+++ /dev/null
-/*
- * 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; }
- }
-}
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