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+/*
+ * utils.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"
+
+
+/*- Private Function -*/
+
+/* Binary search for inverse bwt. */
+static
+saidx_t
+binarysearch_lower(const saidx_t *A, saidx_t size, saidx_t value) {
+ saidx_t half, i;
+ for(i = 0, half = size >> 1;
+ 0 < size;
+ size = half, half >>= 1) {
+ if(A[i + half] < value) {
+ i += half + 1;
+ half -= (size & 1) ^ 1;
+ }
+ }
+ return i;
+}
+
+
+/*- Functions -*/
+
+/* Burrows-Wheeler transform. */
+saint_t
+bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *SA,
+ saidx_t n, saidx_t *idx) {
+ saidx_t *A, i, j, p, t;
+ saint_t c;
+
+ /* Check arguments. */
+ if((T == NULL) || (U == NULL) || (n < 0) || (idx == NULL)) { return -1; }
+ if(n <= 1) {
+ if(n == 1) { U[0] = T[0]; }
+ *idx = n;
+ return 0;
+ }
+
+ if((A = SA) == NULL) {
+ i = divbwt(T, U, NULL, n);
+ if(0 <= i) { *idx = i; i = 0; }
+ return (saint_t)i;
+ }
+
+ /* BW transform. */
+ if(T == U) {
+ t = n;
+ for(i = 0, j = 0; i < n; ++i) {
+ p = t - 1;
+ t = A[i];
+ if(0 <= p) {
+ c = T[j];
+ U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
+ A[j] = c;
+ j++;
+ } else {
+ *idx = i;
+ }
+ }
+ p = t - 1;
+ if(0 <= p) {
+ c = T[j];
+ U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
+ A[j] = c;
+ } else {
+ *idx = i;
+ }
+ } else {
+ U[0] = T[n - 1];
+ for(i = 0; A[i] != 0; ++i) { U[i + 1] = T[A[i] - 1]; }
+ *idx = i + 1;
+ for(++i; i < n; ++i) { U[i] = T[A[i] - 1]; }
+ }
+
+ if(SA == NULL) {
+ /* Deallocate memory. */
+ free(A);
+ }
+
+ return 0;
+}
+
+/* Inverse Burrows-Wheeler transform. */
+saint_t
+inverse_bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *A,
+ saidx_t n, saidx_t idx) {
+ saidx_t C[ALPHABET_SIZE];
+ sauchar_t D[ALPHABET_SIZE];
+ saidx_t *B;
+ saidx_t i, p;
+ saint_t c, d;
+
+ /* Check arguments. */
+ if((T == NULL) || (U == NULL) || (n < 0) || (idx < 0) ||
+ (n < idx) || ((0 < n) && (idx == 0))) {
+ return -1;
+ }
+ if(n <= 1) { return 0; }
+
+ if((B = A) == NULL) {
+ /* Allocate n*sizeof(saidx_t) bytes of memory. */
+ if((B = (saidx_t *)malloc((size_t)n * sizeof(saidx_t))) == NULL) { return -2; }
+ }
+
+ /* Inverse BW transform. */
+ for(c = 0; c < ALPHABET_SIZE; ++c) { C[c] = 0; }
+ for(i = 0; i < n; ++i) { ++C[T[i]]; }
+ for(c = 0, d = 0, i = 0; c < ALPHABET_SIZE; ++c) {
+ p = C[c];
+ if(0 < p) {
+ C[c] = i;
+ D[d++] = (sauchar_t)c;
+ i += p;
+ }
+ }
+ for(i = 0; i < idx; ++i) { B[C[T[i]]++] = i; }
+ for( ; i < n; ++i) { B[C[T[i]]++] = i + 1; }
+ for(c = 0; c < d; ++c) { C[c] = C[D[c]]; }
+ for(i = 0, p = idx; i < n; ++i) {
+ U[i] = D[binarysearch_lower(C, d, p)];
+ p = B[p - 1];
+ }
+
+ if(A == NULL) {
