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This commit is contained in:
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21
3party/bsdiff-courgette/divsufsort/LICENSE
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21
3party/bsdiff-courgette/divsufsort/LICENSE
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The MIT License (MIT)
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Copyright (c) 2003 Yuta Mori All rights reserved.
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Permission is hereby granted, free of charge, to any person obtaining a copy
|
||||
of this software and associated documentation files (the "Software"), to deal
|
||||
in the Software without restriction, including without limitation the rights
|
||||
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
copies of the Software, and to permit persons to whom the Software is
|
||||
furnished to do so, subject to the following conditions:
|
||||
|
||||
The above copyright notice and this permission notice shall be included in all
|
||||
copies or substantial portions of the Software.
|
||||
|
||||
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
||||
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
||||
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
||||
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
||||
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
||||
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
||||
SOFTWARE.
|
||||
35
3party/bsdiff-courgette/divsufsort/README.chromium
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35
3party/bsdiff-courgette/divsufsort/README.chromium
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Name: divsufsort
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URL: https://github.com/y-256/libdivsufsort
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Date: 2016-06-01
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Security Critical: no
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License: MIT
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License File: LICENSE
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Description:
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This directory contains a modified version of Yuta Mori's libdivsufsort,
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available in its original form from:
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https://github.com/y-256/libdivsufsort
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The copy in this directory is so extensively modified that the binary format is
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incompatible with the original and it cannot be compiled outside the Chromium
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source tree or the Courgette project.
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List of changes made to original code:
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- Flattened directory and renamed .c files to .cc files.
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- Extracted top-of-file license to common file LICENCE.
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- Removed unused features, e.g., Burrows-Wheeler transformation.
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- Removed Open EMP usage.
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- Changed static functions to anonymous namespace functions.
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- Moved various #define's from divsufsort_private.h to files that use them.
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- Adapted code to enable PagedArray usage, to reduce effect of memory
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fragmentation:
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- Classified saidx_t* to {saidx_t*, saidx_it, const_saidx_it}.
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- Extracted ss_compare_internal() from ss_compare(), to break awkward usage
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of local array at end of sssort().
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- Defined saidx_it and const_saidx_it to use PagedArray iterators. To
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restore old behavior, we can define DIVSUFSORT_NO_PAGED_ARRAY.
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- Added namespace divsuf.
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- Added divsufsort_with_empty().
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- Added unit tests.
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- Patch to avoid int/uint comparison warnings.
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276
3party/bsdiff-courgette/divsufsort/divsufsort.cc
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276
3party/bsdiff-courgette/divsufsort/divsufsort.cc
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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
|
||||
// obtaining a copy of this software and associated documentation
|
||||
// files (the "Software"), to deal in the Software without
|
||||
// restriction, including without limitation the rights to use,
|
||||
// copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
// copies of the Software, and to permit persons to whom the
|
||||
// Software is furnished to do so, subject to the following
|
||||
// conditions:
|
||||
//
|
||||
// The above copyright notice and this permission notice shall be
|
||||
// included in all copies or substantial portions of the Software.
|
||||
//
|
||||
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
// OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
// HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
// WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
// OTHER DEALINGS IN THE SOFTWARE.
|
||||
//
|
||||
// ChangeLog:
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||||
// 2016-07-22 - Initial commit and adaption to use PagedArray.
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// --Samuel Huang <huangs@chromium.org>
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|
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#include "3party/bsdiff-courgette/divsufsort/divsufsort_private.h"
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#include <stdlib.h>
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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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|
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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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namespace divsuf {
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/*- Private Functions -*/
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namespace {
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/* Sorts suffixes of type B*. */
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saidx_t
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sort_typeBstar(const sauchar_t *T, saidx_it SA,
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saidx_t *bucket_A, saidx_t *bucket_B,
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saidx_t n) {
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saidx_it PAb, ISAb, buf;
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saidx_t i, j, k, t, m, bufsize;
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saint_t c0, c1;
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|
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/* Initialize bucket arrays. */
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for(i = 0; i < static_cast<saidx_t>(BUCKET_A_SIZE); ++i) { bucket_A[i] = 0; }
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for(i = 0; i < static_cast<saidx_t>(BUCKET_B_SIZE); ++i) { bucket_B[i] = 0; }
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|
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/* Count the number of occurrences of the first one or two characters of each
|
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type A, B and B* suffix. Moreover, store the beginning position of all
|
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type B* suffixes into the array SA. */
|
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for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) {
|
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/* type A suffix. */
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do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1));
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if(0 <= i) {
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/* type B* suffix. */
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++BUCKET_BSTAR(c0, c1);
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SA[--m] = i;
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/* type B suffix. */
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for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) {
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++BUCKET_B(c0, c1);
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}
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}
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}
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m = n - m;
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/*
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note:
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A type B* suffix is lexicographically smaller than a type B suffix that
|
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begins with the same first two characters.
