From 2fbdf974338bde8576efdae40a819a76b2391033 Mon Sep 17 00:00:00 2001 From: "Juan J. Martinez" Date: Sun, 5 Nov 2023 11:22:55 +0000 Subject: Initial import of the open source release --- tools/apultra_src/src/apultra.c | 1088 +++++++++++++ tools/apultra_src/src/expand.c | 445 ++++++ tools/apultra_src/src/expand.h | 70 + tools/apultra_src/src/format.h | 47 + tools/apultra_src/src/libapultra.h | 40 + tools/apultra_src/src/libdivsufsort/CHANGELOG.md | 21 + tools/apultra_src/src/libdivsufsort/CMakeLists.txt | 99 ++ .../CMakeModules/AppendCompilerFlags.cmake | 38 + .../CMakeModules/CheckFunctionKeywords.cmake | 15 + .../src/libdivsufsort/CMakeModules/CheckLFS.cmake | 109 ++ .../libdivsufsort/CMakeModules/ProjectCPack.cmake | 38 + .../CMakeModules/cmake_uninstall.cmake.in | 36 + tools/apultra_src/src/libdivsufsort/LICENSE | 21 + tools/apultra_src/src/libdivsufsort/README.md | 140 ++ tools/apultra_src/src/libdivsufsort/VERSION.cmake | 23 + .../src/libdivsufsort/examples/CMakeLists.txt | 11 + tools/apultra_src/src/libdivsufsort/examples/bwt.c | 220 +++ .../src/libdivsufsort/examples/mksary.c | 193 +++ .../src/libdivsufsort/examples/sasearch.c | 165 ++ .../src/libdivsufsort/examples/suftest.c | 164 ++ .../apultra_src/src/libdivsufsort/examples/unbwt.c | 207 +++ .../src/libdivsufsort/include/CMakeLists.txt | 162 ++ .../src/libdivsufsort/include/config.h.cmake | 81 + .../src/libdivsufsort/include/divsufsort.h | 189 +++ .../src/libdivsufsort/include/divsufsort.h.cmake | 180 +++ .../src/libdivsufsort/include/divsufsort_config.h | 9 + .../src/libdivsufsort/include/divsufsort_private.h | 205 +++ .../src/libdivsufsort/include/lfs.h.cmake | 56 + .../src/libdivsufsort/lib/CMakeLists.txt | 31 + .../apultra_src/src/libdivsufsort/lib/divsufsort.c | 431 ++++++ .../src/libdivsufsort/lib/divsufsort_utils.c | 383 +++++ tools/apultra_src/src/libdivsufsort/lib/sssort.c | 815 ++++++++++ tools/apultra_src/src/libdivsufsort/lib/trsort.c | 586 +++++++ .../src/libdivsufsort/pkgconfig/CMakeLists.txt | 9 + .../libdivsufsort/pkgconfig/libdivsufsort.pc.cmake | 11 + tools/apultra_src/src/matchfinder.c | 392 +++++ tools/apultra_src/src/matchfinder.h | 94 ++ tools/apultra_src/src/shrink.c | 1615 ++++++++++++++++++++ tools/apultra_src/src/shrink.h | 166 ++ tools/apultra_src/src/shrink_context.c | 39 + 40 files changed, 8644 insertions(+) create mode 100644 tools/apultra_src/src/apultra.c create mode 100644 tools/apultra_src/src/expand.c create mode 100644 tools/apultra_src/src/expand.h create mode 100644 tools/apultra_src/src/format.h create mode 100644 tools/apultra_src/src/libapultra.h create mode 100644 tools/apultra_src/src/libdivsufsort/CHANGELOG.md create mode 100644 tools/apultra_src/src/libdivsufsort/CMakeLists.txt create mode 100644 tools/apultra_src/src/libdivsufsort/CMakeModules/AppendCompilerFlags.cmake create mode 100644 tools/apultra_src/src/libdivsufsort/CMakeModules/CheckFunctionKeywords.cmake create mode 100644 tools/apultra_src/src/libdivsufsort/CMakeModules/CheckLFS.cmake create mode 100644 tools/apultra_src/src/libdivsufsort/CMakeModules/ProjectCPack.cmake create mode 100644 tools/apultra_src/src/libdivsufsort/CMakeModules/cmake_uninstall.cmake.in create mode 100644 tools/apultra_src/src/libdivsufsort/LICENSE create mode 100644 tools/apultra_src/src/libdivsufsort/README.md create mode 100644 tools/apultra_src/src/libdivsufsort/VERSION.cmake create mode 100644 tools/apultra_src/src/libdivsufsort/examples/CMakeLists.txt create mode 100644 tools/apultra_src/src/libdivsufsort/examples/bwt.c create mode 100644 tools/apultra_src/src/libdivsufsort/examples/mksary.c create mode 100644 tools/apultra_src/src/libdivsufsort/examples/sasearch.c create mode 100644 tools/apultra_src/src/libdivsufsort/examples/suftest.c create mode 100644 tools/apultra_src/src/libdivsufsort/examples/unbwt.c create mode 100644 tools/apultra_src/src/libdivsufsort/include/CMakeLists.txt create mode 100644 tools/apultra_src/src/libdivsufsort/include/config.h.cmake create mode 100644 tools/apultra_src/src/libdivsufsort/include/divsufsort.h create mode 100644 tools/apultra_src/src/libdivsufsort/include/divsufsort.h.cmake create mode 100644 tools/apultra_src/src/libdivsufsort/include/divsufsort_config.h create mode 100644 tools/apultra_src/src/libdivsufsort/include/divsufsort_private.h create mode 100644 tools/apultra_src/src/libdivsufsort/include/lfs.h.cmake create mode 100644 tools/apultra_src/src/libdivsufsort/lib/CMakeLists.txt create mode 100644 tools/apultra_src/src/libdivsufsort/lib/divsufsort.c create mode 100644 tools/apultra_src/src/libdivsufsort/lib/divsufsort_utils.c create mode 100644 tools/apultra_src/src/libdivsufsort/lib/sssort.c create mode 100644 tools/apultra_src/src/libdivsufsort/lib/trsort.c create mode 100644 tools/apultra_src/src/libdivsufsort/pkgconfig/CMakeLists.txt create mode 100644 tools/apultra_src/src/libdivsufsort/pkgconfig/libdivsufsort.pc.cmake create mode 100644 tools/apultra_src/src/matchfinder.c create mode 100644 tools/apultra_src/src/matchfinder.h create mode 100644 tools/apultra_src/src/shrink.c create mode 100644 tools/apultra_src/src/shrink.h create mode 100644 tools/apultra_src/src/shrink_context.c (limited to 'tools/apultra_src/src') diff --git a/tools/apultra_src/src/apultra.c b/tools/apultra_src/src/apultra.c new file mode 100644 index 0000000..e7440e9 --- /dev/null +++ b/tools/apultra_src/src/apultra.c @@ -0,0 +1,1088 @@ +/* + * apultra.c - command line compression utility for the apultra library + * + * Copyright (C) 2019 Emmanuel Marty + * + * This software is provided 'as-is', without any express or implied + * warranty. In no event will the authors be held liable for any damages + * arising from the use of this software. + * + * Permission is granted to anyone to use this software for any purpose, + * including commercial applications, and to alter it and redistribute it + * freely, subject to the following restrictions: + * + * 1. The origin of this software must not be misrepresented; you must not + * claim that you wrote the original software. If you use this software + * in a product, an acknowledgment in the product documentation would be + * appreciated but is not required. + * 2. Altered source versions must be plainly marked as such, and must not be + * misrepresented as being the original software. + * 3. This notice may not be removed or altered from any source distribution. + */ + +/* + * Uses the libdivsufsort library Copyright (c) 2003-2008 Yuta Mori + * + * Inspired by cap by Sven-Åke Dahl. https://github.com/svendahl/cap + * Also inspired by Charles Bloom's compression blog. http://cbloomrants.blogspot.com/ + * With ideas from LZ4 by Yann Collet. https://github.com/lz4/lz4 + * With help and support from spke + * + */ + +#include +#include +#include +#include +#ifdef _WIN32 +#include +#include +#else +#include +#endif +#include "libapultra.h" + +#define OPT_VERBOSE 1 +#define OPT_STATS 2 +#define OPT_ENHANCED 4 + +#define TOOL_VERSION "1.0.9" + +/*---------------------------------------------------------------------------*/ + +#ifdef _WIN32 +LARGE_INTEGER hpc_frequency; +BOOL hpc_available = FALSE; +#endif + +static void do_init_time() { +#ifdef _WIN32 + hpc_frequency.QuadPart = 0; + hpc_available = QueryPerformanceFrequency(&hpc_frequency); +#endif +} + +static long long do_get_time() { + long long nTime; + +#ifdef _WIN32 + if (hpc_available) { + LARGE_INTEGER nCurTime; + + /* Use HPC hardware for best precision */ + QueryPerformanceCounter(&nCurTime); + nTime = (long long)(nCurTime.QuadPart * 1000000LL / hpc_frequency.QuadPart); + } + else { + struct _timeb tb; + _ftime(&tb); + + nTime = ((long long)tb.time * 1000LL + (long long)tb.millitm) * 1000LL; + } +#else + struct timeval tm; + gettimeofday(&tm, NULL); + + nTime = (long long)tm.tv_sec * 1000000LL + (long long)tm.tv_usec; +#endif + return nTime; +} + +/*---------------------------------------------------------------------------*/ + +static void compression_progress(long long nOriginalSize, long long nCompressedSize) { + if (nOriginalSize >= 512 * 1024) { + fprintf(stdout, "\r%lld => %lld (%g %%) \b\b\b\b\b", nOriginalSize, nCompressedSize, (double)(nCompressedSize * 100.0 / nOriginalSize)); + fflush(stdout); + } +} + +static int do_compress(const char *pszInFilename, const char *pszOutFilename, const char *pszDictionaryFilename, const unsigned int nOptions, const unsigned int nMaxWindowSize) { + long long nStartTime = 0LL, nEndTime = 0LL; + size_t nOriginalSize = 0L, nCompressedSize = 0L, nMaxCompressedSize; + int nSafeDist = 0; + int nFlags; + apultra_stats stats; + unsigned char *pDecompressedData; + unsigned char *pCompressedData; + + nFlags = (nOptions & OPT_ENHANCED) ? APULTRA_FLAG_ENHANCED : 0; + + if (nOptions & OPT_VERBOSE) { + nStartTime = do_get_time(); + } + + /* Read the whole original file in memory */ + + FILE *f_in = fopen(pszInFilename, "rb"); + if (!f_in) { + fprintf(stderr, "error opening '%s' for reading\n", pszInFilename); + return 100; + } + + fseek(f_in, 0, SEEK_END); + nOriginalSize = (size_t)ftell(f_in); + fseek(f_in, 0, SEEK_SET); + + pDecompressedData = (unsigned char*)malloc(nOriginalSize); + if (!pDecompressedData) { + fclose(f_in); + fprintf(stderr, "out of memory for reading '%s', %zd bytes needed\n", pszInFilename, nOriginalSize); + return 100; + } + + if (fread(pDecompressedData, 1, nOriginalSize, f_in) != nOriginalSize) { + free(pDecompressedData); + fclose(f_in); + fprintf(stderr, "I/O error while reading '%s'\n", pszInFilename); + return 100; + } + + fclose(f_in); + + /* Allocate max compressed size */ + + nMaxCompressedSize = apultra_get_max_compressed_size(nOriginalSize); + + pCompressedData = (unsigned char*)malloc(nMaxCompressedSize); + if (!pCompressedData) { + free(pDecompressedData); + fprintf(stderr, "out of memory for compressing '%s', %zd bytes needed\n", pszInFilename, nMaxCompressedSize); + return 100; + } + + memset(pCompressedData, 0, nMaxCompressedSize); + + nCompressedSize = apultra_compress(pDecompressedData, pCompressedData, nOriginalSize, nMaxCompressedSize, nFlags, nMaxWindowSize, compression_progress, &stats); + + if ((nOptions & OPT_VERBOSE)) { + nEndTime = do_get_time(); + } + + if (nCompressedSize == -1) { + free(pCompressedData); + free(pDecompressedData); + fprintf(stderr, "compression error for '%s'\n", pszInFilename); + return 100; + } + + if (pszOutFilename) { + FILE *f_out; + + /* Write whole compressed file out */ + + f_out = fopen(pszOutFilename, "wb"); + if (f_out) { + fwrite(pCompressedData, 1, nCompressedSize, f_out); + fclose(f_out); + } + } + + free(pCompressedData); + free(pDecompressedData); + + if ((nOptions & OPT_VERBOSE)) { + double fDelta = ((double)(nEndTime - nStartTime)) / 1000000.0; + double fSpeed = ((double)nOriginalSize / 1048576.0) / fDelta; + fprintf(stdout, "\rCompressed '%s' in %g seconds, %.02g Mb/s, %d tokens (%g bytes/token), %d into %d bytes ==> %g %%\n", + pszInFilename, fDelta, fSpeed, stats.commands_divisor, (double)nOriginalSize / (double)stats.commands_divisor, + (int)nOriginalSize, (int)nCompressedSize, (double)(nCompressedSize * 100.0 / nOriginalSize)); + } + + if (nOptions & OPT_STATS) { + fprintf(stdout, "Tokens: literals: %d short matches: %d normal matches: %d large matches: %d rep matches: %d\n", + stats.num_literals, stats.num_4bit_matches, stats.num_7bit_matches, stats.num_variable_matches, stats.num_rep_matches); + if (stats.match_divisor > 0) { + fprintf(stdout, "Offsets: min: %d avg: %d max: %d count: %d\n", stats.min_offset, (int)(stats.total_offsets / (long long)stats.match_divisor), stats.max_offset, stats.match_divisor); + fprintf(stdout, "Match lens: min: %d avg: %d max: %d count: %d\n", stats.min_match_len, stats.total_match_lens / stats.match_divisor, stats.max_match_len, stats.match_divisor); + } + else { + fprintf(stdout, "Offsets: none\n"); + fprintf(stdout, "Match lens: none\n"); + } + if (stats.rle1_divisor > 0) { + fprintf(stdout, "RLE1 lens: min: %d avg: %d max: %d count: %d\n", stats.min_rle1_len, stats.total_rle1_lens / stats.rle1_divisor, stats.max_rle1_len, stats.rle1_divisor); + } + else { + fprintf(stdout, "RLE1 lens: none\n"); + } + if (stats.rle2_divisor > 0) { + fprintf(stdout, "RLE2 lens: min: %d avg: %d max: %d count: %d\n", stats.min_rle2_len, stats.total_rle2_lens / stats.rle2_divisor, stats.max_rle2_len, stats.rle2_divisor); + } + else { + fprintf(stdout, "RLE2 lens: none\n"); + } + } + return 0; +} + +/*---------------------------------------------------------------------------*/ + +static int do_decompress(const char *pszInFilename, const char *pszOutFilename, const char *pszDictionaryFilename, const unsigned int nOptions) { + long long nStartTime = 0LL, nEndTime = 0LL; + size_t nCompressedSize, nMaxDecompressedSize, nOriginalSize; + unsigned char *pCompressedData; + unsigned char *pDecompressedData; + int nFlags; + + nFlags = (nOptions & OPT_ENHANCED) ? APULTRA_FLAG_ENHANCED : 0; + + /* Read the whole compressed file in memory */ + + FILE *f_in = fopen(pszInFilename, "rb"); + if (!f_in) { + fprintf(stderr, "error opening '%s' for reading\n", pszInFilename); + return 100; + } + + fseek(f_in, 0, SEEK_END); + nCompressedSize = (size_t)ftell(f_in); + fseek(f_in, 0, SEEK_SET); + + pCompressedData = (unsigned char*)malloc(nCompressedSize); + if (!pCompressedData) { + fclose(f_in); + fprintf(stderr, "out of memory for reading '%s', %zd bytes needed\n", pszInFilename, nCompressedSize); + return 100; + } + + if (fread(pCompressedData, 1, nCompressedSize, f_in) != nCompressedSize) { + free(pCompressedData); + fclose(f_in); + fprintf(stderr, "I/O error while reading '%s'\n", pszInFilename); + return 100; + } + + fclose(f_in); + + /* Allocate max decompressed size */ + + nMaxDecompressedSize = apultra_get_max_decompressed_size(pCompressedData, nCompressedSize, nFlags); + if (nMaxDecompressedSize == -1) { + free(pCompressedData); + fprintf(stderr, "invalid compressed format for file '%s'\n", pszInFilename); + return 100; + } + + pDecompressedData = (unsigned char*)malloc(nMaxDecompressedSize); + if (!pDecompressedData) { + free(pCompressedData); + fprintf(stderr, "out of memory for decompressing '%s', %zd bytes needed\n", pszInFilename, nMaxDecompressedSize); + return 100; + } + + memset(pDecompressedData, 0, nMaxDecompressedSize); + + if (nOptions & OPT_VERBOSE) { + nStartTime = do_get_time(); + } + + nOriginalSize = apultra_decompress(pCompressedData, pDecompressedData, nCompressedSize, nMaxDecompressedSize, nFlags); + if (nOriginalSize == -1) { + free(pDecompressedData); + free(pCompressedData); + + fprintf(stderr, "decompression error for '%s'\n", pszInFilename); + return 100; + } + + if (pszOutFilename) { + FILE *f_out; + + /* Write whole decompressed file out */ + + f_out = fopen(pszOutFilename, "wb"); + if (f_out) { + fwrite(pDecompressedData, 1, nOriginalSize, f_out); + fclose(f_out); + } + } + + free(pDecompressedData); + free(pCompressedData); + + if (nOptions & OPT_VERBOSE) { + nEndTime = do_get_time(); + double fDelta = ((double)(nEndTime - nStartTime)) / 1000000.0; + double fSpeed = ((double)nOriginalSize / 1048576.0) / fDelta; + fprintf(stdout, "Decompressed '%s' in %g seconds, %g Mb/s\n", + pszInFilename, fDelta, fSpeed); + } + + return 0; +} + +/*---------------------------------------------------------------------------*/ + +static int do_compare(const char *pszInFilename, const char *pszOutFilename, const char *pszDictionaryFilename, const unsigned int nOptions) { + long long nStartTime = 0LL, nEndTime = 0LL; + size_t nCompressedSize, nMaxDecompressedSize, nOriginalSize, nDecompressedSize; + unsigned char *pCompressedData = NULL; + unsigned char *pOriginalData = NULL; + unsigned char *pDecompressedData = NULL; + int nFlags; + + nFlags = (nOptions & OPT_ENHANCED) ? APULTRA_FLAG_ENHANCED : 0; + + /* Read the whole compressed file in memory */ + + FILE *f_in = fopen(pszInFilename, "rb"); + if (!f_in) { + fprintf(stderr, "error opening '%s' for reading\n", pszInFilename); + return 100; + } + + fseek(f_in, 0, SEEK_END); + nCompressedSize = (size_t)ftell(f_in); + fseek(f_in, 0, SEEK_SET); + + pCompressedData = (unsigned char*)malloc(nCompressedSize); + if (!pCompressedData) { + fclose(f_in); + fprintf(stderr, "out of memory for reading '%s', %zd bytes needed\n", pszInFilename, nCompressedSize); + return 100; + } + + if (fread(pCompressedData, 1, nCompressedSize, f_in) != nCompressedSize) { + free(pCompressedData); + fclose(f_in); + fprintf(stderr, "I/O error while reading '%s'\n", pszInFilename); + return 100; + } + + fclose(f_in); + + /* Read the whole original file in memory */ + + f_in = fopen(pszOutFilename, "rb"); + if (!f_in) { + free(pCompressedData); + fprintf(stderr, "error opening '%s' for reading\n", pszInFilename); + return 100; + } + + fseek(f_in, 0, SEEK_END); + nOriginalSize = (size_t)ftell(f_in); + fseek(f_in, 0, SEEK_SET); + + pOriginalData = (unsigned char*)malloc(nOriginalSize); + if (!pOriginalData) { + fclose(f_in); + free(pCompressedData); + fprintf(stderr, "out of memory for reading '%s', %zd bytes needed\n", pszInFilename, nOriginalSize); + return 100; + } + + if (fread(pOriginalData, 1, nOriginalSize, f_in) != nOriginalSize) { + free(pOriginalData); + fclose(f_in); + free(pCompressedData); + fprintf(stderr, "I/O error while reading '%s'\n", pszInFilename); + return 100; + } + + fclose(f_in); + + /* Allocate max decompressed size */ + + nMaxDecompressedSize = apultra_get_max_decompressed_size(pCompressedData, nCompressedSize, nFlags); + if (nMaxDecompressedSize == -1) { + free(pOriginalData); + free(pCompressedData); + fprintf(stderr, "invalid compressed format for file '%s'\n", pszInFilename); + return 100; + } + + pDecompressedData = (unsigned char*)malloc(nMaxDecompressedSize); + if (!pDecompressedData) { + free(pOriginalData); + free(pCompressedData); + fprintf(stderr, "out of memory for decompressing '%s', %zd bytes needed\n", pszInFilename, nMaxDecompressedSize); + return 100; + } + + memset(pDecompressedData, 0, nMaxDecompressedSize); + + if (nOptions & OPT_VERBOSE) { + nStartTime = do_get_time(); + } + + nDecompressedSize = apultra_decompress(pCompressedData, pDecompressedData, nCompressedSize, nMaxDecompressedSize, nFlags); + if (nDecompressedSize == -1) { + free(pDecompressedData); + free(pOriginalData); + free(pCompressedData); + + fprintf(stderr, "decompression error for '%s'\n", pszInFilename); + return 100; + } + + if (nDecompressedSize != nOriginalSize || memcmp(pDecompressedData, pOriginalData, nOriginalSize)) { + fprintf(stderr, "error comparing compressed file '%s' with original '%s'\n", pszInFilename, pszOutFilename); + return 100; + } + + free(pDecompressedData); + free(pOriginalData); + free(pCompressedData); + + if (nOptions & OPT_VERBOSE) { + nEndTime = do_get_time(); + double fDelta = ((double)(nEndTime - nStartTime)) / 1000000.0; + double fSpeed = ((double)nOriginalSize / 1048576.0) / fDelta; + fprintf(stdout, "Compared '%s' in %g seconds, %g Mb/s\n", + pszInFilename, fDelta, fSpeed); + } + + return 0; +} + +/*---------------------------------------------------------------------------*/ + +static void generate_compressible_data(unsigned char *pBuffer, size_t nBufferSize, unsigned int nSeed, int nNumLiteralValues, float fMatchProbability) { + size_t nIndex = 0; + int nMatchProbability = (int)(fMatchProbability * 1023.0f); + + srand(nSeed); + + if (nIndex >= nBufferSize) return; + pBuffer[nIndex++] = rand() % nNumLiteralValues; + + while (nIndex < nBufferSize) { + if ((rand() & 1023) >= nMatchProbability) { + size_t nLiteralCount = rand() & 127; + if (nLiteralCount > (nBufferSize - nIndex)) + nLiteralCount = nBufferSize - nIndex; + + while (nLiteralCount--) + pBuffer[nIndex++] = rand() % nNumLiteralValues; + } + else { + size_t nMatchLength = MIN_MATCH_SIZE + (rand() & 1023); + size_t nMatchOffset; + + if (nMatchLength > (nBufferSize - nIndex)) + nMatchLength = nBufferSize - nIndex; + if (nMatchLength > nIndex) + nMatchLength = nIndex; + + if (nMatchLength < nIndex) + nMatchOffset = rand() % (nIndex - nMatchLength); + else + nMatchOffset = 0; + + while (nMatchLength--) { + pBuffer[nIndex] = pBuffer[nIndex - nMatchOffset]; + nIndex++; + } + } + } +} + +static void xor_data(unsigned char *pBuffer, size_t nBufferSize, unsigned int nSeed, float fXorProbability) { + size_t nIndex = 0; + int nXorProbability = (int)(fXorProbability * 1023.0f); + + srand(nSeed); + + if (nIndex >= nBufferSize) return; + + while (nIndex < nBufferSize) { + if ((rand() & 1023) < nXorProbability) { + pBuffer[nIndex] ^= 0xff; + } + nIndex++; + } +} + +static int do_self_test(const unsigned int nOptions, const unsigned int nMaxWindowSize, const int nIsQuickTest) { + unsigned char *pGeneratedData; + unsigned char *pCompressedData; + unsigned char *pTmpCompressedData; + unsigned char *pTmpDecompressedData; + size_t nGeneratedDataSize; + size_t nMaxCompressedDataSize; + unsigned int nSeed = 123; + int nFlags; + int i; + + nFlags = (nOptions & OPT_ENHANCED) ? APULTRA_FLAG_ENHANCED : 0; + + pGeneratedData = (unsigned char*)malloc(4 * BLOCK_SIZE); + if (!pGeneratedData) { + fprintf(stderr, "out of memory, %d bytes needed\n", 4 * BLOCK_SIZE); + return 100; + } + + nMaxCompressedDataSize = apultra_get_max_compressed_size(4 * BLOCK_SIZE); + pCompressedData = (unsigned char*)malloc(nMaxCompressedDataSize); + if (!pCompressedData) { + free(pGeneratedData); + pGeneratedData = NULL; + + fprintf(stderr, "out of memory, %zd bytes needed\n", nMaxCompressedDataSize); + return 100; + } + + pTmpCompressedData = (unsigned char*)malloc(nMaxCompressedDataSize); + if (!pTmpCompressedData) { + free(pCompressedData); + pCompressedData = NULL; + free(pGeneratedData); + pGeneratedData = NULL; + + fprintf(stderr, "out of memory, %zd bytes needed\n", nMaxCompressedDataSize); + return 100; + } + + pTmpDecompressedData = (unsigned char*)malloc(4 * BLOCK_SIZE); + if (!pTmpDecompressedData) { + free(pTmpCompressedData); + pTmpCompressedData = NULL; + free(pCompressedData); + pCompressedData = NULL; + free(pGeneratedData); + pGeneratedData = NULL; + + fprintf(stderr, "out of memory, %d bytes needed\n", 4 * BLOCK_SIZE); + return 100; + } + + memset(pGeneratedData, 0, 4 * BLOCK_SIZE); + memset(pCompressedData, 0, nMaxCompressedDataSize); + memset(pTmpCompressedData, 0, nMaxCompressedDataSize); + + /* Test compressing with a too small buffer to do anything, expect to fail cleanly */ + for (i = 0; i < 12; i++) { + generate_compressible_data(pGeneratedData, i, nSeed, 256, 0.5f); + apultra_compress(pGeneratedData, pCompressedData, i, i, nFlags, nMaxWindowSize, NULL, NULL); + } + + size_t nDataSizeStep = 128; + float fProbabilitySizeStep = nIsQuickTest ? 0.005f : 0.0005f; + + for (nGeneratedDataSize = 1024; nGeneratedDataSize <= (nIsQuickTest ? 1024 : (4 * BLOCK_SIZE)); nGeneratedDataSize += nDataSizeStep) { + float fMatchProbability; + + fprintf(stdout, "size %zd", nGeneratedDataSize); + for (fMatchProbability = 0; fMatchProbability <= 0.995f; fMatchProbability += fProbabilitySizeStep) { + int nNumLiteralValues[12] = { 1, 2, 3, 15, 30, 56, 96, 137, 178, 191, 255, 256 }; + float fXorProbability; + + fputc('.', stdout); + fflush(stdout); + + for (i = 0; i < 12; i++) { + /* Generate data to compress */ + generate_compressible_data(pGeneratedData, nGeneratedDataSize, nSeed, nNumLiteralValues[i], fMatchProbability); + + /* Try to compress it, expected to succeed */ + size_t nActualCompressedSize = apultra_compress(pGeneratedData, pCompressedData, nGeneratedDataSize, apultra_get_max_compressed_size(nGeneratedDataSize), + nFlags, nMaxWindowSize, NULL, NULL); + if (nActualCompressedSize == -1 || nActualCompressedSize < (1 + 1 + 1 /* footer */)) { + free(pTmpDecompressedData); + pTmpDecompressedData = NULL; + free(pTmpCompressedData); + pTmpCompressedData = NULL; + free(pCompressedData); + pCompressedData = NULL; + free(pGeneratedData); + pGeneratedData = NULL; + + fprintf(stderr, "\nself-test: error compressing size %zd, seed %d, match probability %f, literals range %d\n", nGeneratedDataSize, nSeed, fMatchProbability, nNumLiteralValues[i]); + return 100; + } + + /* Try to decompress it, expected to succeed */ + size_t nActualDecompressedSize; + nActualDecompressedSize = apultra_decompress(pCompressedData, pTmpDecompressedData, nActualCompressedSize, nGeneratedDataSize, nFlags); + if (nActualDecompressedSize == -1) { + free(pTmpDecompressedData); + pTmpDecompressedData = NULL; + free(pTmpCompressedData); + pTmpCompressedData = NULL; + free(pCompressedData); + pCompressedData = NULL; + free(pGeneratedData); + pGeneratedData = NULL; + + fprintf(stderr, "\nself-test: error decompressing size %zd, seed %d, match probability %f, literals range %d\n", nGeneratedDataSize, nSeed, fMatchProbability, nNumLiteralValues[i]); + return 100; + } + + if (memcmp(pGeneratedData, pTmpDecompressedData, nGeneratedDataSize)) { + free(pTmpDecompressedData); + pTmpDecompressedData = NULL; + free(pTmpCompressedData); + pTmpCompressedData = NULL; + free(pCompressedData); + pCompressedData = NULL; + free(pGeneratedData); + pGeneratedData = NULL; + + fprintf(stderr, "\nself-test: error comparing decompressed and original data, size %zd, seed %d, match probability %f, literals range %d\n", nGeneratedDataSize, nSeed, fMatchProbability, nNumLiteralValues[i]); + return 100; + } + + /* Try to decompress corrupted data, expected to fail cleanly, without crashing or corrupting memory outside the output buffer */ + for (fXorProbability = 0.05f; fXorProbability <= 0.5f; fXorProbability += 0.05f) { + memcpy(pTmpCompressedData, pCompressedData, nActualCompressedSize); + xor_data(pTmpCompressedData, nActualCompressedSize, nSeed, fXorProbability); + apultra_decompress(pTmpCompressedData, pGeneratedData, nActualCompressedSize, nGeneratedDataSize, nFlags); + } + } + + nSeed++; + } + + fputc(10, stdout); + fflush(stdout); + + nDataSizeStep <<= 1; + if (nDataSizeStep > (128 * 4096)) + nDataSizeStep = 128 * 4096; + fProbabilitySizeStep *= 1.25; + if (fProbabilitySizeStep > (0.0005f * 4096)) + fProbabilitySizeStep = 0.0005f * 4096; + } + + free(pTmpDecompressedData); + pTmpDecompressedData = NULL; + + free(pTmpCompressedData); + pTmpCompressedData = NULL; + + free(pCompressedData); + pCompressedData = NULL; + + free(pGeneratedData); + pGeneratedData = NULL; + + fprintf(stdout, "All tests passed.\n"); + return 0; +} + +/*---------------------------------------------------------------------------*/ + +static int do_compr_benchmark(const char *pszInFilename, const char *pszOutFilename, const char *pszDictionaryFilename, const unsigned int nOptions, const unsigned int nMaxWindowSize) { + size_t nFileSize, nMaxCompressedSize; + unsigned char *pFileData; + unsigned char *pCompressedData; + int nFlags; + int i; + + nFlags = (nOptions & OPT_ENHANCED) ? APULTRA_FLAG_ENHANCED : 0; + + if (pszDictionaryFilename) { + fprintf(stderr, "in-memory benchmarking does not support dictionaries\n"); + return 100; + } + + /* Read the whole original file in memory */ + + FILE *f_in = fopen(pszInFilename, "rb"); + if (!f_in) { + fprintf(stderr, "error opening '%s' for reading\n", pszInFilename); + return 100; + } + + fseek(f_in, 0, SEEK_END); + nFileSize = (size_t)ftell(f_in); + fseek(f_in, 0, SEEK_SET); + + pFileData = (unsigned char*)malloc(nFileSize); + if (!pFileData) { + fclose(f_in); + fprintf(stderr, "out of memory for reading '%s', %zd bytes needed\n", pszInFilename, nFileSize); + return 100; + } + + if (fread(pFileData, 1, nFileSize, f_in) != nFileSize) { + free(pFileData); + fclose(f_in); + fprintf(stderr, "I/O error while reading '%s'\n", pszInFilename); + return 100; + } + + fclose(f_in); + + /* Allocate max compressed size */ + + nMaxCompressedSize = apultra_get_max_compressed_size(nFileSize); + + pCompressedData = (unsigned char*)malloc(nMaxCompressedSize + 2048); + if (!pCompressedData) { + free(pFileData); + fprintf(stderr, "out of memory for compressing '%s', %zd bytes needed\n", pszInFilename, nMaxCompressedSize); + return 100; + } + + memset(pCompressedData + 1024, 0, nMaxCompressedSize); + + long long nBestCompTime = -1; + + size_t nActualCompressedSize = 0; + size_t nRightGuardPos = nMaxCompressedSize; + + for (i = 0; i < 5; i++) { + unsigned char nGuard = 0x33 + i; + int j; + + /* Write guard bytes around the output buffer, to help check for writes outside of it by the compressor */ + memset(pCompressedData, nGuard, 1024); + memset(pCompressedData + 1024 + nRightGuardPos, nGuard, 1024); + + long long t0 = do_get_time(); + nActualCompressedSize = apultra_compress(pFileData, pCompressedData + 1024, nFileSize, nRightGuardPos, nFlags, nMaxWindowSize, NULL, NULL); + long long t1 = do_get_time(); + if (nActualCompressedSize == -1) { + free(pCompressedData); + free(pFileData); + fprintf(stderr, "compression error\n"); + return 100; + } + + long long nCurDecTime = t1 - t0; + if (nBestCompTime == -1 || nBestCompTime > nCurDecTime) + nBestCompTime = nCurDecTime; + + /* Check guard bytes before the output buffer */ + for (j = 0; j < 1024; j++) { + if (pCompressedData[j] != nGuard) { + free(pCompressedData); + free(pFileData); + fprintf(stderr, "error, wrote outside of output buffer at %d!\n", j - 1024); + return 100; + } + } + + /* Check guard bytes after the output buffer */ + for (j = 0; j < 1024; j++) { + if (pCompressedData[1024 + nRightGuardPos + j] != nGuard) { + free(pCompressedData); + free(pFileData); + fprintf(stderr, "error, wrote outside of output buffer at %d!