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Change bsdiff to use divsufsort suffix sort library instead of qsufsort,

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which is more efficient.

Note that for now we do not create a separate library for libdivsufsort
because it's not used anywhere else.

Obtained from:	Chromium
MFC after:	2 months
This commit is contained in:
delphij 2016-07-25 03:58:19 +00:00
commit 9c63dcdcf7
14 changed files with 3112 additions and 106 deletions
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# libdivsufsort Change Log
See full changelog at: https://github.com/y-256/libdivsufsort/commits
## [2.0.1] - 2010-11-11
### Fixed
* Wrong variable used in `divbwt` function
* Enclose some string variables with double quotation marks in include/CMakeLists.txt
* Fix typo in include/CMakeLists.txt
## 2.0.0 - 2008-08-23
### Changed
* Switch the build system to [CMake](http://www.cmake.org/)
* Improve the performance of the suffix-sorting algorithm
### Added
* OpenMP support
* 64-bit version of divsufsort
[Unreleased]: https://github.com/y-256/libdivsufsort/compare/2.0.1...HEAD
[2.0.1]: https://github.com/y-256/libdivsufsort/compare/2.0.0...2.0.1

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The MIT License (MIT)
Copyright (c) 2003 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.

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# libdivsufsort
libdivsufsort is a software library that implements a lightweight suffix array construction algorithm.
## News
* 2015-03-21: The project has moved from [Google Code](http://code.google.com/p/libdivsufsort/) to [GitHub](https://github.com/y-256/libdivsufsort)
## Introduction
This library provides a simple and an efficient C API to construct a suffix array and a Burrows-Wheeler transformed string from a given string over a constant-size alphabet.
The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of
the string.
## Build requirements
* An ANSI C Compiler (e.g. GNU GCC)
* [CMake](http://www.cmake.org/ "CMake") version 2.4.2 or newer
* CMake-supported build tool
## Building on GNU/Linux
1. Get the source code from GitHub. You can either
* use git to clone the repository
```
git clone https://github.com/y-256/libdivsufsort.git
```
* or download a [zip file](../../archive/master.zip) directly
2. Create a `build` directory in the package source directory.
```shell
$ cd libdivsufsort
$ mkdir build
$ cd build
```
3. Configure the package for your system.
If you want to install to a different location, change the -DCMAKE_INSTALL_PREFIX option.
```shell
$ cmake -DCMAKE_BUILD_TYPE="Release" \
-DCMAKE_INSTALL_PREFIX="/usr/local" ..
```
4. Compile the package.
```shell
$ make
```
5. (Optional) Install the library and header files.
```shell
$ sudo make install
```
## API
```c
/* Data types */
typedef int32_t saint_t;
typedef int32_t saidx_t;
typedef uint8_t sauchar_t;
/*
* Constructs the suffix array of a given string.
* @param T[0..n-1] The input string.
* @param SA[0..n-1] The output array or 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_t *SA, saidx_t n);
/*
* Constructs the burrows-wheeler transformed string of a given string.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param A[0..n-1] The temporary array. (can be NULL)
* @param n The length of the given string.
* @return The primary index if no error occurred, -1 or -2 otherwise.
*/
saidx_t
divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n);
```
## Example Usage
```c
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <divsufsort.h>
int main() {
// intput data
char *Text = "abracadabra";
int n = strlen(Text);
int i, j;
// allocate
int *SA = (int *)malloc(n * sizeof(int));
// sort
divsufsort((unsigned char *)Text, SA, n);
// output
for(i = 0; i < n; ++i) {
printf("SA[%2d] = %2d: ", i, SA[i]);
for(j = SA[i]; j < n; ++j) {
printf("%c", Text[j]);
}
printf("$\n");
}
// deallocate
free(SA);
return 0;
}
```
See the [examples](examples) directory for a few other examples.
## Benchmarks
See [Benchmarks](https://github.com/y-256/libdivsufsort/blob/wiki/SACA_Benchmarks.md) page for details.
## License
libdivsufsort is released under the [MIT license](LICENSE "MIT license").
> The MIT License (MIT)
>
> Copyright (c) 2003 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.
## Author
* Yuta Mori

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/*
* config.h for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef _CONFIG_H
#define _CONFIG_H 1
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
/** Define to the version of this package. **/
#cmakedefine PROJECT_VERSION_FULL "${PROJECT_VERSION_FULL}"
/** Define to 1 if you have the header files. **/
#cmakedefine HAVE_INTTYPES_H 1
#cmakedefine HAVE_STDDEF_H 1
#cmakedefine HAVE_STDINT_H 1
#cmakedefine HAVE_STDLIB_H 1
#cmakedefine HAVE_STRING_H 1
#cmakedefine HAVE_STRINGS_H 1
#cmakedefine HAVE_MEMORY_H 1
#cmakedefine HAVE_SYS_TYPES_H 1
/** for WinIO **/
#cmakedefine HAVE_IO_H 1
#cmakedefine HAVE_FCNTL_H 1
#cmakedefine HAVE__SETMODE 1
#cmakedefine HAVE_SETMODE 1
#cmakedefine HAVE__FILENO 1
#cmakedefine HAVE_FOPEN_S 1
#cmakedefine HAVE__O_BINARY 1
#ifndef HAVE__SETMODE
# if HAVE_SETMODE
# define _setmode setmode
# define HAVE__SETMODE 1
# endif
# if HAVE__SETMODE && !HAVE__O_BINARY
# define _O_BINARY 0
# define HAVE__O_BINARY 1
# endif
#endif
/** for inline **/
#ifndef INLINE
# define INLINE @INLINE@
#endif
/** for VC++ warning **/
#ifdef _MSC_VER
#pragma warning(disable: 4127)
#endif
#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */
#endif /* _CONFIG_H */

