Commit 7db3f078 authored by Xin LI's avatar Xin LI
Browse files

Vendor import of libdivsufsort, a software library that implements

a lightweight suffix array construction algorithm.

Obtained from:	https://github.com/y-256/libdivsufsort
parents
# Object files
*.o
*.ko
*.obj
*.elf
# Precompiled Headers
*.gch
*.pch
# Libraries
*.lib
*.a
*.la
*.lo
# Shared objects (inc. Windows DLLs)
*.dll
*.so
*.so.*
*.dylib
# Executables
*.exe
*.out
*.app
*.i*86
*.x86_64
*.hex
# CMake files/directories
build/
# 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
### cmake file for building libdivsufsort Package ###
cmake_minimum_required(VERSION 2.4.4)
set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules")
include(AppendCompilerFlags)
## Project information ##
project(libdivsufsort C)
set(PROJECT_VENDOR "Yuta Mori")
set(PROJECT_CONTACT "yuta.256@gmail.com")
set(PROJECT_URL "https://github.com/y-256/libdivsufsort")
set(PROJECT_DESCRIPTION "A lightweight suffix sorting library")
include(VERSION.cmake)
## CPack configuration ##
set(CPACK_GENERATOR "TGZ;TBZ2;ZIP")
set(CPACK_SOURCE_GENERATOR "TGZ;TBZ2;ZIP")
include(ProjectCPack)
## Project options ##
option(BUILD_SHARED_LIBS "Set to OFF to build static libraries" ON)
option(BUILD_EXAMPLES "Build examples" ON)
option(BUILD_DIVSUFSORT64 "Build libdivsufsort64" OFF)
option(USE_OPENMP "Use OpenMP for parallelization" OFF)
option(WITH_LFS "Enable Large File Support" ON)
## Installation directories ##
set(LIB_SUFFIX "" CACHE STRING "Define suffix of directory name (32 or 64)")
set(CMAKE_INSTALL_RUNTIMEDIR "" CACHE PATH "Specify the output directory for dll runtimes (default is bin)")
if(NOT CMAKE_INSTALL_RUNTIMEDIR)
set(CMAKE_INSTALL_RUNTIMEDIR "${CMAKE_INSTALL_PREFIX}/bin")
endif(NOT CMAKE_INSTALL_RUNTIMEDIR)
set(CMAKE_INSTALL_LIBDIR "" CACHE PATH "Specify the output directory for libraries (default is lib)")
if(NOT CMAKE_INSTALL_LIBDIR)
set(CMAKE_INSTALL_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}")
endif(NOT CMAKE_INSTALL_LIBDIR)
set(CMAKE_INSTALL_INCLUDEDIR "" CACHE PATH "Specify the output directory for header files (default is include)")
if(NOT CMAKE_INSTALL_INCLUDEDIR)
set(CMAKE_INSTALL_INCLUDEDIR "${CMAKE_INSTALL_PREFIX}/include")
endif(NOT CMAKE_INSTALL_INCLUDEDIR)
set(CMAKE_INSTALL_PKGCONFIGDIR "" CACHE PATH "Specify the output directory for pkgconfig files (default is lib/pkgconfig)")
if(NOT CMAKE_INSTALL_PKGCONFIGDIR)
set(CMAKE_INSTALL_PKGCONFIGDIR "${CMAKE_INSTALL_LIBDIR}/pkgconfig")
endif(NOT CMAKE_INSTALL_PKGCONFIGDIR)
## Build type ##
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release")
elseif(CMAKE_BUILD_TYPE STREQUAL "Debug")
set(CMAKE_VERBOSE_MAKEFILE ON)
endif(NOT CMAKE_BUILD_TYPE)
## Compiler options ##
if(MSVC)
append_c_compiler_flags("/W4" "VC" CMAKE_C_FLAGS)
append_c_compiler_flags("/Oi;/Ot;/Ox;/Oy" "VC" CMAKE_C_FLAGS_RELEASE)
if(USE_OPENMP)
append_c_compiler_flags("/openmp" "VC" CMAKE_C_FLAGS)
endif(USE_OPENMP)
elseif(BORLAND)
append_c_compiler_flags("-w" "BCC" CMAKE_C_FLAGS)
