extzstd 0.0.2.CONCEPT-x86-mingw32 → 0.0.3.CONCEPT-x86-mingw32

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (72) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +72 -22
  3. data/Rakefile +73 -19
  4. data/contrib/zstd/README.md +68 -0
  5. data/contrib/zstd/common/bitstream.h +414 -0
  6. data/contrib/zstd/common/entropy_common.c +231 -0
  7. data/contrib/zstd/common/error_private.h +125 -0
  8. data/contrib/zstd/common/error_public.h +77 -0
  9. data/contrib/zstd/common/fse.h +628 -0
  10. data/contrib/zstd/common/fse_decompress.c +331 -0
  11. data/contrib/zstd/common/huf.h +228 -0
  12. data/contrib/zstd/common/mem.h +377 -0
  13. data/contrib/zstd/common/xxhash.c +854 -0
  14. data/contrib/zstd/common/xxhash.h +273 -0
  15. data/contrib/zstd/common/zbuff.h +197 -0
  16. data/contrib/zstd/common/zstd.h +475 -0
  17. data/contrib/zstd/common/zstd_common.c +91 -0
  18. data/contrib/zstd/common/zstd_internal.h +238 -0
  19. data/contrib/zstd/compress/fse_compress.c +807 -0
  20. data/contrib/zstd/compress/huf_compress.c +577 -0
  21. data/contrib/zstd/compress/zbuff_compress.c +327 -0
  22. data/contrib/zstd/compress/zstd_compress.c +3074 -0
  23. data/contrib/zstd/compress/zstd_opt.h +1046 -0
  24. data/contrib/zstd/decompress/huf_decompress.c +894 -0
  25. data/contrib/zstd/decompress/zbuff_decompress.c +294 -0
  26. data/contrib/zstd/decompress/zstd_decompress.c +1362 -0
  27. data/contrib/zstd/dictBuilder/divsufsort.c +1913 -0
  28. data/contrib/zstd/dictBuilder/divsufsort.h +67 -0
  29. data/contrib/zstd/dictBuilder/zdict.c +1045 -0
  30. data/contrib/zstd/dictBuilder/zdict.h +113 -0
  31. data/contrib/zstd/legacy/zstd_legacy.h +140 -0
  32. data/contrib/zstd/legacy/zstd_v01.c +2178 -0
  33. data/contrib/zstd/{zstd.h → legacy/zstd_v01.h} +46 -39
  34. data/contrib/zstd/legacy/zstd_v02.c +3748 -0
  35. data/contrib/zstd/legacy/zstd_v02.h +99 -0
  36. data/contrib/zstd/legacy/zstd_v03.c +3389 -0
  37. data/contrib/zstd/legacy/zstd_v03.h +99 -0
  38. data/contrib/zstd/legacy/zstd_v04.c +4056 -0
  39. data/contrib/zstd/legacy/zstd_v04.h +148 -0
  40. data/contrib/zstd/legacy/zstd_v05.c +4325 -0
  41. data/contrib/zstd/legacy/zstd_v05.h +171 -0
  42. data/contrib/zstd/legacy/zstd_v06.c +4581 -0
  43. data/contrib/zstd/legacy/zstd_v06.h +185 -0
  44. data/ext/extconf.rb +10 -12
  45. data/ext/extzstd.c +497 -144
  46. data/ext/extzstd.h +127 -22
  47. data/ext/extzstd_buffered.c +265 -0
  48. data/ext/extzstd_nogvls.h +174 -0
  49. data/ext/zstd_amalgam.c +18 -0
  50. data/ext/zstd_legacy_v01.c +1 -0
  51. data/ext/zstd_legacy_v02.c +1 -0
  52. data/ext/zstd_legacy_v03.c +1 -0
  53. data/ext/zstd_legacy_v04.c +1 -0
  54. data/ext/zstd_legacy_v05.c +1 -0
  55. data/ext/zstd_legacy_v06.c +1 -0
  56. data/gemstub.rb +17 -1
  57. data/lib/2.0/extzstd.so +0 -0
  58. data/lib/2.1/extzstd.so +0 -0
  59. data/lib/2.2/extzstd.so +0 -0
  60. data/lib/2.3/extzstd.so +0 -0
  61. data/lib/extzstd.rb +197 -77
  62. data/lib/extzstd/version.rb +1 -1
  63. data/test/test_basic.rb +41 -0
  64. metadata +71 -20
  65. data/contrib/zstd/Makefile +0 -115
  66. data/contrib/zstd/fse.c +0 -2466
  67. data/contrib/zstd/fse.h +0 -320
  68. data/contrib/zstd/fse_static.h +0 -282
  69. data/contrib/zstd/libzstd.pc.in +0 -14
  70. data/contrib/zstd/zstd.c +0 -1768
  71. data/contrib/zstd/zstd_static.h +0 -89
  72. data/ext/extzstd-stream.c +0 -398
@@ -0,0 +1,1913 @@
1
+ /*
2
+ * divsufsort.c for libdivsufsort-lite
3
+ * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
4
+ *
5
+ * Permission is hereby granted, free of charge, to any person
6
+ * obtaining a copy of this software and associated documentation
7
+ * files (the "Software"), to deal in the Software without
8
+ * restriction, including without limitation the rights to use,
9
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
10
+ * copies of the Software, and to permit persons to whom the
11
+ * Software is furnished to do so, subject to the following
12
+ * conditions:
13
+ *
14
+ * The above copyright notice and this permission notice shall be
15
+ * included in all copies or substantial portions of the Software.
16
+ *
17
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
18
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
19
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
20
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
21
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
22
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
23
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
24
+ * OTHER DEALINGS IN THE SOFTWARE.
25
+ */
26
+
27
+ /*- Compiler specifics -*/
28
+ #ifdef __clang__
29
+ #pragma clang diagnostic ignored "-Wshorten-64-to-32"
30
+ #endif
31
+
32
+ #if defined(_MSC_VER)
33
+ # pragma warning(disable : 4244)
34
+ # pragma warning(disable : 4127) /* C4127 : Condition expression is constant */
35
+ #endif
36
+
37
+
38
+ /*- Dependencies -*/
39
+ #include <assert.h>
40
+ #include <stdio.h>
41
+ #include <stdlib.h>
42
+
43
+ #include "divsufsort.h"
44
+
45
+ /*- Constants -*/
46
+ #if defined(INLINE)
47
+ # undef INLINE
48
+ #endif
49
+ #if !defined(INLINE)
50
+ # define INLINE __inline
51
+ #endif
52
+ #if defined(ALPHABET_SIZE) && (ALPHABET_SIZE < 1)
53
+ # undef ALPHABET_SIZE
54
+ #endif
55
+ #if !defined(ALPHABET_SIZE)
56
+ # define ALPHABET_SIZE (256)
57
+ #endif
58
+ #define BUCKET_A_SIZE (ALPHABET_SIZE)
59
+ #define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE)
60
+ #if defined(SS_INSERTIONSORT_THRESHOLD)
61
+ # if SS_INSERTIONSORT_THRESHOLD < 1
62
+ # undef SS_INSERTIONSORT_THRESHOLD
63
+ # define SS_INSERTIONSORT_THRESHOLD (1)
64
+ # endif
65
+ #else
66
+ # define SS_INSERTIONSORT_THRESHOLD (8)
67
+ #endif
68
+ #if defined(SS_BLOCKSIZE)
69
+ # if SS_BLOCKSIZE < 0
70
+ # undef SS_BLOCKSIZE
71
+ # define SS_BLOCKSIZE (0)
72
+ # elif 32768 <= SS_BLOCKSIZE
73
+ # undef SS_BLOCKSIZE
74
+ # define SS_BLOCKSIZE (32767)
75
+ # endif
76
+ #else
77
+ # define SS_BLOCKSIZE (1024)
78
+ #endif
79
+ /* minstacksize = log(SS_BLOCKSIZE) / log(3) * 2 */
80
+ #if SS_BLOCKSIZE == 0
81
+ # define SS_MISORT_STACKSIZE (96)
82
+ #elif SS_BLOCKSIZE <= 4096
83
+ # define SS_MISORT_STACKSIZE (16)
84
+ #else
85
+ # define SS_MISORT_STACKSIZE (24)
86
+ #endif
87
+ #define SS_SMERGE_STACKSIZE (32)
88
+ #define TR_INSERTIONSORT_THRESHOLD (8)
89
+ #define TR_STACKSIZE (64)
90
+
91
+
92
+ /*- Macros -*/
93
+ #ifndef SWAP
94
+ # define SWAP(_a, _b) do { t = (_a); (_a) = (_b); (_b) = t; } while(0)
95
+ #endif /* SWAP */
96
+ #ifndef MIN
97
+ # define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b))
98
+ #endif /* MIN */
99
+ #ifndef MAX
100
+ # define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b))
101
+ #endif /* MAX */
102
+ #define STACK_PUSH(_a, _b, _c, _d)\
103
+ do {\
104
+ assert(ssize < STACK_SIZE);\
105
+ stack[ssize].a = (_a), stack[ssize].b = (_b),\
106
+ stack[ssize].c = (_c), stack[ssize++].d = (_d);\
107
+ } while(0)
108
+ #define STACK_PUSH5(_a, _b, _c, _d, _e)\
109
+ do {\
110
+ assert(ssize < STACK_SIZE);\
111
+ stack[ssize].a = (_a), stack[ssize].b = (_b),\
112
+ stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\
113
+ } while(0)
114
+ #define STACK_POP(_a, _b, _c, _d)\
115
+ do {\
116
+ assert(0 <= ssize);\
117
+ if(ssize == 0) { return; }\
118
+ (_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
119
+ (_c) = stack[ssize].c, (_d) = stack[ssize].d;\
120
+ } while(0)
121
+ #define STACK_POP5(_a, _b, _c, _d, _e)\
122
+ do {\
123
+ assert(0 <= ssize);\
124
+ if(ssize == 0) { return; }\
125
+ (_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
126
+ (_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\
127
+ } while(0)
128
+ #define BUCKET_A(_c0) bucket_A[(_c0)]
129
+ #if ALPHABET_SIZE == 256
130
+ #define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)])
131
+ #define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)])
132
+ #else
133
+ #define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)])
134
+ #define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)])
135
+ #endif
136
+
137
+
138
+ /*- Private Functions -*/
139
+
140
+ static const int lg_table[256]= {
141
+ -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,
142
+ 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,
143
+ 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,
144
+ 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,
145
+ 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,
146
+ 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,
147
+ 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,
148
+ 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
149
+ };
150
+
151
+ #if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
152
+
153
+ static INLINE
154
+ int
155
+ ss_ilg(int n) {
156
+ #if SS_BLOCKSIZE == 0
157
+ return (n & 0xffff0000) ?
