Vendor import of libdivsufsort, a software library that implements
a lightweight suffix array construction algorithm. Obtained from: https://github.com/y-256/libdivsufsort
This commit is contained in:
commit
7db3f07863
Notes:
svn2git
2020-12-20 02:59:44 +00:00
svn path=/vendor/libdivsufsort/dist/; revision=303275 svn path=/vendor/libdivsufsort/0.0.2015.10.27/; revision=303276; tag=vendor/libdivsufsort/0.0.2015.10.27
32
.gitignore
vendored
Normal file
32
.gitignore
vendored
Normal file
@ -0,0 +1,32 @@
|
||||
# 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/
|
21
CHANGELOG.md
Normal file
21
CHANGELOG.md
Normal file
@ -0,0 +1,21 @@
|
||||
# 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
|
99
CMakeLists.txt
Normal file
99
CMakeLists.txt
Normal file
@ -0,0 +1,99 @@
|
||||
### 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")
|
38
CMakeModules/AppendCompilerFlags.cmake
Normal file
38
CMakeModules/AppendCompilerFlags.cmake
Normal file
@ -0,0 +1,38 @@
|
||||
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 ${SAFE_CMAKE_REQUIRED_FLAGS})
|
||||
endmacro(append_cxx_compiler_flags)
|
15
CMakeModules/CheckFunctionKeywords.cmake
Normal file
15
CMakeModules/CheckFunctionKeywords.cmake
Normal file
@ -0,0 +1,15 @@
|
||||
include(CheckCSourceCompiles)
|
||||
|
||||
macro(check_function_keywords _wordlist)
|
||||
set(${_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 ${_result})
|
||||
endforeach(flag)
|
||||
endmacro(check_function_keywords)
|
109
CMakeModules/CheckLFS.cmake
Normal file
109
CMakeModules/CheckLFS.cmake
Normal file
@ -0,0 +1,109 @@
|
||||
## Checks for large file support ##
|
||||
include(CheckIncludeFile)
|
||||
include(CheckSymbolExists)
|
||||
include(CheckTypeSize)
|
||||
|
||||
macro(check_lfs _isenable)
|
||||
set(LFS_OFF_T "")
|
||||
set(LFS_FOPEN "")
|
||||
set(LFS_FSEEK "")
|
||||
set(LFS_FTELL "")
|
||||
set(LFS_PRID "")
|
||||
|
||||
if(${_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(${_isenable})
|
||||
|
||||
if(NOT LFS_OFF_T)
|
||||
## not found
|
||||
set(LFS_OFF_T "long")
|
||||
set(LFS_FOPEN "fopen")
|
||||
set(LFS_FSEEK "fseek")
|
||||
set(LFS_FTELL "ftell")
|
||||
set(LFS_PRID "\"ld\"")
|
||||
endif(NOT LFS_OFF_T)
|
||||
|
||||
endmacro(check_lfs)
|
38
CMakeModules/ProjectCPack.cmake
Normal file
38
CMakeModules/ProjectCPack.cmake
Normal file
@ -0,0 +1,38 @@
|
||||
# If the cmake version includes cpack, use it
|
||||
IF(EXISTS "${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")
|
36
CMakeModules/cmake_uninstall.cmake.in
Normal file
36
CMakeModules/cmake_uninstall.cmake.in
Normal file
@ -0,0 +1,36 @@
|
||||
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")
|
21
LICENSE
Normal file
21
LICENSE
Normal file
@ -0,0 +1,21 @@
|
||||
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.
|
140
README.md
Normal file
140
README.md
Normal file
@ -0,0 +1,140 @@
|
||||
# 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
|
23
VERSION.cmake
Normal file
23
VERSION.cmake
Normal file
@ -0,0 +1,23 @@
|
||||
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 "${CMAKE_CURRENT_SOURCE_DIR}/.git")
|
11
examples/CMakeLists.txt
Normal file
11
examples/CMakeLists.txt
Normal file
@ -0,0 +1,11 @@
|
||||
## Add definitions ##
|
||||
add_definitions(-D_LARGEFILE_SOURCE -D_LARGE_FILES -D_FILE_OFFSET_BITS=64)
|
||||
|
||||
## Targets ##
|
||||
include_directories("${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)
|
220
examples/bwt.c
Normal file
220
examples/bwt.c
Normal file
@ -0,0 +1,220 @@
|
||||
/*
|
||||
* 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
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
* OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
#if HAVE_CONFIG_H
|
||||
# include "config.h"
|
||||
#endif
|
||||
#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_SYS_TYPES_H
|
||||
# include <sys/types.h>
|
||||
#endif
|
||||
#if HAVE_IO_H && HAVE_FCNTL_H
|
||||
# include <io.h>
|
||||
# include <fcntl.h>
|
||||
#endif
|
||||
#include <time.h>
|
||||
#include <divsufsort.h>
|
||||
#include "lfs.h"
|
||||
|
||||
|
||||
static
|
||||
size_t
|
||||
write_int(FILE *fp, saidx_t n) {
|
||||
unsigned char c[4];
|
||||
c[0] = (unsigned char)((n >> 0) & 0xff), c[1] = (unsigned char)((n >> 8) & 0xff),
|
||||
c[2] = (unsigned char)((n >> 16) & 0xff), c[3] = (unsigned char)((n >> 24) & 0xff);
|
||||
return fwrite(c, sizeof(unsigned char), 4, fp);
|
||||
}
|
||||
|
||||
static
