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libdivsufsort as a project module

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This commit is contained in:
rjawor 2013-11-29 16:19:49 +01:00
parent af33bb0de5
commit 307282a760
66 changed files with 44065 additions and 10 deletions
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4
CMakeLists.txt
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@ -1,7 +1,7 @@
# Tutorial: http://www.cmake.org/cmake/help/cmake_tutorial.html
cmake_minimum_required(VERSION 2.6)
project(concordia CXX)
project(concordia C CXX)
set (CONCORDIA_VERSION_MAJOR 0)
set (CONCORDIA_VERSION_MINOR 1)
@ -117,7 +117,7 @@ configure_file (
# Concordia: sub-projects
# ================================================
set(ALL_DIRECTORIES concordia concordia-console)
set(ALL_DIRECTORIES concordia concordia-console libdivsufsort)
include_directories("${concordia_SOURCE_DIR}")

3
concordia-console/concordia-console.cpp
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@ -1,11 +1,10 @@
#include <divsufsort.h>
#include <iostream>
#include <fstream>
#include <boost/program_options.hpp>
#include <boost/algorithm/string.hpp>
#include "concordia/concordia.hpp"
#include "build/libdivsufsort/include/divsufsort.h"
namespace po = boost::program_options;

2
concordia/concordia.hpp
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@ -8,7 +8,7 @@
#include "concordia/concordia_config.hpp"
#include "concordia/concordia_index.hpp"
#include "concordia/index_searcher.hpp"
#include <divsufsort.h>
#include "build/libdivsufsort/include/divsufsort.h"
/*!

2
concordia/concordia_index.hpp
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@ -1,7 +1,6 @@
#ifndef CONCORDIA_INDEX_HDR
#define CONCORDIA_INDEX_HDR
#include <divsufsort.h>
#include <boost/shared_ptr.hpp>
#include <fstream>
#include <iostream>
@ -9,6 +8,7 @@
#include "concordia/hash_generator.hpp"
#include "concordia/concordia_exception.hpp"
#include "build/libdivsufsort/include/divsufsort.h"
/*!
Class for creating and maintaining the index.

2
concordia/hash_generator.hpp
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@ -8,7 +8,7 @@
#include "concordia/word_map.hpp"
#include "concordia/concordia_exception.hpp"
#include <divsufsort.h>
#include "build/libdivsufsort/include/divsufsort.h"
/*!

2
concordia/index_searcher.hpp
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@ -1,11 +1,11 @@
#ifndef INDEX_SEARCHER_HDR
#define INDEX_SEARCHER_HDR
#include <divsufsort.h>
#include <boost/shared_ptr.hpp>
#include <fstream>
#include <iostream>
#include "build/libdivsufsort/include/divsufsort.h"
#include "concordia/hash_generator.hpp"
#include "concordia/concordia_exception.hpp"

2
concordia/word_map.hpp
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@ -8,7 +8,7 @@
#include <boost/archive/text_iarchive.hpp>
#include <boost/serialization/map.hpp>
#include <divsufsort.h>
#include "build/libdivsufsort/include/divsufsort.h"

3
libdivsufsort/AUTHORS Normal file
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@ -0,0 +1,3 @@
-- AUTHORS for libdivsufsort
Yuta Mori <yuta.256@gmail.com>

101
libdivsufsort/CMakeLists.txt Normal file
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@ -0,0 +1,101 @@
### cmake file for building libdivsufsort Package ###
cmake_minimum_required(VERSION 2.4)
set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules")
include(AppendCompilerFlags)
## SVN revision ##
set(SVN_REVISION "")
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.svn")
execute_process(COMMAND svn info --xml
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
OUTPUT_VARIABLE SVN_INFO ERROR_QUIET)
if(SVN_INFO)
string(REGEX MATCH "<entry[^>]+" SVN_REVISION "${SVN_INFO}")
string(REGEX REPLACE "^.*revision=\"([0-9]+)\".*$" "\\1" SVN_REVISION "${SVN_REVISION}")
endif(SVN_INFO)
endif(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.svn")
## Project information ##
project(libdivsufsort C)
set(PROJECT_VENDOR "Yuta Mori")
set(PROJECT_CONTACT "yuta.256@gmail.com")
set(PROJECT_URL "http://libdivsufsort.googlecode.com/")
set(PROJECT_DESCRIPTION "A lightweight suffix sorting library")
file(READ "${CMAKE_CURRENT_SOURCE_DIR}/VERSION" PROJECT_VERSION_FULL)
string(REGEX REPLACE "[\n\r]" "" PROJECT_VERSION_FULL "${PROJECT_VERSION_FULL}")
string(REGEX REPLACE "^([0-9]+)\\.[0-9]+\\.[0-9]+$" "\\1" PROJECT_VERSION_MAJOR "${PROJECT_VERSION_FULL}")
string(REGEX REPLACE "^[0-9]+\\.([0-9]+)\\.[0-9]+$" "\\1" PROJECT_VERSION_MINOR "${PROJECT_VERSION_FULL}")
string(REGEX REPLACE "^[0-9]+\\.[0-9]+\\.([0-9]+)$" "\\1" PROJECT_VERSION_PATCH "${PROJECT_VERSION_FULL}")
set(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}")
math(EXPR LIBRARY_VERSION_MAJOR "1 + ${PROJECT_VERSION_MAJOR}")
set(LIBRARY_VERSION_MINOR "${PROJECT_VERSION_MINOR}")
set(LIBRARY_VERSION_PATCH "${PROJECT_VERSION_PATCH}")
set(LIBRARY_VERSION "${LIBRARY_VERSION_MAJOR}.${LIBRARY_VERSION_MINOR}")
set(LIBRARY_VERSION_FULL "${LIBRARY_VERSION}.${LIBRARY_VERSION_PATCH}")
if(SVN_REVISION)
set(PROJECT_VERSION_FULL "svn-r${SVN_REVISION}")
endif(SVN_REVISION)
## 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)
## 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
libdivsufsort/CMakeModules/AppendCompilerFlags.cmake Normal file
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@ -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
libdivsufsort/CMakeModules/CheckFunctionKeywords.cmake Normal file
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@ -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)

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libdivsufsort/CMakeModules/CheckLFS.cmake Normal file
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@ -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
libdivsufsort/CMakeModules/ProjectCPack.cmake Normal file
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@ -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}/COPYING")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/COPYING")
SET(CPACK_PACKAGE_VERSION_MAJOR "${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
libdivsufsort/CMakeModules/cmake_uninstall.cmake.in Normal file
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@ -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")

27
libdivsufsort/COPYING Normal file
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@ -0,0 +1,27 @@
The libdivsufsort copyright is as follows:
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.
See also the libdivsufsort web site:
http://libdivsufsort.googlecode.com/ for more information.

329
libdivsufsort/ChangeLog Normal file
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@ -0,0 +1,329 @@
2010-11-11 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/CMakeLists.txt
M /trunk/include/CMakeLists.txt
Fixed some bugs in CMakeLists.txt.
2008-08-24 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/lib/divsufsort.c
bug fix in divbwt.
2008-08-23 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/INSTALL
M /trunk/NEWS
M /trunk/README
M /trunk/include/divsufsort.h.cmake
M /trunk/pkgconfig/CMakeLists.txt
M /trunk/pkgconfig/libdivsufsort.pc.cmake
Update files for 2.0.0.
2008-08-23 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/examples/sasearch.c
M /trunk/lib/sssort.c
A few bug fixes.
2008-07-28 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/CMakeLists.txt
M /trunk/include/CMakeLists.txt
M /trunk/include/divsufsort.h.cmake
M /trunk/include/divsufsort_private.h
M /trunk/lib/CMakeLists.txt
M /trunk/lib/divsufsort.c
M /trunk/lib/trsort.c
M /trunk/lib/utils.c
M /trunk/pkgconfig/CMakeLists.txt
M /trunk/pkgconfig/libdivsufsort.pc.cmake
Added 64-bit version of divsufsort.
2008-07-19 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/include/divsufsort_private.h
M /trunk/lib/sssort.c
Fixed integer overflow in ss_isqrt().
2008-07-14 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/examples/mksary.c
M /trunk/examples/sasearch.c
M /trunk/examples/suftest.c
M /trunk/examples/unbwt.c
Rewrote examples.
2008-07-13 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/examples/bwt.c
Rewrote bwt.c.
2008-07-13 Yuta Mori <yuta.256@gmail.com>
Changed paths:
A /trunk/CMakeModules/CheckLFS.cmake
A /trunk/include/lfs.h.cmake
Added files...
2008-07-13 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/CMakeLists.txt
M /trunk/include/CMakeLists.txt
M /trunk/include/config.h.cmake
Added LFS (Large File Support) files.
2008-07-11 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/CMakeLists.txt
Fix version number.
2008-07-11 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/CMakeLists.txt
A /trunk/CMakeModules/ProjectCPack.cmake
M /trunk/COPYING
M /trunk/examples/bwt.c
M /trunk/examples/mksary.c
M /trunk/examples/sasearch.c
M /trunk/examples/suftest.c
M /trunk/examples/unbwt.c
M /trunk/include/config.h.cmake
M /trunk/include/divsufsort.h.cmake
M /trunk/include/divsufsort_private.h
M /trunk/lib/CMakeLists.txt
M /trunk/lib/divsufsort.c
A /trunk/lib/sssort.c (from /trunk/lib/substringsort.c:5)
D /trunk/lib/substringsort.c
M /trunk/lib/trsort.c
M /trunk/lib/utils.c
A /trunk/pkgconfig
A /trunk/pkgconfig/CMakeLists.txt
A /trunk/pkgconfig/libdivsufsort.pc.cmake
Major rewrite of libdivsufsort.
Added CPack support to create the source package.
Added OpenMP support for sssort.
2008-07-03 Yuta Mori <yuta.256@gmail.com>
Changed paths:
A /trunk/CMakeLists.txt
A /trunk/CMakeModules
A /trunk/CMakeModules/AppendCompilerFlags.cmake
A /trunk/CMakeModules/CheckFunctionKeywords.cmake
A /trunk/CMakeModules/cmake_uninstall.cmake.in
M /trunk/INSTALL
D /trunk/Makefile.am
M /trunk/README
A /trunk/VERSION
D /trunk/configure.ac
A /trunk/examples/CMakeLists.txt
D /trunk/examples/Makefile.am
M /trunk/examples/sasearch.c
A /trunk/include/CMakeLists.txt
D /trunk/include/Makefile.am
A /trunk/include/config.h.cmake
A /trunk/include/divsufsort.h.cmake
D /trunk/include/divsufsort.h.in
A /trunk/include/divsufsort_private.h
D /trunk/include/divsufsort_private.h.in
A /trunk/lib/CMakeLists.txt
D /trunk/lib/Makefile.am
M /trunk/lib/divsufsort.c
D /trunk/lib/libdivsufsort.sym
M /trunk/lib/substringsort.c
M /trunk/lib/trsort.c
The build system was changed to CMake. (http://www.cmake.org/)
2008-06-26 Yuta Mori <yuta.256@gmail.com>
Changed paths:
M /trunk/AUTHORS
M /trunk/configure.ac
AUTHORS: Fixed email address.
2008-02-23 Yuta Mori <yiv01157@nifty.com>
* lib/substringsort.c (_merge_backward): Bug fix.
* lib/trsort.c (_tr_introsort): Bug fix.
2007-09-02 Yuta Mori <yiv01157@nifty.com>
* lib/trsort.c (_ls_introsort): Important bug fix.
2007-07-15 Yuta Mori <yiv01157@nifty.com>
A few bug fixes.
* lib/divsufsort.c (divbwt): Bug fix.
* lib/trsort.c (_tr_introsort): Bug fix.
* lib/utils.c (sa_search, sa_simplesearch): New functions.
* lib/libdivsufsort.sym: Update.
* include/divsufsort.h.in: Update.
* examples/sasearch.c: New file.
* examples/Makefile.am: Update.
* configure.ac: Update.
* NEWS: Update.
* README: Update.
2007-04-14 Yuta Mori <yiv01157@nifty.com>
Change license to the MIT/X11 license.
Update all files for 1.2.0.
* lib/libdivsufsort.sym: New file for libtool.
2007-04-07 Yuta Mori <yiv01157@nifty.com>
Update files for 1.1.7.
2007-04-07 Yuta Mori <yiv01157@nifty.com>
Replace drsort with tandem repeat sorting algorithm and Larsson-Sadakane sorting algorithm.
* lib/trsort.c: New file.
* lib/drsort.c: Delete.
* lib/divsufsort.c: Update.
* lib/Makefile.am: Update.
* lib/divsufsort_private.h.in (LS_INSERTIONSORT_THRESHOLD, TR_INSERTIONSORT_THRESHOLD): New constants.
(DR_INSERTIONSORT_THRESHOLD): Delete.
(STACK_PUSH3, STACK_POP3): New macros.
2007-03-31 Yuta Mori <yiv01157@nifty.com>
Update files for 1.1.6.
2007-03-31 Yuta Mori <yiv01157@nifty.com>
Replace _ss_merge with new merge algorithms.
* lib/substringsort.c (_ss_merge): Delete.
* lib/substringsort.c (_block_swap, _merge_forward, _merge_backward, _merge): New functions.
(substringsort): Update.
* lib/divsufsort.c (_sort_typeBstar, divsufsort, divbwt): Update.
* include/divsufsort_private.h.in (LOCALMERGE_BUFFERSIZE): New constant.
(SS_MERGESORT_QUEUESIZE): Delete.
2007-03-24 Yuta Mori <yiv01157@nifty.com>
Update files for 1.1.5.
2007-03-23 Yuta Mori <yiv01157@nifty.com>
Replace breadth-first introsort with new multikey introsort.
* lib/substringsort.c (_compare): Update.
(_substring_partition): Update.
(_multikey_introsort): New function.
(_introsort, _bfintrosort): Delete.
(substringsort): Update.
* lib/divsufsort.c (_sort_typeBstar): Update.
2007-03-21 Yuta Mori <yiv01157@nifty.com>
* lib/substringsort.c (_introsort): Convert introsort to a non-recursive algorithm.
(substringsort): Update.
* lib/divsufsort.c (_sort_typeBstar): Update.
2007-03-21 Yuta Mori <yiv01157@nifty.com>
* include/divsufsort_private.h.in (STACK_SIZE): Rename from SS_STACK_SIZE.
(SS_BLOCKSIZE): Rename from SS_MKQSORT_THRESHOLD.
(SS_MKQSORT_DMAX, SS_DSWAP, SS_STACK_PUSH, SS_STACK_POP): Delete.
(STACK_PUSH, STACK_POP): New macros.
(substringsort): Update prototype.
2007-03-17 Yuta Mori <yiv01157@nifty.com>
Update files for 1.1.4.
2007-03-17 Yuta Mori <yiv01157@nifty.com>
* substringsort.c (_fixdown, _heapsort, _lg): New function.
(_introsort): Rename from _quicksort. Change to use new partitioning algorithm.
(_bfintrosort): Rename from _bfquicksort.
2007-03-10 Yuta Mori <yiv01157@nifty.com>
Update files for 1.1.3.
2007-03-10 Yuta Mori <yiv01157@nifty.com>
Replace depth-first multikey quicksort with new breadth-first ternary quicksort.
* substringsort.c (_ss_compare_lcp, _ss_tqsort, _ss_mkqsort): Remove.
(_median3): Rename from _ss_median and rewrite.
(_pivot): Rename from _ss_pivot and rewrite.
(_median5, _substring_partition, _quicksort, _bfquicksort): New function.
2007-03-03 Yuta Mori <yiv01157@nifty.com>
Update files for 1.1.2.
2007-03-03 Yuta Mori <yiv01157@nifty.com>
* substringsort.c (_compare): Rename from _ss_compare and rewrite.
(_insertionsort): Rename from _ss_insertionsort and rewrite.
2007-02-24 Yuta Mori <yiv01157@nifty.com>
Update files for 1.1.1.
2007-02-24 Yuta Mori <yiv01157@nifty.com>
* lib/substringsort.c (_ss_getc): Remove.
2007-02-17 Yuta Mori <yiv01157@nifty.com>
Update files for 1.1.0.
2007-02-17 Yuta Mori <yiv01157@nifty.com>
* utils.c (bwtcheck): Remove.
2007-02-11 Yuta Mori <yiv01157@nifty.com>
* lib/divsufsort.c,
include/divsufsort.h.in,
include/divsufsort_private.h.in:
Change to use a new improved two-stage sort algorithm (version 070210).
2007-01-28 Yuta Mori <yiv01157@nifty.com>
* lib/divsufsort.c (_sort): Fix a bug that using wrong index.
2007-01-28 Yuta Mori <yiv01157@nifty.com>
* examples/bwt.c: Rename from examples/bwt2.c.
* examples/unbwt.c: Rename from examples/unbwt2.c.
* examples/bwt1.c: Delete.
* examples/unbwt1.c: Delete.
2007-01-28 Yuta Mori <yiv01157@nifty.com>
* lib/divsufsort.c, include/divsufsort_private.h.in:
Change to use new improved two-stage sort algorithm (version 070128).
2007-01-24 Yuta Mori <yiv01157@nifty.com>
Remove use of libtool.
* include/divsufsort_private.h.in: Rename from include/divsufsort_private.h.
2007-01-24 Yuta Mori <yiv01157@nifty.com>
Initial import.
;; Local Variables:
;; coding: utf-8
;; End:

67
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Version 1.0.2 (2006-01-01):
* Release 1.0.2
Version 1.0.2b (2005-12-11):
* lib/divsufsort.c (_construct_typeBstar): Completely rewrite.
Version 1.0.2a (2005-12-04):
* lib/substringsort.c: Completely rewrite.
* lib/drsort.c: Completely rewrite.
* lib/divsufsort.c (_sort_typeBstar): Fix some bugs.
Version 1.0.1 (2005-11-08):
* Release 1.0.1
Version 1.0.1a (2005-11-06):
* configure.ac: Add AM_ENABLE_STATIC, AM_DISABLE_SHARED and AC_LIBTOOL_WIN32_DLL
* Makefile.am (EXTRA_DIST): Add ChangeLog.old.
* lib/divsufsort.c (_construct_typeBstar): Fix.
* AUTHORS: New file.
* ChangeLog: New file.
* ChangeLog.old: New file.
* INSTALL: New file.
* NEWS: New file.
Version 1.0.0 (2005-10-31)
* Introduced autoconf and automake.
* Added new example programs.
Version 0.2.1 (2005-08-27)
* divsufsort.c: Kao's algorithm was replaced with Improved Two-Stage algorithm.
* divsufsort.c: Reduced memory usage.
* substringsort.c: Added mergesort for sorting large groups of suffixes.
Version 0.1.6 (2005-06-10)
* divsufsort.h: Renamed from libdivsufsort.h. (again...)
* divsufsort.c: Renamed from libdivsufsort.c. (again...)
* divsufsort.c: Reduced memory usage.
* substringsort.c, substringsort.h, drsort.c, drsort.h: Modify.
* mksary_mmap/makefile, mksary_mmap/mksary.c,
mksary_mmap/mmap.c, mksary_mmap/mmap.h: Removed.
Version 0.1.5 (2005-04-07)
* libdivsufsort.c: ranksort and doublingsort were replaced with drsort.
* def.h, drsort.c, drsort.h: New file.
* doublingsort.c, doublingsort.h, ranksort.c, ranksort.h: Removed.
Version 0.1.4 (2005-03-27)
* mksary/mksary.c, mksary_mmap/mksary.c, suftest.c: Added error handling.
Version 0.1.3 (2005-01-28)
* mksary/makefile, mksary/mksary.c, mksary_mmap/makefile,
mksary_mmap/mksary.c, mksary_mmap/mmap.c, mksary_mmap/mmap.h: New file.
* libdivsufsort.c: Modify.
Version 0.1.2 (2005-01-01)
* suftest.c: New file.
* libdivsufsort.c: Renamed from divsufsort.c.
* libdivsufsort.h: Renamed from divsufsort.h.