158
+ ((n & 0xff000000) ?
159
+ 24 + lg_table[(n >> 24) & 0xff] :
160
+ 16 + lg_table[(n >> 16) & 0xff]) :
161
+ ((n & 0x0000ff00) ?
162
+ 8 + lg_table[(n >> 8) & 0xff] :
163
+ 0 + lg_table[(n >> 0) & 0xff]);
164
+ #elif SS_BLOCKSIZE < 256
165
+ return lg_table[n];
166
+ #else
167
+ return (n & 0xff00) ?
168
+ 8 + lg_table[(n >> 8) & 0xff] :
169
+ 0 + lg_table[(n >> 0) & 0xff];
170
+ #endif
171
+ }
172
+
173
+ #endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
174
+
175
+ #if SS_BLOCKSIZE != 0
176
+
177
+ static const int sqq_table[256] = {
178
+ 0, 16, 22, 27, 32, 35, 39, 42, 45, 48, 50, 53, 55, 57, 59, 61,
179
+ 64, 65, 67, 69, 71, 73, 75, 76, 78, 80, 81, 83, 84, 86, 87, 89,
180
+ 90, 91, 93, 94, 96, 97, 98, 99, 101, 102, 103, 104, 106, 107, 108, 109,
181
+ 110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126,
182
+ 128, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
183
+ 143, 144, 144, 145, 146, 147, 148, 149, 150, 150, 151, 152, 153, 154, 155, 155,
184
+ 156, 157, 158, 159, 160, 160, 161, 162, 163, 163, 164, 165, 166, 167, 167, 168,
185
+ 169, 170, 170, 171, 172, 173, 173, 174, 175, 176, 176, 177, 178, 178, 179, 180,
186
+ 181, 181, 182, 183, 183, 184, 185, 185, 186, 187, 187, 188, 189, 189, 190, 191,
187
+ 192, 192, 193, 193, 194, 195, 195, 196, 197, 197, 198, 199, 199, 200, 201, 201,
188
+ 202, 203, 203, 204, 204, 205, 206, 206, 207, 208, 208, 209, 209, 210, 211, 211,
189
+ 212, 212, 213, 214, 214, 215, 215, 216, 217, 217, 218, 218, 219, 219, 220, 221,
190
+ 221, 222, 222, 223, 224, 224, 225, 225, 226, 226, 227, 227, 228, 229, 229, 230,
191
+ 230, 231, 231, 232, 232, 233, 234, 234, 235, 235, 236, 236, 237, 237, 238, 238,
192
+ 239, 240, 240, 241, 241, 242, 242, 243, 243, 244, 244, 245, 245, 246, 246, 247,
193
+ 247, 248, 248, 249, 249, 250, 250, 251, 251, 252, 252, 253, 253, 254, 254, 255
194
+ };
195
+
196
+ static INLINE
197
+ int
198
+ ss_isqrt(int x) {
199
+ int y, e;
200
+
201
+ if(x >= (SS_BLOCKSIZE * SS_BLOCKSIZE)) { return SS_BLOCKSIZE; }
202
+ e = (x & 0xffff0000) ?
203
+ ((x & 0xff000000) ?
204
+ 24 + lg_table[(x >> 24) & 0xff] :
205
+ 16 + lg_table[(x >> 16) & 0xff]) :
206
+ ((x & 0x0000ff00) ?
207
+ 8 + lg_table[(x >> 8) & 0xff] :
208
+ 0 + lg_table[(x >> 0) & 0xff]);
209
+
210
+ if(e >= 16) {
211
+ y = sqq_table[x >> ((e - 6) - (e & 1))] << ((e >> 1) - 7);
212
+ if(e >= 24) { y = (y + 1 + x / y) >> 1; }
213
+ y = (y + 1 + x / y) >> 1;
214
+ } else if(e >= 8) {
215
+ y = (sqq_table[x >> ((e - 6) - (e & 1))] >> (7 - (e >> 1))) + 1;
216
+ } else {
217
+ return sqq_table[x] >> 4;
218
+ }
219
+
220
+ return (x < (y * y)) ? y - 1 : y;
221
+ }
222
+
223
+ #endif /* SS_BLOCKSIZE != 0 */
224
+
225
+
226
+ /*---------------------------------------------------------------------------*/
227
+
228
+ /* Compares two suffixes. */
229
+ static INLINE
230
+ int
231
+ ss_compare(const unsigned char *T,
232
+ const int *p1, const int *p2,
233
+ int depth) {
234
+ const unsigned char *U1, *U2, *U1n, *U2n;
235
+
236
+ for(U1 = T + depth + *p1,
237
+ U2 = T + depth + *p2,
238
+ U1n = T + *(p1 + 1) + 2,
239
+ U2n = T + *(p2 + 1) + 2;
240
+ (U1 < U1n) && (U2 < U2n) && (*U1 == *U2);
241
+ ++U1, ++U2) {
242
+ }
243
+
244
+ return U1 < U1n ?
245
+ (U2 < U2n ? *U1 - *U2 : 1) :
246
+ (U2 < U2n ? -1 : 0);
247
+ }
248
+
249
+
250
+ /*---------------------------------------------------------------------------*/
251
+
252
+ #if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1)
253
+
254
+ /* Insertionsort for small size groups */
255
+ static
256
+ void
257
+ ss_insertionsort(const unsigned char *T, const int *PA,
258
+ int *first, int *last, int depth) {
259
+ int *i, *j;
260
+ int t;
261
+ int r;
262
+
263
+ for(i = last - 2; first <= i; --i) {
264
+ for(t = *i, j = i + 1; 0 < (r = ss_compare(T, PA + t, PA + *j, depth));) {
265
+ do { *(j - 1) = *j; } while((++j < last) && (*j < 0));
266
+ if(last <= j) { break; }
267
+ }
268
+ if(r == 0) { *j = ~*j; }
269
+ *(j - 1) = t;
270
+ }
271
+ }
272
+
273
+ #endif /* (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) */
274
+
275
+
276
+ /*---------------------------------------------------------------------------*/
277
+
278
+ #if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
279
+
280
+ static INLINE
281
+ void
282
+ ss_fixdown(const unsigned char *Td, const int *PA,
283
+ int *SA, int i, int size) {
284
+ int j, k;
285
+ int v;
286
+ int c, d, e;
287
+
288
+ for(v = SA[i], c = Td[PA[v]]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
289
+ d = Td[PA[SA[k = j++]]];
290
+ if(d < (e = Td[PA[SA[j]]])) { k = j; d = e; }
291
+ if(d <= c) { break; }
292
+ }
293
+ SA[i] = v;
294
+ }
295
+
296
+ /* Simple top-down heapsort. */
297
+ static
298
+ void
299
+ ss_heapsort(const unsigned char *Td, const int *PA, int *SA, int size) {
300
+ int i, m;
301
+ int t;
302
+
303
+ m = size;
304
+ if((size % 2) == 0) {
305
+ m--;
306
+ if(Td[PA[SA[m / 2]]] < Td[PA[SA[m]]]) { SWAP(SA[m], SA[m / 2]); }
307
+ }
308
+
309
+ for(i = m / 2 - 1; 0 <= i; --i) { ss_fixdown(Td, PA, SA, i, m); }
310
+ if((size % 2) == 0) { SWAP(SA[0], SA[m]); ss_fixdown(Td, PA, SA, 0, m); }
311
+ for(i = m - 1; 0 < i; --i) {
312
+ t = SA[0], SA[0] = SA[i];
313
+ ss_fixdown(Td, PA, SA, 0, i);
314
+ SA[i] = t;
315
+ }
316
+ }
317
+
318
+
319
+ /*---------------------------------------------------------------------------*/
320
+
321
+ /* Returns the median of three elements. */
322
+ static INLINE
323
+ int *
324
+ ss_median3(const unsigned char *Td, const int *PA,
325
+ int *v1, int *v2, int *v3) {
326
+ int *t;
327
+ if(Td[PA[*v1]] > Td[PA[*v2]]) { SWAP(v1, v2); }
328
+ if(Td[PA[*v2]] > Td[PA[*v3]]) {
329
+ if(Td[PA[*v1]] > Td[PA[*v3]]) { return v1; }
330
+ else { return v3; }
331
+ }
332
+ return v2;
333
+ }
334
+
335
+ /* Returns the median of five elements. */
336
+ static INLINE
337
+ int *
338
+ ss_median5(const unsigned char *Td, const int *PA,
339
+ int *v1, int *v2, int *v3, int *v4, int *v5) {
340
+ int *t;
341
+ if(Td[PA[*v2]] > Td[PA[*v3]]) { SWAP(v2, v3); }
342
+ if(Td[PA[*v4]] > Td[PA[*v5]]) { SWAP(v4, v5); }
343
+ if(Td[PA[*v2]] > Td[PA[*v4]]) { SWAP(v2, v4); SWAP(v3, v5); }
344
+ if(Td[PA[*v1]] > Td[PA[*v3]]) { SWAP(v1, v3); }
345
+ if(Td[PA[*v1]] > Td[PA[*v4]]) { SWAP(v1, v4); SWAP(v3, v5); }
346
+ if(Td[PA[*v3]] > Td[PA[*v4]]) { return v4; }
347
+ return v3;
348
+ }
349
+
350
+ /* Returns the pivot element. */
351
+ static INLINE
352
+ int *
353
+ ss_pivot(const unsigned char *Td, const int *PA, int *first, int *last) {
354
+ int *middle;
355
+ int t;
356
+
357
+ t = last - first;
358
+ middle = first + t / 2;
359
+
360
+ if(t <= 512) {
361
+ if(t <= 32) {
362
+ return ss_median3(Td, PA, first, middle, last - 1);
363
+ } else {
364
+ t >>= 2;
365
+ return ss_median5(Td, PA, first, first + t, middle, last - 1 - t, last - 1);
366
+ }
367
+ }
368
+ t >>= 3;
369
+ first = ss_median3(Td, PA, first, first + t, first + (t << 1));
370
+ middle = ss_median3(Td, PA, middle - t, middle, middle + t);
371
+ last = ss_median3(Td, PA, last - 1 - (t << 1), last - 1 - t, last - 1);
372
+ return ss_median3(Td, PA, first, middle, last);
373
+ }
374
+
375
+
376
+ /*---------------------------------------------------------------------------*/
377
+
378
+ /* Binary partition for substrings. */
379
+ static INLINE
380
+ int *
381
+ ss_partition(const int *PA,
382
+ int *first, int *last, int depth) {
383
+ int *a, *b;
384
+ int t;
385
+ for(a = first - 1, b = last;;) {
386
+ for(; (++a < b) && ((PA[*a] + depth) >= (PA[*a + 1] + 1));) { *a = ~*a; }
