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Replace sais.hxx by submodule hillbig/esaxx.
This commit is contained in:
Ivan Nikulin
parent
4291932022
commit
9294022929
3
.gitmodules
vendored
3
.gitmodules
vendored
@ -1,3 +1,6 @@
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[submodule "terryfy"]
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path = terryfy
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url = https://github.com/MacPython/terryfy.git
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[submodule "research/esaxx"]
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path = research/esaxx
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url = https://github.com/hillbig/esaxx
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1
research/esaxx
Submodule
1
research/esaxx
Submodule
@ -0,0 +1 @@
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Subproject commit ca7cb332011ec37a8436487f210f396b84bd8273
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@ -13,7 +13,7 @@
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#include <cstdio>
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#include <cstring>
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#include "./sais.hxx"
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#include "./esaxx/sais.hxx"
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const int FLAGS_min_length = 1; // Minimal length of found backward references.
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const int FLAGS_skip = 1; // Number of bytes to skip.
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@ -1,364 +0,0 @@
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/*
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* sais.hxx for sais-lite
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* Copyright (c) 2008-2009 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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#ifndef _SAIS_HXX
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#define _SAIS_HXX 1
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#ifdef __cplusplus
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#ifdef __INTEL_COMPILER
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#pragma warning(disable : 383 981 1418)
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// for icc 64-bit
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//#define __builtin_vsnprintf(a, b, c, d) __builtin_vsnprintf(a, b, c, (char *)d)
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#endif
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#include <iterator>
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#ifdef _OPENMP
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# include <omp.h>
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#endif
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namespace saisxx_private {
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/* find the start or end of each bucket */
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template<typename string_type, typename bucket_type, typename index_type>
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void
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getCounts(const string_type T, bucket_type C, index_type n, index_type k) {
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#ifdef _OPENMP
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bucket_type D;
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index_type i, j, p, sum, first, last;
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int thnum, maxthreads = omp_get_max_threads();
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#pragma omp parallel default(shared) private(D, i, thnum, first, last)
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{
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thnum = omp_get_thread_num();
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D = C + thnum * k;
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first = n / maxthreads * thnum;
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last = (thnum < (maxthreads - 1)) ? n / maxthreads * (thnum + 1) : n;
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for(i = 0; i < k; ++i) { D[i] = 0; }
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for(i = first; i < last; ++i) { ++D[T[i]]; }
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}
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if(1 < maxthreads) {
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#pragma omp parallel for default(shared) private(i, j, p, sum)
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for(i = 0; i < k; ++i) {
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for(j = 1, p = i + k, sum = C[i]; j < maxthreads; ++j, p += k) {
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sum += C[p];
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}
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C[i] = sum;
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}
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}
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#else
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index_type i;
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for(i = 0; i < k; ++i) { C[i] = 0; }
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for(i = 0; i < n; ++i) { ++C[T[i]]; }
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#endif
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}
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template<typename bucket_type, typename index_type>
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void
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getBuckets(const bucket_type C, bucket_type B, index_type k, bool end) {
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index_type i, sum = 0;
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if(end) { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum; } }
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else { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum - C[i]; } }
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}
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/* compute SA and BWT */
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template<typename string_type, typename sarray_type,
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typename bucket_type, typename index_type>
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void
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induceSA(string_type T, sarray_type SA, bucket_type C, bucket_type B,
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index_type n, index_type k) {
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typedef typename std::iterator_traits<string_type>::value_type char_type;
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sarray_type b;
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index_type i, j;
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char_type c0, c1;
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/* compute SAl */
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if(C == B) { getCounts(T, C, n, k); }
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getBuckets(C, B, k, false); /* find starts of buckets */
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b = SA + B[c1 = T[j = n - 1]];
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*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
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for(i = 0; i < n; ++i) {
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j = SA[i], SA[i] = ~j;
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if(0 < j) {
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if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
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*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
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}
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}
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/* compute SAs */
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if(C == B) { getCounts(T, C, n, k); }
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getBuckets(C, B, k, true); /* find ends of buckets */
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for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
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if(0 < (j = SA[i])) {
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if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
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*--b = ((j == 0) || (T[j - 1] > c1)) ? ~j : j;
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} else {
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SA[i] = ~j;
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}
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}
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}
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template<typename string_type, typename sarray_type,
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typename bucket_type, typename index_type>
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int
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computeBWT(string_type T, sarray_type SA, bucket_type C, bucket_type B,
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index_type n, index_type k) {
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typedef typename std::iterator_traits<string_type>::value_type char_type;
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sarray_type b;
