commit f0eba24f897981c6cefb439be840440bbc217c3b Author: lib Date: Thu Jun 22 15:57:42 2023 -0500 Initial commit diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 0000000..9cd1b4b --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,31 @@ +cmake_minimum_required(VERSION 2.8) +project(GKlib C) + +option(BUILD_SHARED_LIBS "Build shared libraries (.dll/.so) instead of static ones (.lib/.a)" OFF) + +get_filename_component(abs "." ABSOLUTE) +set(GKLIB_PATH ${abs}) +unset(abs) +include(GKlibSystem.cmake) + +include_directories(".") +if(MSVC) + include_directories("win32") + file(GLOB win32_sources RELATIVE "win32" "*.c") +else(MSVC) + set(win32_sources, "") +endif(MSVC) + +add_library(GKlib ${GKlib_sources} ${win32_sources}) + +if(UNIX) + target_link_libraries(GKlib m) +endif(UNIX) + +include_directories("test") +add_subdirectory("test") + +install(TARGETS GKlib + ARCHIVE DESTINATION lib/${LINSTALL_PATH} + LIBRARY DESTINATION lib/${LINSTALL_PATH}) +install(FILES ${GKlib_includes} DESTINATION include/${HINSTALL_PATH}) diff --git a/DEPENDENCIES b/DEPENDENCIES new file mode 100644 index 0000000..e69de29 diff --git a/GKlib.h b/GKlib.h new file mode 100644 index 0000000..9278fe4 --- /dev/null +++ b/GKlib.h @@ -0,0 +1,85 @@ +/* + * GKlib.h + * + * George's library of most frequently used routines + * + * $Id: GKlib.h 14866 2013-08-03 16:40:04Z karypis $ + * + */ + +#ifndef _GKLIB_H_ +#define _GKLIB_H_ 1 + +#define GKMSPACE + +#if defined(_MSC_VER) +#define __MSC__ +#endif +#if defined(__ICC) +#define __ICC__ +#endif + + +#include "gk_arch.h" /*!< This should be here, prior to the includes */ + + +/************************************************************************* +* Header file inclusion section +**************************************************************************/ +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#if defined(__WITHPCRE__) + #include +#else + #if defined(USE_GKREGEX) + #include "gkregex.h" + #else + #include + #endif /* defined(USE_GKREGEX) */ +#endif /* defined(__WITHPCRE__) */ + + + +#if defined(__OPENMP__) +#include +#endif + + + + +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#include + + +#endif /* GKlib.h */ + + diff --git a/GKlibSystem.cmake b/GKlibSystem.cmake new file mode 100644 index 0000000..31a1cf1 --- /dev/null +++ b/GKlibSystem.cmake @@ -0,0 +1,152 @@ +# Helper modules. +include(CheckFunctionExists) +include(CheckIncludeFile) + +# Setup options. +option(GDB "enable use of GDB" OFF) +option(ASSERT "turn asserts on" OFF) +option(ASSERT2 "additional assertions" OFF) +option(DEBUG "add debugging support" OFF) +option(GPROF "add gprof support" OFF) +option(VALGRIND "add valgrind support" OFF) +option(OPENMP "enable OpenMP support" OFF) +option(PCRE "enable PCRE support" OFF) +option(GKREGEX "enable GKREGEX support" OFF) +option(GKRAND "enable GKRAND support" OFF) +option(NO_X86 "enable NO_X86 support" OFF) + + +# Add compiler flags. +if(MSVC) + set(GKlib_COPTS "/Ox") + set(GKlib_COPTIONS "-DWIN32 -DMSC -D_CRT_SECURE_NO_DEPRECATE -DUSE_GKREGEX") +elseif(MINGW) + set(GKlib_COPTS "-DUSE_GKREGEX") +else() + set(GKlib_COPTIONS "-DLINUX -D_FILE_OFFSET_BITS=64") +endif(MSVC) +if(CYGWIN) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -DCYGWIN") +endif(CYGWIN) +if(CMAKE_COMPILER_IS_GNUCC) +# GCC opts. + set(GKlib_COPTIONS "${GKlib_COPTIONS} -std=c99 -fno-strict-aliasing") +if(VALGRIND) + set(GKlib_COPTIONS "${GK_COPTIONS} -march=x86-64 -mtune=generic") +else() +# -march=native is not a valid flag on PPC: +if(CMAKE_SYSTEM_PROCESSOR MATCHES "power|ppc|powerpc|ppc64|powerpc64" OR (APPLE AND CMAKE_OSX_ARCHITECTURES MATCHES "ppc|ppc64")) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -mtune=native") +else() + set(GKlib_COPTIONS "${GKlib_COPTIONS} -march=native") +endif() +endif(VALGRIND) + if(NOT MINGW) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -fPIC") + endif(NOT MINGW) +# GCC warnings. + set(GKlib_COPTIONS "${GKlib_COPTIONS} -Werror -Wall -pedantic -Wno-unused-function -Wno-unused-but-set-variable -Wno-unused-variable -Wno-unknown-pragmas -Wno-unused-label") +elseif(${CMAKE_C_COMPILER_ID} MATCHES "Sun") +# Sun insists on -xc99. + set(GKlib_COPTIONS "${GKlib_COPTIONS} -xc99") +endif(CMAKE_COMPILER_IS_GNUCC) + +# Intel compiler +if(${CMAKE_C_COMPILER_ID} MATCHES "Intel") + set(GKlib_COPTIONS "${GKlib_COPTIONS} -xHost -std=c99") +endif() + +# Find OpenMP if it is requested. +if(OPENMP) + include(FindOpenMP) + if(OPENMP_FOUND) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__OPENMP__ ${OpenMP_C_FLAGS}") + else() + message(WARNING "OpenMP was requested but support was not found") + endif(OPENMP_FOUND) +endif(OPENMP) + +# Set the CPU type +if(NO_X86) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -DNO_X86=${NO_X86}") +endif(NO_X86) + +# Add various definitions. +if(GDB) + set(GKlib_COPTS "${GKlib_COPTS} -g") + set(GKlib_COPTIONS "${GKlib_COPTIONS} -Werror") +else() + set(GKlib_COPTS "-O3") +endif(GDB) + + +if(DEBUG) + set(GKlib_COPTS "-g") + set(GKlib_COPTIONS "${GKlib_COPTIONS} -DDEBUG") +endif(DEBUG) + +if(GPROF) + set(GKlib_COPTS "-pg") +endif(GPROF) + +if(NOT ASSERT) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -DNDEBUG") +endif(NOT ASSERT) + +if(NOT ASSERT2) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -DNDEBUG2") +endif(NOT ASSERT2) + + +# Add various options +if(PCRE) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__WITHPCRE__") +endif(PCRE) + +if(GKREGEX) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -DUSE_GKREGEX") +endif(GKREGEX) + +if(GKRAND) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -DUSE_GKRAND") +endif(GKRAND) + + +# Check for features. +check_include_file(execinfo.h HAVE_EXECINFO_H) +if(HAVE_EXECINFO_H) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -DHAVE_EXECINFO_H") +endif(HAVE_EXECINFO_H) + +check_function_exists(getline HAVE_GETLINE) +if(HAVE_GETLINE) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -DHAVE_GETLINE") +endif(HAVE_GETLINE) + + +# Custom check for TLS. +if(MSVC) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__thread=__declspec(thread)") + + # This if checks if that value is cached or not. + if("${HAVE_THREADLOCALSTORAGE}" MATCHES "^${HAVE_THREADLOCALSTORAGE}$") + try_compile(HAVE_THREADLOCALSTORAGE + ${CMAKE_BINARY_DIR} + ${GKLIB_PATH}/conf/check_thread_storage.c) + if(HAVE_THREADLOCALSTORAGE) + message(STATUS "checking for thread-local storage - found") + else() + message(STATUS "checking for thread-local storage - not found") + endif() + endif() + if(NOT HAVE_THREADLOCALSTORAGE) + set(GKlib_COPTIONS "${GKlib_COPTIONS} -D__thread=") + endif() +endif() + +# Finally set the official C flags. +set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${GKlib_COPTIONS} ${GKlib_COPTS}") + +# Find GKlib sources. +file(GLOB GKlib_sources ${GKLIB_PATH}/*.c) +file(GLOB GKlib_includes ${GKLIB_PATH}/*.h) diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..b61ca6f --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,18 @@ + +Copyright & License Notice +--------------------------- + +Copyright 1995-2018, Regents of the University of Minnesota + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or +implied. See the License for the specific language governing +permissions and limitations under the License. + diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..6ac97b9 --- /dev/null +++ b/Makefile @@ -0,0 +1,87 @@ +# Configuration options. +cc = gcc +prefix = ~/local +openmp = not-set +gdb = not-set +assert = not-set +assert2 = not-set +debug = not-set +gprof = not-set +valgrind = not-set +pcre = not-set +gkregex = not-set +gkrand = not-set + + +# Basically proxies everything to the builddir cmake. +cputype = $(shell uname -m | sed "s/\\ /_/g") +systype = $(shell uname -s) + +BUILDDIR = build/$(systype)-$(cputype) + +# Process configuration options. +CONFIG_FLAGS = -DCMAKE_VERBOSE_MAKEFILE=1 +ifneq ($(gdb), not-set) + CONFIG_FLAGS += -DGDB=$(gdb) +endif +ifneq ($(assert), not-set) + CONFIG_FLAGS += -DASSERT=$(assert) +endif +ifneq ($(assert2), not-set) + CONFIG_FLAGS += -DASSERT2=$(assert2) +endif +ifneq ($(debug), not-set) + CONFIG_FLAGS += -DDEBUG=$(debug) +endif +ifneq ($(gprof), not-set) + CONFIG_FLAGS += -DGPROF=$(gprof) +endif +ifneq ($(valgrind), not-set) + CONFIG_FLAGS += -DVALGRIND=$(valgrind) +endif +ifneq ($(openmp), not-set) + CONFIG_FLAGS += -DOPENMP=$(openmp) +endif +ifneq ($(pcre), not-set) + CONFIG_FLAGS += -DPCRE=$(pcre) +endif +ifneq ($(gkregex), not-set) + CONFIG_FLAGS += -DGKREGEX=$(pcre) +endif +ifneq ($(gkrand), not-set) + CONFIG_FLAGS += -DGKRAND=$(pcre) +endif +ifneq ($(prefix), not-set) + CONFIG_FLAGS += -DCMAKE_INSTALL_PREFIX=$(prefix) +endif +ifneq ($(cc), not-set) + CONFIG_FLAGS += -DCMAKE_C_COMPILER=$(cc) +endif +ifneq ($(cputype), x86_64) + CONFIG_FLAGS += -DNO_X86=$(cputype) +endif + +define run-config +mkdir -p $(BUILDDIR) +cd $(BUILDDIR) && cmake $(CURDIR) $(CONFIG_FLAGS) +endef + +all clean install: $(BUILDDIR) + make -C $(BUILDDIR) $@ + +uninstall: + xargs rm < $(BUILDDIR)/install_manifest.txt + +$(BUILDDIR): + $(run-config) + +config: distclean + $(run-config) + +distclean: + rm -rf $(BUILDDIR) + +remake: + find . -name CMakeLists.txt -exec touch {} ';' + +.PHONY: config distclean all clean install uninstall remake diff --git a/README.md b/README.md new file mode 100644 index 0000000..f94eeea --- /dev/null +++ b/README.md @@ -0,0 +1,54 @@ +# GKlib +A library of various helper routines and frameworks used by many of the lab's software + +## Build requirements + - CMake 2.8, found at http://www.cmake.org/, as well as GNU make. + +Assuming that the above are available, two commands should suffice to +build the software: +``` +make config +make +``` + +## Configuring the build +It is primarily configured by passing options to make config. For example: +``` +make config cc=icc +``` + +would configure it to be built using icc. + +Configuration options are: +``` +cc=[compiler] - The C compiler to use [default: gcc] +prefix=[PATH] - Set the installation prefix [default: ~/local] +openmp=set - To build a version with OpenMP support +``` + + +## Building and installing +To build and install, run the following +``` +make +make install +``` + +By default, the library file, header file, and binaries will be installed in +``` +~/local/lib +~/local/include +~/local/bin +``` + +## Other make commands + make uninstall + Removes all files installed by 'make install'. + + make clean + Removes all object files but retains the configuration options. + + make distclean + Performs clean and completely removes the build directory. + + diff --git a/SETUP b/SETUP new file mode 100755 index 0000000..a1d187d --- /dev/null +++ b/SETUP @@ -0,0 +1,12 @@ +#!/usr/bin/env bash + +if [ -z "$1" ] +then + printf "Usage: setup.sh install_directory [dependencies].\n" 1>&2 + exit 1 +fi + +cd $(dirname $0) +libname=$(basename $(pwd)) +make config shared=1 prefix="$1" +make install diff --git a/b64.c b/b64.c new file mode 100644 index 0000000..afacd68 --- /dev/null +++ b/b64.c @@ -0,0 +1,95 @@ +/*! +\file b64.c +\brief This file contains some simple 8bit-to-6bit encoding/deconding routines + +Most of these routines are outdated and should be converted using glibc's equivalent +routines. + +\date Started 2/22/05 +\author George +\version\verbatim $Id: b64.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim + +\verbatim +$Copyright$ +$License$ +\endverbatim + +*/ + + +#include "GKlib.h" + +#define B64OFFSET 48 /* This is the '0' number */ + + +/****************************************************************************** +* Encode 3 '8-bit' binary bytes as 4 '6-bit' characters +*******************************************************************************/ +void encodeblock(unsigned char *in, unsigned char *out) +{ + out[0] = (in[0] >> 2); + out[1] = (((in[0] & 0x03) << 4) | (in[1] >> 4)); + out[2] = (((in[1] & 0x0f) << 2) | (in[2] >> 6)); + out[3] = (in[2] & 0x3f); + + out[0] += B64OFFSET; + out[1] += B64OFFSET; + out[2] += B64OFFSET; + out[3] += B64OFFSET; + +// printf("%c %c %c %c %2x %2x %2x %2x %2x %2x %2x\n", out[0], out[1], out[2], out[3], out[0], out[1], out[2], out[3], in[0], in[1], in[2]); +} + +/****************************************************************************** +* Decode 4 '6-bit' characters into 3 '8-bit' binary bytes +*******************************************************************************/ +void decodeblock(unsigned char *in, unsigned char *out) +{ + in[0] -= B64OFFSET; + in[1] -= B64OFFSET; + in[2] -= B64OFFSET; + in[3] -= B64OFFSET; + + out[0] = (in[0] << 2 | in[1] >> 4); + out[1] = (in[1] << 4 | in[2] >> 2); + out[2] = (in[2] << 6 | in[3]); +} + + +/****************************************************************************** +* This function encodes an input array of bytes into a base64 encoding. Memory +* for the output array is assumed to have been allocated by the calling program +* and be sufficiently large. The output string is NULL terminated. +*******************************************************************************/ +void GKEncodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer) +{ + int i, j; + + if (nbytes%3 != 0) + gk_errexit(SIGERR, "GKEncodeBase64: Input buffer size should be a multiple of 3! (%d)\n", nbytes); + + for (j=0, i=0; i + + + +/*************************************************************************/ +/*! Use the templates to generate BLAS routines for the scalar data types */ +/*************************************************************************/ +GK_MKBLAS(gk_c, char, int) +GK_MKBLAS(gk_i, int, int) +GK_MKBLAS(gk_i32, int32_t, int32_t) +GK_MKBLAS(gk_i64, int64_t, int64_t) +GK_MKBLAS(gk_z, ssize_t, ssize_t) +GK_MKBLAS(gk_zu, size_t, size_t) +GK_MKBLAS(gk_f, float, float) +GK_MKBLAS(gk_d, double, double) +GK_MKBLAS(gk_idx, gk_idx_t, gk_idx_t) + + + + diff --git a/cache.c b/cache.c new file mode 100644 index 0000000..932e36d --- /dev/null +++ b/cache.c @@ -0,0 +1,126 @@ +/*! +\file +\brief Functions dealing with simulating cache behavior for performance + modeling and analysis; + +\date Started 4/13/18 +\author George +\author Copyright 1997-2011, Regents of the University of Minnesota +\version $Id: cache.c 21991 2018-04-16 03:08:12Z karypis $ +*/ + +#include + + +/*************************************************************************/ +/*! This function creates a cache + */ +/*************************************************************************/ +gk_cache_t *gk_cacheCreate(uint32_t nway, uint32_t lnbits, size_t cnbits) +{ + gk_cache_t *cache; + + cache = (gk_cache_t *)gk_malloc(sizeof(gk_cache_t), "gk_cacheCreate: cache"); + memset(cache, 0, sizeof(gk_cache_t)); + + cache->nway = nway; + cache->lnbits = lnbits; + cache->cnbits = cnbits; + cache->csize = 1<cmask = cache->csize-1; + + cache->latimes = gk_ui64smalloc(cache->csize*nway, 0, "gk_cacheCreate: latimes"); + cache->clines = gk_zusmalloc(cache->csize*nway, 0, "gk_cacheCreate: clines"); + + return cache; +} + + +/*************************************************************************/ +/*! This function resets a cache + */ +/*************************************************************************/ +void gk_cacheReset(gk_cache_t *cache) +{ + cache->nhits = 0; + cache->nmisses = 0; + + gk_ui64set(cache->csize*cache->nway, 0, cache->latimes); + gk_zuset(cache->csize*cache->nway, 0, cache->clines); + + return; +} + + +/*************************************************************************/ +/*! This function destroys a cache. + */ +/*************************************************************************/ +void gk_cacheDestroy(gk_cache_t **r_cache) +{ + gk_cache_t *cache = *r_cache; + + if (cache == NULL) + return; + + gk_free((void **)&cache->clines, &cache->latimes, &cache, LTERM); + + *r_cache = NULL; +} + + +/*************************************************************************/ +/*! This function simulates a load(ptr) operation. + */ +/*************************************************************************/ +int gk_cacheLoad(gk_cache_t *cache, size_t addr) +{ + uint32_t i, nway=cache->nway; + size_t lru=0; + + //printf("%16"PRIx64" ", (uint64_t)addr); + addr = addr>>(cache->lnbits); + //printf("%16"PRIx64" %16"PRIx64" %16"PRIx64" ", (uint64_t)addr, (uint64_t)addr&(cache->cmask), (uint64_t)cache->cmask); + + size_t *clines = cache->clines + (addr&(cache->cmask)); + uint64_t *latimes = cache->latimes + (addr&(cache->cmask)); + + cache->clock++; + for (i=0; inhits++; + latimes[i] = cache->clock; + goto DONE; + } + } + + for (i=0; inmisses++; + clines[lru] = addr; + latimes[lru] = cache->clock; + +DONE: + //printf(" %"PRIu64" %"PRIu64"\n", cache->nhits, cache->clock); + return 1; +} + + +/*************************************************************************/ +/*! This function returns the cache's hitrate + */ +/*************************************************************************/ +double gk_cacheGetHitRate(gk_cache_t *cache) +{ + return ((double)cache->nhits)/((double)(cache->clock+1)); +} + diff --git a/conf/check_thread_storage.c b/conf/check_thread_storage.c new file mode 100644 index 0000000..e6e1e98 --- /dev/null +++ b/conf/check_thread_storage.c @@ -0,0 +1,5 @@ +extern __thread int x; + +int main(int argc, char **argv) { + return 0; +} diff --git a/csr.c b/csr.c new file mode 100644 index 0000000..7e92a0c --- /dev/null +++ b/csr.c @@ -0,0 +1,3378 @@ +/*! + * \file + * + * \brief Various routines with dealing with CSR matrices + * + * \author George Karypis + * \version\verbatim $Id: csr.c 21044 2017-05-24 22:50:32Z karypis $ \endverbatim + */ + +#include + +#define OMPMINOPS 50000 + +/*************************************************************************/ +/*! Allocate memory for a CSR matrix and initializes it + \returns the allocated matrix. The various fields are set to NULL. +*/ +/**************************************************************************/ +gk_csr_t *gk_csr_Create() +{ + gk_csr_t *mat=NULL; + + if ((mat = (gk_csr_t *)gk_malloc(sizeof(gk_csr_t), "gk_csr_Create: mat"))) + gk_csr_Init(mat); + + return mat; +} + + +/*************************************************************************/ +/*! Initializes the matrix + \param mat is the matrix to be initialized. +*/ +/*************************************************************************/ +void gk_csr_Init(gk_csr_t *mat) +{ + memset(mat, 0, sizeof(gk_csr_t)); + mat->nrows = mat->ncols = 0; +} + + +/*************************************************************************/ +/*! Frees all the memory allocated for matrix. + \param mat is the matrix to be freed. +*/ +/*************************************************************************/ +void gk_csr_Free(gk_csr_t **mat) +{ + if (*mat == NULL) + return; + gk_csr_FreeContents(*mat); + gk_free((void **)mat, LTERM); +} + + +/*************************************************************************/ +/*! Frees only the memory allocated for the matrix's different fields and + sets them to NULL. + \param mat is the matrix whose contents will be freed. +*/ +/*************************************************************************/ +void gk_csr_FreeContents(gk_csr_t *mat) +{ + gk_free((void *)&mat->rowptr, &mat->rowind, &mat->rowval, + &mat->rowids, &mat->rlabels, &mat->rmap, + &mat->colptr, &mat->colind, &mat->colval, + &mat->colids, &mat->clabels, &mat->cmap, + &mat->rnorms, &mat->cnorms, &mat->rsums, &mat->csums, + &mat->rsizes, &mat->csizes, &mat->rvols, &mat->cvols, + &mat->rwgts, &mat->cwgts, + LTERM); +} + + +/*************************************************************************/ +/*! Returns a copy of a matrix. + \param mat is the matrix to be duplicated. + \returns the newly created copy of the matrix. +*/ +/**************************************************************************/ +gk_csr_t *gk_csr_Dup(gk_csr_t *mat) +{ + gk_csr_t *nmat; + + nmat = gk_csr_Create(); + + nmat->nrows = mat->nrows; + nmat->ncols = mat->ncols; + + /* copy the row structure */ + if (mat->rowptr) + nmat->rowptr = gk_zcopy(mat->nrows+1, mat->rowptr, + gk_zmalloc(mat->nrows+1, "gk_csr_Dup: rowptr")); + if (mat->rowids) + nmat->rowids = gk_icopy(mat->nrows, mat->rowids, + gk_imalloc(mat->nrows, "gk_csr_Dup: rowids")); + if (mat->rlabels) + nmat->rlabels = gk_icopy(mat->nrows, mat->rlabels, + gk_imalloc(mat->nrows, "gk_csr_Dup: rlabels")); + if (mat->rnorms) + nmat->rnorms = gk_fcopy(mat->nrows, mat->rnorms, + gk_fmalloc(mat->nrows, "gk_csr_Dup: rnorms")); + if (mat->rsums) + nmat->rsums = gk_fcopy(mat->nrows, mat->rsums, + gk_fmalloc(mat->nrows, "gk_csr_Dup: rsums")); + if (mat->rsizes) + nmat->rsizes = gk_fcopy(mat->nrows, mat->rsizes, + gk_fmalloc(mat->nrows, "gk_csr_Dup: rsizes")); + if (mat->rvols) + nmat->rvols = gk_fcopy(mat->nrows, mat->rvols, + gk_fmalloc(mat->nrows, "gk_csr_Dup: rvols")); + if (mat->rwgts) + nmat->rwgts = gk_fcopy(mat->nrows, mat->rwgts, + gk_fmalloc(mat->nrows, "gk_csr_Dup: rwgts")); + if (mat->rowind) + nmat->rowind = gk_icopy(mat->rowptr[mat->nrows], mat->rowind, + gk_imalloc(mat->rowptr[mat->nrows], "gk_csr_Dup: rowind")); + if (mat->rowval) + nmat->rowval = gk_fcopy(mat->rowptr[mat->nrows], mat->rowval, + gk_fmalloc(mat->rowptr[mat->nrows], "gk_csr_Dup: rowval")); + + /* copy the col structure */ + if (mat->colptr) + nmat->colptr = gk_zcopy(mat->ncols+1, mat->colptr, + gk_zmalloc(mat->ncols+1, "gk_csr_Dup: colptr")); + if (mat->colids) + nmat->colids = gk_icopy(mat->ncols, mat->colids, + gk_imalloc(mat->ncols, "gk_csr_Dup: colids")); + if (mat->clabels) + nmat->clabels = gk_icopy(mat->ncols, mat->clabels, + gk_imalloc(mat->ncols, "gk_csr_Dup: clabels")); + if (mat->cnorms) + nmat->cnorms = gk_fcopy(mat->ncols, mat->cnorms, + gk_fmalloc(mat->ncols, "gk_csr_Dup: cnorms")); + if (mat->csums) + nmat->csums = gk_fcopy(mat->ncols, mat->csums, + gk_fmalloc(mat->ncols, "gk_csr_Dup: csums")); + if (mat->csizes) + nmat->csizes = gk_fcopy(mat->ncols, mat->csizes, + gk_fmalloc(mat->ncols, "gk_csr_Dup: csizes")); + if (mat->cvols) + nmat->cvols = gk_fcopy(mat->ncols, mat->cvols, + gk_fmalloc(mat->ncols, "gk_csr_Dup: cvols")); + if (mat->cwgts) + nmat->cwgts = gk_fcopy(mat->ncols, mat->cwgts, + gk_fmalloc(mat->ncols, "gk_csr_Dup: cwgts")); + if (mat->colind) + nmat->colind = gk_icopy(mat->colptr[mat->ncols], mat->colind, + gk_imalloc(mat->colptr[mat->ncols], "gk_csr_Dup: colind")); + if (mat->colval) + nmat->colval = gk_fcopy(mat->colptr[mat->ncols], mat->colval, + gk_fmalloc(mat->colptr[mat->ncols], "gk_csr_Dup: colval")); + + return nmat; +} + + +/*************************************************************************/ +/*! Returns a submatrix containint a set of consecutive rows. + \param mat is the original matrix. + \param rstart is the starting row. + \param nrows is the number of rows from rstart to extract. + \returns the row structure of the newly created submatrix. +*/ +/**************************************************************************/ +gk_csr_t *gk_csr_ExtractSubmatrix(gk_csr_t *mat, int rstart, int nrows) +{ + ssize_t i; + gk_csr_t *nmat; + + if (rstart+nrows > mat->nrows) + return NULL; + + nmat = gk_csr_Create(); + + nmat->nrows = nrows; + nmat->ncols = mat->ncols; + + /* copy the row structure */ + if (mat->rowptr) + nmat->rowptr = gk_zcopy(nrows+1, mat->rowptr+rstart, + gk_zmalloc(nrows+1, "gk_csr_ExtractSubmatrix: rowptr")); + for (i=nrows; i>=0; i--) + nmat->rowptr[i] -= nmat->rowptr[0]; + ASSERT(nmat->rowptr[0] == 0); + + if (mat->rowids) + nmat->rowids = gk_icopy(nrows, mat->rowids+rstart, + gk_imalloc(nrows, "gk_csr_ExtractSubmatrix: rowids")); + if (mat->rnorms) + nmat->rnorms = gk_fcopy(nrows, mat->rnorms+rstart, + gk_fmalloc(nrows, "gk_csr_ExtractSubmatrix: rnorms")); + + if (mat->rsums) + nmat->rsums = gk_fcopy(nrows, mat->rsums+rstart, + gk_fmalloc(nrows, "gk_csr_ExtractSubmatrix: rsums")); + + ASSERT(nmat->rowptr[nrows] == mat->rowptr[rstart+nrows]-mat->rowptr[rstart]); + if (mat->rowind) + nmat->rowind = gk_icopy(mat->rowptr[rstart+nrows]-mat->rowptr[rstart], + mat->rowind+mat->rowptr[rstart], + gk_imalloc(mat->rowptr[rstart+nrows]-mat->rowptr[rstart], + "gk_csr_ExtractSubmatrix: rowind")); + if (mat->rowval) + nmat->rowval = gk_fcopy(mat->rowptr[rstart+nrows]-mat->rowptr[rstart], + mat->rowval+mat->rowptr[rstart], + gk_fmalloc(mat->rowptr[rstart+nrows]-mat->rowptr[rstart], + "gk_csr_ExtractSubmatrix: rowval")); + + return nmat; +} + + +/*************************************************************************/ +/*! Returns a submatrix containing a certain set of rows. + \param mat is the original matrix. + \param nrows is the number of rows to extract. + \param rind is the set of row numbers to extract. + \returns the row structure of the newly created submatrix. +*/ +/**************************************************************************/ +gk_csr_t *gk_csr_ExtractRows(gk_csr_t *mat, int nrows, int *rind) +{ + ssize_t i, ii, j, nnz; + gk_csr_t *nmat; + + nmat = gk_csr_Create(); + + nmat->nrows = nrows; + nmat->ncols = mat->ncols; + + for (nnz=0, i=0; irowptr[rind[i]+1]-mat->rowptr[rind[i]]; + + nmat->rowptr = gk_zmalloc(nmat->nrows+1, "gk_csr_ExtractPartition: rowptr"); + nmat->rowind = gk_imalloc(nnz, "gk_csr_ExtractPartition: rowind"); + nmat->rowval = gk_fmalloc(nnz, "gk_csr_ExtractPartition: rowval"); + + nmat->rowptr[0] = 0; + for (nnz=0, j=0, ii=0; iirowptr[i+1]-mat->rowptr[i], mat->rowind+mat->rowptr[i], nmat->rowind+nnz); + gk_fcopy(mat->rowptr[i+1]-mat->rowptr[i], mat->rowval+mat->rowptr[i], nmat->rowval+nnz); + nnz += mat->rowptr[i+1]-mat->rowptr[i]; + nmat->rowptr[++j] = nnz; + } + ASSERT(j == nmat->nrows); + + return nmat; +} + + +/*************************************************************************/ +/*! Returns a submatrix corresponding to a specified partitioning of rows. + \param mat is the original matrix. + \param part is the partitioning vector of the rows. + \param pid is the partition ID that will be extracted. + \returns the row structure of the newly created submatrix. +*/ +/**************************************************************************/ +gk_csr_t *gk_csr_ExtractPartition(gk_csr_t *mat, int *part, int pid) +{ + ssize_t i, j, nnz; + gk_csr_t *nmat; + + nmat = gk_csr_Create(); + + nmat->nrows = 0; + nmat->ncols = mat->ncols; + + for (nnz=0, i=0; inrows; i++) { + if (part[i] == pid) { + nmat->nrows++; + nnz += mat->rowptr[i+1]-mat->rowptr[i]; + } + } + + nmat->rowptr = gk_zmalloc(nmat->nrows+1, "gk_csr_ExtractPartition: rowptr"); + nmat->rowind = gk_imalloc(nnz, "gk_csr_ExtractPartition: rowind"); + nmat->rowval = gk_fmalloc(nnz, "gk_csr_ExtractPartition: rowval"); + + nmat->rowptr[0] = 0; + for (nnz=0, j=0, i=0; inrows; i++) { + if (part[i] == pid) { + gk_icopy(mat->rowptr[i+1]-mat->rowptr[i], mat->rowind+mat->rowptr[i], nmat->rowind+nnz); + gk_fcopy(mat->rowptr[i+1]-mat->rowptr[i], mat->rowval+mat->rowptr[i], nmat->rowval+nnz); + nnz += mat->rowptr[i+1]-mat->rowptr[i]; + nmat->rowptr[++j] = nnz; + } + } + ASSERT(j == nmat->nrows); + + return nmat; +} + + +/*************************************************************************/ +/*! Splits the matrix into multiple sub-matrices based on the provided + color array. + \param mat is the original matrix. + \param color is an array of size equal to the number of non-zeros + in the matrix (row-wise structure). The matrix is split into + as many parts as the number of colors. For meaningfull results, + the colors should be numbered consecutively starting from 0. + \returns an array of matrices for each supplied color number. +*/ +/**************************************************************************/ +gk_csr_t **gk_csr_Split(gk_csr_t *mat, int *color) +{ + ssize_t i, j; + int nrows, ncolors; + ssize_t *rowptr; + int *rowind; + float *rowval; + gk_csr_t **smats; + + nrows = mat->nrows; + rowptr = mat->rowptr; + rowind = mat->rowind; + rowval = mat->rowval; + + ncolors = gk_imax(rowptr[nrows], color, 1)+1; + + smats = (gk_csr_t **)gk_malloc(sizeof(gk_csr_t *)*ncolors, "gk_csr_Split: smats"); + for (i=0; inrows = mat->nrows; + smats[i]->ncols = mat->ncols; + smats[i]->rowptr = gk_zsmalloc(nrows+1, 0, "gk_csr_Split: smats[i]->rowptr"); + } + + for (i=0; irowptr[i]++; + } + for (i=0; irowptr); + + for (i=0; irowind = gk_imalloc(smats[i]->rowptr[nrows], "gk_csr_Split: smats[i]->rowind"); + smats[i]->rowval = gk_fmalloc(smats[i]->rowptr[nrows], "gk_csr_Split: smats[i]->rowval"); + } + + for (i=0; irowind[smats[color[j]]->rowptr[i]] = rowind[j]; + smats[color[j]]->rowval[smats[color[j]]->rowptr[i]] = rowval[j]; + smats[color[j]]->rowptr[i]++; + } + } + + for (i=0; irowptr); + + return smats; +} + + +/**************************************************************************/ +/*! Determines the format of the CSR matrix based on the extension. + \param filename is the name of the file. + \param the user-supplied format. + \returns the type. The extension of the file directly maps to the + name of the format. +*/ +/**************************************************************************/ +int gk_csr_DetermineFormat(char *filename, int format) +{ + if (format != GK_CSR_FMT_AUTO) + return format; + + format = GK_CSR_FMT_CSR; + char *extension = gk_getextname(filename); + + if (!strcmp(extension, "csr")) + format = GK_CSR_FMT_CSR; + else if (!strcmp(extension, "ijv")) + format = GK_CSR_FMT_IJV; + else if (!strcmp(extension, "cluto")) + format = GK_CSR_FMT_CLUTO; + else if (!strcmp(extension, "metis")) + format = GK_CSR_FMT_METIS; + else if (!strcmp(extension, "binrow")) + format = GK_CSR_FMT_BINROW; + else if (!strcmp(extension, "bincol")) + format = GK_CSR_FMT_BINCOL; + else if (!strcmp(extension, "bijv")) + format = GK_CSR_FMT_BIJV; + + gk_free((void **)&extension, LTERM); + + return format; +} + + +/**************************************************************************/ +/*! Reads a CSR matrix from the supplied file and stores it the matrix's + forward structure. + \param filename is the file that stores the data. + \param format is either GK_CSR_FMT_METIS, GK_CSR_FMT_CLUTO, + GK_CSR_FMT_CSR, GK_CSR_FMT_BINROW, GK_CSR_FMT_BINCOL + specifying the type of the input format. + The GK_CSR_FMT_CSR does not contain a header + line, whereas the GK_CSR_FMT_BINROW is a binary format written + by gk_csr_Write() using the same format specifier. + \param readvals is either 1 or 0, indicating if the CSR file contains + values or it does not. It only applies when GK_CSR_FMT_CSR is + used. + \param numbering is either 1 or 0, indicating if the numbering of the + indices start from 1 or 0, respectively. If they start from 1, + they are automatically decreamented during input so that they + will start from 0. It only applies when GK_CSR_FMT_CSR is + used. + \returns the matrix that was read. +*/ +/**************************************************************************/ +gk_csr_t *gk_csr_Read(char *filename, int format, int readvals, int numbering) +{ + ssize_t i, k, l; + size_t nfields, nrows, ncols, nnz, fmt, ncon; + size_t lnlen; + ssize_t *rowptr; + int *rowind, *iinds, *jinds, ival; + float *rowval=NULL, *vals, fval; + int readsizes, readwgts; + char *line=NULL, *head, *tail, fmtstr[256]; + FILE *fpin; + gk_csr_t *mat=NULL; + + format = gk_csr_DetermineFormat(filename, format); + + if (!gk_fexists(filename)) + gk_errexit(SIGERR, "File %s does not exist!\n", filename); + + switch (format) { + case GK_CSR_FMT_BINROW: + mat = gk_csr_Create(); + + fpin = gk_fopen(filename, "rb", "gk_csr_Read: fpin"); + if (fread(&(mat->nrows), sizeof(int32_t), 1, fpin) != 1) + gk_errexit(SIGERR, "Failed to read the nrows from file %s!\n", filename); + if (fread(&(mat->ncols), sizeof(int32_t), 1, fpin) != 1) + gk_errexit(SIGERR, "Failed to read the ncols from file %s!\n", filename); + mat->rowptr = gk_zmalloc(mat->nrows+1, "gk_csr_Read: rowptr"); + if (fread(mat->rowptr, sizeof(ssize_t), mat->nrows+1, fpin) != mat->nrows+1) + gk_errexit(SIGERR, "Failed to read the rowptr from file %s!\n", filename); + mat->rowind = gk_imalloc(mat->rowptr[mat->nrows], "gk_csr_Read: rowind"); + if (fread(mat->rowind, sizeof(int32_t), mat->rowptr[mat->nrows], fpin) != mat->rowptr[mat->nrows]) + gk_errexit(SIGERR, "Failed to read the rowind from file %s!\n", filename); + if (readvals == 1) { + mat->rowval = gk_fmalloc(mat->rowptr[mat->nrows], "gk_csr_Read: rowval"); + if (fread(mat->rowval, sizeof(float), mat->rowptr[mat->nrows], fpin) != mat->rowptr[mat->nrows]) + gk_errexit(SIGERR, "Failed to read the rowval from file %s!\n", filename); + } + + gk_fclose(fpin); + return mat; + + break; + + case GK_CSR_FMT_BINCOL: + mat = gk_csr_Create(); + + fpin = gk_fopen(filename, "rb", "gk_csr_Read: fpin"); + if (fread(&(mat->nrows), sizeof(int32_t), 1, fpin) != 1) + gk_errexit(SIGERR, "Failed to read the nrows from file %s!\n", filename); + if (fread(&(mat->ncols), sizeof(int32_t), 1, fpin) != 1) + gk_errexit(SIGERR, "Failed to read the ncols from file %s!\n", filename); + mat->colptr = gk_zmalloc(mat->ncols+1, "gk_csr_Read: colptr"); + if (fread(mat->colptr, sizeof(ssize_t), mat->ncols+1, fpin) != mat->ncols+1) + gk_errexit(SIGERR, "Failed to read the colptr from file %s!\n", filename); + mat->colind = gk_imalloc(mat->colptr[mat->ncols], "gk_csr_Read: colind"); + if (fread(mat->colind, sizeof(int32_t), mat->colptr[mat->ncols], fpin) != mat->colptr[mat->ncols]) + gk_errexit(SIGERR, "Failed to read the colind from file %s!\n", filename); + if (readvals) { + mat->colval = gk_fmalloc(mat->colptr[mat->ncols], "gk_csr_Read: colval"); + if (fread(mat->colval, sizeof(float), mat->colptr[mat->ncols], fpin) != mat->colptr[mat->ncols]) + gk_errexit(SIGERR, "Failed to read the colval from file %s!\n", filename); + } + + gk_fclose(fpin); + return mat; + + break; + + + case GK_CSR_FMT_IJV: + gk_getfilestats(filename, &nrows, &nnz, NULL, NULL); + + if (readvals == 1 && 3*nrows != nnz) + gk_errexit(SIGERR, "Error: The number of numbers (%zd %d) in the input file is not a multiple of 3.\n", nnz, readvals); + if (readvals == 0 && 2*nrows != nnz) + gk_errexit(SIGERR, "Error: The number of numbers (%zd %d) in the input file is not a multiple of 2.\n", nnz, readvals); + + nnz = nrows; + numbering = (numbering ? - 1 : 0); + + /* read the data into three arrays */ + iinds = gk_i32malloc(nnz, "iinds"); + jinds = gk_i32malloc(nnz, "jinds"); + vals = (readvals ? gk_fmalloc(nnz, "vals") : NULL); + + fpin = gk_fopen(filename, "r", "gk_csr_Read: fpin"); + for (nrows=0, ncols=0, i=0; inrows = nrows; + mat->ncols = ncols; + rowptr = mat->rowptr = gk_zsmalloc(nrows+1, 0, "rowptr"); + rowind = mat->rowind = gk_i32malloc(nnz, "rowind"); + if (readvals) + rowval = mat->rowval = gk_fmalloc(nnz, "rowval"); + + for (i=0; inrows), sizeof(int32_t), 1, fpin) != 1) + gk_errexit(SIGERR, "Failed to read the nrows from file %s!\n", filename); + if (fread(&(mat->ncols), sizeof(int32_t), 1, fpin) != 1) + gk_errexit(SIGERR, "Failed to read the ncols from file %s!\n", filename); + if (fread(&nnz, sizeof(size_t), 1, fpin) != 1) + gk_errexit(SIGERR, "Failed to read the nnz from file %s!\n", filename); + if (fread(&readvals, sizeof(int32_t), 1, fpin) != 1) + gk_errexit(SIGERR, "Failed to read the readvals from file %s!\n", filename); + + /* read the data into three arrays */ + iinds = gk_i32malloc(nnz, "iinds"); + jinds = gk_i32malloc(nnz, "jinds"); + vals = (readvals ? gk_fmalloc(nnz, "vals") : NULL); + + for (i=0; irowptr = gk_zsmalloc(mat->nrows+1, 0, "rowptr"); + rowind = mat->rowind = gk_i32malloc(nnz, "rowind"); + if (readvals) + rowval = mat->rowval = gk_fmalloc(nnz, "rowval"); + + for (i=0; inrows, rowptr); + + for (i=0; inrows, rowptr); + + gk_free((void **)&iinds, &jinds, &vals, LTERM); + + return mat; + + break; + + + /* the following are handled by a common input code, that comes after the switch */ + + case GK_CSR_FMT_CLUTO: + fpin = gk_fopen(filename, "r", "gk_csr_Read: fpin"); + do { + if (gk_getline(&line, &lnlen, fpin) <= 0) + gk_errexit(SIGERR, "Premature end of input file: file:%s\n", filename); + } while (line[0] == '%'); + + if (sscanf(line, "%zu %zu %zu", &nrows, &ncols, &nnz) != 3) + gk_errexit(SIGERR, "Header line must contain 3 integers.\n"); + + readsizes = 0; + readwgts = 0; + readvals = 1; + numbering = 1; + + break; + + case GK_CSR_FMT_METIS: + fpin = gk_fopen(filename, "r", "gk_csr_Read: fpin"); + do { + if (gk_getline(&line, &lnlen, fpin) <= 0) + gk_errexit(SIGERR, "Premature end of input file: file:%s\n", filename); + } while (line[0] == '%'); + + fmt = ncon = 0; + nfields = sscanf(line, "%zu %zu %zu %zu", &nrows, &nnz, &fmt, &ncon); + if (nfields < 2) + gk_errexit(SIGERR, "Header line must contain at least 2 integers (#vtxs and #edges).\n"); + + ncols = nrows; + nnz *= 2; + + if (fmt > 111) + gk_errexit(SIGERR, "Cannot read this type of file format [fmt=%zu]!\n", fmt); + + sprintf(fmtstr, "%03zu", fmt%1000); + readsizes = (fmtstr[0] == '1'); + readwgts = (fmtstr[1] == '1'); + readvals = (fmtstr[2] == '1'); + numbering = 1; + ncon = (ncon == 0 ? 1 : ncon); + + break; + + case GK_CSR_FMT_CSR: + readsizes = 0; + readwgts = 0; + + gk_getfilestats(filename, &nrows, &nnz, NULL, NULL); + + if (readvals == 1 && nnz%2 == 1) + gk_errexit(SIGERR, "Error: The number of numbers (%zd %d) in the input file is not even.\n", nnz, readvals); + if (readvals == 1) + nnz = nnz/2; + fpin = gk_fopen(filename, "r", "gk_csr_Read: fpin"); + + break; + + default: + gk_errexit(SIGERR, "Unknown csr format.\n"); + return NULL; + } + + mat = gk_csr_Create(); + + mat->nrows = nrows; + + rowptr = mat->rowptr = gk_zmalloc(nrows+1, "gk_csr_Read: rowptr"); + rowind = mat->rowind = gk_imalloc(nnz, "gk_csr_Read: rowind"); + if (readvals != 2) + rowval = mat->rowval = gk_fsmalloc(nnz, 1.0, "gk_csr_Read: rowval"); + + if (readsizes) + mat->rsizes = gk_fsmalloc(nrows, 0.0, "gk_csr_Read: rsizes"); + + if (readwgts) + mat->rwgts = gk_fsmalloc(nrows*ncon, 0.0, "gk_csr_Read: rwgts"); + + /*---------------------------------------------------------------------- + * Read the sparse matrix file + *---------------------------------------------------------------------*/ + numbering = (numbering ? -1 : 0); + for (ncols=0, rowptr[0]=0, k=0, i=0; irsizes[i] = (float)strtod(head, &tail); +#else + mat->rsizes[i] = strtof(head, &tail); +#endif + if (tail == head) + gk_errexit(SIGERR, "The line for vertex %zd does not have size information\n", i+1); + if (mat->rsizes[i] < 0) + errexit("The size for vertex %zd must be >= 0\n", i+1); + head = tail; + } + + /* Read vertex weights */ + if (readwgts) { + for (l=0; lrwgts[i*ncon+l] = (float)strtod(head, &tail); +#else + mat->rwgts[i*ncon+l] = strtof(head, &tail); +#endif + if (tail == head) + errexit("The line for vertex %zd does not have enough weights " + "for the %d constraints.\n", i+1, ncon); + if (mat->rwgts[i*ncon+l] < 0) + errexit("The weight vertex %zd and constraint %zd must be >= 0\n", i+1, l); + head = tail; + } + } + + + /* Read the rest of the row */ + while (1) { + ival = (int)strtol(head, &tail, 0); + if (tail == head) + break; + head = tail; + + if ((rowind[k] = ival + numbering) < 0) + gk_errexit(SIGERR, "Error: Invalid column number %d at row %zd.\n", ival, i); + + ncols = gk_max(rowind[k], ncols); + + if (readvals == 1) { +#ifdef __MSC__ + fval = (float)strtod(head, &tail); +#else + fval = strtof(head, &tail); +#endif + if (tail == head) + gk_errexit(SIGERR, "Value could not be found for column! Row:%zd, NNZ:%zd\n", i, k); + head = tail; + + rowval[k] = fval; + } + k++; + } + rowptr[i+1] = k; + } + + if (format == GK_CSR_FMT_METIS) { + ASSERT(ncols+1 == mat->nrows); + mat->ncols = mat->nrows; + } + else { + mat->ncols = ncols+1; + } + + if (k != nnz) + gk_errexit(SIGERR, "gk_csr_Read: Something wrong with the number of nonzeros in " + "the input file. NNZ=%zd, ActualNNZ=%zd.\n", nnz, k); + + gk_fclose(fpin); + + gk_free((void **)&line, LTERM); + + return mat; +} + + +/**************************************************************************/ +/*! Writes the row-based structure of a matrix into a file. + \param mat is the matrix to be written, + \param filename is the name of the output file. + \param format is one of: GK_CSR_FMT_CLUTO, GK_CSR_FMT_CSR, + GK_CSR_FMT_BINROW, GK_CSR_FMT_BINCOL, GK_CSR_FMT_BIJV. + \param writevals is either 1 or 0 indicating if the values will be + written or not. This is only applicable when GK_CSR_FMT_CSR + is used. + \param numbering is either 1 or 0 indicating if the internal 0-based + numbering will be shifted by one or not during output. This + is only applicable when GK_CSR_FMT_CSR is used. +*/ +/**************************************************************************/ +void gk_csr_Write(gk_csr_t *mat, char *filename, int format, int writevals, int numbering) +{ + ssize_t i, j; + int32_t edge[2]; + FILE *fpout; + + format = gk_csr_DetermineFormat(filename, format); + + switch (format) { + case GK_CSR_FMT_METIS: + if (mat->nrows != mat->ncols || mat->rowptr[mat->nrows]%2 == 1) + gk_errexit(SIGERR, "METIS output format requires a square symmetric matrix.\n"); + + if (filename) + fpout = gk_fopen(filename, "w", "gk_csr_Write: fpout"); + else + fpout = stdout; + + fprintf(fpout, "%d %zd\n", mat->nrows, mat->rowptr[mat->nrows]/2); + for (i=0; inrows; i++) { + for (j=mat->rowptr[i]; jrowptr[i+1]; j++) + fprintf(fpout, " %d", mat->rowind[j]+1); + fprintf(fpout, "\n"); + } + if (filename) + gk_fclose(fpout); + break; + + case GK_CSR_FMT_BINROW: + if (filename == NULL) + gk_errexit(SIGERR, "The filename parameter cannot be NULL.\n"); + fpout = gk_fopen(filename, "wb", "gk_csr_Write: fpout"); + + fwrite(&(mat->nrows), sizeof(int32_t), 1, fpout); + fwrite(&(mat->ncols), sizeof(int32_t), 1, fpout); + fwrite(mat->rowptr, sizeof(ssize_t), mat->nrows+1, fpout); + fwrite(mat->rowind, sizeof(int32_t), mat->rowptr[mat->nrows], fpout); + if (writevals) + fwrite(mat->rowval, sizeof(float), mat->rowptr[mat->nrows], fpout); + + gk_fclose(fpout); + return; + + break; + + case GK_CSR_FMT_BINCOL: + if (filename == NULL) + gk_errexit(SIGERR, "The filename parameter cannot be NULL.