diff options
| author | Juan J. Martinez <jjm@usebox.net> | 2021-01-09 09:01:05 +0000 |
|---|---|---|
| committer | Juan J. Martinez <jjm@usebox.net> | 2021-01-09 09:01:05 +0000 |
| commit | 9bcf1e97960c0da7322a868efdbc07e2650716fe (patch) | |
| tree | de6d32ad5b0e567991bd3eb262902c15a77074d9 /tools/apultra/src | |
| parent | 3b31adf01305e522f7e28c1435fb47418ce43267 (diff) | |
| download | ubox-msx-lib-9bcf1e97960c0da7322a868efdbc07e2650716fe.tar.gz ubox-msx-lib-9bcf1e97960c0da7322a868efdbc07e2650716fe.zip | |
Extra libs: ap.lib
aPLib support with apultra.
Diffstat (limited to 'tools/apultra/src')
34 files changed, 6624 insertions, 0 deletions
diff --git a/tools/apultra/src/apultra.c b/tools/apultra/src/apultra.c new file mode 100644 index 0000000..1b30fbe --- /dev/null +++ b/tools/apultra/src/apultra.c @@ -0,0 +1,1223 @@ +/*
+ * 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 <zxintrospec@gmail.com>
+ *
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#ifdef _WIN32
+#include <windows.h>
+#include <sys/timeb.h>
+#else
+#include <sys/time.h>
+#endif
+#include "libapultra.h"
+
+#define OPT_VERBOSE 1
+#define OPT_STATS 2
+#define OPT_BACKWARD 4
+
+#define TOOL_VERSION "1.4.0"
+
+/*---------------------------------------------------------------------------*/
+
+#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 do_reverse_buffer(unsigned char *pBuffer, size_t nBufferSize) {
+ size_t nMidPoint = nBufferSize / 2;
+ size_t i, j;
+
+ for (i = 0, j = nBufferSize - 1; i < nMidPoint; i++, j--) {
+ unsigned char c = pBuffer[i];
+ pBuffer[i] = pBuffer[j];
+ pBuffer[j] = c;
+ }
+}
+
+/*---------------------------------------------------------------------------*/
+
+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 nFlags = 0;
+ apultra_stats stats;
+ unsigned char *pDecompressedData;
+ unsigned char *pCompressedData;
+
+ if (nOptions & OPT_VERBOSE) {
+ nStartTime = do_get_time();
+ }
+
+ FILE* f_dict = NULL;
+ size_t nDictionarySize = 0;
+ if (pszDictionaryFilename) {
+ /* Open the dictionary */
+ f_dict = fopen(pszDictionaryFilename, "rb");
+ if (!f_dict) {
+ fprintf(stderr, "error opening dictionary '%s' for reading\n", pszDictionaryFilename);
+ return 100;
+ }
+
+ /* Get dictionary size */
+ fseek(f_dict, 0, SEEK_END);
+ nDictionarySize = (size_t)ftell(f_dict);
+ fseek(f_dict, 0, SEEK_SET);
+
+ if (nDictionarySize > BLOCK_SIZE) nDictionarySize = BLOCK_SIZE;
+ }
+
+ /* Read the whole original file in memory */
+
+ FILE *f_in = fopen(pszInFilename, "rb");
+ if (!f_in) {
+ if (f_dict) fclose(f_dict);
+ 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(nDictionarySize + nOriginalSize);
+ if (!pDecompressedData) {
+ fclose(f_in);
+ if (f_dict) fclose(f_dict);
+ fprintf(stderr, "out of memory for reading '%s', %zd bytes needed\n", pszInFilename, nOriginalSize);
+ return 100;
+ }
+
+ if (f_dict) {
+ /* Read dictionary data */
+ if (fread(pDecompressedData + ((nOptions & OPT_BACKWARD) ? nOriginalSize : 0), 1, nDictionarySize, f_dict) != nDictionarySize) {
+ free(pDecompressedData);
+ fclose(f_in);
+ fclose(f_dict);
+ fprintf(stderr, "I/O error while reading dictionary '%s'\n", pszDictionaryFilename);
+ return 100;
+ }
+
+ fclose(f_dict);
+ f_dict = NULL;
+ }
+
+ /* Read input file data */
+ if (fread(pDecompressedData + ((nOptions & OPT_BACKWARD) ? 0 : nDictionarySize), 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);
+
+ if (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pDecompressedData, nDictionarySize + nOriginalSize);
+
+ /* Allocate max compressed size */
+
+ nMaxCompressedSize = apultra_get_max_compressed_size(nDictionarySize + 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, nDictionarySize + nOriginalSize, nMaxCompressedSize, nFlags, nMaxWindowSize, nDictionarySize, 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 (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pCompressedData, nCompressedSize);
+
+ 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 EOD: %d\n",
+ stats.num_literals, stats.num_4bit_matches, stats.num_7bit_matches, stats.num_variable_matches, stats.num_rep_matches, stats.num_eod);
+ 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");
+ }
+ fprintf(stdout, "Safe distance: %d (0x%X)\n", stats.safe_dist, stats.safe_dist);
+ }
+ 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 = 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);
+
+ if (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pCompressedData, nCompressedSize);
+
+ /* Get 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;
+ }
+
+ FILE* f_dict = NULL;
+ size_t nDictionarySize = 0;
+ if (pszDictionaryFilename) {
+ /* Open the dictionary */
+ f_dict = fopen(pszDictionaryFilename, "rb");
+ if (!f_dict) {
+ fprintf(stderr, "error opening dictionary '%s' for reading\n", pszDictionaryFilename);
+ return 100;
+ }
+
+ /* Get dictionary size */
+ fseek(f_dict, 0, SEEK_END);
+ nDictionarySize = (size_t)ftell(f_dict);
+ fseek(f_dict, 0, SEEK_SET);
+
+ if (nDictionarySize > BLOCK_SIZE) nDictionarySize = BLOCK_SIZE;
+ }
+
+ /* Allocate max decompressed size */
+
+ pDecompressedData = (unsigned char*)malloc(nDictionarySize + nMaxDecompressedSize);
+ if (!pDecompressedData) {
+ free(pCompressedData);
+ if (f_dict) fclose(f_dict);
+ fprintf(stderr, "out of memory for decompressing '%s', %zd bytes needed\n", pszInFilename, nMaxDecompressedSize);
+ return 100;
+ }
+
+ memset(pDecompressedData, 0, nDictionarySize + nMaxDecompressedSize);
+
+ if (f_dict) {
+ /* Read dictionary data */
+ if (fread(pDecompressedData, 1, nDictionarySize, f_dict) != nDictionarySize) {
+ free(pDecompressedData);
+ fclose(f_in);
+ fclose(f_dict);
+ fprintf(stderr, "I/O error while reading dictionary '%s'\n", pszDictionaryFilename);
+ return 100;
+ }
+
+ fclose(f_dict);
+ f_dict = NULL;
+
+ if (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pDecompressedData, nDictionarySize);
+ }
+
+ if (nOptions & OPT_VERBOSE) {
+ nStartTime = do_get_time();
+ }
+
+ nOriginalSize = apultra_decompress(pCompressedData, pDecompressedData, nCompressedSize, nMaxDecompressedSize, nDictionarySize, nFlags);
+ if (nOriginalSize == -1) {
+ free(pDecompressedData);
+ free(pCompressedData);
+
+ fprintf(stderr, "decompression error for '%s'\n", pszInFilename);
+ return 100;
+ }
+
+ if (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pDecompressedData + nDictionarySize, nOriginalSize);
+
+ if (pszOutFilename) {
+ FILE *f_out;
+
+ /* Write whole decompressed file out */
+
+ f_out = fopen(pszOutFilename, "wb");
+ if (f_out) {
+ fwrite(pDecompressedData + nDictionarySize, 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 = 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);
+
+ if (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pCompressedData, nCompressedSize);
+
+ /* 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);
+
+ /* Get 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;
+ }
+
+ FILE* f_dict = NULL;
+ size_t nDictionarySize = 0;
+ if (pszDictionaryFilename) {
+ /* Open the dictionary */
+ f_dict = fopen(pszDictionaryFilename, "rb");
+ if (!f_dict) {
+ fprintf(stderr, "error opening dictionary '%s' for reading\n", pszDictionaryFilename);
+ return 100;
+ }
+
+ /* Get dictionary size */
+ fseek(f_dict, 0, SEEK_END);
+ nDictionarySize = (size_t)ftell(f_dict);
+ fseek(f_dict, 0, SEEK_SET);
+
+ if (nDictionarySize > BLOCK_SIZE) nDictionarySize = BLOCK_SIZE;
+ }
+
+ /* Allocate max decompressed size */
+
+ pDecompressedData = (unsigned char*)malloc(nDictionarySize + nMaxDecompressedSize);
+ if (!pDecompressedData) {
+ free(pOriginalData);
+ free(pCompressedData);
+ if (f_dict) fclose(f_dict);
+ fprintf(stderr, "out of memory for decompressing '%s', %zd bytes needed\n", pszInFilename, nMaxDecompressedSize);
+ return 100;
+ }
+
+ memset(pDecompressedData, 0, nDictionarySize + nMaxDecompressedSize);
+
+ if (f_dict) {
+ /* Read dictionary data */
+ if (fread(pDecompressedData, 1, nDictionarySize, f_dict) != nDictionarySize) {
+ free(pDecompressedData);
+ fclose(f_in);
+ fclose(f_dict);
+ fprintf(stderr, "I/O error while reading dictionary '%s'\n", pszDictionaryFilename);
+ return 100;
+ }
+
+ fclose(f_dict);
+ f_dict = NULL;
+
+ if (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pDecompressedData, nDictionarySize);
+ }
+
+ if (nOptions & OPT_VERBOSE) {
+ nStartTime = do_get_time();
+ }
+
+ nDecompressedSize = apultra_decompress(pCompressedData, pDecompressedData, nCompressedSize, nMaxDecompressedSize, nDictionarySize, nFlags);
+ if (nDecompressedSize == -1) {
+ free(pDecompressedData);
+ free(pOriginalData);
+ free(pCompressedData);
+
+ fprintf(stderr, "decompression error for '%s'\n", pszInFilename);
+ return 100;
+ }
+
+ if (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pDecompressedData + nDictionarySize, nDecompressedSize);
+
+ if (nDecompressedSize != nOriginalSize || memcmp(pDecompressedData + nDictionarySize, 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 = 0;
+ int i;
+
+ 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, 0 /* dictionary size */, NULL, NULL);
+ }
+
+ size_t nDataSizeStep = 128;
+ float fProbabilitySizeStep = nIsQuickTest ? 0.005f : 0.0005f;
+
+ for (nGeneratedDataSize = 1024; nGeneratedDataSize <= (nIsQuickTest ? 1024U : (4U * 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, 0 /* dictionary size */, 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, 0 /* dictionary size */, 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, 0 /* dictionary size */, 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 = 0;
+ int i;
+
+ 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);
+
+ if (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pFileData, nFileSize);
+
+ /* 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, 0 /* dictionary size */, 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 (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pCompressedData + 1024, 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 = 0;
+ int i;
+
+ 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);
+
+ if (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pFileData, nFileSize);
+
+ /* 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, 0 /* dictionary size */, 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 (nOptions & OPT_BACKWARD)
+ do_reverse_buffer(pDecompressedData, nActualDecompressedSize);
+
+ 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;
+ int nArgsError = 0;
+ int nCommandDefined = 0;
+ int nVerifyCompression = 0;
+ char cCommand = 'z';
+ unsigned int nOptions = 0;
+ unsigned int nMaxWindowSize = 0;
+
+ for (i = 1; i < argc; i++) {
+ if (!strcmp(argv[i], "-d")) {
+ if (!nCommandDefined) {
+ nCommandDefined = 1;
+ cCommand = 'd';
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strcmp(argv[i], "-z")) {
+ if (!nCommandDefined) {
+ nCommandDefined = 1;
+ cCommand = 'z';
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strcmp(argv[i], "-c")) {
+ if (!nVerifyCompression) {
+ nVerifyCompression = 1;
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strcmp(argv[i], "-cbench")) {
+ if (!nCommandDefined) {
+ nCommandDefined = 1;
+ cCommand = 'B';
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strcmp(argv[i], "-dbench")) {
+ if (!nCommandDefined) {
+ nCommandDefined = 1;
+ cCommand = 'b';
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strcmp(argv[i], "-test")) {
+ if (!nCommandDefined) {
+ nCommandDefined = 1;
+ cCommand = 't';
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strcmp(argv[i], "-quicktest")) {
+ if (!nCommandDefined) {
+ nCommandDefined = 1;
+ cCommand = 'T';
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strcmp(argv[i], "-D")) {
+ if (!pszDictionaryFilename && (i + 1) < argc) {
+ pszDictionaryFilename = argv[i + 1];
+ i++;
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strncmp(argv[i], "-D", 2)) {
+ if (!pszDictionaryFilename) {
+ pszDictionaryFilename = argv[i] + 2;
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strcmp(argv[i], "-v")) {
+ if ((nOptions & OPT_VERBOSE) == 0) {
+ nOptions |= OPT_VERBOSE;
+ }
+ else
+ nArgsError = 1;
+ }
+ 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 {
+ nArgsError = 1;
+ }
+ }
+ else
+ nArgsError = 1;
+ }
+ 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))) {
+ nArgsError = 1;
+ }
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strcmp(argv[i], "-stats")) {
+ if ((nOptions & OPT_STATS) == 0) {
+ nOptions |= OPT_STATS;
+ }
+ else
+ nArgsError = 1;
+ }
+ else if (!strcmp(argv[i], "-b")) {
+ if ((nOptions & OPT_BACKWARD) == 0) {
+ nOptions |= OPT_BACKWARD;
+ }
+ else
+ nArgsError = 1;
+ }
+ else {
+ if (!pszInFilename)
+ pszInFilename = argv[i];
+ else {
+ if (!pszOutFilename)
+ pszOutFilename = argv[i];
+ else
+ nArgsError = 1;
+ }
+ }
+ }
+
+ if (!nArgsError && cCommand == 't') {
