/* * trsort.c for libdivsufsort * 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. */ #include "divsufsort_private.h" /*- Private Functions -*/ static const saint_t 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 }; static inline saint_t tr_ilg(saidx_t n) { #if defined(BUILD_DIVSUFSORT64) return (n >> 32) ? ((n >> 48) ? ((n >> 56) ? 56 + lg_table[(n >> 56) & 0xff] : 48 + lg_table[(n >> 48) & 0xff]) : ((n >> 40) ? 40 + lg_table[(n >> 40) & 0xff] : 32 + lg_table[(n >> 32) & 0xff])) : ((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])); #else 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]); #endif } /*---------------------------------------------------------------------------*/ /* Simple insertionsort for small size groups. */ static void tr_insertionsort(const saidx_t *ISAd, saidx_t *first, saidx_t *last) { saidx_t *a, *b; saidx_t 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 saidx_t *ISAd, saidx_t *SA, saidx_t i, saidx_t size) { saidx_t j, k; saidx_t v; saidx_t 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 saidx_t *ISAd, saidx_t *SA, saidx_t size) { saidx_t i, m; saidx_t 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 saidx_t * tr_median3(const saidx_t *ISAd, saidx_t *v1, saidx_t *v2, saidx_t *v3) { saidx_t *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 saidx_t * tr_median5(const saidx_t *ISAd, saidx_t *v1, saidx_t *v2, saidx_t *v3, saidx_t *v4, saidx_t *v5) { saidx_t *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 saidx_t * tr_pivot(const saidx_t *ISAd, saidx_t *first, saidx_t *last) { saidx_t *middle; saidx_t 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 { saidx_t chance; saidx_t remain; saidx_t incval; saidx_t count; }; static inline void trbudget_init(trbudget_t *budget, saidx_t chance, saidx_t incval) { budget->chance = chance; budget->remain = budget->incval = incval; } static inline saint_t trbudget_check(trbudget_t *budget, saidx_t 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 saidx_t *ISAd, saidx_t *first, saidx_t *middle, saidx_t *last, saidx_t **pa, saidx_t **pb, saidx_t v) { saidx_t *a, *b, *c, *d, *e, *f; saidx_t t, s; saidx_t 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(saidx_t *ISA, const saidx_t *SA, saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last, saidx_t depth) { /* sort suffixes of middle partition by using sorted order of suffixes of left and right partition. */ saidx_t *c, *d, *e; saidx_t 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(saidx_t *ISA, const saidx_t *SA, saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last, saidx_t depth) { saidx_t *c, *d, *e; saidx_t s, v; saidx_t 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(saidx_t *ISA, const saidx_t *ISAd, saidx_t *SA, saidx_t *first, saidx_t *last, trbudget_t *budget) { #define STACK_SIZE TR_STACKSIZE struct { const saidx_t *a; saidx_t *b, *c; saint_t d, e; }stack[STACK_SIZE]; saidx_t *a, *b, *c; saidx_t t; saidx_t v, x = 0; saidx_t incr = ISAd - ISA; saint_t limit, next; saint_t 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 } /*---------------------------------------------------------------------------*/ /*- Function -*/ /* Tandem repeat sort */ void trsort(saidx_t *ISA, saidx_t *SA, saidx_t n, saidx_t depth) { saidx_t *ISAd; saidx_t *first, *last; trbudget_t budget; saidx_t 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; } } }