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-rw-r--r--lib/trsort.c586
1 files changed, 586 insertions, 0 deletions
diff --git a/lib/trsort.c b/lib/trsort.c
new file mode 100644
index 000000000000..6fe3e67baa4c
--- /dev/null
+++ b/lib/trsort.c
@@ -0,0 +1,586 @@
+/*
+ * 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; }
+ }
+}