+ return do_self_test(nOptions, nMaxWindowSize, 0);
+ }
+ else if (!nArgsError && cCommand == 'T') {
+ return do_self_test(nOptions, nMaxWindowSize, 1);
+ }
+
+ if (nArgsError || !pszInFilename || !pszOutFilename) {
+ fprintf(stderr, "apultra command-line tool v" TOOL_VERSION " by Emmanuel Marty and spke\n");
+ fprintf(stderr, "usage: %s [-c] [-d] [-v] [-b] <infile> <outfile>\n", argv[0]);
+ fprintf(stderr, " -c: check resulting stream after compressing\n");
+ fprintf(stderr, " -d: decompress (default: compress)\n");
+ fprintf(stderr, " -b: backwards compression or decompression\n");
+ fprintf(stderr, " -w <size>: maximum window size, in bytes (16..2097152), defaults to maximum\n");
+ fprintf(stderr, " -D <file>: use dictionary file\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 && nVerifyCompression) {
+ 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/expand.c b/tools/apultra/src/expand.c new file mode 100644 index 0000000..76b3bf1 --- /dev/null +++ b/tools/apultra/src/expand.c @@ -0,0 +1,396 @@ +/*
+ * 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 <zxintrospec@gmail.com>
+ *
+ */
+
+#include <stdlib.h>
+#include <string.h>
+#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 unsigned char *pInBlock = *ppInBlock;
+ int nBit;
+
+ if ((*nCurBitMask) == 0) {
+ if (pInBlock >= pDataEnd) return -1;
+ (*bits) = *pInBlock++;
+ (*nCurBitMask) = 128;
+ }
+
+ nBit = ((*bits) & 128) ? 1 : 0;
+
+ (*bits) <<= 1;
+ (*nCurBitMask) >>= 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) {
+ int bit;
+ unsigned int v = 1;
+
+ do {
+ v = (v << 1) + apultra_read_bit(ppInBlock, pDataEnd, nCurBitMask, bits);
+ bit = apultra_read_bit(ppInBlock, pDataEnd, nCurBitMask, bits);
+ if (bit < 0) return bit;
+ } while (bit);
+
+ return v;
+}
+
+/**
+ * Get maximum decompressed size of compressed data
+ *
+ * @param pInputData compressed data
+ * @param nInputSize compressed size in bytes
+ * @param nFlags compression flags (set to 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 = 0;
+ unsigned char bits = 0;
+ int nMatchOffset = -1;
+ int nFollowsLiteral = 3;
+ size_t nDecompressedSize = 0;
+
+ if (pInputData >= pInputDataEnd)
+ return -1;
+ pInputData++;
+ nDecompressedSize++;
+
+ while (1) {
+ unsigned int nResult;
+
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+
+ if (!nResult) {
+ /* '0': literal */
+ if (pInputData < pInputDataEnd) {
+ pInputData++;
+ nDecompressedSize++;
+ nFollowsLiteral = 3;
+ }
+ else {
+ return -1;
+ }
+ }
+ else {
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+
+ if (nResult == 0) {
+ unsigned int nMatchLen;
+
+ /* '10': 8+n bits offset */
+ int nMatchOffsetHi = apultra_read_gamma2(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ nMatchOffsetHi -= nFollowsLiteral;
+ if (nMatchOffsetHi >= 0) {
+ nMatchOffset = ((unsigned int) nMatchOffsetHi) << 8;
+ nMatchOffset |= (unsigned int)(*pInputData++);
+
+ nMatchLen = apultra_read_gamma2(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+
+ if (nMatchOffset < 128 || nMatchOffset >= MINMATCH4_OFFSET)
+ nMatchLen += 2;
+ else if (nMatchOffset >= MINMATCH3_OFFSET)
+ nMatchLen++;
+ }
+ else {
+ /* else rep-match */
+ nMatchLen = apultra_read_gamma2(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ }
+
+ nFollowsLiteral = 2;
+
+ nDecompressedSize += nMatchLen;
+ }
+ else {
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ 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 = 2;
+ nDecompressedSize += nMatchLen;
+ }
+ else {
+ unsigned int nShortMatchOffset;
+
+ /* '111': 4 bit offset */
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+ nShortMatchOffset = nResult << 3;
+
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+ nShortMatchOffset |= nResult << 2;
+
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+ nShortMatchOffset |= nResult << 1;
+
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+ nShortMatchOffset |= nResult << 0;
+
+ nFollowsLiteral = 3;
+ 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 nDictionarySize size of dictionary in front of input data (0 for none)
+ * @param nFlags compression flags (set to 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, size_t nDictionarySize, const unsigned int nFlags) {
+ const unsigned char *pInputDataEnd = pInputData + nInputSize;
+ unsigned char *pCurOutData = pOutData + nDictionarySize;
+ const unsigned char *pOutDataEnd = pCurOutData + nMaxOutBufferSize;
+ const unsigned char *pOutDataFastEnd = pOutDataEnd - 20;
+ int nCurBitMask = 0;
+ unsigned char bits = 0;
+ int nMatchOffset = -1;
+ int nFollowsLiteral = 3;
+
+ if (pInputData >= pInputDataEnd && pCurOutData < pOutDataEnd)
+ return -1;
+ *pCurOutData++ = *pInputData++;
+
+ while (1) {
+ unsigned int nResult;
+
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+
+ if (!nResult) {
+ /* '0': literal */
+ if (pInputData < pInputDataEnd && pCurOutData < pOutDataEnd) {
+ *pCurOutData++ = *pInputData++;
+ nFollowsLiteral = 3;
+ }
+ else {
+ return -1;
+ }
+ }
+ else {
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+
+ if (nResult == 0) {
+ unsigned int nMatchLen;
+
+ /* '10': 8+n bits offset */
+ int nMatchOffsetHi = apultra_read_gamma2(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ nMatchOffsetHi -= nFollowsLiteral;
+ if (nMatchOffsetHi >= 0) {
+ nMatchOffset = ((unsigned int) nMatchOffsetHi) << 8;
+ nMatchOffset |= (unsigned int)(*pInputData++);
+
+ nMatchLen = apultra_read_gamma2(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+
+ if (nMatchOffset < 128 || nMatchOffset >= MINMATCH4_OFFSET)
+ nMatchLen += 2;
+ else if (nMatchOffset >= MINMATCH3_OFFSET)
+ nMatchLen++;
+ }
+ else {
+ /* else rep-match */
+ nMatchLen = apultra_read_gamma2(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ }
+
+ nFollowsLiteral = 2;
+ const unsigned char *pSrc = pCurOutData - nMatchOffset;
+ if (pSrc >= pOutData && (pSrc + nMatchLen) <= pOutDataEnd) {
+ if (nMatchLen < 11 && nMatchOffset >= 8 && pCurOutData < pOutDataFastEnd) {
+ memcpy(pCurOutData, pSrc, 8);
+ memcpy(pCurOutData + 8, pSrc + 8, 2);
+ pCurOutData += nMatchLen;
+ }
+ else {
+ if ((pCurOutData + 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);
+ 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 = 2;
+ 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);
+ if (nResult < 0) return -1;
+ nShortMatchOffset = nResult << 3;
+
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+ nShortMatchOffset |= nResult << 2;
+
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+ nShortMatchOffset |= nResult << 1;
+
+ nResult = apultra_read_bit(&pInputData, pInputDataEnd, &nCurBitMask, &bits);
+ if (nResult < 0) return -1;
+ nShortMatchOffset |= nResult << 0;
+
+ nFollowsLiteral = 3;
+ 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) - nDictionarySize;
+}
diff --git a/tools/apultra/src/expand.h b/tools/apultra/src/expand.h new file mode 100644 index 0000000..474660c --- /dev/null +++ b/tools/apultra/src/expand.h @@ -0,0 +1,71 @@ +/*
+ * 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 <zxintrospec@gmail.com>
+ *
+ */
+
+#ifndef _EXPAND_H
+#define _EXPAND_H
+
+#include <stdlib.h>
+
+#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 (set to 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 nDictionarySize size of dictionary in front of input data (0 for none)
+ * @param nFlags compression flags (set to 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, size_t nDictionarySize, const unsigned int nFlags);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _EXPAND_H */
diff --git a/tools/apultra/src/format.h b/tools/apultra/src/format.h new file mode 100644 index 0000000..cf949b5 --- /dev/null +++ b/tools/apultra/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 <zxintrospec@gmail.com>
+ *
+ */
+
+#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/libapultra.h b/tools/apultra/src/libapultra.h new file mode 100644 index 0000000..f97e336 --- /dev/null +++ b/tools/apultra/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 <zxintrospec@gmail.com>
+ *
+ */
+
+#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/libdivsufsort/CHANGELOG.md b/tools/apultra/src/libdivsufsort/CHANGELOG.md new file mode 100644 index 0000000..fe9d004 --- /dev/null +++ b/tools/apultra/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/libdivsufsort/CMakeLists.txt b/tools/apultra/src/libdivsufsort/CMakeLists.txt new file mode 100644 index 0000000..7859943 --- /dev/null +++ b/tools/apultra/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/libdivsufsort/CMakeModules/AppendCompilerFlags.cmake b/tools/apultra/src/libdivsufsort/CMakeModules/AppendCompilerFlags.cmake new file mode 100644 index 0000000..58d3f99 --- /dev/null +++ b/tools/apultra/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 ${SAFE_CMAKE_REQUIRED_FLAGS}) +endmacro(append_cxx_compiler_flags) diff --git a/tools/apultra/src/libdivsufsort/CMakeModules/CheckFunctionKeywords.cmake b/tools/apultra/src/libdivsufsort/CMakeModules/CheckFunctionKeywords.cmake new file mode 100644 index 0000000..44601fd --- /dev/null +++ b/tools/apultra/src/libdivsufsort/CMakeModules/CheckFunctionKeywords.cmake @@ -0,0 +1,15 @@ +include(CheckCSourceCompiles) + +macro(check_function_keywords _wordlist) + set(${_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 ${_result}) + endforeach(flag) +endmacro(check_function_keywords) diff --git a/tools/apultra/src/libdivsufsort/CMakeModules/CheckLFS.cmake b/tools/apultra/src/libdivsufsort/CMakeModules/CheckLFS.cmake new file mode 100644 index 0000000..e2b0099 --- /dev/null +++ b/tools/apultra/src/libdivsufsort/CMakeModules/CheckLFS.cmake @@ -0,0 +1,109 @@ +## Checks for large file support ## +include(CheckIncludeFile) +include(CheckSymbolExists) +include(CheckTypeSize) + +macro(check_lfs _isenable) + set(LFS_OFF_T "") + set(LFS_FOPEN "") + set(LFS_FSEEK "") + set(LFS_FTELL "") + set(LFS_PRID "") + + if(${_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(${_isenable}) + + if(NOT LFS_OFF_T) + ## not found + set(LFS_OFF_T "long") + set(LFS_FOPEN "fopen") + set(LFS_FSEEK "fseek") + set(LFS_FTELL "ftell") + set(LFS_PRID "\"ld\"") + endif(NOT LFS_OFF_T) + +endmacro(check_lfs) diff --git a/tools/apultra/src/libdivsufsort/CMakeModules/ProjectCPack.cmake b/tools/apultra/src/libdivsufsort/CMakeModules/ProjectCPack.cmake new file mode 100644 index 0000000..7c105f9 --- /dev/null +++ b/tools/apultra/src/libdivsufsort/CMakeModules/ProjectCPack.cmake @@ -0,0 +1,38 @@ +# If the cmake version includes cpack, use it +IF(EXISTS "${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/libdivsufsort/CMakeModules/cmake_uninstall.cmake.in b/tools/apultra/src/libdivsufsort/CMakeModules/cmake_uninstall.cmake.in new file mode 100644 index 0000000..8366a83 --- /dev/null +++ b/tools/apultra/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/libdivsufsort/LICENSE b/tools/apultra/src/libdivsufsort/LICENSE new file mode 100644 index 0000000..249efa4 --- /dev/null +++ b/tools/apultra/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/libdivsufsort/README.md b/tools/apultra/src/libdivsufsort/README.md new file mode 100644 index 0000000..381a188 --- /dev/null +++ b/tools/apultra/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 <stdio.h> +#include <stdlib.h> +#include <string.h> + +#include <divsufsort.h> + +int main() { + // intput data + char *Text = "abracadabra"; + int n = strlen(Text); + int i, j; + + // allocate + int *SA = (int *)malloc(n * sizeof(int)); + + // sort + divsufsort((unsigned char *)Text, SA, n); + + // output + for(i = 0; i < n; ++i) { + printf("SA[%2d] = %2d: ", i, SA[i]); + for(j = SA[i]; j < n; ++j) { + printf("%c", Text[j]); + } + printf("$\n"); + } + + // deallocate + free(SA); + + return 0; +} +``` +See the [examples](examples) directory for a few other examples. + +## Benchmarks +See [Benchmarks](https://github.com/y-256/libdivsufsort/blob/wiki/SACA_Benchmarks.md) page for details. + +## License +libdivsufsort is released under the [MIT license](LICENSE "MIT license"). +> The MIT License (MIT) +> +> Copyright (c) 2003 Yuta Mori All rights reserved. +> +> Permission is hereby granted, free of charge, to any person obtaining a copy +> of this software and associated documentation files (the "Software"), to deal +> in the Software without restriction, including without limitation the rights +> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +> copies of the Software, and to permit persons to whom the Software is +> furnished to do so, subject to the following conditions: +> +> The above copyright notice and this permission notice shall be included in all +> copies or substantial portions of the Software. +> +> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +> SOFTWARE. + +## Author +* Yuta Mori diff --git a/tools/apultra/src/libdivsufsort/VERSION.cmake