|
||||
void
|
||||
print_help(const char *progname, int status) {
|
||||
fprintf(stderr,
|
||||
"bwt, a burrows-wheeler transform program, version %s.\n",
|
||||
divsufsort_version());
|
||||
fprintf(stderr, "usage: %s [-b num] INFILE OUTFILE\n", progname);
|
||||
fprintf(stderr, " -b num set block size to num MiB [1..512] (default: 32)\n\n");
|
||||
exit(status);
|
||||
}
|
||||
|
||||
int
|
||||
main(int argc, const char *argv[]) {
|
||||
FILE *fp, *ofp;
|
||||
const char *fname, *ofname;
|
||||
sauchar_t *T;
|
||||
saidx_t *SA;
|
||||
LFS_OFF_T n;
|
||||
size_t m;
|
||||
saidx_t pidx;
|
||||
clock_t start,finish;
|
||||
saint_t i, blocksize = 32, needclose = 3;
|
||||
|
||||
/* Check arguments. */
|
||||
if((argc == 1) ||
|
||||
(strcmp(argv[1], "-h") == 0) ||
|
||||
(strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); }
|
||||
if((argc != 3) && (argc != 5)) { print_help(argv[0], EXIT_FAILURE); }
|
||||
i = 1;
|
||||
if(argc == 5) {
|
||||
if(strcmp(argv[i], "-b") != 0) { print_help(argv[0], EXIT_FAILURE); }
|
||||
blocksize = atoi(argv[i + 1]);
|
||||
if(blocksize < 0) { blocksize = 1; }
|
||||
else if(512 < blocksize) { blocksize = 512; }
|
||||
i += 2;
|
||||
}
|
||||
blocksize <<= 20;
|
||||
|
||||
/* Open a file for reading. */
|
||||
if(strcmp(argv[i], "-") != 0) {
|
||||
#if HAVE_FOPEN_S
|
||||
if(fopen_s(&fp, fname = argv[i], "rb") != 0) {
|
||||
#else
|
||||
if((fp = LFS_FOPEN(fname = argv[i], "rb")) == NULL) {
|
||||
#endif
|
||||
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
} else {
|
||||
#if HAVE__SETMODE && HAVE__FILENO
|
||||
if(_setmode(_fileno(stdin), _O_BINARY) == -1) {
|
||||
fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
#endif
|
||||
fp = stdin;
|
||||
fname = "stdin";
|
||||
needclose ^= 1;
|
||||
}
|
||||
i += 1;
|
||||
|
||||
/* Open a file for writing. */
|
||||
if(strcmp(argv[i], "-") != 0) {
|
||||
#if HAVE_FOPEN_S
|
||||
if(fopen_s(&ofp, ofname = argv[i], "wb") != 0) {
|
||||
#else
|
||||
if((ofp = LFS_FOPEN(ofname = argv[i], "wb")) == NULL) {
|
||||
#endif
|
||||
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
} else {
|
||||
#if HAVE__SETMODE && HAVE__FILENO
|
||||
if(_setmode(_fileno(stdout), _O_BINARY) == -1) {
|
||||
fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
#endif
|
||||
ofp = stdout;
|
||||
ofname = "stdout";
|
||||
needclose ^= 2;
|
||||
}
|
||||
|
||||
/* Get the file size. */
|
||||
if(LFS_FSEEK(fp, 0, SEEK_END) == 0) {
|
||||
n = LFS_FTELL(fp);
|
||||
rewind(fp);
|
||||
if(n < 0) {
|
||||
fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
if(0x20000000L < n) { n = 0x20000000L; }
|
||||
if((blocksize == 0) || (n < blocksize)) { blocksize = (saidx_t)n; }
|
||||
} else if(blocksize == 0) { blocksize = 32 << 20; }
|
||||
|
||||
/* Allocate 5blocksize bytes of memory. */
|
||||
T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t));
|
||||
SA = (saidx_t *)malloc(blocksize * sizeof(saidx_t));
|
||||
if((T == NULL) || (SA == NULL)) {
|
||||
fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Write the blocksize. */
|
||||
if(write_int(ofp, blocksize) != 4) {
|
||||
fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
fprintf(stderr, " BWT (blocksize %" PRIdSAINT_T ") ... ", blocksize);
|
||||
start = clock();
|
||||
for(n = 0; 0 < (m = fread(T, sizeof(sauchar_t), blocksize, fp)); n += m) {
|
||||
/* Burrows-Wheeler Transform. */
|
||||
pidx = divbwt(T, T, SA, m);
|
||||
if(pidx < 0) {
|
||||
fprintf(stderr, "%s (bw_transform): %s.\n",
|
||||
argv[0],
|
||||
(pidx == -1) ? "Invalid arguments" : "Cannot allocate memory");
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Write the bwted data. */
|
||||
if((write_int(ofp, pidx) != 4) ||
|
||||
(fwrite(T, sizeof(sauchar_t), m, ofp) != m)) {
|
||||
fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
}
|
||||
if(ferror(fp)) {
|
||||
fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
finish = clock();
|
||||
fprintf(stderr, "%" PRIdOFF_T " bytes: %.4f sec\n",
|
||||
n, (double)(finish - start) / (double)CLOCKS_PER_SEC);
|
||||
|
||||
/* Close files */
|
||||
if(needclose & 1) { fclose(fp); }
|
||||
if(needclose & 2) { fclose(ofp); }
|
||||
|
||||
/* Deallocate memory. */
|
||||
free(SA);
|
||||
free(T);
|
||||
|
||||
return 0;
|
||||
}
|
193
examples/mksary.c
Normal file
193
examples/mksary.c
Normal file
@ -0,0 +1,193 @@
|
||||
/*
|
||||
* mksary.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.