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index_type i, j, pidx = -1;
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char_type c0, c1;
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/* compute SAl */
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if(C == B) { getCounts(T, C, n, k); }
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getBuckets(C, B, k, false); /* find starts of buckets */
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b = SA + B[c1 = T[j = n - 1]];
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*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
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for(i = 0; i < n; ++i) {
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if(0 < (j = SA[i])) {
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SA[i] = ~(c0 = T[--j]);
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if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
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*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
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} else if(j != 0) {
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SA[i] = ~j;
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}
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}
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/* compute SAs */
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if(C == B) { getCounts(T, C, n, k); }
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getBuckets(C, B, k, true); /* find ends of buckets */
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for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
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if(0 < (j = SA[i])) {
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SA[i] = (c0 = T[--j]);
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if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
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*--b = ((0 < j) && (T[j - 1] > c1)) ? ~((index_type)T[j - 1]) : j;
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} else if(j != 0) {
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SA[i] = ~j;
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} else {
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pidx = i;
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}
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}
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return pidx;
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}
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/* find the suffix array SA of T[0..n-1] in {0..k}^n
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use a working space (excluding s and SA) of at most 2n+O(1) for a constant alphabet */
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template<typename string_type, typename sarray_type, typename index_type>
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int
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suffixsort(string_type T, sarray_type SA,
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index_type fs, index_type n, index_type k,
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bool isbwt) {
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typedef typename std::iterator_traits<string_type>::value_type char_type;
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sarray_type RA;
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index_type i, j, m, p, q, plen, qlen, name, pidx = 0;
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bool diff;
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int c;
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#ifdef _OPENMP
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int maxthreads = omp_get_max_threads();
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#else
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# define maxthreads 1
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#endif
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char_type c0, c1;
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/* stage 1: reduce the problem by at least 1/2
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sort all the S-substrings */
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if(fs < (maxthreads * k)) {
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index_type *C, *B;
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if((C = new index_type[maxthreads * k]) == 0) { return -2; }
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B = (1 < maxthreads) ? C + k : C;
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getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
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#ifdef _OPENMP
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#pragma omp parallel for default(shared) private(i)
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#endif
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for(i = 0; i < n; ++i) { SA[i] = 0; }
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for(i = n - 2, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
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if((c0 = T[i]) < (c1 + c)) { c = 1; }
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else if(c != 0) { SA[--B[c1]] = i + 1, c = 0; }
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}
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induceSA(T, SA, C, B, n, k);
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delete [] C;
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} else {
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sarray_type C, B;
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C = SA + n;
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B = ((1 < maxthreads) || (k <= (fs - k))) ? C + k : C;
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getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
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#ifdef _OPENMP
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#pragma omp parallel for default(shared) private(i)
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#endif
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for(i = 0; i < n; ++i) { SA[i] = 0; }
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for(i = n - 2, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
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if((c0 = T[i]) < (c1 + c)) { c = 1; }
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else if(c != 0) { SA[--B[c1]] = i + 1, c = 0; }
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}
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induceSA(T, SA, C, B, n, k);
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}
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/* compact all the sorted substrings into the first m items of SA
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2*m must be not larger than n (proveable) */
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#ifdef _OPENMP
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#pragma omp parallel for default(shared) private(i, j, p, c0, c1)
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for(i = 0; i < n; ++i) {
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p = SA[i];
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if((0 < p) && (T[p - 1] > (c0 = T[p]))) {
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for(j = p + 1; (j < n) && (c0 == (c1 = T[j])); ++j) { }
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if((j < n) && (c0 < c1)) { SA[i] = ~p; }
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}
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}
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for(i = 0, m = 0; i < n; ++i) { if((p = SA[i]) < 0) { SA[m++] = ~p; } }
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#else
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for(i = 0, m = 0; i < n; ++i) {
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p = SA[i];
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if((0 < p) && (T[p - 1] > (c0 = T[p]))) {
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for(j = p + 1; (j < n) && (c0 == (c1 = T[j])); ++j) { }
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if((j < n) && (c0 < c1)) { SA[m++] = p; }
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}
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}
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#endif
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j = m + (n >> 1);
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#ifdef _OPENMP
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#pragma omp parallel for default(shared) private(i)
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#endif
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for(i = m; i < j; ++i) { SA[i] = 0; } /* init the name array buffer */
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/* store the length of all substrings */
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for(i = n - 2, j = n, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
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if((c0 = T[i]) < (c1 + c)) { c = 1; }
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else if(c != 0) { SA[m + ((i + 1) >> 1)] = j - i - 1; j = i + 1; c = 0; }
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}
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/* find the lexicographic names of all substrings */
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for(i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