\n", j); + return 100; + } + } + + nRightGuardPos = nActualCompressedSize; + } + + if (pszOutFilename) { + FILE *f_out; + + /* Write whole compressed file out */ + + f_out = fopen(pszOutFilename, "wb"); + if (f_out) { + fwrite(pCompressedData + 1024, 1, nActualCompressedSize, f_out); + fclose(f_out); + } + } + + free(pCompressedData); + free(pFileData); + + fprintf(stdout, "compressed size: %zd bytes\n", nActualCompressedSize); + fprintf(stdout, "compression time: %lld microseconds (%g Mb/s)\n", nBestCompTime, ((double)nActualCompressedSize / 1024.0) / ((double)nBestCompTime / 1000.0)); + + return 0; +} + +/*---------------------------------------------------------------------------*/ + +static int do_dec_benchmark(const char *pszInFilename, const char *pszOutFilename, const char *pszDictionaryFilename, const unsigned int nOptions) { + size_t nFileSize, nMaxDecompressedSize; + unsigned char *pFileData; + unsigned char *pDecompressedData; + int nFlags; + int i; + + nFlags = (nOptions & OPT_ENHANCED) ? APULTRA_FLAG_ENHANCED : 0; + + if (pszDictionaryFilename) { + fprintf(stderr, "in-memory benchmarking does not support dictionaries\n"); + return 100; + } + + /* Read the whole compressed file in memory */ + + FILE *f_in = fopen(pszInFilename, "rb"); + if (!f_in) { + fprintf(stderr, "error opening '%s' for reading\n", pszInFilename); + return 100; + } + + fseek(f_in, 0, SEEK_END); + nFileSize = (size_t)ftell(f_in); + fseek(f_in, 0, SEEK_SET); + + pFileData = (unsigned char*)malloc(nFileSize); + if (!pFileData) { + fclose(f_in); + fprintf(stderr, "out of memory for reading '%s', %zd bytes needed\n", pszInFilename, nFileSize); + return 100; + } + + if (fread(pFileData, 1, nFileSize, f_in) != nFileSize) { + free(pFileData); + fclose(f_in); + fprintf(stderr, "I/O error while reading '%s'\n", pszInFilename); + return 100; + } + + fclose(f_in); + + /* Allocate max decompressed size */ + + nMaxDecompressedSize = apultra_get_max_decompressed_size(pFileData, nFileSize, nFlags); + if (nMaxDecompressedSize == -1) { + free(pFileData); + fprintf(stderr, "invalid compressed format for file '%s'\n", pszInFilename); + return 100; + } + + pDecompressedData = (unsigned char*)malloc(nMaxDecompressedSize); + if (!pDecompressedData) { + free(pFileData); + fprintf(stderr, "out of memory for decompressing '%s', %zd bytes needed\n", pszInFilename, nMaxDecompressedSize); + return 100; + } + + memset(pDecompressedData, 0, nMaxDecompressedSize); + + long long nBestDecTime = -1; + + size_t nActualDecompressedSize = 0; + for (i = 0; i < 50; i++) { + long long t0 = do_get_time(); + nActualDecompressedSize = apultra_decompress(pFileData, pDecompressedData, nFileSize, nMaxDecompressedSize, nFlags); + long long t1 = do_get_time(); + if (nActualDecompressedSize == -1) { + free(pDecompressedData); + free(pFileData); + fprintf(stderr, "decompression error\n"); + return 100; + } + + long long nCurDecTime = t1 - t0; + if (nBestDecTime == -1 || nBestDecTime > nCurDecTime) + nBestDecTime = nCurDecTime; + } + + if (pszOutFilename) { + FILE *f_out; + + /* Write whole decompressed file out */ + + f_out = fopen(pszOutFilename, "wb"); + if (f_out) { + fwrite(pDecompressedData, 1, nActualDecompressedSize, f_out); + fclose(f_out); + } + } + + free(pDecompressedData); + free(pFileData); + + fprintf(stdout, "decompressed size: %zd bytes\n", nActualDecompressedSize); + fprintf(stdout, "decompression time: %lld microseconds (%g Mb/s)\n", nBestDecTime, ((double)nActualDecompressedSize / 1024.0) / ((double)nBestDecTime / 1000.0)); + + return 0; +} + +/*---------------------------------------------------------------------------*/ + +int main(int argc, char **argv) { + int i; + const char *pszInFilename = NULL; + const char *pszOutFilename = NULL; + const char *pszDictionaryFilename = NULL; + bool bArgsError = false; + bool bCommandDefined = false; + bool bVerifyCompression = false; + bool bMinMatchDefined = false; + bool bFormatVersionDefined = false; + char cCommand = 'z'; + unsigned int nOptions = 0; + unsigned int nMaxWindowSize = 0; + + for (i = 1; i < argc; i++) { + if (!strcmp(argv[i], "-d")) { + if (!bCommandDefined) { + bCommandDefined = true; + cCommand = 'd'; + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-z")) { + if (!bCommandDefined) { + bCommandDefined = true; + cCommand = 'z'; + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-c")) { + if (!bVerifyCompression) { + bVerifyCompression = true; + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-cbench")) { + if (!bCommandDefined) { + bCommandDefined = true; + cCommand = 'B'; + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-dbench")) { + if (!bCommandDefined) { + bCommandDefined = true; + cCommand = 'b'; + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-test")) { + if (!bCommandDefined) { + bCommandDefined = true; + cCommand = 't'; + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-quicktest")) { + if (!bCommandDefined) { + bCommandDefined = true; + cCommand = 'T'; + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-D")) { + if (!pszDictionaryFilename && (i + 1) < argc) { + pszDictionaryFilename = argv[i + 1]; + i++; + } + else + bArgsError = true; + } + else if (!strncmp(argv[i], "-D", 2)) { + if (!pszDictionaryFilename) { + pszDictionaryFilename = argv[i] + 2; + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-v")) { + if ((nOptions & OPT_VERBOSE) == 0) { + nOptions |= OPT_VERBOSE; + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-e")) { + if ((nOptions & OPT_ENHANCED) == 0) { + nOptions |= OPT_ENHANCED; + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-w")) { + if (!nMaxWindowSize && (i + 1) < argc) { + char *pEnd = NULL; + nMaxWindowSize = (int)strtol(argv[i + 1], &pEnd, 10); + if (pEnd && pEnd != argv[i + 1] && (nMaxWindowSize >= 16 && nMaxWindowSize <= 0x200000)) { + i++; + } + else { + bArgsError = true; + } + } + else + bArgsError = true; + } + else if (!strncmp(argv[i], "-w", 2)) { + if (!nMaxWindowSize) { + char *pEnd = NULL; + nMaxWindowSize = (int)strtol(argv[i] + 2, &pEnd, 10); + if (pEnd && pEnd != (argv[i] + 2) && (nMaxWindowSize >= 16 && nMaxWindowSize <= 0x200000)) { + bFormatVersionDefined = true; + } + else { + bArgsError = true; + } + } + else + bArgsError = true; + } + else if (!strcmp(argv[i], "-stats")) { + if ((nOptions & OPT_STATS) == 0) { + nOptions |= OPT_STATS; + } + else + bArgsError = true; + } + else { + if (!pszInFilename) + pszInFilename = argv[i]; + else { + if (!pszOutFilename) + pszOutFilename = argv[i]; + else + bArgsError = true; + } + } + } + + if (!bArgsError && cCommand == 't') { + return do_self_test(nOptions, nMaxWindowSize, 0); + } + else if (!bArgsError && cCommand == 'T') { + return do_self_test(nOptions, nMaxWindowSize, 1); + } + + if (bArgsError || !pszInFilename || !pszOutFilename) { + fprintf(stderr, "apultra command-line tool v" TOOL_VERSION " by Emmanuel Marty and spke\n"); + fprintf(stderr, "usage: %s [-c] [-d] [-v] [-r] \n", argv[0]); + fprintf(stderr, " -c: check resulting stream after compressing\n"); + fprintf(stderr, " -d: decompress (default: compress)\n"); + fprintf(stderr, " -e: use enhanced (incompatible) format for 8-bit micros\n"); + fprintf(stderr, " -w : maximum window size, in bytes (16..2097152), defaults to maximum\n"); + fprintf(stderr, " -cbench: benchmark in-memory compression\n"); + fprintf(stderr, " -dbench: benchmark in-memory decompression\n"); + fprintf(stderr, " -test: run full automated self-tests\n"); + fprintf(stderr, "-quicktest: run quick automated self-tests\n"); + fprintf(stderr, " -stats: show compressed data stats\n"); + fprintf(stderr, " -v: be verbose\n"); + return 100; + } + + do_init_time(); + + if (cCommand == 'z') { + int nResult = do_compress(pszInFilename, pszOutFilename, pszDictionaryFilename, nOptions, nMaxWindowSize); + if (nResult == 0 && bVerifyCompression) { + return do_compare(pszOutFilename, pszInFilename, pszDictionaryFilename, nOptions); + } else { + return nResult; + } + } + else if (cCommand == 'd') { + return do_decompress(pszInFilename, pszOutFilename, pszDictionaryFilename, nOptions); + } + else if (cCommand == 'B') { + return do_compr_benchmark(pszInFilename, pszOutFilename, pszDictionaryFilename, nOptions, nMaxWindowSize); + } + else if (cCommand == 'b') { + return do_dec_benchmark(pszInFilename, pszOutFilename, pszDictionaryFilename, nOptions); + } + else { + return 100; + } +} diff --git a/tools/apultra_src/src/expand.c b/tools/apultra_src/src/expand.c new file mode 100644 index 0000000..1e07bda --- /dev/null +++ b/tools/apultra_src/src/expand.c @@ -0,0 +1,445 @@ +/* + * expand.c - decompressor implementation + * + * Copyright (C) 2019 Emmanuel Marty + * + * This software is provided 'as-is', without any express or implied + * warranty. In no event will the authors be held liable for any damages + * arising from the use of this software. + * + * Permission is granted to anyone to use this software for any purpose, + * including commercial applications, and to alter it and redistribute it + * freely, subject to the following restrictions: + * + * 1. The origin of this software must not be misrepresented; you must not + * claim that you wrote the original software. If you use this software + * in a product, an acknowledgment in the product documentation would be + * appreciated but is not required. + * 2. Altered source versions must be plainly marked as such, and must not be + * misrepresented as being the original software. + * 3. This notice may not be removed or altered from any source distribution. + */ + +/* + * Uses the libdivsufsort library Copyright (c) 2003-2008 Yuta Mori + * + * Inspired by cap by Sven-Åke Dahl. https://github.com/svendahl/cap + * Also inspired by Charles Bloom's compression blog. http://cbloomrants.blogspot.com/ + * With ideas from LZ4 by Yann Collet. https://github.com/lz4/lz4 + * With help and support from spke + * + */ + +#include +#include +#include "format.h" +#include "expand.h" +#include "libapultra.h" + +#ifdef _MSC_VER +#define FORCE_INLINE __forceinline +#else /* _MSC_VER */ +#define FORCE_INLINE __attribute__((always_inline)) +#endif /* _MSC_VER */ + +static inline FORCE_INLINE int apultra_read_bit(const unsigned char **ppInBlock, const unsigned char *pDataEnd, int *nCurBitMask, unsigned char *bits, const int nBitBufferIdx) { + const unsigned char *pInBlock = *ppInBlock; + int nBit; + + if (nCurBitMask[nBitBufferIdx] == 0) { + if (pInBlock >= pDataEnd) return -1; + bits[nBitBufferIdx] = *pInBlock++; + nCurBitMask[nBitBufferIdx] = 128; + } + + nBit = (bits[nBitBufferIdx] & 128) ? 1 : 0; + + bits[nBitBufferIdx] <<= 1; + nCurBitMask[nBitBufferIdx] >>= 1; + + *ppInBlock = pInBlock; + return nBit; +} + +static inline FORCE_INLINE int apultra_read_gamma2(const unsigned char **ppInBlock, const unsigned char *pDataEnd, int *nCurBitMask, unsigned char *bits, const int nBitBufferIdx) { + int bit; + unsigned int v = 1; + + if (nBitBufferIdx == 0) { + /* Standard aPLib encoding. */ + do { + v = (v << 1) + apultra_read_bit(ppInBlock, pDataEnd, nCurBitMask, bits, nBitBufferIdx); + bit = apultra_read_bit(ppInBlock, pDataEnd, nCurBitMask, bits, nBitBufferIdx); + if (bit < 0) return bit; + } while (bit); + } + else { + /* Enhanced encoding for 8-bit microprocessors ... + * 1) Write out values of 256 and higher lo-byte first (so the gamma2 decoder only needs to rotate a byte). + * 2) Swap meaning of continue/stop bits (saves a byte on the 6502, with no effect on other platforms). + */ + int l = 0; + + do { + if ((l == 0) && (v >= 256)) { + l = v; + v = 1; + } + v = (v << 1) + apultra_read_bit(ppInBlock, pDataEnd, nCurBitMask, bits, nBitBufferIdx); + bit = apultra_read_bit(ppInBlock, pDataEnd, nCurBitMask, bits, nBitBufferIdx); + if (bit < 0) return bit; + } while (bit == 0); + + if (l != 0) { + v = (v << 8) + (l & 255); + } + } + + return v; +} + +/** + * Get maximum decompressed size of compressed data + * + * @param pInputData compressed data + * @param nInputSize compressed size in bytes + * @param nFlags compression flags (a bitmask of APULTRA_FLAG_xxx, or 0) + * + * @return maximum decompressed size + */ +size_t apultra_get_max_decompressed_size(const unsigned char *pInputData, size_t nInputSize, const unsigned int nFlags) { + const unsigned char *pInputDataEnd = pInputData + nInputSize; + int nCurBitMask[3] = { 0, 0, 0 }; + unsigned char bits[3] = { 0, 0, 0 }; + int nMatchOffset = 1; + int nFollowsLiteral = 1; + size_t nDecompressedSize = 0; + int nSingleBitBufferIdx = 0; + int nGammaBitBufferIdx = (nFlags & APULTRA_FLAG_ENHANCED) ? 1 : 0; + int nNibblesBitBufferIdx = (nFlags & APULTRA_FLAG_ENHANCED) ? 2 : 0; + + if (pInputData >= pInputDataEnd) + return -1; + pInputData++; + nDecompressedSize++; + + while (1) { + unsigned int nResult; + + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nSingleBitBufferIdx); + if (nResult < 0) return -1; + + if (!nResult) { + /* '0': literal */ + if (pInputData < pInputDataEnd) { + pInputData++; + nDecompressedSize++; + nFollowsLiteral = 1; + } + else { + return -1; + } + } + else { + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nSingleBitBufferIdx); + if (nResult < 0) return -1; + + if (nResult == 0) { + unsigned int nMatchLen; + unsigned int nMatchLenBias = 0; + unsigned int nIsRepMatch = 0; + + /* '10': 8+n bits offset */ + unsigned int nMatchOffsetHi = apultra_read_gamma2(&pInputData, pInputDataEnd, nCurBitMask, bits, nGammaBitBufferIdx); + if (nFollowsLiteral == 0 || nMatchOffsetHi != 2) { + if (nFollowsLiteral) + nMatchOffset = (nMatchOffsetHi - 3) << 8; + else + nMatchOffset = (nMatchOffsetHi - 2) << 8; + nMatchOffset |= (unsigned int)(*pInputData++); + + if (nMatchOffset < 128) + nMatchLenBias = 2; + } + else { + /* else rep-match */ + nIsRepMatch = 1; + } + + nFollowsLiteral = 0; + nMatchLen = apultra_read_gamma2(&pInputData, pInputDataEnd, nCurBitMask, bits, nGammaBitBufferIdx); + + if (!nIsRepMatch) { + if (nMatchOffset >= MINMATCH3_OFFSET) + nMatchLen++; + if (nMatchOffset >= MINMATCH4_OFFSET) + nMatchLen++; + } + + nMatchLen += nMatchLenBias; + nDecompressedSize += nMatchLen; + } + else { + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nSingleBitBufferIdx); + if (nResult < 0) return -1; + + if (nResult == 0) { + unsigned int nCommand; + unsigned int nMatchLen; + + /* '110': 7 bits offset + 1 bit length */ + nCommand = (unsigned int)(*pInputData++); + if (nCommand == 0x00) { + /* EOD. No match len follows. */ + break; + } + + /* Bits 7-1: offset; bit 0: length */ + nMatchOffset = (nCommand >> 1); + nMatchLen = (nCommand & 1) + 2; + + nFollowsLiteral = 0; + nDecompressedSize += nMatchLen; + } + else { + unsigned int nShortMatchOffset; + + /* '111': 4 bit offset */ + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nNibblesBitBufferIdx); + if (nResult < 0) return -1; + nShortMatchOffset = nResult << 3; + + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nNibblesBitBufferIdx); + if (nResult < 0) return -1; + nShortMatchOffset |= nResult << 2; + + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nNibblesBitBufferIdx); + if (nResult < 0) return -1; + nShortMatchOffset |= nResult << 1; + + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nNibblesBitBufferIdx); + if (nResult < 0) return -1; + nShortMatchOffset |= nResult << 0; + + nFollowsLiteral = 1; + nDecompressedSize++; + } + } + } + } + + return nDecompressedSize; +} + +/** + * Decompress data in memory + * + * @param pInputData compressed data + * @param pOutBuffer buffer for decompressed data + * @param nInputSize compressed size in bytes + * @param nMaxOutBufferSize maximum capacity of decompression buffer + * @param nFlags compression flags (a bitmask of APULTRA_FLAG_xxx, or 0) + * + * @return actual decompressed size, or -1 for error + */ +size_t apultra_decompress(const unsigned char *pInputData, unsigned char *pOutData, size_t nInputSize, size_t nMaxOutBufferSize, const unsigned int nFlags) { + const unsigned char *pInputDataEnd = pInputData + nInputSize; + unsigned char *pCurOutData = pOutData; + const unsigned char *pOutDataEnd = pCurOutData + nMaxOutBufferSize; + const unsigned char *pOutDataFastEnd = pOutDataEnd - 20; + int nCurBitMask[3] = { 0, 0, 0 }; + unsigned char bits[3] = { 0, 0, 0 }; + int nMatchOffset = 1; + int nFollowsLiteral = 1; + int nSingleBitBufferIdx = 0; + int nGammaBitBufferIdx = (nFlags & APULTRA_FLAG_ENHANCED) ? 1 : 0; + int nNibblesBitBufferIdx = (nFlags & APULTRA_FLAG_ENHANCED) ? 2 : 0; + + if (pInputData >= pInputDataEnd && pCurOutData < pOutDataEnd) + return -1; + *pCurOutData++ = *pInputData++; + + while (1) { + unsigned int nResult; + + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nSingleBitBufferIdx); + if (nResult < 0) return -1; + + if (!nResult) { + /* '0': literal */ + if (pInputData < pInputDataEnd && pCurOutData < pOutDataEnd) { + *pCurOutData++ = *pInputData++; + nFollowsLiteral = 1; + } + else { + return -1; + } + } + else { + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nSingleBitBufferIdx); + if (nResult < 0) return -1; + + if (nResult == 0) { + unsigned int nMatchLen; + unsigned int nMatchLenBias = 0; + unsigned int nIsRepMatch = 0; + + /* '10': 8+n bits offset */ + unsigned int nMatchOffsetHi = apultra_read_gamma2(&pInputData, pInputDataEnd, nCurBitMask, bits, nGammaBitBufferIdx); + if (nFollowsLiteral == 0 || nMatchOffsetHi != 2) { + if (nFollowsLiteral) + nMatchOffset = (nMatchOffsetHi - 3) << 8; + else + nMatchOffset = (nMatchOffsetHi - 2) << 8; + nMatchOffset |= (unsigned int)(*pInputData++); + + if (nMatchOffset < 128) + nMatchLenBias = 2; + } + else { + /* else rep-match */ + nIsRepMatch = 1; + } + + nFollowsLiteral = 0; + const unsigned char *pSrc = pCurOutData - nMatchOffset; + if (pSrc >= pOutData) { + nMatchLen = apultra_read_gamma2(&pInputData, pInputDataEnd, nCurBitMask, bits, nGammaBitBufferIdx); + + if (!nIsRepMatch) { + if (nMatchOffset >= MINMATCH3_OFFSET) + nMatchLen++; + if (nMatchOffset >= MINMATCH4_OFFSET) + nMatchLen++; + } + + nMatchLen += nMatchLenBias; + + if (nMatchLen < 11 && nMatchOffset >= 8 && pCurOutData < pOutDataFastEnd) { + memcpy(pCurOutData, pSrc, 8); + memcpy(pCurOutData + 8, pSrc + 8, 2); + pCurOutData += nMatchLen; + } + else { + if ((pCurOutData + nMatchLen) <= pOutDataEnd && (pSrc + nMatchLen) <= pOutDataEnd) { + /* Do a deterministic, left to right byte copy instead of memcpy() so as to handle overlaps */ + + if (nMatchOffset >= 16 && (pCurOutData + nMatchLen) < (pOutDataFastEnd - 15)) { + const unsigned char *pCopySrc = pSrc; + unsigned char *pCopyDst = pCurOutData; + const unsigned char *pCopyEndDst = pCurOutData + nMatchLen; + + do { + memcpy(pCopyDst, pCopySrc, 16); + pCopySrc += 16; + pCopyDst += 16; + } while (pCopyDst < pCopyEndDst); + + pCurOutData += nMatchLen; + } + else { + while (nMatchLen) { + *pCurOutData++ = *pSrc++; + nMatchLen--; + } + } + } + else { + return -1; + } + } + } + else { + return -1; + } + } + else { + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nSingleBitBufferIdx); + if (nResult < 0) return -1; + + if (nResult == 0) { + unsigned int nCommand; + unsigned int nMatchLen; + + /* '110': 7 bits offset + 1 bit length */ + nCommand = (unsigned int)(*pInputData++); + if (nCommand == 0x00) { + /* EOD. No match len follows. */ + break; + } + + /* Bits 7-1: offset; bit 0: length */ + nMatchOffset = (nCommand >> 1); + nMatchLen = (nCommand & 1) + 2; + + nFollowsLiteral = 0; + const unsigned char *pSrc = pCurOutData - nMatchOffset; + if (pSrc >= pOutData && (pSrc + nMatchLen) <= pOutDataEnd) { + if (nMatchOffset >= 8 && pCurOutData < pOutDataFastEnd) { + memcpy(pCurOutData, pSrc, 8); + memcpy(pCurOutData + 8, pSrc + 8, 2); + pCurOutData += nMatchLen; + } + else { + if ((pCurOutData + nMatchLen) <= pOutDataEnd) { + while (nMatchLen) { + *pCurOutData++ = *pSrc++; + nMatchLen--; + } + } + else { + return -1; + } + } + } + else { + return -1; + } + } + else { + unsigned int nShortMatchOffset; + + /* '111': 4 bit offset */ + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nNibblesBitBufferIdx); + if (nResult < 0) return -1; + nShortMatchOffset = nResult << 3; + + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nNibblesBitBufferIdx); + if (nResult < 0) return -1; + nShortMatchOffset |= nResult << 2; + + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nNibblesBitBufferIdx); + if (nResult < 0) return -1; + nShortMatchOffset |= nResult << 1; + + nResult = apultra_read_bit(&pInputData, pInputDataEnd, nCurBitMask, bits, nNibblesBitBufferIdx); + if (nResult < 0) return -1; + nShortMatchOffset |= nResult << 0; + + nFollowsLiteral = 1; + if (nShortMatchOffset) { + /* Short offset, 1-15 */ + const unsigned char *pSrc = pCurOutData - nShortMatchOffset; + if (pSrc >= pOutData && (pCurOutData + 1) <= pOutDataEnd && (pSrc + 1) <= pOutDataEnd) { + *pCurOutData++ = *pSrc++; + } + else { + return -1; + } + } + else { + /* Write zero */ + if ((pCurOutData + 1) <= pOutDataEnd) { + *pCurOutData++ = 0; + } + else { + return -1; + } + } + } + } + } + } + + return (size_t)(pCurOutData - pOutData); +} diff --git a/tools/apultra_src/src/expand.h b/tools/apultra_src/src/expand.h new file mode 100644 index 0000000..f56b233 --- /dev/null +++ b/tools/apultra_src/src/expand.h @@ -0,0 +1,70 @@ +/* + * expand.h - decompressor definitions + * + * Copyright (C) 2019 Emmanuel Marty + * + * This software is provided 'as-is', without any express or implied + * warranty. In no event will the authors be held liable for any damages + * arising from the use of this software. + * + * Permission is granted to anyone to use this software for any purpose, + * including commercial applications, and to alter it and redistribute it + * freely, subject to the following restrictions: + * + * 1. The origin of this software must not be misrepresented; you must not + * claim that you wrote the original software. If you use this software + * in a product, an acknowledgment in the product documentation would be + * appreciated but is not required. + * 2. Altered source versions must be plainly marked as such, and must not be + * misrepresented as being the original software. + * 3. This notice may not be removed or altered from any source distribution. + */ + +/* + * Uses the libdivsufsort library Copyright (c) 2003-2008 Yuta Mori + * + * Inspired by cap by Sven-Åke Dahl. https://github.com/svendahl/cap + * Also inspired by Charles Bloom's compression blog. http://cbloomrants.blogspot.com/ + * With ideas from LZ4 by Yann Collet. https://github.com/lz4/lz4 + * With help and support from spke + * + */ + +#ifndef _EXPAND_H +#define _EXPAND_H + +#include + +#ifdef __cplusplus +extern "C" { +#endif + +/** + * Get maximum decompressed size of compressed data + * + * @param pInputData compressed data + * @param nInputSize compressed size in bytes + * @param nFlags compression flags (a bitmask of APULTRA_FLAG_xxx, or 0) + * + * @return maximum decompressed size + */ +size_t apultra_get_max_decompressed_size(const unsigned char *pInputData, size_t nInputSize, const unsigned int nFlags); + +/** + * Decompress data in memory + * + * @param pInputData compressed data + * @param pOutBuffer buffer for decompressed data + * @param nInputSize compressed size in bytes + * @param nMaxOutBufferSize maximum capacity of decompression buffer + * @param nFlags compression flags (a bitmask of APULTRA_FLAG_xxx, or 0) + * + * @return actual decompressed size, or -1 for error + */ +size_t apultra_decompress(const unsigned char *pInputData, unsigned char *pOutBuffer, size_t nInputSize, size_t nMaxOutBufferSize, const unsigned int nFlags); + +#ifdef __cplusplus +} +#endif + +#endif /* _EXPAND_H */ diff --git a/tools/apultra_src/src/format.h b/tools/apultra_src/src/format.h new file mode 100644 index 0000000..cf949b5 --- /dev/null +++ b/tools/apultra_src/src/format.h @@ -0,0 +1,47 @@ +/* + * format.h - byte stream format definitions + * + * Copyright (C) 2019 Emmanuel Marty + * + * This software is provided 'as-is', without any express or implied + * warranty. In no event will the authors be held liable for any damages + * arising from the use of this software. + * + * Permission is granted to anyone to use this software for any purpose, + * including commercial applications, and to alter it and redistribute it + * freely, subject to the following restrictions: + * + * 1. The origin of this software must not be misrepresented; you must not + * claim that you wrote the original software. If you use this software + * in a product, an acknowledgment in the product documentation would be + * appreciated but is not required. + * 2. Altered source versions must be plainly marked as such, and must not be + * misrepresented as being the original software. + * 3. This notice may not be removed or altered from any source distribution. + */ + +/* + * Uses the libdivsufsort library Copyright (c) 2003-2008 Yuta Mori + * + * Inspired by cap by Sven-Åke Dahl. https://github.com/svendahl/cap + * Also inspired by Charles Bloom's compression blog. http://cbloomrants.blogspot.com/ + * With ideas from LZ4 by Yann Collet. https://github.com/lz4/lz4 + * With help and support from spke + * + */ + +#ifndef _FORMAT_H +#define _FORMAT_H + +#define MIN_OFFSET 1 +#define MAX_OFFSET 0x1fffff + +#define MAX_VARLEN 0x1fffff + +#define BLOCK_SIZE 0x100000 + +#define MIN_MATCH_SIZE 1 +#define MINMATCH3_OFFSET 1280 +#define MINMATCH4_OFFSET 32000 + +#endif /* _FORMAT_H */ diff --git a/tools/apultra_src/src/libapultra.h b/tools/apultra_src/src/libapultra.h new file mode 100644 index 0000000..f97e336 --- /dev/null +++ b/tools/apultra_src/src/libapultra.h @@ -0,0 +1,40 @@ +/* + * libapultra.h - library definitions + * + * Copyright (C) 2019 Emmanuel Marty + * + * This software is provided 'as-is', without any express or implied + * warranty. In no event will the authors be held liable for any damages + * arising from the use of this software. + * + * Permission is granted to anyone to use this software for any purpose, + * including commercial applications, and to alter it and redistribute it + * freely, subject to the following restrictions: + * + * 1. The origin of this software must not be misrepresented; you must not + * claim that you wrote the original software. If you use this software + * in a product, an acknowledgment in the product documentation would be + * appreciated but is not required. + * 2. Altered source versions must be plainly marked as such, and must not be + * misrepresented as being the original software. + * 3. This notice may not be removed or altered from any source distribution. + */ + +/* + * Uses the libdivsufsort library Copyright (c) 2003-2008 Yuta Mori + * + * Inspired by cap by Sven-Åke Dahl. https://github.com/svendahl/cap + * Also inspired by Charles Bloom's compression blog. http://cbloomrants.blogspot.com/ + * With ideas from LZ4 by Yann Collet. https://github.com/lz4/lz4 + * With help and support from spke + * + */ + +#ifndef _LIB_APULTRA_H +#define _LIB_APULTRA_H + +#include "format.h" +#include "shrink.h" +#include "expand.h" + +#endif /* _LIB_APULTRA_H */ diff --git a/tools/apultra_src/src/libdivsufsort/CHANGELOG.md b/tools/apultra_src/src/libdivsufsort/CHANGELOG.md new file mode 100644 index 0000000..fe9d004 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/CHANGELOG.md @@ -0,0 +1,21 @@ +# libdivsufsort Change Log + +See full changelog at: https://github.com/y-256/libdivsufsort/commits + +## [2.0.1] - 2010-11-11 +### Fixed +* Wrong variable used in `divbwt` function +* Enclose some string variables with double quotation marks in include/CMakeLists.txt +* Fix typo in include/CMakeLists.txt + +## 2.0.0 - 2008-08-23 +### Changed +* Switch the build system to [CMake](http://www.cmake.org/) +* Improve the performance of the suffix-sorting algorithm + +### Added +* OpenMP support +* 64-bit version of divsufsort + +[Unreleased]: https://github.com/y-256/libdivsufsort/compare/2.0.1...HEAD +[2.0.1]: https://github.com/y-256/libdivsufsort/compare/2.0.0...2.0.1 diff --git a/tools/apultra_src/src/libdivsufsort/CMakeLists.txt b/tools/apultra_src/src/libdivsufsort/CMakeLists.txt new file mode 100644 index 0000000..7859943 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/CMakeLists.txt @@ -0,0 +1,99 @@ +### cmake file for building libdivsufsort Package ### +cmake_minimum_required(VERSION 2.4.4) +set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules") +include(AppendCompilerFlags) + +## Project information ## +project(libdivsufsort C) +set(PROJECT_VENDOR "Yuta Mori") +set(PROJECT_CONTACT "yuta.256@gmail.com") +set(PROJECT_URL "https://github.com/y-256/libdivsufsort") +set(PROJECT_DESCRIPTION "A lightweight suffix sorting library") +include(VERSION.cmake) + +## CPack configuration ## +set(CPACK_GENERATOR "TGZ;TBZ2;ZIP") +set(CPACK_SOURCE_GENERATOR "TGZ;TBZ2;ZIP") +include(ProjectCPack) + +## Project options ## +option(BUILD_SHARED_LIBS "Set to OFF to build static libraries" ON) +option(BUILD_EXAMPLES "Build examples" ON) +option(BUILD_DIVSUFSORT64 "Build libdivsufsort64" OFF) +option(USE_OPENMP "Use OpenMP for parallelization" OFF) +option(WITH_LFS "Enable Large File Support" ON) + +## Installation directories ## +set(LIB_SUFFIX "" CACHE STRING "Define suffix of directory name (32 or 64)") + +set(CMAKE_INSTALL_RUNTIMEDIR "" CACHE PATH "Specify the output directory for dll runtimes (default is bin)") +if(NOT CMAKE_INSTALL_RUNTIMEDIR) + set(CMAKE_INSTALL_RUNTIMEDIR "${CMAKE_INSTALL_PREFIX}/bin") +endif(NOT CMAKE_INSTALL_RUNTIMEDIR) + +set(CMAKE_INSTALL_LIBDIR "" CACHE PATH "Specify the output directory for libraries (default is lib)") +if(NOT CMAKE_INSTALL_LIBDIR) + set(CMAKE_INSTALL_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}") +endif(NOT CMAKE_INSTALL_LIBDIR) + +set(CMAKE_INSTALL_INCLUDEDIR "" CACHE PATH "Specify the output directory for header files (default is include)") +if(NOT CMAKE_INSTALL_INCLUDEDIR) + set(CMAKE_INSTALL_INCLUDEDIR "${CMAKE_INSTALL_PREFIX}/include") +endif(NOT CMAKE_INSTALL_INCLUDEDIR) + +set(CMAKE_INSTALL_PKGCONFIGDIR "" CACHE PATH "Specify the output directory for pkgconfig files (default is lib/pkgconfig)") +if(NOT CMAKE_INSTALL_PKGCONFIGDIR) + set(CMAKE_INSTALL_PKGCONFIGDIR "${CMAKE_INSTALL_LIBDIR}/pkgconfig") +endif(NOT CMAKE_INSTALL_PKGCONFIGDIR) + +## Build type ## +if(NOT CMAKE_BUILD_TYPE) + set(CMAKE_BUILD_TYPE "Release") +elseif(CMAKE_BUILD_TYPE STREQUAL "Debug") + set(CMAKE_VERBOSE_MAKEFILE ON) +endif(NOT CMAKE_BUILD_TYPE) + +## Compiler options ## +if(MSVC) + append_c_compiler_flags("/W4" "VC" CMAKE_C_FLAGS) + append_c_compiler_flags("/Oi;/Ot;/Ox;/Oy" "VC" CMAKE_C_FLAGS_RELEASE) + if(USE_OPENMP) + append_c_compiler_flags("/openmp" "VC" CMAKE_C_FLAGS) + endif(USE_OPENMP) +elseif(BORLAND) + append_c_compiler_flags("-w" "BCC" CMAKE_C_FLAGS) + append_c_compiler_flags("-Oi;-Og;-Os;-Ov;-Ox" "BCC" CMAKE_C_FLAGS_RELEASE) +else(MSVC) + if(CMAKE_COMPILER_IS_GNUCC) + append_c_compiler_flags("-Wall" "GCC" CMAKE_C_FLAGS) + append_c_compiler_flags("-fomit-frame-pointer" "GCC" CMAKE_C_FLAGS_RELEASE) + if(USE_OPENMP) + append_c_compiler_flags("-fopenmp" "GCC" CMAKE_C_FLAGS) + endif(USE_OPENMP) + else(CMAKE_COMPILER_IS_GNUCC) + append_c_compiler_flags("-Wall" "UNKNOWN" CMAKE_C_FLAGS) + append_c_compiler_flags("-fomit-frame-pointer" "UNKNOWN" CMAKE_C_FLAGS_RELEASE) + if(USE_OPENMP) + append_c_compiler_flags("-fopenmp;-openmp;-omp" "UNKNOWN" CMAKE_C_FLAGS) + endif(USE_OPENMP) + endif(CMAKE_COMPILER_IS_GNUCC) +endif(MSVC) + +## Add definitions ## +add_definitions(-DHAVE_CONFIG_H=1 -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS) + +## Add subdirectories ## +add_subdirectory(pkgconfig) +add_subdirectory(include) +add_subdirectory(lib) +if(BUILD_EXAMPLES) + add_subdirectory(examples) +endif(BUILD_EXAMPLES) + +## Add 'uninstall' target ## +CONFIGURE_FILE( + "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/cmake_uninstall.cmake.in" + "${CMAKE_CURRENT_BINARY_DIR}/CMakeModules/cmake_uninstall.cmake" + IMMEDIATE @ONLY) +ADD_CUSTOM_TARGET(uninstall + "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/CMakeModules/cmake_uninstall.cmake") diff --git a/tools/apultra_src/src/libdivsufsort/CMakeModules/AppendCompilerFlags.cmake b/tools/apultra_src/src/libdivsufsort/CMakeModules/AppendCompilerFlags.cmake new file mode 100644 index 0000000..58d3f99 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/CMakeModules/AppendCompilerFlags.cmake @@ -0,0 +1,38 @@ +include(CheckCSourceCompiles) +include(CheckCXXSourceCompiles) + +macro(append_c_compiler_flags _flags _name _result) + set(SAFE_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS}) + string(REGEX REPLACE "[-+/ ]" "_" cname "${_name}") + string(TOUPPER "${cname}" cname) + foreach(flag ${_flags}) + string(REGEX REPLACE "^[-+/ ]+(.*)[-+/ ]*$" "\\1" flagname "${flag}") + string(REGEX REPLACE "[-+/ ]" "_" flagname "${flagname}") + string(TOUPPER "${flagname}" flagname) + set(have_flag "HAVE_${cname}_${flagname}") + set(CMAKE_REQUIRED_FLAGS "${flag}") + check_c_source_compiles("int main() { return 0; }" ${have_flag}) + if(${have_flag}) + set(${_result} "${${_result}} ${flag}") + endif(${have_flag}) + endforeach(flag) + set(CMAKE_REQUIRED_FLAGS ${SAFE_CMAKE_REQUIRED_FLAGS}) +endmacro(append_c_compiler_flags) + +macro(append_cxx_compiler_flags _flags _name _result) + set(SAFE_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS}) + string(REGEX REPLACE "[-+/ ]" "_" cname "${_name}") + string(TOUPPER "${cname}" cname) + foreach(flag ${_flags}) + string(REGEX REPLACE "^[-+/ ]+(.