-/*
- * divsufsort.c for libdivsufsort
- * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
- *
- * 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.
- */
-
-#include "divsufsort_private.h"
-#ifdef _OPENMP
-# include <omp.h>
-#endif
-
-/*- Private Functions -*/
-
-/* Sorts suffixes of type B*. */
-static
-saidx_t
-sort_typeBstar(const sauchar_t *T, saidx_t *SA,
- saidx_t *bucket_A, saidx_t *bucket_B,
- saidx_t n) {
- saidx_t *PAb, *ISAb, *buf;
- saidx_t i, j, k, t, m, bufsize;
- saint_t c0, c1;
-
- /* Initialize bucket arrays. */
- for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; }
- for(uint32_t i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; }
-
- /* Count the number of occurrences of the first one or two characters of each
- type A, B and B* suffix. Moreover, store the beginning position of all
- type B* suffixes into the array SA. */
-
- for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) {
- /* type A suffix. */
- do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1));
- if(0 <= i) {
- /* type B* suffix. */
- ++BUCKET_BSTAR(c0, c1);
- SA[--m] = i;
- /* type B suffix. */
- for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) {
- ++BUCKET_B(c0, c1);
- }
- }
- }
- m = n - m;
-/*
-note:
- A type B* suffix is lexicographically smaller than a type B suffix that
- begins with the same first two characters.
-*/
-
- /* Calculate the index of start/end point of each bucket. */
- for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) {
- t = i + BUCKET_A(c0);
- BUCKET_A(c0) = i + j; /* start point */
- i = t + BUCKET_B(c0, c0);
- for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) {
- j += BUCKET_BSTAR(c0, c1);
- BUCKET_BSTAR(c0, c1) = j; /* end point */
- i += BUCKET_B(c0, c1);
- }
- }
-
- if(0 < m) {
- /* Sort the type B* suffixes by their first two characters. */
- PAb = SA + n - m; ISAb = SA + m;
- for(i = m - 2; 0 <= i; --i) {
- t = PAb[i], c0 = T[t], c1 = T[t + 1];
- SA[--BUCKET_BSTAR(c0, c1)] = i;
- }
- t = PAb[m - 1], c0 = T[t], c1 = T[t + 1];
- SA[--BUCKET_BSTAR(c0, c1)] = m - 1;
-
- /* Sort the type B* substrings using sssort. */
- buf = SA + m, bufsize = n - (2 * m);
- for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
- for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
- i = BUCKET_BSTAR(c0, c1);
- if(1 < (j - i)) {
- sssort(T, PAb, SA + i, SA + j,
- buf, bufsize, 2, n, *(SA + i) == (m - 1));
- }
- }
- }
-
- /* Compute ranks of type B* substrings. */
- for(i = m - 1; 0 <= i; --i) {
- if(0 <= SA[i]) {
- j = i;
- do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i]));
- SA[i + 1] = i - j;
- if(i <= 0) { break; }
- }
- j = i;
- do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0);
- ISAb[SA[i]] = j;
- }
-
- /* Construct the inverse suffix array of type B* suffixes using trsort. */
- trsort(ISAb, SA, m, 1);
-
- /* Set the sorted order of tyoe B* suffixes. */
- for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) {
- for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { }
- if(0 <= i) {
- t = i;
- for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { }
- SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t;
- }
- }
-
- /* Calculate the index of start/end point of each bucket. */
- BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */
- for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) {
- i = BUCKET_A(c0 + 1) - 1;
- for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) {
- t = i - BUCKET_B(c0, c1);
- BUCKET_B(c0, c1) = i; /* end point */
-
- /* Move all type B* suffixes to the correct position. */
- for(i = t, j = BUCKET_BSTAR(c0, c1);
- j <= k;
- --i, --k) { SA[i] = SA[k]; }
- }
- BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */
- BUCKET_B(c0, c0) = i; /* end point */
- }
- }
-
- return m;
-}
-
-/* Constructs the suffix array by using the sorted order of type B* suffixes. */
-static
-void
-construct_SA(const sauchar_t *T, saidx_t *SA,
- saidx_t *bucket_A, saidx_t *bucket_B,
- saidx_t n, saidx_t m) {
- saidx_t *i, *j, *k;
- saidx_t s;
- saint_t c0, c1, c2;
-
- if(0 < m) {
- /* Construct the sorted order of type B suffixes by using
- the sorted order of type B* suffixes. */
- for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
- /* Scan the suffix array from right to left. */
- for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
- j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
- i <= j;
- --j) {
- if(0 < (s = *j)) {
- assert(T[s] == c1);
