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Flips/sais.cpp
Alcaro 24e6c77eb8 Initial commit - version 1.31
2016-01-17 18:14:53 +01:00

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/*
* sais.c for sais-lite
* Copyright (c) 2008-2010 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.
*/
//This file is heavily modified from the original <https://sites.google.com/site/yuta256/sais>;
//while the algorithm is the same, many changes were done.
//- The 'cs' parameters (1 or 4, depending on whether T is int* or uint8_t*) were replaced with C++ templates. This gave a fair speedup.
//- sais_index_type was replaced with a C++ template.
//- bwt, and various other stuff I don't use, was removed.
//- Assertions were removed, as they too showed up heavily in profiles; however, I suspect that just shifted the time taken elsewhere.
#include <stdlib.h>
#include <stdint.h>
#undef assert
#define assert(x)
#ifndef MINBUCKETSIZE
# define MINBUCKETSIZE 256
#endif
#define SAIS_LMSSORT2_LIMIT 0x3fffffff
//static void* allocstack[256];
//static size_t allocstacklen[256];
//static size_t allocstackpos=0;
//static size_t allocstacksum=0;
//static size_t allocstackmax=0;
//static void* mymalloc(size_t n)
//{
// void* ret=malloc(n);
// allocstacksum+=n;
// if(allocstacksum>allocstackmax)allocstackmax=allocstacksum;
// printf("a %p(%i) (max %i)\n",ret,n,allocstackmax);
// allocstacklen[allocstackpos]=n;
// allocstack[allocstackpos]=ret;
// allocstackpos++;
// return ret;
//}
//static void myfree(void* p)
//{
// printf("f %p\n",p);
// allocstackpos--;
// allocstacksum-=allocstacklen[allocstackpos];
// if (p!=allocstack[allocstackpos]) printf("E: not stack\n");
// if (allocstackpos==0) allocstackmax=0;
// free(p);
//}
#define SAIS_MYMALLOC(_num, _type) ((_type *)malloc((_num) * sizeof(_type)))
#define SAIS_MYFREE(_ptr, _num, _type) free((_ptr))
#define chr(_a) T[_a]
/* find the start or end of each bucket */
template<typename sais_index_type, typename TT>
static
void
getCounts(const TT *T, sais_index_type *C, sais_index_type n, sais_index_type k) {
sais_index_type i;
for(i = 0; i < k; ++i) { C[i] = 0; }
for(i = 0; i < n; ++i) { ++C[chr(i)]; }
}
template<typename sais_index_type>
static
void
getBuckets(const sais_index_type *C, sais_index_type *B, sais_index_type k, bool end) {
sais_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]; } }
}
/* sort all type LMS suffixes */
template<typename sais_index_type, typename TT>
static
void
LMSsort1(const TT *T, sais_index_type *SA,
sais_index_type *C, sais_index_type *B,
sais_index_type n, sais_index_type k) {
sais_index_type *b, i, j;
sais_index_type c0, c1;
/* compute SAl */
if(C == B) { getCounts(T, C, n, k); }
getBuckets(C, B, k, false); /* find starts of buckets */
j = n - 1;
b = SA + B[c1 = chr(j)];
--j;
*b++ = (chr(j) < c1) ? ~j : j;
for(i = 0; i < n; ++i) {
if(0 < (j = SA[i])) {
assert(chr(j) >= chr(j + 1));
if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
assert(i < (b - SA));
--j;
*b++ = (chr(j) < c1) ? ~j : j;
SA[i] = 0;
} 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])) {
assert(chr(j) <= chr(j + 1));
if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
assert((b - SA) <= i);
--j;
*--b = (chr(j) > c1) ? ~(j + 1) : j;
SA[i] = 0;
}
}
}
template<typename sais_index_type, typename TT>
static
sais_index_type
LMSpostproc1(const TT *T, sais_index_type *SA,
sais_index_type n, sais_index_type m) {
sais_index_type i, j, p, q, plen, qlen, name;
sais_index_type c0, c1;
bool diff;
/* compact all the sorted substrings into the first m items of SA
2*m must be not larger than n (proveable) */
assert(0 < n);
for(i = 0; (p = SA[i]) < 0; ++i) { SA[i] = ~p; assert((i + 1) < n); }
if(i < m) {
for(j = i, ++i;; ++i) {
assert(i < n);
if((p = SA[i]) < 0) {
SA[j++] = ~p; SA[i] = 0;
if(j == m) { break; }
}
}
}
/* store the length of all substrings */
i = n - 1; j = n - 1; c0 = chr(n - 1);
