diff options
Diffstat (limited to 'debian/vendor-h2o/deps/klib/ksa.c')
| -rw-r--r-- | debian/vendor-h2o/deps/klib/ksa.c | 242 |
1 files changed, 0 insertions, 242 deletions
diff --git a/debian/vendor-h2o/deps/klib/ksa.c b/debian/vendor-h2o/deps/klib/ksa.c deleted file mode 100644 index 18f686d..0000000 --- a/debian/vendor-h2o/deps/klib/ksa.c +++ /dev/null @@ -1,242 +0,0 @@ -/* - * Copyright (c) 2008 Yuta Mori All Rights Reserved. - * 2011 Attractive Chaos <attractor@live.co.uk> - * - * Permission is hereby granted, free of charge, to any person - * obtaining a copy of this software and associated documentation - * files (the "Software"), to deal in the Software without - * restriction, including without limitation the rights to use, - * copy, modify, merge, publish, distribute, sublicense, and/or sell - * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, subject to the following - * conditions: - * - * The above copyright notice and this permission notice shall be - * included in all copies or substantial portions of the Software. - * - * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, - * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING - * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR - * OTHER DEALINGS IN THE SOFTWARE. - */ - -/* This is a library for constructing the suffix array for a string containing - * multiple sentinels with sentinels all represented by 0. The last symbol in - * the string must be a sentinel. The library is modified from an early version - * of Yuta Mori's SAIS library, but is slower than the lastest SAIS by about - * 30%, partly due to the recent optimization Yuta has applied and partly due - * to the extra comparisons between sentinels. This is not the first effort in - * supporting multi-sentinel strings, but is probably the easiest to use. */ - -#include <stdlib.h> - -#ifdef _KSA64 -#include <stdint.h> -typedef int64_t saint_t; -#define SAINT_MAX INT64_MAX -#define SAIS_CORE ksa_core64 -#define SAIS_BWT ksa_bwt64 -#define SAIS_MAIN ksa_sa64 -#else -#include <limits.h> -typedef int saint_t; -#define SAINT_MAX INT_MAX -#define SAIS_CORE ksa_core -#define SAIS_BWT ksa_bwt -#define SAIS_MAIN ksa_sa -#endif - -/* T is of type "const unsigned char*". If T[i] is a sentinel, chr(i) takes a negative value */ -#define chr(i) (cs == sizeof(saint_t) ? ((const saint_t *)T)[i] : (T[i]? (saint_t)T[i] : i - SAINT_MAX)) - -/** Count the occurrences of each symbol */ -static void getCounts(const unsigned char *T, saint_t *C, saint_t n, saint_t k, int cs) -{ - saint_t i; - for (i = 0; i < k; ++i) C[i] = 0; - for (i = 0; i < n; ++i) { - saint_t c = chr(i); - ++C[c > 0? c : 0]; - } -} - -/** - * Find the end of each bucket - * - * @param C occurrences computed by getCounts(); input - * @param B start/end of each bucket; output - * @param k size of alphabet - * @param end compute the end of bucket if true; otherwise compute the end - */ -static inline void getBuckets(const saint_t *C, saint_t *B, saint_t k, saint_t end) -{ - saint_t i, sum = 0; - if (end) for (i = 0; i < k; ++i) sum += C[i], B[i] = sum; - else for (i = 0; i < k; ++i) sum += C[i], B[i] = sum - C[i]; -} - -/** Induced sort */ -static void induceSA(const unsigned char *T, saint_t *SA, saint_t *C, saint_t *B, saint_t n, saint_t k, saint_t cs) -{ - saint_t *b, i, j; - saint_t c0, c1; - /* left-to-right induced sort (for L-type) */ - if (C == B) getCounts(T, C, n, k, cs); - getBuckets(C, B, k, 0); /* find starts of buckets */ - for (i = 0, b = 0, c1 = -1; i < n; ++i) { - j = SA[i], SA[i] = ~j; - if (0 < j) { /* >0 if j-1 is L-type; <0 if S-type; ==0 undefined */ - --j; - if ((c0 = chr(j)) != c1) { - B[c1 > 0? c1 : 0] = b - SA; - c1 = c0; - b = SA + B[c1 > 0? c1 : 0]; - } - *b++ = (0 < j && chr(j - 1) < c1) ? ~j : j; - } - } - /* right-to-left induced sort (for S-type) */ - if (C == B) getCounts(T, C, n, k, cs); - getBuckets(C, B, k, 1); /* find ends of buckets */ - for (i = n - 1, b = 0, c1 = -1; 0 <= i; --i) { - if (0 < (j = SA[i])) { /* the prefix is S-type */ - --j; - if ((c0 = chr(j)) != c1) { - B[c1 > 0? c1 : 0] = b - SA; - c1 = c0; - b = SA + B[c1 > 0? c1 : 0]; - } - if (c0 > 0) *--b = (j == 0 || chr(j - 1) > c1) ? ~j : j; - } else SA[i] = ~j; /* if L-type, change the sign */ - } -} - -/** - * Recursively construct the suffix array for a string containing multiple - * sentinels. NULL is taken as the sentinel. - * - * @param T NULL terminated input string (there can be multiple NULLs) - * @param SA output suffix array - * @param