zstd-ruby 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.gitignore +19 -0
- data/.gitmodules +3 -0
- data/.rspec +2 -0
- data/.travis.yml +11 -0
- data/CODE_OF_CONDUCT.md +74 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +29 -0
- data/README.md +63 -0
- data/Rakefile +22 -0
- data/bin/console +14 -0
- data/bin/setup +8 -0
- data/ext/zstdruby/extconf.rb +23 -0
- data/ext/zstdruby/libzstd/.gitignore +2 -0
- data/ext/zstdruby/libzstd/Makefile +133 -0
- data/ext/zstdruby/libzstd/README.md +77 -0
- data/ext/zstdruby/libzstd/common/bitstream.h +414 -0
- data/ext/zstdruby/libzstd/common/entropy_common.c +227 -0
- data/ext/zstdruby/libzstd/common/error_private.c +43 -0
- data/ext/zstdruby/libzstd/common/error_private.h +76 -0
- data/ext/zstdruby/libzstd/common/fse.h +668 -0
- data/ext/zstdruby/libzstd/common/fse_decompress.c +329 -0
- data/ext/zstdruby/libzstd/common/huf.h +238 -0
- data/ext/zstdruby/libzstd/common/mem.h +372 -0
- data/ext/zstdruby/libzstd/common/xxhash.c +867 -0
- data/ext/zstdruby/libzstd/common/xxhash.h +309 -0
- data/ext/zstdruby/libzstd/common/zstd_common.c +77 -0
- data/ext/zstdruby/libzstd/common/zstd_errors.h +60 -0
- data/ext/zstdruby/libzstd/common/zstd_internal.h +270 -0
- data/ext/zstdruby/libzstd/compress/fse_compress.c +850 -0
- data/ext/zstdruby/libzstd/compress/huf_compress.c +609 -0
- data/ext/zstdruby/libzstd/compress/zstd_compress.c +3291 -0
- data/ext/zstdruby/libzstd/compress/zstd_opt.h +919 -0
- data/ext/zstdruby/libzstd/decompress/huf_decompress.c +885 -0
- data/ext/zstdruby/libzstd/decompress/zstd_decompress.c +2154 -0
- data/ext/zstdruby/libzstd/deprecated/zbuff.h +210 -0
- data/ext/zstdruby/libzstd/deprecated/zbuff_compress.c +145 -0
- data/ext/zstdruby/libzstd/deprecated/zbuff_decompress.c +74 -0
- data/ext/zstdruby/libzstd/dictBuilder/divsufsort.c +1913 -0
- data/ext/zstdruby/libzstd/dictBuilder/divsufsort.h +67 -0
- data/ext/zstdruby/libzstd/dictBuilder/zdict.c +1012 -0
- data/ext/zstdruby/libzstd/dictBuilder/zdict.h +111 -0
- data/ext/zstdruby/libzstd/dll/example/Makefile +47 -0
- data/ext/zstdruby/libzstd/dll/example/README.md +69 -0
- data/ext/zstdruby/libzstd/dll/example/build_package.bat +17 -0
- data/ext/zstdruby/libzstd/dll/example/fullbench-dll.sln +25 -0
- data/ext/zstdruby/libzstd/dll/example/fullbench-dll.vcxproj +179 -0
- data/ext/zstdruby/libzstd/dll/libzstd.def +86 -0
- data/ext/zstdruby/libzstd/legacy/zstd_legacy.h +259 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v01.c +2095 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v01.h +80 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v02.c +3518 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v02.h +79 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v03.c +3159 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v03.h +79 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v04.c +3795 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v04.h +128 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v05.c +4056 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v05.h +149 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v06.c +4167 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v06.h +159 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v07.c +4540 -0
- data/ext/zstdruby/libzstd/legacy/zstd_v07.h +173 -0
- data/ext/zstdruby/libzstd/libzstd.pc.in +14 -0
- data/ext/zstdruby/libzstd/zstd.h +673 -0
- data/ext/zstdruby/zstdruby.c +117 -0
- data/ext/zstdruby/zstdruby.h +6 -0
- data/lib/zstd-ruby.rb +6 -0
- data/lib/zstd-ruby/version.rb +3 -0
- data/zstd-ruby.gemspec +37 -0
- metadata +170 -0
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/**
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* Copyright (c) 2016-present, Yann Collet, Facebook, Inc.
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* All rights reserved.
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*
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* This source code is licensed under the BSD-style license found in the
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* LICENSE file in the root directory of this source tree. An additional grant
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* of patent rights can be found in the PATENTS file in the same directory.
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*/
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/* ***************************************************************
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* NOTES/WARNINGS
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******************************************************************/
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/* The streaming API defined here is deprecated.
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* Consider migrating towards ZSTD_compressStream() API in `zstd.h`
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* See 'lib/README.md'.
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*****************************************************************/
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#if defined (__cplusplus)
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extern "C" {
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#endif
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#ifndef ZSTD_BUFFERED_H_23987
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#define ZSTD_BUFFERED_H_23987
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/* *************************************
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* Dependencies
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***************************************/
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#include <stddef.h> /* size_t */
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#include "zstd.h" /* ZSTD_CStream, ZSTD_DStream, ZSTDLIB_API */
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/* ***************************************************************
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* Compiler specifics
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*****************************************************************/
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/* Deprecation warnings */
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/* Should these warnings be a problem,
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it is generally possible to disable them,
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typically with -Wno-deprecated-declarations for gcc
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or _CRT_SECURE_NO_WARNINGS in Visual.
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Otherwise, it's also possible to define ZBUFF_DISABLE_DEPRECATE_WARNINGS */
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#ifdef ZBUFF_DISABLE_DEPRECATE_WARNINGS
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# define ZBUFF_DEPRECATED(message) ZSTDLIB_API /* disable deprecation warnings */
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#else
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# if (defined(__GNUC__) && (__GNUC__ >= 5)) || defined(__clang__)
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# define ZBUFF_DEPRECATED(message) ZSTDLIB_API __attribute__((deprecated(message)))
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# elif defined(__GNUC__) && (__GNUC__ >= 3)
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# define ZBUFF_DEPRECATED(message) ZSTDLIB_API __attribute__((deprecated))
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# elif defined(_MSC_VER)
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# define ZBUFF_DEPRECATED(message) ZSTDLIB_API __declspec(deprecated(message))
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# else
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# pragma message("WARNING: You need to implement ZBUFF_DEPRECATED for this compiler")
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# define ZBUFF_DEPRECATED(message) ZSTDLIB_API
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# endif
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#endif /* ZBUFF_DISABLE_DEPRECATE_WARNINGS */
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/* *************************************
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* Streaming functions
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***************************************/
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/* This is the easier "buffered" streaming API,
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* using an internal buffer to lift all restrictions on user-provided buffers
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* which can be any size, any place, for both input and output.
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* ZBUFF and ZSTD are 100% interoperable,
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* frames created by one can be decoded by the other one */
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typedef ZSTD_CStream ZBUFF_CCtx;
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ZBUFF_DEPRECATED("use ZSTD_createCStream") ZBUFF_CCtx* ZBUFF_createCCtx(void);
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ZBUFF_DEPRECATED("use ZSTD_freeCStream") size_t ZBUFF_freeCCtx(ZBUFF_CCtx* cctx);
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ZBUFF_DEPRECATED("use ZSTD_initCStream") size_t ZBUFF_compressInit(ZBUFF_CCtx* cctx, int compressionLevel);
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ZBUFF_DEPRECATED("use ZSTD_initCStream_usingDict") size_t ZBUFF_compressInitDictionary(ZBUFF_CCtx* cctx, const void* dict, size_t dictSize, int compressionLevel);
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ZBUFF_DEPRECATED("use ZSTD_compressStream") size_t ZBUFF_compressContinue(ZBUFF_CCtx* cctx, void* dst, size_t* dstCapacityPtr, const void* src, size_t* srcSizePtr);
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ZBUFF_DEPRECATED("use ZSTD_flushStream") size_t ZBUFF_compressFlush(ZBUFF_CCtx* cctx, void* dst, size_t* dstCapacityPtr);
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ZBUFF_DEPRECATED("use ZSTD_endStream") size_t ZBUFF_compressEnd(ZBUFF_CCtx* cctx, void* dst, size_t* dstCapacityPtr);
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/*-*************************************************
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* Streaming compression - howto
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*
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* A ZBUFF_CCtx object is required to track streaming operation.
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* Use ZBUFF_createCCtx() and ZBUFF_freeCCtx() to create/release resources.
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* ZBUFF_CCtx objects can be reused multiple times.
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*
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* Start by initializing ZBUF_CCtx.
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* Use ZBUFF_compressInit() to start a new compression operation.
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* Use ZBUFF_compressInitDictionary() for a compression which requires a dictionary.
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*
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* Use ZBUFF_compressContinue() repetitively to consume input stream.
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* *srcSizePtr and *dstCapacityPtr can be any size.
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* The function will report how many bytes were read or written within *srcSizePtr and *dstCapacityPtr.
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* Note that it may not consume the entire input, in which case it's up to the caller to present again remaining data.
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* The content of `dst` will be overwritten (up to *dstCapacityPtr) at each call, so save its content if it matters or change @dst .
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* @return : a hint to preferred nb of bytes to use as input for next function call (it's just a hint, to improve latency)
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* or an error code, which can be tested using ZBUFF_isError().
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*
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* At any moment, it's possible to flush whatever data remains within buffer, using ZBUFF_compressFlush().
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* The nb of bytes written into `dst` will be reported into *dstCapacityPtr.
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* Note that the function cannot output more than *dstCapacityPtr,
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* therefore, some content might still be left into internal buffer if *dstCapacityPtr is too small.
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* @return : nb of bytes still present into internal buffer (0 if it's empty)
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* or an error code, which can be tested using ZBUFF_isError().
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*
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* ZBUFF_compressEnd() instructs to finish a frame.
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* It will perform a flush and write frame epilogue.
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* The epilogue is required for decoders to consider a frame completed.
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* Similar to ZBUFF_compressFlush(), it may not be able to output the entire internal buffer content if *dstCapacityPtr is too small.
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* In which case, call again ZBUFF_compressFlush() to complete the flush.
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* @return : nb of bytes still present into internal buffer (0 if it's empty)
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* or an error code, which can be tested using ZBUFF_isError().
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*
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* Hint : _recommended buffer_ sizes (not compulsory) : ZBUFF_recommendedCInSize() / ZBUFF_recommendedCOutSize()
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* input : ZBUFF_recommendedCInSize==128 KB block size is the internal unit, use this value to reduce intermediate stages (better latency)
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* output : ZBUFF_recommendedCOutSize==ZSTD_compressBound(128 KB) + 3 + 3 : ensures it's always possible to write/flush/end a full block. Skip some buffering.
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* By using both, it ensures that input will be entirely consumed, and output will always contain the result, reducing intermediate buffering.
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* **************************************************/
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typedef ZSTD_DStream ZBUFF_DCtx;
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ZBUFF_DEPRECATED("use ZSTD_createDStream") ZBUFF_DCtx* ZBUFF_createDCtx(void);
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ZBUFF_DEPRECATED("use ZSTD_freeDStream") size_t ZBUFF_freeDCtx(ZBUFF_DCtx* dctx);
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ZBUFF_DEPRECATED("use ZSTD_initDStream") size_t ZBUFF_decompressInit(ZBUFF_DCtx* dctx);
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ZBUFF_DEPRECATED("use ZSTD_initDStream_usingDict") size_t ZBUFF_decompressInitDictionary(ZBUFF_DCtx* dctx, const void* dict, size_t dictSize);
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ZBUFF_DEPRECATED("use ZSTD_decompressStream") size_t ZBUFF_decompressContinue(ZBUFF_DCtx* dctx,
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void* dst, size_t* dstCapacityPtr,
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const void* src, size_t* srcSizePtr);
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/*-***************************************************************************
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* Streaming decompression howto
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*
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* A ZBUFF_DCtx object is required to track streaming operations.
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* Use ZBUFF_createDCtx() and ZBUFF_freeDCtx() to create/release resources.
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* Use ZBUFF_decompressInit() to start a new decompression operation,
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* or ZBUFF_decompressInitDictionary() if decompression requires a dictionary.
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* Note that ZBUFF_DCtx objects can be re-init multiple times.
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*
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* Use ZBUFF_decompressContinue() repetitively to consume your input.
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* *srcSizePtr and *dstCapacityPtr can be any size.
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* The function will report how many bytes were read or written by modifying *srcSizePtr and *dstCapacityPtr.
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* Note that it may not consume the entire input, in which case it's up to the caller to present remaining input again.
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* The content of `dst` will be overwritten (up to *dstCapacityPtr) at each function call, so save its content if it matters, or change `dst`.
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* @return : 0 when a frame is completely decoded and fully flushed,
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* 1 when there is still some data left within internal buffer to flush,
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* >1 when more data is expected, with value being a suggested next input size (it's just a hint, which helps latency),
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* or an error code, which can be tested using ZBUFF_isError().
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*
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* Hint : recommended buffer sizes (not compulsory) : ZBUFF_recommendedDInSize() and ZBUFF_recommendedDOutSize()
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* output : ZBUFF_recommendedDOutSize== 128 KB block size is the internal unit, it ensures it's always possible to write a full block when decoded.
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* input : ZBUFF_recommendedDInSize == 128KB + 3;
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* just follow indications from ZBUFF_decompressContinue() to minimize latency. It should always be <= 128 KB + 3 .
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* *******************************************************************************/
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/* *************************************
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* Tool functions
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***************************************/
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ZBUFF_DEPRECATED("use ZSTD_isError") unsigned ZBUFF_isError(size_t errorCode);
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ZBUFF_DEPRECATED("use ZSTD_getErrorName") const char* ZBUFF_getErrorName(size_t errorCode);
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/** Functions below provide recommended buffer sizes for Compression or Decompression operations.
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* These sizes are just hints, they tend to offer better latency */
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ZBUFF_DEPRECATED("use ZSTD_CStreamInSize") size_t ZBUFF_recommendedCInSize(void);
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ZBUFF_DEPRECATED("use ZSTD_CStreamOutSize") size_t ZBUFF_recommendedCOutSize(void);
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ZBUFF_DEPRECATED("use ZSTD_DStreamInSize") size_t ZBUFF_recommendedDInSize(void);
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ZBUFF_DEPRECATED("use ZSTD_DStreamOutSize") size_t ZBUFF_recommendedDOutSize(void);
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#endif /* ZSTD_BUFFERED_H_23987 */
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#ifdef ZBUFF_STATIC_LINKING_ONLY
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#ifndef ZBUFF_STATIC_H_30298098432
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#define ZBUFF_STATIC_H_30298098432
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/* ====================================================================================
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* The definitions in this section are considered experimental.
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* They should never be used in association with a dynamic library, as they may change in the future.
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* They are provided for advanced usages.
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* Use them only in association with static linking.
