1914 lines
53 KiB
C
1914 lines
53 KiB
C
/*
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* divsufsort.c for libdivsufsort-lite
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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(_MSC_VER)
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# pragma warning(disable : 4244)
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# pragma warning(disable : 4127) /* C4127 : Condition expression is constant */
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#endif
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/*- Dependencies -*/
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#include <assert.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include "divsufsort.h"
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/*- Constants -*/
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#if defined(INLINE)
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# undef INLINE
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#endif
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#if !defined(INLINE)
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# define INLINE __inline
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#endif
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#if defined(ALPHABET_SIZE) && (ALPHABET_SIZE < 1)
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# undef ALPHABET_SIZE
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#endif
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#if !defined(ALPHABET_SIZE)
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# define ALPHABET_SIZE (256)
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#endif
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#define BUCKET_A_SIZE (ALPHABET_SIZE)
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#define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE)
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#if defined(SS_INSERTIONSORT_THRESHOLD)
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# if SS_INSERTIONSORT_THRESHOLD < 1
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# undef SS_INSERTIONSORT_THRESHOLD
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# define SS_INSERTIONSORT_THRESHOLD (1)
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# endif
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#else
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# define SS_INSERTIONSORT_THRESHOLD (8)
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#endif
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#if defined(SS_BLOCKSIZE)
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# if SS_BLOCKSIZE < 0
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# undef SS_BLOCKSIZE
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# define SS_BLOCKSIZE (0)
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# elif 32768 <= SS_BLOCKSIZE
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# undef SS_BLOCKSIZE
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# define SS_BLOCKSIZE (32767)
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# endif
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#else
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# define SS_BLOCKSIZE (1024)
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#endif
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/* minstacksize = log(SS_BLOCKSIZE) / log(3) * 2 */
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#if SS_BLOCKSIZE == 0
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# define SS_MISORT_STACKSIZE (96)
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#elif SS_BLOCKSIZE <= 4096
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# define SS_MISORT_STACKSIZE (16)
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#else
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# define SS_MISORT_STACKSIZE (24)
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#endif
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#define SS_SMERGE_STACKSIZE (32)
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#define TR_INSERTIONSORT_THRESHOLD (8)
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#define TR_STACKSIZE (64)
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/*- Macros -*/
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#ifndef SWAP
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# define SWAP(_a, _b) do { t = (_a); (_a) = (_b); (_b) = t; } while(0)
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#endif /* SWAP */
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#ifndef MIN
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# define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b))
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#endif /* MIN */
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#ifndef MAX
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# define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b))
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#endif /* MAX */
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#define STACK_PUSH(_a, _b, _c, _d)\
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do {\
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assert(ssize < STACK_SIZE);\
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stack[ssize].a = (_a), stack[ssize].b = (_b),\
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stack[ssize].c = (_c), stack[ssize++].d = (_d);\
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} while(0)
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#define STACK_PUSH5(_a, _b, _c, _d, _e)\
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do {\
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assert(ssize < STACK_SIZE);\
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stack[ssize].a = (_a), stack[ssize].b = (_b),\
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stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\
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} while(0)
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#define STACK_POP(_a, _b, _c, _d)\
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do {\
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assert(0 <= ssize);\
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if(ssize == 0) { return; }\
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(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
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(_c) = stack[ssize].c, (_d) = stack[ssize].d;\
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} while(0)
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#define STACK_POP5(_a, _b, _c, _d, _e)\
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do {\
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assert(0 <= ssize);\
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if(ssize == 0) { return; }\
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(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
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(_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\
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} while(0)
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#define BUCKET_A(_c0) bucket_A[(_c0)]
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#if ALPHABET_SIZE == 256
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#define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)])
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#define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)])
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#else
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#define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)])
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#define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)])
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#endif
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/*- Private Functions -*/
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static const int 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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#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
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static INLINE
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int
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ss_ilg(int n) {
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#if SS_BLOCKSIZE == 0
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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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#elif SS_BLOCKSIZE < 256
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return lg_table[n];
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#else
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return (n & 0xff00) ?
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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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#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
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#if SS_BLOCKSIZE != 0
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static const int sqq_table[256] = {
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0, 16, 22, 27, 32, 35, 39, 42, 45, 48, 50, 53, 55, 57, 59, 61,
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64, 65, 67, 69, 71, 73, 75, 76, 78, 80, 81, 83, 84, 86, 87, 89,
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90, 91, 93, 94, 96, 97, 98, 99, 101, 102, 103, 104, 106, 107, 108, 109,
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110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126,
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128, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
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143, 144, 144, 145, 146, 147, 148, 149, 150, 150, 151, 152, 153, 154, 155, 155,
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156, 157, 158, 159, 160, 160, 161, 162, 163, 163, 164, 165, 166, 167, 167, 168,
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169, 170, 170, 171, 172, 173, 173, 174, 175, 176, 176, 177, 178, 178, 179, 180,
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181, 181, 182, 183, 183, 184, 185, 185, 186, 187, 187, 188, 189, 189, 190, 191,
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192, 192, 193, 193, 194, 195, 195, 196, 197, 197, 198, 199, 199, 200, 201, 201,
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202, 203, 203, 204, 204, 205, 206, 206, 207, 208, 208, 209, 209, 210, 211, 211,
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212, 212, 213, 214, 214, 215, 215, 216, 217, 217, 218, 218, 219, 219, 220, 221,
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221, 222, 222, 223, 224, 224, 225, 225, 226, 226, 227, 227, 228, 229, 229, 230,
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230, 231, 231, 232, 232, 233, 234, 234, 235, 235, 236, 236, 237, 237, 238, 238,
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239, 240, 240, 241, 241, 242, 242, 243, 243, 244, 244, 245, 245, 246, 246, 247,
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247, 248, 248, 249, 249, 250, 250, 251, 251, 252, 252, 253, 253, 254, 254, 255
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};
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static INLINE
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int
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ss_isqrt(int x) {
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int y, e;
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if(x >= (SS_BLOCKSIZE * SS_BLOCKSIZE)) { return SS_BLOCKSIZE; }
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e = (x & 0xffff0000) ?
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((x & 0xff000000) ?
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24 + lg_table[(x >> 24) & 0xff] :
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16 + lg_table[(x >> 16) & 0xff]) :
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((x & 0x0000ff00) ?
