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added dictionary builder utility

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Yann Collet 2016-01-28 00:29:58 +01:00
parent fb810d6053
commit e618f8e221
14 changed files with 4360 additions and 0 deletions
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1
NEWS
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v0.5.0 v0.5.0
Changed streaming & dictionary API Changed streaming & dictionary API
New : dictionary builder utility
v0.4.7 v0.4.7
Improved : small compression speed improvement in HC mode Improved : small compression speed improvement in HC mode

339
dictBuilder/COPYING Normal file
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GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
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67
dictBuilder/Makefile Normal file
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# ##########################################################################
# Dict Builder - Makefile
# Copyright (C) Yann Collet 2015
#
# GPL v2 License
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# You can contact the author at :
# - ZSTD source repository : http://code.google.com/p/zstd/
# - Public forum : https://groups.google.com/forum/#!forum/lz4c
# ##########################################################################
CPPFLAGS= -I../lib
CFLAGS ?= -O3
CFLAGS += -std=c99 -Wall -Wextra -Wshadow -Wcast-qual -Wcast-align -Wundef -Wstrict-prototypes -Wstrict-aliasing=1
FLAGS = $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $(MOREFLAGS)
ZSTDDIR = ../lib
# Define *.exe as extension for Windows systems
ifneq (,$(filter Windows%,$(OS)))
EXT =.exe
VOID = nul
else
EXT =
VOID = /dev/null
endif
.PHONY: default all test
default: dictBuilder
all: dictBuilder
dictBuilder: dictBuilder.c dibcli.c divsufsort.c sssort.c trsort.c $(ZSTDDIR)/huff0.c $(ZSTDDIR)/fse.c $(ZSTDDIR)/zstd_decompress.c
$(CC) $(FLAGS) $^ -o $@$(EXT)
clean:
@rm -f core *.o tmp* result* *.gcda \
dictBuilder$(EXT)
@echo Cleaning completed
test: clean dictBuilder
clangtest: CC = clang
clangtest: CFLAGS += -Werror
clangtest: clean dictBuilder
gpptest: CC = g++
gpptest: CFLAGS=-O3 -Wall -Wextra -Wshadow -Wcast-align -Wcast-qual -Wundef -Werror
gpptest: clean dictBuilder

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dictBuilder/config.h Normal file
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/*
* config.h for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef _CONFIG_H
#define _CONFIG_H 1
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
/** Define to the version of this package. **/
#define PROJECT_VERSION_FULL "2.0.1"
/** Define to 1 if you have the header files. **/
#define HAVE_INTTYPES_H 1
#define HAVE_STDDEF_H 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_STRINGS_H 1
#define HAVE_MEMORY_H 1
#define HAVE_SYS_TYPES_H 1
/** for WinIO **/
/* #undef HAVE_IO_H */
/* #undef HAVE_FCNTL_H */
/* #undef HAVE__SETMODE */
/* #undef HAVE_SETMODE */
/* #undef HAVE__FILENO */
/* #undef HAVE_FOPEN_S */
/* #undef HAVE__O_BINARY */
/*
#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 */

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dictBuilder/dibcli.c Normal file
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/*
dibcli - Command Line Interface (cli) for Dictionary Builder
Copyright (C) Yann Collet 2016
GPL v2 License
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
You can contact the author at :
- zstd source repository : https://github.com/Cyan4973/zstd
- ztsd public forum : https://groups.google.com/forum/#!forum/lz4c
*/
/**************************************
* Compiler Options
**************************************/
#define _CRT_SECURE_NO_WARNINGS /* Visual : removes warning from strcpy */
#define _POSIX_SOURCE 1 /* triggers fileno() within <stdio.h> on unix */
/**************************************
* Includes
**************************************/
#include <stdio.h> /* fprintf, getchar */
#include <stdlib.h> /* exit, calloc, free */
#include <string.h> /* strcmp, strlen */
#include "dictBuilder.h"
/**************************************
* OS-specific Includes
**************************************/
#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(_WIN32) || defined(__CYGWIN__)
# include <fcntl.h> /* _O_BINARY */
# include <io.h> /* _setmode, _isatty */
# define SET_BINARY_MODE(file) _setmode(_fileno(file), _O_BINARY)
# define IS_CONSOLE(stdStream) _isatty(_fileno(stdStream))
#else
# include <unistd.h> /* isatty */
# define SET_BINARY_MODE(file)
# define IS_CONSOLE(stdStream) isatty(fileno(stdStream))
#endif
/**************************************
* Constants
**************************************/
#define PROGRAM_DESCRIPTION "Dictionary builder"
#ifndef PROGRAM_VERSION
# define QUOTE(str) #str
# define EXP_Q(str) QUOTE(str)
# define PROGRAM_VERSION "v" EXP_Q(DiB_VERSION_MAJOR) "." EXP_Q(DiB_VERSION_MINOR) "." EXP_Q(DiB_VERSION_RELEASE)
#endif
#define AUTHOR "Yann Collet"
#define WELCOME_MESSAGE "*** %s %s %i-bits, by %s ***\n", PROGRAM_DESCRIPTION, PROGRAM_VERSION, (int)(sizeof(void*)*8), AUTHOR
#define KB *(1 <<10)
#define MB *(1 <<20)
#define GB *(1U<<30)
static const unsigned selectionLevelDefault = 9; /* determined experimentally */
static const unsigned maxDictSizeDefault = 110 KB;
static const char* dictFileNameDefault = "dictionary";
/**************************************
* Display Macros
**************************************/
#define DISPLAY(...) fprintf(displayOut, __VA_ARGS__)
#define DISPLAYLEVEL(l, ...) if (displayLevel>=l) { DISPLAY(__VA_ARGS__); }
static FILE* displayOut;
static unsigned displayLevel = 2; // 0 : no display // 1: errors // 2 : + result + interaction + warnings ; // 3 : + progression; // 4 : + information
/**************************************
* Exceptions
**************************************/
#define DEBUG 0
#define DEBUGOUTPUT(...) if (DEBUG) DISPLAY(__VA_ARGS__);
#define EXM_THROW(error, ...) \
{ \
DEBUGOUTPUT("Error defined at %s, line %i : \n", __FILE__, __LINE__); \
DISPLAYLEVEL(1, "Error %i : ", error); \
DISPLAYLEVEL(1, __VA_ARGS__); \
DISPLAYLEVEL(1, "\n"); \
exit(error); \
}
/**************************************
* Command Line
**************************************/
static int usage(const char* programName)
{
DISPLAY( "Usage :\n");
DISPLAY( " %s [arg] [filenames]\n", programName);
DISPLAY( "\n");
DISPLAY( "Arguments :\n");
DISPLAY( "--maxdict : limit dictionary to specified size (default : %u) \n", maxDictSizeDefault);
DISPLAY( " -o : name of dictionary file (default: %s) \n", dictFileNameDefault);
DISPLAY( " -h/-H : display help/long help and exit\n");
return 0;
}
static int usage_advanced(const char* programName)
{
DISPLAY(WELCOME_MESSAGE);
usage(programName);
DISPLAY( "\n");
DISPLAY( "Advanced arguments :\n");
DISPLAY( " -# : selection level # (default :%u)\n", selectionLevelDefault);
DISPLAY( " -V : display Version number and exit\n");
DISPLAY( " -v : verbose mode\n");
DISPLAY( " -q : suppress warnings; specify twice to suppress errors too\n");
return 0;
}
static int badusage(const char* programName)
{
DISPLAYLEVEL(1, "Incorrect parameters\n");
if (displayLevel >= 1) usage(programName);
return 1;
}
static void waitEnter(void)
{
int unused;
DISPLAY("Press enter to continue...\n");
unused = getchar();
(void)unused;
}
int main(int argCount, const char** argv)
{
int i,
main_pause=0,
operationResult=0,
nextArgumentIsMaxDict=0,
nextArgumentIsDictFileName=0;
size_t maxDictSize = maxDictSizeDefault;
unsigned selectionLevel = selectionLevelDefault;
const char** filenameTable = (const char**)malloc(argCount * sizeof(const char*)); /* argCount >= 1 */
unsigned filenameIdx = 0;
const char* programName = argv[0];
const char* dictFileName = dictFileNameDefault;
/* init */
displayOut = stderr; /* unfortunately, cannot be set at declaration */
if (filenameTable==NULL) EXM_THROW(1, "not enough memory\n");
/* Pick out program name from path. Don't rely on stdlib because of conflicting behavior */
for (i = (int)strlen(programName); i > 0; i--) { if ((programName[i] == '/') || (programName[i] == '\\')) { i++; break; } }
programName += i;
/* command switches */
for(i=1; i<argCount; i++) {
const char* argument = argv[i];
if(!argument) continue; /* Protection if argument empty */
if (nextArgumentIsDictFileName) {
nextArgumentIsDictFileName=0;
dictFileName = argument;
continue;
}
if (nextArgumentIsMaxDict) {
nextArgumentIsMaxDict = 0;
maxDictSize = 0;
while ((*argument>='0') && (*argument<='9'))
maxDictSize = maxDictSize * 10 + (*argument - '0'), argument++;
if (*argument=='k' || *argument=='K')
maxDictSize <<= 10;
continue;
}
/* long commands (--long-word) */
if (!strcmp(argument, "--version")) { displayOut=stdout; DISPLAY(WELCOME_MESSAGE); return 0; }
if (!strcmp(argument, "--help")) { displayOut=stdout; return usage_advanced(programName); }
if (!strcmp(argument, "--verbose")) { displayLevel=4; continue; }
if (!strcmp(argument, "--quiet")) { displayLevel--; continue; }
if (!strcmp(argument, "--maxdict")) { nextArgumentIsMaxDict=1; continue; }