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p = SA[i], plen = SA[m + (p >> 1)], diff = true;
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if(plen == qlen) {
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for(j = 0; (j < plen) && (T[p + j] == T[q + j]); ++j) { }
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if(j == plen) { diff = false; }
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}
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if(diff != false) { ++name, q = p, qlen = plen; }
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SA[m + (p >> 1)] = name;
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}
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/* stage 2: solve the reduced problem
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recurse if names are not yet unique */
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if(name < m) {
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RA = SA + n + fs - m;
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for(i = m + (n >> 1) - 1, j = m - 1; m <= i; --i) {
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if(SA[i] != 0) { RA[j--] = SA[i] - 1; }
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}
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if(suffixsort(RA, SA, fs + n - m * 2, m, name, false) != 0) { return -2; }
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for(i = n - 2, j = m - 1, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
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if((c0 = T[i]) < (c1 + c)) { c = 1; }
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else if(c != 0) { RA[j--] = i + 1, c = 0; } /* get p1 */
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}
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#ifdef _OPENMP
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#pragma omp parallel for default(shared) private(i)
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#endif
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for(i = 0; i < m; ++i) { SA[i] = RA[SA[i]]; } /* get index in s */
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}
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/* stage 3: induce the result for the original problem */
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if(fs < (maxthreads * k)) {
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index_type *B, *C;
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if((C = new index_type[maxthreads * k]) == 0) { return -2; }
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B = (1 < maxthreads) ? C + k : C;
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/* put all left-most S characters into their buckets */
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getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
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#ifdef _OPENMP
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#pragma omp parallel for default(shared) private(i)
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#endif
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for(i = m; i < n; ++i) { SA[i] = 0; } /* init SA[m..n-1] */
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for(i = m - 1; 0 <= i; --i) {
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j = SA[i], SA[i] = 0;
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SA[--B[T[j]]] = j;
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}
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if(isbwt == false) { induceSA(T, SA, C, B, n, k); }
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else { pidx = computeBWT(T, SA, C, B, n, k); }
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delete [] C;
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} else {
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sarray_type C, B;
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C = SA + n;
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B = ((1 < maxthreads) || (k <= (fs - k))) ? C + k : C;
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/* put all left-most S characters into their buckets */
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getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
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#ifdef _OPENMP
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#pragma omp parallel for default(shared) private(i)
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#endif
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for(i = m; i < n; ++i) { SA[i] = 0; } /* init SA[m..n-1] */
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for(i = m - 1; 0 <= i; --i) {
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j = SA[i], SA[i] = 0;
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SA[--B[T[j]]] = j;
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}
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if(isbwt == false) { induceSA(T, SA, C, B, n, k); }
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else { pidx = computeBWT(T, SA, C, B, n, k); }
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}
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return pidx;
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#ifndef _OPENMP
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# undef maxthreads
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#endif
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}
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} /* namespace saisxx_private */
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/**
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* @brief Constructs the suffix array of a given string in linear time.
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* @param T[0..n-1] The input string. (random access iterator)
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* @param SA[0..n-1] The output array of suffixes. (random access iterator)
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* @param n The length of the given string.
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* @param k The alphabet size.
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* @return 0 if no error occurred, -1 or -2 otherwise.
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*/
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template<typename string_type, typename sarray_type, typename index_type>
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int
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saisxx(string_type T, sarray_type SA, index_type n, index_type k = 256) {
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int err;
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if((n < 0) || (k <= 0)) { return -1; }
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if(n <= 1) { if(n == 1) { SA[0] = 0; } return 0; }
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try { err = saisxx_private::suffixsort(T, SA, 0, n, k, false); }
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catch(...) { err = -2; }
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return err;
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}
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/**
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* @brief Constructs the burrows-wheeler transformed string of a given string in linear time.
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* @param T[0..n-1] The input string. (random access iterator)
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* @param U[0..n-1] The output string. (random access iterator)
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* @param A[0..n-1] The temporary array. (random access iterator)
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* @param n The length of the given string.
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* @param k The alphabet size.
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* @return The primary index if no error occurred, -1 or -2 otherwise.
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*/
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template<typename string_type, typename sarray_type, typename index_type>
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index_type
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saisxx_bwt(string_type T, string_type U, sarray_type A, index_type n, index_type k = 256) {
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typedef typename std::iterator_traits<string_type>::value_type char_type;
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index_type i, pidx;
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if((n < 0) || (k <= 0)) { return -1; }
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if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
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try {
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pidx = saisxx_private::suffixsort(T, A, 0, n, k, true);
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if(0 <= pidx) {
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U[0] = T[n - 1];
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for(i = 0; i < pidx; ++i) { U[i + 1] = (char_type)A[i]; }
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for(i += 1; i < n; ++i) { U[i] = (char_type)A[i]; }
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pidx += 1;
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}
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||||
} catch(...) { pidx = -2; }
|
||||
return pidx;
|
||||
}
|
||||
|
||||
|
||||
#endif /* __cplusplus */
|
||||
#endif /* _SAIS_HXX */
|
||||
Loading…
Reference in New Issue
Block a user