append_c_compiler_flags("-Oi;-Og;-Os;-Ov;-Ox" "BCC" CMAKE_C_FLAGS_RELEASE)
else(MSVC)
if(CMAKE_COMPILER_IS_GNUCC)
append_c_compiler_flags("-Wall" "GCC" CMAKE_C_FLAGS)
append_c_compiler_flags("-fomit-frame-pointer" "GCC" CMAKE_C_FLAGS_RELEASE)
if(USE_OPENMP)
append_c_compiler_flags("-fopenmp" "GCC" CMAKE_C_FLAGS)
endif(USE_OPENMP)
else(CMAKE_COMPILER_IS_GNUCC)
append_c_compiler_flags("-Wall" "UNKNOWN" CMAKE_C_FLAGS)
append_c_compiler_flags("-fomit-frame-pointer" "UNKNOWN" CMAKE_C_FLAGS_RELEASE)
if(USE_OPENMP)
append_c_compiler_flags("-fopenmp;-openmp;-omp" "UNKNOWN" CMAKE_C_FLAGS)
endif(USE_OPENMP)
endif(CMAKE_COMPILER_IS_GNUCC)
endif(MSVC)
## Add definitions ##
add_definitions(-DHAVE_CONFIG_H=1 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS)
## Add subdirectories ##
add_subdirectory(pkgconfig)
add_subdirectory(include)
add_subdirectory(lib)
if(BUILD_EXAMPLES)
add_subdirectory(examples)
endif(BUILD_EXAMPLES)
## Add 'uninstall' target ##
CONFIGURE_FILE(
"${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/cmake_uninstall.cmake.in"
"${CMAKE_CURRENT_BINARY_DIR}/CMakeModules/cmake_uninstall.cmake"
IMMEDIATE @ONLY)
ADD_CUSTOM_TARGET(uninstall
"${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/CMakeModules/cmake_uninstall.cmake")
include(CheckCSourceCompiles)
include(CheckCXXSourceCompiles)
macro(append_c_compiler_flags _flags _name _result)
set(SAFE_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})
string(REGEX REPLACE "[-+/ ]" "_" cname "${_name}")
string(TOUPPER "${cname}" cname)
foreach(flag ${_flags})
string(REGEX REPLACE "^[-+/ ]+(.*)[-+/ ]*$" "\\1" flagname "${flag}")
string(REGEX REPLACE "[-+/ ]" "_" flagname "${flagname}")
string(TOUPPER "${flagname}" flagname)
set(have_flag "HAVE_${cname}_${flagname}")
set(CMAKE_REQUIRED_FLAGS "${flag}")
check_c_source_compiles("int main() { return 0; }" ${have_flag})
if(${have_flag})
set(${_result} "${${_result}} ${flag}")
endif(${have_flag})
endforeach(flag)
set(CMAKE_REQUIRED_FLAGS ${SAFE_CMAKE_REQUIRED_FLAGS})
endmacro(append_c_compiler_flags)
macro(append_cxx_compiler_flags _flags _name _result)
set(SAFE_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})
string(REGEX REPLACE "[-+/ ]" "_" cname "${_name}")
string(TOUPPER "${cname}" cname)
foreach(flag ${_flags})
string(REGEX REPLACE "^[-+/ ]+(.*)[-+/ ]*$" "\\1" flagname "${flag}")
string(REGEX REPLACE "[-+/ ]" "_" flagname "${flagname}")
string(TOUPPER "${flagname}" flagname)
set(have_flag "HAVE_${cname}_${flagname}")
set(CMAKE_REQUIRED_FLAGS "${flag}")
check_cxx_source_compiles("int main() { return 0; }" ${have_flag})
if(${have_flag})
set(${_result} "${${_result}} ${flag}")
endif(${have_flag})
endforeach(flag)
set(CMAKE_REQUIRED_FLAGS ${SAFE_CMAKE_REQUIRED_FLAGS})
endmacro(append_cxx_compiler_flags)
include(CheckCSourceCompiles)
macro(check_function_keywords _wordlist)
set(${_result} "")
foreach(flag ${_wordlist})
string(REGEX REPLACE "[-+/ ()]" "_" flagname "${flag}")
string(TOUPPER "${flagname}" flagname)