b/tools/apultra/src/libdivsufsort/VERSION.cmake new file mode 100644 index 0000000..3f11ac1 --- /dev/null +++ b/tools/apultra/src/libdivsufsort/VERSION.cmake @@ -0,0 +1,23 @@ +set(PROJECT_VERSION_MAJOR "2") +set(PROJECT_VERSION_MINOR "0") +set(PROJECT_VERSION_PATCH "2") +set(PROJECT_VERSION_EXTRA "-1") +set(PROJECT_VERSION "${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 "${CMAKE_CURRENT_SOURCE_DIR}/.git") diff --git a/tools/apultra/src/libdivsufsort/examples/CMakeLists.txt b/tools/apultra/src/libdivsufsort/examples/CMakeLists.txt new file mode 100644 index 0000000..e801c81 --- /dev/null +++ b/tools/apultra/src/libdivsufsort/examples/CMakeLists.txt @@ -0,0 +1,11 @@ +## Add definitions ## +add_definitions(-D_LARGEFILE_SOURCE -D_LARGE_FILES -D_FILE_OFFSET_BITS=64) + +## Targets ## +include_directories("${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/libdivsufsort/examples/bwt.c b/tools/apultra/src/libdivsufsort/examples/bwt.c new file mode 100644 index 0000000..5a362d0 --- /dev/null +++ b/tools/apultra/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 <stdio.h> +#if HAVE_STRING_H +# include <string.h> +#endif +#if HAVE_STDLIB_H +# include <stdlib.h> +#endif +#if HAVE_MEMORY_H +# include <memory.h> +#endif +#if HAVE_STDDEF_H +# include <stddef.h> +#endif +#if HAVE_STRINGS_H +# include <strings.h> +#endif +#if HAVE_SYS_TYPES_H +# include <sys/types.h> +#endif +#if HAVE_IO_H && HAVE_FCNTL_H +# include <io.h> +# include <fcntl.h> +#endif +#include <time.h> +#include <divsufsort.h> +#include "lfs.h" + + +static +size_t +write_int(FILE *fp, saidx_t n) { + unsigned char c[4]; + c[0] = (unsigned char)((n >> 0) & 0xff), c[1] = (unsigned char)((n >> 8) & 0xff), + c[2] = (unsigned char)((n >> 16) & 0xff), c[3] = (unsigned char)((n >> 24) & 0xff); + return fwrite(c, sizeof(unsigned char), 4, fp); +} + +static +void +print_help(const char *progname, int status) { + fprintf(stderr, + "bwt, a burrows-wheeler transform program, version %s.\n", + divsufsort_version()); + fprintf(stderr, "usage: %s [-b num] INFILE OUTFILE\n", progname); + fprintf(stderr, " -b num set block size to num MiB [1..512] (default: 32)\n\n"); + exit(status); +} + +int +main(int argc, const char *argv[]) { + FILE *fp, *ofp; + const char *fname, *ofname; + sauchar_t *T; + saidx_t *SA; + LFS_OFF_T n; + size_t m; + saidx_t pidx; + clock_t start,finish; + saint_t i, blocksize = 32, needclose = 3; + + /* Check arguments. */ + if((argc == 1) || + (strcmp(argv[1], "-h") == 0) || + (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } + if((argc != 3) && (argc != 5)) { print_help(argv[0], EXIT_FAILURE); } + i = 1; + if(argc == 5) { + if(strcmp(argv[i], "-b") != 0) { print_help(argv[0], EXIT_FAILURE); } + blocksize = atoi(argv[i + 1]); + if(blocksize < 0) { blocksize = 1; } + else if(512 < blocksize) { blocksize = 512; } + i += 2; + } + blocksize <<= 20; + + /* Open a file for reading. */ + if(strcmp(argv[i], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&fp, fname = argv[i], "rb") != 0) { +#else + if((fp = LFS_FOPEN(fname = argv[i], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdin), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + fp = stdin; + fname = "stdin"; + needclose ^= 1; + } + i += 1; + + /* Open a file for writing. */ + if(strcmp(argv[i], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&ofp, ofname = argv[i], "wb") != 0) { +#else + if((ofp = LFS_FOPEN(ofname = argv[i], "wb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdout), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + ofp = stdout; + ofname = "stdout"; + needclose ^= 2; + } + + /* Get the file size. */ + if(LFS_FSEEK(fp, 0, SEEK_END) == 0) { + n = LFS_FTELL(fp); + rewind(fp); + if(n < 0) { + fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + if(0x20000000L < n) { n = 0x20000000L; } + if((blocksize == 0) || (n < blocksize)) { blocksize = (saidx_t)n; } + } else if(blocksize == 0) { blocksize = 32 << 20; } + + /* Allocate 5blocksize bytes of memory. */ + T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t)); + SA = (saidx_t *)malloc(blocksize * sizeof(saidx_t)); + if((T == NULL) || (SA == NULL)) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + + /* Write the blocksize. */ + if(write_int(ofp, blocksize) != 4) { + fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + + fprintf(stderr, " BWT (blocksize %" PRIdSAINT_T ") ... ", blocksize); + start = clock(); + for(n = 0; 0 < (m = fread(T, sizeof(sauchar_t), blocksize, fp)); n += m) { + /* Burrows-Wheeler Transform. */ + pidx = divbwt(T, T, SA, m); + if(pidx < 0) { + fprintf(stderr, "%s (bw_transform): %s.\n", + argv[0], + (pidx == -1) ? "Invalid arguments" : "Cannot allocate memory"); + exit(EXIT_FAILURE); + } + + /* Write the bwted data. */ + if((write_int(ofp, pidx) != 4) || + (fwrite(T, sizeof(sauchar_t), m, ofp) != m)) { + fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + } + if(ferror(fp)) { + fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + finish = clock(); + fprintf(stderr, "%" PRIdOFF_T " bytes: %.4f sec\n", + n, (double)(finish - start) / (double)CLOCKS_PER_SEC); + + /* Close files */ + if(needclose & 1) { fclose(fp); } + if(needclose & 2) { fclose(ofp); } + + /* Deallocate memory. */ + free(SA); + free(T); + + return 0; +} diff --git a/tools/apultra/src/libdivsufsort/examples/mksary.c b/tools/apultra/src/libdivsufsort/examples/mksary.c new file mode 100644 index 0000000..b48177c --- /dev/null +++ b/tools/apultra/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 <stdio.h> +#if HAVE_STRING_H +# include <string.h> +#endif +#if HAVE_STDLIB_H +# include <stdlib.h> +#endif +#if HAVE_MEMORY_H +# include <memory.h> +#endif +#if HAVE_STDDEF_H +# include <stddef.h> +#endif +#if HAVE_STRINGS_H +# include <strings.h> +#endif +#if HAVE_SYS_TYPES_H +# include <sys/types.h> +#endif +#if HAVE_IO_H && HAVE_FCNTL_H +# include <io.h> +# include <fcntl.h> +#endif +#include <time.h> +#include <divsufsort.h> +#include "lfs.h" + + +static +void +print_help(const char *progname, int status) { + fprintf(stderr, + "mksary, a simple suffix array builder, version %s.\n", + divsufsort_version()); + fprintf(stderr, "usage: %s INFILE OUTFILE\n\n", progname); + exit(status); +} + +int +main(int argc, const char *argv[]) { + FILE *fp, *ofp; + const char *fname, *ofname; + sauchar_t *T; + saidx_t *SA; + LFS_OFF_T n; + clock_t start, finish; + saint_t needclose = 3; + + /* Check arguments. */ + if((argc == 1) || + (strcmp(argv[1], "-h") == 0) || + (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } + if(argc != 3) { print_help(argv[0], EXIT_FAILURE); } + + /* Open a file for reading. */ + if(strcmp(argv[1], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&fp, fname = argv[1], "rb") != 0) { +#else + if((fp = LFS_FOPEN(fname = argv[1], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdin), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + fp = stdin; + fname = "stdin"; + needclose ^= 1; + } + + /* Open a file for writing. */ + if(strcmp(argv[2], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&ofp, ofname = argv[2], "wb") != 0) { +#else + if((ofp = LFS_FOPEN(ofname = argv[2], "wb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdout), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + ofp = stdout; + ofname = "stdout"; + needclose ^= 2; + } + + /* Get the file size. */ + if(LFS_FSEEK(fp, 0, SEEK_END) == 0) { + n = LFS_FTELL(fp); + rewind(fp); + if(n < 0) { + fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + if(0x7fffffff <= n) { + fprintf(stderr, "%s: Input file `%s' is too big.\n", argv[0], fname); + exit(EXIT_FAILURE); + } + } else { + fprintf(stderr, "%s: Cannot fseek `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Allocate 5blocksize bytes of memory. */ + T = (sauchar_t *)malloc((size_t)n * sizeof(sauchar_t)); + SA = (saidx_t *)malloc((size_t)n * sizeof(saidx_t)); + if((T == NULL) || (SA == NULL)) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + + /* Read n bytes of data. */ + if(fread(T, sizeof(sauchar_t), (size_t)n, fp) != (size_t)n) { + fprintf(stderr, "%s: %s `%s': ", + argv[0], + (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", + fname); + perror(NULL); + exit(EXIT_FAILURE); + } + if(needclose & 1) { fclose(fp); } + + /* Construct the suffix array. */ + fprintf(stderr, "%s: %" PRIdOFF_T " bytes ... ", fname, n); + start = clock(); + if(divsufsort(T, SA, (saidx_t)n) != 0) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + finish = clock(); + fprintf(stderr, "%.4f sec\n", (double)(finish - start) / (double)CLOCKS_PER_SEC); + + /* Write the suffix array. */ + if(fwrite(SA, sizeof(saidx_t), (size_t)n, ofp) != (size_t)n) { + fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + if(needclose & 2) { fclose(ofp); } + + /* Deallocate memory. */ + free(SA); + free(T); + + return 0; +} diff --git a/tools/apultra/src/libdivsufsort/examples/sasearch.c b/tools/apultra/src/libdivsufsort/examples/sasearch.c new file mode 100644 index 0000000..7e5ca4f --- /dev/null +++ b/tools/apultra/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 <stdio.h> +#if HAVE_STRING_H +# include <string.h> +#endif +#if HAVE_STDLIB_H +# include <stdlib.h> +#endif +#if HAVE_MEMORY_H +# include <memory.h> +#endif +#if HAVE_STDDEF_H +# include <stddef.h> +#endif +#if HAVE_STRINGS_H +# include <strings.h> +#endif +#if HAVE_SYS_TYPES_H +# include <sys/types.h> +#endif +#if HAVE_IO_H && HAVE_FCNTL_H +# include <io.h> +# include <fcntl.h> +#endif +#include <divsufsort.h> +#include "lfs.h" + + +static +void +print_help(const char *progname, int status) { + fprintf(stderr, + "sasearch, a simple SA-based full-text search tool, version %s\n", + divsufsort_version()); + fprintf(stderr, "usage: %s PATTERN FILE SAFILE\n\n", progname); + exit(status); +} + +int +main(int argc, const char *argv[]) { + FILE *fp; + const char *P; + sauchar_t *T; + saidx_t *SA; + LFS_OFF_T n; + size_t Psize; + saidx_t i, size, left; + + if((argc == 1) || + (strcmp(argv[1], "-h") == 0) || + (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } + if(argc != 4) { print_help(argv[0], EXIT_FAILURE); } + + P = argv[1]; + Psize = strlen(P); + + /* Open a file for reading. */ +#if HAVE_FOPEN_S + if(fopen_s(&fp, argv[2], "rb") != 0) { +#else + if((fp = LFS_FOPEN(argv[2], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], argv[2]); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Get the file size. */ + if(LFS_FSEEK(fp, 0, SEEK_END) == 0) { + n = LFS_FTELL(fp); + rewind(fp); + if(n < 0) { + fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], argv[2]); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { + fprintf(stderr, "%s: Cannot fseek `%s': ", argv[0], argv[2]); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Allocate 5n bytes of memory. */ + T = (sauchar_t *)malloc((size_t)n * sizeof(sauchar_t)); + SA = (saidx_t *)malloc((size_t)n * sizeof(saidx_t)); + if((T == NULL) || (SA == NULL)) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + + /* Read n bytes of data. */ + if(fread(T, sizeof(sauchar_t), (size_t)n, fp) != (size_t)n) { + fprintf(stderr, "%s: %s `%s': ", + argv[0], + (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", + argv[2]); + perror(NULL); + exit(EXIT_FAILURE); + } + fclose(fp); + + /* Open the SA file for reading. */ +#if HAVE_FOPEN_S + if(fopen_s(&fp, argv[3], "rb") != 0) { +#else + if((fp = LFS_FOPEN(argv[3], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], argv[3]); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Read n * sizeof(saidx_t) bytes of data. */ + if(fread(SA, sizeof(saidx_t), (size_t)n, fp) != (size_t)n) { + fprintf(stderr, "%s: %s `%s': ", + argv[0], + (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", + argv[3]); + perror(NULL); + exit(EXIT_FAILURE); + } + fclose(fp); + + /* Search and print */ + size = sa_search(T, (saidx_t)n, + (const sauchar_t *)P, (saidx_t)Psize, + SA, (saidx_t)n, &left); + for(i = 0; i < size; ++i) { + fprintf(stdout, "%" PRIdSAIDX_T "\n", SA[left + i]); + } + + /* Deallocate memory. */ + free(SA); + free(T); + + return 0; +} diff --git a/tools/apultra/src/libdivsufsort/examples/suftest.c b/tools/apultra/src/libdivsufsort/examples/suftest.c new file mode 100644 index 0000000..71892ac --- /dev/null +++ b/tools/apultra/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 <stdio.h> +#if HAVE_STRING_H +# include <string.h> +#endif +#if HAVE_STDLIB_H +# include <stdlib.h> +#endif +#if HAVE_MEMORY_H +# include <memory.h> +#endif +#if HAVE_STDDEF_H +# include <stddef.h> +#endif +#if HAVE_STRINGS_H +# include <strings.h> +#endif +#if HAVE_SYS_TYPES_H +# include <sys/types.h> +#endif +#if HAVE_IO_H && HAVE_FCNTL_H +# include <io.h> +# include <fcntl.h> +#endif +#include <time.h> +#include <divsufsort.h> +#include "lfs.h" + + +static +void +print_help(const char *progname, int status) { + fprintf(stderr, + "suftest, a suffixsort tester, version %s.