\n"); + fpout = gk_fopen(filename, "wb", "gk_csr_Write: fpout"); + + fwrite(&(mat->nrows), sizeof(int32_t), 1, fpout); + fwrite(&(mat->ncols), sizeof(int32_t), 1, fpout); + fwrite(mat->colptr, sizeof(ssize_t), mat->ncols+1, fpout); + fwrite(mat->colind, sizeof(int32_t), mat->colptr[mat->ncols], fpout); + if (writevals) + fwrite(mat->colval, sizeof(float), mat->colptr[mat->ncols], fpout); + + gk_fclose(fpout); + return; + + break; + + case GK_CSR_FMT_IJV: + if (filename == NULL) + gk_errexit(SIGERR, "The filename parameter cannot be NULL.\n"); + fpout = gk_fopen(filename, "w", "gk_csr_Write: fpout"); + + numbering = (numbering ? 1 : 0); + for (i=0; inrows; i++) { + for (j=mat->rowptr[i]; jrowptr[i+1]; j++) { + if (writevals) + fprintf(fpout, "%zd %d %.8f\n", i+numbering, mat->rowind[j]+numbering, mat->rowval[j]); + else + fprintf(fpout, "%zd %d\n", i+numbering, mat->rowind[j]+numbering); + } + } + + gk_fclose(fpout); + return; + + break; + + case GK_CSR_FMT_BIJV: + if (filename == NULL) + gk_errexit(SIGERR, "The filename parameter cannot be NULL.\n"); + fpout = gk_fopen(filename, "wb", "gk_csr_Write: fpout"); + + fwrite(&(mat->nrows), sizeof(int32_t), 1, fpout); + fwrite(&(mat->ncols), sizeof(int32_t), 1, fpout); + fwrite(&(mat->rowptr[mat->nrows]), sizeof(size_t), 1, fpout); + fwrite(&writevals, sizeof(int32_t), 1, fpout); + + for (i=0; inrows; i++) { + edge[0] = i; + for (j=mat->rowptr[i]; jrowptr[i+1]; j++) { + edge[1] = mat->rowind[j]; + fwrite(edge, sizeof(int32_t), 2, fpout); + if (writevals) + fwrite(&(mat->rowval[j]), sizeof(float), 1, fpout); + } + } + + gk_fclose(fpout); + return; + + break; + + default: + if (filename) + fpout = gk_fopen(filename, "w", "gk_csr_Write: fpout"); + else + fpout = stdout; + + if (format == GK_CSR_FMT_CLUTO) { + fprintf(fpout, "%d %d %zd\n", mat->nrows, mat->ncols, mat->rowptr[mat->nrows]); + writevals = 1; + numbering = 1; + } + + for (i=0; inrows; i++) { + for (j=mat->rowptr[i]; jrowptr[i+1]; j++) { + fprintf(fpout, " %d", mat->rowind[j]+(numbering ? 1 : 0)); + if (writevals) + fprintf(fpout, " %f", mat->rowval[j]); + } + fprintf(fpout, "\n"); + } + if (filename) + gk_fclose(fpout); + } +} + + +/*************************************************************************/ +/*! Prunes certain rows/columns of the matrix. The prunning takes place + by analyzing the row structure of the matrix. The prunning takes place + by removing rows/columns but it does not affect the numbering of the + remaining rows/columns. + + \param mat the matrix to be prunned, + \param what indicates if the rows (GK_CSR_ROW) or the columns (GK_CSR_COL) + of the matrix will be prunned, + \param minf is the minimum number of rows (columns) that a column (row) must + be present in order to be kept, + \param maxf is the maximum number of rows (columns) that a column (row) must + be present at in order to be kept. + \returns the prunned matrix consisting only of its row-based structure. + The input matrix is not modified. +*/ +/**************************************************************************/ +gk_csr_t *gk_csr_Prune(gk_csr_t *mat, int what, int minf, int maxf) +{ + ssize_t i, j, nnz; + int nrows, ncols; + ssize_t *rowptr, *nrowptr; + int *rowind, *nrowind, *collen; + float *rowval, *nrowval; + gk_csr_t *nmat; + + nmat = gk_csr_Create(); + + nrows = nmat->nrows = mat->nrows; + ncols = nmat->ncols = mat->ncols; + + rowptr = mat->rowptr; + rowind = mat->rowind; + rowval = mat->rowval; + + nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_Prune: nrowptr"); + nrowind = nmat->rowind = gk_imalloc(rowptr[nrows], "gk_csr_Prune: nrowind"); + nrowval = nmat->rowval = gk_fmalloc(rowptr[nrows], "gk_csr_Prune: nrowval"); + + + switch (what) { + case GK_CSR_COL: + collen = gk_ismalloc(ncols, 0, "gk_csr_Prune: collen"); + + for (i=0; i= minf && collen[i] <= maxf ? 1 : 0); + + nrowptr[0] = 0; + for (nnz=0, i=0; i= minf && rowptr[i+1]-rowptr[i] <= maxf) { + for (j=rowptr[i]; jnrows = mat->nrows; + ncols = nmat->ncols = mat->ncols; + + rowptr = mat->rowptr; + rowind = mat->rowind; + rowval = mat->rowval; + colptr = mat->colptr; + colind = mat->colind; + colval = mat->colval; + + nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_LowFilter: nrowptr"); + nrowind = nmat->rowind = gk_imalloc(rowptr[nrows], "gk_csr_LowFilter: nrowind"); + nrowval = nmat->rowval = gk_fmalloc(rowptr[nrows], "gk_csr_LowFilter: nrowval"); + + + switch (what) { + case GK_CSR_COL: + if (mat->colptr == NULL) + gk_errexit(SIGERR, "Cannot filter columns when column-based structure has not been created.\n"); + + gk_zcopy(nrows+1, rowptr, nrowptr); + + for (i=0; irowptr == NULL) + gk_errexit(SIGERR, "Cannot filter rows when row-based structure has not been created.\n"); + + for (i=0; inrows = mat->nrows; + ncols = nmat->ncols = mat->ncols; + + rowptr = mat->rowptr; + rowind = mat->rowind; + rowval = mat->rowval; + colptr = mat->colptr; + colind = mat->colind; + colval = mat->colval; + + nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_LowFilter: nrowptr"); + nrowind = nmat->rowind = gk_imalloc(rowptr[nrows], "gk_csr_LowFilter: nrowind"); + nrowval = nmat->rowval = gk_fmalloc(rowptr[nrows], "gk_csr_LowFilter: nrowval"); + + + switch (what) { + case GK_CSR_COL: + if (mat->colptr == NULL) + gk_errexit(SIGERR, "Cannot filter columns when column-based structure has not been created.\n"); + + cand = gk_fkvmalloc(nrows, "gk_csr_LowFilter: cand"); + + gk_zcopy(nrows+1, rowptr, nrowptr); + for (i=0; irowptr == NULL) + gk_errexit(SIGERR, "Cannot filter rows when row-based structure has not been created.\n"); + + cand = gk_fkvmalloc(ncols, "gk_csr_LowFilter: cand"); + + nrowptr[0] = 0; + for (nnz=0, i=0; inrows = mat->nrows; + nmat->ncols = mat->ncols; + + nrows = mat->nrows; + rowptr = mat->rowptr; + rowind = mat->rowind; + rowval = mat->rowval; + + nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_ZScoreFilter: nrowptr"); + nrowind = nmat->rowind = gk_imalloc(rowptr[nrows], "gk_csr_ZScoreFilter: nrowind"); + nrowval = nmat->rowval = gk_fmalloc(rowptr[nrows], "gk_csr_ZScoreFilter: nrowval"); + + + switch (what) { + case GK_CSR_COL: + gk_errexit(SIGERR, "This has not been implemented yet.\n"); + break; + + case GK_CSR_ROW: + if (mat->rowptr == NULL) + gk_errexit(SIGERR, "Cannot filter rows when row-based structure has not been created.\n"); + + nrowptr[0] = 0; + for (nnz=0, i=0; i avgwgt) { + nrowind[nnz] = rowind[j]; + nrowval[nnz] = rowval[j]; + nnz++; + } + } + nrowptr[i+1] = nnz; + } + break; + + default: + gk_csr_Free(&nmat); + gk_errexit(SIGERR, "Unknown prunning type of %d\n", what); + return NULL; + } + + return nmat; +} + + +/*************************************************************************/ +/*! Compacts the column-space of the matrix by removing empty columns. + As a result of the compaction, the column numbers are renumbered. + The compaction operation is done in place and only affects the row-based + representation of the matrix. + The new columns are ordered in decreasing frequency. + + \param mat the matrix whose empty columns will be removed. +*/ +/**************************************************************************/ +void gk_csr_CompactColumns(gk_csr_t *mat) +{ + ssize_t i; + int nrows, ncols, nncols; + ssize_t *rowptr; + int *rowind, *colmap; + gk_ikv_t *clens; + + nrows = mat->nrows; + ncols = mat->ncols; + rowptr = mat->rowptr; + rowind = mat->rowind; + + colmap = gk_imalloc(ncols, "gk_csr_CompactColumns: colmap"); + + clens = gk_ikvmalloc(ncols, "gk_csr_CompactColumns: clens"); + for (i=0; i 0) + colmap[clens[i].val] = nncols++; + else + break; + } + + for (i=0; incols = nncols; + + gk_free((void **)&colmap, &clens, LTERM); +} + + +/*************************************************************************/ +/*! Sorts the indices in increasing order + \param mat the matrix itself, + \param what is either GK_CSR_ROW or GK_CSR_COL indicating which set of + indices to sort. +*/ +/**************************************************************************/ +void gk_csr_SortIndices(gk_csr_t *mat, int what) +{ + int n, nn=0; + ssize_t *ptr; + int *ind; + float *val; + + switch (what) { + case GK_CSR_ROW: + if (!mat->rowptr) + gk_errexit(SIGERR, "Row-based view of the matrix does not exists.\n"); + + n = mat->nrows; + ptr = mat->rowptr; + ind = mat->rowind; + val = mat->rowval; + break; + + case GK_CSR_COL: + if (!mat->colptr) + gk_errexit(SIGERR, "Column-based view of the matrix does not exists.\n"); + + n = mat->ncols; + ptr = mat->colptr; + ind = mat->colind; + val = mat->colval; + break; + + default: + gk_errexit(SIGERR, "Invalid index type of %d.\n", what); + return; + } + + #pragma omp parallel if (n > 100) + { + ssize_t i, j, k; + gk_ikv_t *cand; + float *tval; + + #pragma omp single + for (i=0; i ptr[i] && ind[j] < ind[j-1]) + k = 1; /* an inversion */ + cand[j-ptr[i]].val = j-ptr[i]; + cand[j-ptr[i]].key = ind[j]; + tval[j-ptr[i]] = val[j]; + } + if (k) { + gk_ikvsorti(ptr[i+1]-ptr[i], cand); + for (j=ptr[i]; jnrows; + fptr = mat->rowptr; + find = mat->rowind; + fval = mat->rowval; + + if (mat->colptr) gk_free((void **)&mat->colptr, LTERM); + if (mat->colind) gk_free((void **)&mat->colind, LTERM); + if (mat->colval) gk_free((void **)&mat->colval, LTERM); + + nr = mat->ncols; + rptr = mat->colptr = gk_zsmalloc(nr+1, 0, "gk_csr_CreateIndex: rptr"); + rind = mat->colind = gk_imalloc(fptr[nf], "gk_csr_CreateIndex: rind"); + rval = mat->colval = (fval ? gk_fmalloc(fptr[nf], "gk_csr_CreateIndex: rval") : NULL); + break; + case GK_CSR_ROW: + nf = mat->ncols; + fptr = mat->colptr; + find = mat->colind; + fval = mat->colval; + + if (mat->rowptr) gk_free((void **)&mat->rowptr, LTERM); + if (mat->rowind) gk_free((void **)&mat->rowind, LTERM); + if (mat->rowval) gk_free((void **)&mat->rowval, LTERM); + + nr = mat->nrows; + rptr = mat->rowptr = gk_zsmalloc(nr+1, 0, "gk_csr_CreateIndex: rptr"); + rind = mat->rowind = gk_imalloc(fptr[nf], "gk_csr_CreateIndex: rind"); + rval = mat->rowval = (fval ? gk_fmalloc(fptr[nf], "gk_csr_CreateIndex: rval") : NULL); + break; + default: + gk_errexit(SIGERR, "Invalid index type of %d.\n", what); + return; + } + + + for (i=0; i 6*nr) { + for (i=0; irowval) { + n = mat->nrows; + ptr = mat->rowptr; + val = mat->rowval; + + #pragma omp parallel for if (ptr[n] > OMPMINOPS) private(j,sum) schedule(static) + for (i=0; i 0 */ + if (sum > 0) + sum = 1.0/sum; + } + else if (norm == 2) { + for (j=ptr[i]; j 0) + sum = 1.0/sqrt(sum); + } + for (j=ptr[i]; jcolval) { + n = mat->ncols; + ptr = mat->colptr; + val = mat->colval; + + #pragma omp parallel for if (ptr[n] > OMPMINOPS) private(j,sum) schedule(static) + for (i=0; i 0 */ + if (sum > 0) + sum = 1.0/sum; + } + else if (norm == 2) { + for (j=ptr[i]; j 0) + sum = 1.0/sqrt(sum); + } + for (j=ptr[i]; jnrows; + rowptr = mat->rowptr; + rowind = mat->rowind; + rowval = mat->rowval; + + switch (type) { + case GK_CSR_MAXTF: /* TF' = .5 + .5*TF/MAX(TF) */ + #pragma omp parallel for if (rowptr[nrows] > OMPMINOPS) private(j, maxtf) schedule(static) + for (i=0; i OMPMINOPS) private(j, maxtf) schedule(static) + for (i=0; i OMPMINOPS) private(j) schedule(static) + for (i=0; i OMPMINOPS) private(j) schedule(static) + for (i=0; i OMPMINOPS) private(j) schedule(static) + for (i=0; i OMPMINOPS) private(j) schedule(static) + for (i=0; i OMPMINOPS) private(j) schedule(static) + for (i=0; i OMPMINOPS) schedule(static,32) + for (i=0; i0.0 ? log(rowval[i]) : -log(-rowval[i]))*logscale; + } +#ifdef XXX + #pragma omp parallel for private(j) schedule(static) + for (i=0; i0.0 ? log(rowval[j]) : -log(-rowval[j]))*logscale; + //rowval[j] = 1+sign(rowval[j], log(fabs(rowval[j]))*logscale); + } + } +#endif + break; + + case GK_CSR_IDF: /* TF' = TF*IDF */ + ncols = mat->ncols; + cscale = gk_fmalloc(ncols, "gk_csr_Scale: cscale"); + collen = gk_ismalloc(ncols, 0, "gk_csr_Scale: collen"); + + for (i=0; i OMPMINOPS) schedule(static) + for (i=0; i 0 ? log(1.0*nrows/collen[i]) : 0.0); + + #pragma omp parallel for if (rowptr[nrows] > OMPMINOPS) private(j) schedule(static) + for (i=0; incols; + cscale = gk_fmalloc(ncols, "gk_csr_Scale: cscale"); + collen = gk_ismalloc(ncols, 0, "gk_csr_Scale: collen"); + + for (i=0; i OMPMINOPS) schedule(static) reduction(+:nnzcols) + for (i=0; i 0 ? 1 : 0); + + bgfreq = gk_max(10, (ssize_t)(.5*rowptr[nrows]/nnzcols)); + printf("nnz: %zd, nnzcols: %d, bgfreq: %d\n", rowptr[nrows], nnzcols, bgfreq); + + #pragma omp parallel for if (ncols > OMPMINOPS) schedule(static) + for (i=0; i 0 ? log(1.0*(nrows+2*bgfreq)/(bgfreq+collen[i])) : 0.0); + + #pragma omp parallel for if (rowptr[nrows] > OMPMINOPS) private(j) schedule(static) + for (i=0; inrows; + ptr = mat->rowptr; + val = mat->rowval; + + if (mat->rsums) + gk_free((void **)&mat->rsums, LTERM); + + sums = mat->rsums = gk_fsmalloc(n, 0, "gk_csr_ComputeSums: sums"); + break; + case GK_CSR_COL: + n = mat->ncols; + ptr = mat->colptr; + val = mat->colval; + + if (mat->csums) + gk_free((void **)&mat->csums, LTERM); + + sums = mat->csums = gk_fsmalloc(n, 0, "gk_csr_ComputeSums: sums"); + break; + default: + gk_errexit(SIGERR, "Invalid sum type of %d.\n", what); + return; + } + + if (val) { + #pragma omp parallel for if (ptr[n] > OMPMINOPS) schedule(static) + for (i=0; i OMPMINOPS) schedule(static) + for (i=0; inrows; + ptr = mat->rowptr; + val = mat->rowval; + + if (mat->rnorms) gk_free((void **)&mat->rnorms, LTERM); + + norms = mat->rnorms = gk_fsmalloc(n, 0, "gk_csr_ComputeSums: norms"); + break; + case GK_CSR_COL: + n = mat->ncols; + ptr = mat->colptr; + val = mat->colval; + + if (mat->cnorms) gk_free((void **)&mat->cnorms, LTERM); + + norms = mat->cnorms = gk_fsmalloc(n, 0, "gk_csr_ComputeSums: norms"); + break; + default: + gk_errexit(SIGERR, "Invalid norm type of %d.\n", what); + return; + } + + if (val) { + #pragma omp parallel for if (ptr[n] > OMPMINOPS) schedule(static) + for (i=0; i OMPMINOPS) schedule(static) + for (i=0; inrows; + ptr = mat->rowptr; + val = mat->rowval; + + if (mat->rnorms) gk_free((void **)&mat->rnorms, LTERM); + + norms = mat->rnorms = gk_fsmalloc(n, 0, "gk_csr_ComputeSums: norms"); + break; + case GK_CSR_COL: + n = mat->ncols; + ptr = mat->colptr; + val = mat->colval; + + if (mat->cnorms) gk_free((void **)&mat->cnorms, LTERM); + + norms = mat->cnorms = gk_fsmalloc(n, 0, "gk_csr_ComputeSums: norms"); + break; + default: + gk_errexit(SIGERR, "Invalid norm type of %d.\n", what); + return; + } + + if (val) { + #pragma omp parallel for if (ptr[n] > OMPMINOPS) schedule(static) + for (i=0; i OMPMINOPS) schedule(static) + for (i=0; inrows != mat->ncols) + gk_errexit(SIGERR, "The matrix is not square for a symmetric rowcol shuffling.\n"); + + nrows = mat->nrows; + ncols = mat->ncols; + rowptr = mat->rowptr; + rowind = mat->rowind; + rowval = mat->rowval; + + rperm = gk_imalloc(nrows, "gk_csr_Shuffle: rperm"); + cperm = gk_imalloc(ncols, "gk_csr_Shuffle: cperm"); + + switch (what) { + case GK_CSR_ROW: + gk_RandomPermute(nrows, rperm, 1); + for (i=0; i<20; i++) + gk_RandomPermute(nrows, rperm, 0); + + for (i=0; inrows = nrows; + nmat->ncols = ncols; + + nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_Shuffle: nrowptr"); + nrowind = nmat->rowind = gk_imalloc(rowptr[nrows], "gk_csr_Shuffle: nrowind"); + nrowval = nmat->rowval = (rowval ? gk_fmalloc(rowptr[nrows], "gk_csr_Shuffle: nrowval") : NULL) ; + + for (i=0; icolptr; + colind = mat->colind; + colval = mat->colval; + + mat->colptr = NULL; + mat->colind = NULL; + mat->colval = NULL; + + gk_csr_CreateIndex(mat, GK_CSR_COL); + + nmat = gk_csr_Create(); + nmat->nrows = mat->ncols; + nmat->ncols = mat->nrows; + nmat->rowptr = mat->colptr; + nmat->rowind = mat->colind; + nmat->rowval = mat->colval; + + mat->colptr = colptr; + mat->colind = colind; + mat->colval = colval; + + return nmat; + +} + + +/*************************************************************************/ +/*! Computes the similarity between two rows/columns + + \param mat the matrix itself. The routine assumes that the indices + are sorted in increasing order. + \param i1 is the first row/column, + \param i2 is the second row/column, + \param what is either GK_CSR_ROW or GK_CSR_COL indicating the type of + objects between the similarity will be computed, + \param simtype is the type of similarity and is one of GK_CSR_COS, + GK_CSR_JAC, GK_CSR_MIN, GK_CSR_AMIN + \returns the similarity between the two rows/columns. +*/ +/**************************************************************************/ +float gk_csr_ComputeSimilarity(gk_csr_t *mat, int i1, int i2, int what, + int simtype) +{ + int nind1, nind2; + int *ind1, *ind2; + float *val1, *val2, stat1, stat2, sim; + + switch (what) { + case GK_CSR_ROW: + if (!mat->rowptr) + gk_errexit(SIGERR, "Row-based view of the matrix does not exists.\n"); + nind1 = mat->rowptr[i1+1]-mat->rowptr[i1]; + nind2 = mat->rowptr[i2+1]-mat->rowptr[i2]; + ind1 = mat->rowind + mat->rowptr[i1]; + ind2 = mat->rowind + mat->rowptr[i2]; + val1 = mat->rowval + mat->rowptr[i1]; + val2 = mat->rowval + mat->rowptr[i2]; + break; + + case GK_CSR_COL: + if (!mat->colptr) + gk_errexit(SIGERR, "Column-based view of the matrix does not exists.\n"); + nind1 = mat->colptr[i1+1]-mat->colptr[i1]; + nind2 = mat->colptr[i2+1]-mat->colptr[i2]; + ind1 = mat->colind + mat->colptr[i1]; + ind2 = mat->colind + mat->colptr[i2]; + val1 = mat->colval + mat->colptr[i1]; + val2 = mat->colval + mat->colptr[i2]; + break; + + default: + gk_errexit(SIGERR, "Invalid index type of %d.\n", what); + return 0.0; + } + + + switch (simtype) { + case GK_CSR_COS: + case GK_CSR_JAC: + sim = stat1 = stat2 = 0.0; + i1 = i2 = 0; + while (i1 ind2[i2]) { + stat2 += val2[i2]*val2[i2]; + i2++; + } + else { + sim += val1[i1]*val2[i2]; + stat1 += val1[i1]*val1[i1]; + stat2 += val2[i2]*val2[i2]; + i1++; + i2++; + } + } + if (simtype == GK_CSR_COS) + sim = (stat1*stat2 > 0.0 ? sim/sqrt(stat1*stat2) : 0.0); + else + sim = (stat1+stat2-sim > 0.0 ? sim/(stat1+stat2-sim) : 0.0); + break; + + case GK_CSR_MIN: + sim = stat1 = stat2 = 0.0; + i1 = i2 = 0; + while (i1 ind2[i2]) { + stat2 += val2[i2]; + i2++; + } + else { + sim += gk_min(val1[i1],val2[i2]); + stat1 += val1[i1]; + stat2 += val2[i2]; + i1++; + i2++; + } + } + sim = (stat1+stat2-sim > 0.0 ? sim/(stat1+stat2-sim) : 0.0); + + break; + + case GK_CSR_AMIN: + sim = stat1 = stat2 = 0.0; + i1 = i2 = 0; + while (i1 ind2[i2]) { + stat2 += val2[i2]; + i2++; + } + else { + sim += gk_min(val1[i1],val2[i2]); + stat1 += val1[i1]; + stat2 += val2[i2]; + i1++; + i2++; + } + } + sim = (stat1 > 0.0 ? sim/stat1 : 0.0); + + break; + + default: + gk_errexit(SIGERR, "Unknown similarity measure %d\n", simtype); + return -1; + } + + return sim; + +} + + +/*************************************************************************/ +/*! Computes the similarity between two rows/columns + + \param mat_a the first matrix. The routine assumes that the indices + are sorted in increasing order. + \param mat_b the second matrix. The routine assumes that the indices + are sorted in increasing order. + \param i1 is the row/column from the first matrix (mat_a), + \param i2 is the row/column from the second matrix (mat_b), + \param what is either GK_CSR_ROW or GK_CSR_COL indicating the type of + objects between the similarity will be computed, + \param simtype is the type of similarity and is one of GK_CSR_COS, + GK_CSR_JAC, GK_CSR_MIN, GK_CSR_AMIN + \returns the similarity between the two rows/columns. +*/ +/**************************************************************************/ +float gk_csr_ComputePairSimilarity(gk_csr_t *mat_a, gk_csr_t *mat_b, + int i1, int i2, int what, int simtype) +{ + int nind1, nind2; + int *ind1, *ind2; + float *val1, *val2, stat1, stat2, sim; + + switch (what) { + case GK_CSR_ROW: + if (!mat_a->rowptr || !mat_b->rowptr) + gk_errexit(SIGERR, "Row-based view of the matrix does not exists.\n"); + nind1 = mat_a->rowptr[i1+1]-mat_a->rowptr[i1]; + nind2 = mat_b->rowptr[i2+1]-mat_b->rowptr[i2]; + ind1 = mat_a->rowind + mat_a->rowptr[i1]; + ind2 = mat_b->rowind + mat_b->rowptr[i2]; + val1 = mat_a->rowval + mat_a->rowptr[i1]; + val2 = mat_b->rowval + mat_b->rowptr[i2]; + break; + + case GK_CSR_COL: + if (!mat_a->colptr || !mat_b->colptr) + gk_errexit(SIGERR, "Column-based view of the matrix does not exists.\n"); + nind1 = mat_a->colptr[i1+1]-mat_a->colptr[i1]; + nind2 = mat_b->colptr[i2+1]-mat_b->colptr[i2]; + ind1 = mat_a->colind + mat_a->colptr[i1]; + ind2 = mat_b->colind + mat_b->colptr[i2]; + val1 = mat_a->colval + mat_a->colptr[i1]; + val2 = mat_b->colval + mat_b->colptr[i2]; + break; + + default: + gk_errexit(SIGERR, "Invalid index type of %d.\n", what); + return 0.0; + } + + + switch (simtype) { + case GK_CSR_COS: + case GK_CSR_JAC: + sim = stat1 = stat2 = 0.0; + i1 = i2 = 0; + while (i1 ind2[i2]) { + stat2 += val2[i2]*val2[i2]; + i2++; + } + else { + sim += val1[i1]*val2[i2]; + stat1 += val1[i1]*val1[i1]; + stat2 += val2[i2]*val2[i2]; + i1++; + i2++; + } + } + if (simtype == GK_CSR_COS) + sim = (stat1*stat2 > 0.0 ? sim/sqrt(stat1*stat2) : 0.0); + else + sim = (stat1+stat2-sim > 0.0 ? sim/(stat1+stat2-sim) : 0.0); + break; + + case GK_CSR_MIN: + sim = stat1 = stat2 = 0.0; + i1 = i2 = 0; + while (i1 ind2[i2]) { + stat2 += val2[i2]; + i2++; + } + else { + sim += gk_min(val1[i1],val2[i2]); + stat1 += val1[i1]; + stat2 += val2[i2]; + i1++; + i2++; + } + } + sim = (stat1+stat2-sim > 0.0 ? sim/(stat1+stat2-sim) : 0.0); + + break; + + case GK_CSR_AMIN: + sim = stat1 = stat2 = 0.0; + i1 = i2 = 0; + while (i1 ind2[i2]) { + stat2 += val2[i2]; + i2++; + } + else { + sim += gk_min(val1[i1],val2[i2]); + stat1 += val1[i1]; + stat2 += val2[i2]; + i1++; + i2++; + } + } + sim = (stat1 > 0.0 ? sim/stat1 : 0.0); + + break; + + default: + gk_errexit(SIGERR, "Unknown similarity measure %d\n", simtype); + return -1; + } + + return sim; + +} + +/*************************************************************************/ +/*! Finds the n most similar rows (neighbors) to the query. + + \param mat the matrix itself + \param nqterms is the number of columns in the query + \param qind is the list of query columns + \param qval is the list of correspodning query weights + \param simtype is the type of similarity and is one of GK_CSR_DOTP, + GK_CSR_COS, GK_CSR_JAC, GK_CSR_MIN, GK_CSR_AMIN. In case of + GK_CSR_COS, the rows and the query are assumed to be of unit + length. + \param nsim is the maximum number of requested most similar rows. + If -1 is provided, then everything is returned unsorted. + \param minsim is the minimum similarity of the requested most + similar rows + \param hits is the result set. This array should be at least + of length nsim. + \param i_marker is an array of size equal to the number of rows + whose values are initialized to -1. If NULL is provided + then this array is allocated and freed internally. + \param i_cand is an array of size equal to the number of rows. + If NULL is provided then this array is allocated and freed + internally. + \returns The number of identified most similar rows, which can be + smaller than the requested number of nnbrs in those cases + in which there are no sufficiently many neighbors. +*/ +/**************************************************************************/ +int gk_csr_GetSimilarRows(gk_csr_t *mat, int nqterms, int *qind, + float *qval, int simtype, int nsim, float minsim, gk_fkv_t *hits, + int *i_marker, gk_fkv_t *i_cand) +{ + ssize_t i, ii, j, k; + int nrows, ncols, ncand; + ssize_t *colptr; + int *colind, *marker; + float *colval, *rnorms, mynorm, *rsums, mysum; + gk_fkv_t *cand; + + if (nqterms == 0) + return 0; + + nrows = mat->nrows; + ncols = mat->ncols; + GKASSERT((colptr = mat->colptr) != NULL); + GKASSERT((colind = mat->colind) != NULL); + GKASSERT((colval = mat->colval) != NULL); + + marker = (i_marker ? i_marker : gk_ismalloc(nrows, -1, "gk_csr_SimilarRows: marker")); + cand = (i_cand ? i_cand : gk_fkvmalloc(nrows, "gk_csr_SimilarRows: cand")); + + switch (simtype) { + case GK_CSR_DOTP: + case GK_CSR_COS: + for (ncand=0, ii=0; iirnorms) != NULL); + mynorm = gk_fdot(nqterms, qval, 1, qval, 1); + + for (i=0; irsums) != NULL); + mysum = gk_fsum(nqterms, qval, 1); + + for (i=0; i= minsim) + cand[j++] = cand[i]; + } + ncand = j; + + if (nsim == -1 || nsim >= ncand) { + nsim = ncand; + } + else { + nsim = gk_min(nsim, ncand); + gk_dfkvkselect(ncand, nsim, cand); + gk_fkvsortd(nsim, cand); + } + + gk_fkvcopy(nsim, cand, hits); + + if (i_marker == NULL) + gk_free((void **)&marker, LTERM); + if (i_cand == NULL) + gk_free((void **)&cand, LTERM); + + return nsim; +} + + +/*************************************************************************/ +/*! Returns a symmetric version of a square matrix. The symmetric version + is constructed by applying an A op A^T operation, where op is one of + GK_CSR_SYM_SUM, GK_CSR_SYM_MIN, GK_CSR_SYM_MAX, GK_CSR_SYM_AVG. + + \param mat the matrix to be symmetrized, + \param op indicates the operation to be performed. The possible values are + GK_CSR_SYM_SUM, GK_CSR_SYM_MIN, GK_CSR_SYM_MAX, and GK_CSR_SYM_AVG. + + \returns the symmetrized matrix consisting only of its row-based structure. + The input matrix is not modified. +*/ +/**************************************************************************/ +gk_csr_t *gk_csr_MakeSymmetric(gk_csr_t *mat, int op) +{ + ssize_t i, j, k, nnz; + int nrows, nadj, hasvals; + ssize_t *rowptr, *colptr, *nrowptr; + int *rowind, *colind, *nrowind, *marker, *ids; + float *rowval=NULL, *colval=NULL, *nrowval=NULL, *wgts=NULL; + gk_csr_t *nmat; + + if (mat->nrows != mat->ncols) { + fprintf(stderr, "gk_csr_MakeSymmetric: The matrix needs to be square.\n"); + return NULL; + } + + hasvals = (mat->rowval != NULL); + + nrows = mat->nrows; + rowptr = mat->rowptr; + rowind = mat->rowind; + if (hasvals) + rowval = mat->rowval; + + /* create the column view for efficient processing */ + colptr = gk_zsmalloc(nrows+1, 0, "colptr"); + colind = gk_i32malloc(rowptr[nrows], "colind"); + if (hasvals) + colval = gk_fmalloc(rowptr[nrows], "colval"); + + for (i=0; inrows = mat->nrows; + nmat->ncols = mat->ncols; + + nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_MakeSymmetric: nrowptr"); + nrowind = nmat->rowind = gk_imalloc(2*rowptr[nrows], "gk_csr_MakeSymmetric: nrowind"); + if (hasvals) + nrowval = nmat->rowval = gk_fmalloc(2*rowptr[nrows], "gk_csr_MakeSymmetric: nrowval"); + + marker = gk_ismalloc(nrows, -1, "marker"); + ids = gk_imalloc(nrows, "ids"); + if (hasvals) + wgts = gk_fmalloc(nrows, "wgts"); + + nrowptr[0] = nnz = 0; + for (i=0; inrows+1. + \param cind is the indices structure of the CSR representation of + the components. The length of this vector must be mat->nrows. + \param cids is an array that stores the component # of each vertex + of the graph. The length of this vector must be mat->nrows. + + \returns the number of components that it found. + + \note The cptr, cind, and cids parameters can be NULL, in which case + only the number of connected components is returned. +*/ +/*************************************************************************/ +int gk_csr_FindConnectedComponents(gk_csr_t *mat, int32_t *cptr, int32_t *cind, + int32_t *cids) +{ + ssize_t i, ii, j, jj, k, nvtxs, first, last, ntodo, ncmps; + ssize_t *xadj; + int32_t *adjncy, *pos, *todo; + int32_t mustfree_ccsr=0, mustfree_where=0; + + if (mat->nrows != mat->ncols) { + fprintf(stderr, "gk_csr_FindComponents: The matrix needs to be square.\n"); + return -1; + } + + nvtxs = mat->nrows; + xadj = mat->rowptr; + adjncy = mat->rowind; + + /* Deal with NULL supplied cptr/cind vectors */ + if (cptr == NULL) { + cptr = gk_i32malloc(nvtxs+1, "gk_csr_FindComponents: cptr"); + cind = gk_i32malloc(nvtxs, "gk_csr_FindComponents: cind"); + mustfree_ccsr = 1; + } + + /* The list of vertices that have not been touched yet. + The valid entries are from [0..ntodo). */ + todo = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_csr_FindComponents: todo")); + + /* For a vertex that has not been visited, pos[i] is the position in the + todo list that this vertex is stored. + If a vertex has been visited, pos[i] = -1. */ + pos = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_csr_FindComponents: pos")); + + + /* Find the connected componends */ + ncmps = -1; + ntodo = nvtxs; /* All vertices have not been visited */ + first = last = 0; /* Point to the first and last vertices that have been touched + but not explored. + These vertices are stored in cind[first]...cind[last-1]. */ + + while (first < last || ntodo > 0) { + if (first == last) { /* Find another starting vertex */ + cptr[++ncmps] = first; /* Mark the end of the current CC */ + + /* put the first vertex in the todo list as the start of the new CC */ + ASSERT(pos[todo[0]] != -1); + cind[last++] = todo[0]; + + pos[todo[0]] = -1; + todo[0] = todo[--ntodo]; + pos[todo[0]] = 0; + } + + i = cind[first++]; /* Get the first visited but unexplored vertex */ + + for (j=xadj[i]; jnrows != mat->ncols) { + fprintf(stderr, "gk_csr_ReorderSymmetric: The matrix needs to be square.\n"); + return NULL; + } + + if (perm == NULL && iperm == NULL) + return NULL; + + nrows = mat->nrows; + rowptr = mat->rowptr; + rowind = mat->rowind; + rowval = mat->rowval; + + nmat = gk_csr_Create(); + + nmat->nrows = nrows; + nmat->ncols = nrows; + + nrowptr = nmat->rowptr = gk_zmalloc(nrows+1, "gk_csr_ReorderSymmetric: rowptr"); + nrowind = nmat->rowind = gk_i32malloc(rowptr[nrows], "gk_csr_ReorderSymmetric: rowind"); + nrowval = nmat->rowval = gk_fmalloc(rowptr[nrows], "gk_csr_ReorderSymmetric: rowval"); + + /* allocate memory for the different structures present in the matrix */ + if (mat->rlabels) + nmat->rlabels = gk_i32malloc(nrows, "gk_csr_ReorderSymmetric: rlabels"); + if (mat->rmap) + nmat->rmap = gk_i32malloc(nrows, "gk_csr_ReorderSymmetric: rmap"); + if (mat->rnorms) + nmat->rnorms = gk_fmalloc(nrows, "gk_csr_ReorderSymmetric: rnorms"); + if (mat->rsums) + nmat->rsums = gk_fmalloc(nrows, "gk_csr_ReorderSymmetric: rsums"); + if (mat->rsizes) + nmat->rsizes = gk_fmalloc(nrows, "gk_csr_ReorderSymmetric: rsizes"); + if (mat->rvols) + nmat->rvols = gk_fmalloc(nrows, "gk_csr_ReorderSymmetric: rvols"); + if (mat->rwgts) + nmat->rwgts = gk_fmalloc(nrows, "gk_csr_ReorderSymmetric: rwgts"); + + if (mat->clabels) + nmat->clabels = gk_i32malloc(nrows, "gk_csr_ReorderSymmetric: clabels"); + if (mat->cmap) + nmat->cmap = gk_i32malloc(nrows, "gk_csr_ReorderSymmetric: cmap"); + if (mat->cnorms) + nmat->cnorms = gk_fmalloc(nrows, "gk_csr_ReorderSymmetric: cnorms"); + if (mat->csums) + nmat->csums = gk_fmalloc(nrows, "gk_csr_ReorderSymmetric: csums"); + if (mat->csizes) + nmat->csizes = gk_fmalloc(nrows, "gk_csr_ReorderSymmetric: csizes"); + if (mat->cvols) + nmat->cvols = gk_fmalloc(nrows, "gk_csr_ReorderSymmetric: cvols"); + if (mat->cwgts) + nmat->cwgts = gk_fmalloc(nrows, "gk_csr_ReorderSymmetric: cwgts"); + + + + /* create perm/iperm if not provided */ + if (perm == NULL) { + freeperm = 1; + perm = gk_i32malloc(nrows, "gk_csr_ReorderSymmetric: perm"); + for (i=0; irlabels) + nmat->rlabels[v] = mat->rlabels[u]; + if (mat->rmap) + nmat->rmap[v] = mat->rmap[u]; + if (mat->rnorms) + nmat->rnorms[v] = mat->rnorms[u]; + if (mat->rsums) + nmat->rsums[v] = mat->rsums[u]; + if (mat->rsizes) + nmat->rsizes[v] = mat->rsizes[u]; + if (mat->rvols) + nmat->rvols[v] = mat->rvols[u]; + if (mat->rwgts) + nmat->rwgts[v] = mat->rwgts[u]; + + if (mat->clabels) + nmat->clabels[v] = mat->clabels[u]; + if (mat->cmap) + nmat->cmap[v] = mat->cmap[u]; + if (mat->cnorms) + nmat->cnorms[v] = mat->cnorms[u]; + if (mat->csums) + nmat->csums[v] = mat->csums[u]; + if (mat->csizes) + nmat->csizes[v] = mat->csizes[u]; + if (mat->cvols) + nmat->cvols[v] = mat->cvols[u]; + if (mat->cwgts) + nmat->cwgts[v] = mat->cwgts[u]; + + nrowptr[v+1] = jj; + } + + + /* free memory */ + if (freeperm) + gk_free((void **)&perm, LTERM); + if (freeiperm) + gk_free((void **)&iperm, LTERM); + + return nmat; +} + + +/*************************************************************************/ +/*! This function computes a permutation of the rows/columns of a symmetric + matrix based on a breadth-first-traversal. It can be used for re-ordering + the matrix to reduce its bandwidth for better cache locality. + + \param[IN] mat is the matrix whose ordering to be computed. + \param[IN] maxdegree is the maximum number of nonzeros of the rows that + will participate in the BFS ordering. Rows with more nonzeros + will be put at the front of the ordering in decreasing degree + order. + \param[IN] v is the starting row of the BFS. A value of -1 indicates that + a randomly selected row will be used. + \param[OUT] perm[i] stores the ID of row i in the re-ordered matrix. + \param[OUT] iperm[i] stores the ID of the row that corresponds to + the ith vertex in the re-ordered matrix. + + \note The perm or iperm (but not both) can be NULL, at which point, + the corresponding arrays are not returned. Though the program + works fine when both are NULL, doing that is not smart. + The returned arrays should be freed with gk_free(). +*/ +/*************************************************************************/ +void gk_csr_ComputeBFSOrderingSymmetric(gk_csr_t *mat, int maxdegree, int v, + int32_t **r_perm, int32_t **r_iperm) +{ + int i, k, nrows, first, last; + ssize_t j, *rowptr; + int32_t *rowind, *cot, *pos; + + if (mat->nrows != mat->ncols) { + fprintf(stderr, "gk_csr_ComputeBFSOrderingSymmetric: The matrix needs to be square.\n"); + return; + } + if (maxdegree < mat->nrows && v != -1) { + fprintf(stderr, "gk_csr_ComputeBFSOrderingSymmetric: Since maxdegree node renumbering is requested the starting row should be -1.\n"); + return; + } + if (mat->nrows <= 0) + return; + + nrows = mat->nrows; + rowptr = mat->rowptr; + rowind = mat->rowind; + + /* This array will function like pos + touched of the CC method */ + pos = gk_i32incset(nrows, 0, gk_i32malloc(nrows, "gk_csr_ComputeBFSOrderingSymmetric: pos")); + + /* This array ([C]losed[O]pen[T]odo => cot) serves three purposes. + Positions from [0...first) is the current iperm[] vector of the explored rows; + Positions from [first...last) is the OPEN list (i.e., visited rows); + Positions from [last...nrows) is the todo list. */ + cot = gk_i32incset(nrows, 0, gk_i32malloc(nrows, "gk_csr_ComputeBFSOrderingSymmetric: cot")); + + first = last = 0; + + /* deal with maxdegree handling */ + if (maxdegree < nrows) { + last = nrows; + for (i=nrows-1; i>=0; i--) { + if (rowptr[i+1]-rowptr[i] < maxdegree) { + cot[--last] = i; + pos[i] = last; + } + else { + cot[first++] = i; + pos[i] = -1; + } + } + GKASSERT(first == last); + + if (last > 0) { /* reorder them in degree decreasing order */ + gk_ikv_t *cand = gk_ikvmalloc(first, "gk_csr_ComputeBFSOrderingSymmetric: cand"); + + for (i=0; inrows != mat->ncols) { + fprintf(stderr, "gk_csr_ComputeBestFOrderingSymmetric: The matrix needs to be square.\n"); + return; + } + if (mat->nrows <= 0) + return; + + nrows = mat->nrows; + rowptr = mat->rowptr; + rowind = mat->rowind; + + + /* the degree of the vertices in the closed list */ + degrees = gk_i32smalloc(nrows, 0, "gk_csr_ComputeBestFOrderingSymmetric: degrees"); + + /* the weighted degree of the vertices in the closed list for type==3 */ + wdegrees = gk_i32smalloc(nrows, 0, "gk_csr_ComputeBestFOrderingSymmetric: wdegrees"); + + /* the sum of differences for type==4 */ + sod = gk_i32smalloc(nrows, 0, "gk_csr_ComputeBestFOrderingSymmetric: sod"); + + /* the encountering level of a vertex type==5 */ + level = gk_i32smalloc(nrows, 0, "gk_csr_ComputeBestFOrderingSymmetric: level"); + + /* The open+todo list of vertices. + The vertices from [0..nopen] are the open vertices. + The vertices from [nopen..ntodo) are the todo vertices. + */ + ot = gk_i32incset(nrows, 0, gk_i32malloc(nrows, "gk_csr_ComputeBestFOrderingSymmetric: ot")); + + /* For a vertex that has not been explored, pos[i] is the position in the ot list. */ + pos = gk_i32incset(nrows, 0, gk_i32malloc(nrows, "gk_csr_ComputeBestFOrderingSymmetric: pos")); + + /* if perm[i] >= 0, then perm[i] is the order of vertex i; otherwise perm[i] == -1. */ + perm = gk_i32smalloc(nrows, -1, "gk_csr_ComputeBestFOrderingSymmetric: perm"); + + /* create the queue and put the starting vertex in it */ + queue = gk_i32pqCreate(nrows); + gk_i32pqInsert(queue, v, 1); + + /* put v at the front of the open list */ + pos[0] = ot[0] = v; + pos[v] = ot[v] = 0; + nopen = 1; + ntodo = nrows; + + /* start processing the nodes */ + for (i=0; i= nopen) + gk_errexit(SIGERR, "The position of v is not in open list. pos[%d]=%d is >=%d.\n", v, pos[v], nopen); + + /* remove v from the open list and re-arrange the todo part of the list */ + ot[pos[v]] = ot[nopen-1]; + pos[ot[nopen-1]] = pos[v]; + if (ntodo > nopen) { + ot[nopen-1] = ot[ntodo-1]; + pos[ot[ntodo-1]] = nopen-1; + } + nopen--; + ntodo--; + + for (j=rowptr[v]; j + + +/* These are the jmp_buf for the graceful exit in case of severe errors. + Multiple buffers are defined to allow for recursive invokation. */ +#define MAX_JBUFS 128 +__thread int gk_cur_jbufs=-1; +__thread jmp_buf gk_jbufs[MAX_JBUFS]; +__thread jmp_buf gk_jbuf; + +typedef void (*gksighandler_t)(int); + +/* These are the holders of the old singal handlers for the trapped signals */ +static __thread gksighandler_t old_SIGMEM_handler; /* Custom signal */ +static __thread gksighandler_t old_SIGERR_handler; /* Custom signal */ +static __thread gksighandler_t old_SIGMEM_handlers[MAX_JBUFS]; /* Custom signal */ +static __thread gksighandler_t old_SIGERR_handlers[MAX_JBUFS]; /* Custom signal */ + +/* The following is used to control if the gk_errexit() will actually abort or not. + There is always a single copy of this variable */ +static int gk_exit_on_error = 1; + + +/*************************************************************************/ +/*! This function sets the gk_exit_on_error variable + */ +/*************************************************************************/ +void gk_set_exit_on_error(int value) +{ + gk_exit_on_error = value; +} + + + +/*************************************************************************/ +/*! This function prints an error message and exits + */ +/*************************************************************************/ +void errexit(char *f_str,...) +{ + va_list argp; + + va_start(argp, f_str); + vfprintf(stderr, f_str, argp); + va_end(argp); + + if (strlen(f_str) == 0 || f_str[strlen(f_str)-1] != '\n') + fprintf(stderr,"\n"); + fflush(stderr); + + if (gk_exit_on_error) + exit(-2); + + /* abort(); */ +} + + +/*************************************************************************/ +/*! This function prints an error message and raises a signum signal + */ +/*************************************************************************/ +void gk_errexit(int signum, char *f_str,...) +{ + va_list argp; + + va_start(argp, f_str); + vfprintf(stderr, f_str, argp); + va_end(argp); + + fprintf(stderr,"\n"); + fflush(stderr); + + if (gk_exit_on_error) + raise(signum); +} + + +/***************************************************************************/ +/*! This function sets a number of signal handlers and sets the return point + of a longjmp +*/ +/***************************************************************************/ +int gk_sigtrap() +{ + if (gk_cur_jbufs+1 >= MAX_JBUFS) + return 0; + + gk_cur_jbufs++; + + old_SIGMEM_handlers[gk_cur_jbufs] = signal(SIGMEM, gk_sigthrow); + old_SIGERR_handlers[gk_cur_jbufs] = signal(SIGERR, gk_sigthrow); + + return 1; +} + + +/***************************************************************************/ +/*! This function sets the handlers for the signals to their default handlers + */ +/***************************************************************************/ +int gk_siguntrap() +{ + if (gk_cur_jbufs == -1) + return 0; + + signal(SIGMEM, old_SIGMEM_handlers[gk_cur_jbufs]); + signal(SIGERR, old_SIGERR_handlers[gk_cur_jbufs]); + + gk_cur_jbufs--; + + return 1; +} + + +/*************************************************************************/ +/*! This function is the custome signal handler, which all it does is to + perform a longjump to the most recent saved environment + */ +/*************************************************************************/ +void gk_sigthrow(int signum) +{ + longjmp(gk_jbufs[gk_cur_jbufs], signum); +} + + +/*************************************************************************** +* This function sets a number of signal handlers and sets the return point +* of a longjmp +****************************************************************************/ +void gk_SetSignalHandlers() +{ + old_SIGMEM_handler = signal(SIGMEM, gk_NonLocalExit_Handler); + old_SIGERR_handler = signal(SIGERR, gk_NonLocalExit_Handler); +} + + +/*************************************************************************** +* This function sets the handlers for the signals to their default handlers +****************************************************************************/ +void gk_UnsetSignalHandlers() +{ + signal(SIGMEM, old_SIGMEM_handler); + signal(SIGERR, old_SIGERR_handler); +} + + +/************************************************************************* +* This function is the handler for SIGUSR1 that implements the cleaning up +* process prior to a non-local exit. +**************************************************************************/ +void gk_NonLocalExit_Handler(int signum) +{ + longjmp(gk_jbuf, signum); +} + + +/*************************************************************************/ +/*! \brief Thread-safe implementation of strerror() */ +/**************************************************************************/ +char *gk_strerror(int errnum) +{ +#if defined(WIN32) || defined(__MINGW32__) + return strerror(errnum); +#else +#ifndef SUNOS + static __thread char buf[1024]; + + strerror_r(errnum, buf, 1024); + + buf[1023] = '\0'; + return buf; +#else + return strerror(errnum); +#endif +#endif +} + + + +/************************************************************************* +* This function prints a backtrace of calling functions +**************************************************************************/ +void PrintBackTrace() +{ +#ifdef HAVE_EXECINFO_H + void *array[10]; + int i, size; + char **strings; + + size = backtrace(array, 10); + strings = backtrace_symbols(array, size); + + printf("Obtained %d stack frames.