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* ==================================================================================== */
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/*--- Dependency ---*/
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#define ZSTD_STATIC_LINKING_ONLY /* ZSTD_parameters, ZSTD_customMem */
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#include "zstd.h"
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/*--- Custom memory allocator ---*/
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/*! ZBUFF_createCCtx_advanced() :
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* Create a ZBUFF compression context using external alloc and free functions */
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ZBUFF_DEPRECATED("use ZSTD_createCStream_advanced") ZBUFF_CCtx* ZBUFF_createCCtx_advanced(ZSTD_customMem customMem);
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/*! ZBUFF_createDCtx_advanced() :
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* Create a ZBUFF decompression context using external alloc and free functions */
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ZBUFF_DEPRECATED("use ZSTD_createDStream_advanced") ZBUFF_DCtx* ZBUFF_createDCtx_advanced(ZSTD_customMem customMem);
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/*--- Advanced Streaming Initialization ---*/
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ZBUFF_DEPRECATED("use ZSTD_initDStream_usingDict") size_t ZBUFF_compressInit_advanced(ZBUFF_CCtx* zbc,
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const void* dict, size_t dictSize,
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ZSTD_parameters params, unsigned long long pledgedSrcSize);
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#endif /* ZBUFF_STATIC_H_30298098432 */
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#endif /* ZBUFF_STATIC_LINKING_ONLY */
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#if defined (__cplusplus)
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}
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#endif
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/**
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* Copyright (c) 2016-present, Yann Collet, Facebook, Inc.
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* All rights reserved.
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*
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* This source code is licensed under the BSD-style license found in the
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* LICENSE file in the root directory of this source tree. An additional grant
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* of patent rights can be found in the PATENTS file in the same directory.
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*/
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/* *************************************
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* Dependencies
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***************************************/
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#define ZBUFF_STATIC_LINKING_ONLY
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#include "zbuff.h"
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/*-***********************************************************
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* Streaming compression
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*
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* A ZBUFF_CCtx object is required to track streaming operation.
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* Use ZBUFF_createCCtx() and ZBUFF_freeCCtx() to create/release resources.
|
24
|
+
* Use ZBUFF_compressInit() to start a new compression operation.
|
25
|
+
* ZBUFF_CCtx objects can be reused multiple times.
|
26
|
+
*
|
27
|
+
* Use ZBUFF_compressContinue() repetitively to consume your input.
|
28
|
+
* *srcSizePtr and *dstCapacityPtr can be any size.
|
29
|
+
* The function will report how many bytes were read or written by modifying *srcSizePtr and *dstCapacityPtr.
|
30
|
+
* Note that it may not consume the entire input, in which case it's up to the caller to call again the function with remaining input.
|
31
|
+
* The content of dst will be overwritten (up to *dstCapacityPtr) at each function call, so save its content if it matters or change dst .
|
32
|
+
* @return : a hint to preferred nb of bytes to use as input for next function call (it's only a hint, to improve latency)
|
33
|
+
* or an error code, which can be tested using ZBUFF_isError().
|
34
|
+
*
|
35
|
+
* ZBUFF_compressFlush() can be used to instruct ZBUFF to compress and output whatever remains within its buffer.
|
36
|
+
* Note that it will not output more than *dstCapacityPtr.
|
37
|
+
* Therefore, some content might still be left into its internal buffer if dst buffer is too small.
|
38
|
+
* @return : nb of bytes still present into internal buffer (0 if it's empty)
|
39
|
+
* or an error code, which can be tested using ZBUFF_isError().
|
40
|
+
*
|
41
|
+
* ZBUFF_compressEnd() instructs to finish a frame.
|
42
|
+
* It will perform a flush and write frame epilogue.
|
43
|
+
* Similar to ZBUFF_compressFlush(), it may not be able to output the entire internal buffer content if *dstCapacityPtr is too small.
|
44
|
+
* @return : nb of bytes still present into internal buffer (0 if it's empty)
|
45
|
+
* or an error code, which can be tested using ZBUFF_isError().
|
46
|
+
*
|
47
|
+
* Hint : recommended buffer sizes (not compulsory)
|
48
|
+
* input : ZSTD_BLOCKSIZE_MAX (128 KB), internal unit size, it improves latency to use this value.
|
49
|
+
* output : ZSTD_compressBound(ZSTD_BLOCKSIZE_MAX) + ZSTD_blockHeaderSize + ZBUFF_endFrameSize : ensures it's always possible to write/flush/end a full block at best speed.
|
50
|
+
* ***********************************************************/
|
51
|
+
|
52
|
+
ZBUFF_CCtx* ZBUFF_createCCtx(void)
|
53
|
+
{
|
54
|
+
return ZSTD_createCStream();
|
55
|
+
}
|
56
|
+
|
57
|
+
ZBUFF_CCtx* ZBUFF_createCCtx_advanced(ZSTD_customMem customMem)
|
58
|
+
{
|
59
|
+
return ZSTD_createCStream_advanced(customMem);
|
60
|
+
}
|
61
|
+
|
62
|
+
size_t ZBUFF_freeCCtx(ZBUFF_CCtx* zbc)
|
63
|
+
{
|
64
|
+
return ZSTD_freeCStream(zbc);
|
65
|
+
}
|
66
|
+
|
67
|
+
|
68
|
+
/* ====== Initialization ====== */
|
69
|
+
|
70
|
+
size_t ZBUFF_compressInit_advanced(ZBUFF_CCtx* zbc,
|
71
|
+
const void* dict, size_t dictSize,
|
72
|
+
ZSTD_parameters params, unsigned long long pledgedSrcSize)
|
73
|
+
{
|
74
|
+
return ZSTD_initCStream_advanced(zbc, dict, dictSize, params, pledgedSrcSize);
|
75
|
+
}
|
76
|
+
|
77
|
+
|
78
|
+
size_t ZBUFF_compressInitDictionary(ZBUFF_CCtx* zbc, const void* dict, size_t dictSize, int compressionLevel)
|
79
|
+
{
|
80
|
+
return ZSTD_initCStream_usingDict(zbc, dict, dictSize, compressionLevel);
|
81
|
+
}
|
82
|
+
|
83
|
+
size_t ZBUFF_compressInit(ZBUFF_CCtx* zbc, int compressionLevel)
|
84
|
+
{
|
85
|
+
return ZSTD_initCStream(zbc, compressionLevel);
|
86
|
+
}
|
87
|
+
|
88
|
+
/* ====== Compression ====== */
|
89
|
+
|
90
|
+
|
91
|
+
size_t ZBUFF_compressContinue(ZBUFF_CCtx* zbc,
|
92
|
+
void* dst, size_t* dstCapacityPtr,
|
93
|
+
const void* src, size_t* srcSizePtr)
|
94
|
+
{
|
95
|
+
size_t result;
|
96
|
+
ZSTD_outBuffer outBuff;
|
97
|
+
ZSTD_inBuffer inBuff;
|
98
|
+
outBuff.dst = dst;
|
99
|
+
outBuff.pos = 0;
|
100
|
+
outBuff.size = *dstCapacityPtr;
|
101
|
+
inBuff.src = src;
|
102
|
+
inBuff.pos = 0;
|
103
|
+
inBuff.size = *srcSizePtr;
|
104
|
+
result = ZSTD_compressStream(zbc, &outBuff, &inBuff);
|
105
|
+
*dstCapacityPtr = outBuff.pos;
|
106
|
+
*srcSizePtr = inBuff.pos;
|
107
|
+
return result;
|
108
|
+
}
|
109
|
+
|
110
|
+
|
111
|
+
|
112
|
+
/* ====== Finalize ====== */
|
113
|
+
|
114
|
+
size_t ZBUFF_compressFlush(ZBUFF_CCtx* zbc, void* dst, size_t* dstCapacityPtr)
|
115
|
+
{
|
116
|
+
size_t result;
|
117
|
+
ZSTD_outBuffer outBuff;
|
118
|
+
outBuff.dst = dst;
|
119
|
+
outBuff.pos = 0;
|
120
|
+
outBuff.size = *dstCapacityPtr;
|
121
|
+
result = ZSTD_flushStream(zbc, &outBuff);
|
122
|
+
*dstCapacityPtr = outBuff.pos;
|
123
|
+
return result;
|
124
|
+
}
|
125
|
+
|
126
|
+
|
127
|
+
size_t ZBUFF_compressEnd(ZBUFF_CCtx* zbc, void* dst, size_t* dstCapacityPtr)
|
128
|
+
{
|
129
|
+
size_t result;
|
130
|
+
ZSTD_outBuffer outBuff;
|
131
|
+
outBuff.dst = dst;
|
132
|
+
outBuff.pos = 0;
|
133
|
+
outBuff.size = *dstCapacityPtr;
|
134
|
+
result = ZSTD_endStream(zbc, &outBuff);
|
135
|
+
*dstCapacityPtr = outBuff.pos;
|
136
|
+
return result;
|
137
|
+
}
|
138
|
+
|
139
|
+
|
140
|
+
|
141
|
+
/* *************************************
|
142
|
+
* Tool functions
|
143
|
+
***************************************/
|
144
|
+
size_t ZBUFF_recommendedCInSize(void) { return ZSTD_CStreamInSize(); }
|
145
|
+
size_t ZBUFF_recommendedCOutSize(void) { return ZSTD_CStreamOutSize(); }
|
@@ -0,0 +1,74 @@
|
|
1
|
+
/**
|
2
|
+
* Copyright (c) 2016-present, Yann Collet, Facebook, Inc.
|
3
|
+
* All rights reserved.
|
4
|
+
*
|
5
|
+
* This source code is licensed under the BSD-style license found in the
|
6
|
+
* LICENSE file in the root directory of this source tree. An additional grant
|
7
|
+
* of patent rights can be found in the PATENTS file in the same directory.
|
8
|
+
*/
|
9
|
+
|
10
|
+
|
11
|
+
|
12
|
+
/* *************************************
|
13
|
+
* Dependencies
|
14
|
+
***************************************/
|
15
|
+
#define ZBUFF_STATIC_LINKING_ONLY
|
16
|
+
#include "zbuff.h"
|
17
|
+
|
18
|
+
|
19
|
+
ZBUFF_DCtx* ZBUFF_createDCtx(void)
|
20
|
+
{
|
21
|
+
return ZSTD_createDStream();
|
22
|
+
}
|
23
|
+
|
24
|
+
ZBUFF_DCtx* ZBUFF_createDCtx_advanced(ZSTD_customMem customMem)
|
25
|
+
{
|
26
|
+
return ZSTD_createDStream_advanced(customMem);
|
27
|
+
}
|
28
|
+
|
29
|
+
size_t ZBUFF_freeDCtx(ZBUFF_DCtx* zbd)
|
30
|
+
{
|
31
|
+
return ZSTD_freeDStream(zbd);
|
32
|
+
}
|
33
|
+
|
34
|
+
|
35
|
+
/* *** Initialization *** */
|
36
|
+
|
37
|
+
size_t ZBUFF_decompressInitDictionary(ZBUFF_DCtx* zbd, const void* dict, size_t dictSize)
|
38
|
+
{
|
39
|
+
return ZSTD_initDStream_usingDict(zbd, dict, dictSize);
|
40
|
+
}
|
41
|
+
|
42
|
+
size_t ZBUFF_decompressInit(ZBUFF_DCtx* zbd)
|
43
|
+
{
|
44
|
+
return ZSTD_initDStream(zbd);
|
45
|
+
}
|
46
|
+
|
47
|
+
|
48
|
+
/* *** Decompression *** */
|
49
|
+
|
50
|
+
size_t ZBUFF_decompressContinue(ZBUFF_DCtx* zbd,
|
51
|
+
void* dst, size_t* dstCapacityPtr,
|
52
|
+
const void* src, size_t* srcSizePtr)
|
53
|
+
{
|
54
|
+
ZSTD_outBuffer outBuff;
|
55
|
+
ZSTD_inBuffer inBuff;
|
56
|
+
size_t result;
|
57
|
+
outBuff.dst = dst;
|
58
|
+
outBuff.pos = 0;
|
59
|
+
outBuff.size = *dstCapacityPtr;
|
60
|
+
inBuff.src = src;
|
61
|
+
inBuff.pos = 0;
|
62
|
+
inBuff.size = *srcSizePtr;
|
63
|
+
result = ZSTD_decompressStream(zbd, &outBuff, &inBuff);
|
64
|
+
*dstCapacityPtr = outBuff.pos;
|
65
|
+
*srcSizePtr = inBuff.pos;
|
66
|
+
return result;
|
67
|
+
}
|
68
|
+
|
69
|
+
|
70
|
+
/* *************************************
|
71
|
+
* Tool functions
|
72
|
+
***************************************/
|
73
|
+
size_t ZBUFF_recommendedDInSize(void) { return ZSTD_DStreamInSize(); }
|
74
|
+
size_t ZBUFF_recommendedDOutSize(void) { return ZSTD_DStreamOutSize(); }
|
@@ -0,0 +1,1913 @@
|
|
1
|
+
/*
|
2
|
+
* divsufsort.c for libdivsufsort-lite
|
3
|
+
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
|
4
|
+
*
|
5
|
+
* Permission is hereby granted, free of charge, to any person
|
6
|
+
* obtaining a copy of this software and associated documentation
|
7
|
+
* files (the "Software"), to deal in the Software without
|
8
|
+
* restriction, including without limitation the rights to use,
|
9
|
+
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
10
|
+
* copies of the Software, and to permit persons to whom the
|
11
|
+
* Software is furnished to do so, subject to the following
|
12
|
+
* conditions:
|
13
|
+
*
|
14
|
+
* The above copyright notice and this permission notice shall be
|
15
|
+
* included in all copies or substantial portions of the Software.
|
16
|
+
*
|
17
|
+
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
18
|
+
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
19
|
+
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
20
|
+
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
21
|
+
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
22
|
+
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
23
|
+
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
24
|
+
* OTHER DEALINGS IN THE SOFTWARE.
