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398 lines
12 KiB
398 lines
12 KiB
/* |
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* divsufsort.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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#ifdef _OPENMP |
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# include <omp.h> |
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#endif |
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/*- Private Functions -*/ |
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/* Sorts suffixes of type B*. */ |
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static |
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saidx_t |
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sort_typeBstar(const sauchar_t *T, saidx_t *SA, |
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saidx_t *bucket_A, saidx_t *bucket_B, |
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saidx_t n) { |
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saidx_t *PAb, *ISAb, *buf; |
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#ifdef _OPENMP |
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saidx_t *curbuf; |
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saidx_t l; |
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#endif |
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saidx_t i, j, k, t, m, bufsize; |
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saint_t c0, c1; |
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#ifdef _OPENMP |
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saint_t d0, d1; |
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int tmp; |
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#endif |
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/* Initialize bucket arrays. */ |
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for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; } |
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for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; } |
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/* Count the number of occurrences of the first one or two characters of each |
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type A, B and B* suffix. Moreover, store the beginning position of all |
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type B* suffixes into the array SA. */ |
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for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) { |
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/* type A suffix. */ |
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do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1)); |
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if(0 <= i) { |
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/* type B* suffix. */ |
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++BUCKET_BSTAR(c0, c1); |
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SA[--m] = i; |
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/* type B suffix. */ |
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for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { |
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++BUCKET_B(c0, c1); |
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} |
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} |
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} |
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m = n - m; |
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/* |
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note: |
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A type B* suffix is lexicographically smaller than a type B suffix that |
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begins with the same first two characters. |
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*/ |
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/* Calculate the index of start/end point of each bucket. */ |
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for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) { |
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t = i + BUCKET_A(c0); |
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BUCKET_A(c0) = i + j; /* start point */ |
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i = t + BUCKET_B(c0, c0); |
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for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) { |
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j += BUCKET_BSTAR(c0, c1); |
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BUCKET_BSTAR(c0, c1) = j; /* end point */ |
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i += BUCKET_B(c0, c1); |
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} |
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} |
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if(0 < m) { |
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/* Sort the type B* suffixes by their first two characters. */ |
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PAb = SA + n - m; ISAb = SA + m; |
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for(i = m - 2; 0 <= i; --i) { |
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t = PAb[i], c0 = T[t], c1 = T[t + 1]; |
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SA[--BUCKET_BSTAR(c0, c1)] = i; |
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} |
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t = PAb[m - 1], c0 = T[t], c1 = T[t + 1]; |
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SA[--BUCKET_BSTAR(c0, c1)] = m - 1; |
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/* Sort the type B* substrings using sssort. */ |
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#ifdef _OPENMP |
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tmp = omp_get_max_threads(); |
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buf = SA + m, bufsize = (n - (2 * m)) / tmp; |
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c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m; |
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#pragma omp parallel default(shared) private(curbuf, k, l, d0, d1, tmp) |
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{ |
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tmp = omp_get_thread_num(); |
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curbuf = buf + tmp * bufsize; |
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k = 0; |
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for(;;) { |
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#pragma omp critical(sssort_lock) |
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{ |
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if(0 < (l = j)) { |
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d0 = c0, d1 = c1; |
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do { |
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k = BUCKET_BSTAR(d0, d1); |
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if(--d1 <= d0) { |
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d1 = ALPHABET_SIZE - 1; |
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if(--d0 < 0) { break; } |
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} |
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} while(((l - k) <= 1) && (0 < (l = k))); |
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c0 = d0, c1 = d1, j = k; |
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} |
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} |
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if(l == 0) { break; } |
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sssort(T, PAb, SA + k, SA + l, |
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curbuf, bufsize, 2, n, *(SA + k) == (m - 1)); |
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} |
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} |
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#else |
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buf = SA + m, bufsize = n - (2 * m); |
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for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) { |
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for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) { |
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i = BUCKET_BSTAR(c0, c1); |
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if(1 < (j - i)) { |
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sssort(T, PAb, SA + i, SA + j, |
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buf, bufsize, 2, n, *(SA + i) == (m - 1)); |
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} |
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} |
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} |
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#endif |
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/* Compute ranks of type B* substrings. */ |
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for(i = m - 1; 0 <= i; --i) { |