|
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*/
|
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|
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/* Calculate the index of start/end point of each bucket. */
|
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for(c0 = 0, i = 0, j = 0; c0 < static_cast<saint_t>(ALPHABET_SIZE); ++c0) {
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t = i + BUCKET_A(c0);
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BUCKET_A(c0) = i + j; /* start point */
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i = t + BUCKET_B(c0, c0);
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for(c1 = c0 + 1; c1 < static_cast<saint_t>(ALPHABET_SIZE); ++c1) {
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j += BUCKET_BSTAR(c0, c1);
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BUCKET_BSTAR(c0, c1) = j; /* end point */
|
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i += BUCKET_B(c0, c1);
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}
|
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}
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|
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if(0 < m) {
|
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/* Sort the type B* suffixes by their first two characters. */
|
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PAb = SA + n - m; ISAb = SA + m;
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for(i = m - 2; 0 <= i; --i) {
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t = PAb[i], c0 = T[t], c1 = T[t + 1];
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SA[--BUCKET_BSTAR(c0, c1)] = i;
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}
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t = PAb[m - 1], c0 = T[t], c1 = T[t + 1];
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SA[--BUCKET_BSTAR(c0, c1)] = m - 1;
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/* Sort the type B* substrings using sssort. */
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buf = SA + m, bufsize = n - (2 * m);
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for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
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for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
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i = BUCKET_BSTAR(c0, c1);
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if(1 < (j - i)) {
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sssort(T, PAb, SA + i, SA + j,
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buf, bufsize, 2, n, *(SA + i) == (m - 1));
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}
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}
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}
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/* Compute ranks of type B* substrings. */
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for(i = m - 1; 0 <= i; --i) {
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if(0 <= SA[i]) {
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j = i;
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do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i]));
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SA[i + 1] = i - j;
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if(i <= 0) { break; }
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}
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j = i;
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do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0);
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ISAb[SA[i]] = j;
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}
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/* Construct the inverse suffix array of type B* suffixes using trsort. */
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trsort(ISAb, SA, m, 1);
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|
||||
/* Set the sorted order of tyoe B* suffixes. */
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||||
for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) {
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||||
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { }
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if(0 <= i) {
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t = i;
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||||
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { }
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SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t;
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||||
}
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||||
}
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||||
|
||||
/* 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) {
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||||
i = BUCKET_A(c0 + 1) - 1;
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||||
for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) {
|
||||
t = i - BUCKET_B(c0, c1);
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||||
BUCKET_B(c0, c1) = i; /* end point */
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||||
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||||
/* Move all type B* suffixes to the correct position. */
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||||
for(i = t, j = BUCKET_BSTAR(c0, c1);
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j <= k;
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||||
--i, --k) { SA[i] = SA[k]; }
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||||
}
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||||
BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */
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||||
BUCKET_B(c0, c0) = i; /* end point */
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||||
}
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||||
}
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||||
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||||
return m;
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||||
}
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||||
|
||||
/* Constructs the suffix array by using the sorted order of type B* suffixes. */
|
||||
void
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||||
construct_SA(const sauchar_t *T, saidx_it SA,
|
||||
saidx_t *bucket_A, saidx_t *bucket_B,
|
||||
saidx_t n, saidx_t m) {
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||||
saidx_it i, j, k;
|
||||
saidx_t s;
|
||||
saint_t 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 = nullptr, 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);
|
||||
*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;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
} // namespace
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
/*- Function -*/
|
||||
|
||||
saint_t
|
||||
divsufsort(const sauchar_t *T, saidx_it SA, saidx_t n) {
|
||||
saidx_t *bucket_A, *bucket_B;
|
||||
saidx_t m;
|
||||
saint_t err = 0;
|
||||
|
||||
/* Check arguments. */
|
||||
if ((T == nullptr) || (SA == nullptr) || (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 = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
|
||||
bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
|
||||
|
||||
/* Suffixsort. */
|
||||
if ((bucket_A != nullptr) && (bucket_B != nullptr)) {
|
||||
m = sort_typeBstar(T, SA, bucket_A, bucket_B, n);
|
||||
construct_SA(T, SA, bucket_A, bucket_B, n, m);
|
||||
} else {
|
||||
err = -2;
|
||||
}
|
||||
|
||||
free(bucket_B);
|
||||
free(bucket_A);
|
||||
|
||||
return err;
|
||||
}
|
||||
|
||||
saint_t divsufsort_include_empty(const sauchar_t *T, saidx_it SA, saidx_t n) {
|
||||
SA[0] = n; // Manually add the empty string suffix.
|
||||
return divsufsort(T, SA + 1, n);
|
||||
}
|
||||
|
||||
} // namespace divsuf
|
||||
65
3party/bsdiff-courgette/divsufsort/divsufsort.h
Normal file
65
3party/bsdiff-courgette/divsufsort/divsufsort.h
Normal file
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|
@ -0,0 +1,65 @@
|
|||
// Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
|
||||
//
|
||||
// Permission is hereby granted, free of charge, to any person
|
||||
// obtaining a copy of this software and associated documentation
|
||||
// files (the "Software"), to deal in the Software without
|
||||
// restriction, including without limitation the rights to use,
|
||||
// copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
// copies of the Software, and to permit persons to whom the
|
||||
// Software is furnished to do so, subject to the following
|
||||
// conditions:
|
||||
//
|
||||
// The above copyright notice and this permission notice shall be
|
||||
// included in all copies or substantial portions of the Software.
|
||||
//
|
||||
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
// OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
// HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
// WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
// OTHER DEALINGS IN THE SOFTWARE.
|
||||
//
|
||||
// ChangeLog:
|
||||
// 2016-07-22 - Initial commit and adaption to use PagedArray.
|
||||
// --Samuel Huang <huangs@chromium.org>
|
||||
|
||||
#ifndef COURGETTE_BSDIFF_THIRD_PARTY_DIVSUFSORT_H_
|
||||
#define COURGETTE_BSDIFF_THIRD_PARTY_DIVSUFSORT_H_
|
||||
|
||||
#include <stdint.h>
|
||||
|
||||
namespace divsuf {
|
||||
|
||||
/*- Datatypes -*/
|
||||
typedef int32_t saint_t;
|
||||
typedef int32_t saidx_t;
|
||||
typedef uint8_t sauchar_t;
|
||||
|
||||
typedef saidx_t* saidx_it;
|
||||
typedef const saidx_t* const_saidx_it;
|
||||
|
||||
/*- Prototypes -*/
|
||||
|
||||
/**
|
||||
* Constructs the suffix array of a given string, excluding the empty string.
|
||||
* @param T[0..n-1] The input string.
|
||||
* @param SA[0..n-1] The output array of suffixes.
|
||||
* @param n The length of the given string.
|
||||
* @return 0 if no error occurred, -1 or -2 otherwise.
|
||||
*/
|
||||
saint_t divsufsort(const sauchar_t *T, saidx_it SA, saidx_t n);
|
||||
|
||||
/**
|
||||
* Constructs the suffix array of a given string, including the empty string.
|
||||
* @param T[0..n-1] The input string.
|
||||
* @param SA[0..n] The output array of suffixes (includes empty string).
|
||||
* @param n The length of the given string.
|
||||
* @return 0 if no error occurred, -1 or -2 otherwise.
|
||||
*/
|
||||
saint_t divsufsort_include_empty(const sauchar_t *T, saidx_it SA, saidx_t n);
|
||||
|
||||
} // namespace divsuf
|
||||
|
||||
#endif // COURGETTE_BSDIFF_THIRD_PARTY_DIVSUFSORT_H_
|
||||
75
3party/bsdiff-courgette/divsufsort/divsufsort_private.h
Normal file
75
3party/bsdiff-courgette/divsufsort/divsufsort_private.h
Normal file
|
|
@ -0,0 +1,75 @@
|
|||
// Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
|
||||
//
|
||||
// Permission is hereby granted, free of charge, to any person
|
||||
// obtaining a copy of this software and associated documentation
|
||||
// files (the "Software"), to deal in the Software without
|
||||
// restriction, including without limitation the rights to use,
|
||||
// copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
// copies of the Software, and to permit persons to whom the
|
||||
// Software is furnished to do so, subject to the following
|
||||
// conditions:
|
||||
//
|
||||
// The above copyright notice and this permission notice shall be
|
||||
// included in all copies or substantial portions of the Software.
|
||||
//
|
||||
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
// OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
// HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
// WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
// OTHER DEALINGS IN THE SOFTWARE.