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8 + lg_table[(x >> 8) & 0xff] :
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0 + lg_table[(x >> 0) & 0xff]);
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if(e >= 16) {
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y = sqq_table[x >> ((e - 6) - (e & 1))] << ((e >> 1) - 7);
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if(e >= 24) { y = (y + 1 + x / y) >> 1; }
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y = (y + 1 + x / y) >> 1;
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} else if(e >= 8) {
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y = (sqq_table[x >> ((e - 6) - (e & 1))] >> (7 - (e >> 1))) + 1;
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} else {
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return sqq_table[x] >> 4;
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}
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return (x < (y * y)) ? y - 1 : y;
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}
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#endif /* SS_BLOCKSIZE != 0 */
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/*---------------------------------------------------------------------------*/
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/* Compares two suffixes. */
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static INLINE
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int
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ss_compare(const unsigned char *T,
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const int *p1, const int *p2,
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int depth) {
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const unsigned char *U1, *U2, *U1n, *U2n;
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for(U1 = T + depth + *p1,
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U2 = T + depth + *p2,
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U1n = T + *(p1 + 1) + 2,
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U2n = T + *(p2 + 1) + 2;
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(U1 < U1n) && (U2 < U2n) && (*U1 == *U2);
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++U1, ++U2) {
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}
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return U1 < U1n ?
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(U2 < U2n ? *U1 - *U2 : 1) :
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(U2 < U2n ? -1 : 0);
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}
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/*---------------------------------------------------------------------------*/
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#if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1)
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/* Insertionsort for small size groups */
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static
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void
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ss_insertionsort(const unsigned char *T, const int *PA,
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int *first, int *last, int depth) {
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int *i, *j;
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int t;
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int r;
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for(i = last - 2; first <= i; --i) {
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for(t = *i, j = i + 1; 0 < (r = ss_compare(T, PA + t, PA + *j, depth));) {
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do { *(j - 1) = *j; } while((++j < last) && (*j < 0));
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if(last <= j) { break; }
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}
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if(r == 0) { *j = ~*j; }
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*(j - 1) = t;
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}
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}
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#endif /* (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) */
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/*---------------------------------------------------------------------------*/
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#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
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static INLINE
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void
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ss_fixdown(const unsigned char *Td, const int *PA,
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int *SA, int i, int size) {
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int j, k;
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int v;
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int c, d, e;
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for(v = SA[i], c = Td[PA[v]]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
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d = Td[PA[SA[k = j++]]];
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if(d < (e = Td[PA[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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ss_heapsort(const unsigned char *Td, const int *PA, int *SA, int size) {
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int i, m;
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int 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(Td[PA[SA[m / 2]]] < Td[PA[SA[m]]]) { SWAP(SA[m], SA[m / 2]); }
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}
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for(i = m / 2 - 1; 0 <= i; --i) { ss_fixdown(Td, PA, SA, i, m); }