\n", + divsufsort_version()); + fprintf(stderr, "usage: %s FILE\n\n", progname); + exit(status); +} + +int +main(int argc, const char *argv[]) { + FILE *fp; + const char *fname; + sauchar_t *T; + saidx_t *SA; + LFS_OFF_T n; + clock_t start, finish; + saint_t needclose = 1; + + /* Check arguments. */ + if((argc == 1) || + (strcmp(argv[1], "-h") == 0) || + (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } + if(argc != 2) { print_help(argv[0], EXIT_FAILURE); } + + /* Open a file for reading. */ + if(strcmp(argv[1], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&fp, fname = argv[1], "rb") != 0) { +#else + if((fp = LFS_FOPEN(fname = argv[1], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdin), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + fp = stdin; + fname = "stdin"; + needclose = 0; + } + + /* Get the file size. */ + if(LFS_FSEEK(fp, 0, SEEK_END) == 0) { + n = LFS_FTELL(fp); + rewind(fp); + if(n < 0) { + fprintf(stderr, "%s: Cannot ftell `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + if(0x7fffffff <= n) { + fprintf(stderr, "%s: Input file `%s' is too big.\n", argv[0], fname); + exit(EXIT_FAILURE); + } + } else { + fprintf(stderr, "%s: Cannot fseek `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Allocate 5n bytes of memory. */ + T = (sauchar_t *)malloc((size_t)n * sizeof(sauchar_t)); + SA = (saidx_t *)malloc((size_t)n * sizeof(saidx_t)); + if((T == NULL) || (SA == NULL)) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + + /* Read n bytes of data. */ + if(fread(T, sizeof(sauchar_t), (size_t)n, fp) != (size_t)n) { + fprintf(stderr, "%s: %s `%s': ", + argv[0], + (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", + argv[1]); + perror(NULL); + exit(EXIT_FAILURE); + } + if(needclose & 1) { fclose(fp); } + + /* Construct the suffix array. */ + fprintf(stderr, "%s: %" PRIdOFF_T " bytes ... ", fname, n); + start = clock(); + if(divsufsort(T, SA, (saidx_t)n) != 0) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + finish = clock(); + fprintf(stderr, "%.4f sec\n", (double)(finish - start) / (double)CLOCKS_PER_SEC); + + /* Check the suffix array. */ + if(sufcheck(T, SA, (saidx_t)n, 1) != 0) { exit(EXIT_FAILURE); } + + /* Deallocate memory. */ + free(SA); + free(T); + + return 0; +} diff --git a/tools/apultra/src/libdivsufsort/examples/unbwt.c b/tools/apultra/src/libdivsufsort/examples/unbwt.c new file mode 100644 index 0000000..c0f19e9 --- /dev/null +++ b/tools/apultra/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 <stdio.h> +#if HAVE_STRING_H +# include <string.h> +#endif +#if HAVE_STDLIB_H +# include <stdlib.h> +#endif +#if HAVE_MEMORY_H +# include <memory.h> +#endif +#if HAVE_STDDEF_H +# include <stddef.h> +#endif +#if HAVE_STRINGS_H +# include <strings.h> +#endif +#if HAVE_SYS_TYPES_H +# include <sys/types.h> +#endif +#if HAVE_IO_H && HAVE_FCNTL_H +# include <io.h> +# include <fcntl.h> +#endif +#include <time.h> +#include <divsufsort.h> +#include "lfs.h" + + +static +size_t +read_int(FILE *fp, saidx_t *n) { + unsigned char c[4]; + size_t m = fread(c, sizeof(unsigned char), 4, fp); + if(m == 4) { + *n = (c[0] << 0) | (c[1] << 8) | + (c[2] << 16) | (c[3] << 24); + } + return m; +} + +static +void +print_help(const char *progname, int status) { + fprintf(stderr, + "unbwt, an inverse burrows-wheeler transform program, version %s.\n", + divsufsort_version()); + fprintf(stderr, "usage: %s INFILE OUTFILE\n\n", progname); + exit(status); +} + +int +main(int argc, const char *argv[]) { + FILE *fp, *ofp; + const char *fname, *ofname; + sauchar_t *T; + saidx_t *A; + LFS_OFF_T n; + size_t m; + saidx_t pidx; + clock_t start, finish; + saint_t err, blocksize, needclose = 3; + + /* Check arguments. */ + if((argc == 1) || + (strcmp(argv[1], "-h") == 0) || + (strcmp(argv[1], "--help") == 0)) { print_help(argv[0], EXIT_SUCCESS); } + if(argc != 3) { print_help(argv[0], EXIT_FAILURE); } + + /* Open a file for reading. */ + if(strcmp(argv[1], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&fp, fname = argv[1], "rb") != 0) { +#else + if((fp = LFS_FOPEN(fname = argv[1], "rb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdin), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + fp = stdin; + fname = "stdin"; + needclose ^= 1; + } + + /* Open a file for writing. */ + if(strcmp(argv[2], "-") != 0) { +#if HAVE_FOPEN_S + if(fopen_s(&ofp, ofname = argv[2], "wb") != 0) { +#else + if((ofp = LFS_FOPEN(ofname = argv[2], "wb")) == NULL) { +#endif + fprintf(stderr, "%s: Cannot open file `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + } else { +#if HAVE__SETMODE && HAVE__FILENO + if(_setmode(_fileno(stdout), _O_BINARY) == -1) { + fprintf(stderr, "%s: Cannot set mode: ", argv[0]); + perror(NULL); + exit(EXIT_FAILURE); + } +#endif + ofp = stdout; + ofname = "stdout"; + needclose ^= 2; + } + + /* Read the blocksize. */ + if(read_int(fp, &blocksize) != 4) { + fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Allocate 5blocksize bytes of memory. */ + T = (sauchar_t *)malloc(blocksize * sizeof(sauchar_t)); + A = (saidx_t *)malloc(blocksize * sizeof(saidx_t)); + if((T == NULL) || (A == NULL)) { + fprintf(stderr, "%s: Cannot allocate memory.\n", argv[0]); + exit(EXIT_FAILURE); + } + + fprintf(stderr, "UnBWT (blocksize %" PRIdSAINT_T ") ... ", blocksize); + start = clock(); + for(n = 0; (m = read_int(fp, &pidx)) != 0; n += m) { + /* Read blocksize bytes of data. */ + if((m != 4) || ((m = fread(T, sizeof(sauchar_t), blocksize, fp)) == 0)) { + fprintf(stderr, "%s: %s `%s': ", + argv[0], + (ferror(fp) || !feof(fp)) ? "Cannot read from" : "Unexpected EOF in", + fname); + perror(NULL); + exit(EXIT_FAILURE); + } + + /* Inverse Burrows-Wheeler Transform. */ + if((err = inverse_bw_transform(T, T, A, m, pidx)) != 0) { + fprintf(stderr, "%s (reverseBWT): %s.\n", + argv[0], + (err == -1) ? "Invalid data" : "Cannot allocate memory"); + exit(EXIT_FAILURE); + } + + /* Write m bytes of data. */ + if(fwrite(T, sizeof(sauchar_t), m, ofp) != m) { + fprintf(stderr, "%s: Cannot write to `%s': ", argv[0], ofname); + perror(NULL); + exit(EXIT_FAILURE); + } + } + if(ferror(fp)) { + fprintf(stderr, "%s: Cannot read from `%s': ", argv[0], fname); + perror(NULL); + exit(EXIT_FAILURE); + } + finish = clock(); + fprintf(stderr, "%" PRIdOFF_T " bytes: %.4f sec\n", + n, (double)(finish - start) / (double)CLOCKS_PER_SEC); + + /* Close files */ + if(needclose & 1) { fclose(fp); } + if(needclose & 2) { fclose(ofp); } + + /* Deallocate memory. */ + free(A); + free(T); + + return 0; +} diff --git a/tools/apultra/src/libdivsufsort/include/CMakeLists.txt b/tools/apultra/src/libdivsufsort/include/CMakeLists.txt new file mode 100644 index 0000000..37781cc --- /dev/null +++ b/tools/apultra/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 <inttypes.h>") +elseif(HAVE_STDINT_H) + set(INCFILE "#include <stdint.h>") +else(HAVE_INTTYPES_H) + set(INCFILE "") +endif(HAVE_INTTYPES_H) + +## create configuration files from .cmake file ## +if(BUILD_EXAMPLES) + ## Checks for WinIO ## + if(WIN32) + check_include_file("io.h" HAVE_IO_H) + check_include_file("fcntl.h" HAVE_FCNTL_H) + check_symbol_exists("_setmode" "io.h;fcntl.h" HAVE__SETMODE) + if(NOT HAVE__SETMODE) + check_symbol_exists("setmode" "io.h;fcntl.h" HAVE_SETMODE) + endif(NOT HAVE__SETMODE) + check_symbol_exists("_fileno" "stdio.h" HAVE__FILENO) + check_symbol_exists("fopen_s" "stdio.h" HAVE_FOPEN_S) + check_symbol_exists("_O_BINARY" "fcntl.h" HAVE__O_BINARY) + endif(WIN32) + + ## Checks for large file support ## + check_lfs(WITH_LFS) + configure_file("${CMAKE_CURRENT_SOURCE_DIR}/lfs.h.cmake" "${CMAKE_CURRENT_BINARY_DIR}/lfs.h" @ONLY) +endif(BUILD_EXAMPLES) + +## generate config.h ## +check_function_keywords("inline;__inline;__inline__;__declspec(dllexport);__declspec(dllimport)") +if(HAVE_INLINE) + set(INLINE "inline") +elseif(HAVE___INLINE) + set(INLINE "__inline") +elseif(HAVE___INLINE__) + set(INLINE "__inline__") +else(HAVE_INLINE) + set(INLINE "") +endif(HAVE_INLINE) +configure_file("${CMAKE_CURRENT_SOURCE_DIR}/config.h.cmake" "${CMAKE_CURRENT_BINARY_DIR}/config.h") + +## Checks for types ## +# sauchar_t (8bit) +check_type_size("uint8_t" UINT8_T) +if(HAVE_UINT8_T) + set(SAUCHAR_TYPE "uint8_t") +else(HAVE_UINT8_T) + check_type_size("unsigned char" SIZEOF_UNSIGNED_CHAR) + if("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1") + set(SAUCHAR_TYPE "unsigned char") + else("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1") + message(FATAL_ERROR "Cannot find unsigned 8-bit integer type") + endif("${SIZEOF_UNSIGNED_CHAR}" STREQUAL "1") +endif(HAVE_UINT8_T) +# saint_t (32bit) +check_type_size("int32_t" INT32_T) +if(HAVE_INT32_T) + set(SAINT32_TYPE "int32_t") + check_symbol_exists("PRId32" "inttypes.h" HAVE_PRID32) + if(HAVE_PRID32) + set(SAINT32_PRId "PRId32") + else(HAVE_PRID32) + set(SAINT32_PRId "\"d\"") + endif(HAVE_PRID32) +else(HAVE_INT32_T) + check_type_size("int" SIZEOF_INT) + check_type_size("long" SIZEOF_LONG) + check_type_size("short" SIZEOF_SHORT) + check_type_size("__int32" SIZEOF___INT32) + if("${SIZEOF_INT}" STREQUAL "4") + set(SAINT32_TYPE "int") + set(SAINT32_PRId "\"d\"") + elseif("${SIZEOF_LONG}" STREQUAL "4") + set(SAINT32_TYPE "long") + set(SAINT32_PRId "\"ld\"") + elseif("${SIZEOF_SHORT}" STREQUAL "4") + set(SAINT32_TYPE "short") + set(SAINT32_PRId "\"d\"") + elseif("${SIZEOF___INT32}" STREQUAL "4") + set(SAINT32_TYPE "__int32") + set(SAINT32_PRId "\"d\"") + else("${SIZEOF_INT}" STREQUAL "4") + message(FATAL_ERROR "Cannot find 32-bit integer type") + endif("${SIZEOF_INT}" STREQUAL "4") +endif(HAVE_INT32_T) +# saint64_t (64bit) +if(BUILD_DIVSUFSORT64) + check_type_size("int64_t" INT64_T) + if(HAVE_INT64_T) + set(SAINT64_TYPE "int64_t") + check_symbol_exists("PRId64" "inttypes.h" HAVE_PRID64) + if(HAVE_PRID64) + set(SAINT64_PRId "PRId64") + else(HAVE_PRID64) + set(SAINT64_PRId "\"lld\"") + endif(HAVE_PRID64) + else(HAVE_INT64_T) + check_type_size("int" SIZEOF_INT) + check_type_size("long" SIZEOF_LONG) + check_type_size("long long" SIZEOF_LONG_LONG) + check_type_size("__int64" SIZEOF___INT64) + if("${SIZEOF_INT}" STREQUAL "8") + set(SAINT64_TYPE "int") + set(SAINT64_PRId "\"d\"") + elseif("${SIZEOF_LONG}" STREQUAL "8") + set(SAINT64_TYPE "long") + set(SAINT64_PRId "\"ld\"") + elseif("${SIZEOF_LONG_LONG}" STREQUAL "8") + set(SAINT64_TYPE "long long") + set(SAINT64_PRId "\"lld\"") + elseif("${SIZEOF___INT64}" STREQUAL "8") + set(SAINT64_TYPE "__int64") + set(SAINT64_PRId "\"I64d\"") + else("${SIZEOF_INT}" STREQUAL "8") + message(SEND_ERROR "Cannot find 64-bit integer type") + set(BUILD_DIVSUFSORT64 OFF) + endif("${SIZEOF_INT}" STREQUAL "8") + endif(HAVE_INT64_T) +endif(BUILD_DIVSUFSORT64) + +## generate divsufsort.h ## +set(DIVSUFSORT_IMPORT "") +set(DIVSUFSORT_EXPORT "") +if(BUILD_SHARED_LIBS) + if(HAVE___DECLSPEC_DLLIMPORT_) + set(DIVSUFSORT_IMPORT "__declspec(dllimport)") + endif(HAVE___DECLSPEC_DLLIMPORT_) + if(HAVE___DECLSPEC_DLLEXPORT_) + set(DIVSUFSORT_EXPORT "__declspec(dllexport)") + endif(HAVE___DECLSPEC_DLLEXPORT_) +endif(BUILD_SHARED_LIBS) +set(W64BIT "") +set(SAINDEX_TYPE "${SAINT32_TYPE}") +set(SAINDEX_PRId "${SAINT32_PRId}") +set(SAINT_PRId "${SAINT32_PRId}") +configure_file("${CMAKE_CURRENT_SOURCE_DIR}/divsufsort.h.cmake" + "${CMAKE_CURRENT_BINARY_DIR}/divsufsort.h" @ONLY) +install(FILES "${CMAKE_CURRENT_BINARY_DIR}/divsufsort.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) +if(BUILD_DIVSUFSORT64) + set(W64BIT "64") + set(SAINDEX_TYPE "${SAINT64_TYPE}") + set(SAINDEX_PRId "${SAINT64_PRId}") + configure_file("${CMAKE_CURRENT_SOURCE_DIR}/divsufsort.h.cmake" + "${CMAKE_CURRENT_BINARY_DIR}/divsufsort64.h" @ONLY) + install(FILES "${CMAKE_CURRENT_BINARY_DIR}/divsufsort64.