mirror of
https://github.com/google/brotli.git
synced 2024-11-09 21:50:07 +00:00
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 @@
|
||||
[submodule "terryfy"]
|
||||
path = terryfy
|
||||
url = https://github.com/MacPython/terryfy.git
|
||||
[submodule "research/esaxx"]
|
||||
path = research/esaxx
|
||||
url = https://github.com/hillbig/esaxx
|
||||
|
||||
1
research/esaxx
Submodule
1
research/esaxx
Submodule
@ -0,0 +1 @@
|
||||
Subproject commit ca7cb332011ec37a8436487f210f396b84bd8273
|
||||
@ -13,7 +13,7 @@
|
||||
#include <cstdio>
|
||||
#include <cstring>
|
||||
|
||||
#include "./sais.hxx"
|
||||
#include "./esaxx/sais.hxx"
|
||||
|
||||
const int FLAGS_min_length = 1; // Minimal length of found backward references.
|
||||
const int FLAGS_skip = 1; // Number of bytes to skip.
|
||||
|
||||
@ -1,364 +0,0 @@
|
||||
/*
|
||||
* sais.hxx for sais-lite
|
||||
* Copyright (c) 2008-2009 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.
|
||||
*/
|
||||
|
||||
#ifndef _SAIS_HXX
|
||||
#define _SAIS_HXX 1
|
||||
#ifdef __cplusplus
|
||||
|
||||
#ifdef __INTEL_COMPILER
|
||||
#pragma warning(disable : 383 981 1418)
|
||||
// for icc 64-bit
|
||||
//#define __builtin_vsnprintf(a, b, c, d) __builtin_vsnprintf(a, b, c, (char *)d)
|
||||
#endif
|
||||
|
||||
#include <iterator>
|
||||
#ifdef _OPENMP
|
||||
# include <omp.h>
|
||||
#endif
|
||||
|
||||
namespace saisxx_private {
|
||||
|
||||
/* find the start or end of each bucket */
|
||||
template<typename string_type, typename bucket_type, typename index_type>
|
||||
void
|
||||
getCounts(const string_type T, bucket_type C, index_type n, index_type k) {
|
||||
#ifdef _OPENMP
|
||||
bucket_type D;
|
||||
index_type i, j, p, sum, first, last;
|
||||
int thnum, maxthreads = omp_get_max_threads();
|
||||
#pragma omp parallel default(shared) private(D, i, thnum, first, last)
|
||||
{
|
||||
thnum = omp_get_thread_num();
|
||||
D = C + thnum * k;
|
||||
first = n / maxthreads * thnum;
|
||||
last = (thnum < (maxthreads - 1)) ? n / maxthreads * (thnum + 1) : n;
|
||||
for(i = 0; i < k; ++i) { D[i] = 0; }
|
||||
for(i = first; i < last; ++i) { ++D[T[i]]; }
|
||||
}
|
||||
if(1 < maxthreads) {
|
||||
#pragma omp parallel for default(shared) private(i, j, p, sum)
|
||||
for(i = 0; i < k; ++i) {
|
||||
for(j = 1, p = i + k, sum = C[i]; j < maxthreads; ++j, p += k) {
|
||||
sum += C[p];
|
||||
}
|
||||
C[i] = sum;
|
||||
}
|
||||
}
|
||||
#else
|
||||
index_type i;
|
||||
for(i = 0; i < k; ++i) { C[i] = 0; }
|
||||
for(i = 0; i < n; ++i) { ++C[T[i]]; }
|
||||
#endif
|
||||
}
|
||||
template<typename bucket_type, typename index_type>
|
||||
void
|
||||
getBuckets(const bucket_type C, bucket_type B, index_type k, bool end) {
|
||||
index_type i, sum = 0;
|
||||
if(end) { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum; } }
|
||||
else { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum - C[i]; } }
|
||||
}
|
||||
|
||||
/* compute SA and BWT */
|
||||
template<typename string_type, typename sarray_type,
|
||||
typename bucket_type, typename index_type>
|
||||
void
|
||||
induceSA(string_type T, sarray_type SA, bucket_type C, bucket_type B,
|
||||
index_type n, index_type k) {
|
||||
typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
sarray_type b;
|
||||
index_type i, j;
|
||||
char_type c0, c1;
|
||||
/* compute SAl */
|
||||
if(C == B) { getCounts(T, C, n, k); }
|
||||
getBuckets(C, B, k, false); /* find starts of buckets */
|
||||
b = SA + B[c1 = T[j = n - 1]];
|
||||
*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
for(i = 0; i < n; ++i) {
|
||||
j = SA[i], SA[i] = ~j;
|
||||
if(0 < j) {
|
||||
if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
}
|
||||
}
|
||||
/* compute SAs */
|
||||
if(C == B) { getCounts(T, C, n, k); }
|
||||
getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
|
||||
if(0 < (j = SA[i])) {
|
||||
if((c0 = T[--j]) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
*--b = ((j == 0) || (T[j - 1] > c1)) ? ~j : j;
|
||||
} else {
|
||||
SA[i] = ~j;
|
||||
}
|
||||
}
|
||||
}
|
||||
template<typename string_type, typename sarray_type,
|
||||
typename bucket_type, typename index_type>
|
||||
int
|
||||
computeBWT(string_type T, sarray_type SA, bucket_type C, bucket_type B,
|
||||
index_type n, index_type k) {
|
||||
typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
sarray_type b;
|
||||
index_type i, j, pidx = -1;
|
||||
char_type c0, c1;
|
||||
/* compute SAl */
|
||||
if(C == B) { getCounts(T, C, n, k); }
|
||||
getBuckets(C, B, k, false); /* find starts of buckets */
|
||||
b = SA + B[c1 = T[j = n - 1]];
|
||||
*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
for(i = 0; i < n; ++i) {
|
||||
if(0 < (j = SA[i])) {
|
||||
SA[i] = ~(c0 = T[--j]);
|
||||
if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
*b++ = ((0 < j) && (T[j - 1] < c1)) ? ~j : j;
|
||||
} else if(j != 0) {
|
||||
SA[i] = ~j;
|
||||
}
|
||||
}
|
||||
/* compute SAs */
|
||||
if(C == B) { getCounts(T, C, n, k); }
|
||||
getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
|
||||
if(0 < (j = SA[i])) {
|
||||
SA[i] = (c0 = T[--j]);
|
||||
if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
|
||||
*--b = ((0 < j) && (T[j - 1] > c1)) ? ~((index_type)T[j - 1]) : j;
|
||||
} else if(j != 0) {
|
||||
SA[i] = ~j;
|
||||
} else {
|
||||
pidx = i;
|
||||
}
|
||||
}
|
||||
return pidx;
|
||||
}
|
||||
|
||||
/* find the suffix array SA of T[0..n-1] in {0..k}^n
|
||||
use a working space (excluding s and SA) of at most 2n+O(1) for a constant alphabet */
|
||||
template<typename string_type, typename sarray_type, typename index_type>
|
||||
int
|
||||
suffixsort(string_type T, sarray_type SA,
|
||||
index_type fs, index_type n, index_type k,
|
||||
bool isbwt) {
|
||||
typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
sarray_type RA;
|
||||
index_type i, j, m, p, q, plen, qlen, name, pidx = 0;
|
||||
bool diff;
|
||||
int c;
|
||||
#ifdef _OPENMP
|
||||
int maxthreads = omp_get_max_threads();
|
||||
#else
|
||||
# define maxthreads 1
|
||||
#endif
|
||||
char_type c0, c1;
|
||||
|
||||
/* stage 1: reduce the problem by at least 1/2
|
||||
sort all the S-substrings */
|
||||
if(fs < (maxthreads * k)) {
|
||||
index_type *C, *B;
|
||||
if((C = new index_type[maxthreads * k]) == 0) { return -2; }
|
||||
B = (1 < maxthreads) ? C + k : C;
|
||||
getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = 0; i < n; ++i) { SA[i] = 0; }
|
||||