387
+ for(; (a < --b) && ((PA[*b] + depth) < (PA[*b + 1] + 1));) { }
388
+ if(b <= a) { break; }
389
+ t = ~*b;
390
+ *b = *a;
391
+ *a = t;
392
+ }
393
+ if(first < a) { *first = ~*first; }
394
+ return a;
395
+ }
396
+
397
+ /* Multikey introsort for medium size groups. */
398
+ static
399
+ void
400
+ ss_mintrosort(const unsigned char *T, const int *PA,
401
+ int *first, int *last,
402
+ int depth) {
403
+ #define STACK_SIZE SS_MISORT_STACKSIZE
404
+ struct { int *a, *b, c; int d; } stack[STACK_SIZE];
405
+ const unsigned char *Td;
406
+ int *a, *b, *c, *d, *e, *f;
407
+ int s, t;
408
+ int ssize;
409
+ int limit;
410
+ int v, x = 0;
411
+
412
+ for(ssize = 0, limit = ss_ilg(last - first);;) {
413
+
414
+ if((last - first) <= SS_INSERTIONSORT_THRESHOLD) {
415
+ #if 1 < SS_INSERTIONSORT_THRESHOLD
416
+ if(1 < (last - first)) { ss_insertionsort(T, PA, first, last, depth); }
417
+ #endif
418
+ STACK_POP(first, last, depth, limit);
419
+ continue;
420
+ }
421
+
422
+ Td = T + depth;
423
+ if(limit-- == 0) { ss_heapsort(Td, PA, first, last - first); }
424
+ if(limit < 0) {
425
+ for(a = first + 1, v = Td[PA[*first]]; a < last; ++a) {
426
+ if((x = Td[PA[*a]]) != v) {
427
+ if(1 < (a - first)) { break; }
428
+ v = x;
429
+ first = a;
430
+ }
431
+ }
432
+ if(Td[PA[*first] - 1] < v) {
433
+ first = ss_partition(PA, first, a, depth);
434
+ }
435
+ if((a - first) <= (last - a)) {
436
+ if(1 < (a - first)) {
437
+ STACK_PUSH(a, last, depth, -1);
438
+ last = a, depth += 1, limit = ss_ilg(a - first);
439
+ } else {
440
+ first = a, limit = -1;
441
+ }
442
+ } else {
443
+ if(1 < (last - a)) {
444
+ STACK_PUSH(first, a, depth + 1, ss_ilg(a - first));
445
+ first = a, limit = -1;
446
+ } else {
447
+ last = a, depth += 1, limit = ss_ilg(a - first);
448
+ }
449
+ }
450
+ continue;
451
+ }
452
+
453
+ /* choose pivot */
454
+ a = ss_pivot(Td, PA, first, last);
455
+ v = Td[PA[*a]];
456
+ SWAP(*first, *a);
457
+
458
+ /* partition */
459
+ for(b = first; (++b < last) && ((x = Td[PA[*b]]) == v);) { }
460
+ if(((a = b) < last) && (x < v)) {
461
+ for(; (++b < last) && ((x = Td[PA[*b]]) <= v);) {
462
+ if(x == v) { SWAP(*b, *a); ++a; }
463
+ }
464
+ }
465
+ for(c = last; (b < --c) && ((x = Td[PA[*c]]) == v);) { }
466
+ if((b < (d = c)) && (x > v)) {
467
+ for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
468
+ if(x == v) { SWAP(*c, *d); --d; }
469
+ }
470
+ }
471
+ for(; b < c;) {
472
+ SWAP(*b, *c);
473
+ for(; (++b < c) && ((x = Td[PA[*b]]) <= v);) {
474
+ if(x == v) { SWAP(*b, *a); ++a; }
475
+ }
476
+ for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
477
+ if(x == v) { SWAP(*c, *d); --d; }
478
+ }
479
+ }
480
+
481
+ if(a <= d) {
482
+ c = b - 1;
483
+
484
+ if((s = a - first) > (t = b - a)) { s = t; }
485
+ for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
486
+ if((s = d - c) > (t = last - d - 1)) { s = t; }
487
+ for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
488
+
489
+ a = first + (b - a), c = last - (d - c);
490
+ b = (v <= Td[PA[*a] - 1]) ? a : ss_partition(PA, a, c, depth);
491
+
492
+ if((a - first) <= (last - c)) {
493
+ if((last - c) <= (c - b)) {
494
+ STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
495
+ STACK_PUSH(c, last, depth, limit);
496
+ last = a;
497
+ } else if((a - first) <= (c - b)) {
498
+ STACK_PUSH(c, last, depth, limit);
499
+ STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
500
+ last = a;
501
+ } else {
502
+ STACK_PUSH(c, last, depth, limit);
503
+ STACK_PUSH(first, a, depth, limit);
504
+ first = b, last = c, depth += 1, limit = ss_ilg(c - b);
505
+ }
506
+ } else {
507
+ if((a - first) <= (c - b)) {
508
+ STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
509
+ STACK_PUSH(first, a, depth, limit);
510
+ first = c;
511
+ } else if((last - c) <= (c - b)) {
512
+ STACK_PUSH(first, a, depth, limit);
513
+ STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
514
+ first = c;
515
+ } else {
516
+ STACK_PUSH(first, a, depth, limit);
517
+ STACK_PUSH(c, last, depth, limit);
518
+ first = b, last = c, depth += 1, limit = ss_ilg(c - b);
519
+ }
520
+ }
521
+ } else {
522
+ limit += 1;
523
+ if(Td[PA[*first] - 1] < v) {
524
+ first = ss_partition(PA, first, last, depth);
525
+ limit = ss_ilg(last - first);
526
+ }
527
+ depth += 1;
528
+ }
529
+ }
530
+ #undef STACK_SIZE
531
+ }
532
+
533
+ #endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
534
+
535
+
536
+ /*---------------------------------------------------------------------------*/
537
+
538
+ #if SS_BLOCKSIZE != 0
539
+
540
+ static INLINE
541
+ void
542
+ ss_blockswap(int *a, int *b, int n) {
543
+ int t;
544
+ for(; 0 < n; --n, ++a, ++b) {
545
+ t = *a, *a = *b, *b = t;
546
+ }
547
+ }
548
+
549
+ static INLINE
550
+ void
551
+ ss_rotate(int *first, int *middle, int *last) {
552
+ int *a, *b, t;
553
+ int l, r;
554
+ l = middle - first, r = last - middle;
555
+ for(; (0 < l) && (0 < r);) {
556
+ if(l == r) { ss_blockswap(first, middle, l); break; }
557
+ if(l < r) {
558
+ a = last - 1, b = middle - 1;
559
+ t = *a;
560
+ do {
561
+ *a-- = *b, *b-- = *a;
562
+ if(b < first) {
563
+ *a = t;
564
+ last = a;
565
+ if((r -= l + 1) <= l) { break; }
566
+ a -= 1, b = middle - 1;
567
+ t = *a;
568
+ }
569
+ } while(1);
570
+ } else {
571
+ a = first, b = middle;
572
+ t = *a;
573
+ do {
574
+ *a++ = *b, *b++ = *a;
575
+ if(last <= b) {
576
+ *a = t;
577
+ first = a + 1;
578
+ if((l -= r + 1) <= r) { break; }
579
+ a += 1, b = middle;
580
+ t = *a;
581
+ }
582
+ } while(1);
583
+ }
584
+ }
585
+ }
586
+
587
+
588
+ /*---------------------------------------------------------------------------*/
589
+
590
+ static
591
+ void
592
+ ss_inplacemerge(const unsigned char *T, const int *PA,
593
+ int *first, int *middle, int *last,
594
+ int depth) {
595
+ const int *p;
596
+ int *a, *b;
597
+ int len, half;
598
+ int q, r;
599
+ int x;
600
+
601
+ for(;;) {
602
+ if(*(last - 1) < 0) { x = 1; p = PA + ~*(last - 1); }
603
+ else { x = 0; p = PA + *(last - 1); }
604
+ for(a = first, len = middle - first, half = len >> 1, r = -1;
605
+ 0 < len;
606
+ len = half, half >>= 1) {
607
+ b = a + half;
608
+ q = ss_compare(T, PA + ((0 <= *b) ? *b : ~*b), p, depth);
609
+ if(q < 0) {
610
+ a = b + 1;
611
+ half -= (len & 1) ^ 1;
612
+ } else {
613
+ r = q;
614
+ }
615
+ }
616
+ if(a < middle) {
617
+ if(r == 0) { *a = ~*a; }
618
+ ss_rotate(a, middle, last);
619
+ last -= middle - a;
620
+ middle = a;
621
+ if(first == middle) { break; }
622
+ }
623
+ --last;
624
+ if(x != 0) { while(*--last < 0) { } }
625
+ if(middle == last) { break; }
626
+ }
627
+ }
628
+
629
+
630
+ /*---------------------------------------------------------------------------*/
631
+
632
+ /* Merge-forward with internal buffer. */
633
+ static
634
+ void
635
+ ss_mergeforward(const unsigned char *T, const int *PA,
636
+ int *first, int *middle, int *last,
637
+ int *buf, int depth) {
638
+ int *a, *b, *c, *bufend;
639
+ int t;
640
+ int r;
641
+
642
+ bufend = buf + (middle - first) - 1;
643
+ ss_blockswap(buf, first, middle - first);
644
+
645
+ for(t = *(a = first), b = buf, c = middle;;) {
646
+ r = ss_compare(T, PA + *b, PA + *c, depth);
647
+ if(r < 0) {
648
+ do {
649
+ *a++ = *b;
650
+ if(bufend <= b) { *bufend = t; return; }
651
+ *b++ = *a;
652
+ } while(*b < 0);
653
+ } else if(r > 0) {
654
+ do {
655
+ *a++ = *c, *c++ = *a;
656
+ if(last <= c) {
657
+ while(b < bufend) { *a++ = *b, *b++ = *a; }
658
+ *a = *b, *b = t;
659
+ return;
660
+ }
661
+ } while(*c < 0);
