#pragma once //divsufsort //author: Yuta Mori //license: MIT //class: suffix sort (variant) //average: O(n) //worst: O(n log n) //memory: O(5n) //stable?: yes (all values unique) //omitted functionality: //* OpenMP support //* assertions //* non 8-bit values //* non 32-bit indexes #define ALPHABET_SIZE (256) #define BUCKET_A(_c0) bucket_A[(_c0)] #define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)]) #define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)]) #define BUCKET_A_SIZE (ALPHABET_SIZE) #define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE) #define SS_INSERTIONSORT_THRESHOLD (8) #define SS_BLOCKSIZE (1024) //0..32767 #if SS_BLOCKSIZE == 0 #define SS_MISORT_STACKSIZE (64) #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) #define STACK_PUSH(_a, _b, _c, _d) \ do { \ 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 { \ 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 { \ 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 { \ 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) namespace nall { namespace libdivsufsort { inline auto ilg16(int n) -> int { static int lg_table[256] = {-1}; if(!lg_table[255]) for(uint n : range(1, 256)) lg_table[n] = floor(log2(n)); return (n & 0xff00) ? 8 + lg_table[(n >> 8) & 0xff]: 0 + lg_table[(n >> 0) & 0xff]; } inline auto ilg32(int n) -> int { static int lg_table[256] = {-1}; if(!lg_table[255]) for(uint n : range(1, 256)) lg_table[n] = floor(log2(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]); } // [[sssort.c]] #if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) inline auto ss_ilg(int n) -> int { #if SS_BLOCKSIZE == 0 return ilg32(n); #elif SS_BLOCKSIZE < 256 static int lg_table[256] = {-1}; if(!lg_table[255]) for(uint n : range(1, 256)) lg_table[n] = floor(log2(n)); return lg_table[n]; #else return ilg16(n); #endif } #endif #if SS_BLOCKSIZE != 0 inline auto ss_isqrt(int x) -> int { static int sqq_table[256] = {}; if(!sqq_table[255]) for(uint n : range(256)) sqq_table[n] = floor(sqrt(n) * 16.0); int y, e; if(x >= (SS_BLOCKSIZE * SS_BLOCKSIZE)) { return SS_BLOCKSIZE; } e = ilg32(x); 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 //compare two suffixes inline auto ss_compare(const uint8_t* T, const int* p1, const int* p2, int depth) -> int { const uint8_t *U1, *U2, *U1n, *U2n; for(U1 = T + depth + *p1, U2 = T + depth + *p2, U1n = T + *(p1 + 1) + 2, U2n = T + *(p2 + 1) + 2; (U1 < U1n) && (U2 < U2n) && (*U1 == *U2); ++U1, ++U2 ); return U1 < U1n ? (U2 < U2n ? *U1 - *U2 : 1) : (U2 < U2n ? -1 : 0); } #if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) inline auto ss_insertionsort(const uint8_t* T, const int* PA, int* first, int* last, int depth) -> void { int *i, *j, t, r; for(i = last - 2; first <= i; --i) { for(t = *i, j = i + 1; 0 < (r = ss_compare(T, PA + t, PA + *j, depth));) { do { *(j - 1) = *j; } while((++j < last) && (*j < 0)); if(last <= j) break; } if(r == 0) *j = ~*j; *(j - 1) = t; } } #endif #if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) inline auto ss_fixdown(const uint8_t* Td, const int* PA, int* SA, int i, int size) -> void { int j, k, v, 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 inline auto ss_heapsort(const uint8_t* Td, const int* PA, int* SA, int size) -> void { int i, m, 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 inline auto ss_median3(const uint8_t* Td, const int* PA, int* v1, int* v2, int* v3) -> int* { if(Td[PA[*v1]] > Td[PA[*v2]]) swap(v1, v2); if(Td[PA[*v2]] > Td[PA[*v3]]) return Td[PA[*v1]] > Td[PA[*v3]] ? v1 : v3; return v2; } //returns the median of five elements inline auto ss_median5(const uint8_t* Td, const int* PA, int* v1, int* v2, int* v3, int* v4, int* v5) -> int* { 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 inline auto ss_pivot(const uint8_t* Td, const int* PA, int* first, int* last) -> int* { int *middle, 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 inline auto ss_partition(const int* PA, int* first, int* last, int depth) -> int* { int *a, *b, 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 inline auto ss_mintrosort(const uint8_t* T, const int* PA, int* first, int* last, int depth) -> void { #define STACK_SIZE SS_MISORT_STACKSIZE struct { int *a, *b, c, d; } stack[STACK_SIZE]; const uint8_t* Td; int *a, *b, *c, *d, *e, *f; int s, t, ssize, limit, 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 #if