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/*
* sais.c for sais-lite
* Copyright (c) 2008 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 <stdlib.h>
typedef unsigned char ubyte_t;
#define chr(i) (cs == sizeof(int) ? ((const int *)T)[i]:((const unsigned char *)T)[i])
/* find the start or end of each bucket */
static void getCounts(const unsigned char *T, int *C, int n, int k, int cs)
{
int i;
for (i = 0; i < k; ++i) C[i] = 0;
for (i = 0; i < n; ++i) ++C[chr(i)];
}
static void getBuckets(const int *C, int *B, int k, int end)
{
int 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 */
static void induceSA(const unsigned char *T, int *SA, int *C, int *B, int n, int k, int cs)
{
int *b, i, j;
int 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;
if ((c0 = chr(j)) != c1) {
B[c1] = b - SA;
b = SA + B[c1 = c0];
}
*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;
if ((c0 = chr(j)) != c1) {
B[c1] = b - SA;
b = SA + B[c1 = c0];
}
*--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..k-1}^n use a working
* space (excluding T and SA) of at most 2n+O(1) for a constant alphabet
*/
static int sais_main(const unsigned char *T, int *SA, int fs, int n, int k, int cs)
{
int *C, *B, *RA;
int i, j, c, m, p, q, plen, qlen, name;
int c0, c1;
int diff;
/* stage 1: reduce the problem by at least 1/2 sort all the
* S-substrings */
if (k <= fs) {
C = SA + n;
B = (k <= (fs - k)) ? C + k : C;
} else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
getCounts(T, C, n, k, cs);
getBuckets(C, B, k, 1); /* find ends of buckets */
for (i = 0; i < n; ++i) SA[i] = 0;
for (i = n - 2, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
if ((c0 = chr(i)) < (c1 + c)) c = 1;
else if (c != 0) SA[--B[c1]] = i + 1, c = 0;
}
induceSA(T, SA, C, B, n, k, cs);
if (fs < k) free(C);
/* compact all the sorted substrings into the first m items of SA
* 2*m must be not larger than n (proveable) */
for (i = 0, m = 0; i < n; ++i) {
p = SA[i];
if ((0 < p) && (chr(p - 1) > (c0 = chr(p)))) {
for (j = p + 1; (j < n) && (c0 == (c1 = chr(j))); ++j);
if ((j < n) && (c0 < c1)) SA[m++] = p;
}
}
for (i = m; i < n; ++i) SA[i] = 0; /* init the name array buffer */
/* store the length of all substrings */
for (i = n - 2, j = n, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
if ((c0 = chr(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 = 1;
if (plen == qlen) {
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;
}
/* stage 2: solve the reduced problem recurse if names are not yet
* unique */
if (name < m) {
RA = SA + n + fs - m;
for (i = n - 1, j = m - 1; m <= i; --i) {
if (SA[i] != 0) RA[j--] = SA[i] - 1;
}
if (sais_main((unsigned char *) RA, SA, fs + n - m * 2, m, name, sizeof(int)) != 0) return -2;
for (i = n - 2, j = m - 1, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
if ((c0 = chr(i)) < (c1 + c)) c = 1;
else if (c != 0) RA[j--] = i + 1, c = 0; /* get p1 */
}
for (i = 0; i < m; ++i) SA[i] = RA[SA[i]]; /* get index */
}
/* stage 3: induce the result for the original problem */
if (k <= fs) {
C = SA + n;
B = (k <= (fs - k)) ? C + k : C;
} else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
/* put all left-most S characters into their buckets */
getCounts(T, C, n, k, cs);
getBuckets(C, B, k, 1); /* find ends of buckets */
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[chr(j)]] = j;
}
induceSA(T, SA, C, B, n, k, cs);
if (fs < k) free(C);
return 0;
}
/**
* Constructs the suffix array of a given string.
* @param T[0..n-1] The input string.
* @param SA[0..n] The output array of suffixes.
* @param n The length of the given string.
* @return 0 if no error occurred
*/
int is_sa(const ubyte_t *T, int *SA, int n)
{
if ((T == NULL) || (SA == NULL) || (n < 0)) return -1;
SA[0] = n;
if (n <= 1) {
if (n == 1) SA[1] = 0;
return 0;
}
return sais_main(T, SA+1, 0, n, 256, 1);
}
/**
* Constructs the burrows-wheeler transformed string of a given string.
* @param T[0..n-1] The input string.
* @param n The length of the given string.
* @return The primary index if no error occurred, -1 or -2 otherwise.
*/
int is_bwt(ubyte_t *T, int n)
{
int *SA, i, primary = 0;
SA = (int*)calloc(n+1, sizeof(int));
is_sa(T, SA, n);
for (i = 0; i <= n; ++i) {
if (SA[i] == 0) primary = i;
else SA[i] = T[SA[i] - 1];
}
for (i = 0; i < primary; ++i) T[i] = SA[i];
for (; i < n; ++i) T[i] = SA[i + 1];
free(SA);
return primary;
}
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