662
+ } else {
663
+ *c = ~*c;
664
+ do {
665
+ *a++ = *b;
666
+ if(bufend <= b) { *bufend = t; return; }
667
+ *b++ = *a;
668
+ } while(*b < 0);
669
+
670
+ do {
671
+ *a++ = *c, *c++ = *a;
672
+ if(last <= c) {
673
+ while(b < bufend) { *a++ = *b, *b++ = *a; }
674
+ *a = *b, *b = t;
675
+ return;
676
+ }
677
+ } while(*c < 0);
678
+ }
679
+ }
680
+ }
681
+
682
+ /* Merge-backward with internal buffer. */
683
+ static
684
+ void
685
+ ss_mergebackward(const unsigned char *T, const int *PA,
686
+ int *first, int *middle, int *last,
687
+ int *buf, int depth) {
688
+ const int *p1, *p2;
689
+ int *a, *b, *c, *bufend;
690
+ int t;
691
+ int r;
692
+ int x;
693
+
694
+ bufend = buf + (last - middle) - 1;
695
+ ss_blockswap(buf, middle, last - middle);
696
+
697
+ x = 0;
698
+ if(*bufend < 0) { p1 = PA + ~*bufend; x |= 1; }
699
+ else { p1 = PA + *bufend; }
700
+ if(*(middle - 1) < 0) { p2 = PA + ~*(middle - 1); x |= 2; }
701
+ else { p2 = PA + *(middle - 1); }
702
+ for(t = *(a = last - 1), b = bufend, c = middle - 1;;) {
703
+ r = ss_compare(T, p1, p2, depth);
704
+ if(0 < r) {
705
+ if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
706
+ *a-- = *b;
707
+ if(b <= buf) { *buf = t; break; }
708
+ *b-- = *a;
709
+ if(*b < 0) { p1 = PA + ~*b; x |= 1; }
710
+ else { p1 = PA + *b; }
711
+ } else if(r < 0) {
712
+ if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
713
+ *a-- = *c, *c-- = *a;
714
+ if(c < first) {
715
+ while(buf < b) { *a-- = *b, *b-- = *a; }
716
+ *a = *b, *b = t;
717
+ break;
718
+ }
719
+ if(*c < 0) { p2 = PA + ~*c; x |= 2; }
720
+ else { p2 = PA + *c; }
721
+ } else {
722
+ if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
723
+ *a-- = ~*b;
724
+ if(b <= buf) { *buf = t; break; }
725
+ *b-- = *a;
726
+ if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
727
+ *a-- = *c, *c-- = *a;
728
+ if(c < first) {
729
+ while(buf < b) { *a-- = *b, *b-- = *a; }
730
+ *a = *b, *b = t;
731
+ break;
732
+ }
733
+ if(*b < 0) { p1 = PA + ~*b; x |= 1; }
734
+ else { p1 = PA + *b; }
735
+ if(*c < 0) { p2 = PA + ~*c; x |= 2; }
736
+ else { p2 = PA + *c; }
737
+ }
738
+ }
739
+ }
740
+
741
+ /* D&C based merge. */
742
+ static
743
+ void
744
+ ss_swapmerge(const unsigned char *T, const int *PA,
745
+ int *first, int *middle, int *last,
746
+ int *buf, int bufsize, int depth) {
747
+ #define STACK_SIZE SS_SMERGE_STACKSIZE
748
+ #define GETIDX(a) ((0 <= (a)) ? (a) : (~(a)))
749
+ #define MERGE_CHECK(a, b, c)\
750
+ do {\
751
+ if(((c) & 1) ||\
752
+ (((c) & 2) && (ss_compare(T, PA + GETIDX(*((a) - 1)), PA + *(a), depth) == 0))) {\
753
+ *(a) = ~*(a);\
754
+ }\
755
+ if(((c) & 4) && ((ss_compare(T, PA + GETIDX(*((b) - 1)), PA + *(b), depth) == 0))) {\
756
+ *(b) = ~*(b);\
757
+ }\
758
+ } while(0)
759
+ struct { int *a, *b, *c; int d; } stack[STACK_SIZE];
760
+ int *l, *r, *lm, *rm;
761
+ int m, len, half;
762
+ int ssize;
763
+ int check, next;
764
+
765
+ for(check = 0, ssize = 0;;) {
766
+ if((last - middle) <= bufsize) {
767
+ if((first < middle) && (middle < last)) {
768
+ ss_mergebackward(T, PA, first, middle, last, buf, depth);
769
+ }
770
+ MERGE_CHECK(first, last, check);
771
+ STACK_POP(first, middle, last, check);
772
+ continue;
773
+ }
774
+
775
+ if((middle - first) <= bufsize) {
776
+ if(first < middle) {
777
+ ss_mergeforward(T, PA, first, middle, last, buf, depth);
778
+ }
779
+ MERGE_CHECK(first, last, check);
780
+ STACK_POP(first, middle, last, check);
781
+ continue;
782
+ }
783
+
784
+ for(m = 0, len = MIN(middle - first, last - middle), half = len >> 1;
785
+ 0 < len;
786
+ len = half, half >>= 1) {
787
+ if(ss_compare(T, PA + GETIDX(*(middle + m + half)),
788
+ PA + GETIDX(*(middle - m - half - 1)), depth) < 0) {
789
+ m += half + 1;
790
+ half -= (len & 1) ^ 1;
791
+ }
792
+ }
793
+
794
+ if(0 < m) {
795
+ lm = middle - m, rm = middle + m;
796
+ ss_blockswap(lm, middle, m);
797
+ l = r = middle, next = 0;
798
+ if(rm < last) {
799
+ if(*rm < 0) {
800
+ *rm = ~*rm;
801
+ if(first < lm) { for(; *--l < 0;) { } next |= 4; }
802
+ next |= 1;
803
+ } else if(first < lm) {
804
+ for(; *r < 0; ++r) { }
805
+ next |= 2;
806
+ }
807
+ }
808
+
809
+ if((l - first) <= (last - r)) {
810
+ STACK_PUSH(r, rm, last, (next & 3) | (check & 4));
811
+ middle = lm, last = l, check = (check & 3) | (next & 4);
812
+ } else {
813
+ if((next & 2) && (r == middle)) { next ^= 6; }
814
+ STACK_PUSH(first, lm, l, (check & 3) | (next & 4));
815
+ first = r, middle = rm, check = (next & 3) | (check & 4);
816
+ }
817
+ } else {
818
+ if(ss_compare(T, PA + GETIDX(*(middle - 1)), PA + *middle, depth) == 0) {
819
+ *middle = ~*middle;
820
+ }
821
+ MERGE_CHECK(first, last, check);
822
+ STACK_POP(first, middle, last, check);
823
+ }
824
+ }
825
+ #undef STACK_SIZE
826
+ }
827
+
828
+ #endif /* SS_BLOCKSIZE != 0 */
829
+
830
+
831
+ /*---------------------------------------------------------------------------*/
832
+
833
+ /* Substring sort */
834
+ static
835
+ void
836
+ sssort(const unsigned char *T, const int *PA,
837
+ int *first, int *last,
838
+ int *buf, int bufsize,
839
+ int depth, int n, int lastsuffix) {
840
+ int *a;
841
+ #if SS_BLOCKSIZE != 0
842
+ int *b, *middle, *curbuf;
843
+ int j, k, curbufsize, limit;
844
+ #endif
845
+ int i;
846
+
847
+ if(lastsuffix != 0) { ++first; }
848
+
849
+ #if SS_BLOCKSIZE == 0
850
+ ss_mintrosort(T, PA, first, last, depth);
851
+ #else
852
+ if((bufsize < SS_BLOCKSIZE) &&
853
+ (bufsize < (last - first)) &&
854
+ (bufsize < (limit = ss_isqrt(last - first)))) {
855
+ if(SS_BLOCKSIZE < limit) { limit = SS_BLOCKSIZE; }
856
+ buf = middle = last - limit, bufsize = limit;
857
+ } else {
858
+ middle = last, limit = 0;
859
+ }
860
+ for(a = first, i = 0; SS_BLOCKSIZE < (middle - a); a += SS_BLOCKSIZE, ++i) {
861
+ #if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
862
+ ss_mintrosort(T, PA, a, a + SS_BLOCKSIZE, depth);
863
+ #elif 1 < SS_BLOCKSIZE
864
+ ss_insertionsort(T, PA, a, a + SS_BLOCKSIZE, depth);
865
+ #endif
866
+ curbufsize = last - (a + SS_BLOCKSIZE);
867
+ curbuf = a + SS_BLOCKSIZE;
868
+ if(curbufsize <= bufsize) { curbufsize = bufsize, curbuf = buf; }
869
+ for(b = a, k = SS_BLOCKSIZE, j = i; j & 1; b -= k, k <<= 1, j >>= 1) {
870
+ ss_swapmerge(T, PA, b - k, b, b + k, curbuf, curbufsize, depth);
871
+ }
872
+ }
873
+ #if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
874
+ ss_mintrosort(T, PA, a, middle, depth);
875
+ #elif 1 < SS_BLOCKSIZE
876
+ ss_insertionsort(T, PA, a, middle, depth);
877
+ #endif
878
+ for(k = SS_BLOCKSIZE; i != 0; k <<= 1, i >>= 1) {
879
+ if(i & 1) {
880
+ ss_swapmerge(T, PA, a - k, a, middle, buf, bufsize, depth);
881
+ a -= k;
882
+ }
883
+ }
884
+ if(limit != 0) {
885
+ #if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
886
+ ss_mintrosort(T, PA, middle, last, depth);
887
+ #elif 1 < SS_BLOCKSIZE
888
+ ss_insertionsort(T, PA, middle, last, depth);
889
+ #endif
890
+ ss_inplacemerge(T, PA, first, middle, last, depth);
891
+ }
892
+ #endif
893
+
894
+ if(lastsuffix != 0) {
895
+ /* Insert last type B* suffix. */
896
+ int PAi[2]; PAi[0] = PA[*(first - 1)], PAi[1] = n - 2;
897
+ for(a = first, i = *(first - 1);
898
+ (a < last) && ((*a < 0) || (0 < ss_compare(T, &(PAi[0]), PA + *a, depth)));
899
+ ++a) {
900
+ *(a - 1) = *a;
901
+ }
902
+ *(a - 1) = i;
903
+ }
904
+ }
905
+
906
+
907
+ /*---------------------------------------------------------------------------*/
908
+
909
+ static INLINE
910
+ int
911
+ tr_ilg(int n) {
912
+ return (n & 0xffff0000) ?
