0,0 +1,151 @@
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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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"bufio";
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"bytes";
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"fmt";
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"io";
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"os";
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"sort";
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"strings";
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)
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var in *bufio.Reader
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func count(data string, n int) map[string] int {
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counts := make(map[string] int);
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top := len(data) - n;
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for i := 0; i <= top; i++ {
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s := data[i:i+n];
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if k, ok := counts[s]; ok {
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counts[s] = k+1
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} else {
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counts[s] = 1
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}
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}
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return counts
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}
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func countOne(data string, s string) int {
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counts := count(data, len(s));
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if i, ok := counts[s]; ok {
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return i
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}
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return 0
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}
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type kNuc struct {
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name string;
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count int;
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}
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type kNucArray []kNuc
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func (kn kNucArray) Len() int { return len(kn) }
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func (kn kNucArray) Swap(i, j int) { kn[i], kn[j] = kn[j], kn[i] }
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func (kn kNucArray) Less(i, j int) bool {
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if kn[i].count == kn[j].count {
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return kn[i].name > kn[j].name // sort down
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}
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return kn[i].count > kn[j].count
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}
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func sortedArray(m map[string] int) kNucArray {
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kn := make(kNucArray, len(m));
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i := 0;
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for k, v := range m {
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kn[i].name = k;
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kn[i].count = v;
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i++;
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}
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sort.Sort(kn);
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return kn;
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}
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func print(m map[string] int) {
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a := sortedArray(m);
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sum := 0;
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for _, kn := range a {
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sum += kn.count;
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}
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for _, kn := range a {
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fmt.Printf("%s %.3f\n", kn.name, 100*float64(kn.count)/float64(sum));
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}
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}
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func main() {
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in = bufio.NewReader(os.Stdin);
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buf := new(bytes.Buffer);
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three := strings.Bytes(">THREE ");
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for {
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line, err := in.ReadLineSlice('\n');
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if err != nil {
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fmt.Fprintln(os.Stderr, "ReadLine err:", err);
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os.Exit(2);
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}
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if line[0] == '>' && bytes.Equal(line[0:len(three)], three) {
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break;
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}
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}
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data, err := io.ReadAll(in);
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if err != nil {
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fmt.Fprintln(os.Stderr, "ReadAll err:", err);
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os.Exit(2);
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}
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// delete the newlines and convert to upper case
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j := 0;
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for i := 0; i < len(data); i++ {
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if data[i] != '\n' {
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data[j] = data[i] &^ ' '; // upper case
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j++
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}
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}
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str := string(data[0:j]);
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print(count(str, 1));
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fmt.Print("\n");
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print(count(str, 2));
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fmt.Print("\n");
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interests := []string{"GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT"};
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for _, s := range interests {
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fmt.Printf("%d %s\n", countOne(str, s), s);
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}
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}
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27
test/bench/k-nucleotide.txt
Normal file
27
test/bench/k-nucleotide.txt
Normal file
@ -0,0 +1,27 @@
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A 30.284
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T 29.796
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C 20.312
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G 19.608
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AA 9.212
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AT 8.950
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TT 8.948
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TA 8.936
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CA 6.166
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CT 6.100
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AC 6.086
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TC 6.042
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AG 6.036
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GA 5.968
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TG 5.868
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GT 5.798
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CC 4.140
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GC 4.044
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CG 3.906
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GG 3.798
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562 GGT
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152 GGTA
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15 GGTATT
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0 GGTATTTTAATT
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0 GGTATTTTAATTTATAGT
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@ -66,3 +66,10 @@ spectral-norm 5500
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gc_B spectral-norm 49.69u 0.01s 49.83r
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gc spectral-norm-parallel 24.47u 0.03s 11.05r # has shift >>1 not div /2
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[using >>1 instead of /2 : gc gives 24.33u 0.00s 24.33r]
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August 6, 2009
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k-nucleotide 5000000
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gcc -O2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include k-nucleotide.c -lglib-2.0 k-nucleotide.c: 10.72u 0.01s 10.74r
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gccgo -O2 k-nucleotide.go 22.69u 0.85s 24.09r
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gc k-nucleotide 15.63u 0.26s 16.41r
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@ -84,9 +84,19 @@ spectralnorm() {
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run 'gc_B spectral-norm' $O.out -n 5500
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}
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knucleotide() {
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gcc -O2 fasta.c
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a.out 1000000 > x # should be using 25000000
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echo 'k-nucleotide 1000000'
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run 'gcc -O2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include k-nucleotide.c -lglib-2.0' a.out <x
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run 'gccgo -O2 k-nucleotide.go' a.out <x # warning: pages badly!
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run 'gc k-nucleotide' $O.out <x
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rm x
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}
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case $# in
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0)
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run="fasta revcom nbody binarytree fannkuch regexdna spectralnorm"
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run="fasta revcom nbody binarytree fannkuch regexdna spectralnorm knucleotide"
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;;
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*)
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run=$*
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|
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