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if((size % 2) == 0) { SWAP(SA[0], SA[m]); ss_fixdown(Td, PA, 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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ss_fixdown(Td, PA, 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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int *
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ss_median3(const unsigned char *Td, const int *PA,
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int *v1, int *v2, int *v3) {
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int *t;
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if(Td[PA[*v1]] > Td[PA[*v2]]) { SWAP(v1, v2); }
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if(Td[PA[*v2]] > Td[PA[*v3]]) {
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if(Td[PA[*v1]] > Td[PA[*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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int *
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ss_median5(const unsigned char *Td, const int *PA,
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int *v1, int *v2, int *v3, int *v4, int *v5) {
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int *t;
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if(Td[PA[*v2]] > Td[PA[*v3]]) { SWAP(v2, v3); }
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if(Td[PA[*v4]] > Td[PA[*v5]]) { SWAP(v4, v5); }
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if(Td[PA[*v2]] > Td[PA[*v4]]) { SWAP(v2, v4); SWAP(v3, v5); }
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if(Td[PA[*v1]] > Td[PA[*v3]]) { SWAP(v1, v3); }
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if(Td[PA[*v1]] > Td[PA[*v4]]) { SWAP(v1, v4); SWAP(v3, v5); }
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if(Td[PA[*v3]] > Td[PA[*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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int *
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ss_pivot(const unsigned char *Td, const int *PA, int *first, int *last) {
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int *middle;
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int 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 ss_median3(Td, PA, first, middle, last - 1);
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} else {
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t >>= 2;
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return ss_median5(Td, PA, 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 = ss_median3(Td, PA, first, first + t, first + (t << 1));
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middle = ss_median3(Td, PA, middle - t, middle, middle + t);
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last = ss_median3(Td, PA, last - 1 - (t << 1), last - 1 - t, last - 1);
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return ss_median3(Td, PA, first, middle, last);
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}
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/*---------------------------------------------------------------------------*/
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/* Binary partition for substrings. */
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static INLINE
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int *
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ss_partition(const int *PA,
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int *first, int *last, int depth) {
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int *a, *b;
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int t;
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for(a = first - 1, b = last;;) {
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for(; (++a < b) && ((PA[*a] + depth) >= (PA[*a + 1] + 1));) { *a = ~*a; }
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for(; (a < --b) && ((PA[*b] + depth) < (PA[*b + 1] + 1));) { }
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if(b <= a) { break; }
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t = ~*b;
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*b = *a;
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*a = t;
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}
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if(first < a) { *first = ~*first; }
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return a;
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}
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/* Multikey introsort for medium size groups. */
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static
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void
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ss_mintrosort(const unsigned char *T, const int *PA,
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int *first, int *last,
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int depth) {
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#define STACK_SIZE SS_MISORT_STACKSIZE
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struct { int *a, *b, c; int d; } stack[STACK_SIZE];
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const unsigned char *Td;
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int *a, *b, *c, *d, *e, *f;
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int s, t;
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int ssize;
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int limit;
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int v, x = 0;
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for(ssize = 0, limit = ss_ilg(last - first);;) {
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if((last - first) <= SS_INSERTIONSORT_THRESHOLD) {
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#if 1 < SS_INSERTIONSORT_THRESHOLD