+ /* Deallocate memory. */
+ free(B);
+ }
+
+ return 0;
+}
+
+/* Checks the suffix array SA of the string T. */
+saint_t
+sufcheck(const sauchar_t *T, const saidx_t *SA,
+ saidx_t n, saint_t verbose) {
+ saidx_t C[ALPHABET_SIZE];
+ saidx_t i, p, q, t;
+ saint_t c;
+
+ if(verbose) { fprintf(stderr, "sufcheck: "); }
+
+ /* Check arguments. */
+ if((T == NULL) || (SA == NULL) || (n < 0)) {
+ if(verbose) { fprintf(stderr, "Invalid arguments.\n"); }
+ return -1;
+ }
+ if(n == 0) {
+ if(verbose) { fprintf(stderr, "Done.\n"); }
+ return 0;
+ }
+
+ /* check range: [0..n-1] */
+ for(i = 0; i < n; ++i) {
+ if((SA[i] < 0) || (n <= SA[i])) {
+ if(verbose) {
+ fprintf(stderr, "Out of the range [0,%" PRIdSAIDX_T "].\n"
+ " SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
+ n - 1, i, SA[i]);
+ }
+ return -2;
+ }
+ }
+
+ /* check first characters. */
+ for(i = 1; i < n; ++i) {
+ if(T[SA[i - 1]] > T[SA[i]]) {
+ if(verbose) {
+ fprintf(stderr, "Suffixes in wrong order.\n"
+ " T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d"
+ " > T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d\n",
+ i - 1, SA[i - 1], T[SA[i - 1]], i, SA[i], T[SA[i]]);
+ }
+ return -3;
+ }
+ }
+
+ /* check suffixes. */
+ for(i = 0; i < ALPHABET_SIZE; ++i) { C[i] = 0; }
+ for(i = 0; i < n; ++i) { ++C[T[i]]; }
+ for(i = 0, p = 0; i < ALPHABET_SIZE; ++i) {
+ t = C[i];
+ C[i] = p;
+ p += t;
+ }
+
+ q = C[T[n - 1]];
+ C[T[n - 1]] += 1;
+ for(i = 0; i < n; ++i) {
+ p = SA[i];
+ if(0 < p) {
+ c = T[--p];
+ t = C[c];
+ } else {
+ c = T[p = n - 1];
+ t = q;
+ }
+ if((t < 0) || (p != SA[t])) {
+ if(verbose) {
+ fprintf(stderr, "Suffix in wrong position.\n"
+ " SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T " or\n"
+ " SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
+ t, (0 <= t) ? SA[t] : -1, i, SA[i]);
+ }
+ return -4;
+ }
+ if(t != q) {
+ ++C[c];
+ if((n <= C[c]) || (T[SA[C[c]]] != c)) { C[c] = -1; }
+ }
+ }
+
+ if(1 <= verbose) { fprintf(stderr, "Done.\n"); }
+ return 0;
+}
+
+
+static
+int
+_compare(const sauchar_t *T, saidx_t Tsize,
+ const sauchar_t *P, saidx_t Psize,
+ saidx_t suf, saidx_t *match) {
+ saidx_t i, j;
+ saint_t r;
+ for(i = suf + *match, j = *match, r = 0;
+ (i < Tsize) && (j < Psize) && ((r = T[i] - P[j]) == 0); ++i, ++j) { }
+ *match = j;
+ return (r == 0) ? -(j != Psize) : r;
+}
+
+/* Search for the pattern P in the string T. */
+saidx_t
+sa_search(const sauchar_t *T, saidx_t Tsize,
+ const sauchar_t *P, saidx_t Psize,
+ const saidx_t *SA, saidx_t SAsize,
+ saidx_t *idx) {
+ saidx_t size, lsize, rsize, half;
+ saidx_t match, lmatch, rmatch;
+ saidx_t llmatch, lrmatch, rlmatch, rrmatch;
+ saidx_t i, j, k;
