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-rw-r--r--lib/CMakeLists.txt31
-rw-r--r--lib/divsufsort.c398
-rw-r--r--lib/sssort.c815
-rw-r--r--lib/trsort.c586
-rw-r--r--lib/utils.c381
5 files changed, 2211 insertions, 0 deletions
diff --git a/lib/CMakeLists.txt b/lib/CMakeLists.txt
new file mode 100644
index 000000000000..abc90e61da59
--- /dev/null
+++ b/lib/CMakeLists.txt
@@ -0,0 +1,31 @@
+include_directories("${CMAKE_CURRENT_SOURCE_DIR}/../include"
+ "${CMAKE_CURRENT_BINARY_DIR}/../include")
+
+set(divsufsort_SRCS divsufsort.c sssort.c trsort.c utils.c)
+
+## libdivsufsort ##
+add_library(divsufsort ${divsufsort_SRCS})
+install(TARGETS divsufsort
+ RUNTIME DESTINATION ${CMAKE_INSTALL_RUNTIMEDIR}
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+set_target_properties(divsufsort PROPERTIES
+ VERSION "${LIBRARY_VERSION}"
+ SOVERSION "${LIBRARY_SOVERSION}"
+ DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL
+ RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples")
+
+## libdivsufsort64 ##
+if(BUILD_DIVSUFSORT64)
+ add_library(divsufsort64 ${divsufsort_SRCS})
+ install(TARGETS divsufsort64
+ RUNTIME DESTINATION ${CMAKE_INSTALL_RUNTIMEDIR}
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+ set_target_properties(divsufsort64 PROPERTIES
+ VERSION "${LIBRARY_VERSION}"
+ SOVERSION "${LIBRARY_SOVERSION}"
+ DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL
+ COMPILE_FLAGS "-DBUILD_DIVSUFSORT64"
+ RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples")
+endif(BUILD_DIVSUFSORT64)
diff --git a/lib/divsufsort.c b/lib/divsufsort.c
new file mode 100644
index 000000000000..9f64b4f48adb
--- /dev/null
+++ b/lib/divsufsort.c
@@ -0,0 +1,398 @@
+/*
+ * divsufsort.c for libdivsufsort
+ * Copyright (c) 2003-2008 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 "divsufsort_private.h"
+#ifdef _OPENMP
+# include <omp.h>
+#endif
+
+
+/*- Private Functions -*/
+
+/* Sorts suffixes of type B*. */
+static
+saidx_t
+sort_typeBstar(const sauchar_t *T, saidx_t *SA,
+ saidx_t *bucket_A, saidx_t *bucket_B,
+ saidx_t n) {
+ saidx_t *PAb, *ISAb, *buf;
+#ifdef _OPENMP
+ saidx_t *curbuf;
+ saidx_t l;
+#endif
+ saidx_t i, j, k, t, m, bufsize;
+ saint_t c0, c1;
+#ifdef _OPENMP
+ saint_t d0, d1;
+ int tmp;
+#endif
+
+ /* Initialize bucket arrays. */
+ for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; }
+ for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; }
+
+ /* Count the number of occurrences of the first one or two characters of each
+ type A, B and B* suffix. Moreover, store the beginning position of all
+ type B* suffixes into the array SA. */
+ for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) {
+ /* type A suffix. */
+ do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1));
+ if(0 <= i) {
+ /* type B* suffix. */
+ ++BUCKET_BSTAR(c0, c1);
+ SA[--m] = i;
+ /* type B suffix. */
+ for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) {
+ ++BUCKET_B(c0, c1);
+ }
+ }
+ }
+ m = n - m;
+/*
+note:
+ A type B* suffix is lexicographically smaller than a type B suffix that
+ begins with the same first two characters.
+*/
+
+ /* Calculate the index of start/end point of each bucket. */
+ for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) {
+ t = i + BUCKET_A(c0);
+ BUCKET_A(c0) = i + j; /* start point */
+ i = t + BUCKET_B(c0, c0);
+ for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) {
+ j += BUCKET_BSTAR(c0, c1);
+ BUCKET_BSTAR(c0, c1) = j; /* end point */
+ i += BUCKET_B(c0, c1);
+ }
+ }
+
+ if(0 < m) {
+ /* Sort the type B* suffixes by their first two characters. */
+ PAb = SA + n - m; ISAb = SA + m;
+ for(i = m - 2; 0 <= i; --i) {
+ t = PAb[i], c0 = T[t], c1 = T[t + 1];
+ SA[--BUCKET_BSTAR(c0, c1)] = i;
+ }
+ t = PAb[m - 1], c0 = T[t], c1 = T[t + 1];
+ SA[--BUCKET_BSTAR(c0, c1)] = m - 1;
+
+ /* Sort the type B* substrings using sssort. */
+#ifdef _OPENMP
+ tmp = omp_get_max_threads();
+ buf = SA + m, bufsize = (n - (2 * m)) / tmp;
+ c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m;
+#pragma omp parallel default(shared) private(curbuf, k, l, d0, d1, tmp)
+ {
+ tmp = omp_get_thread_num();
+ curbuf = buf + tmp * bufsize;
+ k = 0;
+ for(;;) {
+ #pragma omp critical(sssort_lock)
+ {
+ if(0 < (l = j)) {
+ d0 = c0, d1 = c1;
+ do {
+ k = BUCKET_BSTAR(d0, d1);
+ if(--d1 <= d0) {
+ d1 = ALPHABET_SIZE - 1;
+ if(--d0 < 0) { break; }
+ }
+ } while(((l - k) <= 1) && (0 < (l = k)));
+ c0 = d0, c1 = d1, j = k;
+ }
+ }
+ if(l == 0) { break; }
+ sssort(T, PAb, SA + k, SA + l,
+ curbuf, bufsize, 2, n, *(SA + k) == (m - 1));
+ }
+ }
+#else
+ buf = SA + m, bufsize = n - (2 * m);
+ for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
+ for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
+ i = BUCKET_BSTAR(c0, c1);
+ if(1 < (j - i)) {
+ sssort(T, PAb, SA + i, SA + j,
+ buf, bufsize, 2, n, *(SA + i) == (m - 1));
+ }
+ }
+ }
+#endif
+
+ /* Compute ranks of type B* substrings. */
+ for(i = m - 1; 0 <= i; --i) {
+ if(0 <= SA[i]) {
+ j = i;
+ do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i]));
+ SA[i + 1] = i - j;
+ if(i <= 0) { break; }
+ }
+ j = i;
+ do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0);
+ ISAb[SA[i]] = j;
+ }
+
+ /* Construct the inverse suffix array of type B* suffixes using trsort. */
+ trsort(ISAb, SA, m, 1);
+
+ /* Set the sorted order of tyoe B* suffixes. */
+ for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) {
+ for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { }
+ if(0 <= i) {
+ t = i;
+ for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { }
+ SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t;
+ }
+ }
+
+ /* Calculate the index of start/end point of each bucket. */
+ BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */
+ for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) {
+ i = BUCKET_A(c0 + 1) - 1;
+ for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) {
+ t = i - BUCKET_B(c0, c1);
+ BUCKET_B(c0, c1) = i; /* end point */
+
+ /* Move all type B* suffixes to the correct position. */
+ for(i = t, j = BUCKET_BSTAR(c0, c1);
+ j <= k;
+ --i, --k) { SA[i] = SA[k]; }
+ }
+ BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */
+ BUCKET_B(c0, c0) = i; /* end point */
+ }
+ }
+
+ return m;
+}
+
+/* Constructs the suffix array by using the sorted order of type B* suffixes. */
+static
+void
+construct_SA(const sauchar_t *T, saidx_t *SA,
+ saidx_t *bucket_A, saidx_t *bucket_B,
+ saidx_t n, saidx_t m) {
+ saidx_t *i, *j, *k;
+ saidx_t s;
+ saint_t c0, c1, c2;
+
+ if(0 < m) {
+ /* Construct the sorted order of type B suffixes by using
+ the sorted order of type B* suffixes. */
+ for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
+ /* Scan the suffix array from right to left. */
+ for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
+ j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
+ i <= j;
+ --j) {
+ if(0 < (s = *j)) {
+ assert(T[s] == c1);
+ assert(((s + 1) < n) && (T[s] <= T[s + 1]));
+ assert(T[s - 1] <= T[s]);
+ *j = ~s;
+ c0 = T[--s];
+ if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
+ if(c0 != c2) {
+ if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
+ k = SA + BUCKET_B(c2 = c0, c1);
+ }
+ assert(k < j);
+ *k-- = s;
+ } else {
+ assert(((s == 0) && (T[s] == c1)) || (s < 0));
+ *j = ~s;
+ }
+ }
+ }
+ }
+
+ /* Construct the suffix array by using
+ the sorted order of type B suffixes. */
+ k = SA + BUCKET_A(c2 = T[n - 1]);
