diff --git a/src/utils.c b/src/utils.c index f7a0ff5..37e5f0c 100644 --- a/src/utils.c +++ b/src/utils.c @@ -116,3 +116,193 @@ void* obi_get_memory_aligned_on_16(int size, int* shift) return (memory); } + +/* + * A generic implementation of binary search for the Linux kernel + * + * Copyright (C) 2008-2009 Ksplice, Inc. + * Author: Tim Abbott + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License as + * published by the Free Software Foundation; version 2. + */ +void* bsearch_user_data(const void* key, const void* base, size_t num, size_t size, const void* user_data, + int (*cmp)(const void *key, const void *elt, const void* user_data)) +{ + size_t start = 0; + size_t end = num; + size_t mid; + int result; + + while (start < end) + { + mid = start + (end - start) / 2; + result = cmp(key, base + mid * size, user_data); + if (result < 0) + end = mid; + else if (result > 0) + start = mid + 1; + else + return (void*)base + mid * size; + } + + return NULL; +} + + +/* + * Copyright (c) 1992, 1993 + * The Regents of the University of California. All rights reserved. + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * 2. 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. + * 3. Neither the name of the University 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 REGENTS 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 REGENTS 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. + */ +/* + * Qsort routine from Bentley & McIlroy's "Engineering a Sort Function". + */ + +#define MIN(a,b) ((a) < (b) ? a : b) + +#define swapcode(TYPE, parmi, parmj, n) { \ + long i = (n) / sizeof (TYPE); \ + register TYPE *pi = (TYPE *) (parmi); \ + register TYPE *pj = (TYPE *) (parmj); \ + do { \ + register TYPE t = *pi; \ + *pi++ = *pj; \ + *pj++ = t; \ + } while (--i > 0); \ +} + +#define SWAPINIT(a, es) swaptype = ((char *)a - (char *)0) % sizeof(long) || \ + es % sizeof(long) ? 2 : es == sizeof(long)? 0 : 1; + +static __inline void +swapfunc(char *a, char *b, int n, int swaptype) +{ + if (swaptype <= 1) + swapcode(long, a, b, n) + else + swapcode(char, a, b, n) +} + +#define swap(a, b) \ + if (swaptype == 0) { \ + long t = *(long *)(a); \ + *(long *)(a) = *(long *)(b); \ + *(long *)(b) = t; \ + } else \ + swapfunc(a, b, es, swaptype) + +#define vecswap(a, b, n) if ((n) > 0) swapfunc(a, b, n, swaptype) + +static __inline char * +med3(char *a, char *b, char *c, const void *user_data, int (*cmp)(const void *, const void *, const void *)) +{ + return cmp(a, b, user_data) < 0 ? + (cmp(b, c, user_data) < 0 ? b : (cmp(a, c, user_data) < 0 ? c : a )) + :(cmp(b, c, user_data) > 0 ? b : (cmp(a, c, user_data) < 0 ? a : c )); +} + +void +qsort_user_data(void *aa, size_t n, size_t es, const void *user_data, int (*cmp)(const void *, const void *, const void *)) +{ + char *pa, *pb, *pc, *pd, *pl, *pm, *pn; + int d, r, swaptype, swap_cnt; + register char *a = aa; + +loop: SWAPINIT(a, es); + swap_cnt = 0; + if (n < 7) { + for (pm = (char *)a + es; pm < (char *) a + n * es; pm += es) + for (pl = pm; pl > (char *) a && cmp(pl - es, pl, user_data) > 0; + pl -= es) + swap(pl, pl - es); + return; + } + pm = (char *)a + (n / 2) * es; + if (n > 7) { + pl = (char *)a; + pn = (char *)a + (n - 1) * es; + if (n > 40) { + d = (n / 8) * es; + pl = med3(pl, pl + d, pl + 2 * d, user_data, cmp); + pm = med3(pm - d, pm, pm + d, user_data, cmp); + pn = med3(pn - 2 * d, pn - d, pn, user_data, cmp); + } + pm = med3(pl, pm, pn, user_data, cmp); + } + swap(a, pm); + pa = pb = (char *)a + es; + + pc = pd = (char *)a + (n - 1) * es; + for (;;) { + while (pb <= pc && (r = cmp(pb, a, user_data)) <= 0) { + if (r == 0) { + swap_cnt = 1; + swap(pa, pb); + pa += es; + } + pb += es; + } + while (pb <= pc && (r = cmp(pc, a, user_data)) >= 0) { + if (r == 0) { + swap_cnt = 1; + swap(pc, pd); + pd -= es; + } + pc -= es; + } + if (pb > pc) + break; + swap(pb, pc); + swap_cnt = 1; + pb += es; + pc -= es; + } + if (swap_cnt == 0) { /* Switch to insertion sort */ + for (pm = (char *) a + es; pm < (char *) a + n * es; pm += es) + for (pl = pm; pl > (char *) a && cmp(pl - es, pl, user_data) > 0; + pl -= es) + swap(pl, pl - es); + return; + } + + pn = (char *)a + n * es; + r = MIN(pa - (char *)a, pb - pa); + vecswap(a, pb - r, r); + r = MIN((long)(pd - pc), (long)(pn - pd - es)); + vecswap(pb, pn - r, r); + if ((r = pb - pa) > (int)es) + qsort_user_data(a, r / es, es, user_data, cmp); + if ((r = pd - pc) > (int)es) { + /* Iterate rather than recurse to save stack space */ + a = pn - r; + n = r / es; + goto loop; + } +/* qsort(pn - r, r / es, es, cmp);*/ +} + diff --git a/src/utils.h b/src/utils.h index 8ac9a6c..ecab62e 100644 --- a/src/utils.h +++ b/src/utils.h @@ -74,4 +74,41 @@ char* obi_format_date(time_t date); void* obi_get_memory_aligned_on_16(int size, int* shift); +/** + * @brief Version of quick sort modified to allow the user to provide an + * additional pointer sent to the comparison function. + * + * @param key This is the pointer to the object that serves as key for the search, type-casted as a void*. + * @param base This is the pointer to the first object of the array where the search is performed, type-casted as a void*. + * @param num This is the number of elements in the array pointed by base. + * @param size This is the size in bytes of each element in the array. + * @param user_data This is an additional pointer passed to the comparison function. + * @param cmp This is the function that compares two elements, eventually with an additional pointer. + * + * @returns A pointer to an entry in the array that matches the search key. + * @retval NULL if key is not found. + * + * @since January 2017 + * @author original code modified by Celine Mercier (celine.mercier@metabarcoding.org) + */ +void* bsearch_user_data(const void* key, const void* base, size_t num, size_t size, const void* user_data, + int (*cmp)(const void *key, const void *elt, const void* user_data)); + + +/** + * @brief Version of quick sort modified to allow the user to provide an + * additional pointer sent to the comparison function. + * + * @param aa This is the pointer to the first element of the array to be sorted. + * @param n This is the number of elements in the array pointed by base. + * @param es This is the size in bytes of each element in the array. + * @param user_data This is an additional pointer passed to the comparison function. + * @param cmp This is the function that compares two elements, eventually with an additional pointer. + * + * @since January 2017 + * @author original code modified by Celine Mercier (celine.mercier@metabarcoding.org) + */ +void qsort_user_data(void *aa, size_t n, size_t es, const void *user_data, int (*cmp)(const void *, const void *, const void *)); + + #endif /* UTILS_H_ */