/*
* 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.
*/
#include <assert.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <time.h>
#include "salcpis.h"
#ifndef UCHAR_SIZE
# define UCHAR_SIZE 256
#endif
#ifndef MINBUCKETSIZE
# define MINBUCKETSIZE 256
#endif
#define sais_index_type int
#define sais_bool_type int
#define SAIS_LMSSORT2_LIMIT 0x3fffffff
#define SAIS_MYMALLOC(_num, _type) ((_type *)malloc((_num) * sizeof(_type)))
#define SAIS_MYFREE(_ptr, _num, _type) free((_ptr))
#define chr(_a) (cs == sizeof(sais_index_type) ? ((sais_index_type *)T)[(_a)] : ((unsigned char *)T)[(_a)])
/* qsort int comparison function */
int int_cmp(const void *a, const void *b)
{
const int *ia = (const int *)a; // casting pointer types
const int *ib = (const int *)b;
return *ia - *ib;
}
/* find the start or end of each bucket */
static
void
getCounts(const void *T, sais_index_type *C, sais_index_type n, sais_index_type k, int cs) {
sais_index_type i;
memset(C, 0, k*sizeof(sais_index_type));
for(i = 0; i < n; ++i) { ++C[chr(i)]; }
}
static
void
getBuckets(const sais_index_type *C, sais_index_type *B, sais_index_type k, sais_bool_type 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 */
static
void
LMSsort1(const void *T, sais_index_type *SA,
sais_index_type *C, sais_index_type *B,
sais_index_type n, sais_index_type k, int cs) {
sais_index_type *b, i, j;
sais_index_type c0, c1;
/* compute SAl */
if(C == B) { getCounts(T, C, n, k, cs); }
getBuckets(C, B, k, 0); /* 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, cs); }
getBuckets(C, B, k, 1); /* 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;
}
}
}
static
sais_index_type
LMSpostproc1(const void *T, sais_index_type *SA,
sais_index_type n, sais_index_type m, int cs) {
sais_index_type i, j, p, q, plen, qlen, name;
sais_index_type c0, c1;
sais_bool_type 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 = 1;
if((plen == qlen) && ((q + plen) < n)) {
for(j = 0; (j < plen) && (chr(p + j) == chr(q + j)); ++j) { }
if(j == plen) { diff = 0; }
}
if(diff != 0) { ++name, q = p, qlen = plen; }
SA[m + (p >> 1)] = name;
}
return name;
}
static
void
LMSsort2(const void *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, int cs) {
sais_index_type *b, i, j, t, d;
sais_index_type c0, c1;
assert(C != B);
/* compute SAl */
getBuckets(C, B, k, 0); /* 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, 1); /* 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;
}
}
}
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 */
static
void
induceSA(const void *T, sais_index_type *SA,
sais_index_type *C, sais_index_type *B,
sais_index_type n, sais_index_type k, int cs) {
sais_index_type *b, i, j;
sais_index_type c0, c1;
/* compute SAl */
if(C == B) { getCounts(T, C, n, k, cs); }
getBuckets(C, B, k, 0); /* 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, cs); }
getBuckets(C, B, k, 1); /* 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;
}
}
}
static void induceSAandLCP(const void *T, sais_index_type *SA,
sais_index_type *LCP,
sais_index_type *C, sais_index_type *B,
sais_index_type n, sais_index_type k, int cs) {
/*
When entering this procedure, we are in the following situation:
all S*-suffixes have been sorted and put at the end of their
corresponding buckets in SA. Further, all their LCP-values have been
computed (in LCP). A value of -1 in LCP means that "this is the first
S*-suffix in its bucket." As in the inducing step an L-suffix
can be placed before the leftmost S*-suffix, this means that the actual
LCP-value at this "L/S-seam" has to be recomputed. All other uncomputed
LCP-entries are marked -2.