\n", size); + for (i=0; i + +/********************************************************************** + * This function computes the max accuracy score of a ranked list, + * given +1/-1 class list + **********************************************************************/ +float ComputeAccuracy(int n, gk_fkv_t *list) +{ + int i, P, N, TP, FN = 0; + float bAccuracy = 0.0; + float acc; + + for (P=0, i=0;i bAccuracy) + bAccuracy = acc; + } + + return bAccuracy; +} + + +/***************************************************************************** + * This function computes the ROC score of a ranked list, given a +1/-1 class + * list. + ******************************************************************************/ +float ComputeROCn(int n, int maxN, gk_fkv_t *list) +{ + int i, P, TP, FP, TPprev, FPprev, AUC; + float prev; + + FP = TP = FPprev = TPprev = AUC = 0; + prev = list[0].key -1; + + for (P=0, i=0; i 0 ? (float)(1.0*AUC/(P*FP)) : 0.0); +} + + +/***************************************************************************** +* This function computes the median rate of false positive for each positive +* instance. +******************************************************************************/ +float ComputeMedianRFP(int n, gk_fkv_t *list) +{ + int i, P, N, TP, FP; + + P = N = 0; + for (i=0; i + +/* Byte-wise swap two items of size SIZE. */ +#define QSSWAP(a, b, stmp) do { stmp = (a); (a) = (b); (b) = stmp; } while (0) + + +/******************************************************************************/ +/*! This function puts the 'topk' largest values in the beginning of the array */ +/*******************************************************************************/ +int gk_dfkvkselect(size_t n, int topk, gk_fkv_t *cand) +{ + int i, j, lo, hi, mid; + gk_fkv_t stmp; + float pivot; + + if (n <= topk) + return n; /* return if the array has fewer elements than we want */ + + for (lo=0, hi=n-1; lo < hi;) { + mid = lo + ((hi-lo) >> 1); + + /* select the median */ + if (cand[lo].key < cand[mid].key) + mid = lo; + if (cand[hi].key > cand[mid].key) + mid = hi; + else + goto jump_over; + if (cand[lo].key < cand[mid].key) + mid = lo; + +jump_over: + QSSWAP(cand[mid], cand[hi], stmp); + pivot = cand[hi].key; + + /* the partitioning algorithm */ + for (i=lo-1, j=lo; j= pivot) { + i++; + QSSWAP(cand[i], cand[j], stmp); + } + } + i++; + QSSWAP(cand[i], cand[hi], stmp); + + + if (i > topk) + hi = i-1; + else if (i < topk) + lo = i+1; + else + break; + } + +/* + if (cand[lo].key < cand[hi].key) + printf("Hmm Error: %d %d %d %f %f\n", i, lo, hi, cand[lo].key, cand[hi].key); + + + for (i=topk; i cand[j].key) + printf("Hmm Error: %d %d %f %f %d %d\n", i, j, cand[i].key, cand[j].key, lo, hi); + } +*/ + + return topk; +} + + +/******************************************************************************/ +/*! This function puts the 'topk' smallest values in the beginning of the array */ +/*******************************************************************************/ +int gk_ifkvkselect(size_t n, int topk, gk_fkv_t *cand) +{ + int i, j, lo, hi, mid; + gk_fkv_t stmp; + float pivot; + + if (n <= topk) + return n; /* return if the array has fewer elements than we want */ + + for (lo=0, hi=n-1; lo < hi;) { + mid = lo + ((hi-lo) >> 1); + + /* select the median */ + if (cand[lo].key > cand[mid].key) + mid = lo; + if (cand[hi].key < cand[mid].key) + mid = hi; + else + goto jump_over; + if (cand[lo].key > cand[mid].key) + mid = lo; + +jump_over: + QSSWAP(cand[mid], cand[hi], stmp); + pivot = cand[hi].key; + + /* the partitioning algorithm */ + for (i=lo-1, j=lo; j topk) + hi = i-1; + else if (i < topk) + lo = i+1; + else + break; + } + +/* + if (cand[lo].key > cand[hi].key) + printf("Hmm Error: %d %d %d %f %f\n", i, lo, hi, cand[lo].key, cand[hi].key); + + + for (i=topk; i + + + +/************************************************************************* +* This function checks if a file exists +**************************************************************************/ +int gk_fexists(char *fname) +{ + struct stat status; + + if (stat(fname, &status) == -1) + return 0; + + return S_ISREG(status.st_mode); +} + + +/************************************************************************* +* This function checks if a directory exists +**************************************************************************/ +int gk_dexists(char *dirname) +{ + struct stat status; + + if (stat(dirname, &status) == -1) + return 0; + + return S_ISDIR(status.st_mode); +} + + +/*************************************************************************/ +/*! \brief Returns the size of the file in bytes + +This function returns the size of a file as a 64 bit integer. If there +were any errors in stat'ing the file, -1 is returned. +\note That due to the -1 return code, the maximum file size is limited to + 63 bits (which I guess is okay for now). +*/ +/**************************************************************************/ +ssize_t gk_getfsize(char *filename) +{ + struct stat status; + + if (stat(filename, &status) == -1) + return -1; + + return (size_t)(status.st_size); +} + + +/*************************************************************************/ +/*! This function gets some basic statistics about the file. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. + \param r_ntokens is the number of tokens in the file. If it is NULL, + this information is not returned. + \param r_max_nlntokens is the maximum number of tokens in any line + in the file. If it is NULL this information is not returned. + \param r_nbytes is the number of bytes in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +void gk_getfilestats(char *fname, size_t *r_nlines, size_t *r_ntokens, + size_t *r_max_nlntokens, size_t *r_nbytes) +{ + size_t nlines=0, ntokens=0, max_nlntokens=0, nbytes=0, oldntokens=0, nread; + int intoken=0; + char buffer[4097], *cptr; + FILE *fpin; + + fpin = gk_fopen(fname, "r", "gk_GetFileStats"); + + while (!feof(fpin)) { + nread = fread(buffer, sizeof(char), 4096, fpin); + nbytes += nread; + + buffer[nread] = '\0'; /* There is space for this one */ + for (cptr=buffer; *cptr!='\0'; cptr++) { + if (*cptr == '\n') { + nlines++; + ntokens += intoken; + intoken = 0; + if (max_nlntokens < ntokens-oldntokens) + max_nlntokens = ntokens-oldntokens; + oldntokens = ntokens; + } + else if (*cptr == ' ' || *cptr == '\t') { + ntokens += intoken; + intoken = 0; + } + else { + intoken = 1; + } + } + } + ntokens += intoken; + if (max_nlntokens < ntokens-oldntokens) + max_nlntokens = ntokens-oldntokens; + + gk_fclose(fpin); + + if (r_nlines != NULL) + *r_nlines = nlines; + if (r_ntokens != NULL) + *r_ntokens = ntokens; + if (r_max_nlntokens != NULL) + *r_max_nlntokens = max_nlntokens; + if (r_nbytes != NULL) + *r_nbytes = nbytes; +} + + +/************************************************************************* +* This function takes in a potentially full path specification of a file +* and just returns a string containing just the basename of the file. +* The basename is derived from the actual filename by stripping the last +* .ext part. +**************************************************************************/ +char *gk_getbasename(char *path) +{ + char *startptr, *endptr; + char *basename; + + if ((startptr = strrchr(path, '/')) == NULL) + startptr = path; + else + startptr = startptr+1; + + basename = gk_strdup(startptr); + + if ((endptr = strrchr(basename, '.')) != NULL) + *endptr = '\0'; + + return basename; +} + +/************************************************************************* +* This function takes in a potentially full path specification of a file +* and just returns a string corresponding to its file extension. The +* extension of a file is considered to be the string right after the +* last '.' character. +**************************************************************************/ +char *gk_getextname(char *path) +{ + char *startptr; + + if ((startptr = strrchr(path, '.')) == NULL) + return gk_strdup(path); + else + return gk_strdup(startptr+1); +} + +/************************************************************************* +* This function takes in a potentially full path specification of a file +* and just returns a string containing just the filename. +**************************************************************************/ +char *gk_getfilename(char *path) +{ + char *startptr; + + if ((startptr = strrchr(path, '/')) == NULL) + return gk_strdup(path); + else + return gk_strdup(startptr+1); +} + +/************************************************************************* +* This function takes in a potentially full path specification of a file +* and extracts the directory path component if it exists, otherwise it +* returns "./" as the path. The memory for it is dynamically allocated. +**************************************************************************/ +char *getpathname(char *path) +{ + char *endptr, *tmp; + + if ((endptr = strrchr(path, '/')) == NULL) { + return gk_strdup("."); + } + else { + tmp = gk_strdup(path); + *(strrchr(tmp, '/')) = '\0'; + return tmp; + } +} + + + +/************************************************************************* +* This function creates a path +**************************************************************************/ +int gk_mkpath(char *pathname) +{ + char tmp[2048]; + + sprintf(tmp, "mkdir -p %s", pathname); + return system(tmp); +} + + +/************************************************************************* +* This function deletes a directory tree and all of its contents +**************************************************************************/ +int gk_rmpath(char *pathname) +{ + char tmp[2048]; + + sprintf(tmp, "rm -r %s", pathname); + return system(tmp); +} diff --git a/getopt.c b/getopt.c new file mode 100644 index 0000000..2e7e042 --- /dev/null +++ b/getopt.c @@ -0,0 +1,855 @@ +/*************************************************************************/ +/*! \file getopt.c +\brief Command line parsing + +This file contains a implementation of GNU's Getopt facility. The purpose +for including it here is to ensure portability across different unix- and +windows-based systems. + +\warning +The implementation provided here uses the \c gk_ prefix for all variables +used by the standard Getopt facility to communicate with the program. +So, do read the documentation here. + +\verbatim + Copyright (C) 1987,88,89,90,91,92,93,94,95,96,98,99,2000,2001 + Free Software Foundation, Inc. This file is part of the GNU C Library. + + The GNU C Library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2.1 of the License, or (at your option) any later version. + + The GNU C Library 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 + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with the GNU C Library; if not, write to the Free + Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA + 02111-1307 USA. +\endverbatim +*/ +/*************************************************************************/ + + +#include + +/*************************************************************************/ +/* Local function prototypes */ +/*************************************************************************/ +static void exchange (char **); +static char *gk_getopt_initialize (int, char **, char *); +static int gk_getopt_internal(int argc, char **argv, char *optstring, + struct gk_option *longopts, int *longind, int long_only); + + + +/*************************************************************************/ +/*! \brief For communication arguments to the caller. + +This variable is set by getopt to point at the value of the option argument, +for those options that accept arguments. +*/ +/*************************************************************************/ +char *gk_optarg; + + +/*************************************************************************/ +/*! \brief Index in ARGV of the next element to be scanned. + +This variable is set by getopt to the index of the next element of the argv +array to be processed. Once getopt has found all of the option arguments, +you can use this variable to determine where the remaining non-option arguments +begin. +*/ +/*************************************************************************/ +int gk_optind = 1; + + +/*************************************************************************/ +/*! \brief Controls error reporting for unrecognized options. + +If the value of this variable is nonzero, then getopt prints an error +message to the standard error stream if it encounters an unknown option +character or an option with a missing required argument. This is the default +behavior. If you set this variable to zero, getopt does not print any messages, +but it still returns the character ? to indicate an error. +*/ +/*************************************************************************/ +int gk_opterr = 1; + + +/*************************************************************************/ +/*! \brief Stores unknown option characters + +When getopt encounters an unknown option character or an option with a +missing required argument, it stores that option character in this +variable. You can use this for providing your own diagnostic messages. +*/ +/*************************************************************************/ +int gk_optopt = '?'; + + +/*************************************************************************/ +/* +Records that the getopt facility has been initialized. +*/ +/*************************************************************************/ +int gk_getopt_initialized; + + +/*************************************************************************/ +/* +The next char to be scanned in the option-element in which the last option +character we returned was found. This allows us to pick up the scan where +we left off. + +If this is zero, or a null string, it means resume the scan by advancing +to the next ARGV-element. +*/ +/*************************************************************************/ +static char *nextchar; + + +/*************************************************************************/ +/* +Value of POSIXLY_CORRECT environment variable. +*/ +/*************************************************************************/ +static char *posixly_correct; + + +/*************************************************************************/ +/* +Describe how to deal with options that follow non-option ARGV-elements. + +If the caller did not specify anything, the default is REQUIRE_ORDER if +the environment variable POSIXLY_CORRECT is defined, PERMUTE otherwise. + +REQUIRE_ORDER means don't recognize them as options; stop option processing +when the first non-option is seen. This is what Unix does. This mode of +operation is selected by either setting the environment variable +POSIXLY_CORRECT, or using `+' as the first character of the list of +option characters. + +PERMUTE is the default. We permute the contents of ARGV as we scan, so +that eventually all the non-options are at the end. This allows options +to be given in any order, even with programs that were not written to +expect this. + +RETURN_IN_ORDER is an option available to programs that were written +to expect options and other ARGV-elements in any order and that care +about the ordering of the two. We describe each non-option ARGV-element +as if it were the argument of an option with character code 1. +Using `-' as the first character of the list of option characters +selects this mode of operation. + +The special argument `--' forces an end of option-scanning regardless +of the value of `ordering'. In the case of RETURN_IN_ORDER, only +`--' can cause `getopt' to return -1 with `gk_optind' != ARGC. +*/ +/*************************************************************************/ +static enum +{ + REQUIRE_ORDER, PERMUTE, RETURN_IN_ORDER +} ordering; + + + +/*************************************************************************/ +/* +Describe the part of ARGV that contains non-options that have +been skipped. `first_nonopt' is the index in ARGV of the first of them; +`last_nonopt' is the index after the last of them. +*/ +/*************************************************************************/ +static int first_nonopt; +static int last_nonopt; + + + + + +/*************************************************************************/ +/* +Handle permutation of arguments. + +Exchange two adjacent subsequences of ARGV. +One subsequence is elements [first_nonopt,last_nonopt) +which contains all the non-options that have been skipped so far. +The other is elements [last_nonopt,gk_optind), which contains all +the options processed since those non-options were skipped. + +`first_nonopt' and `last_nonopt' are relocated so that they describe +the new indices of the non-options in ARGV after they are moved. +*/ +/*************************************************************************/ +static void exchange (char **argv) +{ + int bottom = first_nonopt; + int middle = last_nonopt; + int top = gk_optind; + char *tem; + + /* Exchange the shorter segment with the far end of the longer segment. + That puts the shorter segment into the right place. + It leaves the longer segment in the right place overall, + but it consists of two parts that need to be swapped next. */ + + while (top > middle && middle > bottom) { + if (top - middle > middle - bottom) { + /* Bottom segment is the short one. */ + int len = middle - bottom; + register int i; + + /* Swap it with the top part of the top segment. */ + for (i = 0; i < len; i++) { + tem = argv[bottom + i]; + argv[bottom + i] = argv[top - (middle - bottom) + i]; + argv[top - (middle - bottom) + i] = tem; + } + /* Exclude the moved bottom segment from further swapping. */ + top -= len; + } + else { + /* Top segment is the short one. */ + int len = top - middle; + register int i; + + /* Swap it with the bottom part of the bottom segment. */ + for (i = 0; i < len; i++) { + tem = argv[bottom + i]; + argv[bottom + i] = argv[middle + i]; + argv[middle + i] = tem; + } + /* Exclude the moved top segment from further swapping. */ + bottom += len; + } + } + + /* Update records for the slots the non-options now occupy. */ + + first_nonopt += (gk_optind - last_nonopt); + last_nonopt = gk_optind; +} + + + +/*************************************************************************/ +/* +Initialize the internal data when the first call is made. +*/ +/*************************************************************************/ +static char *gk_getopt_initialize (int argc, char **argv, char *optstring) +{ + /* Start processing options with ARGV-element 1 (since ARGV-element 0 + is the program name); the sequence of previously skipped + non-option ARGV-elements is empty. */ + + first_nonopt = last_nonopt = gk_optind; + + nextchar = NULL; + + posixly_correct = getenv("POSIXLY_CORRECT"); + + /* Determine how to handle the ordering of options and nonoptions. */ + if (optstring[0] == '-') { + ordering = RETURN_IN_ORDER; + ++optstring; + } + else if (optstring[0] == '+') { + ordering = REQUIRE_ORDER; + ++optstring; + } + else if (posixly_correct != NULL) + ordering = REQUIRE_ORDER; + else + ordering = PERMUTE; + + return optstring; +} + + +/*************************************************************************/ +/* + Scan elements of ARGV (whose length is ARGC) for option characters + given in OPTSTRING. + + If an element of ARGV starts with '-', and is not exactly "-" or "--", + then it is an option element. The characters of this element + (aside from the initial '-') are option characters. If `getopt' + is called repeatedly, it returns successively each of the option characters + from each of the option elements. + + If `getopt' finds another option character, it returns that character, + updating `gk_optind' and `nextchar' so that the next call to `getopt' can + resume the scan with the following option character or ARGV-element. + + If there are no more option characters, `getopt' returns -1. + Then `gk_optind' is the index in ARGV of the first ARGV-element + that is not an option. (The ARGV-elements have been permuted + so that those that are not options now come last.) + + OPTSTRING is a string containing the legitimate option characters. + If an option character is seen that is not listed in OPTSTRING, + return '?' after printing an error message. If you set `gk_opterr' to + zero, the error message is suppressed but we still return '?'. + + If a char in OPTSTRING is followed by a colon, that means it wants an arg, + so the following text in the same ARGV-element, or the text of the following + ARGV-element, is returned in `gk_optarg'. Two colons mean an option that + wants an optional arg; if there is text in the current ARGV-element, + it is returned in `gk_optarg', otherwise `gk_optarg' is set to zero. + + If OPTSTRING starts with `-' or `+', it requests different methods of + handling the non-option ARGV-elements. + See the comments about RETURN_IN_ORDER and REQUIRE_ORDER, above. + + Long-named options begin with `--' instead of `-'. + Their names may be abbreviated as long as the abbreviation is unique + or is an exact match for some defined option. If they have an + argument, it follows the option name in the same ARGV-element, separated + from the option name by a `=', or else the in next ARGV-element. + When `getopt' finds a long-named option, it returns 0 if that option's + `flag' field is nonzero, the value of the option's `val' field + if the `flag' field is zero. + + LONGOPTS is a vector of `struct gk_option' terminated by an + element containing a name which is zero. + + LONGIND returns the index in LONGOPT of the long-named option found. + It is only valid when a long-named option has been found by the most + recent call. + + If LONG_ONLY is nonzero, '-' as well as '--' can introduce + long-named options. +*/ +/*************************************************************************/ +static int gk_getopt_internal(int argc, char **argv, char *optstring, + struct gk_option *longopts, int *longind, int long_only) +{ + int print_errors = gk_opterr; + if (optstring[0] == ':') + print_errors = 0; + + if (argc < 1) + return -1; + + gk_optarg = NULL; + + if (gk_optind == 0 || !gk_getopt_initialized) { + if (gk_optind == 0) + gk_optind = 1; /* Don't scan ARGV[0], the program name. */ + + optstring = gk_getopt_initialize (argc, argv, optstring); + gk_getopt_initialized = 1; + } + + /* Test whether ARGV[gk_optind] points to a non-option argument. + Either it does not have option syntax, or there is an environment flag + from the shell indicating it is not an option. The later information + is only used when the used in the GNU libc. */ +# define NONOPTION_P (argv[gk_optind][0] != '-' || argv[gk_optind][1] == '\0') + + if (nextchar == NULL || *nextchar == '\0') { + /* Advance to the next ARGV-element. */ + + /* Give FIRST_NONOPT & LAST_NONOPT rational values if OPTIND has been + moved back by the user (who may also have changed the arguments). */ + if (last_nonopt > gk_optind) + last_nonopt = gk_optind; + if (first_nonopt > gk_optind) + first_nonopt = gk_optind; + + if (ordering == PERMUTE) { + /* If we have just processed some options following some non-options, + exchange them so that the options come first. */ + + if (first_nonopt != last_nonopt && last_nonopt != gk_optind) + exchange ((char **) argv); + else if (last_nonopt != gk_optind) + first_nonopt = gk_optind; + + /* Skip any additional non-options + and extend the range of non-options previously skipped. */ + + while (gk_optind < argc && NONOPTION_P) + gk_optind++; + + last_nonopt = gk_optind; + } + + /* The special ARGV-element `--' means premature end of options. + Skip it like a null option, + then exchange with previous non-options as if it were an option, + then skip everything else like a non-option. */ + + if (gk_optind != argc && !strcmp (argv[gk_optind], "--")) { + gk_optind++; + + if (first_nonopt != last_nonopt && last_nonopt != gk_optind) + exchange ((char **) argv); + else if (first_nonopt == last_nonopt) + first_nonopt = gk_optind; + last_nonopt = argc; + + gk_optind = argc; + } + + /* If we have done all the ARGV-elements, stop the scan + and back over any non-options that we skipped and permuted. */ + + if (gk_optind == argc) { + /* Set the next-arg-index to point at the non-options + that we previously skipped, so the caller will digest them. */ + if (first_nonopt != last_nonopt) + gk_optind = first_nonopt; + return -1; + } + + /* If we have come to a non-option and did not permute it, + either stop the scan or describe it to the caller and pass it by. */ + + if (NONOPTION_P) { + if (ordering == REQUIRE_ORDER) + return -1; + gk_optarg = argv[gk_optind++]; + return 1; + } + + /* We have found another option-ARGV-element. + Skip the initial punctuation. */ + + nextchar = (argv[gk_optind] + 1 + (longopts != NULL && argv[gk_optind][1] == '-')); + } + + /* Decode the current option-ARGV-element. */ + + /* Check whether the ARGV-element is a long option. + + If long_only and the ARGV-element has the form "-f", where f is + a valid short option, don't consider it an abbreviated form of + a long option that starts with f. Otherwise there would be no + way to give the -f short option. + + On the other hand, if there's a long option "fubar" and + the ARGV-element is "-fu", do consider that an abbreviation of + the long option, just like "--fu", and not "-f" with arg "u". + + This distinction seems to be the most useful approach. */ + + if (longopts != NULL && (argv[gk_optind][1] == '-' || (long_only && (argv[gk_optind][2] || !strchr(optstring, argv[gk_optind][1]))))) { + char *nameend; + struct gk_option *p; + struct gk_option *pfound = NULL; + int exact = 0; + int ambig = 0; + int indfound = -1; + int option_index; + + for (nameend = nextchar; *nameend && *nameend != '='; nameend++) + /* Do nothing. */ ; + + /* Test all long options for either exact match or abbreviated matches. */ + for (p = longopts, option_index = 0; p->name; p++, option_index++) { + if (!strncmp (p->name, nextchar, nameend - nextchar)) { + if ((unsigned int) (nameend - nextchar) == (unsigned int) strlen (p->name)) { + /* Exact match found. */ + pfound = p; + indfound = option_index; + exact = 1; + break; + } + else if (pfound == NULL) { + /* First nonexact match found. */ + pfound = p; + indfound = option_index; + } + else if (long_only || pfound->has_arg != p->has_arg || pfound->flag != p->flag || pfound->val != p->val) + /* Second or later nonexact match found. */ + ambig = 1; + } + } + + if (ambig && !exact) { + if (print_errors) + fprintf(stderr, "%s: option `%s' is ambiguous\n", argv[0], argv[gk_optind]); + + nextchar += strlen (nextchar); + gk_optind++; + gk_optopt = 0; + return '?'; + } + + if (pfound != NULL) { + option_index = indfound; + gk_optind++; + if (*nameend) { + /* Don't test has_arg with >, because some C compilers don't allow it to be used on enums. */ + if (pfound->has_arg) + gk_optarg = nameend + 1; + else { + if (print_errors) { + if (argv[gk_optind - 1][1] == '-') + /* --option */ + fprintf(stderr, "%s: option `--%s' doesn't allow an argument\n", argv[0], pfound->name); + else + /* +option or -option */ + fprintf(stderr, "%s: option `%c%s' doesn't allow an argument\n", argv[0], argv[gk_optind - 1][0], pfound->name); + } + + nextchar += strlen (nextchar); + + gk_optopt = pfound->val; + return '?'; + } + } + else if (pfound->has_arg == 1) { + if (gk_optind < argc) + gk_optarg = argv[gk_optind++]; + else { + if (print_errors) + fprintf(stderr, "%s: option `%s' requires an argument\n", argv[0], argv[gk_optind - 1]); + nextchar += strlen (nextchar); + gk_optopt = pfound->val; + return optstring[0] == ':' ? ':' : '?'; + } + } + nextchar += strlen (nextchar); + if (longind != NULL) + *longind = option_index; + if (pfound->flag) { + *(pfound->flag) = pfound->val; + return 0; + } + return pfound->val; + } + + /* Can't find it as a long option. If this is not getopt_long_only, + or the option starts with '--' or is not a valid short + option, then it's an error. Otherwise interpret it as a short option. */ + if (!long_only || argv[gk_optind][1] == '-' || strchr(optstring, *nextchar) == NULL) { + if (print_errors) { + if (argv[gk_optind][1] == '-') + /* --option */ + fprintf(stderr, "%s: unrecognized option `--%s'\n", argv[0], nextchar); + else + /* +option or -option */ + fprintf(stderr, "%s: unrecognized option `%c%s'\n", argv[0], argv[gk_optind][0], nextchar); + } + nextchar = (char *) ""; + gk_optind++; + gk_optopt = 0; + return '?'; + } + } + + /* Look at and handle the next short option-character. */ + { + char c = *nextchar++; + char *temp = strchr(optstring, c); + + /* Increment `gk_optind' when we start to process its last character. */ + if (*nextchar == '\0') + ++gk_optind; + + if (temp == NULL || c == ':') { + if (print_errors) { + if (posixly_correct) + /* 1003.2 specifies the format of this message. */ + fprintf(stderr, "%s: illegal option -- %c\n", argv[0], c); + else + fprintf(stderr, "%s: invalid option -- %c\n", argv[0], c); + } + gk_optopt = c; + return '?'; + } + + /* Convenience. Treat POSIX -W foo same as long option --foo */ + if (temp[0] == 'W' && temp[1] == ';') { + char *nameend; + struct gk_option *p; + struct gk_option *pfound = NULL; + int exact = 0; + int ambig = 0; + int indfound = 0; + int option_index; + + /* This is an option that requires an argument. */ + if (*nextchar != '\0') { + gk_optarg = nextchar; + /* If we end this ARGV-element by taking the rest as an arg, + we must advance to the next element now. */ + gk_optind++; + } + else if (gk_optind == argc) { + if (print_errors) { + /* 1003.2 specifies the format of this message. */ + fprintf(stderr, "%s: option requires an argument -- %c\n", argv[0], c); + } + gk_optopt = c; + if (optstring[0] == ':') + c = ':'; + else + c = '?'; + return c; + } + else + /* We already incremented `gk_optind' once; increment it again when taking next ARGV-elt as argument. */ + gk_optarg = argv[gk_optind++]; + + /* gk_optarg is now the argument, see if it's in the table of longopts. */ + + for (nextchar = nameend = gk_optarg; *nameend && *nameend != '='; nameend++) + /* Do nothing. */ ; + + /* Test all long options for either exact match or abbreviated matches. */ + for (p = longopts, option_index = 0; p->name; p++, option_index++) { + if (!strncmp (p->name, nextchar, nameend - nextchar)) { + if ((unsigned int) (nameend - nextchar) == strlen (p->name)) { + /* Exact match found. */ + pfound = p; + indfound = option_index; + exact = 1; + break; + } + else if (pfound == NULL) { + /* First nonexact match found. */ + pfound = p; + indfound = option_index; + } + else + /* Second or later nonexact match found. */ + ambig = 1; + } + } + if (ambig && !exact) { + if (print_errors) + fprintf(stderr, "%s: option `-W %s' is ambiguous\n", argv[0], argv[gk_optind]); + nextchar += strlen (nextchar); + gk_optind++; + return '?'; + } + if (pfound != NULL) { + option_index = indfound; + if (*nameend) { + /* Don't test has_arg with >, because some C compilers don't allow it to be used on enums. */ + if (pfound->has_arg) + gk_optarg = nameend + 1; + else { + if (print_errors) + fprintf(stderr, "%s: option `-W %s' doesn't allow an argument\n", argv[0], pfound->name); + + nextchar += strlen (nextchar); + return '?'; + } + } + else if (pfound->has_arg == 1) { + if (gk_optind < argc) + gk_optarg = argv[gk_optind++]; + else { + if (print_errors) + fprintf(stderr, "%s: option `%s' requires an argument\n", argv[0], argv[gk_optind - 1]); + nextchar += strlen (nextchar); + return optstring[0] == ':' ? ':' : '?'; + } + } + nextchar += strlen (nextchar); + if (longind != NULL) + *longind = option_index; + if (pfound->flag) { + *(pfound->flag) = pfound->val; + return 0; + } + return pfound->val; + } + nextchar = NULL; + return 'W'; /* Let the application handle it. */ + } + + if (temp[1] == ':') { + if (temp[2] == ':') { + /* This is an option that accepts an argument optionally. */ + if (*nextchar != '\0') { + gk_optarg = nextchar; + gk_optind++; + } + else + gk_optarg = NULL; + nextchar = NULL; + } + else { + /* This is an option that requires an argument. */ + if (*nextchar != '\0') { + gk_optarg = nextchar; + /* If we end this ARGV-element by taking the rest as an arg, we must advance to the next element now. */ + gk_optind++; + } + else if (gk_optind == argc) { + if (print_errors) { + /* 1003.2 specifies the format of this message. */ + fprintf(stderr, "%s: option requires an argument -- %c\n", argv[0], c); + } + gk_optopt = c; + if (optstring[0] == ':') + c = ':'; + else + c = '?'; + } + else + /* We already incremented `gk_optind' once; increment it again when taking next ARGV-elt as argument. */ + gk_optarg = argv[gk_optind++]; + nextchar = NULL; + } + } + return c; + } +} + + + +/*************************************************************************/ +/*! \brief Parse command-line arguments + +The gk_getopt() function gets the next option argument from the argument +list specified by the \c argv and \c argc arguments. Normally these values +come directly from the arguments received by main(). + +\param argc is the number of command line arguments passed to main(). +\param argv is an array of strings storing the above command line + arguments. +\param options is a string that specifies the option characters that + are valid for this program. An option character in this string + can be followed by a colon (`:') to indicate that it takes a + required argument. If an option character is followed by two + colons (`::'), its argument is optional; this is a GNU extension. + +\return +It returns the option character for the next command line option. When no +more option arguments are available, it returns -1. There may still be +more non-option arguments; you must compare the external variable +#gk_optind against the \c argc parameter to check this. + +\return +If the option has an argument, gk_getopt() returns the argument by storing +it in the variable #gk_optarg. You don't ordinarily need to copy the +#gk_optarg string, since it is a pointer into the original \c argv array, +not into a static area that might be overwritten. + +\return +If gk_getopt() finds an option character in \c argv that was not included +in options, or a missing option argument, it returns `?' and sets the +external variable #gk_optopt to the actual option character. +If the first character of options is a colon (`:'), then gk_getopt() +returns `:' instead of `?' to indicate a missing option argument. +In addition, if the external variable #gk_opterr is nonzero (which is +the default), gk_getopt() prints an error message. This variable is +set by gk_getopt() to point at the value of the option argument, +for those options that accept arguments. + + +gk_getopt() has three ways to deal with options that follow non-options +\c argv elements. The special argument `--' forces in all cases +the end of option scanning. + - The default is to permute the contents of \c argv while scanning it + so that eventually all the non-options are at the end. This allows + options to be given in any order, even with programs that were not + written to expect this. + - If the options argument string begins with a hyphen (`-'), this is + treated specially. It permits arguments that are not options to be + returned as if they were associated with option character `\\1'. + - POSIX demands the following behavior: The first non-option stops + option processing. This mode is selected by either setting the + environment variable POSIXLY_CORRECT or beginning the options + argument string with a plus sign (`+'). + +*/ +/*************************************************************************/ +int gk_getopt(int argc, char **argv, char *options) +{ + return gk_getopt_internal(argc, argv, options, NULL, NULL, 0); +} + + +/*************************************************************************/ +/*! \brief Parse command-line arguments with long options + +This function accepts GNU-style long options as well as single-character +options. + +\param argc is the number of command line arguments passed to main(). +\param argv is an array of strings storing the above command line + arguments. +\param options describes the short options to accept, just as it does + in gk_getopt(). +\param long_options describes the long options to accept. See the + defintion of ::gk_option for more information. +\param opt_index this is a returned variable. For any long option, + gk_getopt_long() tells you the index in the array \c long_options + of the options definition, by storing it into *opt_index. + You can get the name of the option with longopts[*opt_index].name. + So you can distinguish among long options either by the values + in their val fields or by their indices. You can also distinguish + in this way among long options that set flags. + + +\return +When gk_getopt_long() encounters a short option, it does the same thing +that gk_getopt() would do: it returns the character code for the option, +and stores the options argument (if it has one) in #gk_optarg. + +\return +When gk_getopt_long() encounters a long option, it takes actions based +on the flag and val fields of the definition of that option. + +\return +If flag is a null pointer, then gk_getopt_long() returns the contents +of val to indicate which option it found. You should arrange distinct +values in the val field for options with different meanings, so you +can decode these values after gk_getopt_long() returns. If the long +option is equivalent to a short option, you can use the short option's +character code in val. + +\return +If flag is not a null pointer, that means this option should just set +a flag in the program. The flag is a variable of type int that you +define. Put the address of the flag in the flag field. Put in the +val field the value you would like this option to store in the flag. +In this case, gk_getopt_long() returns 0. + +\return +When a long option has an argument, gk_getopt_long() puts the argument +value in the variable #gk_optarg before returning. When the option has +no argument, the value in #gk_optarg is a null pointer. This is +how you can tell whether an optional argument was supplied. + +\return +When gk_getopt_long() has no more options to handle, it returns -1, +and leaves in the variable #gk_optind the index in argv of the next +remaining argument. +*/ +/*************************************************************************/ +int gk_getopt_long( int argc, char **argv, char *options, + struct gk_option *long_options, int *opt_index) +{ + return gk_getopt_internal (argc, argv, options, long_options, opt_index, 0); +} + + + +/*************************************************************************/ +/*! \brief Parse command-line arguments with only long options + +Like gk_getopt_long(), but '-' as well as '--' can indicate a long option. +If an option that starts with '-' (not '--') doesn't match a long option, +but does match a short option, it is parsed as a short option instead. +*/ +/*************************************************************************/ +int gk_getopt_long_only(int argc, char **argv, char *options, + struct gk_option *long_options, int *opt_index) +{ + return gk_getopt_internal(argc, argv, options, long_options, opt_index, 1); +} + diff --git a/gk_arch.h b/gk_arch.h new file mode 100644 index 0000000..b82fb6a --- /dev/null +++ b/gk_arch.h @@ -0,0 +1,70 @@ +/*! +\file gk_arch.h +\brief This file contains various architecture-specific declerations + +\date Started 3/27/2007 +\author George +\version\verbatim $Id: gk_arch.h 21637 2018-01-03 22:37:24Z karypis $ \endverbatim +*/ + +#ifndef _GK_ARCH_H_ +#define _GK_ARCH_H_ + +/************************************************************************* +* Architecture-specific differences in header files +**************************************************************************/ +#ifdef LINUX +#if !defined(__USE_XOPEN) +#define __USE_XOPEN +#endif +#if !defined(_XOPEN_SOURCE) +#define _XOPEN_SOURCE 600 +#endif +#if !defined(__USE_XOPEN2K) +#define __USE_XOPEN2K +#endif +#endif + + +#ifdef HAVE_EXECINFO_H +#include +#endif + + +#ifdef __MSC__ + #include "gk_ms_stdint.h" + #include "gk_ms_inttypes.h" + #include "gk_ms_stat.h" + #include "win32/adapt.h" +#else +#ifndef SUNOS + #include +#endif + #include + #include +#ifndef __MINGW32__ + #include +#endif + #include + #include +#endif + + +/************************************************************************* +* Architecture-specific modifications +**************************************************************************/ +#ifdef WIN32 +typedef ptrdiff_t ssize_t; +#endif + + +#ifdef SUNOS +#define PTRDIFF_MAX INT64_MAX +#endif + +/* MSC does not have INFINITY defined */ +#ifndef INFINITY +#define INFINITY FLT_MAX +#endif + +#endif diff --git a/gk_defs.h b/gk_defs.h new file mode 100644 index 0000000..68cb9a4 --- /dev/null +++ b/gk_defs.h @@ -0,0 +1,87 @@ +/*! +\file gk_defs.h +\brief This file contains various constants definitions + +\date Started 3/27/2007 +\author George +\version\verbatim $Id: gk_defs.h 22039 2018-05-26 16:34:48Z karypis $ \endverbatim +*/ + +#ifndef _GK_DEFS_H_ +#define _GK_DEFS_H_ + + +#define LTERM (void **) 0 /* List terminator for GKfree() */ + +/* mopt_t types */ +#define GK_MOPT_MARK 1 +#define GK_MOPT_CORE 2 +#define GK_MOPT_HEAP 3 + +#define HTABLE_EMPTY -1 +#define HTABLE_DELETED -2 +#define HTABLE_FIRST 1 +#define HTABLE_NEXT 2 + +/* pdb corruption bit switches */ +#define CRP_ALTLOCS 1 +#define CRP_MISSINGCA 2 +#define CRP_MISSINGBB 4 +#define CRP_MULTICHAIN 8 +#define CRP_MULTICA 16 +#define CRP_MULTIBB 32 + +#define MAXLINELEN 300000 + +/* GKlib signals to standard signal mapping */ +#define SIGMEM SIGABRT +#define SIGERR SIGTERM + + +/* CSR-related defines */ +#define GK_CSR_ROW 1 +#define GK_CSR_COL 2 +#define GK_CSR_ROWCOL 3 + +#define GK_CSR_MAXTF 1 +#define GK_CSR_SQRT 2 +#define GK_CSR_POW25 3 +#define GK_CSR_POW65 4 +#define GK_CSR_POW75 5 +#define GK_CSR_POW85 6 +#define GK_CSR_LOG 7 +#define GK_CSR_IDF 8 +#define GK_CSR_IDF2 9 +#define GK_CSR_MAXTF2 10 + +#define GK_CSR_DOTP 1 +#define GK_CSR_COS 2 +#define GK_CSR_JAC 3 +#define GK_CSR_MIN 4 +#define GK_CSR_AMIN 5 + +#define GK_CSR_FMT_AUTO 2 +#define GK_CSR_FMT_CLUTO 1 +#define GK_CSR_FMT_CSR 2 +#define GK_CSR_FMT_METIS 3 +#define GK_CSR_FMT_BINROW 4 +#define GK_CSR_FMT_BINCOL 5 +#define GK_CSR_FMT_IJV 6 +#define GK_CSR_FMT_BIJV 7 + +#define GK_CSR_SYM_SUM 1 +#define GK_CSR_SYM_MIN 2 +#define GK_CSR_SYM_MAX 3 +#define GK_CSR_SYM_AVG 4 + + +#define GK_GRAPH_FMT_METIS 1 +#define GK_GRAPH_FMT_IJV 2 +#define GK_GRAPH_FMT_HIJV 3 + +#define GK_GRAPH_SYM_SUM 1 +#define GK_GRAPH_SYM_MIN 2 +#define GK_GRAPH_SYM_MAX 3 +#define GK_GRAPH_SYM_AVG 4 + +#endif diff --git a/gk_externs.h b/gk_externs.h new file mode 100644 index 0000000..2c0fdd9 --- /dev/null +++ b/gk_externs.h @@ -0,0 +1,25 @@ +/*! +\file gk_externs.h +\brief This file contains definitions of external variables created by GKlib + +\date Started 3/27/2007 +\author George +\version\verbatim $Id: gk_externs.