divsufsort.c
1913 lines
| 53.4 KiB
| text/x-c
|
CLexer
Gregory Szorc
|
r30434 | /* | ||
* divsufsort.c for libdivsufsort-lite | ||||
* 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. | ||||
*/ | ||||
/*- Compiler specifics -*/ | ||||
#ifdef __clang__ | ||||
#pragma clang diagnostic ignored "-Wshorten-64-to-32" | ||||
#endif | ||||
#if defined(_MSC_VER) | ||||
# pragma warning(disable : 4244) | ||||
# pragma warning(disable : 4127) /* C4127 : Condition expression is constant */ | ||||
#endif | ||||
/*- Dependencies -*/ | ||||
#include <assert.h> | ||||
#include <stdio.h> | ||||
#include <stdlib.h> | ||||
#include "divsufsort.h" | ||||
/*- Constants -*/ | ||||
#if defined(INLINE) | ||||
# undef INLINE | ||||
#endif | ||||
#if !defined(INLINE) | ||||
# define INLINE __inline | ||||
#endif | ||||
#if defined(ALPHABET_SIZE) && (ALPHABET_SIZE < 1) | ||||
# undef ALPHABET_SIZE | ||||
#endif | ||||
#if !defined(ALPHABET_SIZE) | ||||
# define ALPHABET_SIZE (256) | ||||
#endif | ||||
#define BUCKET_A_SIZE (ALPHABET_SIZE) | ||||
#define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE) | ||||
#if defined(SS_INSERTIONSORT_THRESHOLD) | ||||
# if SS_INSERTIONSORT_THRESHOLD < 1 | ||||
# undef SS_INSERTIONSORT_THRESHOLD | ||||
# define SS_INSERTIONSORT_THRESHOLD (1) | ||||
# endif | ||||
#else | ||||
# define SS_INSERTIONSORT_THRESHOLD (8) | ||||
#endif | ||||
#if defined(SS_BLOCKSIZE) | ||||
# if SS_BLOCKSIZE < 0 | ||||
# undef SS_BLOCKSIZE | ||||
# define SS_BLOCKSIZE (0) | ||||
# elif 32768 <= SS_BLOCKSIZE | ||||
# undef SS_BLOCKSIZE | ||||
# define SS_BLOCKSIZE (32767) | ||||
# endif | ||||
#else | ||||
# define SS_BLOCKSIZE (1024) | ||||
#endif | ||||
/* minstacksize = log(SS_BLOCKSIZE) / log(3) * 2 */ | ||||
#if SS_BLOCKSIZE == 0 | ||||
# define SS_MISORT_STACKSIZE (96) | ||||
#elif SS_BLOCKSIZE <= 4096 | ||||
# define SS_MISORT_STACKSIZE (16) | ||||
#else | ||||
# define SS_MISORT_STACKSIZE (24) | ||||
#endif | ||||
#define SS_SMERGE_STACKSIZE (32) | ||||
#define TR_INSERTIONSORT_THRESHOLD (8) | ||||
#define TR_STACKSIZE (64) | ||||
/*- Macros -*/ | ||||
#ifndef SWAP | ||||
# define SWAP(_a, _b) do { t = (_a); (_a) = (_b); (_b) = t; } while(0) | ||||
#endif /* SWAP */ | ||||
#ifndef MIN | ||||
# define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b)) | ||||
#endif /* MIN */ | ||||
#ifndef MAX | ||||
# define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b)) | ||||
#endif /* MAX */ | ||||
#define STACK_PUSH(_a, _b, _c, _d)\ | ||||
do {\ | ||||
assert(ssize < STACK_SIZE);\ | ||||
stack[ssize].a = (_a), stack[ssize].b = (_b),\ | ||||
stack[ssize].c = (_c), stack[ssize++].d = (_d);\ | ||||
} while(0) | ||||
#define STACK_PUSH5(_a, _b, _c, _d, _e)\ | ||||
do {\ | ||||
assert(ssize < STACK_SIZE);\ | ||||
stack[ssize].a = (_a), stack[ssize].b = (_b),\ | ||||
stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\ | ||||
} while(0) | ||||
#define STACK_POP(_a, _b, _c, _d)\ | ||||
do {\ | ||||
assert(0 <= ssize);\ | ||||
if(ssize == 0) { return; }\ | ||||
(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\ | ||||
(_c) = stack[ssize].c, (_d) = stack[ssize].d;\ | ||||
} while(0) | ||||
#define STACK_POP5(_a, _b, _c, _d, _e)\ | ||||
do {\ | ||||
assert(0 <= ssize);\ | ||||
if(ssize == 0) { return; }\ | ||||
(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\ | ||||
(_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\ | ||||
} while(0) | ||||
#define BUCKET_A(_c0) bucket_A[(_c0)] | ||||
#if ALPHABET_SIZE == 256 | ||||
#define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)]) | ||||
#define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)]) | ||||
#else | ||||
#define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)]) | ||||
#define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)]) | ||||
#endif | ||||
/*- Private Functions -*/ | ||||
static const int 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 | ||||
int | ||||
ss_ilg(int n) { | ||||
#if SS_BLOCKSIZE == 0 | ||||
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]); | ||||
#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 int 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 | ||||
int | ||||
ss_isqrt(int x) { | ||||