|
25
|
+
*/
|
26
|
+
|
27
|
+
/*- Compiler specifics -*/
|
28
|
+
#ifdef __clang__
|
29
|
+
#pragma clang diagnostic ignored "-Wshorten-64-to-32"
|
30
|
+
#endif
|
31
|
+
|
32
|
+
#if defined(_MSC_VER)
|
33
|
+
# pragma warning(disable : 4244)
|
34
|
+
# pragma warning(disable : 4127) /* C4127 : Condition expression is constant */
|
35
|
+
#endif
|
36
|
+
|
37
|
+
|
38
|
+
/*- Dependencies -*/
|
39
|
+
#include <assert.h>
|
40
|
+
#include <stdio.h>
|
41
|
+
#include <stdlib.h>
|
42
|
+
|
43
|
+
#include "divsufsort.h"
|
44
|
+
|
45
|
+
/*- Constants -*/
|
46
|
+
#if defined(INLINE)
|
47
|
+
# undef INLINE
|
48
|
+
#endif
|
49
|
+
#if !defined(INLINE)
|
50
|
+
# define INLINE __inline
|
51
|
+
#endif
|
52
|
+
#if defined(ALPHABET_SIZE) && (ALPHABET_SIZE < 1)
|
53
|
+
# undef ALPHABET_SIZE
|
54
|
+
#endif
|
55
|
+
#if !defined(ALPHABET_SIZE)
|
56
|
+
# define ALPHABET_SIZE (256)
|
57
|
+
#endif
|
58
|
+
#define BUCKET_A_SIZE (ALPHABET_SIZE)
|
59
|
+
#define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE)
|
60
|
+
#if defined(SS_INSERTIONSORT_THRESHOLD)
|
61
|
+
# if SS_INSERTIONSORT_THRESHOLD < 1
|
62
|
+
# undef SS_INSERTIONSORT_THRESHOLD
|
63
|
+
# define SS_INSERTIONSORT_THRESHOLD (1)
|
64
|
+
# endif
|
65
|
+
#else
|
66
|
+
# define SS_INSERTIONSORT_THRESHOLD (8)
|
67
|
+
#endif
|
68
|
+
#if defined(SS_BLOCKSIZE)
|
69
|
+
# if SS_BLOCKSIZE < 0
|
70
|
+
# undef SS_BLOCKSIZE
|
71
|
+
# define SS_BLOCKSIZE (0)
|
72
|
+
# elif 32768 <= SS_BLOCKSIZE
|
73
|
+
# undef SS_BLOCKSIZE
|
74
|
+
# define SS_BLOCKSIZE (32767)
|
75
|
+
# endif
|
76
|
+
#else
|
77
|
+
# define SS_BLOCKSIZE (1024)
|
78
|
+
#endif
|
79
|
+
/* minstacksize = log(SS_BLOCKSIZE) / log(3) * 2 */
|
80
|
+
#if SS_BLOCKSIZE == 0
|
81
|
+
# define SS_MISORT_STACKSIZE (96)
|
82
|
+
#elif SS_BLOCKSIZE <= 4096
|
83
|
+
# define SS_MISORT_STACKSIZE (16)
|
84
|
+
#else
|
85
|
+
# define SS_MISORT_STACKSIZE (24)
|
86
|
+
#endif
|
87
|
+
#define SS_SMERGE_STACKSIZE (32)
|
88
|
+
#define TR_INSERTIONSORT_THRESHOLD (8)
|
89
|
+
#define TR_STACKSIZE (64)
|
90
|
+
|
91
|
+
|
92
|
+
/*- Macros -*/
|
93
|
+
#ifndef SWAP
|
94
|
+
# define SWAP(_a, _b) do { t = (_a); (_a) = (_b); (_b) = t; } while(0)
|
95
|
+
#endif /* SWAP */
|
96
|
+
#ifndef MIN
|
97
|
+
# define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b))
|
98
|
+
#endif /* MIN */
|
99
|
+
#ifndef MAX
|
100
|
+
# define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b))
|
101
|
+
#endif /* MAX */
|
102
|
+
#define STACK_PUSH(_a, _b, _c, _d)\
|
103
|
+
do {\
|
104
|
+
assert(ssize < STACK_SIZE);\
|
105
|
+
stack[ssize].a = (_a), stack[ssize].b = (_b),\
|
106
|
+
stack[ssize].c = (_c), stack[ssize++].d = (_d);\
|
107
|
+
} while(0)
|
108
|
+
#define STACK_PUSH5(_a, _b, _c, _d, _e)\
|
109
|
+
do {\
|
110
|
+
assert(ssize < STACK_SIZE);\
|
111
|
+
stack[ssize].a = (_a), stack[ssize].b = (_b),\
|
112
|
+
stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\
|
113
|
+
} while(0)
|
114
|
+
#define STACK_POP(_a, _b, _c, _d)\
|
115
|
+
do {\
|
116
|
+
assert(0 <= ssize);\
|
117
|
+
if(ssize == 0) { return; }\
|
118
|
+
(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
|
119
|
+
(_c) = stack[ssize].c, (_d) = stack[ssize].d;\
|
120
|
+
} while(0)
|
121
|
+
#define STACK_POP5(_a, _b, _c, _d, _e)\
|
122
|
+
do {\
|
123
|
+
assert(0 <= ssize);\
|
124
|
+
if(ssize == 0) { return; }\
|
125
|
+
(_a) = stack[--ssize].a, (_b) = stack[ssize].b,\
|
126
|
+
(_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\
|
127
|
+
} while(0)
|
128
|
+
#define BUCKET_A(_c0) bucket_A[(_c0)]
|
129
|
+
#if ALPHABET_SIZE == 256
|
130
|
+
#define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)])
|
131
|
+
#define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)])
|
132
|
+
#else
|
133
|
+
#define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)])
|
134
|
+
#define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)])
|
135
|
+
#endif
|
136
|
+
|
137
|
+
|
138
|
+
/*- Private Functions -*/
|
139
|
+
|
140
|
+
static const int lg_table[256]= {
|
141
|
+
-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,
|
142
|
+
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,
|
143
|
+
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
|
144
|
+
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
|
145
|
+
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
146
|
+
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
147
|
+
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
|
148
|
+
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
|
149
|
+
};
|
150
|
+
|
151
|
+
#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
|
152
|
+
|
153
|
+
static INLINE
|
154
|
+
int
|
155
|
+
ss_ilg(int n) {
|
156
|
+
#if SS_BLOCKSIZE == 0
|
157
|
+
return (n & 0xffff0000) ?
|
158
|
+
((n & 0xff000000) ?
|
159
|
+
24 + lg_table[(n >> 24) & 0xff] :
|
160
|
+
16 + lg_table[(n >> 16) & 0xff]) :
|
161
|
+
((n & 0x0000ff00) ?
|
162
|
+
8 + lg_table[(n >> 8) & 0xff] :
|
163
|
+
0 + lg_table[(n >> 0) & 0xff]);
|
164
|
+
#elif SS_BLOCKSIZE < 256
|
165
|
+
return lg_table[n];
|
166
|
+
#else
|
167
|
+
return (n & 0xff00) ?
|
168
|
+
8 + lg_table[(n >> 8) & 0xff] :
|
169
|
+
0 + lg_table[(n >> 0) & 0xff];
|
170
|
+
#endif
|
171
|
+
}
|
172
|
+
|
173
|
+
#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
|
174
|
+
|
175
|
+
#if SS_BLOCKSIZE != 0
|
176
|
+
|
177
|
+
static const int sqq_table[256] = {
|
178
|
+
0, 16, 22, 27, 32, 35, 39, 42, 45, 48, 50, 53, 55, 57, 59, 61,
|
179
|
+
64, 65, 67, 69, 71, 73, 75, 76, 78, 80, 81, 83, 84, 86, 87, 89,
|
180
|
+
90, 91, 93, 94, 96, 97, 98, 99, 101, 102, 103, 104, 106, 107, 108, 109,
|
181
|
+
110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126,
|
182
|
+
128, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
|
183
|
+
143, 144, 144, 145, 146, 147, 148, 149, 150, 150, 151, 152, 153, 154, 155, 155,
|
184
|
+
156, 157, 158, 159, 160, 160, 161, 162, 163, 163, 164, 165, 166, 167, 167, 168,
|
185
|
+
169, 170, 170, 171, 172, 173, 173, 174, 175, 176, 176, 177, 178, 178, 179, 180,
|
186
|
+
181, 181, 182, 183, 183, 184, 185, 185, 186, 187, 187, 188, 189, 189, 190, 191,
|
187
|
+
192, 192, 193, 193, 194, 195, 195, 196, 197, 197, 198, 199, 199, 200, 201, 201,
|
188
|
+
202, 203, 203, 204, 204, 205, 206, 206, 207, 208, 208, 209, 209, 210, 211, 211,
|
189
|
+
212, 212, 213, 214, 214, 215, 215, 216, 217, 217, 218, 218, 219, 219, 220, 221,
|
190
|
+
221, 222, 222, 223, 224, 224, 225, 225, 226, 226, 227, 227, 228, 229, 229, 230,
|
191
|
+
230, 231, 231, 232, 232, 233, 234, 234, 235, 235, 236, 236, 237, 237, 238, 238,
|
192
|
+
239, 240, 240, 241, 241, 242, 242, 243, 243, 244, 244, 245, 245, 246, 246, 247,
|
193
|
+
247, 248, 248, 249, 249, 250, 250, 251, 251, 252, 252, 253, 253, 254, 254, 255
|
194
|
+
};
|
195
|
+
|
196
|
+
static INLINE
|
197
|
+
int
|
198
|
+
ss_isqrt(int x) {
|
199
|
+
int y, e;
|
200
|
+
|
201
|
+
if(x >= (SS_BLOCKSIZE * SS_BLOCKSIZE)) { return SS_BLOCKSIZE; }
|
202
|
+
e = (x & 0xffff0000) ?
|
203
|
+
((x & 0xff000000) ?
|
204
|
+
24 + lg_table[(x >> 24) & 0xff] :
|
205
|
+
16 + lg_table[(x >> 16) & 0xff]) :
|
206
|
+
((x & 0x0000ff00) ?
|
207
|
+
8 + lg_table[(x >> 8) & 0xff] :
|
208
|
+
0 + lg_table[(x >> 0) & 0xff]);
|
209
|
+
|
210
|
+
if(e >= 16) {
|
211
|
+
y = sqq_table[x >> ((e - 6) - (e & 1))] << ((e >> 1) - 7);
|
212
|
+
if(e >= 24) { y = (y + 1 + x / y) >> 1; }
|
213
|
+
y = (y + 1 + x / y) >> 1;
|
214
|
+
} else if(e >= 8) {
|
215
|
+
y = (sqq_table[x >> ((e - 6) - (e & 1))] >> (7 - (e >> 1))) + 1;
|
216
|
+
} else {
|
217
|
+
return sqq_table[x] >> 4;
|
218
|
+
}
|
219
|
+
|
220
|
+
return (x < (y * y)) ? y - 1 : y;
|
221
|
+
}
|
222
|
+
|
223
|
+
#endif /* SS_BLOCKSIZE != 0 */
|
224
|
+
|
225
|
+
|
226
|
+
/*---------------------------------------------------------------------------*/
|
227
|
+
|
228
|
+
/* Compares two suffixes. */
|
229
|
+
static INLINE
|
230
|
+
int
|
231
|
+
ss_compare(const unsigned char *T,
|
232
|
+
const int *p1, const int *p2,
|
233
|
+
int depth) {
|
234
|
+
const unsigned char *U1, *U2, *U1n, *U2n;
|
235
|
+
|
236
|
+
for(U1 = T + depth + *p1,
|
237
|
+
U2 = T + depth + *p2,
|
238
|
+
U1n = T + *(p1 + 1) + 2,
|
239
|
+
U2n = T + *(p2 + 1) + 2;
|
240
|
+
(U1 < U1n) && (U2 < U2n) && (*U1 == *U2);
|
241
|
+
++U1, ++U2) {
|
242
|
+
}
|
243
|
+
|
244
|
+
return U1 < U1n ?
|
245
|
+
(U2 < U2n ? *U1 - *U2 : 1) :
|
246
|
+
(U2 < U2n ? -1 : 0);
|
247
|
+
}
|
248
|
+
|
249
|
+
|
250
|
+
/*---------------------------------------------------------------------------*/
|
251
|
+
|
252
|
+
#if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1)
|
253
|
+
|
254
|
+
/* Insertionsort for small size groups */
|
255
|
+
static
|
256
|
+
void
|
257
|
+
ss_insertionsort(const unsigned char *T, const int *PA,
|
258
|
+
int *first, int *last, int depth) {
|
259
|
+
int *i, *j;
|
260
|
+
int t;
|
261
|
+
int r;
|
262
|
+
|
263
|
+
for(i = last - 2; first <= i; --i) {
|
264
|
+
for(t = *i, j = i + 1; 0 < (r = ss_compare(T, PA + t, PA + *j, depth));) {
|
265
|
+
do { *(j - 1) = *j; } while((++j < last) && (*j < 0));
|
266
|
+
if(last <= j) { break; }
|
267
|
+
}
|
268
|
+
if(r == 0) { *j = ~*j; }
|
269
|
+
*(j - 1) = t;
|
270
|
+
}
|
271
|
+
}
|
272
|
+
|
273
|
+
#endif /* (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) */
|
274
|
+
|
275
|
+
|
276
|
+
/*---------------------------------------------------------------------------*/
|
277
|
+
|
278
|
+
#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
|
279
|
+
|
280
|
+
static INLINE
|
281
|
+
void
|
282
|
+
ss_fixdown(const unsigned char *Td, const int *PA,
|
283
|
+
int *SA, int i, int size) {
|
284
|
+
int j, k;
|
285
|
+
int v;
|
286
|
+
int c, d, e;
|
287
|
+
|
288
|
+
for(v = SA[i], c = Td[PA[v]]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
|
289
|
+
d = Td[PA[SA[k = j++]]];
|
290
|
+
if(d < (e = Td[PA[SA[j]]])) { k = j; d = e; }
|
291
|
+
if(d <= c) { break; }
|
292
|
+
}
|
293
|
+
SA[i] = v;
|
294
|
+
}
|
295
|
+
|
296
|
+
/* Simple top-down heapsort. */
|
297
|
+
static
|
298
|
+
void
|
299
|
+
ss_heapsort(const unsigned char *Td, const int *PA, int *SA, int size) {
|
300
|
+