31
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-- INSTALL for libdivsufsort
Requirements:
=============
* CMake version 2.4.2 or newer (http://www.cmake.org/)
* An ANSI C compiler
* GNU Make
Compilation and Installation (with Unix Makefiles):
===================================================
1. Create a 'build' directory in the package source directory.
$ cd libdivsufsort-?.?.?
$ mkdir build
$ cd build
2. Configure the package for your system.
$ cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_INSTALL_PREFIX="/usr/local" ..
3. Compile the package.
$ make
4. Install the library and header files.
# make install

10
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# Makefile.am for libdivsufsort
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EXTRA_DIST = ChangeLog.old CMakeLists.txt VERSION CMakeModules pkgconfig
ACLOCAL_AMFLAGS = -I m4
libtool: $(LIBTOOL_DEPS)
$(SHELL) ./config.status --recheck

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-- NEWS for libdivsufsort
Changes in release 2.0.0
- The build system was changed to CMake. (http://www.cmake.org/)
- Improved the performance of the suffix-sorting algorithm.
- Added OpenMP support.
- Added 64-bit version of divsufsort.
Changes in release 1.2.3
- Bug fixes.
Changes in release 1.2.2
- An important bug fix.
Changes in release 1.2.1
- A few bug fixes.
- New APIs: sa_search, sa_simplesearch.
Changes in release 1.2.0
- Changed license to the MIT/X11 license, see COPYING.
- Improved the performance of the suffix array construction.
- Change to use a new improved two-stage sorting algorithm.
- Replace substringsort with a new sorting algorithm that uses
multikey introspective sorting algorithm and in-place/recursive
merging algorithm.
- Replace drsort with a new sorting algorithm that uses
multikey introspective sorting algorithm, Maniscalco's tandem
repeat sorting algorithm and Larsson-Sadakane sorting algorithm.
- New API: divbwt.
Changes in release 1.0.2
- The performance of sorting has been improved.
- Fix some bugs.
Changes in release 1.0.1
- The performance of sorting has been improved a little bit.

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libdivsufsort - A lightweight suffix-sorting library.
-----------------------------------------------------
Introduction:
-------------
The libdivsufsort project provides a fast, lightweight, and robust
C API library to construct the suffix array and the Burrows-Wheeler
transformed string for any input string of a constant-size alphabet.
The suffix-sorting 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 input string.
The latest version of libdivsufsort is available at:
http://libdivsufsort.googlecode.com/
License:
--------
libdivsufsort is released under the MIT/X11 license. See the file
COPYING for more details.
APIs:
-----
* 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);
* 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.
saint_t
bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *SA,
saidx_t n, saidx_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.
saint_t
inverse_bw_transform(const sauchar_t *T, sauchar_t *U,
saidx_t *A, saidx_t n, saidx_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.
saint_t
sufcheck(const sauchar_t *T, const saidx_t *SA,
saidx_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.
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);
* 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.
saidx_t
sa_simplesearch(const sauchar_t *T, saidx_t Tsize,
const saidx_t *SA, saidx_t SAsize,
saint_t c, saidx_t *idx);
* Returns the version string of libdivsufsort.
* @return the version string.
const char *
divsufsort_version(void);
Benchmark:
------------------
= Specifications =
Processor: 2.66 GHz Intel Core 2 Duo E6750
L1 Cache: (32 Kb + 32 Kb) x 2
L2 Cache: 4 Mb
RAM: 2 Gb main memory
Operating system: Windows XP Home SP 3 (with Cygwin)
Compiler: GCC version 4.3.1
= Programs =
Archon4r0 kvark's sorting algorithm http://forum.compression.ru/viewtopic.php?t=352
BPR Bucket-Pointer Refinement algorithm http://bibiserv.techfak.uni-bielefeld.de/bpr/
DC Difference-Cover algorithm (v = 32) http://www.cs.helsinki.fi/juha.karkkainen/publications/cpm03.tar.gz
DS Deep-Shallow sorting algorithm http://www.mfn.unipmn.it/~manzini/lightweight/
divsufsort1 libdivsufsort version 1.2.3 http://libdivsufsort.googlecode.com/
divsufsort2 libdivsufsort version 2.0.0 http://libdivsufsort.googlecode.com/
KA Ko-Aluru algorithm http://ko.pang.cn.googlepages.com/software2
KS Kärkkäinen-Sanders algorithm http://www.mpi-inf.mpg.de/~sanders/programs/suffix/
MSufSort3 MSufSort version 3.1.1 beta http://www.michael-maniscalco.com/msufsort.htm
qsufsort Larsson-Sadakane algorithm http://www.larsson.dogma.net/research.html
sais Induced Sorting algorithm http://yuta.256.googlepages.com/sais
All programs were compiled with gcc/g++ using '-O3 -fomit-frame-pointer -DNDEBUG'
optimization options. The times are the average of five runs, in seconds, and were
measured using the standard Unix/Cygwin 'time' command. (user + system) The spaces
were measured using the 'memusage' command.
= Testfiles =
Manzini's Large Corpus http://www.mfn.unipmn.it/~manzini/lightweight/corpus/
The Gauntlet http://www.michael-maniscalco.com/testset/gauntlet/
= Running times =
== Manzini's Corpus ==
Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais
chr22.dna 34553758 6.030 6.196 22.694 7.514 5.404 5.362 16.980 50.006 7.132 10.642 10.796
etext99 105277340 22.160 32.582 79.872 34.264 18.758 18.064 73.236 202.684 24.106 56.612 38.748
gcc-3.0.tar 86630400 13.856 20.692 61.690 35.822 10.382 10.084 40.908 135.174 14.952 40.766 20.990
howto 39422105 5.806 8.326 25.432 8.288 5.472 5.320 20.694 64.834 5.672 16.366 11.388
jdk13c 69728899 18.106 22.252 61.234 32.182 9.260 9.010 34.172 101.096 11.314 39.792 16.396
linux-2.4.5.tar 116254720 18.174 26.226 82.830 25.912 14.672 14.290 58.586 194.412 19.890 54.054 29.614
rctail96 114711151 32.490 55.826 119.026 62.502 18.500 17.914 70.072 190.562 21.060 70.456 33.248
rfc 116421901 20.736 35.404 91.284 29.666 16.116 15.658 64.390 196.500 17.936 61.436 32.224
sprot34.dat 109617186 22.832 36.720 93.122 32.096 17.894 17.404 68.084 187.594 23.352 56.946 34.092
w3c2 104201579 27.264 29.384 89.352 54.682 13.866 13.486 52.660 162.582 17.090 77.804 25.498
totals 896819039 187.454 273.608 726.536 322.928 130.324 126.592 499.782 1485.444 162.504 484.874 252.994
== The Gauntlet ==
Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais
abac 200000 0.044 0.064 0.104 27.914 0.042 0.036 0.058 0.048 0.050 0.062 0.044
abba 10500600 3.270 5.124 10.766 30.702 1.714 1.602 2.570 7.952 3.514 15.272 1.460
book1x20 15375420 4.392 3.530 13.872 97.468 2.312 2.154 7.442 15.756 3.542 22.376 3.912
fib_s14930352 14930352 12.728 10.830 18.524 179.040 3.638 3.588 3.544 10.232 6.700 18.224 2.542
fss10 12078908 11.390 8.974 15.130 85.328 2.828 2.824 3.344 8.646 4.618 14.754 2.076
fss9 2851443 1.002 1.210 1.644 5.256 0.410 0.416 0.618 1.290 0.554 2.836 0.336
houston 3840000 0.344 0.708 2.226 118.960 0.118 0.128 0.520 0.744 0.242 1.230 0.238
paper5x80 981924 0.110 0.154 0.454 0.806 0.092 0.090 0.210 0.256 0.144 0.448 0.110
test1 2097152 0.332 2.132 1.108 8.680 0.268 0.280 0.376 1.066 1.302 2.762 0.202
test2 2097152 0.710 0.616 1.110 8.682 0.180 0.176 0.374 1.076 3.354 2.768 0.206
test3 2097152 0.488 213.154 1.164 1.772 0.220 0.226 0.388 1.082 0.922 3.246 0.212
totals 67050103 34.810 246.496 66.102 564.608 11.822 11.520 19.444 48.148 24.942 83.978 11.338
= Space (in MiBytes) =
== Manzini's Corpus ==
Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais
chr22.dna 34553758 174.66 296.88 193.60 165.18 165.02 165.02 289.97 428.39 199.72 263.62 164.77
etext99 105277340 531.13 915.48 589.85 503.23 502.25 502.25 907.34 1305.20 604.45 803.20 502.00
gcc-3.0.tar 86630400 437.14 756.43 485.38 415.87 413.34 413.34 709.50 1074.01 497.79 660.94 413.09
howto 39422105 199.20 367.53 220.88 188.45 188.23 188.23 331.54 488.75 227.67 300.77 187.98
jdk13c 69728899 351.96 603.99 390.68 333.40 332.74 332.74 609.71 864.48 401.04 531.99 332.49
linux-2.4.5.tar 116254720 586.46 1061.83 651.36 555.76 554.60 554.60 977.81 1441.30 667.39 886.95 554.35
rctail96 114711151 578.68 987.64 642.71 548.32 547.24 547.24 1004.98 1422.16 658.43 875.18 546.99
rfc 116421901 587.30 1005.85 652.29 556.53 555.39 555.39 956.52 1443.37 668.26 888.23 555.14
sprot34.dat 109617186 553.01 941.95 614.17 524.03 522.95 522.95 930.06 1359.01 629.26 836.31 522.70
w3c2 104201579 525.71 958.37 583.82 498.09 497.12 497.12 912.00 1291.87 598.82 795.00 496.87
totals 896819039 4525.25 7895.95 5024.74 4288.86 4278.88 4278.88 7629.43 11118.54 5152.83 6842.19 4276.38
mean - 5.29 9.23 5.88 5.01 5.00 5.00 8.92 13.00 6.02 8.00 5.00
== The Gauntlet ==
Files Size Archon4r0 BPR DC DS divsufsort1 divsufsort2 KA KS MSufSort3 qsufsort sais
abac 200000 1.51 1.73 1.12 0.98 1.21 1.20 1.75 2.48 3.15 1.53 0.95
abba 10500600 53.43 90.19 58.83 50.21 50.32 50.32 86.20 130.18 62.09 80.11 50.07
book1x20 15375420 78.00 134.00 86.15 73.52 73.57 73.57 132.42 190.62 89.99 117.31 73.32
fib_s14930352 14930352 75.75 128.15 83.65 71.71 71.44 71.44 117.16 185.10 87.43 113.91 71.19
fss10 12078908 61.38 103.68 67.68 58.05 57.85 57.85 107.05 149.75 71.12 92.16 57.60
fss9 2851443 14.87 24.48 15.98 13.71 13.85 13.85 25.27 35.35 18.32 21.76 13.60
houston 3840000 19.85 36.96 21.52 18.46 18.56 18.56 28.79 47.58 23.98 29.30 18.31
paper5x80 981924 5.45 11.40 5.50 4.72 4.93 4.93 8.59 12.17 7.63 7.49 4.68
test1 2097152 11.07 82.00 11.75 10.10 10.25 10.25 18.34 25.99 14.01 16.00 10.00
test2 2097152 11.07 82.00 11.75 10.10 10.25 10.25 18.34 25.99 14.01 16.00 10.00
test3 2097152 11.07 82.00 11.75 10.05 10.25 10.25 18.34 26.00 14.63 16.00 10.12
totals 67050103 343.45 776.59 375.68 321.61 322.48 322.47 562.25 831.21 406.36 511.57 319.84
mean - 5.37 12.14 5.88 5.03 5.04 5.04 8.79 13.00 6.35 8.00 5.00
Algorithm:
----------
libdivsufsort uses the following algorithms for suffix sorting.
- The improved version of Itho-Tanaka two-stage sorting algorithm. [2][6]
- A substring sorting/encoding technique. [1][3]
- Maniscalco's tandem repeat sorting algorithm. [5]
- Larsson-Sadakane sorting algorithm. [4]
References:
-----------
1. Stefan Burkhardt and Juha K"arkk"ainen. Fast lightweight suffix
array construction and checking. Proceedings of the 14th Annual
Symposium on Combinatorial Pattern Matching, LNCS 2676,
Springer, pp. 55-69, 2003.
2. Hideo Itoh and Hozumi Tanaka, An Efficient Method for in Memory
Construction of Suffix Arrays, Proceedings of the IEEE String
Processing and Information Retrieval Symposium, pp. 81-88, 1999.
3. Pang Ko and Srinivas Aluru, Space-efficient linear time
construction of suffix arrays, Proceedings of the 14th Annual
Symposium on Combinatorial Pattern Matching, pp. 200-210, 2003.
4. Jesper Larsson and Kunihiko Sadakane, Faster suffix sorting.
Technical report LU-CS-TR:99-214, Department of Computer
Science, Lund University, Sweden, 1999.
5. Michael Maniscalco, MSufSort.
http://www.michael-maniscalco.com/msufsort.htm
6. Yuta Mori, Short description of improved two-stage suffix sorting
algorithm, 2005.
http://homepage3.nifty.com/wpage/software/itssort.txt

1
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m4_include([m4/lt~obsolete.m4])