int 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 | ||||
int | ||||
ss_compare(const unsigned char *T, | ||||
const int *p1, const int *p2, | ||||
int depth) { | ||||
const unsigned char *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 unsigned char *T, const int *PA, | ||||
int *first, int *last, int depth) { | ||||
int *i, *j; | ||||
int t; | ||||
int 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 unsigned char *Td, const int *PA, | ||||
int *SA, int i, int size) { | ||||
int j, k; | ||||
int v; | ||||
int 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 unsigned char *Td, const int *PA, int *SA, int size) { | ||||
int i, m; | ||||
int 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 | ||||
int * | ||||
ss_median3(const unsigned char *Td, const int *PA, | ||||
int *v1, int *v2, int *v3) { | ||||
int *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 | ||||
int * | ||||
ss_median5(const unsigned char *Td, const int *PA, | ||||
int *v1, int *v2, int *v3, int *v4, int *v5) { | ||||
int *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 | ||||
int * | ||||
ss_pivot(const unsigned char *Td, const int *PA, int *first, int *last) { | ||||
int *middle; | ||||
int 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 | ||||
int * | ||||
ss_partition(const int *PA, | ||||
int *first, int *last, int depth) { | ||||
int *a, *b; | ||||
int 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 unsigned char *T, const int *PA, | ||||
int *first, int *last, | ||||
int depth) { | ||||
#define STACK_SIZE SS_MISORT_STACKSIZE | ||||
struct { int *a, *b, c; int d; } stack[STACK_SIZE]; | ||||
const unsigned char *Td; | ||||
int *a, *b, *c, *d, *e, *f; | ||||
int s, t; | ||||
int ssize; | ||||
int limit; | ||||
int 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(int *a, int *b, int n) { | ||||
int t; | ||||
for(; 0 < n; --n, ++a, ++b) { | ||||
t = *a, *a = *b, *b = t; | ||||
} | ||||
} | ||||
static INLINE | ||||
void | ||||
ss_rotate(int *first, int *middle, int *last) { | ||||
int *a, *b, t; | ||||
int 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 unsigned char *T, const int *PA, | ||||
int *first, int *middle, int *last, | ||||
int depth) { | ||||
const int *p; | ||||
int *a, *b; | ||||
int len, half; | ||||
int q, r; | ||||
int 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 unsigned char *T, const int *PA, | ||||
int *first, int *middle, int *last, | ||||
int *buf, int depth) { | ||||
int *a, *b, *c, *bufend; | ||||
int t; | ||||
int 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 unsigned char *T, const int *PA, | ||||
int *first, int *middle, int *last, | ||||
int *buf, int depth) { | ||||
const int *p1, *p2; | ||||
int *a, *b, *c, *bufend; | ||||
int t; | ||||
int r; | ||||
int 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 unsigned char *T, const int *PA, | ||||
int *first, int *middle, int *last, | ||||
int *buf, int bufsize, int 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 { int *a, *b, *c; int d; } stack[STACK_SIZE]; | ||||
int *l, *r, *lm, *rm; | ||||
int m, len, half; | ||||
int ssize; | ||||
int 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 */ | ||||
/*---------------------------------------------------------------------------*/ | ||||
/* Substring sort */ | ||||
static | ||||
void | ||||
sssort(const unsigned char *T, const int *PA, | ||||
int *first, int *last, | ||||
int *buf, int bufsize, | ||||
int depth, int n, int lastsuffix) { | ||||
int *a; | ||||
#if SS_BLOCKSIZE != 0 | ||||
int *b, *middle, *curbuf; | ||||
int j, k, curbufsize, limit; | ||||
#endif | ||||
int 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. */ | ||||
int 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; | ||||
} | ||||
} | ||||
/*---------------------------------------------------------------------------*/ | ||||
static INLINE | ||||
int | ||||
tr_ilg(int n) { | ||||
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]); | ||||
} | ||||
/*---------------------------------------------------------------------------*/ | ||||
/* Simple insertionsort for small size groups. */ | ||||
static | ||||
void | ||||