/* Decode commands (note : aggregated commands are allowed) */
if (argument[0]=='-') {
argument++;
while (argument[0]!=0) {
/* selection Level */
if ((*argument>='0') && (*argument<='9')) {
selectionLevel = 0;
while ((*argument >= '0') && (*argument <= '9')) {
selectionLevel *= 10;
selectionLevel += *argument - '0';
argument++;
}
continue;
}
switch(argument[0])
{
/* Display help */
case 'V': displayOut=stdout; DISPLAY(WELCOME_MESSAGE); return 0; /* Version Only */
case 'H':
case 'h': displayOut=stdout; return usage_advanced(programName);
/* Verbose mode */
case 'v': displayLevel++; if (displayLevel<3) displayLevel=3; argument++; break;
/* Quiet mode */
case 'q': displayLevel--; argument++; break;
/* dictionary name */
case 'o': nextArgumentIsDictFileName=1; argument++; break;
/* Pause at the end (hidden option) */
case 'p': main_pause=1; argument++; break;
/* unknown command */
default : return badusage(programName);
} }
continue;
}
/* add filename to list */
filenameTable[filenameIdx++] = argument;
}
/* Welcome message (if verbose) */
DISPLAYLEVEL(3, WELCOME_MESSAGE);
if (filenameIdx==0) return badusage(programName);
/* building ... */
DiB_setDisplayLevel(displayLevel);
operationResult = DiB_trainFiles(dictFileName, maxDictSize, filenameTable, filenameIdx, selectionLevel);
if (main_pause) waitEnter();
free((void*)filenameTable);
return operationResult;
}

946
dictBuilder/dictBuilder.c Normal file
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@ -0,0 +1,946 @@
/*
dictBuilder.c
Copyright (C) Yann Collet 2016
GPL v2 License
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
You can contact the author at :
- zstd source repository : https://github.com/Cyan4973/zstd
- ztsd public forum : https://groups.google.com/forum/#!forum/lz4c
*/
/* **************************************
* Compiler Options
****************************************/
/* Disable some Visual warning messages */
#ifdef _MSC_VER
# define _CRT_SECURE_NO_WARNINGS /* fopen */
# pragma warning(disable : 4127) /* disable: C4127: conditional expression is constant */
#endif
/* Unix Large Files support (>4GB) */
#define _FILE_OFFSET_BITS 64
#if (defined(__sun__) && (!defined(__LP64__))) /* Sun Solaris 32-bits requires specific definitions */
# define _LARGEFILE_SOURCE
#elif ! defined(__LP64__) /* No point defining Large file for 64 bit */
# define _LARGEFILE64_SOURCE
#endif
/* S_ISREG & gettimeofday() are not supported by MSVC */
#if defined(_MSC_VER) || defined(_WIN32)
# define BMK_LEGACY_TIMER 1
#endif
/* *************************************
* Includes
***************************************/
#include <stdlib.h> /* malloc, free */
#include <string.h> /* memset */
#include <stdio.h> /* fprintf, fopen, ftello64 */
#include <sys/types.h> /* stat64 */
#include <sys/stat.h> /* stat64 */
#include <time.h> /* clock */
#include "mem.h" /* read */
#include "divsufsort.h"
#include "dictBuilder.h"
#include "zstd_compress.c"
#include "huff0_static.h"
/* *************************************
* Compiler specifics
***************************************/
#if !defined(S_ISREG)
# define S_ISREG(x) (((x) & S_IFMT) == S_IFREG)
#endif
#ifdef _MSC_VER
#define snprintf sprintf_s
#endif
/* *************************************
* Constants
***************************************/
#define KB *(1 <<10)
#define MB *(1 <<20)
#define GB *(1U<<30)
#define DICTLISTSIZE 10000
#define MEMMULT 11
static const size_t maxMemory = (sizeof(size_t)==4) ? (2 GB - 64 MB) : (size_t)(3 GB) * MEMMULT;
#define NOISELENGTH 32
#define PRIME1 2654435761U
#define PRIME2 2246822519U
#define MINRATIO 4
/* *************************************
* console display
***************************************/
#define DISPLAY(...) fprintf(stderr, __VA_ARGS__)
#define DISPLAYLEVEL(l, ...) if (g_displayLevel>=l) { DISPLAY(__VA_ARGS__); }
static unsigned g_displayLevel = 2; /* 0 : no display; 1: errors; 2: default; 4: full information */
void DiB_setDisplayLevel(unsigned l) { g_displayLevel=l; }
#define DISPLAYUPDATE(l, ...) if (g_displayLevel>=l) { \
if (DiB_GetMilliSpan(g_time) > refreshRate) \
{ g_time = clock(); DISPLAY(__VA_ARGS__); \
if (g_displayLevel>=4) fflush(stdout); } }
static const unsigned refreshRate = 300;
static clock_t g_time = 0;
void DiB_printHex(U32 dlevel, const void* ptr, size_t length)
{
const BYTE* const b = (const BYTE*)ptr;
size_t u;
for (u=0; u<length; u++)
{
BYTE c = b[u];
if (c<32 || c>126) c = '.'; /* non-printable char */
DISPLAYLEVEL(dlevel, "%c", c);
}
}
/* *************************************
* Exceptions
***************************************/
#ifndef DEBUG
# define DEBUG 0
#endif
#define DEBUGOUTPUT(...) if (DEBUG) DISPLAY(__VA_ARGS__);
#define EXM_THROW(error, ...) \
{ \
DEBUGOUTPUT("Error defined at %s, line %i : \n", __FILE__, __LINE__); \
DISPLAYLEVEL(1, "Error %i : ", error); \
DISPLAYLEVEL(1, __VA_ARGS__); \
DISPLAYLEVEL(1, "\n"); \
exit(error); \
}
/* ********************************************************
* Helper functions
**********************************************************/
unsigned DiB_versionNumber (void) { return DiB_VERSION_NUMBER; }
static unsigned DiB_GetMilliSpan(clock_t nPrevious)
{
clock_t nCurrent = clock();
unsigned nSpan = (unsigned)(((nCurrent - nPrevious) * 1000) / CLOCKS_PER_SEC);
return nSpan;
}
/* ********************************************************
* File related operations
**********************************************************/
static unsigned long long DiB_getFileSize(const char* infilename)
{
int r;
#if defined(_MSC_VER)
struct _stat64 statbuf;
r = _stat64(infilename, &statbuf);
#else
struct stat statbuf;
r = stat(infilename, &statbuf);
#endif
if (r || !S_ISREG(statbuf.st_mode)) return 0; /* No good... */
return (unsigned long long)statbuf.st_size;
}
static unsigned long long DiB_getTotalFileSize(const char** fileNamesTable, unsigned nbFiles)
{
unsigned long long total = 0;
unsigned n;
for (n=0; n<nbFiles; n++)
total += DiB_getFileSize(fileNamesTable[n]);
return total;
}
static void DiB_loadFiles(void* buffer, size_t bufferSize,
size_t* fileSizes,
const char** fileNamesTable, unsigned nbFiles)
{
char* buff = (char*)buffer;
size_t pos = 0;
unsigned n;
for (n=0; n<nbFiles; n++) {
size_t readSize;
unsigned long long fileSize = DiB_getFileSize(fileNamesTable[n]);
FILE* f = fopen(fileNamesTable[n], "rb");
if (f==NULL) EXM_THROW(10, "impossible to open file %s", fileNamesTable[n]);
DISPLAYLEVEL(2, "Loading %s... \r", fileNamesTable[n]);
if (fileSize > bufferSize-pos) fileSize = 0; /* stop there, not enough memory to load all files */
readSize = fread(buff+pos, 1, (size_t)fileSize, f);
if (readSize != (size_t)fileSize) EXM_THROW(11, "could not read %s", fileNamesTable[n]);
pos += readSize;
fileSizes[n] = (size_t)fileSize;
fclose(f);
}
}
/*-********************************************************
* Dictionary training functions
**********************************************************/
static size_t DiB_read_ARCH(const void* p) { size_t r; memcpy(&r, p, sizeof(r)); return r; }
static unsigned DiB_NbCommonBytes (register size_t val)
{
if (MEM_isLittleEndian()) {
if (MEM_64bits()) {
# if defined(_MSC_VER) && defined(_WIN64)
unsigned long r = 0;
_BitScanForward64( &r, (U64)val );
return (unsigned)(r>>3);
# elif defined(__GNUC__) && (__GNUC__ >= 3)
return (__builtin_ctzll((U64)val) >> 3);
# else
static const int DeBruijnBytePos[64] = { 0, 0, 0, 0, 0, 1, 1, 2, 0, 3, 1, 3, 1, 4, 2, 7, 0, 2, 3, 6, 1, 5, 3, 5, 1, 3, 4, 4, 2, 5, 6, 7, 7, 0, 1, 2, 3, 3, 4, 6, 2, 6, 5, 5, 3, 4, 5, 6, 7, 1, 2, 4, 6, 4, 4, 5, 7, 2, 6, 5, 7, 6, 7, 7 };
return DeBruijnBytePos[((U64)((val & -(long long)val) * 0x0218A392CDABBD3FULL)) >> 58];
# endif
} else { /* 32 bits */
# if defined(_MSC_VER)
unsigned long r=0;
_BitScanForward( &r, (U32)val );
return (unsigned)(r>>3);
# elif defined(__GNUC__) && (__GNUC__ >= 3)
return (__builtin_ctz((U32)val) >> 3);
# else
static const int DeBruijnBytePos[32] = { 0, 0, 3, 0, 3, 1, 3, 0, 3, 2, 2, 1, 3, 2, 0, 1, 3, 3, 1, 2, 2, 2, 2, 0, 3, 1, 2, 0, 1, 0, 1, 1 };
return DeBruijnBytePos[((U32)((val & -(S32)val) * 0x077CB531U)) >> 27];
# endif
}
} else { /* Big Endian CPU */
if (MEM_64bits()) {
# if defined(_MSC_VER) && defined(_WIN64)
unsigned long r = 0;
_BitScanReverse64( &r, val );
return (unsigned)(r>>3);
# elif defined(__GNUC__) && (__GNUC__ >= 3)
return (__builtin_clzll(val) >> 3);
# else
unsigned r;
const unsigned n32 = sizeof(size_t)*4; /* calculate this way due to compiler complaining in 32-bits mode */
if (!(val>>n32)) { r=4; } else { r=0; val>>=n32; }
if (!(val>>16)) { r+=2; val>>=8; } else { val>>=24; }
r += (!val);
return r;
# endif
} else { /* 32 bits */
# if defined(_MSC_VER)
unsigned long r = 0;
_BitScanReverse( &r, (unsigned long)val );
return (unsigned)(r>>3);
# elif defined(__GNUC__) && (__GNUC__ >= 3)
return (__builtin_clz((U32)val) >> 3);
# else
unsigned r;
if (!(val>>16)) { r=2; val>>=8; } else { r=0; val>>=24; }
r += (!val);
return r;
# endif
} }
}
/*! DiB_count() :
Count the nb of common bytes between 2 pointers.
Note : this function presumes end of buffer followed by noisy guard band.