*)[-+/ ]*$" "\\1" flagname "${flag}") + string(REGEX REPLACE "[-+/ ]" "_" flagname "${flagname}") + string(TOUPPER "${flagname}" flagname) + set(have_flag "HAVE_${cname}_${flagname}") + set(CMAKE_REQUIRED_FLAGS "${flag}") + check_cxx_source_compiles("int main() { return 0; }" ${have_flag}) + if(${have_flag}) + set(${_result} "${${_result}} ${flag}") + endif(${have_flag}) + endforeach(flag) + set(CMAKE_REQUIRED_FLAGS ${SAFE_CMAKE_REQUIRED_FLAGS}) +endmacro(append_cxx_compiler_flags) diff --git a/tools/apultra_src/src/libdivsufsort/CMakeModules/CheckFunctionKeywords.cmake b/tools/apultra_src/src/libdivsufsort/CMakeModules/CheckFunctionKeywords.cmake new file mode 100644 index 0000000..44601fd --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/CMakeModules/CheckFunctionKeywords.cmake @@ -0,0 +1,15 @@ +include(CheckCSourceCompiles) + +macro(check_function_keywords _wordlist) + set(${_result} "") + foreach(flag ${_wordlist}) + string(REGEX REPLACE "[-+/ ()]" "_" flagname "${flag}") + string(TOUPPER "${flagname}" flagname) + set(have_flag "HAVE_${flagname}") + check_c_source_compiles("${flag} void func(); void func() { } int main() { func(); return 0; }" ${have_flag}) + if(${have_flag} AND NOT ${_result}) + set(${_result} "${flag}") +# break() + endif(${have_flag} AND NOT ${_result}) + endforeach(flag) +endmacro(check_function_keywords) diff --git a/tools/apultra_src/src/libdivsufsort/CMakeModules/CheckLFS.cmake b/tools/apultra_src/src/libdivsufsort/CMakeModules/CheckLFS.cmake new file mode 100644 index 0000000..e2b0099 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/CMakeModules/CheckLFS.cmake @@ -0,0 +1,109 @@ +## Checks for large file support ## +include(CheckIncludeFile) +include(CheckSymbolExists) +include(CheckTypeSize) + +macro(check_lfs _isenable) + set(LFS_OFF_T "") + set(LFS_FOPEN "") + set(LFS_FSEEK "") + set(LFS_FTELL "") + set(LFS_PRID "") + + if(${_isenable}) + set(SAFE_CMAKE_REQUIRED_DEFINITIONS "${CMAKE_REQUIRED_DEFINITIONS}") + set(CMAKE_REQUIRED_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS} + -D_LARGEFILE_SOURCE -D_LARGE_FILES -D_FILE_OFFSET_BITS=64 + -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS) + + check_include_file("sys/types.h" HAVE_SYS_TYPES_H) + check_include_file("inttypes.h" HAVE_INTTYPES_H) + check_include_file("stddef.h" HAVE_STDDEF_H) + check_include_file("stdint.h" HAVE_STDINT_H) + + # LFS type1: 8 <= sizeof(off_t), fseeko, ftello + check_type_size("off_t" SIZEOF_OFF_T) + if(SIZEOF_OFF_T GREATER 7) + check_symbol_exists("fseeko" "stdio.h" HAVE_FSEEKO) + check_symbol_exists("ftello" "stdio.h" HAVE_FTELLO) + if(HAVE_FSEEKO AND HAVE_FTELLO) + set(LFS_OFF_T "off_t") + set(LFS_FOPEN "fopen") + set(LFS_FSEEK "fseeko") + set(LFS_FTELL "ftello") + check_symbol_exists("PRIdMAX" "inttypes.h" HAVE_PRIDMAX) + if(HAVE_PRIDMAX) + set(LFS_PRID "PRIdMAX") + else(HAVE_PRIDMAX) + check_type_size("long" SIZEOF_LONG) + check_type_size("int" SIZEOF_INT) + if(SIZEOF_OFF_T GREATER SIZEOF_LONG) + set(LFS_PRID "\"lld\"") + elseif(SIZEOF_LONG GREATER SIZEOF_INT) + set(LFS_PRID "\"ld\"") + else(SIZEOF_OFF_T GREATER SIZEOF_LONG) + set(LFS_PRID "\"d\"") + endif(SIZEOF_OFF_T GREATER SIZEOF_LONG) + endif(HAVE_PRIDMAX) + endif(HAVE_FSEEKO AND HAVE_FTELLO) + endif(SIZEOF_OFF_T GREATER 7) + + # LFS type2: 8 <= sizeof(off64_t), fopen64, fseeko64, ftello64 + if(NOT LFS_OFF_T) + check_type_size("off64_t" SIZEOF_OFF64_T) + if(SIZEOF_OFF64_T GREATER 7) + check_symbol_exists("fopen64" "stdio.h" HAVE_FOPEN64) + check_symbol_exists("fseeko64" "stdio.h" HAVE_FSEEKO64) + check_symbol_exists("ftello64" "stdio.h" HAVE_FTELLO64) + if(HAVE_FOPEN64 AND HAVE_FSEEKO64 AND HAVE_FTELLO64) + set(LFS_OFF_T "off64_t") + set(LFS_FOPEN "fopen64") + set(LFS_FSEEK "fseeko64") + set(LFS_FTELL "ftello64") + check_symbol_exists("PRIdMAX" "inttypes.h" HAVE_PRIDMAX) + if(HAVE_PRIDMAX) + set(LFS_PRID "PRIdMAX") + else(HAVE_PRIDMAX) + check_type_size("long" SIZEOF_LONG) + check_type_size("int" SIZEOF_INT) + if(SIZEOF_OFF64_T GREATER SIZEOF_LONG) + set(LFS_PRID "\"lld\"") + elseif(SIZEOF_LONG GREATER SIZEOF_INT) + set(LFS_PRID "\"ld\"") + else(SIZEOF_OFF64_T GREATER SIZEOF_LONG) + set(LFS_PRID "\"d\"") + endif(SIZEOF_OFF64_T GREATER SIZEOF_LONG) + endif(HAVE_PRIDMAX) + endif(HAVE_FOPEN64 AND HAVE_FSEEKO64 AND HAVE_FTELLO64) + endif(SIZEOF_OFF64_T GREATER 7) + endif(NOT LFS_OFF_T) + + # LFS type3: 8 <= sizeof(__int64), _fseeki64, _ftelli64 + if(NOT LFS_OFF_T) + check_type_size("__int64" SIZEOF___INT64) + if(SIZEOF___INT64 GREATER 7) + check_symbol_exists("_fseeki64" "stdio.h" HAVE__FSEEKI64) + check_symbol_exists("_ftelli64" "stdio.h" HAVE__FTELLI64) + if(HAVE__FSEEKI64 AND HAVE__FTELLI64) + set(LFS_OFF_T "__int64") + set(LFS_FOPEN "fopen") + set(LFS_FSEEK "_fseeki64") + set(LFS_FTELL "_ftelli64") + set(LFS_PRID "\"I64d\"") + endif(HAVE__FSEEKI64 AND HAVE__FTELLI64) + endif(SIZEOF___INT64 GREATER 7) + endif(NOT LFS_OFF_T) + + set(CMAKE_REQUIRED_DEFINITIONS "${SAFE_CMAKE_REQUIRED_DEFINITIONS}") + endif(${_isenable}) + + if(NOT LFS_OFF_T) + ## not found + set(LFS_OFF_T "long") + set(LFS_FOPEN "fopen") + set(LFS_FSEEK "fseek") + set(LFS_FTELL "ftell") + set(LFS_PRID "\"ld\"") + endif(NOT LFS_OFF_T) + +endmacro(check_lfs) diff --git a/tools/apultra_src/src/libdivsufsort/CMakeModules/ProjectCPack.cmake b/tools/apultra_src/src/libdivsufsort/CMakeModules/ProjectCPack.cmake new file mode 100644 index 0000000..7c105f9 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/CMakeModules/ProjectCPack.cmake @@ -0,0 +1,38 @@ +# If the cmake version includes cpack, use it +IF(EXISTS "${CMAKE_ROOT}/Modules/CPack.cmake") + SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "${PROJECT_DESCRIPTION}") + SET(CPACK_PACKAGE_VENDOR "${PROJECT_VENDOR}") + SET(CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.md") + SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE") + SET(CPACK_PACKAGE_VERSION_MAJOR "${PROJECT_VERSION_MAJOR}") + SET(CPACK_PACKAGE_VERSION_MINOR "${PROJECT_VERSION_MINOR}") + SET(CPACK_PACKAGE_VERSION_PATCH "${PROJECT_VERSION_PATCH}") +# SET(CPACK_PACKAGE_INSTALL_DIRECTORY "${PROJECT_NAME} ${PROJECT_VERSION}") + SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION_FULL}") + + IF(NOT DEFINED CPACK_SYSTEM_NAME) + SET(CPACK_SYSTEM_NAME "${CMAKE_SYSTEM_NAME}-${CMAKE_SYSTEM_PROCESSOR}") + ENDIF(NOT DEFINED CPACK_SYSTEM_NAME) + + IF(${CPACK_SYSTEM_NAME} MATCHES Windows) + IF(CMAKE_CL_64) + SET(CPACK_SYSTEM_NAME win64-${CMAKE_SYSTEM_PROCESSOR}) + ELSE(CMAKE_CL_64) + SET(CPACK_SYSTEM_NAME win32-${CMAKE_SYSTEM_PROCESSOR}) + ENDIF(CMAKE_CL_64) + ENDIF(${CPACK_SYSTEM_NAME} MATCHES Windows) + + IF(NOT DEFINED CPACK_PACKAGE_FILE_NAME) + SET(CPACK_PACKAGE_FILE_NAME "${CPACK_SOURCE_PACKAGE_FILE_NAME}-${CPACK_SYSTEM_NAME}") + ENDIF(NOT DEFINED CPACK_PACKAGE_FILE_NAME) + + SET(CPACK_PACKAGE_CONTACT "${PROJECT_CONTACT}") + IF(UNIX) + SET(CPACK_STRIP_FILES "") + SET(CPACK_SOURCE_STRIP_FILES "") +# SET(CPACK_PACKAGE_EXECUTABLES "ccmake" "CMake") + ENDIF(UNIX) + SET(CPACK_SOURCE_IGNORE_FILES "/CVS/" "/build/" "/\\\\.build/" "/\\\\.svn/" "~$") + # include CPack model once all variables are set + INCLUDE(CPack) +ENDIF(EXISTS "${CMAKE_ROOT}/Modules/CPack.cmake") diff --git a/tools/apultra_src/src/libdivsufsort/CMakeModules/cmake_uninstall.cmake.in b/tools/apultra_src/src/libdivsufsort/CMakeModules/cmake_uninstall.cmake.in new file mode 100644 index 0000000..8366a83 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/CMakeModules/cmake_uninstall.cmake.in @@ -0,0 +1,36 @@ +IF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt") + MESSAGE(FATAL_ERROR "Cannot find install manifest: \"@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt\"") +ENDIF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt") + +FILE(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files) +STRING(REGEX REPLACE "\n" ";" files "${files}") + +SET(NUM 0) +FOREACH(file ${files}) + IF(EXISTS "$ENV{DESTDIR}${file}") + MESSAGE(STATUS "Looking for \"$ENV{DESTDIR}${file}\" - found") + SET(UNINSTALL_CHECK_${NUM} 1) + ELSE(EXISTS "$ENV{DESTDIR}${file}") + MESSAGE(STATUS "Looking for \"$ENV{DESTDIR}${file}\" - not found") + SET(UNINSTALL_CHECK_${NUM} 0) + ENDIF(EXISTS "$ENV{DESTDIR}${file}") + MATH(EXPR NUM "1 + ${NUM}") +ENDFOREACH(file) + +SET(NUM 0) +FOREACH(file ${files}) + IF(${UNINSTALL_CHECK_${NUM}}) + MESSAGE(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"") + EXEC_PROGRAM( + "@CMAKE_COMMAND@" ARGS "-E remove \"$ENV{DESTDIR}${file}\"" + OUTPUT_VARIABLE rm_out + RETURN_VALUE rm_retval + ) + IF(NOT "${rm_retval}" STREQUAL 0) + MESSAGE(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"") + ENDIF(NOT "${rm_retval}" STREQUAL 0) + ENDIF(${UNINSTALL_CHECK_${NUM}}) + MATH(EXPR NUM "1 + ${NUM}") +ENDFOREACH(file) + +FILE(REMOVE "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt") diff --git a/tools/apultra_src/src/libdivsufsort/LICENSE b/tools/apultra_src/src/libdivsufsort/LICENSE new file mode 100644 index 0000000..249efa4 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/LICENSE @@ -0,0 +1,21 @@ +The MIT License (MIT) + +Copyright (c) 2003 Yuta Mori All rights reserved. + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/tools/apultra_src/src/libdivsufsort/README.md b/tools/apultra_src/src/libdivsufsort/README.md new file mode 100644 index 0000000..381a188 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/README.md @@ -0,0 +1,140 @@ +# libdivsufsort + +libdivsufsort is a software library that implements a lightweight suffix array construction algorithm. + +## News +* 2015-03-21: The project has moved from [Google Code](http://code.google.com/p/libdivsufsort/) to [GitHub](https://github.com/y-256/libdivsufsort) + +## Introduction +This library provides a simple and an efficient C API to construct a suffix array and a Burrows-Wheeler transformed string from a given string over a constant-size alphabet. +The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of +the string. + +## Build requirements +* An ANSI C Compiler (e.g. GNU GCC) +* [CMake](http://www.cmake.org/ "CMake") version 2.4.2 or newer +* CMake-supported build tool + +## Building on GNU/Linux +1. Get the source code from GitHub. You can either + * use git to clone the repository + ``` + git clone https://github.com/y-256/libdivsufsort.git + ``` + * or download a [zip file](../../archive/master.zip) directly +2. Create a `build` directory in the package source directory. +```shell +$ cd libdivsufsort +$ mkdir build +$ cd build +``` +3. Configure the package for your system. +If you want to install to a different location, change the -DCMAKE_INSTALL_PREFIX option. +```shell +$ cmake -DCMAKE_BUILD_TYPE="Release" \ +-DCMAKE_INSTALL_PREFIX="/usr/local" .. +``` +4. Compile the package. +```shell +$ make +``` +5. (Optional) Install the library and header files. +```shell +$ sudo make install +``` + +## API +```c +/* Data types */ +typedef int32_t saint_t; +typedef int32_t saidx_t; +typedef uint8_t sauchar_t; + +/* + * Constructs the suffix array of a given string. + * @param T[0..n-1] The input string. + * @param SA[0..n-1] The output array or suffixes. + * @param n The length of the given string. + * @return 0 if no error occurred, -1 or -2 otherwise. + */ +saint_t +divsufsort(const sauchar_t *T, saidx_t *SA, saidx_t n); + +/* + * Constructs the burrows-wheeler transformed string of a given string. + * @param T[0..n-1] The input string. + * @param U[0..n-1] The output string. (can be T) + * @param A[0..n-1] The temporary array. (can be NULL) + * @param n The length of the given string. + * @return The primary index if no error occurred, -1 or -2 otherwise. + */ +saidx_t +divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n); +``` + +## Example Usage +```c +#include +#include +#include + +#include + +int main() { + // intput data + char *Text = "abracadabra"; + int n = strlen(Text); + int i, j; + + // allocate + int *SA = (int *)malloc(n * sizeof(int)); + + // sort + divsufsort((unsigned char *)Text, SA, n); + + // output + for(i = 0; i < n; ++i) { + printf("SA[%2d] = %2d: ", i, SA[i]); + for(j = SA[i]; j < n; ++j) { + printf("%c", Text[j]); + } + printf("$\n"); + } + + // deallocate + free(SA); + + return 0; +} +``` +See the [examples](examples) directory for a few other examples. + +## Benchmarks +See [Benchmarks](https://github.com/y-256/libdivsufsort/blob/wiki/SACA_Benchmarks.md) page for details. + +## License +libdivsufsort is released under the [MIT license](LICENSE "MIT license"). +> The MIT License (MIT) +> +> Copyright (c) 2003 Yuta Mori All rights reserved. +> +> Permission is hereby granted, free of charge, to any person obtaining a copy +> of this software and associated documentation files (the "Software"), to deal +> in the Software without restriction, including without limitation the rights +> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +> copies of the Software, and to permit persons to whom the Software is +> furnished to do so, subject to the following conditions: +> +> The above copyright notice and this permission notice shall be included in all +> copies or substantial portions of the Software. +> +> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +> SOFTWARE. + +## Author +* Yuta Mori diff --git a/tools/apultra_src/src/libdivsufsort/VERSION.cmake b/tools/apultra_src/src/libdivsufsort/VERSION.cmake new file mode 100644 index 0000000..3f11ac1 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/VERSION.cmake @@ -0,0 +1,23 @@ +set(PROJECT_VERSION_MAJOR "2") +set(PROJECT_VERSION_MINOR "0") +set(PROJECT_VERSION_PATCH "2") +set(PROJECT_VERSION_EXTRA "-1") +set(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}") +set(PROJECT_VERSION_FULL "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}${PROJECT_VERSION_EXTRA}") + +set(LIBRARY_VERSION "3.0.1") +set(LIBRARY_SOVERSION "3") + +## Git revision number ## +if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git") + execute_process(COMMAND git describe --tags HEAD + WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}" + OUTPUT_VARIABLE GIT_DESCRIBE_TAGS ERROR_QUIET) + if(GIT_DESCRIBE_TAGS) + string(REGEX REPLACE "^v(.*)" "\\1" GIT_REVISION "${GIT_DESCRIBE_TAGS}") + string(STRIP "${GIT_REVISION}" GIT_REVISION) + if(GIT_REVISION) + set(PROJECT_VERSION_FULL "${GIT_REVISION}") + endif(GIT_REVISION) + endif(GIT_DESCRIBE_TAGS) +endif(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git") diff --git a/tools/apultra_src/src/libdivsufsort/examples/CMakeLists.txt b/tools/apultra_src/src/libdivsufsort/examples/CMakeLists.txt new file mode 100644 index 0000000..e801c81 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/examples/CMakeLists.txt @@ -0,0 +1,11 @@ +## Add definitions ## +add_definitions(-D_LARGEFILE_SOURCE -D_LARGE_FILES -D_FILE_OFFSET_BITS=64) + +## Targets ## +include_directories("${CMAKE_CURRENT_SOURCE_DIR}/../include" + "${CMAKE_CURRENT_BINARY_DIR}/../include") +link_directories("${CMAKE_CURRENT_BINARY_DIR}/../lib") +foreach(src suftest mksary sasearch bwt unbwt) + add_executable(${src} ${src}.c) + target_link_libraries(${src} divsufsort) +endforeach(src) diff --git a/tools/apultra_src/src/libdivsufsort/examples/bwt.c b/tools/apultra_src/src/libdivsufsort/examples/bwt.c new file mode 100644 index 0000000..5a362d0 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/examples/bwt.c @@ -0,0 +1,220 @@ +/* + * bwt.c for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#if HAVE_CONFIG_H +# include "config.h" +#endif +#include +#if HAVE_STRING_H +# include +#endif +#if HAVE_STDLIB_H +# include +#endif +#if HAVE_MEMORY_H +# include +#endif +#if HAVE_STDDEF_H +# include +#endif +#if HAVE_STRINGS_H +# include +#endif +#if HAVE_SYS_TYPES_H +# include +#endif +#if HAVE_IO_H && HAVE_FCNTL_H +# include +# include +#endif +#include +#include +#include "lfs.h" + + +static +size_t +write_int(FILE *fp, saidx_t n) { + unsigned char c[4]; + c[0] = (unsigned char)((n >> 0) & 0xff), c[1] = (unsigned char)((n >> 8) & 0xff), + c[2] = (unsigned char)((n >> 16) & 0xff), c[3] = (unsigned char)((n >> 24) & 0xff); + return fwrite(c, sizeof(unsigned char), 4, fp); +} + +static +void +print_help(const char *progname, int status) { + fprintf(stderr, + "bwt, a burrows-wheeler transform program, version %s.\n", + divsufsort_version()); + fprintf(stderr, "usage: %s [-b num] INFILE OUTFILE\n", progname); + fprintf(stderr, " -b num set block size to num MiB [1..512] (default: 32)\n\n"); + exit(status); +} + +int +main(int argc, const char *argv[]) { + FILE *fp, *ofp; + const char *fname, *ofname; + sauchar_t *T; + saidx_t *SA; + LFS_OFF_T n; + size_t m; + saidx_t pidx; + clock_t start,finish; + saint_t i, blocksize = 32, needclose = 3; + + /* Check arguments. */ + if((argc == 1) || + (strcmp(argv[1], "-h") == 0) || + (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } + if((argc != 3) && (argc != 5)) { print_help(argv[0], EXIT_FAILURE); } + i = 1; + if(argc == 5) { + if(strcmp(argv[i], "-b") != 0) { print_help(argv[0], EXIT_FAILURE); } + blocksize = atoi(argv[i + 1]); + if(blocksize < 0) { blocksize = 1; } + else if(512 < blocksize) { blocksize = 512; } + i += 2; + } + blocksize <<= 20; + + /* Open a file for reading. */ + if(strcmp(argv[i], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&fp, fname = argv[i], "rb") != 0) { +#else + if((fp = LFS_FOPEN(fname = argv[i], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdin), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + fp = stdin; + fname = "stdin"; + needclose ^= 1; + } + i += 1; + + /* Open a file for writing. */ + if(strcmp(argv[i], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&ofp, ofname = argv[i], "wb") != 0) { +#else + if((ofp = LFS_FOPEN(ofname = argv[i], "wb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdout), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + ofp = stdout; + ofname = "stdout"; + needclose ^= 2; + } + + /* Get the file size. */ + if(LFS_FSEEK(fp, 0, SEEK_END) == 0) { + n = LFS_FTELL(fp); + rewind(fp); + if(n < 0) { + fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + if(0x20000000L < n) { n = 0x20000000L; } + if((blocksize == 0) || (n < blocksize)) { blocksize = (saidx_t)n; } + } else if(blocksize == 0) { blocksize = 32 << 20; } + + /* Allocate 5blocksize bytes of memory. */ + T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t)); + SA = (saidx_t *)malloc(blocksize * sizeof(saidx_t)); + if((T == NULL) || (SA == NULL)) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + + /* Write the blocksize. */ + if(write_int(ofp, blocksize) != 4) { + fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + + fprintf(stderr, " BWT (blocksize %" PRIdSAINT_T ") ... ", blocksize); + start = clock(); + for(n = 0; 0 < (m = fread(T, sizeof(sauchar_t), blocksize, fp)); n += m) { + /* Burrows-Wheeler Transform. */ + pidx = divbwt(T, T, SA, m); + if(pidx < 0) { + fprintf(stderr, "%s (bw_transform): %s.\n", + argv[0], + (pidx == -1) ? "Invalid arguments" : "Cannot allocate memory"); + exit(EXIT_FAILURE); + } + + /* Write the bwted data. */ + if((write_int(ofp, pidx) != 4) || + (fwrite(T, sizeof(sauchar_t), m, ofp) != m)) { + fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + } + if(ferror(fp)) { + fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + finish = clock(); + fprintf(stderr, "%" PRIdOFF_T " bytes: %.4f sec\n", + n, (double)(finish - start) / (double)CLOCKS_PER_SEC); + + /* Close files */ + if(needclose & 1) { fclose(fp); } + if(needclose & 2) { fclose(ofp); } + + /* Deallocate memory. */ + free(SA); + free(T); + + return 0; +} diff --git a/tools/apultra_src/src/libdivsufsort/examples/mksary.c b/tools/apultra_src/src/libdivsufsort/examples/mksary.c new file mode 100644 index 0000000..b48177c --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/examples/mksary.c @@ -0,0 +1,193 @@ +/* + * mksary.c for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#if HAVE_CONFIG_H +# include "config.h" +#endif +#include +#if HAVE_STRING_H +# include +#endif +#if HAVE_STDLIB_H +# include +#endif +#if HAVE_MEMORY_H +# include +#endif +#if HAVE_STDDEF_H +# include +#endif +#if HAVE_STRINGS_H +# include +#endif +#if HAVE_SYS_TYPES_H +# include +#endif +#if HAVE_IO_H && HAVE_FCNTL_H +# include +# include +#endif +#include +#include +#include "lfs.h" + + +static +void +print_help(const char *progname, int status) { + fprintf(stderr, + "mksary, a simple suffix array builder, version %s.\n", + divsufsort_version()); + fprintf(stderr, "usage: %s INFILE OUTFILE\n\n", progname); + exit(status); +} + +int +main(int argc, const char *argv[]) { + FILE *fp, *ofp; + const char *fname, *ofname; + sauchar_t *T; + saidx_t *SA; + LFS_OFF_T n; + clock_t start, finish; + saint_t needclose = 3; + + /* Check arguments. */ + if((argc == 1) || + (strcmp(argv[1], "-h") == 0) || + (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } + if(argc != 3) { print_help(argv[0], EXIT_FAILURE); } + + /* Open a file for reading. */ + if(strcmp(argv[1], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&fp, fname = argv[1], "rb") != 0) { +#else + if((fp = LFS_FOPEN(fname = argv[1], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdin), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + fp = stdin; + fname = "stdin"; + needclose ^= 1; + } + + /* Open a file for writing. */ + if(strcmp(argv[2], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&ofp, ofname = argv[2], "wb") != 0) { +#else + if((ofp = LFS_FOPEN(ofname = argv[2], "wb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdout), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + ofp = stdout; + ofname = "stdout"; + needclose ^= 2; + } + + /* Get the file size. */ + if(LFS_FSEEK(fp, 0, SEEK_END) == 0) { + n = LFS_FTELL(fp); + rewind(fp); + if(n < 0) { + fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + if(0x7fffffff <= n) { + fprintf(stderr, "%s: Input file `%s' is too big.\n", argv[0], fname); + exit(EXIT_FAILURE); + } + } else { + fprintf(stderr, "%s: Cannot fseek `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Allocate 5blocksize bytes of memory. */ + T = (sauchar_t *)malloc((size_t)n * sizeof(sauchar_t)); + SA = (saidx_t *)malloc((size_t)n * sizeof(saidx_t)); + if((T == NULL) || (SA == NULL)) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + + /* Read n bytes of data. */ + if(fread(T, sizeof(sauchar_t), (size_t)n, fp) != (size_t)n) { + fprintf(stderr, "%s: %s `%s': ", + argv[0], + (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", + fname); + perror(NULL); + exit(EXIT_FAILURE); + } + if(needclose & 1) { fclose(fp); } + + /* Construct the suffix array. */ + fprintf(stderr, "%s: %" PRIdOFF_T " bytes ... ", fname, n); + start = clock(); + if(divsufsort(T, SA, (saidx_t)n) != 0) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + finish = clock(); + fprintf(stderr, "%.4f sec\n", (double)(finish - start) / (double)CLOCKS_PER_SEC); + + /* Write the suffix array. */ + if(fwrite(SA, sizeof(saidx_t), (size_t)n, ofp) != (size_t)n) { + fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + if(needclose & 2) { fclose(ofp); } + + /* Deallocate memory. */ + free(SA); + free(T); + + return 0; +} diff --git a/tools/apultra_src/src/libdivsufsort/examples/sasearch.c b/tools/apultra_src/src/libdivsufsort/examples/sasearch.c new file mode 100644 index 0000000..7e5ca4f --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/examples/sasearch.c @@ -0,0 +1,165 @@ +/* + * sasearch.c for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#if HAVE_CONFIG_H +# include "config.h" +#endif +#include +#if HAVE_STRING_H +# include +#endif +#if HAVE_STDLIB_H +# include +#endif +#if HAVE_MEMORY_H +# include +#endif +#if HAVE_STDDEF_H +# include +#endif +#if HAVE_STRINGS_H +# include +#endif +#if HAVE_SYS_TYPES_H +# include +#endif +#if HAVE_IO_H && HAVE_FCNTL_H +# include +# include +#endif +#include +#include "lfs.h" + + +static +void +print_help(const char *progname, int status) { + fprintf(stderr, + "sasearch, a simple SA-based full-text search tool, version %s\n", + divsufsort_version()); + fprintf(stderr, "usage: %s PATTERN FILE SAFILE\n\n", progname); + exit(status); +} + +int +main(int argc, const char *argv[]) { + FILE *fp; + const char *P; + sauchar_t *T; + saidx_t *SA; + LFS_OFF_T n; + size_t Psize; + saidx_t i, size, left; + + if((argc == 1) || + (strcmp(argv[1], "-h") == 0) || + (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } + if(argc != 4) { print_help(argv[0], EXIT_FAILURE); } + + P = argv[1]; + Psize = strlen(P); + + /* Open a file for reading. */ +#if HAVE_FOPEN_S + if(fopen_s(&fp, argv[2], "rb") != 0) { +#else + if((fp = LFS_FOPEN(argv[2], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], argv[2]); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Get the file size. */ + if(LFS_FSEEK(fp, 0, SEEK_END) == 0) { + n = LFS_FTELL(fp); + rewind(fp); + if(n < 0) { + fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], argv[2]); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { + fprintf(stderr, "%s: Cannot fseek `%s': ", argv[0], argv[2]); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Allocate 5n bytes of memory. */ + T = (sauchar_t *)malloc((size_t)n * sizeof(sauchar_t)); + SA = (saidx_t *)malloc((size_t)n * sizeof(saidx_t)); + if((T == NULL) || (SA == NULL)) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + + /* Read n bytes of data. */ + if(fread(T, sizeof(sauchar_t), (size_t)n, fp) != (size_t)n) { + fprintf(stderr, "%s: %s `%s': ", + argv[0], + (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", + argv[2]); + perror(NULL); + exit(EXIT_FAILURE); + } + fclose(fp); + + /* Open the SA file for reading. */ +#if HAVE_FOPEN_S + if(fopen_s(&fp, argv[3], "rb") != 0) { +#else + if((fp = LFS_FOPEN(argv[3], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], argv[3]); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Read n * sizeof(saidx_t) bytes of data. */ + if(fread(SA, sizeof(saidx_t), (size_t)n, fp) != (size_t)n) { + fprintf(stderr, "%s: %s `%s': ", + argv[0], + (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", + argv[3]); + perror(NULL); + exit(EXIT_FAILURE); + } + fclose(fp); + + /* Search and print */ + size = sa_search(T, (saidx_t)n, + (const sauchar_t *)P, (saidx_t)Psize, + SA, (saidx_t)n, &left); + for(i = 0; i < size; ++i) { + fprintf(stdout, "%" PRIdSAIDX_T "\n", SA[left + i]); + } + + /* Deallocate memory. */ + free(SA); + free(T); + + return 0; +} diff --git a/tools/apultra_src/src/libdivsufsort/examples/suftest.c b/tools/apultra_src/src/libdivsufsort/examples/suftest.c new file mode 100644 index 0000000..71892ac --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/examples/suftest.c @@ -0,0 +1,164 @@ +/* + * suftest.c for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#if HAVE_CONFIG_H +# include "config.h" +#endif +#include +#if HAVE_STRING_H +# include +#endif +#if HAVE_STDLIB_H +# include +#endif +#if HAVE_MEMORY_H +# include +#endif +#if HAVE_STDDEF_H +# include +#endif +#if HAVE_STRINGS_H +# include +#endif +#if HAVE_SYS_TYPES_H +# include +#endif +#if HAVE_IO_H && HAVE_FCNTL_H +# include +# include +#endif +#include +#include +#include "lfs.h" + + +static +void +print_help(const char *progname, int status) { + fprintf(stderr, + "suftest, a suffixsort tester, version %s.\n", + divsufsort_version()); + fprintf(stderr, "usage: %s FILE\n\n", progname); + exit(status); +} + +int +main(int argc, const char *argv[]) { + FILE *fp; + const char *fname; + sauchar_t *T; + saidx_t *SA; + LFS_OFF_T n; + clock_t start, finish; + saint_t needclose = 1; + + /* Check arguments. */ + if((argc == 1) || + (strcmp(argv[1], "-h") == 0) || + (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } + if(argc != 2) { print_help(argv[0], EXIT_FAILURE); } + + /* Open a file for reading. */ + if(strcmp(argv[1], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&fp, fname = argv[1], "rb") != 0) { +#else + if((fp = LFS_FOPEN(fname = argv[1], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdin), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + fp = stdin; + fname = "stdin"; + needclose = 0; + } + + /* Get the file size. */ + if(LFS_FSEEK(fp, 0, SEEK_END) == 0) { + n = LFS_FTELL(fp); + rewind(fp); + if(n < 0) { + fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + if(0x7fffffff <= n) { + fprintf(stderr, "%s: Input file `%s' is too big.\n", argv[0], fname); + exit(EXIT_FAILURE); + } + } else { + fprintf(stderr, "%s: Cannot fseek `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Allocate 5n bytes of memory. */ + T = (sauchar_t *)malloc((size_t)n * sizeof(sauchar_t)); + SA = (saidx_t *)malloc((size_t)n * sizeof(saidx_t)); + if((T == NULL) || (SA == NULL)) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + + /* Read n bytes of data. */ + if(fread(T, sizeof(sauchar_t), (size_t)n, fp) != (size_t)n) { + fprintf(stderr, "%s: %s `%s': ", + argv[0], + (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", + argv[1]); + perror(NULL); + exit(EXIT_FAILURE); + } + if(needclose & 1) { fclose(fp); } + + /* Construct the suffix array. */ + fprintf(stderr, "%s: %" PRIdOFF_T " bytes ... ", fname, n); + start = clock(); + if(divsufsort(T, SA, (saidx_t)n) != 0) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + finish = clock(); + fprintf(stderr, "%.4f sec\n", (double)(finish - start) / (double)CLOCKS_PER_SEC); + + /* Check the suffix array. */ + if(sufcheck(T, SA, (saidx_t)n, 1) != 0) { exit(EXIT_FAILURE); } + + /* Deallocate memory. */ + free(SA); + free(T); + + return 0; +} diff --git a/tools/apultra_src/src/libdivsufsort/examples/unbwt.c b/tools/apultra_src/src/libdivsufsort/examples/unbwt.c new file mode 100644 index 0000000..c0f19e9 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/examples/unbwt.c @@ -0,0 +1,207 @@ +/* + * unbwt.c for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#if HAVE_CONFIG_H +# include "config.h" +#endif +#include +#if HAVE_STRING_H +# include +#endif +#if HAVE_STDLIB_H +# include +#endif +#if HAVE_MEMORY_H +# include +#endif +#if HAVE_STDDEF_H +# include +#endif +#if HAVE_STRINGS_H +# include +#endif +#if HAVE_SYS_TYPES_H +# include +#endif +#if HAVE_IO_H && HAVE_FCNTL_H +# include +# include +#endif +#include +#include +#include "lfs.h" + + +static +size_t +read_int(FILE *fp, saidx_t *n) { + unsigned char c[4]; + size_t m = fread(c, sizeof(unsigned char), 4, fp); + if(m == 4) { + *n = (c[0] << 0) | (c[1] << 8) | + (c[2] << 16) | (c[3] << 24); + } + return m; +} + +static +void +print_help(const char *progname, int status) { + fprintf(stderr, + "unbwt, an inverse burrows-wheeler transform program, version %s.\n", + divsufsort_version()); + fprintf(stderr, "usage: %s INFILE OUTFILE\n\n", progname); + exit(status); +} + +int +main(int argc, const char *argv[]) { + FILE *fp, *ofp; + const char *fname, *ofname; + sauchar_t *T; + saidx_t *A; + LFS_OFF_T n; + size_t m; + saidx_t pidx; + clock_t start, finish; + saint_t err, blocksize, needclose = 3; + + /* Check arguments. */ + if((argc == 1) || + (strcmp(argv[1], "-h") == 0) || + (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } + if(argc != 3) { print_help(argv[0], EXIT_FAILURE); } + + /* Open a file for reading. */ + if(strcmp(argv[1], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&fp, fname = argv[1], "rb") != 0) { +#else + if((fp = LFS_FOPEN(fname = argv[1], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdin), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + fp = stdin; + fname = "stdin"; + needclose ^= 1; + } + + /* Open a file for writing. */ + if(strcmp(argv[2], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&ofp, ofname = argv[2], "wb") != 0) { +#else + if((ofp = LFS_FOPEN(ofname = argv[2], "wb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdout), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + ofp = stdout; + ofname = "stdout"; + needclose ^= 2; + } + + /* Read the blocksize. */ + if(read_int(fp, &blocksize) != 4) { + fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Allocate 5blocksize bytes of memory. */ + T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t)); + A = (saidx_t *)malloc(blocksize * sizeof(saidx_t)); + if((T == NULL) || (A == NULL)) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + + fprintf(stderr, "UnBWT (blocksize %" PRIdSAINT_T ") ... ", blocksize); + start = clock(); + for(n = 0; (m = read_int(fp, &pidx)) != 0; n += m) { + /* Read blocksize bytes of data. */ + if((m != 4) || ((m = fread(T, sizeof(sauchar_t), blocksize, fp)) == 0)) { + fprintf(stderr, "%s: %s `%s': ", + argv[0], + (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", + fname); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Inverse Burrows-Wheeler Transform. */ + if((err = inverse_bw_transform(T, T, A, m, pidx)) != 0) { + fprintf(stderr, "%s (reverseBWT): %s.