set(have_flag "HAVE_${flagname}")
check_c_source_compiles("${flag} void func(); void func() { } int main() { func(); return 0; }" ${have_flag})
if(${have_flag} AND NOT ${_result})
set(${_result} "${flag}")
# break()
endif(${have_flag} AND NOT ${_result})
endforeach(flag)
endmacro(check_function_keywords)
## Checks for large file support ##
include(CheckIncludeFile)
include(CheckSymbolExists)
include(CheckTypeSize)
macro(check_lfs _isenable)
set(LFS_OFF_T "")
set(LFS_FOPEN "")
set(LFS_FSEEK "")
set(LFS_FTELL "")
set(LFS_PRID "")
if(${_isenable})
set(SAFE_CMAKE_REQUIRED_DEFINITIONS "${CMAKE_REQUIRED_DEFINITIONS}")
set(CMAKE_REQUIRED_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS}
-D_LARGEFILE_SOURCE -D_LARGE_FILES -D_FILE_OFFSET_BITS=64
-D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS)
check_include_file("sys/types.h" HAVE_SYS_TYPES_H)
check_include_file("inttypes.h" HAVE_INTTYPES_H)
check_include_file("stddef.h" HAVE_STDDEF_H)
check_include_file("stdint.h" HAVE_STDINT_H)
# LFS type1: 8 <= sizeof(off_t), fseeko, ftello
check_type_size("off_t" SIZEOF_OFF_T)
if(SIZEOF_OFF_T GREATER 7)
check_symbol_exists("fseeko" "stdio.h" HAVE_FSEEKO)
check_symbol_exists("ftello" "stdio.h" HAVE_FTELLO)
if(HAVE_FSEEKO AND HAVE_FTELLO)
set(LFS_OFF_T "off_t")
set(LFS_FOPEN "fopen")
set(LFS_FSEEK "fseeko")
set(LFS_FTELL "ftello")
check_symbol_exists("PRIdMAX" "inttypes.h" HAVE_PRIDMAX)
if(HAVE_PRIDMAX)
set(LFS_PRID "PRIdMAX")
else(HAVE_PRIDMAX)
check_type_size("long" SIZEOF_LONG)
check_type_size("int" SIZEOF_INT)
if(SIZEOF_OFF_T GREATER SIZEOF_LONG)
set(LFS_PRID "\"lld\"")
elseif(SIZEOF_LONG GREATER SIZEOF_INT)
set(LFS_PRID "\"ld\"")
else(SIZEOF_OFF_T GREATER SIZEOF_LONG)
set(LFS_PRID "\"d\"")
endif(SIZEOF_OFF_T GREATER SIZEOF_LONG)
endif(HAVE_PRIDMAX)
endif(HAVE_FSEEKO AND HAVE_FTELLO)
endif(SIZEOF_OFF_T GREATER 7)
# LFS type2: 8 <= sizeof(off64_t), fopen64, fseeko64, ftello64
if(NOT LFS_OFF_T)
check_type_size("off64_t" SIZEOF_OFF64_T)
if(SIZEOF_OFF64_T GREATER 7)
check_symbol_exists("fopen64" "stdio.h" HAVE_FOPEN64)
check_symbol_exists("fseeko64" "stdio.h" HAVE_FSEEKO64)
check_symbol_exists("ftello64" "stdio.h" HAVE_FTELLO64)
if(HAVE_FOPEN64 AND HAVE_FSEEKO64 AND HAVE_FTELLO64)
set(LFS_OFF_T "off64_t")
set(LFS_FOPEN "fopen64")
set(LFS_FSEEK "fseeko64")
set(LFS_FTELL "ftello64")
check_symbol_exists("PRIdMAX" "inttypes.h" HAVE_PRIDMAX)
if(HAVE_PRIDMAX)
set(LFS_PRID "PRIdMAX")
else(HAVE_PRIDMAX)
check_type_size("long" SIZEOF_LONG)
check_type_size("int" SIZEOF_INT)
if(SIZEOF_OFF64_T GREATER SIZEOF_LONG)
set(LFS_PRID "\"lld\"")
elseif(SIZEOF_LONG GREATER SIZEOF_INT)
set(LFS_PRID "\"ld\"")
else(SIZEOF_OFF64_T GREATER SIZEOF_LONG)
set(LFS_PRID "\"d\"")
endif(SIZEOF_OFF64_T GREATER SIZEOF_LONG)
endif(HAVE_PRIDMAX)
endif(HAVE_FOPEN64 AND HAVE_FSEEKO64 AND HAVE_FTELLO64)
endif(SIZEOF_OFF64_T GREATER 7)
endif(NOT LFS_OFF_T)
# LFS type3: 8 <= sizeof(__int64), _fseeki64, _ftelli64
if(NOT LFS_OFF_T)
check_type_size("__int64" SIZEOF___INT64)
if(SIZEOF___INT64 GREATER 7)