SS_BLOCKSIZE != 0 inline auto ss_blockswap(int* a, int* b, int n) -> void { int t; for(; 0 < n; --n, ++a, ++b) { t = *a, *a = *b, *b = t; } } inline auto ss_rotate(int* first, int* middle, int* last) -> void { int *a, *b, t, l, r; l = middle - first, r = last - middle; for(; (0 < l) && (0 < r);) { if(l == r) { ss_blockswap(first, middle, l); break; } if(l < r) { a = last - 1, b = middle - 1; t = *a; do { *a-- = *b, *b-- = *a; if(b < first) { *a = t; last = a; if((r -= l + 1) <= l) break; a -= 1, b = middle - 1; t = *a; } } while(1); } else { a = first, b = middle; t = *a; do { *a++ = *b, *b++ = *a; if(last <= b) { *a = t; first = a + 1; if((l -= r + 1) <= r) break; a += 1, b = middle; t = *a; } } while(1); } } } inline auto ss_inplacemerge( const uint8_t* T, const int* PA, int* first, int* middle, int* last, int depth ) -> void { const int* p; int *a, *b, len, half, q, r, 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 inline auto ss_mergeforward( const uint8_t* T, const int* PA, int* first, int* middle, int* last, int* buf, int depth ) -> void { int *a, *b, *c, *bufend, t, r; bufend = buf + (middle - first) - 1; ss_blockswap(buf, first, middle - first); for(t = *(a = first), b = buf, c = middle;;) { r = ss_compare(T, PA + *b, PA + *c, depth); if(r < 0) { do { *a++ = *b; if(bufend <= b) { *bufend = t; return; } *b++ = *a; } while(*b < 0); } else if(r > 0) { do { *a++ = *c, *c++ = *a; if(last <= c) { while(b < bufend) { *a++ = *b, *b++ = *a; } *a = *b, *b = t; return; } } while(*c < 0); } else { *c = ~*c; do { *a++ = *b; if(bufend <= b) { *bufend = t; return; } *b++ = *a; } while(*b < 0); do { *a++ = *c, *c++ = *a; if(last <= c) { while(b < bufend) *a++ = *b, *b++ = *a; *a = *b, *b = t; return; } } while(*c < 0); } } } //merge-backward with internal buffer inline auto ss_mergebackward( const uint8_t* T, const int* PA, int* first, int* middle, int* last, int* buf, int depth ) -> void { const int *p1, *p2; int *a, *b, *c, *bufend, t, r, 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 inline auto ss_swapmerge( const uint8_t* T, const int* PA, int* first, int* middle, int* last, int* buf, int bufsize, int depth ) -> void { #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, d; } stack[STACK_SIZE]; int *l, *r, *lm, *rm; int m, len, half, ssize, 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 #undef GETIDX #undef MERGE_CHECK } #endif //substring sort inline auto sssort( const uint8_t* T, const int* PA, int* first, int* last, int* buf, int bufsize, int depth, int n, int lastsuffix ) -> void { 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; } } // [[trsort.c]] inline auto tr_ilg(int n) -> int { return ilg32(n); } //simple insertionsort for small size groups inline auto tr_insertionsort(const int* ISAd, int* first, int* last) -> void { 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; } } inline auto tr_fixdown(const int* ISAd, int* SA, int i, int size) -> void { int j, k, v, 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 inline auto tr_heapsort(const int* ISAd, int* SA, int size) -> void { int i, m, 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 inline auto tr_median3(const int* ISAd, int* v1, int* v2, int* v3) -> int* { if(ISAd[*v1] > ISAd[*v2]) swap(v1, v2); if(ISAd[*v2] > ISAd[*v3]) return ISAd[*v1] > ISAd[*v3] ? v1 : v3; return v2; } //returns the median of five elements inline auto tr_median5(const int* ISAd, int* v1, int* v2, int* v3, int* v4, int* v5) -> int* { 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 inline auto tr_pivot(const int* ISAd, int* first, int* last) -> int* { 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); } struct trbudget_t { int chance; int remain; int incval; int count; }; inline auto trbudget_init(trbudget_t* budget, int chance, int incval) -> void { budget->chance = chance; budget->remain = budget->incval = incval; } inline auto trbudget_check(trbudget_t* budget, int size) -> int { 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; } inline auto tr_partition(const int* ISAd, int* first, int* middle, int* last, int** pa, int** pb, int v) -> void { 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; } //sort suffixes of middle partition by using sorted order of suffixes of left and right partition inline auto tr_copy(int* ISA, int* SA, int* first, int* a, int* b, int* last, int depth) -> void { 