int i, m;
|
301
|
+
int t;
|
302
|
+
|
303
|
+
m = size;
|
304
|
+
if((size % 2) == 0) {
|
305
|
+
m--;
|
306
|
+
if(Td[PA[SA[m / 2]]] < Td[PA[SA[m]]]) { SWAP(SA[m], SA[m / 2]); }
|
307
|
+
}
|
308
|
+
|
309
|
+
for(i = m / 2 - 1; 0 <= i; --i) { ss_fixdown(Td, PA, SA, i, m); }
|
310
|
+
if((size % 2) == 0) { SWAP(SA[0], SA[m]); ss_fixdown(Td, PA, SA, 0, m); }
|
311
|
+
for(i = m - 1; 0 < i; --i) {
|
312
|
+
t = SA[0], SA[0] = SA[i];
|
313
|
+
ss_fixdown(Td, PA, SA, 0, i);
|
314
|
+
SA[i] = t;
|
315
|
+
}
|
316
|
+
}
|
317
|
+
|
318
|
+
|
319
|
+
/*---------------------------------------------------------------------------*/
|
320
|
+
|
321
|
+
/* Returns the median of three elements. */
|
322
|
+
static INLINE
|
323
|
+
int *
|
324
|
+
ss_median3(const unsigned char *Td, const int *PA,
|
325
|
+
int *v1, int *v2, int *v3) {
|
326
|
+
int *t;
|
327
|
+
if(Td[PA[*v1]] > Td[PA[*v2]]) { SWAP(v1, v2); }
|
328
|
+
if(Td[PA[*v2]] > Td[PA[*v3]]) {
|
329
|
+
if(Td[PA[*v1]] > Td[PA[*v3]]) { return v1; }
|
330
|
+
else { return v3; }
|
331
|
+
}
|
332
|
+
return v2;
|
333
|
+
}
|
334
|
+
|
335
|
+
/* Returns the median of five elements. */
|
336
|
+
static INLINE
|
337
|
+
int *
|
338
|
+
ss_median5(const unsigned char *Td, const int *PA,
|
339
|
+
int *v1, int *v2, int *v3, int *v4, int *v5) {
|
340
|
+
int *t;
|
341
|
+
if(Td[PA[*v2]] > Td[PA[*v3]]) { SWAP(v2, v3); }
|
342
|
+
if(Td[PA[*v4]] > Td[PA[*v5]]) { SWAP(v4, v5); }
|
343
|
+
if(Td[PA[*v2]] > Td[PA[*v4]]) { SWAP(v2, v4); SWAP(v3, v5); }
|
344
|
+
if(Td[PA[*v1]] > Td[PA[*v3]]) { SWAP(v1, v3); }
|
345
|
+
if(Td[PA[*v1]] > Td[PA[*v4]]) { SWAP(v1, v4); SWAP(v3, v5); }
|
346
|
+
if(Td[PA[*v3]] > Td[PA[*v4]]) { return v4; }
|
347
|
+
return v3;
|
348
|
+
}
|
349
|
+
|
350
|
+
/* Returns the pivot element. */
|
351
|
+
static INLINE
|
352
|
+
int *
|
353
|
+
ss_pivot(const unsigned char *Td, const int *PA, int *first, int *last) {
|
354
|
+
int *middle;
|
355
|
+
int t;
|
356
|
+
|
357
|
+
t = last - first;
|
358
|
+
middle = first + t / 2;
|
359
|
+
|
360
|
+
if(t <= 512) {
|
361
|
+
if(t <= 32) {
|
362
|
+
return ss_median3(Td, PA, first, middle, last - 1);
|
363
|
+
} else {
|
364
|
+
t >>= 2;
|
365
|
+
return ss_median5(Td, PA, first, first + t, middle, last - 1 - t, last - 1);
|
366
|
+
}
|
367
|
+
}
|
368
|
+
t >>= 3;
|
369
|
+
first = ss_median3(Td, PA, first, first + t, first + (t << 1));
|
370
|
+
middle = ss_median3(Td, PA, middle - t, middle, middle + t);
|
371
|
+
last = ss_median3(Td, PA, last - 1 - (t << 1), last - 1 - t, last - 1);
|
372
|
+
return ss_median3(Td, PA, first, middle, last);
|
373
|
+
}
|
374
|
+
|
375
|
+
|
376
|
+
/*---------------------------------------------------------------------------*/
|
377
|
+
|
378
|
+
/* Binary partition for substrings. */
|
379
|
+
static INLINE
|
380
|
+
int *
|
381
|
+
ss_partition(const int *PA,
|
382
|
+
int *first, int *last, int depth) {
|
383
|
+
int *a, *b;
|
384
|
+
int t;
|
385
|
+
for(a = first - 1, b = last;;) {
|
386
|
+
for(; (++a < b) && ((PA[*a] + depth) >= (PA[*a + 1] + 1));) { *a = ~*a; }
|
387
|
+
for(; (a < --b) && ((PA[*b] + depth) < (PA[*b + 1] + 1));) { }
|
388
|
+
if(b <= a) { break; }
|
389
|
+
t = ~*b;
|
390
|
+
*b = *a;
|
391
|
+
*a = t;
|
392
|
+
}
|
393
|
+
if(first < a) { *first = ~*first; }
|
394
|
+
return a;
|
395
|
+
}
|
396
|
+
|
397
|
+
/* Multikey introsort for medium size groups. */
|
398
|
+
static
|
399
|
+
void
|
400
|
+
ss_mintrosort(const unsigned char *T, const int *PA,
|
401
|
+
int *first, int *last,
|
402
|
+
int depth) {
|
403
|
+
#define STACK_SIZE SS_MISORT_STACKSIZE
|
404
|
+
struct { int *a, *b, c; int d; } stack[STACK_SIZE];
|
405
|
+
const unsigned char *Td;
|
406
|
+
int *a, *b, *c, *d, *e, *f;
|
407
|
+
int s, t;
|
408
|
+
int ssize;
|
409
|
+
int limit;
|
410
|
+
int v, x = 0;
|
411
|
+
|
412
|
+
for(ssize = 0, limit = ss_ilg(last - first);;) {
|
413
|
+
|
414
|
+
if((last - first) <= SS_INSERTIONSORT_THRESHOLD) {
|
415
|
+
#if 1 < SS_INSERTIONSORT_THRESHOLD
|
416
|
+
if(1 < (last - first)) { ss_insertionsort(T, PA, first, last, depth); }
|
417
|
+
#endif
|
418
|
+
STACK_POP(first, last, depth, limit);
|
419
|
+
continue;
|
420
|
+
}
|
421
|
+
|
422
|
+
Td = T + depth;
|
423
|
+
if(limit-- == 0) { ss_heapsort(Td, PA, first, last - first); }
|
424
|
+
if(limit < 0) {
|
425
|
+
for(a = first + 1, v = Td[PA[*first]]; a < last; ++a) {
|
426
|
+
if((x = Td[PA[*a]]) != v) {
|
427
|
+
if(1 < (a - first)) { break; }
|
428
|
+
v = x;
|
429
|
+
first = a;
|
430
|
+
}
|
431
|
+
}
|
432
|
+
if(Td[PA[*first] - 1] < v) {
|
433
|
+
first = ss_partition(PA, first, a, depth);
|
434
|
+
}
|
435
|
+
if((a - first) <= (last - a)) {
|
436
|
+
if(1 < (a - first)) {
|
437
|
+
STACK_PUSH(a, last, depth, -1);
|
438
|
+
last = a, depth += 1, limit = ss_ilg(a - first);
|
439
|
+
} else {
|
440
|
+
first = a, limit = -1;
|
441
|
+
}
|
442
|
+
} else {
|
443
|
+
if(1 < (last - a)) {
|
444
|
+
STACK_PUSH(first, a, depth + 1, ss_ilg(a - first));
|
445
|
+
first = a, limit = -1;
|
446
|
+
} else {
|
447
|
+
last = a, depth += 1, limit = ss_ilg(a - first);
|
448
|
+
}
|
449
|
+
}
|
450
|
+
continue;
|
451
|
+
}
|
452
|
+
|
453
|
+
/* choose pivot */
|
454
|
+
a = ss_pivot(Td, PA, first, last);
|
455
|
+
v = Td[PA[*a]];
|
456
|
+
SWAP(*first, *a);
|
457
|
+
|
458
|
+
/* partition */
|
459
|
+
for(b = first; (++b < last) && ((x = Td[PA[*b]]) == v);) { }
|
460
|
+
if(((a = b) < last) && (x < v)) {
|
461
|
+
for(; (++b < last) && ((x = Td[PA[*b]]) <= v);) {
|
462
|
+
if(x == v) { SWAP(*b, *a); ++a; }
|
463
|
+
}
|
464
|
+
}
|
465
|
+
for(c = last; (b < --c) && ((x = Td[PA[*c]]) == v);) { }
|
466
|
+
if((b < (d = c)) && (x > v)) {
|
467
|
+
for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
|
468
|
+
if(x == v) { SWAP(*c, *d); --d; }
|
469
|
+
}
|
470
|
+
}
|
471
|
+
for(; b < c;) {
|
472
|
+
SWAP(*b, *c);
|
473
|
+
for(; (++b < c) && ((x = Td[PA[*b]]) <= v);) {
|
474
|
+
if(x == v) { SWAP(*b, *a); ++a; }
|
475
|
+
}
|
476
|
+
for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
|
477
|
+
if(x == v) { SWAP(*c, *d); --d; }
|
478
|
+
}
|
479
|
+
}
|
480
|
+
|
481
|
+
if(a <= d) {
|
482
|
+
c = b - 1;
|
483
|
+
|
484
|
+
if((s = a - first) > (t = b - a)) { s = t; }
|
485
|
+
for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
|
486
|
+
if((s = d - c) > (t = last - d - 1)) { s = t; }
|
487
|
+
for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
|
488
|
+
|
489
|
+
a = first + (b - a), c = last - (d - c);
|
490
|
+
b = (v <= Td[PA[*a] - 1]) ? a : ss_partition(PA, a, c, depth);
|
491
|
+
|
492
|
+
if((a - first) <= (last - c)) {
|
493
|
+
if((last - c) <= (c - b)) {
|
494
|
+
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
495
|
+
STACK_PUSH(c, last, depth, limit);
|
496
|
+
last = a;
|
497
|
+
} else if((a - first) <= (c - b)) {
|
498
|
+
STACK_PUSH(c, last, depth, limit);
|
499
|
+
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
500
|
+
last = a;
|
501
|
+
} else {
|
502
|
+
STACK_PUSH(c, last, depth, limit);
|
503
|
+
STACK_PUSH(first, a, depth, limit);
|
504
|
+
first = b, last = c, depth += 1, limit = ss_ilg(c - b);
|
505
|
+
}
|
506
|
+
} else {
|
507
|
+
if((a - first) <= (c - b)) {
|
508
|
+
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
509
|
+
STACK_PUSH(first, a, depth, limit);
|
510
|
+
first = c;
|
511
|
+
} else if((last - c) <= (c - b)) {
|
512
|
+
STACK_PUSH(first, a, depth, limit);
|
513
|
+
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
|
514
|
+
first = c;
|
515
|
+
} else {
|
516
|
+
STACK_PUSH(first, a, depth, limit);
|
517
|
+
STACK_PUSH(c, last, depth, limit);
|
518
|
+
first = b, last = c, depth += 1, limit = ss_ilg(c - b);
|
519
|
+
}
|
520
|
+
}
|
521
|
+
} else {
|
522
|
+
limit += 1;
|
523
|
+
if(Td[PA[*first] - 1] < v) {
|
524
|
+
first = ss_partition(PA, first, last, depth);
|
525
|
+
limit = ss_ilg(last - first);
|
526
|
+
}
|
527
|
+
depth += 1;
|
528
|
+
}
|
529
|
+
}
|
530
|
+
#undef STACK_SIZE
|
531
|
+
}
|
532
|
+
|
533
|
+
#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
|
534
|
+
|
535
|
+
|
536
|
+
/*---------------------------------------------------------------------------*/
|
537
|
+
|
538
|
+
#if SS_BLOCKSIZE != 0
|
539
|
+
|
540
|
+
static INLINE
|
541
|
+
void
|
542
|
+
ss_blockswap(int *a, int *b, int n) {
|
543
|
+
int t;
|
544
|
+
for(; 0 < n; --n, ++a, ++b) {
|
545
|
+
t = *a, *a = *b, *b = t;
|
546
|
+
}
|
547
|
+
}
|
548
|
+
|
549
|
+
static INLINE
|
550
|
+
void
|
551
|
+
ss_rotate(int *first, int *middle, int *last) {
|
552
|
+
int *a, *b, t;
|
553
|
+
int l, r;
|
554
|
+
l = middle - first, r = last - middle;
|
555
|
+
for(; (0 < l) && (0 < r);) {
|
556
|
+
if(l == r) { ss_blockswap(first, middle, l); break; }
|
557
|
+
if(l < r) {
|
558
|
+
a = last - 1, b = middle - 1;
|
559
|
+
t = *a;
|
560
|
+
do {
|
561
|
+
*a-- = *b, *b-- = *a;
|
562
|
+
if(b < first) {
|
563
|
+
*a = t;
|
564
|
+
last = a;
|
565
|
+
if((r -= l + 1) <= l) { break; }
|
566
|
+
a -= 1, b = middle - 1;
|
567
|
+
t = *a;
|
568
|
+
}
|
569
|
+
} while(1);
|
570
|
+
} else {
|
571
|
+
a = first, b = middle;
|
572
|
+
t = *a;
|
573
|
+
do {
|
574
|
+
*a++ = *b, *b++ = *a;
|
575
|
+
if(last <= b) {
|
576
|
+
*a = t;
|
577
|
+
first = a + 1;
|
578
|
+
if((l -= r + 1) <= r) { break; }
|
579
|
+
a += 1, b = middle;
|
580
|
+
t = *a;
|
581
|
+
}
|
582
|
+
} while(1);
|
583
|
+
}
|
584
|
+
}
|
585
|
+
}
|
586
|
+
|
587
|
+
|
588
|
+
/*---------------------------------------------------------------------------*/
|
589
|
+
|
590
|
+
static
|
591
|
+
void
|
592
|
+
ss_inplacemerge(const unsigned char *T, const int *PA,
|
593
|
+
int *first, int *middle, int *last,
|
594
|
+
int depth) {
|
595
|
+
const int *p;
|
596
|
+
int *a, *b;
|
597
|
+
int len, half;
|
598
|
+
int q, r;
|
599
|
+
int x;
|
600
|
+
|
601
|
+
for(;;) {
|
602
|
+
if(*(last - 1) < 0) { x = 1; p = PA + ~*(last - 1); }
|
603
|
+
else { x = 0; p = PA + *(last - 1); }
|
604
|
+
for(a = first, len = middle - first, half = len >> 1, r = -1;
|
605
|
+
0 < len;
|
606
|
+
len = half, half >>= 1) {
|
607
|
+
b = a + half;
|
608
|
+
q = ss_compare(T, PA + ((0 <= *b) ? *b : ~*b), p, depth);
|
609
|
+
if(q < 0) {
