Mercurial > public > mercurial-scm > hg
view contrib/python-zstandard/zstd/dictBuilder/divsufsort.c @ 48674:f7086f6173f8 stable
dirstate-v2: rename the configuration to enable the format
The rename of the old experimental name was overlooked before the 6.0 release.
We rename everything to use the new name (and keep the released name as an alias
for compatibility).
Differential Revision: https://phab.mercurial-scm.org/D12129
| author | Pierre-Yves David <pierre-yves.david@octobus.net> |
|---|---|
| date | Tue, 01 Feb 2022 16:36:20 +0100 |
| parents | 73fef626dae3 |
| children |
line wrap: on
line source
/* * 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); } assert(k < j); assert(k != NULL); *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); } assert(k < j); assert(k != NULL); *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); } assert(k < j); assert(k != NULL); *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; }