|
||||
//
|
||||
// ChangeLog:
|
||||
// 2016-07-22 - Initial commit and adaption to use PagedArray.
|
||||
// --Samuel Huang <huangs@chromium.org>
|
||||
|
||||
#ifndef COURGETTE_BSDIFF_THIRD_PARTY_DIVSUFSORT_PRIVATE_H_
|
||||
#define COURGETTE_BSDIFF_THIRD_PARTY_DIVSUFSORT_PRIVATE_H_
|
||||
|
||||
#include <assert.h>
|
||||
#include <stdint.h>
|
||||
#include <stdio.h>
|
||||
|
||||
#include "3party/bsdiff-courgette/divsufsort/divsufsort.h"
|
||||
|
||||
namespace divsuf {
|
||||
|
||||
/*- Constants -*/
|
||||
#if !defined(UINT8_MAX)
|
||||
# define UINT8_MAX (255)
|
||||
#endif /* UINT8_MAX */
|
||||
#if defined(ALPHABET_SIZE) && (ALPHABET_SIZE < 1)
|
||||
# undef ALPHABET_SIZE
|
||||
#endif
|
||||
#if !defined(ALPHABET_SIZE)
|
||||
# define ALPHABET_SIZE (UINT8_MAX + 1)
|
||||
#endif
|
||||
|
||||
/*- Macros -*/
|
||||
#ifndef SWAP
|
||||
# define SWAP(_a, _b) do { t = (_a); (_a) = (_b); (_b) = t; } while(0)
|
||||
#endif /* SWAP */
|
||||
#ifndef MIN
|
||||
# define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b))
|
||||
#endif /* MIN */
|
||||
#ifndef MAX
|
||||
# define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b))
|
||||
#endif /* MAX */
|
||||
|
||||
/*- Private Prototypes -*/
|
||||
/* sssort.c */
|
||||
void
|
||||
sssort(const sauchar_t *T, const_saidx_it PA,
|
||||
saidx_it first, saidx_it last,
|
||||
saidx_it buf, saidx_t bufsize,
|
||||
saidx_t depth, saidx_t n, saint_t lastsuffix);
|
||||
|
||||
/* trsort.c */
|
||||
void
|
||||
trsort(saidx_it ISA, saidx_it SA, saidx_t n, saidx_t depth);
|
||||
|
||||
} // namespace divsuf
|
||||
|
||||
#endif // COURGETTE_BSDIFF_THIRD_PARTY_DIVSUFSORT_PRIVATE_H_
|
||||
87
3party/bsdiff-courgette/divsufsort/divsufsort_unittest.cc
Normal file
87
3party/bsdiff-courgette/divsufsort/divsufsort_unittest.cc
Normal file
|
|
@ -0,0 +1,87 @@
|
|||
// Copyright 2016 The Chromium Authors. All rights reserved.
|
||||
// Use of this source code is governed by a BSD-style license that can be
|
||||
// found in the LICENSE file.
|
||||
|
||||
#include "courgette/third_party/divsufsort/divsufsort.h"
|
||||
|
||||
#include <algorithm>
|
||||
#include <memory>
|
||||
#include <numeric>
|
||||
#include <string>
|
||||
#include <vector>
|
||||
|
||||
#include "courgette/third_party/bsdiff/bsdiff_search.h"
|
||||
#include "courgette/third_party/bsdiff/paged_array.h"
|
||||
#include "testing/gtest/include/gtest/gtest.h"
|
||||
|
||||
TEST(DivSufSortTest, Sort) {
|
||||
const char* test_strs[] = {
|
||||
"",
|
||||
"a",
|
||||
"za",
|
||||
"CACAO",
|
||||
"banana",
|
||||
"tobeornottobe",
|
||||
"The quick brown fox jumps over the lazy dog.",
|
||||
"elephantelephantelephantelephantelephant",
|
||||
"-------------------------",
|
||||
"011010011001011010010110011010010",
|
||||
"3141592653589793238462643383279502884197169399375105",
|
||||
"\xFF\xFE\xFF\xFE\xFD\x80\x30\x31\x32\x80\x30\xFF\x01\xAB\xCD",
|
||||
};
|
||||
|
||||
for (const std::string& test_str : test_strs) {
|
||||
int len = static_cast<int>(test_str.length());
|
||||
const unsigned char* buf =
|
||||
reinterpret_cast<const unsigned char*>(test_str.data());
|
||||
|
||||
// Generate the suffix array as I.
|
||||
courgette::PagedArray<divsuf::saidx_t> I;
|
||||
ASSERT_TRUE(I.Allocate(len + 1));
|
||||
divsuf::divsufsort_include_empty(buf, I.begin(), len);
|
||||
|
||||
// Expect that I[] is a permutation of [0, len].
|
||||
std::vector<divsuf::saidx_t> I_sorted(I.begin(), I.end());
|
||||
std::sort(I_sorted.begin(), I_sorted.end());
|
||||
for (divsuf::saidx_t i = 0; i < len + 1; ++i)
|
||||
EXPECT_EQ(i, I_sorted[i]);
|
||||
|
||||
// First string must be empty string.
|
||||
EXPECT_EQ(len, I[0]);
|
||||
|
||||
// Expect that the |len + 1| suffixes are strictly ordered.
|
||||
const unsigned char* end = buf + len;
|
||||
for (divsuf::saidx_t i = 1; i <= len; ++i) {
|
||||
const unsigned char* suf1 = buf + I[i - 1];
|
||||
const unsigned char* suf2 = buf + I[i];
|
||||
bool is_less = std::lexicographical_compare(suf1, end, suf2, end);
|
||||
EXPECT_TRUE(is_less);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Test with sequence that has every character.
|
||||
TEST(DivSufSortTest, AllChar) {
|
||||
const int kNumChar = 256;
|
||||
std::vector<unsigned char> all_char(kNumChar);
|
||||
std::iota(all_char.begin(), all_char.end(), 0);
|
||||
|
||||
{
|
||||
courgette::PagedArray<divsuf::saidx_t> I;
|
||||
ASSERT_TRUE(I.Allocate(kNumChar + 1));
|
||||
divsuf::divsufsort_include_empty(&all_char[0], I.begin(), kNumChar);
|
||||
EXPECT_EQ(kNumChar, I[0]); // Empty character.