+ *k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1);
+ /* Scan the suffix array from left to right. */
+ for(i = SA, j = SA + n; i < j; ++i) {
+ if(0 < (s = *i)) {
+ assert(T[s - 1] >= T[s]);
+ c0 = T[--s];
+ if((s == 0) || (T[s - 1] < c0)) { s = ~s; }
+ if(c0 != c2) {
+ BUCKET_A(c2) = k - SA;
+ k = SA + BUCKET_A(c2 = c0);
+ }
+ assert(i < k);
+ *k++ = s;
+ } else {
+ assert(s < 0);
+ *i = ~s;
+ }
+ }
+}
+
+/* Constructs the burrows-wheeler transformed string directly
+ by using the sorted order of type B* suffixes. */
+static
+saidx_t
+construct_BWT(const sauchar_t *T, saidx_t *SA,
+ saidx_t *bucket_A, saidx_t *bucket_B,
+ saidx_t n, saidx_t m) {
+ saidx_t *i, *j, *k, *orig;
+ saidx_t s;
+ saint_t c0, c1, c2;
+
+ if(0 < m) {
+ /* Construct the sorted order of type B suffixes by using
+ the sorted order of type B* suffixes. */
+ for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
+ /* Scan the suffix array from right to left. */
+ for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
+ j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
+ i <= j;
+ --j) {
+ if(0 < (s = *j)) {
+ assert(T[s] == c1);
+ assert(((s + 1) < n) && (T[s] <= T[s + 1]));
+ assert(T[s - 1] <= T[s]);
+ c0 = T[--s];
+ *j = ~((saidx_t)c0);
+ if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
+ if(c0 != c2) {
+ if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
+ k = SA + BUCKET_B(c2 = c0, c1);
+ }
+ assert(k < j);
+ *k-- = s;
+ } else if(s != 0) {
+ *j = ~s;
+#ifndef NDEBUG
+ } else {
+ assert(T[s] == c1);
+#endif
+ }
+ }
+ }
+ }
+
+ /* Construct the BWTed string by using
+ the sorted order of type B suffixes. */
+ k = SA + BUCKET_A(c2 = T[n - 1]);
+ *k++ = (T[n - 2] < c2) ? ~((saidx_t)T[n - 2]) : (n - 1);
+ /* Scan the suffix array from left to right. */
+ for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
+ if(0 < (s = *i)) {
+ assert(T[s - 1] >= T[s]);
+ c0 = T[--s];
+ *i = c0;
+ if((0 < s) && (T[s - 1] < c0)) { s = ~((saidx_t)T[s - 1]); }
+ if(c0 != c2) {
+ BUCKET_A(c2) = k - SA;
+ k = SA + BUCKET_A(c2 = c0);
+ }
+ assert(i < k);
+ *k++ = s;
+ } else if(s != 0) {
+ *i = ~s;
+ } else {
+ orig = i;
+ }
+ }
+
+ return orig - SA;
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+/*- Function -*/
+
+saint_t
+divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n) {
+ saidx_t *bucket_A, *bucket_B;
+ saidx_t m;
+ saint_t err = 0;
+
+ /* Check arguments. */
+ if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; }
+ else if(n == 0) { return 0; }
+ else if(n == 1) { SA[0] = 0; return 0; }
+ else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; }
+
+ bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
+ bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
+
+ /* Suffixsort. */
+ if((bucket_A != NULL) && (bucket_B != NULL)) {
+ m = sort_typeBstar(T, SA, bucket_A, bucket_B, n);
+ construct_SA(T, SA, bucket_A, bucket_B, n, m);
+ } else {
+ err = -2;
+ }
+
+ free(bucket_B);
+ free(bucket_A);
+
+ return err;
+}
+
+saidx_t
+divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n) {
+ saidx_t *B;
+ saidx_t *bucket_A, *bucket_B;
+ saidx_t m, pidx, i;
+
+ /* Check arguments. */
+ if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
+ else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
+
+ if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); }
+ bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
+ bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
+
+ /* Burrows-Wheeler Transform. */
+ if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
+ m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
+ pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
+
+ /* Copy to output string. */
+ U[0] = T[n - 1];
+ for(i = 0; i < pidx; ++i) { U[i + 1] = (sauchar_t)B[i]; }
+ for(i += 1; i < n; ++i) { U[i] = (sauchar_t)B[i]; }
+ pidx += 1;
+ } else {
+ pidx = -2;
+ }
+
+ free(bucket_B);
+ free(bucket_A);
+ if(A == NULL) { free(B); }
+
+ return pidx;
+}
+
+const char *
+divsufsort_version(void) {
+ return PROJECT_VERSION_FULL;
+}
diff --git a/lib/sssort.c b/lib/sssort.c
new file mode 100644
index 000000000000..4a18fd2ab495
--- /dev/null
+++ b/lib/sssort.c
@@ -0,0 +1,815 @@
+/*
+ * sssort.c for libdivsufsort
+ * Copyright (c) 2003-2008 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 "divsufsort_private.h"
+
+
+/*- Private Functions -*/
+
+static const saint_t lg_table[256]= {
+ -1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
+ 5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
+ 6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
+ 6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
+ 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
+ 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
+ 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
+ 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
+};
+
+#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
+
+static INLINE
+saint_t
+ss_ilg(saidx_t n) {
+#if SS_BLOCKSIZE == 0
+# if defined(BUILD_DIVSUFSORT64)
+ return (n >> 32) ?
+ ((n >> 48) ?
+ ((n >> 56) ?
+ 56 + lg_table[(n >> 56) & 0xff] :
+ 48 + lg_table[(n >> 48) & 0xff]) :
+ ((n >> 40) ?
+ 40 + lg_table[(n >> 40) & 0xff] :
+ 32 + lg_table[(n >> 32) & 0xff])) :
+ ((n & 0xffff0000) ?
+ ((n & 0xff000000) ?
+ 24 + lg_table[(n >> 24) & 0xff] :
+ 16 + lg_table[(n >> 16) & 0xff]) :
+ ((n & 0x0000ff00) ?
+ 8 + lg_table[(n >> 8) & 0xff] :
+ 0 + lg_table[(n >> 0) & 0xff]));
+# else
+ return (n & 0xffff0000) ?
+ ((n & 0xff000000) ?
+ 24 + lg_table[(n >> 24) & 0xff] :
+ 16 + lg_table[(n >> 16) & 0xff]) :
+ ((n & 0x0000ff00) ?
+ 8 + lg_table[(n >> 8) & 0xff] :
+ 0 + lg_table[(n >> 0) & 0xff]);
+# endif
+#elif SS_BLOCKSIZE < 256
+ return lg_table[n];
+#else
+ return (n & 0xff00) ?
+ 8 + lg_table[(n >> 8) & 0xff] :
+ 0 + lg_table[(n >> 0) & 0xff];
+#endif
+}
+
+#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
+
+#if SS_BLOCKSIZE != 0
+
+static const saint_t sqq_table[256] = {
+ 0, 16, 22, 27, 32, 35, 39, 42, 45, 48, 50, 53, 55, 57, 59, 61,
+ 64, 65, 67, 69, 71, 73, 75, 76, 78, 80, 81, 83, 84, 86, 87, 89,
+ 90, 91, 93, 94, 96, 97, 98, 99, 101, 102, 103, 104, 106, 107, 108, 109,
+110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126,
+128, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
+143, 144, 144, 145, 146, 147, 148, 149, 150, 150, 151, 152, 153, 154, 155, 155,
+156, 157, 158, 159, 160, 160, 161, 162, 163, 163, 164, 165, 166, 167, 167, 168,
+169, 170, 170, 171, 172, 173, 173, 174, 175, 176, 176, 177, 178, 178, 179, 180,
+181, 181, 182, 183, 183, 184, 185, 185, 186, 187, 187, 188, 189, 189, 190, 191,
+192, 192, 193, 193, 194, 195, 195, 196, 197, 197, 198, 199, 199, 200, 201, 201,
+202, 203, 203, 204, 204, 205, 206, 206, 207, 208, 208, 209, 209, 210, 211, 211,
+212, 212, 213, 214, 214, 215, 215, 216, 217, 217, 218, 218, 219, 219, 220, 221,
+221, 222, 222, 223, 224, 224, 225, 225, 226, 226, 227, 227, 228, 229, 229, 230,
+230, 231, 231, 232, 232, 233, 234, 234, 235, 235, 236, 236, 237, 237, 238, 238,
+239, 240, 240, 241, 241, 242, 242, 243, 243, 244, 244, 245, 245, 246, 246, 247,
+247, 248, 248, 249, 249, 250, 250, 251, 251, 252, 252, 253, 253, 254, 254, 255
+};
+
+static INLINE
+saidx_t
+ss_isqrt(saidx_t x) {
+ saidx_t y, e;
+
+ if(x >= (SS_BLOCKSIZE * SS_BLOCKSIZE)) { return SS_BLOCKSIZE; }
+ e = (x & 0xffff0000) ?
+ ((x & 0xff000000) ?
+ 24 + lg_table[(x >> 24) & 0xff] :
+ 16 + lg_table[(x >> 16) & 0xff]) :
+ ((x & 0x0000ff00) ?