|
610
|
+
a = b + 1;
|
611
|
+
half -= (len & 1) ^ 1;
|
612
|
+
} else {
|
613
|
+
r = q;
|
614
|
+
}
|
615
|
+
}
|
616
|
+
if(a < middle) {
|
617
|
+
if(r == 0) { *a = ~*a; }
|
618
|
+
ss_rotate(a, middle, last);
|
619
|
+
last -= middle - a;
|
620
|
+
middle = a;
|
621
|
+
if(first == middle) { break; }
|
622
|
+
}
|
623
|
+
--last;
|
624
|
+
if(x != 0) { while(*--last < 0) { } }
|
625
|
+
if(middle == last) { break; }
|
626
|
+
}
|
627
|
+
}
|
628
|
+
|
629
|
+
|
630
|
+
/*---------------------------------------------------------------------------*/
|
631
|
+
|
632
|
+
/* Merge-forward with internal buffer. */
|
633
|
+
static
|
634
|
+
void
|
635
|
+
ss_mergeforward(const unsigned char *T, const int *PA,
|
636
|
+
int *first, int *middle, int *last,
|
637
|
+
int *buf, int depth) {
|
638
|
+
int *a, *b, *c, *bufend;
|
639
|
+
int t;
|
640
|
+
int r;
|
641
|
+
|
642
|
+
bufend = buf + (middle - first) - 1;
|
643
|
+
ss_blockswap(buf, first, middle - first);
|
644
|
+
|
645
|
+
for(t = *(a = first), b = buf, c = middle;;) {
|
646
|
+
r = ss_compare(T, PA + *b, PA + *c, depth);
|
647
|
+
if(r < 0) {
|
648
|
+
do {
|
649
|
+
*a++ = *b;
|
650
|
+
if(bufend <= b) { *bufend = t; return; }
|
651
|
+
*b++ = *a;
|
652
|
+
} while(*b < 0);
|
653
|
+
} else if(r > 0) {
|
654
|
+
do {
|
655
|
+
*a++ = *c, *c++ = *a;
|
656
|
+
if(last <= c) {
|
657
|
+
while(b < bufend) { *a++ = *b, *b++ = *a; }
|
658
|
+
*a = *b, *b = t;
|
659
|
+
return;
|
660
|
+
}
|
661
|
+
} while(*c < 0);
|
662
|
+
} else {
|
663
|
+
*c = ~*c;
|
664
|
+
do {
|
665
|
+
*a++ = *b;
|
666
|
+
if(bufend <= b) { *bufend = t; return; }
|
667
|
+
*b++ = *a;
|
668
|
+
} while(*b < 0);
|
669
|
+
|
670
|
+
do {
|
671
|
+
*a++ = *c, *c++ = *a;
|
672
|
+
if(last <= c) {
|
673
|
+
while(b < bufend) { *a++ = *b, *b++ = *a; }
|
674
|
+
*a = *b, *b = t;
|
675
|
+
return;
|
676
|
+
}
|
677
|
+
} while(*c < 0);
|
678
|
+
}
|
679
|
+
}
|
680
|
+
}
|
681
|
+
|
682
|
+
/* Merge-backward with internal buffer. */
|
683
|
+
static
|
684
|
+
void
|
685
|
+
ss_mergebackward(const unsigned char *T, const int *PA,
|
686
|
+
int *first, int *middle, int *last,
|
687
|
+
int *buf, int depth) {
|
688
|
+
const int *p1, *p2;
|
689
|
+
int *a, *b, *c, *bufend;
|
690
|
+
int t;
|
691
|
+
int r;
|
692
|
+
int x;
|
693
|
+
|
694
|
+
bufend = buf + (last - middle) - 1;
|
695
|
+
ss_blockswap(buf, middle, last - middle);
|
696
|
+
|
697
|
+
x = 0;
|
698
|
+
if(*bufend < 0) { p1 = PA + ~*bufend; x |= 1; }
|
699
|
+
else { p1 = PA + *bufend; }
|
700
|
+
if(*(middle - 1) < 0) { p2 = PA + ~*(middle - 1); x |= 2; }
|
701
|
+
else { p2 = PA + *(middle - 1); }
|
702
|
+
for(t = *(a = last - 1), b = bufend, c = middle - 1;;) {
|
703
|
+
r = ss_compare(T, p1, p2, depth);
|
704
|
+
if(0 < r) {
|
705
|
+
if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
|
706
|
+
*a-- = *b;
|
707
|
+
if(b <= buf) { *buf = t; break; }
|
708
|
+
*b-- = *a;
|
709
|
+
if(*b < 0) { p1 = PA + ~*b; x |= 1; }
|
710
|
+
else { p1 = PA + *b; }
|
711
|
+
} else if(r < 0) {
|
712
|
+
if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
|
713
|
+
*a-- = *c, *c-- = *a;
|
714
|
+
if(c < first) {
|
715
|
+
while(buf < b) { *a-- = *b, *b-- = *a; }
|
716
|
+
*a = *b, *b = t;
|
717
|
+
break;
|
718
|
+
}
|
719
|
+
if(*c < 0) { p2 = PA + ~*c; x |= 2; }
|
720
|
+
else { p2 = PA + *c; }
|
721
|
+
} else {
|
722
|
+
if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
|
723
|
+
*a-- = ~*b;
|
724
|
+
if(b <= buf) { *buf = t; break; }
|
725
|
+
*b-- = *a;
|
726
|
+
if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
|
727
|
+
*a-- = *c, *c-- = *a;
|
728
|
+
if(c < first) {
|
729
|
+
while(buf < b) { *a-- = *b, *b-- = *a; }
|
730
|
+
*a = *b, *b = t;
|
731
|
+
break;
|
732
|
+
}
|
733
|
+
if(*b < 0) { p1 = PA + ~*b; x |= 1; }
|
734
|
+
else { p1 = PA + *b; }
|
735
|
+
if(*c < 0) { p2 = PA + ~*c; x |= 2; }
|
736
|
+
else { p2 = PA + *c; }
|
737
|
+
}
|
738
|
+
}
|
739
|
+
}
|
740
|
+
|
741
|
+
/* D&C based merge. */
|
742
|
+
static
|
743
|
+
void
|
744
|
+
ss_swapmerge(const unsigned char *T, const int *PA,
|
745
|
+
int *first, int *middle, int *last,
|
746
|
+
int *buf, int bufsize, int depth) {
|
747
|
+
#define STACK_SIZE SS_SMERGE_STACKSIZE
|
748
|
+
#define GETIDX(a) ((0 <= (a)) ? (a) : (~(a)))
|
749
|
+
#define MERGE_CHECK(a, b, c)\
|
750
|
+
do {\
|
751
|
+
if(((c) & 1) ||\
|
752
|
+
(((c) & 2) && (ss_compare(T, PA + GETIDX(*((a) - 1)), PA + *(a), depth) == 0))) {\
|
753
|
+
*(a) = ~*(a);\
|
754
|
+
}\
|
755
|
+
if(((c) & 4) && ((ss_compare(T, PA + GETIDX(*((b) - 1)), PA + *(b), depth) == 0))) {\
|
756
|
+
*(b) = ~*(b);\
|
757
|
+
}\
|
758
|
+
} while(0)
|
759
|
+
struct { int *a, *b, *c; int d; } stack[STACK_SIZE];
|
760
|
+
int *l, *r, *lm, *rm;
|
761
|
+
int m, len, half;
|
762
|
+
int ssize;
|
763
|
+
int check, next;
|
764
|
+
|
765
|
+
for(check = 0, ssize = 0;;) {
|
766
|
+
if((last - middle) <= bufsize) {
|
767
|
+
if((first < middle) && (middle < last)) {
|
768
|
+
ss_mergebackward(T, PA, first, middle, last, buf, depth);
|
769
|
+
}
|
770
|
+
MERGE_CHECK(first, last, check);
|
771
|
+
STACK_POP(first, middle, last, check);
|
772
|
+
continue;
|
773
|
+
}
|
774
|
+
|
775
|
+
if((middle - first) <= bufsize) {
|
776
|
+
if(first < middle) {
|
777
|
+
ss_mergeforward(T, PA, first, middle, last, buf, depth);
|
778
|
+
}
|
779
|
+
MERGE_CHECK(first, last, check);
|
780
|
+
STACK_POP(first, middle, last, check);
|
781
|
+
continue;
|
782
|
+
}
|
783
|
+
|
784
|
+
for(m = 0, len = MIN(middle - first, last - middle), half = len >> 1;
|
785
|
+
0 < len;
|
786
|
+
len = half, half >>= 1) {
|
787
|
+
if(ss_compare(T, PA + GETIDX(*(middle + m + half)),
|
788
|
+
PA + GETIDX(*(middle - m - half - 1)), depth) < 0) {
|
789
|
+
m += half + 1;
|
790
|
+
half -= (len & 1) ^ 1;
|
791
|
+
}
|
792
|
+
}
|
793
|
+
|
794
|
+
if(0 < m) {
|
795
|
+
lm = middle - m, rm = middle + m;
|
796
|
+
ss_blockswap(lm, middle, m);
|
797
|
+
l = r = middle, next = 0;
|
798
|
+
if(rm < last) {
|
799
|
+
if(*rm < 0) {
|
800
|
+
*rm = ~*rm;
|
801
|
+
if(first < lm) { for(; *--l < 0;) { } next |= 4; }
|
802
|
+
next |= 1;
|
803
|
+
} else if(first < lm) {
|
804
|
+
for(; *r < 0; ++r) { }
|
805
|
+
next |= 2;
|
806
|
+
}
|
807
|
+
}
|
808
|
+
|
809
|
+
if((l - first) <= (last - r)) {
|
810
|
+
STACK_PUSH(r, rm, last, (next & 3) | (check & 4));
|
811
|
+
middle = lm, last = l, check = (check & 3) | (next & 4);
|
812
|
+
} else {
|
813
|
+
if((next & 2) && (r == middle)) { next ^= 6; }
|
814
|
+
STACK_PUSH(first, lm, l, (check & 3) | (next & 4));
|
815
|
+
first = r, middle = rm, check = (next & 3) | (check & 4);
|
816
|
+
}
|
817
|
+
} else {
|
818
|
+
if(ss_compare(T, PA + GETIDX(*(middle - 1)), PA + *middle, depth) == 0) {
|
819
|
+
*middle = ~*middle;
|
820
|
+
}
|
821
|
+
MERGE_CHECK(first, last, check);
|
822
|
+
STACK_POP(first, middle, last, check);
|
823
|
+
}
|
824
|
+
}
|
825
|
+
#undef STACK_SIZE
|
826
|
+
}
|
827
|
+
|
828
|
+
#endif /* SS_BLOCKSIZE != 0 */
|
829
|
+
|
830
|
+
|
831
|
+
/*---------------------------------------------------------------------------*/
|
832
|
+
|
833
|
+
/* Substring sort */
|
834
|
+
static
|
835
|
+
void
|
836
|
+
sssort(const unsigned char *T, const int *PA,
|
837
|
+
int *first, int *last,
|
838
|
+
int *buf, int bufsize,
|
839
|
+
int depth, int n, int lastsuffix) {
|
840
|
+
int *a;
|
841
|
+
#if SS_BLOCKSIZE != 0
|
842
|
+
int *b, *middle, *curbuf;
|
843
|
+
int j, k, curbufsize, limit;
|
844
|
+
#endif
|
845
|
+
int i;
|
846
|
+
|
847
|
+
if(lastsuffix != 0) { ++first; }
|
848
|
+
|
849
|
+
#if SS_BLOCKSIZE == 0
|
850
|
+
ss_mintrosort(T, PA, first, last, depth);
|
851
|
+
#else
|
852
|
+
if((bufsize < SS_BLOCKSIZE) &&
|
853
|
+
(bufsize < (last - first)) &&
|
854
|
+
(bufsize < (limit = ss_isqrt(last - first)))) {
|
855
|
+
if(SS_BLOCKSIZE < limit) { limit = SS_BLOCKSIZE; }
|
856
|
+
buf = middle = last - limit, bufsize = limit;
|
857
|
+
} else {
|
858
|
+
middle = last, limit = 0;
|
859
|
+
}
|
860
|
+
for(a = first, i = 0; SS_BLOCKSIZE < (middle - a); a += SS_BLOCKSIZE, ++i) {
|
861
|
+
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
|
862
|
+
ss_mintrosort(T, PA, a, a + SS_BLOCKSIZE, depth);
|
863
|
+
#elif 1 < SS_BLOCKSIZE
|
864
|
+
ss_insertionsort(T, PA, a, a + SS_BLOCKSIZE, depth);
|
865
|
+
#endif
|
866
|
+
curbufsize = last - (a + SS_BLOCKSIZE);
|
867
|
+
curbuf = a + SS_BLOCKSIZE;
|
868
|
+
if(curbufsize <= bufsize) { curbufsize = bufsize, curbuf = buf; }
|
869
|
+
for(b = a, k = SS_BLOCKSIZE, j = i; j & 1; b -= k, k <<= 1, j >>= 1) {
|
870
|
+
ss_swapmerge(T, PA, b - k, b, b + k, curbuf, curbufsize, depth);
|
871
|
+
}
|
872
|
+
}
|
873
|
+
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
|
874
|
+
ss_mintrosort(T, PA, a, middle, depth);
|
875
|
+
#elif 1 < SS_BLOCKSIZE
|
876
|
+
ss_insertionsort(T, PA, a, middle, depth);
|
877
|
+
#endif
|
878
|
+
for(k = SS_BLOCKSIZE; i != 0; k <<= 1, i >>= 1) {
|
879
|
+
if(i & 1) {
|
880
|
+
ss_swapmerge(T, PA, a - k, a, middle, buf, bufsize, depth);
|
881
|
+
a -= k;
|
882
|
+
}
|
883
|
+
}
|
884
|
+
if(limit != 0) {
|
885
|
+
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
|
886
|
+
ss_mintrosort(T, PA, middle, last, depth);
|
887
|
+
#elif 1 < SS_BLOCKSIZE
|
888
|
+
ss_insertionsort(T, PA, middle, last, depth);
|
889
|
+
#endif
|
890
|
+
ss_inplacemerge(T, PA, first, middle, last, depth);
|
891
|
+
}
|
892
|
+
#endif
|
893
|
+
|
894
|
+
if(lastsuffix != 0) {
|
895
|
+
/* Insert last type B* suffix. */
|
896
|
+
int PAi[2]; PAi[0] = PA[*(first - 1)], PAi[1] = n - 2;
|
897
|
+
for(a = first, i = *(first - 1);
|
898
|
+
(a < last) && ((*a < 0) || (0 < ss_compare(T, &(PAi[0]), PA + *a, depth)));
|
899
|
+
++a) {
|
900
|
+
*(a - 1) = *a;
|
901
|
+
}
|
902
|
+
*(a - 1) = i;
|
903
|
+
}
|
904
|
+
}
|
905
|
+
|
906
|
+
|
907
|
+
/*---------------------------------------------------------------------------*/
|
908
|
+
|
909
|
+
static INLINE
|
910
|
+
int
|
911
|
+
tr_ilg(int n) {
|
912
|
+
return (n & 0xffff0000) ?
|
913
|
+
((n & 0xff000000) ?
|
914
|
+
24 + lg_table[(n >> 24) & 0xff] :
|
915
|
+
16 + lg_table[(n >> 16) & 0xff]) :
|
916
|
+
((n & 0x0000ff00) ?