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if(1 < (last - first)) { ss_insertionsort(T, PA, first, last, depth); }
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#endif
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STACK_POP(first, last, depth, limit);
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continue;
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}
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Td = T + depth;
|
|
if(limit-- == 0) { ss_heapsort(Td, PA, first, last - first); }
|
|
if(limit < 0) {
|
|
for(a = first + 1, v = Td[PA[*first]]; a < last; ++a) {
|
|
if((x = Td[PA[*a]]) != v) {
|
|
if(1 < (a - first)) { break; }
|
|
v = x;
|
|
first = a;
|
|
}
|
|
}
|
|
if(Td[PA[*first] - 1] < v) {
|
|
first = ss_partition(PA, first, a, depth);
|
|
}
|
|
if((a - first) <= (last - a)) {
|
|
if(1 < (a - first)) {
|
|
STACK_PUSH(a, last, depth, -1);
|
|
last = a, depth += 1, limit = ss_ilg(a - first);
|
|
} else {
|
|
first = a, limit = -1;
|
|
}
|
|
} else {
|
|
if(1 < (last - a)) {
|
|
STACK_PUSH(first, a, depth + 1, ss_ilg(a - first));
|
|
first = a, limit = -1;
|
|
} else {
|
|
last = a, depth += 1, limit = ss_ilg(a - first);
|
|
}
|
|
}
|
|
continue;
|
|
}
|
|
|
|
/* choose pivot */
|
|
a = ss_pivot(Td, PA, first, last);
|
|
v = Td[PA[*a]];
|
|
SWAP(*first, *a);
|
|
|
|
/* partition */
|
|
for(b = first; (++b < last) && ((x = Td[PA[*b]]) == v);) { }
|
|
if(((a = b) < last) && (x < v)) {
|
|
for(; (++b < last) && ((x = Td[PA[*b]]) <= v);) {
|
|
if(x == v) { SWAP(*b, *a); ++a; }
|
|
}
|
|
}
|
|
for(c = last; (b < --c) && ((x = Td[PA[*c]]) == v);) { }
|
|
if((b < (d = c)) && (x > v)) {
|
|
for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
|
|
if(x == v) { SWAP(*c, *d); --d; }
|
|
}
|
|
}
|
|
for(; b < c;) {
|
|
SWAP(*b, *c);
|
|
for(; (++b < c) && ((x = Td[PA[*b]]) <= v);) {
|
|
if(x == v) { SWAP(*b, *a); ++a; }
|
|
}
|
|
for(; (b < --c) && ((x = Td[PA[*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); }
|
|
|
|
a = first + (b - a), c = last - (d - c);
|
|
b = (v <= Td[PA[*a] - 1]) ? a : ss_partition(PA, a, c, depth);
|
|
|
|
if((a - first) <= (last - c)) {
|
|
if((last - c) <= (c - b)) {
|
|
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
|
STACK_PUSH(c, last, depth, limit);
|
|
last = a;
|
|
} else if((a - first) <= (c - b)) {
|
|
STACK_PUSH(c, last, depth, limit);
|
|
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
|
last = a;
|
|
} else {
|
|
STACK_PUSH(c, last, depth, limit);
|
|
STACK_PUSH(first, a, depth, limit);
|
|
first = b, last = c, depth += 1, limit = ss_ilg(c - b);
|
|
}
|
|
} else {
|
|
if((a - first) <= (c - b)) {
|
|
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
|
STACK_PUSH(first, a, depth, limit);
|
|
first = c;
|
|
} else if((last - c) <= (c - b)) {
|
|
STACK_PUSH(first, a, depth, limit);
|
|
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
|
first = c;
|
|
} else {
|
|
STACK_PUSH(first, a, depth, limit);
|
|
STACK_PUSH(c, last, depth, limit);
|
|
first = b, last = c, depth += 1, limit = ss_ilg(c - b);
|
|
}
|
|
}
|
|
} else {
|
|
limit += 1;
|
|
if(Td[PA[*first] - 1] < v) {
|
|
first = ss_partition(PA, first, last, depth);
|
|
limit = ss_ilg(last - first);
|
|
}
|
|
depth += 1;
|
|
}
|
|
}
|
|
#undef STACK_SIZE
|
|
}
|
|
|
|
#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
|
|
|
|
|
|
/*---------------------------------------------------------------------------*/
|
|
|
|
#if SS_BLOCKSIZE != 0
|
|
|
|
static INLINE
|
|
void
|
|
ss_blockswap(int *a, int *b, int n) {
|
|
int t;
|
|
for(; 0 < n; --n, ++a, ++b) {
|
|
t = *a, *a = *b, *b = t;
|
|
}
|
|
}
|
|
|
|
static INLINE
|
|
void
|
|
ss_rotate(int *first, int *middle, int *last) {
|
|
int *a, *b, t;
|
|
int l, r;
|
|
l = middle - first, r = last - middle;
|
|
for(; (0 < l) && (0 < r);) {
|
|
if(l == r) { ss_blockswap(first, middle, l); break; }
|
|
if(l < r) {
|
|
a = last - 1, b = middle - 1;
|
|
t = *a;
|
|
do {
|
|
*a-- = *b, *b-- = *a;
|
|
if(b < first) {
|
|
*a = t;
|
|
last = a;
|
|
if((r -= l + 1) <= l) { break; }
|
|
a -= 1, b = middle - 1;
|
|
t = *a;
|
|
}
|
|
} while(1);
|
|
} else {
|
|
a = first, b = middle;
|
|
t = *a;
|
|
do {
|
|
*a++ = *b, *b++ = *a;
|
|
if(last <= b) {
|
|
*a = t;
|
|
first = a + 1;
|
|
if((l -= r + 1) <= r) { break; }
|
|
a += 1, b = middle;
|
|
t = *a;
|
|
}
|
|
} while(1);
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
/*---------------------------------------------------------------------------*/
|
|
|
|
static
|
|
void
|
|
ss_inplacemerge(const unsigned char *T, const int *PA,
|
|
int *first, int *middle, int *last,
|
|
int depth) {
|
|
const int *p;
|
|
int *a, *b;
|
|
int len, half;
|
|
int q, r;
|
|
int x;
|
|
|
|
for(;;) {
|
|
if(*(last - 1) < 0) { x = 1; p = PA + ~*(last - 1); }
|
|
else { x = 0; p = PA + *(last - 1); }
|
|
for(a = first, len = middle - first, half = len >> 1, r = -1;
|
|
0 < len;
|
|
len = half, half >>= 1) {
|
|
b = a + half;
|
|
q = ss_compare(T, PA + ((0 <= *b) ? *b : ~*b), p, depth);
|
|
if(q < 0) {
|
|
a = b + 1;
|
|
half -= (len & 1) ^ 1;
|
|
} else {
|
|
r = q;
|
|
}
|
|
}
|
|
if(a < middle) {
|
|
if(r == 0) { *a = ~*a; }
|
|
ss_rotate(a, middle, last);
|
|
last -= middle - a;
|
|
middle = a;
|
|
if(first == middle) { break; }
|
|
}
|
|
--last;
|
|
if(x != 0) { while(*--last < 0) { } }
|
|
if(middle == last) { break; }
|
|
}
|
|
}
|
|
|
|
|
|
/*---------------------------------------------------------------------------*/
|
|
|
|
/* Merge-forward with internal buffer. */
|
|
static
|
|
void
|
|
ss_mergeforward(const unsigned char *T, const int *PA,
|
|
int *first, int *middle, int *last,
|
|
int *buf, int depth) {
|
|
int *a, *b, *c, *bufend;
|
|
int t;
|
|
int r;
|
|
|
|
bufend = buf + (middle - first) - 1;
|
|
ss_blockswap(buf, first, middle - first);
|
|
|
|
for(t = *(a = first), b = buf, c = middle;;) {