*/
static size_t DiB_count(const void* pIn, const void* pMatch)
{
const char* const pStart = (const char*)pIn;
for (;;) {
size_t diff = DiB_read_ARCH(pMatch) ^ DiB_read_ARCH(pIn);
if (!diff) { pIn = (const char*)pIn+sizeof(size_t); pMatch = (const char*)pMatch+sizeof(size_t); continue; }
pIn = (const char*)pIn+DiB_NbCommonBytes(diff);
return (size_t)((const char*)pIn - pStart);
}
}
typedef struct {
U32 pos;
U32 length;
U32 savings;
} dictItem;
void DiB_initDictItem(dictItem* d)
{
d->pos = 1;
d->length = 0;
d->savings = (U32)(-1);
}
#define LLIMIT 64 /* heuristic determined experimentally */
#define MINMATCHLENGTH 7 /* heuristic determined experimentally */
static dictItem DiB_analyzePos(
BYTE* doneMarks,
const saidx_t* suffix, U32 start,
const void* buffer, U32 minRatio)
{
U32 lengthList[LLIMIT] = {0};
U32 cumulLength[LLIMIT] = {0};
U32 savings[LLIMIT] = {0};
const BYTE* b = (const BYTE*)buffer;
size_t length;
size_t maxLength = LLIMIT;
size_t pos = suffix[start];
U32 end = start;
dictItem solution;
/* init */
memset(&solution, 0, sizeof(solution));
doneMarks[pos] = 1;
/* trivial repetition cases */
if ( (MEM_read16(b+pos+0) == MEM_read16(b+pos+2))
||(MEM_read16(b+pos+1) == MEM_read16(b+pos+3))
||(MEM_read16(b+pos+2) == MEM_read16(b+pos+4)) ) {
/* skip and mark segment */
U16 u16 = MEM_read16(b+pos+4);
U32 u, e = 6;
while (MEM_read16(b+pos+e) == u16) e+=2 ;
if (b[pos+e] == b[pos+e-1]) e++;
for (u=1; u<e; u++)
doneMarks[pos+u] = 1;
return solution;
}
/* look forward */
do {
end++;
length = DiB_count(b + pos, b + suffix[end]);
} while (length >=MINMATCHLENGTH);
/* look backward */
do {
length = DiB_count(b + pos, b + *(suffix+start-1));
if (length >=MINMATCHLENGTH) start--;
} while(length >= MINMATCHLENGTH);
/* exit if not found a minimum nb of repetitions */
if (end-start < minRatio) {
U32 idx;
for(idx=start; idx<end; idx++)
doneMarks[suffix[idx]] = 1;
return solution;
}
{
int i;
U32 searchLength;
U32 refinedStart = start;
U32 refinedEnd = end;
DISPLAYLEVEL(4, "\n");
DISPLAYLEVEL(4, "found %3u matches of length >= %u at pos %7u ", (U32)(end-start), MINMATCHLENGTH, (U32)pos);
DISPLAYLEVEL(4, "\n");
for (searchLength = MINMATCHLENGTH ; ; searchLength++) {
BYTE currentChar = 0;
U32 currentCount = 0;
U32 currentID = refinedStart;
U32 id;
U32 selectedCount = 0;
U32 selectedID = currentID;
for (id =refinedStart; id < refinedEnd; id++) {
if (b[ suffix[id] + searchLength] != currentChar) {
if (currentCount > selectedCount) {
selectedCount = currentCount;
selectedID = currentID;
}
currentID = id;
currentChar = b[ suffix[id] + searchLength];
currentCount = 0;
}
currentCount ++;
}
if (currentCount > selectedCount) { /* for last */
selectedCount = currentCount;
selectedID = currentID;
}
if (selectedCount < minRatio)
break;
//DISPLAYLEVEL(4, "best char at length %u: %02X (seen %u times) (pos %u) \n", searchLength+1, selectedChar, selectedCount, selectedRef);
refinedStart = selectedID;
refinedEnd = refinedStart + selectedCount;
}
/* evaluate gain based on new ref */
start = refinedStart;
pos = suffix[refinedStart];
end = start;
memset(lengthList, 0, sizeof(lengthList));
/* look forward */
do {
end++;
length = DiB_count(b + pos, b + suffix[end]);
if (length >= LLIMIT) length = LLIMIT-1;
lengthList[length]++;
} while (length >=MINMATCHLENGTH);
/* look backward */
do {
length = DiB_count(b + pos, b + suffix[start-1]);
if (length >= LLIMIT) length = LLIMIT-1;
lengthList[length]++;
if (length >=MINMATCHLENGTH) start--;
} while(length >= MINMATCHLENGTH);
/* largest useful length */
memset(cumulLength, 0, sizeof(cumulLength));
cumulLength[maxLength-1] = lengthList[maxLength-1];
for (i=maxLength-2; i>=0; i--)
cumulLength[i] = cumulLength[i+1] + lengthList[i];
for (i=LLIMIT-1; i>=MINMATCHLENGTH; i--) if (cumulLength[i]>=minRatio) break;
maxLength = i;
/* reduce maxLength in case of final into repetitive data */
{
U32 l = maxLength;
BYTE c = b[pos + maxLength-1];
while (b[pos+l-2]==c) l--;
maxLength = l;
}
if (maxLength < MINMATCHLENGTH) return solution; /* skip : no long-enough solution */
/* calculate savings */
savings[5] = 0;
for (i=MINMATCHLENGTH; i<=(int)maxLength; i++)
savings[i] = savings[i-1] + (lengthList[i] * (i-3));
DISPLAYLEVEL(4, "Selected ref at position %u, of length %u : saves %u (ratio: %.2f) \n",
(U32)pos, (U32)maxLength, savings[maxLength], (double)savings[maxLength] / maxLength);
solution.pos = pos;
solution.length = maxLength;
solution.savings = savings[maxLength];
/* mark positions done */
{
U32 id;
U32 testedPos;
for (id=start; id<end; id++) {
U32 p, pEnd;
testedPos = suffix[id];
if (testedPos == pos)
length = solution.length;
else {
length = DiB_count(b+pos, b+testedPos);
if (length > solution.length) length = solution.length;
}
pEnd = testedPos + length;
for (p=testedPos; p<pEnd; p++)
doneMarks[p] = 1;
} } }
return solution;
}
/*! DiB_checkMerge
check if dictItem can be merged, do it if possible
@return : id of destination elt, 0 if not merged
*/
static U32 DiB_checkMerge(dictItem* table, dictItem elt, U32 eltNbToSkip)
{
const U32 tableSize = table->pos;
const U32 max = elt.pos + (elt.length-1);
/* tail overlap */
U32 u; for (u=1; u<tableSize; u++) {
if (u==eltNbToSkip) continue;
if ((table[u].pos > elt.pos) && (table[u].pos < max)) { /* overlap */
/* append */
U32 addedLength = table[u].pos - elt.pos;
table[u].length += addedLength;
table[u].pos = elt.pos;
table[u].savings += elt.savings * addedLength / elt.length; /* rough approx */
table[u].savings += elt.length / 8; /* rough approx */
elt = table[u];
while ((u>1) && (table[u-1].savings < elt.savings))
table[u] = table[u-1], u--;
table[u] = elt;
return u;
} }
/* front overlap */
for (u=1; u<tableSize; u++) {
if (u==eltNbToSkip) continue;
if ((table[u].pos + table[u].length > elt.pos) && (table[u].pos < elt.pos)) { /* overlap */
/* append */
int addedLength = (elt.pos + elt.length) - (table[u].pos + table[u].length);
table[u].savings += elt.length / 8; /* rough approx */
if (addedLength > 0) { /* otherwise, already included */
table[u].length += addedLength;
table[u].savings += elt.savings * addedLength / elt.length; /* rough approx */
}
elt = table[u];
while ((u>1) && (table[u-1].savings < elt.savings))
table[u] = table[u-1], u--;
table[u] = elt;
return u;
} }
return 0;
}
static void DiB_removeDictItem(dictItem* table, U32 id)
{
/* convention : first element is nb of elts */
U32 max = table->pos;
U32 u;
if (!id) return; /* protection, should never happen */
for (u=id; u<max; u++)
table[u] = table[u+1];
table->pos--;
}
static void DiB_insertDictItem(dictItem* table, U32 maxSize, dictItem elt)
{
/* merge if possible */
U32 mergeId = DiB_checkMerge(table, elt, 0);
if (mergeId) {
U32 newMerge = 1;
while (newMerge) {
newMerge = DiB_checkMerge(table, table[mergeId], mergeId);
if (newMerge) DiB_removeDictItem(table, mergeId);
mergeId = newMerge;
}
return;
}
/* insert */
{
U32 current;
U32 nextElt = table->pos;
if (nextElt >= maxSize) nextElt = maxSize-1;
current = nextElt-1;
while (table[current].savings < elt.savings) {
table[current+1] = table[current];
current--;
}
table[current+1] = elt;
table->pos = nextElt+1;
}
}
static U32 DiB_dictSize(const dictItem* dictList)
{
U32 u, dictSize = 0;
for (u=1; u<dictList[0].pos; u++)
dictSize += dictList[u].length;
return dictSize;
}
static void DiB_trainBuffer(dictItem* dictList, U32 dictListSize,
const void* const buffer, const size_t bufferSize, /* buffer must end with noisy guard band */
const char* displayName,
const size_t* fileSizes, size_t nbFiles, unsigned maxDictSize,
U32 shiftRatio)
{
saidx_t* const suffix0 = (saidx_t*)malloc((bufferSize+2)*sizeof(*suffix0));
saidx_t* const suffix = suffix0+1;
U32* reverseSuffix = (U32*)malloc((bufferSize)*sizeof(*reverseSuffix));
BYTE* doneMarks = (BYTE*)malloc((bufferSize+16)*sizeof(*doneMarks)); /* +16 for overflow security */
U32* filePos = (U32*)malloc(nbFiles * sizeof(*filePos));
U32 minRatio = nbFiles >> shiftRatio;
saint_t errorCode;
/* init */
DISPLAYLEVEL(2, "\r%70s\r", ""); /* clean display line */
if (!suffix0 || !reverseSuffix || !doneMarks || !filePos)
EXM_THROW(1, "not enough memory for DiB_trainBuffer");
if (minRatio < MINRATIO) minRatio = MINRATIO;
memset(doneMarks, 0, bufferSize+16);
/* sort */
DISPLAYLEVEL(2, "sorting %s ...\n", displayName);
errorCode = divsufsort((const sauchar_t*)buffer, suffix, bufferSize);
if (errorCode != 0) EXM_THROW(2, "sort failed");
