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-rw-r--r--dependencies/pkg/mod/golang.org/x/exp@v0.0.0-20220613132600-b0d781184e0d/shootout/fasta.c221
1 files changed, 221 insertions, 0 deletions
diff --git a/dependencies/pkg/mod/golang.org/x/exp@v0.0.0-20220613132600-b0d781184e0d/shootout/fasta.c b/dependencies/pkg/mod/golang.org/x/exp@v0.0.0-20220613132600-b0d781184e0d/shootout/fasta.c
new file mode 100644
index 0000000..cf0f2a7
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+++ b/dependencies/pkg/mod/golang.org/x/exp@v0.0.0-20220613132600-b0d781184e0d/shootout/fasta.c
@@ -0,0 +1,221 @@
+// +build ignore
+
+/*
+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.
+*/
+
+/*
+ * http://shootout.alioth.debian.org/u32/program.php?test=fasta&lang=gcc&id=3
+ */
+
+/* The Computer Language Benchmarks Game
+ * http://shootout.alioth.debian.org/
+ *
+ * contributed by Petr Prokhorenkov
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#ifndef fwrite_unlocked
+// not available on OS X
+#define fwrite_unlocked fwrite
+#define fputc_unlocked fputc
+#define fputs_unlocked fputs
+#endif
+
+#define ARRAY_SIZE(a) (sizeof(a)/sizeof(a[0]))
+#define unlikely(x) __builtin_expect((x), 0)
+
+#define IM 139968
+#define IA 3877
+#define IC 29573
+
+#define LINE_LEN 60
+#define LOOKUP_SIZE 4096
+#define LOOKUP_SCALE ((float)(LOOKUP_SIZE - 1))
+
+typedef unsigned random_t;
+
+void
+random_init(random_t *random) {
+ *random = 42;
+}
+
+// Special version with result rescaled to LOOKUP_SCALE.
+static inline
+float
+random_next_lookup(random_t *random) {
+ *random = (*random*IA + IC)%IM;
+
+ return (*random)*(LOOKUP_SCALE/IM);
+}
+
+struct amino_acid {
+ char sym;
+ float prob;
+ float cprob_lookup;
+};
+
+void
+repeat(const char *alu, const char *title, int n) {
+ int len = strlen(alu);
+ char buffer[len + LINE_LEN];
+ int pos = 0;
+
+ memcpy(buffer, alu, len);
+ memcpy(buffer + len, alu, LINE_LEN);
+
+ fputs_unlocked(title, stdout);
+ while (n > 0) {
+ int bytes = n > LINE_LEN ? LINE_LEN : n;
+
+ fwrite_unlocked(buffer + pos, bytes, 1, stdout);
+ pos += bytes;
+ if (pos > len) {
+ pos -= len;
+ }
+ fputc_unlocked('\n', stdout);
+ n -= bytes;
+ }
+}
+
+/*
+ * Lookup table contains mapping from real values to cumulative
+ * probabilities. Careful selection of table size allows lookup
+ * virtually in constant time.
+ *
+ * All cumulative probabilities are rescaled to LOOKUP_SCALE,
+ * this allows to save one multiplication operation on each iteration
+ * in randomize().
+ */
+
+void *
+fill_lookup(struct amino_acid **lookup, struct amino_acid *amino_acid, int amino_acid_size) {
+ float p = 0;
+ int i, j;
+
+ for (i = 0; i < amino_acid_size; i++) {
+ p += amino_acid[i].prob;
+ amino_acid[i].cprob_lookup = p*LOOKUP_SCALE;
+ }
+
+ // Prevent rounding error.
+ amino_acid[amino_acid_size - 1].cprob_lookup = LOOKUP_SIZE - 1;
+
+ for (i = 0, j = 0; i < LOOKUP_SIZE; i++) {
+ while (amino_acid[j].cprob_lookup < i) {
+ j++;
+ }
+ lookup[i] = &amino_acid[j];
+ }
+
+ return 0;
+}
+
+void
+randomize(struct amino_acid *amino_acid, int amino_acid_size,
+ const char *title, int n, random_t *rand) {
+ struct amino_acid *lookup[LOOKUP_SIZE];
+ char line_buffer[LINE_LEN + 1];
+ int i, j;
+
+ line_buffer[LINE_LEN] = '\n';
+
+ fill_lookup(lookup, amino_acid, amino_acid_size);
+
+ fputs_unlocked(title, stdout);
+
+ for (i = 0, j = 0; i < n; i++, j++) {
+ if (j == LINE_LEN) {
+ fwrite_unlocked(line_buffer, LINE_LEN + 1, 1, stdout);
+ j = 0;
+ }
+
+ float r = random_next_lookup(rand);
+ struct amino_acid *u = lookup[(short)r];
+ while (unlikely(u->cprob_lookup < r)) {
+ ++u;
+ }
+ line_buffer[j] = u->sym;
+ }
+ line_buffer[j] = '\n';
+ fwrite_unlocked(line_buffer, j + 1, 1, stdout);
+}
+
+struct amino_acid amino_acid[] = {
+ { 'a', 0.27 },
+ { 'c', 0.12 },
+ { 'g', 0.12 },
+ { 't', 0.27 },
+
+ { 'B', 0.02 },
+ { 'D', 0.02 },
+ { 'H', 0.02 },
+ { 'K', 0.02 },
+ { 'M', 0.02 },
+ { 'N', 0.02 },
+ { 'R', 0.02 },
+ { 'S', 0.02 },
+ { 'V', 0.02 },
+ { 'W', 0.02 },
+ { 'Y', 0.02 },
+};
+
+struct amino_acid homo_sapiens[] = {
+ { 'a', 0.3029549426680 },
+ { 'c', 0.1979883004921 },
+ { 'g', 0.1975473066391 },
+ { 't', 0.3015094502008 },
+};
+
+static const char alu[] =
+ "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTG"
+ "GGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGA"
+ "GACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAA"
+ "AATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAAT"
+ "CCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAAC"
+ "CCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTG"
+ "CACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
+
+int
+main(int argc, const char **argv) {
+ int n = argc > 1 ? atoi( argv[1] ) : 512;
+ random_t rand;
+
+ random_init(&rand);
+
+ repeat(alu, ">ONE Homo sapiens alu\n", n*2);
+ randomize(amino_acid, ARRAY_SIZE(amino_acid),
+ ">TWO IUB ambiguity codes\n", n*3, &rand);
+ randomize(homo_sapiens, ARRAY_SIZE(homo_sapiens),
+ ">THREE Homo sapiens frequency\n", n*5, &rand);
+
+ return 0;
+}