1502
libdivsufsort/config/config.guess vendored Executable file
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630
libdivsufsort/config/depcomp Executable file
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@ -0,0 +1,630 @@
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
scriptversion=2009-04-28.21; # UTC
# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
# Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
case $1 in
'')
echo "$0: No command. Try \`$0 --help' for more information." 1>&2
exit 1;
;;
-h | --h*)
cat <<\EOF
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
Run PROGRAMS ARGS to compile a file, generating dependencies
as side-effects.
Environment variables:
depmode Dependency tracking mode.
source Source file read by `PROGRAMS ARGS'.
object Object file output by `PROGRAMS ARGS'.
DEPDIR directory where to store dependencies.
depfile Dependency file to output.
tmpdepfile Temporary file to use when outputing dependencies.
libtool Whether libtool is used (yes/no).
Report bugs to <bug-automake@gnu.org>.
EOF
exit $?
;;
-v | --v*)
echo "depcomp $scriptversion"
exit $?
;;
esac
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
echo "depcomp: Variables source, object and depmode must be set" 1>&2
exit 1
fi
# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
depfile=${depfile-`echo "$object" |
sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
rm -f "$tmpdepfile"
# Some modes work just like other modes, but use different flags. We
# parameterize here, but still list the modes in the big case below,
# to make depend.m4 easier to write. Note that we *cannot* use a case
# here, because this file can only contain one case statement.
if test "$depmode" = hp; then
# HP compiler uses -M and no extra arg.
gccflag=-M
depmode=gcc
fi
if test "$depmode" = dashXmstdout; then
# This is just like dashmstdout with a different argument.
dashmflag=-xM
depmode=dashmstdout
fi
cygpath_u="cygpath -u -f -"
if test "$depmode" = msvcmsys; then
# This is just like msvisualcpp but w/o cygpath translation.
# Just convert the backslash-escaped backslashes to single forward
# slashes to satisfy depend.m4
cygpath_u="sed s,\\\\\\\\,/,g"
depmode=msvisualcpp
fi
case "$depmode" in
gcc3)
## gcc 3 implements dependency tracking that does exactly what
## we want. Yay! Note: for some reason libtool 1.4 doesn't like
## it if -MD -MP comes after the -MF stuff. Hmm.
## Unfortunately, FreeBSD c89 acceptance of flags depends upon
## the command line argument order; so add the flags where they
## appear in depend2.am. Note that the slowdown incurred here
## affects only configure: in makefiles, %FASTDEP% shortcuts this.
for arg
do
case $arg in
-c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
*) set fnord "$@" "$arg" ;;
esac
shift # fnord
shift # $arg
done
"$@"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
mv "$tmpdepfile" "$depfile"
;;
gcc)
## There are various ways to get dependency output from gcc. Here's
## why we pick this rather obscure method:
## - Don't want to use -MD because we'd like the dependencies to end
## up in a subdir. Having to rename by hand is ugly.
## (We might end up doing this anyway to support other compilers.)
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
## -MM, not -M (despite what the docs say).
## - Using -M directly means running the compiler twice (even worse
## than renaming).
if test -z "$gccflag"; then
gccflag=-MD,
fi
"$@" -Wp,"$gccflag$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
echo "$object : \\" > "$depfile"
alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
## The second -e expression handles DOS-style file names with drive letters.
sed -e 's/^[^:]*: / /' \
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
## This next piece of magic avoids the `deleted header file' problem.
## The problem is that when a header file which appears in a .P file
## is deleted, the dependency causes make to die (because there is
## typically no way to rebuild the header). We avoid this by adding
## dummy dependencies for each header file. Too bad gcc doesn't do
## this for us directly.
tr ' ' '
' < "$tmpdepfile" |
## Some versions of gcc put a space before the `:'. On the theory
## that the space means something, we add a space to the output as
## well.
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
hp)
# This case exists only to let depend.m4 do its work. It works by
# looking at the text of this script. This case will never be run,
# since it is checked for above.
exit 1
;;
sgi)
if test "$libtool" = yes; then
"$@" "-Wp,-MDupdate,$tmpdepfile"
else
"$@" -MDupdate "$tmpdepfile"
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
echo "$object : \\" > "$depfile"
# Clip off the initial element (the dependent). Don't try to be
# clever and replace this with sed code, as IRIX sed won't handle
# lines with more than a fixed number of characters (4096 in
# IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
# the IRIX cc adds comments like `#:fec' to the end of the
# dependency line.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
tr '
' ' ' >> "$depfile"
echo >> "$depfile"
# The second pass generates a dummy entry for each header file.
tr ' ' '
' < "$tmpdepfile" \
| sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
>> "$depfile"
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
aix)
# The C for AIX Compiler uses -M and outputs the dependencies
# in a .u file. In older versions, this file always lives in the
# current directory. Also, the AIX compiler puts `$object:' at the
# start of each line; $object doesn't have directory information.
# Version 6 uses the directory in both cases.
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
test "x$dir" = "x$object" && dir=
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.u
tmpdepfile2=$base.u
tmpdepfile3=$dir.libs/$base.u
"$@" -Wc,-M
else
tmpdepfile1=$dir$base.u
tmpdepfile2=$dir$base.u
tmpdepfile3=$dir$base.u
"$@" -M
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
exit $stat
fi
for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
do
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
# Each line is of the form `foo.o: dependent.h'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
# That's a tab and a space in the [].
sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
else
# The sourcefile does not contain any dependencies, so just
# store a dummy comment line, to avoid errors with the Makefile
# "include basename.Plo" scheme.
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
icc)
# Intel's C compiler understands `-MD -MF file'. However on
# icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
# ICC 7.0 will fill foo.d with something like
# foo.o: sub/foo.c
# foo.o: sub/foo.h
# which is wrong. We want:
# sub/foo.o: sub/foo.c
# sub/foo.o: sub/foo.h
# sub/foo.c:
# sub/foo.h:
# ICC 7.1 will output
# foo.o: sub/foo.c sub/foo.h
# and will wrap long lines using \ :
# foo.o: sub/foo.c ... \
# sub/foo.h ... \
# ...
"$@" -MD -MF "$tmpdepfile"
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
# Each line is of the form `foo.o: dependent.h',
# or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
# Do two passes, one to just change these to
# `$object: dependent.h' and one to simply `dependent.h:'.
sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
# Some versions of the HPUX 10.20 sed can't process this invocation
# correctly. Breaking it into two sed invocations is a workaround.
sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
hp2)
# The "hp" stanza above does not work with aCC (C++) and HP's ia64
# compilers, which have integrated preprocessors. The correct option
# to use with these is +Maked; it writes dependencies to a file named
# 'foo.d', which lands next to the object file, wherever that
# happens to be.
# Much of this is similar to the tru64 case; see comments there.
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
test "x$dir" = "x$object" && dir=
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.d
tmpdepfile2=$dir.libs/$base.d
"$@" -Wc,+Maked
else
tmpdepfile1=$dir$base.d
tmpdepfile2=$dir$base.d
"$@" +Maked
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile1" "$tmpdepfile2"
exit $stat
fi
for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
do
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
# Add `dependent.h:' lines.
sed -ne '2,${
s/^ *//
s/ \\*$//
s/$/:/
p
}' "$tmpdepfile" >> "$depfile"
else
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile" "$tmpdepfile2"
;;
tru64)
# The Tru64 compiler uses -MD to generate dependencies as a side
# effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
# At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
# dependencies in `foo.d' instead, so we check for that too.
# Subdirectories are respected.
dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
test "x$dir" = "x$object" && dir=
base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
if test "$libtool" = yes; then
# With Tru64 cc, shared objects can also be used to make a
# static library. This mechanism is used in libtool 1.4 series to
# handle both shared and static libraries in a single compilation.
# With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
#
# With libtool 1.5 this exception was removed, and libtool now
# generates 2 separate objects for the 2 libraries. These two
# compilations output dependencies in $dir.libs/$base.o.d and
# in $dir$base.o.d. We have to check for both files, because
# one of the two compilations can be disabled. We should prefer
# $dir$base.o.d over $dir.libs/$base.o.d because the latter is
# automatically cleaned when .libs/ is deleted, while ignoring
# the former would cause a distcleancheck panic.
tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
tmpdepfile2=$dir$base.o.d # libtool 1.5
tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
"$@" -Wc,-MD
else
tmpdepfile1=$dir$base.o.d
tmpdepfile2=$dir$base.d
tmpdepfile3=$dir$base.d
tmpdepfile4=$dir$base.d
"$@" -MD
fi
stat=$?
if test $stat -eq 0; then :
else
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
exit $stat
fi
for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
do
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
# That's a tab and a space in the [].
sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
else
echo "#dummy" > "$depfile"
fi
rm -f "$tmpdepfile"
;;
#nosideeffect)
# This comment above is used by automake to tell side-effect
# dependency tracking mechanisms from slower ones.
dashmstdout)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout, regardless of -o.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test "X$1" != 'X--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
test -z "$dashmflag" && dashmflag=-M
# Require at least two characters before searching for `:'
# in the target name. This is to cope with DOS-style filenames:
# a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
"$@" $dashmflag |
sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
tr ' ' '
' < "$tmpdepfile" | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
dashXmstdout)
# This case only exists to satisfy depend.m4. It is never actually
# run, as this mode is specially recognized in the preamble.
exit 1
;;
makedepend)
"$@" || exit $?
# Remove any Libtool call
if test "$libtool" = yes; then
while test "X$1" != 'X--mode=compile'; do
shift
done
shift
fi
# X makedepend
shift
cleared=no eat=no
for arg
do
case $cleared in
no)
set ""; shift
cleared=yes ;;
esac
if test $eat = yes; then
eat=no
continue
fi
case "$arg" in
-D*|-I*)
set fnord "$@" "$arg"; shift ;;
# Strip any option that makedepend may not understand. Remove
# the object too, otherwise makedepend will parse it as a source file.
-arch)
eat=yes ;;
-*|$object)
;;
*)
set fnord "$@" "$arg"; shift ;;
esac
done
obj_suffix=`echo "$object" | sed 's/^.*\././'`
touch "$tmpdepfile"
${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
rm -f "$depfile"
cat < "$tmpdepfile" > "$depfile"
sed '1,2d' "$tmpdepfile" | tr ' ' '
' | \
## Some versions of the HPUX 10.20 sed can't process this invocation
## correctly. Breaking it into two sed invocations is a workaround.
sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile" "$tmpdepfile".bak
;;
cpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test "X$1" != 'X--mode=compile'; do
shift
done
shift
fi
# Remove `-o $object'.
IFS=" "
for arg
do
case $arg in
-o)
shift
;;
$object)
shift
;;
*)
set fnord "$@" "$arg"
shift # fnord
shift # $arg
;;
esac
done
"$@" -E |
sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
-e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
sed '$ s: \\$::' > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
cat < "$tmpdepfile" >> "$depfile"
sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
msvisualcpp)
# Important note: in order to support this mode, a compiler *must*
# always write the preprocessed file to stdout.
"$@" || exit $?
# Remove the call to Libtool.
if test "$libtool" = yes; then
while test "X$1" != 'X--mode=compile'; do
shift
done
shift
fi
IFS=" "
for arg
do
case "$arg" in
-o)
shift
;;
$object)
shift
;;
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
set fnord "$@"
shift
shift
;;
*)
set fnord "$@" "$arg"
shift
shift
;;
esac
done
"$@" -E 2>/dev/null |
sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
rm -f "$depfile"
echo "$object : \\" > "$depfile"
sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
echo " " >> "$depfile"
sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
msvcmsys)
# This case exists only to let depend.m4 do its work. It works by
# looking at the text of this script. This case will never be run,
# since it is checked for above.
exit 1
;;
none)
exec "$@"
;;
*)
echo "Unknown depmode $depmode" 1>&2
exit 1
;;
esac
exit 0
# Local Variables:
# mode: shell-script
# sh-indentation: 2
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:

520
libdivsufsort/config/install-sh Executable file
View File

@ -0,0 +1,520 @@
#!/bin/sh
# install - install a program, script, or datafile
scriptversion=2009-04-28.21; # UTC
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
# following copyright and license.
#
# Copyright (C) 1994 X Consortium
#
# 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
# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# Except as contained in this notice, the name of the X Consortium shall not
# be used in advertising or otherwise to promote the sale, use or other deal-
# ings in this Software without prior written authorization from the X Consor-
# tium.
#
#
# FSF changes to this file are in the public domain.
#
# Calling this script install-sh is preferred over install.sh, to prevent
# `make' implicit rules from creating a file called install from it
# when there is no Makefile.
#
# This script is compatible with the BSD install script, but was written
# from scratch.
nl='
'
IFS=" "" $nl"
# set DOITPROG to echo to test this script
# Don't use :- since 4.3BSD and earlier shells don't like it.
doit=${DOITPROG-}
if test -z "$doit"; then
doit_exec=exec
else
doit_exec=$doit
fi
# Put in absolute file names if you don't have them in your path;
# or use environment vars.
chgrpprog=${CHGRPPROG-chgrp}
chmodprog=${CHMODPROG-chmod}
chownprog=${CHOWNPROG-chown}
cmpprog=${CMPPROG-cmp}
cpprog=${CPPROG-cp}
mkdirprog=${MKDIRPROG-mkdir}
mvprog=${MVPROG-mv}
rmprog=${RMPROG-rm}
stripprog=${STRIPPROG-strip}
posix_glob='?'
initialize_posix_glob='
test "$posix_glob" != "?" || {
if (set -f) 2>/dev/null; then
posix_glob=
else
posix_glob=:
fi
}
'
posix_mkdir=
# Desired mode of installed file.
mode=0755
chgrpcmd=
chmodcmd=$chmodprog
chowncmd=
mvcmd=$mvprog
rmcmd="$rmprog -f"
stripcmd=
src=
dst=
dir_arg=
dst_arg=
copy_on_change=false
no_target_directory=
usage="\
Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
or: $0 [OPTION]... SRCFILES... DIRECTORY
or: $0 [OPTION]... -t DIRECTORY SRCFILES...
or: $0 [OPTION]... -d DIRECTORIES...
In the 1st form, copy SRCFILE to DSTFILE.
In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
In the 4th, create DIRECTORIES.
Options:
--help display this help and exit.
--version display version info and exit.
-c (ignored)
-C install only if different (preserve the last data modification time)
-d create directories instead of installing files.
-g GROUP $chgrpprog installed files to GROUP.
-m MODE $chmodprog installed files to MODE.
-o USER $chownprog installed files to USER.
-s $stripprog installed files.
-t DIRECTORY install into DIRECTORY.
-T report an error if DSTFILE is a directory.
Environment variables override the default commands:
CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
RMPROG STRIPPROG
"
while test $# -ne 0; do
case $1 in
-c) ;;
-C) copy_on_change=true;;
-d) dir_arg=true;;
-g) chgrpcmd="$chgrpprog $2"
shift;;
--help) echo "$usage"; exit $?;;
-m) mode=$2
case $mode in
*' '* | *' '* | *'
'* | *'*'* | *'?'* | *'['*)
echo "$0: invalid mode: $mode" >&2
exit 1;;
esac
shift;;
-o) chowncmd="$chownprog $2"
shift;;
-s) stripcmd=$stripprog;;
-t) dst_arg=$2
shift;;
-T) no_target_directory=true;;
--version) echo "$0 $scriptversion"; exit $?;;
--) shift
break;;
-*) echo "$0: invalid option: $1" >&2
exit 1;;
*) break;;
esac
shift
done
if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
# When -d is used, all remaining arguments are directories to create.
# When -t is used, the destination is already specified.
# Otherwise, the last argument is the destination. Remove it from $@.
for arg
do
if test -n "$dst_arg"; then
# $@ is not empty: it contains at least $arg.
set fnord "$@" "$dst_arg"
shift # fnord
fi
shift # arg
dst_arg=$arg
done
fi
if test $# -eq 0; then
if test -z "$dir_arg"; then
echo "$0: no input file specified." >&2
exit 1
fi
# It's OK to call `install-sh -d' without argument.
# This can happen when creating conditional directories.
exit 0
fi
if test -z "$dir_arg"; then
trap '(exit $?); exit' 1 2 13 15
# Set umask so as not to create temps with too-generous modes.
# However, 'strip' requires both read and write access to temps.
case $mode in
# Optimize common cases.
*644) cp_umask=133;;
*755) cp_umask=22;;
*[0-7])
if test -z "$stripcmd"; then
u_plus_rw=
else
u_plus_rw='% 200'
fi
cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
*)
if test -z "$stripcmd"; then
u_plus_rw=
else
u_plus_rw=,u+rw
fi
cp_umask=$mode$u_plus_rw;;
esac
fi
for src
do
# Protect names starting with `-'.
case $src in
-*) src=./$src;;
esac
if test -n "$dir_arg"; then
dst=$src
dstdir=$dst
test -d "$dstdir"
dstdir_status=$?
else
# Waiting for this to be detected by the "$cpprog $src $dsttmp" command
# might cause directories to be created, which would be especially bad
# if $src (and thus $dsttmp) contains '*'.
if test ! -f "$src" && test ! -d "$src"; then
echo "$0: $src does not exist." >&2
exit 1
fi
if test -z "$dst_arg"; then
echo "$0: no destination specified." >&2
exit 1
fi
dst=$dst_arg
# Protect names starting with `-'.
case $dst in
-*) dst=./$dst;;
esac
# If destination is a directory, append the input filename; won't work
# if double slashes aren't ignored.
if test -d "$dst"; then
if test -n "$no_target_directory"; then
echo "$0: $dst_arg: Is a directory" >&2
exit 1
fi
dstdir=$dst
dst=$dstdir/`basename "$src"`
dstdir_status=0
else
# Prefer dirname, but fall back on a substitute if dirname fails.
dstdir=`
(dirname "$dst") 2>/dev/null ||
expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
X"$dst" : 'X\(//\)[^/]' \| \
X"$dst" : 'X\(//\)$' \| \
X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
echo X"$dst" |
sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
s//\1/
q
}
/^X\(\/\/\)[^/].*/{
s//\1/
q
}
/^X\(\/\/\)$/{
s//\1/
q
}
/^X\(\/\).*/{
s//\1/
q
}
s/.*/./; q'
`
test -d "$dstdir"
dstdir_status=$?
fi
fi
obsolete_mkdir_used=false
if test $dstdir_status != 0; then
case $posix_mkdir in
'')
# Create intermediate dirs using mode 755 as modified by the umask.
# This is like FreeBSD 'install' as of 1997-10-28.
umask=`umask`
case $stripcmd.$umask in
# Optimize common cases.
*[2367][2367]) mkdir_umask=$umask;;
.*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
*[0-7])
mkdir_umask=`expr $umask + 22 \
- $umask % 100 % 40 + $umask % 20 \
- $umask % 10 % 4 + $umask % 2
`;;
*) mkdir_umask=$umask,go-w;;
esac
# With -d, create the new directory with the user-specified mode.
# Otherwise, rely on $mkdir_umask.
if test -n "$dir_arg"; then
mkdir_mode=-m$mode
else
mkdir_mode=
fi
posix_mkdir=false
case $umask in
*[123567][0-7][0-7])
# POSIX mkdir -p sets u+wx bits regardless of umask, which
# is incompatible with FreeBSD 'install' when (umask & 300) != 0.
;;
*)
tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
if (umask $mkdir_umask &&
exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
then
if test -z "$dir_arg" || {
# Check for POSIX incompatibilities with -m.
# HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
# other-writeable bit of parent directory when it shouldn't.
# FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
ls_ld_tmpdir=`ls -ld "$tmpdir"`
case $ls_ld_tmpdir in
d????-?r-*) different_mode=700;;
d????-?--*) different_mode=755;;
*) false;;
esac &&
$mkdirprog -m$different_mode -p -- "$tmpdir" && {
ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
}
}
then posix_mkdir=:
fi
rmdir "$tmpdir/d" "$tmpdir"
else
# Remove any dirs left behind by ancient mkdir implementations.
rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
fi
trap '' 0;;
esac;;
esac
if
$posix_mkdir && (
umask $mkdir_umask &&
$doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
)
then :
else
# The umask is ridiculous, or mkdir does not conform to POSIX,
# or it failed possibly due to a race condition. Create the
# directory the slow way, step by step, checking for races as we go.
case $dstdir in
/*) prefix='/';;
-*) prefix='./';;
*) prefix='';;
esac
eval "$initialize_posix_glob"
oIFS=$IFS
IFS=/
$posix_glob set -f
set fnord $dstdir
shift
$posix_glob set +f
IFS=$oIFS
prefixes=
for d
do
test -z "$d" && continue
prefix=$prefix$d
if test -d "$prefix"; then
prefixes=
else
if $posix_mkdir; then
(umask=$mkdir_umask &&
$doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
# Don't fail if two instances are running concurrently.
test -d "$prefix" || exit 1
else
case $prefix in
*\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
*) qprefix=$prefix;;
esac
prefixes="$prefixes '$qprefix'"
fi
fi
prefix=$prefix/
done
if test -n "$prefixes"; then
# Don't fail if two instances are running concurrently.
(umask $mkdir_umask &&
eval "\$doit_exec \$mkdirprog $prefixes") ||
test -d "$dstdir" || exit 1
obsolete_mkdir_used=true
fi
fi
fi
if test -n "$dir_arg"; then
{ test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
{ test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
{ test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
else
# Make a couple of temp file names in the proper directory.
dsttmp=$dstdir/_inst.$$_
rmtmp=$dstdir/_rm.$$_
# Trap to clean up those temp files at exit.
trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
# Copy the file name to the temp name.
(umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
# and set any options; do chmod last to preserve setuid bits.
#
# If any of these fail, we abort the whole thing. If we want to
# ignore errors from any of these, just make sure not to ignore
# errors from the above "$doit $cpprog $src $dsttmp" command.
#
{ test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
{ test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
{ test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
{ test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
# If -C, don't bother to copy if it wouldn't change the file.
if $copy_on_change &&
old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
eval "$initialize_posix_glob" &&
$posix_glob set -f &&
set X $old && old=:$2:$4:$5:$6 &&
set X $new && new=:$2:$4:$5:$6 &&
$posix_glob set +f &&
test "$old" = "$new" &&
$cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
then
rm -f "$dsttmp"
else
# Rename the file to the real destination.
$doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
# The rename failed, perhaps because mv can't rename something else
# to itself, or perhaps because mv is so ancient that it does not
# support -f.
{
# Now remove or move aside any old file at destination location.
# We try this two ways since rm can't unlink itself on some
# systems and the destination file might be busy for other
# reasons. In this case, the final cleanup might fail but the new
# file should still install successfully.
{
test ! -f "$dst" ||
$doit $rmcmd -f "$dst" 2>/dev/null ||
{ $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
{ $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
} ||
{ echo "$0: cannot unlink or rename $dst" >&2
(exit 1); exit 1
}
} &&
# Now rename the file to the real destination.
$doit $mvcmd "$dsttmp" "$dst"
}
fi || exit 1
trap '' 0
fi
done
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:

8413
libdivsufsort/config/ltmain.sh Executable file
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376
libdivsufsort/config/missing Executable file
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#! /bin/sh
# Common stub for a few missing GNU programs while installing.
scriptversion=2009-04-28.21; # UTC
# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
# 2008, 2009 Free Software Foundation, Inc.
# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
if test $# -eq 0; then
echo 1>&2 "Try \`$0 --help' for more information"
exit 1
fi
run=:
sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
# In the cases where this matters, `missing' is being run in the
# srcdir already.
if test -f configure.ac; then
configure_ac=configure.ac
else
configure_ac=configure.in
fi
msg="missing on your system"
case $1 in
--run)
# Try to run requested program, and just exit if it succeeds.
run=
shift
"$@" && exit 0
# Exit code 63 means version mismatch. This often happens
# when the user try to use an ancient version of a tool on
# a file that requires a minimum version. In this case we
# we should proceed has if the program had been absent, or
# if --run hadn't been passed.
if test $? = 63; then
run=:
msg="probably too old"
fi
;;
-h|--h|--he|--hel|--help)
echo "\
$0 [OPTION]... PROGRAM [ARGUMENT]...
Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
error status if there is no known handling for PROGRAM.
Options:
-h, --help display this help and exit
-v, --version output version information and exit
--run try to run the given command, and emulate it if it fails
Supported PROGRAM values:
aclocal touch file \`aclocal.m4'
autoconf touch file \`configure'
autoheader touch file \`config.h.in'
autom4te touch the output file, or create a stub one
automake touch all \`Makefile.in' files
bison create \`y.tab.[ch]', if possible, from existing .[ch]
flex create \`lex.yy.c', if possible, from existing .c
help2man touch the output file
lex create \`lex.yy.c', if possible, from existing .c
makeinfo touch the output file
tar try tar, gnutar, gtar, then tar without non-portable flags
yacc create \`y.tab.[ch]', if possible, from existing .[ch]
Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
\`g' are ignored when checking the name.
Send bug reports to <bug-automake@gnu.org>."
exit $?
;;
-v|--v|--ve|--ver|--vers|--versi|--versio|--version)
echo "missing $scriptversion (GNU Automake)"
exit $?
;;
-*)
echo 1>&2 "$0: Unknown \`$1' option"
echo 1>&2 "Try \`$0 --help' for more information"
exit 1
;;
esac
# normalize program name to check for.
program=`echo "$1" | sed '
s/^gnu-//; t
s/^gnu//; t
s/^g//; t'`
# Now exit if we have it, but it failed. Also exit now if we
# don't have it and --version was passed (most likely to detect
# the program). This is about non-GNU programs, so use $1 not
# $program.
case $1 in
lex*|yacc*)
# Not GNU programs, they don't have --version.
;;
tar*)
if test -n "$run"; then
echo 1>&2 "ERROR: \`tar' requires --run"
exit 1
elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
exit 1
fi
;;
*)
if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
# We have it, but it failed.
exit 1
elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
# Could not run --version or --help. This is probably someone
# running `$TOOL --version' or `$TOOL --help' to check whether
# $TOOL exists and not knowing $TOOL uses missing.
exit 1
fi
;;
esac
# If it does not exist, or fails to run (possibly an outdated version),
# try to emulate it.
case $program in
aclocal*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified \`acinclude.m4' or \`${configure_ac}'. You might want
to install the \`Automake' and \`Perl' packages. Grab them from
any GNU archive site."
touch aclocal.m4
;;
autoconf*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified \`${configure_ac}'. You might want to install the
\`Autoconf' and \`GNU m4' packages. Grab them from any GNU
archive site."
touch configure
;;
autoheader*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified \`acconfig.h' or \`${configure_ac}'. You might want
to install the \`Autoconf' and \`GNU m4' packages. Grab them
from any GNU archive site."
files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
test -z "$files" && files="config.h"
touch_files=
for f in $files; do
case $f in
*:*) touch_files="$touch_files "`echo "$f" |
sed -e 's/^[^:]*://' -e 's/:.*//'`;;
*) touch_files="$touch_files $f.in";;
esac
done
touch $touch_files
;;
automake*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
You might want to install the \`Automake' and \`Perl' packages.
Grab them from any GNU archive site."
find . -type f -name Makefile.am -print |
sed 's/\.am$/.in/' |
while read f; do touch "$f"; done
;;
autom4te*)
echo 1>&2 "\
WARNING: \`$1' is needed, but is $msg.
You might have modified some files without having the
proper tools for further handling them.
You can get \`$1' as part of \`Autoconf' from any GNU
archive site."
file=`echo "$*" | sed -n "$sed_output"`
test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
if test -f "$file"; then
touch $file
else
test -z "$file" || exec >$file
echo "#! /bin/sh"
echo "# Created by GNU Automake missing as a replacement of"
echo "# $ $@"
echo "exit 0"
chmod +x $file
exit 1
fi
;;
bison*|yacc*)
echo 1>&2 "\
WARNING: \`$1' $msg. You should only need it if
you modified a \`.y' file. You may need the \`Bison' package
in order for those modifications to take effect. You can get
\`Bison' from any GNU archive site."
rm -f y.tab.c y.tab.h
if test $# -ne 1; then
eval LASTARG="\${$#}"
case $LASTARG in
*.y)
SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
if test -f "$SRCFILE"; then
cp "$SRCFILE" y.tab.c
fi
SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
if test -f "$SRCFILE"; then
cp "$SRCFILE" y.tab.h
fi
;;
esac
fi
if test ! -f y.tab.h; then
echo >y.tab.h
fi
if test ! -f y.tab.c; then
echo 'main() { return 0; }' >y.tab.c
fi
;;
lex*|flex*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified a \`.l' file. You may need the \`Flex' package
in order for those modifications to take effect. You can get
\`Flex' from any GNU archive site."
rm -f lex.yy.c
if test $# -ne 1; then
eval LASTARG="\${$#}"
case $LASTARG in
*.l)
SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
if test -f "$SRCFILE"; then
cp "$SRCFILE" lex.yy.c
fi
;;
esac
fi
if test ! -f lex.yy.c; then
echo 'main() { return 0; }' >lex.yy.c
fi
;;
help2man*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified a dependency of a manual page. You may need the
\`Help2man' package in order for those modifications to take
effect. You can get \`Help2man' from any GNU archive site."
file=`echo "$*" | sed -n "$sed_output"`
test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
if test -f "$file"; then
touch $file
else
test -z "$file" || exec >$file
echo ".ab help2man is required to generate this page"
exit $?
fi
;;
makeinfo*)
echo 1>&2 "\
WARNING: \`$1' is $msg. You should only need it if
you modified a \`.texi' or \`.texinfo' file, or any other file
indirectly affecting the aspect of the manual. The spurious
call might also be the consequence of using a buggy \`make' (AIX,
DU, IRIX). You might want to install the \`Texinfo' package or
the \`GNU make' package. Grab either from any GNU archive site."
# The file to touch is that specified with -o ...
file=`echo "$*" | sed -n "$sed_output"`
test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
if test -z "$file"; then
# ... or it is the one specified with @setfilename ...
infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
file=`sed -n '
/^@setfilename/{
s/.* \([^ ]*\) *$/\1/
p
q
}' $infile`
# ... or it is derived from the source name (dir/f.texi becomes f.info)
test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
fi
# If the file does not exist, the user really needs makeinfo;
# let's fail without touching anything.
test -f $file || exit 1
touch $file
;;
tar*)
shift
# We have already tried tar in the generic part.
# Look for gnutar/gtar before invocation to avoid ugly error
# messages.
if (gnutar --version > /dev/null 2>&1); then
gnutar "$@" && exit 0
fi
if (gtar --version > /dev/null 2>&1); then
gtar "$@" && exit 0
fi
firstarg="$1"
if shift; then
case $firstarg in
*o*)
firstarg=`echo "$firstarg" | sed s/o//`
tar "$firstarg" "$@" && exit 0
;;
esac
case $firstarg in
*h*)
firstarg=`echo "$firstarg" | sed s/h//`
tar "$firstarg" "$@" && exit 0
;;
esac
fi
echo 1>&2 "\
WARNING: I can't seem to be able to run \`tar' with the given arguments.
You may want to install GNU tar or Free paxutils, or check the
command line arguments."
exit 1
;;
*)
echo 1>&2 "\
WARNING: \`$1' is needed, and is $msg.
You might have modified some files without having the
proper tools for further handling them. Check the \`README' file,
it often tells you about the needed prerequisites for installing
this package. You may also peek at any GNU archive site, in case
some other package would contain this missing \`$1' program."
exit 1
;;
esac
exit 0
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:

13977
libdivsufsort/configure vendored Executable file
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198
libdivsufsort/configure.ac Normal file
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## configure.ac for libdivsufsort
AC_PREREQ(2.61)
AC_INIT([libdivsufsort], [2.0.1], [yuta.256@gmail.com])
AC_CONFIG_SRCDIR([include/divsufsort.h.cmake])
AC_CONFIG_HEADER([include/config.h])
AC_CONFIG_AUX_DIR([config])
AC_CONFIG_MACRO_DIR([m4])
AC_CANONICAL_TARGET
AM_INIT_AUTOMAKE([-Wall -Werror foreign 1.10.1 no-define dist-bzip2])
AM_MAINTAINER_MODE
# LT_CURRENT = PROJECT_VERSION_MAJOR + PROJECT_VERSION_MINOR + 1
# LT_AGE = PROJECT_VERSION_MINOR
# LT_REVISION = PROJECT_VERSION_PATCH
AC_SUBST(LT_CURRENT, 3)
AC_SUBST(LT_AGE, 0)
AC_SUBST(LT_REVISION, 1)
AC_SUBST([PROJECT_NAME], [libdivsufsort])
AC_SUBST([PROJECT_DESCRIPTION], "A lightweight suffix sorting library")
AC_SUBST([PROJECT_VERSION_FULL], [2.0.0])
AC_SUBST([PROJECT_URL], "http://libdivsufsort.googlecode.com/")
## Checks for programs.
AC_PROG_CC
AC_PROG_INSTALL
AC_PROG_MAKE_SET
## Checks for compiler output filename suffixes.
AC_OBJEXT
AC_EXEEXT
## Check for build configuration.
#AM_DISABLE_STATIC
AM_DISABLE_SHARED
#AC_LIBTOOL_WIN32_DLL
AC_PROG_LIBTOOL
AC_SUBST([LIBTOOL_DEPS])
case "$target_os" in
cygwin* | mingw*)
LDFLAGS="$LDFLAGS -no-undefined"
;;
esac
## Checks for libraries.
## Checks for header files.
AC_HEADER_STDC
AC_CHECK_HEADERS([inttypes.h memory.h stddef.h stdint.h stdlib.h string.h strings.h sys/types.h io.h fcntl.h])
AS_IF([test "$ac_cv_header_inttypes_h" == "yes"],
[AC_SUBST([INCFILE], ["#include <inttypes.h>"])],
[test "$ac_cv_header_stdint_h" == "yes"],
[AC_SUBST([INCFILE], ["#include <stdint.h>"])],
[AC_SUBST([INCFILE], [""])])
## Checks for typedefs, structures, and compiler characteristics.
# sauchar_t
SAUCHAR_TYPE=""
AC_CHECK_TYPES([uint8_t])
if test "$ac_cv_type_uint8_t" = "yes"; then
SAUCHAR_TYPE="uint8_t"
fi
if test -z "$SAUCHAR_TYPE";then
AC_CHECK_SIZEOF([unsigned char], 1)
if test "$ac_cv_sizeof_unsigned_char" = "1";then SAUCHAR_TYPE="unsigned char"; fi
fi
if test -z "$SAUCHAR_TYPE";then
AC_MSG_ERROR([Cannot find unsigned 8-bit integer type])
fi
AC_SUBST([SAUCHAR_TYPE])
# saint_t and saidx_t
SAINT32_TYPE=""
AC_CHECK_TYPES([int32_t])
if test "$ac_cv_type_int32_t" = "yes"; then
SAINT32_TYPE="int32_t";
SAINT32_PRId="PRId32";
fi
if test -z "$SAINT32_TYPE";then
AC_CHECK_SIZEOF([int], 4)
if test "$ac_cv_sizeof_int" = "4";then
SAINT32_TYPE="int";
SAINT32_PRId="\"d\"";
fi
fi
if test -z "$SAINT32_TYPE";then
AC_CHECK_SIZEOF([long], 4)
if test "$ac_cv_sizeof_long" = "4"; then
SAINT32_TYPE="long";
SAINT32_PRId="\"ld\"";
fi
fi
if test -z "$SAINT32_TYPE";then
AC_CHECK_SIZEOF([__int32], 4)
if test "$ac_cv_sizeof___int32" = "4"; then
SAINT32_TYPE="__int32";
SAINT32_PRId="\"I32d\"";
fi
fi
if test -z "$SAINT32_TYPE";then
AC_CHECK_SIZEOF([short], 4)
if test "$ac_cv_sizeof_short" = "4"; then
SAINT32_TYPE="short";
SAINT32_PRId="\"d\"";
fi
fi
if test -z "$SAINT32_TYPE";then
AC_MSG_ERROR([Could not find 32-bit integer type])
fi
AC_SUBST([SAINT32_TYPE])
AC_SUBST([SAINT_PRId], "$SAINT32_PRId")
AC_ARG_ENABLE(divsufsort64, AC_HELP_STRING([--enable-divsufsort64], [build libdivsufsort64]))
if test "$enable_divsufsort64" = "yes"; then
# saint64_t
SAINT64_TYPE=""
AC_CHECK_TYPES([int64_t])
if test "$ac_cv_type_int64_t" = "yes"; then
SAINT64_TYPE="int64_t";
SAINT64_PRId="PRId64";
fi
if test -z "$SAINT64_TYPE";then
AC_CHECK_SIZEOF([long long], 8)
if test "$ac_cv_sizeof_long_long" = "8";then
SAINT64_TYPE="long long";
SAINT64_PRId="\"lld\"";
fi
fi
if test -z "$SAINT64_TYPE";then
AC_CHECK_SIZEOF([long], 8)
if test "$ac_cv_sizeof_long" = "8";then
SAINT64_TYPE="long";
SAINT64_PRId="\"ld\"";
fi
fi
if test -z "$SAINT64_TYPE";then
AC_CHECK_SIZEOF([int], 8)
if test "$ac_cv_sizeof_int" = "8";then
SAINT64_TYPE="int";
SAINT64_PRId="\"d\"";
fi
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if test -z "$SAINT64_TYPE";then
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.NOEXPORT:

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/*
* 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;
}

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/*
* 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;
}

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/*
* 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;
}

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/*
* 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;
}

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/*
* 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;
}