tr_insertionsort(const int *ISAd, int *first, int *last) { | ||||
int *a, *b; | ||||
int 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 int *ISAd, int *SA, int i, int size) { | ||||
int j, k; | ||||
int v; | ||||
int 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 int *ISAd, int *SA, int size) { | ||||
int i, m; | ||||
int 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 | ||||
int * | ||||
tr_median3(const int *ISAd, int *v1, int *v2, int *v3) { | ||||
int *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 | ||||
int * | ||||
tr_median5(const int *ISAd, | ||||
int *v1, int *v2, int *v3, int *v4, int *v5) { | ||||
int *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 | ||||
int * | ||||
tr_pivot(const int *ISAd, int *first, int *last) { | ||||
int *middle; | ||||
int 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 { | ||||
int chance; | ||||
int remain; | ||||
int incval; | ||||
int count; | ||||
}; | ||||
static INLINE | ||||
void | ||||
trbudget_init(trbudget_t *budget, int chance, int incval) { | ||||
budget->chance = chance; | ||||
budget->remain = budget->incval = incval; | ||||
} | ||||
static INLINE | ||||
int | ||||
trbudget_check(trbudget_t *budget, int 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 int *ISAd, | ||||
int *first, int *middle, int *last, | ||||
int **pa, int **pb, int v) { | ||||
int *a, *b, *c, *d, *e, *f; | ||||
int t, s; | ||||
int 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(int *ISA, const int *SA, | ||||
int *first, int *a, int *b, int *last, | ||||
int depth) { | ||||
/* sort suffixes of middle partition | ||||
by using sorted order of suffixes of left and right partition. */ | ||||
int *c, *d, *e; | ||||
int 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(int *ISA, const int *SA, | ||||
int *first, int *a, int *b, int *last, | ||||
int depth) { | ||||
int *c, *d, *e; | ||||
int s, v; | ||||
int 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(int *ISA, const int *ISAd, | ||||
int *SA, int *first, int *last, | ||||
trbudget_t *budget) { | ||||
#define STACK_SIZE TR_STACKSIZE | ||||
struct { const int *a; int *b, *c; int d, e; }stack[STACK_SIZE]; | ||||
int *a, *b, *c; | ||||
int t; | ||||
int v, x = 0; | ||||
int incr = ISAd - ISA; | ||||
int limit, next; | ||||
int 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 | ||||
} | ||||
/*---------------------------------------------------------------------------*/ | ||||
/* Tandem repeat sort */ | ||||
static | ||||
void | ||||
trsort(int *ISA, int *SA, int n, int depth) { | ||||
int *ISAd; | ||||
int *first, *last; | ||||
trbudget_t budget; | ||||
int 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; } | ||||
} | ||||
} | ||||
/*---------------------------------------------------------------------------*/ | ||||
/* Sorts suffixes of type B*. */ | ||||
static | ||||
int | ||||
sort_typeBstar(const unsigned char *T, int *SA, | ||||
int *bucket_A, int *bucket_B, | ||||
int n, int openMP) { | ||||
int *PAb, *ISAb, *buf; | ||||
#ifdef LIBBSC_OPENMP | ||||
int *curbuf; | ||||
int l; | ||||
#endif | ||||
int i, j, k, t, m, bufsize; | ||||
int c0, c1; | ||||
#ifdef LIBBSC_OPENMP | ||||
int d0, d1; | ||||
#endif | ||||
(void)openMP; | ||||
/* 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 LIBBSC_OPENMP | ||||
if (openMP) | ||||
{ | ||||
buf = SA + m; | ||||
c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m; | ||||
#pragma omp parallel default(shared) private(bufsize, curbuf, k, l, d0, d1) | ||||
{ | ||||
bufsize = (n - (2 * m)) / omp_get_num_threads(); | ||||
curbuf = buf + omp_get_thread_num() * 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)); | ||||
} | ||||
} | ||||
} | ||||
} | ||||
#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 unsigned char *T, int *SA, | ||||
int *bucket_A, int *bucket_B, | ||||
int n, int m) { | ||||
int *i, *j, *k; | ||||
int s; | ||||
int 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); | ||||
} | ||||
Gregory Szorc
|
r40157 | assert(k < j); assert(k != NULL); | ||
Gregory Szorc
|
r30434 | *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 | ||||
int | ||||
construct_BWT(const unsigned char *T, int *SA, | ||||
int *bucket_A, int *bucket_B, | ||||