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/*
* divsufsort@W64BIT@.h for libdivsufsort@W64BIT@
* 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.
*/
#ifndef _DIVSUFSORT@W64BIT@_H
#define _DIVSUFSORT@W64BIT@_H 1
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
@INCFILE@
#ifndef DIVSUFSORT_API
# ifdef DIVSUFSORT_BUILD_DLL
# define DIVSUFSORT_API @DIVSUFSORT_EXPORT@
# else
# define DIVSUFSORT_API @DIVSUFSORT_IMPORT@
# endif
#endif
/*- Datatypes -*/
#ifndef SAUCHAR_T
#define SAUCHAR_T
typedef @SAUCHAR_TYPE@ sauchar_t;
#endif /* SAUCHAR_T */
#ifndef SAINT_T
#define SAINT_T
typedef @SAINT32_TYPE@ saint_t;
#endif /* SAINT_T */
#ifndef SAIDX@W64BIT@_T
#define SAIDX@W64BIT@_T
typedef @SAINDEX_TYPE@ saidx@W64BIT@_t;
#endif /* SAIDX@W64BIT@_T */
#ifndef PRIdSAINT_T
#define PRIdSAINT_T @SAINT_PRId@
#endif /* PRIdSAINT_T */
#ifndef PRIdSAIDX@W64BIT@_T
#define PRIdSAIDX@W64BIT@_T @SAINDEX_PRId@
#endif /* PRIdSAIDX@W64BIT@_T */
/*- Prototypes -*/
/**
* Constructs the suffix array of a given 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.
*/
DIVSUFSORT_API
saint_t
divsufsort@W64BIT@(const sauchar_t *T, saidx@W64BIT@_t *SA, saidx@W64BIT@_t n);
/**
* Constructs the burrows-wheeler transformed string of a given string.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param A[0..n-1] The temporary array. (can be NULL)
* @param n The length of the given string.
* @return The primary index if no error occurred, -1 or -2 otherwise.
*/
DIVSUFSORT_API
saidx@W64BIT@_t
divbwt@W64BIT@(const sauchar_t *T, sauchar_t *U, saidx@W64BIT@_t *A, saidx@W64BIT@_t n);
/**
* Returns the version of the divsufsort library.
* @return The version number string.
*/
DIVSUFSORT_API
const char *
divsufsort@W64BIT@_version(void);
/**
* Constructs the burrows-wheeler transformed string of a given string and suffix array.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param SA[0..n-1] The suffix array. (can be NULL)
* @param n The length of the given string.
* @param idx The output primary index.
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
DIVSUFSORT_API
saint_t
bw_transform@W64BIT@(const sauchar_t *T, sauchar_t *U,
saidx@W64BIT@_t *SA /* can NULL */,
saidx@W64BIT@_t n, saidx@W64BIT@_t *idx);
/**
* Inverse BW-transforms a given BWTed string.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param A[0..n-1] The temporary array. (can be NULL)
* @param n The length of the given string.
* @param idx The primary index.
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
DIVSUFSORT_API
saint_t
inverse_bw_transform@W64BIT@(const sauchar_t *T, sauchar_t *U,
saidx@W64BIT@_t *A /* can NULL */,
saidx@W64BIT@_t n, saidx@W64BIT@_t idx);
/**
* Checks the correctness of a given suffix array.
* @param T[0..n-1] The input string.
* @param SA[0..n-1] The input suffix array.
* @param n The length of the given string.
* @param verbose The verbose mode.
* @return 0 if no error occurred.
*/
DIVSUFSORT_API
saint_t
sufcheck@W64BIT@(const sauchar_t *T, const saidx@W64BIT@_t *SA, saidx@W64BIT@_t n, saint_t verbose);
/**
* Search for the pattern P in the string T.
* @param T[0..Tsize-1] The input string.
* @param Tsize The length of the given string.
* @param P[0..Psize-1] The input pattern string.
* @param Psize The length of the given pattern string.
* @param SA[0..SAsize-1] The input suffix array.
* @param SAsize The length of the given suffix array.
* @param idx The output index.
* @return The count of matches if no error occurred, -1 otherwise.
*/
DIVSUFSORT_API
saidx@W64BIT@_t
sa_search@W64BIT@(const sauchar_t *T, saidx@W64BIT@_t Tsize,
const sauchar_t *P, saidx@W64BIT@_t Psize,
const saidx@W64BIT@_t *SA, saidx@W64BIT@_t SAsize,
saidx@W64BIT@_t *left);
/**
* Search for the character c in the string T.
* @param T[0..Tsize-1] The input string.
* @param Tsize The length of the given string.
* @param SA[0..SAsize-1] The input suffix array.
* @param SAsize The length of the given suffix array.
* @param c The input character.
* @param idx The output index.
* @return The count of matches if no error occurred, -1 otherwise.
*/
DIVSUFSORT_API
saidx@W64BIT@_t
sa_simplesearch@W64BIT@(const sauchar_t *T, saidx@W64BIT@_t Tsize,
const saidx@W64BIT@_t *SA, saidx@W64BIT@_t SAsize,
saint_t c, saidx@W64BIT@_t *left);
#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */
#endif /* _DIVSUFSORT@W64BIT@_H */

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/*
* divsufsort_private.h for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef _DIVSUFSORT_PRIVATE_H
#define _DIVSUFSORT_PRIVATE_H 1
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#if HAVE_CONFIG_H
# include "config.h"
#endif
#include <assert.h>
#include <stdio.h>
#if HAVE_STRING_H
# include <string.h>
#endif
#if HAVE_STDLIB_H
# include <stdlib.h>
#endif
#if HAVE_MEMORY_H
# include <memory.h>
#endif
#if HAVE_STDDEF_H
# include <stddef.h>
#endif
#if HAVE_STRINGS_H
# include <strings.h>
#endif
#if HAVE_INTTYPES_H
# include <inttypes.h>
#else
# if HAVE_STDINT_H
# include <stdint.h>
# endif
#endif
#if defined(BUILD_DIVSUFSORT64)
# include "divsufsort64.h"
# ifndef SAIDX_T
# define SAIDX_T
# define saidx_t saidx64_t
# endif /* SAIDX_T */
# ifndef PRIdSAIDX_T
# define PRIdSAIDX_T PRIdSAIDX64_T
# endif /* PRIdSAIDX_T */
# define divsufsort divsufsort64
# define divbwt divbwt64
# define divsufsort_version divsufsort64_version
# define bw_transform bw_transform64
# define inverse_bw_transform inverse_bw_transform64
# define sufcheck sufcheck64
# define sa_search sa_search64
# define sa_simplesearch sa_simplesearch64
# define sssort sssort64
# define trsort trsort64
#else
# include "divsufsort.h"
#endif
/*- 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
/* for divsufsort.c */
#define BUCKET_A_SIZE (ALPHABET_SIZE)
#define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE)
/* for sssort.c */
#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
# if defined(BUILD_DIVSUFSORT64)
# define SS_MISORT_STACKSIZE (96)
# else
# define SS_MISORT_STACKSIZE (64)
# endif
#elif SS_BLOCKSIZE <= 4096
# define SS_MISORT_STACKSIZE (16)
#else
# define SS_MISORT_STACKSIZE (24)
#endif
#if defined(BUILD_DIVSUFSORT64)
# define SS_SMERGE_STACKSIZE (64)
#else
# define SS_SMERGE_STACKSIZE (32)
#endif
/* for trsort.c */
#define TR_INSERTIONSORT_THRESHOLD (8)
#if defined(BUILD_DIVSUFSORT64)
# define TR_STACKSIZE (96)
#else
# define TR_STACKSIZE (64)
#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 */
#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_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_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)
#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)
/* for divsufsort.c */
#define BUCKET_A(_c0) bucket_A[(_c0)]
#if ALPHABET_SIZE == 256
#define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)])
#define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)])
#else
#define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)])
#define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)])
#endif
/*- Private Prototypes -*/
/* sssort.c */
void
sssort(const sauchar_t *Td, const saidx_t *PA,
saidx_t *first, saidx_t *last,
saidx_t *buf, saidx_t bufsize,
saidx_t depth, saidx_t n, saint_t lastsuffix);
/* trsort.c */
void
trsort(saidx_t *ISA, saidx_t *SA, saidx_t n, saidx_t depth);
#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */
#endif /* _DIVSUFSORT_PRIVATE_H */