suffix[bufferSize] = bufferSize; /* leads into noise */
suffix0[0] = bufferSize; /* leads into noise */
{
/* build reverse suffix sort */
size_t pos;
for (pos=0; pos < bufferSize; pos++)
reverseSuffix[suffix[pos]] = pos;
/* build file pos */
filePos[0] = 0;
for (pos=1; pos<nbFiles; pos++)
filePos[pos] = filePos[pos-1] + fileSizes[pos-1];
}
DISPLAYLEVEL(2, "finding patterns ... \n");
DISPLAYLEVEL(4, "minimum ratio : %u \n", minRatio);
{
U32 cursor; for (cursor=0; cursor < bufferSize; ) {
dictItem solution;
if (doneMarks[cursor]) { cursor++; continue; }
solution = DiB_analyzePos(doneMarks, suffix, reverseSuffix[cursor], buffer, minRatio);
if (solution.length==0) { cursor++; continue; }
DiB_insertDictItem(dictList, dictListSize, solution);
cursor += solution.length;
DISPLAYUPDATE(2, "\r%4.2f %% \r", (double)cursor / bufferSize * 100);
}
#if 0
/* 2nd scan */
for (cursor=0; cursor < bufferSize; cursor++ )
{
dictItem solution;
if (doneMarks[cursor]) continue;
solution = DiB_analyzePos(doneMarks, suffix, reverseSuffix[cursor], buffer, minRatio);
if (solution.length==0) continue;
DiB_insertDictItem(dictList, dictListSize, solution);
DISPLAYUPDATE(2, "\r%4.2f %% \r", (double)cursor / bufferSize * 100);
}
#endif
}
/* limit dictionary size */
{
U32 max = dictList->pos; /* convention : nb of useful elts within dictList */
U32 currentSize = 0;
U32 n; for (n=1; n<max; n++) {
currentSize += dictList[n].length;
if (currentSize > maxDictSize) break;
}
dictList->pos = n;
}
free(suffix0);
free(reverseSuffix);
free(doneMarks);
free(filePos);
}
static size_t DiB_findMaxMem(unsigned long long requiredMem)
{
size_t step = 8 MB;
void* testmem = NULL;
requiredMem = (((requiredMem >> 23) + 1) << 23);
requiredMem += 2 * step;
if (requiredMem > maxMemory) requiredMem = maxMemory;
while (!testmem) {
requiredMem -= step;
testmem = malloc((size_t)requiredMem);
}
free(testmem);
return (size_t)(requiredMem - step);
}
static void DiB_fillNoise(void* buffer, size_t length)
{
unsigned acc = PRIME1;
size_t p=0;;
for (p=0; p<length; p++) {
acc *= PRIME2;
((unsigned char*)buffer)[p] = (unsigned char)(acc >> 21);
}
}
typedef struct
{
ZSTD_CCtx* ref;
ZSTD_CCtx* zc;
void* workPlace; /* must be BLOCKSIZE allocated */
} EStats_ress_t;
static void DiB_countEStats(EStats_ress_t esr,
U32* countLit, U32* offsetcodeCount, U32* matchlengthCount, U32* litlengthCount,
const void* src, size_t srcSize)
{
const BYTE* bytePtr;
const U32* u32Ptr;
if (srcSize > BLOCKSIZE) srcSize = BLOCKSIZE; /* protection vs large samples */
ZSTD_copyCCtx(esr.zc, esr.ref);
ZSTD_compressBlock(esr.zc, esr.workPlace, BLOCKSIZE, src, srcSize);
/* count stats */
for(bytePtr = esr.zc->seqStore.litStart; bytePtr < esr.zc->seqStore.lit; bytePtr++)
countLit[*bytePtr]++;
for(u32Ptr = esr.zc->seqStore.offsetStart; u32Ptr < esr.zc->seqStore.offset; u32Ptr++) {
BYTE offcode = (BYTE)ZSTD_highbit(*u32Ptr) + 1;
if (*u32Ptr==0) offcode=0;
offsetcodeCount[offcode]++;
}
for(bytePtr = esr.zc->seqStore.matchLengthStart; bytePtr < esr.zc->seqStore.matchLength; bytePtr++)
matchlengthCount[*bytePtr]++;
for(bytePtr = esr.zc->seqStore.litLengthStart; bytePtr < esr.zc->seqStore.litLength; bytePtr++)
litlengthCount[*bytePtr]++;
}
#define OFFCODE_MAX 18
static size_t DiB_analyzeEntropy(void* dstBuffer, size_t maxDstSize,
const void* srcBuffer, size_t* fileSizes, unsigned nbFiles,
const void* dictBuffer, size_t dictBufferSize)
{
U32 countLit[256];
U32 offcodeCount[MaxOff+1];
HUF_CREATE_STATIC_CTABLE(hufTable, 255);
short offcodeNCount[MaxOff+1];
U32 matchLengthCount[MaxML+1];
short matchLengthNCount[MaxML+1];
U32 litlengthCount[MaxLL+1];
short litlengthNCount[MaxLL+1];
EStats_ress_t esr;
ZSTD_parameters params;
U32 u, huffLog = 12, Offlog = OffFSELog, mlLog = MLFSELog, llLog = LLFSELog, total;
size_t pos = 0, errorCode;
size_t eSize = 0;
/* init */
for (u=0; u<256; u++) countLit[u]=1; /* any character must be described */
for (u=0; u<=OFFCODE_MAX; u++) offcodeCount[u]=1;
for (u=0; u<=MaxML; u++) matchLengthCount[u]=1;
for (u=0; u<=MaxLL; u++) litlengthCount[u]=1;
esr.ref = ZSTD_createCCtx();
esr.zc = ZSTD_createCCtx();
esr.workPlace = malloc(BLOCKSIZE);
if (!esr.ref || !esr.zc || !esr.workPlace) EXM_THROW(30, "Not enough memory");
params = ZSTD_getParams(5, dictBufferSize + 15 KB);
params.strategy = ZSTD_greedy;
ZSTD_compressBegin_advanced(esr.ref, dictBuffer, dictBufferSize, params);
/* collect stats on all files */
for (u=0; u<nbFiles; u++) {
DiB_countEStats(esr,
countLit, offcodeCount, matchLengthCount, litlengthCount,
(const char*)srcBuffer + pos, fileSizes[u]);
pos += fileSizes[u];
}
/* analyze */
errorCode = HUF_buildCTable (hufTable, countLit, 255, huffLog);
if (HUF_isError(errorCode)) EXM_THROW(31, "HUF_buildCTable error");
huffLog = (U32)errorCode;
total=0; for (u=0; u<=OFFCODE_MAX; u++) total+=offcodeCount[u];
errorCode = FSE_normalizeCount(offcodeNCount, Offlog, offcodeCount, total, OFFCODE_MAX);
if (FSE_isError(errorCode)) EXM_THROW(32, "FSE_normalizeCount error with offcodeCount");
Offlog = (U32)errorCode;
total=0; for (u=0; u<=MaxML; u++) total+=matchLengthCount[u];
errorCode = FSE_normalizeCount(matchLengthNCount, mlLog, matchLengthCount, total, MaxML);
if (FSE_isError(errorCode)) EXM_THROW(33, "FSE_normalizeCount error with matchLengthCount");
mlLog = (U32)errorCode;
total=0; for (u=0; u<=MaxLL; u++) total+=litlengthCount[u];
errorCode = FSE_normalizeCount(litlengthNCount, llLog, litlengthCount, total, MaxLL);
if (FSE_isError(errorCode)) EXM_THROW(34, "FSE_normalizeCount error with litlengthCount");
llLog = (U32)errorCode;
/* write result to buffer */
errorCode = HUF_writeCTable(dstBuffer, maxDstSize, hufTable, 255, huffLog);
if (HUF_isError(errorCode)) EXM_THROW(41, "HUF_writeCTable error");
dstBuffer = (char*)dstBuffer + errorCode;
maxDstSize -= errorCode;
eSize += errorCode;
errorCode = FSE_writeNCount(dstBuffer, maxDstSize, offcodeNCount, OFFCODE_MAX, Offlog);
if (FSE_isError(errorCode)) EXM_THROW(42, "FSE_writeNCount error with offcodeNCount");
dstBuffer = (char*)dstBuffer + errorCode;
maxDstSize -= errorCode;
eSize += errorCode;
errorCode = FSE_writeNCount(dstBuffer, maxDstSize, matchLengthNCount, MaxML, mlLog);
if (FSE_isError(errorCode)) EXM_THROW(43, "FSE_writeNCount error with matchLengthNCount");
dstBuffer = (char*)dstBuffer + errorCode;
maxDstSize -= errorCode;
eSize += errorCode;
errorCode = FSE_writeNCount(dstBuffer, maxDstSize, litlengthNCount, MaxLL, llLog);
if (FSE_isError(errorCode)) EXM_THROW(43, "FSE_writeNCount error with litlengthNCount");
dstBuffer = (char*)dstBuffer + errorCode;
maxDstSize -= errorCode;
eSize += errorCode;
/* clean */
ZSTD_freeCCtx(esr.ref);
ZSTD_freeCCtx(esr.zc);
free(esr.workPlace);
return eSize;
}
static void DiB_saveDict(const char* dictFileName,
const void* buff1, size_t buff1Size,
const void* buff2, size_t buff2Size)
{
FILE* f;
size_t n;
f = fopen(dictFileName, "wb");
if (f==NULL) EXM_THROW(3, "cannot open %s ", dictFileName);
n = fwrite(buff1, 1, buff1Size, f);
if (n!=buff1Size) EXM_THROW(4, "%s : write error", dictFileName)
n = fwrite(buff2, 1, buff2Size, f);
if (n!=buff2Size) EXM_THROW(4, "%s : write error", dictFileName)
n = (size_t)fclose(f);
if (n!=0) EXM_THROW(5, "%s : flush error", dictFileName)
}
int DiB_trainFiles(const char* dictFileName, unsigned maxDictSize,
const char** fileNamesTable, unsigned nbFiles,
unsigned shiftRatio)
{
void* srcBuffer;
size_t benchedSize;
size_t* fileSizes = (size_t*)malloc(nbFiles * sizeof(size_t));
unsigned long long totalSizeToLoad = DiB_getTotalFileSize(fileNamesTable, nbFiles);
const U32 dictListSize = DICTLISTSIZE;
dictItem* dictList = (dictItem*)malloc(dictListSize * sizeof(*dictList));
char mfName[20] = {0};
const char* displayName = NULL;
/* init */
benchedSize = DiB_findMaxMem(totalSizeToLoad * MEMMULT) / MEMMULT;
if ((unsigned long long)benchedSize > totalSizeToLoad) benchedSize = (size_t)totalSizeToLoad;
if (benchedSize < totalSizeToLoad)
DISPLAY("Not enough memory; training on %u MB only...\n", (unsigned)(benchedSize >> 20));
/* Memory allocation & restrictions */
srcBuffer = malloc(benchedSize+NOISELENGTH); /* + noise */
if ((!fileSizes) || (!srcBuffer) || (!dictList)) EXM_THROW(12, "not enough memory for DiB_trainFiles"); /* should not happen */
DiB_initDictItem(dictList);
/* Load input buffer */
DiB_loadFiles(srcBuffer, benchedSize, fileSizes, fileNamesTable, nbFiles);
DiB_fillNoise((char*)srcBuffer + benchedSize, NOISELENGTH); /* for end of buffer condition */
