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1 /*
2  * divsufsort.c for libdivsufsort
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 #include "divsufsort_private.h"
28 #ifdef _OPENMP
29 # include <omp.h>
30 #endif
31 
32 
33 /*- Private Functions -*/
34 
35 /* Sorts suffixes of type B*. */
36 static
37 saidx_t
sort_typeBstar(const sauchar_t * T,saidx_t * SA,saidx_t * bucket_A,saidx_t * bucket_B,saidx_t n)38 sort_typeBstar(const sauchar_t *T, saidx_t *SA,
39                saidx_t *bucket_A, saidx_t *bucket_B,
40                saidx_t n) {
41   saidx_t *PAb, *ISAb, *buf;
42 #ifdef _OPENMP
43   saidx_t *curbuf;
44   saidx_t l;
45 #endif
46   saidx_t i, j, k, t, m, bufsize;
47   saint_t c0, c1;
48 #ifdef _OPENMP
49   saint_t d0, d1;
50   int tmp;
51 #endif
52 
53   /* Initialize bucket arrays. */
54   for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; }
55   for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; }
56 
57   /* Count the number of occurrences of the first one or two characters of each
58      type A, B and B* suffix. Moreover, store the beginning position of all
59      type B* suffixes into the array SA. */
60   for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) {
61     /* type A suffix. */
62     do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1));
63     if(0 <= i) {
64       /* type B* suffix. */
65       ++BUCKET_BSTAR(c0, c1);
66       SA[--m] = i;
67       /* type B suffix. */
68       for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) {
69         ++BUCKET_B(c0, c1);
70       }
71     }
72   }
73   m = n - m;
74 /*
75 note:
76   A type B* suffix is lexicographically smaller than a type B suffix that
77   begins with the same first two characters.
78 */
79 
80   /* Calculate the index of start/end point of each bucket. */
81   for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) {
82     t = i + BUCKET_A(c0);
83     BUCKET_A(c0) = i + j; /* start point */
84     i = t + BUCKET_B(c0, c0);
85     for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) {
86       j += BUCKET_BSTAR(c0, c1);
87       BUCKET_BSTAR(c0, c1) = j; /* end point */
88       i += BUCKET_B(c0, c1);
89     }
90   }
91 
92   if(0 < m) {
93     /* Sort the type B* suffixes by their first two characters. */
94     PAb = SA + n - m; ISAb = SA + m;
95     for(i = m - 2; 0 <= i; --i) {
96       t = PAb[i], c0 = T[t], c1 = T[t + 1];
97       SA[--BUCKET_BSTAR(c0, c1)] = i;
98     }
99     t = PAb[m - 1], c0 = T[t], c1 = T[t + 1];
100     SA[--BUCKET_BSTAR(c0, c1)] = m - 1;
101 
102     /* Sort the type B* substrings using sssort. */
103 #ifdef _OPENMP
104     tmp = omp_get_max_threads();
105     buf = SA + m, bufsize = (n - (2 * m)) / tmp;
106     c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m;
107 #pragma omp parallel default(shared) private(curbuf, k, l, d0, d1, tmp)
108     {
109       tmp = omp_get_thread_num();
110       curbuf = buf + tmp * bufsize;
111       k = 0;
112       for(;;) {
113         #pragma omp critical(sssort_lock)
114         {
115           if(0 < (l = j)) {
116             d0 = c0, d1 = c1;
117             do {
118               k = BUCKET_BSTAR(d0, d1);
119               if(--d1 <= d0) {
120                 d1 = ALPHABET_SIZE - 1;
121                 if(--d0 < 0) { break; }
122               }
123             } while(((l - k) <= 1) && (0 < (l = k)));
124             c0 = d0, c1 = d1, j = k;
125           }
126         }
127         if(l == 0) { break; }
128         sssort(T, PAb, SA + k, SA + l,
129                curbuf, bufsize, 2, n, *(SA + k) == (m - 1));
130       }
131     }
132 #else
133     buf = SA + m, bufsize = n - (2 * m);
134     for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
135       for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
136         i = BUCKET_BSTAR(c0, c1);
137         if(1 < (j - i)) {
138           sssort(T, PAb, SA + i, SA + j,
139                  buf, bufsize, 2, n, *(SA + i) == (m - 1));
140         }
141       }
142     }
143 #endif
144 
145     /* Compute ranks of type B* substrings. */
146     for(i = m - 1; 0 <= i; --i) {
147       if(0 <= SA[i]) {
148         j = i;