+ 8 + lg_table[(x >> 8) & 0xff] :
+ 0 + lg_table[(x >> 0) & 0xff]);
+
+ if(e >= 16) {
+ y = sqq_table[x >> ((e - 6) - (e & 1))] << ((e >> 1) - 7);
+ if(e >= 24) { y = (y + 1 + x / y) >> 1; }
+ y = (y + 1 + x / y) >> 1;
+ } else if(e >= 8) {
+ y = (sqq_table[x >> ((e - 6) - (e & 1))] >> (7 - (e >> 1))) + 1;
+ } else {
+ return sqq_table[x] >> 4;
+ }
+
+ return (x < (y * y)) ? y - 1 : y;
+}
+
+#endif /* SS_BLOCKSIZE != 0 */
+
+
+/*---------------------------------------------------------------------------*/
+
+/* Compares two suffixes. */
+static INLINE
+saint_t
+ss_compare(const sauchar_t *T,
+ const saidx_t *p1, const saidx_t *p2,
+ saidx_t depth) {
+ const sauchar_t *U1, *U2, *U1n, *U2n;
+
+ for(U1 = T + depth + *p1,
+ U2 = T + depth + *p2,
+ U1n = T + *(p1 + 1) + 2,
+ U2n = T + *(p2 + 1) + 2;
+ (U1 < U1n) && (U2 < U2n) && (*U1 == *U2);
+ ++U1, ++U2) {
+ }
+
+ return U1 < U1n ?
+ (U2 < U2n ? *U1 - *U2 : 1) :
+ (U2 < U2n ? -1 : 0);
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+#if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1)
+
+/* Insertionsort for small size groups */
+static
+void
+ss_insertionsort(const sauchar_t *T, const saidx_t *PA,
+ saidx_t *first, saidx_t *last, saidx_t depth) {
+ saidx_t *i, *j;
+ saidx_t t;
+ saint_t r;
+
+ for(i = last - 2; first <= i; --i) {
+ for(t = *i, j = i + 1; 0 < (r = ss_compare(T, PA + t, PA + *j, depth));) {
+ do { *(j - 1) = *j; } while((++j < last) && (*j < 0));
+ if(last <= j) { break; }
+ }
+ if(r == 0) { *j = ~*j; }
+ *(j - 1) = t;
+ }
+}
+
+#endif /* (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) */
+
+
+/*---------------------------------------------------------------------------*/
+
+#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
+
+static INLINE
+void
+ss_fixdown(const sauchar_t *Td, const saidx_t *PA,
+ saidx_t *SA, saidx_t i, saidx_t size) {
+ saidx_t j, k;
+ saidx_t v;
+ saint_t c, d, e;
+
+ for(v = SA[i], c = Td[PA[v]]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
+ d = Td[PA[SA[k = j++]]];
+ if(d < (e = Td[PA[SA[j]]])) { k = j; d = e; }
+ if(d <= c) { break; }
+ }
+ SA[i] = v;
+}
+
+/* Simple top-down heapsort. */
+static
+void
+ss_heapsort(const sauchar_t *Td, const saidx_t *PA, saidx_t *SA, saidx_t size) {
+ saidx_t i, m;
+ saidx_t t;
+
+ m = size;
+ if((size % 2) == 0) {
+ m--;
+ if(Td[PA[SA[m / 2]]] < Td[PA[SA[m]]]) { SWAP(SA[m], SA[m / 2]); }
+ }
+
+ for(i = m / 2 - 1; 0 <= i; --i) { ss_fixdown(Td, PA, SA, i, m); }
+ if((size % 2) == 0) { SWAP(SA[0], SA[m]); ss_fixdown(Td, PA, SA, 0, m); }
+ for(i = m - 1; 0 < i; --i) {
+ t = SA[0], SA[0] = SA[i];
+ ss_fixdown(Td, PA, SA, 0, i);
+ SA[i] = t;
+ }
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+/* Returns the median of three elements. */
+static INLINE
+saidx_t *
+ss_median3(const sauchar_t *Td, const saidx_t *PA,
+ saidx_t *v1, saidx_t *v2, saidx_t *v3) {
+ saidx_t *t;
+ if(Td[PA[*v1]] > Td[PA[*v2]]) { SWAP(v1, v2); }
+ if(Td[PA[*v2]] > Td[PA[*v3]]) {
+ if(Td[PA[*v1]] > Td[PA[*v3]]) { return v1; }
+ else { return v3; }
+ }
+ return v2;
+}
+
+/* Returns the median of five elements. */
+static INLINE
+saidx_t *
+ss_median5(const sauchar_t *Td, const saidx_t *PA,
+ saidx_t *v1, saidx_t *v2, saidx_t *v3, saidx_t *v4, saidx_t *v5) {
+ saidx_t *t;
+ if(Td[PA[*v2]] > Td[PA[*v3]]) { SWAP(v2, v3); }
+ if(Td[PA[*v4]] > Td[PA[*v5]]) { SWAP(v4, v5); }
+ if(Td[PA[*v2]] > Td[PA[*v4]]) { SWAP(v2, v4); SWAP(v3, v5); }
+ if(Td[PA[*v1]] > Td[PA[*v3]]) { SWAP(v1, v3); }
+ if(Td[PA[*v1]] > Td[PA[*v4]]) { SWAP(v1, v4); SWAP(v3, v5); }
+ if(Td[PA[*v3]] > Td[PA[*v4]]) { return v4; }
+ return v3;
+}
+
+/* Returns the pivot element. */
+static INLINE
+saidx_t *
+ss_pivot(const sauchar_t *Td, const saidx_t *PA, saidx_t *first, saidx_t *last) {
+ saidx_t *middle;
+ saidx_t t;
+
+ t = last - first;
+ middle = first + t / 2;
+
+ if(t <= 512) {
+ if(t <= 32) {
+ return ss_median3(Td, PA, first, middle, last - 1);
+ } else {
+ t >>= 2;
+ return ss_median5(Td, PA, first, first + t, middle, last - 1 - t, last - 1);
+ }
+ }
+ t >>= 3;
+ first = ss_median3(Td, PA, first, first + t, first + (t << 1));
+ middle = ss_median3(Td, PA, middle - t, middle, middle + t);
+ last = ss_median3(Td, PA, last - 1 - (t << 1), last - 1 - t, last - 1);
+ return ss_median3(Td, PA, first, middle, last);
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+/* Binary partition for substrings. */
+static INLINE
+saidx_t *
+ss_partition(const saidx_t *PA,
+ saidx_t *first, saidx_t *last, saidx_t depth) {
+ saidx_t *a, *b;
+ saidx_t t;
+ for(a = first - 1, b = last;;) {
+ for(; (++a < b) && ((PA[*a] + depth) >= (PA[*a + 1] + 1));) { *a = ~*a; }
+ for(; (a < --b) && ((PA[*b] + depth) < (PA[*b + 1] + 1));) { }
+ if(b <= a) { break; }
+ t = ~*b;
+ *b = *a;
+ *a = t;
+ }
+ if(first < a) { *first = ~*first; }
+ return a;
+}
+
+/* Multikey introsort for medium size groups. */
+static
+void
+ss_mintrosort(const sauchar_t *T, const saidx_t *PA,
+ saidx_t *first, saidx_t *last,
+ saidx_t depth) {
+#define STACK_SIZE SS_MISORT_STACKSIZE
+ struct { saidx_t *a, *b, c; saint_t d; } stack[STACK_SIZE];
+ const sauchar_t *Td;
+ saidx_t *a, *b, *c, *d, *e, *f;
+ saidx_t s, t;
+ saint_t ssize;
+ saint_t limit;
+ saint_t v, x = 0;
+
+ for(ssize = 0, limit = ss_ilg(last - first);;) {
+
+ if((last - first) <= SS_INSERTIONSORT_THRESHOLD) {
+#if 1 < SS_INSERTIONSORT_THRESHOLD
+ if(1 < (last - first)) { ss_insertionsort(T, PA, first, last, depth); }
+#endif
+ STACK_POP(first, last, depth, limit);
+ continue;
+ }
+
+ Td = T + depth;
+ if(limit-- == 0) { ss_heapsort(Td, PA, first, last - first); }
+ if(limit < 0) {
+ for(a = first + 1, v = Td[PA[*first]]; a < last; ++a) {
+ if((x = Td[PA[*a]]) != v) {
+ if(1 < (a - first)) { break; }
+ v = x;
+ first = a;
+ }
+ }
+ if(Td[PA[*first] - 1] < v) {
+ first = ss_partition(PA, first, a, depth);
+ }
+ if((a - first) <= (last - a)) {
+ if(1 < (a - first)) {
+ STACK_PUSH(a, last, depth, -1);
+ last = a, depth += 1, limit = ss_ilg(a - first);
+ } else {
+ first = a, limit = -1;
+ }
+ } else {
+ if(1 < (last - a)) {
+ STACK_PUSH(first, a, depth + 1, ss_ilg(a - first));
+ first = a, limit = -1;
+ } else {
+ last = a, depth += 1, limit = ss_ilg(a - first);
+ }
+ }
+ continue;
+ }
+
+ /* choose pivot */
+ a = ss_pivot(Td, PA, first, last);
+ v = Td[PA[*a]];
+ SWAP(*first, *a);
+
+ /* partition */