|
917
|
+
8 + lg_table[(n >> 8) & 0xff] :
|
918
|
+
0 + lg_table[(n >> 0) & 0xff]);
|
919
|
+
}
|
920
|
+
|
921
|
+
|
922
|
+
/*---------------------------------------------------------------------------*/
|
923
|
+
|
924
|
+
/* Simple insertionsort for small size groups. */
|
925
|
+
static
|
926
|
+
void
|
927
|
+
tr_insertionsort(const int *ISAd, int *first, int *last) {
|
928
|
+
int *a, *b;
|
929
|
+
int t, r;
|
930
|
+
|
931
|
+
for(a = first + 1; a < last; ++a) {
|
932
|
+
for(t = *a, b = a - 1; 0 > (r = ISAd[t] - ISAd[*b]);) {
|
933
|
+
do { *(b + 1) = *b; } while((first <= --b) && (*b < 0));
|
934
|
+
if(b < first) { break; }
|
935
|
+
}
|
936
|
+
if(r == 0) { *b = ~*b; }
|
937
|
+
*(b + 1) = t;
|
938
|
+
}
|
939
|
+
}
|
940
|
+
|
941
|
+
|
942
|
+
/*---------------------------------------------------------------------------*/
|
943
|
+
|
944
|
+
static INLINE
|
945
|
+
void
|
946
|
+
tr_fixdown(const int *ISAd, int *SA, int i, int size) {
|
947
|
+
int j, k;
|
948
|
+
int v;
|
949
|
+
int c, d, e;
|
950
|
+
|
951
|
+
for(v = SA[i], c = ISAd[v]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
|
952
|
+
d = ISAd[SA[k = j++]];
|
953
|
+
if(d < (e = ISAd[SA[j]])) { k = j; d = e; }
|
954
|
+
if(d <= c) { break; }
|
955
|
+
}
|
956
|
+
SA[i] = v;
|
957
|
+
}
|
958
|
+
|
959
|
+
/* Simple top-down heapsort. */
|
960
|
+
static
|
961
|
+
void
|
962
|
+
tr_heapsort(const int *ISAd, int *SA, int size) {
|
963
|
+
int i, m;
|
964
|
+
int t;
|
965
|
+
|
966
|
+
m = size;
|
967
|
+
if((size % 2) == 0) {
|
968
|
+
m--;
|
969
|
+
if(ISAd[SA[m / 2]] < ISAd[SA[m]]) { SWAP(SA[m], SA[m / 2]); }
|
970
|
+
}
|
971
|
+
|
972
|
+
for(i = m / 2 - 1; 0 <= i; --i) { tr_fixdown(ISAd, SA, i, m); }
|
973
|
+
if((size % 2) == 0) { SWAP(SA[0], SA[m]); tr_fixdown(ISAd, SA, 0, m); }
|
974
|
+
for(i = m - 1; 0 < i; --i) {
|
975
|
+
t = SA[0], SA[0] = SA[i];
|
976
|
+
tr_fixdown(ISAd, SA, 0, i);
|
977
|
+
SA[i] = t;
|
978
|
+
}
|
979
|
+
}
|
980
|
+
|
981
|
+
|
982
|
+
/*---------------------------------------------------------------------------*/
|
983
|
+
|
984
|
+
/* Returns the median of three elements. */
|
985
|
+
static INLINE
|
986
|
+
int *
|
987
|
+
tr_median3(const int *ISAd, int *v1, int *v2, int *v3) {
|
988
|
+
int *t;
|
989
|
+
if(ISAd[*v1] > ISAd[*v2]) { SWAP(v1, v2); }
|
990
|
+
if(ISAd[*v2] > ISAd[*v3]) {
|
991
|
+
if(ISAd[*v1] > ISAd[*v3]) { return v1; }
|
992
|
+
else { return v3; }
|
993
|
+
}
|
994
|
+
return v2;
|
995
|
+
}
|
996
|
+
|
997
|
+
/* Returns the median of five elements. */
|
998
|
+
static INLINE
|
999
|
+
int *
|
1000
|
+
tr_median5(const int *ISAd,
|
1001
|
+
int *v1, int *v2, int *v3, int *v4, int *v5) {
|
1002
|
+
int *t;
|
1003
|
+
if(ISAd[*v2] > ISAd[*v3]) { SWAP(v2, v3); }
|
1004
|
+
if(ISAd[*v4] > ISAd[*v5]) { SWAP(v4, v5); }
|
1005
|
+
if(ISAd[*v2] > ISAd[*v4]) { SWAP(v2, v4); SWAP(v3, v5); }
|
1006
|
+
if(ISAd[*v1] > ISAd[*v3]) { SWAP(v1, v3); }
|
1007
|
+
if(ISAd[*v1] > ISAd[*v4]) { SWAP(v1, v4); SWAP(v3, v5); }
|
1008
|
+
if(ISAd[*v3] > ISAd[*v4]) { return v4; }
|
1009
|
+
return v3;
|
1010
|
+
}
|
1011
|
+
|
1012
|
+
/* Returns the pivot element. */
|
1013
|
+
static INLINE
|
1014
|
+
int *
|
1015
|
+
tr_pivot(const int *ISAd, int *first, int *last) {
|
1016
|
+
int *middle;
|
1017
|
+
int t;
|
1018
|
+
|
1019
|
+
t = last - first;
|
1020
|
+
middle = first + t / 2;
|
1021
|
+
|
1022
|
+
if(t <= 512) {
|
1023
|
+
if(t <= 32) {
|
1024
|
+
return tr_median3(ISAd, first, middle, last - 1);
|
1025
|
+
} else {
|
1026
|
+
t >>= 2;
|
1027
|
+
return tr_median5(ISAd, first, first + t, middle, last - 1 - t, last - 1);
|
1028
|
+
}
|
1029
|
+
}
|
1030
|
+
t >>= 3;
|
1031
|
+
first = tr_median3(ISAd, first, first + t, first + (t << 1));
|
1032
|
+
middle = tr_median3(ISAd, middle - t, middle, middle + t);
|
1033
|
+
last = tr_median3(ISAd, last - 1 - (t << 1), last - 1 - t, last - 1);
|
1034
|
+
return tr_median3(ISAd, first, middle, last);
|
1035
|
+
}
|
1036
|
+
|
1037
|
+
|
1038
|
+
/*---------------------------------------------------------------------------*/
|
1039
|
+
|
1040
|
+
typedef struct _trbudget_t trbudget_t;
|
1041
|
+
struct _trbudget_t {
|
1042
|
+
int chance;
|
1043
|
+
int remain;
|
1044
|
+
int incval;
|
1045
|
+
int count;
|
1046
|
+
};
|
1047
|
+
|
1048
|
+
static INLINE
|
1049
|
+
void
|
1050
|
+
trbudget_init(trbudget_t *budget, int chance, int incval) {
|
1051
|
+
budget->chance = chance;
|
1052
|
+
budget->remain = budget->incval = incval;
|
1053
|
+
}
|
1054
|
+
|
1055
|
+
static INLINE
|
1056
|
+
int
|
1057
|
+
trbudget_check(trbudget_t *budget, int size) {
|
1058
|
+
if(size <= budget->remain) { budget->remain -= size; return 1; }
|
1059
|
+
if(budget->chance == 0) { budget->count += size; return 0; }
|
1060
|
+
budget->remain += budget->incval - size;
|
1061
|
+
budget->chance -= 1;
|
1062
|
+
return 1;
|
1063
|
+
}
|
1064
|
+
|
1065
|
+
|
1066
|
+
/*---------------------------------------------------------------------------*/
|
1067
|
+
|
1068
|
+
static INLINE
|
1069
|
+
void
|
1070
|
+
tr_partition(const int *ISAd,
|
1071
|
+
int *first, int *middle, int *last,
|
1072
|
+
int **pa, int **pb, int v) {
|
1073
|
+
int *a, *b, *c, *d, *e, *f;
|
1074
|
+
int t, s;
|
1075
|
+
int x = 0;
|
1076
|
+
|
1077
|
+
for(b = middle - 1; (++b < last) && ((x = ISAd[*b]) == v);) { }
|
1078
|
+
if(((a = b) < last) && (x < v)) {
|
1079
|
+
for(; (++b < last) && ((x = ISAd[*b]) <= v);) {
|
1080
|
+
if(x == v) { SWAP(*b, *a); ++a; }
|
1081
|
+
}
|
1082
|
+
}
|
1083
|
+
for(c = last; (b < --c) && ((x = ISAd[*c]) == v);) { }
|
1084
|
+
if((b < (d = c)) && (x > v)) {
|
1085
|
+
for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
|
1086
|
+
if(x == v) { SWAP(*c, *d); --d; }
|
1087
|
+
}
|
1088
|
+
}
|
1089
|
+
for(; b < c;) {
|
1090
|
+
SWAP(*b, *c);
|
1091
|
+
for(; (++b < c) && ((x = ISAd[*b]) <= v);) {
|
1092
|
+
if(x == v) { SWAP(*b, *a); ++a; }
|
1093
|
+
}
|
1094
|
+
for(; (b < --c) && ((x = ISAd[*c]) >= v);) {
|
1095
|
+
if(x == v) { SWAP(*c, *d); --d; }
|
1096
|
+
}
|
1097
|
+
}
|
1098
|
+
|
1099
|
+
if(a <= d) {
|
1100
|
+
c = b - 1;
|
1101
|
+
if((s = a - first) > (t = b - a)) { s = t; }
|
1102
|
+
for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
|
1103
|
+
if((s = d - c) > (t = last - d - 1)) { s = t; }
|
1104
|
+
for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
|
1105
|
+
first += (b - a), last -= (d - c);
|
1106
|
+
}
|
1107
|
+
*pa = first, *pb = last;
|
1108
|
+
}
|
1109
|
+
|
1110
|
+
static
|
1111
|
+
void
|
1112
|
+
tr_copy(int *ISA, const int *SA,
|
1113
|
+
int *first, int *a, int *b, int *last,
|
1114
|
+
int depth) {
|
1115
|
+
/* sort suffixes of middle partition
|
1116
|
+
by using sorted order of suffixes of left and right partition. */
|
1117
|
+
int *c, *d, *e;
|
1118
|
+
int s, v;
|
1119
|
+
|
1120
|
+
v = b - SA - 1;
|
1121
|
+
for(c = first, d = a - 1; c <= d; ++c) {
|
1122
|
+
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
1123
|
+
*++d = s;
|
1124
|
+
ISA[s] = d - SA;
|
1125
|
+
}
|
1126
|
+
}
|
1127
|
+
for(c = last - 1, e = d + 1, d = b; e < d; --c) {
|
1128
|
+
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
1129
|
+
*--d = s;
|
1130
|
+
ISA[s] = d - SA;
|
1131
|
+
}
|
1132
|
+
}
|
1133
|
+
}
|
1134
|
+
|
1135
|
+
static
|
1136
|
+
void
|
1137
|
+
tr_partialcopy(int *ISA, const int *SA,
|
1138
|
+
int *first, int *a, int *b, int *last,
|
1139
|
+
int depth) {
|
1140
|
+
int *c, *d, *e;
|
1141
|
+
int s, v;
|
1142
|
+
int rank, lastrank, newrank = -1;
|
1143
|
+
|
1144
|
+
v = b - SA - 1;
|
1145
|
+
lastrank = -1;
|
1146
|
+
for(c = first, d = a - 1; c <= d; ++c) {
|
1147
|
+
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
1148
|
+
*++d = s;
|
1149
|
+
rank = ISA[s + depth];
|
1150
|
+
if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
|
1151
|
+
ISA[s] = newrank;
|
1152
|
+
}
|
1153
|
+
}
|
1154
|
+
|
1155
|
+
lastrank = -1;
|
1156
|
+
for(e = d; first <= e; --e) {
|
1157
|
+
rank = ISA[*e];
|
1158
|
+
if(lastrank != rank) { lastrank = rank; newrank = e - SA; }
|
1159
|
+
if(newrank != rank) { ISA[*e] = newrank; }
|
1160
|
+
}
|
1161
|
+
|
1162
|
+
lastrank = -1;
|
1163
|
+
for(c = last - 1, e = d + 1, d = b; e < d; --c) {
|
1164
|
+
if((0 <= (s = *c - depth)) && (ISA[s] == v)) {
|
1165
|
+
*--d = s;
|
1166
|
+
rank = ISA[s + depth];
|
1167
|
+
if(lastrank != rank) { lastrank = rank; newrank = d - SA; }
|
1168
|
+
ISA[s] = newrank;
|
1169
|
+
}
|
1170
|
+
}
|
1171
|
+
}
|
1172
|
+
|
1173
|
+
static
|
1174
|
+
void
|
1175
|
+
tr_introsort(int *ISA, const int *ISAd,
|
1176
|
+
int *SA, int *first, int *last,
|
1177
|
+
trbudget_t *budget) {
|
1178
|
+
#define STACK_SIZE TR_STACKSIZE
|
1179
|
+
struct { const int *a; int *b, *c; int d, e; }stack[STACK_SIZE];
|
1180
|
+
int *a, *b, *c;
|
1181
|
+
int t;
|
1182
|
+
int v, x = 0;
|
1183
|
+
int incr = ISAd - ISA;
|
1184
|
+
int limit, next;
|
1185
|
+
int ssize, trlink = -1;
|
1186
|
+
|
1187
|
+
for(ssize = 0, limit = tr_ilg(last - first);;) {
|
1188
|
+
|
1189
|
+
if(limit < 0) {
|
1190
|
+
if(limit == -1) {
|
1191
|
+
/* tandem repeat partition */
|
1192
|
+
tr_partition(ISAd - incr, first, first, last, &a, &b, last - SA - 1);
|
1193
|
+
|
1194
|
+
/* update ranks */
|
1195
|
+
if(a < last) {
|
1196
|
+
for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
|
1197
|
+
}
|
1198
|
+
if(b < last) {
|
1199
|
+
for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; }
|
1200
|
+
}
|
1201
|
+
|
1202
|
+
/* push */
|
1203
|
+
if(1 < (b - a)) {
|
1204
|
+
STACK_PUSH5(NULL, a, b, 0, 0);
|
1205
|
+
STACK_PUSH5(ISAd - incr, first, last, -2, trlink);
|
1206
|
+
trlink = ssize - 2;
|
1207
|
+
}
|
1208
|
+
if((a - first) <= (last - b)) {
|
1209
|
+
if(1 < (a - first)) {
|
1210
|
+
STACK_PUSH5(ISAd, b, last, tr_ilg(last - b), trlink);
|
1211
|
+
last = a, limit = tr_ilg(a - first);
|
1212
|
+
} else if(1 < (last - b)) {
|
1213
|
+
first = b, limit = tr_ilg(last - b);
|
1214
|
+
} else {
|
1215
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1216
|
+
}
|
1217
|
+
} else {
|
1218
|
+
if(1 < (last - b)) {
|
1219
|
+
STACK_PUSH5(ISAd, first, a, tr_ilg(a - first), trlink);
|
1220
|
+
first = b, limit = tr_ilg(last - b);
|
1221
|
+
} else if(1 < (a - first)) {
|
1222
|
+
last = a, limit = tr_ilg(a - first);
|
1223
|
+
} else {
|
1224
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1225
|
+
}
|
1226
|
+
}
|
1227
|
+
} else if(limit == -2) {
|
1228
|
+
/* tandem repeat copy */
|
1229
|
+
a = stack[--ssize].b, b = stack[ssize].c;
|
1230
|
+
if(stack[ssize].d == 0) {
|
1231
|
+
tr_copy(ISA, SA, first, a, b, last, ISAd - ISA);
|
1232
|
+
} else {
|
1233
|
+
if(0 <= trlink) { stack[trlink].d = -1; }
|
1234
|
+
tr_partialcopy(ISA, SA, first, a, b, last, ISAd - ISA);
|
1235
|
+
}
|
1236
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1237
|
+
} else {
|
1238
|
+
/* sorted partition */
|
1239
|
+
if(0 <= *first) {
|
1240
|
+
a = first;
|
1241
|
+
do { ISA[*a] = a - SA; } while((++a < last) && (0 <= *a));
|
1242
|
+
first = a;
|
1243
|
+
}
|
1244
|
+
if(first < last) {
|
1245
|
+
a = first; do { *a = ~*a; } while(*++a < 0);
|
1246
|
+
next = (ISA[*a] != ISAd[*a]) ? tr_ilg(a - first + 1) : -1;
|
1247
|
+
if(++a < last) { for(b = first, v = a - SA - 1; b < a; ++b) { ISA[*b] = v; } }
|
1248
|
+
|
1249
|
+
/* push */
|
1250
|
+
if(trbudget_check(budget, a - first)) {
|
1251
|
+
if((a - first) <= (last - a)) {
|
1252
|
+
STACK_PUSH5(ISAd, a, last, -3, trlink);
|
1253
|
+