do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1));
for(; 0 <= i;) {
do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) <= c1));
if(0 <= i) {
SA[m + ((i + 1) >> 1)] = j - i; j = i + 1;
do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1));
}
}
/* 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) && ((q + plen) < n)) {
for(j = 0; (j < plen) && (chr(p + j) == chr(q + j)); ++j) { }
if(j == plen) { diff = false; }
}
if(diff) { ++name, q = p, qlen = plen; }
SA[m + (p >> 1)] = name;
}
return name;
}
template<typename sais_index_type, typename TT>
static
void
LMSsort2(const TT *T, sais_index_type *SA,
sais_index_type *C, sais_index_type *B, sais_index_type *D,
sais_index_type n, sais_index_type k) {
sais_index_type *b, i, j, t, d;
sais_index_type c0, c1;
assert(C != B);
/* compute SAl */
getBuckets(C, B, k, false); /* find starts of buckets */
j = n - 1;
b = SA + B[c1 = chr(j)];
--j;
t = (chr(j) < c1);
j += n;
*b++ = (t & 1) ? ~j : j;
for(i = 0, d = 0; i < n; ++i) {
if(0 < (j = SA[i])) {
if(n <= j) { d += 1; j -= n; }
assert(chr(j) >= chr(j + 1));
if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
assert(i < (b - SA));
--j;
t = c0; t = (t << 1) | (chr(j) < c1);
if(D[t] != d) { j += n; D[t] = d; }
*b++ = (t & 1) ? ~j : j;
SA[i] = 0;
} else if(j < 0) {
SA[i] = ~j;
}
}
for(i = n - 1; 0 <= i; --i) {
if(0 < SA[i]) {
if(SA[i] < n) {
SA[i] += n;
for(j = i - 1; SA[j] < n; --j) { }
SA[j] -= n;
i = j;
}
}
}
/* compute SAs */
getBuckets(C, B, k, true); /* find ends of buckets */
for(i = n - 1, d += 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
if(0 < (j = SA[i])) {
if(n <= j) { d += 1; j -= n; }
assert(chr(j) <= chr(j + 1));
if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
assert((b - SA) <= i);
--j;
t = c0; t = (t << 1) | (chr(j) > c1);
if(D[t] != d) { j += n; D[t] = d; }
*--b = (t & 1) ? ~(j + 1) : j;
SA[i] = 0;
}
}
}
template<typename sais_index_type>
static
sais_index_type
LMSpostproc2(sais_index_type *SA, sais_index_type n, sais_index_type m) {
sais_index_type i, j, d, name;
/* compact all the sorted LMS substrings into the first m items of SA */
assert(0 < n);
for(i = 0, name = 0; (j = SA[i]) < 0; ++i) {
j = ~j;
if(n <= j) { name += 1; }
SA[i] = j;
assert((i + 1) < n);
}
if(i < m) {
for(d = i, ++i;; ++i) {
assert(i < n);
if((j = SA[i]) < 0) {
j = ~j;
if(n <= j) { name += 1; }
SA[d++] = j; SA[i] = 0;
if(d == m) { break; }
}
}
}
if(name < m) {
/* store the lexicographic names */
for(i = m - 1, d = name + 1; 0 <= i; --i) {
if(n <= (j = SA[i])) { j -= n; --d; }
SA[m + (j >> 1)] = d;
}
} else {
/* unset flags */
for(i = 0; i < m; ++i) {
if(n <= (j = SA[i])) { j -= n; SA[i] = j; }
}
}
return name;
}
/* compute SA and BWT */
template<typename sais_index_type, typename TT>
static
void
induceSA(const TT *T, sais_index_type *SA,
sais_index_type *C, sais_index_type *B,
sais_index_type n, sais_index_type k) {
sais_index_type *b, i, j;
sais_index_type c0, c1;
/* compute SAl */
if(C == B) { getCounts(T, C, n, k); }
getBuckets(C, B, k, false); /* find starts of buckets */
j = n - 1;
b = SA + B[c1 = chr(j)];
*b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
for(i = 0; i < n; ++i) {
j = SA[i], SA[i] = ~j;
if(0 < j) {
--j;
assert(chr(j) >= chr(j + 1));
if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
assert(i < (b - SA));
*b++ = ((0 < j) && (chr(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])) {
--j;
assert(chr(j) <= chr(j + 1));
if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
assert((b - SA) <= i);
*--b = ((j == 0) || (chr(j - 1) > c1)) ? ~j : j;
} else {
SA[i] = ~j;
}
}
}
/* find the suffix array SA of T[0..n-1] in {0..255}^n */
template<typename sais_index_type, typename TT>
static
sais_index_type
sais_main(const TT *T, sais_index_type *SA,
sais_index_type fs, sais_index_type n, sais_index_type k) {
sais_index_type *C, *B, *D, *RA, *b;
sais_index_type i, j, m, p, q, t, name, pidx = 0, newfs;