149         do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i]));
150         SA[i + 1] = i - j;
151         if(i <= 0) { break; }
152       }
153       j = i;
154       do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0);
155       ISAb[SA[i]] = j;
156     }
157 
158     /* Construct the inverse suffix array of type B* suffixes using trsort. */
159     trsort(ISAb, SA, m, 1);
160 
161     /* Set the sorted order of tyoe B* suffixes. */
162     for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) {
163       for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { }
164       if(0 <= i) {
165         t = i;
166         for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { }
167         SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t;
168       }
169     }
170 
171     /* Calculate the index of start/end point of each bucket. */
172     BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */
173     for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) {
174       i = BUCKET_A(c0 + 1) - 1;
175       for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) {
176         t = i - BUCKET_B(c0, c1);
177         BUCKET_B(c0, c1) = i; /* end point */
178 
179         /* Move all type B* suffixes to the correct position. */
180         for(i = t, j = BUCKET_BSTAR(c0, c1);
181             j <= k;
182             --i, --k) { SA[i] = SA[k]; }
183       }
184       BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */
185       BUCKET_B(c0, c0) = i; /* end point */
186     }
187   }
188 
189   return m;
190 }
191 
192 /* Constructs the suffix array by using the sorted order of type B* suffixes. */
193 static
194 void
construct_SA(const sauchar_t * T,saidx_t * SA,saidx_t * bucket_A,saidx_t * bucket_B,saidx_t n,saidx_t m)195 construct_SA(const sauchar_t *T, saidx_t *SA,
196              saidx_t *bucket_A, saidx_t *bucket_B,
197              saidx_t n, saidx_t m) {
198   saidx_t *i, *j, *k;
199   saidx_t s;
200   saint_t c0, c1, c2;
201 
202   if(0 < m) {
203     /* Construct the sorted order of type B suffixes by using
204        the sorted order of type B* suffixes. */
205     for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
206       /* Scan the suffix array from right to left. */
207       for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
208           j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
209           i <= j;
210           --j) {
211         if(0 < (s = *j)) {
212           assert(T[s] == c1);
213           assert(((s + 1) < n) && (T[s] <= T[s + 1]));
214           assert(T[s - 1] <= T[s]);
215           *j = ~s;
216           c0 = T[--s];
217           if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
218           if(c0 != c2) {
219             if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
220             k = SA + BUCKET_B(c2 = c0, c1);
221           }
222           assert(k < j);
223           *k-- = s;
224         } else {
225           assert(((s == 0) && (T[s] == c1)) || (s < 0));
226           *j = ~s;
227         }
228       }
229     }
230   }
231 
232   /* Construct the suffix array by using
233      the sorted order of type B suffixes. */
234   k = SA + BUCKET_A(c2 = T[n - 1]);
235   *k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1);
236   /* Scan the suffix array from left to right. */
237   for(i = SA, j = SA + n; i < j; ++i) {
238     if(0 < (s = *i)) {
239       assert(T[s - 1] >= T[s]);
240       c0 = T[--s];
241       if((s == 0) || (T[s - 1] < c0)) { s = ~s; }
242       if(c0 != c2) {
243         BUCKET_A(c2) = k - SA;
244         k = SA + BUCKET_A(c2 = c0);
245       }
246       assert(i < k);
247       *k++ = s;
248     } else {
249       assert(s < 0);
250       *i = ~s;
251     }
252   }
253 }
254 
255 /* Constructs the burrows-wheeler transformed string directly
256    by using the sorted order of type B* suffixes. */
257 static
258 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)259 construct_BWT(const sauchar_t *T, saidx_t *SA,
260               saidx_t *bucket_A, saidx_t *bucket_B,
261               saidx_t n, saidx_t m) {
262   saidx_t *i, *j, *k, *orig;
263   saidx_t s;
264   saint_t c0, c1, c2;
265 
266   if(0 < m) {