for(i = n - 2, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
else if(c != 0) { SA[--B[c1]] = i + 1, c = 0; }
|
||||
}
|
||||
induceSA(T, SA, C, B, n, k);
|
||||
delete [] C;
|
||||
} else {
|
||||
sarray_type C, B;
|
||||
C = SA + n;
|
||||
B = ((1 < maxthreads) || (k <= (fs - k))) ? C + k : C;
|
||||
getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = 0; i < n; ++i) { SA[i] = 0; }
|
||||
for(i = n - 2, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
else if(c != 0) { SA[--B[c1]] = i + 1, c = 0; }
|
||||
}
|
||||
induceSA(T, SA, C, B, n, k);
|
||||
}
|
||||
|
||||
/* compact all the sorted substrings into the first m items of SA
|
||||
2*m must be not larger than n (proveable) */
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i, j, p, c0, c1)
|
||||
for(i = 0; i < n; ++i) {
|
||||
p = SA[i];
|
||||
if((0 < p) && (T[p - 1] > (c0 = T[p]))) {
|
||||
for(j = p + 1; (j < n) && (c0 == (c1 = T[j])); ++j) { }
|
||||
if((j < n) && (c0 < c1)) { SA[i] = ~p; }
|
||||
}
|
||||
}
|
||||
for(i = 0, m = 0; i < n; ++i) { if((p = SA[i]) < 0) { SA[m++] = ~p; } }
|
||||
#else
|
||||
for(i = 0, m = 0; i < n; ++i) {
|
||||
p = SA[i];
|
||||
if((0 < p) && (T[p - 1] > (c0 = T[p]))) {
|
||||
for(j = p + 1; (j < n) && (c0 == (c1 = T[j])); ++j) { }
|
||||
if((j < n) && (c0 < c1)) { SA[m++] = p; }
|
||||
}
|
||||
}
|
||||
#endif
|
||||
j = m + (n >> 1);
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = m; i < j; ++i) { SA[i] = 0; } /* init the name array buffer */
|
||||
/* store the length of all substrings */
|
||||
for(i = n - 2, j = n, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
else if(c != 0) { SA[m + ((i + 1) >> 1)] = j - i - 1; j = i + 1; c = 0; }
|
||||
}
|
||||
/* find the lexicographic names of all substrings */
|
||||
for(i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
|
||||
p = SA[i], plen = SA[m + (p >> 1)], diff = true;
|
||||
if(plen == qlen) {
|
||||
for(j = 0; (j < plen) && (T[p + j] == T[q + j]); ++j) { }
|
||||
if(j == plen) { diff = false; }
|
||||
}
|
||||
if(diff != false) { ++name, q = p, qlen = plen; }
|
||||
SA[m + (p >> 1)] = name;
|
||||
}
|
||||
|
||||
/* stage 2: solve the reduced problem
|
||||
recurse if names are not yet unique */
|
||||
if(name < m) {
|
||||
RA = SA + n + fs - m;
|
||||
for(i = m + (n >> 1) - 1, j = m - 1; m <= i; --i) {
|
||||
if(SA[i] != 0) { RA[j--] = SA[i] - 1; }
|
||||
}
|
||||
if(suffixsort(RA, SA, fs + n - m * 2, m, name, false) != 0) { return -2; }
|
||||
for(i = n - 2, j = m - 1, c = 0, c1 = T[n - 1]; 0 <= i; --i, c1 = c0) {
|
||||
if((c0 = T[i]) < (c1 + c)) { c = 1; }
|
||||
else if(c != 0) { RA[j--] = i + 1, c = 0; } /* get p1 */
|
||||
}
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = 0; i < m; ++i) { SA[i] = RA[SA[i]]; } /* get index in s */
|
||||
}
|
||||
|
||||
/* stage 3: induce the result for the original problem */
|
||||
if(fs < (maxthreads * k)) {
|
||||
index_type *B, *C;
|
||||
if((C = new index_type[maxthreads * k]) == 0) { return -2; }
|
||||
B = (1 < maxthreads) ? C + k : C;
|
||||
/* put all left-most S characters into their buckets */
|
||||
getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = m; i < n; ++i) { SA[i] = 0; } /* init SA[m..n-1] */
|
||||