int n, int m) { | ||||
int *i, *j, *k, *orig; | ||||
int s; | ||||
int 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 = ~((int)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); | ||||
} | ||||
Gregory Szorc
|
r40157 | assert(k < j); assert(k != NULL); | ||
Gregory Szorc
|
r30434 | *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) ? ~((int)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 = ~((int)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; | ||||
} | ||||
/* Constructs the burrows-wheeler transformed string directly | ||||
by using the sorted order of type B* suffixes. */ | ||||
static | ||||
int | ||||
construct_BWT_indexes(const unsigned char *T, int *SA, | ||||
int *bucket_A, int *bucket_B, | ||||
int n, int m, | ||||
unsigned char * num_indexes, int * indexes) { | ||||
int *i, *j, *k, *orig; | ||||
int s; | ||||
int c0, c1, c2; | ||||
int mod = n / 8; | ||||
{ | ||||
mod |= mod >> 1; mod |= mod >> 2; | ||||
mod |= mod >> 4; mod |= mod >> 8; | ||||
mod |= mod >> 16; mod >>= 1; | ||||
*num_indexes = (unsigned char)((n - 1) / (mod + 1)); | ||||
} | ||||
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]); | ||||
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = j - SA; | ||||
c0 = T[--s]; | ||||
*j = ~((int)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); | ||||
} | ||||
Gregory Szorc
|
r40157 | assert(k < j); assert(k != NULL); | ||
Gregory Szorc
|
r30434 | *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]); | ||||
if (T[n - 2] < c2) { | ||||
if (((n - 1) & mod) == 0) indexes[(n - 1) / (mod + 1) - 1] = k - SA; | ||||
*k++ = ~((int)T[n - 2]); | ||||
} | ||||
else { | ||||
*k++ = 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]); | ||||
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = i - SA; | ||||
c0 = T[--s]; | ||||
*i = c0; | ||||
if(c0 != c2) { | ||||
BUCKET_A(c2) = k - SA; | ||||
k = SA + BUCKET_A(c2 = c0); | ||||
} | ||||
assert(i < k); | ||||
if((0 < s) && (T[s - 1] < c0)) { | ||||
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = k - SA; | ||||
*k++ = ~((int)T[s - 1]); | ||||
} else | ||||
*k++ = s; | ||||
} else if(s != 0) { | ||||
*i = ~s; | ||||
} else { | ||||
orig = i; | ||||
} | ||||
} | ||||
return orig - SA; | ||||
} | ||||
/*---------------------------------------------------------------------------*/ | ||||
/*- Function -*/ | ||||
int | ||||
divsufsort(const unsigned char *T, int *SA, int n, int openMP) { | ||||
int *bucket_A, *bucket_B; | ||||
int m; | ||||
int 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 = (int *)malloc(BUCKET_A_SIZE * sizeof(int)); | ||||
bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int)); | ||||
/* Suffixsort. */ | ||||
if((bucket_A != NULL) && (bucket_B != NULL)) { | ||||
m = sort_typeBstar(T, SA, bucket_A, bucket_B, n, openMP); | ||||
construct_SA(T, SA, bucket_A, bucket_B, n, m); | ||||
} else { | ||||
err = -2; | ||||
} | ||||
free(bucket_B); | ||||
free(bucket_A); | ||||
return err; | ||||
} | ||||
int | ||||
divbwt(const unsigned char *T, unsigned char *U, int *A, int n, unsigned char * num_indexes, int * indexes, int openMP) { | ||||
int *B; | ||||
int *bucket_A, *bucket_B; | ||||
int 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 = (int *)malloc((size_t)(n + 1) * sizeof(int)); } | ||||
bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int)); | ||||
bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int)); | ||||
/* Burrows-Wheeler Transform. */ | ||||
if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) { | ||||
m = sort_typeBstar(T, B, bucket_A, bucket_B, n, openMP); | ||||
if (num_indexes == NULL || indexes == NULL) { | ||||
pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m); | ||||
} else { | ||||
pidx = construct_BWT_indexes(T, B, bucket_A, bucket_B, n, m, num_indexes, indexes); | ||||
} | ||||
/* Copy to output string. */ | ||||
U[0] = T[n - 1]; | ||||
for(i = 0; i < pidx; ++i) { U[i + 1] = (unsigned char)B[i]; } | ||||
for(i += 1; i < n; ++i) { U[i] = (unsigned char)B[i]; } | ||||
pidx += 1; | ||||
} else { | ||||
pidx = -2; | ||||
} | ||||
free(bucket_B); | ||||
free(bucket_A); | ||||
if(A == NULL) { free(B); } | ||||
return pidx; | ||||
} | ||||