|
||||
*/
|
||||
|
||||
#if HAVE_CONFIG_H
|
||||
# include "config.h"
|
||||
#endif
|
||||
#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_SYS_TYPES_H
|
||||
# include <sys/types.h>
|
||||
#endif
|
||||
#if HAVE_IO_H && HAVE_FCNTL_H
|
||||
# include <io.h>
|
||||
# include <fcntl.h>
|
||||
#endif
|
||||
#include <time.h>
|
||||
#include <divsufsort.h>
|
||||
#include "lfs.h"
|
||||
|
||||
|
||||
static
|
||||
void
|
||||
print_help(const char *progname, int status) {
|
||||
fprintf(stderr,
|
||||
"mksary, a simple suffix array builder, version %s.\n",
|
||||
divsufsort_version());
|
||||
fprintf(stderr, "usage: %s INFILE OUTFILE\n\n", progname);
|
||||
exit(status);
|
||||
}
|
||||
|
||||
int
|
||||
main(int argc, const char *argv[]) {
|
||||
FILE *fp, *ofp;
|
||||
const char *fname, *ofname;
|
||||
sauchar_t *T;
|
||||
saidx_t *SA;
|
||||
LFS_OFF_T n;
|
||||
clock_t start, finish;
|
||||
saint_t needclose = 3;
|
||||
|
||||
/* Check arguments. */
|
||||
if((argc == 1) ||
|
||||
(strcmp(argv[1], "-h") == 0) ||
|
||||
(strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); }
|
||||
if(argc != 3) { print_help(argv[0], EXIT_FAILURE); }
|
||||
|
||||
/* Open a file for reading. */
|
||||
if(strcmp(argv[1], "-") != 0) {
|
||||
#if HAVE_FOPEN_S
|
||||
if(fopen_s(&fp, fname = argv[1], "rb") != 0) {
|
||||
#else
|
||||
if((fp = LFS_FOPEN(fname = argv[1], "rb")) == NULL) {
|
||||
#endif
|
||||
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
} else {
|
||||
#if HAVE__SETMODE && HAVE__FILENO
|
||||
if(_setmode(_fileno(stdin), _O_BINARY) == -1) {
|
||||
fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
#endif
|
||||
fp = stdin;
|
||||
fname = "stdin";
|
||||
needclose ^= 1;
|
||||
}
|
||||
|
||||
/* Open a file for writing. */
|
||||
if(strcmp(argv[2], "-") != 0) {
|
||||
#if HAVE_FOPEN_S
|
||||
if(fopen_s(&ofp, ofname = argv[2], "wb") != 0) {
|
||||
#else
|
||||
if((ofp = LFS_FOPEN(ofname = argv[2], "wb")) == NULL) {
|
||||
#endif
|
||||
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
} else {
|
||||
#if HAVE__SETMODE && HAVE__FILENO
|
||||
if(_setmode(_fileno(stdout), _O_BINARY) == -1) {
|
||||
fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
#endif
|
||||
ofp = stdout;
|
||||
ofname = "stdout";
|
||||
needclose ^= 2;
|
||||
}
|
||||
|
||||
/* Get the file size. */
|
||||
if(LFS_FSEEK(fp, 0, SEEK_END) == 0) {
|
||||
n = LFS_FTELL(fp);
|
||||
rewind(fp);
|
||||
if(n < 0) {
|
||||
fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
if(0x7fffffff <= n) {
|
||||
fprintf(stderr, "%s: Input file `%s' is too big.\n", argv[0], fname);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
} else {
|
||||
fprintf(stderr, "%s: Cannot fseek `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Allocate 5blocksize bytes of memory. */
|
||||
T = (sauchar_t *)malloc((size_t)n * sizeof(sauchar_t));
|
||||
SA = (saidx_t *)malloc((size_t)n * sizeof(saidx_t));
|
||||
if((T == NULL) || (SA == NULL)) {
|
||||
fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Read n bytes of data. */
|
||||
if(fread(T, sizeof(sauchar_t), (size_t)n, fp) != (size_t)n) {
|
||||
fprintf(stderr, "%s: %s `%s': ",
|
||||
argv[0],
|
||||
(ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in",
|
||||
fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
if(needclose & 1) { fclose(fp); }
|
||||
|
||||
/* Construct the suffix array. */
|
||||
fprintf(stderr, "%s: %" PRIdOFF_T " bytes ... ", fname, n);
|
||||
start = clock();
|
||||
if(divsufsort(T, SA, (saidx_t)n) != 0) {
|
||||
fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
finish = clock();
|
||||
fprintf(stderr, "%.4f sec\n", (double)(finish - start) / (double)CLOCKS_PER_SEC);
|
||||
|
||||
/* Write the suffix array. */
|
||||
if(fwrite(SA, sizeof(saidx_t), (size_t)n, ofp) != (size_t)n) {
|
||||
fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
if(needclose & 2) { fclose(ofp); }
|
||||
|
||||
/* Deallocate memory. */
|
||||
free(SA);
|
||||
free(T);
|
||||
|
||||
return 0;
|
||||
}
|
165
examples/sasearch.c
Normal file
165
examples/sasearch.c
Normal file
@ -0,0 +1,165 @@
|
||||
/*
|
||||
* sasearch.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.