+ for(b = first; (++b < last) && ((x = Td[PA[*b]]) == v);) { }
+ if(((a = b) < last) && (x < v)) {
+ for(; (++b < last) && ((x = Td[PA[*b]]) <= v);) {
+ if(x == v) { SWAP(*b, *a); ++a; }
+ }
+ }
+ for(c = last; (b < --c) && ((x = Td[PA[*c]]) == v);) { }
+ if((b < (d = c)) && (x > v)) {
+ for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
+ if(x == v) { SWAP(*c, *d); --d; }
+ }
+ }
+ for(; b < c;) {
+ SWAP(*b, *c);
+ for(; (++b < c) && ((x = Td[PA[*b]]) <= v);) {
+ if(x == v) { SWAP(*b, *a); ++a; }
+ }
+ for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
+ if(x == v) { SWAP(*c, *d); --d; }
+ }
+ }
+
+ if(a <= d) {
+ c = b - 1;
+
+ if((s = a - first) > (t = b - a)) { s = t; }
+ for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
+ if((s = d - c) > (t = last - d - 1)) { s = t; }
+ for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
+
+ a = first + (b - a), c = last - (d - c);
+ b = (v <= Td[PA[*a] - 1]) ? a : ss_partition(PA, a, c, depth);
+
+ if((a - first) <= (last - c)) {
+ if((last - c) <= (c - b)) {
+ STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
+ STACK_PUSH(c, last, depth, limit);
+ last = a;
+ } else if((a - first) <= (c - b)) {
+ STACK_PUSH(c, last, depth, limit);
+ STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
+ last = a;
+ } else {
+ STACK_PUSH(c, last, depth, limit);
+ STACK_PUSH(first, a, depth, limit);
+ first = b, last = c, depth += 1, limit = ss_ilg(c - b);
+ }
+ } else {
+ if((a - first) <= (c - b)) {
+ STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
+ STACK_PUSH(first, a, depth, limit);
+ first = c;
+ } else if((last - c) <= (c - b)) {
+ STACK_PUSH(first, a, depth, limit);
+ STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
+ first = c;
+ } else {
+ STACK_PUSH(first, a, depth, limit);
+ STACK_PUSH(c, last, depth, limit);
+ first = b, last = c, depth += 1, limit = ss_ilg(c - b);
+ }
+ }
+ } else {
+ limit += 1;
+ if(Td[PA[*first] - 1] < v) {
+ first = ss_partition(PA, first, last, depth);
+ limit = ss_ilg(last - first);
+ }
+ depth += 1;
+ }
+ }
+#undef STACK_SIZE
+}
+
+#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
+
+
+/*---------------------------------------------------------------------------*/
+
+#if SS_BLOCKSIZE != 0
+
+static INLINE
+void
+ss_blockswap(saidx_t *a, saidx_t *b, saidx_t n) {
+ saidx_t t;
+ for(; 0 < n; --n, ++a, ++b) {
+ t = *a, *a = *b, *b = t;
+ }
+}
+
+static INLINE
+void
+ss_rotate(saidx_t *first, saidx_t *middle, saidx_t *last) {
+ saidx_t *a, *b, t;
+ saidx_t l, r;
+ l = middle - first, r = last - middle;
+ for(; (0 < l) && (0 < r);) {
+ if(l == r) { ss_blockswap(first, middle, l); break; }
+ if(l < r) {
+ a = last - 1, b = middle - 1;
+ t = *a;
+ do {
+ *a-- = *b, *b-- = *a;
+ if(b < first) {
+ *a = t;
+ last = a;
+ if((r -= l + 1) <= l) { break; }
+ a -= 1, b = middle - 1;
+ t = *a;
+ }
+ } while(1);
+ } else {
+ a = first, b = middle;
+ t = *a;
+ do {
+ *a++ = *b, *b++ = *a;
+ if(last <= b) {
+ *a = t;
+ first = a + 1;
+ if((l -= r + 1) <= r) { break; }
+ a += 1, b = middle;
+ t = *a;
+ }
+ } while(1);
+ }
+ }
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+static
+void
+ss_inplacemerge(const sauchar_t *T, const saidx_t *PA,
+ saidx_t *first, saidx_t *middle, saidx_t *last,
+ saidx_t depth) {
+ const saidx_t *p;
+ saidx_t *a, *b;
+ saidx_t len, half;
+ saint_t q, r;
+ saint_t x;
+
+ for(;;) {
+ if(*(last - 1) < 0) { x = 1; p = PA + ~*(last - 1); }
+ else { x = 0; p = PA + *(last - 1); }
+ for(a = first, len = middle - first, half = len >> 1, r = -1;
+ 0 < len;
+ len = half, half >>= 1) {
+ b = a + half;
+ q = ss_compare(T, PA + ((0 <= *b) ? *b : ~*b), p, depth);
+ if(q < 0) {
+ a = b + 1;
+ half -= (len & 1) ^ 1;
+ } else {
+ r = q;
+ }
+ }
+ if(a < middle) {
+ if(r == 0) { *a = ~*a; }
+ ss_rotate(a, middle, last);
+ last -= middle - a;
+ middle = a;
+ if(first == middle) { break; }
+ }
+ --last;
+ if(x != 0) { while(*--last < 0) { } }
+ if(middle == last) { break; }
+ }
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+/* Merge-forward with internal buffer. */
+static
+void
+ss_mergeforward(const sauchar_t *T, const saidx_t *PA,
+ saidx_t *first, saidx_t *middle, saidx_t *last,
+ saidx_t *buf, saidx_t depth) {
+ saidx_t *a, *b, *c, *bufend;
+ saidx_t t;
+ saint_t r;
+
+ bufend = buf + (middle - first) - 1;
+ ss_blockswap(buf, first, middle - first);
+
+ for(t = *(a = first), b = buf, c = middle;;) {
+ r = ss_compare(T, PA + *b, PA + *c, depth);
+ if(r < 0) {
+ do {
+ *a++ = *b;
+ if(bufend <= b) { *bufend = t; return; }
+ *b++ = *a;
+ } while(*b < 0);
+ } else if(r > 0) {
+ do {
+ *a++ = *c, *c++ = *a;
+ if(last <= c) {
+ while(b < bufend) { *a++ = *b, *b++ = *a; }
+ *a = *b, *b = t;
+ return;
+ }
+ } while(*c < 0);
+ } else {
+ *c = ~*c;
+ do {
+ *a++ = *b;
+ if(bufend <= b) { *bufend = t; return; }
+ *b++ = *a;
+ } while(*b < 0);
+
+ do {
+ *a++ = *c, *c++ = *a;
+ if(last <= c) {
+ while(b < bufend) { *a++ = *b, *b++ = *a; }
+ *a = *b, *b = t;
+ return;
+ }
+ } while(*c < 0);
+ }
+ }
+}
+
+/* Merge-backward with internal buffer. */
+static
+void
+ss_mergebackward(const sauchar_t *T, const saidx_t *PA,
+ saidx_t *first, saidx_t *middle, saidx_t *last,
+ saidx_t *buf, saidx_t depth) {
+ const saidx_t *p1, *p2;
+ saidx_t *a, *b, *c, *bufend;
+ saidx_t t;
+ saint_t r;
+ saint_t x;
+
+ bufend = buf + (last - middle) - 1;
+ ss_blockswap(buf, middle, last - middle);
+
+ x = 0;
+ if(*bufend < 0) { p1 = PA + ~*bufend; x |= 1; }
+ else { p1 = PA + *bufend; }
+ if(*(middle - 1) < 0) { p2 = PA + ~*(middle - 1); x |= 2; }
+ else { p2 = PA + *(middle - 1); }
+ for(t = *(a = last - 1), b = bufend, c = middle - 1;;) {
+ r = ss_compare(T, p1, p2, depth);
+ if(0 < r) {
+ if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
+ *a-- = *b;
+ if(b <= buf) { *buf = t; break; }
+ *b-- = *a;
+ if(*b < 0) { p1 = PA + ~*b; x |= 1; }
+ else { p1 = PA + *b; }
+ } else if(r < 0) {
+ if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
+ *a-- = *c, *c-- = *a;
+ if(c < first) {
+ while(buf < b) { *a-- = *b, *b-- = *a; }
+ *a = *b, *b = t;
+ break;
+ }
+ if(*c < 0) { p2 = PA + ~*c; x |= 2; }
+ else { p2 = PA + *c; }
+ } else {
+ if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
+ *a-- = ~*b;
+ if(b <= buf) { *buf = t; break; }
+ *b-- = *a;
+ if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