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; } } } inline auto tr_partialcopy(int* ISA, int* SA, int* first, int* a, int* b, int* last, int depth) -> void { 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; } } } inline auto tr_introsort(int* ISA, const int* ISAd, int* SA, int* first, int* last, trbudget_t* budget) -> void { struct { const int *a; int *b, *c; int d, e; } stack[TR_STACKSIZE]; 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(nullptr, 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); } } } } //tandem repeat sort inline auto trsort(int* ISA, int* SA, int n, int depth) -> void { int *ISAd; int *first, *last; trbudget_t budget; int t, skip, unsorted; trbudget_init(&budget, tr_ilg(n) * 2 / 3, 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; } } // [[divsufsort.c]] inline auto sort_typeBstar(const uint8_t* T, int* SA, int* bucket_A, int* bucket_B, int n) -> int { int *PAb, *ISAb, *buf; int i, j, k, t, m, bufsize; int c0, c1; //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(int 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 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)); } } } //compare 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 type 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; } inline auto construct_SA(const uint8_t* T, int* SA, int* bucket_A, int* bucket_B, int n, int m) -> void { 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 = nullptr, c2 = -1; i <= j; --j) { if(0 < (s = *j)) { *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); } *k-- = s; } else { *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)) { 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); } *k++ = s; } else { *i = ~s; } } } //constructs the burrows-wheeler transformed string directly by using the sorted order of type B* suffixes inline auto construct_BWT(const uint8_t* T, int* SA, int* bucket_A, int* bucket_B, int n, int m) -> int { int *i, *j, *k, *orig, s, 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 = nullptr, c2 = -1; i <= j; --j) { if(0 < (s = *j)) { 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); } *k-- = s; } else if(s != 0) { *j = ~s; } } } } //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)) { 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); } *k++ = s; } else if(s != 0) { *i = ~s; } else { orig = i; } } return orig - SA; } }} namespace nall { inline auto div_suf_sort(int* SA, const uint8_t* T, int n) -> int { int m, err = 0; if(T == nullptr || SA == nullptr || n < 0) return -1; if(n == 0) return 0; if(n == 1) { SA[0] = 0; return 0; } if(n == 2) { m = T[0] < T[1]; SA[m ^ 1] = 0; SA[m] = 1; return 0; } auto bucket_A = memory::allocate(BUCKET_A_SIZE); auto bucket_B = memory::allocate(BUCKET_B_SIZE); if(bucket_A && bucket_B) { m = libdivsufsort::sort_typeBstar(T, SA, bucket_A, bucket_B, n); libdivsufsort::construct_SA(T, SA, bucket_A, bucket_B, n, m); } else { err = -2; } memory::free(bucket_A); memory::free(bucket_B); return err; } //byuu: note that this function is broken, and not just in my port of it to nall //even with the original library, it is incapable of producing a correct BWT result in *any* case inline auto div_suf_sort_bwt(const uint8_t* T, uint8_t* U, int* A, int n) -> int { int *B, *bucket_A, *bucket_B, m, pidx, i; if(T == nullptr || U == nullptr || n < 0) return -1; if(n == 0) return 0; if(n == 1) return U[0] = T[0], 1; if((B = A) == nullptr) B = memory::allocate(n + 1); bucket_A = memory::allocate(BUCKET_A_SIZE); bucket_B = memory::allocate(BUCKET_B_SIZE); //burrows-wheeler transform if((B != nullptr) && (bucket_A != nullptr) && (bucket_B != nullptr)) { m = libdivsufsort::sort_typeBstar(T, B, bucket_A, bucket_B, n); pidx = libdivsufsort::construct_BWT(T, B, bucket_A, bucket_B, n, m); //copy to output string U[0] = T[n - 1]; for(i = 0; i < pidx; ++i) U[i + 1] = (uint8_t)B[i]; for(i += 1; i < n; ++i) U[i] = (uint8_t)B[i]; pidx += 1; } else { pidx -= 2; } memory::free(bucket_A); memory::free(bucket_B); if(A == nullptr) memory::free(B); return pidx; } #undef ALPHABET_SIZE #undef BUCKET_A #undef BUCKET_B #undef BUCKET_BSTAR #undef BUCKET_A_SIZE #undef BUCKET_B_SIZE #undef SS_INSERTIONSORT_THRESHOLD #undef SS_BLOCKSIZE #undef SS_MISORT_STACKSIZE #undef SS_SMERGE_STACKSIZE #undef TR_INSERTIONSORT_THRESHOLD #undef TR_STACKSIZE #undef STACK_PUSH #undef STACK_PUSH5 #undef STACK_POP #undef STACK_POP5 }