|
|
r = ss_compare(T, PA + *b, PA + *c, depth);
|
|
if(r < 0) {
|
|
do {
|
|
*a++ = *b;
|
|
if(bufend <= b) { *bufend = t; return; }
|
|
*b++ = *a;
|
|
} while(*b < 0);
|
|
} else if(r > 0) {
|
|
do {
|
|
*a++ = *c, *c++ = *a;
|
|
if(last <= c) {
|
|
while(b < bufend) { *a++ = *b, *b++ = *a; }
|
|
*a = *b, *b = t;
|
|
return;
|
|
}
|
|
} while(*c < 0);
|
|
} else {
|
|
*c = ~*c;
|
|
do {
|
|
*a++ = *b;
|
|
if(bufend <= b) { *bufend = t; return; }
|
|
*b++ = *a;
|
|
} while(*b < 0);
|
|
|
|
do {
|
|
*a++ = *c, *c++ = *a;
|
|
if(last <= c) {
|
|
while(b < bufend) { *a++ = *b, *b++ = *a; }
|
|
*a = *b, *b = t;
|
|
return;
|
|
}
|
|
} while(*c < 0);
|
|
}
|
|
}
|
|
}
|
|
|
|
/* Merge-backward with internal buffer. */
|
|
static
|
|
void
|
|
ss_mergebackward(const unsigned char *T, const int *PA,
|
|
int *first, int *middle, int *last,
|
|
int *buf, int depth) {
|
|
const int *p1, *p2;
|
|
int *a, *b, *c, *bufend;
|
|
int t;
|
|
int r;
|
|
int x;
|
|
|
|
bufend = buf + (last - middle) - 1;
|
|
ss_blockswap(buf, middle, last - middle);
|
|
|
|
x = 0;
|
|
if(*bufend < 0) { p1 = PA + ~*bufend; x |= 1; }
|
|
else { p1 = PA + *bufend; }
|
|
if(*(middle - 1) < 0) { p2 = PA + ~*(middle - 1); x |= 2; }
|
|
else { p2 = PA + *(middle - 1); }
|
|
for(t = *(a = last - 1), b = bufend, c = middle - 1;;) {
|
|
r = ss_compare(T, p1, p2, depth);
|
|
if(0 < r) {
|
|
if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
|
|
*a-- = *b;
|
|
if(b <= buf) { *buf = t; break; }
|
|
*b-- = *a;
|
|
if(*b < 0) { p1 = PA + ~*b; x |= 1; }
|
|
else { p1 = PA + *b; }
|
|
} else if(r < 0) {
|
|
if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
|
|
*a-- = *c, *c-- = *a;
|
|
if(c < first) {
|
|
while(buf < b) { *a-- = *b, *b-- = *a; }
|
|
*a = *b, *b = t;
|
|
break;
|
|
}
|
|
if(*c < 0) { p2 = PA + ~*c; x |= 2; }
|
|
else { p2 = PA + *c; }
|
|
} else {
|
|
if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
|
|
*a-- = ~*b;
|
|
if(b <= buf) { *buf = t; break; }
|
|
*b-- = *a;
|
|
if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
|
|
*a-- = *c, *c-- = *a;
|
|
if(c < first) {
|
|
while(buf < b) { *a-- = *b, *b-- = *a; }
|
|
*a = *b, *b = t;
|
|
break;
|
|
}
|
|
if(*b < 0) { p1 = PA + ~*b; x |= 1; }
|
|
else { p1 = PA + *b; }
|
|
if(*c < 0) { p2 = PA + ~*c; x |= 2; }
|
|
else { p2 = PA + *c; }
|
|
}
|
|
}
|
|
}
|
|
|
|
/* D&C based merge. */
|
|
static
|
|
void
|
|
ss_swapmerge(const unsigned char *T, const int *PA,
|
|
int *first, int *middle, int *last,
|
|
int *buf, int bufsize, int depth) {
|
|
#define STACK_SIZE SS_SMERGE_STACKSIZE
|
|
#define GETIDX(a) ((0 <= (a)) ? (a) : (~(a)))
|
|
#define MERGE_CHECK(a, b, c)\
|
|
do {\
|
|
if(((c) & 1) ||\
|
|
(((c) & 2) && (ss_compare(T, PA + GETIDX(*((a) - 1)), PA + *(a), depth) == 0))) {\
|
|
*(a) = ~*(a);\
|
|
}\
|
|
if(((c) & 4) && ((ss_compare(T, PA + GETIDX(*((b) - 1)), PA + *(b), depth) == 0))) {\
|
|
*(b) = ~*(b);\
|
|
}\
|
|
} while(0)
|
|
struct { int *a, *b, *c; int d; } stack[STACK_SIZE];
|
|
int *l, *r, *lm, *rm;
|
|
int m, len, half;
|
|
int ssize;
|
|
int check, next;
|
|
|
|
for(check = 0, ssize = 0;;) {
|
|
if((last - middle) <= bufsize) {
|
|
if((first < middle) && (middle < last)) {
|
|
ss_mergebackward(T, PA, first, middle, last, buf, depth);
|
|
}
|
|
MERGE_CHECK(first, last, check);
|
|
STACK_POP(first, middle, last, check);
|
|
continue;
|
|
}
|
|
|
|
if((middle - first) <= bufsize) {
|
|
if(first < middle) {
|
|
ss_mergeforward(T, PA, first, middle, last, buf, depth);
|
|
}
|
|
MERGE_CHECK(first, last, check);
|
|
STACK_POP(first, middle, last, check);
|
|
continue;
|
|
}
|
|
|
|
for(m = 0, len = MIN(middle - first, last - middle), half = len >> 1;
|
|
0 < len;
|
|
len = half, half >>= 1) {
|
|
if(ss_compare(T, PA + GETIDX(*(middle + m + half)),
|
|
PA + GETIDX(*(middle - m - half - 1)), depth) < 0) {
|
|
m += half + 1;
|
|
half -= (len & 1) ^ 1;
|
|
}
|
|
}
|
|
|
|
if(0 < m) {
|
|
lm = middle - m, rm = middle + m;
|
|
ss_blockswap(lm, middle, m);
|
|
l = r = middle, next = 0;
|
|
if(rm < last) {
|
|
if(*rm < 0) {
|
|
*rm = ~*rm;
|
|
if(first < lm) { for(; *--l < 0;) { } next |= 4; }
|
|
next |= 1;
|
|
} else if(first < lm) {
|
|
for(; *r < 0; ++r) { }
|
|
next |= 2;
|
|
}
|
|
}
|
|
|
|
if((l - first) <= (last - r)) {
|
|
STACK_PUSH(r, rm, last, (next & 3) | (check & 4));
|
|
middle = lm, last = l, check = (check & 3) | (next & 4);
|
|
} else {
|
|
if((next & 2) && (r == middle)) { next ^= 6; }
|
|
STACK_PUSH(first, lm, l, (check & 3) | (next & 4));
|
|
first = r, middle = rm, check = (next & 3) | (check & 4);
|
|
}
|
|
} else {
|
|
if(ss_compare(T, PA + GETIDX(*(middle - 1)), PA + *middle, depth) == 0) {
|
|
*middle = ~*middle;
|
|
}
|
|
MERGE_CHECK(first, last, check);
|
|
STACK_POP(first, middle, last, check);
|
|
}
|
|
}
|
|
#undef STACK_SIZE
|
|
}
|
|
|
|
#endif /* SS_BLOCKSIZE != 0 */
|
|
|
|
|
|
/*---------------------------------------------------------------------------*/
|
|
|
|
/* Substring sort */
|
|
static
|
|
void
|
|
sssort(const unsigned char *T, const int *PA,
|
|
int *first, int *last,
|
|
int *buf, int bufsize,
|
|
int depth, int n, int lastsuffix) {
|
|
int *a;
|
|
#if SS_BLOCKSIZE != 0
|
|
int *b, *middle, *curbuf;
|
|
int j, k, curbufsize, limit;
|
|
#endif
|
|
int i;
|
|
|
|
if(lastsuffix != 0) { ++first; }
|
|
|
|
#if SS_BLOCKSIZE == 0
|
|
ss_mintrosort(T, PA, first, last, depth);
|
|
#else
|
|
if((bufsize < SS_BLOCKSIZE) &&
|
|
(bufsize < (last - first)) &&
|
|
(bufsize < (limit = ss_isqrt(last - first)))) {
|
|
if(SS_BLOCKSIZE < limit) { limit = SS_BLOCKSIZE; }
|
|
buf = middle = last - limit, bufsize = limit;
|
|
} else {
|
|
middle = last, limit = 0;
|
|
}
|
|
for(a = first, i = 0; SS_BLOCKSIZE < (middle - a); a += SS_BLOCKSIZE, ++i) {
|
|
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
|
|
ss_mintrosort(T, PA, a, a + SS_BLOCKSIZE, depth);
|
|
#elif 1 < SS_BLOCKSIZE
|
|