+ *a-- = *c, *c-- = *a;
+ if(c < first) {
+ while(buf < b) { *a-- = *b, *b-- = *a; }
+ *a = *b, *b = t;
+ break;
+ }
+ if(*b < 0) { p1 = PA + ~*b; x |= 1; }
+ else { p1 = PA + *b; }
+ if(*c < 0) { p2 = PA + ~*c; x |= 2; }
+ else { p2 = PA + *c; }
+ }
+ }
+}
+
+/* D&C based merge. */
+static
+void
+ss_swapmerge(const sauchar_t *T, const saidx_t *PA,
+ saidx_t *first, saidx_t *middle, saidx_t *last,
+ saidx_t *buf, saidx_t bufsize, saidx_t depth) {
+#define STACK_SIZE SS_SMERGE_STACKSIZE
+#define GETIDX(a) ((0 <= (a)) ? (a) : (~(a)))
+#define MERGE_CHECK(a, b, c)\
+ do {\
+ if(((c) & 1) ||\
+ (((c) & 2) && (ss_compare(T, PA + GETIDX(*((a) - 1)), PA + *(a), depth) == 0))) {\
+ *(a) = ~*(a);\
+ }\
+ if(((c) & 4) && ((ss_compare(T, PA + GETIDX(*((b) - 1)), PA + *(b), depth) == 0))) {\
+ *(b) = ~*(b);\
+ }\
+ } while(0)
+ struct { saidx_t *a, *b, *c; saint_t d; } stack[STACK_SIZE];
+ saidx_t *l, *r, *lm, *rm;
+ saidx_t m, len, half;
+ saint_t ssize;
+ saint_t check, next;
+
+ for(check = 0, ssize = 0;;) {
+ if((last - middle) <= bufsize) {
+ if((first < middle) && (middle < last)) {
+ ss_mergebackward(T, PA, first, middle, last, buf, depth);
+ }
+ MERGE_CHECK(first, last, check);
+ STACK_POP(first, middle, last, check);
+ continue;
+ }
+
+ if((middle - first) <= bufsize) {
+ if(first < middle) {
+ ss_mergeforward(T, PA, first, middle, last, buf, depth);
+ }
+ MERGE_CHECK(first, last, check);
+ STACK_POP(first, middle, last, check);
+ continue;
+ }
+
+ for(m = 0, len = MIN(middle - first, last - middle), half = len >> 1;
+ 0 < len;
+ len = half, half >>= 1) {
+ if(ss_compare(T, PA + GETIDX(*(middle + m + half)),
+ PA + GETIDX(*(middle - m - half - 1)), depth) < 0) {
+ m += half + 1;
+ half -= (len & 1) ^ 1;
+ }
+ }
+
+ if(0 < m) {
+ lm = middle - m, rm = middle + m;
+ ss_blockswap(lm, middle, m);
+ l = r = middle, next = 0;
+ if(rm < last) {
+ if(*rm < 0) {
+ *rm = ~*rm;
+ if(first < lm) { for(; *--l < 0;) { } next |= 4; }
+ next |= 1;
+ } else if(first < lm) {
+ for(; *r < 0; ++r) { }
+ next |= 2;
+ }
+ }
+
+ if((l - first) <= (last - r)) {
+ STACK_PUSH(r, rm, last, (next & 3) | (check & 4));
+ middle = lm, last = l, check = (check & 3) | (next & 4);
+ } else {
+ if((next & 2) && (r == middle)) { next ^= 6; }
+ STACK_PUSH(first, lm, l, (check & 3) | (next & 4));
+ first = r, middle = rm, check = (next & 3) | (check & 4);
+ }
+ } else {
+ if(ss_compare(T, PA + GETIDX(*(middle - 1)), PA + *middle, depth) == 0) {
+ *middle = ~*middle;
+ }
+ MERGE_CHECK(first, last, check);
+ STACK_POP(first, middle, last, check);
+ }
+ }
+#undef STACK_SIZE
+}
+
+#endif /* SS_BLOCKSIZE != 0 */
+
+
+/*---------------------------------------------------------------------------*/
+
+/*- Function -*/
+
+/* Substring sort */
+void
+sssort(const sauchar_t *T, const saidx_t *PA,
+ saidx_t *first, saidx_t *last,
+ saidx_t *buf, saidx_t bufsize,
+ saidx_t depth, saidx_t n, saint_t lastsuffix) {
+ saidx_t *a;
+#if SS_BLOCKSIZE != 0
+ saidx_t *b, *middle, *curbuf;
+ saidx_t j, k, curbufsize, limit;
+#endif
+ saidx_t i;
+
+ if(lastsuffix != 0) { ++first; }
+
+#if SS_BLOCKSIZE == 0
+ ss_mintrosort(T, PA, first, last, depth);
+#else
+ if((bufsize < SS_BLOCKSIZE) &&
+ (bufsize < (last - first)) &&
+ (bufsize < (limit = ss_isqrt(last - first)))) {
+ if(SS_BLOCKSIZE < limit) { limit = SS_BLOCKSIZE; }
+ buf = middle = last - limit, bufsize = limit;
+ } else {
+ middle = last, limit = 0;
+ }
+ for(a = first, i = 0; SS_BLOCKSIZE < (middle - a); a += SS_BLOCKSIZE, ++i) {
+#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
+ ss_mintrosort(T, PA, a, a + SS_BLOCKSIZE, depth);
+#elif 1 < SS_BLOCKSIZE
+ ss_insertionsort(T, PA, a, a + SS_BLOCKSIZE, depth);
+#endif
+ curbufsize = last - (a + SS_BLOCKSIZE);
+ curbuf = a + SS_BLOCKSIZE;
+ if(curbufsize <= bufsize) { curbufsize = bufsize, curbuf = buf; }
+ for(b = a, k = SS_BLOCKSIZE, j = i; j & 1; b -= k, k <<= 1, j >>= 1) {
+ ss_swapmerge(T, PA, b - k, b, b + k, curbuf, curbufsize, depth);
+ }
+ }
+#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
+ ss_mintrosort(T, PA, a, middle, depth);
+#elif 1 < SS_BLOCKSIZE
+ ss_insertionsort(T, PA, a, middle, depth);
+#endif
+ for(k = SS_BLOCKSIZE; i != 0; k <<= 1, i >>= 1) {
+ if(i & 1) {
+ ss_swapmerge(T, PA, a - k, a, middle, buf, bufsize, depth);
+ a -= k;
+ }
+ }
+ if(limit != 0) {
+#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
+ ss_mintrosort(T, PA, middle, last, depth);
+#elif 1 < SS_BLOCKSIZE
+ ss_insertionsort(T, PA, middle, last, depth);
+#endif
+ ss_inplacemerge(T, PA, first, middle, last, depth);
+ }
+#endif
+
+ if(lastsuffix != 0) {
+ /* Insert last type B* suffix. */
+ saidx_t PAi[2]; PAi[0] = PA[*(first - 1)], PAi[1] = n - 2;
+ for(a = first, i = *(first - 1);
+ (a < last) && ((*a < 0) || (0 < ss_compare(T, &(PAi[0]), PA + *a, depth)));
+ ++a) {
+ *(a - 1) = *a;
+ }
+ *(a - 1) = i;
+ }
+}
diff --git a/lib/trsort.c b/lib/trsort.c
new file mode 100644
index 000000000000..6fe3e67baa4c
--- /dev/null
+++ b/lib/trsort.c
@@ -0,0 +1,586 @@
+/*
+ * trsort.c for libdivsufsort
+ * Copyright (c) 2003-2008 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 "divsufsort_private.h"
+
+
+/*- Private Functions -*/
+
+static const saint_t lg_table[256]= {
+ -1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
+ 5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
+ 6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
+ 6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
+ 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
+ 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
+ 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
+ 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
+};
+
+static INLINE
+saint_t
+tr_ilg(saidx_t n) {
+#if defined(BUILD_DIVSUFSORT64)
+ return (n >> 32) ?
+ ((n >> 48) ?
+ ((n >> 56) ?
+ 56 + lg_table[(n >> 56) & 0xff] :
+ 48 + lg_table[(n >> 48) & 0xff]) :
+ ((n >> 40) ?
+ 40 + lg_table[(n >> 40) & 0xff] :
+ 32 + lg_table[(n >> 32) & 0xff])) :
+ ((n & 0xffff0000) ?
+ ((n & 0xff000000) ?
+ 24 + lg_table[(n >> 24) & 0xff] :
+ 16 + lg_table[(n >> 16) & 0xff]) :
+ ((n & 0x0000ff00) ?
+ 8 + lg_table[(n >> 8) & 0xff] :
+ 0 + lg_table[(n >> 0) & 0xff]));
+#else
+ return (n & 0xffff0000) ?
+ ((n & 0xff000000) ?
+ 24 + lg_table[(n >> 24) & 0xff] :
+ 16 + lg_table[(n >> 16) & 0xff]) :
+ ((n & 0x0000ff00) ?