for(i = m - 1; 0 <= i; --i) {
|
||||
j = SA[i], SA[i] = 0;
|
||||
SA[--B[T[j]]] = j;
|
||||
}
|
||||
if(isbwt == false) { induceSA(T, SA, C, B, n, k); }
|
||||
else { pidx = computeBWT(T, SA, C, B, n, k); }
|
||||
delete [] C;
|
||||
} else {
|
||||
sarray_type C, B;
|
||||
C = SA + n;
|
||||
B = ((1 < maxthreads) || (k <= (fs - k))) ? C + k : C;
|
||||
/* put all left-most S characters into their buckets */
|
||||
getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
|
||||
#ifdef _OPENMP
|
||||
#pragma omp parallel for default(shared) private(i)
|
||||
#endif
|
||||
for(i = m; i < n; ++i) { SA[i] = 0; } /* init SA[m..n-1] */
|
||||
for(i = m - 1; 0 <= i; --i) {
|
||||
j = SA[i], SA[i] = 0;
|
||||
SA[--B[T[j]]] = j;
|
||||
}
|
||||
if(isbwt == false) { induceSA(T, SA, C, B, n, k); }
|
||||
else { pidx = computeBWT(T, SA, C, B, n, k); }
|
||||
}
|
||||
|
||||
return pidx;
|
||||
#ifndef _OPENMP
|
||||
# undef maxthreads
|
||||
#endif
|
||||
}
|
||||
|
||||
} /* namespace saisxx_private */
|
||||
|
||||
|
||||
/**
|
||||
* @brief Constructs the suffix array of a given string in linear time.
|
||||
* @param T[0..n-1] The input string. (random access iterator)
|
||||
* @param SA[0..n-1] The output array of suffixes. (random access iterator)
|
||||
* @param n The length of the given string.
|
||||
* @param k The alphabet size.
|
||||
* @return 0 if no error occurred, -1 or -2 otherwise.
|
||||
*/
|
||||
template<typename string_type, typename sarray_type, typename index_type>
|
||||
int
|
||||
saisxx(string_type T, sarray_type SA, index_type n, index_type k = 256) {
|
||||
int err;
|
||||
if((n < 0) || (k <= 0)) { return -1; }
|
||||
if(n <= 1) { if(n == 1) { SA[0] = 0; } return 0; }
|
||||
try { err = saisxx_private::suffixsort(T, SA, 0, n, k, false); }
|
||||
catch(...) { err = -2; }
|
||||
return err;
|
||||
}
|
||||
|
||||
/**
|
||||
* @brief Constructs the burrows-wheeler transformed string of a given string in linear time.
|
||||
* @param T[0..n-1] The input string. (random access iterator)
|
||||
* @param U[0..n-1] The output string. (random access iterator)
|
||||
* @param A[0..n-1] The temporary array. (random access iterator)
|
||||
* @param n The length of the given string.
|
||||
* @param k The alphabet size.
|
||||
* @return The primary index if no error occurred, -1 or -2 otherwise.
|
||||
*/
|
||||
template<typename string_type, typename sarray_type, typename index_type>
|
||||
index_type
|
||||
saisxx_bwt(string_type T, string_type U, sarray_type A, index_type n, index_type k = 256) {
|
||||
typedef typename std::iterator_traits<string_type>::value_type char_type;
|
||||
index_type i, pidx;
|
||||
if((n < 0) || (k <= 0)) { return -1; }
|
||||
if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
|
||||
try {
|
||||
pidx = saisxx_private::suffixsort(T, A, 0, n, k, true);
|
||||
if(0 <= pidx) {
|
||||
U[0] = T[n - 1];
|
||||
for(i = 0; i < pidx; ++i) { U[i + 1] = (char_type)A[i]; }
|
||||
for(i += 1; i < n; ++i) { U[i] = (char_type)A[i]; }
|
||||
pidx += 1;
|
||||
}
|
||||
} catch(...) { pidx = -2; }
|
||||
return pidx;
|
||||
}
|
||||
|
||||
|
||||
#endif /* __cplusplus */
|
||||
#endif /* _SAIS_HXX */
|
||||
Loading…
Reference in New Issue
Block a user