fs working space available in SA (typically 0 when first called) - * @param n length of T, including the trailing NULL - * @param k size of the alphabet (typically 256 when first called) - * @param cs # bytes per element in T; 1 or sizeof(saint_t) (typically 1 when first called) - * - * @return 0 upon success - */ -int SAIS_CORE(const unsigned char *T, saint_t *SA, saint_t fs, saint_t n, saint_t k, int cs) -{ - saint_t *C, *B; - saint_t i, j, c, m, q, qlen, name; - saint_t c0, c1; - - /* STAGE I: reduce the problem by at least 1/2 sort all the S-substrings */ - if (k <= fs) C = SA + n, B = (k <= fs - k) ? C + k : C; - else { - if ((C = (saint_t*)malloc(k * (1 + (cs == 1)) * sizeof(saint_t))) == NULL) return -2; - B = cs == 1? C + k : C; - } - getCounts(T, C, n, k, cs); - getBuckets(C, B, k, 1); /* find ends of buckets */ - for (i = 0; i < n; ++i) SA[i] = 0; - /* mark L and S (the t array in Nong et al.), and keep the positions of LMS in the buckets */ - for (i = n - 2, c = 1, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) { - if ((c0 = chr(i)) < c1 + c) c = 1; /* c1 = chr(i+1); c==1 if in an S run */ - else if (c) SA[--B[c1 > 0? c1 : 0]] = i + 1, c = 0; - } - induceSA(T, SA, C, B, n, k, cs); - if (fs < k) free(C); - /* pack all the sorted LMS into the first m items of SA - 2*m must be not larger than n (see Nong et al. for the proof) */ - for (i = 0, m = 0; i < n; ++i) { - saint_t p = SA[i]; - if (p == n - 1) SA[m++] = p; - else if (0 < p && chr(p - 1) > (c0 = chr(p))) { - for (j = p + 1; j < n && c0 == (c1 = chr(j)); ++j); - if (j < n && c0 < c1) SA[m++] = p; - } - } - for (i = m; i < n; ++i) SA[i] = 0; /* init the name array buffer */ - /* store the length of all substrings */ - for (i = n - 2, j = n, c = 1, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) { - if ((c0 = chr(i)) < c1 + c) c = 1; /* c1 = chr(i+1) */ - else if (c) SA[m + ((i + 1) >> 1)] = j - i - 1, j = i + 1, c = 0; - } - /* find the lexicographic names of all substrings */ - for (i = 0, name = 0, q = n, qlen = 0; i < m; ++i) { - saint_t p = SA[i], plen = SA[m + (p >> 1)], diff = 1; - if (plen == qlen) { - for (j = 0; j < plen && chr(p + j) == chr(q + j); j++); - if (j == plen) diff = 0; - } - if (diff) ++name, q = p, qlen = plen; - SA[m + (p >> 1)] = name; - } - - /* STAGE II: solve the reduced problem; recurse if names are not yet unique */ - if (name < m) { - saint_t *RA = SA + n + fs - m - 1; - for (i = n - 1, j = m - 1; m <= i; --i) - if (SA[i] != 0) RA[j--] = SA[i]; - RA[m] = 0; // add a sentinel; in the resulting SA, SA[0]==m always stands - if (SAIS_CORE((unsigned char *)RA, SA, fs + n - m * 2 - 2, m + 1, name + 1, sizeof(saint_t)) != 0) return -2; - for (i = n - 2, j = m - 1, c = 1, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) { - if ((c0 = chr(i)) < c1 + c) c = 1; - else if (c) RA[j--] = i + 1, c = 0; /* get p1 */ - } - for (i = 0; i < m; ++i) SA[i] = RA[SA[i+1]]; /* get index */ - } - - /* STAGE III: induce the result for the original problem */ - if (k <= fs) C = SA + n, B = (k <= fs - k) ? C + k : C; - else { - if ((C = (saint_t*)malloc(k * (1 + (cs == 1)) * sizeof(saint_t))) == NULL) return -2; - B = cs == 1? C + k : C; - } - /* put all LMS characters into their buckets */ - getCounts(T, C, n, k, cs); - getBuckets(C, B, k, 1); /* find ends of buckets */ - for (i = m; i < n; ++i) SA[i] = 0; /* init SA[m..n-1] */ - for (i = m - 1; 0 <= i; --i) { - j = SA[i], SA[i] = 0; - c = chr(j); - SA[--B[c > 0? c : 0]] = j; - } - induceSA(T, SA, C, B, n, k, cs); - if (fs < k) free(C); - return 0; -} - -/** - * Construct the suffix array for a NULL terminated string possibly containing - * multiple sentinels (NULLs). - * - * @param T[0..n-1] NULL terminated input string - * @param SA[0..n-1] output suffix array - * @param n length of the given string, including NULL - * @param k size of the alphabet including the sentinel; no more than 256 - * @return 0 upon success - */ -int SAIS_MAIN(const unsigned char *T, saint_t *SA, saint_t n, int k) -{ - if (T == NULL || SA == NULL || T[n - 1] != '\0' || n <= 0) return -1; - if (k < 0 || k > 256) k = 256; - return SAIS_CORE(T, SA, 0, n, (saint_t)k, 1); -} - -int SAIS_BWT(unsigned char *T, saint_t n, int k) -{ - saint_t *SA, i; - int ret; - if ((SA = malloc(n * sizeof(saint_t))) == 0) return -1; - if ((ret = SAIS_MAIN(T, SA, n, k)) != 0) return ret; - for (i = 0; i < n; ++i) - if (SA[i]) SA[i] = T[SA[i] - 1]; // if SA[i]==0, SA[i]=0 - for (i = 0; i < n; ++i) T[i] = SA[i]; - free(SA); - return 0; -} |