ISAd += incr, last = a, limit = next;
|
1254
|
+
} else {
|
1255
|
+
if(1 < (last - a)) {
|
1256
|
+
STACK_PUSH5(ISAd + incr, first, a, next, trlink);
|
1257
|
+
first = a, limit = -3;
|
1258
|
+
} else {
|
1259
|
+
ISAd += incr, last = a, limit = next;
|
1260
|
+
}
|
1261
|
+
}
|
1262
|
+
} else {
|
1263
|
+
if(0 <= trlink) { stack[trlink].d = -1; }
|
1264
|
+
if(1 < (last - a)) {
|
1265
|
+
first = a, limit = -3;
|
1266
|
+
} else {
|
1267
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1268
|
+
}
|
1269
|
+
}
|
1270
|
+
} else {
|
1271
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1272
|
+
}
|
1273
|
+
}
|
1274
|
+
continue;
|
1275
|
+
}
|
1276
|
+
|
1277
|
+
if((last - first) <= TR_INSERTIONSORT_THRESHOLD) {
|
1278
|
+
tr_insertionsort(ISAd, first, last);
|
1279
|
+
limit = -3;
|
1280
|
+
continue;
|
1281
|
+
}
|
1282
|
+
|
1283
|
+
if(limit-- == 0) {
|
1284
|
+
tr_heapsort(ISAd, first, last - first);
|
1285
|
+
for(a = last - 1; first < a; a = b) {
|
1286
|
+
for(x = ISAd[*a], b = a - 1; (first <= b) && (ISAd[*b] == x); --b) { *b = ~*b; }
|
1287
|
+
}
|
1288
|
+
limit = -3;
|
1289
|
+
continue;
|
1290
|
+
}
|
1291
|
+
|
1292
|
+
/* choose pivot */
|
1293
|
+
a = tr_pivot(ISAd, first, last);
|
1294
|
+
SWAP(*first, *a);
|
1295
|
+
v = ISAd[*first];
|
1296
|
+
|
1297
|
+
/* partition */
|
1298
|
+
tr_partition(ISAd, first, first + 1, last, &a, &b, v);
|
1299
|
+
if((last - first) != (b - a)) {
|
1300
|
+
next = (ISA[*a] != v) ? tr_ilg(b - a) : -1;
|
1301
|
+
|
1302
|
+
/* update ranks */
|
1303
|
+
for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; }
|
1304
|
+
if(b < last) { for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; } }
|
1305
|
+
|
1306
|
+
/* push */
|
1307
|
+
if((1 < (b - a)) && (trbudget_check(budget, b - a))) {
|
1308
|
+
if((a - first) <= (last - b)) {
|
1309
|
+
if((last - b) <= (b - a)) {
|
1310
|
+
if(1 < (a - first)) {
|
1311
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1312
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1313
|
+
last = a;
|
1314
|
+
} else if(1 < (last - b)) {
|
1315
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1316
|
+
first = b;
|
1317
|
+
} else {
|
1318
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1319
|
+
}
|
1320
|
+
} else if((a - first) <= (b - a)) {
|
1321
|
+
if(1 < (a - first)) {
|
1322
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1323
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1324
|
+
last = a;
|
1325
|
+
} else {
|
1326
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1327
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1328
|
+
}
|
1329
|
+
} else {
|
1330
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1331
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1332
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1333
|
+
}
|
1334
|
+
} else {
|
1335
|
+
if((a - first) <= (b - a)) {
|
1336
|
+
if(1 < (last - b)) {
|
1337
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1338
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1339
|
+
first = b;
|
1340
|
+
} else if(1 < (a - first)) {
|
1341
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1342
|
+
last = a;
|
1343
|
+
} else {
|
1344
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1345
|
+
}
|
1346
|
+
} else if((last - b) <= (b - a)) {
|
1347
|
+
if(1 < (last - b)) {
|
1348
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1349
|
+
STACK_PUSH5(ISAd + incr, a, b, next, trlink);
|
1350
|
+
first = b;
|
1351
|
+
} else {
|
1352
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1353
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1354
|
+
}
|
1355
|
+
} else {
|
1356
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1357
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1358
|
+
ISAd += incr, first = a, last = b, limit = next;
|
1359
|
+
}
|
1360
|
+
}
|
1361
|
+
} else {
|
1362
|
+
if((1 < (b - a)) && (0 <= trlink)) { stack[trlink].d = -1; }
|
1363
|
+
if((a - first) <= (last - b)) {
|
1364
|
+
if(1 < (a - first)) {
|
1365
|
+
STACK_PUSH5(ISAd, b, last, limit, trlink);
|
1366
|
+
last = a;
|
1367
|
+
} else if(1 < (last - b)) {
|
1368
|
+
first = b;
|
1369
|
+
} else {
|
1370
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1371
|
+
}
|
1372
|
+
} else {
|
1373
|
+
if(1 < (last - b)) {
|
1374
|
+
STACK_PUSH5(ISAd, first, a, limit, trlink);
|
1375
|
+
first = b;
|
1376
|
+
} else if(1 < (a - first)) {
|
1377
|
+
last = a;
|
1378
|
+
} else {
|
1379
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1380
|
+
}
|
1381
|
+
}
|
1382
|
+
}
|
1383
|
+
} else {
|
1384
|
+
if(trbudget_check(budget, last - first)) {
|
1385
|
+
limit = tr_ilg(last - first), ISAd += incr;
|
1386
|
+
} else {
|
1387
|
+
if(0 <= trlink) { stack[trlink].d = -1; }
|
1388
|
+
STACK_POP5(ISAd, first, last, limit, trlink);
|
1389
|
+
}
|
1390
|
+
}
|
1391
|
+
}
|
1392
|
+
#undef STACK_SIZE
|
1393
|
+
}
|
1394
|
+
|
1395
|
+
|
1396
|
+
|
1397
|
+
/*---------------------------------------------------------------------------*/
|
1398
|
+
|
1399
|
+
/* Tandem repeat sort */
|
1400
|
+
static
|
1401
|
+
void
|
1402
|
+
trsort(int *ISA, int *SA, int n, int depth) {
|
1403
|
+
int *ISAd;
|
1404
|
+
int *first, *last;
|
1405
|
+
trbudget_t budget;
|
1406
|
+
int t, skip, unsorted;
|
1407
|
+
|
1408
|
+
trbudget_init(&budget, tr_ilg(n) * 2 / 3, n);
|
1409
|
+
/* trbudget_init(&budget, tr_ilg(n) * 3 / 4, n); */
|
1410
|
+
for(ISAd = ISA + depth; -n < *SA; ISAd += ISAd - ISA) {
|
1411
|
+
first = SA;
|
1412
|
+
skip = 0;
|
1413
|
+
unsorted = 0;
|
1414
|
+
do {
|
1415
|
+
if((t = *first) < 0) { first -= t; skip += t; }
|
1416
|
+
else {
|
1417
|
+
if(skip != 0) { *(first + skip) = skip; skip = 0; }
|
1418
|
+
last = SA + ISA[t] + 1;
|
1419
|
+
if(1 < (last - first)) {
|
1420
|
+
budget.count = 0;
|
1421
|
+
tr_introsort(ISA, ISAd, SA, first, last, &budget);
|
1422
|
+
if(budget.count != 0) { unsorted += budget.count; }
|
1423
|
+
else { skip = first - last; }
|
1424
|
+
} else if((last - first) == 1) {
|
1425
|
+
skip = -1;
|
1426
|
+
}
|
1427
|
+
first = last;
|
1428
|
+
}
|
1429
|
+
} while(first < (SA + n));
|
1430
|
+
if(skip != 0) { *(first + skip) = skip; }
|
1431
|
+
if(unsorted == 0) { break; }
|
1432
|
+
}
|
1433
|
+
}
|
1434
|
+
|
1435
|
+
|
1436
|
+
/*---------------------------------------------------------------------------*/
|
1437
|
+
|
1438
|
+
/* Sorts suffixes of type B*. */
|
1439
|
+
static
|
1440
|
+
int
|
1441
|
+
sort_typeBstar(const unsigned char *T, int *SA,
|
1442
|
+
int *bucket_A, int *bucket_B,
|
1443
|
+
int n, int openMP) {
|
1444
|
+
int *PAb, *ISAb, *buf;
|
1445
|
+
#ifdef LIBBSC_OPENMP
|
1446
|
+
int *curbuf;
|
1447
|
+
int l;
|
1448
|
+
#endif
|
1449
|
+
int i, j, k, t, m, bufsize;
|
1450
|
+
int c0, c1;
|
1451
|
+
#ifdef LIBBSC_OPENMP
|
1452
|
+
int d0, d1;
|
1453
|
+
#endif
|
1454
|
+
(void)openMP;
|
1455
|
+
|
1456
|
+
/* Initialize bucket arrays. */
|
1457
|
+
for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; }
|
1458
|
+
for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; }
|
1459
|
+
|
1460
|
+
/* Count the number of occurrences of the first one or two characters of each
|
1461
|
+
type A, B and B* suffix. Moreover, store the beginning position of all
|
1462
|
+
type B* suffixes into the array SA. */
|
1463
|
+
for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) {
|
1464
|
+
/* type A suffix. */
|
1465
|
+
do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1));
|
1466
|
+
if(0 <= i) {
|
1467
|
+
/* type B* suffix. */
|
1468
|
+
++BUCKET_BSTAR(c0, c1);
|
1469
|
+
SA[--m] = i;
|
1470
|
+
/* type B suffix. */
|
1471
|
+
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) {
|
1472
|
+
++BUCKET_B(c0, c1);
|
1473
|
+
}
|
1474
|
+
}
|
1475
|
+
}
|
1476
|
+
m = n - m;
|
1477
|
+
/*
|
1478
|
+
note:
|
1479
|
+
A type B* suffix is lexicographically smaller than a type B suffix that
|
1480
|
+
begins with the same first two characters.
|
1481
|
+
*/
|
1482
|
+
|
1483
|
+
/* Calculate the index of start/end point of each bucket. */
|
1484
|
+
for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) {
|
1485
|
+
t = i + BUCKET_A(c0);
|
1486
|
+
BUCKET_A(c0) = i + j; /* start point */
|
1487
|
+
i = t + BUCKET_B(c0, c0);
|
1488
|
+
for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) {
|
1489
|
+
j += BUCKET_BSTAR(c0, c1);
|
1490
|
+
BUCKET_BSTAR(c0, c1) = j; /* end point */
|
1491
|
+
i += BUCKET_B(c0, c1);
|
1492
|
+
}
|
1493
|
+
}
|
1494
|
+
|
1495
|
+
if(0 < m) {
|
1496
|
+
/* Sort the type B* suffixes by their first two characters. */
|
1497
|
+
PAb = SA + n - m; ISAb = SA + m;
|
1498
|
+
for(i = m - 2; 0 <= i; --i) {
|
1499
|
+
t = PAb[i], c0 = T[t], c1 = T[t + 1];
|
1500
|
+
SA[--BUCKET_BSTAR(c0, c1)] = i;
|
1501
|
+
}
|
1502
|
+
t = PAb[m - 1], c0 = T[t], c1 = T[t + 1];
|
1503
|
+
SA[--BUCKET_BSTAR(c0, c1)] = m - 1;
|
1504
|
+
|
1505
|
+
/* Sort the type B* substrings using sssort. */
|
1506
|
+
#ifdef LIBBSC_OPENMP
|
1507
|
+
if (openMP)
|
1508
|
+
{
|
1509
|
+
buf = SA + m;
|
1510
|
+
c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m;
|
1511
|
+
#pragma omp parallel default(shared) private(bufsize, curbuf, k, l, d0, d1)
|
1512
|
+
{
|
1513
|
+
bufsize = (n - (2 * m)) / omp_get_num_threads();
|
1514
|
+
curbuf = buf + omp_get_thread_num() * bufsize;
|
1515
|
+
k = 0;
|
1516
|
+
for(;;) {
|
1517
|
+
#pragma omp critical(sssort_lock)
|
1518
|
+
{
|
1519
|
+
if(0 < (l = j)) {
|
1520
|
+
d0 = c0, d1 = c1;
|
1521
|
+
do {
|
1522
|
+
k = BUCKET_BSTAR(d0, d1);
|
1523
|
+
if(--d1 <= d0) {
|
1524
|
+
d1 = ALPHABET_SIZE - 1;
|
1525
|
+
if(--d0 < 0) { break; }
|
1526
|
+
}
|
1527
|
+
} while(((l - k) <= 1) && (0 < (l = k)));
|
1528
|
+
c0 = d0, c1 = d1, j = k;
|
1529
|
+
}
|
1530
|
+
}
|
1531
|
+
if(l == 0) { break; }
|
1532
|
+
sssort(T, PAb, SA + k, SA + l,
|
1533
|
+
curbuf, bufsize, 2, n, *(SA + k) == (m - 1));
|
1534
|
+
}
|
1535
|
+
}
|
1536
|
+
}
|
1537
|
+
else
|
1538
|
+
{
|
1539
|
+
buf = SA + m, bufsize = n - (2 * m);
|
1540
|
+
for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
|
1541
|
+
for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
|
1542
|
+
i = BUCKET_BSTAR(c0, c1);
|
1543
|
+
if(1 < (j - i)) {
|
1544
|
+
sssort(T, PAb, SA + i, SA + j,
|
1545
|
+
buf, bufsize, 2, n, *(SA + i) == (m - 1));
|
1546
|
+
}
|
1547
|
+
}
|
1548
|
+
}
|
1549
|
+
}
|
1550
|
+
#else
|
1551
|
+
buf = SA + m, bufsize = n - (2 * m);
|
1552
|
+
for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) {
|
1553
|
+
for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) {
|
1554
|
+
i = BUCKET_BSTAR(c0, c1);
|
1555
|
+
if(1 < (j - i)) {
|
1556
|
+
sssort(T, PAb, SA + i, SA + j,
|
1557
|
+
buf, bufsize, 2, n, *(SA + i) == (m - 1));
|
1558
|
+
}
|
1559
|
+
}
|
1560
|
+
}
|
1561
|
+
#endif
|
1562
|
+
|
1563
|
+
/* Compute ranks of type B* substrings. */
|
1564
|
+
for(i = m - 1; 0 <= i; --i) {
|
1565
|
+
if(0 <= SA[i]) {
|
1566
|
+
j = i;
|
1567
|
+
do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i]));
|
1568
|
+
SA[i + 1] = i - j;
|
1569
|
+
if(i <= 0) { break; }
|
1570
|
+
}
|
1571
|
+
j = i;
|
1572
|
+
do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0);
|
1573
|
+
ISAb[SA[i]] = j;
|
1574
|
+
}
|
1575
|
+
|
1576
|
+
/* Construct the inverse suffix array of type B* suffixes using trsort. */
|
1577
|
+
trsort(ISAb, SA, m, 1);
|
1578
|
+
|
1579
|
+
/* Set the sorted order of tyoe B* suffixes. */
|
1580
|
+
for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) {