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim +*/ + +#ifndef _GK_EXTERNS_H_ +#define _GK_EXTERNS_H_ + + +/************************************************************************* +* Extern variable definition. Hopefully, the __thread makes them thread-safe. +**************************************************************************/ +#ifndef _GK_ERROR_C_ +/* declared in error.c */ +extern __thread int gk_cur_jbufs; +extern __thread jmp_buf gk_jbufs[]; +extern __thread jmp_buf gk_jbuf; + +#endif + +#endif diff --git a/gk_getopt.h b/gk_getopt.h new file mode 100644 index 0000000..597c080 --- /dev/null +++ b/gk_getopt.h @@ -0,0 +1,64 @@ +/*! +\file gk_getopt.h +\brief This file contains GNU's externs/structs/prototypes + +\date Started 3/27/2007 +\author George +\version\verbatim $Id: gk_getopt.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim +*/ + +#ifndef _GK_GETOPT_H_ +#define _GK_GETOPT_H_ + + +/* Externals from getopt.c */ +extern char *gk_optarg; +extern int gk_optind; +extern int gk_opterr; +extern int gk_optopt; + + +/*! \brief The structure that stores the information about the command-line options + +This structure describes a single long option name for the sake of +gk_getopt_long(). The argument long_options must be an array +of these structures, one for each long option. Terminate the array with +an element containing all zeros. +*/ +struct gk_option { + char *name; /*!< This field is the name of the option. */ + int has_arg; /*!< This field says whether the option takes an argument. + It is an integer, and there are three legitimate values: + no_argument, required_argument and optional_argument. + */ + int *flag; /*!< See the discussion on ::gk_option#val */ + int val; /*!< These fields control how to report or act on the option + when it occurs. + + If flag is a null pointer, then the val is a value which + identifies this option. Often these values are chosen + to uniquely identify particular long options. + + If flag is not a null pointer, it should be the address + of an int variable which is the flag for this option. + The value in val is the value to store in the flag to + indicate that the option was seen. */ +}; + +/* Names for the values of the `has_arg' field of `struct gk_option'. */ +#define no_argument 0 +#define required_argument 1 +#define optional_argument 2 + + +/* Function prototypes */ +extern int gk_getopt(int argc, char **argv, char *shortopts); +extern int gk_getopt_long(int argc, char **argv, char *shortopts, + struct gk_option *longopts, int *longind); +extern int gk_getopt_long_only (int argc, char **argv, + char *shortopts, struct gk_option *longopts, int *longind); + + + +#endif + diff --git a/gk_macros.h b/gk_macros.h new file mode 100644 index 0000000..c3f1b45 --- /dev/null +++ b/gk_macros.h @@ -0,0 +1,169 @@ +/*! +\file gk_macros.h +\brief This file contains various macros + +\date Started 3/27/2007 +\author George +\version\verbatim $Id: gk_macros.h 15048 2013-08-31 19:38:14Z karypis $ \endverbatim +*/ + +#ifndef _GK_MACROS_H_ +#define _GK_MACROS_H_ + +/*------------------------------------------------------------- + * Usefull commands + *-------------------------------------------------------------*/ +#define gk_max(a, b) ((a) >= (b) ? (a) : (b)) +#define gk_min(a, b) ((a) >= (b) ? (b) : (a)) +#define gk_max3(a, b, c) ((a) >= (b) && (a) >= (c) ? (a) : ((b) >= (a) && (b) >= (c) ? (b) : (c))) +#define gk_SWAP(a, b, tmp) do {(tmp) = (a); (a) = (b); (b) = (tmp);} while(0) +#define INC_DEC(a, b, val) do {(a) += (val); (b) -= (val);} while(0) +#define sign(a, b) ((a >= 0 ? b : -b)) + +#define ONEOVERRANDMAX (1.0/(RAND_MAX+1.0)) +#define RandomInRange(u) ((int) (ONEOVERRANDMAX*(u)*rand())) +#define RandomInRange_r(s, u) ((int) (ONEOVERRANDMAX*(u)*rand_r(s))) + +#define gk_abs(x) ((x) >= 0 ? (x) : -(x)) + + +/*------------------------------------------------------------- + * Timing macros + *-------------------------------------------------------------*/ +#define gk_clearcputimer(tmr) (tmr = 0.0) +#define gk_startcputimer(tmr) (tmr -= gk_CPUSeconds()) +#define gk_stopcputimer(tmr) (tmr += gk_CPUSeconds()) +#define gk_getcputimer(tmr) (tmr) + +#define gk_clearwctimer(tmr) (tmr = 0.0) +#define gk_startwctimer(tmr) (tmr -= gk_WClockSeconds()) +#define gk_stopwctimer(tmr) (tmr += gk_WClockSeconds()) +#define gk_getwctimer(tmr) (tmr) + +/*------------------------------------------------------------- + * dbglvl handling macros + *-------------------------------------------------------------*/ +#define IFSET(a, flag, cmd) if ((a)&(flag)) (cmd); + + +/*------------------------------------------------------------- + * gracefull library exit macro + *-------------------------------------------------------------*/ +#define GKSETJMP() (setjmp(gk_return_to_entry)) +#define gk_sigcatch() (setjmp(gk_jbufs[gk_cur_jbufs])) + + +/*------------------------------------------------------------- + * Debuging memory leaks + *-------------------------------------------------------------*/ +#ifdef DMALLOC +# define MALLOC_CHECK(ptr) \ + if (malloc_verify((ptr)) == DMALLOC_VERIFY_ERROR) { \ + printf("***MALLOC_CHECK failed on line %d of file %s: " #ptr "\n", \ + __LINE__, __FILE__); \ + abort(); \ + } +#else +# define MALLOC_CHECK(ptr) ; +#endif + + +/*------------------------------------------------------------- + * CSR conversion macros + *-------------------------------------------------------------*/ +#define MAKECSR(i, n, a) \ + do { \ + for (i=1; i0; i--) a[i] = a[i-1]; \ + a[0] = 0; \ + } while(0) + +#define SHIFTCSR(i, n, a) \ + do { \ + for (i=n; i>0; i--) a[i] = a[i-1]; \ + a[0] = 0; \ + } while(0) + + +/*------------------------------------------------------------- + * ASSERTS that cannot be turned off! + *-------------------------------------------------------------*/ +#define GKASSERT(expr) \ + if (!(expr)) { \ + printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \ + __LINE__, __FILE__); \ + abort(); \ + } + +#define GKASSERTP(expr,msg) \ + if (!(expr)) { \ + printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \ + __LINE__, __FILE__); \ + printf msg ; \ + printf("\n"); \ + abort(); \ + } + +#define GKCUASSERT(expr) \ + if (!(expr)) { \ + printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \ + __LINE__, __FILE__); \ + } + +#define GKWARN(expr) \ + if (!(expr)) { \ + printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \ + __LINE__, __FILE__); \ + } + +#define GKCUASSERTP(expr,msg) \ + if (!(expr)) { \ + printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \ + __LINE__, __FILE__); \ + printf msg ; \ + printf("\n"); \ + } + +#define GKWARNP(expr,msg) \ + if (!(expr)) { \ + printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \ + __LINE__, __FILE__); \ + printf msg ; \ + printf("\n"); \ + } + + +/*------------------------------------------------------------- + * Program Assertions + *-------------------------------------------------------------*/ +#ifndef NDEBUG +# define ASSERT(expr) \ + if (!(expr)) { \ + printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \ + __LINE__, __FILE__); \ + assert(expr); \ + } + +# define ASSERTP(expr,msg) \ + if (!(expr)) { \ + printf("***ASSERTION failed on line %d of file %s: " #expr "\n", \ + __LINE__, __FILE__); \ + printf msg ; \ + printf("\n"); \ + assert(expr); \ + } +#else +# define ASSERT(expr) ; +# define ASSERTP(expr,msg) ; +#endif + +#ifndef NDEBUG2 +# define ASSERT2 ASSERT +# define ASSERTP2 ASSERTP +#else +# define ASSERT2(expr) ; +# define ASSERTP2(expr,msg) ; +#endif + + +#endif diff --git a/gk_mkblas.h b/gk_mkblas.h new file mode 100644 index 0000000..1231669 --- /dev/null +++ b/gk_mkblas.h @@ -0,0 +1,203 @@ +/*! +\file gk_mkblas.h +\brief Templates for BLAS-like routines + +\date Started 3/28/07 +\author George +\version\verbatim $Id: gk_mkblas.h 16304 2014-02-25 14:27:19Z karypis $ \endverbatim +*/ + +#ifndef _GK_MKBLAS_H_ +#define _GK_MKBLAS_H_ + + +#define GK_MKBLAS(PRFX, TYPE, OUTTYPE) \ +/*************************************************************************/\ +/*! The macro for gk_?incset()-class of routines */\ +/*************************************************************************/\ +TYPE *PRFX ## incset(size_t n, TYPE baseval, TYPE *x)\ +{\ + size_t i;\ +\ + for (i=0; i max ? (*x) : max);\ +\ + return max;\ +}\ +\ +\ +/*************************************************************************/\ +/*! The macro for gk_?min()-class of routines */\ +/*************************************************************************/\ +TYPE PRFX ## min(size_t n, TYPE *x, size_t incx)\ +{\ + size_t i;\ + TYPE min;\ +\ + if (n <= 0) return (TYPE) 0;\ +\ + for (min=(*x), x+=incx, i=1; i x[max] ? j : max);\ +\ + return (size_t)(max/incx);\ +}\ +\ +\ +/*************************************************************************/\ +/*! The macro for gk_?argmin()-class of routines */\ +/*************************************************************************/\ +size_t PRFX ## argmin(size_t n, TYPE *x, size_t incx)\ +{\ + size_t i, j, min=0;\ +\ + for (i=1, j=incx; i 0 ? (OUTTYPE)sqrt((double)partial) : (OUTTYPE)0);\ +}\ +\ +\ +/*************************************************************************/\ +/*! The macro for gk_?dot()-class of routines */\ +/**************************************************************************/\ +OUTTYPE PRFX ## dot(size_t n, TYPE *x, size_t incx, TYPE *y, size_t incy)\ +{\ + size_t i;\ + OUTTYPE partial = 0.0;\ + \ + for (i=0; innodes = 0;\ + queue->maxnodes = maxnodes;\ +\ + queue->heap = KVMALLOC(maxnodes, "gk_PQInit: heap");\ + queue->locator = gk_idxsmalloc(maxnodes, -1, "gk_PQInit: locator");\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function resets the priority queue */\ +/**************************************************************************/\ +void FPRFX ## Reset(PQT *queue)\ +{\ + ssize_t i;\ + ssize_t *locator=queue->locator;\ + KVT *heap=queue->heap;\ +\ + for (i=queue->nnodes-1; i>=0; i--)\ + locator[heap[i].val] = -1;\ + queue->nnodes = 0;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function frees the internal datastructures of the priority queue */\ +/**************************************************************************/\ +void FPRFX ## Free(PQT *queue)\ +{\ + if (queue == NULL) return;\ + gk_free((void **)&queue->heap, &queue->locator, LTERM);\ + queue->maxnodes = 0;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function frees the internal datastructures of the priority queue \ + and the queue itself */\ +/**************************************************************************/\ +void FPRFX ## Destroy(PQT *queue)\ +{\ + if (queue == NULL) return;\ + FPRFX ## Free(queue);\ + gk_free((void **)&queue, LTERM);\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function returns the length of the queue */\ +/**************************************************************************/\ +size_t FPRFX ## Length(PQT *queue)\ +{\ + return queue->nnodes;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function adds an item in the priority queue */\ +/**************************************************************************/\ +int FPRFX ## Insert(PQT *queue, VT node, KT key)\ +{\ + ssize_t i, j;\ + ssize_t *locator=queue->locator;\ + KVT *heap=queue->heap;\ +\ + ASSERT2(FPRFX ## CheckHeap(queue));\ +\ + ASSERT(locator[node] == -1);\ +\ + i = queue->nnodes++;\ + while (i > 0) {\ + j = (i-1)>>1;\ + if (KEY_LT(key, heap[j].key)) {\ + heap[i] = heap[j];\ + locator[heap[i].val] = i;\ + i = j;\ + }\ + else\ + break;\ + }\ + ASSERT(i >= 0);\ + heap[i].key = key;\ + heap[i].val = node;\ + locator[node] = i;\ +\ + ASSERT2(FPRFX ## CheckHeap(queue));\ +\ + return 0;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function deletes an item from the priority queue */\ +/**************************************************************************/\ +int FPRFX ## Delete(PQT *queue, VT node)\ +{\ + ssize_t i, j;\ + size_t nnodes;\ + KT newkey, oldkey;\ + ssize_t *locator=queue->locator;\ + KVT *heap=queue->heap;\ +\ + ASSERT(locator[node] != -1);\ + ASSERT(heap[locator[node]].val == node);\ +\ + ASSERT2(FPRFX ## CheckHeap(queue));\ +\ + i = locator[node];\ + locator[node] = -1;\ +\ + if (--queue->nnodes > 0 && heap[queue->nnodes].val != node) {\ + node = heap[queue->nnodes].val;\ + newkey = heap[queue->nnodes].key;\ + oldkey = heap[i].key;\ +\ + if (KEY_LT(newkey, oldkey)) { /* Filter-up */\ + while (i > 0) {\ + j = (i-1)>>1;\ + if (KEY_LT(newkey, heap[j].key)) {\ + heap[i] = heap[j];\ + locator[heap[i].val] = i;\ + i = j;\ + }\ + else\ + break;\ + }\ + }\ + else { /* Filter down */\ + nnodes = queue->nnodes;\ + while ((j=(i<<1)+1) < nnodes) {\ + if (KEY_LT(heap[j].key, newkey)) {\ + if (j+1 < nnodes && KEY_LT(heap[j+1].key, heap[j].key))\ + j++;\ + heap[i] = heap[j];\ + locator[heap[i].val] = i;\ + i = j;\ + }\ + else if (j+1 < nnodes && KEY_LT(heap[j+1].key, newkey)) {\ + j++;\ + heap[i] = heap[j];\ + locator[heap[i].val] = i;\ + i = j;\ + }\ + else\ + break;\ + }\ + }\ +\ + heap[i].key = newkey;\ + heap[i].val = node;\ + locator[node] = i;\ + }\ +\ + ASSERT2(FPRFX ## CheckHeap(queue));\ +\ + return 0;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function updates the key values associated for a particular item */ \ +/**************************************************************************/\ +void FPRFX ## Update(PQT *queue, VT node, KT newkey)\ +{\ + ssize_t i, j;\ + size_t nnodes;\ + KT oldkey;\ + ssize_t *locator=queue->locator;\ + KVT *heap=queue->heap;\ +\ + oldkey = heap[locator[node]].key;\ + if (!KEY_LT(newkey, oldkey) && !KEY_LT(oldkey, newkey)) return;\ +\ + ASSERT(locator[node] != -1);\ + ASSERT(heap[locator[node]].val == node);\ + ASSERT2(FPRFX ## CheckHeap(queue));\ +\ + i = locator[node];\ +\ + if (KEY_LT(newkey, oldkey)) { /* Filter-up */\ + while (i > 0) {\ + j = (i-1)>>1;\ + if (KEY_LT(newkey, heap[j].key)) {\ + heap[i] = heap[j];\ + locator[heap[i].val] = i;\ + i = j;\ + }\ + else\ + break;\ + }\ + }\ + else { /* Filter down */\ + nnodes = queue->nnodes;\ + while ((j=(i<<1)+1) < nnodes) {\ + if (KEY_LT(heap[j].key, newkey)) {\ + if (j+1 < nnodes && KEY_LT(heap[j+1].key, heap[j].key))\ + j++;\ + heap[i] = heap[j];\ + locator[heap[i].val] = i;\ + i = j;\ + }\ + else if (j+1 < nnodes && KEY_LT(heap[j+1].key, newkey)) {\ + j++;\ + heap[i] = heap[j];\ + locator[heap[i].val] = i;\ + i = j;\ + }\ + else\ + break;\ + }\ + }\ +\ + heap[i].key = newkey;\ + heap[i].val = node;\ + locator[node] = i;\ +\ + ASSERT2(FPRFX ## CheckHeap(queue));\ +\ + return;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function returns the item at the top of the queue and removes\ + it from the priority queue */\ +/**************************************************************************/\ +VT FPRFX ## GetTop(PQT *queue)\ +{\ + ssize_t i, j;\ + ssize_t *locator;\ + KVT *heap;\ + VT vtx, node;\ + KT key;\ +\ + ASSERT2(FPRFX ## CheckHeap(queue));\ +\ + if (queue->nnodes == 0)\ + return -1;\ +\ + queue->nnodes--;\ +\ + heap = queue->heap;\ + locator = queue->locator;\ +\ + vtx = heap[0].val;\ + locator[vtx] = -1;\ +\ + if ((i = queue->nnodes) > 0) {\ + key = heap[i].key;\ + node = heap[i].val;\ + i = 0;\ + while ((j=2*i+1) < queue->nnodes) {\ + if (KEY_LT(heap[j].key, key)) {\ + if (j+1 < queue->nnodes && KEY_LT(heap[j+1].key, heap[j].key))\ + j = j+1;\ + heap[i] = heap[j];\ + locator[heap[i].val] = i;\ + i = j;\ + }\ + else if (j+1 < queue->nnodes && KEY_LT(heap[j+1].key, key)) {\ + j = j+1;\ + heap[i] = heap[j];\ + locator[heap[i].val] = i;\ + i = j;\ + }\ + else\ + break;\ + }\ +\ + heap[i].key = key;\ + heap[i].val = node;\ + locator[node] = i;\ + }\ +\ + ASSERT2(FPRFX ## CheckHeap(queue));\ + return vtx;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function returns the item at the top of the queue. The item is not\ + deleted from the queue. */\ +/**************************************************************************/\ +VT FPRFX ## SeeTopVal(PQT *queue)\ +{\ + return (queue->nnodes == 0 ? -1 : queue->heap[0].val);\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function returns the key of the top item. The item is not\ + deleted from the queue. */\ +/**************************************************************************/\ +KT FPRFX ## SeeTopKey(PQT *queue)\ +{\ + return (queue->nnodes == 0 ? KMAX : queue->heap[0].key);\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function returns the key of a specific item */\ +/**************************************************************************/\ +KT FPRFX ## SeeKey(PQT *queue, VT node)\ +{\ + ssize_t *locator;\ + KVT *heap;\ +\ + heap = queue->heap;\ + locator = queue->locator;\ +\ + return heap[locator[node]].key;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function returns the first item in a breadth-first traversal of\ + the heap whose key is less than maxwgt. This function is here due to\ + hMETIS and is not general!*/\ +/**************************************************************************/\ +/*\ +VT FPRFX ## SeeConstraintTop(PQT *queue, KT maxwgt, KT *wgts)\ +{\ + ssize_t i;\ +\ + if (queue->nnodes == 0)\ + return -1;\ +\ + if (maxwgt <= 1000)\ + return FPRFX ## SeeTopVal(queue);\ +\ + for (i=0; innodes; i++) {\ + if (queue->heap[i].key > 0) {\ + if (wgts[queue->heap[i].val] <= maxwgt)\ + return queue->heap[i].val;\ + }\ + else {\ + if (queue->heap[i/2].key <= 0)\ + break;\ + }\ + }\ +\ + return queue->heap[0].val;\ +\ +}\ +*/\ +\ +\ +/*************************************************************************/\ +/*! This functions checks the consistency of the heap */\ +/**************************************************************************/\ +int FPRFX ## CheckHeap(PQT *queue)\ +{\ + ssize_t i, j;\ + size_t nnodes;\ + ssize_t *locator;\ + KVT *heap;\ +\ + heap = queue->heap;\ + locator = queue->locator;\ + nnodes = queue->nnodes;\ +\ + if (nnodes == 0)\ + return 1;\ +\ + ASSERT(locator[heap[0].val] == 0);\ + for (i=1; imaxnodes; i++) {\ + if (locator[i] != -1)\ + j++;\ + }\ + ASSERTP(j == nnodes, ("%jd %jd\n", (intmax_t)j, (intmax_t)nnodes));\ +\ + return 1;\ +}\ + + +#define GK_MKPQUEUE_PROTO(FPRFX, PQT, KT, VT)\ + PQT * FPRFX ## Create(size_t maxnodes);\ + void FPRFX ## Init(PQT *queue, size_t maxnodes);\ + void FPRFX ## Reset(PQT *queue);\ + void FPRFX ## Free(PQT *queue);\ + void FPRFX ## Destroy(PQT *queue);\ + size_t FPRFX ## Length(PQT *queue);\ + int FPRFX ## Insert(PQT *queue, VT node, KT key);\ + int FPRFX ## Delete(PQT *queue, VT node);\ + void FPRFX ## Update(PQT *queue, VT node, KT newkey);\ + VT FPRFX ## GetTop(PQT *queue);\ + VT FPRFX ## SeeTopVal(PQT *queue);\ + KT FPRFX ## SeeTopKey(PQT *queue);\ + KT FPRFX ## SeeKey(PQT *queue, VT node);\ + VT FPRFX ## SeeConstraintTop(PQT *queue, KT maxwgt, KT *wgts);\ + int FPRFX ## CheckHeap(PQT *queue);\ + + +/* This is how these macros are used +GK_MKPQUEUE(gk_dkvPQ, gk_dkvPQ_t, double, gk_idx_t, gk_dkvmalloc, DBL_MAX) +GK_MKPQUEUE_PROTO(gk_dkvPQ, gk_dkvPQ_t, double, gk_idx_t) +*/ + + +#endif diff --git a/gk_mkpqueue2.h b/gk_mkpqueue2.h new file mode 100644 index 0000000..10e8ee4 --- /dev/null +++ b/gk_mkpqueue2.h @@ -0,0 +1,215 @@ +/*! +\file gk_mkpqueue2.h +\brief Templates for priority queues that do not utilize locators and as such + they can use different types of values. + +\date Started 4/09/07 +\author George +\version\verbatim $Id: gk_mkpqueue2.h 13005 2012-10-23 22:34:36Z karypis $ \endverbatim +*/ + + +#ifndef _GK_MKPQUEUE2_H +#define _GK_MKPQUEUE2_H + + +#define GK_MKPQUEUE2(FPRFX, PQT, KT, VT, KMALLOC, VMALLOC, KMAX, KEY_LT)\ +/*************************************************************************/\ +/*! This function creates and initializes a priority queue */\ +/**************************************************************************/\ +PQT *FPRFX ## Create2(ssize_t maxnodes)\ +{\ + PQT *queue; \ +\ + if ((queue = (PQT *)gk_malloc(sizeof(PQT), "gk_pqCreate2: queue")) != NULL) {\ + memset(queue, 0, sizeof(PQT));\ + queue->nnodes = 0;\ + queue->maxnodes = maxnodes;\ + queue->keys = KMALLOC(maxnodes, "gk_pqCreate2: keys");\ + queue->vals = VMALLOC(maxnodes, "gk_pqCreate2: vals");\ +\ + if (queue->keys == NULL || queue->vals == NULL)\ + gk_free((void **)&queue->keys, &queue->vals, &queue, LTERM);\ + }\ +\ + return queue;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function resets the priority queue */\ +/**************************************************************************/\ +void FPRFX ## Reset2(PQT *queue)\ +{\ + queue->nnodes = 0;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function frees the internal datastructures of the priority queue */\ +/**************************************************************************/\ +void FPRFX ## Destroy2(PQT **r_queue)\ +{\ + PQT *queue = *r_queue; \ + if (queue == NULL) return;\ + gk_free((void **)&queue->keys, &queue->vals, &queue, LTERM);\ + *r_queue = NULL;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function returns the length of the queue */\ +/**************************************************************************/\ +size_t FPRFX ## Length2(PQT *queue)\ +{\ + return queue->nnodes;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function adds an item in the priority queue. */\ +/**************************************************************************/\ +int FPRFX ## Insert2(PQT *queue, VT val, KT key)\ +{\ + ssize_t i, j;\ + KT *keys=queue->keys;\ + VT *vals=queue->vals;\ +\ + ASSERT2(FPRFX ## CheckHeap2(queue));\ +\ + if (queue->nnodes == queue->maxnodes) \ + return 0;\ +\ + ASSERT2(FPRFX ## CheckHeap2(queue));\ +\ + i = queue->nnodes++;\ + while (i > 0) {\ + j = (i-1)>>1;\ + if (KEY_LT(key, keys[j])) {\ + keys[i] = keys[j];\ + vals[i] = vals[j];\ + i = j;\ + }\ + else\ + break;\ + }\ + ASSERT(i >= 0);\ + keys[i] = key;\ + vals[i] = val;\ +\ + ASSERT2(FPRFX ## CheckHeap2(queue));\ +\ + return 1;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function returns the item at the top of the queue and removes\ + it from the priority queue */\ +/**************************************************************************/\ +int FPRFX ## GetTop2(PQT *queue, VT *r_val)\ +{\ + ssize_t i, j;\ + KT key, *keys=queue->keys;\ + VT val, *vals=queue->vals;\ +\ + ASSERT2(FPRFX ## CheckHeap2(queue));\ +\ + if (queue->nnodes == 0)\ + return 0;\ +\ + queue->nnodes--;\ +\ + *r_val = vals[0];\ +\ + if ((i = queue->nnodes) > 0) {\ + key = keys[i];\ + val = vals[i];\ + i = 0;\ + while ((j=2*i+1) < queue->nnodes) {\ + if (KEY_LT(keys[j], key)) {\ + if (j+1 < queue->nnodes && KEY_LT(keys[j+1], keys[j]))\ + j = j+1;\ + keys[i] = keys[j];\ + vals[i] = vals[j];\ + i = j;\ + }\ + else if (j+1 < queue->nnodes && KEY_LT(keys[j+1], key)) {\ + j = j+1;\ + keys[i] = keys[j];\ + vals[i] = vals[j];\ + i = j;\ + }\ + else\ + break;\ + }\ +\ + keys[i] = key;\ + vals[i] = val;\ + }\ +\ + ASSERT2(FPRFX ## CheckHeap2(queue));\ +\ + return 1;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function returns the item at the top of the queue. The item is not\ + deleted from the queue. */\ +/**************************************************************************/\ +int FPRFX ## SeeTopVal2(PQT *queue, VT *r_val)\ +{\ + if (queue->nnodes == 0) \ + return 0;\ +\ + *r_val = queue->vals[0];\ +\ + return 1;\ +}\ +\ +\ +/*************************************************************************/\ +/*! This function returns the key of the top item. The item is not\ + deleted from the queue. */\ +/**************************************************************************/\ +KT FPRFX ## SeeTopKey2(PQT *queue)\ +{\ + return (queue->nnodes == 0 ? KMAX : queue->keys[0]);\ +}\ +\ +\ +/*************************************************************************/\ +/*! This functions checks the consistency of the heap */\ +/**************************************************************************/\ +int FPRFX ## CheckHeap2(PQT *queue)\ +{\ + ssize_t i;\ + KT *keys=queue->keys;\ +\ + if (queue->nnodes == 0)\ + return 1;\ +\ + for (i=1; innodes; i++) {\ + ASSERT(!KEY_LT(keys[i], keys[(i-1)/2]));\ + }\ + for (i=1; innodes; i++)\ + ASSERT(!KEY_LT(keys[i], keys[0]));\ +\ + return 1;\ +}\ + + +#define GK_MKPQUEUE2_PROTO(FPRFX, PQT, KT, VT)\ + PQT * FPRFX ## Create2(ssize_t maxnodes);\ + void FPRFX ## Reset2(PQT *queue);\ + void FPRFX ## Destroy2(PQT **r_queue);\ + size_t FPRFX ## Length2(PQT *queue);\ + int FPRFX ## Insert2(PQT *queue, VT node, KT key);\ + int FPRFX ## GetTop2(PQT *queue, VT *r_val);\ + int FPRFX ## SeeTopVal2(PQT *queue, VT *r_val);\ + KT FPRFX ## SeeTopKey2(PQT *queue);\ + int FPRFX ## CheckHeap2(PQT *queue);\ + + +#endif diff --git a/gk_mkrandom.h b/gk_mkrandom.h new file mode 100644 index 0000000..68d54fa --- /dev/null +++ b/gk_mkrandom.h @@ -0,0 +1,123 @@ +/*! +\file +\brief Templates for portable random number generation + +\date Started 5/17/07 +\author George +\version\verbatim $Id: gk_mkrandom.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim +*/ + + +#ifndef _GK_MKRANDOM_H +#define _GK_MKRANDOM_H + +/*************************************************************************/\ +/*! The generator for the rand() related routines. \ + \params RNGT the datatype that defines the range of values over which\ + random numbers will be generated\ + \params VALT the datatype that defines the contents of the array to \ + be permuted by randArrayPermute() \ + \params FPRFX the function prefix \ +*/\ +/**************************************************************************/\ +#define GK_MKRANDOM(FPRFX, RNGT, VALT)\ +/*************************************************************************/\ +/*! Initializes the generator */ \ +/**************************************************************************/\ +void FPRFX ## srand(RNGT seed) \ +{\ + gk_randinit((uint64_t) seed);\ +}\ +\ +\ +/*************************************************************************/\ +/*! Returns a random number */ \ +/**************************************************************************/\ +RNGT FPRFX ## rand() \ +{\ + if (sizeof(RNGT) <= sizeof(int32_t)) \ + return (RNGT)gk_randint32(); \ + else \ + return (RNGT)gk_randint64(); \ +}\ +\ +\ +/*************************************************************************/\ +/*! Returns a random number between [0, max) */ \ +/**************************************************************************/\ +RNGT FPRFX ## randInRange(RNGT max) \ +{\ + return (RNGT)((FPRFX ## rand())%max); \ +}\ +\ +\ +/*************************************************************************/\ +/*! Randomly permutes the elements of an array p[]. \ + flag == 1, p[i] = i prior to permutation, \ + flag == 0, p[] is not initialized. */\ +/**************************************************************************/\ +void FPRFX ## randArrayPermute(RNGT n, VALT *p, RNGT nshuffles, int flag)\ +{\ + RNGT i, u, v;\ + VALT tmp;\ +\ + if (flag == 1) {\ + for (i=0; ikey < (b)->key) + * GKQSORT(struct elt, arr, n, elt_lt); + * } + * + * And so on. + */ + +/* Swap two items pointed to by A and B using temporary buffer t. */ +#define _GKQSORT_SWAP(a, b, t) ((void)((t = *a), (*a = *b), (*b = t))) + +/* Discontinue quicksort algorithm when partition gets below this size. */ +#define _GKQSORT_MAX_THRESH 8 + +/* The next 4 #defines implement a very fast in-line stack abstraction. */ +#define _GKQSORT_STACK_SIZE (8 * sizeof(size_t)) +#define _GKQSORT_PUSH(top, low, high) (((top->_lo = (low)), (top->_hi = (high)), ++top)) +#define _GKQSORT_POP(low, high, top) ((--top, (low = top->_lo), (high = top->_hi))) +#define _GKQSORT_STACK_NOT_EMPTY (_stack < _top) + + +/* The main code starts here... */ +#define GK_MKQSORT(GKQSORT_TYPE,GKQSORT_BASE,GKQSORT_NELT,GKQSORT_LT) \ +{ \ + GKQSORT_TYPE *const _base = (GKQSORT_BASE); \ + const size_t _elems = (GKQSORT_NELT); \ + GKQSORT_TYPE _hold; \ + \ + if (_elems < 1) \ + return; \ + \ + /* Don't declare two variables of type GKQSORT_TYPE in a single \ + * statement: eg `TYPE a, b;', in case if TYPE is a pointer, \ + * expands to `type* a, b;' wich isn't what we want. \ + */ \ + \ + if (_elems > _GKQSORT_MAX_THRESH) { \ + GKQSORT_TYPE *_lo = _base; \ + GKQSORT_TYPE *_hi = _lo + _elems - 1; \ + struct { \ + GKQSORT_TYPE *_hi; GKQSORT_TYPE *_lo; \ + } _stack[_GKQSORT_STACK_SIZE], *_top = _stack + 1; \ + \ + while (_GKQSORT_STACK_NOT_EMPTY) { \ + GKQSORT_TYPE *_left_ptr; GKQSORT_TYPE *_right_ptr; \ + \ + /* Select median value from among LO, MID, and HI. Rearrange \ + LO and HI so the three values are sorted. This lowers the \ + probability of picking a pathological pivot value and \ + skips a comparison for both the LEFT_PTR and RIGHT_PTR in \ + the while loops. */ \ + \ + GKQSORT_TYPE *_mid = _lo + ((_hi - _lo) >> 1); \ + \ + if (GKQSORT_LT (_mid, _lo)) \ + _GKQSORT_SWAP (_mid, _lo, _hold); \ + if (GKQSORT_LT (_hi, _mid)) \ + _GKQSORT_SWAP (_mid, _hi, _hold); \ + else \ + goto _jump_over; \ + if (GKQSORT_LT (_mid, _lo)) \ + _GKQSORT_SWAP (_mid, _lo, _hold); \ + _jump_over:; \ + \ + _left_ptr = _lo + 1; \ + _right_ptr = _hi - 1; \ + \ + /* Here's the famous ``collapse the walls'' section of quicksort. \ + Gotta like those tight inner loops! They are the main reason \ + that this algorithm runs much faster than others. */ \ + do { \ + while (GKQSORT_LT (_left_ptr, _mid)) \ + ++_left_ptr; \ + \ + while (GKQSORT_LT (_mid, _right_ptr)) \ + --_right_ptr; \ + \ + if (_left_ptr < _right_ptr) { \ + _GKQSORT_SWAP (_left_ptr, _right_ptr, _hold); \ + if (_mid == _left_ptr) \ + _mid = _right_ptr; \ + else if (_mid == _right_ptr) \ + _mid = _left_ptr; \ + ++_left_ptr; \ + --_right_ptr; \ + } \ + else if (_left_ptr == _right_ptr) { \ + ++_left_ptr; \ + --_right_ptr; \ + break; \ + } \ + } while (_left_ptr <= _right_ptr); \ + \ + /* Set up pointers for next iteration. First determine whether \ + left and right partitions are below the threshold size. If so, \ + ignore one or both. Otherwise, push the larger partition's \ + bounds on the stack and continue sorting the smaller one. */ \ + \ + if (_right_ptr - _lo <= _GKQSORT_MAX_THRESH) { \ + if (_hi - _left_ptr <= _GKQSORT_MAX_THRESH) \ + /* Ignore both small partitions. */ \ + _GKQSORT_POP (_lo, _hi, _top); \ + else \ + /* Ignore small left partition. */ \ + _lo = _left_ptr; \ + } \ + else if (_hi - _left_ptr <= _GKQSORT_MAX_THRESH) \ + /* Ignore small right partition. */ \ + _hi = _right_ptr; \ + else if (_right_ptr - _lo > _hi - _left_ptr) { \ + /* Push larger left partition indices. */ \ + _GKQSORT_PUSH (_top, _lo, _right_ptr); \ + _lo = _left_ptr; \ + } \ + else { \ + /* Push larger right partition indices. */ \ + _GKQSORT_PUSH (_top, _left_ptr, _hi); \ + _hi = _right_ptr; \ + } \ + } \ + } \ + \ + /* Once the BASE array is partially sorted by quicksort the rest \ + is completely sorted using insertion sort, since this is efficient \ + for partitions below MAX_THRESH size. BASE points to the \ + beginning of the array to sort, and END_PTR points at the very \ + last element in the array (*not* one beyond it!). */ \ + \ + { \ + GKQSORT_TYPE *const _end_ptr = _base + _elems - 1; \ + GKQSORT_TYPE *_tmp_ptr = _base; \ + register GKQSORT_TYPE *_run_ptr; \ + GKQSORT_TYPE *_thresh; \ + \ + _thresh = _base + _GKQSORT_MAX_THRESH; \ + if (_thresh > _end_ptr) \ + _thresh = _end_ptr; \ + \ + /* Find smallest element in first threshold and place it at the \ + array's beginning. This is the smallest array element, \ + and the operation speeds up insertion sort's inner loop. */ \ + \ + for (_run_ptr = _tmp_ptr + 1; _run_ptr <= _thresh; ++_run_ptr) \ + if (GKQSORT_LT (_run_ptr, _tmp_ptr)) \ + _tmp_ptr = _run_ptr; \ + \ + if (_tmp_ptr != _base) \ + _GKQSORT_SWAP (_tmp_ptr, _base, _hold); \ + \ + /* Insertion sort, running from left-hand-side \ + * up to right-hand-side. */ \ + \ + _run_ptr = _base + 1; \ + while (++_run_ptr <= _end_ptr) { \ + _tmp_ptr = _run_ptr - 1; \ + while (GKQSORT_LT (_run_ptr, _tmp_ptr)) \ + --_tmp_ptr; \ + \ + ++_tmp_ptr; \ + if (_tmp_ptr != _run_ptr) { \ + GKQSORT_TYPE *_trav = _run_ptr + 1; \ + while (--_trav >= _run_ptr) { \ + GKQSORT_TYPE *_hi; GKQSORT_TYPE *_lo; \ + _hold = *_trav; \ + \ + for (_hi = _lo = _trav; --_lo >= _tmp_ptr; _hi = _lo) \ + *_hi = *_lo; \ + *_hi = _hold; \ + } \ + } \ + } \ + } \ + \ +} + +#endif diff --git a/gk_mkutils.h b/gk_mkutils.h new file mode 100644 index 0000000..a092f22 --- /dev/null +++ b/gk_mkutils.h @@ -0,0 +1,40 @@ +/*! +\file +\brief Templates for various utility routines + +\date Started 5/28/07 +\author George +\version\verbatim $Id: gk_mkutils.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim +*/ + +#ifndef _GK_MKUTILS_H_ +#define _GK_MKUTILS_H_ + + +#define GK_MKARRAY2CSR(PRFX, TYPE)\ +/*************************************************************************/\ +/*! The macro for gk_?array2csr() routine */\ +/**************************************************************************/\ +void PRFX ## array2csr(TYPE n, TYPE range, TYPE *array, TYPE *ptr, TYPE *ind)\ +{\ + TYPE i;\ +\ + for (i=0; i<=range; i++)\ + ptr[i] = 0;\ +\ + for (i=0; i 1000 +#pragma once +#endif + +#include "gk_ms_stdint.h" + +// 7.8 Format conversion of integer types + +typedef struct { + intmax_t quot; + intmax_t rem; +} imaxdiv_t; + +// 7.8.1 Macros for format specifiers + +// The fprintf macros for signed integers are: +#define PRId8 "d" +#define PRIi8 "i" +#define PRIdLEAST8 "d" +#define PRIiLEAST8 "i" +#define PRIdFAST8 "d" +#define PRIiFAST8 "i" + +#define PRId16 "hd" +#define PRIi16 "hi" +#define PRIdLEAST16 "hd" +#define PRIiLEAST16 "hi" +#define PRIdFAST16 "hd" +#define PRIiFAST16 "hi" + +#define PRId32 "I32d" +#define PRIi32 "I32i" +#define PRIdLEAST32 "I32d" +#define PRIiLEAST32 "I32i" +#define PRIdFAST32 "I32d" +#define PRIiFAST32 "I32i" + +#define PRId64 "I64d" +#define PRIi64 "I64i" +#define PRIdLEAST64 "I64d" +#define PRIiLEAST64 "I64i" +#define PRIdFAST64 "I64d" +#define PRIiFAST64 "I64i" + +#define PRIdMAX "I64d" +#define PRIiMAX "I64i" + +#define PRIdPTR "Id" +#define PRIiPTR "Ii" + +// The fprintf macros for unsigned integers are: +#define PRIo8 "o" +#define PRIu8 "u" +#define PRIx8 "x" +#define PRIX8 "X" +#define PRIoLEAST8 "o" +#define PRIuLEAST8 "u" +#define PRIxLEAST8 "x" +#define PRIXLEAST8 "X" +#define PRIoFAST8 "o" +#define PRIuFAST8 "u" +#define PRIxFAST8 "x" +#define PRIXFAST8 "X" + +#define PRIo16 "ho" +#define PRIu16 "hu" +#define PRIx16 "hx" +#define PRIX16 "hX" +#define PRIoLEAST16 "ho" +#define PRIuLEAST16 "hu" +#define PRIxLEAST16 "hx" +#define PRIXLEAST16 "hX" +#define PRIoFAST16 "ho" +#define PRIuFAST16 "hu" +#define PRIxFAST16 "hx" +#define PRIXFAST16 "hX" + +#define PRIo32 "I32o" +#define PRIu32 "I32u" +#define PRIx32 "I32x" +#define PRIX32 "I32X" +#define PRIoLEAST32 "I32o" +#define PRIuLEAST32 "I32u" +#define PRIxLEAST32 "I32x" +#define PRIXLEAST32 "I32X" +#define PRIoFAST32 "I32o" +#define PRIuFAST32 "I32u" +#define PRIxFAST32 "I32x" +#define PRIXFAST32 "I32X" + +#define PRIo64 "I64o" +#define PRIu64 "I64u" +#define PRIx64 "I64x" +#define PRIX64 "I64X" +#define PRIoLEAST64 "I64o" +#define PRIuLEAST64 "I64u" +#define PRIxLEAST64 "I64x" +#define PRIXLEAST64 "I64X" +#define PRIoFAST64 "I64o" +#define PRIuFAST64 "I64u" +#define PRIxFAST64 "I64x" +#define PRIXFAST64 "I64X" + +#define PRIoMAX "I64o" +#define PRIuMAX "I64u" +#define PRIxMAX "I64x" +#define PRIXMAX "I64X" + +#define PRIoPTR "Io" +#define PRIuPTR "Iu" +#define PRIxPTR "Ix" +#define PRIXPTR "IX" + +// The fscanf macros for signed integers are: +#define SCNd8 "d" +#define SCNi8 "i" +#define SCNdLEAST8 "d" +#define SCNiLEAST8 "i" +#define SCNdFAST8 "d" +#define SCNiFAST8 "i" + +#define SCNd16 "hd" +#define SCNi16 "hi" +#define SCNdLEAST16 "hd" +#define SCNiLEAST16 "hi" +#define SCNdFAST16 "hd" +#define SCNiFAST16 "hi" + +#define SCNd32 "ld" +#define SCNi32 "li" +#define SCNdLEAST32 "ld" +#define SCNiLEAST32 "li" +#define SCNdFAST32 "ld" +#define SCNiFAST32 "li" + +#define SCNd64 "I64d" +#define SCNi64 "I64i" +#define SCNdLEAST64 "I64d" +#define SCNiLEAST64 "I64i" +#define SCNdFAST64 "I64d" +#define SCNiFAST64 "I64i" + +#define SCNdMAX "I64d" +#define SCNiMAX "I64i" + +#ifdef _WIN64 // [ +# define SCNdPTR "I64d" +# define SCNiPTR "I64i" +#else // _WIN64 ][ +# define SCNdPTR "ld" +# define SCNiPTR "li" +#endif // _WIN64 ] + +// The fscanf macros for unsigned integers are: +#define SCNo8 "o" +#define SCNu8 "u" +#define SCNx8 "x" +#define SCNX8 "X" +#define SCNoLEAST8 "o" +#define SCNuLEAST8 "u" +#define SCNxLEAST8 "x" +#define SCNXLEAST8 "X" +#define SCNoFAST8 "o" +#define SCNuFAST8 "u" +#define SCNxFAST8 "x" +#define SCNXFAST8 "X" + +#define SCNo16 "ho" +#define SCNu16 "hu" +#define SCNx16 "hx" +#define SCNX16 "hX" +#define SCNoLEAST16 "ho" +#define SCNuLEAST16 "hu" +#define SCNxLEAST16 "hx" +#define SCNXLEAST16 "hX" +#define SCNoFAST16 "ho" +#define SCNuFAST16 "hu" +#define SCNxFAST16 "hx" +#define SCNXFAST16 "hX" + +#define SCNo32 "lo" +#define SCNu32 "lu" +#define SCNx32 "lx" +#define SCNX32 "lX" +#define SCNoLEAST32 "lo" +#define SCNuLEAST32 "lu" +#define SCNxLEAST32 "lx" +#define SCNXLEAST32 "lX" +#define SCNoFAST32 "lo" +#define SCNuFAST32 "lu" +#define SCNxFAST32 "lx" +#define SCNXFAST32 "lX" + +#define SCNo64 "I64o" +#define SCNu64 "I64u" +#define SCNx64 "I64x" +#define SCNX64 "I64X" +#define SCNoLEAST64 "I64o" +#define SCNuLEAST64 "I64u" +#define SCNxLEAST64 "I64x" +#define SCNXLEAST64 "I64X" +#define SCNoFAST64 "I64o" +#define SCNuFAST64 "I64u" +#define SCNxFAST64 "I64x" +#define SCNXFAST64 "I64X" + +#define SCNoMAX "I64o" +#define SCNuMAX "I64u" +#define SCNxMAX "I64x" +#define SCNXMAX "I64X" + +#ifdef _WIN64 // [ +# define SCNoPTR "I64o" +# define SCNuPTR "I64u" +# define SCNxPTR "I64x" +# define SCNXPTR "I64X" +#else // _WIN64 ][ +# define SCNoPTR "lo" +# define SCNuPTR "lu" +# define SCNxPTR "lx" +# define SCNXPTR "lX" +#endif // _WIN64 ] + +// 7.8.2 Functions for greatest-width integer types + +// 7.8.2.1 The imaxabs function +#define imaxabs _abs64 + +// 7.8.2.2 The imaxdiv function + +// This is modified version of div() function from Microsoft's div.c found +// in %MSVC.NET%\crt\src\div.c +#ifdef STATIC_IMAXDIV // [ +static +#else // STATIC_IMAXDIV ][ +_inline +#endif // STATIC_IMAXDIV ] +imaxdiv_t __cdecl imaxdiv(intmax_t numer, intmax_t denom) +{ + imaxdiv_t result; + + result.quot = numer / denom; + result.rem = numer % denom; + + if (numer < 0 && result.rem > 0) { + // did division wrong; must fix up + ++result.quot; + result.rem -= denom; + } + + return result; +} + +// 7.8.2.3 The strtoimax and strtoumax functions +#define strtoimax _strtoi64 +#define strtoumax _strtoui64 + +// 7.8.2.4 The wcstoimax and wcstoumax functions +#define wcstoimax _wcstoi64 +#define wcstoumax _wcstoui64 + + +#endif // _MSC_INTTYPES_H_ ] diff --git a/gk_ms_stat.h b/gk_ms_stat.h new file mode 100644 index 0000000..a1ef6fa --- /dev/null +++ b/gk_ms_stat.h @@ -0,0 +1,22 @@ +#ifndef _MSC_VER // [ +#error "Use this header only with Microsoft Visual C++ compilers!" +#endif // _MSC_VER ] + +#ifndef _MS_STAT_H_ +#define _MS_STAT_H_ + +#if _MSC_VER > 1000 +#pragma once +#endif + +#include +/* Test macros for file types. */ + +#define __S_ISTYPE(mode, mask) (((mode) & S_IFMT) == (mask)) + +#define S_ISDIR(mode) __S_ISTYPE((mode), S_IFDIR) +#define S_ISCHR(mode) __S_ISTYPE((mode), S_IFCHR) +#define S_ISBLK(mode) __S_ISTYPE((mode), S_IFBLK) +#define S_ISREG(mode) __S_ISTYPE((mode), S_IFREG) + +#endif diff --git a/gk_ms_stdint.h b/gk_ms_stdint.h new file mode 100644 index 0000000..7e200dc --- /dev/null +++ b/gk_ms_stdint.h @@ -0,0 +1,222 @@ +// ISO C9x compliant stdint.h for Microsoft Visual Studio +// Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124 +// +// Copyright (c) 2006 Alexander Chemeris +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are met: +// +// 1. Redistributions of source code must retain the above copyright notice, +// this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. The name of the author may be used to endorse or promote products +// derived from this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED +// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +// MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +// EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +/////////////////////////////////////////////////////////////////////////////// + +#ifndef _MSC_VER // [ +#error "Use this header only with Microsoft Visual C++ compilers!" +#endif // _MSC_VER ] + +#ifndef _MSC_STDINT_H_ // [ +#define _MSC_STDINT_H_ + +#if _MSC_VER > 1000 +#pragma once +#endif + +#include + +// For Visual Studio 6 in C++ mode wrap include with 'extern "C++" {}' +// or compiler give many errors like this: +// error C2733: second C linkage of overloaded function 'wmemchr' not allowed +#if (_MSC_VER < 1300) && defined(__cplusplus) + extern "C++" { +#endif +# include +#if (_MSC_VER < 1300) && defined(__cplusplus) + } +#endif + +// 7.18.1 Integer types + +// 7.18.1.1 Exact-width integer types +typedef __int8 int8_t; +typedef __int16 int16_t; +typedef __int32 int32_t; +typedef __int64 int64_t; +typedef unsigned __int8 uint8_t; +typedef unsigned __int16 uint16_t; +typedef unsigned __int32 uint32_t; +typedef unsigned __int64 uint64_t; + +// 7.18.1.2 Minimum-width integer types +typedef int8_t int_least8_t; +typedef int16_t int_least16_t; +typedef int32_t int_least32_t; +typedef int64_t int_least64_t; +typedef uint8_t uint_least8_t; +typedef uint16_t uint_least16_t; +typedef uint32_t uint_least32_t; +typedef uint64_t uint_least64_t; + +// 7.18.1.3 Fastest minimum-width integer types +typedef int8_t int_fast8_t; +typedef int16_t int_fast16_t; +typedef int32_t int_fast32_t; +typedef int64_t int_fast64_t; +typedef uint8_t uint_fast8_t; +typedef uint16_t uint_fast16_t; +typedef uint32_t uint_fast32_t; +typedef uint64_t uint_fast64_t; + +// 7.18.1.4 Integer types capable of holding object pointers +#ifdef _WIN64 // [ + typedef __int64 intptr_t; + typedef unsigned __int64 uintptr_t; +#else // _WIN64 ][ + typedef int intptr_t; + typedef unsigned int uintptr_t; +#endif // _WIN64 ] + +// 7.18.1.5 Greatest-width integer types +typedef int64_t intmax_t; +typedef uint64_t uintmax_t; + + +// 7.18.2 Limits of specified-width integer types + +#if !defined(__cplusplus) || defined(__STDC_LIMIT_MACROS) // [ See footnote 220 at page 257 and footnote 221 at page 259 + +// 7.18.2.1 Limits of exact-width integer types +#define INT8_MIN ((int8_t)_I8_MIN) +#define INT8_MAX _I8_MAX +#define INT16_MIN ((int16_t)_I16_MIN) +#define INT16_MAX _I16_MAX +#define INT32_MIN ((int32_t)_I32_MIN) +#define INT32_MAX _I32_MAX +#define INT64_MIN ((int64_t)_I64_MIN) +#define INT64_MAX _I64_MAX +#define UINT8_MAX _UI8_MAX +#define UINT16_MAX _UI16_MAX +#define UINT32_MAX _UI32_MAX +#define UINT64_MAX _UI64_MAX + +// 7.18.2.2 Limits of minimum-width integer types +#define INT_LEAST8_MIN INT8_MIN +#define INT_LEAST8_MAX INT8_MAX +#define INT_LEAST16_MIN INT16_MIN +#define INT_LEAST16_MAX INT16_MAX +#define INT_LEAST32_MIN INT32_MIN +#define INT_LEAST32_MAX INT32_MAX +#define INT_LEAST64_MIN INT64_MIN +#define INT_LEAST64_MAX INT64_MAX +#define UINT_LEAST8_MAX UINT8_MAX +#define UINT_LEAST16_MAX UINT16_MAX +#define UINT_LEAST32_MAX UINT32_MAX +#define UINT_LEAST64_MAX UINT64_MAX + +// 7.18.2.3 Limits of fastest minimum-width integer types +#define INT_FAST8_MIN INT8_MIN +#define INT_FAST8_MAX INT8_MAX +#define INT_FAST16_MIN INT16_MIN +#define INT_FAST16_MAX INT16_MAX +#define INT_FAST32_MIN INT32_MIN +#define INT_FAST32_MAX INT32_MAX +#define INT_FAST64_MIN INT64_MIN +#define INT_FAST64_MAX INT64_MAX +#define UINT_FAST8_MAX UINT8_MAX +#define UINT_FAST16_MAX UINT16_MAX +#define UINT_FAST32_MAX UINT32_MAX +#define UINT_FAST64_MAX UINT64_MAX + +// 7.18.2.4 Limits of integer types capable of holding object pointers +#ifdef _WIN64 // [ +# define INTPTR_MIN INT64_MIN +# define INTPTR_MAX INT64_MAX +# define UINTPTR_MAX UINT64_MAX +#else // _WIN64 ][ +# define INTPTR_MIN INT32_MIN +# define INTPTR_MAX INT32_MAX +# define UINTPTR_MAX UINT32_MAX +#endif // _WIN64 ] + +// 7.18.2.5 Limits of greatest-width integer types +#define INTMAX_MIN INT64_MIN +#define INTMAX_MAX INT64_MAX +#define UINTMAX_MAX UINT64_MAX + +// 7.18.3 Limits of other integer types + +#ifdef _WIN64 // [ +# define PTRDIFF_MIN _I64_MIN +# define PTRDIFF_MAX _I64_MAX +#else // _WIN64 ][ +# define PTRDIFF_MIN _I32_MIN +# define PTRDIFF_MAX _I32_MAX +#endif // _WIN64 ] + +#define SIG_ATOMIC_MIN INT_MIN +#define SIG_ATOMIC_MAX INT_MAX + +#ifndef SIZE_MAX // [ +# ifdef _WIN64 // [ +# define SIZE_MAX _UI64_MAX +# else // _WIN64 ][ +# define SIZE_MAX _UI32_MAX +# endif // _WIN64 ] +#endif // SIZE_MAX ] + +// WCHAR_MIN and WCHAR_MAX are also defined in +#ifndef WCHAR_MIN // [ +# define WCHAR_MIN 0 +#endif // WCHAR_MIN ] +#ifndef WCHAR_MAX // [ +# define WCHAR_MAX _UI16_MAX +#endif // WCHAR_MAX ] + +#define WINT_MIN 0 +#define WINT_MAX _UI16_MAX + +#endif // __STDC_LIMIT_MACROS ] + + +// 7.18.4 Limits of other integer types + +#if !defined(__cplusplus) || defined(__STDC_CONSTANT_MACROS) // [ See footnote 224 at page 260 + +// 7.18.4.1 Macros for minimum-width integer constants + +#define INT8_C(val) val##i8 +#define INT16_C(val) val##i16 +#define INT32_C(val) val##i32 +#define INT64_C(val) val##i64 + +#define UINT8_C(val) val##ui8 +#define UINT16_C(val) val##ui16 +#define UINT32_C(val) val##ui32 +#define UINT64_C(val) val##ui64 + +// 7.18.4.2 Macros for greatest-width integer constants +#define INTMAX_C INT64_C +#define UINTMAX_C UINT64_C + +#endif // __STDC_CONSTANT_MACROS ] + + +#endif // _MSC_STDINT_H_ ] diff --git a/gk_proto.h b/gk_proto.h new file mode 100644 index 0000000..6fd6bd4 --- /dev/null +++ b/gk_proto.h @@ -0,0 +1,426 @@ +/*! +\file gk_proto.h +\brief This file contains function prototypes + +\date Started 3/27/2007 +\author George +\version\verbatim $Id: gk_proto.h 22010 2018-05-14 20:20:26Z karypis $ \endverbatim +*/ + +#ifndef _GK_PROTO_H_ +#define _GK_PROTO_H_ + +#ifdef __cplusplus +extern "C" { +#endif + +/*------------------------------------------------------------- + * blas.c + *-------------------------------------------------------------*/ +GK_MKBLAS_PROTO(gk_c, char, int) +GK_MKBLAS_PROTO(gk_i, int, int) +GK_MKBLAS_PROTO(gk_i8, int8_t, int8_t) +GK_MKBLAS_PROTO(gk_i16, int16_t, int16_t) +GK_MKBLAS_PROTO(gk_i32, int32_t, int32_t) +GK_MKBLAS_PROTO(gk_i64, int64_t, int64_t) +GK_MKBLAS_PROTO(gk_z, ssize_t, ssize_t) +GK_MKBLAS_PROTO(gk_zu, size_t, size_t) +GK_MKBLAS_PROTO(gk_f, float, float) +GK_MKBLAS_PROTO(gk_d, double, double) +GK_MKBLAS_PROTO(gk_idx, gk_idx_t, gk_idx_t) + + + + +/*------------------------------------------------------------- + * io.c + *-------------------------------------------------------------*/ +FILE *gk_fopen(char *, char *, const char *); +void gk_fclose(FILE *); +ssize_t gk_read(int fd, void *vbuf, size_t count); +ssize_t gk_write(int fd, void *vbuf, size_t count); +ssize_t gk_getline(char **lineptr, size_t *n, FILE *stream); +char **gk_readfile(char *fname, size_t *r_nlines); +int32_t *gk_i32readfile(char *fname, size_t *r_nlines); +int64_t *gk_i64readfile(char *fname, size_t *r_nlines); +ssize_t *gk_zreadfile(char *fname, size_t *r_nlines); +char *gk_creadfilebin(char *fname, size_t *r_nelmnts); +size_t gk_cwritefilebin(char *fname, size_t n, char *a); +int32_t *gk_i32readfilebin(char *fname, size_t *r_nelmnts); +size_t gk_i32writefilebin(char *fname, size_t n, int32_t *a); +int64_t *gk_i64readfilebin(char *fname, size_t *r_nelmnts); +size_t gk_i64writefilebin(char *fname, size_t n, int64_t *a); +ssize_t *gk_zreadfilebin(char *fname, size_t *r_nelmnts); +size_t gk_zwritefilebin(char *fname, size_t n, ssize_t *a); +float *gk_freadfilebin(char *fname, size_t *r_nelmnts); +size_t gk_fwritefilebin(char *fname, size_t n, float *a); +double *gk_dreadfilebin(char *fname, size_t *r_nelmnts); +size_t gk_dwritefilebin(char *fname, size_t n, double *a); + + + + +/*------------------------------------------------------------- + * fs.c + *-------------------------------------------------------------*/ +int gk_fexists(char *); +int gk_dexists(char *); +ssize_t gk_getfsize(char *); +void gk_getfilestats(char *fname, size_t *r_nlines, size_t *r_ntokens, + size_t *r_max_nlntokens, size_t *r_nbytes); +char *gk_getbasename(char *path); +char *gk_getextname(char *path); +char *gk_getfilename(char *path); +char *gk_getpathname(char *path); +int gk_mkpath(char *); +int gk_rmpath(char *); + + + +/*------------------------------------------------------------- + * memory.c + *-------------------------------------------------------------*/ +GK_MKALLOC_PROTO(gk_c, char) +GK_MKALLOC_PROTO(gk_i, int) +GK_MKALLOC_PROTO(gk_i8, int8_t) +GK_MKALLOC_PROTO(gk_i16, int16_t) +GK_MKALLOC_PROTO(gk_i32, int32_t) +GK_MKALLOC_PROTO(gk_i64, int64_t) +GK_MKALLOC_PROTO(gk_ui8, uint8_t) +GK_MKALLOC_PROTO(gk_ui16, uint16_t) +GK_MKALLOC_PROTO(gk_ui32, uint32_t) +GK_MKALLOC_PROTO(gk_ui64, uint64_t) +GK_MKALLOC_PROTO(gk_z, ssize_t) +GK_MKALLOC_PROTO(gk_zu, size_t) +GK_MKALLOC_PROTO(gk_f, float) +GK_MKALLOC_PROTO(gk_d, double) +GK_MKALLOC_PROTO(gk_idx, gk_idx_t) + +GK_MKALLOC_PROTO(gk_ckv, gk_ckv_t) +GK_MKALLOC_PROTO(gk_ikv, gk_ikv_t) +GK_MKALLOC_PROTO(gk_i8kv, gk_i8kv_t) +GK_MKALLOC_PROTO(gk_i16kv, gk_i16kv_t) +GK_MKALLOC_PROTO(gk_i32kv, gk_i32kv_t) +GK_MKALLOC_PROTO(gk_i64kv, gk_i64kv_t) +GK_MKALLOC_PROTO(gk_zkv, gk_zkv_t) +GK_MKALLOC_PROTO(gk_zukv, gk_zukv_t) +GK_MKALLOC_PROTO(gk_fkv, gk_fkv_t) +GK_MKALLOC_PROTO(gk_dkv, gk_dkv_t) +GK_MKALLOC_PROTO(gk_skv, gk_skv_t) +GK_MKALLOC_PROTO(gk_idxkv, gk_idxkv_t) + +void gk_AllocMatrix(void ***, size_t, size_t , size_t); +void gk_FreeMatrix(void ***, size_t, size_t); +int gk_malloc_init(); +void gk_malloc_cleanup(int showstats); +void *gk_malloc(size_t nbytes, char *msg); +void *gk_realloc(void *oldptr, size_t nbytes, char *msg); +void gk_free(void **ptr1,...); +size_t gk_GetCurMemoryUsed(); +size_t gk_GetMaxMemoryUsed(); +void gk_GetVMInfo(size_t *vmsize, size_t *vmrss); +size_t gk_GetProcVmPeak(); + + + +/*------------------------------------------------------------- + * seq.c + *-------------------------------------------------------------*/ +gk_seq_t *gk_seq_ReadGKMODPSSM(char *file_name); +gk_i2cc2i_t *gk_i2cc2i_create_common(char *alphabet); +void gk_seq_init(gk_seq_t *seq); + + + +/*------------------------------------------------------------- + * error.c + *-------------------------------------------------------------*/ +void gk_set_exit_on_error(int value); +void errexit(char *,...); +void gk_errexit(int signum, char *,...); +int gk_sigtrap(); +int gk_siguntrap(); +void gk_sigthrow(int signum); +void gk_SetSignalHandlers(); +void gk_UnsetSignalHandlers(); +void gk_NonLocalExit_Handler(int signum); +char *gk_strerror(int errnum); +void PrintBackTrace(); + + +/*------------------------------------------------------------- + * util.c + *-------------------------------------------------------------*/ +void gk_RandomPermute(size_t, int *, int); +void gk_array2csr(size_t n, size_t range, int *array, int *ptr, int *ind); +int gk_log2(int); +int gk_ispow2(int); +float gk_flog2(float); + + +/*------------------------------------------------------------- + * time.c + *-------------------------------------------------------------*/ +gk_wclock_t gk_WClockSeconds(void); +double gk_CPUSeconds(void); + +/*------------------------------------------------------------- + * string.c + *-------------------------------------------------------------*/ +char *gk_strchr_replace(char *str, char *fromlist, char *tolist); +int gk_strstr_replace(char *str, char *pattern, char *replacement, char *options, char **new_str); +char *gk_strtprune(char *, char *); +char *gk_strhprune(char *, char *); +char *gk_strtoupper(char *); +char *gk_strtolower(char *); +char *gk_strdup(char *orgstr); +int gk_strcasecmp(char *s1, char *s2); +int gk_strrcmp(char *s1, char *s2); +char *gk_time2str(time_t time); +time_t gk_str2time(char *str); +int gk_GetStringID(gk_StringMap_t *strmap, char *key); + + + +/*------------------------------------------------------------- + * sort.c + *-------------------------------------------------------------*/ +void gk_csorti(size_t, char *); +void gk_csortd(size_t, char *); +void gk_isorti(size_t, int *); +void gk_isortd(size_t, int *); +void gk_i32sorti(size_t, int32_t *); +void gk_i32sortd(size_t, int32_t *); +void gk_i64sorti(size_t, int64_t *); +void gk_i64sortd(size_t, int64_t *); +void gk_ui32sorti(size_t, uint32_t *); +void gk_ui32sortd(size_t, uint32_t *); +void gk_ui64sorti(size_t, uint64_t *); +void gk_ui64sortd(size_t, uint64_t *); +void gk_fsorti(size_t, float *); +void gk_fsortd(size_t, float *); +void gk_dsorti(size_t, double *); +void gk_dsortd(size_t, double *); +void gk_idxsorti(size_t, gk_idx_t *); +void gk_idxsortd(size_t, gk_idx_t *); +void gk_ckvsorti(size_t, gk_ckv_t *); +void gk_ckvsortd(size_t, gk_ckv_t *); +void gk_ikvsorti(size_t, gk_ikv_t *); +void gk_ikvsortd(size_t, gk_ikv_t *); +void gk_i32kvsorti(size_t, gk_i32kv_t *); +void gk_i32kvsortd(size_t, gk_i32kv_t *); +void gk_i64kvsorti(size_t, gk_i64kv_t *); +void gk_i64kvsortd(size_t, gk_i64kv_t *); +void gk_zkvsorti(size_t, gk_zkv_t *); +void gk_zkvsortd(size_t, gk_zkv_t *); +void gk_zukvsorti(size_t, gk_zukv_t *); +void gk_zukvsortd(size_t, gk_zukv_t *); +void gk_fkvsorti(size_t, gk_fkv_t *); +void gk_fkvsortd(size_t, gk_fkv_t *); +void gk_dkvsorti(size_t, gk_dkv_t *); +void gk_dkvsortd(size_t, gk_dkv_t *); +void gk_skvsorti(size_t, gk_skv_t *); +void gk_skvsortd(size_t, gk_skv_t *); +void gk_idxkvsorti(size_t, gk_idxkv_t *); +void gk_idxkvsortd(size_t, gk_idxkv_t *); + + +/*------------------------------------------------------------- + * Selection routines + *-------------------------------------------------------------*/ +int gk_dfkvkselect(size_t, int, gk_fkv_t *); +int gk_ifkvkselect(size_t, int, gk_fkv_t *); + + +/*------------------------------------------------------------- + * Priority queue + *-------------------------------------------------------------*/ +GK_MKPQUEUE_PROTO(gk_ipq, gk_ipq_t, int, gk_idx_t) +GK_MKPQUEUE_PROTO(gk_i32pq, gk_i32pq_t, int32_t, gk_idx_t) +GK_MKPQUEUE_PROTO(gk_i64pq, gk_i64pq_t, int64_t, gk_idx_t) +GK_MKPQUEUE_PROTO(gk_fpq, gk_fpq_t, float, gk_idx_t) +GK_MKPQUEUE_PROTO(gk_dpq, gk_dpq_t, double, gk_idx_t) +GK_MKPQUEUE_PROTO(gk_idxpq, gk_idxpq_t, gk_idx_t, gk_idx_t) + + +/*------------------------------------------------------------- + * HTable routines + *-------------------------------------------------------------*/ +gk_HTable_t *HTable_Create(int nelements); +void HTable_Reset(gk_HTable_t *htable); +void HTable_Resize(gk_HTable_t *htable, int nelements); +void HTable_Insert(gk_HTable_t *htable, int key, int val); +void HTable_Delete(gk_HTable_t *htable, int key); +int HTable_Search(gk_HTable_t *htable, int key); +int HTable_GetNext(gk_HTable_t *htable, int key, int *val, int type); +int HTable_SearchAndDelete(gk_HTable_t *htable, int key); +void HTable_Destroy(gk_HTable_t *htable); +int HTable_HFunction(int nelements, int key); + + +/*------------------------------------------------------------- + * Tokenizer routines + *-------------------------------------------------------------*/ +void gk_strtokenize(char *line, char *delim, gk_Tokens_t *tokens); +void gk_freetokenslist(gk_Tokens_t *tokens); + +/*------------------------------------------------------------- + * Encoder/Decoder + *-------------------------------------------------------------*/ +void encodeblock(unsigned char *in, unsigned char *out); +void decodeblock(unsigned char *in, unsigned char *out); +void GKEncodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer); +void GKDecodeBase64(int nbytes, unsigned char *inbuffer, unsigned char *outbuffer); + + +/*------------------------------------------------------------- + * random.c + *-------------------------------------------------------------*/ +GK_MKRANDOM_PROTO(gk_c, size_t, char) +GK_MKRANDOM_PROTO(gk_i, size_t, int) +GK_MKRANDOM_PROTO(gk_i32, size_t, int32_t) +GK_MKRANDOM_PROTO(gk_f, size_t, float) +GK_MKRANDOM_PROTO(gk_d, size_t, double) +GK_MKRANDOM_PROTO(gk_idx, size_t, gk_idx_t) +GK_MKRANDOM_PROTO(gk_z, size_t, ssize_t) +GK_MKRANDOM_PROTO(gk_zu, size_t, size_t) +void gk_randinit(uint64_t); +uint64_t gk_randint64(void); +uint32_t gk_randint32(void); + + +/*------------------------------------------------------------- + * OpenMP fake functions + *-------------------------------------------------------------*/ +#if !defined(__OPENMP__) +void omp_set_num_threads(int num_threads); +int omp_get_num_threads(void); +int omp_get_max_threads(void); +int omp_get_thread_num(void); +int omp_get_num_procs(void); +int omp_in_parallel(void); +void omp_set_dynamic(int num_threads); +int omp_get_dynamic(void); +void omp_set_nested(int nested); +int omp_get_nested(void); +#endif /* __OPENMP__ */ + + +/*------------------------------------------------------------- + * CSR-related functions + *-------------------------------------------------------------*/ +gk_csr_t *gk_csr_Create(); +void gk_csr_Init(gk_csr_t *mat); +void gk_csr_Free(gk_csr_t **mat); +void gk_csr_FreeContents(gk_csr_t *mat); +gk_csr_t *gk_csr_Dup(gk_csr_t *mat); +gk_csr_t *gk_csr_ExtractSubmatrix(gk_csr_t *mat, int rstart, int nrows); +gk_csr_t *gk_csr_ExtractRows(gk_csr_t *mat, int nrows, int *rind); +gk_csr_t *gk_csr_ExtractPartition(gk_csr_t *mat, int *part, int pid); +gk_csr_t **gk_csr_Split(gk_csr_t *mat, int *color); +int gk_csr_DetermineFormat(char *filename, int format); +gk_csr_t *gk_csr_Read(char *filename, int format, int readvals, int numbering); +void gk_csr_Write(gk_csr_t *mat, char *filename, int format, int writevals, int numbering); +gk_csr_t *gk_csr_Prune(gk_csr_t *mat, int what, int minf, int maxf); +gk_csr_t *gk_csr_LowFilter(gk_csr_t *mat, int what, int norm, float fraction); +gk_csr_t *gk_csr_TopKPlusFilter(gk_csr_t *mat, int what, int topk, float keepval); +gk_csr_t *gk_csr_ZScoreFilter(gk_csr_t *mat, int what, float zscore); +void gk_csr_CompactColumns(gk_csr_t *mat); +void gk_csr_SortIndices(gk_csr_t *mat, int what); +void gk_csr_CreateIndex(gk_csr_t *mat, int what); +void gk_csr_Normalize(gk_csr_t *mat, int what, int norm); +void gk_csr_Scale(gk_csr_t *mat, int type); +void gk_csr_ComputeSums(gk_csr_t *mat, int what); +void gk_csr_ComputeNorms(gk_csr_t *mat, int what); +void gk_csr_ComputeSquaredNorms(gk_csr_t *mat, int what); +gk_csr_t *gk_csr_Shuffle(gk_csr_t *mat, int what, int summetric); +gk_csr_t *gk_csr_Transpose(gk_csr_t *mat); +float gk_csr_ComputeSimilarity(gk_csr_t *mat, int i1, int i2, int what, int simtype); +float gk_csr_ComputePairSimilarity(gk_csr_t *mat_a, gk_csr_t *mat_b, int i1, int i2, int what, int simtype); +int gk_csr_GetSimilarRows(gk_csr_t *mat, int nqterms, int *qind, float *qval, + int simtype, int nsim, float minsim, gk_fkv_t *hits, int *_imarker, + gk_fkv_t *i_cand); +int gk_csr_FindConnectedComponents(gk_csr_t *mat, int32_t *cptr, int32_t *cind, + int32_t *cids); +gk_csr_t *gk_csr_MakeSymmetric(gk_csr_t *mat, int op); +gk_csr_t *gk_csr_ReorderSymmetric(gk_csr_t *mat, int32_t *perm, int32_t *iperm); +void gk_csr_ComputeBFSOrderingSymmetric(gk_csr_t *mat, int maxdegree, int v, + int32_t **r_perm, int32_t **r_iperm); +void gk_csr_ComputeBestFOrderingSymmetric(gk_csr_t *mat, int v, int type, + int32_t **r_perm, int32_t **r_iperm); + + +/* itemsets.c */ +void gk_find_frequent_itemsets(int ntrans, ssize_t *tranptr, int *tranind, + int minfreq, int maxfreq, int minlen, int maxlen, + void (*process_itemset)(void *stateptr, int nitems, int *itemind, + int ntrans, int *tranind), + void *stateptr); + + +/* evaluate.c */ +float ComputeAccuracy(int n, gk_fkv_t *list); +float ComputeROCn(int n, int maxN, gk_fkv_t *list); +float ComputeMedianRFP(int n, gk_fkv_t *list); +float ComputeMean (int n, float *values); +float ComputeStdDev(int n, float *values); + + +/* mcore.c */ +gk_mcore_t *gk_mcoreCreate(size_t coresize); +gk_mcore_t *gk_gkmcoreCreate(); +void gk_mcoreDestroy(gk_mcore_t **r_mcore, int showstats); +void gk_gkmcoreDestroy(gk_mcore_t **r_mcore, int showstats); +void *gk_mcoreMalloc(gk_mcore_t *mcore, size_t nbytes); +void gk_mcorePush(gk_mcore_t *mcore); +void gk_gkmcorePush(gk_mcore_t *mcore); +void gk_mcorePop(gk_mcore_t *mcore); +void gk_gkmcorePop(gk_mcore_t *mcore); +void gk_mcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr); +void gk_gkmcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr); +void gk_mcoreDel(gk_mcore_t *mcore, void *ptr); +void gk_gkmcoreDel(gk_mcore_t *mcore, void *ptr); + +/* rw.c */ +int gk_rw_PageRank(gk_csr_t *mat, float lamda, float eps, int max_niter, float *pr); + + +/* graph.c */ +gk_graph_t *gk_graph_Create(); +void gk_graph_Init(gk_graph_t *graph); +void gk_graph_Free(gk_graph_t **graph); +void gk_graph_FreeContents(gk_graph_t *graph); +gk_graph_t *gk_graph_Read(char *filename, int format, int hasvals, + int numbering, int isfewgts, int isfvwgts, int isfvsizes); +void gk_graph_Write(gk_graph_t *graph, char *filename, int format, int numbering); +gk_graph_t *gk_graph_Dup(gk_graph_t *graph); +gk_graph_t *gk_graph_Transpose(gk_graph_t *graph); +gk_graph_t *gk_graph_ExtractSubgraph(gk_graph_t *graph, int vstart, int nvtxs); +gk_graph_t *gk_graph_Reorder(gk_graph_t *graph, int32_t *perm, int32_t *iperm); +int gk_graph_FindComponents(gk_graph_t *graph, int32_t *cptr, int32_t *cind); +void gk_graph_ComputeBFSOrdering(gk_graph_t *graph, int v, int32_t **r_perm, + int32_t **r_iperm); +void gk_graph_ComputeBestFOrdering0(gk_graph_t *graph, int v, int type, + int32_t **r_perm, int32_t **r_iperm); +void gk_graph_ComputeBestFOrdering(gk_graph_t *graph, int v, int type, + int32_t **r_perm, int32_t **r_iperm); +void gk_graph_SingleSourceShortestPaths(gk_graph_t *graph, int v, void **r_sps); +void gk_graph_SortAdjacencies(gk_graph_t *graph); +gk_graph_t *gk_graph_MakeSymmetric(gk_graph_t *graph, int op); + + +/* cache.c */ +gk_cache_t *gk_cacheCreate(uint32_t nway, uint32_t lnbits, size_t cnbits); +void gk_cacheReset(gk_cache_t *cache); +void gk_cacheDestroy(gk_cache_t **r_cache); +int gk_cacheLoad(gk_cache_t *cache, size_t addr); +double gk_cacheGetHitRate(gk_cache_t *cache); + + +#ifdef __cplusplus +} +#endif + + +#endif + diff --git a/gk_struct.h b/gk_struct.h new file mode 100644 index 0000000..2925e98 --- /dev/null +++ b/gk_struct.h @@ -0,0 +1,296 @@ +/*! +\file gk_struct.h +\brief This file contains various datastructures used/provided by GKlib + +\date Started 3/27/2007 +\author George +\version\verbatim $Id: gk_struct.h 21988 2018-04-16 00:11:19Z karypis $ \endverbatim +*/ + +#ifndef _GK_STRUCT_H_ +#define _GK_STRUCT_H_ + + +/********************************************************************/ +/*! Generator for gk_??KeyVal_t data structure */ +/********************************************************************/ +#define GK_MKKEYVALUE_T(NAME, KEYTYPE, VALTYPE) \ +typedef struct {\ + KEYTYPE key;\ + VALTYPE val;\ +} NAME;\ + +/* The actual KeyVal data structures */ +GK_MKKEYVALUE_T(gk_ckv_t, char, ssize_t) +GK_MKKEYVALUE_T(gk_ikv_t, int, ssize_t) +GK_MKKEYVALUE_T(gk_i8kv_t, int8_t, ssize_t) +GK_MKKEYVALUE_T(gk_i16kv_t, int16_t, ssize_t) +GK_MKKEYVALUE_T(gk_i32kv_t, int32_t, ssize_t) +GK_MKKEYVALUE_T(gk_i64kv_t, int64_t, ssize_t) +GK_MKKEYVALUE_T(gk_zkv_t, ssize_t, ssize_t) +GK_MKKEYVALUE_T(gk_zukv_t, size_t, ssize_t) +GK_MKKEYVALUE_T(gk_fkv_t, float, ssize_t) +GK_MKKEYVALUE_T(gk_dkv_t, double, ssize_t) +GK_MKKEYVALUE_T(gk_skv_t, char *, ssize_t) +GK_MKKEYVALUE_T(gk_idxkv_t, gk_idx_t, gk_idx_t) + + + +/********************************************************************/ +/*! Generator for gk_?pq_t data structure */ +/********************************************************************/ +#define GK_MKPQUEUE_T(NAME, KVTYPE)\ +typedef struct {\ + size_t nnodes;\ + size_t maxnodes;\ +\ + /* Heap version of the data structure */ \ + KVTYPE *heap;\ + ssize_t *locator;\ +} NAME;\ + +GK_MKPQUEUE_T(gk_ipq_t, gk_ikv_t) +GK_MKPQUEUE_T(gk_i32pq_t, gk_i32kv_t) +GK_MKPQUEUE_T(gk_i64pq_t, gk_i64kv_t) +GK_MKPQUEUE_T(gk_fpq_t, gk_fkv_t) +GK_MKPQUEUE_T(gk_dpq_t, gk_dkv_t) +GK_MKPQUEUE_T(gk_idxpq_t, gk_idxkv_t) + + +#define GK_MKPQUEUE2_T(NAME, KTYPE, VTYPE)\ +typedef struct {\ + ssize_t nnodes;\ + ssize_t maxnodes;\ +\ + /* Heap version of the data structure */ \ + KTYPE *keys;\ + VTYPE *vals;\ +} NAME;\ + + + +/*------------------------------------------------------------- + * The following data structure stores a sparse CSR format + *-------------------------------------------------------------*/ +typedef struct gk_csr_t { + int32_t nrows, ncols; + ssize_t *rowptr, *colptr; + int32_t *rowind, *colind; + int32_t *rowids, *colids; + int32_t *rlabels, *clabels; + int32_t *rmap, *cmap; + float *rowval, *colval; + float *rnorms, *cnorms; + float *rsums, *csums; + float *rsizes, *csizes; + float *rvols, *cvols; + float *rwgts, *cwgts; +} gk_csr_t; + + +/*------------------------------------------------------------- + * The following data structure stores a sparse graph + *-------------------------------------------------------------*/ +typedef struct gk_graph_t { + int32_t nvtxs; /*!< The number of vertices in the graph */ + ssize_t *xadj; /*!< The ptr-structure of the adjncy list */ + int32_t *adjncy; /*!< The adjacency list of the graph */ + int32_t *iadjwgt; /*!< The integer edge weights */ + float *fadjwgt; /*!< The floating point edge weights */ + int32_t *ivwgts; /*!< The integer vertex weights */ + float *fvwgts; /*!< The floating point vertex weights */ + int32_t *ivsizes; /*!< The integer vertex sizes */ + float *fvsizes; /*!< The floating point vertex sizes */ + int32_t *vlabels; /*!< The labels of the vertices */ +} gk_graph_t; + + +/*------------------------------------------------------------- + * The following data structure stores stores a string as a + * pair of its allocated buffer and the buffer itself. + *-------------------------------------------------------------*/ +typedef struct gk_str_t { + size_t len; + char *buf; +} gk_str_t; + + + + +/*------------------------------------------------------------- +* The following data structure implements a string-2-int mapping +* table used for parsing command-line options +*-------------------------------------------------------------*/ +typedef struct gk_StringMap_t { + char *name; + int id; +} gk_StringMap_t; + + +/*------------------------------------------------------------ + * This structure implements a simple hash table + *------------------------------------------------------------*/ +typedef struct gk_HTable_t { + int nelements; /* The overall size of the hash-table */ + int htsize; /* The current size of the hash-table */ + gk_ikv_t *harray; /* The actual hash-table */ +} gk_HTable_t; + + +/*------------------------------------------------------------ + * This structure implements a gk_Tokens_t list returned by the + * string tokenizer + *------------------------------------------------------------*/ +typedef struct gk_Tokens_t { + int ntoks; /* The number of tokens in the input string */ + char *strbuf; /* The memory that stores all the entries */ + char **list; /* Pointers to the strbuf for each element */ +} gk_Tokens_t; + + +/*------------------------------------------------------------ + * This structure implements storage for an atom in a pdb file + *------------------------------------------------------------*/ +typedef struct atom { + int serial; + char *name; + char altLoc; + char *resname; + char chainid; + int rserial; + char icode; + char element; + double x; + double y; + double z; + double opcy; + double tmpt; +} atom; + + +/*------------------------------------------------------------ + * This structure implements storage for a center of mass for + * a single residue. + *------------------------------------------------------------*/ +typedef struct center_of_mass { + char name; + double x; + double y; + double z; +} center_of_mass; + + +/*------------------------------------------------------------ + * This structure implements storage for a pdb protein + *------------------------------------------------------------*/ +typedef struct pdbf { + int natoms; /* Number of atoms */ + int nresidues; /* Number of residues based on coordinates */ + int ncas; + int nbbs; + int corruption; + char *resSeq; /* Residue sequence based on coordinates */ + char **threeresSeq; /* three-letter residue sequence */ + atom *atoms; + atom **bbs; + atom **cas; + center_of_mass *cm; +} pdbf; + + + +/************************************************************* +* Localization Structures for converting characters to integers +**************************************************************/ +typedef struct gk_i2cc2i_t { + int n; + char *i2c; + int *c2i; +} gk_i2cc2i_t; + + +/******************************************************************* + *This structure implements storage of a protein sequence + * *****************************************************************/ +typedef struct gk_seq_t { + + int len; /*Number of Residues */ + int *sequence; /* Stores the sequence*/ + + + int **pssm; /* Stores the pssm matrix */ + int **psfm; /* Stores the psfm matrix */ + char *name; /* Stores the name of the sequence */ + + int nsymbols; + + +} gk_seq_t; + + + + +/*************************************************************************/ +/*! The following data structure stores information about a memory + allocation operation that can either be served from gk_mcore_t or by + a gk_malloc if not sufficient workspace memory is available. */ +/*************************************************************************/ +typedef struct gk_mop_t { + int type; + ssize_t nbytes; + void *ptr; +} gk_mop_t; + + +/*************************************************************************/ +/*! The following structure defines the mcore for GKlib's customized + memory allocations. */ +/*************************************************************************/ +typedef struct gk_mcore_t { + /* Workspace information */ + size_t coresize; /*!< The amount of core memory that has been allocated */ + size_t corecpos; /*!< Index of the first free location in core */ + void *core; /*!< Pointer to the core itself */ + + /* These are for implementing a stack-based allocation scheme using both + core and also dynamically allocated memory */ + size_t nmops; /*!< The number of maop_t entries that have been allocated */ + size_t cmop; /*!< Index of the first free location in maops */ + gk_mop_t *mops; /*!< The array recording the maop_t operations */ + + /* These are for keeping various statistics for wspacemalloc */ + size_t num_callocs; /*!< The number of core mallocs */ + size_t num_hallocs; /*!< The number of heap mallocs */ + size_t size_callocs; /*!< The total # of bytes in core mallocs */ + size_t size_hallocs; /*!< The total # of bytes in heap mallocs */ + size_t cur_callocs; /*!< The current # of bytes in core mallocs */ + size_t cur_hallocs; /*!< The current # of bytes in heap mallocs */ + size_t max_callocs; /*!< The maximum # of bytes in core mallocs at any given time */ + size_t max_hallocs; /*!< The maximum # of bytes in heap mallocs at any given time */ + +} gk_mcore_t; + + +/*************************************************************************/ +/*! The following structure is used for cache simulation for performance + modeling and analysis. */ +/*************************************************************************/ +typedef struct gk_cache_t { + /*! The total cache is nway*(2^(cnbits+lnbits)) bytes */ + uint32_t nway; /*!< the associativity of the cache */ + uint32_t lnbits; /*!< the number of address bits indexing the cache line */ + uint32_t cnbits; /*!< the number of address bits indexing the cache */ + size_t csize; /*!< 2^cnbits */ + size_t cmask; /*!< csize-1 */ + + uint64_t clock; /*!< a clock in terms of accesses */ + + uint64_t *latimes; /*!< a cacheline-level last access time */ + size_t *clines; /*!< the cache in terms of cachelines */ + + uint64_t nhits; /*!< counts the number of hits */ + uint64_t nmisses; /*!< counts the number of misses */ +} gk_cache_t; + + +#endif diff --git a/gk_types.h b/gk_types.h new file mode 100644 index 0000000..57c1191 --- /dev/null +++ b/gk_types.h @@ -0,0 +1,38 @@ +/*! +\file gk_types.h +\brief This file contains basic scalar datatype used in GKlib + +\date Started 3/27/2007 +\author George +\version\verbatim $Id: gk_types.h 10711 2011-08-31 22:23:04Z karypis $ \endverbatim +*/ + +#ifndef _GK_TYPES_H_ +#define _GK_TYPES_H_ + +/************************************************************************* +* Basic data type definitions. These definitions allow GKlib to separate +* the following elemental types: +* - loop iterator variables, which are set to size_t +* - signed and unsigned int variables that can be set to any # of bits +* - signed and unsigned long variables that can be set to any # of bits +* - real variables, which can be set to single or double precision. +**************************************************************************/ +/*typedef ptrdiff_t gk_idx_t; */ /* index variable */ +typedef ssize_t gk_idx_t; /* index variable */ +typedef int32_t gk_int_t; /* integer values */ +typedef uint32_t gk_uint_t; /* unsigned integer values */ +typedef int64_t gk_long_t; /* long integer values */ +typedef uint64_t gk_ulong_t; /* unsigned long integer values */ +typedef float gk_real_t; /* real type */ +typedef double gk_dreal_t; /* double precission real type */ +typedef double gk_wclock_t; /* wall-clock time */ + +/*#define GK_IDX_MAX PTRDIFF_MAX*/ +#define GK_IDX_MAX ((SIZE_MAX>>1)-2) + +#define PRIGKIDX "zd" +#define SCNGKIDX "zd" + + +#endif diff --git a/gk_util.c b/gk_util.c new file mode 100644 index 0000000..e1e68db --- /dev/null +++ b/gk_util.c @@ -0,0 +1,107 @@ +/*! +\file util.c +\brief Various utility routines + +\date Started 4/12/2007 +\author George +\version\verbatim $Id: gk_util.c 16223 2014-02-15 21:34:09Z karypis $ \endverbatim +*/ + + +#include + + +/************************************************************************* +* This file randomly permutes the contents of an array. +* flag == 0, don't initialize perm +* flag == 1, set p[i] = i +**************************************************************************/ +void gk_RandomPermute(size_t n, int *p, int flag) +{ + size_t i, u, v; + int tmp; + + if (flag == 1) { + for (i=0; i 1; i++, a = a>>1); + return i-1; +} + + +/************************************************************************* +* This function checks if the argument is a power of 2 +**************************************************************************/ +int gk_ispow2(int a) +{ + return (a == (1<. + + The GNU C Library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2.1 of the License, or (at your option) any later version. + + The GNU C Library 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 + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with the GNU C Library; if not, write to the Free + Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA + 02111-1307 USA. */ + +/* this is for removing a compiler warning */ +void gkfooo() { return; } + +#ifdef USE_GKREGEX + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#ifdef _LIBC +/* We have to keep the namespace clean. */ +# define regfree(preg) __regfree (preg) +# define regexec(pr, st, nm, pm, ef) __regexec (pr, st, nm, pm, ef) +# define regcomp(preg, pattern, cflags) __regcomp (preg, pattern, cflags) +# define regerror(errcode, preg, errbuf, errbuf_size) \ + __regerror(errcode, preg, errbuf, errbuf_size) +# define re_set_registers(bu, re, nu, st, en) \ + __re_set_registers (bu, re, nu, st, en) +# define re_match_2(bufp, string1, size1, string2, size2, pos, regs, stop) \ + __re_match_2 (bufp, string1, size1, string2, size2, pos, regs, stop) +# define re_match(bufp, string, size, pos, regs) \ + __re_match (bufp, string, size, pos, regs) +# define re_search(bufp, string, size, startpos, range, regs) \ + __re_search (bufp, string, size, startpos, range, regs) +# define re_compile_pattern(pattern, length, bufp) \ + __re_compile_pattern (pattern, length, bufp) +# define re_set_syntax(syntax) __re_set_syntax (syntax) +# define re_search_2(bufp, st1, s1, st2, s2, startpos, range, regs, stop) \ + __re_search_2 (bufp, st1, s1, st2, s2, startpos, range, regs, stop) +# define re_compile_fastmap(bufp) __re_compile_fastmap (bufp) + +# include "../locale/localeinfo.h" +#endif + +#include "GKlib.h" + + +/******************************************************************************/ +/******************************************************************************/ +/******************************************************************************/ +/* GKINCLUDE #include "regex_internal.h" */ +/******************************************************************************/ +/******************************************************************************/ +/******************************************************************************/ +/* Extended regular expression matching and search library. + Copyright (C) 2002, 2003, 2004, 2005 Free Software Foundation, Inc. + This file is part of the GNU C Library. + Contributed by Isamu Hasegawa . + + The GNU C Library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2.1 of the License, or (at your option) any later version. + + The GNU C Library 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 + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with the GNU C Library; if not, write to the Free + Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA + 02111-1307 USA. */ + +#ifndef _REGEX_INTERNAL_H +#define _REGEX_INTERNAL_H 1 + +#include +#include +#include +#include +#include + +#if defined(__MINGW32_VERSION) || defined(_MSC_VER) +#define strcasecmp stricmp +#endif + +#if defined HAVE_LANGINFO_H || defined HAVE_LANGINFO_CODESET || defined _LIBC +# include +#endif +#if defined HAVE_LOCALE_H || defined _LIBC +# include +#endif +#if defined HAVE_WCHAR_H || defined _LIBC +# include +#endif /* HAVE_WCHAR_H || _LIBC */ +#if defined HAVE_WCTYPE_H || defined _LIBC +# include +#endif /* HAVE_WCTYPE_H || _LIBC */ +#if defined HAVE_STDBOOL_H || defined _LIBC +# include +#else +typedef enum { false, true } bool; +#endif /* HAVE_STDBOOL_H || _LIBC */ +#if defined HAVE_STDINT_H || defined _LIBC +# include +#endif /* HAVE_STDINT_H || _LIBC */ +#if defined _LIBC +# include +#else +# define __libc_lock_define(CLASS,NAME) +# define __libc_lock_init(NAME) do { } while (0) +# define __libc_lock_lock(NAME) do { } while (0) +# define __libc_lock_unlock(NAME) do { } while (0) +#endif + +/* In case that the system doesn't have isblank(). */ +#if !defined _LIBC && !defined HAVE_ISBLANK && !defined isblank +# define isblank(ch) ((ch) == ' ' || (ch) == '\t') +#endif + +#ifdef _LIBC +# ifndef _RE_DEFINE_LOCALE_FUNCTIONS +# define _RE_DEFINE_LOCALE_FUNCTIONS 1 +# include +# include +# include +# endif +#endif + +/* This is for other GNU distributions with internationalized messages. */ +#if (HAVE_LIBINTL_H && ENABLE_NLS) || defined _LIBC +# include +# ifdef _LIBC +# undef gettext +# define gettext(msgid) \ + INTUSE(__dcgettext) (_libc_intl_domainname, msgid, LC_MESSAGES) +# endif +#else +# define gettext(msgid) (msgid) +#endif + +#ifndef gettext_noop +/* This define is so xgettext can find the internationalizable + strings. */ +# define gettext_noop(String) String +#endif + +/* For loser systems without the definition. */ +#ifndef SIZE_MAX +# define SIZE_MAX ((size_t) -1) +#endif + +#if (defined MB_CUR_MAX && HAVE_LOCALE_H && HAVE_WCTYPE_H && HAVE_WCHAR_H && HAVE_WCRTOMB && HAVE_MBRTOWC && HAVE_WCSCOLL) || _LIBC +# define RE_ENABLE_I18N +#endif + +#if __GNUC__ >= 3 +# define BE(expr, val) __builtin_expect (expr, val) +#else +# define BE(expr, val) (expr) +# define inline +#endif + +/* Number of single byte character. */ +#define SBC_MAX 256 + +#define COLL_ELEM_LEN_MAX 8 + +/* The character which represents newline. */ +#define NEWLINE_CHAR '\n' +#define WIDE_NEWLINE_CHAR L'\n' + +/* Rename to standard API for using out of glibc. */ +#ifndef _LIBC +# define __wctype wctype +# define __iswctype iswctype +# define __btowc btowc +# define __mempcpy mempcpy +# define __wcrtomb wcrtomb +# define __regfree regfree +# define attribute_hidden +#endif /* not _LIBC */ + +#ifdef __GNUC__ +# define __attribute(arg) __attribute__ (arg) +#else +# define __attribute(arg) +#endif + +extern const char __re_error_msgid[] attribute_hidden; +extern const size_t __re_error_msgid_idx[] attribute_hidden; + +/* An integer used to represent a set of bits. It must be unsigned, + and must be at least as wide as unsigned int. */ +typedef unsigned long int bitset_word_t; +/* All bits set in a bitset_word_t. */ +#define BITSET_WORD_MAX ULONG_MAX +/* Number of bits in a bitset_word_t. */ +#define BITSET_WORD_BITS (sizeof (bitset_word_t) * CHAR_BIT) +/* Number of bitset_word_t in a bit_set. */ +#define BITSET_WORDS (SBC_MAX / BITSET_WORD_BITS) +typedef bitset_word_t bitset_t[BITSET_WORDS]; +typedef bitset_word_t *re_bitset_ptr_t; +typedef const bitset_word_t *re_const_bitset_ptr_t; + +#define bitset_set(set,i) \ + (set[i / BITSET_WORD_BITS] |= (bitset_word_t) 1 << i % BITSET_WORD_BITS) +#define bitset_clear(set,i) \ + (set[i / BITSET_WORD_BITS] &= ~((bitset_word_t) 1 << i % BITSET_WORD_BITS)) +#define bitset_contain(set,i) \ + (set[i / BITSET_WORD_BITS] & ((bitset_word_t) 1 << i % BITSET_WORD_BITS)) +#define bitset_empty(set) memset (set, '\0', sizeof (bitset_t)) +#define bitset_set_all(set) memset (set, '\xff', sizeof (bitset_t)) +#define bitset_copy(dest,src) memcpy (dest, src, sizeof (bitset_t)) + +#define PREV_WORD_CONSTRAINT 0x0001 +#define PREV_NOTWORD_CONSTRAINT 0x0002 +#define NEXT_WORD_CONSTRAINT 0x0004 +#define NEXT_NOTWORD_CONSTRAINT 0x0008 +#define PREV_NEWLINE_CONSTRAINT 0x0010 +#define NEXT_NEWLINE_CONSTRAINT 0x0020 +#define PREV_BEGBUF_CONSTRAINT 0x0040 +#define NEXT_ENDBUF_CONSTRAINT 0x0080 +#define WORD_DELIM_CONSTRAINT 0x0100 +#define NOT_WORD_DELIM_CONSTRAINT 0x0200 + +typedef enum +{ + INSIDE_WORD = PREV_WORD_CONSTRAINT | NEXT_WORD_CONSTRAINT, + WORD_FIRST = PREV_NOTWORD_CONSTRAINT | NEXT_WORD_CONSTRAINT, + WORD_LAST = PREV_WORD_CONSTRAINT | NEXT_NOTWORD_CONSTRAINT, + INSIDE_NOTWORD = PREV_NOTWORD_CONSTRAINT | NEXT_NOTWORD_CONSTRAINT, + LINE_FIRST = PREV_NEWLINE_CONSTRAINT, + LINE_LAST = NEXT_NEWLINE_CONSTRAINT, + BUF_FIRST = PREV_BEGBUF_CONSTRAINT, + BUF_LAST = NEXT_ENDBUF_CONSTRAINT, + WORD_DELIM = WORD_DELIM_CONSTRAINT, + NOT_WORD_DELIM = NOT_WORD_DELIM_CONSTRAINT +} re_context_type; + +typedef struct +{ + int alloc; + int nelem; + int *elems; +} re_node_set; + +typedef enum +{ + NON_TYPE = 0, + + /* Node type, These are used by token, node, tree. */ + CHARACTER = 1, + END_OF_RE = 2, + SIMPLE_BRACKET = 3, + OP_BACK_REF = 4, + OP_PERIOD = 5, +#ifdef RE_ENABLE_I18N + COMPLEX_BRACKET = 6, + OP_UTF8_PERIOD = 7, +#endif /* RE_ENABLE_I18N */ + + /* We define EPSILON_BIT as a macro so that OP_OPEN_SUBEXP is used + when the debugger shows values of this enum type. */ +#define EPSILON_BIT 8 + OP_OPEN_SUBEXP = EPSILON_BIT | 0, + OP_CLOSE_SUBEXP = EPSILON_BIT | 1, + OP_ALT = EPSILON_BIT | 2, + OP_DUP_ASTERISK = EPSILON_BIT | 3, + ANCHOR = EPSILON_BIT | 4, + + /* Tree type, these are used only by tree. */ + CONCAT = 16, + SUBEXP = 17, + + /* Token type, these are used only by token. */ + OP_DUP_PLUS = 18, + OP_DUP_QUESTION, + OP_OPEN_BRACKET, + OP_CLOSE_BRACKET, + OP_CHARSET_RANGE, + OP_OPEN_DUP_NUM, + OP_CLOSE_DUP_NUM, + OP_NON_MATCH_LIST, + OP_OPEN_COLL_ELEM, + OP_CLOSE_COLL_ELEM, + OP_OPEN_EQUIV_CLASS, + OP_CLOSE_EQUIV_CLASS, + OP_OPEN_CHAR_CLASS, + OP_CLOSE_CHAR_CLASS, + OP_WORD, + OP_NOTWORD, + OP_SPACE, + OP_NOTSPACE, + BACK_SLASH + +} re_token_type_t; + +#ifdef RE_ENABLE_I18N +typedef struct +{ + /* Multibyte characters. */ + wchar_t *mbchars; + + /* Collating symbols. */ +# ifdef _LIBC + int32_t *coll_syms; +# endif + + /* Equivalence classes. */ +# ifdef _LIBC + int32_t *equiv_classes; +# endif + + /* Range expressions. */ +# ifdef _LIBC + uint32_t *range_starts; + uint32_t *range_ends; +# else /* not _LIBC */ + wchar_t *range_starts; + wchar_t *range_ends; +# endif /* not _LIBC */ + + /* Character classes. */ + wctype_t *char_classes; + + /* If this character set is the non-matching list. */ + unsigned int non_match : 1; + + /* # of multibyte characters. */ + int nmbchars; + + /* # of collating symbols. */ + int ncoll_syms; + + /* # of equivalence classes. */ + int nequiv_classes; + + /* # of range expressions. */ + int nranges; + + /* # of character classes. */ + int nchar_classes; +} re_charset_t; +#endif /* RE_ENABLE_I18N */ + +typedef struct +{ + union + { + unsigned char c; /* for CHARACTER */ + re_bitset_ptr_t sbcset; /* for SIMPLE_BRACKET */ +#ifdef RE_ENABLE_I18N + re_charset_t *mbcset; /* for COMPLEX_BRACKET */ +#endif /* RE_ENABLE_I18N */ + int idx; /* for BACK_REF */ + re_context_type ctx_type; /* for ANCHOR */ + } opr; +#if __GNUC__ >= 2 + re_token_type_t type : 8; +#else + re_token_type_t type; +#endif + unsigned int constraint : 10; /* context constraint */ + unsigned int duplicated : 1; + unsigned int opt_subexp : 1; +#ifdef RE_ENABLE_I18N + unsigned int accept_mb : 1; + /* These 2 bits can be moved into the union if needed (e.g. if running out + of bits; move opr.c to opr.c.c and move the flags to opr.c.flags). */ + unsigned int mb_partial : 1; +#endif + unsigned int word_char : 1; +} re_token_t; + +#define IS_EPSILON_NODE(type) ((type) & EPSILON_BIT) + +struct re_string_t +{ + /* Indicate the raw buffer which is the original string passed as an + argument of regexec(), re_search(), etc.. */ + const unsigned char *raw_mbs; + /* Store the multibyte string. In case of "case insensitive mode" like + REG_ICASE, upper cases of the string are stored, otherwise MBS points + the same address that RAW_MBS points. */ + unsigned char *mbs; +#ifdef RE_ENABLE_I18N + /* Store the wide character string which is corresponding to MBS. */ + wint_t *wcs; + int *offsets; + mbstate_t cur_state; +#endif + /* Index in RAW_MBS. Each character mbs[i] corresponds to + raw_mbs[raw_mbs_idx + i]. */ + int raw_mbs_idx; + /* The length of the valid characters in the buffers. */ + int valid_len; + /* The corresponding number of bytes in raw_mbs array. */ + int valid_raw_len; + /* The length of the buffers MBS and WCS. */ + int bufs_len; + /* The index in MBS, which is updated by re_string_fetch_byte. */ + int cur_idx; + /* length of RAW_MBS array. */ + int raw_len; + /* This is RAW_LEN - RAW_MBS_IDX + VALID_LEN - VALID_RAW_LEN. */ + int len; + /* End of the buffer may be shorter than its length in the cases such + as re_match_2, re_search_2. Then, we use STOP for end of the buffer + instead of LEN. */ + int raw_stop; + /* This is RAW_STOP - RAW_MBS_IDX adjusted through OFFSETS. */ + int stop; + + /* The context of mbs[0]. We store the context independently, since + the context of mbs[0] may be different from raw_mbs[0], which is + the beginning of the input string. */ + unsigned int tip_context; + /* The translation passed as a part of an argument of re_compile_pattern. */ + RE_TRANSLATE_TYPE trans; + /* Copy of re_dfa_t's word_char. */ + re_const_bitset_ptr_t word_char; + /* 1 if REG_ICASE. */ + unsigned char icase; + unsigned char is_utf8; + unsigned char map_notascii; + unsigned char mbs_allocated; + unsigned char offsets_needed; + unsigned char newline_anchor; + unsigned char word_ops_used; + int mb_cur_max; +}; +typedef struct re_string_t re_string_t; + + +struct re_dfa_t; +typedef struct re_dfa_t re_dfa_t; + +#ifndef _LIBC +# ifdef __i386__ +# define internal_function __attribute ((regparm (3), stdcall)) +# else +# define internal_function +# endif +#endif + +static reg_errcode_t re_string_realloc_buffers (re_string_t *pstr, + int new_buf_len) + internal_function; +#ifdef RE_ENABLE_I18N +static void build_wcs_buffer (re_string_t *pstr) internal_function; +static int build_wcs_upper_buffer (re_string_t *pstr) internal_function; +#endif /* RE_ENABLE_I18N */ +static void build_upper_buffer (re_string_t *pstr) internal_function; +static void re_string_translate_buffer (re_string_t *pstr) internal_function; +static unsigned int re_string_context_at (const re_string_t *input, int idx, + int eflags) + internal_function __attribute ((pure)); +#define re_string_peek_byte(pstr, offset) \ + ((pstr)->mbs[(pstr)->cur_idx + offset]) +#define re_string_fetch_byte(pstr) \ + ((pstr)->mbs[(pstr)->cur_idx++]) +#define re_string_first_byte(pstr, idx) \ + ((idx) == (pstr)->valid_len || (pstr)->wcs[idx] != WEOF) +#define re_string_is_single_byte_char(pstr, idx) \ + ((pstr)->wcs[idx] != WEOF && ((pstr)->valid_len == (idx) + 1 \ + || (pstr)->wcs[(idx) + 1] != WEOF)) +#define re_string_eoi(pstr) ((pstr)->stop <= (pstr)->cur_idx) +#define re_string_cur_idx(pstr) ((pstr)->cur_idx) +#define re_string_get_buffer(pstr) ((pstr)->mbs) +#define re_string_length(pstr) ((pstr)->len) +#define re_string_byte_at(pstr,idx) ((pstr)->mbs[idx]) +#define re_string_skip_bytes(pstr,idx) ((pstr)->cur_idx += (idx)) +#define re_string_set_index(pstr,idx) ((pstr)->cur_idx = (idx)) + +#ifdef __GNUC__ +# define alloca(size) __builtin_alloca (size) +# define HAVE_ALLOCA 1 +#elif defined(_MSC_VER) +# include +# define alloca _alloca +# define HAVE_ALLOCA 1 +#else +# error No alloca() +#endif + +#ifndef _LIBC +# if HAVE_ALLOCA +/* The OS usually guarantees only one guard page at the bottom of the stack, + and a page size can be as small as 4096 bytes. So we cannot safely + allocate anything larger than 4096 bytes. Also care for the possibility + of a few compiler-allocated temporary stack slots. */ +# define __libc_use_alloca(n) ((n) < 4032) +# else +/* alloca is implemented with malloc, so just use malloc. */ +# define __libc_use_alloca(n) 0 +# endif +#endif + +#define re_malloc(t,n) ((t *) malloc ((n) * sizeof (t))) +#define re_realloc(p,t,n) ((t *) realloc (p, (n) * sizeof (t))) +#define re_free(p) free (p) + +struct bin_tree_t +{ + struct bin_tree_t *parent; + struct bin_tree_t *left; + struct bin_tree_t *right; + struct bin_tree_t *first; + struct bin_tree_t *next; + + re_token_t token; + + /* `node_idx' is the index in dfa->nodes, if `type' == 0. + Otherwise `type' indicate the type of this node. */ + int node_idx; +}; +typedef struct bin_tree_t bin_tree_t; + +#define BIN_TREE_STORAGE_SIZE \ + ((1024 - sizeof (void *)) / sizeof (bin_tree_t)) + +struct bin_tree_storage_t +{ + struct bin_tree_storage_t *next; + bin_tree_t data[BIN_TREE_STORAGE_SIZE]; +}; +typedef struct bin_tree_storage_t bin_tree_storage_t; + +#define CONTEXT_WORD 1 +#define CONTEXT_NEWLINE (CONTEXT_WORD << 1) +#define CONTEXT_BEGBUF (CONTEXT_NEWLINE << 1) +#define CONTEXT_ENDBUF (CONTEXT_BEGBUF << 1) + +#define IS_WORD_CONTEXT(c) ((c) & CONTEXT_WORD) +#define IS_NEWLINE_CONTEXT(c) ((c) & CONTEXT_NEWLINE) +#define IS_BEGBUF_CONTEXT(c) ((c) & CONTEXT_BEGBUF) +#define IS_ENDBUF_CONTEXT(c) ((c) & CONTEXT_ENDBUF) +#define IS_ORDINARY_CONTEXT(c) ((c) == 0) + +#define IS_WORD_CHAR(ch) (isalnum (ch) || (ch) == '_') +#define IS_NEWLINE(ch) ((ch) == NEWLINE_CHAR) +#define IS_WIDE_WORD_CHAR(ch) (iswalnum (ch) || (ch) == L'_') +#define IS_WIDE_NEWLINE(ch) ((ch) == WIDE_NEWLINE_CHAR) + +#define NOT_SATISFY_PREV_CONSTRAINT(constraint,context) \ + ((((constraint) & PREV_WORD_CONSTRAINT) && !IS_WORD_CONTEXT (context)) \ + || ((constraint & PREV_NOTWORD_CONSTRAINT) && IS_WORD_CONTEXT (context)) \ + || ((constraint & PREV_NEWLINE_CONSTRAINT) && !IS_NEWLINE_CONTEXT (context))\ + || ((constraint & PREV_BEGBUF_CONSTRAINT) && !IS_BEGBUF_CONTEXT (context))) + +#define NOT_SATISFY_NEXT_CONSTRAINT(constraint,context) \ + ((((constraint) & NEXT_WORD_CONSTRAINT) && !IS_WORD_CONTEXT (context)) \ + || (((constraint) & NEXT_NOTWORD_CONSTRAINT) && IS_WORD_CONTEXT (context)) \ + || (((constraint) & NEXT_NEWLINE_CONSTRAINT) && !IS_NEWLINE_CONTEXT (context)) \ + || (((constraint) & NEXT_ENDBUF_CONSTRAINT) && !IS_ENDBUF_CONTEXT (context))) + +struct re_dfastate_t +{ + unsigned int hash; + re_node_set nodes; + re_node_set non_eps_nodes; + re_node_set inveclosure; + re_node_set *entrance_nodes; + struct re_dfastate_t **trtable, **word_trtable; + unsigned int context : 4; + unsigned int halt : 1; + /* If this state can accept `multi byte'. + Note that we refer to multibyte characters, and multi character + collating elements as `multi byte'. */ + unsigned int accept_mb : 1; + /* If this state has backreference node(s). */ + unsigned int has_backref : 1; + unsigned int has_constraint : 1; +}; +typedef struct re_dfastate_t re_dfastate_t; + +struct re_state_table_entry +{ + int num; + int alloc; + re_dfastate_t **array; +}; + +/* Array type used in re_sub_match_last_t and re_sub_match_top_t. */ + +typedef struct +{ + int next_idx; + int alloc; + re_dfastate_t **array; +} state_array_t; + +/* Store information about the node NODE whose type is OP_CLOSE_SUBEXP. */ + +typedef struct +{ + int node; + int str_idx; /* The position NODE match at. */ + state_array_t path; +} re_sub_match_last_t; + +/* Store information about the node NODE whose type is OP_OPEN_SUBEXP. + And information about the node, whose type is OP_CLOSE_SUBEXP, + corresponding to NODE is stored in LASTS. */ + +typedef struct +{ + int str_idx; + int node; + state_array_t *path; + int alasts; /* Allocation size of LASTS. */ + int nlasts; /* The number of LASTS. */ + re_sub_match_last_t **lasts; +} re_sub_match_top_t; + +struct re_backref_cache_entry +{ + int node; + int str_idx; + int subexp_from; + int subexp_to; + char more; + char unused; + unsigned short int eps_reachable_subexps_map; +}; + +typedef struct +{ + /* The string object corresponding to the input string. */ + re_string_t input; +#if defined _LIBC || (defined __STDC_VERSION__ && __STDC_VERSION__ >= 199901L) + const re_dfa_t *const dfa; +#else + const re_dfa_t *dfa; +#endif + /* EFLAGS of the argument of regexec. */ + int eflags; + /* Where the matching ends. */ + int match_last; + int last_node; + /* The state log used by the matcher. */ + re_dfastate_t **state_log; + int state_log_top; + /* Back reference cache. */ + int nbkref_ents; + int abkref_ents; + struct re_backref_cache_entry *bkref_ents; + int max_mb_elem_len; + int nsub_tops; + int asub_tops; + re_sub_match_top_t **sub_tops; +} re_match_context_t; + +typedef struct +{ + re_dfastate_t **sifted_states; + re_dfastate_t **limited_states; + int last_node; + int last_str_idx; + re_node_set limits; +} re_sift_context_t; + +struct re_fail_stack_ent_t +{ + int idx; + int node; + regmatch_t *regs; + re_node_set eps_via_nodes; +}; + +struct re_fail_stack_t +{ + int num; + int alloc; + struct re_fail_stack_ent_t *stack; +}; + +struct re_dfa_t +{ + re_token_t *nodes; + size_t nodes_alloc; + size_t nodes_len; + int *nexts; + int *org_indices; + re_node_set *edests; + re_node_set *eclosures; + re_node_set *inveclosures; + struct re_state_table_entry *state_table; + re_dfastate_t *init_state; + re_dfastate_t *init_state_word; + re_dfastate_t *init_state_nl; + re_dfastate_t *init_state_begbuf; + bin_tree_t *str_tree; + bin_tree_storage_t *str_tree_storage; + re_bitset_ptr_t sb_char; + int str_tree_storage_idx; + + /* number of subexpressions `re_nsub' is in regex_t. */ + unsigned int state_hash_mask; + int init_node; + int nbackref; /* The number of backreference in this dfa. */ + + /* Bitmap expressing which backreference is used. */ + bitset_word_t used_bkref_map; + bitset_word_t completed_bkref_map; + + unsigned int has_plural_match : 1; + /* If this dfa has "multibyte node", which is a backreference or + a node which can accept multibyte character or multi character + collating element. */ + unsigned int has_mb_node : 1; + unsigned int is_utf8 : 1; + unsigned int map_notascii : 1; + unsigned int word_ops_used : 1; + int mb_cur_max; + bitset_t word_char; + reg_syntax_t syntax; + int *subexp_map; +#ifdef DEBUG + char* re_str; +#endif + __libc_lock_define (, lock) +}; + +#define re_node_set_init_empty(set) memset (set, '\0', sizeof (re_node_set)) +#define re_node_set_remove(set,id) \ + (re_node_set_remove_at (set, re_node_set_contains (set, id) - 1)) +#define re_node_set_empty(p) ((p)->nelem = 0) +#define re_node_set_free(set) re_free ((set)->elems) + + +typedef enum +{ + SB_CHAR, + MB_CHAR, + EQUIV_CLASS, + COLL_SYM, + CHAR_CLASS +} bracket_elem_type; + +typedef struct +{ + bracket_elem_type type; + union + { + unsigned char ch; + unsigned char *name; + wchar_t wch; + } opr; +} bracket_elem_t; + + +/* Inline functions for bitset operation. */ +static inline void +bitset_not (bitset_t set) +{ + int bitset_i; + for (bitset_i = 0; bitset_i < BITSET_WORDS; ++bitset_i) + set[bitset_i] = ~set[bitset_i]; +} + +static inline void +bitset_merge (bitset_t dest, const bitset_t src) +{ + int bitset_i; + for (bitset_i = 0; bitset_i < BITSET_WORDS; ++bitset_i) + dest[bitset_i] |= src[bitset_i]; +} + +static inline void +bitset_mask (bitset_t dest, const bitset_t src) +{ + int bitset_i; + for (bitset_i = 0; bitset_i < BITSET_WORDS; ++bitset_i) + dest[bitset_i] &= src[bitset_i]; +} + +#ifdef RE_ENABLE_I18N +/* Inline functions for re_string. */ +static inline int +internal_function __attribute ((pure)) +re_string_char_size_at (const re_string_t *pstr, int idx) +{ + int byte_idx; + if (pstr->mb_cur_max == 1) + return 1; + for (byte_idx = 1; idx + byte_idx < pstr->valid_len; ++byte_idx) + if (pstr->wcs[idx + byte_idx] != WEOF) + break; + return byte_idx; +} + +static inline wint_t +internal_function __attribute ((pure)) +re_string_wchar_at (const re_string_t *pstr, int idx) +{ + if (pstr->mb_cur_max == 1) + return (wint_t) pstr->mbs[idx]; + return (wint_t) pstr->wcs[idx]; +} + +static int +internal_function __attribute ((pure)) +re_string_elem_size_at (const re_string_t *pstr, int idx) +{ +# ifdef _LIBC + const unsigned char *p, *extra; + const int32_t *table, *indirect; + int32_t tmp; +# include + uint_fast32_t nrules = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES); + + if (nrules != 0) + { + table = (const int32_t *) _NL_CURRENT (LC_COLLATE, _NL_COLLATE_TABLEMB); + extra = (const unsigned char *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_EXTRAMB); + indirect = (const int32_t *) _NL_CURRENT (LC_COLLATE, + _NL_COLLATE_INDIRECTMB); + p = pstr->mbs + idx; + tmp = findidx (&p); + return p - pstr->mbs - idx; + } + else +# endif /* _LIBC */ + return 1; +} +#endif /* RE_ENABLE_I18N */ + +#endif /* _REGEX_INTERNAL_H */ + +/******************************************************************************/ +/******************************************************************************/ +/******************************************************************************/ +/* GKINCLUDE #include "regex_internal.c" */ +/******************************************************************************/ +/******************************************************************************/ +/******************************************************************************/ +/* Extended regular expression matching and search library. + Copyright (C) 2002, 2003, 2004, 2005, 2006 Free Software Foundation, Inc. + This file is part of the GNU C Library. + Contributed by Isamu Hasegawa . + + The GNU C Library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2.1 of the License, or (at your option) any later version. + + The GNU C Library 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 + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with the GNU C Library; if not, write to the Free + Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA + 02111-1307 USA. */ + +static void re_string_construct_common (const char *str, int len, + re_string_t *pstr, + RE_TRANSLATE_TYPE trans, int icase, + const re_dfa_t *dfa) internal_function; +static re_dfastate_t *create_ci_newstate (const re_dfa_t *dfa, + const re_node_set *nodes, + unsigned int hash) internal_function; +static re_dfastate_t *create_cd_newstate (const re_dfa_t *dfa, + const re_node_set *nodes, + unsigned int context, + unsigned int hash) internal_function; + +/* Functions for string operation. */ + +/* This function allocate the buffers. It is necessary to call + re_string_reconstruct before using the object. */ + +static reg_errcode_t +internal_function +re_string_allocate (re_string_t *pstr, const char *str, int len, int init_len, + RE_TRANSLATE_TYPE trans, int icase, const re_dfa_t *dfa) +{ + reg_errcode_t ret; + int init_buf_len; + + /* Ensure at least one character fits into the buffers. */ + if (init_len < dfa->mb_cur_max) + init_len = dfa->mb_cur_max; + init_buf_len = (len + 1 < init_len) ? len + 1: init_len; + re_string_construct_common (str, len, pstr, trans, icase, dfa); + + ret = re_string_realloc_buffers (pstr, init_buf_len); + if (BE (ret != REG_NOERROR, 0)) + return ret; + + pstr->word_char = dfa->word_char; + pstr->word_ops_used = dfa->word_ops_used; + pstr->mbs = pstr->mbs_allocated ? pstr->mbs : (unsigned char *) str; + pstr->valid_len = (pstr->mbs_allocated || dfa->mb_cur_max > 1) ? 0 : len; + pstr->valid_raw_len = pstr->valid_len; + return REG_NOERROR; +} + +/* This function allocate the buffers, and initialize them. */ + +static reg_errcode_t +internal_function +re_string_construct (re_string_t *pstr, const char *str, int len, + RE_TRANSLATE_TYPE trans, int icase, const re_dfa_t *dfa) +{ + reg_errcode_t ret; + memset (pstr, '\0', sizeof (re_string_t)); + re_string_construct_common (str, len, pstr, trans, icase, dfa); + + if (len > 0) + { + ret = re_string_realloc_buffers (pstr, len + 1); + if (BE (ret != REG_NOERROR, 0)) + return ret; + } + pstr->mbs = pstr->mbs_allocated ? pstr->mbs : (unsigned char *) str; + + if (icase) + { +#ifdef RE_ENABLE_I18N + if (dfa->mb_cur_max > 1) + { + while (1) + { + ret = build_wcs_upper_buffer (pstr); + if (BE (ret != REG_NOERROR, 0)) + return ret; + if (pstr->valid_raw_len >= len) + break; + if (pstr->bufs_len > pstr->valid_len + dfa->mb_cur_max) + break; + ret = re_string_realloc_buffers (pstr, pstr->bufs_len * 2); + if (BE (ret != REG_NOERROR, 0)) + return ret; + } + } + else +#endif /* RE_ENABLE_I18N */ + build_upper_buffer (pstr); + } + else + { +#ifdef RE_ENABLE_I18N + if (dfa->mb_cur_max > 1) + build_wcs_buffer (pstr); + else +#endif /* RE_ENABLE_I18N */ + { + if (trans != NULL) + re_string_translate_buffer (pstr); + else + { + pstr->valid_len = pstr->bufs_len; + pstr->valid_raw_len = pstr->bufs_len; + } + } + } + + return REG_NOERROR; +} + +/* Helper functions for re_string_allocate, and re_string_construct. */ + +static reg_errcode_t +internal_function +re_string_realloc_buffers (re_string_t *pstr, int new_buf_len) +{ +#ifdef RE_ENABLE_I18N + if (pstr->mb_cur_max > 1) + { + wint_t *new_wcs = re_realloc (pstr->wcs, wint_t, new_buf_len); + if (BE (new_wcs == NULL, 0)) + return REG_ESPACE; + pstr->wcs = new_wcs; + if (pstr->offsets != NULL) + { + int *new_offsets = re_realloc (pstr->offsets, int, new_buf_len); + if (BE (new_offsets == NULL, 0)) + return REG_ESPACE; + pstr->offsets = new_offsets; + } + } +#endif /* RE_ENABLE_I18N */ + if (pstr->mbs_allocated) + { + unsigned char *new_mbs = re_realloc (pstr->mbs, unsigned char, + new_buf_len); + if (BE (new_mbs == NULL, 0)) + return REG_ESPACE; + pstr->mbs = new_mbs; + } + pstr->bufs_len = new_buf_len; + return REG_NOERROR; +} + + +static void +internal_function +re_string_construct_common (const char *str, int len, re_string_t *pstr, + RE_TRANSLATE_TYPE trans, int icase, + const re_dfa_t *dfa) +{ + pstr->raw_mbs = (const unsigned char *) str; + pstr->len = len; + pstr->raw_len = len; + pstr->trans = trans; + pstr->icase = icase ? 1 : 0; + pstr->mbs_allocated = (trans != NULL || icase); + pstr->mb_cur_max = dfa->mb_cur_max; + pstr->is_utf8 = dfa->is_utf8; + pstr->map_notascii = dfa->map_notascii; + pstr->stop = pstr->len; + pstr->raw_stop = pstr->stop; +} + +#ifdef RE_ENABLE_I18N + +/* Build wide character buffer PSTR->WCS. + If the byte sequence of the string are: + (0), (1), (0), (1), + Then wide character buffer will be: + , WEOF , , WEOF , + We use WEOF for padding, they indicate that the position isn't + a first byte of a multibyte character. + + Note that this function assumes PSTR->VALID_LEN elements are already + built and starts from PSTR->VALID_LEN. */ + +static void +internal_function +build_wcs_buffer (re_string_t *pstr) +{ +#ifdef _LIBC + unsigned char buf[MB_LEN_MAX]; + assert (MB_LEN_MAX >= pstr->mb_cur_max); +#else + unsigned char buf[64]; +#endif + mbstate_t prev_st; + int byte_idx, end_idx, remain_len; + size_t mbclen; + + /* Build the buffers from pstr->valid_len to either pstr->len or + pstr->bufs_len. */ + end_idx = (pstr->bufs_len > pstr->len) ? pstr->len : pstr->bufs_len; + for (byte_idx = pstr->valid_len; byte_idx < end_idx;) + { + wchar_t wc; + const char *p; + + remain_len = end_idx - byte_idx; + prev_st = pstr->cur_state; + /* Apply the translation if we need. */ + if (BE (pstr->trans != NULL, 0)) + { + int i, ch; + + for (i = 0; i < pstr->mb_cur_max && i < remain_len; ++i) + { + ch = pstr->raw_mbs [pstr->raw_mbs_idx + byte_idx + i]; + buf[i] = pstr->mbs[byte_idx + i] = pstr->trans[ch]; + } + p = (const char *) buf; + } + else + p = (const char *) pstr->raw_mbs + pstr->raw_mbs_idx + byte_idx; + mbclen = mbrtowc (&wc, p, remain_len, &pstr->cur_state); + if (BE (mbclen == (size_t) -2, 0)) + { + /* The buffer doesn't have enough space, finish to build. */ + pstr->cur_state = prev_st; + break; + } + else if (BE (mbclen == (size_t) -1 || mbclen == 0, 0)) + { + /* We treat these cases as a singlebyte character. */ + mbclen = 1; + wc = (wchar_t) pstr->raw_mbs[pstr->raw_mbs_idx + byte_idx]; + if (BE (pstr->trans != NULL, 0)) + wc = pstr->trans[wc]; + pstr->cur_state = prev_st; + } + + /* Write wide character and padding. */ + pstr->wcs[byte_idx++] = wc; + /* Write paddings. */ + for (remain_len = byte_idx + mbclen - 1; byte_idx < remain_len ;) + pstr->wcs[byte_idx++] = WEOF; + } + pstr->valid_len = byte_idx; + pstr->valid_raw_len = byte_idx; +} + +/* Build wide character buffer PSTR->WCS like build_wcs_buffer, + but for REG_ICASE. */ + +static reg_errcode_t +internal_function +build_wcs_upper_buffer (re_string_t *pstr) +{ + mbstate_t prev_st; + int src_idx, byte_idx, end_idx, remain_len; + size_t mbclen; +#ifdef _LIBC + char buf[MB_LEN_MAX]; + assert (MB_LEN_MAX >= pstr->mb_cur_max); +#else + char buf[64]; +#endif + + byte_idx = pstr->valid_len; + end_idx = (pstr->bufs_len > pstr->len) ? pstr->len : pstr->bufs_len; + + /* The following optimization assumes that ASCII characters can be + mapped to wide characters with a simple cast. */ + if (! pstr->map_notascii && pstr->trans == NULL && !pstr->offsets_needed) + { + while (byte_idx < end_idx) + { + wchar_t wc; + + if (isascii (pstr->raw_mbs[pstr->raw_mbs_idx + byte_idx]) + && mbsinit (&pstr->cur_state)) + { + /* In case of a singlebyte character. */ + pstr->mbs[byte_idx] + = toupper (pstr->raw_mbs[pstr->raw_mbs_idx + byte_idx]); + /* The next step uses the assumption that wchar_t is encoded + ASCII-safe: all ASCII values can be converted like this. */ + pstr->wcs[byte_idx] = (wchar_t) pstr->mbs[byte_idx]; + ++byte_idx; + continue; + } + + remain_len = end_idx - byte_idx; + prev_st = pstr->cur_state; + mbclen = mbrtowc (&wc, + ((const char *) pstr->raw_mbs + pstr->raw_mbs_idx + + byte_idx), remain_len, &pstr->cur_state); + if (BE (mbclen + 2 > 2, 1)) + { + wchar_t wcu = wc; + if (iswlower (wc)) + { + size_t mbcdlen; + + wcu = towupper (wc); + mbcdlen = wcrtomb (buf, wcu, &prev_st); + if (BE (mbclen == mbcdlen, 1)) + memcpy (pstr->mbs + byte_idx, buf, mbclen); + else + { + src_idx = byte_idx; + goto offsets_needed; + } + } + else + memcpy (pstr->mbs + byte_idx, + pstr->raw_mbs + pstr->raw_mbs_idx + byte_idx, mbclen); + pstr->wcs[byte_idx++] = wcu; + /* Write paddings. */ + for (remain_len = byte_idx + mbclen - 1; byte_idx < remain_len ;) + pstr->wcs[byte_idx++] = WEOF; + } + else if (mbclen == (size_t) -1 || mbclen == 0) + { + /* It is an invalid character or '\0'. Just use the byte. */ + int ch = pstr->raw_mbs[pstr->raw_mbs_idx + byte_idx]; + pstr->mbs[byte_idx] = ch; + /* And also cast it to wide char. */ + pstr->wcs[byte_idx++] = (wchar_t) ch; + if (BE (mbclen == (size_t) -1, 0)) + pstr->cur_state = prev_st; + } + else + { + /* The buffer doesn't have enough space, finish to build. */ + pstr->cur_state = prev_st; + break; + } + } + pstr->valid_len = byte_idx; + pstr->valid_raw_len = byte_idx; + return REG_NOERROR; + } + else + for (src_idx = pstr->valid_raw_len; byte_idx < end_idx;) + { + wchar_t wc; + const char *p; + offsets_needed: + remain_len = end_idx - byte_idx; + prev_st = pstr->cur_state; + if (BE (pstr->trans != NULL, 0)) + { + int i, ch; + + for (i = 0; i < pstr->mb_cur_max && i < remain_len; ++i) + { + ch = pstr->raw_mbs [pstr->raw_mbs_idx + src_idx + i]; + buf[i] = pstr->trans[ch]; + } + p = (const char *) buf; + } + else + p = (const char *) pstr->raw_mbs + pstr->raw_mbs_idx + src_idx; + mbclen = mbrtowc (&wc, p, remain_len, &pstr->cur_state); + if (BE (mbclen + 2 > 2, 1)) + { + wchar_t wcu = wc; + if (iswlower (wc)) + { + size_t mbcdlen; + + wcu = towupper (wc); + mbcdlen = wcrtomb ((char *) buf, wcu, &prev_st); + if (BE (mbclen == mbcdlen, 1)) + memcpy (pstr->mbs + byte_idx, buf, mbclen); + else if (mbcdlen != (size_t) -1) + { + size_t i; + + if (byte_idx + mbcdlen > pstr->bufs_len) + { + pstr->cur_state = prev_st; + break; + } + + if (pstr->offsets == NULL) + { + pstr->offsets = re_malloc (int, pstr->bufs_len); + + if (pstr->offsets == NULL) + return REG_ESPACE; + } + if (!pstr->offsets_needed) + { + for (i = 0; i < (size_t) byte_idx; ++i) + pstr->offsets[i] = i; + pstr->offsets_needed = 1; + } + + memcpy (pstr->mbs + byte_idx, buf, mbcdlen); + pstr->wcs[byte_idx] = wcu; + pstr->offsets[byte_idx] = src_idx; + for (i = 1; i < mbcdlen; ++i) + { + pstr->offsets[byte_idx + i] + = src_idx + (i < mbclen ? i : mbclen - 1); + pstr->wcs[byte_idx + i] = WEOF; + } + pstr->len += mbcdlen - mbclen; + if (pstr->raw_stop > src_idx) + pstr->stop += mbcdlen - mbclen; + end_idx = (pstr->bufs_len > pstr->len) + ? pstr->len : pstr->bufs_len; + byte_idx += mbcdlen; + src_idx += mbclen; + continue; + } + else + memcpy (pstr->mbs + byte_idx, p, mbclen); + } + else + memcpy (pstr->mbs + byte_idx, p, mbclen); + + if (BE (pstr->offsets_needed != 0, 0)) + { + size_t i; + for (i = 0; i < mbclen; ++i) + pstr->offsets[byte_idx + i] = src_idx + i; + } + src_idx += mbclen; + + pstr->wcs[byte_idx++] = wcu; + /* Write paddings. */ + for (remain_len = byte_idx + mbclen - 1; byte_idx < remain_len ;) + pstr->wcs[byte_idx++] = WEOF; + } + else if (mbclen == (size_t) -1 || mbclen == 0) + { + /* It is an invalid character or '\0'. Just use the byte. */ + int ch = pstr->raw_mbs[pstr->raw_mbs_idx + src_idx]; + + if (BE (pstr->trans != NULL, 0)) + ch = pstr->trans [ch]; + pstr->mbs[byte_idx] = ch; + + if (BE (pstr->offsets_needed != 0, 0)) + pstr->offsets[byte_idx] = src_idx; + ++src_idx; + + /* And also cast it to wide char. */ + pstr->wcs[byte_idx++] = (wchar_t) ch; + if (BE (mbclen == (size_t) -1, 0)) + pstr->cur_state = prev_st; + } + else + { + /* The buffer doesn't have enough space, finish to build. */ + pstr->cur_state = prev_st; + break; + } + } + pstr->valid_len = byte_idx; + pstr->valid_raw_len = src_idx; + return REG_NOERROR; +} + +/* Skip characters until the index becomes greater than NEW_RAW_IDX. + Return the index. */ + +static int +internal_function +re_string_skip_chars (re_string_t *pstr, int new_raw_idx, wint_t *last_wc) +{ + mbstate_t prev_st; + int rawbuf_idx; + size_t mbclen; + wchar_t wc = WEOF; + + /* Skip the characters which are not necessary to check. */ + for (rawbuf_idx = pstr->raw_mbs_idx + pstr->valid_raw_len; + rawbuf_idx < new_raw_idx;) + { + int remain_len; + remain_len = pstr->len - rawbuf_idx; + prev_st = pstr->cur_state; + mbclen = mbrtowc (&wc, (const char *) pstr->raw_mbs + rawbuf_idx, + remain_len, &pstr->cur_state); + if (BE (mbclen == (size_t) -2 || mbclen == (size_t) -1 || mbclen == 0, 0)) + { + /* We treat these cases as a single byte character. */ + if (mbclen == 0 || remain_len == 0) + wc = L'\0'; + else + wc = *(unsigned char *) (pstr->raw_mbs + rawbuf_idx); + mbclen = 1; + pstr->cur_state = prev_st; + } + /* Then proceed the next character. */ + rawbuf_idx += mbclen; + } + *last_wc = (wint_t) wc; + return rawbuf_idx; +} +#endif /* RE_ENABLE_I18N */ + +/* Build the buffer PSTR->MBS, and apply the translation if we need. + This function is used in case of REG_ICASE. */ + +static void +internal_function +build_upper_buffer (re_string_t *pstr) +{ + int char_idx, end_idx; + end_idx = (pstr->bufs_len > pstr->len) ? pstr->len : pstr->bufs_len; + + for (char_idx = pstr->valid_len; char_idx < end_idx; ++char_idx) + { + int ch = pstr->raw_mbs[pstr->raw_mbs_idx + char_idx]; + if (BE (pstr->trans != NULL, 0)) + ch = pstr->trans[ch]; + if (islower (ch)) + pstr->mbs[char_idx] = toupper (ch); + else + pstr->mbs[char_idx] = ch; + } + pstr->valid_len = char_idx; + pstr->valid_raw_len = char_idx; +} + +/* Apply TRANS to the buffer in PSTR. */ + +static void +internal_function +re_string_translate_buffer (re_string_t *pstr) +{ + int buf_idx, end_idx; + end_idx = (pstr->bufs_len > pstr->len) ? pstr->len : pstr->bufs_len; + + for (buf_idx = pstr->valid_len; buf_idx < end_idx; ++buf_idx) + { + int ch = pstr->raw_mbs[pstr->raw_mbs_idx + buf_idx]; + pstr->mbs[buf_idx] = pstr->trans[ch]; + } + + pstr->valid_len = buf_idx; + pstr->valid_raw_len = buf_idx; +} + +/* This function re-construct the buffers. + Concretely, convert to wide character in case of pstr->mb_cur_max > 1, + convert to upper case in case of REG_ICASE, apply translation. */ + +static reg_errcode_t +internal_function +re_string_reconstruct (re_string_t *pstr, int idx, int eflags) +{ + int offset = idx - pstr->raw_mbs_idx; + if (BE (offset < 0, 0)) + { + /* Reset buffer. */ +#ifdef RE_ENABLE_I18N + if (pstr->mb_cur_max > 1) + memset (&pstr->cur_state, '\0', sizeof (mbstate_t)); +#endif /* RE_ENABLE_I18N */ + pstr->len = pstr->raw_len; + pstr->stop = pstr->raw_stop; + pstr->valid_len = 0; + pstr->raw_mbs_idx = 0; + pstr->valid_raw_len = 0; + pstr->offsets_needed = 0; + pstr->tip_context = ((eflags & REG_NOTBOL) ? CONTEXT_BEGBUF + : CONTEXT_NEWLINE | CONTEXT_BEGBUF); + if (!pstr->mbs_allocated) + pstr->mbs = (unsigned char *) pstr->raw_mbs; + offset = idx; + } + + if (BE (offset != 0, 1)) + { + /* Should the already checked characters be kept? */ + if (BE (offset < pstr->valid_raw_len, 1)) + { + /* Yes, move them to the front of the buffer. */ +#ifdef RE_ENABLE_I18N + if (BE (pstr->offsets_needed, 0)) + { + int low = 0, high = pstr->valid_len, mid; + do + { + mid = (high + low) / 2; + if (pstr->offsets[mid] > offset) + high = mid; + else if (pstr->offsets[mid] < offset) + low = mid + 1; + else + break; + } + while (low < high); + if (pstr->offsets[mid] < offset) + ++mid; + pstr->tip_context = re_string_context_at (pstr, mid - 1, + eflags); + /* This can be quite complicated, so handle specially + only the common and easy case where the character with + different length representation of lower and upper + case is present at or after offset. */ + if (pstr->valid_len > offset + && mid == offset && pstr->offsets[mid] == offset) + { + memmove (pstr->wcs, pstr->wcs + offset, + (pstr->valid_len - offset) * sizeof (wint_t)); + memmove (pstr->mbs, pstr->mbs + offset, pstr->valid_len - offset); + pstr->valid_len -= offset; + pstr->valid_raw_len -= offset; + for (low = 0; low < pstr->valid_len; low++) + pstr->offsets[low] = pstr->offsets[low + offset] - offset; + } + else + { + /* Otherwise, just find out how long the partial multibyte + character at offset is and fill it with WEOF/255. */ + pstr->len = pstr->raw_len - idx + offset; + pstr->stop = pstr->raw_stop - idx + offset; + pstr->offsets_needed = 0; + while (mid > 0 && pstr->offsets[mid - 1] == offset) + --mid; + while (mid < pstr->valid_len) + if (pstr->wcs[mid] != WEOF) + break; + else + ++mid; + if (mid == pstr->valid_len) + pstr->valid_len = 0; + else + { + pstr->valid_len = pstr->offsets[mid] - offset; + if (pstr->valid_len) + { + for (low = 0; low < pstr->valid_len; ++low) + pstr->wcs[low] = WEOF; + memset (pstr->mbs, 255, pstr->valid_len); + } + } + pstr->valid_raw_len = pstr->valid_len; + } + } + else +#endif + { + pstr->tip_context = re_string_context_at (pstr, offset - 1, + eflags); +#ifdef RE_ENABLE_I18N + if (pstr->mb_cur_max > 1) + memmove (pstr->wcs, pstr->wcs + offset, + (pstr->valid_len - offset) * sizeof (wint_t)); +#endif /* RE_ENABLE_I18N */ + if (BE (pstr->mbs_allocated, 0)) + memmove (pstr->mbs, pstr->mbs + offset, + pstr->valid_len - offset); + pstr->valid_len -= offset; + pstr->valid_raw_len -= offset; +#if DEBUG + assert (pstr->valid_len > 0); +#endif + } + } + else + { + /* No, skip all characters until IDX. */ + int prev_valid_len = pstr->valid_len; + +#ifdef RE_ENABLE_I18N + if (BE (pstr->offsets_needed, 0)) + { + pstr->len = pstr->raw_len - idx + offset; + pstr->stop = pstr->raw_stop - idx + offset; + pstr->offsets_needed = 0; + } +#endif + pstr->valid_len = 0; +#ifdef RE_ENABLE_I18N + if (pstr->mb_cur_max > 1) + { + int wcs_idx; + wint_t wc = WEOF; + + if (pstr->is_utf8) + { + const unsigned char *raw, *p, *q, *end; + + /* Special case UTF-8. Multi-byte chars start with any + byte other than 0x80 - 0xbf. */ + raw = pstr->raw_mbs + pstr->raw_mbs_idx; + end = raw + (offset - pstr->mb_cur_max); + if (end < pstr->raw_mbs) + end = pstr->raw_mbs; + p = raw + offset - 1; +#ifdef _LIBC + /* We know the wchar_t encoding is UCS4, so for the simple + case, ASCII characters, skip the conversion step. */ + if (isascii (*p) && BE (pstr->trans == NULL, 1)) + { + memset (&pstr->cur_state, '\0', sizeof (mbstate_t)); + /* pstr->valid_len = 0; */ + wc = (wchar_t) *p; + } + else +#endif + for (; p >= end; --p) + if ((*p & 0xc0) != 0x80) + { + mbstate_t cur_state; + wchar_t wc2; + int mlen = raw + pstr->len - p; + unsigned char buf[6]; + size_t mbclen; + + q = p; + if (BE (pstr->trans != NULL, 0)) + { + int i = mlen < 6 ? mlen : 6; + while (--i >= 0) + buf[i] = pstr->trans[p[i]]; + q = buf; + } + /* XXX Don't use mbrtowc, we know which conversion + to use (UTF-8 -> UCS4). */ + memset (&cur_state, 0, sizeof (cur_state)); + mbclen = mbrtowc (&wc2, (const char *) p, mlen, + &cur_state); + if (raw + offset - p <= mbclen + && mbclen < (size_t) -2) + { + memset (&pstr->cur_state, '\0', + sizeof (mbstate_t)); + pstr->valid_len = mbclen - (raw + offset - p); + wc = wc2; + } + break; + } + } + + if (wc == WEOF) + pstr->valid_len = re_string_skip_chars (pstr, idx, &wc) - idx; + if (wc == WEOF) + pstr->tip_context + = re_string_context_at (pstr, prev_valid_len - 1, eflags); + else + pstr->tip_context = ((BE (pstr->word_ops_used != 0, 0) + && IS_WIDE_WORD_CHAR (wc)) + ? CONTEXT_WORD + : ((IS_WIDE_NEWLINE (wc) + && pstr->newline_anchor) + ? CONTEXT_NEWLINE : 0)); + if (BE (pstr->valid_len, 0)) + { + for (wcs_idx = 0; wcs_idx < pstr->valid_len; ++wcs_idx) + pstr->wcs[wcs_idx] = WEOF; + if (pstr->mbs_allocated) + memset (pstr->mbs, 255, pstr->valid_len); + } + pstr->valid_raw_len = pstr->valid_len; + } + else +#endif /* RE_ENABLE_I18N */ + { + int c = pstr->raw_mbs[pstr->raw_mbs_idx + offset - 1]; + pstr->valid_raw_len = 0; + if (pstr->trans) + c = pstr->trans[c]; + pstr->tip_context = (bitset_contain (pstr->word_char, c) + ? CONTEXT_WORD + : ((IS_NEWLINE (c) && pstr->newline_anchor) + ? CONTEXT_NEWLINE : 0)); + } + } + if (!BE (pstr->mbs_allocated, 0)) + pstr->mbs += offset; + } + pstr->raw_mbs_idx = idx; + pstr->len -= offset; + pstr->stop -= offset; + + /* Then build the buffers. */ +#ifdef RE_ENABLE_I18N + if (pstr->mb_cur_max > 1) + { + if (pstr->icase) + { + reg_errcode_t ret = build_wcs_upper_buffer (pstr); + if (BE (ret != REG_NOERROR, 0)) + return ret; + } + else + build_wcs_buffer (pstr); + } + else +#endif /* RE_ENABLE_I18N */ + if (BE (pstr->mbs_allocated, 0)) + { + if (pstr->icase) + build_upper_buffer (pstr); + else if (pstr->trans != NULL) + re_string_translate_buffer (pstr); + } + else + pstr->valid_len = pstr->len; + + pstr->cur_idx = 0; + return REG_NOERROR; +} + +static unsigned char +internal_function __attribute ((pure)) +re_string_peek_byte_case (const re_string_t *pstr, int idx) +{ + int ch, off; + + /* Handle the common (easiest) cases first. */ + if (BE (!pstr->mbs_allocated, 1)) + return re_string_peek_byte (pstr, idx); + +#ifdef RE_ENABLE_I18N + if (pstr->mb_cur_max > 1 + && ! re_string_is_single_byte_char (pstr, pstr->cur_idx + idx)) + return re_string_peek_byte (pstr, idx); +#endif + + off = pstr->cur_idx + idx; +#ifdef RE_ENABLE_I18N + if (pstr->offsets_needed) + off = pstr->offsets[off]; +#endif + + ch = pstr->raw_mbs[pstr->raw_mbs_idx + off]; + +#ifdef RE_ENABLE_I18N + /* Ensure that e.g. for tr_TR.UTF-8 BACKSLASH DOTLESS SMALL LETTER I + this function returns CAPITAL LETTER I instead of first byte of + DOTLESS SMALL LETTER I. The latter would confuse the parser, + since peek_byte_case doesn't advance cur_idx in any way. */ + if (pstr->offsets_needed && !isascii (ch)) + return re_string_peek_byte (pstr, idx); +#endif + + return ch; +} + +static unsigned char +internal_function __attribute ((pure)) +re_string_fetch_byte_case (re_string_t *pstr) +{ + if (BE (!pstr->mbs_allocated, 1)) + return re_string_fetch_byte (pstr); + +#ifdef RE_ENABLE_I18N + if (pstr->offsets_needed) + { + int off, ch; + + /* For tr_TR.UTF-8 [[:islower:]] there is + [[: CAPITAL LETTER I WITH DOT lower:]] in mbs. Skip + in that case the whole multi-byte character and return + the original letter. On the other side, with + [[: DOTLESS SMALL LETTER I return [[:I, as doing + anything else would complicate things too much. */ + + if (!re_string_first_byte (pstr, pstr->cur_idx)) + return re_string_fetch_byte (pstr); + + off = pstr->offsets[pstr->cur_idx]; + ch = pstr->raw_mbs[pstr->raw_mbs_idx + off]; + + if (! isascii (ch)) + return re_string_fetch_byte (pstr); + + re_string_skip_bytes (pstr, + re_string_char_size_at (pstr, pstr->cur_idx)); + return ch; + } +#endif + + return pstr->raw_mbs[pstr->raw_mbs_idx + pstr->cur_idx++]; +} + +static void +internal_function +re_string_destruct (re_string_t *pstr) +{ +#ifdef RE_ENABLE_I18N + re_free (pstr->wcs); + re_free (pstr->offsets); +#endif /* RE_ENABLE_I18N */ + if (pstr->mbs_allocated) + re_free (pstr->mbs); +} + +/* Return the context at IDX in INPUT. */ + +static unsigned int +internal_function +re_string_context_at (const re_string_t *input, int idx, int eflags) +{ + int c; + if (BE (idx < 0, 0)) + /* In this case, we use the value stored in input->tip_context, + since we can't know the character in input->mbs[-1] here. */ + return input->tip_context; + if (BE (idx == input->len, 0)) + return ((eflags & REG_NOTEOL) ? CONTEXT_ENDBUF + : CONTEXT_NEWLINE | CONTEXT_ENDBUF); +#ifdef RE_ENABLE_I18N + if (input->mb_cur_max > 1) + { + wint_t wc; + int wc_idx = idx; + while(input->wcs[wc_idx] == WEOF) + { +#ifdef DEBUG + /* It must not happen. */ + assert (wc_idx >= 0); +#endif + --wc_idx; + if (wc_idx < 0) + return input->tip_context; + } + wc = input->wcs[wc_idx]; + if (BE (input->word_ops_used != 0, 0) && IS_WIDE_WORD_CHAR (wc)) + return CONTEXT_WORD; + return (IS_WIDE_NEWLINE (wc) && input->newline_anchor + ? CONTEXT_NEWLINE : 0); + } + else +#endif + { + c = re_string_byte_at (input, idx); + if (bitset_contain (input->word_char, c)) + return CONTEXT_WORD; + return IS_NEWLINE (c) && input->newline_anchor ? CONTEXT_NEWLINE : 0; + } +} + +/* Functions for set operation. */ + +static reg_errcode_t +internal_function +re_node_set_alloc (re_node_set *set, int size) +{ + set->alloc = size; + set->nelem = 0; + set->elems = re_malloc (int, size); + if (BE (set->elems == NULL, 0)) + return REG_ESPACE; + return REG_NOERROR; +} + +static reg_errcode_t +internal_function +re_node_set_init_1 (re_node_set *set, int elem) +{ + set->alloc = 1; + set->nelem = 1; + set->elems = re_malloc (int, 1); + if (BE (set->elems == NULL, 0)) + { + set->alloc = set->nelem = 0; + return REG_ESPACE; + } + set->elems[0] = elem; + return REG_NOERROR; +} + +static