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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 "${CMAKE_CURRENT_BINARY_DIR}/divsufsort.h" DESTINATION include)
if(BUILD_DIVSUFSORT64)
set(W64BIT "64")
set(SAINDEX_TYPE "${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 include)
endif(BUILD_DIVSUFSORT64)

7
libdivsufsort/include/Makefile.am Normal file
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# Makefile.am for libdivsufsort
nodist_include_HEADERS = divsufsort.h
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nodist_include_HEADERS += divsufsort64.h
endif
EXTRA_DIST = divsufsort_private.h divsufsort.h.cmake divsufsort64.h.in config.h.cmake CMakeLists.txt lfs.h.cmake

508
libdivsufsort/include/Makefile.in Normal file
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# @configure_input@
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# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
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/*
* config.h for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef _CONFIG_H
#define _CONFIG_H 1
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
/** Define to the version of this package. **/
#cmakedefine PROJECT_VERSION_FULL "${PROJECT_VERSION_FULL}"
/** Define to 1 if you have the header files. **/
#cmakedefine HAVE_INTTYPES_H 1
#cmakedefine HAVE_STDDEF_H 1
#cmakedefine HAVE_STDINT_H 1
#cmakedefine HAVE_STDLIB_H 1
#cmakedefine HAVE_STRING_H 1
#cmakedefine HAVE_STRINGS_H 1
#cmakedefine HAVE_MEMORY_H 1
#cmakedefine HAVE_SYS_TYPES_H 1
/** for WinIO **/
#cmakedefine HAVE_IO_H 1
#cmakedefine HAVE_FCNTL_H 1
#cmakedefine HAVE__SETMODE 1
#cmakedefine HAVE_SETMODE 1
#cmakedefine HAVE__FILENO 1
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# endif
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# define _O_BINARY 0
# define HAVE__O_BINARY 1
# endif
#endif
/** for inline **/
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# define INLINE @INLINE@
#endif
/** for VC++ warning **/
#ifdef _MSC_VER
#pragma warning(disable: 4127)
#endif
#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */
#endif /* _CONFIG_H */

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/* Define to 1 if your system has a GNU libc compatible `malloc' function, and
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/* Define to 1 if you have the <memory.h> header file. */
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/* The size of `int', as computed by sizeof. */
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/* The size of `long', as computed by sizeof. */
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/* The size of `long long', as computed by sizeof. */
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/* The size of `short', as computed by sizeof. */
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#undef malloc

180
libdivsufsort/include/divsufsort.h.cmake Normal file
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@ -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 */

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/*
* divsufsort64.h for libdivsufsort64
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef _DIVSUFSORT64_H
#define _DIVSUFSORT64_H 1
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
@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 SAIDX64_T
#define SAIDX64_T
typedef @SAINT64_TYPE@ saidx64_t;
#endif /* SAIDX64_T */
#ifndef PRIdSAINT_T
#define PRIdSAINT_T @SAINT_PRId@
#endif /* PRIdSAINT_T */
#ifndef PRIdSAIDX64_T
#define PRIdSAIDX64_T @SAINT64_PRId@
#endif /* PRIdSAIDX64_T */
/*- Prototypes -*/
/**
* Constructs the suffix array of a given string.
* @param T[0..n-1] The input string.
* @param SA[0..n-1] The output array of suffixes.
* @param n The length of the given string.
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
DIVSUFSORT_API
saint_t
divsufsort64(const sauchar_t *T, saidx64_t *SA, saidx64_t n);
/**
* Constructs the burrows-wheeler transformed string of a given string.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param A[0..n-1] The temporary array. (can be NULL)
* @param n The length of the given string.
* @return The primary index if no error occurred, -1 or -2 otherwise.
*/
DIVSUFSORT_API
saidx64_t
divbwt64(const sauchar_t *T, sauchar_t *U, saidx64_t *A, saidx64_t n);
/**
* Returns the version of the divsufsort library.
* @return The version number string.
*/
DIVSUFSORT_API
const char *
divsufsort64_version(void);
/**
* Constructs the burrows-wheeler transformed string of a given string and suffix array.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param SA[0..n-1] The suffix array. (can be NULL)
* @param n The length of the given string.
* @param idx The output primary index.
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
DIVSUFSORT_API
saint_t
bw_transform64(const sauchar_t *T, sauchar_t *U,
saidx64_t *SA /* can NULL */,
saidx64_t n, saidx64_t *idx);
/**
* Inverse BW-transforms a given BWTed string.
* @param T[0..n-1] The input string.
* @param U[0..n-1] The output string. (can be T)
* @param A[0..n-1] The temporary array. (can be NULL)
* @param n The length of the given string.
* @param idx The primary index.
* @return 0 if no error occurred, -1 or -2 otherwise.
*/
DIVSUFSORT_API
saint_t
inverse_bw_transform64(const sauchar_t *T, sauchar_t *U,
saidx64_t *A /* can NULL */,
saidx64_t n, saidx64_t idx);
/**
* Checks the correctness of a given suffix array.
* @param T[0..n-1] The input string.
* @param SA[0..n-1] The input suffix array.
* @param n The length of the given string.
* @param verbose The verbose mode.
* @return 0 if no error occurred.
*/
DIVSUFSORT_API
saint_t
sufcheck64(const sauchar_t *T, const saidx64_t *SA, saidx64_t n, saint_t verbose);
/**
* Search for the pattern P in the string T.
* @param T[0..Tsize-1] The input string.
* @param Tsize The length of the given string.
* @param P[0..Psize-1] The input pattern string.
* @param Psize The length of the given pattern string.
* @param SA[0..SAsize-1] The input suffix array.
* @param SAsize The length of the given suffix array.
* @param idx The output index.
* @return The count of matches if no error occurred, -1 otherwise.
*/
DIVSUFSORT_API
saidx64_t
sa_search64(const sauchar_t *T, saidx64_t Tsize,
const sauchar_t *P, saidx64_t Psize,
const saidx64_t *SA, saidx64_t SAsize,
saidx64_t *left);
/**
* Search for the character c in the string T.
* @param T[0..Tsize-1] The input string.
* @param Tsize The length of the given string.
* @param SA[0..SAsize-1] The input suffix array.
* @param SAsize The length of the given suffix array.
* @param c The input character.
* @param idx The output index.
* @return The count of matches if no error occurred, -1 otherwise.
*/
DIVSUFSORT_API
saidx64_t
sa_simplesearch64(const sauchar_t *T, saidx64_t Tsize,
const saidx64_t *SA, saidx64_t SAsize,
saint_t c, saidx64_t *left);
#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */
#endif /* _DIVSUFSORT64_H */

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/*
* divsufsort_private.h for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef _DIVSUFSORT_PRIVATE_H
#define _DIVSUFSORT_PRIVATE_H 1
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#if HAVE_CONFIG_H
# include "config.h"
#endif
#include <assert.h>
#include <stdio.h>
#if HAVE_STRING_H
# include <string.h>
#endif
#if HAVE_STDLIB_H
# include <stdlib.h>
#endif
#if HAVE_MEMORY_H
# include <memory.h>
#endif
#if HAVE_STDDEF_H
# include <stddef.h>
#endif
#if HAVE_STRINGS_H
# include <strings.h>
#endif
#if HAVE_INTTYPES_H
# include <inttypes.h>
#else
# if HAVE_STDINT_H
# include <stdint.h>
# endif
#endif
#if defined(BUILD_DIVSUFSORT64)
# include "divsufsort64.h"
# ifndef SAIDX_T
# define SAIDX_T
# define saidx_t saidx64_t
# endif /* SAIDX_T */
# ifndef PRIdSAIDX_T
# define PRIdSAIDX_T PRIdSAIDX64_T
# endif /* PRIdSAIDX_T */
# define divsufsort divsufsort64
# define divbwt divbwt64
# define divsufsort_version divsufsort64_version
# define bw_transform bw_transform64
# define inverse_bw_transform inverse_bw_transform64
# define sufcheck sufcheck64
# define sa_search sa_search64
# define sa_simplesearch sa_simplesearch64
# define sssort sssort64
# define trsort trsort64
#else
# include "divsufsort.h"
#endif
/*- Constants -*/
#if !defined(UINT8_MAX)
# define UINT8_MAX (255)
#endif /* UINT8_MAX */
#if defined(ALPHABET_SIZE) && (ALPHABET_SIZE < 1)
# undef ALPHABET_SIZE
#endif
#if !defined(ALPHABET_SIZE)
# define ALPHABET_SIZE (UINT8_MAX + 1)
#endif
/* for divsufsort.c */
#define BUCKET_A_SIZE (ALPHABET_SIZE)
#define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE)
/* for sssort.c */
#if defined(SS_INSERTIONSORT_THRESHOLD)
# if SS_INSERTIONSORT_THRESHOLD < 1
# undef SS_INSERTIONSORT_THRESHOLD
# define SS_INSERTIONSORT_THRESHOLD (1)
# endif
#else
# define SS_INSERTIONSORT_THRESHOLD (8)
#endif
#if defined(SS_BLOCKSIZE)
# if SS_BLOCKSIZE < 0
# undef SS_BLOCKSIZE
# define SS_BLOCKSIZE (0)
# elif 32768 <= SS_BLOCKSIZE
# undef SS_BLOCKSIZE
# define SS_BLOCKSIZE (32767)
# endif
#else
# define SS_BLOCKSIZE (1024)
#endif
/* minstacksize = log(SS_BLOCKSIZE) / log(3) * 2 */
#if SS_BLOCKSIZE == 0
# if defined(BUILD_DIVSUFSORT64)
# define SS_MISORT_STACKSIZE (96)
# else
# define SS_MISORT_STACKSIZE (64)
# endif
#elif SS_BLOCKSIZE <= 4096
# define SS_MISORT_STACKSIZE (16)
#else
# define SS_MISORT_STACKSIZE (24)
#endif
#if defined(BUILD_DIVSUFSORT64)
# define SS_SMERGE_STACKSIZE (64)
#else
# define SS_SMERGE_STACKSIZE (32)
#endif
/* for trsort.c */
#define TR_INSERTIONSORT_THRESHOLD (8)
#if defined(BUILD_DIVSUFSORT64)
# define TR_STACKSIZE (96)
#else
# define TR_STACKSIZE (64)
#endif
/*- Macros -*/
#ifndef SWAP
# define SWAP(_a, _b) do { t = (_a); (_a) = (_b); (_b) = t; } while(0)
#endif /* SWAP */
#ifndef MIN
# define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b))
#endif /* MIN */
#ifndef MAX
# define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b))
#endif /* MAX */
#define STACK_PUSH(_a, _b, _c, _d)\
do {\
assert(ssize < STACK_SIZE);\
stack[ssize].a = (_a), stack[ssize].b = (_b),\
stack[ssize].c = (_c), stack[ssize++].d = (_d);\
} while(0)
#define STACK_PUSH5(_a, _b, _c, _d, _e)\
do {\
assert(ssize < STACK_SIZE);\
stack[ssize].a = (_a), stack[ssize].b = (_b),\
stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\
} while(0)
#define STACK_POP(_a, _b, _c, _d)\
do {\
assert(0 <= ssize);\
if(ssize == 0) { return; }\
(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
(_c) = stack[ssize].c, (_d) = stack[ssize].d;\
} while(0)
#define STACK_POP5(_a, _b, _c, _d, _e)\
do {\
assert(0 <= ssize);\
if(ssize == 0) { return; }\
(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
(_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\
} while(0)
/* for divsufsort.c */
#define BUCKET_A(_c0) bucket_A[(_c0)]
#if ALPHABET_SIZE == 256
#define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)])
#define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)])
#else
#define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)])
#define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)])
#endif
/*- Private Prototypes -*/
/* sssort.c */
void
sssort(const sauchar_t *Td, const saidx_t *PA,
saidx_t *first, saidx_t *last,
saidx_t *buf, saidx_t bufsize,
saidx_t depth, saidx_t n, saint_t lastsuffix);
/* trsort.c */
void
trsort(saidx_t *ISA, saidx_t *SA, saidx_t n, saidx_t depth);
#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */
#endif /* _DIVSUFSORT_PRIVATE_H */

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/*
* 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 */

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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 ${divsufsort_SRCS})
install(TARGETS divsufsort
RUNTIME DESTINATION bin
LIBRARY DESTINATION lib
ARCHIVE DESTINATION lib)
set_target_properties(divsufsort PROPERTIES
VERSION "${LIBRARY_VERSION_FULL}"
SOVERSION "${LIBRARY_VERSION_MAJOR}"
DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL
RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples")
## libdivsufsort64 ##
if(BUILD_DIVSUFSORT64)
add_library(divsufsort64 ${divsufsort_SRCS})
install(TARGETS divsufsort64
RUNTIME DESTINATION bin
LIBRARY DESTINATION lib
ARCHIVE DESTINATION lib)
set_target_properties(divsufsort64 PROPERTIES
VERSION "${LIBRARY_VERSION_FULL}"
SOVERSION "${LIBRARY_VERSION_MAJOR}"
DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL
COMPILE_FLAGS "-DBUILD_DIVSUFSORT64"
RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples")
endif(BUILD_DIVSUFSORT64)

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# Makefile.am for libdivsufsort
lib_LTLIBRARIES = libdivsufsort.la
libdivsufsort_la_SOURCES = divsufsort.c sssort.c trsort.c utils.c
libdivsufsort_la_CPPFLAGS = -I$(top_srcdir)/include
libdivsufsort_la_LDFLAGS = -version-info @LT_CURRENT@:@LT_REVISION@:@LT_AGE@ -export-symbols $(srcdir)/libdivsufsort.sym
if DIVSUFSORT64
lib_LTLIBRARIES += libdivsufsort64.la
libdivsufsort64_la_SOURCES = divsufsort.c sssort.c trsort.c utils.c
libdivsufsort64_la_CPPFLAGS = -I$(top_srcdir)/include -DBUILD_DIVSUFSORT64
libdivsufsort64_la_LDFLAGS = -version-info @LT_CURRENT@:@LT_REVISION@:@LT_AGE@ -export-symbols $(srcdir)/libdivsufsort64.sym
endif
EXTRA_DIST = libdivsufsort.sym libdivsufsort64.sym CMakeLists.txt

637
libdivsufsort/lib/Makefile.in Normal file
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# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation,
# Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
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test -f "$(distdir)/$$file" \
|| cp -p $$d/$$file "$(distdir)/$$file" \
|| exit 1; \
fi; \
done
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all-am: Makefile $(LTLIBRARIES)
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distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
@echo "it deletes files that may require special tools to rebuild."
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clean-am: clean-generic clean-libLTLIBRARIES clean-libtool \
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distclean: distclean-am
-rm -rf ./$(DEPDIR)
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# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:

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/*
* divsufsort.c for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#include "divsufsort_private.h"
#ifdef _OPENMP
# include <omp.h>
#endif
/*- Private Functions -*/
/* Sorts suffixes of type B*. */
static
saidx_t
sort_typeBstar(const sauchar_t *T, saidx_t *SA,
saidx_t *bucket_A, saidx_t *bucket_B,
saidx_t n) {
saidx_t *PAb, *ISAb, *buf;
#ifdef _OPENMP
saidx_t *curbuf;
saidx_t l;
#endif
saidx_t i, j, k, t, m, bufsize;
saint_t c0, c1;
#ifdef _OPENMP
saint_t d0, d1;
int tmp;
#endif
/* Initialize bucket arrays. */
for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; }
for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; }
/* Count the number of occurrences of the first one or two characters of each
type A, B and B* suffix. Moreover, store the beginning position of all
type B* suffixes into the array SA. */
for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) {
/* type A suffix. */
do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1));
if(0 <= i) {
/* type B* suffix. */
++BUCKET_BSTAR(c0, c1);
SA[--m] = i;
/* type B suffix. */
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) {
++BUCKET_B(c0, c1);
}
}
}
m = n - m;
/*
note:
A type B* suffix is lexicographically smaller than a type B suffix that
begins with the same first two characters.
*/
/* Calculate the index of start/end point of each bucket. */
for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) {
t = i + BUCKET_A(c0);
BUCKET_A(c0) = i + j; /* start point */
i = t + BUCKET_B(c0, c0);
for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) {
j += BUCKET_BSTAR(c0, c1);
BUCKET_BSTAR(c0, c1) = j; /* end point */
i += BUCKET_B(c0, c1);
}
}
if(0 < m) {
/* Sort the type B* suffixes by their first two characters. */
PAb = SA + n - m; ISAb = SA + m;
for(i = m - 2; 0 <= i; --i) {
t = PAb[i], c0 = T[t], c1 = T[t + 1];
SA[--BUCKET_BSTAR(c0, c1)] = i;
}
t = PAb[m - 1], c0 = T[t], c1 = T[t + 1];
SA[--BUCKET_BSTAR(c0, c1)] = m - 1;
/* Sort the type B* substrings using sssort. */
#ifdef _OPENMP
tmp = omp_get_max_threads();
buf = SA + m, bufsize = (n - (2 * m)) / tmp;
c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m;
#pragma omp parallel default(shared) private(curbuf, k, l, d0, d1, tmp)
{
tmp = omp_get_thread_num();
curbuf = buf + tmp * bufsize;
k = 0;
for(;;) {
#pragma omp critical(sssort_lock)
{
if(0 < (l = j)) {
d0 = c0, d1 = c1;
do {
k = BUCKET_BSTAR(d0, d1);
if(--d1 <= d0) {
d1 = ALPHABET_SIZE - 1;
if(--d0 < 0) { break; }
}
} while(((l - k) <= 1) && (0 < (l = k)));
c0 = d0, c1 = d1, j = k;
}
}
if(l == 0) { break; }
sssort(T, PAb, SA + k, SA + l,
curbuf, bufsize, 2, n, *(SA + k) == (m - 1));
}
}
#else
buf = SA + m, bufsize = n - (2 * m);
for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
i = BUCKET_BSTAR(c0, c1);
if(1 < (j - i)) {
sssort(T, PAb, SA + i, SA + j,
buf, bufsize, 2, n, *(SA + i) == (m - 1));
}
}
}
#endif
/* Compute ranks of type B* substrings. */
for(i = m - 1; 0 <= i; --i) {
if(0 <= SA[i]) {
j = i;
do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i]));
SA[i + 1] = i - j;
if(i <= 0) { break; }
}
j = i;
do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0);
ISAb[SA[i]] = j;
}
/* Construct the inverse suffix array of type B* suffixes using trsort. */
trsort(ISAb, SA, m, 1);
/* Set the sorted order of tyoe B* suffixes. */
for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) {
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { }
if(0 <= i) {
t = i;
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { }
SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t;
}
}
/* Calculate the index of start/end point of each bucket. */
BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */
for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) {
i = BUCKET_A(c0 + 1) - 1;
for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) {
t = i - BUCKET_B(c0, c1);
BUCKET_B(c0, c1) = i; /* end point */
/* Move all type B* suffixes to the correct position. */
for(i = t, j = BUCKET_BSTAR(c0, c1);
j <= k;
--i, --k) { SA[i] = SA[k]; }
}
BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */
BUCKET_B(c0, c0) = i; /* end point */
}
}
return m;
}
/* Constructs the suffix array by using the sorted order of type B* suffixes. */
static
void
construct_SA(const sauchar_t *T, saidx_t *SA,
saidx_t *bucket_A, saidx_t *bucket_B,
saidx_t n, saidx_t m) {
saidx_t *i, *j, *k;
saidx_t s;
saint_t c0, c1, c2;
if(0 < m) {
/* Construct the sorted order of type B suffixes by using
the sorted order of type B* suffixes. */
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
/* Scan the suffix array from right to left. */
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
i <= j;
--j) {
if(0 < (s = *j)) {
assert(T[s] == c1);
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
assert(T[s - 1] <= T[s]);
*j = ~s;
c0 = T[--s];
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
if(c0 != c2) {
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
k = SA + BUCKET_B(c2 = c0, c1);
}
assert(k < j);
*k-- = s;
} else {
assert(((s == 0) && (T[s] == c1)) || (s < 0));
*j = ~s;
}
}
}
}
/* Construct the suffix array by using
the sorted order of type B suffixes. */
k = SA + BUCKET_A(c2 = T[n - 1]);
*k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1);
/* Scan the suffix array from left to right. */
for(i = SA, j = SA + n; i < j; ++i) {
if(0 < (s = *i)) {
assert(T[s - 1] >= T[s]);
c0 = T[--s];
if((s == 0) || (T[s - 1] < c0)) { s = ~s; }
if(c0 != c2) {
BUCKET_A(c2) = k - SA;
k = SA + BUCKET_A(c2 = c0);
}
assert(i < k);
*k++ = s;
} else {
assert(s < 0);
*i = ~s;
}
}
}
/* Constructs the burrows-wheeler transformed string directly
by using the sorted order of type B* suffixes. */
static
saidx_t
construct_BWT(const sauchar_t *T, saidx_t *SA,
saidx_t *bucket_A, saidx_t *bucket_B,
saidx_t n, saidx_t m) {
saidx_t *i, *j, *k, *orig;
saidx_t s;
saint_t c0, c1, c2;
if(0 < m) {
/* Construct the sorted order of type B suffixes by using
the sorted order of type B* suffixes. */
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
/* Scan the suffix array from right to left. */
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
i <= j;
--j) {
if(0 < (s = *j)) {
assert(T[s] == c1);
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
assert(T[s - 1] <= T[s]);
c0 = T[--s];
*j = ~((saidx_t)c0);
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
if(c0 != c2) {
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
k = SA + BUCKET_B(c2 = c0, c1);
}
assert(k < j);
*k-- = s;
} else if(s != 0) {
*j = ~s;
#ifndef NDEBUG
} else {
assert(T[s] == c1);
#endif
}
}
}
}
/* Construct the BWTed string by using
the sorted order of type B suffixes. */
k = SA + BUCKET_A(c2 = T[n - 1]);
*k++ = (T[n - 2] < c2) ? ~((saidx_t)T[n - 2]) : (n - 1);
/* Scan the suffix array from left to right. */
for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
if(0 < (s = *i)) {
assert(T[s - 1] >= T[s]);
c0 = T[--s];
*i = c0;
if((0 < s) && (T[s - 1] < c0)) { s = ~((saidx_t)T[s - 1]); }
if(c0 != c2) {
BUCKET_A(c2) = k - SA;
k = SA + BUCKET_A(c2 = c0);
}
assert(i < k);
*k++ = s;
} else if(s != 0) {
*i = ~s;
} else {
orig = i;
}
}
return orig - SA;
}
/*---------------------------------------------------------------------------*/
/*- Function -*/
saint_t
divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n) {
saidx_t *bucket_A, *bucket_B;
saidx_t m;
saint_t err = 0;
/* Check arguments. */
if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; }
else if(n == 0) { return 0; }
else if(n == 1) { SA[0] = 0; return 0; }
else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; }
bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
/* Suffixsort. */
if((bucket_A != NULL) && (bucket_B != NULL)) {
m = sort_typeBstar(T, SA, bucket_A, bucket_B, n);
construct_SA(T, SA, bucket_A, bucket_B, n, m);
} else {
err = -2;
}
free(bucket_B);
free(bucket_A);
return err;
}
saidx_t
divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n) {
saidx_t *B;
saidx_t *bucket_A, *bucket_B;
saidx_t m, pidx, i;
/* Check arguments. */
if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); }
bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t));
bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t));
/* Burrows-Wheeler Transform. */
if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
m = sort_typeBstar(T, B, bucket_A, bucket_B, n);
pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
/* Copy to output string. */
U[0] = T[n - 1];
for(i = 0; i < pidx; ++i) { U[i + 1] = (sauchar_t)B[i]; }
for(i += 1; i < n; ++i) { U[i] = (sauchar_t)B[i]; }
pidx += 1;
} else {
pidx = -2;
}
free(bucket_B);
free(bucket_A);
if(A == NULL) { free(B); }
return pidx;
}
const char *
divsufsort_version(void) {
return PROJECT_VERSION_FULL;
}

8
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divsufsort
divbwt
divsufsort_version
bw_transform
inverse_bw_transform
sufcheck
sa_search
sa_simplesearch

8
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divsufsort64
divbwt64
divsufsort64_version
bw_transform64
inverse_bw_transform64
sufcheck64
sa_search64
sa_simplesearch64

815
libdivsufsort/lib/sssort.c Normal file
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/*
* 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
libdivsufsort/lib/trsort.c Normal file
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@ -0,0 +1,586 @@
/*
* trsort.c for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#include "divsufsort_private.h"
/*- Private Functions -*/
static const saint_t lg_table[256]= {
-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
};
static INLINE
saint_t
tr_ilg(saidx_t n) {
#if defined(BUILD_DIVSUFSORT64)
return (n >> 32) ?
((n >> 48) ?
((n >> 56) ?
56 + lg_table[(n >> 56) & 0xff] :
48 + lg_table[(n >> 48) & 0xff]) :
((n >> 40) ?
40 + lg_table[(n >> 40) & 0xff] :
32 + lg_table[(n >> 32) & 0xff])) :
((n & 0xffff0000) ?
((n & 0xff000000) ?
24 + lg_table[(n >> 24) & 0xff] :
16 + lg_table[(n >> 16) & 0xff]) :
((n & 0x0000ff00) ?
8 + lg_table[(n >> 8) & 0xff] :
0 + lg_table[(n >> 0) & 0xff]));
#else
return (n & 0xffff0000) ?
((n & 0xff000000) ?
24 + lg_table[(n >> 24) & 0xff] :
16 + lg_table[(n >> 16) & 0xff]) :
((n & 0x0000ff00) ?
8 + lg_table[(n >> 8) & 0xff] :
0 + lg_table[(n >> 0) & 0xff]);
#endif
}
/*---------------------------------------------------------------------------*/
/* Simple insertionsort for small size groups. */
static
void
tr_insertionsort(const saidx_t *ISAd, saidx_t *first, saidx_t *last) {
saidx_t *a, *b;
saidx_t t, r;
for(a = first + 1; a < last; ++a) {
for(t = *a, b = a - 1; 0 > (r = ISAd[t] - ISAd[*b]);) {
do { *(b + 1) = *b; } while((first <= --b) && (*b < 0));
if(b < first) { break; }
}
if(r == 0) { *b = ~*b; }
*(b + 1) = t;
}
}
/*---------------------------------------------------------------------------*/
static INLINE
void
tr_fixdown(const saidx_t *ISAd, saidx_t *SA, saidx_t i, saidx_t size) {
saidx_t j, k;
saidx_t v;
saidx_t c, d, e;
for(v = SA[i], c = ISAd[v]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
d = ISAd[SA[k = j++]];
if(d < (e = ISAd[SA[j]])) { k = j; d = e; }
if(d <= c) { break; }
}
SA[i] = v;
}
/* Simple top-down heapsort. */
static
void
tr_heapsort(const saidx_t *ISAd, saidx_t *SA, saidx_t size) {
saidx_t i, m;
saidx_t t;
m = size;
if((size % 2) == 0) {
m--;
if(ISAd[SA[m / 2]] < ISAd[SA[m]]) { SWAP(SA[m], SA[m / 2]); }
}
for(i = m / 2 - 1; 0 <= i; --i) { tr_fixdown(ISAd, SA, i, m); }
if((size % 2) == 0) { SWAP(SA[0], SA[m]); tr_fixdown(ISAd, SA, 0, m); }
for(i = m - 1; 0 < i; --i) {
t = SA[0], SA[0] = SA[i];
tr_fixdown(ISAd, SA, 0, i);
SA[i] = t;
}
}
/*---------------------------------------------------------------------------*/
/* Returns the median of three elements. */
static INLINE
saidx_t *
tr_median3(const saidx_t *ISAd, saidx_t *v1, saidx_t *v2, saidx_t *v3) {
saidx_t *t;
if(ISAd[*v1] > ISAd[*v2]) { SWAP(v1, v2); }
if(ISAd[*v2] > ISAd[*v3]) {
if(ISAd[*v1] > ISAd[*v3]) { return v1; }
else { return v3; }
}
return v2;
}
/* Returns the median of five elements. */
static INLINE
saidx_t *
tr_median5(const saidx_t *ISAd,
saidx_t *v1, saidx_t *v2, saidx_t *v3, saidx_t *v4, saidx_t *v5) {
saidx_t *t;
if(ISAd[*v2] > ISAd[*v3]) { SWAP(v2, v3); }
if(ISAd[*v4] > ISAd[*v5]) { SWAP(v4, v5); }
if(ISAd[*v2] > ISAd[*v4]) { SWAP(v2, v4); SWAP(v3, v5); }
if(ISAd[*v1] > ISAd[*v3]) { SWAP(v1, v3); }
if(ISAd[*v1] > ISAd[*v4]) { SWAP(v1, v4); SWAP(v3, v5); }
if(ISAd[*v3] > ISAd[*v4]) { return v4; }
return v3;
}
/* Returns the pivot element. */
static INLINE
saidx_t *
tr_pivot(const saidx_t *ISAd, saidx_t *first, saidx_t *last) {
saidx_t *middle;
saidx_t t;
t = last - first;
middle = first + t / 2;
if(t <= 512) {
if(t <= 32) {
return tr_median3(ISAd, first, middle, last - 1);
} else {
t >>= 2;
return tr_median5(ISAd, first, first + t, middle, last - 1 - t, last - 1);
}
}
t >>= 3;
first = tr_median3(ISAd, first, first + t, first + (t << 1));
middle = tr_median3(ISAd, middle - t, middle, middle + t);
last = tr_median3(ISAd, last - 1 - (t << 1), last - 1 - t, last - 1);
return tr_median3(ISAd, first, middle, last);
}
/*---------------------------------------------------------------------------*/
typedef struct _trbudget_t trbudget_t;
struct _trbudget_t {
saidx_t chance;
saidx_t remain;
saidx_t incval;
saidx_t count;
};
static INLINE
void
trbudget_init(trbudget_t *budget, saidx_t chance, saidx_t incval) {
budget->chance = chance;
budget->remain = budget->incval = incval;
}
static INLINE
saint_t
trbudget_check(trbudget_t *budget, saidx_t size) {
if(size <= budget->remain) { budget->remain -= size; return 1; }
if(budget->chance == 0) { budget->count += size; return 0; }
budget->remain += budget->incval - size;
budget->chance -= 1;
return 1;
}
/*---------------------------------------------------------------------------*/
static INLINE
void
tr_partition(const saidx_t *ISAd,
saidx_t *first, saidx_t *middle, saidx_t *last,
saidx_t **pa, saidx_t **pb, saidx_t v) {
saidx_t *a, *b, *c, *d, *e, *f;
saidx_t t, s;
saidx_t x = 0;
for(b = middle - 1; (++b < last) && ((x = ISAd[*b]) == v);) { }
if(((a = b) < last) && (x < v)) {
for(; (++b < last) && ((x = ISAd[*b]) <= v);) {
if(x == v) { SWAP(*b, *a); ++a; }
}
}
for(c = last; (b < --c) && ((x = ISAd[*c]) == v);) { }
if((b < (d = c)) && (x > v)) {
for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
if(x == v) { SWAP(*c, *d); --d; }
}
}
for(; b < c;) {
SWAP(*b, *c);
for(; (++b < c) && ((x = ISAd[*b]) <= v);) {
if(x == v) { SWAP(*b, *a); ++a; }
}
for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
if(x == v) { SWAP(*c, *d); --d; }
}
}
if(a <= d) {
c = b - 1;
if((s = a - first) > (t = b - a)) { s = t; }
for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
if((s = d - c) > (t = last - d - 1)) { s = t; }
for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
first += (b - a), last -= (d - c);
}
*pa = first, *pb = last;
}
static
void
tr_copy(saidx_t *ISA, const saidx_t *SA,
saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last,
saidx_t depth) {
/* sort suffixes of middle partition
by using sorted order of suffixes of left and right partition. */
saidx_t *c, *d, *e;
saidx_t s, v;
v = b - SA - 1;
for(c = first, d = a - 1; c <= d; ++c) {
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
*++d = s;
ISA[s] = d - SA;
}
}
for(c = last - 1, e = d + 1, d = b; e < d; --c) {
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
*--d = s;
ISA[s] = d - SA;
}
}
}
static
void
tr_partialcopy(saidx_t *ISA, const saidx_t *SA,
saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last,
saidx_t depth) {
saidx_t *c, *d, *e;
saidx_t s, v;
saidx_t rank, lastrank, newrank = -1;
v = b - SA - 1;
lastrank = -1;
for(c = first, d = a - 1; c <= d; ++c) {
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
*++d = s;
rank = ISA[s + depth];
if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
ISA[s] = newrank;
}
}
lastrank = -1;
for(e = d; first <= e; --e) {
rank = ISA[*e];
if(lastrank != rank) { lastrank = rank; newrank = e - SA; }
if(newrank != rank) { ISA[*e] = newrank; }
}
lastrank = -1;
for(c = last - 1, e = d + 1, d = b; e < d; --c) {
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
*--d = s;
rank = ISA[s + depth];
if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
ISA[s] = newrank;
}
}
}
static
void
tr_introsort(saidx_t *ISA, const saidx_t *ISAd,
saidx_t *SA, saidx_t *first, saidx_t *last,
trbudget_t *budget) {
#define STACK_SIZE TR_STACKSIZE
struct { const saidx_t *a; saidx_t *b, *c; saint_t d, e; }stack[STACK_SIZE];
saidx_t *a, *b, *c;
saidx_t t;
saidx_t v, x = 0;
saidx_t incr = ISAd - ISA;
saint_t limit, next;
saint_t ssize, trlink = -1;
for(ssize = 0, limit = tr_ilg(last - first);;) {
if(limit < 0) {
if(limit == -1) {
/* tandem repeat partition */
tr_partition(ISAd - incr, first, first, last, &a, &b, last - SA - 1);
/* update ranks */
if(a < last) {
for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
}
if(b < last) {
for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; }
}
/* push */
if(1 < (b - a)) {
STACK_PUSH5(NULL, a, b, 0, 0);
STACK_PUSH5(ISAd - incr, first, last, -2, trlink);
trlink = ssize - 2;
}
if((a - first) <= (last - b)) {
if(1 < (a - first)) {
STACK_PUSH5(ISAd, b, last, tr_ilg(last - b), trlink);
last = a, limit = tr_ilg(a - first);
} else if(1 < (last - b)) {
first = b, limit = tr_ilg(last - b);
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
} else {
if(1 < (last - b)) {
STACK_PUSH5(ISAd, first, a, tr_ilg(a - first), trlink);
first = b, limit = tr_ilg(last - b);
} else if(1 < (a - first)) {
last = a, limit = tr_ilg(a - first);
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
}
} else if(limit == -2) {
/* tandem repeat copy */
a = stack[--ssize].b, b = stack[ssize].c;
if(stack[ssize].d == 0) {
tr_copy(ISA, SA, first, a, b, last, ISAd - ISA);
} else {
if(0 <= trlink) { stack[trlink].d = -1; }
tr_partialcopy(ISA, SA, first, a, b, last, ISAd - ISA);
}
STACK_POP5(ISAd, first, last, limit, trlink);
} else {
/* sorted partition */
if(0 <= *first) {
a = first;
do { ISA[*a] = a - SA; } while((++a < last) && (0 <= *a));
first = a;
}
if(first < last) {
a = first; do { *a = ~*a; } while(*++a < 0);
next = (ISA[*a] != ISAd[*a]) ? tr_ilg(a - first + 1) : -1;
if(++a < last) { for(b = first, v = a - SA - 1; b < a; ++b) { ISA[*b] = v; } }
/* push */
if(trbudget_check(budget, a - first)) {
if((a - first) <= (last - a)) {
STACK_PUSH5(ISAd, a, last, -3, trlink);
ISAd += incr, last = a, limit = next;
} else {
if(1 < (last - a)) {
STACK_PUSH5(ISAd + incr, first, a, next, trlink);
first = a, limit = -3;
} else {
ISAd += incr, last = a, limit = next;
}
}
} else {
if(0 <= trlink) { stack[trlink].d = -1; }
if(1 < (last - a)) {
first = a, limit = -3;
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
}
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
}
continue;
}
if((last - first) <= TR_INSERTIONSORT_THRESHOLD) {
tr_insertionsort(ISAd, first, last);
limit = -3;
continue;
}
if(limit-- == 0) {
tr_heapsort(ISAd, first, last - first);
for(a = last - 1; first < a; a = b) {
for(x = ISAd[*a], b = a - 1; (first <= b) && (ISAd[*b] == x); --b) { *b = ~*b; }
}
limit = -3;
continue;
}
/* choose pivot */
a = tr_pivot(ISAd, first, last);
SWAP(*first, *a);
v = ISAd[*first];
/* partition */
tr_partition(ISAd, first, first + 1, last, &a, &b, v);
if((last - first) != (b - a)) {
next = (ISA[*a] != v) ? tr_ilg(b - a) : -1;
/* update ranks */
for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
if(b < last) { for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; } }
/* push */
if((1 < (b - a)) && (trbudget_check(budget, b - a))) {
if((a - first) <= (last - b)) {
if((last - b) <= (b - a)) {
if(1 < (a - first)) {
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
STACK_PUSH5(ISAd, b, last, limit, trlink);
last = a;
} else if(1 < (last - b)) {
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
first = b;
} else {
ISAd += incr, first = a, last = b, limit = next;
}
} else if((a - first) <= (b - a)) {
if(1 < (a - first)) {
STACK_PUSH5(ISAd, b, last, limit, trlink);
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
last = a;
} else {
STACK_PUSH5(ISAd, b, last, limit, trlink);
ISAd += incr, first = a, last = b, limit = next;
}
} else {
STACK_PUSH5(ISAd, b, last, limit, trlink);
STACK_PUSH5(ISAd, first, a, limit, trlink);
ISAd += incr, first = a, last = b, limit = next;
}
} else {
if((a - first) <= (b - a)) {
if(1 < (last - b)) {
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
STACK_PUSH5(ISAd, first, a, limit, trlink);
first = b;
} else if(1 < (a - first)) {
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
last = a;
} else {
ISAd += incr, first = a, last = b, limit = next;
}
} else if((last - b) <= (b - a)) {
if(1 < (last - b)) {
STACK_PUSH5(ISAd, first, a, limit, trlink);
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
first = b;
} else {
STACK_PUSH5(ISAd, first, a, limit, trlink);
ISAd += incr, first = a, last = b, limit = next;
}
} else {
STACK_PUSH5(ISAd, first, a, limit, trlink);
STACK_PUSH5(ISAd, b, last, limit, trlink);
ISAd += incr, first = a, last = b, limit = next;
}
}
} else {
if((1 < (b - a)) && (0 <= trlink)) { stack[trlink].d = -1; }
if((a - first) <= (last - b)) {
if(1 < (a - first)) {
STACK_PUSH5(ISAd, b, last, limit, trlink);
last = a;
} else if(1 < (last - b)) {
first = b;
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
} else {
if(1 < (last - b)) {
STACK_PUSH5(ISAd, first, a, limit, trlink);
first = b;
} else if(1 < (a - first)) {
last = a;
} else {
STACK_POP5(ISAd, first, last, limit, trlink);
}
}
}
} else {
if(trbudget_check(budget, last - first)) {
limit = tr_ilg(last - first), ISAd += incr;
} else {
if(0 <= trlink) { stack[trlink].d = -1; }
STACK_POP5(ISAd, first, last, limit, trlink);
}
}
}
#undef STACK_SIZE
}
/*---------------------------------------------------------------------------*/
/*- Function -*/
/* Tandem repeat sort */
void
trsort(saidx_t *ISA, saidx_t *SA, saidx_t n, saidx_t depth) {
saidx_t *ISAd;
saidx_t *first, *last;
trbudget_t budget;
saidx_t t, skip, unsorted;
trbudget_init(&budget, tr_ilg(n) * 2 / 3, n);
/* trbudget_init(&budget, tr_ilg(n) * 3 / 4, n); */
for(ISAd = ISA + depth; -n < *SA; ISAd += ISAd - ISA) {
first = SA;
skip = 0;
unsorted = 0;
do {
if((t = *first) < 0) { first -= t; skip += t; }
else {
if(skip != 0) { *(first + skip) = skip; skip = 0; }
last = SA + ISA[t] + 1;
if(1 < (last - first)) {
budget.count = 0;
tr_introsort(ISA, ISAd, SA, first, last, &budget);
if(budget.count != 0) { unsorted += budget.count; }
else { skip = first - last; }
} else if((last - first) == 1) {
skip = -1;
}
first = last;
}
} while(first < (SA + n));
if(skip != 0) { *(first + skip) = skip; }
if(unsorted == 0) { break; }
}
}

