| /* |
| * 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; } |
| } |
| } |