*/
sais_index_type i, bb; // indices in SA/LCP (origin/target)
sais_index_type j; // position in text
sais_index_type c0, c1; // characters (new/last)
sais_index_type lcp; // LCP-value
sais_index_type l; // for finding LCP at L/S-seam
sais_index_type start, end, stack_end; // for inducing the LCP-values
sais_index_type *D; // store beginnings of buckets (not CURRENT beginnings!)
sais_index_type *LastW; // store last written L or S-suffix for every bucket
sais_index_type *TranslateSigma; // general to effective alphabet ([0..k-1] |--> [0..sigma-1])
sais_index_type *LastOcc; // store last occurrences of characters
sais_index_type sigma = 0; // (true) alphabet size
if ((D = SAIS_MYMALLOC(k, sais_index_type)) == NULL) { exit(-1); } // TODO: check if D is necessary!!! (first write to bucket=>0)
if ((LastW = SAIS_MYMALLOC(k, sais_index_type)) == NULL) { exit(-1); }
for (i = 0; i < k; ++i) LastW[i] = n-1; // point to $
// todo: move memory management to sais_main
/* compute SAl and LCPl*/
if(C == B) { getCounts(T, C, n, k, cs); } // re-calculate character counts
getBuckets(C, B, k, 0); // find starts of buckets
memcpy(D,B,k*sizeof(sais_index_type)); // store starts of buckets
j = n - 1; // go to last character $
bb = B[c1 = chr(j)]; // bb = position in induced bucket
LCP[bb] = 0; // set LCP-value of $ (first value in bucket => 0)
SA[bb++] = (chr(j - 1) < c1) ? ~j : j; // put last character $ into its bucket
// negative values mean "don't induce from here anymore"
//// in case LCP[0], which is always 0, hadn't been set yet
//LCP[0] = 0;
// Variant 3: stack
if ((TranslateSigma = SAIS_MYMALLOC(k, sais_index_type)) == NULL) { exit(-1); }
for (i = 0; i < k; ++i) { // calculate effective alphabet size
TranslateSigma[i] = sigma; // (also stores values for unused characters)
if (C[i] > 0) ++sigma; // count characters
}
if ((LastOcc = SAIS_MYMALLOC(sigma, sais_index_type)) == NULL) { exit(-1); }
for (i = 0; i < sigma; ++i) LastOcc[i] = -1; // init with impossible values
{
const sais_index_type stack_extra_space = 1024; // this is the same Min-Stack as in Gog's sdsl
const sais_index_type stack_size = 2 * (stack_extra_space + sigma + 4);
sais_index_type *MinStack; // Min-Stack
if ((MinStack = SAIS_MYMALLOC(stack_size+4, sais_index_type)) == NULL) { exit(-1); }
MinStack[0] = -1; MinStack[1] = -1; // (pos, LCP-value)
stack_end = 1;
for(i = 0; i < n; ++i) {
j = SA[i], SA[i] = ~j;
if (0 < j) { // otherwise don't induce anymore from j
lcp = LCP[i];
if (lcp == -1) {
// here we are at the seam between L and S in the same bucket
c0 = chr(j); // i's bucket
lcp = 0;
while (chr(j+lcp) == chr(LastW[c0]+lcp)) lcp++; // naive LCP-computation (overall linear!)
// no need to store LCP[i]=lcp (will be re-calculated in right-to-left scan!)
}
--j; // move to suffix T[SA[i]-1]
assert(chr(j) >= chr(j + 1)); // induced suffix must be type L
if((c0 = chr(j)) != c1) { // induced SA-value in new bucket c0
B[c1] = bb; // store current end in old bucket
bb = B[c1 = c0]; // go to position in new bucket
}
assert(i < bb); // can only induce to the right
LastW[c0] = j; // store last written L-suffix for every bucket
SA[bb] = ((0 < j) && (chr(j - 1) < c0)) ? ~j : j;
// Variant 3: use stack:
assert(lcp >= 0); // lcp already computed
while (lcp <= MinStack[stack_end]) stack_end -= 2; // pop from stack
MinStack[++stack_end] = i; // push position on stack
MinStack[++stack_end] = lcp; // push lcp-value
start = LastOcc[TranslateSigma[c0]] + 1; // start of query
assert(stack_end-3 >= 0); // stopper (-1) and last (i) are on stack
end = stack_end - 3;
while (start <= MinStack[end]) end -= 2; // search until smaller element found
if (bb == D[c0]) LCP[bb] = 0; // store 0 at bucket beginnings
else LCP[bb] = MinStack[end+3] + 1; // induce LCP-value!