|
||||
for (int i = 1; i <= kNumChar; ++i)
|
||||
EXPECT_EQ(i - 1, I[i]);
|
||||
}
|
||||
|
||||
std::vector<unsigned char> all_char_reverse(
|
||||
all_char.rbegin(), all_char.rend());
|
||||
{
|
||||
courgette::PagedArray<divsuf::saidx_t> I;
|
||||
ASSERT_TRUE(I.Allocate(kNumChar + 1));
|
||||
divsuf::divsufsort_include_empty(&all_char_reverse[0], I.begin(), kNumChar);
|
||||
for (int i = 0; i <= kNumChar; ++i)
|
||||
EXPECT_EQ(kNumChar - i, I[i]);
|
||||
}
|
||||
}
|
||||
855
3party/bsdiff-courgette/divsufsort/sssort.cc
Normal file
855
3party/bsdiff-courgette/divsufsort/sssort.cc
Normal file
|
|
@ -0,0 +1,855 @@
|
|||
// Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
|
||||
//
|
||||
// Permission is hereby granted, free of charge, to any person
|
||||
// obtaining a copy of this software and associated documentation
|
||||
// files (the "Software"), to deal in the Software without
|
||||
// restriction, including without limitation the rights to use,
|
||||
// copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
// copies of the Software, and to permit persons to whom the
|
||||
// Software is furnished to do so, subject to the following
|
||||
// conditions:
|
||||
//
|
||||
// The above copyright notice and this permission notice shall be
|
||||
// included in all copies or substantial portions of the Software.
|
||||
//
|
||||
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
// OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
// HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
// WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
// OTHER DEALINGS IN THE SOFTWARE.
|
||||
//
|
||||
// ChangeLog:
|
||||
// 2016-07-22 - Initial commit and adaption to use PagedArray.
|
||||
// --Samuel Huang <huangs@chromium.org>
|
||||
|
||||
#include "3party/bsdiff-courgette/divsufsort/divsufsort_private.h"
|
||||
|
||||
#if defined(SS_INSERTIONSORT_THRESHOLD)
|
||||
# if SS_INSERTIONSORT_THRESHOLD < 1
|
||||
# undef SS_INSERTIONSORT_THRESHOLD
|
||||
# define SS_INSERTIONSORT_THRESHOLD (1)
|
||||
# endif
|
||||
#else
|
||||
# define SS_INSERTIONSORT_THRESHOLD (8)
|
||||
#endif
|
||||
#if defined(SS_BLOCKSIZE)
|
||||
# if SS_BLOCKSIZE < 0
|
||||
# undef SS_BLOCKSIZE
|
||||
# define SS_BLOCKSIZE (0)
|
||||
# elif 32768 <= SS_BLOCKSIZE
|
||||
# undef SS_BLOCKSIZE
|
||||
# define SS_BLOCKSIZE (32767)
|
||||
# endif
|
||||
#else
|
||||
# define SS_BLOCKSIZE (1024)
|
||||
#endif
|
||||
/* minstacksize = log(SS_BLOCKSIZE) / log(3) * 2 */
|
||||
#if SS_BLOCKSIZE == 0
|
||||
# define SS_MISORT_STACKSIZE (64)
|
||||
#elif SS_BLOCKSIZE <= 4096
|
||||
# define SS_MISORT_STACKSIZE (16)
|
||||
#else
|
||||
# define SS_MISORT_STACKSIZE (24)
|
||||
#endif
|
||||
#define SS_SMERGE_STACKSIZE (32)
|
||||
|
||||
#define STACK_PUSH(_a, _b, _c, _d)\
|
||||
do {\
|
||||
assert(ssize < STACK_SIZE);\
|
||||
stack[ssize].a = (_a), stack[ssize].b = (_b),\
|
||||
stack[ssize].c = (_c), stack[ssize++].d = (_d);\
|
||||
} while(0)
|
||||
#define STACK_POP(_a, _b, _c, _d)\
|
||||
do {\
|
||||
assert(0 <= ssize);\
|
||||
if(ssize == 0) { return; }\
|
||||
(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
|
||||
(_c) = stack[ssize].c, (_d) = stack[ssize].d;\
|
||||
} while(0)
|
||||
|
||||
namespace divsuf {
|
||||
|
||||
namespace {
|
||||
|
||||
/*- Private Functions -*/
|
||||
|
||||
const saint_t lg_table[256]= {
|
||||
-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
|
||||
5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
|
||||
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
|
||||
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
|
||||
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
||||
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
||||
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
||||
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
|
||||
};
|
||||
|
||||
#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
|
||||
|
||||
inline
|
||||
saint_t
|
||||
ss_ilg(saidx_t n) {
|
||||
#if SS_BLOCKSIZE == 0
|
||||
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]);
|
||||
#elif SS_BLOCKSIZE < 256
|
||||
return lg_table[n];
|
||||
#else
|
||||
return (n & 0xff00) ?
|
||||
8 + lg_table[(n >> 8) & 0xff] :
|
||||
0 + lg_table[(n >> 0) & 0xff];
|
||||
#endif
|
||||
}
|
||||
|
||||
#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
|
||||
|
||||
#if SS_BLOCKSIZE != 0
|
||||
|
||||
const saint_t sqq_table[256] = {
|
||||
0, 16, 22, 27, 32, 35, 39, 42, 45, 48, 50, 53, 55, 57, 59, 61,
|
||||
64, 65, 67, 69, 71, 73, 75, 76, 78, 80, 81, 83, 84, 86, 87, 89,
|
||||
90, 91, 93, 94, 96, 97, 98, 99, 101, 102, 103, 104, 106, 107, 108, 109,
|
||||
110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126,
|
||||
128, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
|
||||
143, 144, 144, 145, 146, 147, 148, 149, 150, 150, 151, 152, 153, 154, 155, 155,
|
||||
156, 157, 158, 159, 160, 160, 161, 162, 163, 163, 164, 165, 166, 167, 167, 168,
|
||||
169, 170, 170, 171, 172, 173, 173, 174, 175, 176, 176, 177, 178, 178, 179, 180,
|
||||
181, 181, 182, 183, 183, 184, 185, 185, 186, 187, 187, 188, 189, 189, 190, 191,
|
||||
192, 192, 193, 193, 194, 195, 195, 196, 197, 197, 198, 199, 199, 200, 201, 201,
|
||||
202, 203, 203, 204, 204, 205, 206, 206, 207, 208, 208, 209, 209, 210, 211, 211,
|
||||
212, 212, 213, 214, 214, 215, 215, 216, 217, 217, 218, 218, 219, 219, 220, 221,
|
||||
221, 222, 222, 223, 224, 224, 225, 225, 226, 226, 227, 227, 228, 229, 229, 230,
|
||||
230, 231, 231, 232, 232, 233, 234, 234, 235, 235, 236, 236, 237, 237, 238, 238,
|
||||
239, 240, 240, 241, 241, 242, 242, 243, 243, 244, 244, 245, 245, 246, 246, 247,
|
||||
247, 248, 248, 249, 249, 250, 250, 251, 251, 252, 252, 253, 253, 254, 254, 255
|
||||
};
|
||||
|
||||
inline
|
||||
saidx_t
|
||||
ss_isqrt(saidx_t x) {
|
||||
saidx_t y, e;
|
||||
|
||||
if(x >= (SS_BLOCKSIZE * SS_BLOCKSIZE)) { return SS_BLOCKSIZE; }
|
||||
e = (x & 0xffff0000) ?
