diff options
Diffstat (limited to 'test/bench/k-nucleotide.c')
| -rw-r--r-- | test/bench/k-nucleotide.c | 228 |
1 files changed, 0 insertions, 228 deletions
diff --git a/test/bench/k-nucleotide.c b/test/bench/k-nucleotide.c deleted file mode 100644 index 3bace391c..000000000 --- a/test/bench/k-nucleotide.c +++ /dev/null @@ -1,228 +0,0 @@ -/* -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. -*/ - -#include <stdio.h> -#include <string.h> -#include <ctype.h> -#include <stdlib.h> -#include <glib.h> - -typedef struct stat_s stat_t; -struct stat_s -{ - const gchar *key; - long stat; -}; - -#define MAX_ELM (8192 / sizeof (stat_t)) - -static int -generate_frequencies (int fl, char *buffer, long buflen, - GHashTable *ht, GTrashStack **ts, GPtrArray *roots, GStringChunk *sc) -{ - gchar *key; - long i; - - if (fl > buflen) return 0; - if (fl == 0) return 0; - - for (i = 0; i < buflen - fl + 1; ++i) - { - char nulled; - stat_t *stat; - - nulled = buffer[i + fl]; - buffer[i + fl] = '\0'; - - key = g_string_chunk_insert_const(sc, buffer + i); - - stat = g_hash_table_lookup(ht, key); - if (!stat) - { - stat = g_trash_stack_pop(ts); - if (!stat) - { - int j; - - stat = malloc(sizeof (stat_t) * MAX_ELM); - g_ptr_array_add(roots, stat); - - for (j = 1; j < MAX_ELM; ++j) - g_trash_stack_push(ts, stat + j); - } - stat->stat = 1; - stat->key = key; - - g_hash_table_insert(ht, key, stat); - } - else - stat->stat++; - - buffer[i + fl] = nulled; - } - - return buflen - fl + 1; -} - -static int -cmp_func(gconstpointer a, gconstpointer b) -{ - const stat_t *left = a; - const stat_t *right = b; - - return right->stat - left->stat; -} - -static void -sorted_list(gpointer key, gpointer value, gpointer user_data) -{ - stat_t *data = value; - GList **lst = user_data; - - *lst = g_list_insert_sorted(*lst, data, cmp_func); -} - -static void -display_stat(gpointer data, gpointer user_data) -{ - long *total = user_data; - stat_t *st = data; - - printf("%s %.3f\n", st->key, 100 * (float) st->stat / *total); -} - -void -write_frequencies (int fl, char *buffer, long buflen, GTrashStack **ts, GPtrArray *roots) -{ - GStringChunk *sc; - GHashTable *ht; - GList *lst; - long total; - - ht = g_hash_table_new_full(g_str_hash, g_str_equal, NULL /* free key */, NULL /* free value */); - sc = g_string_chunk_new(buflen); - lst = NULL; - - total = generate_frequencies (fl, buffer, buflen, ht, ts, roots, sc); - - if (!total) goto on_error; - - g_hash_table_foreach(ht, sorted_list, &lst); - g_list_foreach(lst, display_stat, &total); - g_list_free(lst); - - on_error: - g_hash_table_destroy(ht); - g_string_chunk_free(sc); -} - -void -write_count (char *searchFor, char *buffer, long buflen, GTrashStack **ts, GPtrArray *roots) -{ - GStringChunk *sc; - GHashTable *ht; - stat_t *result; - GList *lst; - long total; - long fl; - - fl = strlen(searchFor); - - ht = g_hash_table_new_full(g_str_hash, g_str_equal, NULL /* free key */, NULL /* free value */); - sc = g_string_chunk_new(buflen); - lst = NULL; - result = NULL; - - total = generate_frequencies (fl, buffer, buflen, ht, ts, roots, sc); - - if (!total) goto on_error; - - result = g_hash_table_lookup(ht, searchFor); - - on_error: - printf("%ld\t%s\n", result ? result->stat : 0, searchFor); - - g_hash_table_destroy(ht); - g_string_chunk_free(sc); -} - -int -main () -{ - char buffer[4096]; - GTrashStack *ts; - GPtrArray *roots; - GString *stuff; - gchar *s; - int len; - - roots = g_ptr_array_new(); - ts = NULL; - - while (fgets(buffer, sizeof (buffer), stdin)) - if (strncmp(buffer, ">THREE", 6) == 0) - break; - - stuff = g_string_new(NULL); - - while (fgets(buffer, sizeof (buffer), stdin)) - { - size_t sz; - - if (buffer[0] == '>') - break; - - sz = strlen(buffer); - if (buffer[sz - 1] == '\n') - --sz; - - stuff = g_string_append_len(stuff, buffer, sz); - } - - stuff = g_string_ascii_up(stuff); - len = stuff->len; - s = g_string_free(stuff, FALSE); - - write_frequencies(1, s, len, &ts, roots); - printf("\n"); - write_frequencies(2, s, len, &ts, roots); - printf("\n"); - write_count("GGT", s, len, &ts, roots); - write_count("GGTA", s, len, &ts, roots); - write_count("GGTATT", s, len, &ts, roots); - write_count("GGTATTTTAATT", s, len, &ts, roots); - write_count("GGTATTTTAATTTATAGT", s, len, &ts, roots); - - free(s); - - g_ptr_array_foreach(roots, free, NULL); - g_ptr_array_free(roots, TRUE); - - return 0; -} |