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/*
* divsufsort.c for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#include "divsufsort_private.h"
#ifdef _OPENMP
# include <omp.h>
#endif
/*- Private Functions -*/
/* Sorts suffixes of type B*. */
static
saidx_t
sort_typeBstar(const sauchar_t *T, saidx_t *SA,
saidx_t *bucket_A, saidx_t *bucket_B,
saidx_t n) {
saidx_t *PAb, *ISAb, *buf;
#ifdef _OPENMP
saidx_t *curbuf;
saidx_t l;
#endif
saidx_t i, j, k, t, m, bufsize;
saint_t c0, c1;
#ifdef _OPENMP
saint_t d0, d1;
int tmp;
#endif
/* 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 _OPENMP
tmp = omp_get_max_threads();
buf = SA + m, bufsize = (n - (2 * m)) / tmp;
c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m;
#pragma omp parallel default(shared) private(curbuf, k, l, d0, d1, tmp)
{
tmp = omp_get_thread_num();
curbuf = buf + tmp * 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));
}
}
}
#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 sauchar_t *T, saidx_t *SA,
saidx_t *bucket_A, saidx_t *bucket_B,
saidx_t n, saidx_t m) {
saidx_t *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 = 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);
*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
saidx_t
construct_BWT(const sauchar_t *T, saidx_t *SA,
saidx_t *bucket_A, saidx_t *bucket_B,
saidx_t n, saidx_t m) {
saidx_t *i, *j, *k, *orig;
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 = 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 = ~((saidx_t)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);
*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) ? ~((saidx_t)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 = ~((saidx_t)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;
}
/*---------------------------------------------------------------------------*/
/*- Function -*/
saint_t
divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n) {
saidx_t *bucket_A, *bucket_B;
saidx_t m;
saint_t 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 = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
/* Suffixsort. */
if((bucket_A != NULL) && (bucket_B != NULL)) {
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;
}
saidx_t
divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n) {
saidx_t *B;
saidx_t *bucket_A, *bucket_B;
saidx_t 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 = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); }
bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
/* Burrows-Wheeler Transform. */
if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
/* Copy to output string. */
U[0] = T[n - 1];
for(i = 0; i < pidx; ++i) { U[i + 1] = (sauchar_t)B[i]; }
for(i += 1; i < n; ++i) { U[i] = (sauchar_t)B[i]; }
pidx += 1;
} else {
pidx = -2;
}
free(bucket_B);
free(bucket_A);
if(A == NULL) { free(B); }
return pidx;
}
const char *
divsufsort_version(void) {
return PROJECT_VERSION_FULL;
}

815
contrib/libdivsufsort/lib/sssort.c Normal file
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@ -0,0 +1,815 @@
/*
* sssort.c for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#include "divsufsort_private.h"
/*- Private Functions -*/
static const saint_t lg_table[256]= {
-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
};
#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
static INLINE
saint_t
ss_ilg(saidx_t n) {
#if SS_BLOCKSIZE == 0
# if defined(BUILD_DIVSUFSORT64)
return (n >> 32) ?
((n >> 48) ?
((n >> 56) ?
56 + lg_table[(n >> 56) & 0xff] :
48 + lg_table[(n >> 48) & 0xff]) :
((n >> 40) ?
40 + lg_table[(n >> 40) & 0xff] :
32 + lg_table[(n >> 32) & 0xff])) :
((n & 0xffff0000) ?
((n & 0xff000000) ?
24 + lg_table[(n >> 24) & 0xff] :
16 + lg_table[(n >> 16) & 0xff]) :
((n & 0x0000ff00) ?
8 + lg_table[(n >> 8) & 0xff] :
0 + lg_table[(n >> 0) & 0xff]));
# else
return (n & 0xffff0000) ?
((n & 0xff000000) ?
24 + lg_table[(n >> 24) & 0xff] :
16 + lg_table[(n >> 16) & 0xff]) :
((n & 0x0000ff00) ?
8 + lg_table[(n >> 8) & 0xff] :
0 + lg_table[(n >> 0) & 0xff]);
# endif
#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
static 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
};
static 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. */
static INLINE
saint_t
ss_compare(const sauchar_t *T,
const saidx_t *p1, const saidx_t *p2,
saidx_t depth) {
const sauchar_t *U1, *U2, *U1n, *U2n;
for(U1 = T + depth + *p1,
U2 = T + depth + *p2,
U1n = T + *(p1 + 1) + 2,
U2n = T + *(p2 + 1) + 2;
(U1 < U1n) && (U2 < U2n) && (*U1 == *U2);
++U1, ++U2) {
}
return U1 < U1n ?
(U2 < U2n ? *U1 - *U2 : 1) :
(U2 < U2n ? -1 : 0);
}
/*---------------------------------------------------------------------------*/
#if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1)
/* Insertionsort for small size groups */
static
void
ss_insertionsort(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *last, saidx_t depth) {
saidx_t *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)
static INLINE
void
ss_fixdown(const sauchar_t *Td, const saidx_t *PA,
saidx_t *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. */
static
void
ss_heapsort(const sauchar_t *Td, const saidx_t *PA, saidx_t *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. */
static INLINE
saidx_t *
ss_median3(const sauchar_t *Td, const saidx_t *PA,
saidx_t *v1, saidx_t *v2, saidx_t *v3) {
saidx_t *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. */
static INLINE
saidx_t *
ss_median5(const sauchar_t *Td, const saidx_t *PA,
saidx_t *v1, saidx_t *v2, saidx_t *v3, saidx_t *v4, saidx_t *v5) {
saidx_t *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. */
static INLINE
saidx_t *
ss_pivot(const sauchar_t *Td, const saidx_t *PA, saidx_t *first, saidx_t *last) {
saidx_t *middle;
saidx_t t;
t = last - first;
middle = first + t / 2;
if(t <= 512) {
if(t <= 32) {
return 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. */
static INLINE
saidx_t *
ss_partition(const saidx_t *PA,
saidx_t *first, saidx_t *last, saidx_t depth) {
saidx_t *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. */
static
void
ss_mintrosort(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *last,
saidx_t depth) {
#define STACK_SIZE SS_MISORT_STACKSIZE
struct { saidx_t *a, *b, c; saint_t d; } stack[STACK_SIZE];
const sauchar_t *Td;
saidx_t *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
static INLINE
void
ss_blockswap(saidx_t *a, saidx_t *b, saidx_t n) {
saidx_t t;
for(; 0 < n; --n, ++a, ++b) {
t = *a, *a = *b, *b = t;
}
}
static INLINE
void
ss_rotate(saidx_t *first, saidx_t *middle, saidx_t *last) {
saidx_t *a, *b, 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);
}
}
}
/*---------------------------------------------------------------------------*/
static
void
ss_inplacemerge(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *middle, saidx_t *last,
saidx_t depth) {
const saidx_t *p;
saidx_t *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_t *PA,
saidx_t *first, saidx_t *middle, saidx_t *last,
saidx_t *buf, saidx_t depth) {
saidx_t *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. */
static
void
ss_mergebackward(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *middle, saidx_t *last,
saidx_t *buf, saidx_t depth) {
const saidx_t *p1, *p2;
saidx_t *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. */
static
void
ss_swapmerge(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *middle, saidx_t *last,
saidx_t *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_t *a, *b, *c; saint_t d; } stack[STACK_SIZE];
saidx_t *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 */
/*---------------------------------------------------------------------------*/
/*- Function -*/
/* Substring sort */
void
sssort(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *last,
saidx_t *buf, saidx_t bufsize,
saidx_t depth, saidx_t n, saint_t lastsuffix) {
saidx_t *a;
#if SS_BLOCKSIZE != 0
saidx_t *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. */
saidx_t 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;
}
}