|
||||
((x & 0xff000000) ?
|
||||
24 + lg_table[(x >> 24) & 0xff] :
|
||||
16 + lg_table[(x >> 16) & 0xff]) :
|
||||
((x & 0x0000ff00) ?
|
||||
8 + lg_table[(x >> 8) & 0xff] :
|
||||
0 + lg_table[(x >> 0) & 0xff]);
|
||||
|
||||
if(e >= 16) {
|
||||
y = sqq_table[x >> ((e - 6) - (e & 1))] << ((e >> 1) - 7);
|
||||
if(e >= 24) { y = (y + 1 + x / y) >> 1; }
|
||||
y = (y + 1 + x / y) >> 1;
|
||||
} else if(e >= 8) {
|
||||
y = (sqq_table[x >> ((e - 6) - (e & 1))] >> (7 - (e >> 1))) + 1;
|
||||
} else {
|
||||
return sqq_table[x] >> 4;
|
||||
}
|
||||
|
||||
return (x < (y * y)) ? y - 1 : y;
|
||||
}
|
||||
|
||||
#endif /* SS_BLOCKSIZE != 0 */
|
||||
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
/* Compares two suffixes. */
|
||||
inline
|
||||
saint_t
|
||||
ss_compare_internal(const sauchar_t *T,
|
||||
saidx_t p1_lo,
|
||||
saidx_t p1_hi,
|
||||
saidx_t p2_lo,
|
||||
saidx_t p2_hi,
|
||||
saidx_t depth) {
|
||||
const sauchar_t *U1, *U2, *U1n, *U2n;
|
||||
|
||||
for(U1 = T + depth + p1_lo,
|
||||
U2 = T + depth + p2_lo,
|
||||
U1n = T + p1_hi + 2,
|
||||
U2n = T + p2_hi + 2;
|
||||
(U1 < U1n) && (U2 < U2n) && (*U1 == *U2);
|
||||
++U1, ++U2) {
|
||||
}
|
||||
|
||||
return U1 < U1n ?
|
||||
(U2 < U2n ? *U1 - *U2 : 1) :
|
||||
(U2 < U2n ? -1 : 0);
|
||||
}
|
||||
|
||||
/* Compares two suffixes. */
|
||||
inline
|
||||
saint_t
|
||||
ss_compare(const sauchar_t *T,
|
||||
const_saidx_it p1, const_saidx_it p2,
|
||||
saidx_t depth) {
|
||||
return ss_compare_internal(T, *p1, *(p1 + 1), *p2, *(p2 + 1), depth);
|
||||
}
|
||||
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
#if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1)
|
||||
|
||||
/* Insertionsort for small size groups */
|
||||
void
|
||||
ss_insertionsort(const sauchar_t *T, const_saidx_it PA,
|
||||
saidx_it first, saidx_it last, saidx_t depth) {
|
||||
saidx_it i, j;
|
||||
saidx_t t;
|
||||
saint_t r;
|
||||
|
||||
for(i = last - 2; first <= i; --i) {
|
||||
for(t = *i, j = i + 1; 0 < (r = ss_compare(T, PA + t, PA + *j, depth));) {
|
||||
do { *(j - 1) = *j; } while((++j < last) && (*j < 0));
|
||||
if(last <= j) { break; }
|
||||
}
|
||||
if(r == 0) { *j = ~*j; }
|
||||
*(j - 1) = t;
|
||||
}
|
||||
}
|
||||
|
||||
#endif /* (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) */
|
||||
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
|
||||
|
||||
inline
|
||||
void
|
||||
ss_fixdown(const sauchar_t *Td, const_saidx_it PA,
|
||||
saidx_it SA, saidx_t i, saidx_t size) {
|
||||
saidx_t j, k;
|
||||
saidx_t v;
|
||||
saint_t c, d, e;
|
||||
|
||||
for(v = SA[i], c = Td[PA[v]]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
|
||||
d = Td[PA[SA[k = j++]]];
|
||||
if(d < (e = Td[PA[SA[j]]])) { k = j; d = e; }
|
||||
if(d <= c) { break; }
|
||||
}
|
||||
SA[i] = v;
|
||||
}
|
||||
|
||||
/* Simple top-down heapsort. */
|
||||
void
|
||||
ss_heapsort(const sauchar_t *Td, const_saidx_it PA, saidx_it SA, saidx_t size) {
|
||||
saidx_t i, m;
|
||||
saidx_t t;
|
||||
|
||||
m = size;
|
||||
if((size % 2) == 0) {
|
||||
m--;
|
||||
if(Td[PA[SA[m / 2]]] < Td[PA[SA[m]]]) { SWAP(SA[m], SA[m / 2]); }
|
||||
}
|
||||
|
||||
for(i = m / 2 - 1; 0 <= i; --i) { ss_fixdown(Td, PA, SA, i, m); }
|
||||
if((size % 2) == 0) { SWAP(SA[0], SA[m]); ss_fixdown(Td, PA, SA, 0, m); }
|
||||
for(i = m - 1; 0 < i; --i) {
|
||||
t = SA[0], SA[0] = SA[i];
|
||||
ss_fixdown(Td, PA, SA, 0, i);
|
||||
SA[i] = t;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
/* Returns the median of three elements. */
|
||||
inline
|
||||
saidx_it
|
||||
ss_median3(const sauchar_t *Td, const_saidx_it PA,
|
||||
saidx_it v1, saidx_it v2, saidx_it v3) {
|
||||
saidx_it t;
|
||||
if(Td[PA[*v1]] > Td[PA[*v2]]) { SWAP(v1, v2); }
|
||||
if(Td[PA[*v2]] > Td[PA[*v3]]) {
|
||||
if(Td[PA[*v1]] > Td[PA[*v3]]) { return v1; }
|
||||
else { return v3; }
|
||||
}
|
||||
return v2;
|
||||
}
|
||||
|
||||
/* Returns the median of five elements. */
|
||||
inline
|
||||
saidx_it
|
||||
ss_median5(const sauchar_t *Td, const_saidx_it PA,
|
||||
saidx_it v1, saidx_it v2, saidx_it v3, saidx_it v4, saidx_it v5) {
|
||||
saidx_it t;
|
||||
if(Td[PA[*v2]] > Td[PA[*v3]]) { SWAP(v2, v3); }
|
||||
if(Td[PA[*v4]] > Td[PA[*v5]]) { SWAP(v4, v5); }
|
||||
if(Td[PA[*v2]] > Td[PA[*v4]]) { SWAP(v2, v4); SWAP(v3, v5); }
|
||||
if(Td[PA[*v1]] > Td[PA[*v3]]) { SWAP(v1, v3); }
|
||||
if(Td[PA[*v1]] > Td[PA[*v4]]) { SWAP(v1, v4); SWAP(v3, v5); }
|
||||
if(Td[PA[*v3]] > Td[PA[*v4]]) { return v4; }
|
||||
return v3;
|
||||
}
|
||||
|
||||
/* Returns the pivot element. */
|
||||
inline
|
||||
saidx_it
|
||||
ss_pivot(const sauchar_t *Td, const_saidx_it PA, saidx_it first, saidx_it last) {
|
||||
saidx_it middle;
|
||||
saidx_t t;
|
||||
|
||||
t = last - first;
|
||||
middle = first + t / 2;
|
||||
|
||||
if(t <= 512) {
|
||||
if(t <= 32) {
|
||||
return ss_median3(Td, PA, first, middle, last - 1);
|
||||
} else {
|
||||
t >>= 2;
|
||||
return ss_median5(Td, PA, first, first + t, middle, last - 1 - t, last - 1);
|
||||
}
|
||||
}
|
||||
t >>= 3;
|
||||
first = ss_median3(Td, PA, first, first + t, first + (t << 1));
|
||||
middle = ss_median3(Td, PA, middle - t, middle, middle + t);