\n", + argv[0], + (err == -1) ? "Invalid data" : "Cannot allocate memory"); + exit(EXIT_FAILURE); + } + + /* Write m bytes of data. */ + if(fwrite(T, sizeof(sauchar_t), m, ofp) != m) { + fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + } + if(ferror(fp)) { + fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + finish = clock(); + fprintf(stderr, "%" PRIdOFF_T " bytes: %.4f sec\n", + n, (double)(finish - start) / (double)CLOCKS_PER_SEC); + + /* Close files */ + if(needclose & 1) { fclose(fp); } + if(needclose & 2) { fclose(ofp); } + + /* Deallocate memory. */ + free(A); + free(T); + + return 0; +} diff --git a/tools/apultra_src/src/libdivsufsort/include/CMakeLists.txt b/tools/apultra_src/src/libdivsufsort/include/CMakeLists.txt new file mode 100644 index 0000000..37781cc --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/include/CMakeLists.txt @@ -0,0 +1,162 @@ +include(CheckIncludeFiles) +include(CheckIncludeFile) +include(CheckSymbolExists) +include(CheckTypeSize) +include(CheckFunctionKeywords) +include(CheckLFS) + +## Checks for header files ## +check_include_file("inttypes.h" HAVE_INTTYPES_H) +check_include_file("memory.h" HAVE_MEMORY_H) +check_include_file("stddef.h" HAVE_STDDEF_H) +check_include_file("stdint.h" HAVE_STDINT_H) +check_include_file("stdlib.h" HAVE_STDLIB_H) +check_include_file("string.h" HAVE_STRING_H) +check_include_file("strings.h" HAVE_STRINGS_H) +check_include_file("sys/types.h" HAVE_SYS_TYPES_H) +if(HAVE_INTTYPES_H) + set(INCFILE "#include ") +elseif(HAVE_STDINT_H) + set(INCFILE "#include ") +else(HAVE_INTTYPES_H) + set(INCFILE "") +endif(HAVE_INTTYPES_H) + +## create configuration files from .cmake file ## +if(BUILD_EXAMPLES) + ## Checks for WinIO ## + if(WIN32) + check_include_file("io.h" HAVE_IO_H) + check_include_file("fcntl.h" HAVE_FCNTL_H) + check_symbol_exists("_setmode" "io.h;fcntl.h" HAVE__SETMODE) + if(NOT HAVE__SETMODE) + check_symbol_exists("setmode" "io.h;fcntl.h" HAVE_SETMODE) + endif(NOT HAVE__SETMODE) + check_symbol_exists("_fileno" "stdio.h" HAVE__FILENO) + check_symbol_exists("fopen_s" "stdio.h" HAVE_FOPEN_S) + check_symbol_exists("_O_BINARY" "fcntl.h" HAVE__O_BINARY) + endif(WIN32) + + ## Checks for large file support ## + check_lfs(WITH_LFS) + configure_file("${CMAKE_CURRENT_SOURCE_DIR}/lfs.h.cmake" "${CMAKE_CURRENT_BINARY_DIR}/lfs.h" @ONLY) +endif(BUILD_EXAMPLES) + +## generate config.h ## +check_function_keywords("inline;__inline;__inline__;__declspec(dllexport);__declspec(dllimport)") +if(HAVE_INLINE) + set(INLINE "inline") +elseif(HAVE___INLINE) + set(INLINE "__inline") +elseif(HAVE___INLINE__) + set(INLINE "__inline__") +else(HAVE_INLINE) + set(INLINE "") +endif(HAVE_INLINE) +configure_file("${CMAKE_CURRENT_SOURCE_DIR}/config.h.cmake" "${CMAKE_CURRENT_BINARY_DIR}/config.h") + +## Checks for types ## +# sauchar_t (8bit) +check_type_size("uint8_t" UINT8_T) +if(HAVE_UINT8_T) + set(SAUCHAR_TYPE "uint8_t") +else(HAVE_UINT8_T) + check_type_size("unsigned char" SIZEOF_UNSIGNED_CHAR) + if("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1") + set(SAUCHAR_TYPE "unsigned char") + else("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1") + message(FATAL_ERROR "Cannot find unsigned 8-bit integer type") + endif("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1") +endif(HAVE_UINT8_T) +# saint_t (32bit) +check_type_size("int32_t" INT32_T) +if(HAVE_INT32_T) + set(SAINT32_TYPE "int32_t") + check_symbol_exists("PRId32" "inttypes.h" HAVE_PRID32) + if(HAVE_PRID32) + set(SAINT32_PRId "PRId32") + else(HAVE_PRID32) + set(SAINT32_PRId "\"d\"") + endif(HAVE_PRID32) +else(HAVE_INT32_T) + check_type_size("int" SIZEOF_INT) + check_type_size("long" SIZEOF_LONG) + check_type_size("short" SIZEOF_SHORT) + check_type_size("__int32" SIZEOF___INT32) + if("${SIZEOF_INT}" STREQUAL "4") + set(SAINT32_TYPE "int") + set(SAINT32_PRId "\"d\"") + elseif("${SIZEOF_LONG}" STREQUAL "4") + set(SAINT32_TYPE "long") + set(SAINT32_PRId "\"ld\"") + elseif("${SIZEOF_SHORT}" STREQUAL "4") + set(SAINT32_TYPE "short") + set(SAINT32_PRId "\"d\"") + elseif("${SIZEOF___INT32}" STREQUAL "4") + set(SAINT32_TYPE "__int32") + set(SAINT32_PRId "\"d\"") + else("${SIZEOF_INT}" STREQUAL "4") + message(FATAL_ERROR "Cannot find 32-bit integer type") + endif("${SIZEOF_INT}" STREQUAL "4") +endif(HAVE_INT32_T) +# saint64_t (64bit) +if(BUILD_DIVSUFSORT64) + check_type_size("int64_t" INT64_T) + if(HAVE_INT64_T) + set(SAINT64_TYPE "int64_t") + check_symbol_exists("PRId64" "inttypes.h" HAVE_PRID64) + if(HAVE_PRID64) + set(SAINT64_PRId "PRId64") + else(HAVE_PRID64) + set(SAINT64_PRId "\"lld\"") + endif(HAVE_PRID64) + else(HAVE_INT64_T) + check_type_size("int" SIZEOF_INT) + check_type_size("long" SIZEOF_LONG) + check_type_size("long long" SIZEOF_LONG_LONG) + check_type_size("__int64" SIZEOF___INT64) + if("${SIZEOF_INT}" STREQUAL "8") + set(SAINT64_TYPE "int") + set(SAINT64_PRId "\"d\"") + elseif("${SIZEOF_LONG}" STREQUAL "8") + set(SAINT64_TYPE "long") + set(SAINT64_PRId "\"ld\"") + elseif("${SIZEOF_LONG_LONG}" STREQUAL "8") + set(SAINT64_TYPE "long long") + set(SAINT64_PRId "\"lld\"") + elseif("${SIZEOF___INT64}" STREQUAL "8") + set(SAINT64_TYPE "__int64") + set(SAINT64_PRId "\"I64d\"") + else("${SIZEOF_INT}" STREQUAL "8") + message(SEND_ERROR "Cannot find 64-bit integer type") + set(BUILD_DIVSUFSORT64 OFF) + endif("${SIZEOF_INT}" STREQUAL "8") + endif(HAVE_INT64_T) +endif(BUILD_DIVSUFSORT64) + +## generate divsufsort.h ## +set(DIVSUFSORT_IMPORT "") +set(DIVSUFSORT_EXPORT "") +if(BUILD_SHARED_LIBS) + if(HAVE___DECLSPEC_DLLIMPORT_) + set(DIVSUFSORT_IMPORT "__declspec(dllimport)") + endif(HAVE___DECLSPEC_DLLIMPORT_) + if(HAVE___DECLSPEC_DLLEXPORT_) + set(DIVSUFSORT_EXPORT "__declspec(dllexport)") + endif(HAVE___DECLSPEC_DLLEXPORT_) +endif(BUILD_SHARED_LIBS) +set(W64BIT "") +set(SAINDEX_TYPE "${SAINT32_TYPE}") +set(SAINDEX_PRId "${SAINT32_PRId}") +set(SAINT_PRId "${SAINT32_PRId}") +configure_file("${CMAKE_CURRENT_SOURCE_DIR}/divsufsort.h.cmake" + "${CMAKE_CURRENT_BINARY_DIR}/divsufsort.h" @ONLY) +install(FILES "${CMAKE_CURRENT_BINARY_DIR}/divsufsort.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) +if(BUILD_DIVSUFSORT64) + set(W64BIT "64") + set(SAINDEX_TYPE "${SAINT64_TYPE}") + set(SAINDEX_PRId "${SAINT64_PRId}") + configure_file("${CMAKE_CURRENT_SOURCE_DIR}/divsufsort.h.cmake" + "${CMAKE_CURRENT_BINARY_DIR}/divsufsort64.h" @ONLY) + install(FILES "${CMAKE_CURRENT_BINARY_DIR}/divsufsort64.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) +endif(BUILD_DIVSUFSORT64) diff --git a/tools/apultra_src/src/libdivsufsort/include/config.h.cmake b/tools/apultra_src/src/libdivsufsort/include/config.h.cmake new file mode 100644 index 0000000..6a1cf47 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/include/config.h.cmake @@ -0,0 +1,81 @@ +/* + * config.h for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#ifndef _CONFIG_H +#define _CONFIG_H 1 + +#ifdef __cplusplus +extern "C" { +#endif /* __cplusplus */ + +/** Define to the version of this package. **/ +#cmakedefine PROJECT_VERSION_FULL "${PROJECT_VERSION_FULL}" + +/** Define to 1 if you have the header files. **/ +#cmakedefine HAVE_INTTYPES_H 1 +#cmakedefine HAVE_STDDEF_H 1 +#cmakedefine HAVE_STDINT_H 1 +#cmakedefine HAVE_STDLIB_H 1 +#cmakedefine HAVE_STRING_H 1 +#cmakedefine HAVE_STRINGS_H 1 +#cmakedefine HAVE_MEMORY_H 1 +#cmakedefine HAVE_SYS_TYPES_H 1 + +/** for WinIO **/ +#cmakedefine HAVE_IO_H 1 +#cmakedefine HAVE_FCNTL_H 1 +#cmakedefine HAVE__SETMODE 1 +#cmakedefine HAVE_SETMODE 1 +#cmakedefine HAVE__FILENO 1 +#cmakedefine HAVE_FOPEN_S 1 +#cmakedefine HAVE__O_BINARY 1 +#ifndef HAVE__SETMODE +# if HAVE_SETMODE +# define _setmode setmode +# define HAVE__SETMODE 1 +# endif +# if HAVE__SETMODE && !HAVE__O_BINARY +# define _O_BINARY 0 +# define HAVE__O_BINARY 1 +# endif +#endif + +/** for inline **/ +#ifndef INLINE +# define INLINE @INLINE@ +#endif + +/** for VC++ warning **/ +#ifdef _MSC_VER +#pragma warning(disable: 4127) +#endif + + +#ifdef __cplusplus +} /* extern "C" */ +#endif /* __cplusplus */ + +#endif /* _CONFIG_H */ diff --git a/tools/apultra_src/src/libdivsufsort/include/divsufsort.h b/tools/apultra_src/src/libdivsufsort/include/divsufsort.h new file mode 100644 index 0000000..7ebb412 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/include/divsufsort.h @@ -0,0 +1,189 @@ +/* + * divsufsort.h for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#ifndef _DIVSUFSORT_H +#define _DIVSUFSORT_H 1 + +#ifdef __cplusplus +extern "C" { +#endif /* __cplusplus */ + +#define DIVSUFSORT_API + +/*- Datatypes -*/ +#ifndef SAUCHAR_T +#define SAUCHAR_T +typedef unsigned char sauchar_t; +#endif /* SAUCHAR_T */ +#ifndef SAINT_T +#define SAINT_T +typedef int saint_t; +#endif /* SAINT_T */ +#ifndef SAIDX_T +#define SAIDX_T +typedef int saidx_t; +#endif /* SAIDX_T */ +#ifndef PRIdSAIDX_T +#define PRIdSAIDX_T "d" +#endif + +/*- divsufsort context */ +typedef struct _divsufsort_ctx_t { + saidx_t *bucket_A; + saidx_t *bucket_B; +} divsufsort_ctx_t; + +/*- Prototypes -*/ + +/** + * Initialize suffix array context + * + * @return 0 for success, or non-zero in case of an error + */ +int divsufsort_init(divsufsort_ctx_t *ctx); + +/** + * Destroy suffix array context + * + * @param ctx suffix array context to destroy + */ +void divsufsort_destroy(divsufsort_ctx_t *ctx); + +/** + * Constructs the suffix array of a given string. + * @param ctx suffix array context + * @param T[0..n-1] The input string. + * @param SA[0..n-1] The output array of suffixes. + * @param n The length of the given string. + * @return 0 if no error occurred, -1 or -2 otherwise. + */ +DIVSUFSORT_API +saint_t divsufsort_build_array(divsufsort_ctx_t *ctx, const sauchar_t *T, saidx_t *SA, saidx_t n); + +#if 0 +/** + * Constructs the burrows-wheeler transformed string of a given string. + * @param T[0..n-1] The input string. + * @param U[0..n-1] The output string. (can be T) + * @param A[0..n-1] The temporary array. (can be NULL) + * @param n The length of the given string. + * @return The primary index if no error occurred, -1 or -2 otherwise. + */ +DIVSUFSORT_API +saidx_t +divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n); + +/** + * Returns the version of the divsufsort library. + * @return The version number string. + */ +DIVSUFSORT_API +const char * +divsufsort_version(void); + + +/** + * Constructs the burrows-wheeler transformed string of a given string and suffix array. + * @param T[0..n-1] The input string. + * @param U[0..n-1] The output string. (can be T) + * @param SA[0..n-1] The suffix array. (can be NULL) + * @param n The length of the given string. + * @param idx The output primary index. + * @return 0 if no error occurred, -1 or -2 otherwise. + */ +DIVSUFSORT_API +saint_t +bw_transform(const sauchar_t *T, sauchar_t *U, + saidx_t *SA /* can NULL */, + saidx_t n, saidx_t *idx); + +/** + * Inverse BW-transforms a given BWTed string. + * @param T[0..n-1] The input string. + * @param U[0..n-1] The output string. (can be T) + * @param A[0..n-1] The temporary array. (can be NULL) + * @param n The length of the given string. + * @param idx The primary index. + * @return 0 if no error occurred, -1 or -2 otherwise. + */ +DIVSUFSORT_API +saint_t +inverse_bw_transform(const sauchar_t *T, sauchar_t *U, + saidx_t *A /* can NULL */, + saidx_t n, saidx_t idx); + +/** + * Checks the correctness of a given suffix array. + * @param T[0..n-1] The input string. + * @param SA[0..n-1] The input suffix array. + * @param n The length of the given string. + * @param verbose The verbose mode. + * @return 0 if no error occurred. + */ +DIVSUFSORT_API +saint_t +sufcheck(const sauchar_t *T, const saidx_t *SA, saidx_t n, saint_t verbose); + +/** + * Search for the pattern P in the string T. + * @param T[0..Tsize-1] The input string. + * @param Tsize The length of the given string. + * @param P[0..Psize-1] The input pattern string. + * @param Psize The length of the given pattern string. + * @param SA[0..SAsize-1] The input suffix array. + * @param SAsize The length of the given suffix array. + * @param idx The output index. + * @return The count of matches if no error occurred, -1 otherwise. + */ +DIVSUFSORT_API +saidx_t +sa_search(const sauchar_t *T, saidx_t Tsize, + const sauchar_t *P, saidx_t Psize, + const saidx_t *SA, saidx_t SAsize, + saidx_t *left); + +/** + * Search for the character c in the string T. + * @param T[0..Tsize-1] The input string. + * @param Tsize The length of the given string. + * @param SA[0..SAsize-1] The input suffix array. + * @param SAsize The length of the given suffix array. + * @param c The input character. + * @param idx The output index. + * @return The count of matches if no error occurred, -1 otherwise. + */ +DIVSUFSORT_API +saidx_t +sa_simplesearch(const sauchar_t *T, saidx_t Tsize, + const saidx_t *SA, saidx_t SAsize, + saint_t c, saidx_t *left); +#endif + +#ifdef __cplusplus +} /* extern "C" */ +#endif /* __cplusplus */ + +#endif /* _DIVSUFSORT_H */ diff --git a/tools/apultra_src/src/libdivsufsort/include/divsufsort.h.cmake b/tools/apultra_src/src/libdivsufsort/include/divsufsort.h.cmake new file mode 100644 index 0000000..bcaba7c --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/include/divsufsort.h.cmake @@ -0,0 +1,180 @@ +/* + * divsufsort@W64BIT@.h for libdivsufsort@W64BIT@ + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#ifndef _DIVSUFSORT@W64BIT@_H +#define _DIVSUFSORT@W64BIT@_H 1 + +#ifdef __cplusplus +extern "C" { +#endif /* __cplusplus */ + +@INCFILE@ + +#ifndef DIVSUFSORT_API +# ifdef DIVSUFSORT_BUILD_DLL +# define DIVSUFSORT_API @DIVSUFSORT_EXPORT@ +# else +# define DIVSUFSORT_API @DIVSUFSORT_IMPORT@ +# endif +#endif + +/*- Datatypes -*/ +#ifndef SAUCHAR_T +#define SAUCHAR_T +typedef @SAUCHAR_TYPE@ sauchar_t; +#endif /* SAUCHAR_T */ +#ifndef SAINT_T +#define SAINT_T +typedef @SAINT32_TYPE@ saint_t; +#endif /* SAINT_T */ +#ifndef SAIDX@W64BIT@_T +#define SAIDX@W64BIT@_T +typedef @SAINDEX_TYPE@ saidx@W64BIT@_t; +#endif /* SAIDX@W64BIT@_T */ +#ifndef PRIdSAINT_T +#define PRIdSAINT_T @SAINT_PRId@ +#endif /* PRIdSAINT_T */ +#ifndef PRIdSAIDX@W64BIT@_T +#define PRIdSAIDX@W64BIT@_T @SAINDEX_PRId@ +#endif /* PRIdSAIDX@W64BIT@_T */ + + +/*- Prototypes -*/ + +/** + * Constructs the suffix array of a given string. + * @param T[0..n-1] The input string. + * @param SA[0..n-1] The output array of suffixes. + * @param n The length of the given string. + * @return 0 if no error occurred, -1 or -2 otherwise. + */ +DIVSUFSORT_API +saint_t +divsufsort@W64BIT@(const sauchar_t *T, saidx@W64BIT@_t *SA, saidx@W64BIT@_t n); + +/** + * Constructs the burrows-wheeler transformed string of a given string. + * @param T[0..n-1] The input string. + * @param U[0..n-1] The output string. (can be T) + * @param A[0..n-1] The temporary array. (can be NULL) + * @param n The length of the given string. + * @return The primary index if no error occurred, -1 or -2 otherwise. + */ +DIVSUFSORT_API +saidx@W64BIT@_t +divbwt@W64BIT@(const sauchar_t *T, sauchar_t *U, saidx@W64BIT@_t *A, saidx@W64BIT@_t n); + +/** + * Returns the version of the divsufsort library. + * @return The version number string. + */ +DIVSUFSORT_API +const char * +divsufsort@W64BIT@_version(void); + + +/** + * Constructs the burrows-wheeler transformed string of a given string and suffix array. + * @param T[0..n-1] The input string. + * @param U[0..n-1] The output string. (can be T) + * @param SA[0..n-1] The suffix array. (can be NULL) + * @param n The length of the given string. + * @param idx The output primary index. + * @return 0 if no error occurred, -1 or -2 otherwise. + */ +DIVSUFSORT_API +saint_t +bw_transform@W64BIT@(const sauchar_t *T, sauchar_t *U, + saidx@W64BIT@_t *SA /* can NULL */, + saidx@W64BIT@_t n, saidx@W64BIT@_t *idx); + +/** + * Inverse BW-transforms a given BWTed string. + * @param T[0..n-1] The input string. + * @param U[0..n-1] The output string. (can be T) + * @param A[0..n-1] The temporary array. (can be NULL) + * @param n The length of the given string. + * @param idx The primary index. + * @return 0 if no error occurred, -1 or -2 otherwise. + */ +DIVSUFSORT_API +saint_t +inverse_bw_transform@W64BIT@(const sauchar_t *T, sauchar_t *U, + saidx@W64BIT@_t *A /* can NULL */, + saidx@W64BIT@_t n, saidx@W64BIT@_t idx); + +/** + * Checks the correctness of a given suffix array. + * @param T[0..n-1] The input string. + * @param SA[0..n-1] The input suffix array. + * @param n The length of the given string. + * @param verbose The verbose mode. + * @return 0 if no error occurred. + */ +DIVSUFSORT_API +saint_t +sufcheck@W64BIT@(const sauchar_t *T, const saidx@W64BIT@_t *SA, saidx@W64BIT@_t n, saint_t verbose); + +/** + * Search for the pattern P in the string T. + * @param T[0..Tsize-1] The input string. + * @param Tsize The length of the given string. + * @param P[0..Psize-1] The input pattern string. + * @param Psize The length of the given pattern string. + * @param SA[0..SAsize-1] The input suffix array. + * @param SAsize The length of the given suffix array. + * @param idx The output index. + * @return The count of matches if no error occurred, -1 otherwise. + */ +DIVSUFSORT_API +saidx@W64BIT@_t +sa_search@W64BIT@(const sauchar_t *T, saidx@W64BIT@_t Tsize, + const sauchar_t *P, saidx@W64BIT@_t Psize, + const saidx@W64BIT@_t *SA, saidx@W64BIT@_t SAsize, + saidx@W64BIT@_t *left); + +/** + * Search for the character c in the string T. + * @param T[0..Tsize-1] The input string. + * @param Tsize The length of the given string. + * @param SA[0..SAsize-1] The input suffix array. + * @param SAsize The length of the given suffix array. + * @param c The input character. + * @param idx The output index. + * @return The count of matches if no error occurred, -1 otherwise. + */ +DIVSUFSORT_API +saidx@W64BIT@_t +sa_simplesearch@W64BIT@(const sauchar_t *T, saidx@W64BIT@_t Tsize, + const saidx@W64BIT@_t *SA, saidx@W64BIT@_t SAsize, + saint_t c, saidx@W64BIT@_t *left); + + +#ifdef __cplusplus +} /* extern "C" */ +#endif /* __cplusplus */ + +#endif /* _DIVSUFSORT@W64BIT@_H */ diff --git a/tools/apultra_src/src/libdivsufsort/include/divsufsort_config.h b/tools/apultra_src/src/libdivsufsort/include/divsufsort_config.h new file mode 100644 index 0000000..4054a8a --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/include/divsufsort_config.h @@ -0,0 +1,9 @@ +#define HAVE_STRING_H 1 +#define HAVE_STDLIB_H 1 +#define HAVE_MEMORY_H 1 +#define HAVE_STDINT_H 1 +#define INLINE inline + +#ifdef _MSC_VER +#pragma warning( disable : 4244 ) +#endif /* _MSC_VER */ diff --git a/tools/apultra_src/src/libdivsufsort/include/divsufsort_private.h b/tools/apultra_src/src/libdivsufsort/include/divsufsort_private.h new file mode 100644 index 0000000..b4d97ad --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/include/divsufsort_private.h @@ -0,0 +1,205 @@ +/* + * divsufsort_private.h for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#ifndef _DIVSUFSORT_PRIVATE_H +#define _DIVSUFSORT_PRIVATE_H 1 + +#ifdef __cplusplus +extern "C" { +#endif /* __cplusplus */ + +#include "divsufsort_config.h" +#include +#include +#if HAVE_STRING_H +# include +#endif +#if HAVE_STDLIB_H +# include +#endif +#if HAVE_MEMORY_H +# include +#endif +#if HAVE_STDDEF_H +# include +#endif +#if HAVE_STRINGS_H +# include +#endif +#if HAVE_INTTYPES_H +# include +#else +# if HAVE_STDINT_H +# include +# endif +#endif +#if defined(BUILD_DIVSUFSORT64) +# include "divsufsort64.h" +# ifndef SAIDX_T +# define SAIDX_T +# define saidx_t saidx64_t +# endif /* SAIDX_T */ +# ifndef PRIdSAIDX_T +# define PRIdSAIDX_T PRIdSAIDX64_T +# endif /* PRIdSAIDX_T */ +# define divsufsort divsufsort64 +# define divbwt divbwt64 +# define divsufsort_version divsufsort64_version +# define bw_transform bw_transform64 +# define inverse_bw_transform inverse_bw_transform64 +# define sufcheck sufcheck64 +# define sa_search sa_search64 +# define sa_simplesearch sa_simplesearch64 +# define sssort sssort64 +# define trsort trsort64 +#else +# include "divsufsort.h" +#endif + + +/*- Constants -*/ +#if !defined(UINT8_MAX) +# define UINT8_MAX (255) +#endif /* UINT8_MAX */ +#if defined(ALPHABET_SIZE) && (ALPHABET_SIZE < 1) +# undef ALPHABET_SIZE +#endif +#if !defined(ALPHABET_SIZE) +# define ALPHABET_SIZE (UINT8_MAX + 1) +#endif +/* for divsufsort.c */ +#define BUCKET_A_SIZE (ALPHABET_SIZE) +#define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE) +/* for sssort.c */ +#if defined(SS_INSERTIONSORT_THRESHOLD) +# if SS_INSERTIONSORT_THRESHOLD < 1 +# undef SS_INSERTIONSORT_THRESHOLD +# define SS_INSERTIONSORT_THRESHOLD (1) +# endif +#else +# define SS_INSERTIONSORT_THRESHOLD (8) +#endif +#if defined(SS_BLOCKSIZE) +# if SS_BLOCKSIZE < 0 +# undef SS_BLOCKSIZE +# define SS_BLOCKSIZE (0) +# elif 32768 <= SS_BLOCKSIZE +# undef SS_BLOCKSIZE +# define SS_BLOCKSIZE (32767) +# endif +#else +# define SS_BLOCKSIZE (1024) +#endif +/* minstacksize = log(SS_BLOCKSIZE) / log(3) * 2 */ +#if SS_BLOCKSIZE == 0 +# if defined(BUILD_DIVSUFSORT64) +# define SS_MISORT_STACKSIZE (96) +# else +# define SS_MISORT_STACKSIZE (64) +# endif +#elif SS_BLOCKSIZE <= 4096 +# define SS_MISORT_STACKSIZE (16) +#else +# define SS_MISORT_STACKSIZE (24) +#endif +#if defined(BUILD_DIVSUFSORT64) +# define SS_SMERGE_STACKSIZE (64) +#else +# define SS_SMERGE_STACKSIZE (32) +#endif +/* for trsort.c */ +#define TR_INSERTIONSORT_THRESHOLD (8) +#if defined(BUILD_DIVSUFSORT64) +# define TR_STACKSIZE (96) +#else +# define TR_STACKSIZE (64) +#endif + + +/*- Macros -*/ +#ifndef SWAP +# define SWAP(_a, _b) do { t = (_a); (_a) = (_b); (_b) = t; } while(0) +#endif /* SWAP */ +#ifndef MIN +# define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b)) +#endif /* MIN */ +#ifndef MAX +# define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b)) +#endif /* MAX */ +#define STACK_PUSH(_a, _b, _c, _d)\ + do {\ + assert(ssize < STACK_SIZE);\ + stack[ssize].a = (_a), stack[ssize].b = (_b),\ + stack[ssize].c = (_c), stack[ssize++].d = (_d);\ + } while(0) +#define STACK_PUSH5(_a, _b, _c, _d, _e)\ + do {\ + assert(ssize < STACK_SIZE);\ + stack[ssize].a = (_a), stack[ssize].b = (_b),\ + stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\ + } while(0) +#define STACK_POP(_a, _b, _c, _d)\ + do {\ + assert(0 <= ssize);\ + if(ssize == 0) { return; }\ + (_a) = stack[--ssize].a, (_b) = stack[ssize].b,\ + (_c) = stack[ssize].c, (_d) = stack[ssize].d;\ + } while(0) +#define STACK_POP5(_a, _b, _c, _d, _e)\ + do {\ + assert(0 <= ssize);\ + if(ssize == 0) { return; }\ + (_a) = stack[--ssize].a, (_b) = stack[ssize].b,\ + (_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\ + } while(0) +/* for divsufsort.c */ +#define BUCKET_A(_c0) bucket_A[(_c0)] +#if ALPHABET_SIZE == 256 +#define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)]) +#define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)]) +#else +#define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)]) +#define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)]) +#endif + + +/*- Private Prototypes -*/ +/* sssort.c */ +void +sssort(const sauchar_t *Td, const saidx_t *PA, + saidx_t *first, saidx_t *last, + saidx_t *buf, saidx_t bufsize, + saidx_t depth, saidx_t n, saint_t lastsuffix); +/* trsort.c */ +void +trsort(saidx_t *ISA, saidx_t *SA, saidx_t n, saidx_t depth); + + +#ifdef __cplusplus +} /* extern "C" */ +#endif /* __cplusplus */ + +#endif /* _DIVSUFSORT_PRIVATE_H */ diff --git a/tools/apultra_src/src/libdivsufsort/include/lfs.h.cmake b/tools/apultra_src/src/libdivsufsort/include/lfs.h.cmake new file mode 100644 index 0000000..d5b84a8 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/include/lfs.h.cmake @@ -0,0 +1,56 @@ +/* + * lfs.h for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#ifndef _LFS_H +#define _LFS_H 1 + +#ifdef __cplusplus +extern "C" { +#endif /* __cplusplus */ + +#ifndef __STRICT_ANSI__ +# define LFS_OFF_T @LFS_OFF_T@ +# define LFS_FOPEN @LFS_FOPEN@ +# define LFS_FTELL @LFS_FTELL@ +# define LFS_FSEEK @LFS_FSEEK@ +# define LFS_PRId @LFS_PRID@ +#else +# define LFS_OFF_T long +# define LFS_FOPEN fopen +# define LFS_FTELL ftell +# define LFS_FSEEK fseek +# define LFS_PRId "ld" +#endif +#ifndef PRIdOFF_T +# define PRIdOFF_T LFS_PRId +#endif + + +#ifdef __cplusplus +} /* extern "C" */ +#endif /* __cplusplus */ + +#endif /* _LFS_H */ diff --git a/tools/apultra_src/src/libdivsufsort/lib/CMakeLists.txt b/tools/apultra_src/src/libdivsufsort/lib/CMakeLists.txt new file mode 100644 index 0000000..abc90e6 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/lib/CMakeLists.txt @@ -0,0 +1,31 @@ +include_directories("${CMAKE_CURRENT_SOURCE_DIR}/../include" + "${CMAKE_CURRENT_BINARY_DIR}/../include") + +set(divsufsort_SRCS divsufsort.c sssort.c trsort.c utils.c) + +## libdivsufsort ## +add_library(divsufsort ${divsufsort_SRCS}) +install(TARGETS divsufsort + RUNTIME DESTINATION ${CMAKE_INSTALL_RUNTIMEDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) +set_target_properties(divsufsort PROPERTIES + VERSION "${LIBRARY_VERSION}" + SOVERSION "${LIBRARY_SOVERSION}" + DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL + RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples") + +## libdivsufsort64 ## +if(BUILD_DIVSUFSORT64) + add_library(divsufsort64 ${divsufsort_SRCS}) + install(TARGETS divsufsort64 + RUNTIME DESTINATION ${CMAKE_INSTALL_RUNTIMEDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) + set_target_properties(divsufsort64 PROPERTIES + VERSION "${LIBRARY_VERSION}" + SOVERSION "${LIBRARY_SOVERSION}" + DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL + COMPILE_FLAGS "-DBUILD_DIVSUFSORT64" + RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples") +endif(BUILD_DIVSUFSORT64) diff --git a/tools/apultra_src/src/libdivsufsort/lib/divsufsort.c b/tools/apultra_src/src/libdivsufsort/lib/divsufsort.c new file mode 100644 index 0000000..50631ac --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/lib/divsufsort.c @@ -0,0 +1,431 @@ +/* + * divsufsort.c for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#include "divsufsort_private.h" +#ifdef _OPENMP +# include +#endif + + +/*- Private Functions -*/ + +/* Sorts suffixes of type B*. */ +static +saidx_t +sort_typeBstar(const sauchar_t *T, saidx_t *SA, + saidx_t *bucket_A, saidx_t *bucket_B, + saidx_t n) { + saidx_t *PAb, *ISAb, *buf; +#ifdef _OPENMP + saidx_t *curbuf; + saidx_t l; +#endif + saidx_t i, j, k, t, m, bufsize; + saint_t c0, c1; +#ifdef _OPENMP + saint_t d0, d1; + int tmp; +#endif + + /* Initialize bucket arrays. */ + for(i = 0; i < BUCKET_A_SIZE; ++i) { bucket_A[i] = 0; } + for(i = 0; i < BUCKET_B_SIZE; ++i) { bucket_B[i] = 0; } + + /* Count the number of occurrences of the first one or two characters of each + type A, B and B* suffix. Moreover, store the beginning position of all + type B* suffixes into the array SA. */ + for(i = n - 1, m = n, c0 = T[n - 1]; 0 <= i;) { + /* type A suffix. */ + do { ++BUCKET_A(c1 = c0); } while((0 <= --i) && ((c0 = T[i]) >= c1)); + if(0 <= i) { + /* type B* suffix. */ + ++BUCKET_BSTAR(c0, c1); + SA[--m] = i; + /* type B suffix. */ + for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { + ++BUCKET_B(c0, c1); + } + } + } + m = n - m; +/* +note: + A type B* suffix is lexicographically smaller than a type B suffix that + begins with the same first two characters. +*/ + + /* Calculate the index of start/end point of each bucket. */ + for(c0 = 0, i = 0, j = 0; c0 < ALPHABET_SIZE; ++c0) { + t = i + BUCKET_A(c0); + BUCKET_A(c0) = i + j; /* start point */ + i = t + BUCKET_B(c0, c0); + for(c1 = c0 + 1; c1 < ALPHABET_SIZE; ++c1) { + j += BUCKET_BSTAR(c0, c1); + BUCKET_BSTAR(c0, c1) = j; /* end point */ + i += BUCKET_B(c0, c1); + } + } + + if(0 < m) { + /* Sort the type B* suffixes by their first two characters. */ + PAb = SA + n - m; ISAb = SA + m; + for(i = m - 2; 0 <= i; --i) { + t = PAb[i], c0 = T[t], c1 = T[t + 1]; + SA[--BUCKET_BSTAR(c0, c1)] = i; + } + t = PAb[m - 1], c0 = T[t], c1 = T[t + 1]; + SA[--BUCKET_BSTAR(c0, c1)] = m - 1; + + /* Sort the type B* substrings using sssort. */ +#ifdef _OPENMP + tmp = omp_get_max_threads(); + buf = SA + m, bufsize = (n - (2 * m)) / tmp; + c0 = ALPHABET_SIZE - 2, c1 = ALPHABET_SIZE - 1, j = m; +#pragma omp parallel default(shared) private(curbuf, k, l, d0, d1, tmp) + { + tmp = omp_get_thread_num(); + curbuf = buf + tmp * bufsize; + k = 0; + for(;;) { + #pragma omp critical(sssort_lock) + { + if(0 < (l = j)) { + d0 = c0, d1 = c1; + do { + k = BUCKET_BSTAR(d0, d1); + if(--d1 <= d0) { + d1 = ALPHABET_SIZE - 1; + if(--d0 < 0) { break; } + } + } while(((l - k) <= 1) && (0 < (l = k))); + c0 = d0, c1 = d1, j = k; + } + } + if(l == 0) { break; } + sssort(T, PAb, SA + k, SA + l, + curbuf, bufsize, 2, n, *(SA + k) == (m - 1)); + } + } +#else + buf = SA + m, bufsize = n - (2 * m); + for(c0 = ALPHABET_SIZE - 2, j = m; 0 < j; --c0) { + for(c1 = ALPHABET_SIZE - 1; c0 < c1; j = i, --c1) { + i = BUCKET_BSTAR(c0, c1); + if(1 < (j - i)) { + sssort(T, PAb, SA + i, SA + j, + buf, bufsize, 2, n, *(SA + i) == (m - 1)); + } + } + } +#endif + + /* Compute ranks of type B* substrings. */ + for(i = m - 1; 0 <= i; --i) { + if(0 <= SA[i]) { + j = i; + do { ISAb[SA[i]] = i; } while((0 <= --i) && (0 <= SA[i])); + SA[i + 1] = i - j; + if(i <= 0) { break; } + } + j = i; + do { ISAb[SA[i] = ~SA[i]] = j; } while(SA[--i] < 0); + ISAb[SA[i]] = j; + } + + /* Construct the inverse suffix array of type B* suffixes using trsort. */ + trsort(ISAb, SA, m, 1); + + /* Set the sorted order of tyoe B* suffixes. */ + for(i = n - 1, j = m, c0 = T[n - 1]; 0 <= i;) { + for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) >= c1); --i, c1 = c0) { } + if(0 <= i) { + t = i; + for(--i, c1 = c0; (0 <= i) && ((c0 = T[i]) <= c1); --i, c1 = c0) { } + SA[ISAb[--j]] = ((t == 0) || (1 < (t - i))) ? t : ~t; + } + } + + /* Calculate the index of start/end point of each bucket. */ + BUCKET_B(ALPHABET_SIZE - 1, ALPHABET_SIZE - 1) = n; /* end point */ + for(c0 = ALPHABET_SIZE - 2, k = m - 1; 0 <= c0; --c0) { + i = BUCKET_A(c0 + 1) - 1; + for(c1 = ALPHABET_SIZE - 1; c0 < c1; --c1) { + t = i - BUCKET_B(c0, c1); + BUCKET_B(c0, c1) = i; /* end point */ + + /* Move all type B* suffixes to the correct position. */ + for(i = t, j = BUCKET_BSTAR(c0, c1); + j <= k; + --i, --k) { SA[i] = SA[k]; } + } + BUCKET_BSTAR(c0, c0 + 1) = i - BUCKET_B(c0, c0) + 1; /* start point */ + BUCKET_B(c0, c0) = i; /* end point */ + } + } + + return m; +} + +/* Constructs the suffix array by using the sorted order of type B* suffixes. */ +static +void +construct_SA(const sauchar_t *T, saidx_t *SA, + saidx_t *bucket_A, saidx_t *bucket_B, + saidx_t n, saidx_t m) { + saidx_t *i, *j, *k; + saidx_t s; + saint_t c0, c1, c2; + + if(0 < m) { + /* Construct the sorted order of type B suffixes by using + the sorted order of type B* suffixes. */ + for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) { + /* Scan the suffix array from right to left. */ + for(i = SA + BUCKET_BSTAR(c1, c1 + 1), + j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1; + i <= j; + --j) { + if(0 < (s = *j)) { + assert(T[s] == c1); + assert(((s + 1) < n) && (T[s] <= T[s + 1])); + assert(T[s - 1] <= T[s]); + *j = ~s; + c0 = T[--s]; + if((0 < s) && (T[s - 1] > c0)) { s = ~s; } + if(c0 != c2) { + if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; } + k = SA + BUCKET_B(c2 = c0, c1); + } + assert(k < j); + *k-- = s; + } else { + assert(((s == 0) && (T[s] == c1)) || (s < 0)); + *j = ~s; + } + } + } + } + + /* Construct the suffix array by using + the sorted order of type B suffixes. */ + k = SA + BUCKET_A(c2 = T[n - 1]); + *k++ = (T[n - 2] < c2) ? ~(n - 1) : (n - 1); + /* Scan the suffix array from left to right. */ + for(i = SA, j = SA + n; i < j; ++i) { + if(0 < (s = *i)) { + assert(T[s - 1] >= T[s]); + c0 = T[--s]; + if((s == 0) || (T[s - 1] < c0)) { s = ~s; } + if(c0 != c2) { + BUCKET_A(c2) = k - SA; + k = SA + BUCKET_A(c2 = c0); + } + assert(i < k); + *k++ = s; + } else { + assert(s < 0); + *i = ~s; + } + } +} + +#if 0 +/* Constructs the burrows-wheeler transformed string directly + by using the sorted order of type B* suffixes. */ +static +saidx_t +construct_BWT(const sauchar_t *T, saidx_t *SA, + saidx_t *bucket_A, saidx_t *bucket_B, + saidx_t n, saidx_t m) { + saidx_t *i, *j, *k, *orig; + saidx_t s; + saint_t c0, c1, c2; + + if(0 < m) { + /* Construct the sorted order of type B suffixes by using + the sorted order of type B* suffixes. */ + for(c1 = ALPHABET_SIZE - 2; 0 <= c1; --c1) { + /* Scan the suffix array from right to left. */ + for(i = SA + BUCKET_BSTAR(c1, c1 + 1), + j = SA + BUCKET_A(c1 + 1) - 1, k = NULL, c2 = -1; + i <= j; + --j) { + if(0 < (s = *j)) { + assert(T[s] == c1); + assert(((s + 1) < n) && (T[s] <= T[s + 1])); + assert(T[s - 1] <= T[s]); + c0 = T[--s]; + *j = ~((saidx_t)c0); + if((0 < s) && (T[s - 1] > c0)) { s = ~s; } + if(c0 != c2) { + if(0 <= c2) { BUCKET_B(c2, c1) = k - SA; } + k = SA + BUCKET_B(c2 = c0, c1); + } + assert(k < j); + *k-- = s; + } else if(s != 0) { + *j = ~s; +#ifndef NDEBUG + } else { + assert(T[s] == c1); +#endif + } + } + } + } + + /* Construct the BWTed string by using + the sorted order of type B suffixes. */ + k = SA + BUCKET_A(c2 = T[n - 1]); + *k++ = (T[n - 2] < c2) ? ~((saidx_t)T[n - 2]) : (n - 1); + /* Scan the suffix array from left to right. */ + for(i = SA, j = SA + n, orig = SA; i < j; ++i) { + if(0 < (s = *i)) { + assert(T[s - 1] >= T[s]); + c0 = T[--s]; + *i = c0; + if((0 < s) && (T[s - 1] < c0)) { s = ~((saidx_t)T[s - 1]); } + if(c0 != c2) { + BUCKET_A(c2) = k - SA; + k = SA + BUCKET_A(c2 = c0); + } + assert(i < k); + *k++ = s; + } else if(s != 0) { + *i = ~s; + } else { + orig = i; + } + } + + return orig - SA; +} +#endif + +/*---------------------------------------------------------------------------*/ + +/** + * Initialize suffix array context + * + * @return 0 for success, or non-zero in case of an error + */ +int divsufsort_init(divsufsort_ctx_t *ctx) { + ctx->bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t)); + ctx->bucket_B = NULL; + + if (ctx->bucket_A) { + ctx->bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t)); + + if (ctx->bucket_B) + return 0; + } + + divsufsort_destroy(ctx); + return -1; +} + +/** + * Destroy suffix array context + * + * @param ctx suffix array context to destroy + */ +void