913
+ ((n & 0xff000000) ?
914
+ 24 + lg_table[(n >> 24) & 0xff] :
915
+ 16 + lg_table[(n >> 16) & 0xff]) :
916
+ ((n & 0x0000ff00) ?
917
+ 8 + lg_table[(n >> 8) & 0xff] :
918
+ 0 + lg_table[(n >> 0) & 0xff]);
919
+ }
920
+
921
+
922
+ /*---------------------------------------------------------------------------*/
923
+
924
+ /* Simple insertionsort for small size groups. */
925
+ static
926
+ void
927
+ tr_insertionsort(const int *ISAd, int *first, int *last) {
928
+ int *a, *b;
929
+ int t, r;
930
+
931
+ for(a = first + 1; a < last; ++a) {
932
+ for(t = *a, b = a - 1; 0 > (r = ISAd[t] - ISAd[*b]);) {
933
+ do { *(b + 1) = *b; } while((first <= --b) && (*b < 0));
934
+ if(b < first) { break; }
935
+ }
936
+ if(r == 0) { *b = ~*b; }
937
+ *(b + 1) = t;
938
+ }
939
+ }
940
+
941
+
942
+ /*---------------------------------------------------------------------------*/
943
+
944
+ static INLINE
945
+ void
946
+ tr_fixdown(const int *ISAd, int *SA, int i, int size) {
947
+ int j, k;
948
+ int v;
949
+ int c, d, e;
950
+
951
+ for(v = SA[i], c = ISAd[v]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
952
+ d = ISAd[SA[k = j++]];
953
+ if(d < (e = ISAd[SA[j]])) { k = j; d = e; }
954
+ if(d <= c) { break; }
955
+ }
956
+ SA[i] = v;
957
+ }
958
+
959
+ /* Simple top-down heapsort. */
960
+ static
961
+ void
962
+ tr_heapsort(const int *ISAd, int *SA, int size) {
963
+ int i, m;
964
+ int t;
965
+
966
+ m = size;
967
+ if((size % 2) == 0) {
968
+ m--;
969
+ if(ISAd[SA[m / 2]] < ISAd[SA[m]]) { SWAP(SA[m], SA[m / 2]); }
970
+ }
971
+
972
+ for(i = m / 2 - 1; 0 <= i; --i) { tr_fixdown(ISAd, SA, i, m); }
973
+ if((size % 2) == 0) { SWAP(SA[0], SA[m]); tr_fixdown(ISAd, SA, 0, m); }
974
+ for(i = m - 1; 0 < i; --i) {
975
+ t = SA[0], SA[0] = SA[i];
976
+ tr_fixdown(ISAd, SA, 0, i);
977
+ SA[i] = t;
978
+ }
979
+ }
980
+
981
+
982
+ /*---------------------------------------------------------------------------*/
983
+
984
+ /* Returns the median of three elements. */
985
+ static INLINE
986
+ int *
987
+ tr_median3(const int *ISAd, int *v1, int *v2, int *v3) {
988
+ int *t;
989
+ if(ISAd[*v1] > ISAd[*v2]) { SWAP(v1, v2); }
990
+ if(ISAd[*v2] > ISAd[*v3]) {
991
+ if(ISAd[*v1] > ISAd[*v3]) { return v1; }
992
+ else { return v3; }
993
+ }
994
+ return v2;
995
+ }
996
+
997
+ /* Returns the median of five elements. */
998
+ static INLINE
999
+ int *
1000
+ tr_median5(const int *ISAd,
1001
+ int *v1, int *v2, int *v3, int *v4, int *v5) {
1002
+ int *t;
1003
+ if(ISAd[*v2] > ISAd[*v3]) { SWAP(v2, v3); }
1004
+ if(ISAd[*v4] > ISAd[*v5]) { SWAP(v4, v5); }
1005
+ if(ISAd[*v2] > ISAd[*v4]) { SWAP(v2, v4); SWAP(v3, v5); }
1006
+ if(ISAd[*v1] > ISAd[*v3]) { SWAP(v1, v3); }
1007
+ if(ISAd[*v1] > ISAd[*v4]) { SWAP(v1, v4); SWAP(v3, v5); }
1008
+ if(ISAd[*v3] > ISAd[*v4]) { return v4; }
1009
+ return v3;
1010
+ }
1011
+
1012
+ /* Returns the pivot element. */
1013
+ static INLINE
1014
+ int *
1015
+ tr_pivot(const int *ISAd, int *first, int *last) {
1016
+ int *middle;
1017
+ int t;
1018
+
1019
+ t = last - first;
1020
+ middle = first + t / 2;
1021
+
1022
+ if(t <= 512) {
1023
+ if(t <= 32) {
1024
+ return tr_median3(ISAd, first, middle, last - 1);
1025
+ } else {
1026
+ t >>= 2;
1027
+ return tr_median5(ISAd, first, first + t, middle, last - 1 - t, last - 1);
1028
+ }
1029
+ }
1030
+ t >>= 3;
1031
+ first = tr_median3(ISAd, first, first + t, first + (t << 1));
1032
+ middle = tr_median3(ISAd, middle - t, middle, middle + t);
1033
+ last = tr_median3(ISAd, last - 1 - (t << 1), last - 1 - t, last - 1);
1034
+ return tr_median3(ISAd, first, middle, last);
1035
+ }
1036
+
1037
+
1038
+ /*---------------------------------------------------------------------------*/
1039
+
1040
+ typedef struct _trbudget_t trbudget_t;
1041
+ struct _trbudget_t {
1042
+ int chance;
1043
+ int remain;
1044
+ int incval;
1045
+ int count;
1046
+ };
1047
+
1048
+ static INLINE
1049
+ void
1050
+ trbudget_init(trbudget_t *budget, int chance, int incval) {
1051
+ budget->chance = chance;
1052
+ budget->remain = budget->incval = incval;
1053
+ }
1054
+
1055
+ static INLINE
1056
+ int
1057
+ trbudget_check(trbudget_t *budget, int size) {
1058
+ if(size <= budget->remain) { budget->remain -= size; return 1; }
1059
+ if(budget->chance == 0) { budget->count += size; return 0; }
1060
+ budget->remain += budget->incval - size;
1061
+ budget->chance -= 1;
1062
+ return 1;
1063
+ }
1064
+
1065
+
1066
+ /*---------------------------------------------------------------------------*/
1067
+
1068
+ static INLINE
1069
+ void
1070
+ tr_partition(const int *ISAd,
1071
+ int *first, int *middle, int *last,
1072
+ int **pa, int **pb, int v) {
1073
+ int *a, *b, *c, *d, *e, *f;
1074
+ int t, s;
1075
+ int x = 0;
1076
+
1077
+ for(b = middle - 1; (++b < last) && ((x = ISAd[*b]) == v);) { }
1078
+ if(((a = b) < last) && (x < v)) {
1079
+ for(; (++b < last) && ((x = ISAd[*b]) <= v);) {
1080
+ if(x == v) { SWAP(*b, *a); ++a; }
1081
+ }
1082
+ }
1083
+ for(c = last; (b < --c) && ((x = ISAd[*c]) == v);) { }
1084
+ if((b < (d = c)) && (x > v)) {
1085
+ for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
1086
+ if(x == v) { SWAP(*c, *d); --d; }
1087
+ }
1088
+ }
1089
+ for(; b < c;) {
1090
+ SWAP(*b, *c);
1091
+ for(; (++b < c) && ((x = ISAd[*b]) <= v);) {
1092
+ if(x == v) { SWAP(*b, *a); ++a; }
1093
+ }
1094
+ for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
1095
+ if(x == v) { SWAP(*c, *d); --d; }
1096
+ }
1097
+ }
1098
+
1099
+ if(a <= d) {
1100
+ c = b - 1;
1101
+ if((s = a - first) > (t = b - a)) { s = t; }
1102
+ for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
1103
+ if((s = d - c) > (t = last - d - 1)) { s = t; }
1104
+ for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
1105
+ first += (b - a), last -= (d - c);
1106
+ }
1107
+ *pa = first, *pb = last;
1108
+ }
1109
+
1110
+ static
1111
+ void
1112
+ tr_copy(int *ISA, const int *SA,
1113
+ int *first, int *a, int *b, int *last,
1114
+ int depth) {
1115
+ /* sort suffixes of middle partition
1116
+ by using sorted order of suffixes of left and right partition. */
1117
+ int *c, *d, *e;
1118
+ int s, v;
1119
+
1120
+ v = b - SA - 1;
1121
+ for(c = first, d = a - 1; c <= d; ++c) {
1122
+ if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
1123
+ *++d = s;
1124
+ ISA[s] = d - SA;
1125
+ }
1126
+ }
1127
+ for(c = last - 1, e = d + 1, d = b; e < d; --c) {
1128
+ if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
1129
+ *--d = s;
1130
+ ISA[s] = d - SA;
1131
+ }
1132
+ }
1133
+ }
1134
+
1135
+ static
1136
+ void
1137
+ tr_partialcopy(int *ISA, const int *SA,
1138
+ int *first, int *a, int *b, int *last,
1139
+ int depth) {
1140
+ int *c, *d, *e;
1141
+ int s, v;
1142
+ int rank, lastrank, newrank = -1;
1143
+
1144
+ v = b - SA - 1;
1145
+ lastrank = -1;
1146
+ for(c = first, d = a - 1; c <= d; ++c) {
1147
+ if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
1148
+ *++d = s;
1149
+ rank = ISA[s + depth];
1150
+ if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
1151
+ ISA[s] = newrank;
1152
+ }
1153
+ }
1154
+
1155
+ lastrank = -1;
1156
+ for(e = d; first <= e; --e) {
1157
+ rank = ISA[*e];
1158
+ if(lastrank != rank) { lastrank = rank; newrank = e - SA; }
1159
+ if(newrank != rank) { ISA[*e] = newrank; }
1160
+ }
1161
+
1162
+ lastrank = -1;
1163
+ for(c = last - 1, e = d + 1, d = b; e < d; --c) {
1164
+ if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
1165
+ *--d = s;
1166
+ rank = ISA[s + depth];
1167
+ if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
1168
+ ISA[s] = newrank;
1169
+ }
1170
+ }
1171
+ }
1172
+
1173
+ static
1174
+ void
1175
+ tr_introsort(int *ISA, const int *ISAd,