|
1581
|
+
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { }
|
1582
|
+
if(0 <= i) {
|
1583
|
+
t = i;
|
1584
|
+
for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { }
|
1585
|
+
SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t;
|
1586
|
+
}
|
1587
|
+
}
|
1588
|
+
|
1589
|
+
/* Calculate the index of start/end point of each bucket. */
|
1590
|
+
BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */
|
1591
|
+
for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) {
|
1592
|
+
i = BUCKET_A(c0 + 1) - 1;
|
1593
|
+
for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) {
|
1594
|
+
t = i - BUCKET_B(c0, c1);
|
1595
|
+
BUCKET_B(c0, c1) = i; /* end point */
|
1596
|
+
|
1597
|
+
/* Move all type B* suffixes to the correct position. */
|
1598
|
+
for(i = t, j = BUCKET_BSTAR(c0, c1);
|
1599
|
+
j <= k;
|
1600
|
+
--i, --k) { SA[i] = SA[k]; }
|
1601
|
+
}
|
1602
|
+
BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */
|
1603
|
+
BUCKET_B(c0, c0) = i; /* end point */
|
1604
|
+
}
|
1605
|
+
}
|
1606
|
+
|
1607
|
+
return m;
|
1608
|
+
}
|
1609
|
+
|
1610
|
+
/* Constructs the suffix array by using the sorted order of type B* suffixes. */
|
1611
|
+
static
|
1612
|
+
void
|
1613
|
+
construct_SA(const unsigned char *T, int *SA,
|
1614
|
+
int *bucket_A, int *bucket_B,
|
1615
|
+
int n, int m) {
|
1616
|
+
int *i, *j, *k;
|
1617
|
+
int s;
|
1618
|
+
int c0, c1, c2;
|
1619
|
+
|
1620
|
+
if(0 < m) {
|
1621
|
+
/* Construct the sorted order of type B suffixes by using
|
1622
|
+
the sorted order of type B* suffixes. */
|
1623
|
+
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
|
1624
|
+
/* Scan the suffix array from right to left. */
|
1625
|
+
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
|
1626
|
+
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
|
1627
|
+
i <= j;
|
1628
|
+
--j) {
|
1629
|
+
if(0 < (s = *j)) {
|
1630
|
+
assert(T[s] == c1);
|
1631
|
+
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
|
1632
|
+
assert(T[s - 1] <= T[s]);
|
1633
|
+
*j = ~s;
|
1634
|
+
c0 = T[--s];
|
1635
|
+
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
|
1636
|
+
if(c0 != c2) {
|
1637
|
+
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
|
1638
|
+
k = SA + BUCKET_B(c2 = c0, c1);
|
1639
|
+
}
|
1640
|
+
assert(k < j);
|
1641
|
+
*k-- = s;
|
1642
|
+
} else {
|
1643
|
+
assert(((s == 0) && (T[s] == c1)) || (s < 0));
|
1644
|
+
*j = ~s;
|
1645
|
+
}
|
1646
|
+
}
|
1647
|
+
}
|
1648
|
+
}
|
1649
|
+
|
1650
|
+
/* Construct the suffix array by using
|
1651
|
+
the sorted order of type B suffixes. */
|
1652
|
+
k = SA + BUCKET_A(c2 = T[n - 1]);
|
1653
|
+
*k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1);
|
1654
|
+
/* Scan the suffix array from left to right. */
|
1655
|
+
for(i = SA, j = SA + n; i < j; ++i) {
|
1656
|
+
if(0 < (s = *i)) {
|
1657
|
+
assert(T[s - 1] >= T[s]);
|
1658
|
+
c0 = T[--s];
|
1659
|
+
if((s == 0) || (T[s - 1] < c0)) { s = ~s; }
|
1660
|
+
if(c0 != c2) {
|
1661
|
+
BUCKET_A(c2) = k - SA;
|
1662
|
+
k = SA + BUCKET_A(c2 = c0);
|
1663
|
+
}
|
1664
|
+
assert(i < k);
|
1665
|
+
*k++ = s;
|
1666
|
+
} else {
|
1667
|
+
assert(s < 0);
|
1668
|
+
*i = ~s;
|
1669
|
+
}
|
1670
|
+
}
|
1671
|
+
}
|
1672
|
+
|
1673
|
+
/* Constructs the burrows-wheeler transformed string directly
|
1674
|
+
by using the sorted order of type B* suffixes. */
|
1675
|
+
static
|
1676
|
+
int
|
1677
|
+
construct_BWT(const unsigned char *T, int *SA,
|
1678
|
+
int *bucket_A, int *bucket_B,
|
1679
|
+
int n, int m) {
|
1680
|
+
int *i, *j, *k, *orig;
|
1681
|
+
int s;
|
1682
|
+
int c0, c1, c2;
|
1683
|
+
|
1684
|
+
if(0 < m) {
|
1685
|
+
/* Construct the sorted order of type B suffixes by using
|
1686
|
+
the sorted order of type B* suffixes. */
|
1687
|
+
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
|
1688
|
+
/* Scan the suffix array from right to left. */
|
1689
|
+
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
|
1690
|
+
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
|
1691
|
+
i <= j;
|
1692
|
+
--j) {
|
1693
|
+
if(0 < (s = *j)) {
|
1694
|
+
assert(T[s] == c1);
|
1695
|
+
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
|
1696
|
+
assert(T[s - 1] <= T[s]);
|
1697
|
+
c0 = T[--s];
|
1698
|
+
*j = ~((int)c0);
|
1699
|
+
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
|
1700
|
+
if(c0 != c2) {
|
1701
|
+
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
|
1702
|
+
k = SA + BUCKET_B(c2 = c0, c1);
|
1703
|
+
}
|
1704
|
+
assert(k < j);
|
1705
|
+
*k-- = s;
|
1706
|
+
} else if(s != 0) {
|
1707
|
+
*j = ~s;
|
1708
|
+
#ifndef NDEBUG
|
1709
|
+
} else {
|
1710
|
+
assert(T[s] == c1);
|
1711
|
+
#endif
|
1712
|
+
}
|
1713
|
+
}
|
1714
|
+
}
|
1715
|
+
}
|
1716
|
+
|
1717
|
+
/* Construct the BWTed string by using
|
1718
|
+
the sorted order of type B suffixes. */
|
1719
|
+
k = SA + BUCKET_A(c2 = T[n - 1]);
|
1720
|
+
*k++ = (T[n - 2] < c2) ? ~((int)T[n - 2]) : (n - 1);
|
1721
|
+
/* Scan the suffix array from left to right. */
|
1722
|
+
for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
|
1723
|
+
if(0 < (s = *i)) {
|
1724
|
+
assert(T[s - 1] >= T[s]);
|
1725
|
+
c0 = T[--s];
|
1726
|
+
*i = c0;
|
1727
|
+
if((0 < s) && (T[s - 1] < c0)) { s = ~((int)T[s - 1]); }
|
1728
|
+
if(c0 != c2) {
|
1729
|
+
BUCKET_A(c2) = k - SA;
|
1730
|
+
k = SA + BUCKET_A(c2 = c0);
|
1731
|
+
}
|
1732
|
+
assert(i < k);
|
1733
|
+
*k++ = s;
|
1734
|
+
} else if(s != 0) {
|
1735
|
+
*i = ~s;
|
1736
|
+
} else {
|
1737
|
+
orig = i;
|
1738
|
+
}
|
1739
|
+
}
|
1740
|
+
|
1741
|
+
return orig - SA;
|
1742
|
+
}
|
1743
|
+
|
1744
|
+
/* Constructs the burrows-wheeler transformed string directly
|
1745
|
+
by using the sorted order of type B* suffixes. */
|
1746
|
+
static
|
1747
|
+
int
|
1748
|
+
construct_BWT_indexes(const unsigned char *T, int *SA,
|
1749
|
+
int *bucket_A, int *bucket_B,
|
1750
|
+
int n, int m,
|
1751
|
+
unsigned char * num_indexes, int * indexes) {
|
1752
|
+
int *i, *j, *k, *orig;
|
1753
|
+
int s;
|
1754
|
+
int c0, c1, c2;
|
1755
|
+
|
1756
|
+
int mod = n / 8;
|
1757
|
+
{
|
1758
|
+
mod |= mod >> 1; mod |= mod >> 2;
|
1759
|
+
mod |= mod >> 4; mod |= mod >> 8;
|
1760
|
+
mod |= mod >> 16; mod >>= 1;
|
1761
|
+
|
1762
|
+
*num_indexes = (unsigned char)((n - 1) / (mod + 1));
|
1763
|
+
}
|
1764
|
+
|
1765
|
+
if(0 < m) {
|
1766
|
+
/* Construct the sorted order of type B suffixes by using
|
1767
|
+
the sorted order of type B* suffixes. */
|
1768
|
+
for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) {
|
1769
|
+
/* Scan the suffix array from right to left. */
|
1770
|
+
for(i = SA + BUCKET_BSTAR(c1, c1 + 1),
|
1771
|
+
j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1;
|
1772
|
+
i <= j;
|
1773
|
+
--j) {
|
1774
|
+
if(0 < (s = *j)) {
|
1775
|
+
assert(T[s] == c1);
|
1776
|
+
assert(((s + 1) < n) && (T[s] <= T[s + 1]));
|
1777
|
+
assert(T[s - 1] <= T[s]);
|
1778
|
+
|
1779
|
+
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = j - SA;
|
1780
|
+
|
1781
|
+
c0 = T[--s];
|
1782
|
+
*j = ~((int)c0);
|
1783
|
+
if((0 < s) && (T[s - 1] > c0)) { s = ~s; }
|
1784
|
+
if(c0 != c2) {
|
1785
|
+
if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; }
|
1786
|
+
k = SA + BUCKET_B(c2 = c0, c1);
|
1787
|
+
}
|
1788
|
+
assert(k < j);
|
1789
|
+
*k-- = s;
|
1790
|
+
} else if(s != 0) {
|
1791
|
+
*j = ~s;
|
1792
|
+
#ifndef NDEBUG
|
1793
|
+
} else {
|
1794
|
+
assert(T[s] == c1);
|
1795
|
+
#endif
|
1796
|
+
}
|
1797
|
+
}
|
1798
|
+
}
|
1799
|
+
}
|
1800
|
+
|
1801
|
+
/* Construct the BWTed string by using
|
1802
|
+
the sorted order of type B suffixes. */
|
1803
|
+
k = SA + BUCKET_A(c2 = T[n - 1]);
|
1804
|
+
if (T[n - 2] < c2) {
|
1805
|
+
if (((n - 1) & mod) == 0) indexes[(n - 1) / (mod + 1) - 1] = k - SA;
|
1806
|
+
*k++ = ~((int)T[n - 2]);
|
1807
|
+
}
|
1808
|
+
else {
|
1809
|
+
*k++ = n - 1;
|
1810
|
+
}
|
1811
|
+
|
1812
|
+
/* Scan the suffix array from left to right. */
|
1813
|
+
for(i = SA, j = SA + n, orig = SA; i < j; ++i) {
|
1814
|
+
if(0 < (s = *i)) {
|
1815
|
+
assert(T[s - 1] >= T[s]);
|
1816
|
+
|
1817
|
+
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = i - SA;
|
1818
|
+
|
1819
|
+
c0 = T[--s];
|
1820
|
+
*i = c0;
|
1821
|
+
if(c0 != c2) {
|
1822
|
+
BUCKET_A(c2) = k - SA;
|
1823
|
+
k = SA + BUCKET_A(c2 = c0);
|
1824
|
+
}
|
1825
|
+
assert(i < k);
|
1826
|
+
if((0 < s) && (T[s - 1] < c0)) {
|
1827
|
+
if ((s & mod) == 0) indexes[s / (mod + 1) - 1] = k - SA;
|
1828
|
+
*k++ = ~((int)T[s - 1]);
|
1829
|
+
} else
|
1830
|
+
*k++ = s;
|
1831
|
+
} else if(s != 0) {
|
1832
|
+
*i = ~s;
|
1833
|
+
} else {
|
1834
|
+
orig = i;
|
1835
|
+
}
|
1836
|
+
}
|
1837
|
+
|
1838
|
+
return orig - SA;
|
1839
|
+
}
|
1840
|
+
|
1841
|
+
|
1842
|
+
/*---------------------------------------------------------------------------*/
|
1843
|
+
|
1844
|
+
/*- Function -*/
|
1845
|
+
|
1846
|
+
int
|
1847
|
+
divsufsort(const unsigned char *T, int *SA, int n, int openMP) {
|
1848
|
+
int *bucket_A, *bucket_B;
|
1849
|
+
int m;
|
1850
|
+
int err = 0;
|
1851
|
+
|
1852
|
+
/* Check arguments. */
|
1853
|
+
if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; }
|
1854
|
+
else if(n == 0) { return 0; }
|
1855
|
+
else if(n == 1) { SA[0] = 0; return 0; }
|
1856
|
+
else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; }
|
1857
|
+
|
1858
|
+
bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int));
|
1859
|
+
bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int));
|
1860
|
+
|
1861
|
+
/* Suffixsort. */
|
1862
|
+
if((bucket_A != NULL) && (bucket_B != NULL)) {
|
1863
|
+
m = sort_typeBstar(T, SA, bucket_A, bucket_B, n, openMP);
|
1864
|
+
construct_SA(T, SA, bucket_A, bucket_B, n, m);
|
1865
|
+
} else {
|
1866
|
+
err = -2;
|
1867
|
+
}
|
1868
|
+
|
1869
|
+
free(bucket_B);
|
1870
|
+
free(bucket_A);
|
1871
|
+
|
1872
|
+
return err;
|
1873
|
+
}
|
1874
|
+
|
1875
|
+
int
|
1876
|
+
divbwt(const unsigned char *T, unsigned char *U, int *A, int n, unsigned char * num_indexes, int * indexes, int openMP) {
|
1877
|
+
int *B;
|
1878
|
+
int *bucket_A, *bucket_B;
|
1879
|
+
int m, pidx, i;
|
1880
|
+
|
1881
|
+
/* Check arguments. */
|
1882
|
+
if((T == NULL) || (U == NULL) || (n < 0)) { return -1; }
|
1883
|
+
else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; }
|
1884
|
+
|
1885
|
+
if((B = A) == NULL) { B = (int *)malloc((size_t)(n + 1) * sizeof(int)); }
|
1886
|
+
bucket_A = (int *)malloc(BUCKET_A_SIZE * sizeof(int));
|
1887
|
+
bucket_B = (int *)malloc(BUCKET_B_SIZE * sizeof(int));
|
1888
|
+
|
1889
|
+
/* Burrows-Wheeler Transform. */
|
1890
|
+
if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) {
|
1891
|
+
m = sort_typeBstar(T, B, bucket_A, bucket_B, n, openMP);
|
1892
|
+
|
1893
|
+
if (num_indexes == NULL || indexes == NULL) {
|
1894
|
+
pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m);
|
1895
|
+
} else {
|
1896
|
+
pidx = construct_BWT_indexes(T, B, bucket_A, bucket_B, n, m, num_indexes, indexes);
|
1897
|
+
}
|
1898
|
+
|
1899
|
+
/* Copy to output string. */
|
1900
|
+
U[0] = T[n - 1];
|
1901
|
+
for(i = 0; i < pidx; ++i) { U[i + 1] = (unsigned char)B[i]; }
|
1902
|
+
for(i += 1; i < n; ++i) { U[i] = (unsigned char)B[i]; }
|
1903
|
+
pidx += 1;
|
1904
|
+
} else {
|
1905
|
+
pidx = -2;
|
1906
|
+
}
|
1907
|
+
|
1908
|
+
free(bucket_B);
|
1909
|
+
free(bucket_A);
|
1910
|
+
if(A == NULL) { free(B); }
|
1911
|
+
|
1912
|
+
return pidx;
|
1913
|
+
}
|