+ 8 + lg_table[(n >> 8) & 0xff] :
+ 0 + lg_table[(n >> 0) & 0xff]);
+#endif
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+/* Simple insertionsort for small size groups. */
+static
+void
+tr_insertionsort(const saidx_t *ISAd, saidx_t *first, saidx_t *last) {
+ saidx_t *a, *b;
+ saidx_t t, r;
+
+ for(a = first + 1; a < last; ++a) {
+ for(t = *a, b = a - 1; 0 > (r = ISAd[t] - ISAd[*b]);) {
+ do { *(b + 1) = *b; } while((first <= --b) && (*b < 0));
+ if(b < first) { break; }
+ }
+ if(r == 0) { *b = ~*b; }
+ *(b + 1) = t;
+ }
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+static INLINE
+void
+tr_fixdown(const saidx_t *ISAd, saidx_t *SA, saidx_t i, saidx_t size) {
+ saidx_t j, k;
+ saidx_t v;
+ saidx_t c, d, e;
+
+ for(v = SA[i], c = ISAd[v]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
+ d = ISAd[SA[k = j++]];
+ if(d < (e = ISAd[SA[j]])) { k = j; d = e; }
+ if(d <= c) { break; }
+ }
+ SA[i] = v;
+}
+
+/* Simple top-down heapsort. */
+static
+void
+tr_heapsort(const saidx_t *ISAd, saidx_t *SA, saidx_t size) {
+ saidx_t i, m;
+ saidx_t t;
+
+ m = size;
+ if((size % 2) == 0) {
+ m--;
+ if(ISAd[SA[m / 2]] < ISAd[SA[m]]) { SWAP(SA[m], SA[m / 2]); }
+ }
+
+ for(i = m / 2 - 1; 0 <= i; --i) { tr_fixdown(ISAd, SA, i, m); }
+ if((size % 2) == 0) { SWAP(SA[0], SA[m]); tr_fixdown(ISAd, SA, 0, m); }
+ for(i = m - 1; 0 < i; --i) {
+ t = SA[0], SA[0] = SA[i];
+ tr_fixdown(ISAd, SA, 0, i);
+ SA[i] = t;
+ }
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+/* Returns the median of three elements. */
+static INLINE
+saidx_t *
+tr_median3(const saidx_t *ISAd, saidx_t *v1, saidx_t *v2, saidx_t *v3) {
+ saidx_t *t;
+ if(ISAd[*v1] > ISAd[*v2]) { SWAP(v1, v2); }
+ if(ISAd[*v2] > ISAd[*v3]) {
+ if(ISAd[*v1] > ISAd[*v3]) { return v1; }
+ else { return v3; }
+ }
+ return v2;
+}
+
+/* Returns the median of five elements. */
+static INLINE
+saidx_t *
+tr_median5(const saidx_t *ISAd,
+ saidx_t *v1, saidx_t *v2, saidx_t *v3, saidx_t *v4, saidx_t *v5) {
+ saidx_t *t;
+ if(ISAd[*v2] > ISAd[*v3]) { SWAP(v2, v3); }
+ if(ISAd[*v4] > ISAd[*v5]) { SWAP(v4, v5); }
+ if(ISAd[*v2] > ISAd[*v4]) { SWAP(v2, v4); SWAP(v3, v5); }
+ if(ISAd[*v1] > ISAd[*v3]) { SWAP(v1, v3); }
+ if(ISAd[*v1] > ISAd[*v4]) { SWAP(v1, v4); SWAP(v3, v5); }
+ if(ISAd[*v3] > ISAd[*v4]) { return v4; }
+ return v3;
+}
+
+/* Returns the pivot element. */
+static INLINE
+saidx_t *
+tr_pivot(const saidx_t *ISAd, saidx_t *first, saidx_t *last) {
+ saidx_t *middle;
+ saidx_t t;
+
+ t = last - first;
+ middle = first + t / 2;
+
+ if(t <= 512) {
+ if(t <= 32) {
+ return tr_median3(ISAd, first, middle, last - 1);
+ } else {
+ t >>= 2;
+ return tr_median5(ISAd, first, first + t, middle, last - 1 - t, last - 1);
+ }
+ }
+ t >>= 3;
+ first = tr_median3(ISAd, first, first + t, first + (t << 1));
+ middle = tr_median3(ISAd, middle - t, middle, middle + t);
+ last = tr_median3(ISAd, last - 1 - (t << 1), last - 1 - t, last - 1);
+ return tr_median3(ISAd, first, middle, last);
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+typedef struct _trbudget_t trbudget_t;
+struct _trbudget_t {
+ saidx_t chance;
+ saidx_t remain;
+ saidx_t incval;
+ saidx_t count;
+};
+
+static INLINE
+void
+trbudget_init(trbudget_t *budget, saidx_t chance, saidx_t incval) {
+ budget->chance = chance;
+ budget->remain = budget->incval = incval;
+}
+
+static INLINE
+saint_t
+trbudget_check(trbudget_t *budget, saidx_t size) {
+ if(size <= budget->remain) { budget->remain -= size; return 1; }
+ if(budget->chance == 0) { budget->count += size; return 0; }
+ budget->remain += budget->incval - size;
+ budget->chance -= 1;
+ return 1;
+}
+
+
+/*---------------------------------------------------------------------------*/
+
+static INLINE
+void
+tr_partition(const saidx_t *ISAd,
+ saidx_t *first, saidx_t *middle, saidx_t *last,
+ saidx_t **pa, saidx_t **pb, saidx_t v) {
+ saidx_t *a, *b, *c, *d, *e, *f;
+ saidx_t t, s;
+ saidx_t x = 0;
+
+ for(b = middle - 1; (++b < last) && ((x = ISAd[*b]) == v);) { }
+ if(((a = b) < last) && (x < v)) {
+ for(; (++b < last) && ((x = ISAd[*b]) <= v);) {
+ if(x == v) { SWAP(*b, *a); ++a; }
+ }
+ }
+ for(c = last; (b < --c) && ((x = ISAd[*c]) == v);) { }
+ if((b < (d = c)) && (x > v)) {
+ for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
+ if(x == v) { SWAP(*c, *d); --d; }
+ }
+ }
+ for(; b < c;) {
+ SWAP(*b, *c);
+ for(; (++b < c) && ((x = ISAd[*b]) <= v);) {
+ if(x == v) { SWAP(*b, *a); ++a; }
+ }
+ for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
+ if(x == v) { SWAP(*c, *d); --d; }
+ }
+ }
+
+ if(a <= d) {
+ c = b - 1;
+ if((s = a - first) > (t = b - a)) { s = t; }
+ for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
+ if((s = d - c) > (t = last - d - 1)) { s = t; }
+ for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
+ first += (b - a), last -= (d - c);
+ }
+ *pa = first, *pb = last;
+}
+
+static
+void
+tr_copy(saidx_t *ISA, const saidx_t *SA,
+ saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last,
+ saidx_t depth) {
+ /* sort suffixes of middle partition
+ by using sorted order of suffixes of left and right partition. */
+ saidx_t *c, *d, *e;
+ saidx_t s, v;
+
+ v = b - SA - 1;
+ for(c = first, d = a - 1; c <= d; ++c) {
+ if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
+ *++d = s;
+ ISA[s] = d - SA;
+ }
+ }
+ for(c = last - 1, e = d + 1, d = b; e < d; --c) {
+ if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
+ *--d = s;
+ ISA[s] = d - SA;
+ }
+ }
+}
+
+static
+void
+tr_partialcopy(saidx_t *ISA, const saidx_t *SA,
+ saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last,
+ saidx_t depth) {
+ saidx_t *c, *d, *e;
+ saidx_t s, v;
+ saidx_t rank, lastrank, newrank = -1;
+
+ v = b - SA - 1;
+ lastrank = -1;
+ for(c = first, d = a - 1; c <= d; ++c) {
+ if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
+ *++d = s;
+ rank = ISA[s + depth];
+ if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
+ ISA[s] = newrank;
+ }
+ }
+
+ lastrank = -1;
+ for(e = d; first <= e; --e) {
+ rank = ISA[*e];
+ if(lastrank != rank) { lastrank = rank; newrank = e - SA; }
+ if(newrank != rank) { ISA[*e] = newrank; }
+ }
+
+ lastrank = -1;
+ for(c = last - 1, e = d + 1, d = b; e < d; --c) {
+ if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
+ *--d = s;
+ rank = ISA[s + depth];
+ if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
+ ISA[s] = newrank;
+ }
+ }
+}
+
+static
+void
+tr_introsort(saidx_t *ISA, const saidx_t *ISAd,
+ saidx_t *SA, saidx_t *first, saidx_t *last,
+ trbudget_t *budget) {
+#define STACK_SIZE TR_STACKSIZE
+ struct { const saidx_t *a; saidx_t *b, *c; saint_t d, e; }stack[STACK_SIZE];
+ saidx_t *a, *b, *c;
+ saidx_t t;
+ saidx_t v, x = 0;
+ saidx_t incr = ISAd - ISA;
+ saint_t limit, next;
+ saint_t ssize, trlink = -1;
+
+ for(ssize = 0, limit = tr_ilg(last - first);;) {
+
+ if(limit < 0) {
+ if(limit == -1) {
+ /* tandem repeat partition */
+ tr_partition(ISAd - incr, first, first, last, &a, &b, last - SA - 1);
+
+ /* update ranks */
+ if(a < last) {
+ for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
+ }
+ if(b < last) {