LastOcc[TranslateSigma[c0]] = i; // store origin of last occurrence of c0
++bb; // advance in bucket
}
else { // don't induce, but update stack with LCP[i]
lcp = LCP[i]; // get current LCP-value
assert(lcp != -1); // -1 only for S*, but we induce from S*
if (lcp >= 0) { // check if already computed
while (lcp <= MinStack[stack_end]) stack_end -= 2; // pop from stack
MinStack[++stack_end] = i; // push position on stack
MinStack[++stack_end] = lcp; // push lcp-value
}
}
if (stack_end > stack_size) { // re-adjust stack:
sais_index_type *LastOccCopy; // Copy of LastOcc
if ((LastOccCopy = SAIS_MYMALLOC(sigma, sais_index_type)) == NULL) { exit(-1); }
memcpy(LastOccCopy, LastOcc, sigma*sizeof(sais_index_type));
qsort(LastOccCopy, sigma, sizeof(sais_index_type), int_cmp);
end = 1;
for (j = 0, l=2; j < sigma; ++j) {
start = LastOccCopy[j] + 1; // start of next largest query
if (start > MinStack[end-1]) { // otherwise correct element already taken
while (l < stack_end && start > MinStack[l]) l += 2;
if (l > stack_end) break;
assert(l < stack_end);
MinStack[++end] = MinStack[l]; // take first element >= start
MinStack[++end] = MinStack[l+1];
}
}
stack_end = end;
free(LastOccCopy);
}
}
/* compute SAs and LCPl */
if(C == B) { getCounts(T, C, n, k, cs); }
getBuckets(C, B, k, 1); /* find ends of buckets */
for (i = 0; i < sigma; ++i) LastOcc[i] = n-1; // init with impossible values
MinStack[0] = n; MinStack[1] = -1; // (pos, LCP-value)
stack_end = 1;
for(i = n - 1, bb = B[c1 = 0]; 0 <= i; --i) {
lcp = LCP[i];
if (0 < i && lcp < 0 && LCP[i-1] >= 0) { // calculate LCP at L/S-seam
j = SA[i]; // go to suffix
if (j < 0) j = ~j; // entry in SA could be negative => adjust
l = SA[i-1]; // go to lex. previous suffix
if (l < 0) l = ~l; // entry in SA could be negative => adjust
lcp = 0;
while (chr(j+lcp) == chr(l+lcp)) lcp++; // naive LCP-computation (overall linear!)
LCP[i] = lcp; // this time set LCP-value at seam
}
if(0 < (j = SA[i])) { // induce SA and LCP
--j; // go to suffix T[SA[i]-1] (to be induced)
assert(chr(j) <= chr(j + 1)); // must be type S
if((c0 = chr(j)) != c1) {
B[c1] = bb; bb = B[c1 = c0]; // switch bucket
}
assert(bb <= i); // induced suffix must be placed to the left of i
SA[--bb] = ((j == 0) || (chr(j - 1) > c0)) ? ~j : j; // continue if type L
assert(c0+1<k); // we cannot induce into the last bucket
// search MinStack:
start = LastOcc[TranslateSigma[c0]]; // end of query
assert(stack_end-1 >= 0); // stopper (-1) is on stack
end = stack_end - 1;
while (start >= MinStack[end]) end -= 2; // search until smaller element found
if (bb+1 == D[c0+1]) LCP[bb+1] = 0; // store 0 at bucket beginnings
else LCP[bb+1] = MinStack[end+3] + 1; // induce LCP-value!