586
contrib/libdivsufsort/lib/trsort.c Normal file
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@ -0,0 +1,586 @@
/*
* trsort.c for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#include "divsufsort_private.h"
/*- Private Functions -*/
static const saint_t lg_table[256]= {
-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
};
static INLINE
saint_t
tr_ilg(saidx_t n) {
#if defined(BUILD_DIVSUFSORT64)
return (n >> 32) ?
((n >> 48) ?
((n >> 56) ?
56 + lg_table[(n >> 56) & 0xff] :
48 + lg_table[(n >> 48) & 0xff]) :
((n >> 40) ?
40 + lg_table[(n >> 40) & 0xff] :
32 + lg_table[(n >> 32) & 0xff])) :
((n & 0xffff0000) ?
((n & 0xff000000) ?
24 + lg_table[(n >> 24) & 0xff] :
16 + lg_table[(n >> 16) & 0xff]) :
((n & 0x0000ff00) ?
8 + lg_table[(n >> 8) & 0xff] :
0 + lg_table[(n >> 0) & 0xff]));
#else
return (n & 0xffff0000) ?
((n & 0xff000000) ?
24 + lg_table[(n >> 24) & 0xff] :
16 + lg_table[(n >> 16) & 0xff]) :
((n & 0x0000ff00) ?
8 + lg_table[(n >> 8) & 0xff] :
0 + lg_table[(n >> 0) & 0xff]);
#endif
}
/*---------------------------------------------------------------------------*/
/* Simple insertionsort for small size groups. */
static
void
tr_insertionsort(const saidx_t *ISAd, saidx_t *first, saidx_t *last) {
saidx_t *a, *b;
saidx_t t, r;
for(a = first + 1; a < last; ++a) {
for(t = *a, b = a - 1; 0 > (r = ISAd[t] - ISAd[*b]);) {
do { *(b + 1) = *b; } while((first <= --b) && (*b < 0));
if(b < first) { break; }
}
if(r == 0) { *b = ~*b; }
*(b + 1) = t;
}
}
/*---------------------------------------------------------------------------*/
static INLINE
void
tr_fixdown(const saidx_t *ISAd, saidx_t *SA, saidx_t i, saidx_t size) {
saidx_t j, k;
saidx_t v;
saidx_t c, d, e;
for(v = SA[i], c = ISAd[v]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
d = ISAd[SA[k = j++]];
if(d < (e = ISAd[SA[j]])) { k = j; d = e; }
if(d <= c) { break; }
}
SA[i] = v;
}
/* Simple top-down heapsort. */
static
void
tr_heapsort(const saidx_t *ISAd, saidx_t *SA, saidx_t size) {
saidx_t i, m;
saidx_t t;
m = size;
if((size % 2) == 0) {
m--;
if(ISAd[SA[m / 2]] < ISAd[SA[m]]) { SWAP(SA[m], SA[m / 2]); }
}
for(i = m / 2 - 1; 0 <= i; --i) { tr_fixdown(ISAd, SA, i, m); }
if((size % 2) == 0) { SWAP(SA[0], SA[m]); tr_fixdown(ISAd, SA, 0, m); }
for(i = m - 1; 0 < i; --i) {
t = SA[0], SA[0] = SA[i];
tr_fixdown(ISAd, SA, 0, i);
SA[i] = t;
}
}
/*---------------------------------------------------------------------------*/
/* Returns the median of three elements. */
static INLINE
saidx_t *
tr_median3(const saidx_t *ISAd, saidx_t *v1, saidx_t *v2, saidx_t *v3) {
saidx_t *t;
if(ISAd[*v1] > ISAd[*v2]) { SWAP(v1, v2); }
if(ISAd[*v2] > ISAd[*v3]) {
if(ISAd[*v1] > ISAd[*v3]) { return v1; }
else { return v3; }
}
return v2;
}
/* Returns the median of five elements. */
static INLINE
saidx_t *
tr_median5(const saidx_t *ISAd,
saidx_t *v1, saidx_t *v2, saidx_t *v3, saidx_t *v4, saidx_t *v5) {
saidx_t *t;
if(ISAd[*v2] > ISAd[*v3]) { SWAP(v2, v3); }
if(ISAd[*v4] > ISAd[*v5]) { SWAP(v4, v5); }
if(ISAd[*v2] > ISAd[*v4]) { SWAP(v2, v4); SWAP(v3, v5); }
if(ISAd[*v1] > ISAd[*v3]) { SWAP(v1, v3); }
if(ISAd[*v1] > ISAd[*v4]) { SWAP(v1, v4); SWAP(v3, v5); }
if(ISAd[*v3] > ISAd[*v4]) { return v4; }
return v3;
}
/* Returns the pivot element. */
static INLINE
saidx_t *
tr_pivot(const saidx_t *ISAd, saidx_t *first, saidx_t *last) {
saidx_t *middle;
saidx_t t;
t = last - first;
middle = first + t / 2;
if(t <= 512) {
if(t <= 32) {
return tr_median3(ISAd, first, middle, last - 1);
} else {
t >>= 2;
return tr_median5(ISAd, first, first + t, middle, last - 1 - t, last - 1);
}
}
t >>= 3;
first = tr_median3(ISAd, first, first + t, first + (t << 1));
middle = tr_median3(ISAd, middle - t, middle, middle + t);
last = tr_median3(ISAd, last - 1 - (t << 1), last - 1 - t, last - 1);
return tr_median3(ISAd, first, middle, last);
}
/*---------------------------------------------------------------------------*/
typedef struct _trbudget_t trbudget_t;
struct _trbudget_t {
saidx_t chance;
saidx_t remain;
saidx_t incval;
saidx_t count;
};
static INLINE
void
trbudget_init(trbudget_t *budget, saidx_t chance, saidx_t incval) {
budget->chance = chance;
budget->remain = budget->incval = incval;
}
static INLINE
saint_t
trbudget_check(trbudget_t *budget, saidx_t size) {
if(size <= budget->remain) { budget->remain -= size; return 1; }
if(budget->chance == 0) { budget->count += size; return 0; }
budget->remain += budget->incval - size;
budget->chance -= 1;
return 1;
}
/*---------------------------------------------------------------------------*/
static INLINE
void
tr_partition(const saidx_t *ISAd,
saidx_t *first, saidx_t *middle, saidx_t *last,
saidx_t **pa, saidx_t **pb, saidx_t v) {
saidx_t *a, *b, *c, *d, *e, *f;
saidx_t t, s;
saidx_t x = 0;
for(b = middle - 1; (++b < last) && ((x = ISAd[*b]) == v);) { }
if(((a = b) < last) && (x < v)) {
for(; (++b < last) && ((x = ISAd[*b]) <= v);) {
if(x == v) { SWAP(*b, *a); ++a; }
}
}
for(c = last; (b < --c) && ((x = ISAd[*c]) == v);) { }
if((b < (d = c)) && (x > v)) {
for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
if(x == v) { SWAP(*c, *d); --d; }
}
}
for(; b < c;) {
SWAP(*b, *c);
for(; (++b < c) && ((x = ISAd[*b]) <= v);) {
if(x == v) { SWAP(*b, *a); ++a; }
}
for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
if(x == v) { SWAP(*c, *d); --d; }
}
}
if(a <= d) {
c = b - 1;
if((s = a - first) > (t = b - a)) { s = t; }
for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
if((s = d - c) > (t = last - d - 1)) { s = t; }
for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
first += (b - a), last -= (d - c);
}
*pa = first, *pb = last;
}
static
void
tr_copy(saidx_t *ISA, const saidx_t *SA,
saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last,
saidx_t depth) {
/* sort suffixes of middle partition
by using sorted order of suffixes of left and right partition. */
saidx_t *c, *d, *e;
saidx_t s, v;
v = b - SA - 1;
for(c = first, d = a - 1; c <= d; ++c) {
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
*++d = s;
ISA[s] = d - SA;
}
}
for(c = last - 1, e = d + 1, d = b; e < d; --c) {
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
*--d = s;
ISA[s] = d - SA;
}
}
}
static
void
tr_partialcopy(saidx_t *ISA, const saidx_t *SA,
saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last,
saidx_t depth) {
saidx_t *c, *d, *e;
saidx_t s, v;
saidx_t rank, lastrank, newrank = -1;
v = b - SA - 1;
lastrank = -1;
for(c = first, d = a - 1; c <= d; ++c) {
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
*++d = s;
rank = ISA[s + depth];
if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
ISA[s] = newrank;
}
}
lastrank = -1;
for(e = d; first <= e; --e) {
rank = ISA[*e];
if(lastrank != rank) { lastrank = rank; newrank = e - SA; }