+ for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; }
+ }
+
+ /* push */
+ if(1 < (b - a)) {
+ STACK_PUSH5(NULL, a, b, 0, 0);
+ STACK_PUSH5(ISAd - incr, first, last, -2, trlink);
+ trlink = ssize - 2;
+ }
+ if((a - first) <= (last - b)) {
+ if(1 < (a - first)) {
+ STACK_PUSH5(ISAd, b, last, tr_ilg(last - b), trlink);
+ last = a, limit = tr_ilg(a - first);
+ } else if(1 < (last - b)) {
+ first = b, limit = tr_ilg(last - b);
+ } else {
+ STACK_POP5(ISAd, first, last, limit, trlink);
+ }
+ } else {
+ if(1 < (last - b)) {
+ STACK_PUSH5(ISAd, first, a, tr_ilg(a - first), trlink);
+ first = b, limit = tr_ilg(last - b);
+ } else if(1 < (a - first)) {
+ last = a, limit = tr_ilg(a - first);
+ } else {
+ STACK_POP5(ISAd, first, last, limit, trlink);
+ }
+ }
+ } else if(limit == -2) {
+ /* tandem repeat copy */
+ a = stack[--ssize].b, b = stack[ssize].c;
+ if(stack[ssize].d == 0) {
+ tr_copy(ISA, SA, first, a, b, last, ISAd - ISA);
+ } else {
+ if(0 <= trlink) { stack[trlink].d = -1; }
+ tr_partialcopy(ISA, SA, first, a, b, last, ISAd - ISA);
+ }
+ STACK_POP5(ISAd, first, last, limit, trlink);
+ } else {
+ /* sorted partition */
+ if(0 <= *first) {
+ a = first;
+ do { ISA[*a] = a - SA; } while((++a < last) && (0 <= *a));
+ first = a;
+ }
+ if(first < last) {
+ a = first; do { *a = ~*a; } while(*++a < 0);
+ next = (ISA[*a] != ISAd[*a]) ? tr_ilg(a - first + 1) : -1;
+ if(++a < last) { for(b = first, v = a - SA - 1; b < a; ++b) { ISA[*b] = v; } }
+
+ /* push */
+ if(trbudget_check(budget, a - first)) {
+ if((a - first) <= (last - a)) {
+ STACK_PUSH5(ISAd, a, last, -3, trlink);
+ ISAd += incr, last = a, limit = next;
+ } else {
+ if(1 < (last - a)) {
+ STACK_PUSH5(ISAd + incr, first, a, next, trlink);
+ first = a, limit = -3;
+ } else {
+ ISAd += incr, last = a, limit = next;
+ }
+ }
+ } else {
+ if(0 <= trlink) { stack[trlink].d = -1; }
+ if(1 < (last - a)) {
+ first = a, limit = -3;
+ } else {
+ STACK_POP5(ISAd, first, last, limit, trlink);
+ }
+ }
+ } else {
+ STACK_POP5(ISAd, first, last, limit, trlink);
+ }
+ }
+ continue;
+ }
+
+ if((last - first) <= TR_INSERTIONSORT_THRESHOLD) {
+ tr_insertionsort(ISAd, first, last);
+ limit = -3;
+ continue;
+ }
+
+ if(limit-- == 0) {
+ tr_heapsort(ISAd, first, last - first);
+ for(a = last - 1; first < a; a = b) {
+ for(x = ISAd[*a], b = a - 1; (first <= b) && (ISAd[*b] == x); --b) { *b = ~*b; }
+ }
+ limit = -3;
+ continue;
+ }
+
+ /* choose pivot */
+ a = tr_pivot(ISAd, first, last);
+ SWAP(*first, *a);
+ v = ISAd[*first];
+
+ /* partition */
+ tr_partition(ISAd, first, first + 1, last, &a, &b, v);
+ if((last - first) != (b - a)) {
+ next = (ISA[*a] != v) ? tr_ilg(b - a) : -1;
+
+ /* update ranks */
+ for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
+ if(b < last) { for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; } }
+
+ /* push */
+ if((1 < (b - a)) && (trbudget_check(budget, b - a))) {
+ if((a - first) <= (last - b)) {
+ if((last - b) <= (b - a)) {
+ if(1 < (a - first)) {
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
+ last = a;
+ } else if(1 < (last - b)) {
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
+ first = b;
+ } else {
+ ISAd += incr, first = a, last = b, limit = next;
+ }
+ } else if((a - first) <= (b - a)) {
+ if(1 < (a - first)) {
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
+ last = a;
+ } else {
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
+ ISAd += incr, first = a, last = b, limit = next;
+ }
+ } else {
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
+ ISAd += incr, first = a, last = b, limit = next;
+ }
+ } else {
+ if((a - first) <= (b - a)) {
+ if(1 < (last - b)) {
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
+ first = b;
+ } else if(1 < (a - first)) {
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
+ last = a;
+ } else {
+ ISAd += incr, first = a, last = b, limit = next;
+ }
+ } else if((last - b) <= (b - a)) {
+ if(1 < (last - b)) {
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
+ first = b;
+ } else {
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
+ ISAd += incr, first = a, last = b, limit = next;
+ }
+ } else {
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
+ ISAd += incr, first = a, last = b, limit = next;
+ }
+ }
+ } else {
+ if((1 < (b - a)) && (0 <= trlink)) { stack[trlink].d = -1; }
+ if((a - first) <= (last - b)) {
+ if(1 < (a - first)) {
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
+ last = a;
+ } else if(1 < (last - b)) {
+ first = b;
+ } else {
+ STACK_POP5(ISAd, first, last, limit, trlink);
+ }
+ } else {
+ if(1 < (last - b)) {
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
+ first = b;
+ } else if(1 < (a - first)) {
+ last = a;
+ } else {
+ STACK_POP5(ISAd, first, last, limit, trlink);
+ }
+ }
+ }
+ } else {
+ if(trbudget_check(budget, last - first)) {
+ limit = tr_ilg(last - first), ISAd += incr;
+ } else {
+ if(0 <= trlink) { stack[trlink].d = -1; }
+ STACK_POP5(ISAd, first, last, limit, trlink);
+ }
+ }
+ }
+#undef STACK_SIZE
+}
+
+
+
+/*---------------------------------------------------------------------------*/
+
+/*- Function -*/
+
+/* Tandem repeat sort */
+void
+trsort(saidx_t *ISA, saidx_t *SA, saidx_t n, saidx_t depth) {
+ saidx_t *ISAd;
+ saidx_t *first, *last;
+ trbudget_t budget;
+ saidx_t t, skip, unsorted;
+
+ trbudget_init(&budget, tr_ilg(n) * 2 / 3, n);
+/* trbudget_init(&budget, tr_ilg(n) * 3 / 4, n); */
+ for(ISAd = ISA + depth; -n < *SA; ISAd += ISAd - ISA) {
+ first = SA;
+ skip = 0;
+ unsorted = 0;
+ do {
+ if((t = *first) < 0) { first -= t; skip += t; }
+ else {
+ if(skip != 0) { *(first + skip) = skip; skip = 0; }
+ last = SA + ISA[t] + 1;
+ if(1 < (last - first)) {
+ budget.count = 0;
+ tr_introsort(ISA, ISAd, SA, first, last, &budget);
+ if(budget.count != 0) { unsorted += budget.count; }
+ else { skip = first - last; }
+ } else if((last - first) == 1) {
+ skip = -1;
+ }
+ first = last;
+ }
+ } while(first < (SA + n));
+ if(skip != 0) { *(first + skip) = skip; }
+ if(unsorted == 0) { break; }
+ }
+}
diff --git a/lib/utils.c b/lib/utils.c
new file mode 100644
index 000000000000..90fb23efa89a
--- /dev/null
+++ b/lib/utils.c
@@ -0,0 +1,381 @@
+/*
+ * utils.c for libdivsufsort
+ * Copyright (c) 2003-2008 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 "divsufsort_private.h"
+
+
+/*- Private Function -*/
+
+/* Binary search for inverse bwt. */
+static
+saidx_t
+binarysearch_lower(const saidx_t *A, saidx_t size, saidx_t value) {
+ saidx_t half, i;
+ for(i = 0, half = size >> 1;
+ 0 < size;
+ size = half, half >>= 1) {
+ if(A[i + half] < value) {
+ i += half + 1;
+ half -= (size & 1) ^ 1;
+ }
+ }
+ return i;
+}
+
+
+/*- Functions -*/
+
+/* Burrows-Wheeler transform. */
+saint_t
+bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *SA,
+ saidx_t n, saidx_t *idx) {
+ saidx_t *A, i, j, p, t;
+ saint_t c;
+
+ /* Check arguments. */
+ if((T == NULL) || (U == NULL) || (n < 0) || (idx == NULL)) { return -1; }
+ if(n <= 1) {
+ if(n == 1) { U[0] = T[0]; }
+ *idx = n;
+ return 0;
+ }
+
+ if((A = SA) == NULL) {
+ i = divbwt(T, U, NULL, n);