/* Train */
snprintf (mfName, sizeof(mfName), " %u files", nbFiles);
if (nbFiles > 1) displayName = mfName;
else displayName = fileNamesTable[0];
DiB_trainBuffer(dictList, dictListSize,
srcBuffer, benchedSize,
displayName,
fileSizes, nbFiles, maxDictSize,
shiftRatio);
/* display best matches */
if (g_displayLevel>= 3) {
const U32 nb = 25;
U32 u;
U32 dictContentSize = DiB_dictSize(dictList);
DISPLAYLEVEL(3, "\n %u segments found, of total size %u \n", dictList[0].pos, dictContentSize);
DISPLAYLEVEL(3, "list %u best segments \n", nb);
for (u=1; u<=nb; u++) {
U32 p = dictList[u].pos;
U32 l = dictList[u].length;
U32 d = MIN(40, l);
DISPLAYLEVEL(3, "%3u:%3u bytes at pos %8u, savings %7u bytes |",
u, l, p, dictList[u].savings);
DiB_printHex(3, (char*)srcBuffer+p, d);
DISPLAYLEVEL(3, "| \n");
} }
/* create dictionary */
{
void* dictContent;
U32 dictContentSize = DiB_dictSize(dictList);
void* dictHeader;
size_t dictHeaderSize, hSize;
BYTE* ptr;
U32 u;
/* build dict */
#define EBSIZE (2 KB)
dictHeaderSize = EBSIZE;
dictHeader = malloc(dictHeaderSize);
dictContent = malloc(dictContentSize);
if (!dictHeader || !dictContent) EXM_THROW(2, "not enough memory");
/* build dict content */
ptr = (BYTE*)dictContent + dictContentSize;
for (u=1; u<dictList->pos; u++) {
U32 l = dictList[u].length;
ptr -= l;
memcpy(ptr, (char*)srcBuffer+dictList[u].pos, l);
}
/* dictionary header */
MEM_writeLE32(dictHeader, ZSTD_DICT_MAGIC);
hSize = 4;
dictHeaderSize -= 4;
/* entropic tables */
DISPLAYLEVEL(2, "statistics ... \n");
hSize += DiB_analyzeEntropy((char*)dictHeader+4, dictHeaderSize,
srcBuffer, fileSizes, nbFiles,
dictContent, dictContentSize);
/* save dict */
{
size_t dictSize = hSize + dictContentSize;
DISPLAYLEVEL(2, "Save dictionary of size %u into file %s \n", (U32)dictSize, dictFileName);
DiB_saveDict(dictFileName, dictHeader, hSize, dictContent, dictContentSize);
//DiB_saveDict(dictFileName, NULL, 0, dictContent, dictContentSize); // content only
}
/* clean */
free(dictHeader);
free(dictContent);
}
/* clean up */
free(srcBuffer);
free(fileSizes);
free(dictList);
return 0;
}

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/*
dictBuilder.h
Copyright (C) Yann Collet 2016
GPL v2 License
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
You can contact the author at :
- zstd source repository : https://github.com/Cyan4973/zstd
- ztsd public forum : https://groups.google.com/forum/#!forum/lz4c
*/
/* *************************************
* Version
***************************************/
#define DiB_VERSION_MAJOR 0 /* for breaking interface changes */
#define DiB_VERSION_MINOR 0 /* for new (non-breaking) interface capabilities */
#define DiB_VERSION_RELEASE 1 /* for tweaks, bug-fixes, or development */
#define DiB_VERSION_NUMBER (DiB_VERSION_MAJOR *100*100 + DiB_VERSION_MINOR *100 + DiB_VERSION_RELEASE)
unsigned DiB_versionNumber (void);
/* *************************************
* Main functions
***************************************/
int DiB_trainFiles(const char* dictFileName, unsigned maxDictSize,
const char** fileNamesTable, unsigned nbFiles,
unsigned selectionLevel);
void DiB_setDisplayLevel(unsigned l);

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

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/*
* 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 */
#include <inttypes.h>
#ifndef DIVSUFSORT_API
# ifdef DIVSUFSORT_BUILD_DLL
# define DIVSUFSORT_API
# else
# define DIVSUFSORT_API
# endif
#endif
/*- Datatypes -*/
#ifndef SAUCHAR_T
#define SAUCHAR_T
typedef uint8_t sauchar_t;
#endif /* SAUCHAR_T */
#ifndef SAINT_T
#define SAINT_T
typedef int32_t saint_t;
#endif /* SAINT_T */
#ifndef SAIDX_T
#define SAIDX_T
typedef int32_t saidx_t;
#endif /* SAIDX_T */
#ifndef PRIdSAINT_T
#define PRIdSAINT_T PRId32
#endif /* PRIdSAINT_T */
#ifndef PRIdSAIDX_T
#define PRIdSAIDX_T PRId32
#endif /* PRIdSAIDX_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(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.
*/
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);
#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */
#endif /* _DIVSUFSORT_H */

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

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/*
* lfs.h for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef _LFS_H
#define _LFS_H 1
#ifdef __cplusplus
extern "C" {
#endif /* __cplusplus */
#ifndef __STRICT_ANSI__
# define LFS_OFF_T off_t
# define LFS_FOPEN fopen
# define LFS_FTELL ftello
# define LFS_FSEEK fseeko
# define LFS_PRId PRIdMAX
#else
# define LFS_OFF_T long
# define LFS_FOPEN fopen
# define LFS_FTELL ftell
# define LFS_FSEEK fseek
# define LFS_PRId "ld"
#endif
#ifndef PRIdOFF_T
# define PRIdOFF_T LFS_PRId
#endif
#ifdef __cplusplus
} /* extern "C" */
#endif /* __cplusplus */
#endif /* _LFS_H */

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/*
* sssort.c for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#include "divsufsort_private.h"
/*- Private Functions -*/
static const saint_t lg_table[256]= {
-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7
};
#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
static INLINE
saint_t
ss_ilg(saidx_t n) {
#if SS_BLOCKSIZE == 0
# if defined(BUILD_DIVSUFSORT64)
return (n >> 32) ?
((n >> 48) ?
((n >> 56) ?
56 + lg_table[(n >> 56) & 0xff] :
48 + lg_table[(n >> 48) & 0xff]) :
((n >> 40) ?
40 + lg_table[(n >> 40) & 0xff] :
32 + lg_table[(n >> 32) & 0xff])) :
((n & 0xffff0000) ?
((n & 0xff000000) ?
24 + lg_table[(n >> 24) & 0xff] :
16 + lg_table[(n >> 16) & 0xff]) :
((n & 0x0000ff00) ?
8 + lg_table[(n >> 8) & 0xff] :
0 + lg_table[(n >> 0) & 0xff]));
# else
return (n & 0xffff0000) ?
((n & 0xff000000) ?
24 + lg_table[(n >> 24) & 0xff] :
16 + lg_table[(n >> 16) & 0xff]) :
((n & 0x0000ff00) ?
8 + lg_table[(n >> 8) & 0xff] :
0 + lg_table[(n >> 0) & 0xff]);
# endif
#elif SS_BLOCKSIZE < 256
return lg_table[n];
#else
return (n & 0xff00) ?
8 + lg_table[(n >> 8) & 0xff] :
0 + lg_table[(n >> 0) & 0xff];
#endif
}
#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
#if SS_BLOCKSIZE != 0
static const saint_t sqq_table[256] = {
0, 16, 22, 27, 32, 35, 39, 42, 45, 48, 50, 53, 55, 57, 59, 61,
64, 65, 67, 69, 71, 73, 75, 76, 78, 80, 81, 83, 84, 86, 87, 89,
90, 91, 93, 94, 96, 97, 98, 99, 101, 102, 103, 104, 106, 107, 108, 109,
110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126,
128, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
143, 144, 144, 145, 146, 147, 148, 149, 150, 150, 151, 152, 153, 154, 155, 155,
156, 157, 158, 159, 160, 160, 161, 162, 163, 163, 164, 165, 166, 167, 167, 168,
169, 170, 170, 171, 172, 173, 173, 174, 175, 176, 176, 177, 178, 178, 179, 180,
181, 181, 182, 183, 183, 184, 185, 185, 186, 187, 187, 188, 189, 189, 190, 191,
192, 192, 193, 193, 194, 195, 195, 196, 197, 197, 198, 199, 199, 200, 201, 201,
202, 203, 203, 204, 204, 205, 206, 206, 207, 208, 208, 209, 209, 210, 211, 211,
212, 212, 213, 214, 214, 215, 215, 216, 217, 217, 218, 218, 219, 219, 220, 221,
221, 222, 222, 223, 224, 224, 225, 225, 226, 226, 227, 227, 228, 229, 229, 230,
230, 231, 231, 232, 232, 233, 234, 234, 235, 235, 236, 236, 237, 237, 238, 238,
239, 240, 240, 241, 241, 242, 242, 243, 243, 244, 244, 245, 245, 246, 246, 247,
247, 248, 248, 249, 249, 250, 250, 251, 251, 252, 252, 253, 253, 254, 254, 255
};
static INLINE
saidx_t
ss_isqrt(saidx_t x) {
saidx_t y, e;
if(x >= (SS_BLOCKSIZE * SS_BLOCKSIZE)) { return SS_BLOCKSIZE; }
e = (x & 0xffff0000) ?
((x & 0xff000000) ?
24 + lg_table[(x >> 24) & 0xff] :
16 + lg_table[(x >> 16) & 0xff]) :
((x & 0x0000ff00) ?
8 + lg_table[(x >> 8) & 0xff] :
0 + lg_table[(x >> 0) & 0xff]);
if(e >= 16) {
y = sqq_table[x >> ((e - 6) - (e & 1))] << ((e >> 1) - 7);
if(e >= 24) { y = (y + 1 + x / y) >> 1; }
y = (y + 1 + x / y) >> 1;
} else if(e >= 8) {
y = (sqq_table[x >> ((e - 6) - (e & 1))] >> (7 - (e >> 1))) + 1;
} else {
return sqq_table[x] >> 4;
}
return (x < (y * y)) ? y - 1 : y;
}
#endif /* SS_BLOCKSIZE != 0 */
/*---------------------------------------------------------------------------*/
/* Compares two suffixes. */
static INLINE
saint_t
ss_compare(const sauchar_t *T,
const saidx_t *p1, const saidx_t *p2,
saidx_t depth) {
const sauchar_t *U1, *U2, *U1n, *U2n;
for(U1 = T + depth + *p1,
U2 = T + depth + *p2,
U1n = T + *(p1 + 1) + 2,
U2n = T + *(p2 + 1) + 2;
(U1 < U1n) && (U2 < U2n) && (*U1 == *U2);
++U1, ++U2) {
}
return U1 < U1n ?