|
||||
*/
|
||||
|
||||
#if HAVE_CONFIG_H
|
||||
# include "config.h"
|
||||
#endif
|
||||
#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_SYS_TYPES_H
|
||||
# include <sys/types.h>
|
||||
#endif
|
||||
#if HAVE_IO_H && HAVE_FCNTL_H
|
||||
# include <io.h>
|
||||
# include <fcntl.h>
|
||||
#endif
|
||||
#include <divsufsort.h>
|
||||
#include "lfs.h"
|
||||
|
||||
|
||||
static
|
||||
void
|
||||
print_help(const char *progname, int status) {
|
||||
fprintf(stderr,
|
||||
"sasearch, a simple SA-based full-text search tool, version %s\n",
|
||||
divsufsort_version());
|
||||
fprintf(stderr, "usage: %s PATTERN FILE SAFILE\n\n", progname);
|
||||
exit(status);
|
||||
}
|
||||
|
||||
int
|
||||
main(int argc, const char *argv[]) {
|
||||
FILE *fp;
|
||||
const char *P;
|
||||
sauchar_t *T;
|
||||
saidx_t *SA;
|
||||
LFS_OFF_T n;
|
||||
size_t Psize;
|
||||
saidx_t i, size, left;
|
||||
|
||||
if((argc == 1) ||
|
||||
(strcmp(argv[1], "-h") == 0) ||
|
||||
(strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); }
|
||||
if(argc != 4) { print_help(argv[0], EXIT_FAILURE); }
|
||||
|
||||
P = argv[1];
|
||||
Psize = strlen(P);
|
||||
|
||||
/* Open a file for reading. */
|
||||
#if HAVE_FOPEN_S
|
||||
if(fopen_s(&fp, argv[2], "rb") != 0) {
|
||||
#else
|
||||
if((fp = LFS_FOPEN(argv[2], "rb")) == NULL) {
|
||||
#endif
|
||||
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], argv[2]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Get the file size. */
|
||||
if(LFS_FSEEK(fp, 0, SEEK_END) == 0) {
|
||||
n = LFS_FTELL(fp);
|
||||
rewind(fp);
|
||||
if(n < 0) {
|
||||
fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], argv[2]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
} else {
|
||||
fprintf(stderr, "%s: Cannot fseek `%s': ", argv[0], argv[2]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Allocate 5n bytes of memory. */
|
||||
T = (sauchar_t *)malloc((size_t)n * sizeof(sauchar_t));
|
||||
SA = (saidx_t *)malloc((size_t)n * sizeof(saidx_t));
|
||||
if((T == NULL) || (SA == NULL)) {
|
||||
fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Read n bytes of data. */
|
||||
if(fread(T, sizeof(sauchar_t), (size_t)n, fp) != (size_t)n) {
|
||||
fprintf(stderr, "%s: %s `%s': ",
|
||||
argv[0],
|
||||
(ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in",
|
||||
argv[2]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
fclose(fp);
|
||||
|
||||
/* Open the SA file for reading. */
|
||||
#if HAVE_FOPEN_S
|
||||
if(fopen_s(&fp, argv[3], "rb") != 0) {
|
||||
#else
|
||||
if((fp = LFS_FOPEN(argv[3], "rb")) == NULL) {
|
||||
#endif
|
||||
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], argv[3]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Read n * sizeof(saidx_t) bytes of data. */
|
||||
if(fread(SA, sizeof(saidx_t), (size_t)n, fp) != (size_t)n) {
|
||||
fprintf(stderr, "%s: %s `%s': ",
|
||||
argv[0],
|
||||
(ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in",
|
||||
argv[3]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
fclose(fp);
|
||||
|
||||
/* Search and print */
|
||||
size = sa_search(T, (saidx_t)n,
|
||||
(const sauchar_t *)P, (saidx_t)Psize,
|
||||
SA, (saidx_t)n, &left);
|
||||
for(i = 0; i < size; ++i) {
|
||||
fprintf(stdout, "%" PRIdSAIDX_T "\n", SA[left + i]);
|
||||
}
|
||||
|
||||
/* Deallocate memory. */
|
||||
free(SA);
|
||||
free(T);
|
||||
|
||||
return 0;
|
||||
}
|
164
examples/suftest.c
Normal file
164
examples/suftest.c
Normal file
@ -0,0 +1,164 @@
|
||||
/*
|
||||
* suftest.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.
|
||||
*/
|
||||
|
||||
#if HAVE_CONFIG_H
|
||||
# include "config.h"
|
||||
#endif
|
||||
#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_SYS_TYPES_H
|
||||
# include <sys/types.h>
|
||||
#endif
|
||||
#if HAVE_IO_H && HAVE_FCNTL_H
|
||||
# include <io.h>
|
||||
# include <fcntl.h>
|
||||
#endif
|
||||
#include <time.h>
|
||||
#include <divsufsort.h>
|
||||
#include "lfs.h"
|
||||
|
||||
|
||||
static
|
||||
void
|
||||
print_help(const char *progname, int status) {
|
||||
fprintf(stderr,
|
||||
"suftest, a suffixsort tester, version %s.\n",
|
||||
divsufsort_version());
|
||||
fprintf(stderr, "usage: %s FILE\n\n", progname);
|
||||
exit(status);
|
||||
}
|
||||
|
||||
int
|
||||
main(int argc, const char *argv[]) {
|
||||
FILE *fp;
|
||||
const char *fname;
|
||||
sauchar_t *T;
|
||||
saidx_t *SA;
|
||||
LFS_OFF_T n;
|
||||
clock_t start, finish;
|
||||
saint_t needclose = 1;
|
||||
|
||||
/* Check arguments. */
|
||||
if((argc == 1) ||
|
||||
(strcmp(argv[1], "-h") == 0) ||
|
||||
(strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); }
|
||||
if(argc != 2) { print_help(argv[0], EXIT_FAILURE); }
|
||||
|
||||
/* Open a file for reading. */
|
||||
if(strcmp(argv[1], "-") != 0) {
|
||||
#if HAVE_FOPEN_S
|
||||
if(fopen_s(&fp, fname = argv[1], "rb") != 0) {
|
||||
#else
|
||||
if((fp = LFS_FOPEN(fname = argv[1], "rb")) == NULL) {
|
||||
#endif
|
||||
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
} else {
|
||||
#if HAVE__SETMODE && HAVE__FILENO
|
||||
if(_setmode(_fileno(stdin), _O_BINARY) == -1) {
|
||||
fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
#endif
|
||||
fp = stdin;
|
||||
fname = "stdin";
|
||||
needclose = 0;
|
||||
}
|
||||
|
||||
/* Get the file size. */
|
||||
if(LFS_FSEEK(fp, 0, SEEK_END) == 0) {
|
||||
n = LFS_FTELL(fp);
|
||||
rewind(fp);
|
||||
if(n < 0) {
|
||||
fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
if(0x7fffffff <= n) {
|
||||
fprintf(stderr, "%s: Input file `%s' is too big.\n", argv[0], fname);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
} else {
|
||||
fprintf(stderr, "%s: Cannot fseek `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Allocate 5n bytes of memory. */
|
||||
T = (sauchar_t *)malloc((size_t)n * sizeof(sauchar_t));
|
||||
SA = (saidx_t *)malloc((size_t)n * sizeof(saidx_t));
|
||||
if((T == NULL) || (SA == NULL)) {
|
||||
fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Read n bytes of data. */
|
||||
if(fread(T, sizeof(sauchar_t), (size_t)n, fp) != (size_t)n) {
|
||||
fprintf(stderr, "%s: %s `%s': ",
|
||||
argv[0],
|
||||
(ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in",
|
||||
argv[1]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
if(needclose & 1) { fclose(fp); }
|
||||
|
||||
/* Construct the suffix array. */
|
||||
fprintf(stderr, "%s: %" PRIdOFF_T " bytes ... ", fname, n);
|
||||
start = clock();
|
||||
if(divsufsort(T, SA, (saidx_t)n) != 0) {
|
||||
fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
finish = clock();
|
||||
fprintf(stderr, "%.4f sec\n", (double)(finish - start) / (double)CLOCKS_PER_SEC);
|
||||
|
||||
/* Check the suffix array. */
|
||||
if(sufcheck(T, SA, (saidx_t)n, 1) != 0) { exit(EXIT_FAILURE); }
|
||||
|
||||
/* Deallocate memory. */
|
||||
free(SA);
|
||||
free(T);
|
||||
|
||||
return 0;
|
||||
}
|
207
examples/unbwt.c
Normal file
207
examples/unbwt.c
Normal file
@ -0,0 +1,207 @@
|
||||
/*
|
||||
* unbwt.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.