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) +endif(BUILD_DIVSUFSORT64) diff --git a/tools/apultra/src/libdivsufsort/include/config.h.cmake b/tools/apultra/src/libdivsufsort/include/config.h.cmake new file mode 100644 index 0000000..6a1cf47 --- /dev/null +++ b/tools/apultra/src/libdivsufsort/include/config.h.cmake @@ -0,0 +1,81 @@ +/* + * config.h for libdivsufsort + * Copyright (c) 2003-2008 Yuta Mori All Rights Reserved. + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR + * OTHER DEALINGS IN THE SOFTWARE. + */ + +#ifndef _CONFIG_H +#define _CONFIG_H 1 + +#ifdef __cplusplus +extern "C" { +#endif /* __cplusplus */ + +/** Define to the version of this package. **/ +#cmakedefine PROJECT_VERSION_FULL "${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/libdivsufsort/include/divsufsort.h b/tools/apultra/src/libdivsufsort/include/divsufsort.h new file mode 100644 index 0000000..7ebb412 --- /dev/null +++ b/tools/apultra/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/libdivsufsort/include/divsufsort.h.cmake b/tools/apultra/src/libdivsufsort/include/divsufsort.h.cmake new file mode 100644 index 0000000..bcaba7c --- /dev/null +++ b/tools/apultra/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/libdivsufsort/include/divsufsort_config.h b/tools/apultra/src/libdivsufsort/include/divsufsort_config.h new file mode 100644 index 0000000..4054a8a --- /dev/null +++ b/tools/apultra/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/libdivsufsort/include/divsufsort_private.h b/tools/apultra/src/libdivsufsort/include/divsufsort_private.h new file mode 100644 index 0000000..b4d97ad --- /dev/null +++ b/tools/apultra/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 <assert.h> +#include <stdio.h> +#if HAVE_STRING_H +# include <string.h> +#endif +#if HAVE_STDLIB_H +# include <stdlib.h> +#endif +#if HAVE_MEMORY_H +# include <memory.h> +#endif +#if HAVE_STDDEF_H +# include <stddef.h> +#endif +#if HAVE_STRINGS_H +# include <strings.h> +#endif +#if HAVE_INTTYPES_H +# include <inttypes.h> +#else +# if HAVE_STDINT_H +# include <stdint.h> +# endif +#endif +#if defined(BUILD_DIVSUFSORT64) +# include "divsufsort64.h" +# ifndef SAIDX_T +# define SAIDX_T +# define saidx_t saidx64_t +# endif /* SAIDX_T */ +# ifndef PRIdSAIDX_T +# define PRIdSAIDX_T PRIdSAIDX64_T +# endif /* PRIdSAIDX_T */ +# define divsufsort divsufsort64 +# define divbwt divbwt64 +# define divsufsort_version divsufsort64_version +# define bw_transform bw_transform64 +# define inverse_bw_transform inverse_bw_transform64 +# define sufcheck sufcheck64 +# define sa_search sa_search64 +# define sa_simplesearch sa_simplesearch64 +# define sssort sssort64 +# define trsort trsort64 +#else +# include "divsufsort.h" +#endif + + +/*- Constants -*/ +#if !defined(UINT8_MAX) +# define UINT8_MAX (255) +#endif /* UINT8_MAX */ +#if defined(ALPHABET_SIZE) && (ALPHABET_SIZE < 1) +# undef ALPHABET_SIZE +#endif +#if !defined(ALPHABET_SIZE) +# define ALPHABET_SIZE (UINT8_MAX + 1) +#endif +/* for divsufsort.c */ +#define BUCKET_A_SIZE (ALPHABET_SIZE) +#define BUCKET_B_SIZE (ALPHABET_SIZE * ALPHABET_SIZE) +/* for sssort.c */ +#if defined(SS_INSERTIONSORT_THRESHOLD) +# if SS_INSERTIONSORT_THRESHOLD < 1 +# undef SS_INSERTIONSORT_THRESHOLD +# define SS_INSERTIONSORT_THRESHOLD (1) +# endif +#else +# define SS_INSERTIONSORT_THRESHOLD (8) +#endif +#if defined(SS_BLOCKSIZE) +# if SS_BLOCKSIZE < 0 +# undef SS_BLOCKSIZE +# define SS_BLOCKSIZE (0) +# elif 32768 <= SS_BLOCKSIZE +# undef SS_BLOCKSIZE +# define SS_BLOCKSIZE (32767) +# endif +#else +# define SS_BLOCKSIZE (1024) +#endif +/* minstacksize = log(SS_BLOCKSIZE) / log(3) * 2 */ +#if SS_BLOCKSIZE == 0 +# if defined(BUILD_DIVSUFSORT64) +# define SS_MISORT_STACKSIZE (96) +# else +# define SS_MISORT_STACKSIZE (64) +# endif +#elif SS_BLOCKSIZE <= 4096 +# define SS_MISORT_STACKSIZE (16) +#else +# define SS_MISORT_STACKSIZE (24) +#endif +#if defined(BUILD_DIVSUFSORT64) +# define SS_SMERGE_STACKSIZE (64) +#else +# define SS_SMERGE_STACKSIZE (32) +#endif +/* for trsort.c */ +#define TR_INSERTIONSORT_THRESHOLD (8) +#if defined(BUILD_DIVSUFSORT64) +# define TR_STACKSIZE (96) +#else +# define TR_STACKSIZE (64) +#endif + + +/*- Macros -*/ +#ifndef SWAP +# define SWAP(_a, _b) do { t = (_a); (_a) = (_b); (_b) = t; } while(0) +#endif /* SWAP */ +#ifndef MIN +# define MIN(_a, _b) (((_a) < (_b)) ? (_a) : (_b)) +#endif /* MIN */ +#ifndef MAX +# define MAX(_a, _b) (((_a) > (_b)) ? (_a) : (_b)) +#endif /* MAX */ +#define STACK_PUSH(_a, _b, _c, _d)\ + do {\ + assert(ssize < STACK_SIZE);\ + stack[ssize].a = (_a), stack[ssize].b = (_b),\ + stack[ssize].c = (_c), stack[ssize++].d = (_d);\ + } while(0) +#define STACK_PUSH5(_a, _b, _c, _d, _e)\ + do {\ + assert(ssize < STACK_SIZE);\ + stack[ssize].a = (_a), stack[ssize].b = (_b),\ + stack[ssize].c = (_c), stack[ssize].d = (_d), stack[ssize++].e = (_e);\ + } while(0) +#define STACK_POP(_a, _b, _c, _d)\ + do {\ + assert(0 <= ssize);\ + if(ssize == 0) { return; }\ + (_a) = stack[--ssize].a, (_b) = stack[ssize].b,\ + (_c) = stack[ssize].c, (_d) = stack[ssize].d;\ + } while(0) +#define STACK_POP5(_a, _b, _c, _d, _e)\ + do {\ + assert(0 <= ssize);\ + if(ssize == 0) { return; }\ + (_a) = stack[--ssize].a, (_b) = stack[ssize].b,\ + (_c) = stack[ssize].c, (_d) = stack[ssize].d, (_e) = stack[ssize].e;\ + } while(0) +/* for divsufsort.c */ +#define BUCKET_A(_c0) bucket_A[(_c0)] +#if ALPHABET_SIZE == 256 +#define BUCKET_B(_c0, _c1) (bucket_B[((_c1) << 8) | (_c0)]) +#define BUCKET_BSTAR(_c0, _c1) (bucket_B[((_c0) << 8) | (_c1)]) +#else +#define BUCKET_B(_c0, _c1) (bucket_B[(_c1) * ALPHABET_SIZE + (_c0)]) +#define BUCKET_BSTAR(_c0, _c1) (bucket_B[(_c0) * ALPHABET_SIZE + (_c1)]) +#endif + + +/*- Private Prototypes -*/ +/* sssort.c */ +void +sssort(const sauchar_t *Td, const saidx_t *PA, + saidx_t *first, saidx_t *last, + saidx_t *buf, saidx_t bufsize, + saidx_t depth, saidx_t n, saint_t lastsuffix); +/* trsort.c */ +void +trsort(saidx_t *ISA, saidx_t *SA, saidx_t n, saidx_t depth); + + +#ifdef __cplusplus +} /* extern "C" */ +#endif /* __cplusplus */ + +#endif /* _DIVSUFSORT_PRIVATE_H */ diff --git a/tools/apultra/src/libdivsufsort/include/lfs.h.cmake b/tools/apultra/src/libdivsufsort/include/lfs.h.cmake new file mode 100644 index 0000000..d5b84a8 --- /dev/null +++ b/tools/apultra/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/libdivsufsort/pkgconfig/CMakeLists.txt b/tools/apultra/src/libdivsufsort/pkgconfig/CMakeLists.txt new file mode 100644 index 0000000..ee7063c --- /dev/null +++ b/tools/apultra/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 ${CMAKE_INSTALL_PKGCONFIGDIR}) +endif(BUILD_DIVSUFSORT64) diff --git a/tools/apultra/src/libdivsufsort/pkgconfig/libdivsufsort.pc.cmake b/tools/apultra/src/libdivsufsort/pkgconfig/libdivsufsort.pc.cmake new file mode 100644 index 0000000..6419d1e --- /dev/null +++ b/tools/apultra/src/libdivsufsort/pkgconfig/libdivsufsort.pc.cmake @@ -0,0 +1,11 @@ +prefix=@CMAKE_INSTALL_PREFIX@ +exec_prefix=${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/matchfinder.c b/tools/apultra/src/matchfinder.c new file mode 100644 index 0000000..a9987f9 --- /dev/null +++ b/tools/apultra/src/matchfinder.c @@ -0,0 +1,449 @@ +/*
+ * matchfinder.c - LZ match finder implementation
+ *
+ * The following copying information applies to this specific source code file:
+ *
+ * Written in 2019 by Emmanuel Marty <marty.emmanuel@gmail.com>
+ * Portions written in 2014-2015 by Eric Biggers <ebiggers3@gmail.com>
+ *
+ * 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 <http://creativecommons.org/publicdomain/zero/1.0/>.
+ */
+
+/*
+ * 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 <zxintrospec@gmail.com>
+ *
+ */
+
+#include <stdlib.h>
+#include <string.h>
+#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, r;
+
+ 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 (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;
+ const int nMaxOffset = pCompressor->max_offset;
+
+ *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 <= nMaxOffset) {
+ 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 <= nMaxOffset && abs(nMatchOffset - nPrevOffset) >= 128) {
+ 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;
+
+ 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 <= nMaxOffset && (nMatchLen >= 3 || (nMatchLen >= 2 && (matchptr - pMatches) < (nMaxMatches - 1))) && nMatchLen < 1280 && abs(nMatchOffset - nPrevOffset) >= 128) {
+ 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;
+ }
+ }
+ }
+ }
+
+ 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 <= nMaxOffset && 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;
+
+ 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 <= nMaxOffset && nMatchLen >= 2 && abs(nMatchOffset - nPrevOffset) >= 128) {
+ 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;
+ }
+ }
+ }
+ }
+
+ 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/matchfinder.h b/tools/apultra/src/matchfinder.h new file mode 100644 index 0000000..7d68eaf --- /dev/null +++ b/tools/apultra/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 <zxintrospec@gmail.com>
+ *
+ */
+
+#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/shrink.c b/tools/apultra/src/shrink.c new file mode 100644 index 0000000..c6c9826 --- /dev/null +++ b/tools/apultra/src/shrink.c @@ -0,0 +1,1728 @@ +/*
+ * 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 <zxintrospec@gmail.com>
+ *
+ */
+
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
+#include "libapultra.h"
+#include "matchfinder.h"
+#include "shrink.h"
+#include "format.h"
+
+#define TOKEN_CODE_LARGE_MATCH 2 /* 10 */
+#define TOKEN_SIZE_LARGE_MATCH 2
+
+#define TOKEN_CODE_7BIT_MATCH 6 /* 110 */
+#define TOKEN_SIZE_7BIT_MATCH 3
+
+#define TOKEN_CODE_4BIT_MATCH 7 /* 111 */
+#define TOKEN_SIZE_4BIT_MATCH 3
+
+#define CountShift(N,bits) if ((N)>>(bits)) { (N)>>=(bits); (n) += (bits); }
+
+/** 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 bitpacked 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 to write
+ * @param nBits number of least significant bits to write in value
+ * @param nCurBitsOffset write index into output buffer, of current byte being filled with bits
+ * @param nCurBitShift bit shift count
+ *
+ * @return updated write index into output buffer, or -1 in case of an error
+ */
+static int apultra_write_bits(unsigned char *pOutData, int nOutOffset, const int nMaxOutDataSize, const int nValue, const int nBits, int *nCurBitsOffset, int *nCurBitShift) {
+ int i;
+
+ if (nOutOffset < 0) return -1;
+
+ for (i = nBits - 1; i >= 0; i--) {
+ if ((*nCurBitsOffset) == INT_MIN) {
+ /* Allocate a new byte in the stream to pack bits in */
+ if (nOutOffset >= nMaxOutDataSize) return -1;
+ (*nCurBitsOffset) = nOutOffset;
+ (*nCurBitShift) = 7;
+ pOutData[nOutOffset++] = 0;
+ }
+
+ pOutData[(*nCurBitsOffset)] |= ((nValue >> i) & 1) << (*nCurBitShift);
+
+ (*nCurBitShift) --;
+ if ((*nCurBitShift) == -1) {
+ /* Current byte is full */
+ (*nCurBitsOffset) = 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 nCurBitShift bit shift count
+ *
+ * @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 *nCurBitShift) {
+ int msb = 30;
+ while ((nValue >> msb--) == 0);
+
+ while (msb > 0) {
+ int bit = (nValue >> msb) & 1;
+
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, bit, 1, nCurBitsOffset, nCurBitShift);
+ msb--;
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, 1, 1, nCurBitsOffset, nCurBitShift);
+ }
+
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, nValue & 1, 1, nCurBitsOffset, nCurBitShift);
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, 0, 1, nCurBitsOffset, nCurBitShift);
+ return nOutOffset;
+}
+
+/**
+ * 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 <= 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 match length
+ *
+ * @param nLength match length
+ * @param nMatchOffset match offset
+ *
+ * @return number of extra bits required
+ */
+static inline int apultra_get_match_varlen_size(int nLength, const int nMatchOffset) {
+ if (nLength <= 3 && nMatchOffset < 128)
+ return 0;
+ else {
+ if (nMatchOffset < 128 || nMatchOffset >= MINMATCH4_OFFSET)
+ return apultra_get_gamma2_size(nLength - 2);
+ else if (nMatchOffset < MINMATCH3_OFFSET)
+ return apultra_get_gamma2_size(nLength);
+ else
+ return apultra_get_gamma2_size(nLength - 1);
+ }
+}
+
+/**
+ * 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 nArrivalsPerPosition maximum number of arrivals per input buffer position
+ * @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 nArrivalsPerPosition, int nDepth) {
+ const apultra_arrival *arrival = pCompressor->arrival + ((i - nStartOffset) * nArrivalsPerPosition);
+ const int *rle_len = (int*)pCompressor->intervals /* reuse */;
+ int* visited = ((int*)pCompressor->pos_data) - nStartOffset /* reuse */;
+ int j;
+
+ for (j = 0; j < nArrivalsPerPosition && arrival[j].from_slot; j++) {
+ if (arrival[j].follows_literal) {
+ int nRepOffset = arrival[j].rep_offset;
+
+ if (nMatchOffset != nRepOffset && nRepOffset) {
+ int nRepPos = arrival[j].rep_pos;
+
+ if (nRepPos >= nStartOffset &&
+ nRepPos < nEndOffset &&
+ visited[nRepPos] != nMatchOffset) {
+
+ visited[nRepPos] = nMatchOffset;
+
+ if (nRepPos >= nMatchOffset && pCompressor->match[((nRepPos - nStartOffset) << MATCHES_PER_INDEX_SHIFT) + NMATCHES_PER_INDEX - 1].length == 0) {
+ const unsigned char* pInWindowAtRepOffset = pInWindow + nRepPos;
+
+ if (pInWindowAtRepOffset[0] == pInWindowAtRepOffset[-nMatchOffset]) {
+ int nLen0 = rle_len[nRepPos - nMatchOffset];
+ int nLen1 = rle_len[nRepPos];
+ int nMinLen = (nLen0 < nLen1) ? nLen0 : nLen1;
+
+ int nMaxRepLen = nEndOffset - nRepPos;
+ if (nMaxRepLen > LCP_MAX)
+ nMaxRepLen = LCP_MAX;
+
+ if (nMinLen > nMaxRepLen)
+ nMinLen = nMaxRepLen;
+
+ const unsigned char* pInWindowMax = pInWindowAtRepOffset + nMaxRepLen;