|
||||
last = ss_median3(Td, PA, last - 1 - (t << 1), last - 1 - t, last - 1);
|
||||
return ss_median3(Td, PA, first, middle, last);
|
||||
}
|
||||
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
/* Binary partition for substrings. */
|
||||
inline
|
||||
saidx_it
|
||||
ss_partition(const_saidx_it PA,
|
||||
saidx_it first, saidx_it last, saidx_t depth) {
|
||||
saidx_it a, b;
|
||||
saidx_t t;
|
||||
for(a = first - 1, b = last;;) {
|
||||
for(; (++a < b) && ((PA[*a] + depth) >= (PA[*a + 1] + 1));) { *a = ~*a; }
|
||||
for(; (a < --b) && ((PA[*b] + depth) < (PA[*b + 1] + 1));) { }
|
||||
if(b <= a) { break; }
|
||||
t = ~*b;
|
||||
*b = *a;
|
||||
*a = t;
|
||||
}
|
||||
if(first < a) { *first = ~*first; }
|
||||
return a;
|
||||
}
|
||||
|
||||
/* Multikey introsort for medium size groups. */
|
||||
void
|
||||
ss_mintrosort(const sauchar_t *T, const_saidx_it PA,
|
||||
saidx_it first, saidx_it last,
|
||||
saidx_t depth) {
|
||||
#define STACK_SIZE SS_MISORT_STACKSIZE
|
||||
struct { saidx_it a, b; saidx_t c; saint_t d; } stack[STACK_SIZE];
|
||||
const sauchar_t *Td;
|
||||
saidx_it a, b, c, d, e, f;
|
||||
saidx_t s, t;
|
||||
saint_t ssize;
|
||||
saint_t limit;
|
||||
saint_t v, x = 0;
|
||||
|
||||
for(ssize = 0, limit = ss_ilg(last - first);;) {
|
||||
|
||||
if((last - first) <= SS_INSERTIONSORT_THRESHOLD) {
|
||||
#if 1 < SS_INSERTIONSORT_THRESHOLD
|
||||
if(1 < (last - first)) { ss_insertionsort(T, PA, first, last, depth); }
|
||||
#endif
|
||||
STACK_POP(first, last, depth, limit);
|
||||
continue;
|
||||
}
|
||||
|
||||
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
|
||||
|
||||
inline
|
||||
void
|
||||
ss_blockswap(saidx_it a, saidx_it b, saidx_t n) {
|
||||
saidx_t t;
|
||||
for(; 0 < n; --n, ++a, ++b) {
|
||||
t = *a, *a = *b, *b = t;
|
||||
}
|
||||
}
|
||||
|
||||
inline
|
||||
void
|
||||
ss_rotate(saidx_it first, saidx_it middle, saidx_it last) {
|
||||
saidx_it a, b;
|
||||
saidx_t t;
|
||||
saidx_t 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);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
void
|
||||
ss_inplacemerge(const sauchar_t *T, const_saidx_it PA,
|
||||
saidx_it first, saidx_it middle, saidx_it last,
|
||||
saidx_t depth) {
|
||||
const_saidx_it p;
|
||||
saidx_it a, b;
|
||||
saidx_t len, half;
|
||||
saint_t q, r;
|
||||
saint_t 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 sauchar_t *T, const_saidx_it PA,
|
||||
saidx_it first, saidx_it middle, saidx_it last,
|
||||
saidx_it buf, saidx_t depth) {
|
||||
saidx_it a, b, c, bufend;
|
||||
saidx_t t;
|
||||
saint_t 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. */
|
||||
void
|
||||
ss_mergebackward(const sauchar_t *T, const_saidx_it PA,
|
||||
saidx_it first, saidx_it middle, saidx_it last,
|
||||
saidx_it buf, saidx_t depth) {
|
||||
const_saidx_it p1, p2;
|
||||
saidx_it a, b, c, bufend;
|
||||
saidx_t t;
|
||||
saint_t r;
|
||||
saint_t 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. */
|
||||
void
|
||||
ss_swapmerge(const sauchar_t *T, const_saidx_it PA,
|
||||
saidx_it first, saidx_it middle, saidx_it last,
|
||||
saidx_it buf, saidx_t bufsize, saidx_t 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 { saidx_it a, b, c; saint_t d; } stack[STACK_SIZE];
|
||||
saidx_it l, r, lm, rm;
|
||||
saidx_t m, len, half;
|
||||
saint_t ssize;
|
||||
saint_t 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 */
|
||||
|
||||
} // namespace
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
/*- Function -*/
|
||||
|
||||
/* Substring sort */
|
||||
void
|
||||
sssort(const sauchar_t *T, const_saidx_it PA,
|
||||
saidx_it first, saidx_it last,
|
||||
saidx_it buf, saidx_t bufsize,
|
||||
saidx_t depth, saidx_t n, saint_t lastsuffix) {
|
||||
saidx_it a;
|
||||
#if SS_BLOCKSIZE != 0
|
||||
saidx_it b, middle, curbuf;
|
||||
saidx_t j, k, curbufsize, limit;
|
||||
#endif
|
||||
saidx_t 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. */
|
||||
for(a = first, i = *(first - 1);
|
||||
(a < last) && ((*a < 0) ||
|
||||
(0 < ss_compare_internal(T, PA[*(first - 1)], n - 2,
|
||||
PA[*a], PA[*a + 1], depth)));
|
||||
++a) {
|
||||
*(a - 1) = *a;
|
||||
}
|
||||
*(a - 1) = i;
|
||||
}
|
||||
}
|
||||
|
||||
} // namespace divsuf
|
||||
587
3party/bsdiff-courgette/divsufsort/trsort.cc
Normal file
587
3party/bsdiff-courgette/divsufsort/trsort.cc
Normal file
|
|
@ -0,0 +1,587 @@
|
|||
// Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
|
||||
//
|
||||
// Permission is hereby granted, free of charge, to any person
|
||||
// obtaining a copy of this software and associated documentation
|
||||
// files (the "Software"), to deal in the Software without
|
||||
// restriction, including without limitation the rights to use,
|
||||
// copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
// copies of the Software, and to permit persons to whom the
|
||||
// Software is furnished to do so, subject to the following
|
||||
// conditions:
|
||||
//
|
||||
// The above copyright notice and this permission notice shall be
|
||||
// included in all copies or substantial portions of the Software.