|
||||
*/
|
||||
|
||||
#if HAVE_CONFIG_H
|
||||
# include "config.h"
|
||||
#endif
|
||||
#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_SYS_TYPES_H
|
||||
# include <sys/types.h>
|
||||
#endif
|
||||
#if HAVE_IO_H && HAVE_FCNTL_H
|
||||
# include <io.h>
|
||||
# include <fcntl.h>
|
||||
#endif
|
||||
#include <time.h>
|
||||
#include <divsufsort.h>
|
||||
#include "lfs.h"
|
||||
|
||||
|
||||
static
|
||||
size_t
|
||||
read_int(FILE *fp, saidx_t *n) {
|
||||
unsigned char c[4];
|
||||
size_t m = fread(c, sizeof(unsigned char), 4, fp);
|
||||
if(m == 4) {
|
||||
*n = (c[0] << 0) | (c[1] << 8) |
|
||||
(c[2] << 16) | (c[3] << 24);
|
||||
}
|
||||
return m;
|
||||
}
|
||||
|
||||
static
|
||||
void
|
||||
print_help(const char *progname, int status) {
|
||||
fprintf(stderr,
|
||||
"unbwt, an inverse burrows-wheeler transform program, version %s.\n",
|
||||
divsufsort_version());
|
||||
fprintf(stderr, "usage: %s INFILE OUTFILE\n\n", progname);
|
||||
exit(status);
|
||||
}
|
||||
|
||||
int
|
||||
main(int argc, const char *argv[]) {
|
||||
FILE *fp, *ofp;
|
||||
const char *fname, *ofname;
|
||||
sauchar_t *T;
|
||||
saidx_t *A;
|
||||
LFS_OFF_T n;
|
||||
size_t m;
|
||||
saidx_t pidx;
|
||||
clock_t start, finish;
|
||||
saint_t err, blocksize, needclose = 3;
|
||||
|
||||
/* Check arguments. */
|
||||
if((argc == 1) ||
|
||||
(strcmp(argv[1], "-h") == 0) ||
|
||||
(strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); }
|
||||
if(argc != 3) { print_help(argv[0], EXIT_FAILURE); }
|
||||
|
||||
/* Open a file for reading. */
|
||||
if(strcmp(argv[1], "-") != 0) {
|
||||
#if HAVE_FOPEN_S
|
||||
if(fopen_s(&fp, fname = argv[1], "rb") != 0) {
|
||||
#else
|
||||
if((fp = LFS_FOPEN(fname = argv[1], "rb")) == NULL) {
|
||||
#endif
|
||||
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
} else {
|
||||
#if HAVE__SETMODE && HAVE__FILENO
|
||||
if(_setmode(_fileno(stdin), _O_BINARY) == -1) {
|
||||
fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
#endif
|
||||
fp = stdin;
|
||||
fname = "stdin";
|
||||
needclose ^= 1;
|
||||
}
|
||||
|
||||
/* Open a file for writing. */
|
||||
if(strcmp(argv[2], "-") != 0) {
|
||||
#if HAVE_FOPEN_S
|
||||
if(fopen_s(&ofp, ofname = argv[2], "wb") != 0) {
|
||||
#else
|
||||
if((ofp = LFS_FOPEN(ofname = argv[2], "wb")) == NULL) {
|
||||
#endif
|
||||
fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
} else {
|
||||
#if HAVE__SETMODE && HAVE__FILENO
|
||||
if(_setmode(_fileno(stdout), _O_BINARY) == -1) {
|
||||
fprintf(stderr, "%s: Cannot set mode: ", argv[0]);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
#endif
|
||||
ofp = stdout;
|
||||
ofname = "stdout";
|
||||
needclose ^= 2;
|
||||
}
|
||||
|
||||
/* Read the blocksize. */
|
||||
if(read_int(fp, &blocksize) != 4) {
|
||||
fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Allocate 5blocksize bytes of memory. */
|
||||
T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t));
|
||||
A = (saidx_t *)malloc(blocksize * sizeof(saidx_t));
|
||||
if((T == NULL) || (A == NULL)) {
|
||||
fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
fprintf(stderr, "UnBWT (blocksize %" PRIdSAINT_T ") ... ", blocksize);
|
||||
start = clock();
|
||||
for(n = 0; (m = read_int(fp, &pidx)) != 0; n += m) {
|
||||
/* Read blocksize bytes of data. */
|
||||
if((m != 4) || ((m = fread(T, sizeof(sauchar_t), blocksize, fp)) == 0)) {
|
||||
fprintf(stderr, "%s: %s `%s': ",
|
||||
argv[0],
|
||||
(ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in",
|
||||
fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Inverse Burrows-Wheeler Transform. */
|
||||
if((err = inverse_bw_transform(T, T, A, m, pidx)) != 0) {
|
||||
fprintf(stderr, "%s (reverseBWT): %s.\n",
|
||||
argv[0],
|
||||
(err == -1) ? "Invalid data" : "Cannot allocate memory");
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
/* Write m bytes of data. */
|
||||
if(fwrite(T, sizeof(sauchar_t), m, ofp) != m) {
|
||||
fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
}
|
||||
if(ferror(fp)) {
|
||||
fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname);