divsufsort_destroy(divsufsort_ctx_t *ctx) { + if (ctx->bucket_B) { + free(ctx->bucket_B); + ctx->bucket_B = NULL; + } + + if (ctx->bucket_A) { + free(ctx->bucket_A); + ctx->bucket_A = NULL; + } +} + +/*- Function -*/ + +saint_t +divsufsort_build_array(divsufsort_ctx_t *ctx, const sauchar_t *T, saidx_t *SA, saidx_t n) { + saidx_t m; + saint_t err = 0; + + /* Check arguments. */ + if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; } + else if(n == 0) { return 0; } + else if(n == 1) { SA[0] = 0; return 0; } + else if(n == 2) { m = (T[0] < T[1]); SA[m ^ 1] = 0, SA[m] = 1; return 0; } + + /* Suffixsort. */ + if((ctx->bucket_A != NULL) && (ctx->bucket_B != NULL)) { + m = sort_typeBstar(T, SA, ctx->bucket_A, ctx->bucket_B, n); + construct_SA(T, SA, ctx->bucket_A, ctx->bucket_B, n, m); + } else { + err = -2; + } + + return err; +} + +#if 0 +saidx_t +divbwt(const sauchar_t *T, sauchar_t *U, saidx_t *A, saidx_t n) { + saidx_t *B; + saidx_t *bucket_A, *bucket_B; + saidx_t m, pidx, i; + + /* Check arguments. */ + if((T == NULL) || (U == NULL) || (n < 0)) { return -1; } + else if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; } + + if((B = A) == NULL) { B = (saidx_t *)malloc((size_t)(n + 1) * sizeof(saidx_t)); } + bucket_A = (saidx_t *)malloc(BUCKET_A_SIZE * sizeof(saidx_t)); + bucket_B = (saidx_t *)malloc(BUCKET_B_SIZE * sizeof(saidx_t)); + + /* Burrows-Wheeler Transform. */ + if((B != NULL) && (bucket_A != NULL) && (bucket_B != NULL)) { + m = sort_typeBstar(T, B, bucket_A, bucket_B, n); + pidx = construct_BWT(T, B, bucket_A, bucket_B, n, m); + + /* Copy to output string. */ + U[0] = T[n - 1]; + for(i = 0; i < pidx; ++i) { U[i + 1] = (sauchar_t)B[i]; } + for(i += 1; i < n; ++i) { U[i] = (sauchar_t)B[i]; } + pidx += 1; + } else { + pidx = -2; + } + + free(bucket_B); + free(bucket_A); + if(A == NULL) { free(B); } + + return pidx; +} + +const char * +divsufsort_version(void) { + return PROJECT_VERSION_FULL; +} +#endif diff --git a/tools/apultra_src/src/libdivsufsort/lib/divsufsort_utils.c b/tools/apultra_src/src/libdivsufsort/lib/divsufsort_utils.c new file mode 100644 index 0000000..f7cbc0d --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/lib/divsufsort_utils.c @@ -0,0 +1,383 @@ +/* + * utils.c for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#include "divsufsort_private.h" + + +/*- Private Function -*/ + +#if 0 +/* Binary search for inverse bwt. */ +static +saidx_t +binarysearch_lower(const saidx_t *A, saidx_t size, saidx_t value) { + saidx_t half, i; + for(i = 0, half = size >> 1; + 0 < size; + size = half, half >>= 1) { + if(A[i + half] < value) { + i += half + 1; + half -= (size & 1) ^ 1; + } + } + return i; +} + + +/*- Functions -*/ + +/* Burrows-Wheeler transform. */ +saint_t +bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *SA, + saidx_t n, saidx_t *idx) { + saidx_t *A, i, j, p, t; + saint_t c; + + /* Check arguments. */ + if((T == NULL) || (U == NULL) || (n < 0) || (idx == NULL)) { return -1; } + if(n <= 1) { + if(n == 1) { U[0] = T[0]; } + *idx = n; + return 0; + } + + if((A = SA) == NULL) { + i = divbwt(T, U, NULL, n); + if(0 <= i) { *idx = i; i = 0; } + return (saint_t)i; + } + + /* BW transform. */ + if(T == U) { + t = n; + for(i = 0, j = 0; i < n; ++i) { + p = t - 1; + t = A[i]; + if(0 <= p) { + c = T[j]; + U[j] = (j <= p) ? T[p] : (sauchar_t)A[p]; + A[j] = c; + j++; + } else { + *idx = i; + } + } + p = t - 1; + if(0 <= p) { + c = T[j]; + U[j] = (j <= p) ? T[p] : (sauchar_t)A[p]; + A[j] = c; + } else { + *idx = i; + } + } else { + U[0] = T[n - 1]; + for(i = 0; A[i] != 0; ++i) { U[i + 1] = T[A[i] - 1]; } + *idx = i + 1; + for(++i; i < n; ++i) { U[i] = T[A[i] - 1]; } + } + + if(SA == NULL) { + /* Deallocate memory. */ + free(A); + } + + return 0; +} + +/* Inverse Burrows-Wheeler transform. */ +saint_t +inverse_bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *A, + saidx_t n, saidx_t idx) { + saidx_t C[ALPHABET_SIZE]; + sauchar_t D[ALPHABET_SIZE]; + saidx_t *B; + saidx_t i, p; + saint_t c, d; + + /* Check arguments. */ + if((T == NULL) || (U == NULL) || (n < 0) || (idx < 0) || + (n < idx) || ((0 < n) && (idx == 0))) { + return -1; + } + if(n <= 1) { return 0; } + + if((B = A) == NULL) { + /* Allocate n*sizeof(saidx_t) bytes of memory. */ + if((B = (saidx_t *)malloc((size_t)n * sizeof(saidx_t))) == NULL) { return -2; } + } + + /* Inverse BW transform. */ + for(c = 0; c < ALPHABET_SIZE; ++c) { C[c] = 0; } + for(i = 0; i < n; ++i) { ++C[T[i]]; } + for(c = 0, d = 0, i = 0; c < ALPHABET_SIZE; ++c) { + p = C[c]; + if(0 < p) { + C[c] = i; + D[d++] = (sauchar_t)c; + i += p; + } + } + for(i = 0; i < idx; ++i) { B[C[T[i]]++] = i; } + for( ; i < n; ++i) { B[C[T[i]]++] = i + 1; } + for(c = 0; c < d; ++c) { C[c] = C[D[c]]; } + for(i = 0, p = idx; i < n; ++i) { + U[i] = D[binarysearch_lower(C, d, p)]; + p = B[p - 1]; + } + + if(A == NULL) { + /* Deallocate memory. */ + free(B); + } + + return 0; +} + +/* Checks the suffix array SA of the string T. */ +saint_t +sufcheck(const sauchar_t *T, const saidx_t *SA, + saidx_t n, saint_t verbose) { + saidx_t C[ALPHABET_SIZE]; + saidx_t i, p, q, t; + saint_t c; + + if(verbose) { fprintf(stderr, "sufcheck: "); } + + /* Check arguments. */ + if((T == NULL) || (SA == NULL) || (n < 0)) { + if(verbose) { fprintf(stderr, "Invalid arguments.\n"); } + return -1; + } + if(n == 0) { + if(verbose) { fprintf(stderr, "Done.\n"); } + return 0; + } + + /* check range: [0..n-1] */ + for(i = 0; i < n; ++i) { + if((SA[i] < 0) || (n <= SA[i])) { + if(verbose) { + fprintf(stderr, "Out of the range [0,%" PRIdSAIDX_T "].\n" + " SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n", + n - 1, i, SA[i]); + } + return -2; + } + } + + /* check first characters. */ + for(i = 1; i < n; ++i) { + if(T[SA[i - 1]] > T[SA[i]]) { + if(verbose) { + fprintf(stderr, "Suffixes in wrong order.\n" + " T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d" + " > T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d\n", + i - 1, SA[i - 1], T[SA[i - 1]], i, SA[i], T[SA[i]]); + } + return -3; + } + } + + /* check suffixes. */ + for(i = 0; i < ALPHABET_SIZE; ++i) { C[i] = 0; } + for(i = 0; i < n; ++i) { ++C[T[i]]; } + for(i = 0, p = 0; i < ALPHABET_SIZE; ++i) { + t = C[i]; + C[i] = p; + p += t; + } + + q = C[T[n - 1]]; + C[T[n - 1]] += 1; + for(i = 0; i < n; ++i) { + p = SA[i]; + if(0 < p) { + c = T[--p]; + t = C[c]; + } else { + c = T[p = n - 1]; + t = q; + } + if((t < 0) || (p != SA[t])) { + if(verbose) { + fprintf(stderr, "Suffix in wrong position.\n" + " SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T " or\n" + " SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n", + t, (0 <= t) ? SA[t] : -1, i, SA[i]); + } + return -4; + } + if(t != q) { + ++C[c]; + if((n <= C[c]) || (T[SA[C[c]]] != c)) { C[c] = -1; } + } + } + + if(1 <= verbose) { fprintf(stderr, "Done.\n"); } + return 0; +} + + +static +int +_compare(const sauchar_t *T, saidx_t Tsize, + const sauchar_t *P, saidx_t Psize, + saidx_t suf, saidx_t *match) { + saidx_t i, j; + saint_t r; + for(i = suf + *match, j = *match, r = 0; + (i < Tsize) && (j < Psize) && ((r = T[i] - P[j]) == 0); ++i, ++j) { } + *match = j; + return (r == 0) ? -(j != Psize) : r; +} + +/* Search for the pattern P in the string T. */ +saidx_t +sa_search(const sauchar_t *T, saidx_t Tsize, + const sauchar_t *P, saidx_t Psize, + const saidx_t *SA, saidx_t SAsize, + saidx_t *idx) { + saidx_t size, lsize, rsize, half; + saidx_t match, lmatch, rmatch; + saidx_t llmatch, lrmatch, rlmatch, rrmatch; + saidx_t i, j, k; + saint_t r; + + if(idx != NULL) { *idx = -1; } + if((T == NULL) || (P == NULL) || (SA == NULL) || + (Tsize < 0) || (Psize < 0) || (SAsize < 0)) { return -1; } + if((Tsize == 0) || (SAsize == 0)) { return 0; } + if(Psize == 0) { if(idx != NULL) { *idx = 0; } return SAsize; } + + for(i = j = k = 0, lmatch = rmatch = 0, size = SAsize, half = size >> 1; + 0 < size; + size = half, half >>= 1) { + match = MIN(lmatch, rmatch); + r = _compare(T, Tsize, P, Psize, SA[i + half], &match); + if(r < 0) { + i += half + 1; + half -= (size & 1) ^ 1; + lmatch = match; + } else if(r > 0) { + rmatch = match; + } else { + lsize = half, j = i, rsize = size - half - 1, k = i + half + 1; + + /* left part */ + for(llmatch = lmatch, lrmatch = match, half = lsize >> 1; + 0 < lsize; + lsize = half, half >>= 1) { + lmatch = MIN(llmatch, lrmatch); + r = _compare(T, Tsize, P, Psize, SA[j + half], &lmatch); + if(r < 0) { + j += half + 1; + half -= (lsize & 1) ^ 1; + llmatch = lmatch; + } else { + lrmatch = lmatch; + } + } + + /* right part */ + for(rlmatch = match, rrmatch = rmatch, half = rsize >> 1; + 0 < rsize; + rsize = half, half >>= 1) { + rmatch = MIN(rlmatch, rrmatch); + r = _compare(T, Tsize, P, Psize, SA[k + half], &rmatch); + if(r <= 0) { + k += half + 1; + half -= (rsize & 1) ^ 1; + rlmatch = rmatch; + } else { + rrmatch = rmatch; + } + } + + break; + } + } + + if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; } + return k - j; +} + +/* Search for the character c in the string T. */ +saidx_t +sa_simplesearch(const sauchar_t *T, saidx_t Tsize, + const saidx_t *SA, saidx_t SAsize, + saint_t c, saidx_t *idx) { + saidx_t size, lsize, rsize, half; + saidx_t i, j, k, p; + saint_t r; + + if(idx != NULL) { *idx = -1; } + if((T == NULL) || (SA == NULL) || (Tsize < 0) || (SAsize < 0)) { return -1; } + if((Tsize == 0) || (SAsize == 0)) { return 0; } + + for(i = j = k = 0, size = SAsize, half = size >> 1; + 0 < size; + size = half, half >>= 1) { + p = SA[i + half]; + r = (p < Tsize) ? T[p] - c : -1; + if(r < 0) { + i += half + 1; + half -= (size & 1) ^ 1; + } else if(r == 0) { + lsize = half, j = i, rsize = size - half - 1, k = i + half + 1; + + /* left part */ + for(half = lsize >> 1; + 0 < lsize; + lsize = half, half >>= 1) { + p = SA[j + half]; + r = (p < Tsize) ? T[p] - c : -1; + if(r < 0) { + j += half + 1; + half -= (lsize & 1) ^ 1; + } + } + + /* right part */ + for(half = rsize >> 1; + 0 < rsize; + rsize = half, half >>= 1) { + p = SA[k + half]; + r = (p < Tsize) ? T[p] - c : -1; + if(r <= 0) { + k += half + 1; + half -= (rsize & 1) ^ 1; + } + } + + break; + } + } + + if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; } + return k - j; +} +#endif diff --git a/tools/apultra_src/src/libdivsufsort/lib/sssort.c b/tools/apultra_src/src/libdivsufsort/lib/sssort.c new file mode 100644 index 0000000..4a18fd2 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/lib/sssort.c @@ -0,0 +1,815 @@ +/* + * sssort.c for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#include "divsufsort_private.h" + + +/*- Private Functions -*/ + +static const saint_t lg_table[256]= { + -1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, + 5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5, + 6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6, + 6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7 +}; + +#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) + +static INLINE +saint_t +ss_ilg(saidx_t n) { +#if SS_BLOCKSIZE == 0 +# if defined(BUILD_DIVSUFSORT64) + return (n >> 32) ? + ((n >> 48) ? + ((n >> 56) ? + 56 + lg_table[(n >> 56) & 0xff] : + 48 + lg_table[(n >> 48) & 0xff]) : + ((n >> 40) ? + 40 + lg_table[(n >> 40) & 0xff] : + 32 + lg_table[(n >> 32) & 0xff])) : + ((n & 0xffff0000) ? + ((n & 0xff000000) ? + 24 + lg_table[(n >> 24) & 0xff] : + 16 + lg_table[(n >> 16) & 0xff]) : + ((n & 0x0000ff00) ? + 8 + lg_table[(n >> 8) & 0xff] : + 0 + lg_table[(n >> 0) & 0xff])); +# else + return (n & 0xffff0000) ? + ((n & 0xff000000) ? + 24 + lg_table[(n >> 24) & 0xff] : + 16 + lg_table[(n >> 16) & 0xff]) : + ((n & 0x0000ff00) ? + 8 + lg_table[(n >> 8) & 0xff] : + 0 + lg_table[(n >> 0) & 0xff]); +# endif +#elif SS_BLOCKSIZE < 256 + return lg_table[n]; +#else + return (n & 0xff00) ? + 8 + lg_table[(n >> 8) & 0xff] : + 0 + lg_table[(n >> 0) & 0xff]; +#endif +} + +#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */ + +#if SS_BLOCKSIZE != 0 + +static const saint_t sqq_table[256] = { + 0, 16, 22, 27, 32, 35, 39, 42, 45, 48, 50, 53, 55, 57, 59, 61, + 64, 65, 67, 69, 71, 73, 75, 76, 78, 80, 81, 83, 84, 86, 87, 89, + 90, 91, 93, 94, 96, 97, 98, 99, 101, 102, 103, 104, 106, 107, 108, 109, +110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, +128, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, +143, 144, 144, 145, 146, 147, 148, 149, 150, 150, 151, 152, 153, 154, 155, 155, +156, 157, 158, 159, 160, 160, 161, 162, 163, 163, 164, 165, 166, 167, 167, 168, +169, 170, 170, 171, 172, 173, 173, 174, 175, 176, 176, 177, 178, 178, 179, 180, +181, 181, 182, 183, 183, 184, 185, 185, 186, 187, 187, 188, 189, 189, 190, 191, +192, 192, 193, 193, 194, 195, 195, 196, 197, 197, 198, 199, 199, 200, 201, 201, +202, 203, 203, 204, 204, 205, 206, 206, 207, 208, 208, 209, 209, 210, 211, 211, +212, 212, 213, 214, 214, 215, 215, 216, 217, 217, 218, 218, 219, 219, 220, 221, +221, 222, 222, 223, 224, 224, 225, 225, 226, 226, 227, 227, 228, 229, 229, 230, +230, 231, 231, 232, 232, 233, 234, 234, 235, 235, 236, 236, 237, 237, 238, 238, +239, 240, 240, 241, 241, 242, 242, 243, 243, 244, 244, 245, 245, 246, 246, 247, +247, 248, 248, 249, 249, 250, 250, 251, 251, 252, 252, 253, 253, 254, 254, 255 +}; + +static INLINE +saidx_t +ss_isqrt(saidx_t x) { + saidx_t y, e; + + if(x >= (SS_BLOCKSIZE * SS_BLOCKSIZE)) { return SS_BLOCKSIZE; } + e = (x & 0xffff0000) ? + ((x & 0xff000000) ? + 24 + lg_table[(x >> 24) & 0xff] : + 16 + lg_table[(x >> 16) & 0xff]) : + ((x & 0x0000ff00) ? + 8 + lg_table[(x >> 8) & 0xff] : + 0 + lg_table[(x >> 0) & 0xff]); + + if(e >= 16) { + y = sqq_table[x >> ((e - 6) - (e & 1))] << ((e >> 1) - 7); + if(e >= 24) { y = (y + 1 + x / y) >> 1; } + y = (y + 1 + x / y) >> 1; + } else if(e >= 8) { + y = (sqq_table[x >> ((e - 6) - (e & 1))] >> (7 - (e >> 1))) + 1; + } else { + return sqq_table[x] >> 4; + } + + return (x < (y * y)) ? y - 1 : y; +} + +#endif /* SS_BLOCKSIZE != 0 */ + + +/*---------------------------------------------------------------------------*/ + +/* Compares two suffixes. */ +static INLINE +saint_t +ss_compare(const sauchar_t *T, + const saidx_t *p1, const saidx_t *p2, + saidx_t depth) { + const sauchar_t *U1, *U2, *U1n, *U2n; + + for(U1 = T + depth + *p1, + U2 = T + depth + *p2, + U1n = T + *(p1 + 1) + 2, + U2n = T + *(p2 + 1) + 2; + (U1 < U1n) && (U2 < U2n) && (*U1 == *U2); + ++U1, ++U2) { + } + + return U1 < U1n ? + (U2 < U2n ? *U1 - *U2 : 1) : + (U2 < U2n ? -1 : 0); +} + + +/*---------------------------------------------------------------------------*/ + +#if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) + +/* Insertionsort for small size groups */ +static +void +ss_insertionsort(const sauchar_t *T, const saidx_t *PA, + saidx_t *first, saidx_t *last, saidx_t depth) { + saidx_t *i, *j; + saidx_t t; + saint_t r; + + for(i = last - 2; first <= i; --i) { + for(t = *i, j = i + 1; 0 < (r = ss_compare(T, PA + t, PA + *j, depth));) { + do { *(j - 1) = *j; } while((++j < last) && (*j < 0)); + if(last <= j) { break; } + } + if(r == 0) { *j = ~*j; } + *(j - 1) = t; + } +} + +#endif /* (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) */ + + +/*---------------------------------------------------------------------------*/ + +#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) + +static INLINE +void +ss_fixdown(const sauchar_t *Td, const saidx_t *PA, + saidx_t *SA, saidx_t i, saidx_t size) { + saidx_t j, k; + saidx_t v; + saint_t c, d, e; + + for(v = SA[i], c = Td[PA[v]]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) { + d = Td[PA[SA[k = j++]]]; + if(d < (e = Td[PA[SA[j]]])) { k = j; d = e; } + if(d <= c) { break; } + } + SA[i] = v; +} + +/* Simple top-down heapsort. */ +static +void +ss_heapsort(const sauchar_t *Td, const saidx_t *PA, saidx_t *SA, saidx_t size) { + saidx_t i, m; + saidx_t t; + + m = size; + if((size % 2) == 0) { + m--; + if(Td[PA[SA[m / 2]]] < Td[PA[SA[m]]]) { SWAP(SA[m], SA[m / 2]); } + } + + for(i = m / 2 - 1; 0 <= i; --i) { ss_fixdown(Td, PA, SA, i, m); } + if((size % 2) == 0) { SWAP(SA[0], SA[m]); ss_fixdown(Td, PA, SA, 0, m); } + for(i = m - 1; 0 < i; --i) { + t = SA[0], SA[0] = SA[i]; + ss_fixdown(Td, PA, SA, 0, i); + SA[i] = t; + } +} + + +/*---------------------------------------------------------------------------*/ + +/* Returns the median of three elements. */ +static INLINE +saidx_t * +ss_median3(const sauchar_t *Td, const saidx_t *PA, + saidx_t *v1, saidx_t *v2, saidx_t *v3) { + saidx_t *t; + if(Td[PA[*v1]] > Td[PA[*v2]]) { SWAP(v1, v2); } + if(Td[PA[*v2]] > Td[PA[*v3]]) { + if(Td[PA[*v1]] > Td[PA[*v3]]) { return v1; } + else { return v3; } + } + return v2; +} + +/* Returns the median of five elements. */ +static INLINE +saidx_t * +ss_median5(const sauchar_t *Td, const saidx_t *PA, + saidx_t *v1, saidx_t *v2, saidx_t *v3, saidx_t *v4, saidx_t *v5) { + saidx_t *t; + if(Td[PA[*v2]] > Td[PA[*v3]]) { SWAP(v2, v3); } + if(Td[PA[*v4]] > Td[PA[*v5]]) { SWAP(v4, v5); } + if(Td[PA[*v2]] > Td[PA[*v4]]) { SWAP(v2, v4); SWAP(v3, v5); } + if(Td[PA[*v1]] > Td[PA[*v3]]) { SWAP(v1, v3); } + if(Td[PA[*v1]] > Td[PA[*v4]]) { SWAP(v1, v4); SWAP(v3, v5); } + if(Td[PA[*v3]] > Td[PA[*v4]]) { return v4; } + return v3; +} + +/* Returns the pivot element. */ +static INLINE +saidx_t * +ss_pivot(const sauchar_t *Td, const saidx_t *PA, saidx_t *first, saidx_t *last) { + saidx_t *middle; + saidx_t t; + + t = last - first; + middle = first + t / 2; + + if(t <= 512) { + if(t <= 32) { + return ss_median3(Td, PA, first, middle, last - 1); + } else { + t >>= 2; + return ss_median5(Td, PA, first, first + t, middle, last - 1 - t, last - 1); + } + } + t >>= 3; + first = ss_median3(Td, PA, first, first + t, first + (t << 1)); + middle = ss_median3(Td, PA, middle - t, middle, middle + t); + last = ss_median3(Td, PA, last - 1 - (t << 1), last - 1 - t, last - 1); + return ss_median3(Td, PA, first, middle, last); +} + + +/*---------------------------------------------------------------------------*/ + +/* Binary partition for substrings. */ +static INLINE +saidx_t * +ss_partition(const saidx_t *PA, + saidx_t *first, saidx_t *last, saidx_t depth) { + saidx_t *a, *b; + saidx_t t; + for(a = first - 1, b = last;;) { + for(; (++a < b) && ((PA[*a] + depth) >= (PA[*a + 1] + 1));) { *a = ~*a; } + for(; (a < --b) && ((PA[*b] + depth) < (PA[*b + 1] + 1));) { } + if(b <= a) { break; } + t = ~*b; + *b = *a; + *a = t; + } + if(first < a) { *first = ~*first; } + return a; +} + +/* Multikey introsort for medium size groups. */ +static +void +ss_mintrosort(const sauchar_t *T, const saidx_t *PA, + saidx_t *first, saidx_t *last, + saidx_t depth) { +#define STACK_SIZE SS_MISORT_STACKSIZE + struct { saidx_t *a, *b, c; saint_t d; } stack[STACK_SIZE]; + const sauchar_t *Td; + saidx_t *a, *b, *c, *d, *e, *f; + saidx_t s, t; + saint_t ssize; + saint_t limit; + saint_t v, x = 0; + + for(ssize = 0, limit = ss_ilg(last - first);;) { + + if((last - first) <= SS_INSERTIONSORT_THRESHOLD) { +#if 1 < SS_INSERTIONSORT_THRESHOLD + if(1 < (last - first)) { ss_insertionsort(T, PA, first, last, depth); } +#endif + STACK_POP(first, last, depth, limit); + continue; + } + + Td = T + depth; + if(limit-- == 0) { ss_heapsort(Td, PA, first, last - first); } + if(limit < 0) { + for(a = first + 1, v = Td[PA[*first]]; a < last; ++a) { + if((x = Td[PA[*a]]) != v) { + if(1 < (a - first)) { break; } + v = x; + first = a; + } + } + if(Td[PA[*first] - 1] < v) { + first = ss_partition(PA, first, a, depth); + } + if((a - first) <= (last - a)) { + if(1 < (a - first)) { + STACK_PUSH(a, last, depth, -1); + last = a, depth += 1, limit = ss_ilg(a - first); + } else { + first = a, limit = -1; + } + } else { + if(1 < (last - a)) { + STACK_PUSH(first, a, depth + 1, ss_ilg(a - first)); + first = a, limit = -1; + } else { + last = a, depth += 1, limit = ss_ilg(a - first); + } + } + continue; + } + + /* choose pivot */ + a = ss_pivot(Td, PA, first, last); + v = Td[PA[*a]]; + SWAP(*first, *a); + + /* partition */ + for(b = first; (++b < last) && ((x = Td[PA[*b]]) == v);) { } + if(((a = b) < last) && (x < v)) { + for(; (++b < last) && ((x = Td[PA[*b]]) <= v);) { + if(x == v) { SWAP(*b, *a); ++a; } + } + } + for(c = last; (b < --c) && ((x = Td[PA[*c]]) == v);) { } + if((b < (d = c)) && (x > v)) { + for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) { + if(x == v) { SWAP(*c, *d); --d; } + } + } + for(; b < c;) { + SWAP(*b, *c); + for(; (++b < c) && ((x = Td[PA[*b]]) <= v);) { + if(x == v) { SWAP(*b, *a); ++a; } + } + for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) { + if(x == v) { SWAP(*c, *d); --d; } + } + } + + if(a <= d) { + c = b - 1; + + if((s = a - first) > (t = b - a)) { s = t; } + for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); } + if((s = d - c) > (t = last - d - 1)) { s = t; } + for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); } + + a = first + (b - a), c = last - (d - c); + b = (v <= Td[PA[*a] - 1]) ? a : ss_partition(PA, a, c, depth); + + if((a - first) <= (last - c)) { + if((last - c) <= (c - b)) { + STACK_PUSH(b, c, depth + 1, ss_ilg(c - b)); + STACK_PUSH(c, last, depth, limit); + last = a; + } else if((a - first) <= (c - b)) { + STACK_PUSH(c, last, depth, limit); + STACK_PUSH(b, c, depth + 1, ss_ilg(c - b)); + last = a; + } else { + STACK_PUSH(c, last, depth, limit); + STACK_PUSH(first, a, depth, limit); + first = b, last = c, depth += 1, limit = ss_ilg(c - b); + } + } else { + if((a - first) <= (c - b)) { + STACK_PUSH(b, c, depth + 1, ss_ilg(c - b)); + STACK_PUSH(first, a, depth, limit); + first = c; + } else if((last - c) <= (c - b)) { + STACK_PUSH(first, a, depth, limit); + STACK_PUSH(b, c, depth + 1, ss_ilg(c - b)); + first = c; + } else { + STACK_PUSH(first, a, depth, limit); + STACK_PUSH(c, last, depth, limit); + first = b, last = c, depth += 1, limit = ss_ilg(c - b); + } + } + } else { + limit += 1; + if(Td[PA[*first] - 1] < v) { + first = ss_partition(PA, first, last, depth); + limit = ss_ilg(last - first); + } + depth += 1; + } + } +#undef STACK_SIZE +} + +#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */ + + +/*---------------------------------------------------------------------------*/ + +#if SS_BLOCKSIZE != 0 + +static INLINE +void +ss_blockswap(saidx_t *a, saidx_t *b, saidx_t n) { + saidx_t t; + for(; 0 < n; --n, ++a, ++b) { + t = *a, *a = *b, *b = t; + } +} + +static INLINE +void +ss_rotate(saidx_t *first, saidx_t *middle, saidx_t *last) { + saidx_t *a, *b, t; + saidx_t l, r; + l = middle - first, r = last - middle; + for(; (0 < l) && (0 < r);) { + if(l == r) { ss_blockswap(first, middle, l); break; } + if(l < r) { + a = last - 1, b = middle - 1; + t = *a; + do { + *a-- = *b, *b-- = *a; + if(b < first) { + *a = t; + last = a; + if((r -= l + 1) <= l) { break; } + a -= 1, b = middle - 1; + t = *a; + } + } while(1); + } else { + a = first, b = middle; + t = *a; + do { + *a++ = *b, *b++ = *a; + if(last <= b) { + *a = t; + first = a + 1; + if((l -= r + 1) <= r) { break; } + a += 1, b = middle; + t = *a; + } + } while(1); + } + } +} + + +/*---------------------------------------------------------------------------*/ + +static +void +ss_inplacemerge(const sauchar_t *T, const saidx_t *PA, + saidx_t *first, saidx_t *middle, saidx_t *last, + saidx_t depth) { + const saidx_t *p; + saidx_t *a, *b; + saidx_t len, half; + saint_t q, r; + saint_t x; + + for(;;) { + if(*(last - 1) < 0) { x = 1; p = PA + ~*(last - 1); } + else { x = 0; p = PA + *(last - 1); } + for(a = first, len = middle - first, half = len >> 1, r = -1; + 0 < len; + len = half, half >>= 1) { + b = a + half; + q = ss_compare(T, PA + ((0 <= *b) ? *b : ~*b), p, depth); + if(q < 0) { + a = b + 1; + half -= (len & 1) ^ 1; + } else { + r = q; + } + } + if(a < middle) { + if(r == 0) { *a = ~*a; } + ss_rotate(a, middle, last); + last -= middle - a; + middle = a; + if(first == middle) { break; } + } + --last; + if(x != 0) { while(*--last < 0) { } } + if(middle == last) { break; } + } +} + + +/*---------------------------------------------------------------------------*/ + +/* Merge-forward with internal buffer. */ +static +void +ss_mergeforward(const sauchar_t *T, const saidx_t *PA, + saidx_t *first, saidx_t *middle, saidx_t *last, + saidx_t *buf, saidx_t depth) { + saidx_t *a, *b, *c, *bufend; + saidx_t t; + saint_t r; + + bufend = buf + (middle - first) - 1; + ss_blockswap(buf, first, middle - first); + + for(t = *(a = first), b = buf, c = middle;;) { + r = ss_compare(T, PA + *b, PA + *c, depth); + if(r < 0) { + do { + *a++ = *b; + if(bufend <= b) { *bufend = t; return; } + *b++ = *a; + } while(*b < 0); + } else if(r > 0) { + do { + *a++ = *c, *c++ = *a; + if(last <= c) { + while(b < bufend) { *a++ = *b, *b++ = *a; } + *a = *b, *b = t; + return; + } + } while(*c < 0); + } else { + *c = ~*c; + do { + *a++ = *b; + if(bufend <= b) { *bufend = t; return; } + *b++ = *a; + } while(*b < 0); + + do { + *a++ = *c, *c++ = *a; + if(last <= c) { + while(b < bufend) { *a++ = *b, *b++ = *a; } + *a = *b, *b = t; + return; + } + } while(*c < 0); + } + } +} + +/* Merge-backward with internal buffer. */ +static +void +ss_mergebackward(const sauchar_t *T, const saidx_t *PA, + saidx_t *first, saidx_t *middle, saidx_t *last, + saidx_t *buf, saidx_t depth) { + const saidx_t *p1, *p2; + saidx_t *a, *b, *c, *bufend; + saidx_t t; + saint_t r; + saint_t x; + + bufend = buf + (last - middle) - 1; + ss_blockswap(buf, middle, last - middle); + + x = 0; + if(*bufend < 0) { p1 = PA + ~*bufend; x |= 1; } + else { p1 = PA + *bufend; } + if(*(middle - 1) < 0) { p2 = PA + ~*(middle - 1); x |= 2; } + else { p2 = PA + *(middle - 1); } + for(t = *(a = last - 1), b = bufend, c = middle - 1;;) { + r = ss_compare(T, p1, p2, depth); + if(0 < r) { + if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; } + *a-- = *b; + if(b <= buf) { *buf = t; break; } + *b-- = *a; + if(*b < 0) { p1 = PA + ~*b; x |= 1; } + else { p1 = PA + *b; } + } else if(r < 0) { + if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; } + *a-- = *c, *c-- = *a; + if(c < first) { + while(buf < b) { *a-- = *b, *b-- = *a; } + *a = *b, *b = t; + break; + } + if(*c < 0) { p2 = PA + ~*c; x |= 2; } + else { p2 = PA + *c; } + } else { + if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; } + *a-- = ~*b; + if(b <= buf) { *buf = t; break; } + *b-- = *a; + if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; } + *a-- = *c, *c-- = *a; + if(c < first) { + while(buf < b) { *a-- = *b, *b-- = *a; } + *a = *b, *b = t; + break; + } + if(*b < 0) { p1 = PA + ~*b; x |= 1; } + else { p1 = PA + *b; } + if(*c < 0) { p2 = PA + ~*c; x |= 2; } + else { p2 = PA + *c; } + } + } +} + +/* D&C based merge. */ +static +void +ss_swapmerge(const sauchar_t *T, const saidx_t *PA, + saidx_t *first, saidx_t *middle, saidx_t *last, + saidx_t *buf, saidx_t bufsize, saidx_t depth) { +#define STACK_SIZE SS_SMERGE_STACKSIZE +#define GETIDX(a) ((0 <= (a)) ? (a) : (~(a))) +#define MERGE_CHECK(a, b, c)\ + do {\ + if(((c) & 1) ||\ + (((c) & 2) && (ss_compare(T, PA + GETIDX(*((a) - 1)), PA + *(a), depth) == 0))) {\ + *(a) = ~*(a);\ + }\ + if(((c) & 4) && ((ss_compare(T, PA + GETIDX(*((b) - 1)), PA + *(b), depth) == 0))) {\ + *(b) = ~*(b);\ + }\ + } while(0) + struct { saidx_t *a, *b, *c; saint_t d; } stack[STACK_SIZE]; + saidx_t *l, *r, *lm, *rm; + saidx_t m, len, half; + saint_t ssize; + saint_t check, next; + + for(check = 0, ssize = 0;;) { + if((last - middle) <= bufsize) { + if((first < middle) && (middle < last)) { + ss_mergebackward(T, PA, first, middle, last, buf, depth); + } + MERGE_CHECK(first, last, check); + STACK_POP(first, middle, last, check); + continue; + } + + if((middle - first) <= bufsize) { + if(first < middle) { + ss_mergeforward(T, PA, first, middle, last, buf, depth); + } + MERGE_CHECK(first, last, check); + STACK_POP(first, middle, last, check); + continue; + } + + for(m = 0, len = MIN(middle - first, last - middle), half = len >> 1; + 0 < len; + len = half, half >>= 1) { + if(ss_compare(T, PA + GETIDX(*(middle + m + half)), + PA + GETIDX(*(middle - m - half - 1)), depth) < 0) { + m += half + 1; + half -= (len & 1) ^ 1; + } + } + + if(0 < m) { + lm = middle - m, rm = middle + m; + ss_blockswap(lm, middle, m); + l = r = middle, next = 0; + if(rm < last) { + if(*rm < 0) { + *rm = ~*rm; + if(first < lm) { for(; *--l < 0;) { } next |= 4; } + next |= 1; + } else if(first < lm) { + for(; *r < 0; ++r) { } + next |= 2; + } + } + + if((l - first) <= (last - r)) { + STACK_PUSH(r, rm, last, (next & 3) | (check & 4)); + middle = lm, last = l, check = (check & 3) | (next & 4); + } else { + if((next & 2) && (r == middle)) { next ^= 6; } + STACK_PUSH(first, lm, l, (check & 3) | (next & 4)); + first = r, middle = rm, check = (next & 3) | (check & 4); + } + } else { + if(ss_compare(T, PA + GETIDX(*(middle - 1)), PA + *middle, depth) == 0) { + *middle = ~*middle; + } + MERGE_CHECK(first, last, check); + STACK_POP(first, middle, last, check); + } + } +#undef STACK_SIZE +} + +#endif /* SS_BLOCKSIZE != 0 */ + + +/*---------------------------------------------------------------------------*/ + +/*- Function -*/ + +/* Substring sort */ +void +sssort(const sauchar_t *T, const saidx_t *PA, + saidx_t *first, saidx_t *last, + saidx_t *buf, saidx_t bufsize, + saidx_t depth, saidx_t n, saint_t lastsuffix) { + saidx_t *a; +#if SS_BLOCKSIZE != 0 + saidx_t *b, *middle, *curbuf; + saidx_t j, k, curbufsize, limit; +#endif + saidx_t i; + + if(lastsuffix != 0) { ++first; } + +#if SS_BLOCKSIZE == 0 + ss_mintrosort(T, PA, first, last, depth); +#else + if((bufsize < SS_BLOCKSIZE) && + (bufsize < (last - first)) && + (bufsize < (limit = ss_isqrt(last - first)))) { + if(SS_BLOCKSIZE < limit) { limit = SS_BLOCKSIZE; } + buf = middle = last - limit, bufsize = limit; + } else { + middle = last, limit = 0; + } + for(a = first, i = 0; SS_BLOCKSIZE < (middle - a); a += SS_BLOCKSIZE, ++i) { +#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE + ss_mintrosort(T, PA, a, a + SS_BLOCKSIZE, depth); +#elif 1 < SS_BLOCKSIZE + ss_insertionsort(T, PA, a, a + SS_BLOCKSIZE, depth); +#endif + curbufsize = last - (a + SS_BLOCKSIZE); + curbuf = a + SS_BLOCKSIZE; + if(curbufsize <= bufsize) { curbufsize = bufsize, curbuf = buf; } + for(b = a, k = SS_BLOCKSIZE, j = i; j & 1; b -= k, k <<= 1, j >>= 1) { + ss_swapmerge(T, PA, b - k, b, b + k, curbuf, curbufsize, depth); + } + } +#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE + ss_mintrosort(T, PA, a, middle, depth); +#elif 1 < SS_BLOCKSIZE + ss_insertionsort(T, PA, a, middle, depth); +#endif + for(k = SS_BLOCKSIZE; i != 0; k <<= 1, i >>= 1) { + if(i & 1) { + ss_swapmerge(T, PA, a - k, a, middle, buf, bufsize, depth); + a -= k; + } + } + if(limit != 0) { +#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE + ss_mintrosort(T, PA, middle, last, depth); +#elif 1 < SS_BLOCKSIZE + ss_insertionsort(T, PA, middle, last, depth); +#endif + ss_inplacemerge(T, PA, first, middle, last, depth); + } +#endif + + if(lastsuffix != 0) { + /* Insert last type B* suffix. */ + saidx_t PAi[2]; PAi[0] = PA[*(first - 1)], PAi[1] = n - 2; + for(a = first, i = *(first - 1); + (a < last) && ((*a < 0) || (0 < ss_compare(T, &(PAi[0]), PA + *a, depth))); + ++a) { + *(a - 1) = *a; + } + *(a - 1) = i; + } +} diff --git a/tools/apultra_src/src/libdivsufsort/lib/trsort.c b/tools/apultra_src/src/libdivsufsort/lib/trsort.c new file mode 100644 index 0000000..6fe3e67 --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/lib/trsort.c @@ -0,0 +1,586 @@ +/* + * trsort.c for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#include "divsufsort_private.h" + + +/*- Private Functions -*/ + +static const saint_t lg_table[256]= { + -1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4, + 5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5, + 6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6, + 6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7 +}; + +static INLINE +saint_t +tr_ilg(saidx_t n) { +#if defined(BUILD_DIVSUFSORT64) + return (n >> 32) ? + ((n >> 48) ? + ((n >> 56) ? + 56 + lg_table[(n >> 56) & 0xff] : + 48 + lg_table[(n >> 48) & 0xff]) : + ((n >> 40) ? + 40 + lg_table[(n >> 40) & 0xff] : + 32 + lg_table[(n >> 32) & 0xff])) : + ((n & 0xffff0000) ? + ((n & 0xff000000) ? + 24 + lg_table[(n >> 24) & 0xff] : + 16 + lg_table[(n >> 16) & 0xff]) : + ((n & 0x0000ff00) ? + 8 + lg_table[(n >> 8) & 0xff] : + 0 + lg_table[(n >> 0) & 0xff])); +#else + return (n & 0xffff0000) ? + ((n & 0xff000000) ? + 24 + lg_table[(n >> 24) & 0xff] : + 16 + lg_table[(n >> 16) & 0xff]) : + ((n & 0x0000ff00) ? + 8 + lg_table[(n >> 8) & 0xff] : + 0 + lg_table[(n >> 0) & 