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Emmanuel Marty
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/*
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* utils.c for libdivsufsort
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* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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#include "divsufsort_private.h"
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/*- Private Function -*/
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#if 0
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/* Binary search for inverse bwt. */
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static
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saidx_t
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binarysearch_lower(const saidx_t *A, saidx_t size, saidx_t value) {
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saidx_t half, i;
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for(i = 0, half = size >> 1;
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0 < size;
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size = half, half >>= 1) {
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if(A[i + half] < value) {
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i += half + 1;
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half -= (size & 1) ^ 1;
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}
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}
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return i;
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}
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/*- Functions -*/
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/* Burrows-Wheeler transform. */
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saint_t
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bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *SA,
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saidx_t n, saidx_t *idx) {
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saidx_t *A, i, j, p, t;
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saint_t c;
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/* Check arguments. */
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if((T == NULL) || (U == NULL) || (n < 0) || (idx == NULL)) { return -1; }
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if(n <= 1) {
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if(n == 1) { U[0] = T[0]; }
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*idx = n;
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return 0;
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}
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if((A = SA) == NULL) {
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i = divbwt(T, U, NULL, n);
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if(0 <= i) { *idx = i; i = 0; }
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return (saint_t)i;
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}
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/* BW transform. */
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if(T == U) {
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t = n;
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for(i = 0, j = 0; i < n; ++i) {
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p = t - 1;
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t = A[i];
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if(0 <= p) {
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c = T[j];
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U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
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A[j] = c;
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j++;
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} else {
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*idx = i;
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}
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}
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p = t - 1;
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if(0 <= p) {
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c = T[j];
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U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
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A[j] = c;
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} else {
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*idx = i;
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}
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} else {
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U[0] = T[n - 1];
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for(i = 0; A[i] != 0; ++i) { U[i + 1] = T[A[i] - 1]; }
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*idx = i + 1;
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for(++i; i < n; ++i) { U[i] = T[A[i] - 1]; }
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}
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if(SA == NULL) {
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/* Deallocate memory. */
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free(A);
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}
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return 0;
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}
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/* Inverse Burrows-Wheeler transform. */
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saint_t
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inverse_bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *A,
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saidx_t n, saidx_t idx) {
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saidx_t C[ALPHABET_SIZE];
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sauchar_t D[ALPHABET_SIZE];
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saidx_t *B;
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saidx_t i, p;
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saint_t c, d;
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/* Check arguments. */
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if((T == NULL) || (U == NULL) || (n < 0) || (idx < 0) ||
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(n < idx) || ((0 < n) && (idx == 0))) {
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return -1;
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}
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if(n <= 1) { return 0; }
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if((B = A) == NULL) {
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/* Allocate n*sizeof(saidx_t) bytes of memory. */
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if((B = (saidx_t *)malloc((size_t)n * sizeof(saidx_t))) == NULL) { return -2; }
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}
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/* Inverse BW transform. */
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for(c = 0; c < ALPHABET_SIZE; ++c) { C[c] = 0; }
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for(i = 0; i < n; ++i) { ++C[T[i]]; }
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for(c = 0, d = 0, i = 0; c < ALPHABET_SIZE; ++c) {
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p = C[c];
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if(0 < p) {
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C[c] = i;
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D[d++] = (sauchar_t)c;
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i += p;
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}
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}
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for(i = 0; i < idx; ++i) { B[C[T[i]]++] = i; }
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for( ; i < n; ++i) { B[C[T[i]]++] = i + 1; }
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for(c = 0; c < d; ++c) { C[c] = C[D[c]]; }
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for(i = 0, p = idx; i < n; ++i) {
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U[i] = D[binarysearch_lower(C, d, p)];
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p = B[p - 1];
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}
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if(A == NULL) {
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/* Deallocate memory. */
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free(B);
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}
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return 0;
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}
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/* Checks the suffix array SA of the string T. */
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saint_t
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sufcheck(const sauchar_t *T, const saidx_t *SA,
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saidx_t n, saint_t verbose) {
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saidx_t C[ALPHABET_SIZE];
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saidx_t i, p, q, t;
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saint_t c;
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if(verbose) { fprintf(stderr, "sufcheck: "); }
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/* Check arguments. */
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if((T == NULL) || (SA == NULL) || (n < 0)) {
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if(verbose) { fprintf(stderr, "Invalid arguments.\n"); }
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return -1;
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}
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if(n == 0) {
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if(verbose) { fprintf(stderr, "Done.\n"); }
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return 0;
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}
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/* check range: [0..n-1] */
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for(i = 0; i < n; ++i) {
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if((SA[i] < 0) || (n <= SA[i])) {
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if(verbose) {
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fprintf(stderr, "Out of the range [0,%" PRIdSAIDX_T "].\n"
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" SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
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n - 1, i, SA[i]);
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}
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return -2;
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}
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}
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/* check first characters. */
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for(i = 1; i < n; ++i) {
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if(T[SA[i - 1]] > T[SA[i]]) {
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if(verbose) {
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fprintf(stderr, "Suffixes in wrong order.\n"
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" T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d"
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" > T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d\n",
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i - 1, SA[i - 1], T[SA[i - 1]], i, SA[i], T[SA[i]]);
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}
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return -3;
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}
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}
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/* check suffixes. */
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for(i = 0; i < ALPHABET_SIZE; ++i) { C[i] = 0; }