if (bb+1 == i) lcp = LCP[i]; // update if inducing changed my LCP-value
LastOcc[TranslateSigma[c0]] = i; // store origin of last occurrence of c0
} else { // don't induce
SA[i] = ~j;
}
// update MinStack:
assert(lcp >= 0); // LCP must already have been computed
while ((stack_end >= 0) && (lcp <= MinStack[stack_end])) stack_end -= 2; // pop from stack
MinStack[++stack_end] = i; // push position on stack
MinStack[++stack_end] = lcp; // push lcp-value
if (stack_end > stack_size) { // re-adjust stack:
sais_index_type *LastOccCopy; // Copy of LastOcc
if ((LastOccCopy = SAIS_MYMALLOC(sigma, sais_index_type)) == NULL) { exit(-1); }
memcpy(LastOccCopy, LastOcc, sigma*sizeof(sais_index_type));
qsort(LastOccCopy, sigma, sizeof(sais_index_type), int_cmp);
end = 1;
for (j = sigma-1, l=2; j >= 0; --j) {
start = LastOccCopy[j]; // start of next largest query
if (start < MinStack[end-1]) { // otherwise correct element already taken
while (l < stack_end && start < MinStack[l]) l += 2;
if (l > stack_end) break;
assert(l < stack_end);
MinStack[++end] = MinStack[l]; // take first element >= start
MinStack[++end] = MinStack[l+1];
}
}
stack_end = end;
free(LastOccCopy);
}
}
free(MinStack);
}
free(LastOcc);
free(TranslateSigma);
free(LastW);
free(D);
}
static
sais_index_type
computeBWT(const void *T, sais_index_type *SA,
sais_index_type *C, sais_index_type *B,
sais_index_type n, sais_index_type k, int cs) {
sais_index_type *b, i, j, pidx = -1;
sais_index_type c0, c1;
/* compute SAl */
if(C == B) { getCounts(T, C, n, k, cs); }
getBuckets(C, B, k, 0); /* 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) {
if(0 < (j = SA[i])) {
--j;
assert(chr(j) >= chr(j + 1));
SA[i] = ~((sais_index_type)(c0 = chr(j)));
if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
assert(i < (b - SA));
*b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
} else if(j != 0) {
SA[i] = ~j;
}
}
/* compute SAs */
if(C == B) { getCounts(T, C, n, k, cs); }
getBuckets(C, B, k, 1); /* 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));
SA[i] = (c0 = chr(j));
if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; }
assert((b - SA) <= i);
*--b = ((0 < j) && (chr(j - 1) > c1)) ? ~((sais_index_type)chr(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..255}^n */
static
sais_index_type
sais_main(const void *T, sais_index_type *SA,
sais_index_type *LCP,
sais_index_type fs, sais_index_type n, sais_index_type k, int cs,
sais_bool_type isbwt,
sais_bool_type level0) { // level0 = 1 iff recursion depth is 0
sais_index_type *C, *B, *D, *RA, *PLCP, *PHI, *DELTA, *b;
sais_index_type i, j, m, // m: number of S*-suffixes
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, cs); getBuckets(C, B, k, 1); /* find ends of buckets */
//for(i = 0; i < n; ++i) { SA[i] = 0; }
memset(SA, 0, n * sizeof(sais_index_type));
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, cs);
name = LMSpostproc2(SA, n, m);
if(flags & 16) { SAIS_MYFREE(D, k * 2, sais_index_type); }
} else {
LMSsort1(T, SA, C, B, n, k, cs);
name = LMSpostproc1(T, SA, n, m, cs);
}
} else if (m == 1) { // only one S*-suffix => set immediately
*b = j + 1; // set entry in SA
if (level0) { LCP[b-SA] = -1; } // mark first (=only) S*-suffix in bucket
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, NULL, newfs, m, name, sizeof(sais_index_type), 0, 0) != 0) {
if(flags & 1) { SAIS_MYFREE(C, k, sais_index_type); }
return -2;
}
// (re)compute starting positions of S*-suffixes (stored in RA):
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));
}
}
// construct LCP for S*-suffixes:
// PHI: "to whom I want to be compared" (pos. in T)
// DELTA: "distance (in T) to next S*" (in PHI-order)
if (level0) {
if (m < n/3) { // hence we can store PHI and DELTA interleaved
PHI = LCP+m; // use space in LCP-array for PHI and DELTA
RA[m] = n; // stopper
j = SA[0]; // j stores SA[i-1] in the following loop
PHI[j<<1] = n-1; // set PHI[SA[0]] to $ (causes mismatch in char. comp.)