+ pInWindowAtRepOffset += nMinLen;
+
+ while ((pInWindowAtRepOffset + 8) < pInWindowMax && !memcmp(pInWindowAtRepOffset, pInWindowAtRepOffset - nMatchOffset, 8))
+ pInWindowAtRepOffset += 8;
+ while ((pInWindowAtRepOffset + 4) < pInWindowMax && !memcmp(pInWindowAtRepOffset, pInWindowAtRepOffset - nMatchOffset, 4))
+ pInWindowAtRepOffset += 4;
+ while (pInWindowAtRepOffset < pInWindowMax && pInWindowAtRepOffset[0] == pInWindowAtRepOffset[-nMatchOffset])
+ pInWindowAtRepOffset++;
+
+ int nCurRepLen = (int)(pInWindowAtRepOffset - (pInWindow + nRepPos));
+
+ 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 r;
+
+ for (r = 0; fwd_match[r].length >= MIN_MATCH_SIZE; r++) {
+ if (fwd_match[r].offset == nMatchOffset && (fwd_depth[r] & 0x3fff) == 0) {
+ if ((int)fwd_match[r].length < nCurRepLen) {
+ fwd_match[r].length = nCurRepLen;
+ fwd_depth[r] = 0;
+ }
+ r = NMATCHES_PER_INDEX;
+ break;
+ }
+ }
+
+ if (r < NMATCHES_PER_INDEX) {
+ fwd_match[r].offset = nMatchOffset;
+ fwd_match[r].length = nCurRepLen;
+ fwd_depth[r] = 0;
+
+ if (nDepth < 9)
+ apultra_insert_forward_match(pCompressor, pInWindow, nRepPos, nMatchOffset, nStartOffset, nEndOffset, nArrivalsPerPosition, 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
+ * @param nArrivalsPerPosition maximum number of arrivals per input buffer position
+ */
+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 nArrivalsPerPosition) {
+ apultra_arrival *arrival = pCompressor->arrival - (nStartOffset * nArrivalsPerPosition);
+ const int* rle_len = (int*)pCompressor->intervals /* reuse */;
+ int* visited = ((int*)pCompressor->pos_data) - nStartOffset /* reuse */;
+ int i, j, n;
+
+ if ((nEndOffset - nStartOffset) > pCompressor->block_size) return;
+
+ memset(arrival + (nStartOffset * nArrivalsPerPosition), 0, sizeof(apultra_arrival) * ((nEndOffset - nStartOffset + 1) * nArrivalsPerPosition));
+
+ arrival[nStartOffset * nArrivalsPerPosition].from_slot = -1;
+ arrival[nStartOffset * nArrivalsPerPosition].rep_offset = *nCurRepMatchOffset;
+
+ for (i = (nStartOffset * nArrivalsPerPosition); i != ((nEndOffset+1) * nArrivalsPerPosition); i++) {
+ arrival[i].cost = 0x40000000;
+ }
+
+ if (nInsertForwardReps) {
+ memset(visited + nStartOffset, 0, (nEndOffset - nStartOffset) * sizeof(int));
+ }
+
+ for (i = nStartOffset; i != nEndOffset; i++) {
+ apultra_arrival *cur_arrival = &arrival[i * nArrivalsPerPosition];
+ int m;
+
+ const unsigned char nMatch1Offs = pCompressor->match1[i - nStartOffset];
+ int nShortOffset;
+ int nShortLen;
+ int nLiteralScore;
+ int nLiteralCost;
+
+ if ((pInWindow[i] != 0 && nMatch1Offs == 0) || (i == nStartOffset && (nBlockFlags & 1))) {
+ nShortOffset = 0;
+ nShortLen = 0;
+ nLiteralCost = 9 /* literal bit + literal byte */;
+ }
+ else {
+ nShortOffset = (pInWindow[i] == 0) ? 0 : nMatch1Offs;
+ nShortLen = 1;
+ nLiteralCost = 4 + TOKEN_SIZE_4BIT_MATCH /* command and offset cost; no length cost */;
+ }
+
+ nLiteralScore = nShortOffset ? 3 : 1;
+
+ if (cur_arrival[nArrivalsPerPosition].from_slot) {
+ for (j = 0; j < nArrivalsPerPosition && cur_arrival[j].from_slot; j++) {
+ int nPrevCost = cur_arrival[j].cost & 0x3fffffff;
+ int nCodingChoiceCost = nPrevCost + nLiteralCost;
+ int nScore = cur_arrival[j].score + nLiteralScore;
+
+ apultra_arrival* pDestSlots = &cur_arrival[nArrivalsPerPosition];
+ if (nCodingChoiceCost < pDestSlots[nArrivalsPerPosition - 1].cost ||
+ (nCodingChoiceCost == pDestSlots[nArrivalsPerPosition - 1].cost && nScore < pDestSlots[nArrivalsPerPosition - 1].score)) {
+ int nRepOffset = cur_arrival[j].rep_offset;
+ int exists = 0;
+
+ for (n = 0;
+ n < nArrivalsPerPosition && pDestSlots[n].cost < nCodingChoiceCost;
+ n++) {
+ if (pDestSlots[n].rep_offset == nRepOffset) {
+ exists = 1;
+ break;
+ }
+ }
+
+ if (!exists) {
+ for (;
+ n < nArrivalsPerPosition && pDestSlots[n].cost == nCodingChoiceCost && nScore >= pDestSlots[n].score;
+ n++) {
+ if (pDestSlots[n].rep_offset == nRepOffset) {
+ exists = 1;
+ break;
+ }
+ }
+
+ if (!exists) {
+ if (n < nArrivalsPerPosition) {
+ int nn;
+
+ for (nn = n;
+ nn < nArrivalsPerPosition && pDestSlots[nn].cost == nCodingChoiceCost;
+ nn++) {
+ if (pDestSlots[nn].rep_offset == nRepOffset) {
+ exists = 1;
+ break;
+ }
+ }
+
+ if (!exists) {
+ int z;
+
+ for (z = n; z < nArrivalsPerPosition - 1 && pDestSlots[z].from_slot; z++) {
+ if (pDestSlots[z].rep_offset == nRepOffset)
+ break;
+ }
+
+ apultra_arrival* pDestArrival = &pDestSlots[n];
+ 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->rep_offset = nRepOffset;
+ pDestArrival->short_offset = nShortOffset;
+ pDestArrival->rep_pos = cur_arrival[j].rep_pos;
+ pDestArrival->match_len = nShortLen;
+ pDestArrival->score = nScore;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ else {
+ for (j = 0; j < nArrivalsPerPosition && cur_arrival[j].from_slot; j++) {
+ int nPrevCost = cur_arrival[j].cost & 0x3fffffff;
+ int nCodingChoiceCost = nPrevCost + nLiteralCost;
+ int nScore = cur_arrival[j].score + nLiteralScore;
+
+ apultra_arrival* pDestArrival = &cur_arrival[nArrivalsPerPosition + j];
+
+ pDestArrival->cost = nCodingChoiceCost;
+ pDestArrival->from_pos = i;
+ pDestArrival->from_slot = j + 1;
+ pDestArrival->follows_literal = 1;
+ pDestArrival->rep_offset = cur_arrival[j].rep_offset;
+ pDestArrival->short_offset = nShortOffset;
+ pDestArrival->rep_pos = cur_arrival[j].rep_pos;
+ pDestArrival->match_len = nShortLen;
+ pDestArrival->score = nScore;
+ }
+ }
+
+ if (i == nStartOffset && (nBlockFlags & 1)) continue;
+
+ const apultra_match *match = pCompressor->match + ((i - nStartOffset) << MATCHES_PER_INDEX_SHIFT);
+ const unsigned short *match_depth = pCompressor->match_depth + ((i - nStartOffset) << MATCHES_PER_INDEX_SHIFT);
+ int nNumArrivalsForThisPos = j, nOverallMinRepLen = 0, nOverallMaxRepLen = 0;
+
+ int nRepLenForArrival[NARRIVALS_PER_POSITION_MAX];
+ memset(nRepLenForArrival, 0, nArrivalsPerPosition * sizeof(int));
+
+ int nRepMatchArrivalIdx[NARRIVALS_PER_POSITION_MAX + 1];
+ int nNumRepMatchArrivals = 0;
+
+ int nMaxRepLenForPos = nEndOffset - i;
+ if (nMaxRepLenForPos > LCP_MAX)
+ nMaxRepLenForPos = LCP_MAX;
+ const unsigned char* pInWindowStart = pInWindow + i;
+ const unsigned char* pInWindowMax = pInWindowStart + nMaxRepLenForPos;
+ const int nLen1 = rle_len[i];
+
+ for (j = 0; j < nNumArrivalsForThisPos && (i + 2) <= nEndOffset; j++) {
+ if (cur_arrival[j].follows_literal) {
+ int nRepOffset = cur_arrival[j].rep_offset;
+
+ if (nRepOffset && i >= nRepOffset) {
+ if (pInWindowStart[0] == pInWindowStart[-nRepOffset]) {
+ int nLen0 = rle_len[i - nRepOffset];
+ int nMinLen = (nLen0 < nLen1) ? nLen0 : nLen1;
+
+ if (nMinLen > nMaxRepLenForPos)
+ nMinLen = nMaxRepLenForPos;
+
+ const unsigned char* pInWindowAtRepOffset = pInWindowStart + nMinLen;
+ while ((pInWindowAtRepOffset + 8) < pInWindowMax && !memcmp(pInWindowAtRepOffset, pInWindowAtRepOffset - nRepOffset, 8))
+ pInWindowAtRepOffset += 8;
+ while ((pInWindowAtRepOffset + 4) < pInWindowMax && !memcmp(pInWindowAtRepOffset, pInWindowAtRepOffset - nRepOffset, 4))
+ pInWindowAtRepOffset += 4;
+ while (pInWindowAtRepOffset < pInWindowMax && pInWindowAtRepOffset[0] == pInWindowAtRepOffset[-nRepOffset])
+ pInWindowAtRepOffset++;
+
+ int nCurMaxLen = (int)(pInWindowAtRepOffset - pInWindowStart);
+
+ if (nCurMaxLen >= 2) {
+ nRepLenForArrival[j] = nCurMaxLen;
+ nRepMatchArrivalIdx[nNumRepMatchArrivals++] = j;
+
+ if (nOverallMaxRepLen < nCurMaxLen)
+ nOverallMaxRepLen = nCurMaxLen;
+ }
+ }
+ }
+ }
+ }
+ nRepMatchArrivalIdx[nNumRepMatchArrivals] = -1;
+
+ 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] & 0x3fff;
+ const int nScorePenalty = 3 + ((match_depth[m] & 0x8000) >> 15);
+ unsigned int d;
+
+ for (d = 0; d <= nOrigMatchDepth; d += (nOrigMatchDepth ? nOrigMatchDepth : 1)) {
+ const int nMatchOffset = nOrigMatchOffset - d;
+ int nMatchLen = nOrigMatchLen - d;
+
+ if ((i + nMatchLen) > nEndOffset)
+ nMatchLen = nEndOffset - i;
+
+ if (nInsertForwardReps) {
+ apultra_insert_forward_match(pCompressor, pInWindow, i, nMatchOffset, nStartOffset, nEndOffset, nArrivalsPerPosition, 0);
+ }
+
+ if (nMatchLen >= 2) {
+ int nStartingMatchLen, nJumpMatchLen, k;
+ int nNoRepMatchOffsetCostForLit[2], nNoRepMatchOffsetCostDelta;
+ int nMinMatchLenForOffset;
+ int nNoRepCostAdjusment = (nMatchLen >= LCP_MAX) ? 1 : 0;
+
+ if (nMatchOffset < MINMATCH3_OFFSET)
+ nMinMatchLenForOffset = 2;
+ else {
+ if (nMatchOffset < MINMATCH4_OFFSET)
+ nMinMatchLenForOffset = 3;
+ else
+ nMinMatchLenForOffset = 4;
+ }
+
+ if (nMatchLen >= LEAVE_ALONE_MATCH_SIZE && i >= nMatchLen)
+ nStartingMatchLen = nMatchLen;
+ else
+ nStartingMatchLen = 2;
+
+ if ((nBlockFlags & 3) == 3 && nMatchLen > 90 && i >= 90)
+ nJumpMatchLen = 90;
+ else
+ nJumpMatchLen = nMatchLen + 1;
+
+ if (nStartingMatchLen <= 3 && nMatchOffset < 128) {
+ nNoRepMatchOffsetCostForLit[0] = 8 + TOKEN_SIZE_7BIT_MATCH;
+ nNoRepMatchOffsetCostForLit[1] = 8 + TOKEN_SIZE_7BIT_MATCH;
+ }
+ else {
+ nNoRepMatchOffsetCostForLit[0] = 8 + TOKEN_SIZE_LARGE_MATCH + apultra_get_gamma2_size((nMatchOffset >> 8) + 2);
+ nNoRepMatchOffsetCostForLit[1] = 8 + TOKEN_SIZE_LARGE_MATCH + apultra_get_gamma2_size((nMatchOffset >> 8) + 3);
+ }
+ nNoRepMatchOffsetCostDelta = nNoRepMatchOffsetCostForLit[1] - nNoRepMatchOffsetCostForLit[0];
+
+ for (k = nStartingMatchLen; k <= nMatchLen; k++) {
+ int nRepMatchMatchLenCost = apultra_get_gamma2_size(k);
+ apultra_arrival *pDestSlots = &cur_arrival[k * nArrivalsPerPosition];
+
+ /* Insert non-repmatch candidate */
+
+ if (k >= nMinMatchLenForOffset) {
+ int nNoRepMatchMatchLenCost;
+
+ 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);
+ }
+
+ for (j = 0; j < nNumArrivalsForThisPos; j++) {
+ if (nMatchOffset != cur_arrival[j].rep_offset || cur_arrival[j].follows_literal == 0) {
+ int nPrevCost = cur_arrival[j].cost & 0x3fffffff;
+ int nMatchCmdCost = nNoRepMatchMatchLenCost + nNoRepMatchOffsetCostForLit[cur_arrival[j].follows_literal];
+ int nCodingChoiceCost = nPrevCost + nMatchCmdCost;
+
+ if (nCodingChoiceCost <= (pDestSlots[nArrivalsPerPosition - 1].cost + 1)) {
+ int nScore = cur_arrival[j].score + nScorePenalty;
+
+ if (nCodingChoiceCost < pDestSlots[nArrivalsPerPosition - 2].cost ||
+ (nCodingChoiceCost == pDestSlots[nArrivalsPerPosition - 2].cost && nScore < pDestSlots[nArrivalsPerPosition - 2].score)) {
+ int exists = 0;
+
+ for (n = 0;
+ n < nArrivalsPerPosition && pDestSlots[n].cost < nCodingChoiceCost;
+ n++) {
+ if (pDestSlots[n].rep_offset == nMatchOffset) {
+ exists = 1;
+ break;
+ }
+ }
+
+ if (!exists) {
+ int nRevisedCodingChoiceCost = nCodingChoiceCost - nNoRepCostAdjusment;
+
+ for (;
+ n < nArrivalsPerPosition - 1 && pDestSlots[n].cost == nRevisedCodingChoiceCost && nScore >= pDestSlots[n].score;
+ n++) {
+ if (pDestSlots[n].rep_offset == nMatchOffset) {
+ exists = 1;
+ break;
+ }
+ }
+
+ if (!exists) {
+ if (n < nArrivalsPerPosition - 1) {
+ int nn;
+
+ for (nn = n;
+ nn < nArrivalsPerPosition && pDestSlots[nn].cost == nCodingChoiceCost;
+ nn++) {
+ if (pDestSlots[nn].rep_offset == nMatchOffset) {
+ exists = 1;
+ break;
+ }
+ }
+
+ if (!exists) {
+ int z;
+
+ for (z = n; z < nArrivalsPerPosition - 1 && pDestSlots[z].from_slot; z++) {
+ if (pDestSlots[z].rep_offset == nMatchOffset)
+ break;
+ }
+
+ apultra_arrival* pDestArrival = &pDestSlots[n];
+ memmove(&pDestSlots[n + 1],
+ &pDestSlots[n],
+ sizeof(apultra_arrival) * (z - n));
+
+ pDestArrival->cost = nRevisedCodingChoiceCost;
+ pDestArrival->from_pos = i;
+ pDestArrival->from_slot = j + 1;
+ pDestArrival->follows_literal = 0;
+ pDestArrival->rep_offset = nMatchOffset;
+ pDestArrival->short_offset = 0;
+ pDestArrival->rep_pos = i;
+ pDestArrival->match_len = k;
+ pDestArrival->score = nScore;
+ }
+ }
+ }
+ }
+ else {
+ if ((nCodingChoiceCost - pDestSlots[n].cost) >= nNoRepMatchOffsetCostDelta)
+ break;
+ }
+ }
+ if (cur_arrival[j].follows_literal == 0 || nNoRepMatchOffsetCostDelta == 0)
+ break;
+ }
+ else {
+ break;
+ }
+ }
+ }
+ }
+
+ /* Insert repmatch candidate */
+
+ if (k > nOverallMinRepLen && k <= nOverallMaxRepLen) {
+ int nRepMatchCmdCost = TOKEN_SIZE_LARGE_MATCH + 2 /* apultra_get_gamma2_size(2) */ + nRepMatchMatchLenCost;
+ int nCurRepMatchArrival;
+
+ if (k <= 90)
+ nOverallMinRepLen = k;
+ else if (nOverallMaxRepLen == k)
+ nOverallMaxRepLen--;
+
+ for (nCurRepMatchArrival = 0; (j = nRepMatchArrivalIdx[nCurRepMatchArrival]) >= 0; nCurRepMatchArrival++) {
+ if (nRepLenForArrival[j] >= k) {
+ int nPrevCost = cur_arrival[j].cost & 0x3fffffff;
+ int nRepCodingChoiceCost = nPrevCost + nRepMatchCmdCost;
+ int nScore = cur_arrival[j].score + 2;
+
+ if (nRepCodingChoiceCost < pDestSlots[nArrivalsPerPosition - 1].cost ||
+ (nRepCodingChoiceCost == pDestSlots[nArrivalsPerPosition - 1].cost && nScore < pDestSlots[nArrivalsPerPosition - 1].score)) {