|
||||
//
|
||||
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
// OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
// HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
// WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
// OTHER DEALINGS IN THE SOFTWARE.
|
||||
//
|
||||
// ChangeLog:
|
||||
// 2016-07-22 - Initial commit and adaption to use PagedArray.
|
||||
// --Samuel Huang <huangs@chromium.org>
|
||||
|
||||
#include "3party/bsdiff-courgette/divsufsort/divsufsort_private.h"
|
||||
|
||||
#define TR_INSERTIONSORT_THRESHOLD (8)
|
||||
#define TR_STACKSIZE (64)
|
||||
|
||||
#define STACK_PUSH5(_a, _b, _c, _d, _e)\
|
||||
do {\
|
||||
assert(ssize < STACK_SIZE);\
|
||||
stack[ssize].a = (_a), stack[ssize].b = (_b),\
|
||||
stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\
|
||||
} while(0)
|
||||
#define STACK_POP5(_a, _b, _c, _d, _e)\
|
||||
do {\
|
||||
assert(0 <= ssize);\
|
||||
if(ssize == 0) { return; }\
|
||||
(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
|
||||
(_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\
|
||||
} while(0)
|
||||
|
||||
|
||||
namespace divsuf {
|
||||
|
||||
namespace {
|
||||
|
||||
/*- Private Functions -*/
|
||||
|
||||
const saint_t lg_table_[256]= {
|
||||
-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
|
||||
5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
|
||||
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
|
||||
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
|
||||
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
||||
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
||||
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
||||
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
|
||||
};
|
||||
|
||||
inline
|
||||
saint_t
|
||||
tr_ilg(saidx_t 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. */
|
||||
void
|
||||
tr_insertionsort(const_saidx_it ISAd, saidx_it first, saidx_it last) {
|
||||
saidx_it a, b;
|
||||
saidx_t t, r;
|
||||
|
||||
for(a = first + 1; a < last; ++a) {
|
||||
for(t = *a, b = a - 1; 0 > (r = ISAd[t] - ISAd[*b]);) {
|
||||
do { *(b + 1) = *b; } while((first <= --b) && (*b < 0));
|
||||
if(b < first) { break; }
|
||||
}
|
||||
if(r == 0) { *b = ~*b; }
|
||||
*(b + 1) = t;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
inline
|
||||
void
|
||||
tr_fixdown(const_saidx_it ISAd, saidx_it SA, saidx_t i, saidx_t size) {
|
||||
saidx_t j, k;
|
||||
saidx_t v;
|
||||
saidx_t c, d, e;
|
||||
|
||||
for(v = SA[i], c = ISAd[v]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
|
||||
d = ISAd[SA[k = j++]];
|
||||
if(d < (e = ISAd[SA[j]])) { k = j; d = e; }
|
||||
if(d <= c) { break; }
|
||||
}
|
||||
SA[i] = v;
|
||||
}
|
||||
|
||||
/* Simple top-down heapsort. */
|
||||
void
|
||||
tr_heapsort(const_saidx_it ISAd, saidx_it SA, saidx_t size) {
|
||||
saidx_t i, m;
|
||||
saidx_t t;
|
||||
|
||||
m = size;
|
||||
if((size % 2) == 0) {
|
||||
m--;
|
||||
if(ISAd[SA[m / 2]] < ISAd[SA[m]]) { SWAP(SA[m], SA[m / 2]); }
|
||||
}
|
||||
|
||||
for(i = m / 2 - 1; 0 <= i; --i) { tr_fixdown(ISAd, SA, i, m); }
|
||||
if((size % 2) == 0) { SWAP(SA[0], SA[m]); tr_fixdown(ISAd, SA, 0, m); }
|
||||
for(i = m - 1; 0 < i; --i) {
|
||||
t = SA[0], SA[0] = SA[i];
|
||||
tr_fixdown(ISAd, SA, 0, i);
|
||||
SA[i] = t;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
/* Returns the median of three elements. */
|
||||
inline
|
||||
saidx_it
|
||||
tr_median3(const_saidx_it ISAd, saidx_it v1, saidx_it v2, saidx_it v3) {
|
||||
saidx_it 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. */
|
||||
inline
|
||||
saidx_it
|
||||
tr_median5(const_saidx_it ISAd,
|
||||
saidx_it v1, saidx_it v2, saidx_it v3, saidx_it v4, saidx_it v5) {
|
||||
saidx_it 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. */
|
||||
inline
|
||||
saidx_it
|
||||
tr_pivot(const_saidx_it ISAd, saidx_it first, saidx_it last) {
|
||||
saidx_it middle;
|
||||
saidx_t t;
|
||||
|
||||
t = last - first;
|
||||
middle = first + t / 2;
|
||||
|
||||
if(t <= 512) {
|
||||
if(t <= 32) {
|
||||
return tr_median3(ISAd, first, middle, last - 1);
|
||||
} else {
|
||||
t >>= 2;
|
||||
return tr_median5(ISAd, first, first + t, middle, last - 1 - t, last - 1);
|
||||
}
|
||||
}
|
||||
t >>= 3;
|
||||
first = tr_median3(ISAd, first, first + t, first + (t << 1));
|
||||
middle = tr_median3(ISAd, middle - t, middle, middle + t);
|
||||
last = tr_median3(ISAd, last - 1 - (t << 1), last - 1 - t, last - 1);
|
||||
return tr_median3(ISAd, first, middle, last);
|
||||
}
|
||||
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
typedef struct _trbudget_t trbudget_t;
|
||||
struct _trbudget_t {
|
||||
saidx_t chance;
|
||||
saidx_t remain;
|
||||
saidx_t incval;
|
||||
saidx_t count;
|
||||
};
|
||||
|
||||
inline
|
||||
void
|
||||
trbudget_init(trbudget_t *budget, saidx_t chance, saidx_t incval) {
|
||||
budget->chance = chance;
|
||||
budget->remain = budget->incval = incval;
|
||||
}
|
||||
|
||||
inline
|
||||
saint_t
|
||||