267     /* Construct the sorted order of type B suffixes by using
268        the sorted order of type B* suffixes. */
269     for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
270       /* Scan the suffix array from right to left. */
271       for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
272           j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
273           i <= j;
274           --j) {
275         if(0 < (s = *j)) {
276           assert(T[s] == c1);
277           assert(((s + 1) < n) && (T[s] <= T[s + 1]));
278           assert(T[s - 1] <= T[s]);
279           c0 = T[--s];
280           *j = ~((saidx_t)c0);
281           if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
282           if(c0 != c2) {
283             if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
284             k = SA + BUCKET_B(c2 = c0, c1);
285           }
286           assert(k < j);
287           *k-- = s;
288         } else if(s != 0) {
289           *j = ~s;
290 #ifndef NDEBUG
291         } else {
292           assert(T[s] == c1);
293 #endif
294         }
295       }
296     }
297   }
298 
299   /* Construct the BWTed string by using
300      the sorted order of type B suffixes. */
301   k = SA + BUCKET_A(c2 = T[n - 1]);
302   *k++ = (T[n - 2] < c2) ? ~((saidx_t)T[n - 2]) : (n - 1);
303   /* Scan the suffix array from left to right. */
304   for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
305     if(0 < (s = *i)) {
306       assert(T[s - 1] >= T[s]);
307       c0 = T[--s];
308       *i = c0;
309       if((0 < s) && (T[s - 1] < c0)) { s = ~((saidx_t)T[s - 1]); }
310       if(c0 != c2) {
311         BUCKET_A(c2) = k - SA;
312         k = SA + BUCKET_A(c2 = c0);
313       }
314       assert(i < k);
315       *k++ = s;
316     } else if(s != 0) {
317       *i = ~s;
318     } else {
319       orig = i;
320     }
321   }
322 
323   return orig - SA;
324 }
325 
326 
327 /*---------------------------------------------------------------------------*/
328 
329 /*- Function -*/
330 
331 saint_t
divsufsort(const sauchar_t * T,saidx_t * SA,saidx_t n)332 divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n) {
333   saidx_t *bucket_A, *bucket_B;
334   saidx_t m;
335   saint_t err = 0;
336 
337   /* Check arguments. */
338   if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; }
339   else if(n == 0) { return 0; }
340   else if(n == 1) { SA[0] = 0; return 0; }
341   else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; }
342 
343   bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
344   bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
345 
346   /* Suffixsort. */
347   if((bucket_A != NULL) && (bucket_B != NULL)) {
348     m = sort_typeBstar(T, SA, bucket_A, bucket_B, n);
349     construct_SA(T, SA, bucket_A, bucket_B, n, m);
350   } else {
351     err = -2;
352   }
353 
354   free(bucket_B);
355   free(bucket_A);
356 
357   return err;
358 }
359 
360 saidx_t
divbwt(const sauchar_t * T,sauchar_t * U,saidx_t * A,saidx_t n)361 divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n) {
362   saidx_t *B;
363   saidx_t *bucket_A, *bucket_B;
364   saidx_t m, pidx, i;
365 
366   /* Check arguments. */
367   if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
368   else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
369 
370   if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); }
371   bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
372   bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
373 
374   /* Burrows-Wheeler Transform. */
375   if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
376     m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
377     pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
378 
379     /* Copy to output string. */
380     U[0] = T[n - 1];
381     for(i = 0; i < pidx; ++i) { U[i + 1] = (sauchar_t)B[i]; }
382     for(i += 1; i < n; ++i) { U[i] = (sauchar_t)B[i]; }
383     pidx += 1;
384   } else {
385     pidx = -2;
386   }
387 
388   free(bucket_B);
389   free(bucket_A);
390   if(A == NULL) { free(B); }
391 
392   return pidx;
393 }
394 
395 const char *
divsufsort_version(void)396 divsufsort_version(void) {
397   return PROJECT_VERSION_FULL;
398 }
399