ss_insertionsort(T, PA, a, a + SS_BLOCKSIZE, depth);
|
|
#endif
|
|
curbufsize = last - (a + SS_BLOCKSIZE);
|
|
curbuf = a + SS_BLOCKSIZE;
|
|
if(curbufsize <= bufsize) { curbufsize = bufsize, curbuf = buf; }
|
|
for(b = a, k = SS_BLOCKSIZE, j = i; j & 1; b -= k, k <<= 1, j >>= 1) {
|
|
ss_swapmerge(T, PA, b - k, b, b + k, curbuf, curbufsize, depth);
|
|
}
|
|
}
|
|
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
|
|
ss_mintrosort(T, PA, a, middle, depth);
|
|
#elif 1 < SS_BLOCKSIZE
|
|
ss_insertionsort(T, PA, a, middle, depth);
|
|
#endif
|
|
for(k = SS_BLOCKSIZE; i != 0; k <<= 1, i >>= 1) {
|
|
if(i & 1) {
|
|
ss_swapmerge(T, PA, a - k, a, middle, buf, bufsize, depth);
|
|
a -= k;
|
|
}
|
|
}
|
|
if(limit != 0) {
|
|
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
|
|
ss_mintrosort(T, PA, middle, last, depth);
|
|
#elif 1 < SS_BLOCKSIZE
|
|
ss_insertionsort(T, PA, middle, last, depth);
|
|
#endif
|
|
ss_inplacemerge(T, PA, first, middle, last, depth);
|
|
}
|
|
#endif
|
|
|
|
if(lastsuffix != 0) {
|
|
/* Insert last type B* suffix. */
|
|
int PAi[2]; PAi[0] = PA[*(first - 1)], PAi[1] = n - 2;
|
|
for(a = first, i = *(first - 1);
|
|
(a < last) && ((*a < 0) || (0 < ss_compare(T, &(PAi[0]), PA + *a, depth)));
|
|
++a) {
|
|
*(a - 1) = *a;
|
|
}
|
|
*(a - 1) = i;
|
|
}
|
|
}
|
|
|
|
|
|
/*---------------------------------------------------------------------------*/
|
|
|
|
static INLINE
|
|
int
|
|
tr_ilg(int n) {
|
|
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]);
|
|
}
|
|
|
|
|
|
/*---------------------------------------------------------------------------*/
|
|
|
|
/* Simple insertionsort for small size groups. */
|
|
static
|
|
void
|
|
tr_insertionsort(const int *ISAd, int *first, int *last) {
|
|
int *a, *b;
|
|
int 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 int *ISAd, int *SA, int i, int size) {
|
|
int j, k;
|
|
int v;
|
|
int 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 int *ISAd, int *SA, int size) {
|
|
int i, m;
|
|
int 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
|
|
int *
|
|
tr_median3(const int *ISAd, int *v1, int *v2, int *v3) {
|
|
int *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
|
|
int *
|
|
tr_median5(const int *ISAd,
|
|
int *v1, int *v2, int *v3, int *v4, int *v5) {
|
|
int *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
|
|
int *
|
|
tr_pivot(const int *ISAd, int *first, int *last) {
|
|
int *middle;
|
|
int 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 {
|
|
int chance;
|
|
int remain;
|
|
int incval;
|
|
int count;
|
|
};
|
|
|
|
static INLINE
|
|
void
|
|
trbudget_init(trbudget_t *budget, int chance, int incval) {
|
|
budget->chance = chance;
|
|
budget->remain = budget->incval = incval;
|
|
}
|
|
|
|
static INLINE
|
|
int
|
|
trbudget_check(trbudget_t *budget, int 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 int *ISAd,
|
|
int *first, int *middle, int *last,
|
|
int **pa, int **pb, int v) {
|
|
int *a, *b, *c, *d, *e, *f;
|
|
int t, s;
|
|
int 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(int *ISA, const int *SA,
|
|
int *first, int *a, int *b, int *last,
|
|
int depth) {
|
|
/* sort suffixes of middle partition
|
|
by using sorted order of suffixes of left and right partition. */
|
|
int *c, *d, *e;
|
|
int 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(int *ISA, const int *SA,
|
|
int *first, int *a, int *b, int *last,
|
|
int depth) {
|
|
int *c, *d, *e;
|
|
int s, v;
|
|
int 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(int *ISA, const int *ISAd,
|
|
int *SA, int *first, int *last,
|
|
trbudget_t *budget) {
|
|
#define STACK_SIZE TR_STACKSIZE
|
|
struct { const int *a; int *b, *c; int d, e; }stack[STACK_SIZE];
|
|
int *a, *b, *c;
|
|
int t;
|
|
int v, x = 0;
|
|
int incr = ISAd - ISA;
|
|
int limit, next;
|
|
int 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
|
|
}
|
|
|
|
|
|
|
|
/*---------------------------------------------------------------------------*/
|
|
|
|
/* Tandem repeat sort */
|
|
static
|
|
void
|
|
trsort(int *ISA, int *SA, int n, int depth) {
|
|
int *ISAd;
|
|
int *first, *last;
|
|
trbudget_t budget;
|
|
int 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; }
|
|
}
|
|
}
|
|
|
|
|
|
/*---------------------------------------------------------------------------*/
|
|
|
|
/* Sorts suffixes of type B*. */
|
|
static
|
|
int
|
|
sort_typeBstar(const unsigned char *T, int *SA,
|
|
int *bucket_A, int *bucket_B,
|
|
int n, int openMP) {
|
|
int *PAb, *ISAb, *buf;
|
|
#ifdef LIBBSC_OPENMP
|
|
int *curbuf;
|
|
int l;
|
|
#endif
|
|
int i, j, k, t, m, bufsize;
|
|
int c0, c1;
|
|
#ifdef LIBBSC_OPENMP
|
|
int d0, d1;
|
|
#endif
|
|
(void)openMP;
|
|
|
|
/* Initialize bucket arrays. */
|
|
for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; }
|
|
for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; }
|
|
|
|
/* Count the number of occurrences of the first one or two characters of each
|
|
type A, B and B* suffix. Moreover, store the beginning position of all
|
|
type B* suffixes into the array SA. */
|
|
for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) {
|
|
/* type A suffix. */
|
|
do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1));
|
|
if(0 <= i) {
|
|
/* type B* suffix. */
|
|
++BUCKET_BSTAR(c0, c1);
|
|
SA[--m] = i;
|
|
/* type B suffix. */
|
|
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) {
|
|
++BUCKET_B(c0, c1);
|
|
}
|
|
}
|
|
}
|
|
m = n - m;
|
|
/*
|
|
note:
|
|
A type B* suffix is lexicographically smaller than a type B suffix that
|
|
begins with the same first two characters.
|
|
*/
|
|
|
|
/* Calculate the index of start/end point of each bucket. */
|
|
for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) {
|
|
t = i + BUCKET_A(c0);
|
|
BUCKET_A(c0) = i + j; /* start point */
|
|
i = t + BUCKET_B(c0, c0);
|
|
for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) {
|
|