PHI[(j<<1)+1] = 0; // set DELTA
for (i = 1; i < m; ++i) {
q = SA[i]; // text position
p = q<<1; // for interleaving
PHI[p]=RA[j]; // set PHI-array
PHI[p+1]=RA[j+1]-RA[j]; // set DELTA
j = q; // store for next loop iteration
}
PLCP = PHI; // overwrite DELTA in following loop
p = 0; // guaranteed LCP-value
j = 0; // position in PLCP and RA
for (i = 0; i < n; ++i) {
if (i == RA[j]) {
sais_index_type twoj;
if (p < 0) p = 0;
twoj = j << 1;
while (chr(i+p) == chr(PHI[twoj]+p)) ++p;
t = PHI[twoj+1]; // accesses DELTA-value
q = RA[j+1]-RA[j]; // length difference
PLCP[twoj] = p; // overwrite PHI with PLCP
++j;
p -= (t > q) ? t : q; // decrease p by larger of t and q
}
}
// translate PLCP-values to SA-order:
for (j = 0; j < m; ++j) LCP[j] = PLCP[SA[j]<<1];
}
else { // non-interleaved
PHI = LCP; // use space in LCP-array for PHI
DELTA = LCP+m; // because we compute only m < n/2 values, this is valid
RA[m] = n; // stopper
j = SA[0]; // j stores SA[i-1] in the following loop
PHI[j] = n-1; // set PHI[SA[0]] to $ (causes mismatch in char. comp.)
DELTA[j] = 0;
for (i = 1; i < m; ++i) {
q = SA[i]; // text position
PHI[q]=RA[j]; // set PHI-array
DELTA[q]=RA[j+1]-RA[j]; // set DELTA
j = q; // store for next loop iteration
}
PLCP = DELTA; // overwrite DELTA in following loop
p = 0; // guaranteed LCP-value
j = 0; // position in PLCP and RA
for (i = 0; i < n; ++i) {
if (i == RA[j]) {
if (p < 0) p = 0;
while (chr(i+p) == chr(PHI[j]+p)) ++p;
t = PLCP[j]; // accesses DELTA-value
q = RA[j+1]-RA[j]; // length difference
PLCP[j++] = p;
p -= (t > q) ? t : q; // decrease p by larger of t and q
}
}
// translate PLCP-values to SA-order:
for (j = 0; j < m; ++j) LCP[j] = PLCP[SA[j]];
}
}
// translate indices in RA to indices in T:
for(i = 0; i < m; ++i) { SA[i] = RA[SA[i]]; }
if(flags & 4) {
if((C = B = SAIS_MYMALLOC(k, int)) == NULL) { return -2; }
}
if(flags & 2) {
if((B = SAIS_MYMALLOC(k, int)) == NULL) {
if(flags & 1) { SAIS_MYFREE(C, k, sais_index_type); }
return -2;
}
}
} // endif (name < m)
else if (level0) { // this should only occur for small or pathetic inputs
// all names unique => computing LCP for *S naively takes linear time
// printf("*** computing LCP naively...");
j = SA[0]; // j = SA[i-1] in the following loop
for (i = 1; i < m; ++i) {
p = 0;
while (chr(SA[i]+p) == chr(j+p)) p++;
LCP[i] = p;
j = SA[i];
}
// printf("done.\n");
}
/* stage 3: induce the result for the original problem */
if(flags & 8) { getCounts(T, C, n, k, cs); }
/* put all S*-suffixes (and their LCP-values) into their buckets */
if(1 < m) { // otherwise SA (and LCP) is already correct
getBuckets(C, B, k, 1); /* find ends of buckets */
i = m - 1, j = n, p = SA[m - 1], c1 = chr(p);
if (level0) {
newfs = LCP[m-1]; // newfs stores LCP[i] in the following loop
do {
q = B[c0 = c1];
while(q < j) {
SA[--j] = 0; LCP[j] = -2; // set remaining entries in old bucket to 0/-2
}
do { // step through bucket c0 and write S*-suffixes to SA:
SA[--j] = p; LCP[j] = newfs;
if(--i < 0) break;
newfs = LCP[i]; p = SA[i];
