616 lines
18 KiB
C
616 lines
18 KiB
C
/*
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* trsort.c for libdivsufsort
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* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/*- Compiler specifics -*/
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#ifdef __clang__
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#pragma clang diagnostic ignored "-Wshorten-64-to-32"
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#endif
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#if defined (__cplusplus) || (defined (__STDC_VERSION__) && (__STDC_VERSION__ >= 199901L) /* C99 */)
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/* inline is defined */
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#elif defined(_MSC_VER)
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# define inline __inline
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#else
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# define inline /* disable inline */
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#endif
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#ifdef _MSC_VER /* Visual Studio */
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# pragma warning(disable : 4127) /* disable: C4127: conditional expression is constant */
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# define FORCE_INLINE static __forceinline
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#else
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# if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L /* C99 */
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# ifdef __GNUC__
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# define FORCE_INLINE static inline __attribute__((always_inline))
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# else
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# define FORCE_INLINE static inline
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# endif
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# else
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# define FORCE_INLINE static
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# endif /* __STDC_VERSION__ */
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#endif
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/*- Dependencies -*/
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#include "divsufsort_private.h"
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/*- Private Functions -*/
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static const saint_t lg_table[256]= {
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-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,
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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,
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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,
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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,
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7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
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7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
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7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
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7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
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};
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static INLINE
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saint_t
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tr_ilg(saidx_t n) {
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#if defined(BUILD_DIVSUFSORT64)
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return (n >> 32) ?
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((n >> 48) ?
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((n >> 56) ?
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56 + lg_table[(n >> 56) & 0xff] :
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48 + lg_table[(n >> 48) & 0xff]) :
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((n >> 40) ?
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40 + lg_table[(n >> 40) & 0xff] :
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32 + lg_table[(n >> 32) & 0xff])) :
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((n & 0xffff0000) ?
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((n & 0xff000000) ?
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24 + lg_table[(n >> 24) & 0xff] :
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16 + lg_table[(n >> 16) & 0xff]) :
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((n & 0x0000ff00) ?
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8 + lg_table[(n >> 8) & 0xff] :
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0 + lg_table[(n >> 0) & 0xff]));
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#else
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return (n & 0xffff0000) ?
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((n & 0xff000000) ?
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24 + lg_table[(n >> 24) & 0xff] :
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16 + lg_table[(n >> 16) & 0xff]) :
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((n & 0x0000ff00) ?
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8 + lg_table[(n >> 8) & 0xff] :
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0 + lg_table[(n >> 0) & 0xff]);
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#endif
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}
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/*---------------------------------------------------------------------------*/
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/* Simple insertionsort for small size groups. */
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static
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void
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tr_insertionsort(const saidx_t *ISAd, saidx_t *first, saidx_t *last) {
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saidx_t *a, *b;
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saidx_t t, r;
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for(a = first + 1; a < last; ++a) {
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for(t = *a, b = a - 1; 0 > (r = ISAd[t] - ISAd[*b]);) {
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do { *(b + 1) = *b; } while((first <= --b) && (*b < 0));
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if(b < first) { break; }
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}
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if(r == 0) { *b = ~*b; }
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*(b + 1) = t;
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}
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}
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/*---------------------------------------------------------------------------*/
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static INLINE
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void
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tr_fixdown(const saidx_t *ISAd, saidx_t *SA, saidx_t i, saidx_t size) {
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saidx_t j, k;
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saidx_t v;
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saidx_t c, d, e;
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for(v = SA[i], c = ISAd[v]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
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d = ISAd[SA[k = j++]];
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if(d < (e = ISAd[SA[j]])) { k = j; d = e; }
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if(d <= c) { break; }
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}
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SA[i] = v;
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}
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/* Simple top-down heapsort. */
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static
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void
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tr_heapsort(const saidx_t *ISAd, saidx_t *SA, saidx_t size) {
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saidx_t i, m;
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saidx_t t;
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m = size;
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if((size % 2) == 0) {
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m--;
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if(ISAd[SA[m / 2]] < ISAd[SA[m]]) { SWAP(SA[m], SA[m / 2]); }
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}
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for(i = m / 2 - 1; 0 <= i; --i) { tr_fixdown(ISAd, SA, i, m); }
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if((size % 2) == 0) { SWAP(SA[0], SA[m]); tr_fixdown(ISAd, SA, 0, m); }
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for(i = m - 1; 0 < i; --i) {
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t = SA[0], SA[0] = SA[i];
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tr_fixdown(ISAd, SA, 0, i);
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SA[i] = t;
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}
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}
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/*---------------------------------------------------------------------------*/
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/* Returns the median of three elements. */