j += BUCKET_BSTAR(c0, c1);
|
|
BUCKET_BSTAR(c0, c1) = j; /* end point */
|
|
i += BUCKET_B(c0, c1);
|
|
}
|
|
}
|
|
|
|
if(0 < m) {
|
|
/* Sort the type B* suffixes by their first two characters. */
|
|
PAb = SA + n - m; ISAb = SA + m;
|
|
for(i = m - 2; 0 <= i; --i) {
|
|
t = PAb[i], c0 = T[t], c1 = T[t + 1];
|
|
SA[--BUCKET_BSTAR(c0, c1)] = i;
|
|
}
|
|
t = PAb[m - 1], c0 = T[t], c1 = T[t + 1];
|
|
SA[--BUCKET_BSTAR(c0, c1)] = m - 1;
|
|
|
|
/* Sort the type B* substrings using sssort. */
|
|
#ifdef LIBBSC_OPENMP
|
|
if (openMP)
|
|
{
|
|
buf = SA + m;
|
|
c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m;
|
|
#pragma omp parallel default(shared) private(bufsize, curbuf, k, l, d0, d1)
|
|
{
|
|
bufsize = (n - (2 * m)) / omp_get_num_threads();
|
|
curbuf = buf + omp_get_thread_num() * bufsize;
|
|
k = 0;
|
|
for(;;) {
|
|
#pragma omp critical(sssort_lock)
|
|
{
|
|
if(0 < (l = j)) {
|
|
d0 = c0, d1 = c1;
|
|
do {
|
|
k = BUCKET_BSTAR(d0, d1);
|
|
if(--d1 <= d0) {
|
|
d1 = ALPHABET_SIZE - 1;
|
|
if(--d0 < 0) { break; }
|
|
}
|
|
} while(((l - k) <= 1) && (0 < (l = k)));
|
|
c0 = d0, c1 = d1, j = k;
|
|
}
|
|
}
|
|
if(l == 0) { break; }
|
|
sssort(T, PAb, SA + k, SA + l,
|
|
curbuf, bufsize, 2, n, *(SA + k) == (m - 1));
|
|
}
|
|
}
|
|
}
|
|
else
|
|
{
|
|
buf = SA + m, bufsize = n - (2 * m);
|
|
for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
|
|
for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
|
|
i = BUCKET_BSTAR(c0, c1);
|
|
if(1 < (j - i)) {
|
|
sssort(T, PAb, SA + i, SA + j,
|
|
buf, bufsize, 2, n, *(SA + i) == (m - 1));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
#else
|
|
buf = SA + m, bufsize = n - (2 * m);
|
|
for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
|
|
for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
|
|
i = BUCKET_BSTAR(c0, c1);
|
|
if(1 < (j - i)) {
|
|
sssort(T, PAb, SA + i, SA + j,
|
|
buf, bufsize, 2, n, *(SA + i) == (m - 1));
|
|
}
|
|
}
|
|
}
|
|
#endif
|
|
|
|
/* Compute ranks of type B* substrings. */
|
|
for(i = m - 1; 0 <= i; --i) {
|
|
if(0 <= SA[i]) {
|
|
j = i;
|
|
do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i]));
|
|
SA[i + 1] = i - j;
|
|
if(i <= 0) { break; }
|
|
}
|
|
j = i;
|
|
do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0);
|
|
ISAb[SA[i]] = j;
|
|
}
|
|
|
|
/* Construct the inverse suffix array of type B* suffixes using trsort. */
|
|
trsort(ISAb, SA, m, 1);
|
|
|
|
/* Set the sorted order of tyoe B* suffixes. */
|
|
for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) {
|
|
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { }
|
|
if(0 <= i) {
|
|
t = i;
|
|
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { }
|
|
SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t;
|
|
}
|
|
}
|
|
|
|
/* Calculate the index of start/end point of each bucket. */
|
|
BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */
|
|
for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) {
|
|
i = BUCKET_A(c0 + 1) - 1;
|
|
for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) {
|
|
t = i - BUCKET_B(c0, c1);
|
|
BUCKET_B(c0, c1) = i; /* end point */
|
|
|
|
/* Move all type B* suffixes to the correct position. */
|
|
for(i = t, j = BUCKET_BSTAR(c0, c1);
|
|
j <= k;
|
|
--i, --k) { SA[i] = SA[k]; }
|
|
}
|
|
BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */
|
|
BUCKET_B(c0, c0) = i; /* end point */
|
|
}
|
|
}
|
|
|
|
return m;
|
|
}
|
|
|
|
/* Constructs the suffix array by using the sorted order of type B* suffixes. */
|
|
static
|
|
void
|
|
construct_SA(const unsigned char *T, int *SA,
|
|
int *bucket_A, int *bucket_B,
|
|
int n, int m) {
|
|
int *i, *j, *k;
|
|
int s;
|
|
int c0, c1, c2;
|
|
|
|
if(0 < m) {
|
|
/* Construct the sorted order of type B suffixes by using
|
|
the sorted order of type B* suffixes. */
|
|
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
|
|
/* Scan the suffix array from right to left. */
|
|
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
|
|
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
|
|
i <= j;
|
|
--j) {
|
|
if(0 < (s = *j)) {
|
|
assert(T[s] == c1);
|
|
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
|
|
assert(T[s - 1] <= T[s]);
|
|
*j = ~s;
|
|
c0 = T[--s];
|
|
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
|
|
if(c0 != c2) {
|
|
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
|
|
k = SA + BUCKET_B(c2 = c0, c1);
|
|
}
|
|
assert(k < j); assert(k != NULL);
|
|
*k-- = s;
|
|
} else {
|
|
assert(((s == 0) && (T[s] == c1)) || (s < 0));
|
|
*j = ~s;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
/* Construct the suffix array by using
|
|
the sorted order of type B suffixes. */
|
|
k = SA + BUCKET_A(c2 = T[n - 1]);
|
|
*k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1);
|
|
/* Scan the suffix array from left to right. */
|
|
for(i = SA, j = SA + n; i < j; ++i) {
|
|
if(0 < (s = *i)) {
|
|
assert(T[s - 1] >= T[s]);
|
|
c0 = T[--s];
|
|
if((s == 0) || (T[s - 1] < c0)) { s = ~s; }
|
|
if(c0 != c2) {
|
|
BUCKET_A(c2) = k - SA;
|
|
k = SA + BUCKET_A(c2 = c0);
|
|
}
|
|
assert(i < k);
|
|
*k++ = s;
|
|
} else {
|
|
assert(s < 0);
|
|
*i = ~s;
|
|
}
|
|
}
|
|
}
|
|
|
|
/* Constructs the burrows-wheeler transformed string directly
|
|
by using the sorted order of type B* suffixes. */
|
|
static
|
|
int
|
|
construct_BWT(const unsigned char *T, int *SA,
|
|
int *bucket_A, int *bucket_B,
|
|
int n, int m) {
|
|
int *i, *j, *k, *orig;
|
|
int s;
|
|
int c0, c1, c2;
|
|
|
|
if(0 < m) {
|
|
/* Construct the sorted order of type B suffixes by using
|
|
the sorted order of type B* suffixes. */
|
|
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
|
|
/* Scan the suffix array from right to left. */
|
|
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
|
|
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
|
|
i <= j;
|
|
--j) {
|
|
if(0 < (s = *j)) {
|
|
assert(T[s] == c1);
|
|