(U2 < U2n ? *U1 - *U2 : 1) :
(U2 < U2n ? -1 : 0);
}
/*---------------------------------------------------------------------------*/
#if (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1)
/* Insertionsort for small size groups */
static
void
ss_insertionsort(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *last, saidx_t depth) {
saidx_t *i, *j;
saidx_t t;
saint_t r;
for(i = last - 2; first <= i; --i) {
for(t = *i, j = i + 1; 0 < (r = ss_compare(T, PA + t, PA + *j, depth));) {
do { *(j - 1) = *j; } while((++j < last) && (*j < 0));
if(last <= j) { break; }
}
if(r == 0) { *j = ~*j; }
*(j - 1) = t;
}
}
#endif /* (SS_BLOCKSIZE != 1) && (SS_INSERTIONSORT_THRESHOLD != 1) */
/*---------------------------------------------------------------------------*/
#if (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE)
static INLINE
void
ss_fixdown(const sauchar_t *Td, const saidx_t *PA,
saidx_t *SA, saidx_t i, saidx_t size) {
saidx_t j, k;
saidx_t v;
saint_t c, d, e;
for(v = SA[i], c = Td[PA[v]]; (j = 2 * i + 1) < size; SA[i] = SA[k], i = k) {
d = Td[PA[SA[k = j++]]];
if(d < (e = Td[PA[SA[j]]])) { k = j; d = e; }
if(d <= c) { break; }
}
SA[i] = v;
}
/* Simple top-down heapsort. */
static
void
ss_heapsort(const sauchar_t *Td, const saidx_t *PA, saidx_t *SA, saidx_t size) {
saidx_t i, m;
saidx_t t;
m = size;
if((size % 2) == 0) {
m--;
if(Td[PA[SA[m / 2]]] < Td[PA[SA[m]]]) { SWAP(SA[m], SA[m / 2]); }
}
for(i = m / 2 - 1; 0 <= i; --i) { ss_fixdown(Td, PA, SA, i, m); }
if((size % 2) == 0) { SWAP(SA[0], SA[m]); ss_fixdown(Td, PA, SA, 0, m); }
for(i = m - 1; 0 < i; --i) {
t = SA[0], SA[0] = SA[i];
ss_fixdown(Td, PA, SA, 0, i);
SA[i] = t;
}
}
/*---------------------------------------------------------------------------*/
/* Returns the median of three elements. */
static INLINE
saidx_t *
ss_median3(const sauchar_t *Td, const saidx_t *PA,
saidx_t *v1, saidx_t *v2, saidx_t *v3) {
saidx_t *t;
if(Td[PA[*v1]] > Td[PA[*v2]]) { SWAP(v1, v2); }
if(Td[PA[*v2]] > Td[PA[*v3]]) {
if(Td[PA[*v1]] > Td[PA[*v3]]) { return v1; }
else { return v3; }
}
return v2;
}
/* Returns the median of five elements. */
static INLINE
saidx_t *
ss_median5(const sauchar_t *Td, const saidx_t *PA,
saidx_t *v1, saidx_t *v2, saidx_t *v3, saidx_t *v4, saidx_t *v5) {
saidx_t *t;
if(Td[PA[*v2]] > Td[PA[*v3]]) { SWAP(v2, v3); }
if(Td[PA[*v4]] > Td[PA[*v5]]) { SWAP(v4, v5); }
if(Td[PA[*v2]] > Td[PA[*v4]]) { SWAP(v2, v4); SWAP(v3, v5); }
if(Td[PA[*v1]] > Td[PA[*v3]]) { SWAP(v1, v3); }
if(Td[PA[*v1]] > Td[PA[*v4]]) { SWAP(v1, v4); SWAP(v3, v5); }
if(Td[PA[*v3]] > Td[PA[*v4]]) { return v4; }
return v3;
}
/* Returns the pivot element. */
static INLINE
saidx_t *
ss_pivot(const sauchar_t *Td, const saidx_t *PA, saidx_t *first, saidx_t *last) {
saidx_t *middle;
saidx_t t;
t = last - first;
middle = first + t / 2;
if(t <= 512) {
if(t <= 32) {
return ss_median3(Td, PA, first, middle, last - 1);
} else {
t >>= 2;
return ss_median5(Td, PA, first, first + t, middle, last - 1 - t, last - 1);
}
}
t >>= 3;
first = ss_median3(Td, PA, first, first + t, first + (t << 1));
middle = ss_median3(Td, PA, middle - t, middle, middle + t);
last = ss_median3(Td, PA, last - 1 - (t << 1), last - 1 - t, last - 1);
return ss_median3(Td, PA, first, middle, last);
}
/*---------------------------------------------------------------------------*/
/* Binary partition for substrings. */
static INLINE
saidx_t *
ss_partition(const saidx_t *PA,
saidx_t *first, saidx_t *last, saidx_t depth) {
saidx_t *a, *b;
saidx_t t;
for(a = first - 1, b = last;;) {
for(; (++a < b) && ((PA[*a] + depth) >= (PA[*a + 1] + 1));) { *a = ~*a; }
for(; (a < --b) && ((PA[*b] + depth) < (PA[*b + 1] + 1));) { }
if(b <= a) { break; }
t = ~*b;
*b = *a;
*a = t;
}
if(first < a) { *first = ~*first; }
return a;
}
/* Multikey introsort for medium size groups. */
static
void
ss_mintrosort(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *last,
saidx_t depth) {
#define STACK_SIZE SS_MISORT_STACKSIZE
struct { saidx_t *a, *b, c; saint_t d; } stack[STACK_SIZE];
const sauchar_t *Td;
saidx_t *a, *b, *c, *d, *e, *f;
saidx_t s, t;
saint_t ssize;
saint_t limit;
saint_t v, x = 0;
for(ssize = 0, limit = ss_ilg(last - first);;) {
if((last - first) <= SS_INSERTIONSORT_THRESHOLD) {
#if 1 < SS_INSERTIONSORT_THRESHOLD
if(1 < (last - first)) { ss_insertionsort(T, PA, first, last, depth); }
#endif
STACK_POP(first, last, depth, limit);
continue;
}
Td = T + depth;
if(limit-- == 0) { ss_heapsort(Td, PA, first, last - first); }
if(limit < 0) {
for(a = first + 1, v = Td[PA[*first]]; a < last; ++a) {
if((x = Td[PA[*a]]) != v) {
if(1 < (a - first)) { break; }
v = x;
first = a;
}
}
if(Td[PA[*first] - 1] < v) {
first = ss_partition(PA, first, a, depth);
}
if((a - first) <= (last - a)) {
if(1 < (a - first)) {
STACK_PUSH(a, last, depth, -1);
last = a, depth += 1, limit = ss_ilg(a - first);
} else {
first = a, limit = -1;
}
} else {
if(1 < (last - a)) {
STACK_PUSH(first, a, depth + 1, ss_ilg(a - first));
first = a, limit = -1;
} else {
last = a, depth += 1, limit = ss_ilg(a - first);
}
}
continue;
}
/* choose pivot */
a = ss_pivot(Td, PA, first, last);
v = Td[PA[*a]];
SWAP(*first, *a);
/* partition */
for(b = first; (++b < last) && ((x = Td[PA[*b]]) == v);) { }
if(((a = b) < last) && (x < v)) {
for(; (++b < last) && ((x = Td[PA[*b]]) <= v);) {
if(x == v) { SWAP(*b, *a); ++a; }
}
}
for(c = last; (b < --c) && ((x = Td[PA[*c]]) == v);) { }
if((b < (d = c)) && (x > v)) {
for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
if(x == v) { SWAP(*c, *d); --d; }
}
}
for(; b < c;) {
SWAP(*b, *c);
for(; (++b < c) && ((x = Td[PA[*b]]) <= v);) {
if(x == v) { SWAP(*b, *a); ++a; }
}
for(; (b < --c) && ((x = Td[PA[*c]]) >= v);) {
if(x == v) { SWAP(*c, *d); --d; }
}
}
if(a <= d) {
c = b - 1;
if((s = a - first) > (t = b - a)) { s = t; }
for(e = first, f = b - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
if((s = d - c) > (t = last - d - 1)) { s = t; }
for(e = b, f = last - s; 0 < s; --s, ++e, ++f) { SWAP(*e, *f); }
a = first + (b - a), c = last - (d - c);
b = (v <= Td[PA[*a] - 1]) ? a : ss_partition(PA, a, c, depth);
if((a - first) <= (last - c)) {
if((last - c) <= (c - b)) {
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
STACK_PUSH(c, last, depth, limit);
last = a;
} else if((a - first) <= (c - b)) {
STACK_PUSH(c, last, depth, limit);
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
last = a;
} else {
STACK_PUSH(c, last, depth, limit);
STACK_PUSH(first, a, depth, limit);
first = b, last = c, depth += 1, limit = ss_ilg(c - b);
}
} else {
if((a - first) <= (c - b)) {
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
STACK_PUSH(first, a, depth, limit);
first = c;
} else if((last - c) <= (c - b)) {
STACK_PUSH(first, a, depth, limit);
STACK_PUSH(b, c, depth + 1, ss_ilg(c - b));
first = c;
} else {
STACK_PUSH(first, a, depth, limit);
STACK_PUSH(c, last, depth, limit);
first = b, last = c, depth += 1, limit = ss_ilg(c - b);
}
}
} else {
limit += 1;
if(Td[PA[*first] - 1] < v) {
first = ss_partition(PA, first, last, depth);
limit = ss_ilg(last - first);
}
depth += 1;
}
}
#undef STACK_SIZE
}
#endif /* (SS_BLOCKSIZE == 0) || (SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE) */
/*---------------------------------------------------------------------------*/
#if SS_BLOCKSIZE != 0
static INLINE
void
ss_blockswap(saidx_t *a, saidx_t *b, saidx_t n) {
saidx_t t;
for(; 0 < n; --n, ++a, ++b) {
t = *a, *a = *b, *b = t;
}
}
static INLINE
void
ss_rotate(saidx_t *first, saidx_t *middle, saidx_t *last) {
saidx_t *a, *b, t;
saidx_t l, r;
l = middle - first, r = last - middle;
for(; (0 < l) && (0 < r);) {
if(l == r) { ss_blockswap(first, middle, l); break; }