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static INLINE
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saidx_t *
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tr_median3(const saidx_t *ISAd, saidx_t *v1, saidx_t *v2, saidx_t *v3) {
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saidx_t *t;
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if(ISAd[*v1] > ISAd[*v2]) { SWAP(v1, v2); }
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if(ISAd[*v2] > ISAd[*v3]) {
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if(ISAd[*v1] > ISAd[*v3]) { return v1; }
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else { return v3; }
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}
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return v2;
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}
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/* Returns the median of five elements. */
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static INLINE
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saidx_t *
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tr_median5(const saidx_t *ISAd,
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saidx_t *v1, saidx_t *v2, saidx_t *v3, saidx_t *v4, saidx_t *v5) {
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saidx_t *t;
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if(ISAd[*v2] > ISAd[*v3]) { SWAP(v2, v3); }
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if(ISAd[*v4] > ISAd[*v5]) { SWAP(v4, v5); }
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if(ISAd[*v2] > ISAd[*v4]) { SWAP(v2, v4); SWAP(v3, v5); }
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if(ISAd[*v1] > ISAd[*v3]) { SWAP(v1, v3); }
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if(ISAd[*v1] > ISAd[*v4]) { SWAP(v1, v4); SWAP(v3, v5); }
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if(ISAd[*v3] > ISAd[*v4]) { return v4; }
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return v3;
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}
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/* Returns the pivot element. */
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static INLINE
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saidx_t *
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tr_pivot(const saidx_t *ISAd, saidx_t *first, saidx_t *last) {
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saidx_t *middle;
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saidx_t t;
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t = last - first;
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middle = first + t / 2;
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if(t <= 512) {
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if(t <= 32) {
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return tr_median3(ISAd, first, middle, last - 1);
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} else {
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t >>= 2;
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return tr_median5(ISAd, first, first + t, middle, last - 1 - t, last - 1);
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}
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}
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t >>= 3;
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first = tr_median3(ISAd, first, first + t, first + (t << 1));
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middle = tr_median3(ISAd, middle - t, middle, middle + t);
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last = tr_median3(ISAd, last - 1 - (t << 1), last - 1 - t, last - 1);
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return tr_median3(ISAd, first, middle, last);
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}
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/*---------------------------------------------------------------------------*/
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typedef struct _trbudget_t trbudget_t;
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struct _trbudget_t {
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saidx_t chance;
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saidx_t remain;
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saidx_t incval;
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saidx_t count;
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};
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static INLINE
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void
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trbudget_init(trbudget_t *budget, saidx_t chance, saidx_t incval) {
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budget->chance = chance;
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budget->remain = budget->incval = incval;
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}
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static INLINE
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saint_t
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trbudget_check(trbudget_t *budget, saidx_t size) {
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if(size <= budget->remain) { budget->remain -= size; return 1; }
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if(budget->chance == 0) { budget->count += size; return 0; }
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budget->remain += budget->incval - size;
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budget->chance -= 1;
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return 1;
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}
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/*---------------------------------------------------------------------------*/
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static INLINE
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void
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tr_partition(const saidx_t *ISAd,
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saidx_t *first, saidx_t *middle, saidx_t *last,
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saidx_t **pa, saidx_t **pb, saidx_t v) {
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saidx_t *a, *b, *c, *d, *e, *f;
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saidx_t t, s;
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saidx_t x = 0;
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for(b = middle - 1; (++b < last) && ((x = ISAd[*b]) == v);) { }
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if(((a = b) < last) && (x < v)) {
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for(; (++b < last) && ((x = ISAd[*b]) <= v);) {
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if(x == v) { SWAP(*b, *a); ++a; }
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}
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}
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for(c = last; (b < --c) && ((x = ISAd[*c]) == v);) { }
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if((b < (d = c)) && (x > v)) {
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for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
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if(x == v) { SWAP(*c, *d); --d; }
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}
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}
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for(; b < c;) {
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SWAP(*b, *c);
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for(; (++b < c) && ((x = ISAd[*b]) <= v);) {
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if(x == v) { SWAP(*b, *a); ++a; }
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}
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for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
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if(x == v) { SWAP(*c, *d); --d; }
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}
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}
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if(a <= d) {
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c = b - 1;
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if((s = a - first) > (t = b - a)) { s = t; }
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for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
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if((s = d - c) > (t = last - d - 1)) { s = t; }
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for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
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first += (b - a), last -= (d - c);
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}
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*pa = first, *pb = last;
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}
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static
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void
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tr_copy(saidx_t *ISA, const saidx_t *SA,
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saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last,
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saidx_t depth) {
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/* sort suffixes of middle partition
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by using sorted order of suffixes of left and right partition. */
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saidx_t *c, *d, *e;
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saidx_t s, v;
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v = b - SA - 1;
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for(c = first, d = a - 1; c <= d; ++c) {