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for(i = 0; i < n; ++i) { ++C[T[i]]; }
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for(i = 0, p = 0; i < ALPHABET_SIZE; ++i) {
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t = C[i];
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C[i] = p;
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p += t;
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}
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q = C[T[n - 1]];
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C[T[n - 1]] += 1;
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for(i = 0; i < n; ++i) {
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p = SA[i];
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if(0 < p) {
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c = T[--p];
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t = C[c];
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} else {
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c = T[p = n - 1];
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t = q;
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}
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if((t < 0) || (p != SA[t])) {
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if(verbose) {
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fprintf(stderr, "Suffix in wrong position.\n"
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" SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T " or\n"
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" SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
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t, (0 <= t) ? SA[t] : -1, i, SA[i]);
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}
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return -4;
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}
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if(t != q) {
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++C[c];
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if((n <= C[c]) || (T[SA[C[c]]] != c)) { C[c] = -1; }
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}
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}
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if(1 <= verbose) { fprintf(stderr, "Done.\n"); }
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return 0;
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}
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static
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int
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_compare(const sauchar_t *T, saidx_t Tsize,
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const sauchar_t *P, saidx_t Psize,
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saidx_t suf, saidx_t *match) {
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saidx_t i, j;
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saint_t r;
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for(i = suf + *match, j = *match, r = 0;
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(i < Tsize) && (j < Psize) && ((r = T[i] - P[j]) == 0); ++i, ++j) { }
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*match = j;
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return (r == 0) ? -(j != Psize) : r;
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}
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/* Search for the pattern P in the string T. */
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saidx_t
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sa_search(const sauchar_t *T, saidx_t Tsize,
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const sauchar_t *P, saidx_t Psize,
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const saidx_t *SA, saidx_t SAsize,
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saidx_t *idx) {
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saidx_t size, lsize, rsize, half;
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saidx_t match, lmatch, rmatch;
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saidx_t llmatch, lrmatch, rlmatch, rrmatch;
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saidx_t i, j, k;
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saint_t r;
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if(idx != NULL) { *idx = -1; }
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if((T == NULL) || (P == NULL) || (SA == NULL) ||
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(Tsize < 0) || (Psize < 0) || (SAsize < 0)) { return -1; }
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if((Tsize == 0) || (SAsize == 0)) { return 0; }
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if(Psize == 0) { if(idx != NULL) { *idx = 0; } return SAsize; }
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for(i = j = k = 0, lmatch = rmatch = 0, size = SAsize, half = size >> 1;
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0 < size;
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size = half, half >>= 1) {
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match = MIN(lmatch, rmatch);
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r = _compare(T, Tsize, P, Psize, SA[i + half], &match);
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if(r < 0) {
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i += half + 1;
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half -= (size & 1) ^ 1;
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lmatch = match;
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} else if(r > 0) {
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rmatch = match;
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} else {
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lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
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/* left part */
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for(llmatch = lmatch, lrmatch = match, half = lsize >> 1;
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0 < lsize;
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lsize = half, half >>= 1) {
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lmatch = MIN(llmatch, lrmatch);
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r = _compare(T, Tsize, P, Psize, SA[j + half], &lmatch);
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if(r < 0) {
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j += half + 1;
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half -= (lsize & 1) ^ 1;
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llmatch = lmatch;
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} else {
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lrmatch = lmatch;
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}
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}
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/* right part */
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for(rlmatch = match, rrmatch = rmatch, half = rsize >> 1;
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0 < rsize;
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rsize = half, half >>= 1) {
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rmatch = MIN(rlmatch, rrmatch);
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r = _compare(T, Tsize, P, Psize, SA[k + half], &rmatch);
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if(r <= 0) {
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k += half + 1;
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half -= (rsize & 1) ^ 1;
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rlmatch = rmatch;
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} else {
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rrmatch = rmatch;
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}
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}
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break;
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}
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}
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if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
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return k - j;
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}
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/* Search for the character c in the string T. */
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saidx_t
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sa_simplesearch(const sauchar_t *T, saidx_t Tsize,
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const saidx_t *SA, saidx_t SAsize,
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saint_t c, saidx_t *idx) {
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saidx_t size, lsize, rsize, half;
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saidx_t i, j, k, p;
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saint_t r;
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if(idx != NULL) { *idx = -1; }
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if((T == NULL) || (SA == NULL) || (Tsize < 0) || (SAsize < 0)) { return -1; }
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if((Tsize == 0) || (SAsize == 0)) { return 0; }
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for(i = j = k = 0, size = SAsize, half = size >> 1;
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0 < size;
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size = half, half >>= 1) {
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p = SA[i + half];
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r = (p < Tsize) ? T[p] - c : -1;
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if(r < 0) {
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i += half + 1;
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half -= (size & 1) ^ 1;
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} else if(r == 0) {
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lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
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/* left part */
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for(half = lsize >> 1;
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0 < lsize;
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lsize = half, half >>= 1) {
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p = SA[j + half];
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r = (p < Tsize) ? T[p] - c : -1;
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if(r < 0) {
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j += half + 1;
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half -= (lsize & 1) ^ 1;
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}
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}
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/* right part */
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for(half = rsize >> 1;
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0 < rsize;
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rsize = half, half >>= 1) {
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p = SA[k + half];
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r = (p < Tsize) ? T[p] - c : -1;
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if(r <= 0) {
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k += half + 1;
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half -= (rsize & 1) ^ 1;
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}
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}
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break;
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}
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}
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if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
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return k - j;
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}
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#endif
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