+ saint_t r;
+
+ if(idx != NULL) { *idx = -1; }
+ if((T == NULL) || (P == NULL) || (SA == NULL) ||
+ (Tsize < 0) || (Psize < 0) || (SAsize < 0)) { return -1; }
+ if((Tsize == 0) || (SAsize == 0)) { return 0; }
+ if(Psize == 0) { if(idx != NULL) { *idx = 0; } return SAsize; }
+
+ for(i = j = k = 0, lmatch = rmatch = 0, size = SAsize, half = size >> 1;
+ 0 < size;
+ size = half, half >>= 1) {
+ match = MIN(lmatch, rmatch);
+ r = _compare(T, Tsize, P, Psize, SA[i + half], &match);
+ if(r < 0) {
+ i += half + 1;
+ half -= (size & 1) ^ 1;
+ lmatch = match;
+ } else if(r > 0) {
+ rmatch = match;
+ } else {
+ lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
+
+ /* left part */
+ for(llmatch = lmatch, lrmatch = match, half = lsize >> 1;
+ 0 < lsize;
+ lsize = half, half >>= 1) {
+ lmatch = MIN(llmatch, lrmatch);
+ r = _compare(T, Tsize, P, Psize, SA[j + half], &lmatch);
+ if(r < 0) {
+ j += half + 1;
+ half -= (lsize & 1) ^ 1;
+ llmatch = lmatch;
+ } else {
+ lrmatch = lmatch;
+ }
+ }
+
+ /* right part */
+ for(rlmatch = match, rrmatch = rmatch, half = rsize >> 1;
+ 0 < rsize;
+ rsize = half, half >>= 1) {
+ rmatch = MIN(rlmatch, rrmatch);
+ r = _compare(T, Tsize, P, Psize, SA[k + half], &rmatch);
+ if(r <= 0) {
+ k += half + 1;
+ half -= (rsize & 1) ^ 1;
+ rlmatch = rmatch;
+ } else {
+ rrmatch = rmatch;
+ }
+ }
+
+ break;
+ }
+ }
+
+ if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
+ return k - j;
+}
+
+/* Search for the character c in the string T. */
+saidx_t
+sa_simplesearch(const sauchar_t *T, saidx_t Tsize,
+ const saidx_t *SA, saidx_t SAsize,
+ saint_t c, saidx_t *idx) {
+ saidx_t size, lsize, rsize, half;
+ saidx_t i, j, k, p;
+ saint_t r;
+
+ if(idx != NULL) { *idx = -1; }
+ if((T == NULL) || (SA == NULL) || (Tsize < 0) || (SAsize < 0)) { return -1; }
+ if((Tsize == 0) || (SAsize == 0)) { return 0; }
+
+ for(i = j = k = 0, size = SAsize, half = size >> 1;
+ 0 < size;
+ size = half, half >>= 1) {
+ p = SA[i + half];
+ r = (p < Tsize) ? T[p] - c : -1;
+ if(r < 0) {
+ i += half + 1;
+ half -= (size & 1) ^ 1;
+ } else if(r == 0) {
+ lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
+
+ /* left part */
+ for(half = lsize >> 1;
+ 0 < lsize;
+ lsize = half, half >>= 1) {
+ p = SA[j + half];
+ r = (p < Tsize) ? T[p] - c : -1;
+ if(r < 0) {
+ j += half + 1;
+ half -= (lsize & 1) ^ 1;
+ }
+ }
+
+ /* right part */
+ for(half = rsize >> 1;
+ 0 < rsize;
+ rsize = half, half >>= 1) {
+ p = SA[k + half];
+ r = (p < Tsize) ? T[p] - c : -1;
+ if(r <= 0) {
+ k += half + 1;
+ half -= (rsize & 1) ^ 1;
+ }
+ }
+
+ break;
+ }
+ }
+
+ if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
+ return k - j;
+}