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if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
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*++d = s;
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ISA[s] = d - SA;
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}
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}
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for(c = last - 1, e = d + 1, d = b; e < d; --c) {
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if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
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*--d = s;
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ISA[s] = d - SA;
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}
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}
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}
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static
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void
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tr_partialcopy(saidx_t *ISA, const saidx_t *SA,
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saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last,
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saidx_t depth) {
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saidx_t *c, *d, *e;
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saidx_t s, v;
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saidx_t rank, lastrank, newrank = -1;
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v = b - SA - 1;
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lastrank = -1;
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for(c = first, d = a - 1; c <= d; ++c) {
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if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
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*++d = s;
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rank = ISA[s + depth];
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if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
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ISA[s] = newrank;
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}
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}
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lastrank = -1;
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for(e = d; first <= e; --e) {
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rank = ISA[*e];
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if(lastrank != rank) { lastrank = rank; newrank = e - SA; }
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if(newrank != rank) { ISA[*e] = newrank; }
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}
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lastrank = -1;
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for(c = last - 1, e = d + 1, d = b; e < d; --c) {
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if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
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*--d = s;
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rank = ISA[s + depth];
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if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
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ISA[s] = newrank;
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}
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}
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}
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static
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void
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tr_introsort(saidx_t *ISA, const saidx_t *ISAd,
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saidx_t *SA, saidx_t *first, saidx_t *last,
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trbudget_t *budget) {
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#define STACK_SIZE TR_STACKSIZE
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struct { const saidx_t *a; saidx_t *b, *c; saint_t d, e; }stack[STACK_SIZE];
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saidx_t *a, *b, *c;
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saidx_t t;
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saidx_t v, x = 0;
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saidx_t incr = ISAd - ISA;
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saint_t limit, next;
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saint_t ssize, trlink = -1;
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for(ssize = 0, limit = tr_ilg(last - first);;) {
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if(limit < 0) {
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if(limit == -1) {
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/* tandem repeat partition */
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tr_partition(ISAd - incr, first, first, last, &a, &b, last - SA - 1);
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/* update ranks */
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if(a < last) {
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for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
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}
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if(b < last) {
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for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; }
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}
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/* push */
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if(1 < (b - a)) {
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STACK_PUSH5(NULL, a, b, 0, 0);
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STACK_PUSH5(ISAd - incr, first, last, -2, trlink);
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trlink = ssize - 2;
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}
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if((a - first) <= (last - b)) {
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if(1 < (a - first)) {
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STACK_PUSH5(ISAd, b, last, tr_ilg(last - b), trlink);
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last = a, limit = tr_ilg(a - first);
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} else if(1 < (last - b)) {
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first = b, limit = tr_ilg(last - b);
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} else {
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STACK_POP5(ISAd, first, last, limit, trlink);
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}
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} else {
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if(1 < (last - b)) {
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STACK_PUSH5(ISAd, first, a, tr_ilg(a - first), trlink);
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first = b, limit = tr_ilg(last - b);
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} else if(1 < (a - first)) {
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last = a, limit = tr_ilg(a - first);
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} else {
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STACK_POP5(ISAd, first, last, limit, trlink);
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}
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}
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} else if(limit == -2) {
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/* tandem repeat copy */
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a = stack[--ssize].b, b = stack[ssize].c;
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if(stack[ssize].d == 0) {
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tr_copy(ISA, SA, first, a, b, last, ISAd - ISA);
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} else {
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if(0 <= trlink) { stack[trlink].d = -1; }
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tr_partialcopy(ISA, SA, first, a, b, last, ISAd - ISA);
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}
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STACK_POP5(ISAd, first, last, limit, trlink);
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} else {
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/* sorted partition */
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if(0 <= *first) {
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a = first;
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do { ISA[*a] = a - SA; } while((++a < last) && (0 <= *a));
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first = a;
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}
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if(first < last) {
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a = first; do { *a = ~*a; } while(*++a < 0);
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next = (ISA[*a] != ISAd[*a]) ? tr_ilg(a - first + 1) : -1;
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if(++a < last) { for(b = first, v = a - SA - 1; b < a; ++b) { ISA[*b] = v; } }
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/* push */
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if(trbudget_check(budget, a - first)) {
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if((a - first) <= (last - a)) {
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STACK_PUSH5(ISAd, a, last, -3, trlink);
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ISAd += incr, last = a, limit = next;
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|
} 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; }
|
|
}
|
|
}
|