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if(0 <= SA[i]) { |
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j = i; |
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do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i])); |
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SA[i + 1] = i - j; |
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if(i <= 0) { break; } |
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} |
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j = i; |
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do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0); |
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ISAb[SA[i]] = j; |
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} |
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/* Construct the inverse suffix array of type B* suffixes using trsort. */ |
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trsort(ISAb, SA, m, 1); |
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/* Set the sorted order of tyoe B* suffixes. */ |
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for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) { |
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for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { } |
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if(0 <= i) { |
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t = i; |
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for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { } |
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SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t; |
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} |
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} |
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/* Calculate the index of start/end point of each bucket. */ |
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BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */ |
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for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) { |
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i = BUCKET_A(c0 + 1) - 1; |
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for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) { |
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t = i - BUCKET_B(c0, c1); |
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BUCKET_B(c0, c1) = i; /* end point */ |
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/* Move all type B* suffixes to the correct position. */ |
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for(i = t, j = BUCKET_BSTAR(c0, c1); |
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j <= k; |
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--i, --k) { SA[i] = SA[k]; } |
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} |
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BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */ |
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BUCKET_B(c0, c0) = i; /* end point */ |
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} |
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} |
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return m; |
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} |
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/* Constructs the suffix array by using the sorted order of type B* suffixes. */ |
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static |
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void |
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construct_SA(const sauchar_t *T, saidx_t *SA, |
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saidx_t *bucket_A, saidx_t *bucket_B, |
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saidx_t n, saidx_t m) { |
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saidx_t *i, *j, *k; |
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saidx_t s; |
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saint_t c0, c1, c2; |
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if(0 < m) { |
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/* Construct the sorted order of type B suffixes by using |
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the sorted order of type B* suffixes. */ |
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for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) { |
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/* Scan the suffix array from right to left. */ |
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for(i = SA + BUCKET_BSTAR(c1, c1 + 1), |
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j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1; |
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i <= j; |
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--j) { |
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if(0 < (s = *j)) { |
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assert(T[s] == c1); |
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assert(((s + 1) < n) && (T[s] <= T[s + 1])); |
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assert(T[s - 1] <= T[s]); |
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*j = ~s; |
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c0 = T[--s]; |
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if((0 < s) && (T[s - 1] > c0)) { s = ~s; } |
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if(c0 != c2) { |
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if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; } |
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k = SA + BUCKET_B(c2 = c0, c1); |
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} |
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assert(k < j); |
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*k-- = s; |
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} else { |
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assert(((s == 0) && (T[s] == c1)) || (s < 0)); |
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*j = ~s; |
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} |
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} |
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} |
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} |
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/* Construct the suffix array by using |
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the sorted order of type B suffixes. */ |
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k = SA + BUCKET_A(c2 = T[n - 1]); |
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*k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1); |
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/* Scan the suffix array from left to right. */ |
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for(i = SA, j = SA + n; i < j; ++i) { |
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if(0 < (s = *i)) { |
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assert(T[s - 1] >= T[s]); |
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c0 = T[--s]; |
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if((s == 0) || (T[s - 1] < c0)) { s = ~s; } |
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if(c0 != c2) { |
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BUCKET_A(c2) = k - SA; |
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k = SA + BUCKET_A(c2 = c0); |
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} |
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assert(i < k); |
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*k++ = s; |
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} else { |
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assert(s < 0); |
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*i = ~s; |
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} |
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} |
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} |
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/* Constructs the burrows-wheeler transformed string directly |
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by using the sorted order of type B* suffixes. */ |
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static |
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saidx_t |
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construct_BWT(const sauchar_t *T, saidx_t *SA, |
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saidx_t *bucket_A, saidx_t *bucket_B, |
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saidx_t n, saidx_t m) { |
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saidx_t *i, *j, *k, *orig; |
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saidx_t s; |
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saint_t c0, c1, c2; |
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if(0 < m) { |
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/* Construct the sorted order of type B suffixes by using |
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the sorted order of type B* suffixes. */ |