trbudget_check(trbudget_t *budget, saidx_t size) {
|
||||
if(size <= budget->remain) { budget->remain -= size; return 1; }
|
||||
if(budget->chance == 0) { budget->count += size; return 0; }
|
||||
budget->remain += budget->incval - size;
|
||||
budget->chance -= 1;
|
||||
return 1;
|
||||
}
|
||||
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
inline
|
||||
void
|
||||
tr_partition(const_saidx_it ISAd,
|
||||
saidx_it first, saidx_it middle, saidx_it last,
|
||||
saidx_it* pa, saidx_it* pb, saidx_t v) {
|
||||
saidx_it a, b, c, d, e, f;
|
||||
saidx_t t, s;
|
||||
saidx_t x = 0;
|
||||
|
||||
for(b = middle - 1; (++b < last) && ((x = ISAd[*b]) == v);) { }
|
||||
if(((a = b) < last) && (x < v)) {
|
||||
for(; (++b < last) && ((x = ISAd[*b]) <= v);) {
|
||||
if(x == v) { SWAP(*b, *a); ++a; }
|
||||
}
|
||||
}
|
||||
for(c = last; (b < --c) && ((x = ISAd[*c]) == v);) { }
|
||||
if((b < (d = c)) && (x > v)) {
|
||||
for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
|
||||
if(x == v) { SWAP(*c, *d); --d; }
|
||||
}
|
||||
}
|
||||
for(; b < c;) {
|
||||
SWAP(*b, *c);
|
||||
for(; (++b < c) && ((x = ISAd[*b]) <= v);) {
|
||||
if(x == v) { SWAP(*b, *a); ++a; }
|
||||
}
|
||||
for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
|
||||
if(x == v) { SWAP(*c, *d); --d; }
|
||||
}
|
||||
}
|
||||
|
||||
if(a <= d) {
|
||||
c = b - 1;
|
||||
if((s = a - first) > (t = b - a)) { s = t; }
|
||||
for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
|
||||
if((s = d - c) > (t = last - d - 1)) { s = t; }
|
||||
for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
|
||||
first += (b - a), last -= (d - c);
|
||||
}
|
||||
*pa = first, *pb = last;
|
||||
}
|
||||
|
||||
void
|
||||
tr_copy(saidx_it ISA, const_saidx_it SA,
|
||||
saidx_it first, saidx_it a, saidx_it b, saidx_it last,
|
||||
saidx_t depth) {
|
||||
/* sort suffixes of middle partition
|
||||
by using sorted order of suffixes of left and right partition. */
|
||||
saidx_it c, d, e;
|
||||
saidx_t s, v;
|
||||
|
||||
v = b - SA - 1;
|
||||
for(c = first, d = a - 1; c <= d; ++c) {
|
||||
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
||||
*++d = s;
|
||||
ISA[s] = d - SA;
|
||||
}
|
||||
}
|
||||
for(c = last - 1, e = d + 1, d = b; e < d; --c) {
|
||||
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
||||
*--d = s;
|
||||
ISA[s] = d - SA;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void
|
||||
tr_partialcopy(saidx_it ISA, const_saidx_it SA,
|
||||
saidx_it first, saidx_it a, saidx_it b, saidx_it last,
|
||||
saidx_t depth) {
|
||||
saidx_it c, d, e;
|
||||
saidx_t s, v;
|
||||
saidx_t rank, lastrank, newrank = -1;
|
||||
|
||||
v = b - SA - 1;
|
||||
lastrank = -1;
|
||||
for(c = first, d = a - 1; c <= d; ++c) {
|
||||
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
||||
*++d = s;
|
||||
rank = ISA[s + depth];
|
||||
if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
|
||||
ISA[s] = newrank;
|
||||
}
|
||||
}
|
||||
|
||||
lastrank = -1;
|
||||
for(e = d; first <= e; --e) {
|
||||
rank = ISA[*e];
|
||||
if(lastrank != rank) { lastrank = rank; newrank = e - SA; }
|
||||
if(newrank != rank) { ISA[*e] = newrank; }
|
||||
}
|
||||
|
||||
lastrank = -1;
|
||||
for(c = last - 1, e = d + 1, d = b; e < d; --c) {
|
||||
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
||||
*--d = s;
|
||||
rank = ISA[s + depth];
|
||||
if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
|
||||
ISA[s] = newrank;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void
|
||||
tr_introsort(saidx_it ISA, const_saidx_it ISAd,
|
||||
saidx_it SA, saidx_it first, saidx_it last,
|
||||
trbudget_t *budget) {
|
||||
#define STACK_SIZE TR_STACKSIZE
|
||||
struct { const_saidx_it a; saidx_it b, c; saint_t d, e; }stack[STACK_SIZE];
|
||||
saidx_it a, b, c;
|
||||
saidx_t t;
|
||||
saidx_t v, x = 0;
|
||||
saidx_t incr = ISAd - ISA;
|
||||
saint_t limit, next;
|
||||
saint_t ssize, trlink = -1;
|
||||
|
||||
for(ssize = 0, limit = tr_ilg(last - first);;) {
|
||||
|
||||
if(limit < 0) {
|
||||
if(limit == -1) {
|
||||
/* tandem repeat partition */
|
||||
tr_partition(ISAd - incr, first, first, last, &a, &b, last - SA - 1);
|
||||
|
||||
/* update ranks */
|
||||
if(a < last) {
|
||||
for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
|
||||
}
|
||||
if(b < last) {
|
||||
for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; }
|
||||
}
|
||||
|
||||
/* push */
|
||||
if(1 < (b - a)) {
|
||||
STACK_PUSH5(nullptr, 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
|
||||
}
|
||||
|
||||
} // namespace
|
||||
|
||||
/*---------------------------------------------------------------------------*/
|
||||
|
||||
/*- Function -*/
|
||||
|
||||
/* Tandem repeat sort */
|
||||
void
|
||||
trsort(saidx_it ISA, saidx_it SA, saidx_t n, saidx_t depth) {
|
||||
saidx_it ISAd;
|
||||
saidx_it 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; }
|
||||
}
|
||||
}
|
||||
|
||||
} // namespace divsuf
|
||||
Loading…
Add table
Add a link
Reference in a new issue