if(newrank != rank) { ISA[*e] = newrank; }
}
lastrank = -1;
for(c = last - 1, e = d + 1, d = b; e < d; --c) {
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
*--d = s;
rank = ISA[s + depth];
if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
ISA[s] = newrank;
}
}
}
static
void
tr_introsort(saidx_t *ISA, const saidx_t *ISAd,
saidx_t *SA, saidx_t *first, saidx_t *last,
trbudget_t *budget) {
#define STACK_SIZE TR_STACKSIZE
struct { const saidx_t *a; saidx_t *b, *c; saint_t d, e; }stack[STACK_SIZE];
saidx_t *a, *b, *c;
saidx_t t;
saidx_t v, x = 0;
saidx_t incr = ISAd - ISA;
saint_t limit, next;
saint_t ssize, trlink = -1;
for(ssize = 0, limit = tr_ilg(last - first);;) {
if(limit < 0) {
if(limit == -1) {
/* tandem repeat partition */
tr_partition(ISAd - incr, first, first, last, &a, &b, last - SA - 1);
/* update ranks */
if(a < last) {
for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
}
if(b < last) {
for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; }
}
/* push */
if(1 < (b - a)) {
STACK_PUSH5(NULL, a, b, 0, 0);
STACK_PUSH5(ISAd - incr, first, last, -2, trlink);
trlink = ssize - 2;
}
if((a - first) <= (last - b)) {
if(1 < (a - first)) {
STACK_PUSH5(ISAd, b, last, tr_ilg(last - b), trlink);
last = a, limit = tr_ilg(a - first);
} else if(1 < (last - b)) {
first = b, limit = tr_ilg(last - b);
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
} else {
if(1 < (last - b)) {
STACK_PUSH5(ISAd, first, a, tr_ilg(a - first), trlink);
first = b, limit = tr_ilg(last - b);
} else if(1 < (a - first)) {
last = a, limit = tr_ilg(a - first);
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
}
} else if(limit == -2) {
/* tandem repeat copy */
a = stack[--ssize].b, b = stack[ssize].c;
if(stack[ssize].d == 0) {
tr_copy(ISA, SA, first, a, b, last, ISAd - ISA);
} else {
if(0 <= trlink) { stack[trlink].d = -1; }
tr_partialcopy(ISA, SA, first, a, b, last, ISAd - ISA);
}
STACK_POP5(ISAd, first, last, limit, trlink);
} else {
/* sorted partition */
if(0 <= *first) {
a = first;
do { ISA[*a] = a - SA; } while((++a < last) && (0 <= *a));
first = a;
}
if(first < last) {
a = first; do { *a = ~*a; } while(*++a < 0);
next = (ISA[*a] != ISAd[*a]) ? tr_ilg(a - first + 1) : -1;
if(++a < last) { for(b = first, v = a - SA - 1; b < a; ++b) { ISA[*b] = v; } }
/* push */
if(trbudget_check(budget, a - first)) {
if((a - first) <= (last - a)) {
STACK_PUSH5(ISAd, a, last, -3, trlink);
ISAd += incr, last = a, limit = next;
} else {
if(1 < (last - a)) {
STACK_PUSH5(ISAd + incr, first, a, next, trlink);
first = a, limit = -3;
} else {
ISAd += incr, last = a, limit = next;
}
}
} else {
if(0 <= trlink) { stack[trlink].d = -1; }
if(1 < (last - a)) {
first = a, limit = -3;
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
}
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
}
continue;
}
if((last - first) <= TR_INSERTIONSORT_THRESHOLD) {
tr_insertionsort(ISAd, first, last);
limit = -3;
continue;
}
if(limit-- == 0) {
tr_heapsort(ISAd, first, last - first);
for(a = last - 1; first < a; a = b) {
for(x = ISAd[*a], b = a - 1; (first <= b) && (ISAd[*b] == x); --b) { *b = ~*b; }
}
limit = -3;
continue;
}
/* choose pivot */
a = tr_pivot(ISAd, first, last);
SWAP(*first, *a);
v = ISAd[*first];
/* partition */
tr_partition(ISAd, first, first + 1, last, &a, &b, v);
if((last - first) != (b - a)) {
next = (ISA[*a] != v) ? tr_ilg(b - a) : -1;
/* update ranks */
for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
if(b < last) { for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; } }
/* push */
if((1 < (b - a)) && (trbudget_check(budget, b - a))) {
if((a - first) <= (last - b)) {
if((last - b) <= (b - a)) {
if(1 < (a - first)) {
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
STACK_PUSH5(ISAd, b, last, limit, trlink);
last = a;
} else if(1 < (last - b)) {
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
first = b;
} else {
ISAd += incr, first = a, last = b, limit = next;
}
} else if((a - first) <= (b - a)) {
if(1 < (a - first)) {
STACK_PUSH5(ISAd, b, last, limit, trlink);
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
last = a;
} else {
STACK_PUSH5(ISAd, b, last, limit, trlink);
ISAd += incr, first = a, last = b, limit = next;
}
} else {
STACK_PUSH5(ISAd, b, last, limit, trlink);
STACK_PUSH5(ISAd, first, a, limit, trlink);
ISAd += incr, first = a, last = b, limit = next;
}
} else {
if((a - first) <= (b - a)) {
if(1 < (last - b)) {
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
STACK_PUSH5(ISAd, first, a, limit, trlink);
first = b;
} else if(1 < (a - first)) {
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
last = a;
} else {
ISAd += incr, first = a, last = b, limit = next;
}
} else if((last - b) <= (b - a)) {
if(1 < (last - b)) {
STACK_PUSH5(ISAd, first, a, limit, trlink);
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
first = b;
} else {
STACK_PUSH5(ISAd, first, a, limit, trlink);
ISAd += incr, first = a, last = b, limit = next;
}
} else {
STACK_PUSH5(ISAd, first, a, limit, trlink);
STACK_PUSH5(ISAd, b, last, limit, trlink);
ISAd += incr, first = a, last = b, limit = next;
}
}
} else {
if((1 < (b - a)) && (0 <= trlink)) { stack[trlink].d = -1; }
if((a - first) <= (last - b)) {
if(1 < (a - first)) {
STACK_PUSH5(ISAd, b, last, limit, trlink);
last = a;
} else if(1 < (last - b)) {
first = b;
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
} else {
if(1 < (last - b)) {
STACK_PUSH5(ISAd, first, a, limit, trlink);
first = b;
} else if(1 < (a - first)) {
last = a;
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
}
}
} else {
if(trbudget_check(budget, last - first)) {
limit = tr_ilg(last - first), ISAd += incr;
} else {
if(0 <= trlink) { stack[trlink].d = -1; }
STACK_POP5(ISAd, first, last, limit, trlink);
}
}
}
#undef STACK_SIZE
}
/*---------------------------------------------------------------------------*/
/*- Function -*/
/* Tandem repeat sort */
void
trsort(saidx_t *ISA, saidx_t *SA, saidx_t n, saidx_t depth) {
saidx_t *ISAd;
saidx_t *first, *last;
trbudget_t budget;
saidx_t t, skip, unsorted;
trbudget_init(&budget, tr_ilg(n) * 2 / 3, n);
/* trbudget_init(&budget, tr_ilg(n) * 3 / 4, n); */
for(ISAd = ISA + depth; -n < *SA; ISAd += ISAd - ISA) {
first = SA;
skip = 0;
unsorted = 0;
do {
if((t = *first) < 0) { first -= t; skip += t; }
else {
if(skip != 0) { *(first + skip) = skip; skip = 0; }
last = SA + ISA[t] + 1;
if(1 < (last - first)) {
budget.count = 0;
tr_introsort(ISA, ISAd, SA, first, last, &budget);
if(budget.count != 0) { unsorted += budget.count; }
else { skip = first - last; }
} else if((last - first) == 1) {
skip = -1;
}
first = last;
}
} while(first < (SA + n));
if(skip != 0) { *(first + skip) = skip; }
if(unsorted == 0) { break; }
}
}