|
||||
perror(NULL);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
finish = clock();
|
||||
fprintf(stderr, "%" PRIdOFF_T " bytes: %.4f sec\n",
|
||||
n, (double)(finish - start) / (double)CLOCKS_PER_SEC);
|
||||
|
||||
/* Close files */
|
||||
if(needclose & 1) { fclose(fp); }
|
||||
if(needclose & 2) { fclose(ofp); }
|
||||
|
||||
/* Deallocate memory. */
|
||||
free(A);
|
||||
free(T);
|
||||
|
||||
return 0;
|
||||
}
|
162
include/CMakeLists.txt
Normal file
162
include/CMakeLists.txt
Normal file
@ -0,0 +1,162 @@
|
||||
include(CheckIncludeFiles)
|
||||
include(CheckIncludeFile)
|
||||
include(CheckSymbolExists)
|
||||
include(CheckTypeSize)
|
||||
include(CheckFunctionKeywords)
|
||||
include(CheckLFS)
|
||||
|
||||
## Checks for header files ##
|
||||
check_include_file("inttypes.h" HAVE_INTTYPES_H)
|
||||
check_include_file("memory.h" HAVE_MEMORY_H)
|
||||
check_include_file("stddef.h" HAVE_STDDEF_H)
|
||||
check_include_file("stdint.h" HAVE_STDINT_H)
|
||||
check_include_file("stdlib.h" HAVE_STDLIB_H)
|
||||
check_include_file("string.h" HAVE_STRING_H)
|
||||
check_include_file("strings.h" HAVE_STRINGS_H)
|
||||
check_include_file("sys/types.h" HAVE_SYS_TYPES_H)
|
||||
if(HAVE_INTTYPES_H)
|
||||
set(INCFILE "#include <inttypes.h>")
|
||||
elseif(HAVE_STDINT_H)
|
||||
set(INCFILE "#include <stdint.h>")
|
||||
else(HAVE_INTTYPES_H)
|
||||
set(INCFILE "")
|
||||
endif(HAVE_INTTYPES_H)
|
||||
|
||||
## create configuration files from .cmake file ##
|
||||
if(BUILD_EXAMPLES)
|
||||
## Checks for WinIO ##
|
||||
if(WIN32)
|
||||
check_include_file("io.h" HAVE_IO_H)
|
||||
check_include_file("fcntl.h" HAVE_FCNTL_H)
|
||||
check_symbol_exists("_setmode" "io.h;fcntl.h" HAVE__SETMODE)
|
||||
if(NOT HAVE__SETMODE)
|
||||
check_symbol_exists("setmode" "io.h;fcntl.h" HAVE_SETMODE)
|
||||
endif(NOT HAVE__SETMODE)
|
||||
check_symbol_exists("_fileno" "stdio.h" HAVE__FILENO)
|
||||
check_symbol_exists("fopen_s" "stdio.h" HAVE_FOPEN_S)
|
||||
check_symbol_exists("_O_BINARY" "fcntl.h" HAVE__O_BINARY)
|
||||
endif(WIN32)
|
||||
|
||||
## Checks for large file support ##
|
||||
check_lfs(WITH_LFS)
|
||||
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/lfs.h.cmake" "${CMAKE_CURRENT_BINARY_DIR}/lfs.h" @ONLY)
|
||||
endif(BUILD_EXAMPLES)
|
||||
|
||||
## generate config.h ##
|
||||
check_function_keywords("inline;__inline;__inline__;__declspec(dllexport);__declspec(dllimport)")
|
||||
if(HAVE_INLINE)
|
||||
set(INLINE "inline")
|
||||
elseif(HAVE___INLINE)
|
||||
set(INLINE "__inline")
|
||||
elseif(HAVE___INLINE__)
|
||||
set(INLINE "__inline__")
|
||||
else(HAVE_INLINE)
|
||||
set(INLINE "")
|
||||
endif(HAVE_INLINE)
|
||||
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/config.h.cmake" "${CMAKE_CURRENT_BINARY_DIR}/config.h")
|
||||
|
||||
## Checks for types ##
|
||||
# sauchar_t (8bit)
|
||||
check_type_size("uint8_t" UINT8_T)
|
||||
if(HAVE_UINT8_T)
|
||||
set(SAUCHAR_TYPE "uint8_t")
|
||||
else(HAVE_UINT8_T)
|
||||
check_type_size("unsigned char" SIZEOF_UNSIGNED_CHAR)
|
||||
if("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1")
|
||||
set(SAUCHAR_TYPE "unsigned char")
|
||||
else("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1")
|
||||
message(FATAL_ERROR "Cannot find unsigned 8-bit integer type")
|
||||
endif("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1")
|
||||
endif(HAVE_UINT8_T)
|
||||
# saint_t (32bit)
|
||||
check_type_size("int32_t" INT32_T)
|
||||
if(HAVE_INT32_T)
|
||||
set(SAINT32_TYPE "int32_t")
|
||||
check_symbol_exists("PRId32" "inttypes.h" HAVE_PRID32)
|
||||
if(HAVE_PRID32)
|
||||
set(SAINT32_PRId "PRId32")
|
||||
else(HAVE_PRID32)
|
||||
set(SAINT32_PRId "\"d\"")
|
||||
endif(HAVE_PRID32)
|
||||
else(HAVE_INT32_T)
|
||||
check_type_size("int" SIZEOF_INT)
|
||||
check_type_size("long" SIZEOF_LONG)
|
||||
check_type_size("short" SIZEOF_SHORT)
|
||||
check_type_size("__int32" SIZEOF___INT32)
|
||||
if("${SIZEOF_INT}" STREQUAL "4")
|
||||
set(SAINT32_TYPE "int")
|
||||
set(SAINT32_PRId "\"d\"")
|
||||
elseif("${SIZEOF_LONG}" STREQUAL "4")