0xff]); +#endif +} + + +/*---------------------------------------------------------------------------*/ + +/* Simple insertionsort for small size groups. */ +static +void +tr_insertionsort(const saidx_t *ISAd, saidx_t *first, saidx_t *last) { + saidx_t *a, *b; + saidx_t t, r; + + for(a = first + 1; a < last; ++a) { + for(t = *a, b = a - 1; 0 > (r = ISAd[t] - ISAd[*b]);) { + do { *(b + 1) = *b; } while((first <= --b) && (*b < 0)); + if(b < first) { break; } + } + if(r == 0) { *b = ~*b; } + *(b + 1) = t; + } +} + + +/*---------------------------------------------------------------------------*/ + +static INLINE +void +tr_fixdown(const saidx_t *ISAd, saidx_t *SA, saidx_t i, saidx_t size) { + saidx_t j, k; + saidx_t v; + saidx_t c, d, e; + + for(v = SA[i], c = ISAd[v]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) { + d = ISAd[SA[k = j++]]; + if(d < (e = ISAd[SA[j]])) { k = j; d = e; } + if(d <= c) { break; } + } + SA[i] = v; +} + +/* Simple top-down heapsort. */ +static +void +tr_heapsort(const saidx_t *ISAd, saidx_t *SA, saidx_t size) { + saidx_t i, m; + saidx_t t; + + m = size; + if((size % 2) == 0) { + m--; + if(ISAd[SA[m / 2]] < ISAd[SA[m]]) { SWAP(SA[m], SA[m / 2]); } + } + + for(i = m / 2 - 1; 0 <= i; --i) { tr_fixdown(ISAd, SA, i, m); } + if((size % 2) == 0) { SWAP(SA[0], SA[m]); tr_fixdown(ISAd, SA, 0, m); } + for(i = m - 1; 0 < i; --i) { + t = SA[0], SA[0] = SA[i]; + tr_fixdown(ISAd, SA, 0, i); + SA[i] = t; + } +} + + +/*---------------------------------------------------------------------------*/ + +/* Returns the median of three elements. */ +static INLINE +saidx_t * +tr_median3(const saidx_t *ISAd, saidx_t *v1, saidx_t *v2, saidx_t *v3) { + saidx_t *t; + if(ISAd[*v1] > ISAd[*v2]) { SWAP(v1, v2); } + if(ISAd[*v2] > ISAd[*v3]) { + if(ISAd[*v1] > ISAd[*v3]) { return v1; } + else { return v3; } + } + return v2; +} + +/* Returns the median of five elements. */ +static INLINE +saidx_t * +tr_median5(const saidx_t *ISAd, + saidx_t *v1, saidx_t *v2, saidx_t *v3, saidx_t *v4, saidx_t *v5) { + saidx_t *t; + if(ISAd[*v2] > ISAd[*v3]) { SWAP(v2, v3); } + if(ISAd[*v4] > ISAd[*v5]) { SWAP(v4, v5); } + if(ISAd[*v2] > ISAd[*v4]) { SWAP(v2, v4); SWAP(v3, v5); } + if(ISAd[*v1] > ISAd[*v3]) { SWAP(v1, v3); } + if(ISAd[*v1] > ISAd[*v4]) { SWAP(v1, v4); SWAP(v3, v5); } + if(ISAd[*v3] > ISAd[*v4]) { return v4; } + return v3; +} + +/* Returns the pivot element. */ +static INLINE +saidx_t * +tr_pivot(const saidx_t *ISAd, saidx_t *first, saidx_t *last) { + saidx_t *middle; + saidx_t t; + + t = last - first; + middle = first + t / 2; + + if(t <= 512) { + if(t <= 32) { + return tr_median3(ISAd, first, middle, last - 1); + } else { + t >>= 2; + return tr_median5(ISAd, first, first + t, middle, last - 1 - t, last - 1); + } + } + t >>= 3; + first = tr_median3(ISAd, first, first + t, first + (t << 1)); + middle = tr_median3(ISAd, middle - t, middle, middle + t); + last = tr_median3(ISAd, last - 1 - (t << 1), last - 1 - t, last - 1); + return tr_median3(ISAd, first, middle, last); +} + + +/*---------------------------------------------------------------------------*/ + +typedef struct _trbudget_t trbudget_t; +struct _trbudget_t { + saidx_t chance; + saidx_t remain; + saidx_t incval; + saidx_t count; +}; + +static INLINE +void +trbudget_init(trbudget_t *budget, saidx_t chance, saidx_t incval) { + budget->chance = chance; + budget->remain = budget->incval = incval; +} + +static INLINE +saint_t +trbudget_check(trbudget_t *budget, saidx_t size) { + if(size <= budget->remain) { budget->remain -= size; return 1; } + if(budget->chance == 0) { budget->count += size; return 0; } + budget->remain += budget->incval - size; + budget->chance -= 1; + return 1; +} + + +/*---------------------------------------------------------------------------*/ + +static INLINE +void +tr_partition(const saidx_t *ISAd, + saidx_t *first, saidx_t *middle, saidx_t *last, + saidx_t **pa, saidx_t **pb, saidx_t v) { + saidx_t *a, *b, *c, *d, *e, *f; + saidx_t t, s; + saidx_t x = 0; + + for(b = middle - 1; (++b < last) && ((x = ISAd[*b]) == v);) { } + if(((a = b) < last) && (x < v)) { + for(; (++b < last) && ((x = ISAd[*b]) <= v);) { + if(x == v) { SWAP(*b, *a); ++a; } + } + } + for(c = last; (b < --c) && ((x = ISAd[*c]) == v);) { } + if((b < (d = c)) && (x > v)) { + for(; (b < --c) && ((x = ISAd[*c]) >= v);) { + if(x == v) { SWAP(*c, *d); --d; } + } + } + for(; b < c;) { + SWAP(*b, *c); + for(; (++b < c) && ((x = ISAd[*b]) <= v);) { + if(x == v) { SWAP(*b, *a); ++a; } + } + for(; (b < --c) && ((x = ISAd[*c]) >= v);) { + if(x == v) { SWAP(*c, *d); --d; } + } + } + + if(a <= d) { + c = b - 1; + if((s = a - first) > (t = b - a)) { s = t; } + for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); } + if((s = d - c) > (t = last - d - 1)) { s = t; } + for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); } + first += (b - a), last -= (d - c); + } + *pa = first, *pb = last; +} + +static +void +tr_copy(saidx_t *ISA, const saidx_t *SA, + saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last, + saidx_t depth) { + /* sort suffixes of middle partition + by using sorted order of suffixes of left and right partition. */ + saidx_t *c, *d, *e; + saidx_t s, v; + + v = b - SA - 1; + for(c = first, d = a - 1; c <= d; ++c) { + if((0 <= (s = *c - depth)) && (ISA[s] == v)) { + *++d = s; + ISA[s] = d - SA; + } + } + for(c = last - 1, e = d + 1, d = b; e < d; --c) { + if((0 <= (s = *c - depth)) && (ISA[s] == v)) { + *--d = s; + ISA[s] = d - SA; + } + } +} + +static +void +tr_partialcopy(saidx_t *ISA, const saidx_t *SA, + saidx_t *first, saidx_t *a, saidx_t *b, saidx_t *last, + saidx_t depth) { + saidx_t *c, *d, *e; + saidx_t s, v; + saidx_t rank, lastrank, newrank = -1; + + v = b - SA - 1; + lastrank = -1; + for(c = first, d = a - 1; c <= d; ++c) { + if((0 <= (s = *c - depth)) && (ISA[s] == v)) { + *++d = s; + rank = ISA[s + depth]; + if(lastrank != rank) { lastrank = rank; newrank = d - SA; } + ISA[s] = newrank; + } + } + + lastrank = -1; + for(e = d; first <= e; --e) { + rank = ISA[*e]; + if(lastrank != rank) { lastrank = rank; newrank = e - SA; } + if(newrank != rank) { ISA[*e] = newrank; } + } + + lastrank = -1; + for(c = last - 1, e = d + 1, d = b; e < d; --c) { + if((0 <= (s = *c - depth)) && (ISA[s] == v)) { + *--d = s; + rank = ISA[s + depth]; + if(lastrank != rank) { lastrank = rank; newrank = d - SA; } + ISA[s] = newrank; + } + } +} + +static +void +tr_introsort(saidx_t *ISA, const saidx_t *ISAd, + saidx_t *SA, saidx_t *first, saidx_t *last, + trbudget_t *budget) { +#define STACK_SIZE TR_STACKSIZE + struct { const saidx_t *a; saidx_t *b, *c; saint_t d, e; }stack[STACK_SIZE]; + saidx_t *a, *b, *c; + saidx_t t; + saidx_t v, x = 0; + saidx_t incr = ISAd - ISA; + saint_t limit, next; + saint_t ssize, trlink = -1; + + for(ssize = 0, limit = tr_ilg(last - first);;) { + + if(limit < 0) { + if(limit == -1) { + /* tandem repeat partition */ + tr_partition(ISAd - incr, first, first, last, &a, &b, last - SA - 1); + + /* update ranks */ + if(a < last) { + for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; } + } + if(b < last) { + for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; } + } + + /* push */ + if(1 < (b - a)) { + STACK_PUSH5(NULL, a, b, 0, 0); + STACK_PUSH5(ISAd - incr, first, last, -2, trlink); + trlink = ssize - 2; + } + if((a - first) <= (last - b)) { + if(1 < (a - first)) { + STACK_PUSH5(ISAd, b, last, tr_ilg(last - b), trlink); + last = a, limit = tr_ilg(a - first); + } else if(1 < (last - b)) { + first = b, limit = tr_ilg(last - b); + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } else { + if(1 < (last - b)) { + STACK_PUSH5(ISAd, first, a, tr_ilg(a - first), trlink); + first = b, limit = tr_ilg(last - b); + } else if(1 < (a - first)) { + last = a, limit = tr_ilg(a - first); + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } + } else if(limit == -2) { + /* tandem repeat copy */ + a = stack[--ssize].b, b = stack[ssize].c; + if(stack[ssize].d == 0) { + tr_copy(ISA, SA, first, a, b, last, ISAd - ISA); + } else { + if(0 <= trlink) { stack[trlink].d = -1; } + tr_partialcopy(ISA, SA, first, a, b, last, ISAd - ISA); + } + STACK_POP5(ISAd, first, last, limit, trlink); + } else { + /* sorted partition */ + if(0 <= *first) { + a = first; + do { ISA[*a] = a - SA; } while((++a < last) && (0 <= *a)); + first = a; + } + if(first < last) { + a = first; do { *a = ~*a; } while(*++a < 0); + next = (ISA[*a] != ISAd[*a]) ? tr_ilg(a - first + 1) : -1; + if(++a < last) { for(b = first, v = a - SA - 1; b < a; ++b) { ISA[*b] = v; } } + + /* push */ + if(trbudget_check(budget, a - first)) { + if((a - first) <= (last - a)) { + STACK_PUSH5(ISAd, a, last, -3, trlink); + ISAd += incr, last = a, limit = next; + } else { + if(1 < (last - a)) { + STACK_PUSH5(ISAd + incr, first, a, next, trlink); + first = a, limit = -3; + } else { + ISAd += incr, last = a, limit = next; + } + } + } else { + if(0 <= trlink) { stack[trlink].d = -1; } + if(1 < (last - a)) { + first = a, limit = -3; + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } + continue; + } + + if((last - first) <= TR_INSERTIONSORT_THRESHOLD) { + tr_insertionsort(ISAd, first, last); + limit = -3; + continue; + } + + if(limit-- == 0) { + tr_heapsort(ISAd, first, last - first); + for(a = last - 1; first < a; a = b) { + for(x = ISAd[*a], b = a - 1; (first <= b) && (ISAd[*b] == x); --b) { *b = ~*b; } + } + limit = -3; + continue; + } + + /* choose pivot */ + a = tr_pivot(ISAd, first, last); + SWAP(*first, *a); + v = ISAd[*first]; + + /* partition */ + tr_partition(ISAd, first, first + 1, last, &a, &b, v); + if((last - first) != (b - a)) { + next = (ISA[*a] != v) ? tr_ilg(b - a) : -1; + + /* update ranks */ + for(c = first, v = a - SA - 1; c < a; ++c) { ISA[*c] = v; } + if(b < last) { for(c = a, v = b - SA - 1; c < b; ++c) { ISA[*c] = v; } } + + /* push */ + if((1 < (b - a)) && (trbudget_check(budget, b - a))) { + if((a - first) <= (last - b)) { + if((last - b) <= (b - a)) { + if(1 < (a - first)) { + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + STACK_PUSH5(ISAd, b, last, limit, trlink); + last = a; + } else if(1 < (last - b)) { + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + first = b; + } else { + ISAd += incr, first = a, last = b, limit = next; + } + } else if((a - first) <= (b - a)) { + if(1 < (a - first)) { + STACK_PUSH5(ISAd, b, last, limit, trlink); + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + last = a; + } else { + STACK_PUSH5(ISAd, b, last, limit, trlink); + ISAd += incr, first = a, last = b, limit = next; + } + } else { + STACK_PUSH5(ISAd, b, last, limit, trlink); + STACK_PUSH5(ISAd, first, a, limit, trlink); + ISAd += incr, first = a, last = b, limit = next; + } + } else { + if((a - first) <= (b - a)) { + if(1 < (last - b)) { + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + STACK_PUSH5(ISAd, first, a, limit, trlink); + first = b; + } else if(1 < (a - first)) { + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + last = a; + } else { + ISAd += incr, first = a, last = b, limit = next; + } + } else if((last - b) <= (b - a)) { + if(1 < (last - b)) { + STACK_PUSH5(ISAd, first, a, limit, trlink); + STACK_PUSH5(ISAd + incr, a, b, next, trlink); + first = b; + } else { + STACK_PUSH5(ISAd, first, a, limit, trlink); + ISAd += incr, first = a, last = b, limit = next; + } + } else { + STACK_PUSH5(ISAd, first, a, limit, trlink); + STACK_PUSH5(ISAd, b, last, limit, trlink); + ISAd += incr, first = a, last = b, limit = next; + } + } + } else { + if((1 < (b - a)) && (0 <= trlink)) { stack[trlink].d = -1; } + if((a - first) <= (last - b)) { + if(1 < (a - first)) { + STACK_PUSH5(ISAd, b, last, limit, trlink); + last = a; + } else if(1 < (last - b)) { + first = b; + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } else { + if(1 < (last - b)) { + STACK_PUSH5(ISAd, first, a, limit, trlink); + first = b; + } else if(1 < (a - first)) { + last = a; + } else { + STACK_POP5(ISAd, first, last, limit, trlink); + } + } + } + } else { + if(trbudget_check(budget, last - first)) { + limit = tr_ilg(last - first), ISAd += incr; + } else { + if(0 <= trlink) { stack[trlink].d = -1; } + STACK_POP5(ISAd, first, last, limit, trlink); + } + } + } +#undef STACK_SIZE +} + + + +/*---------------------------------------------------------------------------*/ + +/*- Function -*/ + +/* Tandem repeat sort */ +void +trsort(saidx_t *ISA, saidx_t *SA, saidx_t n, saidx_t depth) { + saidx_t *ISAd; + saidx_t *first, *last; + trbudget_t budget; + saidx_t t, skip, unsorted; + + trbudget_init(&budget, tr_ilg(n) * 2 / 3, n); +/* trbudget_init(&budget, tr_ilg(n) * 3 / 4, n); */ + for(ISAd = ISA + depth; -n < *SA; ISAd += ISAd - ISA) { + first = SA; + skip = 0; + unsorted = 0; + do { + if((t = *first) < 0) { first -= t; skip += t; } + else { + if(skip != 0) { *(first + skip) = skip; skip = 0; } + last = SA + ISA[t] + 1; + if(1 < (last - first)) { + budget.count = 0; + tr_introsort(ISA, ISAd, SA, first, last, &budget); + if(budget.count != 0) { unsorted += budget.count; } + else { skip = first - last; } + } else if((last - first) == 1) { + skip = -1; + } + first = last; + } + } while(first < (SA + n)); + if(skip != 0) { *(first + skip) = skip; } + if(unsorted == 0) { break; } + } +} diff --git a/tools/apultra_src/src/libdivsufsort/pkgconfig/CMakeLists.txt b/tools/apultra_src/src/libdivsufsort/pkgconfig/CMakeLists.txt new file mode 100644 index 0000000..ee7063c --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/pkgconfig/CMakeLists.txt @@ -0,0 +1,9 @@ +## generate libdivsufsort.pc ## +set(W64BIT "") +configure_file("${CMAKE_CURRENT_SOURCE_DIR}/libdivsufsort.pc.cmake" "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort.pc" @ONLY) +install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort.pc" DESTINATION ${CMAKE_INSTALL_PKGCONFIGDIR}) +if(BUILD_DIVSUFSORT64) + set(W64BIT "64") + configure_file("${CMAKE_CURRENT_SOURCE_DIR}/libdivsufsort.pc.cmake" "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort64.pc" @ONLY) + install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort64.pc" DESTINATION ${CMAKE_INSTALL_PKGCONFIGDIR}) +endif(BUILD_DIVSUFSORT64) diff --git a/tools/apultra_src/src/libdivsufsort/pkgconfig/libdivsufsort.pc.cmake b/tools/apultra_src/src/libdivsufsort/pkgconfig/libdivsufsort.pc.cmake new file mode 100644 index 0000000..6419d1e --- /dev/null +++ b/tools/apultra_src/src/libdivsufsort/pkgconfig/libdivsufsort.pc.cmake @@ -0,0 +1,11 @@ +prefix=@CMAKE_INSTALL_PREFIX@ +exec_prefix=${prefix} +libdir=@CMAKE_INSTALL_LIBDIR@ +includedir=@CMAKE_INSTALL_INCLUDEDIR@ + +Name: @PROJECT_NAME@@W64BIT@ +Description: @PROJECT_DESCRIPTION@ +Version: @PROJECT_VERSION_FULL@ +URL: @PROJECT_URL@ +Libs: -L${libdir} -ldivsufsort@W64BIT@ +Cflags: -I${includedir} diff --git a/tools/apultra_src/src/matchfinder.c b/tools/apultra_src/src/matchfinder.c new file mode 100644 index 0000000..dcf3464 --- /dev/null +++ b/tools/apultra_src/src/matchfinder.c @@ -0,0 +1,392 @@ +/* + * matchfinder.c - LZ match finder implementation + * + * The following copying information applies to this specific source code file: + * + * Written in 2019 by Emmanuel Marty + * Portions written in 2014-2015 by Eric Biggers + * + * To the extent possible under law, the author(s) have dedicated all copyright + * and related and neighboring rights to this software to the public domain + * worldwide via the Creative Commons Zero 1.0 Universal Public Domain + * Dedication (the "CC0"). + * + * This software is distributed in the hope that it will be useful, but WITHOUT + * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS + * FOR A PARTICULAR PURPOSE. See the CC0 for more details. + * + * You should have received a copy of the CC0 along with this software; if not + * see . + */ + +/* + * Uses the libdivsufsort library Copyright (c) 2003-2008 Yuta Mori + * + * Inspired by cap by Sven-Åke Dahl. https://github.com/svendahl/cap + * Also inspired by Charles Bloom's compression blog. http://cbloomrants.blogspot.com/ + * With ideas from LZ4 by Yann Collet. https://github.com/lz4/lz4 + * With help and support from spke + * + */ + +#include +#include +#include "matchfinder.h" +#include "format.h" +#include "libapultra.h" + +/** + * Hash index into TAG_BITS + * + * @param nIndex index value + * + * @return hash + */ +static inline int apultra_get_index_tag(unsigned int nIndex) { + return (int)(((unsigned long long)nIndex * 11400714819323198485ULL) >> (64ULL - TAG_BITS)); +} + +/** + * Parse input data, build suffix array and overlaid data structures to speed up match finding + * + * @param pCompressor compression context + * @param pInWindow pointer to input data window (previously compressed bytes + bytes to compress) + * @param nInWindowSize total input size in bytes (previously compressed bytes + bytes to compress) + * + * @return 0 for success, non-zero for failure + */ +int apultra_build_suffix_array(apultra_compressor *pCompressor, const unsigned char *pInWindow, const int nInWindowSize) { + unsigned long long *intervals = pCompressor->intervals; + + /* Build suffix array from input data */ + saidx_t *suffixArray = (saidx_t*)intervals; + if (divsufsort_build_array(&pCompressor->divsufsort_context, pInWindow, suffixArray, nInWindowSize) != 0) { + return 100; + } + + int i; + + for (i = nInWindowSize - 1; i >= 0; i--) { + intervals[i] = suffixArray[i]; + } + + int *PLCP = (int*)pCompressor->pos_data; /* Use temporarily */ + int *Phi = PLCP; + int nCurLen = 0; + + /* Compute the permuted LCP first (Kärkkäinen method) */ + Phi[intervals[0]] = -1; + for (i = 1; i < nInWindowSize; i++) + Phi[intervals[i]] = (unsigned int)intervals[i - 1]; + for (i = 0; i < nInWindowSize; i++) { + if (Phi[i] == -1) { + PLCP[i] = 0; + continue; + } + int nMaxLen = (i > Phi[i]) ? (nInWindowSize - i) : (nInWindowSize - Phi[i]); + while (nCurLen < nMaxLen && pInWindow[i + nCurLen] == pInWindow[Phi[i] + nCurLen]) nCurLen++; + PLCP[i] = nCurLen; + if (nCurLen > 0) + nCurLen--; + } + + /* Rotate permuted LCP into the LCP. This has better cache locality than the direct Kasai LCP method. This also + * saves us from having to build the inverse suffix array index, as the LCP is calculated without it using this method, + * and the interval builder below doesn't need it either. */ + intervals[0] &= POS_MASK; + + for (i = 1; i < nInWindowSize; i++) { + int nIndex = (int)(intervals[i] & POS_MASK); + int nLen = PLCP[nIndex]; + if (nLen < MIN_MATCH_SIZE) + nLen = 0; + if (nLen > LCP_MAX) + nLen = LCP_MAX; + int nTaggedLen = 0; + if (nLen) + nTaggedLen = (nLen << TAG_BITS) | (apultra_get_index_tag((unsigned int)nIndex) & ((1 << TAG_BITS) - 1)); + intervals[i] = ((unsigned long long)nIndex) | (((unsigned long long)nTaggedLen) << LCP_SHIFT); + } + + /** + * Build intervals for finding matches + * + * Methodology and code fragment taken from wimlib (CC0 license): + * https://wimlib.net/git/?p=wimlib;a=blob_plain;f=src/lcpit_matchfinder.c;h=a2d6a1e0cd95200d1f3a5464d8359d5736b14cbe;hb=HEAD + */ + unsigned long long * const SA_and_LCP = intervals; + unsigned long long *pos_data = pCompressor->pos_data; + unsigned long long next_interval_idx; + unsigned long long *top = pCompressor->open_intervals; + unsigned long long prev_pos = SA_and_LCP[0] & POS_MASK; + + *top = 0; + intervals[0] = 0; + next_interval_idx = 1; + + for (int r = 1; r < nInWindowSize; r++) { + const unsigned long long next_pos = SA_and_LCP[r] & POS_MASK; + const unsigned long long next_lcp = SA_and_LCP[r] & LCP_MASK; + const unsigned long long top_lcp = *top & LCP_MASK; + + if (next_lcp == top_lcp) { + /* Continuing the deepest open interval */ + pos_data[prev_pos] = *top; + } + else if (next_lcp > top_lcp) { + /* Opening a new interval */ + *++top = next_lcp | next_interval_idx++; + pos_data[prev_pos] = *top; + } + else { + /* Closing the deepest open interval */ + pos_data[prev_pos] = *top; + for (;;) { + const unsigned long long closed_interval_idx = *top-- & POS_MASK; + const unsigned long long superinterval_lcp = *top & LCP_MASK; + + if (next_lcp == superinterval_lcp) { + /* Continuing the superinterval */ + intervals[closed_interval_idx] = *top; + break; + } + else if (next_lcp > superinterval_lcp) { + /* Creating a new interval that is a + * superinterval of the one being + * closed, but still a subinterval of + * its superinterval */ + *++top = next_lcp | next_interval_idx++; + intervals[closed_interval_idx] = *top; + break; + } + else { + /* Also closing the superinterval */ + intervals[closed_interval_idx] = *top; + } + } + } + prev_pos = next_pos; + } + + /* Close any still-open intervals. */ + pos_data[prev_pos] = *top; + for (; top > pCompressor->open_intervals; top--) + intervals[*top & POS_MASK] = *(top - 1); + + /* Success */ + return 0; +} + +/** + * Find matches at the specified offset in the input window + * + * @param pCompressor compression context + * @param nOffset offset to find matches at, in the input window + * @param pMatches pointer to returned matches + * @param pMatchDepth pointer to returned match depths + * @param pMatch1 pointer to 1-byte length, 4 bit offset match + * @param nMaxMatches maximum number of matches to return (0 for none) + * @param nBlockFlags bit 0: 1 for first block, 0 otherwise; bit 1: 1 for last block, 0 otherwise + * + * @return number of matches + */ +int apultra_find_matches_at(apultra_compressor *pCompressor, const int nOffset, apultra_match *pMatches, unsigned short *pMatchDepth, unsigned char *pMatch1, const int nMaxMatches, const int nBlockFlags) { + unsigned long long *intervals = pCompressor->intervals; + unsigned long long *pos_data = pCompressor->pos_data; + unsigned long long ref; + unsigned long long super_ref; + unsigned long long match_pos; + apultra_match *matchptr; + unsigned short *depthptr; + + *pMatch1 = 0; + + /** + * Find matches using intervals + * + * Taken from wimlib (CC0 license): + * https://wimlib.net/git/?p=wimlib;a=blob_plain;f=src/lcpit_matchfinder.c;h=a2d6a1e0cd95200d1f3a5464d8359d5736b14cbe;hb=HEAD + */ + + /* Get the deepest lcp-interval containing the current suffix. */ + ref = pos_data[nOffset]; + + pos_data[nOffset] = 0; + + /* Ascend until we reach a visited interval, the root, or a child of the + * root. Link unvisited intervals to the current suffix as we go. */ + while ((super_ref = intervals[ref & POS_MASK]) & LCP_MASK) { + intervals[ref & POS_MASK] = nOffset | VISITED_FLAG; + ref = super_ref; + } + + if (super_ref == 0) { + /* In this case, the current interval may be any of: + * (1) the root; + * (2) an unvisited child of the root */ + + if (ref != 0) /* Not the root? */ + intervals[ref & POS_MASK] = nOffset | VISITED_FLAG; + return 0; + } + + /* Ascend indirectly via pos_data[] links. */ + match_pos = super_ref & EXCL_VISITED_MASK; + matchptr = pMatches; + depthptr = pMatchDepth; + int nPrevOffset = 0; + int nPrevLen = 0; + int nCurDepth = 0; + unsigned short *cur_depth = NULL; + + if (nOffset > match_pos && (nBlockFlags & 3) == 3) { + int nMatchOffset = (int)(nOffset - match_pos); + int nMatchLen = (int)(ref >> (LCP_SHIFT + TAG_BITS)); + + if ((matchptr - pMatches) < nMaxMatches) { + if (nMatchOffset <= MAX_OFFSET) { + if (nPrevOffset && nPrevLen > 2 && nMatchOffset == (nPrevOffset - 1) && nMatchLen == (nPrevLen - 1) && cur_depth && nCurDepth < LCP_MAX) { + nCurDepth++; + *cur_depth = nCurDepth; + } + else { + nCurDepth = 0; + + cur_depth = depthptr; + matchptr->length = nMatchLen; + matchptr->offset = nMatchOffset; + *depthptr = 0; + matchptr++; + depthptr++; + } + + nPrevLen = nMatchLen; + nPrevOffset = nMatchOffset; + } + } + } + + for (;;) { + if ((super_ref = pos_data[match_pos]) > ref) { + match_pos = intervals[super_ref & POS_MASK] & EXCL_VISITED_MASK; + + if (nOffset > match_pos && (nBlockFlags & 3) == 3) { + int nMatchOffset = (int)(nOffset - match_pos); + int nMatchLen = (int)(ref >> (LCP_SHIFT + TAG_BITS)); + + if ((matchptr - pMatches) < nMaxMatches) { + if (nMatchOffset <= MAX_OFFSET && abs(nMatchOffset - nPrevOffset) >= 288) { + if (nPrevOffset && nPrevLen > 2 && nMatchOffset == (nPrevOffset - 1) && nMatchLen == (nPrevLen - 1) && cur_depth && nCurDepth < LCP_MAX) { + nCurDepth++; + *cur_depth = nCurDepth | 0x8000; + } + else { + nCurDepth = 0; + + cur_depth = depthptr; + matchptr->length = nMatchLen; + matchptr->offset = nMatchOffset; + *depthptr = 0x8000; + matchptr++; + depthptr++; + } + + nPrevLen = nMatchLen; + nPrevOffset = nMatchOffset; + } + } + } + } + + while ((super_ref = pos_data[match_pos]) > ref) + match_pos = intervals[super_ref & POS_MASK] & EXCL_VISITED_MASK; + intervals[ref & POS_MASK] = nOffset | VISITED_FLAG; + pos_data[match_pos] = (unsigned long long)ref; + + int nMatchOffset = (int)(nOffset - match_pos); + int nMatchLen = (int)(ref >> (LCP_SHIFT + TAG_BITS)); + + if ((matchptr - pMatches) < nMaxMatches) { + if (nMatchOffset <= MAX_OFFSET && nMatchOffset != nPrevOffset) { + if (nPrevOffset && nPrevLen > 2 && nMatchOffset == (nPrevOffset - 1) && nMatchLen == (nPrevLen - 1) && cur_depth && nCurDepth < LCP_MAX) { + nCurDepth++; + *cur_depth = nCurDepth; + } + else { + nCurDepth = 0; + + cur_depth = depthptr; + matchptr->length = nMatchLen; + matchptr->offset = nMatchOffset; + *depthptr = 0; + matchptr++; + depthptr++; + } + + nPrevLen = nMatchLen; + nPrevOffset = nMatchOffset; + } + } + + if (nMatchOffset && nMatchOffset < 16 && nMatchLen) + *pMatch1 = nMatchOffset; + + if (super_ref == 0) + break; + ref = super_ref; + match_pos = intervals[ref & POS_MASK] & EXCL_VISITED_MASK; + } + + return (int)(matchptr - pMatches); +} + +/** + * Skip previously compressed bytes + * + * @param pCompressor compression context + * @param nStartOffset current offset in input window (typically 0) + * @param nEndOffset offset to skip to in input window (typically the number of previously compressed bytes) + */ +void apultra_skip_matches(apultra_compressor *pCompressor, const int nStartOffset, const int nEndOffset) { + apultra_match match; + unsigned short depth; + unsigned char match1; + int i; + + /* Skipping still requires scanning for matches, as this also performs a lazy update of the intervals. However, + * we don't store the matches. */ + for (i = nStartOffset; i < nEndOffset; i++) { + apultra_find_matches_at(pCompressor, i, &match, &depth, &match1, 0, 0); + } +} + +/** + * Find all matches for the data to be compressed + * + * @param pCompressor compression context + * @param nMatchesPerOffset maximum number of matches to store for each offset + * @param nStartOffset current offset in input window (typically the number of previously compressed bytes) + * @param nEndOffset offset to end finding matches at (typically the size of the total input window in bytes + * @param nBlockFlags bit 0: 1 for first block, 0 otherwise; bit 1: 1 for last block, 0 otherwise + */ +void apultra_find_all_matches(apultra_compressor *pCompressor, const int nMatchesPerOffset, const int nStartOffset, const int nEndOffset, const int nBlockFlags) { + apultra_match *pMatch = pCompressor->match; + unsigned short *pMatchDepth = pCompressor->match_depth; + unsigned char *pMatch1 = pCompressor->match1; + int i; + + for (i = nStartOffset; i < nEndOffset; i++) { + int nMatches = apultra_find_matches_at(pCompressor, i, pMatch, pMatchDepth, pMatch1, nMatchesPerOffset, nBlockFlags); + + while (nMatches < nMatchesPerOffset) { + pMatch[nMatches].length = 0; + pMatch[nMatches].offset = 0; + pMatchDepth[nMatches] = 0; + nMatches++; + } + + pMatch += nMatchesPerOffset; + pMatchDepth += nMatchesPerOffset; + pMatch1++; + } +} diff --git a/tools/apultra_src/src/matchfinder.h b/tools/apultra_src/src/matchfinder.h new file mode 100644 index 0000000..7d68eaf --- /dev/null +++ b/tools/apultra_src/src/matchfinder.h @@ -0,0 +1,94 @@ +/* + * matchfinder.h - LZ match finder definitions + * + * Copyright (C) 2019 Emmanuel Marty + * + * This software is provided 'as-is', without any express or implied + * warranty. In no event will the authors be held liable for any damages + * arising from the use of this software. + * + * Permission is granted to anyone to use this software for any purpose, + * including commercial applications, and to alter it and redistribute it + * freely, subject to the following restrictions: + * + * 1. The origin of this software must not be misrepresented; you must not + * claim that you wrote the original software. If you use this software + * in a product, an acknowledgment in the product documentation would be + * appreciated but is not required. + * 2. Altered source versions must be plainly marked as such, and must not be + * misrepresented as being the original software. + * 3. This notice may not be removed or altered from any source distribution. + */ + +/* + * Uses the libdivsufsort library Copyright (c) 2003-2008 Yuta Mori + * + * Inspired by cap by Sven-Åke Dahl. https://github.com/svendahl/cap + * Also inspired by Charles Bloom's compression blog. http://cbloomrants.blogspot.com/ + * With ideas from LZ4 by Yann Collet. https://github.com/lz4/lz4 + * With help and support from spke + * + */ + +#ifndef _MATCHFINDER_H +#define _MATCHFINDER_H + +#ifdef __cplusplus +extern "C" { +#endif + +/* Forward declarations */ +typedef struct _apultra_match apultra_match; +typedef struct _apultra_compressor apultra_compressor; + +/** + * Parse input data, build suffix array and overlaid data structures to speed up match finding + * + * @param pCompressor compression context + * @param pInWindow pointer to input data window (previously compressed bytes + bytes to compress) + * @param nInWindowSize total input size in bytes (previously compressed bytes + bytes to compress) + * + * @return 0 for success, non-zero for failure + */ +int apultra_build_suffix_array(apultra_compressor *pCompressor, const unsigned char *pInWindow, const int nInWindowSize); + +/** + * Find matches at the specified offset in the input window + * + * @param pCompressor compression context + * @param nOffset offset to find matches at, in the input window + * @param pMatches pointer to returned matches + * @param pMatchDepth pointer to returned match depths + * @param pMatch1 pointer to 1-byte length, 4 bit offset match + * @param nMaxMatches maximum number of matches to return (0 for none) + * @param nBlockFlags bit 0: 1 for first block, 0 otherwise; bit 1: 1 for last block, 0 otherwise + * + * @return number of matches + */ +int apultra_find_matches_at(apultra_compressor *pCompressor, const int nOffset, apultra_match *pMatches, unsigned short *pMatchDepth, unsigned char *pMatch1, const int nMaxMatches, const int nBlockFlags); + +/** + * Skip previously compressed bytes + * + * @param pCompressor compression context + * @param nStartOffset current offset in input window (typically 0) + * @param nEndOffset offset to skip to in input window (typically the number of previously compressed bytes) + */ +void apultra_skip_matches(apultra_compressor *pCompressor, const int nStartOffset, const int nEndOffset); + +/** + * Find all matches for the data to be compressed + * + * @param pCompressor compression context + * @param nMatchesPerOffset maximum number of matches to store for each offset + * @param nStartOffset current offset in input window (typically the number of previously compressed bytes) + * @param nEndOffset offset to end finding matches at (typically the size of the total input window in bytes + * @param nBlockFlags bit 0: 1 for first block, 0 otherwise; bit 1: 1 for last block, 0 otherwise + */ +void apultra_find_all_matches(apultra_compressor *pCompressor, const int nMatchesPerOffset, const int nStartOffset, const int nEndOffset, const int nBlockFlags); + +#ifdef __cplusplus +} +#endif + +#endif /* _MATCHFINDER_H */ diff --git a/tools/apultra_src/src/shrink.c b/tools/apultra_src/src/shrink.c new file mode 100644 index 0000000..127c6fb --- /dev/null +++ b/tools/apultra_src/src/shrink.c @@ -0,0 +1,1615 @@ +/* + * shrink.c - compressor implementation + * + * Copyright (C) 2019 Emmanuel Marty + * + * This software is provided 'as-is', without any express or implied + * warranty. In no event will the authors be held liable for any damages + * arising from the use of this software. + * + * Permission is granted to anyone to use this software for any purpose, + * including commercial applications, and to alter it and redistribute it + * freely, subject to the following restrictions: + * + * 1. The origin of this software must not be misrepresented; you must not + * claim that you wrote the original software. If you use this software + * in a product, an acknowledgment in the product documentation would be + * appreciated but is not required. + * 2. Altered source versions must be plainly marked as such, and must not be + * misrepresented as being the original software. + * 3. This notice may not be removed or altered from any source distribution. + */ + +/* + * Uses the libdivsufsort library Copyright (c) 2003-2008 Yuta Mori + * + * Inspired by cap by Sven-Åke Dahl. https://github.com/svendahl/cap + * Also inspired by Charles Bloom's compression blog. http://cbloomrants.blogspot.com/ + * With ideas from LZ4 by Yann Collet. https://github.com/lz4/lz4 + * With help and support from spke + * + */ + +#include +#include +#include +#include "libapultra.h" +#include "matchfinder.h" +#include "shrink.h" +#include "format.h" + +#define TOKEN_PREFIX_SIZE 1 /* literal/ match bit */ + +#define TOKEN_CODE_LARGE_MATCH 0 /* 0 */ +#define TOKEN_SIZE_LARGE_MATCH 1 + +#define TOKEN_CODE_7BIT_MATCH 2 /* 10 */ +#define TOKEN_SIZE_7BIT_MATCH 2 + +#define TOKEN_CODE_4BIT_MATCH 3 /* 11 */ +#define TOKEN_SIZE_4BIT_MATCH 2 + +#define CountShift(N,bits) if ((N)>>(bits)) { (N)>>=(bits); (n) += (bits); } + +/** Code values for variable 8+gamma2 bits offset + gamma2 len match; 7 bits offset + 1 bit len match; and 4 bits offset + fixed 1 byte len match */ +static const int _token_code[3] = { TOKEN_CODE_LARGE_MATCH, TOKEN_CODE_7BIT_MATCH, TOKEN_CODE_4BIT_MATCH }; + +/** Code sizes for variable 8+gamma2 bits offset + gamma2 len match; 7 bits offset + 1 bit len match; and 4 bits offset + fixed 1 byte len match */ +static const int _token_size[3] = { TOKEN_SIZE_LARGE_MATCH, TOKEN_SIZE_7BIT_MATCH, TOKEN_SIZE_4BIT_MATCH }; + +/** Gamma2 bit counts for common values, up to 255 */ +static char _gamma2_size[256] = { + 0, 0, 2, 2, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, +}; + +/** + * Write bit to output (compressed) buffer + * + * @param pOutData pointer to output buffer + * @param nOutOffset current write index into output buffer + * @param nMaxOutDataSize maximum size of output buffer, in bytes + * @param nBit value of bit to write (0 or 1) + * @param nCurBitsOffset write index into output buffer, of current byte being filled with bits + * @param nCurBitMask bit shifter + * @param nBitBufferIdx index of bit buffer to write to + * + * @return updated write index into output buffer, or -1 in case of an error + */ +static int apultra_write_bit(unsigned char *pOutData, int nOutOffset, const int nMaxOutDataSize, const int nBit, int *nCurBitsOffset, int *nCurBitMask, const int nBitBufferIdx) { + if (nOutOffset < 0) return -1; + + if (nCurBitsOffset[nBitBufferIdx] == INT_MIN) { + /* Allocate a new byte in the stream to pack bits in */ + if (nOutOffset >= nMaxOutDataSize) return -1; + nCurBitsOffset[nBitBufferIdx] = nOutOffset; + nCurBitMask[nBitBufferIdx] = 1 << 7; + pOutData[nOutOffset++] = 0; + } + + if (nBit) { + pOutData[nCurBitsOffset[nBitBufferIdx]] |= nCurBitMask[nBitBufferIdx]; + } + + nCurBitMask[nBitBufferIdx] >>= 1; + if (nCurBitMask[nBitBufferIdx] == 0) { + /* Current byte is full */ + nCurBitsOffset[nBitBufferIdx] = INT_MIN; + } + + return nOutOffset; +} + +/** + * Get size of gamma2 encoded value + * + * @param nValue value of evaluate (2..n) + * + * @return number of bits required + */ +static int apultra_get_gamma2_size(int nValue) { + if (nValue >= 0 && nValue < 256) + return _gamma2_size[nValue]; + else { + unsigned int n = 0; + CountShift(nValue, 16); + CountShift(nValue, 8); + CountShift(nValue, 4); + CountShift(nValue, 2); + CountShift(nValue, 1); + + return n << 1; + } +} + +/** + * Write gamma2 encoded value to output (compressed) buffer + * + * @param pOutData pointer to output buffer + * @param nOutOffset current write index into output buffer + * @param nMaxOutDataSize maximum size of output buffer, in bytes + * @param nValue value of write (2..n) + * @param nCurBitsOffset write index into output buffer, of current byte being filled with bits + * @param nCurBitMask bit shifter + * @param nBitBufferIdx index of bit buffer to write to + * + * @return updated write index into output buffer, or -1 in case of an error + */ +static int apultra_write_gamma2_value(unsigned char *pOutData, int nOutOffset, const int nMaxOutDataSize, int nValue, int *nCurBitsOffset, int *nCurBitMask, const int nBitBufferIdx) { + int msb = 30; + while ((nValue >> msb--) == 0); + + if (nBitBufferIdx == 0) { + /* Standard aPLib encoding. */ + while (msb >= 0) { + int bit = (nValue >> msb) & 1; + + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, bit ? 