381
libdivsufsort/lib/utils.c Normal file
View 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;
}

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libdivsufsort/m4/libtool.m4 vendored Normal file
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368
libdivsufsort/m4/ltoptions.m4 vendored Normal file
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@ -0,0 +1,368 @@
# Helper functions for option handling. -*- Autoconf -*-
#
# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
# Written by Gary V. Vaughan, 2004
#
# This file is free software; the Free Software Foundation gives
# unlimited permission to copy and/or distribute it, with or without
# modifications, as long as this notice is preserved.
# serial 6 ltoptions.m4
# This is to help aclocal find these macros, as it can't see m4_define.
AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])])
# _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME)
# ------------------------------------------
m4_define([_LT_MANGLE_OPTION],
[[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])])
# _LT_SET_OPTION(MACRO-NAME, OPTION-NAME)
# ---------------------------------------
# Set option OPTION-NAME for macro MACRO-NAME, and if there is a
# matching handler defined, dispatch to it. Other OPTION-NAMEs are
# saved as a flag.
m4_define([_LT_SET_OPTION],
[m4_define(_LT_MANGLE_OPTION([$1], [$2]))dnl
m4_ifdef(_LT_MANGLE_DEFUN([$1], [$2]),
_LT_MANGLE_DEFUN([$1], [$2]),
[m4_warning([Unknown $1 option `$2'])])[]dnl
])
# _LT_IF_OPTION(MACRO-NAME, OPTION-NAME, IF-SET, [IF-NOT-SET])
# ------------------------------------------------------------
# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise.
m4_define([_LT_IF_OPTION],
[m4_ifdef(_LT_MANGLE_OPTION([$1], [$2]), [$3], [$4])])
# _LT_UNLESS_OPTIONS(MACRO-NAME, OPTION-LIST, IF-NOT-SET)
# -------------------------------------------------------
# Execute IF-NOT-SET unless all options in OPTION-LIST for MACRO-NAME
# are set.
m4_define([_LT_UNLESS_OPTIONS],
[m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),
[m4_ifdef(_LT_MANGLE_OPTION([$1], _LT_Option),
[m4_define([$0_found])])])[]dnl
m4_ifdef([$0_found], [m4_undefine([$0_found])], [$3
])[]dnl
])
# _LT_SET_OPTIONS(MACRO-NAME, OPTION-LIST)
# ----------------------------------------
# OPTION-LIST is a space-separated list of Libtool options associated
# with MACRO-NAME. If any OPTION has a matching handler declared with
# LT_OPTION_DEFINE, dispatch to that macro; otherwise complain about
# the unknown option and exit.
m4_defun([_LT_SET_OPTIONS],
[# Set options
m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),
[_LT_SET_OPTION([$1], _LT_Option)])
m4_if([$1],[LT_INIT],[
dnl
dnl Simply set some default values (i.e off) if boolean options were not
dnl specified:
_LT_UNLESS_OPTIONS([LT_INIT], [dlopen], [enable_dlopen=no
])
_LT_UNLESS_OPTIONS([LT_INIT], [win32-dll], [enable_win32_dll=no
])
dnl
dnl If no reference was made to various pairs of opposing options, then
dnl we run the default mode handler for the pair. For example, if neither
dnl `shared' nor `disable-shared' was passed, we enable building of shared
dnl archives by default:
_LT_UNLESS_OPTIONS([LT_INIT], [shared disable-shared], [_LT_ENABLE_SHARED])
_LT_UNLESS_OPTIONS([LT_INIT], [static disable-static], [_LT_ENABLE_STATIC])
_LT_UNLESS_OPTIONS([LT_INIT], [pic-only no-pic], [_LT_WITH_PIC])
_LT_UNLESS_OPTIONS([LT_INIT], [fast-install disable-fast-install],
[_LT_ENABLE_FAST_INSTALL])
])
])# _LT_SET_OPTIONS
## --------------------------------- ##
## Macros to handle LT_INIT options. ##
## --------------------------------- ##
# _LT_MANGLE_DEFUN(MACRO-NAME, OPTION-NAME)
# -----------------------------------------
m4_define([_LT_MANGLE_DEFUN],
[[_LT_OPTION_DEFUN_]m4_bpatsubst(m4_toupper([$1__$2]), [[^A-Z0-9_]], [_])])
# LT_OPTION_DEFINE(MACRO-NAME, OPTION-NAME, CODE)
# -----------------------------------------------
m4_define([LT_OPTION_DEFINE],
[m4_define(_LT_MANGLE_DEFUN([$1], [$2]), [$3])[]dnl
])# LT_OPTION_DEFINE
# dlopen
# ------
LT_OPTION_DEFINE([LT_INIT], [dlopen], [enable_dlopen=yes
])
AU_DEFUN([AC_LIBTOOL_DLOPEN],
[_LT_SET_OPTION([LT_INIT], [dlopen])
AC_DIAGNOSE([obsolete],
[$0: Remove this warning and the call to _LT_SET_OPTION when you
put the `dlopen' option into LT_INIT's first parameter.])
])
dnl aclocal-1.4 backwards compatibility:
dnl AC_DEFUN([AC_LIBTOOL_DLOPEN], [])
# win32-dll
# ---------
# Declare package support for building win32 dll's.
LT_OPTION_DEFINE([LT_INIT], [win32-dll],
[enable_win32_dll=yes
case $host in
*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-cegcc*)
AC_CHECK_TOOL(AS, as, false)
AC_CHECK_TOOL(DLLTOOL, dlltool, false)
AC_CHECK_TOOL(OBJDUMP, objdump, false)
;;
esac
test -z "$AS" && AS=as
_LT_DECL([], [AS], [0], [Assembler program])dnl
test -z "$DLLTOOL" && DLLTOOL=dlltool
_LT_DECL([], [DLLTOOL], [0], [DLL creation program])dnl
test -z "$OBJDUMP" && OBJDUMP=objdump
_LT_DECL([], [OBJDUMP], [0], [Object dumper program])dnl
])# win32-dll
AU_DEFUN([AC_LIBTOOL_WIN32_DLL],
[AC_REQUIRE([AC_CANONICAL_HOST])dnl
_LT_SET_OPTION([LT_INIT], [win32-dll])
AC_DIAGNOSE([obsolete],
[$0: Remove this warning and the call to _LT_SET_OPTION when you
put the `win32-dll' option into LT_INIT's first parameter.])
])
dnl aclocal-1.4 backwards compatibility:
dnl AC_DEFUN([AC_LIBTOOL_WIN32_DLL], [])
# _LT_ENABLE_SHARED([DEFAULT])
# ----------------------------
# implement the --enable-shared flag, and supports the `shared' and
# `disable-shared' LT_INIT options.
# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
m4_define([_LT_ENABLE_SHARED],
[m4_define([_LT_ENABLE_SHARED_DEFAULT], [m4_if($1, no, no, yes)])dnl
AC_ARG_ENABLE([shared],
[AS_HELP_STRING([--enable-shared@<:@=PKGS@:>@],
[build shared libraries @<:@default=]_LT_ENABLE_SHARED_DEFAULT[@:>@])],
[p=${PACKAGE-default}
case $enableval in
yes) enable_shared=yes ;;
no) enable_shared=no ;;
*)
enable_shared=no
# Look at the argument we got. We use all the common list separators.
lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
for pkg in $enableval; do
IFS="$lt_save_ifs"
if test "X$pkg" = "X$p"; then
enable_shared=yes
fi
done
IFS="$lt_save_ifs"
;;
esac],
[enable_shared=]_LT_ENABLE_SHARED_DEFAULT)
_LT_DECL([build_libtool_libs], [enable_shared], [0],
[Whether or not to build shared libraries])
])# _LT_ENABLE_SHARED
LT_OPTION_DEFINE([LT_INIT], [shared], [_LT_ENABLE_SHARED([yes])])
LT_OPTION_DEFINE([LT_INIT], [disable-shared], [_LT_ENABLE_SHARED([no])])
# Old names:
AC_DEFUN([AC_ENABLE_SHARED],
[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[shared])
])
AC_DEFUN([AC_DISABLE_SHARED],
[_LT_SET_OPTION([LT_INIT], [disable-shared])
])
AU_DEFUN([AM_ENABLE_SHARED], [AC_ENABLE_SHARED($@)])
AU_DEFUN([AM_DISABLE_SHARED], [AC_DISABLE_SHARED($@)])
dnl aclocal-1.4 backwards compatibility:
dnl AC_DEFUN([AM_ENABLE_SHARED], [])
dnl AC_DEFUN([AM_DISABLE_SHARED], [])
# _LT_ENABLE_STATIC([DEFAULT])
# ----------------------------
# implement the --enable-static flag, and support the `static' and
# `disable-static' LT_INIT options.
# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
m4_define([_LT_ENABLE_STATIC],
[m4_define([_LT_ENABLE_STATIC_DEFAULT], [m4_if($1, no, no, yes)])dnl
AC_ARG_ENABLE([static],
[AS_HELP_STRING([--enable-static@<:@=PKGS@:>@],
[build static libraries @<:@default=]_LT_ENABLE_STATIC_DEFAULT[@:>@])],
[p=${PACKAGE-default}
case $enableval in
yes) enable_static=yes ;;
no) enable_static=no ;;
*)
enable_static=no
# Look at the argument we got. We use all the common list separators.
lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
for pkg in $enableval; do
IFS="$lt_save_ifs"
if test "X$pkg" = "X$p"; then
enable_static=yes
fi
done
IFS="$lt_save_ifs"
;;
esac],
[enable_static=]_LT_ENABLE_STATIC_DEFAULT)
_LT_DECL([build_old_libs], [enable_static], [0],
[Whether or not to build static libraries])
])# _LT_ENABLE_STATIC
LT_OPTION_DEFINE([LT_INIT], [static], [_LT_ENABLE_STATIC([yes])])
LT_OPTION_DEFINE([LT_INIT], [disable-static], [_LT_ENABLE_STATIC([no])])
# Old names:
AC_DEFUN([AC_ENABLE_STATIC],
[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[static])
])
AC_DEFUN([AC_DISABLE_STATIC],
[_LT_SET_OPTION([LT_INIT], [disable-static])
])
AU_DEFUN([AM_ENABLE_STATIC], [AC_ENABLE_STATIC($@)])
AU_DEFUN([AM_DISABLE_STATIC], [AC_DISABLE_STATIC($@)])
dnl aclocal-1.4 backwards compatibility:
dnl AC_DEFUN([AM_ENABLE_STATIC], [])
dnl AC_DEFUN([AM_DISABLE_STATIC], [])
# _LT_ENABLE_FAST_INSTALL([DEFAULT])
# ----------------------------------
# implement the --enable-fast-install flag, and support the `fast-install'
# and `disable-fast-install' LT_INIT options.
# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
m4_define([_LT_ENABLE_FAST_INSTALL],
[m4_define([_LT_ENABLE_FAST_INSTALL_DEFAULT], [m4_if($1, no, no, yes)])dnl
AC_ARG_ENABLE([fast-install],
[AS_HELP_STRING([--enable-fast-install@<:@=PKGS@:>@],
[optimize for fast installation @<:@default=]_LT_ENABLE_FAST_INSTALL_DEFAULT[@:>@])],
[p=${PACKAGE-default}
case $enableval in
yes) enable_fast_install=yes ;;
no) enable_fast_install=no ;;
*)
enable_fast_install=no
# Look at the argument we got. We use all the common list separators.
lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
for pkg in $enableval; do
IFS="$lt_save_ifs"
if test "X$pkg" = "X$p"; then
enable_fast_install=yes
fi
done
IFS="$lt_save_ifs"
;;
esac],
[enable_fast_install=]_LT_ENABLE_FAST_INSTALL_DEFAULT)
_LT_DECL([fast_install], [enable_fast_install], [0],
[Whether or not to optimize for fast installation])dnl
])# _LT_ENABLE_FAST_INSTALL
LT_OPTION_DEFINE([LT_INIT], [fast-install], [_LT_ENABLE_FAST_INSTALL([yes])])
LT_OPTION_DEFINE([LT_INIT], [disable-fast-install], [_LT_ENABLE_FAST_INSTALL([no])])
# Old names:
AU_DEFUN([AC_ENABLE_FAST_INSTALL],
[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[fast-install])
AC_DIAGNOSE([obsolete],
[$0: Remove this warning and the call to _LT_SET_OPTION when you put
the `fast-install' option into LT_INIT's first parameter.])
])
AU_DEFUN([AC_DISABLE_FAST_INSTALL],
[_LT_SET_OPTION([LT_INIT], [disable-fast-install])
AC_DIAGNOSE([obsolete],
[$0: Remove this warning and the call to _LT_SET_OPTION when you put
the `disable-fast-install' option into LT_INIT's first parameter.])
])
dnl aclocal-1.4 backwards compatibility:
dnl AC_DEFUN([AC_ENABLE_FAST_INSTALL], [])
dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], [])
# _LT_WITH_PIC([MODE])
# --------------------
# implement the --with-pic flag, and support the `pic-only' and `no-pic'
# LT_INIT options.
# MODE is either `yes' or `no'. If omitted, it defaults to `both'.
m4_define([_LT_WITH_PIC],
[AC_ARG_WITH([pic],
[AS_HELP_STRING([--with-pic],
[try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
[pic_mode="$withval"],
[pic_mode=default])
test -z "$pic_mode" && pic_mode=m4_default([$1], [default])
_LT_DECL([], [pic_mode], [0], [What type of objects to build])dnl
])# _LT_WITH_PIC
LT_OPTION_DEFINE([LT_INIT], [pic-only], [_LT_WITH_PIC([yes])])
LT_OPTION_DEFINE([LT_INIT], [no-pic], [_LT_WITH_PIC([no])])
# Old name:
AU_DEFUN([AC_LIBTOOL_PICMODE],
[_LT_SET_OPTION([LT_INIT], [pic-only])
AC_DIAGNOSE([obsolete],
[$0: Remove this warning and the call to _LT_SET_OPTION when you
put the `pic-only' option into LT_INIT's first parameter.])
])
dnl aclocal-1.4 backwards compatibility:
dnl AC_DEFUN([AC_LIBTOOL_PICMODE], [])
## ----------------- ##
## LTDL_INIT Options ##
## ----------------- ##
m4_define([_LTDL_MODE], [])
LT_OPTION_DEFINE([LTDL_INIT], [nonrecursive],
[m4_define([_LTDL_MODE], [nonrecursive])])
LT_OPTION_DEFINE([LTDL_INIT], [recursive],
[m4_define([_LTDL_MODE], [recursive])])
LT_OPTION_DEFINE([LTDL_INIT], [subproject],
[m4_define([_LTDL_MODE], [subproject])])
m4_define([_LTDL_TYPE], [])
LT_OPTION_DEFINE([LTDL_INIT], [installable],
[m4_define([_LTDL_TYPE], [installable])])
LT_OPTION_DEFINE([LTDL_INIT], [convenience],
[m4_define([_LTDL_TYPE], [convenience])])