|
||||
set(SAINT32_TYPE "long")
|
||||
set(SAINT32_PRId "\"ld\"")
|
||||
elseif("${SIZEOF_SHORT}" STREQUAL "4")
|
||||
set(SAINT32_TYPE "short")
|
||||
set(SAINT32_PRId "\"d\"")
|
||||
elseif("${SIZEOF___INT32}" STREQUAL "4")
|
||||
set(SAINT32_TYPE "__int32")
|
||||
set(SAINT32_PRId "\"d\"")
|
||||
else("${SIZEOF_INT}" STREQUAL "4")
|
||||
message(FATAL_ERROR "Cannot find 32-bit integer type")
|
||||
endif("${SIZEOF_INT}" STREQUAL "4")
|
||||
endif(HAVE_INT32_T)
|
||||
# saint64_t (64bit)
|
||||
if(BUILD_DIVSUFSORT64)
|
||||
check_type_size("int64_t" INT64_T)
|
||||
if(HAVE_INT64_T)
|
||||
set(SAINT64_TYPE "int64_t")
|
||||
check_symbol_exists("PRId64" "inttypes.h" HAVE_PRID64)
|
||||
if(HAVE_PRID64)
|
||||
set(SAINT64_PRId "PRId64")
|
||||
else(HAVE_PRID64)
|
||||
set(SAINT64_PRId "\"lld\"")
|
||||
endif(HAVE_PRID64)
|
||||
else(HAVE_INT64_T)
|
||||
check_type_size("int" SIZEOF_INT)
|
||||
check_type_size("long" SIZEOF_LONG)
|
||||
check_type_size("long long" SIZEOF_LONG_LONG)
|
||||
check_type_size("__int64" SIZEOF___INT64)
|
||||
if("${SIZEOF_INT}" STREQUAL "8")
|
||||
set(SAINT64_TYPE "int")
|
||||
set(SAINT64_PRId "\"d\"")
|
||||
elseif("${SIZEOF_LONG}" STREQUAL "8")
|
||||
set(SAINT64_TYPE "long")
|
||||
set(SAINT64_PRId "\"ld\"")
|
||||
elseif("${SIZEOF_LONG_LONG}" STREQUAL "8")
|
||||
set(SAINT64_TYPE "long long")
|
||||
set(SAINT64_PRId "\"lld\"")
|
||||
elseif("${SIZEOF___INT64}" STREQUAL "8")
|
||||
set(SAINT64_TYPE "__int64")
|
||||
set(SAINT64_PRId "\"I64d\"")
|
||||
else("${SIZEOF_INT}" STREQUAL "8")
|
||||
message(SEND_ERROR "Cannot find 64-bit integer type")
|
||||
set(BUILD_DIVSUFSORT64 OFF)
|
||||
endif("${SIZEOF_INT}" STREQUAL "8")
|
||||
endif(HAVE_INT64_T)
|
||||
endif(BUILD_DIVSUFSORT64)
|
||||
|
||||
## generate divsufsort.h ##
|
||||
set(DIVSUFSORT_IMPORT "")
|
||||
set(DIVSUFSORT_EXPORT "")
|
||||
if(BUILD_SHARED_LIBS)
|
||||
if(HAVE___DECLSPEC_DLLIMPORT_)
|
||||
set(DIVSUFSORT_IMPORT "__declspec(dllimport)")
|
||||
endif(HAVE___DECLSPEC_DLLIMPORT_)
|
||||
if(HAVE___DECLSPEC_DLLEXPORT_)
|
||||
set(DIVSUFSORT_EXPORT "__declspec(dllexport)")
|
||||
endif(HAVE___DECLSPEC_DLLEXPORT_)
|
||||
endif(BUILD_SHARED_LIBS)
|
||||
set(W64BIT "")
|
||||
set(SAINDEX_TYPE "${SAINT32_TYPE}")
|
||||
set(SAINDEX_PRId "${SAINT32_PRId}")
|
||||
set(SAINT_PRId "${SAINT32_PRId}")
|
||||
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/divsufsort.h.cmake"
|
||||
"${CMAKE_CURRENT_BINARY_DIR}/divsufsort.h" @ONLY)
|
||||
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/divsufsort.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
|
||||
if(BUILD_DIVSUFSORT64)
|
||||
set(W64BIT "64")
|
||||
set(SAINDEX_TYPE "${SAINT64_TYPE}")
|
||||
set(SAINDEX_PRId "${SAINT64_PRId}")
|
||||
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/divsufsort.h.cmake"
|
||||
"${CMAKE_CURRENT_BINARY_DIR}/divsufsort64.h" @ONLY)
|
||||
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/divsufsort64.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
|
||||
endif(BUILD_DIVSUFSORT64)
|
81
include/config.h.cmake
Normal file
81
include/config.h.cmake
Normal file
@ -0,0 +1,81 @@
|
||||
/*
|
||||
* config.h for libdivsufsort
|
||||
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
* OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
#ifndef _CONFIG_H
|
||||
#define _CONFIG_H 1
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif /* __cplusplus */
|
||||
|
||||
/** Define to the version of this package. **/
|
||||
#cmakedefine PROJECT_VERSION_FULL "${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 */
|
180
include/divsufsort.h.cmake
Normal file
180
include/divsufsort.h.cmake
Normal file
@ -0,0 +1,180 @@
|
||||
/*
|
||||
* 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 */
|
207
include/divsufsort_private.h
Normal file
207
include/divsufsort_private.h
Normal file
@ -0,0 +1,207 @@
|
||||
/*
|
||||
* 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 */
|
56
include/lfs.h.cmake
Normal file
56
include/lfs.h.cmake
Normal file
@ -0,0 +1,56 @@
|
||||
/*
|
||||