1 : 0, nCurBitsOffset, nCurBitMask, nBitBufferIdx); + msb--; + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, msb >= 0 ? 1 : 0, nCurBitsOffset, nCurBitMask, nBitBufferIdx); + } + } + else { + /* Enhanced encoding for 8-bit microprocessors ... + * 1) Write out values of 256 and higher lo-byte first (so the gamma2 decoder only needs to rotate a byte). + * 2) Swap meaning of continue/stop bits (saves a byte on the 6502, with no effect on other platforms). + */ + if (msb >= 8) { + int btm = 7; + /* Write lo-byte of nValue first. */ + while (btm >= 0) { + int bit = (nValue >> btm) & 1; + + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, bit ? 1 : 0, nCurBitsOffset, nCurBitMask, nBitBufferIdx); + btm--; + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, 0, nCurBitsOffset, nCurBitMask, nBitBufferIdx); + } + /* Then write the remaining bits. */ + nValue >>= 8; + msb -= 8; + } + + while (msb >= 0) { + int bit = (nValue >> msb) & 1; + + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, bit ? 1 : 0, nCurBitsOffset, nCurBitMask, nBitBufferIdx); + msb--; + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, msb >= 0 ? 0 : 1, nCurBitsOffset, nCurBitMask, nBitBufferIdx); + } + } + + return nOutOffset; +} + +/** + * Get the number of extra bits required to represent a literals length + * + * @param nLength literals length + * + * @return number of extra bits required + */ +static inline int apultra_get_literals_varlen_size(const int nLength) { + return nLength; +} + +/** + * Get the number of extra bits required to represent a match offset + * + * @param nLength match length + * @param nMatchOffset match offset + * @param nFollowsLiteral non-zero if the match follows a literal, zero if it immediately follows another match + * + * @return number of extra bits required + */ +static inline int apultra_get_offset_varlen_size(const int nLength, const int nMatchOffset, const int nFollowsLiteral) { + if (nLength == 1 && nMatchOffset < 16) + return 4 + TOKEN_SIZE_4BIT_MATCH; + else { + if (nLength <= 3 && nMatchOffset < 128) + return 8 + TOKEN_SIZE_7BIT_MATCH; + else { + if (nFollowsLiteral) + return 8 + TOKEN_SIZE_LARGE_MATCH + apultra_get_gamma2_size((nMatchOffset >> 8) + 3); + else + return 8 + TOKEN_SIZE_LARGE_MATCH + apultra_get_gamma2_size((nMatchOffset >> 8) + 2); + } + } +} + +/** + * Get the number of extra bits required to represent a rep-match + * + * @return number of extra bits required + */ +static inline int apultra_get_rep_offset_varlen_size(void) { + return TOKEN_SIZE_LARGE_MATCH + 2 /* apultra_get_gamma2_size(2) */; +} + +/** + * Get the number of extra bits required to represent a match length + * + * @param nLength match length + * @param nMatchOffset match offset + * @param nIsRepMatch non-zero if this is a rep-match, zero if it is a regular match + * + * @return number of extra bits required + */ +static inline int apultra_get_match_varlen_size(int nLength, const int nMatchOffset, const int nIsRepMatch) { + if (nLength == 1 && nMatchOffset < 16) + return 0; + else { + if (nLength <= 3 && nMatchOffset < 128 && !nIsRepMatch) + return 0; + else { + if (nMatchOffset < 128 && !nIsRepMatch) + nLength -= 2; + if (nMatchOffset < MINMATCH3_OFFSET || nIsRepMatch) + return apultra_get_gamma2_size(nLength); + else if (nMatchOffset < MINMATCH4_OFFSET) + return apultra_get_gamma2_size(nLength - 1); + else + return apultra_get_gamma2_size(nLength - 2); + } + } +} + +/** + * Write extra encoded match length bytes to output (compressed) buffer. The caller must first check that there is enough + * room to write the bytes. + * + * @param pOutData pointer to output buffer + * @param nOutOffset current write index into output buffer + * @param nMaxOutDataSize maximum size of output buffer, in bytes + * @param nCurBitsOffset write index into output buffer, of current byte being filled with bits + * @param nCurBitMask bit shifter + * @param nLength match length + * @param nMatchOffset match offset + * @param nIsRepMatch non-zero if this is a rep-match, zero if it is a regular match + * @param nBitBufferIdx index of bit buffer to write to + * + * @return updated write index into output buffer, or -1 in case of an error + */ +static inline int apultra_write_match_varlen(unsigned char *pOutData, int nOutOffset, const int nMaxOutDataSize, int *nCurBitsOffset, int *nCurBitMask, const int nBitBufferIdx, int nLength, const int nMatchOffset, const int nIsRepMatch) { + if (nLength < 2) + return -1; + + if (nMatchOffset < 128 && !nIsRepMatch) + nLength -= 2; + if (nMatchOffset < MINMATCH3_OFFSET || nIsRepMatch) + return apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, nLength, nCurBitsOffset, nCurBitMask, nBitBufferIdx); + else if (nMatchOffset < MINMATCH4_OFFSET) + return apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, nLength - 1, nCurBitsOffset, nCurBitMask, nBitBufferIdx); + else + return apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, nLength - 2, nCurBitsOffset, nCurBitMask, nBitBufferIdx); +} + +/** + * Insert forward rep candidate + * + * @param pCompressor compression context + * @param pInWindow pointer to input data window (previously compressed bytes + bytes to compress) + * @param i input data window position whose matches are being considered + * @param nMatchOffset match offset to use as rep candidate + * @param nStartOffset current offset in input window (typically the number of previously compressed bytes) + * @param nEndOffset offset to end finding matches at (typically the size of the total input window in bytes + * @param nDepth current insertion depth + */ +static void apultra_insert_forward_match(apultra_compressor *pCompressor, const unsigned char *pInWindow, const int i, const int nMatchOffset, const int nStartOffset, const int nEndOffset, const int nMatchesPerArrival, int nDepth) { + apultra_arrival *arrival = pCompressor->arrival - (nStartOffset * NMATCHES_PER_ARRIVAL); + int j; + + if (nDepth >= 10) return; + + for (j = 0; j < nMatchesPerArrival && arrival[(i * NMATCHES_PER_ARRIVAL) + j].from_slot; j++) { + int nRepOffset = arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_offset; + + if (nMatchOffset != nRepOffset && nRepOffset) { + int nRepPos = arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_pos; + + if (arrival[(i * NMATCHES_PER_ARRIVAL) + j].follows_literal && + nRepPos && + nRepPos > nMatchOffset && + nRepPos < nEndOffset) { + int nCurRepLen = 0; + + int nMaxRepLen = nEndOffset - nRepPos; + if (nMaxRepLen > LCP_MAX) + nMaxRepLen = LCP_MAX; + while ((nCurRepLen + 8) < nMaxRepLen && !memcmp(pInWindow + nRepPos + nCurRepLen, pInWindow + nRepPos - nMatchOffset + nCurRepLen, 8)) + nCurRepLen += 8; + while ((nCurRepLen + 4) < nMaxRepLen && !memcmp(pInWindow + nRepPos + nCurRepLen, pInWindow + nRepPos - nMatchOffset + nCurRepLen, 4)) + nCurRepLen += 4; + while (nCurRepLen < nMaxRepLen && pInWindow[nRepPos + nCurRepLen] == pInWindow[nRepPos - nMatchOffset + nCurRepLen]) + nCurRepLen++; + + if (nCurRepLen >= 2) { + apultra_match *fwd_match = pCompressor->match + ((nRepPos - nStartOffset) << MATCHES_PER_INDEX_SHIFT); + unsigned short *fwd_depth = pCompressor->match_depth + ((nRepPos - nStartOffset) << MATCHES_PER_INDEX_SHIFT); + int exists = 0; + int r; + + for (r = 0; r < NMATCHES_PER_INDEX && fwd_match[r].length >= MIN_MATCH_SIZE; r++) { + if (fwd_match[r].offset == nMatchOffset && (fwd_depth[r] & 0x7fff) == 0) { + exists = 1; + + if ((int)fwd_match[r].length < nCurRepLen) { + fwd_match[r].length = nCurRepLen; + fwd_depth[r] = 0; + apultra_insert_forward_match(pCompressor, pInWindow, nRepPos, nMatchOffset, nStartOffset, nEndOffset, nMatchesPerArrival, nDepth + 1); + } + break; + } + } + + if (!exists && r < NMATCHES_PER_INDEX) { + fwd_match[r].offset = nMatchOffset; + fwd_match[r].length = nCurRepLen; + fwd_depth[r] = 0; + + apultra_insert_forward_match(pCompressor, pInWindow, nRepPos, nMatchOffset, nStartOffset, nEndOffset, nMatchesPerArrival, nDepth + 1); + } + } + } + } + } +} + +/** + * Attempt to pick optimal matches, so as to produce the smallest possible output that decompresses to the same input + * + * @param pCompressor compression context + * @param pInWindow pointer to input data window (previously compressed bytes + bytes to compress) + * @param nStartOffset current offset in input window (typically the number of previously compressed bytes) + * @param nEndOffset offset to end finding matches at (typically the size of the total input window in bytes + * @param nInsertForwardReps non-zero to insert forward repmatch candidates, zero to use the previously inserted candidates + * @param nCurRepMatchOffset starting rep offset for this block + * @param nBlockFlags bit 0: 1 for first block, 0 otherwise; bit 1: 1 for last block, 0 otherwise + */ +static void apultra_optimize_forward(apultra_compressor *pCompressor, const unsigned char *pInWindow, const int nStartOffset, const int nEndOffset, const int nInsertForwardReps, const int *nCurRepMatchOffset, const int nBlockFlags, const int nMatchesPerArrival) { + apultra_arrival *arrival = pCompressor->arrival - (nStartOffset * NMATCHES_PER_ARRIVAL); + int i, j, n; + + if ((nEndOffset - nStartOffset) > pCompressor->block_size) return; + + memset(arrival + (nStartOffset * NMATCHES_PER_ARRIVAL), 0, sizeof(apultra_arrival) * ((nEndOffset - nStartOffset + 1) * NMATCHES_PER_ARRIVAL)); + + arrival[nStartOffset * NMATCHES_PER_ARRIVAL].from_slot = -1; + arrival[nStartOffset * NMATCHES_PER_ARRIVAL].rep_offset = *nCurRepMatchOffset; + + for (i = (nStartOffset * NMATCHES_PER_ARRIVAL); i != ((nEndOffset+1) * NMATCHES_PER_ARRIVAL); i++) { + arrival[i].cost = 0x40000000; + } + + for (i = nStartOffset; i != nEndOffset; i++) { + int m; + + unsigned char *match1 = pCompressor->match1 + (i - nStartOffset); + + if ((pInWindow[i] != 0 && (*match1) == 0) || (i == nStartOffset && (nBlockFlags & 1))) { + for (j = 0; j < nMatchesPerArrival && arrival[(i * NMATCHES_PER_ARRIVAL) + j].from_slot; j++) { + int nPrevCost = arrival[(i * NMATCHES_PER_ARRIVAL) + j].cost & 0x3fffffff; + int nCodingChoiceCost = nPrevCost + 8 /* literal */; + + nCodingChoiceCost ++ /* Literal bit */; + + apultra_arrival *pDestSlots = &arrival[(i + 1) * NMATCHES_PER_ARRIVAL]; + if (nCodingChoiceCost <= pDestSlots[nMatchesPerArrival - 1].cost) { + int nScore = arrival[(i * NMATCHES_PER_ARRIVAL) + j].score + 1; + int exists = 0; + + for (n = 0; + n < nMatchesPerArrival && pDestSlots[n].cost <= nCodingChoiceCost; + n++) { + if (pDestSlots[n].rep_offset == arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_offset) { + exists = 1; + break; + } + } + + if (!exists) { + for (n = 0; n < nMatchesPerArrival; n++) { + apultra_arrival *pDestArrival = &pDestSlots[n]; + if (nCodingChoiceCost < pDestArrival->cost || + (nCodingChoiceCost == pDestArrival->cost && nScore < pDestArrival->score)) { + int z; + + for (z = n; z < nMatchesPerArrival - 1; z++) { + if (pDestSlots[z].rep_offset == arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_offset) + break; + } + + memmove(&pDestSlots[n + 1], + &pDestSlots[n], + sizeof(apultra_arrival) * (z - n)); + + pDestArrival->cost = nCodingChoiceCost; + pDestArrival->from_pos = i; + pDestArrival->from_slot = j + 1; + pDestArrival->follows_literal = 1; + pDestArrival->match_offset = 0; + pDestArrival->match_len = 0; + pDestArrival->score = nScore; + pDestArrival->rep_offset = arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_offset; + pDestArrival->rep_pos = arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_pos; + break; + } + } + } + } + } + } + else { + int nShortOffset = (pInWindow[i] == 0) ? 0 : (*match1); + + for (j = 0; j < nMatchesPerArrival && arrival[(i * NMATCHES_PER_ARRIVAL) + j].from_slot; j++) { + int nPrevCost = arrival[(i * NMATCHES_PER_ARRIVAL) + j].cost & 0x3fffffff; + int nCodingChoiceCost = nPrevCost + TOKEN_PREFIX_SIZE /* token */ /* the actual cost of the literals themselves accumulates up the chain */ + (4 + TOKEN_SIZE_4BIT_MATCH) /* command and offset cost; no length cost */; + + apultra_arrival *pDestSlots = &arrival[(i + 1) * NMATCHES_PER_ARRIVAL]; + if (nCodingChoiceCost <= pDestSlots[nMatchesPerArrival - 1].cost) { + int nScore = arrival[(i * NMATCHES_PER_ARRIVAL) + j].score + (nShortOffset ? 3 : 1); + int exists = 0; + + for (n = 0; + n < nMatchesPerArrival && pDestSlots[n].cost <= nCodingChoiceCost; + n++) { + if (pDestSlots[n].rep_offset == arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_offset) { + exists = 1; + break; + } + } + + if (!exists) { + for (n = 0; n < nMatchesPerArrival; n++) { + apultra_arrival *pDestArrival = &pDestSlots[n]; + + if (nCodingChoiceCost < pDestArrival->cost || + (nCodingChoiceCost == pDestArrival->cost && nScore < pDestArrival->score)) { + int z; + + for (z = n; z < nMatchesPerArrival - 1; z++) { + if (pDestSlots[z].rep_offset == arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_offset) + break; + } + + memmove(&pDestSlots[n + 1], + &pDestSlots[n], + sizeof(apultra_arrival) * (z - n)); + + pDestArrival->cost = nCodingChoiceCost; + pDestArrival->from_pos = i; + pDestArrival->from_slot = j + 1; + pDestArrival->match_offset = nShortOffset; + pDestArrival->match_len = 1; + pDestArrival->follows_literal = 1; + pDestArrival->score = nScore; + pDestArrival->rep_offset = arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_offset; + pDestArrival->rep_pos = arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_pos; + break; + } + } + } + } + } + } + + if (i == nStartOffset && (nBlockFlags & 1)) continue; + + apultra_match *match = pCompressor->match + ((i - nStartOffset) << MATCHES_PER_INDEX_SHIFT); + unsigned short *match_depth = pCompressor->match_depth + ((i - nStartOffset) << MATCHES_PER_INDEX_SHIFT); + const int nRepMatchOffsetCost = TOKEN_PREFIX_SIZE /* token */ + apultra_get_rep_offset_varlen_size(); + + int nMinRepLen[NMATCHES_PER_ARRIVAL]; + memset(nMinRepLen, 0, NMATCHES_PER_ARRIVAL * sizeof(int)); + + for (m = 0; m < NMATCHES_PER_INDEX && match[m].length; m++) { + const int nOrigMatchLen = match[m].length; + const int nOrigMatchOffset = match[m].offset; + const unsigned int nOrigMatchDepth = match_depth[m] & 0x7fff; + const int nScorePenalty = 3 + ((match_depth[m] & 0x8000) >> 15); + + for (unsigned int d = 0; d <= nOrigMatchDepth; d += (nOrigMatchDepth ? nOrigMatchDepth : 1)) { + int nStartingMatchLen, k; + int nMaxRepLen[NMATCHES_PER_ARRIVAL]; + int nMinMatchLen[NMATCHES_PER_ARRIVAL]; + + const int nMatchOffset = nOrigMatchOffset - d; + int nMatchLen = nOrigMatchLen - d; + + if ((i + nMatchLen) > nEndOffset) + nMatchLen = nEndOffset - i; + + for (j = 0; j < nMatchesPerArrival && arrival[(i * NMATCHES_PER_ARRIVAL) + j].from_slot; j++) { + int nRepOffset = arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_offset; + int nCurMaxLen = 0; + + if (arrival[(i * NMATCHES_PER_ARRIVAL) + j].follows_literal && + nRepOffset) { + + if (nMatchOffset == nRepOffset) + nCurMaxLen = nMatchLen; + else { + if (i > nRepOffset && + (i - nRepOffset + nMatchLen) <= nEndOffset) { + nCurMaxLen = nMinRepLen[j]; + while ((nCurMaxLen + 8) < nMatchLen && !memcmp(pInWindow + i - nRepOffset + nCurMaxLen, pInWindow + i - nMatchOffset + nCurMaxLen, 8)) + nCurMaxLen += 8; + while ((nCurMaxLen + 4) < nMatchLen && !memcmp(pInWindow + i - nRepOffset + nCurMaxLen, pInWindow + i - nMatchOffset + nCurMaxLen, 4)) + nCurMaxLen += 4; + while (nCurMaxLen < nMatchLen && pInWindow[i - nRepOffset + nCurMaxLen] == pInWindow[i - nMatchOffset + nCurMaxLen]) + nCurMaxLen++; + nMinRepLen[j] = nCurMaxLen; + } + } + } + + nMaxRepLen[j] = nCurMaxLen; + + int nIsRepMatch = (nMatchOffset == nRepOffset && + arrival[(i * NMATCHES_PER_ARRIVAL) + j].follows_literal) ? 1 : 0; + + if (nIsRepMatch == 0) { + if (nMatchOffset < MINMATCH3_OFFSET) + nMinMatchLen[j] = 2; + else { + if (nMatchOffset < MINMATCH4_OFFSET) + nMinMatchLen[j] = 3; + else + nMinMatchLen[j] = 4; + } + } + else { + nMinMatchLen[j] = nMatchLen + 1; + } + } + while (j < NMATCHES_PER_ARRIVAL) { + nMaxRepLen[j] = 0; + nMinMatchLen[j++] = 0; + } + + if (nInsertForwardReps) + apultra_insert_forward_match(pCompressor, pInWindow, i, nMatchOffset, nStartOffset, nEndOffset, nMatchesPerArrival, 0); + + if (nMatchLen >= LEAVE_ALONE_MATCH_SIZE && i >= nMatchLen) + nStartingMatchLen = nMatchLen; + else + nStartingMatchLen = 2; + + if (nStartingMatchLen <= nMatchLen) { + int nNoRepMatchOffsetCostForLit[2]; + + if (nStartingMatchLen <= 3) { + nNoRepMatchOffsetCostForLit[0] = TOKEN_PREFIX_SIZE /* token */ + apultra_get_offset_varlen_size(2, nMatchOffset, 0); + nNoRepMatchOffsetCostForLit[1] = TOKEN_PREFIX_SIZE /* token */ + apultra_get_offset_varlen_size(2, nMatchOffset, 1); + } + else { + nNoRepMatchOffsetCostForLit[0] = TOKEN_PREFIX_SIZE /* token */ + apultra_get_offset_varlen_size(4, nMatchOffset, 0); + nNoRepMatchOffsetCostForLit[1] = TOKEN_PREFIX_SIZE /* token */ + apultra_get_offset_varlen_size(4, nMatchOffset, 1); + } + + for (k = nStartingMatchLen; k <= nMatchLen; k++) { + int nNoRepMatchMatchLenCost; + int nRepMatchMatchLenCost = apultra_get_gamma2_size(k); + + if (k <= 3 && nMatchOffset < 128) + nNoRepMatchMatchLenCost = 0; + else { + if (nMatchOffset < 128 || nMatchOffset >= MINMATCH4_OFFSET) + nNoRepMatchMatchLenCost = apultra_get_gamma2_size(k - 2); + else if (nMatchOffset < MINMATCH3_OFFSET) + nNoRepMatchMatchLenCost = nRepMatchMatchLenCost; + else + nNoRepMatchMatchLenCost = apultra_get_gamma2_size(k - 1); + } + + int nRepMatchCmdCost = nRepMatchOffsetCost + nRepMatchMatchLenCost; + apultra_arrival *pDestSlots = &arrival[(i + k) * NMATCHES_PER_ARRIVAL]; + + for (j = 0; j < nMatchesPerArrival && arrival[(i * NMATCHES_PER_ARRIVAL) + j].from_slot; j++) { + int nPrevCost = arrival[(i * NMATCHES_PER_ARRIVAL) + j].cost & 0x3fffffff; + + int nRepCodingChoiceCost = nPrevCost /* the actual cost of the literals themselves accumulates up the chain */ + nRepMatchCmdCost; + + if (nRepCodingChoiceCost <= pDestSlots[nMatchesPerArrival - 1].cost) { + if (k >= nMinMatchLen[j]) { + int nMatchCmdCost = nNoRepMatchMatchLenCost + nNoRepMatchOffsetCostForLit[arrival[(i * NMATCHES_PER_ARRIVAL) + j].follows_literal]; + int nCodingChoiceCost = nPrevCost /* the actual cost of the literals themselves accumulates up the chain */ + nMatchCmdCost; + + if (nCodingChoiceCost <= pDestSlots[nMatchesPerArrival - 1].cost) { + int exists = 0; + + for (n = 0; + n < nMatchesPerArrival && pDestSlots[n].cost <= nCodingChoiceCost; + n++) { + if (pDestSlots[n].rep_offset == nMatchOffset) { + exists = 1; + break; + } + } + + if (!exists) { + int nScore = arrival[(i * NMATCHES_PER_ARRIVAL) + j].score + nScorePenalty; + + if (nMatchLen >= LCP_MAX) + nCodingChoiceCost -= 1; + + for (n = 0; n < nMatchesPerArrival - 1; n++) { + apultra_arrival *pDestArrival = &pDestSlots[n]; + + if (nCodingChoiceCost < pDestArrival->cost || + (nCodingChoiceCost == pDestArrival->cost && nScore < pDestArrival->score)) { + int z; + + for (z = n; z < nMatchesPerArrival - 1; z++) { + if (pDestSlots[z].rep_offset == nMatchOffset) + break; + } + + if (z == (nMatchesPerArrival - 1) && pDestSlots[z].from_slot && pDestSlots[z].match_len < 2) + z--; + + memmove(&pDestSlots[n + 1], + &pDestSlots[n], + sizeof(apultra_arrival) * (z - n)); + + pDestArrival->cost = nCodingChoiceCost; + pDestArrival->from_pos = i; + pDestArrival->from_slot = j + 1; + pDestArrival->match_offset = nMatchOffset; + pDestArrival->match_len = k; + pDestArrival->follows_literal = 0; + pDestArrival->score = nScore; + pDestArrival->rep_offset = nMatchOffset; + pDestArrival->rep_pos = i; + nMinMatchLen[j] = k + 1; + break; + } + } + } + } + } + + /* If this coding choice doesn't rep-match, see if we still get a match by using the current repmatch offset for this arrival. This can occur (and not have the + * matchfinder offer the offset in the first place, or have too many choices with the same cost to retain the repmatchable offset) when compressing regions + * of identical bytes, for instance. Checking for this provides a big compression win on some files. */ + + if (nMaxRepLen[j] >= k) { + int nRepOffset = arrival[(i * NMATCHES_PER_ARRIVAL) + j].rep_offset; + + /* A match is possible at the rep offset; insert the extra coding choice. */ + + int exists = 0; + + for (n = 0; + n < nMatchesPerArrival && pDestSlots[n].cost <= nRepCodingChoiceCost; + n++) { + if (pDestSlots[n].rep_offset == nRepOffset) { + exists = 1; + break; + } + } + + if (!exists) { + int nScore = arrival[(i * NMATCHES_PER_ARRIVAL) + j].score + 2; + + for (n = 0; n < nMatchesPerArrival; n++) { + apultra_arrival *pDestArrival = &pDestSlots[n]; + + if (nRepCodingChoiceCost < pDestArrival->cost || + (nRepCodingChoiceCost == pDestArrival->cost && nScore < pDestArrival->score)) { + int z; + + for (z = n; z < nMatchesPerArrival - 1; z++) { + if (pDestSlots[z].rep_offset == nRepOffset) + break; + } + + memmove(&pDestSlots[n + 1], + &pDestSlots[n], + sizeof(apultra_arrival) * (z - n)); + + pDestArrival->cost = nRepCodingChoiceCost; + pDestArrival->from_pos = i; + pDestArrival->from_slot = j + 1; + pDestArrival->match_offset = nRepOffset; + pDestArrival->match_len = k; + pDestArrival->follows_literal = 0; + pDestArrival->score = nScore; + pDestArrival->rep_offset = nRepOffset; + pDestArrival->rep_pos = i; + break; + } + } + } + } + } + else { + break; + } + } + + if (k == 3) { + nNoRepMatchOffsetCostForLit[0] = TOKEN_PREFIX_SIZE /* token */ + apultra_get_offset_varlen_size(4, nMatchOffset, 0); + nNoRepMatchOffsetCostForLit[1] = TOKEN_PREFIX_SIZE /* token */ + apultra_get_offset_varlen_size(4, nMatchOffset, 1); + } + } + } + + if (nOrigMatchLen >= 512) + break; + } + } + } + + apultra_arrival *end_arrival = &arrival[(i * NMATCHES_PER_ARRIVAL) + 0]; + apultra_final_match *pBestMatch = pCompressor->best_match - nStartOffset; + + int nEndCost = end_arrival->cost; + + while (end_arrival->from_slot > 0 && end_arrival->from_pos >= 0 && (int)end_arrival->from_pos < nEndOffset) { + pBestMatch[end_arrival->from_pos].length = end_arrival->match_len; + pBestMatch[end_arrival->from_pos].offset = end_arrival->match_offset; + + end_arrival = &arrival[(end_arrival->from_pos * NMATCHES_PER_ARRIVAL) + (end_arrival->from_slot-1)]; + } +} + +/** + * Attempt to replace matches by literals when it makes the final bitstream smaller, and merge large matches + * + * @param pCompressor compression context + * @param pInWindow pointer to input data window (previously compressed bytes + bytes to compress) + * @param pBestMatch optimal matches to evaluate and update + * @param nStartOffset current offset in input window (typically the number of previously compressed bytes) + * @param nEndOffset offset to end finding matches at (typically the size of the total input window in bytes + * @param nCurRepMatchOffset starting rep offset for this block + * + * @return non-zero if the number of tokens was reduced, 0 if it wasn't + */ +static int apultra_reduce_commands(apultra_compressor *pCompressor, const unsigned char *pInWindow, apultra_final_match *pBestMatch, const int nStartOffset, const int nEndOffset, const int *nCurRepMatchOffset) { + int i; + int nNumLiterals = 0; + int nRepMatchOffset = *nCurRepMatchOffset; + int nFollowsLiteral = 0; + int nDidReduce = 0; + int nLastMatchLen = 0; + const unsigned char *match1 = pCompressor->match1 - nStartOffset; + + for (i = nStartOffset; i < nEndOffset; ) { + apultra_final_match *pMatch = pBestMatch + i; + + if (pMatch->length <= 1 && + (i + 1) < nEndOffset && + pBestMatch[i + 1].length >= 2 && + pBestMatch[i + 1].length < MAX_VARLEN && + pBestMatch[i + 1].offset && + i >= pBestMatch[i + 1].offset && + (i + pBestMatch[i + 1].length + 1) <= nEndOffset && + !memcmp(pInWindow + i - (pBestMatch[i + 1].offset), pInWindow + i, pBestMatch[i + 1].length + 1)) { + if ((pBestMatch[i + 1].offset < MINMATCH3_OFFSET || (pBestMatch[i + 1].length + 1) >= 3 || (pBestMatch[i + 1].offset == nRepMatchOffset && nFollowsLiteral)) && + (pBestMatch[i + 1].offset < MINMATCH4_OFFSET || (pBestMatch[i + 1].length + 1) >= 4 || (pBestMatch[i + 1].offset == nRepMatchOffset && nFollowsLiteral))) { + + int nCurPartialCommandSize = TOKEN_PREFIX_SIZE /* literal bit */ + ((pMatch->length == 1) ? (TOKEN_SIZE_4BIT_MATCH + 4) : 8 /* literal size */); + if (pBestMatch[i + 1].offset == nRepMatchOffset /* always follows a literal, the one at the current position */) { + nCurPartialCommandSize += apultra_get_rep_offset_varlen_size() + apultra_get_match_varlen_size(pBestMatch[i + 1].length, pBestMatch[i + 1].offset, 1); + } + else { + nCurPartialCommandSize += apultra_get_offset_varlen_size(pBestMatch[i + 1].length, pBestMatch[i + 1].offset, 1) + apultra_get_match_varlen_size(pBestMatch[i + 1].length, pBestMatch[i + 1].offset, 0); + } + + int nReducedPartialCommandSize; + if (pBestMatch[i + 1].offset == nRepMatchOffset && nFollowsLiteral) { + nReducedPartialCommandSize = apultra_get_rep_offset_varlen_size() + apultra_get_match_varlen_size(pBestMatch[i + 1].length, pBestMatch[i + 1].offset, 1); + } + else { + nReducedPartialCommandSize = apultra_get_offset_varlen_size(pBestMatch[i + 1].length, pBestMatch[i + 1].offset, nFollowsLiteral) + apultra_get_match_varlen_size(pBestMatch[i + 1].length, pBestMatch[i + 1].offset, 0); + } + + if (nReducedPartialCommandSize < nCurPartialCommandSize || (nFollowsLiteral == 0 && nLastMatchLen >= LCP_MAX)) { + /* Merge */ + pBestMatch[i].length = pBestMatch[i + 1].length + 1; + pBestMatch[i].offset = pBestMatch[i + 1].offset; + pBestMatch[i + 1].length = 0; + pBestMatch[i + 1].offset = 0; + nDidReduce = 1; + continue; + } + } + } + + if (pMatch->length >= MIN_MATCH_SIZE) { + if (pMatch->length < 8 && /* Don't waste time considering large matches, they will always win over literals */ + (i + pMatch->length) < nEndOffset /* Don't consider the last match in the block, we can only reduce a match inbetween other tokens */) { + int nNextIndex = i + pMatch->length; + int nNextLiterals = 0; + int nNextFollowsLiteral = (pMatch->length >= 2) ? 0 : 1; + int nCannotEncode = 0; + + while (nNextIndex < nEndOffset && pBestMatch[nNextIndex].length < 2) { + nNextLiterals++; + nNextIndex++; + nNextFollowsLiteral = 1; + } + + if (nNextIndex < nEndOffset && pBestMatch[nNextIndex].length >= 2) { + if (pMatch->length >= 2 && nRepMatchOffset && nRepMatchOffset != pMatch->offset && pBestMatch[nNextIndex].offset && pMatch->offset != pBestMatch[nNextIndex].offset && + nNextFollowsLiteral) { + /* Try to gain a match forward */ + if (i >= pBestMatch[nNextIndex].offset && (i - pBestMatch[nNextIndex].offset + pMatch->length) <= nEndOffset) { + if ((pBestMatch[nNextIndex].offset < MINMATCH3_OFFSET || pMatch->length >= 3) && + (pBestMatch[nNextIndex].offset < MINMATCH4_OFFSET || pMatch->length >= 4)) { + int nMaxLen = 0; + while (nMaxLen < pMatch->length && pInWindow[i - pBestMatch[nNextIndex].offset + nMaxLen] == pInWindow[i - pMatch->offset + nMaxLen]) + nMaxLen++; + + if (nMaxLen >= pMatch->length) { + /* Replace */ + pMatch->offset = pBestMatch[nNextIndex].offset; + nDidReduce = 1; + } + else if (nMaxLen >= 2) { + if ((nFollowsLiteral && nRepMatchOffset == pBestMatch[nNextIndex].offset) || + ((pBestMatch[nNextIndex].offset < MINMATCH3_OFFSET || nMaxLen >= 3) && + (pBestMatch[nNextIndex].offset < MINMATCH4_OFFSET || nMaxLen >= 4))) { + + int nPartialSizeBefore, nPartialSizeAfter; + + nPartialSizeBefore = apultra_get_offset_varlen_size(pMatch->length, pMatch->offset, nFollowsLiteral); + nPartialSizeBefore += apultra_get_match_varlen_size(pMatch->length, pMatch->offset, 0); + + nPartialSizeBefore += apultra_get_offset_varlen_size(pBestMatch[nNextIndex].length, pBestMatch[nNextIndex].offset, 1); + nPartialSizeBefore += apultra_get_match_varlen_size(pBestMatch[nNextIndex].length, pBestMatch[nNextIndex].offset, 0); + + nPartialSizeAfter = apultra_get_offset_varlen_size(nMaxLen, pBestMatch[nNextIndex].offset, nFollowsLiteral); + nPartialSizeAfter += apultra_get_match_varlen_size(nMaxLen, pBestMatch[nNextIndex].offset, (nFollowsLiteral && nRepMatchOffset == pBestMatch[nNextIndex].offset) ? 