+ if(0 <= i) { *idx = i; i = 0; }
+ return (saint_t)i;
+ }
+
+ /* BW transform. */
+ if(T == U) {
+ t = n;
+ for(i = 0, j = 0; i < n; ++i) {
+ p = t - 1;
+ t = A[i];
+ if(0 <= p) {
+ c = T[j];
+ U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
+ A[j] = c;
+ j++;
+ } else {
+ *idx = i;
+ }
+ }
+ p = t - 1;
+ if(0 <= p) {
+ c = T[j];
+ U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
+ A[j] = c;
+ } else {
+ *idx = i;
+ }
+ } else {
+ U[0] = T[n - 1];
+ for(i = 0; A[i] != 0; ++i) { U[i + 1] = T[A[i] - 1]; }
+ *idx = i + 1;
+ for(++i; i < n; ++i) { U[i] = T[A[i] - 1]; }
+ }
+
+ if(SA == NULL) {
+ /* Deallocate memory. */
+ free(A);
+ }
+
+ return 0;
+}
+
+/* Inverse Burrows-Wheeler transform. */
+saint_t
+inverse_bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *A,
+ saidx_t n, saidx_t idx) {
+ saidx_t C[ALPHABET_SIZE];
+ sauchar_t D[ALPHABET_SIZE];
+ saidx_t *B;
+ saidx_t i, p;
+ saint_t c, d;
+
+ /* Check arguments. */
+ if((T == NULL) || (U == NULL) || (n < 0) || (idx < 0) ||
+ (n < idx) || ((0 < n) && (idx == 0))) {
+ return -1;
+ }
+ if(n <= 1) { return 0; }
+
+ if((B = A) == NULL) {
+ /* Allocate n*sizeof(saidx_t) bytes of memory. */
+ if((B = (saidx_t *)malloc((size_t)n * sizeof(saidx_t))) == NULL) { return -2; }
+ }
+
+ /* Inverse BW transform. */
+ for(c = 0; c < ALPHABET_SIZE; ++c) { C[c] = 0; }
+ for(i = 0; i < n; ++i) { ++C[T[i]]; }
+ for(c = 0, d = 0, i = 0; c < ALPHABET_SIZE; ++c) {
+ p = C[c];
+ if(0 < p) {
+ C[c] = i;
+ D[d++] = (sauchar_t)c;
+ i += p;
+ }
+ }
+ for(i = 0; i < idx; ++i) { B[C[T[i]]++] = i; }
+ for( ; i < n; ++i) { B[C[T[i]]++] = i + 1; }
+ for(c = 0; c < d; ++c) { C[c] = C[D[c]]; }
+ for(i = 0, p = idx; i < n; ++i) {
+ U[i] = D[binarysearch_lower(C, d, p)];
+ p = B[p - 1];
+ }
+
+ if(A == NULL) {
+ /* Deallocate memory. */
+ free(B);
+ }
+
+ return 0;
+}
+
+/* Checks the suffix array SA of the string T. */
+saint_t
+sufcheck(const sauchar_t *T, const saidx_t *SA,
+ saidx_t n, saint_t verbose) {
+ saidx_t C[ALPHABET_SIZE];
+ saidx_t i, p, q, t;
+ saint_t c;
+
+ if(verbose) { fprintf(stderr, "sufcheck: "); }
+
+ /* Check arguments. */
+ if((T == NULL) || (SA == NULL) || (n < 0)) {
+ if(verbose) { fprintf(stderr, "Invalid arguments.\n"); }
+ return -1;
+ }
+ if(n == 0) {
+ if(verbose) { fprintf(stderr, "Done.\n"); }
+ return 0;
+ }
+
+ /* check range: [0..n-1] */
+ for(i = 0; i < n; ++i) {
+ if((SA[i] < 0) || (n <= SA[i])) {
+ if(verbose) {
+ fprintf(stderr, "Out of the range [0,%" PRIdSAIDX_T "].\n"
+ " SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
+ n - 1, i, SA[i]);
+ }
+ return -2;
+ }
+ }
+
+ /* check first characters. */
+ for(i = 1; i < n; ++i) {
+ if(T[SA[i - 1]] > T[SA[i]]) {
+ if(verbose) {
+ fprintf(stderr, "Suffixes in wrong order.\n"
+ " T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d"
+ " > T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d\n",
+ i - 1, SA[i - 1], T[SA[i - 1]], i, SA[i], T[SA[i]]);
+ }
+ return -3;
+ }
+ }
+
+ /* check suffixes. */
+ for(i = 0; i < ALPHABET_SIZE; ++i) { C[i] = 0; }
+ for(i = 0; i < n; ++i) { ++C[T[i]]; }
+ for(i = 0, p = 0; i < ALPHABET_SIZE; ++i) {
+ t = C[i];
+ C[i] = p;
+ p += t;
+ }
+
+ q = C[T[n - 1]];
+ C[T[n - 1]] += 1;
+ for(i = 0; i < n; ++i) {
+ p = SA[i];
+ if(0 < p) {
+ c = T[--p];
+ t = C[c];
+ } else {
+ c = T[p = n - 1];
+ t = q;
+ }
+ if((t < 0) || (p != SA[t])) {
+ if(verbose) {
+ fprintf(stderr, "Suffix in wrong position.\n"
+ " SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T " or\n"
+ " SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
+ t, (0 <= t) ? SA[t] : -1, i, SA[i]);
+ }
+ return -4;
+ }
+ if(t != q) {
+ ++C[c];
+ if((n <= C[c]) || (T[SA[C[c]]] != c)) { C[c] = -1; }
+ }
+ }
+
+ if(1 <= verbose) { fprintf(stderr, "Done.\n"); }
+ return 0;
+}
+
+
+static
+int
+_compare(const sauchar_t *T, saidx_t Tsize,
+ const sauchar_t *P, saidx_t Psize,
+ saidx_t suf, saidx_t *match) {
+ saidx_t i, j;
+ saint_t r;
+ for(i = suf + *match, j = *match, r = 0;
+ (i < Tsize) && (j < Psize) && ((r = T[i] - P[j]) == 0); ++i, ++j) { }
+ *match = j;
+ return (r == 0) ? -(j != Psize) : r;
+}
+
+/* Search for the pattern P in the string T. */
+saidx_t
+sa_search(const sauchar_t *T, saidx_t Tsize,
+ const sauchar_t *P, saidx_t Psize,
+ const saidx_t *SA, saidx_t SAsize,
+ saidx_t *idx) {
+ saidx_t size, lsize, rsize, half;
+ saidx_t match, lmatch, rmatch;
+ saidx_t llmatch, lrmatch, rlmatch, rrmatch;
+ saidx_t i, j, k;
+ saint_t r;
+
+ if(idx != NULL) { *idx = -1; }
+ if((T == NULL) || (P == NULL) || (SA == NULL) ||
+ (Tsize < 0) || (Psize < 0) || (SAsize < 0)) { return -1; }
+ if((Tsize == 0) || (SAsize == 0)) { return 0; }
+ if(Psize == 0) { if(idx != NULL) { *idx = 0; } return SAsize; }
+
+ for(i = j = k = 0, lmatch = rmatch = 0, size = SAsize, half = size >> 1;
+ 0 < size;
+ size = half, half >>= 1) {
+ match = MIN(lmatch, rmatch);
+ r = _compare(T, Tsize, P, Psize, SA[i + half], &match);
+ if(r < 0) {
+ i += half + 1;
+ half -= (size & 1) ^ 1;
+ lmatch = match;
+ } else if(r > 0) {
+ rmatch = match;
+ } else {
+ lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
+
+ /* left part */
+ for(llmatch = lmatch, lrmatch = match, half = lsize >> 1;
+ 0 < lsize;
+ lsize = half, half >>= 1) {
+ lmatch = MIN(llmatch, lrmatch);
+ r = _compare(T, Tsize, P, Psize, SA[j + half], &lmatch);
+ if(r < 0) {
+ j += half + 1;
+ half -= (lsize & 1) ^ 1;
+ llmatch = lmatch;
+ } else {
+ lrmatch = lmatch;
+ }
+ }
+
+ /* right part */
+ for(rlmatch = match, rrmatch = rmatch, half = rsize >> 1;
+ 0 < rsize;
+ rsize = half, half >>= 1) {
+ rmatch = MIN(rlmatch, rrmatch);
+ r = _compare(T, Tsize, P, Psize, SA[k + half], &rmatch);
+ if(r <= 0) {
+ k += half + 1;
+ half -= (rsize & 1) ^ 1;
+ rlmatch = rmatch;
+ } else {
+ rrmatch = rmatch;
+ }
+ }
+
+ break;
+ }
+ }
+
+ if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
+ return k - j;
+}
+
+/* Search for the character c in the string T. */
+saidx_t
+sa_simplesearch(const sauchar_t *T, saidx_t Tsize,
+ const saidx_t *SA, saidx_t SAsize,
+ saint_t c, saidx_t *idx) {
+ saidx_t size, lsize, rsize, half;
+ saidx_t i, j, k, p;
+ saint_t r;
+
+ if(idx != NULL) { *idx = -1; }
+ if((T == NULL) || (SA == NULL) || (Tsize < 0) || (SAsize < 0)) { return -1; }
+ if((Tsize == 0) || (SAsize == 0)) { return 0; }
+
+ for(i = j = k = 0, size = SAsize, half = size >> 1;
+ 0 < size;
+ size = half, half >>= 1) {
+ p = SA[i + half];
+ r = (p < Tsize) ? T[p] - c : -1;
+ if(r < 0) {
+ i += half + 1;
+ half -= (size & 1) ^ 1;
+ } else if(r == 0) {
+ lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
+
+ /* left part */
+ for(half = lsize >> 1;
+ 0 < lsize;
+ lsize = half, half >>= 1) {
+ p = SA[j + half];
+ r = (p < Tsize) ? T[p] - c : -1;
+ if(r < 0) {
+ j += half + 1;
+ half -= (lsize & 1) ^ 1;
+ }
+ }
+
+ /* right part */
+ for(half = rsize >> 1;
+ 0 < rsize;
+ rsize = half, half >>= 1) {
+ p = SA[k + half];
+ r = (p < Tsize) ? T[p] - c : -1;
+ if(r <= 0) {
+ k += half + 1;
+ half -= (rsize & 1) ^ 1;
+ }
+ }
+
+ break;
+ }
+ }
+
+ if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
+ return k - j;
+}