381
contrib/libdivsufsort/lib/utils.c Normal file
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@ -0,0 +1,381 @@
/*
* utils.c for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#include "divsufsort_private.h"
/*- Private Function -*/
/* Binary search for inverse bwt. */
static
saidx_t
binarysearch_lower(const saidx_t *A, saidx_t size, saidx_t value) {
saidx_t half, i;
for(i = 0, half = size >> 1;
0 < size;
size = half, half >>= 1) {
if(A[i + half] < value) {
i += half + 1;
half -= (size & 1) ^ 1;
}
}
return i;
}
/*- Functions -*/
/* Burrows-Wheeler transform. */
saint_t
bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *SA,
saidx_t n, saidx_t *idx) {
saidx_t *A, i, j, p, t;
saint_t c;
/* Check arguments. */
if((T == NULL) || (U == NULL) || (n < 0) || (idx == NULL)) { return -1; }
if(n <= 1) {
if(n == 1) { U[0] = T[0]; }
*idx = n;
return 0;
}
if((A = SA) == NULL) {
i = divbwt(T, U, NULL, n);
if(0 <= i) { *idx = i; i = 0; }
return (saint_t)i;
}
/* BW transform. */
if(T == U) {
t = n;
for(i = 0, j = 0; i < n; ++i) {
p = t - 1;
t = A[i];
if(0 <= p) {
c = T[j];
U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
A[j] = c;
j++;
} else {
*idx = i;
}
}
p = t - 1;
if(0 <= p) {
c = T[j];
U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
A[j] = c;
} else {
*idx = i;
}
} else {
U[0] = T[n - 1];
for(i = 0; A[i] != 0; ++i) { U[i + 1] = T[A[i] - 1]; }
*idx = i + 1;
for(++i; i < n; ++i) { U[i] = T[A[i] - 1]; }
}
if(SA == NULL) {
/* Deallocate memory. */
free(A);
}
return 0;
}
/* Inverse Burrows-Wheeler transform. */
saint_t
inverse_bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *A,
saidx_t n, saidx_t idx) {
saidx_t C[ALPHABET_SIZE];
sauchar_t D[ALPHABET_SIZE];
saidx_t *B;
saidx_t i, p;
saint_t c, d;
/* Check arguments. */
if((T == NULL) || (U == NULL) || (n < 0) || (idx < 0) ||
(n < idx) || ((0 < n) && (idx == 0))) {
return -1;
}
if(n <= 1) { return 0; }
if((B = A) == NULL) {
/* Allocate n*sizeof(saidx_t) bytes of memory. */
if((B = (saidx_t *)malloc((size_t)n * sizeof(saidx_t))) == NULL) { return -2; }
}
/* Inverse BW transform. */
for(c = 0; c < ALPHABET_SIZE; ++c) { C[c] = 0; }
for(i = 0; i < n; ++i) { ++C[T[i]]; }
for(c = 0, d = 0, i = 0; c < ALPHABET_SIZE; ++c) {
p = C[c];
if(0 < p) {
C[c] = i;
D[d++] = (sauchar_t)c;
i += p;
}
}
for(i = 0; i < idx; ++i) { B[C[T[i]]++] = i; }
for( ; i < n; ++i) { B[C[T[i]]++] = i + 1; }
for(c = 0; c < d; ++c) { C[c] = C[D[c]]; }
for(i = 0, p = idx; i < n; ++i) {
U[i] = D[binarysearch_lower(C, d, p)];
p = B[p - 1];
}
if(A == NULL) {
/* Deallocate memory. */
free(B);
}
return 0;
}
/* Checks the suffix array SA of the string T. */
saint_t
sufcheck(const sauchar_t *T, const saidx_t *SA,
saidx_t n, saint_t verbose) {
saidx_t C[ALPHABET_SIZE];
saidx_t i, p, q, t;
saint_t c;
if(verbose) { fprintf(stderr, "sufcheck: "); }
/* Check arguments. */
if((T == NULL) || (SA == NULL) || (n < 0)) {
if(verbose) { fprintf(stderr, "Invalid arguments.\n"); }
return -1;
}
if(n == 0) {
if(verbose) { fprintf(stderr, "Done.\n"); }
return 0;
}
/* check range: [0..n-1] */
for(i = 0; i < n; ++i) {
if((SA[i] < 0) || (n <= SA[i])) {
if(verbose) {
fprintf(stderr, "Out of the range [0,%" PRIdSAIDX_T "].\n"
" SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
n - 1, i, SA[i]);
}
return -2;
}
}
/* check first characters. */
for(i = 1; i < n; ++i) {
if(T[SA[i - 1]] > T[SA[i]]) {
if(verbose) {
fprintf(stderr, "Suffixes in wrong order.\n"
" T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d"
" > T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d\n",
i - 1, SA[i - 1], T[SA[i - 1]], i, SA[i], T[SA[i]]);
}
return -3;
}
}
/* check suffixes. */
for(i = 0; i < ALPHABET_SIZE; ++i) { C[i] = 0; }
for(i = 0; i < n; ++i) { ++C[T[i]]; }
for(i = 0, p = 0; i < ALPHABET_SIZE; ++i) {
t = C[i];
C[i] = p;
p += t;
}
q = C[T[n - 1]];
C[T[n - 1]] += 1;
for(i = 0; i < n; ++i) {
p = SA[i];
if(0 < p) {
c = T[--p];
t = C[c];
} else {
c = T[p = n - 1];
t = q;
}
if((t < 0) || (p != SA[t])) {
if(verbose) {
fprintf(stderr, "Suffix in wrong position.\n"
" SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T " or\n"
" SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
t, (0 <= t) ? SA[t] : -1, i, SA[i]);
}
return -4;
}
if(t != q) {
++C[c];
if((n <= C[c]) || (T[SA[C[c]]] != c)) { C[c] = -1; }
}
}
if(1 <= verbose) { fprintf(stderr, "Done.\n"); }
return 0;
}
static
int
_compare(const sauchar_t *T, saidx_t Tsize,
const sauchar_t *P, saidx_t Psize,
saidx_t suf, saidx_t *match) {
saidx_t i, j;
saint_t r;
for(i = suf + *match, j = *match, r = 0;
(i < Tsize) && (j < Psize) && ((r = T[i] - P[j]) == 0); ++i, ++j) { }
*match = j;
return (r == 0) ? -(j != Psize) : r;
}
/* Search for the pattern P in the string T. */
saidx_t
sa_search(const sauchar_t *T, saidx_t Tsize,
const sauchar_t *P, saidx_t Psize,
const saidx_t *SA, saidx_t SAsize,
saidx_t *idx) {
saidx_t size, lsize, rsize, half;
saidx_t match, lmatch, rmatch;
saidx_t llmatch, lrmatch, rlmatch, rrmatch;
saidx_t i, j, k;
saint_t r;
if(idx != NULL) { *idx = -1; }
if((T == NULL) || (P == NULL) || (SA == NULL) ||
(Tsize < 0) || (Psize < 0) || (SAsize < 0)) { return -1; }
if((Tsize == 0) || (SAsize == 0)) { return 0; }
if(Psize == 0) { if(idx != NULL) { *idx = 0; } return SAsize; }
for(i = j = k = 0, lmatch = rmatch = 0, size = SAsize, half = size >> 1;
0 < size;
size = half, half >>= 1) {
match = MIN(lmatch, rmatch);
r = _compare(T, Tsize, P, Psize, SA[i + half], &match);
if(r < 0) {
i += half + 1;
half -= (size & 1) ^ 1;
lmatch = match;
} else if(r > 0) {
rmatch = match;
} else {
lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
/* left part */
for(llmatch = lmatch, lrmatch = match, half = lsize >> 1;
0 < lsize;
lsize = half, half >>= 1) {
lmatch = MIN(llmatch, lrmatch);
r = _compare(T, Tsize, P, Psize, SA[j + half], &lmatch);
if(r < 0) {
j += half + 1;
half -= (lsize & 1) ^ 1;
llmatch = lmatch;
} else {
lrmatch = lmatch;
}
}
/* right part */
for(rlmatch = match, rrmatch = rmatch, half = rsize >> 1;
0 < rsize;
rsize = half, half >>= 1) {
rmatch = MIN(rlmatch, rrmatch);
r = _compare(T, Tsize, P, Psize, SA[k + half], &rmatch);
if(r <= 0) {
k += half + 1;
half -= (rsize & 1) ^ 1;
rlmatch = rmatch;
} else {
rrmatch = rmatch;
}
}
break;
}
}
if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
return k - j;
}
/* Search for the character c in the string T. */
saidx_t
sa_simplesearch(const sauchar_t *T, saidx_t Tsize,
const saidx_t *SA, saidx_t SAsize,
saint_t c, saidx_t *idx) {
saidx_t size, lsize, rsize, half;
saidx_t i, j, k, p;
saint_t r;
if(idx != NULL) { *idx = -1; }
if((T == NULL) || (SA == NULL) || (Tsize < 0) || (SAsize < 0)) { return -1; }
if((Tsize == 0) || (SAsize == 0)) { return 0; }
for(i = j = k = 0, size = SAsize, half = size >> 1;
0 < size;
size = half, half >>= 1) {
p = SA[i + half];
r = (p < Tsize) ? T[p] - c : -1;
if(r < 0) {
i += half + 1;
half -= (size & 1) ^ 1;
} else if(r == 0) {
lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
/* left part */
for(half = lsize >> 1;
0 < lsize;
lsize = half, half >>= 1) {
p = SA[j + half];
r = (p < Tsize) ? T[p] - c : -1;
if(r < 0) {
j += half + 1;
half -= (lsize & 1) ^ 1;
}
}
/* right part */
for(half = rsize >> 1;
0 < rsize;
rsize = half, half >>= 1) {
p = SA[k + half];
r = (p < Tsize) ? T[p] - c : -1;
if(r <= 0) {
k += half + 1;
half -= (rsize & 1) ^ 1;
}
}
break;
}
}
if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
return k - j;
}