* lfs.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 _LFS_H
|
||||
#define _LFS_H 1
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif /* __cplusplus */
|
||||
|
||||
#ifndef __STRICT_ANSI__
|
||||
# define LFS_OFF_T @LFS_OFF_T@
|
||||
# define LFS_FOPEN @LFS_FOPEN@
|
||||
# define LFS_FTELL @LFS_FTELL@
|
||||
# define LFS_FSEEK @LFS_FSEEK@
|
||||
# define LFS_PRId @LFS_PRID@
|
||||
#else
|
||||
# define LFS_OFF_T long
|
||||
# define LFS_FOPEN fopen
|
||||
# define LFS_FTELL ftell
|
||||
# define LFS_FSEEK fseek
|
||||
# define LFS_PRId "ld"
|
||||
#endif
|
||||
#ifndef PRIdOFF_T
|
||||
# define PRIdOFF_T LFS_PRId
|
||||
#endif
|
||||
|
||||
|
||||
#ifdef __cplusplus
|
||||
} /* extern "C" */
|
||||
#endif /* __cplusplus */
|
||||
|
||||
#endif /* _LFS_H */
|
31
lib/CMakeLists.txt
Normal file
31
lib/CMakeLists.txt
Normal file
@ -0,0 +1,31 @@
|
||||
include_directories("${CMAKE_CURRENT_SOURCE_DIR}/../include"
|
||||
"${CMAKE_CURRENT_BINARY_DIR}/../include")
|
||||
|
||||
set(divsufsort_SRCS divsufsort.c sssort.c trsort.c utils.c)
|
||||
|
||||
## libdivsufsort ##
|
||||
add_library(divsufsort ${divsufsort_SRCS})
|
||||
install(TARGETS divsufsort
|
||||
RUNTIME DESTINATION ${CMAKE_INSTALL_RUNTIMEDIR}
|
||||
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
|
||||
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
|
||||
set_target_properties(divsufsort PROPERTIES
|
||||
VERSION "${LIBRARY_VERSION}"
|
||||
SOVERSION "${LIBRARY_SOVERSION}"
|
||||
DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL
|
||||
RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples")
|
||||
|
||||
## libdivsufsort64 ##
|
||||
if(BUILD_DIVSUFSORT64)
|
||||
add_library(divsufsort64 ${divsufsort_SRCS})
|
||||
install(TARGETS divsufsort64
|
||||
RUNTIME DESTINATION ${CMAKE_INSTALL_RUNTIMEDIR}
|
||||
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
|
||||
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
|
||||
set_target_properties(divsufsort64 PROPERTIES
|
||||
VERSION "${LIBRARY_VERSION}"
|
||||
SOVERSION "${LIBRARY_SOVERSION}"
|
||||
DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL
|
||||
COMPILE_FLAGS "-DBUILD_DIVSUFSORT64"
|
||||
RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples")
|
||||
endif(BUILD_DIVSUFSORT64)
|
398
lib/divsufsort.c
Normal file
398
lib/divsufsort.c
Normal file
@ -0,0 +1,398 @@
|
||||
/*
|
||||
* 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
lib/sssort.c
Normal file
815
lib/sssort.c
Normal file
@ -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
lib/trsort.c
Normal file
586
lib/trsort.c
Normal file
@ -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
lib/utils.c
Normal file
381
lib/utils.c
Normal file
@ -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;
|
||||
}
|
9
pkgconfig/CMakeLists.txt
Normal file
9
pkgconfig/CMakeLists.txt
Normal file
@ -0,0 +1,9 @@
|
||||
## generate libdivsufsort.pc ##
|
||||
set(W64BIT "")
|
||||
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/libdivsufsort.pc.cmake" "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort.pc" @ONLY)
|
||||
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort.pc" DESTINATION ${CMAKE_INSTALL_PKGCONFIGDIR})
|
||||
if(BUILD_DIVSUFSORT64)
|
||||
set(W64BIT "64")
|
||||
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/libdivsufsort.pc.cmake" "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort64.pc" @ONLY)
|
||||
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort64.pc" DESTINATION ${CMAKE_INSTALL_PKGCONFIGDIR})
|
||||
endif(BUILD_DIVSUFSORT64)
|
11
pkgconfig/libdivsufsort.pc.cmake
Normal file
11
pkgconfig/libdivsufsort.pc.cmake
Normal file
@ -0,0 +1,11 @@
|
||||
prefix=@CMAKE_INSTALL_PREFIX@
|
||||
exec_prefix=${prefix}
|
||||
libdir=@CMAKE_INSTALL_LIBDIR@
|
||||
includedir=@CMAKE_INSTALL_INCLUDEDIR@
|
||||
|
||||
Name: @PROJECT_NAME@@W64BIT@
|
||||
Description: @PROJECT_DESCRIPTION@
|
||||
Version: @PROJECT_VERSION_FULL@
|
||||
URL: @PROJECT_URL@
|
||||
Libs: -L${libdir} -ldivsufsort@W64BIT@
|
||||
Cflags: -I${includedir}
|
Loading…
Reference in New Issue
Block a user