1176
+ int *SA, int *first, int *last,
1177
+ trbudget_t *budget) {
1178
+ #define STACK_SIZE TR_STACKSIZE
1179
+ struct { const int *a; int *b, *c; int d, e; }stack[STACK_SIZE];
1180
+ int *a, *b, *c;
1181
+ int t;
1182
+ int v, x = 0;
1183
+ int incr = ISAd - ISA;
1184
+ int limit, next;
1185
+ int ssize, trlink = -1;
1186
+
1187
+ for(ssize = 0, limit = tr_ilg(last - first);;) {
1188
+
1189
+ if(limit < 0) {
1190
+ if(limit == -1) {
1191
+ /* tandem repeat partition */
1192
+ tr_partition(ISAd - incr, first, first, last, &a, &b, last - SA - 1);
1193
+
1194
+ /* update ranks */
1195
+ if(a < last) {
1196
+ for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
1197
+ }
1198
+ if(b < last) {
1199
+ for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; }
1200
+ }
1201
+
1202
+ /* push */
1203
+ if(1 < (b - a)) {
1204
+ STACK_PUSH5(NULL, a, b, 0, 0);
1205
+ STACK_PUSH5(ISAd - incr, first, last, -2, trlink);
1206
+ trlink = ssize - 2;
1207
+ }
1208
+ if((a - first) <= (last - b)) {
1209
+ if(1 < (a - first)) {
1210
+ STACK_PUSH5(ISAd, b, last, tr_ilg(last - b), trlink);
1211
+ last = a, limit = tr_ilg(a - first);
1212
+ } else if(1 < (last - b)) {
1213
+ first = b, limit = tr_ilg(last - b);
1214
+ } else {
1215
+ STACK_POP5(ISAd, first, last, limit, trlink);
1216
+ }
1217
+ } else {
1218
+ if(1 < (last - b)) {
1219
+ STACK_PUSH5(ISAd, first, a, tr_ilg(a - first), trlink);
1220
+ first = b, limit = tr_ilg(last - b);
1221
+ } else if(1 < (a - first)) {
1222
+ last = a, limit = tr_ilg(a - first);
1223
+ } else {
1224
+ STACK_POP5(ISAd, first, last, limit, trlink);
1225
+ }
1226
+ }
1227
+ } else if(limit == -2) {
1228
+ /* tandem repeat copy */
1229
+ a = stack[--ssize].b, b = stack[ssize].c;
1230
+ if(stack[ssize].d == 0) {
1231
+ tr_copy(ISA, SA, first, a, b, last, ISAd - ISA);
1232
+ } else {
1233
+ if(0 <= trlink) { stack[trlink].d = -1; }
1234
+ tr_partialcopy(ISA, SA, first, a, b, last, ISAd - ISA);
1235
+ }
1236
+ STACK_POP5(ISAd, first, last, limit, trlink);
1237
+ } else {
1238
+ /* sorted partition */
1239
+ if(0 <= *first) {
1240
+ a = first;
1241
+ do { ISA[*a] = a - SA; } while((++a < last) && (0 <= *a));
1242
+ first = a;
1243
+ }
1244
+ if(first < last) {
1245
+ a = first; do { *a = ~*a; } while(*++a < 0);
1246
+ next = (ISA[*a] != ISAd[*a]) ? tr_ilg(a - first + 1) : -1;
1247
+ if(++a < last) { for(b = first, v = a - SA - 1; b < a; ++b) { ISA[*b] = v; } }
1248
+
1249
+ /* push */
1250
+ if(trbudget_check(budget, a - first)) {
1251
+ if((a - first) <= (last - a)) {
1252
+ STACK_PUSH5(ISAd, a, last, -3, trlink);
1253
+ ISAd += incr, last = a, limit = next;
1254
+ } else {
1255
+ if(1 < (last - a)) {
1256
+ STACK_PUSH5(ISAd + incr, first, a, next, trlink);
1257
+ first = a, limit = -3;
1258
+ } else {
1259
+ ISAd += incr, last = a, limit = next;
1260
+ }
1261
+ }
1262
+ } else {
1263
+ if(0 <= trlink) { stack[trlink].d = -1; }
1264
+ if(1 < (last - a)) {
1265
+ first = a, limit = -3;
1266
+ } else {
1267
+ STACK_POP5(ISAd, first, last, limit, trlink);
1268
+ }
1269
+ }
1270
+ } else {
1271
+ STACK_POP5(ISAd, first, last, limit, trlink);
1272
+ }
1273
+ }
1274
+ continue;
1275
+ }
1276
+
1277
+ if((last - first) <= TR_INSERTIONSORT_THRESHOLD) {
1278
+ tr_insertionsort(ISAd, first, last);
1279
+ limit = -3;
1280
+ continue;
1281
+ }
1282
+
1283
+ if(limit-- == 0) {
1284
+ tr_heapsort(ISAd, first, last - first);
1285
+ for(a = last - 1; first < a; a = b) {
1286
+ for(x = ISAd[*a], b = a - 1; (first <= b) && (ISAd[*b] == x); --b) { *b = ~*b; }
1287
+ }
1288
+ limit = -3;
1289
+ continue;
1290
+ }
1291
+
1292
+ /* choose pivot */
1293
+ a = tr_pivot(ISAd, first, last);
1294
+ SWAP(*first, *a);
1295
+ v = ISAd[*first];
1296
+
1297
+ /* partition */
1298
+ tr_partition(ISAd, first, first + 1, last, &a, &b, v);
1299
+ if((last - first) != (b - a)) {
1300
+ next = (ISA[*a] != v) ? tr_ilg(b - a) : -1;
1301
+
1302
+ /* update ranks */
1303
+ for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
1304
+ if(b < last) { for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; } }
1305
+
1306
+ /* push */
1307
+ if((1 < (b - a)) && (trbudget_check(budget, b - a))) {
1308
+ if((a - first) <= (last - b)) {
1309
+ if((last - b) <= (b - a)) {
1310
+ if(1 < (a - first)) {
1311
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
1312
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
1313
+ last = a;
1314
+ } else if(1 < (last - b)) {
1315
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
1316
+ first = b;
1317
+ } else {
1318
+ ISAd += incr, first = a, last = b, limit = next;
1319
+ }
1320
+ } else if((a - first) <= (b - a)) {
1321
+ if(1 < (a - first)) {
1322
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
1323
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
1324
+ last = a;
1325
+ } else {
1326
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
1327
+ ISAd += incr, first = a, last = b, limit = next;
1328
+ }
1329
+ } else {
1330
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
1331
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
1332
+ ISAd += incr, first = a, last = b, limit = next;
1333
+ }
1334
+ } else {
1335
+ if((a - first) <= (b - a)) {
1336
+ if(1 < (last - b)) {
1337
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
1338
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
1339
+ first = b;
1340
+ } else if(1 < (a - first)) {
1341
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
1342
+ last = a;
1343
+ } else {
1344
+ ISAd += incr, first = a, last = b, limit = next;
1345
+ }
1346
+ } else if((last - b) <= (b - a)) {
1347
+ if(1 < (last - b)) {
1348
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
1349
+ STACK_PUSH5(ISAd + incr, a, b, next, trlink);
1350
+ first = b;
1351
+ } else {
1352
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
1353
+ ISAd += incr, first = a, last = b, limit = next;
1354
+ }
1355
+ } else {
1356
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
1357
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
1358
+ ISAd += incr, first = a, last = b, limit = next;
1359
+ }
1360
+ }
1361
+ } else {
1362
+ if((1 < (b - a)) && (0 <= trlink)) { stack[trlink].d = -1; }
1363
+ if((a - first) <= (last - b)) {
1364
+ if(1 < (a - first)) {
1365
+ STACK_PUSH5(ISAd, b, last, limit, trlink);
1366
+ last = a;
1367
+ } else if(1 < (last - b)) {
1368
+ first = b;
1369
+ } else {
1370
+ STACK_POP5(ISAd, first, last, limit, trlink);
1371
+ }
1372
+ } else {
1373
+ if(1 < (last - b)) {
1374
+ STACK_PUSH5(ISAd, first, a, limit, trlink);
1375
+ first = b;
1376
+ } else if(1 < (a - first)) {
1377
+ last = a;
1378
+ } else {
1379
+ STACK_POP5(ISAd, first, last, limit, trlink);
1380
+ }
1381
+ }
1382
+ }
1383
+ } else {
1384
+ if(trbudget_check(budget, last - first)) {
1385
+ limit = tr_ilg(last - first), ISAd += incr;
1386
+ } else {
1387
+ if(0 <= trlink) { stack[trlink].d = -1; }
1388
+ STACK_POP5(ISAd, first, last, limit, trlink);
1389
+ }
1390
+ }
1391
+ }
1392
+ #undef STACK_SIZE
1393
+ }
1394
+
1395
+
1396
+
1397
+ /*---------------------------------------------------------------------------*/
1398
+
1399
+ /* Tandem repeat sort */
1400
+ static
1401
+ void
1402
+ trsort(int *ISA, int *SA, int n, int depth) {
1403
+ int *ISAd;
1404
+ int *first, *last;
1405
+ trbudget_t budget;
1406
+ int t, skip, unsorted;
1407
+
1408
+ trbudget_init(&budget, tr_ilg(n) * 2 / 3, n);
1409
+ /* trbudget_init(&budget, tr_ilg(n) * 3 / 4, n); */
1410
+ for(ISAd = ISA + depth; -n < *SA; ISAd += ISAd - ISA) {
1411
+ first = SA;
1412
+ skip = 0;
1413
+ unsorted = 0;
1414
+ do {
1415
+ if((t = *first) < 0) { first -= t; skip += t; }
1416
+ else {