13
usr.bin/bsdiff/bsdiff/Makefile
View File

@ -1,6 +1,17 @@
# $FreeBSD$
PROG= bsdiff
PROG= bsdiff
# libdivsufsort configured with:
# cmake -DCMAKE_BUILD_TYPE="Release" -DBUILD_DIVSUFSORT64=ON
.PATH: ${.CURDIR}/../../../contrib/libdivsufsort/lib
CFLAGS+= -DHAVE_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
CFLAGS+= -D_LARGE_FILES -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS
CFLAGS+= -D__STDC_LIMIT_MACROS -DBUILD_DIVSUFSORT64
CFLAGS+= -I${.CURDIR}/../../../contrib/libdivsufsort/include -I${.CURDIR}
SRCS= divsufsort.c sssort.c trsort.c utils.c
SRCS+= bsdiff.c
LIBADD= bz2

112
usr.bin/bsdiff/bsdiff/bsdiff.c
View File

@ -44,107 +44,12 @@ __FBSDID("$FreeBSD$");
#define O_BINARY 0
#endif
#include "divsufsort64.h"
#define saidx_t saidx64_t
#define divsufsort divsufsort64
#define MIN(x,y) (((x)<(y)) ? (x) : (y))
static void split(off_t *I,off_t *V,off_t start,off_t len,off_t h)
{
off_t i,j,k,x,tmp,jj,kk;
if(len<16) {
for(k=start;k<start+len;k+=j) {
j=1;x=V[I[k]+h];
for(i=1;k+i<start+len;i++) {
if(V[I[k+i]+h]<x) {
x=V[I[k+i]+h];
j=0;
}
if(V[I[k+i]+h]==x) {
tmp=I[k+j];I[k+j]=I[k+i];I[k+i]=tmp;
j++;
}
}
for(i=0;i<j;i++) V[I[k+i]]=k+j-1;
if(j==1) I[k]=-1;
}
return;
}
x=V[I[start+len/2]+h];
jj=0;kk=0;
for(i=start;i<start+len;i++) {
if(V[I[i]+h]<x) jj++;
if(V[I[i]+h]==x) kk++;
}
jj+=start;kk+=jj;
i=start;j=0;k=0;
while(i<jj) {
if(V[I[i]+h]<x) {
i++;
} else if(V[I[i]+h]==x) {
tmp=I[i];I[i]=I[jj+j];I[jj+j]=tmp;
j++;
} else {
tmp=I[i];I[i]=I[kk+k];I[kk+k]=tmp;
k++;
}
}
while(jj+j<kk) {
if(V[I[jj+j]+h]==x) {
j++;
} else {
tmp=I[jj+j];I[jj+j]=I[kk+k];I[kk+k]=tmp;
k++;
}
}
if(jj>start) split(I,V,start,jj-start,h);
for(i=0;i<kk-jj;i++) V[I[jj+i]]=kk-1;
if(jj==kk-1) I[jj]=-1;
if(start+len>kk) split(I,V,kk,start+len-kk,h);
}
static void qsufsort(off_t *I,off_t *V,u_char *old,off_t oldsize)
{
off_t buckets[256];
off_t i,h,len;
for(i=0;i<256;i++) buckets[i]=0;
for(i=0;i<oldsize;i++) buckets[old[i]]++;
for(i=1;i<256;i++) buckets[i]+=buckets[i-1];
for(i=255;i>0;i--) buckets[i]=buckets[i-1];
buckets[0]=0;
for(i=0;i<oldsize;i++) I[++buckets[old[i]]]=i;
I[0]=oldsize;
for(i=0;i<oldsize;i++) V[i]=buckets[old[i]];
V[oldsize]=0;
for(i=1;i<256;i++) if(buckets[i]==buckets[i-1]+1) I[buckets[i]]=-1;
I[0]=-1;
for(h=1;I[0]!=-(oldsize+1);h+=h) {
len=0;
for(i=0;i<oldsize+1;) {
if(I[i]<0) {
len-=I[i];
i-=I[i];
} else {
if(len) I[i-len]=-len;
len=V[I[i]]+1-i;
split(I,V,i,len,h);
i+=len;
len=0;
}
}
if(len) I[i-len]=-len;
}
for(i=0;i<oldsize+1;i++) I[V[i]]=i;
}
static off_t matchlen(u_char *old,off_t oldsize,u_char *new,off_t newsize)
{
off_t i;
@ -212,7 +117,7 @@ int main(int argc,char *argv[])
int fd;
u_char *old,*new;
off_t oldsize,newsize;
off_t *I,*V;
saidx_t *I;
off_t scan,pos,len;
off_t lastscan,lastpos,lastoffset;
off_t oldscore,scsc;
@ -248,12 +153,9 @@ int main(int argc,char *argv[])
(read(fd,old,oldsize)!=oldsize) ||
(close(fd)==-1)) err(1,"%s",argv[1]);
if(((I=malloc((oldsize+1)*sizeof(off_t)))==NULL) ||
((V=malloc((oldsize+1)*sizeof(off_t)))==NULL)) err(1,NULL);
if(((I=malloc((oldsize+1)*sizeof(saidx_t)))==NULL)) err(1,NULL);
qsufsort(I,V,old,oldsize);
free(V);
if(divsufsort(old, I, oldsize)) err(1, "divsufsort");
/* Allocate newsize+1 bytes instead of newsize bytes to ensure
that we never try to malloc(0) and get a NULL pointer */