check_symbol_exists("_fseeki64" "stdio.h" HAVE__FSEEKI64)
check_symbol_exists("_ftelli64" "stdio.h" HAVE__FTELLI64)
if(HAVE__FSEEKI64 AND HAVE__FTELLI64)
set(LFS_OFF_T "__int64")
set(LFS_FOPEN "fopen")
set(LFS_FSEEK "_fseeki64")
set(LFS_FTELL "_ftelli64")
set(LFS_PRID "\"I64d\"")
endif(HAVE__FSEEKI64 AND HAVE__FTELLI64)
endif(SIZEOF___INT64 GREATER 7)
endif(NOT LFS_OFF_T)
set(CMAKE_REQUIRED_DEFINITIONS "${SAFE_CMAKE_REQUIRED_DEFINITIONS}")
endif(${_isenable})
if(NOT LFS_OFF_T)
## not found
set(LFS_OFF_T "long")
set(LFS_FOPEN "fopen")
set(LFS_FSEEK "fseek")
set(LFS_FTELL "ftell")
set(LFS_PRID "\"ld\"")
endif(NOT LFS_OFF_T)
endmacro(check_lfs)
# If the cmake version includes cpack, use it
IF(EXISTS "${CMAKE_ROOT}/Modules/CPack.cmake")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "${PROJECT_DESCRIPTION}")
SET(CPACK_PACKAGE_VENDOR "${PROJECT_VENDOR}")
SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.md")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
SET(CPACK_PACKAGE_VERSION_MAJOR "${PROJECT_VERSION_MAJOR}")
SET(CPACK_PACKAGE_VERSION_MINOR "${PROJECT_VERSION_MINOR}")
SET(CPACK_PACKAGE_VERSION_PATCH "${PROJECT_VERSION_PATCH}")
# SET(CPACK_PACKAGE_INSTALL_DIRECTORY "${PROJECT_NAME} ${PROJECT_VERSION}")
SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION_FULL}")
IF(NOT DEFINED CPACK_SYSTEM_NAME)
SET(CPACK_SYSTEM_NAME "${CMAKE_SYSTEM_NAME}-${CMAKE_SYSTEM_PROCESSOR}")
ENDIF(NOT DEFINED CPACK_SYSTEM_NAME)
IF(${CPACK_SYSTEM_NAME} MATCHES Windows)
IF(CMAKE_CL_64)
SET(CPACK_SYSTEM_NAME win64-${CMAKE_SYSTEM_PROCESSOR})
ELSE(CMAKE_CL_64)
SET(CPACK_SYSTEM_NAME win32-${CMAKE_SYSTEM_PROCESSOR})
ENDIF(CMAKE_CL_64)
ENDIF(${CPACK_SYSTEM_NAME} MATCHES Windows)
IF(NOT DEFINED CPACK_PACKAGE_FILE_NAME)
SET(CPACK_PACKAGE_FILE_NAME "${CPACK_SOURCE_PACKAGE_FILE_NAME}-${CPACK_SYSTEM_NAME}")
ENDIF(NOT DEFINED CPACK_PACKAGE_FILE_NAME)
SET(CPACK_PACKAGE_CONTACT "${PROJECT_CONTACT}")
IF(UNIX)
SET(CPACK_STRIP_FILES "")
SET(CPACK_SOURCE_STRIP_FILES "")
# SET(CPACK_PACKAGE_EXECUTABLES "ccmake" "CMake")
ENDIF(UNIX)
SET(CPACK_SOURCE_IGNORE_FILES "/CVS/" "/build/" "/\\\\.build/" "/\\\\.svn/" "~$")
# include CPack model once all variables are set
INCLUDE(CPack)
ENDIF(EXISTS "${CMAKE_ROOT}/Modules/CPack.cmake")
IF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
MESSAGE(FATAL_ERROR "Cannot find install manifest: \"@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt\"")
ENDIF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
FILE(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files)
STRING(REGEX REPLACE "\n" ";" files "${files}")
SET(NUM 0)
FOREACH(file ${files})
IF(EXISTS "$ENV{DESTDIR}${file}")
MESSAGE(STATUS "Looking for \"$ENV{DESTDIR}${file}\" - found")
SET(UNINSTALL_CHECK_${NUM} 1)
ELSE(EXISTS "$ENV{DESTDIR}${file}")
MESSAGE(STATUS "Looking for \"$ENV{DESTDIR}${file}\" - not found")
SET(UNINSTALL_CHECK_${NUM} 0)
ENDIF(EXISTS "$ENV{DESTDIR}${file}")
MATH(EXPR NUM "1 + ${NUM}")
ENDFOREACH(file)
SET(NUM 0)
FOREACH(file ${files})