1417
+ if(skip != 0) { *(first + skip) = skip; skip = 0; }
1418
+ last = SA + ISA[t] + 1;
1419
+ if(1 < (last - first)) {
1420
+ budget.count = 0;
1421
+ tr_introsort(ISA, ISAd, SA, first, last, &budget);
1422
+ if(budget.count != 0) { unsorted += budget.count; }
1423
+ else { skip = first - last; }
1424
+ } else if((last - first) == 1) {
1425
+ skip = -1;
1426
+ }
1427
+ first = last;
1428
+ }
1429
+ } while(first < (SA + n));
1430
+ if(skip != 0) { *(first + skip) = skip; }
1431
+ if(unsorted == 0) { break; }
1432
+ }
1433
+ }
1434
+
1435
+
1436
+ /*---------------------------------------------------------------------------*/
1437
+
1438
+ /* Sorts suffixes of type B*. */
1439
+ static
1440
+ int
1441
+ sort_typeBstar(const unsigned char *T, int *SA,
1442
+ int *bucket_A, int *bucket_B,
1443
+ int n, int openMP) {
1444
+ int *PAb, *ISAb, *buf;
1445
+ #ifdef LIBBSC_OPENMP
1446
+ int *curbuf;
1447
+ int l;
1448
+ #endif
1449
+ int i, j, k, t, m, bufsize;
1450
+ int c0, c1;
1451
+ #ifdef LIBBSC_OPENMP
1452
+ int d0, d1;
1453
+ #endif
1454
+ (void)openMP;
1455
+
1456
+ /* Initialize bucket arrays. */
1457
+ for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; }
1458
+ for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; }
1459
+
1460
+ /* Count the number of occurrences of the first one or two characters of each
1461
+ type A, B and B* suffix. Moreover, store the beginning position of all
1462
+ type B* suffixes into the array SA. */
1463
+ for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) {
1464
+ /* type A suffix. */
1465
+ do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1));
1466
+ if(0 <= i) {
1467
+ /* type B* suffix. */
1468
+ ++BUCKET_BSTAR(c0, c1);
1469
+ SA[--m] = i;
1470
+ /* type B suffix. */
1471
+ for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) {
1472
+ ++BUCKET_B(c0, c1);
1473
+ }
1474
+ }
1475
+ }
1476
+ m = n - m;
1477
+ /*
1478
+ note:
1479
+ A type B* suffix is lexicographically smaller than a type B suffix that
1480
+ begins with the same first two characters.
1481
+ */
1482
+
1483
+ /* Calculate the index of start/end point of each bucket. */
1484
+ for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) {
1485
+ t = i + BUCKET_A(c0);
1486
+ BUCKET_A(c0) = i + j; /* start point */
1487
+ i = t + BUCKET_B(c0, c0);
1488
+ for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) {
1489
+ j += BUCKET_BSTAR(c0, c1);
1490
+ BUCKET_BSTAR(c0, c1) = j; /* end point */
1491
+ i += BUCKET_B(c0, c1);
1492
+ }
1493
+ }
1494
+
1495
+ if(0 < m) {
1496
+ /* Sort the type B* suffixes by their first two characters. */
1497
+ PAb = SA + n - m; ISAb = SA + m;
1498
+ for(i = m - 2; 0 <= i; --i) {
1499
+ t = PAb[i], c0 = T[t], c1 = T[t + 1];
1500
+ SA[--BUCKET_BSTAR(c0, c1)] = i;
1501
+ }
1502
+ t = PAb[m - 1], c0 = T[t], c1 = T[t + 1];
1503
+ SA[--BUCKET_BSTAR(c0, c1)] = m - 1;
1504
+
1505
+ /* Sort the type B* substrings using sssort. */
1506
+ #ifdef LIBBSC_OPENMP
1507
+ if (openMP)
1508
+ {
1509
+ buf = SA + m;
1510
+ c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m;
1511
+ #pragma omp parallel default(shared) private(bufsize, curbuf, k, l, d0, d1)
1512
+ {
1513
+ bufsize = (n - (2 * m)) / omp_get_num_threads();
1514
+ curbuf = buf + omp_get_thread_num() * bufsize;
1515
+ k = 0;
1516
+ for(;;) {
1517
+ #pragma omp critical(sssort_lock)
1518
+ {
1519
+ if(0 < (l = j)) {
1520
+ d0 = c0, d1 = c1;
1521
+ do {
1522
+ k = BUCKET_BSTAR(d0, d1);
1523
+ if(--d1 <= d0) {
1524
+ d1 = ALPHABET_SIZE - 1;
1525
+ if(--d0 < 0) { break; }
1526
+ }
1527
+ } while(((l - k) <= 1) && (0 < (l = k)));
1528
+ c0 = d0, c1 = d1, j = k;
1529
+ }
1530
+ }
1531
+ if(l == 0) { break; }
1532
+ sssort(T, PAb, SA + k, SA + l,
1533
+ curbuf, bufsize, 2, n, *(SA + k) == (m - 1));
1534
+ }
1535
+ }
1536
+ }
1537
+ else
1538
+ {
1539
+ buf = SA + m, bufsize = n - (2 * m);
1540
+ for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
1541
+ for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
1542
+ i = BUCKET_BSTAR(c0, c1);
1543
+ if(1 < (j - i)) {
1544
+ sssort(T, PAb, SA + i, SA + j,
1545
+ buf, bufsize, 2, n, *(SA + i) == (m - 1));
1546
+ }
1547
+ }
1548
+ }
1549
+ }
1550
+ #else
1551
+ buf = SA + m, bufsize = n - (2 * m);
1552
+ for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
1553
+ for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
1554
+ i = BUCKET_BSTAR(c0, c1);
1555
+ if(1 < (j - i)) {
1556
+ sssort(T, PAb, SA + i, SA + j,
1557
+ buf, bufsize, 2, n, *(SA + i) == (m - 1));
1558
+ }
1559
+ }
1560
+ }
1561
+ #endif
1562
+
1563
+ /* Compute ranks of type B* substrings. */
1564
+ for(i = m - 1; 0 <= i; --i) {
1565
+ if(0 <= SA[i]) {
1566
+ j = i;
1567
+ do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i]));
1568
+ SA[i + 1] = i - j;
1569
+ if(i <= 0) { break; }
1570
+ }
1571
+ j = i;
1572
+ do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0);
1573
+ ISAb[SA[i]] = j;
1574
+ }
1575
+
1576
+ /* Construct the inverse suffix array of type B* suffixes using trsort. */
1577
+ trsort(ISAb, SA, m, 1);
1578
+
1579
+ /* Set the sorted order of tyoe B* suffixes. */
1580
+ for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) {
1581
+ for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { }
1582
+ if(0 <= i) {
1583
+ t = i;
1584
+ for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { }
1585
+ SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t;
1586
+ }
1587
+ }
1588
+
1589
+ /* Calculate the index of start/end point of each bucket. */
1590
+ BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */
1591
+ for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) {
1592
+ i = BUCKET_A(c0 + 1) - 1;
1593
+ for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) {
1594
+ t = i - BUCKET_B(c0, c1);
1595
+ BUCKET_B(c0, c1) = i; /* end point */
1596
+
1597
+ /* Move all type B* suffixes to the correct position. */
1598
+ for(i = t, j = BUCKET_BSTAR(c0, c1);
1599
+ j <= k;
1600
+ --i, --k) { SA[i] = SA[k]; }
1601
+ }
1602
+ BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */
1603
+ BUCKET_B(c0, c0) = i; /* end point */
1604
+ }
1605
+ }
1606
+
1607
+ return m;
1608
+ }
1609
+
1610
+ /* Constructs the suffix array by using the sorted order of type B* suffixes. */
1611
+ static
1612
+ void
1613
+ construct_SA(const unsigned char *T, int *SA,
1614
+ int *bucket_A, int *bucket_B,
1615
+ int n, int m) {
1616
+ int *i, *j, *k;
1617
+ int s;
1618
+ int c0, c1, c2;
1619
+
1620
+ if(0 < m) {
1621
+ /* Construct the sorted order of type B suffixes by using
1622
+ the sorted order of type B* suffixes. */
1623
+ for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
1624
+ /* Scan the suffix array from right to left. */
1625
+ for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
1626
+ j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
1627
+ i <= j;
1628
+ --j) {
1629
+ if(0 < (s = *j)) {
1630
+ assert(T[s] == c1);
1631
+ assert(((s + 1) < n) && (T[s] <= T[s + 1]));
1632
+ assert(T[s - 1] <= T[s]);
1633
+ *j = ~s;
1634
+ c0 = T[--s];
1635
+ if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
1636
+ if(c0 != c2) {
1637
+ if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
1638
+ k = SA + BUCKET_B(c2 = c0, c1);
1639
+ }
1640
+ assert(k < j);
1641
+ *k-- = s;
1642
+ } else {
1643
+ assert(((s == 0) && (T[s] == c1)) || (s < 0));
1644
+ *j = ~s;
1645
+ }
1646
+ }
1647
+ }
1648
+ }
1649
+
1650
+ /* Construct the suffix array by using
1651
+ the sorted order of type B suffixes. */
1652
+ k = SA + BUCKET_A(c2 = T[n - 1]);
1653
+ *k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1);
1654
+ /* Scan the suffix array from left to right. */
1655
