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+/*
+ * 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 */