+ int nRepOffset = cur_arrival[j].rep_offset;
+ int exists = 0;
+
+ for (n = 0;
+ n < nArrivalsPerPosition && pDestSlots[n].cost < nRepCodingChoiceCost;
+ n++) {
+ if (pDestSlots[n].rep_offset == nRepOffset) {
+ exists = 1;
+ break;
+ }
+ }
+
+ if (!exists) {
+ for (;
+ n < nArrivalsPerPosition && pDestSlots[n].cost == nRepCodingChoiceCost && nScore >= pDestSlots[n].score;
+ n++) {
+ if (pDestSlots[n].rep_offset == nRepOffset) {
+ exists = 1;
+ break;
+ }
+ }
+
+ if (!exists) {
+ if (n < nArrivalsPerPosition) {
+ int nn;
+
+ for (nn = n;
+ nn < nArrivalsPerPosition && pDestSlots[nn].cost == nRepCodingChoiceCost;
+ nn++) {
+ if (pDestSlots[nn].rep_offset == nRepOffset) {
+ exists = 1;
+ break;
+ }
+ }
+
+ if (!exists) {
+ int z;
+
+ for (z = n; z < nArrivalsPerPosition - 1 && pDestSlots[z].from_slot; z++) {
+ if (pDestSlots[z].rep_offset == nRepOffset)
+ break;
+ }
+
+ apultra_arrival* pDestArrival = &pDestSlots[n];
+ memmove(&pDestSlots[n + 1],
+ &pDestSlots[n],
+ sizeof(apultra_arrival) * (z - n));
+
+ pDestArrival->cost = nRepCodingChoiceCost;
+ pDestArrival->from_pos = i;
+ pDestArrival->from_slot = j + 1;
+ pDestArrival->follows_literal = 0;
+ pDestArrival->rep_offset = nRepOffset;
+ pDestArrival->short_offset = 0;
+ pDestArrival->rep_pos = i;
+ pDestArrival->match_len = k;
+ pDestArrival->score = nScore;
+ }
+ }
+ }
+ }
+ }
+ else {
+ break;
+ }
+ }
+ }
+ }
+
+ if (k == 3 && nMatchOffset < 128) {
+ nNoRepMatchOffsetCostForLit[0] = 8 + TOKEN_SIZE_LARGE_MATCH + 2 /* apultra_get_gamma2_size((nMatchOffset >> 8) + 2) */;
+ nNoRepMatchOffsetCostForLit[1] = 8 + TOKEN_SIZE_LARGE_MATCH + 2 /* apultra_get_gamma2_size((nMatchOffset >> 8) + 3) */;
+ }
+
+ if (k == nJumpMatchLen)
+ k = nMatchLen - 1;
+ }
+ }
+
+ if (nOrigMatchLen >= 512)
+ break;
+ }
+ }
+ }
+
+ if (!nInsertForwardReps) {
+ const apultra_arrival* end_arrival = &arrival[(i * nArrivalsPerPosition) + 0];
+ apultra_final_match* pBestMatch = pCompressor->best_match - nStartOffset;
+
+ 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;
+ if (end_arrival->match_len >= 2)
+ pBestMatch[end_arrival->from_pos].offset = end_arrival->rep_offset;
+ else
+ pBestMatch[end_arrival->from_pos].offset = end_arrival->short_offset;
+
+ end_arrival = &arrival[(end_arrival->from_pos * nArrivalsPerPosition) + (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
+ * @param nBlockFlags bit 0: 1 for first block, 0 otherwise; bit 1: 1 for last block, 0 otherwise
+ *
+ * @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, const int nBlockFlags) {
+ int i;
+ int nRepMatchOffset = *nCurRepMatchOffset;
+ int nFollowsLiteral = 0;
+ int nDidReduce = 0;
+ int nLastMatchLen = 0;
+ const unsigned char *match1 = pCompressor->match1 - nStartOffset;
+
+ for (i = nStartOffset + ((nBlockFlags & 1) ? 1 : 0); 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 = (pMatch->length == 1) ? (TOKEN_SIZE_4BIT_MATCH + 4) : (1 /* literal bit */ + 8 /* literal size */);
+ if (pBestMatch[i + 1].offset == nRepMatchOffset /* always follows a literal, the one at the current position */) {
+ nCurPartialCommandSize += TOKEN_SIZE_LARGE_MATCH + 2 /* apultra_get_gamma2_size(2) */ + apultra_get_gamma2_size(pBestMatch[i + 1].length);
+ }
+ 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);
+ }
+
+ int nReducedPartialCommandSize;
+ if (pBestMatch[i + 1].offset == nRepMatchOffset && nFollowsLiteral) {
+ nReducedPartialCommandSize = TOKEN_SIZE_LARGE_MATCH + 2 /* apultra_get_gamma2_size(2) */ + apultra_get_gamma2_size(pBestMatch[i + 1].length);
+ }
+ 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);
+ }
+
+ 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 >= 2) {
+ if (pMatch->length < 32 && /* 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 nNextFollowsLiteral = 0;
+ int nCannotEncode = 0;
+
+ while (nNextIndex < nEndOffset && pBestMatch[nNextIndex].length < 2) {
+ nNextIndex++;
+ nNextFollowsLiteral = 1;
+ }
+
+ if (nNextIndex < nEndOffset && pBestMatch[nNextIndex].length >= 2) {
+ if (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;
+ const unsigned char* pInWindowAtPos = pInWindow + i;
+ while (nMaxLen < pMatch->length && pInWindowAtPos[nMaxLen - pBestMatch[nNextIndex].offset] == pInWindowAtPos[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, j;
+
+ nPartialSizeBefore = apultra_get_offset_varlen_size(pMatch->length, pMatch->offset, nFollowsLiteral);
+ nPartialSizeBefore += apultra_get_match_varlen_size(pMatch->length, pMatch->offset);
+
+ 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);
+
+ nPartialSizeAfter = apultra_get_offset_varlen_size(nMaxLen, pBestMatch[nNextIndex].offset, nFollowsLiteral);
+ if (nFollowsLiteral && nRepMatchOffset == pBestMatch[nNextIndex].offset)
+ nPartialSizeAfter += apultra_get_gamma2_size(nMaxLen);
+ else
+ nPartialSizeAfter += apultra_get_match_varlen_size(nMaxLen, pBestMatch[nNextIndex].offset);
+
+ nPartialSizeAfter += TOKEN_SIZE_LARGE_MATCH + 2 /* apultra_get_gamma2_size(2) */;
+ nPartialSizeAfter += apultra_get_gamma2_size(pBestMatch[nNextIndex].length);
+
+ for (j = nMaxLen; j < pMatch->length; j++) {
+ if (pInWindow[i + j] == 0 || match1[i + j])
+ nPartialSizeAfter += TOKEN_SIZE_4BIT_MATCH + 4;
+ else
+ nPartialSizeAfter += 1 /* literal bit */ + 8 /* literal byte */;
+ }
+
+ 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;
+ int j;
+
+ pMatch->offset = pBestMatch[nNextIndex].offset;
+ pMatch->length = nMaxLen;
+
+ for (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;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /* Calculate this command's current cost */
+
+ int nCurCommandSize;
+ if (pMatch->offset == nRepMatchOffset && nFollowsLiteral) {
+ nCurCommandSize = TOKEN_SIZE_LARGE_MATCH + 2 /* apultra_get_gamma2_size(2) */ + apultra_get_gamma2_size(pMatch->length);
+ }
+ else {
+ nCurCommandSize = apultra_get_offset_varlen_size(pMatch->length, pMatch->offset, nFollowsLiteral) + apultra_get_match_varlen_size(pMatch->length, pMatch->offset);
+ }
+
+ /* Calculate the next command's current cost */
+ int nNextCommandSize;
+ if (pBestMatch[nNextIndex].offset == pMatch->offset && nNextFollowsLiteral && pBestMatch[nNextIndex].length >= 2) {
+ nNextCommandSize = TOKEN_SIZE_LARGE_MATCH + 2 /* apultra_get_gamma2_size(2) */ + apultra_get_gamma2_size(pBestMatch[nNextIndex].length);
+ }
+ 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);
+ }
+
+ int nOriginalCombinedCommandSize = nCurCommandSize + nNextCommandSize;
+
+ /* Calculate the cost of replacing this match command by literals + the effect on the cost of the next command */
+ int nReducedCommandSize = 0;
+ int j;
+
+ for (j = 0; j < pMatch->length; j++) {
+ if (pInWindow[i + j] == 0 || match1[i + j])
+ nReducedCommandSize += TOKEN_SIZE_4BIT_MATCH + 4;
+ else
+ nReducedCommandSize += 1 /* literal bit */ + 8;
+ }
+
+ if (pBestMatch[nNextIndex].offset == nRepMatchOffset /* the new command would always follow literals, the ones we create */ && pBestMatch[nNextIndex].length >= 2) {
+ nReducedCommandSize += TOKEN_SIZE_LARGE_MATCH + 2 /* apultra_get_gamma2_size(2) */ + apultra_get_gamma2_size(pBestMatch[nNextIndex].length);
+ }
+ 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, 1 /* follows literals */) + apultra_get_match_varlen_size(pBestMatch[nNextIndex].length, pBestMatch[nNextIndex].offset);
+ }
+ }
+
+ 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 &&
+ 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;
+ }
+ }
+
+ nRepMatchOffset = pMatch->offset;
+ nFollowsLiteral = 0;
+ nLastMatchLen = pMatch->length;
+
+ i += pMatch->length;
+ }
+ else {
+ /* 4 bits offset (1 byte match) or literal */
+ 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 nCurBitShift bit shift count
+ * @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 *nCurBitShift, int *nFollowsLiteral, int *nCurRepMatchOffset, const int nBlockFlags) {
+ int i;
+ int nRepMatchOffset = *nCurRepMatchOffset;
+ const int nMaxOffset = pCompressor->max_offset;
+
+ 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 >= 2) {
+ int nMatchOffset = pMatch->offset;
+ int nMatchLen = pMatch->length;
+
+ if (nMatchOffset < MIN_OFFSET || nMatchOffset > nMaxOffset)
+ return -1;
+
+ if (nMatchOffset == nRepMatchOffset && *nFollowsLiteral) {
+ /* Rep-match */
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, TOKEN_CODE_LARGE_MATCH, TOKEN_SIZE_LARGE_MATCH, nCurBitsOffset, nCurBitShift);
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, 0 /* length of 2 encoded as gamma 2 */, 2, nCurBitsOffset, nCurBitShift);
+
+ /* The match length isn't encoded in the command, emit elias gamma value */
+ nOutOffset = apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, nMatchLen, nCurBitsOffset, nCurBitShift);
+ if (nOutOffset < 0) return -1;
+
+ *nFollowsLiteral = 0;
+
+ pCompressor->stats.num_rep_matches++;
+ }
+ else {
+ if (nMatchLen <= 3 && nMatchOffset < 128) {
+ /* 7 bits offset + 1 bit length */
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, TOKEN_CODE_7BIT_MATCH, TOKEN_SIZE_7BIT_MATCH, nCurBitsOffset, nCurBitShift);
+
+ if (nOutOffset < 0 || nOutOffset >= nMaxOutDataSize)
+ return -1;
+ pOutData[nOutOffset++] = ((nMatchOffset) & 0x7f) << 1 | (nMatchLen - 2);
+
+ *nFollowsLiteral = 0;
+ nRepMatchOffset = nMatchOffset;
+
+ pCompressor->stats.num_7bit_matches++;
+ }
+ else {
+ /* 8+n bits offset */
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, TOKEN_CODE_LARGE_MATCH, TOKEN_SIZE_LARGE_MATCH, nCurBitsOffset, nCurBitShift);
+
+ if (nOutOffset < 0 || nOutOffset >= nMaxOutDataSize)
+ return -1;
+ if (*nFollowsLiteral)
+ nOutOffset = apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, (nMatchOffset >> 8) + 3, nCurBitsOffset, nCurBitShift);
+ else
+ nOutOffset = apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, (nMatchOffset >> 8) + 2, nCurBitsOffset, nCurBitShift);
+ pOutData[nOutOffset++] = nMatchOffset & 0xff;
+
+ /* The match length isn't encoded in the command, emit elias gamma value */
+
+ if (nMatchOffset < 128 || nMatchOffset >= MINMATCH4_OFFSET)
+ nOutOffset = apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, nMatchLen - 2, nCurBitsOffset, nCurBitShift);
+ else if (nMatchOffset < MINMATCH3_OFFSET)
+ nOutOffset = apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, nMatchLen, nCurBitsOffset, nCurBitShift);
+ else
+ nOutOffset = apultra_write_gamma2_value(pOutData, nOutOffset, nMaxOutDataSize, nMatchLen - 1, nCurBitsOffset, nCurBitShift);
+ if (nOutOffset < 0) return -1;
+
+ *nFollowsLiteral = 0;
+ nRepMatchOffset = nMatchOffset;
+
+ pCompressor->stats.num_variable_matches++;
+ }
+ }
+
+ 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 if (pMatch->length == 1) {
+ int nMatchOffset = pMatch->offset;
+
+ /* 4 bits offset */
+
+ if (nMatchOffset < 0 || nMatchOffset > 15)
+ return -1;
+
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, TOKEN_CODE_4BIT_MATCH, TOKEN_SIZE_4BIT_MATCH, nCurBitsOffset, nCurBitShift);
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, nMatchOffset, 4, nCurBitsOffset, nCurBitShift);
+ if (nOutOffset < 0) return -1;
+
+ pCompressor->stats.num_4bit_matches++;
+ pCompressor->stats.commands_divisor++;
+
+ i++;
+ *nFollowsLiteral = 1;
+ }
+ else {
+ /* Literal */
+
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, 0 /* literal */, 1, nCurBitsOffset, nCurBitShift);
+
+ if (nOutOffset < 0 || nOutOffset >= nMaxOutDataSize)
+ return -1;
+ pOutData[nOutOffset++] = pInWindow[i];
+
+ pCompressor->stats.num_literals++;
+ pCompressor->stats.commands_divisor++;
+ i++;
+ *nFollowsLiteral = 1;
+ }
+
+ int nCurSafeDist = (i - nStartOffset) - nOutOffset;
+ if (nCurSafeDist >= 0 && pCompressor->stats.safe_dist < nCurSafeDist)
+ pCompressor->stats.safe_dist = nCurSafeDist;
+ }
+
+ if (nBlockFlags & 2) {
+ /* 8 bits offset */
+
+ nOutOffset = apultra_write_bits(pOutData, nOutOffset, nMaxOutDataSize, TOKEN_CODE_7BIT_MATCH, TOKEN_SIZE_7BIT_MATCH, nCurBitsOffset, nCurBitShift);
+
+ if (nOutOffset < 0 || nOutOffset >= nMaxOutDataSize)
+ return -1;
+ pOutData[nOutOffset++] = 0x00; /* Offset: EOD */
+ pCompressor->stats.num_eod++;
+ pCompressor->stats.commands_divisor++;
+
+ int nCurSafeDist = (i - nStartOffset) - nOutOffset;
+ if (nCurSafeDist >= 0 && pCompressor->stats.safe_dist < nCurSafeDist)
+ pCompressor->stats.safe_dist = nCurSafeDist;
+ }
+
+ *nCurRepMatchOffset = nRepMatchOffset;
+ 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 nCurBitShift bit shift count
+ * @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 *nCurBitShift, int *nCurFollowsLiteral, int *nCurRepMatchOffset, const int nBlockFlags) {
+ int nOutOffset = 0;
+ const int nEndOffset = nPreviousBlockSize + nInDataSize;
+ const int nArrivalsPerPosition = pCompressor->max_arrivals;
+ int *rle_len = (int*)pCompressor->intervals /* reuse */;
+ int i, nPosition;
+