83
usr.bin/bsdiff/bsdiff/config.h Normal file
View File

@ -0,0 +1,83 @@
/*
* config.h for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*
* $FreeBSD$
*/
#ifndef _CONFIG_H
#define _CONFIG_H 1
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
/** Define to the version of this package. **/
#define PROJECT_VERSION_FULL "2.0.1-14-g5f60d6f"
/** Define to 1 if you have the header files. **/
#define HAVE_INTTYPES_H 1
#define HAVE_STDDEF_H 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_STRINGS_H 1
#define HAVE_MEMORY_H 1
#define HAVE_SYS_TYPES_H 1
/** for WinIO **/
/* #undef HAVE_IO_H */
/* #undef HAVE_FCNTL_H */
/* #undef HAVE__SETMODE */
/* #undef HAVE_SETMODE */
/* #undef HAVE__FILENO */
/* #undef HAVE_FOPEN_S */
/* #undef HAVE__O_BINARY */
#ifndef HAVE__SETMODE
# if HAVE_SETMODE
# define _setmode setmode
# define HAVE__SETMODE 1
# endif
# if HAVE__SETMODE && !HAVE__O_BINARY
# define _O_BINARY 0
# define HAVE__O_BINARY 1
# endif
#endif
/** for inline **/
#ifndef INLINE
# define INLINE inline
#endif
/** for VC++ warning **/
#ifdef _MSC_VER
#pragma warning(disable: 4127)
#endif
#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */
#endif /* _CONFIG_H */

180
usr.bin/bsdiff/bsdiff/divsufsort64.h Normal file
View File

@ -0,0 +1,180 @@
/*
* divsufsort64.h for libdivsufsort64
* 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.
*/
#ifndef _DIVSUFSORT64_H
#define _DIVSUFSORT64_H 1
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#include <inttypes.h>
#ifndef DIVSUFSORT_API
# ifdef DIVSUFSORT_BUILD_DLL
# define DIVSUFSORT_API
# else
# define DIVSUFSORT_API
# endif
#endif
/*- Datatypes -*/
#ifndef SAUCHAR_T
#define SAUCHAR_T
typedef uint8_t sauchar_t;
#endif /* SAUCHAR_T */
#ifndef SAINT_T
#define SAINT_T
typedef int32_t saint_t;
#endif /* SAINT_T */
#ifndef SAIDX64_T
#define SAIDX64_T
typedef int64_t saidx64_t;
#endif /* SAIDX64_T */
#ifndef PRIdSAINT_T
#define PRIdSAINT_T PRId32
#endif /* PRIdSAINT_T */
#ifndef PRIdSAIDX64_T
#define PRIdSAIDX64_T PRId64
#endif /* PRIdSAIDX64_T */
/*- Prototypes -*/
/**
* Constructs the suffix array of a given 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.
*/
DIVSUFSORT_API
saint_t
divsufsort64(const sauchar_t *T, saidx64_t *SA, saidx64_t n);
/**
* Constructs the burrows-wheeler transformed string of a given string.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param A[0..n-1] The temporary array. (can be NULL)
* @param n The length of the given string.
* @return The primary index if no error occurred, -1 or -2 otherwise.
*/
DIVSUFSORT_API
saidx64_t
divbwt64(const sauchar_t *T, sauchar_t *U, saidx64_t *A, saidx64_t n);
/**
* Returns the version of the divsufsort library.
* @return The version number string.
*/
DIVSUFSORT_API
const char *
divsufsort64_version(void);
/**
* Constructs the burrows-wheeler transformed string of a given string and suffix array.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param SA[0..n-1] The suffix array. (can be NULL)
* @param n The length of the given string.
* @param idx The output primary index.
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
DIVSUFSORT_API
saint_t
bw_transform64(const sauchar_t *T, sauchar_t *U,
saidx64_t *SA /* can NULL */,
saidx64_t n, saidx64_t *idx);
/**
* Inverse BW-transforms a given BWTed string.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param A[0..n-1] The temporary array. (can be NULL)
* @param n The length of the given string.
* @param idx The primary index.
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
DIVSUFSORT_API
saint_t
inverse_bw_transform64(const sauchar_t *T, sauchar_t *U,
saidx64_t *A /* can NULL */,
saidx64_t n, saidx64_t idx);
/**
* Checks the correctness of a given suffix array.
* @param T[0..n-1] The input string.
* @param SA[0..n-1] The input suffix array.
* @param n The length of the given string.
* @param verbose The verbose mode.
* @return 0 if no error occurred.
*/
DIVSUFSORT_API
saint_t
sufcheck64(const sauchar_t *T, const saidx64_t *SA, saidx64_t n, saint_t verbose);
/**
* Search for the pattern P in the string T.
* @param T[0..Tsize-1] The input string.
* @param Tsize The length of the given string.
* @param P[0..Psize-1] The input pattern string.
* @param Psize The length of the given pattern string.
* @param SA[0..SAsize-1] The input suffix array.
* @param SAsize The length of the given suffix array.
* @param idx The output index.
* @return The count of matches if no error occurred, -1 otherwise.
*/
DIVSUFSORT_API
saidx64_t
sa_search64(const sauchar_t *T, saidx64_t Tsize,
const sauchar_t *P, saidx64_t Psize,
const saidx64_t *SA, saidx64_t SAsize,
saidx64_t *left);
/**
* Search for the character c in the string T.
* @param T[0..Tsize-1] The input string.
* @param Tsize The length of the given string.
* @param SA[0..SAsize-1] The input suffix array.
* @param SAsize The length of the given suffix array.
* @param c The input character.
* @param idx The output index.
* @return The count of matches if no error occurred, -1 otherwise.
*/
DIVSUFSORT_API
saidx64_t
sa_simplesearch64(const sauchar_t *T, saidx64_t Tsize,
const saidx64_t *SA, saidx64_t SAsize,
saint_t c, saidx64_t *left);
#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */
#endif /* _DIVSUFSORT64_H */