- assert(((s + 1) < n) && (T[s] <= T[s + 1]));
- assert(T[s - 1] <= T[s]);
- *j = ~s;
- c0 = T[--s];
- if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
- if(c0 != c2) {
- if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
- k = SA + BUCKET_B(c2 = c0, c1);
- }
- assert(k < j);
- *k-- = s;
- } else {
- assert(((s == 0) && (T[s] == c1)) || (s < 0));
- *j = ~s;
- }
- }
- }
- }
-
- /* Construct the suffix array by using
- the sorted order of type B suffixes. */
- k = SA + BUCKET_A(c2 = T[n - 1]);
- *k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1);
- /* Scan the suffix array from left to right. */
- for(i = SA, j = SA + n; i < j; ++i) {
- if(0 < (s = *i)) {
- assert(T[s - 1] >= T[s]);
- c0 = T[--s];
- if((s == 0) || (T[s - 1] < c0)) { s = ~s; }
- if(c0 != c2) {
- BUCKET_A(c2) = k - SA;
- k = SA + BUCKET_A(c2 = c0);
- }
- assert(i < k);
- *k++ = s;
- } else {
- assert(s < 0);
- *i = ~s;
- }
- }
-}
-
-#if 0
-/* Constructs the burrows-wheeler transformed string directly
- by using the sorted order of type B* suffixes. */
-static
-saidx_t
-construct_BWT(const sauchar_t *T, saidx_t *SA,
- saidx_t *bucket_A, saidx_t *bucket_B,
- saidx_t n, saidx_t m) {
- saidx_t *i, *j, *k, *orig;
- saidx_t s;
- saint_t c0, c1, c2;
-
- if(0 < m) {
- /* Construct the sorted order of type B suffixes by using
- the sorted order of type B* suffixes. */
- for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
- /* Scan the suffix array from right to left. */
- for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
- j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
- i <= j;
- --j) {
- if(0 < (s = *j)) {
- assert(T[s] == c1);
- assert(((s + 1) < n) && (T[s] <= T[s + 1]));
- assert(T[s - 1] <= T[s]);
- c0 = T[--s];
- *j = ~((saidx_t)c0);
- if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
- if(c0 != c2) {
- if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
- k = SA + BUCKET_B(c2 = c0, c1);
- }
- assert(k < j);
- *k-- = s;
- } else if(s != 0) {
- *j = ~s;
-#ifndef NDEBUG
- } else {
- assert(T[s] == c1);
-#endif
- }
- }
- }
- }
-
- /* Construct the BWTed string by using
- the sorted order of type B suffixes. */
- k = SA + BUCKET_A(c2 = T[n - 1]);
- *k++ = (T[n - 2] < c2) ? ~((saidx_t)T[n - 2]) : (n - 1);
- /* Scan the suffix array from left to right. */
- for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
- if(0 < (s = *i)) {
- assert(T[s - 1] >= T[s]);
- c0 = T[--s];
- *i = c0;
- if((0 < s) && (T[s - 1] < c0)) { s = ~((saidx_t)T[s - 1]); }
- if(c0 != c2) {
- BUCKET_A(c2) = k - SA;
- k = SA + BUCKET_A(c2 = c0);
- }
- assert(i < k);
- *k++ = s;
- } else if(s != 0) {
- *i = ~s;
- } else {
- orig = i;
- }
- }
-
- return orig - SA;
-}
-#endif
-
-
-/*---------------------------------------------------------------------------*/
-
-/*- Function -*/
-
-/* XXX Modified from original: use provided temporary space instead of
- * allocating it. */
-saint_t
-divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n,
- saidx_t *bucket_A, saidx_t *bucket_B) {
- saidx_t m;
-
- switch (n) {
- case 0:
- break;
-
- case 1:
- SA[0] = 0;
- break;
-
- case 2:
- m = (T[0] < T[1]);
- SA[m ^ 1] = 0;
- SA[m] = 1;
- break;
-
- default:
- m = sort_typeBstar(T, SA, bucket_A, bucket_B, n);
- construct_SA(T, SA, bucket_A, bucket_B, n, m);
- break;
- }
- return 0;
-}
-
-#if 0
-saidx_t
-divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n) {
- saidx_t *B;
- saidx_t *bucket_A, *bucket_B;
- saidx_t m, pidx, i;
-
- /* Check arguments. */
- if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
- else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
-
- if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); }
- bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
- bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
-
- /* Burrows-Wheeler Transform. */
- if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
- m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
- pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
-
- /* Copy to output string. */
- U[0] = T[n - 1];
- for(i = 0; i < pidx; ++i) { U[i + 1] = (sauchar_t)B[i]; }
- for(i += 1; i < n; ++i) { U[i] = (sauchar_t)B[i]; }
- pidx += 1;
- } else {
- pidx = -2;
- }
-
- free(bucket_B);
- free(bucket_A);
- if(A == NULL) { free(B); }
-
- return pidx;
-}
-#endif
-
-#if 0
-const char *
-divsufsort_version(void) {
- return PROJECT_VERSION_FULL;
-}
-#endif
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