IF(${UNINSTALL_CHECK_${NUM}})
MESSAGE(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"")
EXEC_PROGRAM(
"@CMAKE_COMMAND@" ARGS "-E remove \"$ENV{DESTDIR}${file}\""
OUTPUT_VARIABLE rm_out
RETURN_VALUE rm_retval
)
IF(NOT "${rm_retval}" STREQUAL 0)
MESSAGE(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"")
ENDIF(NOT "${rm_retval}" STREQUAL 0)
ENDIF(${UNINSTALL_CHECK_${NUM}})
MATH(EXPR NUM "1 + ${NUM}")
ENDFOREACH(file)
FILE(REMOVE "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
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.
# 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("$\n");
}
// deallocate
free(SA);
return 0;
}
```
See the [examples](examples) directory for a few other examples.
## Benchmarks
See [Benchmarks](https://github.com/y-256/libdivsufsort/blob/wiki/SACA_Benchmarks.md) page for details.
## License
libdivsufsort is released under the [MIT license](LICENSE "MIT license").
> The MIT License (MIT)
>
> Copyright (c) 2003 Yuta Mori All rights reserved.
>
> Permission is hereby granted, free of charge, to any person obtaining a copy
> of this software and associated documentation files (the "Software"), to deal
> in the Software without restriction, including without limitation the rights
> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
> copies of the Software, and to permit persons to whom the Software is
> furnished to do so, subject to the following conditions:
>
> The above copyright notice and this permission notice shall be included in all
> copies or substantial portions of the Software.
>
> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
> SOFTWARE.
## Author
* Yuta Mori
set(PROJECT_VERSION_MAJOR "2")
set(PROJECT_VERSION_MINOR "0")
set(PROJECT_VERSION_PATCH "2")
set(PROJECT_VERSION_EXTRA "-1")
set(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}")
set(PROJECT_VERSION_FULL "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}${PROJECT_VERSION_EXTRA}")
set(LIBRARY_VERSION "3.0.1")
set(LIBRARY_SOVERSION "3")
## Git revision number ##
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
execute_process(COMMAND git describe --tags HEAD
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
OUTPUT_VARIABLE GIT_DESCRIBE_TAGS ERROR_QUIET)
if(GIT_DESCRIBE_TAGS)
string(REGEX REPLACE "^v(.*)" "\\1" GIT_REVISION "${GIT_DESCRIBE_TAGS}")
string(STRIP "${GIT_REVISION}" GIT_REVISION)
if(GIT_REVISION)
set(PROJECT_VERSION_FULL "${GIT_REVISION}")
endif(GIT_REVISION)
endif(GIT_DESCRIBE_TAGS)
endif(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
## Add definitions ##
add_definitions(-D_LARGEFILE_SOURCE -D_LARGE_FILES -D_FILE_OFFSET_BITS=64)
## Targets ##
include_directories("${CMAKE_CURRENT_SOURCE_DIR}/../include"
"${CMAKE_CURRENT_BINARY_DIR}/../include")
link_directories("${CMAKE_CURRENT_BINARY_DIR}/../lib")
foreach(src suftest mksary sasearch bwt unbwt)
add_executable(${src} ${src}.c)
target_link_libraries(${src} divsufsort)
endforeach(src)
/*
* bwt.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