} while((c1 = chr(p)) == c0);
//assert(LCP[j]==0); // first S*-suffix in bucket must have LCP-value 0
#ifndef NDEBUG
if (LCP[j]!=0) { // first S*-suffix in bucket must have LCP-value 0
fprintf(stderr, "\n\nassert in line %u: LCP@%u == %u != 0\n\n\n", __LINE__ - 3, j, LCP[j]);
}
#endif
LCP[j] = -1; // mark first S*-suffix in every bucket
} while(0 <= i);
while(0 < j) {
SA[--j] = 0; LCP[j] = -2; // set remaining entries in smallest buckets to 0/-2
}
}
else {
do {
q = B[c0 = c1];
while(q < j) SA[--j] = 0; // set remaining entries in old bucket to 0
do { // step through bucket c0
SA[--j] = p;
if(--i < 0) break;
p = SA[i];
} while((c1 = chr(p)) == c0);
} while(0 <= i);
while(0 < j) SA[--j] = 0; // set remaining entries in 1st bucket to 0
}
}
if(isbwt == 0) {
if (level0 && m > 1) induceSAandLCP(T, SA, LCP, C, B, n, k, cs);
else if (level0) {
// Buggy -> crashes
induceSA(T, SA, C, B, n, k, cs);
//Compute the LCP naively. This is only done if the instance is very simple
//and most likely constructed. Still this could be done by a more efficient
//algorithm (phi-algorithm).
for(i = 1; i < n; ++i){
p = 0;
while (chr(SA[i - 1] + p) == chr(SA[i] + p)) { ++p; }
LCP[i] = p;
}
LCP[0] = 0;
}
else induceSA(T, SA, C, B, n, k, cs);
}
else { pidx = computeBWT(T, SA, C, B, n, k, cs); }
if(flags & (1 | 4)) { SAIS_MYFREE(C, k, sais_index_type); }
if(flags & 2) { SAIS_MYFREE(B, k, sais_index_type); }
return pidx;
}
/*---------------------------------------------------------------------------*/
int
sais(const unsigned char *T, int *SA, int* LCP, int n) {
if((T == NULL) || (SA == NULL) || (LCP == NULL) || (n < 0)) { return -1; }
if(n <= 1) { if(n == 1) { SA[0] = 0; LCP[0] = 0; } return 0; }
#ifndef NDEBUG
memset(LCP, 0x01, n*sizeof(int));
#endif
return sais_main(T, SA, LCP, 0, n, UCHAR_SIZE, sizeof(unsigned char), 0, 1);
}
int
sais_int(const int *T, int *SA, int n, int k) {
if((T == NULL) || (SA == NULL) || (n < 0) || (k <= 0)) { return -1; }
if(n <= 1) { if(n == 1) { SA[0] = 0; } return 0; }
return sais_main(T, SA, NULL, 0, n, k, sizeof(int), 0, 1);
}
int
sais_bwt(const unsigned char *T, unsigned char *U, int *A, int n) {
int i, pidx;
if((T == NULL) || (U == NULL) || (A == NULL) || (n < 0)) { return -1; }
if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
pidx = sais_main(T, A, NULL, 0, n, UCHAR_SIZE, sizeof(unsigned char), 1, 1);
if(pidx < 0) { return pidx; }
U[0] = T[n - 1];
for(i = 0; i < pidx; ++i) { U[i + 1] = (unsigned char)A[i]; }
for(i += 1; i < n; ++i) { U[i] = (unsigned char)A[i]; }
pidx += 1;
return pidx;
}
int
sais_int_bwt(const int *T, int *U, int *A, int n, int k) {
int i, pidx;
if((T == NULL) || (U == NULL) || (A == NULL) || (n < 0) || (k <= 0)) { return -1; }
if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
pidx = sais_main(T, A, NULL, 0, n, k, sizeof(int), 1, 1);
if(pidx < 0) { return pidx; }
U[0] = T[n - 1];
for(i = 0; i < pidx; ++i) { U[i + 1] = A[i]; }
for(i += 1; i < n; ++i) { U[i] = A[i]; }
pidx += 1;
return pidx;
}