reg_errcode_t +internal_function +re_node_set_init_2 (re_node_set *set, int elem1, int elem2) +{ + set->alloc = 2; + set->elems = re_malloc (int, 2); + if (BE (set->elems == NULL, 0)) + return REG_ESPACE; + if (elem1 == elem2) + { + set->nelem = 1; + set->elems[0] = elem1; + } + else + { + set->nelem = 2; + if (elem1 < elem2) + { + set->elems[0] = elem1; + set->elems[1] = elem2; + } + else + { + set->elems[0] = elem2; + set->elems[1] = elem1; + } + } + return REG_NOERROR; +} + +static reg_errcode_t +internal_function +re_node_set_init_copy (re_node_set *dest, const re_node_set *src) +{ + dest->nelem = src->nelem; + if (src->nelem > 0) + { + dest->alloc = dest->nelem; + dest->elems = re_malloc (int, dest->alloc); + if (BE (dest->elems == NULL, 0)) + { + dest->alloc = dest->nelem = 0; + return REG_ESPACE; + } + memcpy (dest->elems, src->elems, src->nelem * sizeof (int)); + } + else + re_node_set_init_empty (dest); + return REG_NOERROR; +} + +/* Calculate the intersection of the sets SRC1 and SRC2. And merge it to + DEST. Return value indicate the error code or REG_NOERROR if succeeded. + Note: We assume dest->elems is NULL, when dest->alloc is 0. */ + +static reg_errcode_t +internal_function +re_node_set_add_intersect (re_node_set *dest, const re_node_set *src1, + const re_node_set *src2) +{ + int i1, i2, is, id, delta, sbase; + if (src1->nelem == 0 || src2->nelem == 0) + return REG_NOERROR; + + /* We need dest->nelem + 2 * elems_in_intersection; this is a + conservative estimate. */ + if (src1->nelem + src2->nelem + dest->nelem > dest->alloc) + { + int new_alloc = src1->nelem + src2->nelem + dest->alloc; + int *new_elems = re_realloc (dest->elems, int, new_alloc); + if (BE (new_elems == NULL, 0)) + return REG_ESPACE; + dest->elems = new_elems; + dest->alloc = new_alloc; + } + + /* Find the items in the intersection of SRC1 and SRC2, and copy + into the top of DEST those that are not already in DEST itself. */ + sbase = dest->nelem + src1->nelem + src2->nelem; + i1 = src1->nelem - 1; + i2 = src2->nelem - 1; + id = dest->nelem - 1; + for (;;) + { + if (src1->elems[i1] == src2->elems[i2]) + { + /* Try to find the item in DEST. Maybe we could binary search? */ + while (id >= 0 && dest->elems[id] > src1->elems[i1]) + --id; + + if (id < 0 || dest->elems[id] != src1->elems[i1]) + dest->elems[--sbase] = src1->elems[i1]; + + if (--i1 < 0 || --i2 < 0) + break; + } + + /* Lower the highest of the two items. */ + else if (src1->elems[i1] < src2->elems[i2]) + { + if (--i2 < 0) + break; + } + else + { + if (--i1 < 0) + break; + } + } + + id = dest->nelem - 1; + is = dest->nelem + src1->nelem + src2->nelem - 1; + delta = is - sbase + 1; + + /* Now copy. When DELTA becomes zero, the remaining + DEST elements are already in place; this is more or + less the same loop that is in re_node_set_merge. */ + dest->nelem += delta; + if (delta > 0 && id >= 0) + for (;;) + { + if (dest->elems[is] > dest->elems[id]) + { + /* Copy from the top. */ + dest->elems[id + delta--] = dest->elems[is--]; + if (delta == 0) + break; + } + else + { + /* Slide from the bottom. */ + dest->elems[id + delta] = dest->elems[id]; + if (--id < 0) + break; + } + } + + /* Copy remaining SRC elements. */ + memcpy (dest->elems, dest->elems + sbase, delta * sizeof (int)); + + return REG_NOERROR; +} + +/* Calculate the union set of the sets SRC1 and SRC2. And store it to + DEST. Return value indicate the error code or REG_NOERROR if succeeded. */ + +static reg_errcode_t +internal_function +re_node_set_init_union (re_node_set *dest, const re_node_set *src1, + const re_node_set *src2) +{ + int i1, i2, id; + if (src1 != NULL && src1->nelem > 0 && src2 != NULL && src2->nelem > 0) + { + dest->alloc = src1->nelem + src2->nelem; + dest->elems = re_malloc (int, dest->alloc); + if (BE (dest->elems == NULL, 0)) + return REG_ESPACE; + } + else + { + if (src1 != NULL && src1->nelem > 0) + return re_node_set_init_copy (dest, src1); + else if (src2 != NULL && src2->nelem > 0) + return re_node_set_init_copy (dest, src2); + else + re_node_set_init_empty (dest); + return REG_NOERROR; + } + for (i1 = i2 = id = 0 ; i1 < src1->nelem && i2 < src2->nelem ;) + { + if (src1->elems[i1] > src2->elems[i2]) + { + dest->elems[id++] = src2->elems[i2++]; + continue; + } + if (src1->elems[i1] == src2->elems[i2]) + ++i2; + dest->elems[id++] = src1->elems[i1++]; + } + if (i1 < src1->nelem) + { + memcpy (dest->elems + id, src1->elems + i1, + (src1->nelem - i1) * sizeof (int)); + id += src1->nelem - i1; + } + else if (i2 < src2->nelem) + { + memcpy (dest->elems + id, src2->elems + i2, + (src2->nelem - i2) * sizeof (int)); + id += src2->nelem - i2; + } + dest->nelem = id; + return REG_NOERROR; +} + +/* Calculate the union set of the sets DEST and SRC. And store it to + DEST. Return value indicate the error code or REG_NOERROR if succeeded. */ + +static reg_errcode_t +internal_function +re_node_set_merge (re_node_set *dest, const re_node_set *src) +{ + int is, id, sbase, delta; + if (src == NULL || src->nelem == 0) + return REG_NOERROR; + if (dest->alloc < 2 * src->nelem + dest->nelem) + { + int new_alloc = 2 * (src->nelem + dest->alloc); + int *new_buffer = re_realloc (dest->elems, int, new_alloc); + if (BE (new_buffer == NULL, 0)) + return REG_ESPACE; + dest->elems = new_buffer; + dest->alloc = new_alloc; + } + + if (BE (dest->nelem == 0, 0)) + { + dest->nelem = src->nelem; + memcpy (dest->elems, src->elems, src->nelem * sizeof (int)); + return REG_NOERROR; + } + + /* Copy into the top of DEST the items of SRC that are not + found in DEST. Maybe we could binary search in DEST? */ + for (sbase = dest->nelem + 2 * src->nelem, + is = src->nelem - 1, id = dest->nelem - 1; is >= 0 && id >= 0; ) + { + if (dest->elems[id] == src->elems[is]) + is--, id--; + else if (dest->elems[id] < src->elems[is]) + dest->elems[--sbase] = src->elems[is--]; + else /* if (dest->elems[id] > src->elems[is]) */ + --id; + } + + if (is >= 0) + { + /* If DEST is exhausted, the remaining items of SRC must be unique. */ + sbase -= is + 1; + memcpy (dest->elems + sbase, src->elems, (is + 1) * sizeof (int)); + } + + id = dest->nelem - 1; + is = dest->nelem + 2 * src->nelem - 1; + delta = is - sbase + 1; + if (delta == 0) + return REG_NOERROR; + + /* Now copy. When DELTA becomes zero, the remaining + DEST elements are already in place. */ + dest->nelem += delta; + for (;;) + { + if (dest->elems[is] > dest->elems[id]) + { + /* Copy from the top. */ + dest->elems[id + delta--] = dest->elems[is--]; + if (delta == 0) + break; + } + else + { + /* Slide from the bottom. */ + dest->elems[id + delta] = dest->elems[id]; + if (--id < 0) + { + /* Copy remaining SRC elements. */ + memcpy (dest->elems, dest->elems + sbase, + delta * sizeof (int)); + break; + } + } + } + + return REG_NOERROR; +} + +/* Insert the new element ELEM to the re_node_set* SET. + SET should not already have ELEM. + return -1 if an error is occured, return 1 otherwise. */ + +static int +internal_function +re_node_set_insert (re_node_set *set, int elem) +{ + int idx; + /* In case the set is empty. */ + if (set->alloc == 0) + { + if (BE (re_node_set_init_1 (set, elem) == REG_NOERROR, 1)) + return 1; + else + return -1; + } + + if (BE (set->nelem, 0) == 0) + { + /* We already guaranteed above that set->alloc != 0. */ + set->elems[0] = elem; + ++set->nelem; + return 1; + } + + /* Realloc if we need. */ + if (set->alloc == set->nelem) + { + int *new_elems; + set->alloc = set->alloc * 2; + new_elems = re_realloc (set->elems, int, set->alloc); + if (BE (new_elems == NULL, 0)) + return -1; + set->elems = new_elems; + } + + /* Move the elements which follows the new element. Test the + first element separately to skip a check in the inner loop. */ + if (elem < set->elems[0]) + { + idx = 0; + for (idx = set->nelem; idx > 0; idx--) + set->elems[idx] = set->elems[idx - 1]; + } + else + { + for (idx = set->nelem; set->elems[idx - 1] > elem; idx--) + set->elems[idx] = set->elems[idx - 1]; + } + + /* Insert the new element. */ + set->elems[idx] = elem; + ++set->nelem; + return 1; +} + +/* Insert the new element ELEM to the re_node_set* SET. + SET should not already have any element greater than or equal to ELEM. + Return -1 if an error is occured, return 1 otherwise. */ + +static int +internal_function +re_node_set_insert_last (re_node_set *set, int elem) +{ + /* Realloc if we need. */ + if (set->alloc == set->nelem) + { + int *new_elems; + set->alloc = (set->alloc + 1) * 2; + new_elems = re_realloc (set->elems, int, set->alloc); + if (BE (new_elems == NULL, 0)) + return -1; + set->elems = new_elems; + } + + /* Insert the new element. */ + set->elems[set->nelem++] = elem; + return 1; +} + +/* Compare two node sets SET1 and SET2. + return 1 if SET1 and SET2 are equivalent, return 0 otherwise. */ + +static int +internal_function __attribute ((pure)) +re_node_set_compare (const re_node_set *set1, const re_node_set *set2) +{ + int i; + if (set1 == NULL || set2 == NULL || set1->nelem != set2->nelem) + return 0; + for (i = set1->nelem ; --i >= 0 ; ) + if (set1->elems[i] != set2->elems[i]) + return 0; + return 1; +} + +/* Return (idx + 1) if SET contains the element ELEM, return 0 otherwise. */ + +static int +internal_function __attribute ((pure)) +re_node_set_contains (const re_node_set *set, int elem) +{ + unsigned int idx, right, mid; + if (set->nelem <= 0) + return 0; + + /* Binary search the element. */ + idx = 0; + right = set->nelem - 1; + while (idx < right) + { + mid = (idx + right) / 2; + if (set->elems[mid] < elem) + idx = mid + 1; + else + right = mid; + } + return set->elems[idx] == elem ? idx + 1 : 0; +} + +static void +internal_function +re_node_set_remove_at (re_node_set *set, int idx) +{ + if (idx < 0 || idx >= set->nelem) + return; + --set->nelem; + for (; idx < set->nelem; idx++) + set->elems[idx] = set->elems[idx + 1]; +} + + +/* Add the token TOKEN to dfa->nodes, and return the index of the token. + Or return -1, if an error will be occured. */ + +static int +internal_function +re_dfa_add_node (re_dfa_t *dfa, re_token_t token) +{ + int type = token.type; + if (BE (dfa->nodes_len >= dfa->nodes_alloc, 0)) + { + size_t new_nodes_alloc = dfa->nodes_alloc * 2; + int *new_nexts, *new_indices; + re_node_set *new_edests, *new_eclosures; + re_token_t *new_nodes; + + /* Avoid overflows. */ + if (BE (new_nodes_alloc < dfa->nodes_alloc, 0)) + return -1; + + new_nodes = re_realloc (dfa->nodes, re_token_t, new_nodes_alloc); + if (BE (new_nodes == NULL, 0)) + return -1; + dfa->nodes = new_nodes; + new_nexts = re_realloc (dfa->nexts, int, new_nodes_alloc); + new_indices = re_realloc (dfa->org_indices, int, new_nodes_alloc); + new_edests = re_realloc (dfa->edests, re_node_set, new_nodes_alloc); + new_eclosures = re_realloc (dfa->eclosures, re_node_set, new_nodes_alloc); + if (BE (new_nexts == NULL || new_indices == NULL + || new_edests == NULL || new_eclosures == NULL, 0)) + return -1; + dfa->nexts = new_nexts; + dfa->org_indices = new_indices; + dfa->edests = new_edests; + dfa->eclosures = new_eclosures; + dfa->nodes_alloc = new_nodes_alloc; + } + dfa->nodes[dfa->nodes_len] = token; + dfa->nodes[dfa->nodes_len].constraint = 0; +#ifdef RE_ENABLE_I18N + dfa->nodes[dfa->nodes_len].accept_mb = + (type == OP_PERIOD && dfa->mb_cur_max > 1) || type == COMPLEX_BRACKET; +#endif + dfa->nexts[dfa->nodes_len] = -1; + re_node_set_init_empty (dfa->edests + dfa->nodes_len); + re_node_set_init_empty (dfa->eclosures + dfa->nodes_len); + return dfa->nodes_len++; +} + +static inline unsigned int +internal_function +calc_state_hash (const re_node_set *nodes, unsigned int context) +{ + unsigned int hash = nodes->nelem + context; + int i; + for (i = 0 ; i < nodes->nelem ; i++) + hash += nodes->elems[i]; + return hash; +} + +/* Search for the state whose node_set is equivalent to NODES. + Return the pointer to the state, if we found it in the DFA. + Otherwise create the new one and return it. In case of an error + return NULL and set the error code in ERR. + Note: - We assume NULL as the invalid state, then it is possible that + return value is NULL and ERR is REG_NOERROR. + - We never return non-NULL value in case of any errors, it is for + optimization. */ + +static re_dfastate_t * +internal_function +re_acquire_state (reg_errcode_t *err, const re_dfa_t *dfa, + const re_node_set *nodes) +{ + unsigned int hash; + re_dfastate_t *new_state; + struct re_state_table_entry *spot; + int i; + if (BE (nodes->nelem == 0, 0)) + { + *err = REG_NOERROR; + return NULL; + } + hash = calc_state_hash (nodes, 0); + spot = dfa->state_table + (hash & dfa->state_hash_mask); + + for (i = 0 ; i < spot->num ; i++) + { + re_dfastate_t *state = spot->array[i]; + if (hash != state->hash) + continue; + if (re_node_set_compare (&state->nodes, nodes)) + return state; + } + + /* There are no appropriate state in the dfa, create the new one. */ + new_state = create_ci_newstate (dfa, nodes, hash); + if (BE (new_state == NULL, 0)) + *err = REG_ESPACE; + + return new_state; +} + +/* Search for the state whose node_set is equivalent to NODES and + whose context is equivalent to CONTEXT. + Return the pointer to the state, if we found it in the DFA. + Otherwise create the new one and return it. In case of an error + return NULL and set the error code in ERR. + Note: - We assume NULL as the invalid state, then it is possible that + return value is NULL and ERR is REG_NOERROR. + - We never return non-NULL value in case of any errors, it is for + optimization. */ + +static re_dfastate_t * +internal_function +re_acquire_state_context (reg_errcode_t *err, const re_dfa_t *dfa, + const re_node_set *nodes, unsigned int context) +{ + unsigned int hash; + re_dfastate_t *new_state; + struct re_state_table_entry *spot; + int i; + if (nodes->nelem == 0) + { + *err = REG_NOERROR; + return NULL; + } + hash = calc_state_hash (nodes, context); + spot = dfa->state_table + (hash & dfa->state_hash_mask); + + for (i = 0 ; i < spot->num ; i++) + { + re_dfastate_t *state = spot->array[i]; + if (state->hash == hash + && state->context == context + && re_node_set_compare (state->entrance_nodes, nodes)) + return state; + } + /* There are no appropriate state in `dfa', create the new one. */ + new_state = create_cd_newstate (dfa, nodes, context, hash); + if (BE (new_state == NULL, 0)) + *err = REG_ESPACE; + + return new_state; +} + +/* Finish initialization of the new state NEWSTATE, and using its hash value + HASH put in the appropriate bucket of DFA's state table. Return value + indicates the error code if failed. */ + +static reg_errcode_t +register_state (const re_dfa_t *dfa, re_dfastate_t *newstate, + unsigned int hash) +{ + struct re_state_table_entry *spot; + reg_errcode_t err; + int i; + + newstate->hash = hash; + err = re_node_set_alloc (&newstate->non_eps_nodes, newstate->nodes.nelem); + if (BE (err != REG_NOERROR, 0)) + return REG_ESPACE; + for (i = 0; i < newstate->nodes.nelem; i++) + { + int elem = newstate->nodes.elems[i]; + if (!IS_EPSILON_NODE (dfa->nodes[elem].type)) + re_node_set_insert_last (&newstate->non_eps_nodes, elem); + } + + spot = dfa->state_table + (hash & dfa->state_hash_mask); + if (BE (spot->alloc <= spot->num, 0)) + { + int new_alloc = 2 * spot->num + 2; + re_dfastate_t **new_array = re_realloc (spot->array, re_dfastate_t *, + new_alloc); + if (BE (new_array == NULL, 0)) + return REG_ESPACE; + spot->array = new_array; + spot->alloc = new_alloc; + } + spot->array[spot->num++] = newstate; + return REG_NOERROR; +} + +static void +free_state (re_dfastate_t *state) +{ + re_node_set_free (&state->non_eps_nodes); + re_node_set_free (&state->inveclosure); + if (state->entrance_nodes != &state->nodes) + { + re_node_set_free (state->entrance_nodes); + re_free (state->entrance_nodes); + } + re_node_set_free (&state->nodes); + re_free (state->word_trtable); + re_free (state->trtable); + re_free (state); +} + +/* Create the new state which is independ of contexts. + Return the new state if succeeded, otherwise return NULL. */ + +static re_dfastate_t * +internal_function +create_ci_newstate (const re_dfa_t *dfa, const re_node_set *nodes, + unsigned int hash) +{ + int i; + reg_errcode_t err; + re_dfastate_t *newstate; + + newstate = (re_dfastate_t *) calloc (sizeof (re_dfastate_t), 1); + if (BE (newstate == NULL, 0)) + return NULL; + err = re_node_set_init_copy (&newstate->nodes, nodes); + if (BE (err != REG_NOERROR, 0)) + { + re_free (newstate); + return NULL; + } + + newstate->entrance_nodes = &newstate->nodes; + for (i = 0 ; i < nodes->nelem ; i++) + { + re_token_t *node = dfa->nodes + nodes->elems[i]; + re_token_type_t type = node->type; + if (type == CHARACTER && !node->constraint) + continue; +#ifdef RE_ENABLE_I18N + newstate->accept_mb |= node->accept_mb; +#endif /* RE_ENABLE_I18N */ + + /* If the state has the halt node, the state is a halt state. */ + if (type == END_OF_RE) + newstate->halt = 1; + else if (type == OP_BACK_REF) + newstate->has_backref = 1; + else if (type == ANCHOR || node->constraint) + newstate->has_constraint = 1; + } + err = register_state (dfa, newstate, hash); + if (BE (err != REG_NOERROR, 0)) + { + free_state (newstate); + newstate = NULL; + } + return newstate; +} + +/* Create the new state which is depend on the context CONTEXT. + Return the new state if succeeded, otherwise return NULL. */ + +static re_dfastate_t * +internal_function +create_cd_newstate (const re_dfa_t *dfa, const re_node_set *nodes, + unsigned int context, unsigned int hash) +{ + int i, nctx_nodes = 0; + reg_errcode_t err; + re_dfastate_t *newstate; + + newstate = (re_dfastate_t *) calloc (sizeof (re_dfastate_t), 1); + if (BE (newstate == NULL, 0)) + return NULL; + err = re_node_set_init_copy (&newstate->nodes, nodes); + if (BE (err != REG_NOERROR, 0)) + { + re_free (newstate); + return NULL; + } + + newstate->context = context; + newstate->entrance_nodes = &newstate->nodes; + + for (i = 0 ; i < nodes->nelem ; i++) + { + unsigned int constraint = 0; + re_token_t *node = dfa->nodes + nodes->elems[i]; + re_token_type_t type = node->type; + if (node->constraint) + constraint = node->constraint; + + if (type == CHARACTER && !constraint) + continue; +#ifdef RE_ENABLE_I18N + newstate->accept_mb |= node->accept_mb; +#endif /* RE_ENABLE_I18N */ + + /* If the state has the halt node, the state is a halt state. */ + if (type == END_OF_RE) + newstate->halt = 1; + else if (type == OP_BACK_REF) + newstate->has_backref = 1; + else if (type == ANCHOR) + constraint = node->opr.ctx_type; + + if (constraint) + { + if (newstate->entrance_nodes == &newstate->nodes) + { + newstate->entrance_nodes = re_malloc (re_node_set, 1); + if (BE (newstate->entrance_nodes == NULL, 0)) + { + free_state (newstate); + return NULL; + } + re_node_set_init_copy (newstate->entrance_nodes, nodes); + nctx_nodes = 0; + newstate->has_constraint = 1; + } + + if (NOT_SATISFY_PREV_CONSTRAINT (constraint,context)) + { + re_node_set_remove_at (&newstate->nodes, i - nctx_nodes); + ++nctx_nodes; + } + } + } + err = register_state (dfa, newstate, hash); + if (BE (err != REG_NOERROR, 0)) + { + free_state (newstate); + newstate = NULL; + } + return newstate; +} + +/******************************************************************************/ +/******************************************************************************/ +/******************************************************************************/ +/* GKINCLUDE #include "regcomp.c" */ +/******************************************************************************/ +/******************************************************************************/ +/******************************************************************************/ +/* Extended regular expression matching and search library. + Copyright (C) 2002,2003,2004,2005,2006 Free Software Foundation, Inc. + This file is part of the GNU C Library. + Contributed by Isamu Hasegawa . + + The GNU C Library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2.1 of the License, or (at your option) any later version. + + The GNU C Library 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 + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with the GNU C Library; if not, write to the Free + Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA + 02111-1307 USA. */ + +static reg_errcode_t re_compile_internal (regex_t *preg, const char * pattern, + size_t length, reg_syntax_t syntax); +static void re_compile_fastmap_iter (regex_t *bufp, + const re_dfastate_t *init_state, + char *fastmap); +static reg_errcode_t init_dfa (re_dfa_t *dfa, size_t pat_len); +#ifdef RE_ENABLE_I18N +static void free_charset (re_charset_t *cset); +#endif /* RE_ENABLE_I18N */ +static void free_workarea_compile (regex_t *preg); +static reg_errcode_t create_initial_state (re_dfa_t *dfa); +#ifdef RE_ENABLE_I18N +static void optimize_utf8 (re_dfa_t *dfa); +#endif +static reg_errcode_t analyze (regex_t *preg); +static reg_errcode_t preorder (bin_tree_t *root, + reg_errcode_t (fn (void *, bin_tree_t *)), + void *extra); +static reg_errcode_t postorder (bin_tree_t *root, + reg_errcode_t (fn (void *, bin_tree_t *)), + void *extra); +static reg_errcode_t optimize_subexps (void *extra, bin_tree_t *node); +static reg_errcode_t lower_subexps (void *extra, bin_tree_t *node); +static bin_tree_t *lower_subexp (reg_errcode_t *err, regex_t *preg, + bin_tree_t *node); +static reg_errcode_t calc_first (void *extra, bin_tree_t *node); +static reg_errcode_t calc_next (void *extra, bin_tree_t *node); +static reg_errcode_t link_nfa_nodes (void *extra, bin_tree_t *node); +static int duplicate_node (re_dfa_t *dfa, int org_idx, unsigned int constraint); +static int search_duplicated_node (const re_dfa_t *dfa, int org_node, + unsigned int constraint); +static reg_errcode_t calc_eclosure (re_dfa_t *dfa); +static reg_errcode_t calc_eclosure_iter (re_node_set *new_set, re_dfa_t *dfa, + int node, int root); +static reg_errcode_t calc_inveclosure (re_dfa_t *dfa); +static int fetch_number (re_string_t *input, re_token_t *token, + reg_syntax_t syntax); +static int peek_token (re_token_t *token, re_string_t *input, + reg_syntax_t syntax) internal_function; +static bin_tree_t *parse (re_string_t *regexp, regex_t *preg, + reg_syntax_t syntax, reg_errcode_t *err); +static bin_tree_t *parse_reg_exp (re_string_t *regexp, regex_t *preg, + re_token_t *token, reg_syntax_t syntax, + int nest, reg_errcode_t *err); +static bin_tree_t *parse_branch (re_string_t *regexp, regex_t *preg, + re_token_t *token, reg_syntax_t syntax, + int nest, reg_errcode_t *err); +static bin_tree_t *parse_expression (re_string_t *regexp, regex_t *preg, + re_token_t *token, reg_syntax_t syntax, + int nest, reg_errcode_t *err); +static bin_tree_t *parse_sub_exp (re_string_t *regexp, regex_t *preg, + re_token_t *token, reg_syntax_t syntax, + int nest, reg_errcode_t *err); +static bin_tree_t *parse_dup_op (bin_tree_t *dup_elem, re_string_t *regexp, + re_dfa_t *dfa, re_token_t *token, + reg_syntax_t syntax, reg_errcode_t *err); +static bin_tree_t *parse_bracket_exp (re_string_t *regexp, re_dfa_t *dfa, + re_token_t *token, reg_syntax_t syntax, + reg_errcode_t *err); +static reg_errcode_t parse_bracket_element (bracket_elem_t *elem, + re_string_t *regexp, + re_token_t *token, int token_len, + re_dfa_t *dfa, + reg_syntax_t syntax, + int accept_hyphen); +static reg_errcode_t parse_bracket_symbol (bracket_elem_t *elem, + re_string_t *regexp, + re_token_t *token); +#ifdef RE_ENABLE_I18N +static reg_errcode_t build_equiv_class (bitset_t sbcset, + re_charset_t *mbcset, + int *equiv_class_alloc, + const unsigned char *name); +static reg_errcode_t build_charclass (RE_TRANSLATE_TYPE trans, + bitset_t sbcset, + re_charset_t *mbcset, + int *char_class_alloc, + const unsigned char *class_name, + reg_syntax_t syntax); +#else /* not RE_ENABLE_I18N */ +static reg_errcode_t build_equiv_class (bitset_t sbcset, + const unsigned char *name); +static reg_errcode_t build_charclass (RE_TRANSLATE_TYPE trans, + bitset_t sbcset, + const unsigned char *class_name, + reg_syntax_t syntax); +#endif /* not RE_ENABLE_I18N */ +static bin_tree_t *build_charclass_op (re_dfa_t *dfa, + RE_TRANSLATE_TYPE trans, + const unsigned char *class_name, + const unsigned char *extra, + int non_match, reg_errcode_t *err); +static bin_tree_t *create_tree (re_dfa_t *dfa, + bin_tree_t *left, bin_tree_t *right, + re_token_type_t type); +static bin_tree_t *create_token_tree (re_dfa_t *dfa, + bin_tree_t *left, bin_tree_t *right, + const re_token_t *token); +static bin_tree_t *duplicate_tree (const bin_tree_t *src, re_dfa_t *dfa); +static void free_token (re_token_t *node); +static reg_errcode_t free_tree (void *extra, bin_tree_t *node); +static reg_errcode_t mark_opt_subexp (void *extra, bin_tree_t *node); + +/* This table gives an error message for each of the error codes listed + in regex.h. Obviously the order here has to be same as there. + POSIX doesn't require that we do anything for REG_NOERROR, + but why not be nice? */ + +const char __re_error_msgid[] attribute_hidden = + { +#define REG_NOERROR_IDX 0 + gettext_noop ("Success") /* REG_NOERROR */ + "\0" +#define REG_NOMATCH_IDX (REG_NOERROR_IDX + sizeof "Success") + gettext_noop ("No match") /* REG_NOMATCH */ + "\0" +#define REG_BADPAT_IDX (REG_NOMATCH_IDX + sizeof "No match") + gettext_noop ("Invalid regular expression") /* REG_BADPAT */ + "\0" +#define REG_ECOLLATE_IDX (REG_BADPAT_IDX + sizeof "Invalid regular expression") + gettext_noop ("Invalid collation character") /* REG_ECOLLATE */ + "\0" +#define REG_ECTYPE_IDX (REG_ECOLLATE_IDX + sizeof "Invalid collation character") + gettext_noop ("Invalid character class name") /* REG_ECTYPE */ + "\0" +#define REG_EESCAPE_IDX (REG_ECTYPE_IDX + sizeof "Invalid character class name") + gettext_noop ("Trailing backslash") /* REG_EESCAPE */ + "\0" +#define REG_ESUBREG_IDX (REG_EESCAPE_IDX + sizeof "Trailing backslash") + gettext_noop ("Invalid back reference") /* REG_ESUBREG */ + "\0" +#define REG_EBRACK_IDX (REG_ESUBREG_IDX + sizeof "Invalid back reference") + gettext_noop ("Unmatched [ or [^") /* REG_EBRACK */ + "\0" +#define REG_EPAREN_IDX (REG_EBRACK_IDX + sizeof "Unmatched [ or [^") + gettext_noop ("Unmatched ( or \\(") /* REG_EPAREN */ + "\0" +#define REG_EBRACE_IDX (REG_EPAREN_IDX + sizeof "Unmatched ( or \\(") + gettext_noop ("Unmatched \\{") /* REG_EBRACE */ + "\0" +#define REG_BADBR_IDX (REG_EBRACE_IDX + sizeof "Unmatched \\{") + gettext_noop ("Invalid content of \\{\\}") /* REG_BADBR */ + "\0" +#define REG_ERANGE_IDX (REG_BADBR_IDX + sizeof "Invalid content of \\{\\}") + gettext_noop ("Invalid range end") /* REG_ERANGE */ + "\0" +#define REG_ESPACE_IDX (REG_ERANGE_IDX + sizeof "Invalid range end") + gettext_noop ("Memory exhausted") /* REG_ESPACE */ + "\0" +#define REG_BADRPT_IDX (REG_ESPACE_IDX + sizeof "Memory exhausted") + gettext_noop ("Invalid preceding regular expression") /* REG_BADRPT */ + "\0" +#define REG_EEND_IDX (REG_BADRPT_IDX + sizeof "Invalid preceding regular expression") + gettext_noop ("Premature end of regular expression") /* REG_EEND */ + "\0" +#define REG_ESIZE_IDX (REG_EEND_IDX + sizeof "Premature end of regular expression") + gettext_noop ("Regular expression too big") /* REG_ESIZE */ + "\0" +#define REG_ERPAREN_IDX (REG_ESIZE_IDX + sizeof "Regular expression too big") + gettext_noop ("Unmatched ) or \\)") /* REG_ERPAREN */ + }; + +const size_t __re_error_msgid_idx[] attribute_hidden = + { + REG_NOERROR_IDX, + REG_NOMATCH_IDX, + REG_BADPAT_IDX, + REG_ECOLLATE_IDX, + REG_ECTYPE_IDX, + REG_EESCAPE_IDX, + REG_ESUBREG_IDX, + REG_EBRACK_IDX, + REG_EPAREN_IDX, + REG_EBRACE_IDX, + REG_BADBR_IDX, + REG_ERANGE_IDX, + REG_ESPACE_IDX, + REG_BADRPT_IDX, + REG_EEND_IDX, + REG_ESIZE_IDX, + REG_ERPAREN_IDX + }; + +/* Entry points for GNU code. */ + +/* re_compile_pattern is the GNU regular expression compiler: it + compiles PATTERN (of length LENGTH) and puts the result in BUFP. + Returns 0 if the pattern was valid, otherwise an error string. + + Assumes the `allocated' (and perhaps `buffer') and `translate' fields + are set in BUFP on entry. */ + +const char * +re_compile_pattern (pattern, length, bufp) + const char *pattern; + size_t length; + struct re_pattern_buffer *bufp; +{ + reg_errcode_t ret; + + /* And GNU code determines whether or not to get register information + by passing null for the REGS argument to re_match, etc., not by + setting no_sub, unless RE_NO_SUB is set. */ + bufp->no_sub = !!(re_syntax_options & RE_NO_SUB); + + /* Match anchors at newline. */ + bufp->newline_anchor = 1; + + ret = re_compile_internal (bufp, pattern, length, re_syntax_options); + + if (!ret) + return NULL; + return gettext (__re_error_msgid + __re_error_msgid_idx[(int) ret]); +} +#ifdef _LIBC +weak_alias (__re_compile_pattern, re_compile_pattern) +#endif + +/* Set by `re_set_syntax' to the current regexp syntax to recognize. Can + also be assigned to arbitrarily: each pattern buffer stores its own + syntax, so it can be changed between regex compilations. */ +/* This has no initializer because initialized variables in Emacs + become read-only after dumping. */ +reg_syntax_t re_syntax_options; + + +/* Specify the precise syntax of regexps for compilation. This provides + for compatibility for various utilities which historically have + different, incompatible syntaxes. + + The argument SYNTAX is a bit mask comprised of the various bits + defined in regex.h. We return the old syntax. */ + +reg_syntax_t +re_set_syntax (syntax) + reg_syntax_t syntax; +{ + reg_syntax_t ret = re_syntax_options; + + re_syntax_options = syntax; + return ret; +} +#ifdef _LIBC +weak_alias (__re_set_syntax, re_set_syntax) +#endif + +int +re_compile_fastmap (bufp) + struct re_pattern_buffer *bufp; +{ + re_dfa_t *dfa = (re_dfa_t *) bufp->buffer; + char *fastmap = bufp->fastmap; + + memset (fastmap, '\0', sizeof (char) * SBC_MAX); + re_compile_fastmap_iter (bufp, dfa->init_state, fastmap); + if (dfa->init_state != dfa->init_state_word) + re_compile_fastmap_iter (bufp, dfa->init_state_word, fastmap); + if (dfa->init_state != dfa->init_state_nl) + re_compile_fastmap_iter (bufp, dfa->init_state_nl, fastmap); + if (dfa->init_state != dfa->init_state_begbuf) + re_compile_fastmap_iter (bufp, dfa->init_state_begbuf, fastmap); + bufp->fastmap_accurate = 1; + return 0; +} +#ifdef _LIBC +weak_alias (__re_compile_fastmap, re_compile_fastmap) +#endif + +static inline void +__attribute ((always_inline)) +re_set_fastmap (char *fastmap, int icase, int ch) +{ + fastmap[ch] = 1; + if (icase) + fastmap[tolower (ch)] = 1; +} + +/* Helper function for re_compile_fastmap. + Compile fastmap for the initial_state INIT_STATE. */ + +static void +re_compile_fastmap_iter (regex_t *bufp, const re_dfastate_t *init_state, + char *fastmap) +{ + re_dfa_t *dfa = (re_dfa_t *) bufp->buffer; + int node_cnt; + int icase = (dfa->mb_cur_max == 1 && (bufp->syntax & RE_ICASE)); + for (node_cnt = 0; node_cnt < init_state->nodes.nelem; ++node_cnt) + { + int node = init_state->nodes.elems[node_cnt]; + re_token_type_t type = dfa->nodes[node].type; + + if (type == CHARACTER) + { + re_set_fastmap (fastmap, icase, dfa->nodes[node].opr.c); +#ifdef RE_ENABLE_I18N + if ((bufp->syntax & RE_ICASE) && dfa->mb_cur_max > 1) + { + unsigned char *buf = alloca (dfa->mb_cur_max), *p; + wchar_t wc; + mbstate_t state; + + p = buf; + *p++ = dfa->nodes[node].opr.c; + while (++node < dfa->nodes_len + && dfa->nodes[node].type == CHARACTER + && dfa->nodes[node].mb_partial) + *p++ = dfa->nodes[node].opr.c; + memset (&state, '\0', sizeof (state)); + if (mbrtowc (&wc, (const char *) buf, p - buf, + &state) == p - buf + && (__wcrtomb ((char *) buf, towlower (wc), &state) + != (size_t) -1)) + re_set_fastmap (fastmap, 0, buf[0]); + } +#endif + } + else if (type == SIMPLE_BRACKET) + { + int i, ch; + for (i = 0, ch = 0; i < BITSET_WORDS; ++i) + { + int j; + bitset_word_t w = dfa->nodes[node].opr.sbcset[i]; + for (j = 0; j < BITSET_WORD_BITS; ++j, ++ch) + if (w & ((bitset_word_t) 1 << j)) + re_set_fastmap (fastmap, icase, ch); + } + } +#ifdef RE_ENABLE_I18N + else if (type == COMPLEX_BRACKET) + { + int i; + re_charset_t *cset = dfa->nodes[node].opr.mbcset; + if (cset->non_match || cset->ncoll_syms || cset->nequiv_classes + || cset->nranges || cset->nchar_classes) + { +# ifdef _LIBC + if (_NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES) != 0) + { + /* In this case we want to catch the bytes which are + the first byte of any collation elements. + e.g. In da_DK, we want to catch 'a' since "aa" + is a valid collation element, and don't catch + 'b' since 'b' is the only collation element + which starts from 'b'. */ + const int32_t *table = (const int32_t *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_TABLEMB); + for (i = 0; i < SBC_MAX; ++i) + if (table[i] < 0) + re_set_fastmap (fastmap, icase, i); + } +# else + if (dfa->mb_cur_max > 1) + for (i = 0; i < SBC_MAX; ++i) + if (__btowc (i) == WEOF) + re_set_fastmap (fastmap, icase, i); +# endif /* not _LIBC */ + } + for (i = 0; i < cset->nmbchars; ++i) + { + char buf[256]; + mbstate_t state; + memset (&state, '\0', sizeof (state)); + if (__wcrtomb (buf, cset->mbchars[i], &state) != (size_t) -1) + re_set_fastmap (fastmap, icase, *(unsigned char *) buf); + if ((bufp->syntax & RE_ICASE) && dfa->mb_cur_max > 1) + { + if (__wcrtomb (buf, towlower (cset->mbchars[i]), &state) + != (size_t) -1) + re_set_fastmap (fastmap, 0, *(unsigned char *) buf); + } + } + } +#endif /* RE_ENABLE_I18N */ + else if (type == OP_PERIOD +#ifdef RE_ENABLE_I18N + || type == OP_UTF8_PERIOD +#endif /* RE_ENABLE_I18N */ + || type == END_OF_RE) + { + memset (fastmap, '\1', sizeof (char) * SBC_MAX); + if (type == END_OF_RE) + bufp->can_be_null = 1; + return; + } + } +} + +/* Entry point for POSIX code. */ +/* regcomp takes a regular expression as a string and compiles it. + + PREG is a regex_t *. We do not expect any fields to be initialized, + since POSIX says we shouldn't. Thus, we set + + `buffer' to the compiled pattern; + `used' to the length of the compiled pattern; + `syntax' to RE_SYNTAX_POSIX_EXTENDED if the + REG_EXTENDED bit in CFLAGS is set; otherwise, to + RE_SYNTAX_POSIX_BASIC; + `newline_anchor' to REG_NEWLINE being set in CFLAGS; + `fastmap' to an allocated space for the fastmap; + `fastmap_accurate' to zero; + `re_nsub' to the number of subexpressions in PATTERN. + + PATTERN is the address of the pattern string. + + CFLAGS is a series of bits which affect compilation. + + If REG_EXTENDED is set, we use POSIX extended syntax; otherwise, we + use POSIX basic syntax. + + If REG_NEWLINE is set, then . and [^...] don't match newline. + Also, regexec will try a match beginning after every newline. + + If REG_ICASE is set, then we considers upper- and lowercase + versions of letters to be equivalent when matching. + + If REG_NOSUB is set, then when PREG is passed to regexec, that + routine will report only success or failure, and nothing about the + registers. + + It returns 0 if it succeeds, nonzero if it doesn't. (See regex.h for + the return codes and their meanings.) */ + +int +regcomp (preg, pattern, cflags) + regex_t *__restrict preg; + const char *__restrict pattern; + int cflags; +{ + reg_errcode_t ret; + reg_syntax_t syntax = ((cflags & REG_EXTENDED) ? RE_SYNTAX_POSIX_EXTENDED + : RE_SYNTAX_POSIX_BASIC); + + preg->buffer = NULL; + preg->allocated = 0; + preg->used = 0; + + /* Try to allocate space for the fastmap. */ + preg->fastmap = re_malloc (char, SBC_MAX); + if (BE (preg->fastmap == NULL, 0)) + return REG_ESPACE; + + syntax |= (cflags & REG_ICASE) ? RE_ICASE : 0; + + /* If REG_NEWLINE is set, newlines are treated differently. */ + if (cflags & REG_NEWLINE) + { /* REG_NEWLINE implies neither . nor [^...] match newline. */ + syntax &= ~RE_DOT_NEWLINE; + syntax |= RE_HAT_LISTS_NOT_NEWLINE; + /* It also changes the matching behavior. */ + preg->newline_anchor = 1; + } + else + preg->newline_anchor = 0; + preg->no_sub = !!(cflags & REG_NOSUB); + preg->translate = NULL; + + ret = re_compile_internal (preg, pattern, strlen (pattern), syntax); + + /* POSIX doesn't distinguish between an unmatched open-group and an + unmatched close-group: both are REG_EPAREN. */ + if (ret == REG_ERPAREN) + ret = REG_EPAREN; + + /* We have already checked preg->fastmap != NULL. */ + if (BE (ret == REG_NOERROR, 1)) + /* Compute the fastmap now, since regexec cannot modify the pattern + buffer. This function never fails in this implementation. */ + (void) re_compile_fastmap (preg); + else + { + /* Some error occurred while compiling the expression. */ + re_free (preg->fastmap); + preg->fastmap = NULL; + } + + return (int) ret; +} +#ifdef _LIBC +weak_alias (__regcomp, regcomp) +#endif + +/* Returns a message corresponding to an error code, ERRCODE, returned + from either regcomp or regexec. We don't use PREG here. */ + +/* regerror ( int errcode, preg, errbuf, errbuf_size) */ +size_t +regerror ( + int errcode, + const regex_t *__restrict preg, + char *__restrict errbuf, + size_t errbuf_size) +{ + const char *msg; + size_t msg_size; + + if (BE (errcode < 0 + || errcode >= (int) (sizeof (__re_error_msgid_idx) + / sizeof (__re_error_msgid_idx[0])), 0)) + /* Only error codes returned by the rest of the code should be passed + to this routine. If we are given anything else, or if other regex + code generates an invalid error code, then the program has a bug. + Dump core so we can fix it. */ + abort (); + + msg = gettext (__re_error_msgid + __re_error_msgid_idx[errcode]); + + msg_size = strlen (msg) + 1; /* Includes the null. */ + + if (BE (errbuf_size != 0, 1)) + { + if (BE (msg_size > errbuf_size, 0)) + { +#if defined HAVE_MEMPCPY || defined _LIBC + *((char *) __mempcpy (errbuf, msg, errbuf_size - 1)) = '\0'; +#else + memcpy (errbuf, msg, errbuf_size - 1); + errbuf[errbuf_size - 1] = 0; +#endif + } + else + memcpy (errbuf, msg, msg_size); + } + + return msg_size; +} +#ifdef _LIBC +weak_alias (__regerror, regerror) +#endif + + +#ifdef RE_ENABLE_I18N +/* This static array is used for the map to single-byte characters when + UTF-8 is used. Otherwise we would allocate memory just to initialize + it the same all the time. UTF-8 is the preferred encoding so this is + a worthwhile optimization. */ +static const bitset_t utf8_sb_map = +{ + /* Set the first 128 bits. */ + [0 ... 0x80 / BITSET_WORD_BITS - 1] = BITSET_WORD_MAX +}; +#endif + + +static void +free_dfa_content (re_dfa_t *dfa) +{ + int i, j; + + if (dfa->nodes) + for (i = 0; i < dfa->nodes_len; ++i) + free_token (dfa->nodes + i); + re_free (dfa->nexts); + for (i = 0; i < dfa->nodes_len; ++i) + { + if (dfa->eclosures != NULL) + re_node_set_free (dfa->eclosures + i); + if (dfa->inveclosures != NULL) + re_node_set_free (dfa->inveclosures + i); + if (dfa->edests != NULL) + re_node_set_free (dfa->edests + i); + } + re_free (dfa->edests); + re_free (dfa->eclosures); + re_free (dfa->inveclosures); + re_free (dfa->nodes); + + if (dfa->state_table) + for (i = 0; i <= dfa->state_hash_mask; ++i) + { + struct re_state_table_entry *entry = dfa->state_table + i; + for (j = 0; j < entry->num; ++j) + { + re_dfastate_t *state = entry->array[j]; + free_state (state); + } + re_free (entry->array); + } + re_free (dfa->state_table); +#ifdef RE_ENABLE_I18N + if (dfa->sb_char != utf8_sb_map) + re_free (dfa->sb_char); +#endif + re_free (dfa->subexp_map); +#ifdef DEBUG + re_free (dfa->re_str); +#endif + + re_free (dfa); +} + + +/* Free dynamically allocated space used by PREG. */ + +void +regfree (preg) + regex_t *preg; +{ + re_dfa_t *dfa = (re_dfa_t *) preg->buffer; + if (BE (dfa != NULL, 1)) + free_dfa_content (dfa); + preg->buffer = NULL; + preg->allocated = 0; + + re_free (preg->fastmap); + preg->fastmap = NULL; + + re_free (preg->translate); + preg->translate = NULL; +} +#ifdef _LIBC +weak_alias (__regfree, regfree) +#endif + +/* Entry points compatible with 4.2 BSD regex library. We don't define + them unless specifically requested. */ + +#if defined _REGEX_RE_COMP || defined _LIBC + +/* BSD has one and only one pattern buffer. */ +static struct re_pattern_buffer re_comp_buf; + +char * +# ifdef _LIBC +/* Make these definitions weak in libc, so POSIX programs can redefine + these names if they don't use our functions, and still use + regcomp/regexec above without link errors. */ +weak_function +# endif +re_comp (s) + const char *s; +{ + reg_errcode_t ret; + char *fastmap; + + if (!s) + { + if (!re_comp_buf.buffer) + return gettext ("No previous regular expression"); + return 0; + } + + if (re_comp_buf.buffer) + { + fastmap = re_comp_buf.fastmap; + re_comp_buf.fastmap = NULL; + __regfree (&re_comp_buf); + memset (&re_comp_buf, '\0', sizeof (re_comp_buf)); + re_comp_buf.fastmap = fastmap; + } + + if (re_comp_buf.fastmap == NULL) + { + re_comp_buf.fastmap = (char *) malloc (SBC_MAX); + if (re_comp_buf.fastmap == NULL) + return (char *) gettext (__re_error_msgid + + __re_error_msgid_idx[(int) REG_ESPACE]); + } + + /* Since `re_exec' always passes NULL for the `regs' argument, we + don't need to initialize the pattern buffer fields which affect it. */ + + /* Match anchors at newlines. */ + re_comp_buf.newline_anchor = 1; + + ret = re_compile_internal (&re_comp_buf, s, strlen (s), re_syntax_options); + + if (!ret) + return NULL; + + /* Yes, we're discarding `const' here if !HAVE_LIBINTL. */ + return (char *) gettext (__re_error_msgid + __re_error_msgid_idx[(int) ret]); +} + +#ifdef _LIBC +libc_freeres_fn (free_mem) +{ + __regfree (&re_comp_buf); +} +#endif + +#endif /* _REGEX_RE_COMP */ + +/* Internal entry point. + Compile the regular expression PATTERN, whose length is LENGTH. + SYNTAX indicate regular expression's syntax. */ + +static reg_errcode_t +re_compile_internal (regex_t *preg, const char * pattern, size_t length, + reg_syntax_t syntax) +{ + reg_errcode_t err = REG_NOERROR; + re_dfa_t *dfa; + re_string_t regexp; + + /* Initialize the pattern buffer. */ + preg->fastmap_accurate = 0; + preg->syntax = syntax; + preg->not_bol = preg->not_eol = 0; + preg->used = 0; + preg->re_nsub = 0; + preg->can_be_null = 0; + preg->regs_allocated = REGS_UNALLOCATED; + + /* Initialize the dfa. */ + dfa = (re_dfa_t *) preg->buffer; + if (BE (preg->allocated < sizeof (re_dfa_t), 0)) + { + /* If zero allocated, but buffer is non-null, try to realloc + enough space. This loses if buffer's address is bogus, but + that is the user's responsibility. If ->buffer is NULL this + is a simple allocation. */ + dfa = re_realloc (preg->buffer, re_dfa_t, 1); + if (dfa == NULL) + return REG_ESPACE; + preg->allocated = sizeof (re_dfa_t); + preg->buffer = (unsigned char *) dfa; + } + preg->used = sizeof (re_dfa_t); + + err = init_dfa (dfa, length); + if (BE (err != REG_NOERROR, 0)) + { + free_dfa_content (dfa); + preg->buffer = NULL; + preg->allocated = 0; + return err; + } +#ifdef DEBUG + /* Note: length+1 will not overflow since it is checked in init_dfa. */ + dfa->re_str = re_malloc (char, length + 1); + strncpy (dfa->re_str, pattern, length + 1); +#endif + + __libc_lock_init (dfa->lock); + + err = re_string_construct (®exp, pattern, length, preg->translate, + syntax & RE_ICASE, dfa); + if (BE (err != REG_NOERROR, 0)) + { + re_compile_internal_free_return: + free_workarea_compile (preg); + re_string_destruct (®exp); + free_dfa_content (dfa); + preg->buffer = NULL; + preg->allocated = 0; + return err; + } + + /* Parse the regular expression, and build a structure tree. */ + preg->re_nsub = 0; + dfa->str_tree = parse (®exp, preg, syntax, &err); + if (BE (dfa->str_tree == NULL, 0)) + goto re_compile_internal_free_return; + + /* Analyze the tree and create the nfa. */ + err = analyze (preg); + if (BE (err != REG_NOERROR, 0)) + goto re_compile_internal_free_return; + +#ifdef RE_ENABLE_I18N + /* If possible, do searching in single byte encoding to speed things up. */ + if (dfa->is_utf8 && !