sais_index_type c0, c1;
unsigned int flags;
assert((T != NULL) && (SA != NULL));
assert((0 <= fs) && (0 < n) && (1 <= k));
if(k <= MINBUCKETSIZE) {
if((C = SAIS_MYMALLOC(k, sais_index_type)) == NULL) { return -2; }
if(k <= fs) {
B = SA + (n + fs - k);
flags = 1;
} else {
if((B = SAIS_MYMALLOC(k, sais_index_type)) == NULL) { SAIS_MYFREE(C, k, sais_index_type); return -2; }
flags = 3;
}
} else if(k <= fs) {
C = SA + (n + fs - k);
if(k <= (fs - k)) {
B = C - k;
flags = 0;
} else if(k <= (MINBUCKETSIZE * 4)) {
if((B = SAIS_MYMALLOC(k, sais_index_type)) == NULL) { return -2; }
flags = 2;
} else {
B = C;
flags = 8;
}
} else {
if((C = B = SAIS_MYMALLOC(k, sais_index_type)) == NULL) { return -2; }
flags = 4 | 8;
}
if((n <= SAIS_LMSSORT2_LIMIT) && (2 <= (n / k))) {
if(flags & 1) { flags |= ((k * 2) <= (fs - k)) ? 32 : 16; }
else if((flags == 0) && ((k * 2) <= (fs - k * 2))) { flags |= 32; }
}
/* stage 1: reduce the problem by at least 1/2
sort all the LMS-substrings */
getCounts(T, C, n, k); getBuckets(C, B, k, true); /* find ends of buckets */
for(i = 0; i < n; ++i) { SA[i] = 0; }
b = &t; i = n - 1; j = n; m = 0; c0 = chr(n - 1);
do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1));
for(; 0 <= i;) {
do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) <= c1));
if(0 <= i) {
*b = j; b = SA + --B[c1]; j = i; ++m;
do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1));
}
}
if(1 < m) {
if(flags & (16 | 32)) {
if(flags & 16) {
if((D = SAIS_MYMALLOC(k * 2, sais_index_type)) == NULL) {
if(flags & (1 | 4)) { SAIS_MYFREE(C, k, sais_index_type); }
if(flags & 2) { SAIS_MYFREE(B, k, sais_index_type); }
return -2;
}
} else {
D = B - k * 2;
}
assert((j + 1) < n);
++B[chr(j + 1)];
for(i = 0, j = 0; i < k; ++i) {
j += C[i];
if(B[i] != j) { assert(SA[B[i]] != 0); SA[B[i]] += n; }
D[i] = D[i + k] = 0;
}
LMSsort2(T, SA, C, B, D, n, k);
name = LMSpostproc2(SA, n, m);
if(flags & 16) { SAIS_MYFREE(D, k * 2, sais_index_type); }
} else {
LMSsort1(T, SA, C, B, n, k);
name = LMSpostproc1(T, SA, n, m);
}
} else if(m == 1) {
*b = j + 1;
name = 1;
} else {
name = 0;
}
/* stage 2: solve the reduced problem
recurse if names are not yet unique */
if(name < m) {
if(flags & 4) { SAIS_MYFREE(C, k, sais_index_type); }
if(flags & 2) { SAIS_MYFREE(B, k, sais_index_type); }
newfs = (n + fs) - (m * 2);
if((flags & (1 | 4 | 8)) == 0) {
if((k + name) <= newfs) { newfs -= k; }
else { flags |= 8; }
}
assert((n >> 1) <= (newfs + m));
RA = SA + m + newfs;
for(i = m + (n >> 1) - 1, j = m - 1; m <= i; --i) {
if(SA[i] != 0) {
RA[j--] = SA[i] - 1;
}
}
if(sais_main(RA, SA, newfs, m, name) != 0) {
if(flags & 1) { SAIS_MYFREE(C, k, sais_index_type); }
return -2;
}
i = n - 1; j = m - 1; c0 = chr(n - 1);
do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1));
for(; 0 <= i;) {
do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) <= c1));
if(0 <= i) {
RA[j--] = i + 1;
do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1));
}
}
for(i = 0; i < m; ++i) { SA[i] = RA[SA[i]]; }
if(flags & 4) {
if((C = B = SAIS_MYMALLOC(k, sais_index_type)) == NULL) { return -2; }
}
if(flags & 2) {
if((B = SAIS_MYMALLOC(k, sais_index_type)) == NULL) {
if(flags & 1) { SAIS_MYFREE(C, k, sais_index_type); }
return -2;
}
}
}
/* stage 3: induce the result for the original problem */
if(flags & 8) { getCounts(T, C, n, k); }
/* put all left-most S characters into their buckets */
if(1 < m) {
getBuckets(C, B, k, true); /* find ends of buckets */
i = m - 1, j = n, p = SA[m - 1], c1 = chr(p);
do {
q = B[c0 = c1];
while(q < j) { SA[--j] = 0; }
do {
SA[--j] = p;
if(--i < 0) { break; }
p = SA[i];
} while((c1 = chr(p)) == c0);
} while(0 <= i);
while(0 < j) { SA[--j] = 0; }
}
induceSA(T, SA, C, B, n, k);
if(flags & 2) { SAIS_MYFREE(B, k, sais_index_type); }
if(flags & (1 | 4)) { SAIS_MYFREE(C, k, sais_index_type); }
return pidx;
}
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