+ for(i = SA, j = SA + n; i < j; ++i) {
1656
+ if(0 < (s = *i)) {
1657
+ assert(T[s - 1] >= T[s]);
1658
+ c0 = T[--s];
1659
+ if((s == 0) || (T[s - 1] < c0)) { s = ~s; }
1660
+ if(c0 != c2) {
1661
+ BUCKET_A(c2) = k - SA;
1662
+ k = SA + BUCKET_A(c2 = c0);
1663
+ }
1664
+ assert(i < k);
1665
+ *k++ = s;
1666
+ } else {
1667
+ assert(s < 0);
1668
+ *i = ~s;
1669
+ }
1670
+ }
1671
+ }
1672
+
1673
+ /* Constructs the burrows-wheeler transformed string directly
1674
+ by using the sorted order of type B* suffixes. */
1675
+ static
1676
+ int
1677
+ construct_BWT(const unsigned char *T, int *SA,
1678
+ int *bucket_A, int *bucket_B,
1679
+ int n, int m) {
1680
+ int *i, *j, *k, *orig;
1681
+ int s;
1682
+ int c0, c1, c2;
1683
+
1684
+ if(0 < m) {
1685
+ /* Construct the sorted order of type B suffixes by using
1686
+ the sorted order of type B* suffixes. */
1687
+ for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
1688
+ /* Scan the suffix array from right to left. */
1689
+ for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
1690
+ j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
1691
+ i <= j;
1692
+ --j) {
1693
+ if(0 < (s = *j)) {
1694
+ assert(T[s] == c1);
1695
+ assert(((s + 1) < n) && (T[s] <= T[s + 1]));
1696
+ assert(T[s - 1] <= T[s]);
1697
+ c0 = T[--s];
1698
+ *j = ~((int)c0);
1699
+ if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
1700
+ if(c0 != c2) {
1701
+ if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
1702
+ k = SA + BUCKET_B(c2 = c0, c1);
1703
+ }
1704
+ assert(k < j);
1705
+ *k-- = s;
1706
+ } else if(s != 0) {
1707
+ *j = ~s;
1708
+ #ifndef NDEBUG
1709
+ } else {
1710
+ assert(T[s] == c1);
1711
+ #endif
1712
+ }
1713
+ }
1714
+ }
1715
+ }
1716
+
1717
+ /* Construct the BWTed string by using
1718
+ the sorted order of type B suffixes. */
1719
+ k = SA + BUCKET_A(c2 = T[n - 1]);
1720
+ *k++ = (T[n - 2] < c2) ? ~((int)T[n - 2]) : (n - 1);
1721
+ /* Scan the suffix array from left to right. */
1722
+ for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
1723
+ if(0 < (s = *i)) {
1724
+ assert(T[s - 1] >= T[s]);
1725
+ c0 = T[--s];
1726
+ *i = c0;
1727
+ if((0 < s) && (T[s - 1] < c0)) { s = ~((int)T[s - 1]); }
1728
+ if(c0 != c2) {
1729
+ BUCKET_A(c2) = k - SA;
1730
+ k = SA + BUCKET_A(c2 = c0);
1731
+ }
1732
+ assert(i < k);
1733
+ *k++ = s;
1734
+ } else if(s != 0) {
1735
+ *i = ~s;
1736
+ } else {
1737
+ orig = i;
1738
+ }
1739
+ }
1740
+
1741
+ return orig - SA;
1742
+ }
1743
+
1744
+ /* Constructs the burrows-wheeler transformed string directly
1745
+ by using the sorted order of type B* suffixes. */
1746
+ static
1747
+ int
1748
+ construct_BWT_indexes(const unsigned char *T, int *SA,
1749
+ int *bucket_A, int *bucket_B,
1750
+ int n, int m,
1751
+ unsigned char * num_indexes, int * indexes) {
1752
+ int *i, *j, *k, *orig;
1753
+ int s;
1754
+ int c0, c1, c2;
1755
+
1756
+ int mod = n / 8;
1757
+ {
1758
+ mod |= mod >> 1; mod |= mod >> 2;
1759
+ mod |= mod >> 4; mod |= mod >> 8;
1760
+ mod |= mod >> 16; mod >>= 1;
1761
+
1762
+ *num_indexes = (unsigned char)((n - 1) / (mod + 1));
1763
+ }
1764
+
1765
+ if(0 < m) {
1766
+ /* Construct the sorted order of type B suffixes by using
1767
+ the sorted order of type B* suffixes. */
1768
+ for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
1769
+ /* Scan the suffix array from right to left. */
1770
+ for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
1771
+ j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
1772
+ i <= j;
1773
+ --j) {
1774
+ if(0 < (s = *j)) {
1775
+ assert(T[s] == c1);
1776
+ assert(((s + 1) < n) && (T[s] <= T[s + 1]));
1777
+ assert(T[s - 1] <= T[s]);
1778
+
1779
+ if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = j - SA;
1780
+
1781
+ c0 = T[--s];
1782
+ *j = ~((int)c0);
1783
+ if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
1784
+ if(c0 != c2) {
1785
+ if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
1786
+ k = SA + BUCKET_B(c2 = c0, c1);
1787
+ }
1788
+ assert(k < j);
1789
+ *k-- = s;
1790
+ } else if(s != 0) {
1791
+ *j = ~s;
1792
+ #ifndef NDEBUG
1793
+ } else {
1794
+ assert(T[s] == c1);
1795
+ #endif
1796
+ }
1797
+ }
1798
+ }
1799
+ }
1800
+
1801
+ /* Construct the BWTed string by using
1802
+ the sorted order of type B suffixes. */
1803
+ k = SA + BUCKET_A(c2 = T[n - 1]);
1804
+ if (T[n - 2] < c2) {
1805
+ if (((n - 1) & mod) == 0) indexes[(n - 1) / (mod + 1) - 1] = k - SA;
1806
+ *k++ = ~((int)T[n - 2]);
1807
+ }
1808
+ else {
1809
+ *k++ = n - 1;
1810
+ }
1811
+
1812
+ /* Scan the suffix array from left to right. */
1813
+ for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
1814
+ if(0 < (s = *i)) {
1815
+ assert(T[s - 1] >= T[s]);
1816
+
1817
+ if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = i - SA;
1818
+
1819
+ c0 = T[--s];
1820
+ *i = c0;
1821
+ if(c0 != c2) {
1822
+ BUCKET_A(c2) = k - SA;
1823
+ k = SA + BUCKET_A(c2 = c0);
1824
+ }
1825
+ assert(i < k);
1826
+ if((0 < s) && (T[s - 1] < c0)) {
1827
+ if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = k - SA;
1828
+ *k++ = ~((int)T[s - 1]);
1829
+ } else
1830
+ *k++ = s;
1831
+ } else if(s != 0) {
1832
+ *i = ~s;
1833
+ } else {
1834
+ orig = i;
1835
+ }
1836
+ }
1837
+
1838
+ return orig - SA;
1839
+ }
1840
+
1841
+
1842
+ /*---------------------------------------------------------------------------*/
1843
+
1844
+ /*- Function -*/
1845
+
1846
+ int
1847
+ divsufsort(const unsigned char *T, int *SA, int n, int openMP) {
1848
+ int *bucket_A, *bucket_B;
1849
+ int m;
1850
+ int err = 0;
1851
+
1852
+ /* Check arguments. */
1853
+ if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; }
1854
+ else if(n == 0) { return 0; }
1855
+ else if(n == 1) { SA[0] = 0; return 0; }
1856
+ else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; }
1857
+
1858
+ bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int));
1859
+ bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int));
1860
+
1861
+ /* Suffixsort. */
1862
+ if((bucket_A != NULL) && (bucket_B != NULL)) {
1863
+ m = sort_typeBstar(T, SA, bucket_A, bucket_B, n, openMP);
1864
+ construct_SA(T, SA, bucket_A, bucket_B, n, m);
1865
+ } else {
1866
+ err = -2;
1867
+ }
1868
+
1869
+ free(bucket_B);
1870
+ free(bucket_A);
1871
+
1872
+ return err;
1873
+ }
1874
+
1875
+ int
1876
+ divbwt(const unsigned char *T, unsigned char *U, int *A, int n, unsigned char * num_indexes, int * indexes, int openMP) {
1877
+ int *B;
1878
+ int *bucket_A, *bucket_B;
1879
+ int m, pidx, i;
1880
+
1881
+ /* Check arguments. */
1882
+ if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
1883
+ else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
1884
+
1885
+ if((B = A) == NULL) { B = (int *)malloc((size_t)(n + 1) * sizeof(int)); }
1886
+ bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int));
1887
+ bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int));
1888
+
1889
+ /* Burrows-Wheeler Transform. */
1890
+ if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
1891
+ m = sort_typeBstar(T, B, bucket_A, bucket_B, n, openMP);
1892
+
1893
+ if (num_indexes == NULL || indexes == NULL) {
1894
+ pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
1895
+ } else {
1896
+ pidx = construct_BWT_indexes(T, B, bucket_A, bucket_B, n, m, num_indexes, indexes);
1897
+ }
1898
+
1899
+ /* Copy to output string. */
1900
+ U[0] = T[n - 1];
1901
+ for(i = 0; i < pidx; ++i) { U[i + 1] = (unsigned char)B[i]; }
1902
+ for(i += 1; i < n; ++i) { U[i] = (unsigned char)B[i]; }
1903
+ pidx += 1;
1904
+ } else {
1905
+ pidx = -2;
1906
+ }
1907
+
1908
+ free(bucket_B);
1909
+ free(bucket_A);
1910
+ if(A == NULL) { free(B); }
1911
+
1912
+ return pidx;
1913
+ }