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
|
|
assert(T[s - 1] <= T[s]);
|
|
c0 = T[--s];
|
|
*j = ~((int)c0);
|
|
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
|
|
if(c0 != c2) {
|
|
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
|
|
k = SA + BUCKET_B(c2 = c0, c1);
|
|
}
|
|
assert(k < j); assert(k != NULL);
|
|
*k-- = s;
|
|
} else if(s != 0) {
|
|
*j = ~s;
|
|
#ifndef NDEBUG
|
|
} else {
|
|
assert(T[s] == c1);
|
|
#endif
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
/* Construct the BWTed string by using
|
|
the sorted order of type B suffixes. */
|
|
k = SA + BUCKET_A(c2 = T[n - 1]);
|
|
*k++ = (T[n - 2] < c2) ? ~((int)T[n - 2]) : (n - 1);
|
|
/* Scan the suffix array from left to right. */
|
|
for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
|
|
if(0 < (s = *i)) {
|
|
assert(T[s - 1] >= T[s]);
|
|
c0 = T[--s];
|
|
*i = c0;
|
|
if((0 < s) && (T[s - 1] < c0)) { s = ~((int)T[s - 1]); }
|
|
if(c0 != c2) {
|
|
BUCKET_A(c2) = k - SA;
|
|
k = SA + BUCKET_A(c2 = c0);
|
|
}
|
|
assert(i < k);
|
|
*k++ = s;
|
|
} else if(s != 0) {
|
|
*i = ~s;
|
|
} else {
|
|
orig = i;
|
|
}
|
|
}
|
|
|
|
return orig - SA;
|
|
}
|
|
|
|
/* Constructs the burrows-wheeler transformed string directly
|
|
by using the sorted order of type B* suffixes. */
|
|
static
|
|
int
|
|
construct_BWT_indexes(const unsigned char *T, int *SA,
|
|
int *bucket_A, int *bucket_B,
|
|
int n, int m,
|
|
unsigned char * num_indexes, int * indexes) {
|
|
int *i, *j, *k, *orig;
|
|
int s;
|
|
int c0, c1, c2;
|
|
|
|
int mod = n / 8;
|
|
{
|
|
mod |= mod >> 1; mod |= mod >> 2;
|
|
mod |= mod >> 4; mod |= mod >> 8;
|
|
mod |= mod >> 16; mod >>= 1;
|
|
|
|
*num_indexes = (unsigned char)((n - 1) / (mod + 1));
|
|
}
|
|
|
|
if(0 < m) {
|
|
/* Construct the sorted order of type B suffixes by using
|
|
the sorted order of type B* suffixes. */
|
|
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
|
|
/* Scan the suffix array from right to left. */
|
|
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
|
|
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
|
|
i <= j;
|
|
--j) {
|
|
if(0 < (s = *j)) {
|
|
assert(T[s] == c1);
|
|
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
|
|
assert(T[s - 1] <= T[s]);
|
|
|
|
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = j - SA;
|
|
|
|
c0 = T[--s];
|
|
*j = ~((int)c0);
|
|
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
|
|
if(c0 != c2) {
|
|
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
|
|
k = SA + BUCKET_B(c2 = c0, c1);
|
|
}
|
|
assert(k < j); assert(k != NULL);
|
|
*k-- = s;
|
|
} else if(s != 0) {
|
|
*j = ~s;
|
|
#ifndef NDEBUG
|
|
} else {
|
|
assert(T[s] == c1);
|
|
#endif
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
/* Construct the BWTed string by using
|
|
the sorted order of type B suffixes. */
|
|
k = SA + BUCKET_A(c2 = T[n - 1]);
|
|
if (T[n - 2] < c2) {
|
|
if (((n - 1) & mod) == 0) indexes[(n - 1) / (mod + 1) - 1] = k - SA;
|
|
*k++ = ~((int)T[n - 2]);
|
|
}
|
|
else {
|
|
*k++ = n - 1;
|
|
}
|
|
|
|
/* Scan the suffix array from left to right. */
|
|
for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
|
|
if(0 < (s = *i)) {
|
|
assert(T[s - 1] >= T[s]);
|
|
|
|
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = i - SA;
|
|
|
|
c0 = T[--s];
|
|
*i = c0;
|
|
if(c0 != c2) {
|
|
BUCKET_A(c2) = k - SA;
|
|
k = SA + BUCKET_A(c2 = c0);
|
|
}
|
|
assert(i < k);
|
|
if((0 < s) && (T[s - 1] < c0)) {
|
|
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = k - SA;
|
|
*k++ = ~((int)T[s - 1]);
|
|
} else
|
|
*k++ = s;
|
|
} else if(s != 0) {
|
|
*i = ~s;
|
|
} else {
|
|
orig = i;
|
|
}
|
|
}
|
|
|
|
return orig - SA;
|
|
}
|
|
|
|
|
|
/*---------------------------------------------------------------------------*/
|
|
|
|
/*- Function -*/
|
|
|
|
int
|
|
divsufsort(const unsigned char *T, int *SA, int n, int openMP) {
|
|
int *bucket_A, *bucket_B;
|
|
int m;
|
|
int err = 0;
|
|
|
|
/* Check arguments. */
|
|
if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; }
|
|
else if(n == 0) { return 0; }
|
|
else if(n == 1) { SA[0] = 0; return 0; }
|
|
else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; }
|
|
|
|
bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int));
|
|
bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int));
|
|
|
|
/* Suffixsort. */
|
|
if((bucket_A != NULL) && (bucket_B != NULL)) {
|
|
m = sort_typeBstar(T, SA, bucket_A, bucket_B, n, openMP);
|
|
construct_SA(T, SA, bucket_A, bucket_B, n, m);
|
|
} else {
|
|
err = -2;
|
|
}
|
|
|
|
free(bucket_B);
|
|
free(bucket_A);
|
|
|
|
return err;
|
|
}
|
|
|
|
int
|
|
divbwt(const unsigned char *T, unsigned char *U, int *A, int n, unsigned char * num_indexes, int * indexes, int openMP) {
|
|
int *B;
|
|
int *bucket_A, *bucket_B;
|
|
int m, pidx, i;
|
|
|
|
/* Check arguments. */
|
|
if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
|
|
else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
|
|
|
|
if((B = A) == NULL) { B = (int *)malloc((size_t)(n + 1) * sizeof(int)); }
|
|
bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int));
|
|
bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int));
|
|
|
|
/* Burrows-Wheeler Transform. */
|
|
if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
|
|
m = sort_typeBstar(T, B, bucket_A, bucket_B, n, openMP);
|
|
|
|
if (num_indexes == NULL || indexes == NULL) {
|
|
pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
|
|
} else {
|
|
pidx = construct_BWT_indexes(T, B, bucket_A, bucket_B, n, m, num_indexes, indexes);
|
|
}
|
|
|
|
/* Copy to output string. */
|
|
U[0] = T[n - 1];
|
|
for(i = 0; i < pidx; ++i) { U[i + 1] = (unsigned char)B[i]; }
|
|
for(i += 1; i < n; ++i) { U[i] = (unsigned char)B[i]; }
|
|
pidx += 1;
|
|
} else {
|
|
pidx = -2;
|
|
}
|
|
|
|
free(bucket_B);
|
|
free(bucket_A);
|
|
if(A == NULL) { free(B); }
|
|
|
|
return pidx;
|
|
}
|