if(l < r) {
a = last - 1, b = middle - 1;
t = *a;
do {
*a-- = *b, *b-- = *a;
if(b < first) {
*a = t;
last = a;
if((r -= l + 1) <= l) { break; }
a -= 1, b = middle - 1;
t = *a;
}
} while(1);
} else {
a = first, b = middle;
t = *a;
do {
*a++ = *b, *b++ = *a;
if(last <= b) {
*a = t;
first = a + 1;
if((l -= r + 1) <= r) { break; }
a += 1, b = middle;
t = *a;
}
} while(1);
}
}
}
/*---------------------------------------------------------------------------*/
static
void
ss_inplacemerge(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *middle, saidx_t *last,
saidx_t depth) {
const saidx_t *p;
saidx_t *a, *b;
saidx_t len, half;
saint_t q, r;
saint_t x;
for(;;) {
if(*(last - 1) < 0) { x = 1; p = PA + ~*(last - 1); }
else { x = 0; p = PA + *(last - 1); }
for(a = first, len = middle - first, half = len >> 1, r = -1;
0 < len;
len = half, half >>= 1) {
b = a + half;
q = ss_compare(T, PA + ((0 <= *b) ? *b : ~*b), p, depth);
if(q < 0) {
a = b + 1;
half -= (len & 1) ^ 1;
} else {
r = q;
}
}
if(a < middle) {
if(r == 0) { *a = ~*a; }
ss_rotate(a, middle, last);
last -= middle - a;
middle = a;
if(first == middle) { break; }
}
--last;
if(x != 0) { while(*--last < 0) { } }
if(middle == last) { break; }
}
}
/*---------------------------------------------------------------------------*/
/* Merge-forward with internal buffer. */
static
void
ss_mergeforward(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *middle, saidx_t *last,
saidx_t *buf, saidx_t depth) {
saidx_t *a, *b, *c, *bufend;
saidx_t t;
saint_t r;
bufend = buf + (middle - first) - 1;
ss_blockswap(buf, first, middle - first);
for(t = *(a = first), b = buf, c = middle;;) {
r = ss_compare(T, PA + *b, PA + *c, depth);
if(r < 0) {
do {
*a++ = *b;
if(bufend <= b) { *bufend = t; return; }
*b++ = *a;
} while(*b < 0);
} else if(r > 0) {
do {
*a++ = *c, *c++ = *a;
if(last <= c) {
while(b < bufend) { *a++ = *b, *b++ = *a; }
*a = *b, *b = t;
return;
}
} while(*c < 0);
} else {
*c = ~*c;
do {
*a++ = *b;
if(bufend <= b) { *bufend = t; return; }
*b++ = *a;
} while(*b < 0);
do {
*a++ = *c, *c++ = *a;
if(last <= c) {
while(b < bufend) { *a++ = *b, *b++ = *a; }
*a = *b, *b = t;
return;
}
} while(*c < 0);
}
}
}
/* Merge-backward with internal buffer. */
static
void
ss_mergebackward(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *middle, saidx_t *last,
saidx_t *buf, saidx_t depth) {
const saidx_t *p1, *p2;
saidx_t *a, *b, *c, *bufend;
saidx_t t;
saint_t r;
saint_t x;
bufend = buf + (last - middle) - 1;
ss_blockswap(buf, middle, last - middle);
x = 0;
if(*bufend < 0) { p1 = PA + ~*bufend; x |= 1; }
else { p1 = PA + *bufend; }
if(*(middle - 1) < 0) { p2 = PA + ~*(middle - 1); x |= 2; }
else { p2 = PA + *(middle - 1); }
for(t = *(a = last - 1), b = bufend, c = middle - 1;;) {
r = ss_compare(T, p1, p2, depth);
if(0 < r) {
if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
*a-- = *b;
if(b <= buf) { *buf = t; break; }
*b-- = *a;
if(*b < 0) { p1 = PA + ~*b; x |= 1; }
else { p1 = PA + *b; }
} else if(r < 0) {
if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
*a-- = *c, *c-- = *a;
if(c < first) {
while(buf < b) { *a-- = *b, *b-- = *a; }
*a = *b, *b = t;
break;
}
if(*c < 0) { p2 = PA + ~*c; x |= 2; }
else { p2 = PA + *c; }
} else {
if(x & 1) { do { *a-- = *b, *b-- = *a; } while(*b < 0); x ^= 1; }
*a-- = ~*b;
if(b <= buf) { *buf = t; break; }
*b-- = *a;
if(x & 2) { do { *a-- = *c, *c-- = *a; } while(*c < 0); x ^= 2; }
*a-- = *c, *c-- = *a;
if(c < first) {
while(buf < b) { *a-- = *b, *b-- = *a; }
*a = *b, *b = t;
break;
}
if(*b < 0) { p1 = PA + ~*b; x |= 1; }
else { p1 = PA + *b; }
if(*c < 0) { p2 = PA + ~*c; x |= 2; }
else { p2 = PA + *c; }
}
}
}
/* D&C based merge. */
static
void
ss_swapmerge(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *middle, saidx_t *last,
saidx_t *buf, saidx_t bufsize, saidx_t depth) {
#define STACK_SIZE SS_SMERGE_STACKSIZE
#define GETIDX(a) ((0 <= (a)) ? (a) : (~(a)))
#define MERGE_CHECK(a, b, c)\
do {\
if(((c) & 1) ||\
(((c) & 2) && (ss_compare(T, PA + GETIDX(*((a) - 1)), PA + *(a), depth) == 0))) {\
*(a) = ~*(a);\
}\
if(((c) & 4) && ((ss_compare(T, PA + GETIDX(*((b) - 1)), PA + *(b), depth) == 0))) {\
*(b) = ~*(b);\
}\
} while(0)
struct { saidx_t *a, *b, *c; saint_t d; } stack[STACK_SIZE];
saidx_t *l, *r, *lm, *rm;
saidx_t m, len, half;
saint_t ssize;
saint_t check, next;
for(check = 0, ssize = 0;;) {
if((last - middle) <= bufsize) {
if((first < middle) && (middle < last)) {
ss_mergebackward(T, PA, first, middle, last, buf, depth);
}
MERGE_CHECK(first, last, check);
STACK_POP(first, middle, last, check);
continue;
}
if((middle - first) <= bufsize) {
if(first < middle) {
ss_mergeforward(T, PA, first, middle, last, buf, depth);
}
MERGE_CHECK(first, last, check);
STACK_POP(first, middle, last, check);
continue;
}
for(m = 0, len = MIN(middle - first, last - middle), half = len >> 1;
0 < len;
len = half, half >>= 1) {
if(ss_compare(T, PA + GETIDX(*(middle + m + half)),
PA + GETIDX(*(middle - m - half - 1)), depth) < 0) {
m += half + 1;
half -= (len & 1) ^ 1;
}
}
if(0 < m) {
lm = middle - m, rm = middle + m;
ss_blockswap(lm, middle, m);
l = r = middle, next = 0;
if(rm < last) {
if(*rm < 0) {
*rm = ~*rm;
if(first < lm) { for(; *--l < 0;) { } next |= 4; }
next |= 1;
} else if(first < lm) {
for(; *r < 0; ++r) { }
next |= 2;
}
}
if((l - first) <= (last - r)) {
STACK_PUSH(r, rm, last, (next & 3) | (check & 4));
middle = lm, last = l, check = (check & 3) | (next & 4);
} else {
if((next & 2) && (r == middle)) { next ^= 6; }
STACK_PUSH(first, lm, l, (check & 3) | (next & 4));
first = r, middle = rm, check = (next & 3) | (check & 4);
}
} else {
if(ss_compare(T, PA + GETIDX(*(middle - 1)), PA + *middle, depth) == 0) {
*middle = ~*middle;
}
MERGE_CHECK(first, last, check);
STACK_POP(first, middle, last, check);
}
}
#undef STACK_SIZE
}
#endif /* SS_BLOCKSIZE != 0 */
/*---------------------------------------------------------------------------*/
/*- Function -*/
/* Substring sort */
void
sssort(const sauchar_t *T, const saidx_t *PA,
saidx_t *first, saidx_t *last,
saidx_t *buf, saidx_t bufsize,
saidx_t depth, saidx_t n, saint_t lastsuffix) {
saidx_t *a;
#if SS_BLOCKSIZE != 0
saidx_t *b, *middle, *curbuf;
saidx_t j, k, curbufsize, limit;
#endif
saidx_t i;
if(lastsuffix != 0) { ++first; }
#if SS_BLOCKSIZE == 0
ss_mintrosort(T, PA, first, last, depth);
#else
if((bufsize < SS_BLOCKSIZE) &&
(bufsize < (last - first)) &&
(bufsize < (limit = ss_isqrt(last - first)))) {
if(SS_BLOCKSIZE < limit) { limit = SS_BLOCKSIZE; }
buf = middle = last - limit, bufsize = limit;
} else {
middle = last, limit = 0;
}
for(a = first, i = 0; SS_BLOCKSIZE < (middle - a); a += SS_BLOCKSIZE, ++i) {
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
ss_mintrosort(T, PA, a, a + SS_BLOCKSIZE, depth);
#elif 1 < SS_BLOCKSIZE
ss_insertionsort(T, PA, a, a + SS_BLOCKSIZE, depth);
#endif
curbufsize = last - (a + SS_BLOCKSIZE);
curbuf = a + SS_BLOCKSIZE;
if(curbufsize <= bufsize) { curbufsize = bufsize, curbuf = buf; }
for(b = a, k = SS_BLOCKSIZE, j = i; j & 1; b -= k, k <<= 1, j >>= 1) {
ss_swapmerge(T, PA, b - k, b, b + k, curbuf, curbufsize, depth);
}
}
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
ss_mintrosort(T, PA, a, middle, depth);
#elif 1 < SS_BLOCKSIZE
ss_insertionsort(T, PA, a, middle, depth);
#endif
for(k = SS_BLOCKSIZE; i != 0; k <<= 1, i >>= 1) {
if(i & 1) {
ss_swapmerge(T, PA, a - k, a, middle, buf, bufsize, depth);
a -= k;
}
}
if(limit != 0) {
#if SS_INSERTIONSORT_THRESHOLD < SS_BLOCKSIZE
ss_mintrosort(T, PA, middle, last, depth);
#elif 1 < SS_BLOCKSIZE
ss_insertionsort(T, PA, middle, last, depth);
#endif
ss_inplacemerge(T, PA, first, middle, last, depth);
}
#endif