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for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) { |
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/* Scan the suffix array from right to left. */ |
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for(i = SA + BUCKET_BSTAR(c1, c1 + 1), |
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j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1; |
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i <= j; |
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--j) { |
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if(0 < (s = *j)) { |
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assert(T[s] == c1); |
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assert(((s + 1) < n) && (T[s] <= T[s + 1])); |
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assert(T[s - 1] <= T[s]); |
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c0 = T[--s]; |
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*j = ~((saidx_t)c0); |
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if((0 < s) && (T[s - 1] > c0)) { s = ~s; } |
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if(c0 != c2) { |
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if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; } |
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k = SA + BUCKET_B(c2 = c0, c1); |
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} |
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assert(k < j); |
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*k-- = s; |
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} else if(s != 0) { |
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*j = ~s; |
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#ifndef NDEBUG |
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} else { |
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assert(T[s] == c1); |
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#endif |
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} |
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} |
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} |
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} |
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/* Construct the BWTed string by using |
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the sorted order of type B suffixes. */ |
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k = SA + BUCKET_A(c2 = T[n - 1]); |
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*k++ = (T[n - 2] < c2) ? ~((saidx_t)T[n - 2]) : (n - 1); |
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/* Scan the suffix array from left to right. */ |
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for(i = SA, j = SA + n, orig = SA; i < j; ++i) { |
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if(0 < (s = *i)) { |
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assert(T[s - 1] >= T[s]); |
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c0 = T[--s]; |
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*i = c0; |
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if((0 < s) && (T[s - 1] < c0)) { s = ~((saidx_t)T[s - 1]); } |
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if(c0 != c2) { |
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BUCKET_A(c2) = k - SA; |
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k = SA + BUCKET_A(c2 = c0); |
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} |
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assert(i < k); |
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*k++ = s; |
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} else if(s != 0) { |
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*i = ~s; |
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} else { |
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orig = i; |
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} |
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} |
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return orig - SA; |
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} |
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/*---------------------------------------------------------------------------*/ |
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/*- Function -*/ |
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saint_t |
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divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n) { |
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saidx_t *bucket_A, *bucket_B; |
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saidx_t m; |
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saint_t err = 0; |
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/* Check arguments. */ |
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if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; } |
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else if(n == 0) { return 0; } |
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else if(n == 1) { SA[0] = 0; return 0; } |
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else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; } |
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bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t)); |
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bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t)); |
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/* Suffixsort. */ |
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if((bucket_A != NULL) && (bucket_B != NULL)) { |
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m = sort_typeBstar(T, SA, bucket_A, bucket_B, n); |
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construct_SA(T, SA, bucket_A, bucket_B, n, m); |
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} else { |
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err = -2; |
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} |
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free(bucket_B); |
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free(bucket_A); |
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return err; |
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} |
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saidx_t |
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divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n) { |
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saidx_t *B; |
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saidx_t *bucket_A, *bucket_B; |
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saidx_t m, pidx, i; |
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/* Check arguments. */ |
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if((T == NULL) || (U == NULL) || (n < 0)) { return -1; } |
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else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; } |
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if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); } |
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bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t)); |
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bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t)); |
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/* Burrows-Wheeler Transform. */ |
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if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) { |
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m = sort_typeBstar(T, B, bucket_A, bucket_B, n); |
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pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m); |
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/* Copy to output string. */ |
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U[0] = T[n - 1]; |
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for(i = 0; i < pidx; ++i) { U[i + 1] = (sauchar_t)B[i]; } |
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for(i += 1; i < n; ++i) { U[i] = (sauchar_t)B[i]; } |
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pidx += 1; |
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} else { |
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pidx = -2; |
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} |
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free(bucket_B); |
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free(bucket_A); |
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if(A == NULL) { free(B); } |
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return pidx; |
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} |
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const char * |
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divsufsort_version(void) { |
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return PROJECT_VERSION_FULL; |
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}
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