+ memset(pCompressor->best_match, 0, pCompressor->block_size * sizeof(apultra_final_match));
+
+ if ((nBlockFlags & 3) == 3) {
+ int *first_offset_for_byte = pCompressor->first_offset_for_byte;
+ int *next_offset_for_pos = pCompressor->next_offset_for_pos;
+
+ /* Supplement 2 and 3-byte matches */
+
+ memset(first_offset_for_byte, 0xff, sizeof(int) * 65536);
+ memset(next_offset_for_pos, 0xff, sizeof(int) * nInDataSize);
+
+ for (nPosition = nPreviousBlockSize; nPosition < (nEndOffset - 1); nPosition++) {
+ next_offset_for_pos[nPosition - nPreviousBlockSize] = first_offset_for_byte[((unsigned int)pInWindow[nPosition]) | (((unsigned int)pInWindow[nPosition + 1]) << 8)];
+ first_offset_for_byte[((unsigned int)pInWindow[nPosition]) | (((unsigned int)pInWindow[nPosition + 1]) << 8)] = nPosition;
+ }
+
+ for (nPosition = nPreviousBlockSize + 1; nPosition < (nEndOffset - 1); nPosition++) {
+ apultra_match *match = pCompressor->match + ((nPosition - nPreviousBlockSize) << MATCHES_PER_INDEX_SHIFT);
+ unsigned short *match_depth = pCompressor->match_depth + ((nPosition - nPreviousBlockSize) << MATCHES_PER_INDEX_SHIFT);
+ int m = 0, nInserted = 0;
+ int nMatchPos;
+
+ while (m < 15 && match[m].length)
+ m++;
+
+ for (nMatchPos = next_offset_for_pos[nPosition - nPreviousBlockSize]; m < 15 && nMatchPos >= 0; nMatchPos = next_offset_for_pos[nMatchPos - nPreviousBlockSize]) {
+ int nMatchOffset = nPosition - nMatchPos;
+
+ if (nMatchOffset <= pCompressor->max_offset) {
+ int nExistingMatchIdx;
+ int nAlreadyExists = 0;
+
+ for (nExistingMatchIdx = 0; nExistingMatchIdx < m; nExistingMatchIdx++) {
+ if (match[nExistingMatchIdx].offset == nMatchOffset ||
+ (match[nExistingMatchIdx].offset - (match_depth[nExistingMatchIdx] & 0x3fff)) == nMatchOffset) {
+ nAlreadyExists = 1;
+ break;
+ }
+ }
+
+ if (!nAlreadyExists) {
+ match[m].length = (nPosition < (nEndOffset - 2) && pInWindow[nMatchPos + 2] == pInWindow[nPosition + 2]) ? 3 : 2;
+ match[m].offset = nMatchOffset;
+ match_depth[m] = 0x4000;
+ m++;
+ nInserted++;
+ if (nInserted >= 6)
+ break;
+ }
+ }
+ else {
+ break;
+ }
+ }
+ }
+ }
+
+ i = 0;
+ while (i < nEndOffset) {
+ int nRangeStartIdx = i;
+ unsigned char c = pInWindow[nRangeStartIdx];
+ do {
+ i++;
+ }
+ while (i < nEndOffset && pInWindow[i] == c);
+ while (nRangeStartIdx < i) {
+ rle_len[nRangeStartIdx] = i - nRangeStartIdx;
+ nRangeStartIdx++;
+ }
+ }
+
+ apultra_optimize_forward(pCompressor, pInWindow, nPreviousBlockSize, nEndOffset, 1 /* nInsertForwardReps */, nCurRepMatchOffset, nBlockFlags, nArrivalsPerPosition);
+
+ if ((nBlockFlags & 3) == 3 && nArrivalsPerPosition == NARRIVALS_PER_POSITION_MAX) {
+ const int* next_offset_for_pos = pCompressor->next_offset_for_pos;
+ int* offset_cache = pCompressor->offset_cache;
+
+ /* Supplement matches further */
+
+ memset(offset_cache, 0xff, sizeof(int) * 2048);
+
+ for (nPosition = nPreviousBlockSize + 1; nPosition < (nEndOffset - 1); nPosition++) {
+ apultra_match* match = pCompressor->match + ((nPosition - nPreviousBlockSize) << MATCHES_PER_INDEX_SHIFT);
+
+ if (match[0].length < 8) {
+ unsigned short* match_depth = pCompressor->match_depth + ((nPosition - nPreviousBlockSize) << MATCHES_PER_INDEX_SHIFT);
+ int m = 0, nInserted = 0;
+ int nMatchPos;
+
+ while (m < 42 && match[m].length) {
+ offset_cache[match[m].offset & 2047] = nPosition;
+ offset_cache[(match[m].offset - (match_depth[m] & 0x3fff)) & 2047] = nPosition;
+ m++;
+ }
+
+ for (nMatchPos = next_offset_for_pos[nPosition - nPreviousBlockSize]; m < 42 && nMatchPos >= 0; nMatchPos = next_offset_for_pos[nMatchPos - nPreviousBlockSize]) {
+ int nMatchOffset = nPosition - nMatchPos;
+
+ if (nMatchOffset <= pCompressor->max_offset) {
+ int nAlreadyExists = 0;
+
+ if (offset_cache[nMatchOffset & 2047] == nPosition) {
+ int nExistingMatchIdx;
+
+ for (nExistingMatchIdx = 0; nExistingMatchIdx < m; nExistingMatchIdx++) {
+ if (match[nExistingMatchIdx].offset == nMatchOffset ||
+ (match[nExistingMatchIdx].offset - (match_depth[nExistingMatchIdx] & 0x3fff)) == nMatchOffset) {
+ nAlreadyExists = 1;
+
+ if (match_depth[nExistingMatchIdx] == 0x4000) {
+ int nMatchLen = 2;
+ while (nMatchLen < 16 && nPosition < (nEndOffset - nMatchLen) && pInWindow[nMatchPos + nMatchLen] == pInWindow[nPosition + nMatchLen])
+ nMatchLen++;
+ if (nMatchLen > (int)match[nExistingMatchIdx].length)
+ match[nExistingMatchIdx].length = nMatchLen;
+ }
+
+ break;
+ }
+ }
+ }
+
+ if (!nAlreadyExists) {
+ int nForwardPos = nPosition + 2 + 1;
+ int nGotMatch = 0;
+
+ while (nForwardPos >= nMatchOffset && (nForwardPos + 2) < nEndOffset && nForwardPos < (nPosition + 2 + 1 + 5)) {
+ if (!memcmp(pInWindow + nForwardPos, pInWindow + nForwardPos - nMatchOffset, 2)) {
+ nGotMatch = 1;
+ break;
+ }
+ nForwardPos++;
+ }
+
+ if (nGotMatch) {
+ int nMatchLen = 2;
+ while (nMatchLen < 16 && nPosition < (nEndOffset - nMatchLen) && pInWindow[nMatchPos + nMatchLen] == pInWindow[nPosition + nMatchLen])
+ nMatchLen++;
+ match[m].length = nMatchLen;
+ match[m].offset = nMatchOffset;
+ match_depth[m] = 0;
+ m++;
+
+ apultra_insert_forward_match(pCompressor, pInWindow, nPosition, nMatchOffset, nPreviousBlockSize, nEndOffset, nArrivalsPerPosition, 8);
+
+ nInserted++;
+ if (nInserted >= 6)
+ break;
+ }
+ }
+ }
+ else {
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ /* Pick optimal matches */
+ apultra_optimize_forward(pCompressor, pInWindow, nPreviousBlockSize, nEndOffset, 0 /* nInsertForwardReps */, nCurRepMatchOffset, nBlockFlags, nArrivalsPerPosition);
+
+ /* Apply reduction and merge pass */
+ int nDidReduce;
+ int nPasses = 0;
+ do {
+ nDidReduce = apultra_reduce_commands(pCompressor, pInWindow, pCompressor->best_match - nPreviousBlockSize, nPreviousBlockSize, nEndOffset, nCurRepMatchOffset, nBlockFlags);
+ nPasses++;
+ } while (nDidReduce && nPasses < 20);
+
+ /* Write compressed block */
+
+ return apultra_write_block(pCompressor, pCompressor->best_match - nPreviousBlockSize, pInWindow, nPreviousBlockSize, nEndOffset, pOutData, nOutOffset, nMaxOutDataSize, nCurBitsOffset, nCurBitShift, nCurFollowsLiteral, nCurRepMatchOffset, nBlockFlags);
+}
+
+/* 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 nMaxArrivals maximum number of arrivals per position
+ * @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 nMaxArrivals, 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->first_offset_for_byte = NULL;
+ pCompressor->next_offset_for_pos = NULL;
+ pCompressor->offset_cache = NULL;
+ pCompressor->flags = nFlags;
+ pCompressor->block_size = nBlockSize;
+ pCompressor->max_arrivals = nMaxArrivals;
+
+ 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) * nMaxArrivals * 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) {
+ pCompressor->first_offset_for_byte = (int*)malloc(65536 * sizeof(int));
+ if (pCompressor->first_offset_for_byte) {
+ pCompressor->next_offset_for_pos = (int*)malloc(nBlockSize * sizeof(int));
+ if (pCompressor->next_offset_for_pos) {
+ if (nMaxArrivals == NARRIVALS_PER_POSITION_MAX) {
+ pCompressor->offset_cache = (int*)malloc(2048 * sizeof(int));
+ if (pCompressor->offset_cache) {
+ return 0;
+ }
+ }
+ else {
+ 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->offset_cache) {
+ free(pCompressor->offset_cache);
+ pCompressor->offset_cache = NULL;
+ }
+
+ if (pCompressor->next_offset_for_pos) {
+ free(pCompressor->next_offset_for_pos);
+ pCompressor->next_offset_for_pos = NULL;
+ }
+
+ if (pCompressor->first_offset_for_byte) {
+ free(pCompressor->first_offset_for_byte);
+ pCompressor->first_offset_for_byte = NULL;
+ }
+
+ 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 nCurBitShift bit shift count
+ * @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 *nCurBitShift, 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, nCurBitShift, 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 (set to 0)
+ * @param nMaxWindowSize maximum window size to use (0 for default)
+ * @param nDictionarySize size of dictionary in front of input data (0 for none)
+ * @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
+ *
+ * @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, size_t nDictionarySize, 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 nMaxArrivals = NARRIVALS_PER_POSITION_SMALL;
+ int nError = 0;
+ const int nBlockSize = (nInputSize < BLOCK_SIZE) ? ((nInputSize < 1024) ? 1024 : (int)nInputSize) : BLOCK_SIZE;
+ const int nMaxOutBlockSize = (int)apultra_get_max_compressed_size(nBlockSize);
+
+ if (nDictionarySize < nInputSize) {
+ int nInDataSize = (int)(nInputSize - nDictionarySize);
+ if (nInDataSize > nBlockSize)
+ nInDataSize = nBlockSize;
+
+ if (nInDataSize > 0 && (nDictionarySize + nInDataSize) >= nInputSize) {
+ if (nInputSize <= 65536)
+ nMaxArrivals = NARRIVALS_PER_POSITION_MAX;
+ else
+ nMaxArrivals = NARRIVALS_PER_POSITION_NORMAL;
+ }
+ }
+
+ nResult = apultra_compressor_init(&compressor, nBlockSize, nBlockSize * 2, nMaxArrivals, nFlags);
+ if (nResult != 0) {
+ return -1;
+ }
+
+ compressor.max_offset = nMaxWindowSize ? (int)nMaxWindowSize : MAX_OFFSET;
+
+ int nPreviousBlockSize = 0;
+ int nNumBlocks = 0;
+ int nCurBitsOffset = INT_MIN, nCurBitShift = 0, nCurFollowsLiteral = 0;
+ int nBlockFlags = 1;
+ int nCurRepMatchOffset = 0;
+
+ if (nDictionarySize) {
+ nOriginalSize = (int)nDictionarySize;
+ nPreviousBlockSize = (int)nDictionarySize;
+ }
+
+ 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, &nCurBitShift, &nCurFollowsLiteral, &nCurRepMatchOffset, nBlockFlags);
+ nBlockFlags &= (~1);
+
+ if (nOutDataSize >= 0) {
+ /* Write compressed block */
+
+ if (!nError) {
+ nOriginalSize += nInDataSize;
+ nCompressedSize += nOutDataSize;
+ if (nCurBitsOffset != INT_MIN)
+ nCurBitsOffset -= 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/shrink.h b/tools/apultra/src/shrink.h new file mode 100644 index 0000000..0057d68 --- /dev/null +++ b/tools/apultra/src/shrink.h @@ -0,0 +1,174 @@ +/*
+ * 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 <zxintrospec@gmail.com>
+ *
+ */
+
+#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<<LCP_BITS) - 1)
+#define LCP_SHIFT (63-LCP_BITS)
+#define LCP_MASK (((1ULL<<LCP_BITS) - 1) << LCP_SHIFT)
+#define POS_MASK ((1ULL<<LCP_SHIFT) - 1)
+#define VISITED_FLAG 0x8000000000000000ULL
+#define EXCL_VISITED_MASK 0x7fffffffffffffffULL
+
+#define NARRIVALS_PER_POSITION_MAX 55
+#define NARRIVALS_PER_POSITION_NORMAL 46
+#define NARRIVALS_PER_POSITION_SMALL 9
+
+#define NMATCHES_PER_INDEX 64
+#define MATCHES_PER_INDEX_SHIFT 6
+
+#define LEAVE_ALONE_MATCH_SIZE 120
+
+/** One match option */
+typedef struct _apultra_match {
+ unsigned int length:11;
+ unsigned int offset:21;
+} apultra_match;
+
+/** One finalized match */
+typedef struct _apultra_final_match {
+ int length;
+ int offset;
+} apultra_final_match;
+
+/** Forward arrival slot */
+typedef struct {
+ int cost;
+
+ unsigned int from_pos:21;
+ int from_slot:7;
+ unsigned int follows_literal:1;
+
+ unsigned int rep_offset:21;
+ unsigned int short_offset:4;
+ unsigned int rep_pos:21;
+ unsigned int match_len:11;
+
+ int score;
+} apultra_arrival;
+
+/** Compression statistics */
+typedef struct _apultra_stats {
+ int num_literals;
+ int num_4bit_matches;
+ int num_7bit_matches;
+ int num_variable_matches;
+ int num_rep_matches;
+ int num_eod;
+
+ int safe_dist;
+
+ int min_offset;
+ int max_offset;
+ long long total_offsets;
+
+ int min_match_len;
+ int max_match_len;
+ int total_match_lens;
+
+ int min_rle1_len;
+ int max_rle1_len;
+ int total_rle1_lens;
+
+ int min_rle2_len;
+ int max_rle2_len;
+ int total_rle2_lens;
+
+ int commands_divisor;
+ int match_divisor;
+ int rle1_divisor;
+ int rle2_divisor;
+} apultra_stats;
+
+/** Compression context */
+typedef struct _apultra_compressor {
+ divsufsort_ctx_t divsufsort_context;
+ unsigned long long *intervals;
+ unsigned long long *pos_data;
+ unsigned long long *open_intervals;
+ apultra_match *match;
+ unsigned short *match_depth;
+ unsigned char *match1;
+ apultra_final_match *best_match;
+ apultra_arrival *arrival;
+ int *first_offset_for_byte;
+ int *next_offset_for_pos;
+ int *offset_cache;
+ int flags;
+ int block_size;
+ int max_offset;
+ int max_arrivals;
+ apultra_stats stats;
+} apultra_compressor;
+
+/**
+ * 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);
+
+/**
+ * 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 (set to 0)
+ * @param nMaxWindowSize maximum window size to use (0 for default)
+ * @param nDictionarySize size of dictionary in front of input data (0 for none)
+ * @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
+ *
+ * @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, size_t nDictionarySize, void(*progress)(long long nOriginalSize, long long nCompressedSize), apultra_stats *pStats);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _SHRINK_H */
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