if(lastsuffix != 0) {
/* Insert last type B* suffix. */
saidx_t PAi[2]; PAi[0] = PA[*(first - 1)], PAi[1] = n - 2;
for(a = first, i = *(first - 1);
(a < last) && ((*a < 0) || (0 < ss_compare(T, &(PAi[0]), PA + *a, depth)));
++a) {
*(a - 1) = *a;
}
*(a - 1) = i;
}
}

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

381
dictBuilder/utils.c Normal file
View File

@ -0,0 +1,381 @@
/*
* utils.c for libdivsufsort
* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
#include "divsufsort_private.h"
/*- Private Function -*/
/* Binary search for inverse bwt. */
static
saidx_t
binarysearch_lower(const saidx_t *A, saidx_t size, saidx_t value) {
saidx_t half, i;
for(i = 0, half = size >> 1;
0 < size;
size = half, half >>= 1) {
if(A[i + half] < value) {
i += half + 1;
half -= (size & 1) ^ 1;
}
}
return i;
}
/*- Functions -*/
/* Burrows-Wheeler transform. */
saint_t
bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *SA,
saidx_t n, saidx_t *idx) {
saidx_t *A, i, j, p, t;
saint_t c;
/* Check arguments. */
if((T == NULL) || (U == NULL) || (n < 0) || (idx == NULL)) { return -1; }
if(n <= 1) {
if(n == 1) { U[0] = T[0]; }
*idx = n;
return 0;
}
if((A = SA) == NULL) {
i = divbwt(T, U, NULL, n);
if(0 <= i) { *idx = i; i = 0; }
return (saint_t)i;
}
/* BW transform. */
if(T == U) {
t = n;
for(i = 0, j = 0; i < n; ++i) {
p = t - 1;
t = A[i];
if(0 <= p) {
c = T[j];
U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
A[j] = c;
j++;
} else {
*idx = i;
}
}
p = t - 1;
if(0 <= p) {
c = T[j];
U[j] = (j <= p) ? T[p] : (sauchar_t)A[p];
A[j] = c;
} else {
*idx = i;
}
} else {
U[0] = T[n - 1];
for(i = 0; A[i] != 0; ++i) { U[i + 1] = T[A[i] - 1]; }
*idx = i + 1;
for(++i; i < n; ++i) { U[i] = T[A[i] - 1]; }
}
if(SA == NULL) {
/* Deallocate memory. */
free(A);
}
return 0;
}
/* Inverse Burrows-Wheeler transform. */
saint_t
inverse_bw_transform(const sauchar_t *T, sauchar_t *U, saidx_t *A,
saidx_t n, saidx_t idx) {
saidx_t C[ALPHABET_SIZE];
sauchar_t D[ALPHABET_SIZE];
saidx_t *B;
saidx_t i, p;
saint_t c, d;
/* Check arguments. */
if((T == NULL) || (U == NULL) || (n < 0) || (idx < 0) ||
(n < idx) || ((0 < n) && (idx == 0))) {
return -1;
}
if(n <= 1) { return 0; }
if((B = A) == NULL) {
/* Allocate n*sizeof(saidx_t) bytes of memory. */
if((B = (saidx_t *)malloc((size_t)n * sizeof(saidx_t))) == NULL) { return -2; }
}
/* Inverse BW transform. */
for(c = 0; c < ALPHABET_SIZE; ++c) { C[c] = 0; }
for(i = 0; i < n; ++i) { ++C[T[i]]; }
for(c = 0, d = 0, i = 0; c < ALPHABET_SIZE; ++c) {
p = C[c];
if(0 < p) {
C[c] = i;
D[d++] = (sauchar_t)c;
i += p;
}
}
for(i = 0; i < idx; ++i) { B[C[T[i]]++] = i; }
for( ; i < n; ++i) { B[C[T[i]]++] = i + 1; }
for(c = 0; c < d; ++c) { C[c] = C[D[c]]; }
for(i = 0, p = idx; i < n; ++i) {
U[i] = D[binarysearch_lower(C, d, p)];
p = B[p - 1];
}
if(A == NULL) {
/* Deallocate memory. */
free(B);
}
return 0;
}
/* Checks the suffix array SA of the string T. */
saint_t
sufcheck(const sauchar_t *T, const saidx_t *SA,
saidx_t n, saint_t verbose) {
saidx_t C[ALPHABET_SIZE];
saidx_t i, p, q, t;
saint_t c;
if(verbose) { fprintf(stderr, "sufcheck: "); }
/* Check arguments. */
if((T == NULL) || (SA == NULL) || (n < 0)) {
if(verbose) { fprintf(stderr, "Invalid arguments.\n"); }
return -1;
}
if(n == 0) {
if(verbose) { fprintf(stderr, "Done.\n"); }
return 0;
}
/* check range: [0..n-1] */
for(i = 0; i < n; ++i) {
if((SA[i] < 0) || (n <= SA[i])) {
if(verbose) {
fprintf(stderr, "Out of the range [0,%" PRIdSAIDX_T "].\n"
" SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
n - 1, i, SA[i]);
}
return -2;
}
}
/* check first characters. */
for(i = 1; i < n; ++i) {
if(T[SA[i - 1]] > T[SA[i]]) {
if(verbose) {
fprintf(stderr, "Suffixes in wrong order.\n"
" T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d"
" > T[SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "]=%d\n",
i - 1, SA[i - 1], T[SA[i - 1]], i, SA[i], T[SA[i]]);
}
return -3;
}
}
/* check suffixes. */
for(i = 0; i < ALPHABET_SIZE; ++i) { C[i] = 0; }
for(i = 0; i < n; ++i) { ++C[T[i]]; }
for(i = 0, p = 0; i < ALPHABET_SIZE; ++i) {
t = C[i];
C[i] = p;
p += t;
}
q = C[T[n - 1]];
C[T[n - 1]] += 1;
for(i = 0; i < n; ++i) {
p = SA[i];
if(0 < p) {
c = T[--p];
t = C[c];
} else {
c = T[p = n - 1];
t = q;
}
if((t < 0) || (p != SA[t])) {
if(verbose) {
fprintf(stderr, "Suffix in wrong position.\n"
" SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T " or\n"
" SA[%" PRIdSAIDX_T "]=%" PRIdSAIDX_T "\n",
t, (0 <= t) ? SA[t] : -1, i, SA[i]);
}
return -4;
}
if(t != q) {
++C[c];
if((n <= C[c]) || (T[SA[C[c]]] != c)) { C[c] = -1; }
}
}
if(1 <= verbose) { fprintf(stderr, "Done.\n"); }
return 0;
}
static
int
_compare(const sauchar_t *T, saidx_t Tsize,
const sauchar_t *P, saidx_t Psize,
saidx_t suf, saidx_t *match) {
saidx_t i, j;
saint_t r;
for(i = suf + *match, j = *match, r = 0;
(i < Tsize) && (j < Psize) && ((r = T[i] - P[j]) == 0); ++i, ++j) { }
*match = j;
return (r == 0) ? -(j != Psize) : r;
}
/* Search for the pattern P in the string T. */
saidx_t
sa_search(const sauchar_t *T, saidx_t Tsize,
const sauchar_t *P, saidx_t Psize,
const saidx_t *SA, saidx_t SAsize,
saidx_t *idx) {
saidx_t size, lsize, rsize, half;
saidx_t match, lmatch, rmatch;
saidx_t llmatch, lrmatch, rlmatch, rrmatch;
saidx_t i, j, k;
saint_t r;
if(idx != NULL) { *idx = -1; }
if((T == NULL) || (P == NULL) || (SA == NULL) ||
(Tsize < 0) || (Psize < 0) || (SAsize < 0)) { return -1; }
if((Tsize == 0) || (SAsize == 0)) { return 0; }
if(Psize == 0) { if(idx != NULL) { *idx = 0; } return SAsize; }
for(i = j = k = 0, lmatch = rmatch = 0, size = SAsize, half = size >> 1;
0 < size;
size = half, half >>= 1) {
match = MIN(lmatch, rmatch);
r = _compare(T, Tsize, P, Psize, SA[i + half], &match);
if(r < 0) {
i += half + 1;
half -= (size & 1) ^ 1;
lmatch = match;
} else if(r > 0) {
rmatch = match;
} else {
lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
/* left part */
for(llmatch = lmatch, lrmatch = match, half = lsize >> 1;
0 < lsize;
lsize = half, half >>= 1) {
lmatch = MIN(llmatch, lrmatch);
r = _compare(T, Tsize, P, Psize, SA[j + half], &lmatch);
if(r < 0) {
j += half + 1;
half -= (lsize & 1) ^ 1;
llmatch = lmatch;
} else {
lrmatch = lmatch;
}
}
/* right part */
for(rlmatch = match, rrmatch = rmatch, half = rsize >> 1;
0 < rsize;
rsize = half, half >>= 1) {
rmatch = MIN(rlmatch, rrmatch);
r = _compare(T, Tsize, P, Psize, SA[k + half], &rmatch);
if(r <= 0) {
k += half + 1;
half -= (rsize & 1) ^ 1;
rlmatch = rmatch;
} else {
rrmatch = rmatch;
}
}
break;
}
}
if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
return k - j;
}
/* Search for the character c in the string T. */
saidx_t
sa_simplesearch(const sauchar_t *T, saidx_t Tsize,
const saidx_t *SA, saidx_t SAsize,
saint_t c, saidx_t *idx) {
saidx_t size, lsize, rsize, half;
saidx_t i, j, k, p;
saint_t r;
if(idx != NULL) { *idx = -1; }
if((T == NULL) || (SA == NULL) || (Tsize < 0) || (SAsize < 0)) { return -1; }
if((Tsize == 0) || (SAsize == 0)) { return 0; }
for(i = j = k = 0, size = SAsize, half = size >> 1;
0 < size;
size = half, half >>= 1) {
p = SA[i + half];
r = (p < Tsize) ? T[p] - c : -1;
if(r < 0) {
i += half + 1;
half -= (size & 1) ^ 1;
} else if(r == 0) {
lsize = half, j = i, rsize = size - half - 1, k = i + half + 1;
/* left part */
for(half = lsize >> 1;
0 < lsize;
lsize = half, half >>= 1) {
p = SA[j + half];
r = (p < Tsize) ? T[p] - c : -1;
if(r < 0) {
j += half + 1;
half -= (lsize & 1) ^ 1;
}
}
/* right part */
for(half = rsize >> 1;
0 < rsize;
rsize = half, half >>= 1) {
p = SA[k + half];
r = (p < Tsize) ? T[p] - c : -1;
if(r <= 0) {
k += half + 1;
half -= (rsize & 1) ^ 1;
}
}
break;
}
}
if(idx != NULL) { *idx = (0 < (k - j)) ? j : i; }
return k - j;
}