1 : 0); + + nPartialSizeAfter += apultra_get_rep_offset_varlen_size(); + nPartialSizeAfter += apultra_get_match_varlen_size(pBestMatch[nNextIndex].length, pBestMatch[nNextIndex].offset, 1); + nPartialSizeAfter += apultra_get_literals_varlen_size(pMatch->length - nMaxLen); + + for (int j = nMaxLen; j < pMatch->length; j++) { + if (pInWindow[i + j] == 0 || match1[i + j]) + nPartialSizeAfter += TOKEN_SIZE_4BIT_MATCH + 4; + else + nPartialSizeAfter += 8; + } + + if (nPartialSizeAfter < nPartialSizeBefore) { + /* We gain a repmatch that is shorter than the original match as this is the best we can do, so it is followed by extra literals, but + * we have calculated that this is shorter */ + + int nOrigLen = pMatch->length; + pMatch->offset = pBestMatch[nNextIndex].offset; + pMatch->length = nMaxLen; + + for (int j = nMaxLen; j < nOrigLen; j++) { + pBestMatch[i + j].offset = match1[i + j]; + pBestMatch[i + j].length = (pInWindow[i + j] && match1[i+j] == 0) ? 0 : 1; + } + + nDidReduce = 1; + continue; + } + } + } + } + } + } + + /* This command is a match, is followed by 'nNextLiterals' literals and then by another match. Calculate this command's current cost (excluding 'nNumLiterals' bytes) */ + + int nCurCommandSize = TOKEN_PREFIX_SIZE /* token */ + apultra_get_literals_varlen_size(nNumLiterals); + if (pMatch->offset == nRepMatchOffset && nFollowsLiteral && pMatch->length >= 2) { + nCurCommandSize += apultra_get_rep_offset_varlen_size() + apultra_get_match_varlen_size(pMatch->length, pMatch->offset, 1); + } + else { + nCurCommandSize += apultra_get_offset_varlen_size(pMatch->length, pMatch->offset, nFollowsLiteral) + apultra_get_match_varlen_size(pMatch->length, pMatch->offset, 0); + } + + /* Calculate the next command's current cost */ + int nNextCommandSize = TOKEN_PREFIX_SIZE /* token */ + apultra_get_literals_varlen_size(nNextLiterals) + (nNextLiterals << 3); + int nCurRepOffset = (pMatch->length >= 2) ? pMatch->offset : nRepMatchOffset; + if (pBestMatch[nNextIndex].offset == nCurRepOffset && nNextFollowsLiteral && pBestMatch[nNextIndex].length >= 2) { + nNextCommandSize += apultra_get_rep_offset_varlen_size() + apultra_get_match_varlen_size(pBestMatch[nNextIndex].length, pBestMatch[nNextIndex].offset, 1); + } + else { + nNextCommandSize += apultra_get_offset_varlen_size(pBestMatch[nNextIndex].length, pBestMatch[nNextIndex].offset, nNextFollowsLiteral) + apultra_get_match_varlen_size(pBestMatch[nNextIndex].length, pBestMatch[nNextIndex].offset, 0); + } + + int nOriginalCombinedCommandSize = nCurCommandSize + nNextCommandSize; + + /* Calculate the cost of replacing this match command by literals + the next command with the cost of encoding these literals (excluding 'nNumLiterals' bytes) */ + int nReducedFollowsLiteral = (nNumLiterals + pMatch->length) ? 1 : 0; + int nReducedCommandSize = TOKEN_PREFIX_SIZE /* token */ + apultra_get_literals_varlen_size(nNumLiterals + pMatch->length + nNextLiterals) + (nNextLiterals << 3); + + for (int j = 0; j < pMatch->length; j++) { + if (pInWindow[i + j] == 0 || match1[i + j]) + nReducedCommandSize += TOKEN_SIZE_4BIT_MATCH + 4; + else + nReducedCommandSize += 8; + } + + if (pBestMatch[nNextIndex].offset == nRepMatchOffset && nReducedFollowsLiteral && pBestMatch[nNextIndex].length >= 2) { + nReducedCommandSize += apultra_get_rep_offset_varlen_size() + apultra_get_match_varlen_size(pBestMatch[nNextIndex].length, pBestMatch[nNextIndex].offset, 1); + } + else { + if ((pBestMatch[nNextIndex].length < 3 && pBestMatch[nNextIndex].offset >= MINMATCH3_OFFSET) || + (pBestMatch[nNextIndex].length < 4 && pBestMatch[nNextIndex].offset >= MINMATCH4_OFFSET)) { + /* This match length can only be encoded with a rep-match */ + nCannotEncode = 1; + } + else { + nReducedCommandSize += apultra_get_offset_varlen_size(pBestMatch[nNextIndex].length, pBestMatch[nNextIndex].offset, nReducedFollowsLiteral) + apultra_get_match_varlen_size(pBestMatch[nNextIndex].length, pBestMatch[nNextIndex].offset, 0); + } + } + + if (!nCannotEncode && nOriginalCombinedCommandSize > nReducedCommandSize) { + /* Reduce */ + int nMatchLen = pMatch->length; + int j; + + for (j = 0; j < nMatchLen; j++) { + pBestMatch[i + j].offset = match1[i + j]; + pBestMatch[i + j].length = (pInWindow[i + j] && match1[i + j] == 0) ? 0 : 1; + } + + nDidReduce = 1; + continue; + } + } + } + + if ((i + pMatch->length) < nEndOffset && pMatch->offset > 0 && pMatch->length >= 2 && + pBestMatch[i + pMatch->length].offset > 0 && + pBestMatch[i + pMatch->length].length >= 2 && + (pMatch->length + pBestMatch[i + pMatch->length].length) >= LEAVE_ALONE_MATCH_SIZE && + (pMatch->length + pBestMatch[i + pMatch->length].length) <= MAX_VARLEN && + (i + pMatch->length) > pMatch->offset && + (i + pMatch->length) > pBestMatch[i + pMatch->length].offset && + (i + pMatch->length + pBestMatch[i + pMatch->length].length) <= nEndOffset && + !memcmp(pInWindow + i + pMatch->length - pMatch->offset, + pInWindow + i + pMatch->length - pBestMatch[i + pMatch->length].offset, + pBestMatch[i + pMatch->length].length)) { + int nMatchLen = pMatch->length; + + /* Join large matches */ + + int nNextIndex = i + pMatch->length + pBestMatch[i + pMatch->length].length; + int nNextFollowsLiteral = 0; + int nCannotEncode = 0; + + while (nNextIndex < nEndOffset && pBestMatch[nNextIndex].length < 2) { + nNextIndex++; + nNextFollowsLiteral = 1; + } + + if (nNextIndex < nEndOffset && nNextFollowsLiteral && pBestMatch[nNextIndex].length >= 2 && + pBestMatch[nNextIndex].offset == pBestMatch[i + pMatch->length].offset) { + if ((pBestMatch[nNextIndex].offset >= MINMATCH3_OFFSET && pBestMatch[nNextIndex].length < 3) || + (pBestMatch[nNextIndex].offset >= MINMATCH4_OFFSET && pBestMatch[nNextIndex].length < 4)) { + nCannotEncode = 1; + } + } + + if (!nCannotEncode) { + pMatch->length += pBestMatch[i + nMatchLen].length; + pBestMatch[i + nMatchLen].offset = 0; + pBestMatch[i + nMatchLen].length = -1; + nDidReduce = 1; + continue; + } + } + + if (pMatch->offset == nRepMatchOffset && nFollowsLiteral && pMatch->length >= 2) { + /* Rep-match */ + nRepMatchOffset = pMatch->offset; + nFollowsLiteral = 0; + nLastMatchLen = pMatch->length; + } + else { + if (pMatch->length == 1 && pMatch->offset < 16) { + /* 4 bits offset */ + nFollowsLiteral = 1; + nLastMatchLen = 0; + } + else if (pMatch->length <= 3 && pMatch->offset < 128) { + /* 7 bits offset + 1 bit length */ + nRepMatchOffset = pMatch->offset; + nFollowsLiteral = 0; + nLastMatchLen = pMatch->length; + } + else { + /* 8+n bits offset */ + nRepMatchOffset = pMatch->offset; + nFollowsLiteral = 0; + nLastMatchLen = pMatch->length; + } + } + + i += pMatch->length; + nNumLiterals = 0; + } + else { + nNumLiterals++; + i++; + nFollowsLiteral = 1; + nLastMatchLen = 0; + } + } + + return nDidReduce; +} + +/** + * Emit a block of compressed data + * + * @param pCompressor compression context + * @param pBestMatch optimal matches to emit + * @param pInWindow pointer to input data window (previously compressed bytes + bytes to compress) + * @param nStartOffset current offset in input window (typically the number of previously compressed bytes) + * @param nEndOffset offset to end finding matches at (typically the size of the total input window in bytes + * @param pOutData pointer to output buffer + * @param nMaxOutDataSize maximum size of output buffer, in bytes + * @param nCurBitsOffset write index into output buffer, of current byte being filled with bits + * @param nCurBitMask bit shifter + * @param nFollowsLiteral non-zero if the next command to be issued follows a literal, 0 if not + * @param nCurRepMatchOffset starting rep offset for this block, updated after the block is compressed successfully + * @param nBlockFlags bit 0: 1 for first block, 0 otherwise; bit 1: 1 for last block, 0 otherwise + * + * @return size of compressed data in output buffer, or -1 if the data is uncompressible + */ +static int apultra_write_block(apultra_compressor *pCompressor, apultra_final_match *pBestMatch, const unsigned char *pInWindow, const int nStartOffset, const int nEndOffset, unsigned char *pOutData, int nOutOffset, const int nMaxOutDataSize, int *nCurBitsOffset, int *nCurBitMask, int *nFollowsLiteral, int *nCurRepMatchOffset, const int nBlockFlags) { + int i, j; + int nInFirstLiteralOffset = 0; + int nRepMatchOffset = *nCurRepMatchOffset; + int nSingleBitBufferIdx = 0; + int nGammaBitBufferIdx = (pCompressor->flags & APULTRA_FLAG_ENHANCED) ? 1 : 0; + int nNibblesBitBufferIdx = (pCompressor->flags & APULTRA_FLAG_ENHANCED) ? 2 : 0; + + if (nBlockFlags & 1) { + if (nOutOffset < 0 || nOutOffset >= nMaxOutDataSize) + return -1; + pOutData[nOutOffset++] = pInWindow[nStartOffset]; + *nFollowsLiteral = 1; + } + + for (i = nStartOffset + ((nBlockFlags & 1) ? 1 : 0); i < nEndOffset; ) { + const apultra_final_match *pMatch = pBestMatch + i; + + if (pMatch->length >= MIN_MATCH_SIZE) { + int nMatchOffset = pMatch->offset; + int nMatchLen = pMatch->length; + int nTokenOffsetMode; + int nOffsetSize; + + if (nMatchOffset == nRepMatchOffset && *nFollowsLiteral && nMatchLen >= 2) { + /* Rep-match */ + nTokenOffsetMode = 3; + nOffsetSize = TOKEN_SIZE_LARGE_MATCH + apultra_get_gamma2_size(2); + } + else { + if (nMatchLen == 1 && nMatchOffset < 16) { + /* 4 bits offset */ + nTokenOffsetMode = 2; + nOffsetSize = 4 + TOKEN_SIZE_4BIT_MATCH; + } + else if (nMatchLen <= 3 && nMatchOffset < 128) { + /* 7 bits offset + 1 bit length */ + nTokenOffsetMode = 1; + nOffsetSize = 8 + TOKEN_SIZE_7BIT_MATCH; + } + else { + /* 8+n bits offset */ + nTokenOffsetMode = 0; + if (*nFollowsLiteral) + nOffsetSize = 8 + TOKEN_SIZE_LARGE_MATCH + apultra_get_gamma2_size((nMatchOffset >> 8) + 3); + else + nOffsetSize = 8 + TOKEN_SIZE_LARGE_MATCH + apultra_get_gamma2_size((nMatchOffset >> 8) + 2); + } + } + + int nCommandSize = TOKEN_PREFIX_SIZE /* token */ + nOffsetSize /* match offset */ + apultra_get_match_varlen_size(nMatchLen, nMatchOffset, (nTokenOffsetMode == 3) ? 1 : 0); + + if ((nOutOffset + ((nCommandSize + 7) >> 3)) > nMaxOutDataSize) + return -1; + if (nMatchOffset < ((nMatchLen == 1) ? 0 : MIN_OFFSET) || nMatchOffset > MAX_OFFSET) + return -1; + + int nActualTokenOffsetMode = nTokenOffsetMode; + if (nActualTokenOffsetMode == 3) + nActualTokenOffsetMode = 0; + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, 1 /* match */, nCurBitsOffset, nCurBitMask, nSingleBitBufferIdx); + for (j = _token_size[nActualTokenOffsetMode] - 1; j >= 0; j--) + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, (_token_code[nActualTokenOffsetMode] & (1 << j)) ? 1 : 0, nCurBitsOffset, nCurBitMask, nSingleBitBufferIdx); + + int nEmitMatchLength = 0; + + if (nTokenOffsetMode == 0) { + /* 8+n bits offset */ + + if (nOutOffset < 0 || nOutOffset >= nMaxOutDataSize) + return -1; + if (*nFollowsLiteral) + nOutOffset = apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, (nMatchOffset >> 8) + 3, nCurBitsOffset, nCurBitMask, nGammaBitBufferIdx); + else + nOutOffset = apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, (nMatchOffset >> 8) + 2, nCurBitsOffset, nCurBitMask, nGammaBitBufferIdx); + pOutData[nOutOffset++] = nMatchOffset & 0xff; + + if (nMatchOffset < 128 && nMatchLen <= 3) { + /* A shorter match must have been encoded as a 4 bits offset or a 7 bits offset + 1 bit match length command */ + return -1; + } + + nEmitMatchLength = 1; + *nFollowsLiteral = 0; + nRepMatchOffset = nMatchOffset; + + pCompressor->stats.num_variable_matches++; + } + else if (nTokenOffsetMode == 1) { + /* 7 bits offset + 1 bit length */ + + if (nOutOffset < 0 || nOutOffset >= nMaxOutDataSize) + return -1; + pOutData[nOutOffset++] = ((nMatchOffset) & 0x7f) << 1 | (nMatchLen - 2); + + *nFollowsLiteral = 0; + nRepMatchOffset = nMatchOffset; + + pCompressor->stats.num_7bit_matches++; + } + else if (nTokenOffsetMode == 2) { + /* 4 bits offset */ + + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, (nMatchOffset & 0x08) ? 1 : 0, nCurBitsOffset, nCurBitMask, nNibblesBitBufferIdx); + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, (nMatchOffset & 0x04) ? 1 : 0, nCurBitsOffset, nCurBitMask, nNibblesBitBufferIdx); + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, (nMatchOffset & 0x02) ? 1 : 0, nCurBitsOffset, nCurBitMask, nNibblesBitBufferIdx); + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, (nMatchOffset & 0x01) ? 1 : 0, nCurBitsOffset, nCurBitMask, nNibblesBitBufferIdx); + if (nOutOffset < 0) return -1; + + *nFollowsLiteral = 1; + + pCompressor->stats.num_4bit_matches++; + } + else { + /* rep match */ + nOutOffset = apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, 2, nCurBitsOffset, nCurBitMask, nGammaBitBufferIdx); + + nEmitMatchLength = 1; + *nFollowsLiteral = 0; + + pCompressor->stats.num_rep_matches++; + } + + if (nEmitMatchLength) { + /* The match length isn't encoded in the command, emit elias gamma value */ + nOutOffset = apultra_write_match_varlen(pOutData, nOutOffset, nMaxOutDataSize, nCurBitsOffset, nCurBitMask, nGammaBitBufferIdx, nMatchLen, nMatchOffset, (nTokenOffsetMode == 3) ? 1 : 0); + if (nOutOffset < 0) return -1; + } + + if (nMatchOffset < pCompressor->stats.min_offset || pCompressor->stats.min_offset == -1) + pCompressor->stats.min_offset = nMatchOffset; + if (nMatchOffset > pCompressor->stats.max_offset) + pCompressor->stats.max_offset = nMatchOffset; + pCompressor->stats.total_offsets += (long long)nMatchOffset; + + if (nMatchLen < pCompressor->stats.min_match_len || pCompressor->stats.min_match_len == -1) + pCompressor->stats.min_match_len = nMatchLen; + if (nMatchLen > pCompressor->stats.max_match_len) + pCompressor->stats.max_match_len = nMatchLen; + pCompressor->stats.total_match_lens += nMatchLen; + pCompressor->stats.match_divisor++; + + if (nMatchOffset == 1) { + if (nMatchLen < pCompressor->stats.min_rle1_len || pCompressor->stats.min_rle1_len == -1) + pCompressor->stats.min_rle1_len = nMatchLen; + if (nMatchLen > pCompressor->stats.max_rle1_len) + pCompressor->stats.max_rle1_len = nMatchLen; + pCompressor->stats.total_rle1_lens += nMatchLen; + pCompressor->stats.rle1_divisor++; + } + else if (nMatchOffset == 2) { + if (nMatchLen < pCompressor->stats.min_rle2_len || pCompressor->stats.min_rle2_len == -1) + pCompressor->stats.min_rle2_len = nMatchLen; + if (nMatchLen > pCompressor->stats.max_rle2_len) + pCompressor->stats.max_rle2_len = nMatchLen; + pCompressor->stats.total_rle2_lens += nMatchLen; + pCompressor->stats.rle2_divisor++; + } + + i += nMatchLen; + + pCompressor->stats.commands_divisor++; + } + else { + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, 0 /* literal */, nCurBitsOffset, nCurBitMask, nSingleBitBufferIdx); + + if (nOutOffset < 0 || nOutOffset >= nMaxOutDataSize) + return -1; + pOutData[nOutOffset++] = pInWindow[i]; + + pCompressor->stats.num_literals++; + pCompressor->stats.commands_divisor++; + i++; + *nFollowsLiteral = 1; + } + } + + if (nBlockFlags & 2) { + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, 1 /* match */, nCurBitsOffset, nCurBitMask, nSingleBitBufferIdx); + + /* 8 bits offset */ + + for (j = TOKEN_SIZE_7BIT_MATCH - 1; j >= 0; j--) + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, (_token_code[1] & (1 << j)) ? 1 : 0, nCurBitsOffset, nCurBitMask, nSingleBitBufferIdx); + + if (nOutOffset < 0 || nOutOffset >= nMaxOutDataSize) + return -1; + pOutData[nOutOffset++] = 0x00; /* Offset: EOD */ + pCompressor->stats.commands_divisor++; + } + + *nCurRepMatchOffset = nRepMatchOffset; + return nOutOffset; +} + +/** + * Emit raw block of uncompressible data + * + * @param pCompressor compression context + * @param pInWindow pointer to input data window (previously compressed bytes + bytes to compress) + * @param nStartOffset current offset in input window (typically the number of previously compressed bytes) + * @param nEndOffset offset to end finding matches at (typically the size of the total input window in bytes + * @param pOutData pointer to output buffer + * @param nMaxOutDataSize maximum size of output buffer, in bytes + * @param nBlockFlags bit 0: 1 for first block, 0 otherwise; bit 1: 1 for last block, 0 otherwise + * @param nCurBitsOffset write index into output buffer, of current byte being filled with bits + * @param nCurBitMask bit shifter + * @param nFollowsLiteral non-zero if the next command to be issued follows a literal, 0 if not + * + * @return size of compressed data in output buffer, or -1 if the data is uncompressible + */ +static int apultra_write_raw_uncompressed_block_v3(apultra_compressor *pCompressor, const unsigned char *pInWindow, const int nStartOffset, const int nEndOffset, unsigned char *pOutData, int nOutOffset, const int nMaxOutDataSize, const int nBlockFlags, int *nCurBitsOffset, int *nCurBitMask, int *nFollowsLiteral) { + int nNumLiterals = nEndOffset - nStartOffset; + int j; + int nInOffset = nStartOffset; + int nSingleBitBufferIdx = 0; + + int nCommandSize = apultra_get_literals_varlen_size(nNumLiterals) + (nNumLiterals << 3) + TOKEN_PREFIX_SIZE + TOKEN_SIZE_7BIT_MATCH /* token */ + 8 /* match offset */; + if ((nOutOffset + ((nCommandSize + 7) >> 3)) > nMaxOutDataSize) + return -1; + + pCompressor->stats.commands_divisor = 0; + *nFollowsLiteral = 1; + + for (j = 0; j < nNumLiterals; j++) { + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, 0 /* literal */, nCurBitsOffset, nCurBitMask, nSingleBitBufferIdx); + pOutData[nOutOffset++] = pInWindow[nInOffset + j]; + } + + nNumLiterals = 0; + + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, 1 /* match */, nCurBitsOffset, nCurBitMask, nSingleBitBufferIdx); + + /* 8 bits offset */ + for (j = TOKEN_SIZE_7BIT_MATCH - 1; j >= 0; j--) + nOutOffset = apultra_write_bit(pOutData, nOutOffset, nMaxOutDataSize, (_token_code[1] & (1 << j)) ? 1 : 0, nCurBitsOffset, nCurBitMask, nSingleBitBufferIdx); + + if (nOutOffset < 0 || nOutOffset >= nMaxOutDataSize) + return -1; + pOutData[nOutOffset++] = 0x00; /* Offset: EOD */ + + pCompressor->stats.commands_divisor++; + + return nOutOffset; +} + +/** + * Select the most optimal matches, reduce the token count if possible, and then emit a block of compressed data + * + * @param pCompressor compression context + * @param pInWindow pointer to input data window (previously compressed bytes + bytes to compress) + * @param nPreviousBlockSize number of previously compressed bytes (or 0 for none) + * @param nInDataSize number of input bytes to compress + * @param pOutData pointer to output buffer + * @param nMaxOutDataSize maximum size of output buffer, in bytes + * @param nCurBitsOffset write index into output buffer, of current byte being filled with bits + * @param nCurBitMask bit shifter + * @param nCurFollowsLiteral non-zero if the next command to be issued follows a literal, 0 if not + * @param nCurRepMatchOffset starting rep offset for this block, updated after the block is compressed successfully + * @param nBlockFlags bit 0: 1 for first block, 0 otherwise; bit 1: 1 for last block, 0 otherwise + * + * @return size of compressed data in output buffer, or -1 if the data is uncompressible + */ +static int apultra_optimize_and_write_block(apultra_compressor *pCompressor, const unsigned char *pInWindow, const int nPreviousBlockSize, const int nInDataSize, unsigned char *pOutData, const int nMaxOutDataSize, int *nCurBitsOffset, int *nCurBitMask, int *nCurFollowsLiteral, int *nCurRepMatchOffset, const int nBlockFlags) { + int nResult; + int nOutOffset = 0; + const int nMatchesPerArrival = ((nBlockFlags & 3) == 3) ? NMATCHES_PER_ARRIVAL : NMATCHES_PER_ARRIVAL_SMALL; + + memset(pCompressor->best_match, 0, pCompressor->block_size * sizeof(apultra_final_match)); + apultra_optimize_forward(pCompressor, pInWindow, nPreviousBlockSize, nPreviousBlockSize + nInDataSize, 1 /* nInsertForwardReps */, nCurRepMatchOffset, nBlockFlags, nMatchesPerArrival); + + /* Pick optimal matches */ + apultra_optimize_forward(pCompressor, pInWindow, nPreviousBlockSize, nPreviousBlockSize + nInDataSize, 0 /* nInsertForwardReps */, nCurRepMatchOffset, nBlockFlags, nMatchesPerArrival); + + /* Apply reduction and merge pass */ + int nDidReduce; + int nPasses = 0; + do { + nDidReduce = apultra_reduce_commands(pCompressor, pInWindow, pCompressor->best_match - nPreviousBlockSize, nPreviousBlockSize, nPreviousBlockSize + nInDataSize, nCurRepMatchOffset); + nPasses++; + } while (nDidReduce && nPasses < 20); + + /* Write compressed block */ + + nResult = apultra_write_block(pCompressor, pCompressor->best_match - nPreviousBlockSize, pInWindow, nPreviousBlockSize, nPreviousBlockSize + nInDataSize, pOutData, nOutOffset, nMaxOutDataSize, nCurBitsOffset, nCurBitMask, nCurFollowsLiteral, nCurRepMatchOffset, nBlockFlags); + if (nResult < 0) { + /* Try to write block as all literals */ + *nCurRepMatchOffset = 0; + nResult = apultra_write_raw_uncompressed_block_v3(pCompressor, pInWindow, nPreviousBlockSize, nPreviousBlockSize + nInDataSize, pOutData, nOutOffset, nMaxOutDataSize, nBlockFlags, nCurBitsOffset, nCurBitMask, nCurFollowsLiteral); + } + + return nResult; +} + +/* Forward declaration */ +static void apultra_compressor_destroy(apultra_compressor *pCompressor); + +/** + * Initialize compression context + * + * @param pCompressor compression context to initialize + * @param nBlockSize maximum size of input data (bytes to compress only) + * @param nMaxWindowSize maximum size of input data window (previously compressed bytes + bytes to compress) + * @param nFlags compression flags + * + * @return 0 for success, non-zero for failure + */ +static int apultra_compressor_init(apultra_compressor *pCompressor, const int nBlockSize, const int nMaxWindowSize, const int nFlags) { + int nResult; + + nResult = divsufsort_init(&pCompressor->divsufsort_context); + pCompressor->intervals = NULL; + pCompressor->pos_data = NULL; + pCompressor->open_intervals = NULL; + pCompressor->match = NULL; + pCompressor->match_depth = NULL; + pCompressor->match1 = NULL; + pCompressor->best_match = NULL; + pCompressor->arrival = NULL; + pCompressor->flags = nFlags; + pCompressor->block_size = nBlockSize; + + memset(&pCompressor->stats, 0, sizeof(pCompressor->stats)); + pCompressor->stats.min_match_len = -1; + pCompressor->stats.min_offset = -1; + pCompressor->stats.min_rle1_len = -1; + pCompressor->stats.min_rle2_len = -1; + + if (!nResult) { + pCompressor->intervals = (unsigned long long *)malloc(nMaxWindowSize * sizeof(unsigned long long)); + + if (pCompressor->intervals) { + pCompressor->pos_data = (unsigned long long *)malloc(nMaxWindowSize * sizeof(unsigned long long)); + + if (pCompressor->pos_data) { + pCompressor->open_intervals = (unsigned long long *)malloc((LCP_AND_TAG_MAX + 1) * sizeof(unsigned long long)); + + if (pCompressor->open_intervals) { + pCompressor->arrival = (apultra_arrival *)malloc((nBlockSize + 1) * NMATCHES_PER_ARRIVAL * sizeof(apultra_arrival)); + + if (pCompressor->arrival) { + pCompressor->best_match = (apultra_final_match *)malloc(nBlockSize * sizeof(apultra_final_match)); + + if (pCompressor->best_match) { + pCompressor->match = (apultra_match *)malloc(nBlockSize * NMATCHES_PER_INDEX * sizeof(apultra_match)); + if (pCompressor->match) { + pCompressor->match_depth = (unsigned short *)malloc(nBlockSize * NMATCHES_PER_INDEX * sizeof(unsigned short)); + if (pCompressor->match_depth) { + pCompressor->match1 = (unsigned char *)malloc(nBlockSize * sizeof(unsigned char)); + if (pCompressor->match1) + return 0; + } + } + } + } + } + } + } + } + + apultra_compressor_destroy(pCompressor); + return 100; +} + +/** + * Clean up compression context and free up any associated resources + * + * @param pCompressor compression context to clean up + */ +static void apultra_compressor_destroy(apultra_compressor *pCompressor) { + divsufsort_destroy(&pCompressor->divsufsort_context); + + if (pCompressor->match1) { + free(pCompressor->match1); + pCompressor->match1 = NULL; + } + + if (pCompressor->match_depth) { + free(pCompressor->match_depth); + pCompressor->match_depth = NULL; + } + + if (pCompressor->match) { + free(pCompressor->match); + pCompressor->match = NULL; + } + + if (pCompressor->arrival) { + free(pCompressor->arrival); + pCompressor->arrival = NULL; + } + + if (pCompressor->best_match) { + free(pCompressor->best_match); + pCompressor->best_match = NULL; + } + + if (pCompressor->open_intervals) { + free(pCompressor->open_intervals); + pCompressor->open_intervals = NULL; + } + + if (pCompressor->pos_data) { + free(pCompressor->pos_data); + pCompressor->pos_data = NULL; + } + + if (pCompressor->intervals) { + free(pCompressor->intervals); + pCompressor->intervals = NULL; + } +} + +/** + * Compress one block of data + * + * @param pCompressor compression context + * @param pInWindow pointer to input data window (previously compressed bytes + bytes to compress) + * @param nPreviousBlockSize number of previously compressed bytes (or 0 for none) + * @param nInDataSize number of input bytes to compress + * @param pOutData pointer to output buffer + * @param nMaxOutDataSize maximum size of output buffer, in bytes + * @param nCurBitsOffset write index into output buffer, of current byte being filled with bits + * @param nCurBitMask bit shifter + * @param nCurFollowsLiteral non-zero if the next command to be issued follows a literal, 0 if not + * @param nCurRepMatchOffset starting rep offset for this block, updated after the block is compressed successfully + * @param nBlockFlags bit 0: 1 for first block, 0 otherwise; bit 1: 1 for last block, 0 otherwise + * + * @return size of compressed data in output buffer, or -1 if the data is uncompressible + */ +static int apultra_compressor_shrink_block(apultra_compressor *pCompressor, const unsigned char *pInWindow, const int nPreviousBlockSize, const int nInDataSize, unsigned char *pOutData, const int nMaxOutDataSize, int *nCurBitsOffset, int *nCurBitMask, int *nCurFollowsLiteral, int *nCurRepMatchOffset, const int nBlockFlags) { + int nCompressedSize; + + if (apultra_build_suffix_array(pCompressor, pInWindow, nPreviousBlockSize + nInDataSize)) + nCompressedSize = -1; + else { + if (nPreviousBlockSize) { + apultra_skip_matches(pCompressor, 0, nPreviousBlockSize); + } + apultra_find_all_matches(pCompressor, NMATCHES_PER_INDEX, nPreviousBlockSize, nPreviousBlockSize + nInDataSize, nBlockFlags); + + nCompressedSize = apultra_optimize_and_write_block(pCompressor, pInWindow, nPreviousBlockSize, nInDataSize, pOutData, nMaxOutDataSize, nCurBitsOffset, nCurBitMask, nCurFollowsLiteral, nCurRepMatchOffset, nBlockFlags); + } + + return nCompressedSize; +} + +/** + * Get maximum compressed size of input(source) data + * + * @param nInputSize input(source) size in bytes + * + * @return maximum compressed size + */ +size_t apultra_get_max_compressed_size(size_t nInputSize) { + return ((nInputSize * 9 /* literals + literal bits */ + 1 /* match bit */ + 2 /* 7+1 command bits */ + 8 /* EOD offset bits */) + 7) >> 3; +} + +/** + * Compress memory + * + * @param pInputData pointer to input(source) data to compress + * @param pOutBuffer buffer for compressed data + * @param nInputSize input(source) size in bytes + * @param nMaxOutBufferSize maximum capacity of compression buffer + * @param nFlags compression flags (a bitmask of APULTRA_FLAG_xxx, or 0) + * @param progress progress function, called after compressing each block, or NULL for none + * @param pStats pointer to compression stats that are filled if this function is successful, or NULL + * @param nMaxWindowSize maximum window size to use (0 for default) + * + * @return actual compressed size, or -1 for error + */ +size_t apultra_compress(const unsigned char *pInputData, unsigned char *pOutBuffer, size_t nInputSize, size_t nMaxOutBufferSize, + const unsigned int nFlags, size_t nMaxWindowSize, void(*progress)(long long nOriginalSize, long long nCompressedSize), apultra_stats *pStats) { + apultra_compressor compressor; + size_t nOriginalSize = 0; + size_t nCompressedSize = 0L; + int nResult; + int nError = 0; + const int nDefaultBlockSize = (nInputSize < BLOCK_SIZE) ? ((nInputSize < 1024) ? 1024 : (int)nInputSize) : BLOCK_SIZE; + const int nBlockSize = nMaxWindowSize ? ((nDefaultBlockSize < nMaxWindowSize / 2) ? nDefaultBlockSize : (int)nMaxWindowSize / 2) : nDefaultBlockSize; + const int nMaxOutBlockSize = (int)apultra_get_max_compressed_size(nBlockSize); + + nResult = apultra_compressor_init(&compressor, nBlockSize, nBlockSize * 2, nFlags); + if (nResult != 0) { + return -1; + } + + int nPreviousBlockSize = 0; + int nNumBlocks = 0; + int nCurBitsOffset[3] = { INT_MIN, INT_MIN, INT_MIN }, nCurBitMask[3] = { 0, 0, 0 }, nCurFollowsLiteral = 0; + int nBlockFlags = 1; + int nCurRepMatchOffset = 0; + + while (nOriginalSize < nInputSize && !nError) { + int nInDataSize; + + nInDataSize = (int)(nInputSize - nOriginalSize); + if (nInDataSize > nBlockSize) + nInDataSize = nBlockSize; + + if (nInDataSize > 0) { + int nOutDataSize; + int nOutDataEnd = (int)(nMaxOutBufferSize - nCompressedSize); + + if (nOutDataEnd > nMaxOutBlockSize) + nOutDataEnd = nMaxOutBlockSize; + + if ((nOriginalSize + nInDataSize) >= nInputSize) + nBlockFlags |= 2; + nOutDataSize = apultra_compressor_shrink_block(&compressor, pInputData + nOriginalSize - nPreviousBlockSize, nPreviousBlockSize, nInDataSize, pOutBuffer + nCompressedSize, nOutDataEnd, + nCurBitsOffset, nCurBitMask, &nCurFollowsLiteral, &nCurRepMatchOffset, nBlockFlags); + nBlockFlags &= (~1); + + if (nOutDataSize >= 0) { + /* Write compressed block */ + + if (!nError) { + nOriginalSize += nInDataSize; + nCompressedSize += nOutDataSize; + if (nCurBitsOffset[0] != INT_MIN) + nCurBitsOffset[0] -= nOutDataSize; + if (nCurBitsOffset[1] != INT_MIN) + nCurBitsOffset[1] -= nOutDataSize; + if (nCurBitsOffset[2] != INT_MIN) + nCurBitsOffset[2] -= nOutDataSize; + } + } + else { + nError = -1; + } + + nPreviousBlockSize = nInDataSize; + nNumBlocks++; + } + + if (!nError && nOriginalSize < nInputSize) { + if (progress) + progress(nOriginalSize, nCompressedSize); + } + } + + if (progress) + progress(nOriginalSize, nCompressedSize); + if (pStats) + *pStats = compressor.stats; + + apultra_compressor_destroy(&compressor); + + if (nError) { + return -1; + } + else { + return nCompressedSize; + } +} diff --git a/tools/apultra_src/src/shrink.h b/tools/apultra_src/src/shrink.h new file mode 100644 index 0000000..0ed8a8f --- /dev/null +++ b/tools/apultra_src/src/shrink.h @@ -0,0 +1,166 @@ +/* + * shrink.h - compressor definitions + * + * Copyright (C) 2019 Emmanuel Marty + * + * This software is provided 'as-is', without any express or implied + * warranty. In no event will the authors be held liable for any damages + * arising from the use of this software. + * + * Permission is granted to anyone to use this software for any purpose, + * including commercial applications, and to alter it and redistribute it + * freely, subject to the following restrictions: + * + * 1. The origin of this software must not be misrepresented; you must not + * claim that you wrote the original software. If you use this software + * in a product, an acknowledgment in the product documentation would be + * appreciated but is not required. + * 2. Altered source versions must be plainly marked as such, and must not be + * misrepresented as being the original software. + * 3. This notice may not be removed or altered from any source distribution. + */ + +/* + * Uses the libdivsufsort library Copyright (c) 2003-2008 Yuta Mori + * + * Inspired by cap by Sven-Åke Dahl. https://github.com/svendahl/cap + * Also inspired by Charles Bloom's compression blog. http://cbloomrants.blogspot.com/ + * With ideas from LZ4 by Yann Collet. https://github.com/lz4/lz4 + * With help and support from spke + * + */ + +#ifndef _SHRINK_H +#define _SHRINK_H + +#include "divsufsort.h" + +#ifdef __cplusplus +extern "C" { +#endif + +#define LCP_BITS 15 +#define TAG_BITS 4 +#define LCP_MAX ((1U<<(LCP_BITS - TAG_BITS)) - 1) +#define LCP_AND_TAG_MAX ((1U< + * With ideas from Lizard by Przemyslaw Skibinski and Yann Collet. https://github.com/inikep/lizard + * Also with ideas from smallz4 by Stephan Brumme. https://create.stephan-brumme.com/smallz4/ + * + */ + +#include +#include +#include "shrink_context.h" +#include "shrink_block.h" +#include "format.h" +#include "matchfinder.h" +#include "lib.h" -- cgit v1.2.3