123
libdivsufsort/m4/ltsugar.m4 vendored Normal file
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@ -0,0 +1,123 @@
# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*-
#
# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
# Written by Gary V. Vaughan, 2004
#
# This file is free software; the Free Software Foundation gives
# unlimited permission to copy and/or distribute it, with or without
# modifications, as long as this notice is preserved.
# serial 6 ltsugar.m4
# This is to help aclocal find these macros, as it can't see m4_define.
AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])])
# lt_join(SEP, ARG1, [ARG2...])
# -----------------------------
# Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their
# associated separator.
# Needed until we can rely on m4_join from Autoconf 2.62, since all earlier
# versions in m4sugar had bugs.
m4_define([lt_join],
[m4_if([$#], [1], [],
[$#], [2], [[$2]],
[m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])])
m4_define([_lt_join],
[m4_if([$#$2], [2], [],
[m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])])
# lt_car(LIST)
# lt_cdr(LIST)
# ------------
# Manipulate m4 lists.
# These macros are necessary as long as will still need to support
# Autoconf-2.59 which quotes differently.
m4_define([lt_car], [[$1]])
m4_define([lt_cdr],
[m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])],
[$#], 1, [],
[m4_dquote(m4_shift($@))])])
m4_define([lt_unquote], $1)
# lt_append(MACRO-NAME, STRING, [SEPARATOR])
# ------------------------------------------
# Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'.
# Note that neither SEPARATOR nor STRING are expanded; they are appended
# to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked).
# No SEPARATOR is output if MACRO-NAME was previously undefined (different
# than defined and empty).
#
# This macro is needed until we can rely on Autoconf 2.62, since earlier
# versions of m4sugar mistakenly expanded SEPARATOR but not STRING.
m4_define([lt_append],
[m4_define([$1],
m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])])
# lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...])
# ----------------------------------------------------------
# Produce a SEP delimited list of all paired combinations of elements of
# PREFIX-LIST with SUFFIX1 through SUFFIXn. Each element of the list
# has the form PREFIXmINFIXSUFFIXn.
# Needed until we can rely on m4_combine added in Autoconf 2.62.
m4_define([lt_combine],
[m4_if(m4_eval([$# > 3]), [1],
[m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl
[[m4_foreach([_Lt_prefix], [$2],
[m4_foreach([_Lt_suffix],
]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[,
[_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])])
# lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ])
# -----------------------------------------------------------------------
# Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited
# by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ.
m4_define([lt_if_append_uniq],
[m4_ifdef([$1],
[m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1],
[lt_append([$1], [$2], [$3])$4],
[$5])],
[lt_append([$1], [$2], [$3])$4])])
# lt_dict_add(DICT, KEY, VALUE)
# -----------------------------
m4_define([lt_dict_add],
[m4_define([$1($2)], [$3])])
# lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE)
# --------------------------------------------
m4_define([lt_dict_add_subkey],
[m4_define([$1($2:$3)], [$4])])
# lt_dict_fetch(DICT, KEY, [SUBKEY])
# ----------------------------------
m4_define([lt_dict_fetch],
[m4_ifval([$3],
m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]),
m4_ifdef([$1($2)], [m4_defn([$1($2)])]))])
# lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE])
# -----------------------------------------------------------------
m4_define([lt_if_dict_fetch],
[m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4],
[$5],
[$6])])
# lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...])
# --------------------------------------------------------------
m4_define([lt_dict_filter],
[m4_if([$5], [], [],
[lt_join(m4_quote(m4_default([$4], [[, ]])),
lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]),
[lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl
])

23
libdivsufsort/m4/ltversion.m4 vendored Normal file
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@ -0,0 +1,23 @@
# ltversion.m4 -- version numbers -*- Autoconf -*-
#
# Copyright (C) 2004 Free Software Foundation, Inc.
# Written by Scott James Remnant, 2004
#
# This file is free software; the Free Software Foundation gives
# unlimited permission to copy and/or distribute it, with or without
# modifications, as long as this notice is preserved.
# Generated from ltversion.in.
# serial 3017 ltversion.m4
# This file is part of GNU Libtool
m4_define([LT_PACKAGE_VERSION], [2.2.6b])
m4_define([LT_PACKAGE_REVISION], [1.3017])
AC_DEFUN([LTVERSION_VERSION],
[macro_version='2.2.6b'
macro_revision='1.3017'
_LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?])
_LT_DECL(, macro_revision, 0)
])

92
libdivsufsort/m4/lt~obsolete.m4 vendored Normal file
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@ -0,0 +1,92 @@
# lt~obsolete.m4 -- aclocal satisfying obsolete definitions. -*-Autoconf-*-
#
# Copyright (C) 2004, 2005, 2007 Free Software Foundation, Inc.
# Written by Scott James Remnant, 2004.
#
# This file is free software; the Free Software Foundation gives
# unlimited permission to copy and/or distribute it, with or without
# modifications, as long as this notice is preserved.
# serial 4 lt~obsolete.m4
# These exist entirely to fool aclocal when bootstrapping libtool.
#
# In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN)
# which have later been changed to m4_define as they aren't part of the
# exported API, or moved to Autoconf or Automake where they belong.
#
# The trouble is, aclocal is a bit thick. It'll see the old AC_DEFUN
# in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us
# using a macro with the same name in our local m4/libtool.m4 it'll
# pull the old libtool.m4 in (it doesn't see our shiny new m4_define
# and doesn't know about Autoconf macros at all.)
#
# So we provide this file, which has a silly filename so it's always
# included after everything else. This provides aclocal with the
# AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything
# because those macros already exist, or will be overwritten later.
# We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6.
#
# Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here.
# Yes, that means every name once taken will need to remain here until
# we give up compatibility with versions before 1.7, at which point
# we need to keep only those names which we still refer to.
# This is to help aclocal find these macros, as it can't see m4_define.
AC_DEFUN([LTOBSOLETE_VERSION], [m4_if([1])])
m4_ifndef([AC_LIBTOOL_LINKER_OPTION], [AC_DEFUN([AC_LIBTOOL_LINKER_OPTION])])
m4_ifndef([AC_PROG_EGREP], [AC_DEFUN([AC_PROG_EGREP])])
m4_ifndef([_LT_AC_PROG_ECHO_BACKSLASH], [AC_DEFUN([_LT_AC_PROG_ECHO_BACKSLASH])])
m4_ifndef([_LT_AC_SHELL_INIT], [AC_DEFUN([_LT_AC_SHELL_INIT])])
m4_ifndef([_LT_AC_SYS_LIBPATH_AIX], [AC_DEFUN([_LT_AC_SYS_LIBPATH_AIX])])
m4_ifndef([_LT_PROG_LTMAIN], [AC_DEFUN([_LT_PROG_LTMAIN])])
m4_ifndef([_LT_AC_TAGVAR], [AC_DEFUN([_LT_AC_TAGVAR])])
m4_ifndef([AC_LTDL_ENABLE_INSTALL], [AC_DEFUN([AC_LTDL_ENABLE_INSTALL])])
m4_ifndef([AC_LTDL_PREOPEN], [AC_DEFUN([AC_LTDL_PREOPEN])])
m4_ifndef([_LT_AC_SYS_COMPILER], [AC_DEFUN([_LT_AC_SYS_COMPILER])])
m4_ifndef([_LT_AC_LOCK], [AC_DEFUN([_LT_AC_LOCK])])
m4_ifndef([AC_LIBTOOL_SYS_OLD_ARCHIVE], [AC_DEFUN([AC_LIBTOOL_SYS_OLD_ARCHIVE])])
m4_ifndef([_LT_AC_TRY_DLOPEN_SELF], [AC_DEFUN([_LT_AC_TRY_DLOPEN_SELF])])
m4_ifndef([AC_LIBTOOL_PROG_CC_C_O], [AC_DEFUN([AC_LIBTOOL_PROG_CC_C_O])])
m4_ifndef([AC_LIBTOOL_SYS_HARD_LINK_LOCKS], [AC_DEFUN([AC_LIBTOOL_SYS_HARD_LINK_LOCKS])])
m4_ifndef([AC_LIBTOOL_OBJDIR], [AC_DEFUN([AC_LIBTOOL_OBJDIR])])
m4_ifndef([AC_LTDL_OBJDIR], [AC_DEFUN([AC_LTDL_OBJDIR])])
m4_ifndef([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH], [AC_DEFUN([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH])])
m4_ifndef([AC_LIBTOOL_SYS_LIB_STRIP], [AC_DEFUN([AC_LIBTOOL_SYS_LIB_STRIP])])
m4_ifndef([AC_PATH_MAGIC], [AC_DEFUN([AC_PATH_MAGIC])])
m4_ifndef([AC_PROG_LD_GNU], [AC_DEFUN([AC_PROG_LD_GNU])])
m4_ifndef([AC_PROG_LD_RELOAD_FLAG], [AC_DEFUN([AC_PROG_LD_RELOAD_FLAG])])
m4_ifndef([AC_DEPLIBS_CHECK_METHOD], [AC_DEFUN([AC_DEPLIBS_CHECK_METHOD])])
m4_ifndef([AC_LIBTOOL_PROG_COMPILER_NO_RTTI], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_NO_RTTI])])
m4_ifndef([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE], [AC_DEFUN([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE])])
m4_ifndef([AC_LIBTOOL_PROG_COMPILER_PIC], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_PIC])])
m4_ifndef([AC_LIBTOOL_PROG_LD_SHLIBS], [AC_DEFUN([AC_LIBTOOL_PROG_LD_SHLIBS])])
m4_ifndef([AC_LIBTOOL_POSTDEP_PREDEP], [AC_DEFUN([AC_LIBTOOL_POSTDEP_PREDEP])])
m4_ifndef([LT_AC_PROG_EGREP], [AC_DEFUN([LT_AC_PROG_EGREP])])
m4_ifndef([LT_AC_PROG_SED], [AC_DEFUN([LT_AC_PROG_SED])])
m4_ifndef([_LT_CC_BASENAME], [AC_DEFUN([_LT_CC_BASENAME])])
m4_ifndef([_LT_COMPILER_BOILERPLATE], [AC_DEFUN([_LT_COMPILER_BOILERPLATE])])
m4_ifndef([_LT_LINKER_BOILERPLATE], [AC_DEFUN([_LT_LINKER_BOILERPLATE])])
m4_ifndef([_AC_PROG_LIBTOOL], [AC_DEFUN([_AC_PROG_LIBTOOL])])
m4_ifndef([AC_LIBTOOL_SETUP], [AC_DEFUN([AC_LIBTOOL_SETUP])])
m4_ifndef([_LT_AC_CHECK_DLFCN], [AC_DEFUN([_LT_AC_CHECK_DLFCN])])
m4_ifndef([AC_LIBTOOL_SYS_DYNAMIC_LINKER], [AC_DEFUN([AC_LIBTOOL_SYS_DYNAMIC_LINKER])])
m4_ifndef([_LT_AC_TAGCONFIG], [AC_DEFUN([_LT_AC_TAGCONFIG])])
m4_ifndef([AC_DISABLE_FAST_INSTALL], [AC_DEFUN([AC_DISABLE_FAST_INSTALL])])
m4_ifndef([_LT_AC_LANG_CXX], [AC_DEFUN([_LT_AC_LANG_CXX])])
m4_ifndef([_LT_AC_LANG_F77], [AC_DEFUN([_LT_AC_LANG_F77])])
m4_ifndef([_LT_AC_LANG_GCJ], [AC_DEFUN([_LT_AC_LANG_GCJ])])
m4_ifndef([AC_LIBTOOL_RC], [AC_DEFUN([AC_LIBTOOL_RC])])
m4_ifndef([AC_LIBTOOL_LANG_C_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_C_CONFIG])])
m4_ifndef([_LT_AC_LANG_C_CONFIG], [AC_DEFUN([_LT_AC_LANG_C_CONFIG])])
m4_ifndef([AC_LIBTOOL_LANG_CXX_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_CXX_CONFIG])])
m4_ifndef([_LT_AC_LANG_CXX_CONFIG], [AC_DEFUN([_LT_AC_LANG_CXX_CONFIG])])
m4_ifndef([AC_LIBTOOL_LANG_F77_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_F77_CONFIG])])
m4_ifndef([_LT_AC_LANG_F77_CONFIG], [AC_DEFUN([_LT_AC_LANG_F77_CONFIG])])
m4_ifndef([AC_LIBTOOL_LANG_GCJ_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_GCJ_CONFIG])])
m4_ifndef([_LT_AC_LANG_GCJ_CONFIG], [AC_DEFUN([_LT_AC_LANG_GCJ_CONFIG])])
m4_ifndef([AC_LIBTOOL_LANG_RC_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_RC_CONFIG])])
m4_ifndef([_LT_AC_LANG_RC_CONFIG], [AC_DEFUN([_LT_AC_LANG_RC_CONFIG])])
m4_ifndef([AC_LIBTOOL_CONFIG], [AC_DEFUN([AC_LIBTOOL_CONFIG])])
m4_ifndef([_LT_AC_FILE_LTDLL_C], [AC_DEFUN([_LT_AC_FILE_LTDLL_C])])

10
libdivsufsort/pkgconfig/CMakeLists.txt Normal file
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@ -0,0 +1,10 @@
## generate libdivsufsort.pc ##
set(prefix "${CMAKE_INSTALL_PREFIX}")
set(W64BIT "")
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/libdivsufsort.pc.cmake" "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort.pc" @ONLY)
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort.pc" DESTINATION lib/pkgconfig)
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 lib/pkgconfig)
endif(BUILD_DIVSUFSORT64)

11
libdivsufsort/pkgconfig/libdivsufsort.pc.cmake Normal file
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@ -0,0 +1,11 @@
prefix=@prefix@
exec_prefix=${prefix}
libdir=${exec_prefix}/lib
includedir=${prefix}/include
Name: @PROJECT_NAME@@W64BIT@
Description: @PROJECT_DESCRIPTION@
Version: @PROJECT_VERSION_FULL@
URL: @PROJECT_URL@
Libs: -L${libdir} -ldivsufsort@W64BIT@
Cflags: -I${includedir}

2
run-checkers.sh
View File

@ -4,4 +4,4 @@ TARGET_DIR=build
./cpplint.py --filter=-legal,-build/namespaces,-whitespace/labels,-build/include_what_you_use,-runtime/int,-readability/streams,-build/include_order `find concordia concordia-console -type f -regextype posix-extended -regex '.*\.(cpp|hpp|h|c)' ! -regex '.*\./build.*' ! -regex '.*concordia/common/config.hpp' ! -regex '.*/(t|tests)/.*'` 2> cpplint-result.txt
cppcheck -D__cplusplus -D__GNUC__=3 -f --enable=all echo `find . -type d ! -path './.git*' ! -path "./${TARGET_DIR}"'*' | perl -ne 'chomp; print "-I$_ "'` `find . -type f -regextype posix-extended -regex '.*\.(cpp|hpp|h|c)' ! -regex '.*\./build.*'` 2> cppcheck-result.txt
cppcheck -D__cplusplus -D__GNUC__=3 -f --enable=all echo `find . -type d ! -path './.git*' ! -path "./${TARGET_DIR}"'*' | perl -ne 'chomp; print "-I$_ "'` `find . -type f -regextype posix-extended -regex '.*\.(cpp|hpp)' ! -regex '.*\./build.*'` 2> cppcheck-result.txt