(syntax & RE_ICASE) && preg->translate == NULL) + optimize_utf8 (dfa); +#endif + + /* Then create the initial state of the dfa. */ + err = create_initial_state (dfa); + + /* Release work areas. */ + free_workarea_compile (preg); + re_string_destruct (®exp); + + if (BE (err != REG_NOERROR, 0)) + { + free_dfa_content (dfa); + preg->buffer = NULL; + preg->allocated = 0; + } + + return err; +} + +/* Initialize DFA. We use the length of the regular expression PAT_LEN + as the initial length of some arrays. */ + +static reg_errcode_t +init_dfa (re_dfa_t *dfa, size_t pat_len) +{ + unsigned int table_size; +#ifndef _LIBC + char *codeset_name; +#endif + + memset (dfa, '\0', sizeof (re_dfa_t)); + + /* Force allocation of str_tree_storage the first time. */ + dfa->str_tree_storage_idx = BIN_TREE_STORAGE_SIZE; + + /* Avoid overflows. */ + if (pat_len == SIZE_MAX) + return REG_ESPACE; + + dfa->nodes_alloc = pat_len + 1; + dfa->nodes = re_malloc (re_token_t, dfa->nodes_alloc); + + /* table_size = 2 ^ ceil(log pat_len) */ + for (table_size = 1; ; table_size <<= 1) + if (table_size > pat_len) + break; + + dfa->state_table = calloc (sizeof (struct re_state_table_entry), table_size); + dfa->state_hash_mask = table_size - 1; + + dfa->mb_cur_max = MB_CUR_MAX; +#ifdef _LIBC + if (dfa->mb_cur_max == 6 + && strcmp (_NL_CURRENT (LC_CTYPE, _NL_CTYPE_CODESET_NAME), "UTF-8") == 0) + dfa->is_utf8 = 1; + dfa->map_notascii = (_NL_CURRENT_WORD (LC_CTYPE, _NL_CTYPE_MAP_TO_NONASCII) + != 0); +#else +# ifdef HAVE_LANGINFO_CODESET + codeset_name = nl_langinfo (CODESET); +# else + codeset_name = getenv ("LC_ALL"); + if (codeset_name == NULL || codeset_name[0] == '\0') + codeset_name = getenv ("LC_CTYPE"); + if (codeset_name == NULL || codeset_name[0] == '\0') + codeset_name = getenv ("LANG"); + if (codeset_name == NULL) + codeset_name = ""; + else if (strchr (codeset_name, '.') != NULL) + codeset_name = strchr (codeset_name, '.') + 1; +# endif + + if (strcasecmp (codeset_name, "UTF-8") == 0 + || strcasecmp (codeset_name, "UTF8") == 0) + dfa->is_utf8 = 1; + + /* We check exhaustively in the loop below if this charset is a + superset of ASCII. */ + dfa->map_notascii = 0; +#endif + +#ifdef RE_ENABLE_I18N + if (dfa->mb_cur_max > 1) + { + if (dfa->is_utf8) + dfa->sb_char = (re_bitset_ptr_t) utf8_sb_map; + else + { + int i, j, ch; + + dfa->sb_char = (re_bitset_ptr_t) calloc (sizeof (bitset_t), 1); + if (BE (dfa->sb_char == NULL, 0)) + return REG_ESPACE; + + /* Set the bits corresponding to single byte chars. */ + for (i = 0, ch = 0; i < BITSET_WORDS; ++i) + for (j = 0; j < BITSET_WORD_BITS; ++j, ++ch) + { + wint_t wch = __btowc (ch); + if (wch != WEOF) + dfa->sb_char[i] |= (bitset_word_t) 1 << j; +# ifndef _LIBC + if (isascii (ch) && wch != ch) + dfa->map_notascii = 1; +# endif + } + } + } +#endif + + if (BE (dfa->nodes == NULL || dfa->state_table == NULL, 0)) + return REG_ESPACE; + return REG_NOERROR; +} + +/* Initialize WORD_CHAR table, which indicate which character is + "word". In this case "word" means that it is the word construction + character used by some operators like "\<", "\>", etc. */ + +static void +internal_function +init_word_char (re_dfa_t *dfa) +{ + int i, j, ch; + dfa->word_ops_used = 1; + for (i = 0, ch = 0; i < BITSET_WORDS; ++i) + for (j = 0; j < BITSET_WORD_BITS; ++j, ++ch) + if (isalnum (ch) || ch == '_') + dfa->word_char[i] |= (bitset_word_t) 1 << j; +} + +/* Free the work area which are only used while compiling. */ + +static void +free_workarea_compile (regex_t *preg) +{ + re_dfa_t *dfa = (re_dfa_t *) preg->buffer; + bin_tree_storage_t *storage, *next; + for (storage = dfa->str_tree_storage; storage; storage = next) + { + next = storage->next; + re_free (storage); + } + dfa->str_tree_storage = NULL; + dfa->str_tree_storage_idx = BIN_TREE_STORAGE_SIZE; + dfa->str_tree = NULL; + re_free (dfa->org_indices); + dfa->org_indices = NULL; +} + +/* Create initial states for all contexts. */ + +static reg_errcode_t +create_initial_state (re_dfa_t *dfa) +{ + int first, i; + reg_errcode_t err; + re_node_set init_nodes; + + /* Initial states have the epsilon closure of the node which is + the first node of the regular expression. */ + first = dfa->str_tree->first->node_idx; + dfa->init_node = first; + err = re_node_set_init_copy (&init_nodes, dfa->eclosures + first); + if (BE (err != REG_NOERROR, 0)) + return err; + + /* The back-references which are in initial states can epsilon transit, + since in this case all of the subexpressions can be null. + Then we add epsilon closures of the nodes which are the next nodes of + the back-references. */ + if (dfa->nbackref > 0) + for (i = 0; i < init_nodes.nelem; ++i) + { + int node_idx = init_nodes.elems[i]; + re_token_type_t type = dfa->nodes[node_idx].type; + + int clexp_idx; + if (type != OP_BACK_REF) + continue; + for (clexp_idx = 0; clexp_idx < init_nodes.nelem; ++clexp_idx) + { + re_token_t *clexp_node; + clexp_node = dfa->nodes + init_nodes.elems[clexp_idx]; + if (clexp_node->type == OP_CLOSE_SUBEXP + && clexp_node->opr.idx == dfa->nodes[node_idx].opr.idx) + break; + } + if (clexp_idx == init_nodes.nelem) + continue; + + if (type == OP_BACK_REF) + { + int dest_idx = dfa->edests[node_idx].elems[0]; + if (!re_node_set_contains (&init_nodes, dest_idx)) + { + re_node_set_merge (&init_nodes, dfa->eclosures + dest_idx); + i = 0; + } + } + } + + /* It must be the first time to invoke acquire_state. */ + dfa->init_state = re_acquire_state_context (&err, dfa, &init_nodes, 0); + /* We don't check ERR here, since the initial state must not be NULL. */ + if (BE (dfa->init_state == NULL, 0)) + return err; + if (dfa->init_state->has_constraint) + { + dfa->init_state_word = re_acquire_state_context (&err, dfa, &init_nodes, + CONTEXT_WORD); + dfa->init_state_nl = re_acquire_state_context (&err, dfa, &init_nodes, + CONTEXT_NEWLINE); + dfa->init_state_begbuf = re_acquire_state_context (&err, dfa, + &init_nodes, + CONTEXT_NEWLINE + | CONTEXT_BEGBUF); + if (BE (dfa->init_state_word == NULL || dfa->init_state_nl == NULL + || dfa->init_state_begbuf == NULL, 0)) + return err; + } + else + dfa->init_state_word = dfa->init_state_nl + = dfa->init_state_begbuf = dfa->init_state; + + re_node_set_free (&init_nodes); + return REG_NOERROR; +} + +#ifdef RE_ENABLE_I18N +/* If it is possible to do searching in single byte encoding instead of UTF-8 + to speed things up, set dfa->mb_cur_max to 1, clear is_utf8 and change + DFA nodes where needed. */ + +static void +optimize_utf8 (re_dfa_t *dfa) +{ + int node, i, mb_chars = 0, has_period = 0; + + for (node = 0; node < dfa->nodes_len; ++node) + switch (dfa->nodes[node].type) + { + case CHARACTER: + if (dfa->nodes[node].opr.c >= 0x80) + mb_chars = 1; + break; + case ANCHOR: + switch (dfa->nodes[node].opr.idx) + { + case LINE_FIRST: + case LINE_LAST: + case BUF_FIRST: + case BUF_LAST: + break; + default: + /* Word anchors etc. cannot be handled. */ + return; + } + break; + case OP_PERIOD: + has_period = 1; + break; + case OP_BACK_REF: + case OP_ALT: + case END_OF_RE: + case OP_DUP_ASTERISK: + case OP_OPEN_SUBEXP: + case OP_CLOSE_SUBEXP: + break; + case COMPLEX_BRACKET: + return; + case SIMPLE_BRACKET: + /* Just double check. The non-ASCII range starts at 0x80. */ + assert (0x80 % BITSET_WORD_BITS == 0); + for (i = 0x80 / BITSET_WORD_BITS; i < BITSET_WORDS; ++i) + if (dfa->nodes[node].opr.sbcset[i]) + return; + break; + default: + abort (); + } + + if (mb_chars || has_period) + for (node = 0; node < dfa->nodes_len; ++node) + { + if (dfa->nodes[node].type == CHARACTER + && dfa->nodes[node].opr.c >= 0x80) + dfa->nodes[node].mb_partial = 0; + else if (dfa->nodes[node].type == OP_PERIOD) + dfa->nodes[node].type = OP_UTF8_PERIOD; + } + + /* The search can be in single byte locale. */ + dfa->mb_cur_max = 1; + dfa->is_utf8 = 0; + dfa->has_mb_node = dfa->nbackref > 0 || has_period; +} +#endif + +/* Analyze the structure tree, and calculate "first", "next", "edest", + "eclosure", and "inveclosure". */ + +static reg_errcode_t +analyze (regex_t *preg) +{ + re_dfa_t *dfa = (re_dfa_t *) preg->buffer; + reg_errcode_t ret; + + /* Allocate arrays. */ + dfa->nexts = re_malloc (int, dfa->nodes_alloc); + dfa->org_indices = re_malloc (int, dfa->nodes_alloc); + dfa->edests = re_malloc (re_node_set, dfa->nodes_alloc); + dfa->eclosures = re_malloc (re_node_set, dfa->nodes_alloc); + if (BE (dfa->nexts == NULL || dfa->org_indices == NULL || dfa->edests == NULL + || dfa->eclosures == NULL, 0)) + return REG_ESPACE; + + dfa->subexp_map = re_malloc (int, preg->re_nsub); + if (dfa->subexp_map != NULL) + { + int i; + for (i = 0; i < preg->re_nsub; i++) + dfa->subexp_map[i] = i; + preorder (dfa->str_tree, optimize_subexps, dfa); + for (i = 0; i < preg->re_nsub; i++) + if (dfa->subexp_map[i] != i) + break; + if (i == preg->re_nsub) + { + free (dfa->subexp_map); + dfa->subexp_map = NULL; + } + } + + ret = postorder (dfa->str_tree, lower_subexps, preg); + if (BE (ret != REG_NOERROR, 0)) + return ret; + ret = postorder (dfa->str_tree, calc_first, dfa); + if (BE (ret != REG_NOERROR, 0)) + return ret; + preorder (dfa->str_tree, calc_next, dfa); + ret = preorder (dfa->str_tree, link_nfa_nodes, dfa); + if (BE (ret != REG_NOERROR, 0)) + return ret; + ret = calc_eclosure (dfa); + if (BE (ret != REG_NOERROR, 0)) + return ret; + + /* We only need this during the prune_impossible_nodes pass in regexec.c; + skip it if p_i_n will not run, as calc_inveclosure can be quadratic. */ + if ((!preg->no_sub && preg->re_nsub > 0 && dfa->has_plural_match) + || dfa->nbackref) + { + dfa->inveclosures = re_malloc (re_node_set, dfa->nodes_len); + if (BE (dfa->inveclosures == NULL, 0)) + return REG_ESPACE; + ret = calc_inveclosure (dfa); + } + + return ret; +} + +/* Our parse trees are very unbalanced, so we cannot use a stack to + implement parse tree visits. Instead, we use parent pointers and + some hairy code in these two functions. */ +static reg_errcode_t +postorder (bin_tree_t *root, reg_errcode_t (fn (void *, bin_tree_t *)), + void *extra) +{ + bin_tree_t *node, *prev; + + for (node = root; ; ) + { + /* Descend down the tree, preferably to the left (or to the right + if that's the only child). */ + while (node->left || node->right) + if (node->left) + node = node->left; + else + node = node->right; + + do + { + reg_errcode_t err = fn (extra, node); + if (BE (err != REG_NOERROR, 0)) + return err; + if (node->parent == NULL) + return REG_NOERROR; + prev = node; + node = node->parent; + } + /* Go up while we have a node that is reached from the right. */ + while (node->right == prev || node->right == NULL); + node = node->right; + } +} + +static reg_errcode_t +preorder (bin_tree_t *root, reg_errcode_t (fn (void *, bin_tree_t *)), + void *extra) +{ + bin_tree_t *node; + + for (node = root; ; ) + { + reg_errcode_t err = fn (extra, node); + if (BE (err != REG_NOERROR, 0)) + return err; + + /* Go to the left node, or up and to the right. */ + if (node->left) + node = node->left; + else + { + bin_tree_t *prev = NULL; + while (node->right == prev || node->right == NULL) + { + prev = node; + node = node->parent; + if (!node) + return REG_NOERROR; + } + node = node->right; + } + } +} + +/* Optimization pass: if a SUBEXP is entirely contained, strip it and tell + re_search_internal to map the inner one's opr.idx to this one's. Adjust + backreferences as well. Requires a preorder visit. */ +static reg_errcode_t +optimize_subexps (void *extra, bin_tree_t *node) +{ + re_dfa_t *dfa = (re_dfa_t *) extra; + + if (node->token.type == OP_BACK_REF && dfa->subexp_map) + { + int idx = node->token.opr.idx; + node->token.opr.idx = dfa->subexp_map[idx]; + dfa->used_bkref_map |= 1 << node->token.opr.idx; + } + + else if (node->token.type == SUBEXP + && node->left && node->left->token.type == SUBEXP) + { + int other_idx = node->left->token.opr.idx; + + node->left = node->left->left; + if (node->left) + node->left->parent = node; + + dfa->subexp_map[other_idx] = dfa->subexp_map[node->token.opr.idx]; + if (other_idx < BITSET_WORD_BITS) + dfa->used_bkref_map &= ~((bitset_word_t) 1 << other_idx); + } + + return REG_NOERROR; +} + +/* Lowering pass: Turn each SUBEXP node into the appropriate concatenation + of OP_OPEN_SUBEXP, the body of the SUBEXP (if any) and OP_CLOSE_SUBEXP. */ +static reg_errcode_t +lower_subexps (void *extra, bin_tree_t *node) +{ + regex_t *preg = (regex_t *) extra; + reg_errcode_t err = REG_NOERROR; + + if (node->left && node->left->token.type == SUBEXP) + { + node->left = lower_subexp (&err, preg, node->left); + if (node->left) + node->left->parent = node; + } + if (node->right && node->right->token.type == SUBEXP) + { + node->right = lower_subexp (&err, preg, node->right); + if (node->right) + node->right->parent = node; + } + + return err; +} + +static bin_tree_t * +lower_subexp (reg_errcode_t *err, regex_t *preg, bin_tree_t *node) +{ + re_dfa_t *dfa = (re_dfa_t *) preg->buffer; + bin_tree_t *body = node->left; + bin_tree_t *op, *cls, *tree1, *tree; + + if (preg->no_sub + /* We do not optimize empty subexpressions, because otherwise we may + have bad CONCAT nodes with NULL children. This is obviously not + very common, so we do not lose much. An example that triggers + this case is the sed "script" /\(\)/x. */ + && node->left != NULL + && (node->token.opr.idx >= BITSET_WORD_BITS + || !(dfa->used_bkref_map + & ((bitset_word_t) 1 << node->token.opr.idx)))) + return node->left; + + /* Convert the SUBEXP node to the concatenation of an + OP_OPEN_SUBEXP, the contents, and an OP_CLOSE_SUBEXP. */ + op = create_tree (dfa, NULL, NULL, OP_OPEN_SUBEXP); + cls = create_tree (dfa, NULL, NULL, OP_CLOSE_SUBEXP); + tree1 = body ? create_tree (dfa, body, cls, CONCAT) : cls; + tree = create_tree (dfa, op, tree1, CONCAT); + if (BE (tree == NULL || tree1 == NULL || op == NULL || cls == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } + + op->token.opr.idx = cls->token.opr.idx = node->token.opr.idx; + op->token.opt_subexp = cls->token.opt_subexp = node->token.opt_subexp; + return tree; +} + +/* Pass 1 in building the NFA: compute FIRST and create unlinked automaton + nodes. Requires a postorder visit. */ +static reg_errcode_t +calc_first (void *extra, bin_tree_t *node) +{ + re_dfa_t *dfa = (re_dfa_t *) extra; + if (node->token.type == CONCAT) + { + node->first = node->left->first; + node->node_idx = node->left->node_idx; + } + else + { + node->first = node; + node->node_idx = re_dfa_add_node (dfa, node->token); + if (BE (node->node_idx == -1, 0)) + return REG_ESPACE; + } + return REG_NOERROR; +} + +/* Pass 2: compute NEXT on the tree. Preorder visit. */ +static reg_errcode_t +calc_next (void *extra, bin_tree_t *node) +{ + switch (node->token.type) + { + case OP_DUP_ASTERISK: + node->left->next = node; + break; + case CONCAT: + node->left->next = node->right->first; + node->right->next = node->next; + break; + default: + if (node->left) + node->left->next = node->next; + if (node->right) + node->right->next = node->next; + break; + } + return REG_NOERROR; +} + +/* Pass 3: link all DFA nodes to their NEXT node (any order will do). */ +static reg_errcode_t +link_nfa_nodes (void *extra, bin_tree_t *node) +{ + re_dfa_t *dfa = (re_dfa_t *) extra; + int idx = node->node_idx; + reg_errcode_t err = REG_NOERROR; + + switch (node->token.type) + { + case CONCAT: + break; + + case END_OF_RE: + assert (node->next == NULL); + break; + + case OP_DUP_ASTERISK: + case OP_ALT: + { + int left, right; + dfa->has_plural_match = 1; + if (node->left != NULL) + left = node->left->first->node_idx; + else + left = node->next->node_idx; + if (node->right != NULL) + right = node->right->first->node_idx; + else + right = node->next->node_idx; + assert (left > -1); + assert (right > -1); + err = re_node_set_init_2 (dfa->edests + idx, left, right); + } + break; + + case ANCHOR: + case OP_OPEN_SUBEXP: + case OP_CLOSE_SUBEXP: + err = re_node_set_init_1 (dfa->edests + idx, node->next->node_idx); + break; + + case OP_BACK_REF: + dfa->nexts[idx] = node->next->node_idx; + if (node->token.type == OP_BACK_REF) + re_node_set_init_1 (dfa->edests + idx, dfa->nexts[idx]); + break; + + default: + assert (!IS_EPSILON_NODE (node->token.type)); + dfa->nexts[idx] = node->next->node_idx; + break; + } + + return err; +} + +/* Duplicate the epsilon closure of the node ROOT_NODE. + Note that duplicated nodes have constraint INIT_CONSTRAINT in addition + to their own constraint. */ + +static reg_errcode_t +internal_function +duplicate_node_closure (re_dfa_t *dfa, int top_org_node, int top_clone_node, + int root_node, unsigned int init_constraint) +{ + int org_node, clone_node, ret; + unsigned int constraint = init_constraint; + for (org_node = top_org_node, clone_node = top_clone_node;;) + { + int org_dest, clone_dest; + if (dfa->nodes[org_node].type == OP_BACK_REF) + { + /* If the back reference epsilon-transit, its destination must + also have the constraint. Then duplicate the epsilon closure + of the destination of the back reference, and store it in + edests of the back reference. */ + org_dest = dfa->nexts[org_node]; + re_node_set_empty (dfa->edests + clone_node); + clone_dest = duplicate_node (dfa, org_dest, constraint); + if (BE (clone_dest == -1, 0)) + return REG_ESPACE; + dfa->nexts[clone_node] = dfa->nexts[org_node]; + ret = re_node_set_insert (dfa->edests + clone_node, clone_dest); + if (BE (ret < 0, 0)) + return REG_ESPACE; + } + else if (dfa->edests[org_node].nelem == 0) + { + /* In case of the node can't epsilon-transit, don't duplicate the + destination and store the original destination as the + destination of the node. */ + dfa->nexts[clone_node] = dfa->nexts[org_node]; + break; + } + else if (dfa->edests[org_node].nelem == 1) + { + /* In case of the node can epsilon-transit, and it has only one + destination. */ + org_dest = dfa->edests[org_node].elems[0]; + re_node_set_empty (dfa->edests + clone_node); + if (dfa->nodes[org_node].type == ANCHOR) + { + /* In case of the node has another constraint, append it. */ + if (org_node == root_node && clone_node != org_node) + { + /* ...but if the node is root_node itself, it means the + epsilon closure have a loop, then tie it to the + destination of the root_node. */ + ret = re_node_set_insert (dfa->edests + clone_node, + org_dest); + if (BE (ret < 0, 0)) + return REG_ESPACE; + break; + } + constraint |= dfa->nodes[org_node].opr.ctx_type; + } + clone_dest = duplicate_node (dfa, org_dest, constraint); + if (BE (clone_dest == -1, 0)) + return REG_ESPACE; + ret = re_node_set_insert (dfa->edests + clone_node, clone_dest); + if (BE (ret < 0, 0)) + return REG_ESPACE; + } + else /* dfa->edests[org_node].nelem == 2 */ + { + /* In case of the node can epsilon-transit, and it has two + destinations. In the bin_tree_t and DFA, that's '|' and '*'. */ + org_dest = dfa->edests[org_node].elems[0]; + re_node_set_empty (dfa->edests + clone_node); + /* Search for a duplicated node which satisfies the constraint. */ + clone_dest = search_duplicated_node (dfa, org_dest, constraint); + if (clone_dest == -1) + { + /* There are no such a duplicated node, create a new one. */ + reg_errcode_t err; + clone_dest = duplicate_node (dfa, org_dest, constraint); + if (BE (clone_dest == -1, 0)) + return REG_ESPACE; + ret = re_node_set_insert (dfa->edests + clone_node, clone_dest); + if (BE (ret < 0, 0)) + return REG_ESPACE; + err = duplicate_node_closure (dfa, org_dest, clone_dest, + root_node, constraint); + if (BE (err != REG_NOERROR, 0)) + return err; + } + else + { + /* There are a duplicated node which satisfy the constraint, + use it to avoid infinite loop. */ + ret = re_node_set_insert (dfa->edests + clone_node, clone_dest); + if (BE (ret < 0, 0)) + return REG_ESPACE; + } + + org_dest = dfa->edests[org_node].elems[1]; + clone_dest = duplicate_node (dfa, org_dest, constraint); + if (BE (clone_dest == -1, 0)) + return REG_ESPACE; + ret = re_node_set_insert (dfa->edests + clone_node, clone_dest); + if (BE (ret < 0, 0)) + return REG_ESPACE; + } + org_node = org_dest; + clone_node = clone_dest; + } + return REG_NOERROR; +} + +/* Search for a node which is duplicated from the node ORG_NODE, and + satisfies the constraint CONSTRAINT. */ + +static int +search_duplicated_node (const re_dfa_t *dfa, int org_node, + unsigned int constraint) +{ + int idx; + for (idx = dfa->nodes_len - 1; dfa->nodes[idx].duplicated && idx > 0; --idx) + { + if (org_node == dfa->org_indices[idx] + && constraint == dfa->nodes[idx].constraint) + return idx; /* Found. */ + } + return -1; /* Not found. */ +} + +/* Duplicate the node whose index is ORG_IDX and set the constraint CONSTRAINT. + Return the index of the new node, or -1 if insufficient storage is + available. */ + +static int +duplicate_node (re_dfa_t *dfa, int org_idx, unsigned int constraint) +{ + int dup_idx = re_dfa_add_node (dfa, dfa->nodes[org_idx]); + if (BE (dup_idx != -1, 1)) + { + dfa->nodes[dup_idx].constraint = constraint; + if (dfa->nodes[org_idx].type == ANCHOR) + dfa->nodes[dup_idx].constraint |= dfa->nodes[org_idx].opr.ctx_type; + dfa->nodes[dup_idx].duplicated = 1; + + /* Store the index of the original node. */ + dfa->org_indices[dup_idx] = org_idx; + } + return dup_idx; +} + +static reg_errcode_t +calc_inveclosure (re_dfa_t *dfa) +{ + int src, idx, ret; + for (idx = 0; idx < dfa->nodes_len; ++idx) + re_node_set_init_empty (dfa->inveclosures + idx); + + for (src = 0; src < dfa->nodes_len; ++src) + { + int *elems = dfa->eclosures[src].elems; + for (idx = 0; idx < dfa->eclosures[src].nelem; ++idx) + { + ret = re_node_set_insert_last (dfa->inveclosures + elems[idx], src); + if (BE (ret == -1, 0)) + return REG_ESPACE; + } + } + + return REG_NOERROR; +} + +/* Calculate "eclosure" for all the node in DFA. */ + +static reg_errcode_t +calc_eclosure (re_dfa_t *dfa) +{ + int node_idx, incomplete; +#ifdef DEBUG + assert (dfa->nodes_len > 0); +#endif + incomplete = 0; + /* For each nodes, calculate epsilon closure. */ + for (node_idx = 0; ; ++node_idx) + { + reg_errcode_t err; + re_node_set eclosure_elem; + if (node_idx == dfa->nodes_len) + { + if (!incomplete) + break; + incomplete = 0; + node_idx = 0; + } + +#ifdef DEBUG + assert (dfa->eclosures[node_idx].nelem != -1); +#endif + + /* If we have already calculated, skip it. */ + if (dfa->eclosures[node_idx].nelem != 0) + continue; + /* Calculate epsilon closure of `node_idx'. */ + err = calc_eclosure_iter (&eclosure_elem, dfa, node_idx, 1); + if (BE (err != REG_NOERROR, 0)) + return err; + + if (dfa->eclosures[node_idx].nelem == 0) + { + incomplete = 1; + re_node_set_free (&eclosure_elem); + } + } + return REG_NOERROR; +} + +/* Calculate epsilon closure of NODE. */ + +static reg_errcode_t +calc_eclosure_iter (re_node_set *new_set, re_dfa_t *dfa, int node, int root) +{ + reg_errcode_t err; + unsigned int constraint; + int i, incomplete; + re_node_set eclosure; + incomplete = 0; + err = re_node_set_alloc (&eclosure, dfa->edests[node].nelem + 1); + if (BE (err != REG_NOERROR, 0)) + return err; + + /* This indicates that we are calculating this node now. + We reference this value to avoid infinite loop. */ + dfa->eclosures[node].nelem = -1; + + constraint = ((dfa->nodes[node].type == ANCHOR) + ? dfa->nodes[node].opr.ctx_type : 0); + /* If the current node has constraints, duplicate all nodes. + Since they must inherit the constraints. */ + if (constraint + && dfa->edests[node].nelem + && !dfa->nodes[dfa->edests[node].elems[0]].duplicated) + { + err = duplicate_node_closure (dfa, node, node, node, constraint); + if (BE (err != REG_NOERROR, 0)) + return err; + } + + /* Expand each epsilon destination nodes. */ + if (IS_EPSILON_NODE(dfa->nodes[node].type)) + for (i = 0; i < dfa->edests[node].nelem; ++i) + { + re_node_set eclosure_elem; + int edest = dfa->edests[node].elems[i]; + /* If calculating the epsilon closure of `edest' is in progress, + return intermediate result. */ + if (dfa->eclosures[edest].nelem == -1) + { + incomplete = 1; + continue; + } + /* If we haven't calculated the epsilon closure of `edest' yet, + calculate now. Otherwise use calculated epsilon closure. */ + if (dfa->eclosures[edest].nelem == 0) + { + err = calc_eclosure_iter (&eclosure_elem, dfa, edest, 0); + if (BE (err != REG_NOERROR, 0)) + return err; + } + else + eclosure_elem = dfa->eclosures[edest]; + /* Merge the epsilon closure of `edest'. */ + re_node_set_merge (&eclosure, &eclosure_elem); + /* If the epsilon closure of `edest' is incomplete, + the epsilon closure of this node is also incomplete. */ + if (dfa->eclosures[edest].nelem == 0) + { + incomplete = 1; + re_node_set_free (&eclosure_elem); + } + } + + /* Epsilon closures include itself. */ + re_node_set_insert (&eclosure, node); + if (incomplete && !root) + dfa->eclosures[node].nelem = 0; + else + dfa->eclosures[node] = eclosure; + *new_set = eclosure; + return REG_NOERROR; +} + +/* Functions for token which are used in the parser. */ + +/* Fetch a token from INPUT. + We must not use this function inside bracket expressions. */ + +static void +internal_function +fetch_token (re_token_t *result, re_string_t *input, reg_syntax_t syntax) +{ + re_string_skip_bytes (input, peek_token (result, input, syntax)); +} + +/* Peek a token from INPUT, and return the length of the token. + We must not use this function inside bracket expressions. */ + +static int +internal_function +peek_token (re_token_t *token, re_string_t *input, reg_syntax_t syntax) +{ + unsigned char c; + + if (re_string_eoi (input)) + { + token->type = END_OF_RE; + return 0; + } + + c = re_string_peek_byte (input, 0); + token->opr.c = c; + + token->word_char = 0; +#ifdef RE_ENABLE_I18N + token->mb_partial = 0; + if (input->mb_cur_max > 1 && + !re_string_first_byte (input, re_string_cur_idx (input))) + { + token->type = CHARACTER; + token->mb_partial = 1; + return 1; + } +#endif + if (c == '\\') + { + unsigned char c2; + if (re_string_cur_idx (input) + 1 >= re_string_length (input)) + { + token->type = BACK_SLASH; + return 1; + } + + c2 = re_string_peek_byte_case (input, 1); + token->opr.c = c2; + token->type = CHARACTER; +#ifdef RE_ENABLE_I18N + if (input->mb_cur_max > 1) + { + wint_t wc = re_string_wchar_at (input, + re_string_cur_idx (input) + 1); + token->word_char = IS_WIDE_WORD_CHAR (wc) != 0; + } + else +#endif + token->word_char = IS_WORD_CHAR (c2) != 0; + + switch (c2) + { + case '|': + if (!(syntax & RE_LIMITED_OPS) && !(syntax & RE_NO_BK_VBAR)) + token->type = OP_ALT; + break; + case '1': case '2': case '3': case '4': case '5': + case '6': case '7': case '8': case '9': + if (!(syntax & RE_NO_BK_REFS)) + { + token->type = OP_BACK_REF; + token->opr.idx = c2 - '1'; + } + break; + case '<': + if (!(syntax & RE_NO_GNU_OPS)) + { + token->type = ANCHOR; + token->opr.ctx_type = WORD_FIRST; + } + break; + case '>': + if (!(syntax & RE_NO_GNU_OPS)) + { + token->type = ANCHOR; + token->opr.ctx_type = WORD_LAST; + } + break; + case 'b': + if (!(syntax & RE_NO_GNU_OPS)) + { + token->type = ANCHOR; + token->opr.ctx_type = WORD_DELIM; + } + break; + case 'B': + if (!(syntax & RE_NO_GNU_OPS)) + { + token->type = ANCHOR; + token->opr.ctx_type = NOT_WORD_DELIM; + } + break; + case 'w': + if (!(syntax & RE_NO_GNU_OPS)) + token->type = OP_WORD; + break; + case 'W': + if (!(syntax & RE_NO_GNU_OPS)) + token->type = OP_NOTWORD; + break; + case 's': + if (!(syntax & RE_NO_GNU_OPS)) + token->type = OP_SPACE; + break; + case 'S': + if (!(syntax & RE_NO_GNU_OPS)) + token->type = OP_NOTSPACE; + break; + case '`': + if (!(syntax & RE_NO_GNU_OPS)) + { + token->type = ANCHOR; + token->opr.ctx_type = BUF_FIRST; + } + break; + case '\'': + if (!(syntax & RE_NO_GNU_OPS)) + { + token->type = ANCHOR; + token->opr.ctx_type = BUF_LAST; + } + break; + case '(': + if (!(syntax & RE_NO_BK_PARENS)) + token->type = OP_OPEN_SUBEXP; + break; + case ')': + if (!(syntax & RE_NO_BK_PARENS)) + token->type = OP_CLOSE_SUBEXP; + break; + case '+': + if (!(syntax & RE_LIMITED_OPS) && (syntax & RE_BK_PLUS_QM)) + token->type = OP_DUP_PLUS; + break; + case '?': + if (!(syntax & RE_LIMITED_OPS) && (syntax & RE_BK_PLUS_QM)) + token->type = OP_DUP_QUESTION; + break; + case '{': + if ((syntax & RE_INTERVALS) && (!(syntax & RE_NO_BK_BRACES))) + token->type = OP_OPEN_DUP_NUM; + break; + case '}': + if ((syntax & RE_INTERVALS) && (!(syntax & RE_NO_BK_BRACES))) + token->type = OP_CLOSE_DUP_NUM; + break; + default: + break; + } + return 2; + } + + token->type = CHARACTER; +#ifdef RE_ENABLE_I18N + if (input->mb_cur_max > 1) + { + wint_t wc = re_string_wchar_at (input, re_string_cur_idx (input)); + token->word_char = IS_WIDE_WORD_CHAR (wc) != 0; + } + else +#endif + token->word_char = IS_WORD_CHAR (token->opr.c); + + switch (c) + { + case '\n': + if (syntax & RE_NEWLINE_ALT) + token->type = OP_ALT; + break; + case '|': + if (!(syntax & RE_LIMITED_OPS) && (syntax & RE_NO_BK_VBAR)) + token->type = OP_ALT; + break; + case '*': + token->type = OP_DUP_ASTERISK; + break; + case '+': + if (!(syntax & RE_LIMITED_OPS) && !(syntax & RE_BK_PLUS_QM)) + token->type = OP_DUP_PLUS; + break; + case '?': + if (!(syntax & RE_LIMITED_OPS) && !(syntax & RE_BK_PLUS_QM)) + token->type = OP_DUP_QUESTION; + break; + case '{': + if ((syntax & RE_INTERVALS) && (syntax & RE_NO_BK_BRACES)) + token->type = OP_OPEN_DUP_NUM; + break; + case '}': + if ((syntax & RE_INTERVALS) && (syntax & RE_NO_BK_BRACES)) + token->type = OP_CLOSE_DUP_NUM; + break; + case '(': + if (syntax & RE_NO_BK_PARENS) + token->type = OP_OPEN_SUBEXP; + break; + case ')': + if (syntax & RE_NO_BK_PARENS) + token->type = OP_CLOSE_SUBEXP; + break; + case '[': + token->type = OP_OPEN_BRACKET; + break; + case '.': + token->type = OP_PERIOD; + break; + case '^': + if (!(syntax & (RE_CONTEXT_INDEP_ANCHORS | RE_CARET_ANCHORS_HERE)) && + re_string_cur_idx (input) != 0) + { + char prev = re_string_peek_byte (input, -1); + if (!(syntax & RE_NEWLINE_ALT) || prev != '\n') + break; + } + token->type = ANCHOR; + token->opr.ctx_type = LINE_FIRST; + break; + case '$': + if (!(syntax & RE_CONTEXT_INDEP_ANCHORS) && + re_string_cur_idx (input) + 1 != re_string_length (input)) + { + re_token_t next; + re_string_skip_bytes (input, 1); + peek_token (&next, input, syntax); + re_string_skip_bytes (input, -1); + if (next.type != OP_ALT && next.type != OP_CLOSE_SUBEXP) + break; + } + token->type = ANCHOR; + token->opr.ctx_type = LINE_LAST; + break; + default: + break; + } + return 1; +} + +/* Peek a token from INPUT, and return the length of the token. + We must not use this function out of bracket expressions. */ + +static int +internal_function +peek_token_bracket (re_token_t *token, re_string_t *input, reg_syntax_t syntax) +{ + unsigned char c; + if (re_string_eoi (input)) + { + token->type = END_OF_RE; + return 0; + } + c = re_string_peek_byte (input, 0); + token->opr.c = c; + +#ifdef RE_ENABLE_I18N + if (input->mb_cur_max > 1 && + !re_string_first_byte (input, re_string_cur_idx (input))) + { + token->type = CHARACTER; + return 1; + } +#endif /* RE_ENABLE_I18N */ + + if (c == '\\' && (syntax & RE_BACKSLASH_ESCAPE_IN_LISTS) + && re_string_cur_idx (input) + 1 < re_string_length (input)) + { + /* In this case, '\' escape a character. */ + unsigned char c2; + re_string_skip_bytes (input, 1); + c2 = re_string_peek_byte (input, 0); + token->opr.c = c2; + token->type = CHARACTER; + return 1; + } + if (c == '[') /* '[' is a special char in a bracket exps. */ + { + unsigned char c2; + int token_len; + if (re_string_cur_idx (input) + 1 < re_string_length (input)) + c2 = re_string_peek_byte (input, 1); + else + c2 = 0; + token->opr.c = c2; + token_len = 2; + switch (c2) + { + case '.': + token->type = OP_OPEN_COLL_ELEM; + break; + case '=': + token->type = OP_OPEN_EQUIV_CLASS; + break; + case ':': + if (syntax & RE_CHAR_CLASSES) + { + token->type = OP_OPEN_CHAR_CLASS; + break; + } + /* else fall through. */ + default: + token->type = CHARACTER; + token->opr.c = c; + token_len = 1; + break; + } + return token_len; + } + switch (c) + { + case '-': + token->type = OP_CHARSET_RANGE; + break; + case ']': + token->type = OP_CLOSE_BRACKET; + break; + case '^': + token->type = OP_NON_MATCH_LIST; + break; + default: + token->type = CHARACTER; + } + return 1; +} + +/* Functions for parser. */ + +/* Entry point of the parser. + Parse the regular expression REGEXP and return the structure tree. + If an error is occured, ERR is set by error code, and return NULL. + This function build the following tree, from regular expression : + CAT + / \ + / \ + EOR + + CAT means concatenation. + EOR means end of regular expression. */ + +static bin_tree_t * +parse (re_string_t *regexp, regex_t *preg, reg_syntax_t syntax, + reg_errcode_t *err) +{ + re_dfa_t *dfa = (re_dfa_t *) preg->buffer; + bin_tree_t *tree, *eor, *root; + re_token_t current_token; + dfa->syntax = syntax; + fetch_token (¤t_token, regexp, syntax | RE_CARET_ANCHORS_HERE); + tree = parse_reg_exp (regexp, preg, ¤t_token, syntax, 0, err); + if (BE (*err != REG_NOERROR && tree == NULL, 0)) + return NULL; + eor = create_tree (dfa, NULL, NULL, END_OF_RE); + if (tree != NULL) + root = create_tree (dfa, tree, eor, CONCAT); + else + root = eor; + if (BE (eor == NULL || root == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } + return root; +} + +/* This function build the following tree, from regular expression + |: + ALT + / \ + / \ + + + ALT means alternative, which represents the operator `|'. */ + +static bin_tree_t * +parse_reg_exp (re_string_t *regexp, regex_t *preg, re_token_t *token, + reg_syntax_t syntax, int nest, reg_errcode_t *err) +{ + re_dfa_t *dfa = (re_dfa_t *) preg->buffer; + bin_tree_t *tree, *branch = NULL; + tree = parse_branch (regexp, preg, token, syntax, nest, err); + if (BE (*err != REG_NOERROR && tree == NULL, 0)) + return NULL; + + while (token->type == OP_ALT) + { + fetch_token (token, regexp, syntax | RE_CARET_ANCHORS_HERE); + if (token->type != OP_ALT && token->type != END_OF_RE + && (nest == 0 || token->type != OP_CLOSE_SUBEXP)) + { + branch = parse_branch (regexp, preg, token, syntax, nest, err); + if (BE (*err != REG_NOERROR && branch == NULL, 0)) + return NULL; + } + else + branch = NULL; + tree = create_tree (dfa, tree, branch, OP_ALT); + if (BE (tree == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } + } + return tree; +} + +/* This function build the following tree, from regular expression + : + CAT + / \ + / \ + + + CAT means concatenation. */ + +static bin_tree_t * +parse_branch (re_string_t *regexp, regex_t *preg, re_token_t *token, + reg_syntax_t syntax, int nest, reg_errcode_t *err) +{ + bin_tree_t *tree, *exp; + re_dfa_t *dfa = (re_dfa_t *) preg->buffer; + tree = parse_expression (regexp, preg, token, syntax, nest, err); + if (BE (*err != REG_NOERROR && tree == NULL, 0)) + return NULL; + + while (token->type != OP_ALT && token->type != END_OF_RE + && (nest == 0 || token->type != OP_CLOSE_SUBEXP)) + { + exp = parse_expression (regexp, preg, token, syntax, nest, err); + if (BE (*err != REG_NOERROR && exp == NULL, 0)) + { + return NULL; + } + if (tree != NULL && exp != NULL) + { + tree = create_tree (dfa, tree, exp, CONCAT); + if (tree == NULL) + { + *err = REG_ESPACE; + return NULL; + } + } + else if (tree == NULL) + tree = exp; + /* Otherwise exp == NULL, we don't need to create new tree. */ + } + return tree; +} + +/* This function build the following tree, from regular expression a*: + * + | + a +*/ + +static bin_tree_t * +parse_expression (re_string_t *regexp, regex_t *preg, re_token_t *token, + reg_syntax_t syntax, int nest, reg_errcode_t *err) +{ + re_dfa_t *dfa = (re_dfa_t *) preg->buffer; + bin_tree_t *tree; + switch (token->type) + { + case CHARACTER: + tree = create_token_tree (dfa, NULL, NULL, token); + if (BE (tree == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } +#ifdef RE_ENABLE_I18N + if (dfa->mb_cur_max > 1) + { + while (!re_string_eoi (regexp) + && !re_string_first_byte (regexp, re_string_cur_idx (regexp))) + { + bin_tree_t *mbc_remain; + fetch_token (token, regexp, syntax); + mbc_remain = create_token_tree (dfa, NULL, NULL, token); + tree = create_tree (dfa, tree, mbc_remain, CONCAT); + if (BE (mbc_remain == NULL || tree == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } + } + } +#endif + break; + case OP_OPEN_SUBEXP: + tree = parse_sub_exp (regexp, preg, token, syntax, nest + 1, err); + if (BE (*err != REG_NOERROR && tree == NULL, 0)) + return NULL; + break; + case OP_OPEN_BRACKET: + tree = parse_bracket_exp (regexp, dfa, token, syntax, err); + if (BE (*err != REG_NOERROR && tree == NULL, 0)) + return NULL; + break; + case OP_BACK_REF: + if (!BE (dfa->completed_bkref_map & (1 << token->opr.idx), 1)) + { + *err = REG_ESUBREG; + return NULL; + } + dfa->used_bkref_map |= 1 << token->opr.idx; + tree = create_token_tree (dfa, NULL, NULL, token); + if (BE (tree == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } + ++dfa->nbackref; + dfa->has_mb_node = 1; + break; + case OP_OPEN_DUP_NUM: + if (syntax & RE_CONTEXT_INVALID_DUP) + { + *err = REG_BADRPT; + return NULL; + } + /* FALLTHROUGH */ + case OP_DUP_ASTERISK: + case OP_DUP_PLUS: + case OP_DUP_QUESTION: + if (syntax & RE_CONTEXT_INVALID_OPS) + { + *err = REG_BADRPT; + return NULL; + } + else if (syntax & RE_CONTEXT_INDEP_OPS) + { + fetch_token (token, regexp, syntax); + return parse_expression (regexp, preg, token, syntax, nest, err); + } + /* else fall through */ + case OP_CLOSE_SUBEXP: + if ((token->type == OP_CLOSE_SUBEXP) && + !(syntax & RE_UNMATCHED_RIGHT_PAREN_ORD)) + { + *err = REG_ERPAREN; + return NULL; + } + /* else fall through */ + case OP_CLOSE_DUP_NUM: + /* We treat it as a normal character. */ + + /* Then we can these characters as normal characters. */ + token->type = CHARACTER; + /* mb_partial and word_char bits should be initialized already + by peek_token. */ + tree = create_token_tree (dfa, NULL, NULL, token); + if (BE (tree == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } + break; + case ANCHOR: + if ((token->opr.ctx_type + & (WORD_DELIM | NOT_WORD_DELIM | WORD_FIRST | WORD_LAST)) + && dfa->word_ops_used == 0) + init_word_char (dfa); + if (token->opr.ctx_type == WORD_DELIM + || token->opr.ctx_type == NOT_WORD_DELIM) + { + bin_tree_t *tree_first, *tree_last; + if (token->opr.ctx_type == WORD_DELIM) + { + token->opr.ctx_type = WORD_FIRST; + tree_first = create_token_tree (dfa, NULL, NULL, token); + token->opr.ctx_type = WORD_LAST; + } + else + { + token->opr.ctx_type = INSIDE_WORD; + tree_first = create_token_tree (dfa, NULL, NULL, token); + token->opr.ctx_type = INSIDE_NOTWORD; + } + tree_last = create_token_tree (dfa, NULL, NULL, token); + tree = create_tree (dfa, tree_first, tree_last, OP_ALT); + if (BE (tree_first == NULL || tree_last == NULL || tree == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } + } + else + { + tree = create_token_tree (dfa, NULL, NULL, token); + if (BE (tree == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } + } + /* We must return here, since ANCHORs can't be followed + by repetition operators. + eg. RE"^*" is invalid or "", + it must not be "". */ + fetch_token (token, regexp, syntax); + return tree; + case OP_PERIOD: + tree = create_token_tree (dfa, NULL, NULL, token); + if (BE (tree == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } + if (dfa->mb_cur_max > 1) + dfa->has_mb_node = 1; + break; + case OP_WORD: + case OP_NOTWORD: + tree = build_charclass_op (dfa, regexp->trans, + (const unsigned char *) "alnum", + (const unsigned char *) "_", + token->type == OP_NOTWORD, err); + if (BE (*err != REG_NOERROR && tree == NULL, 0)) + return NULL; + break; + case OP_SPACE: + case OP_NOTSPACE: + tree = build_charclass_op (dfa, regexp->trans, + (const unsigned char *) "space", + (const unsigned char *) "", + token->type == OP_NOTSPACE, err); + if (BE (*err != REG_NOERROR && tree == NULL, 0)) + return NULL; + break; + case OP_ALT: + case END_OF_RE: + return NULL; + case BACK_SLASH: + *err = REG_EESCAPE; + return NULL; + default: + /* Must not happen? */ +#ifdef DEBUG + assert (0); +#endif + return NULL; + } + fetch_token (token, regexp, syntax); + + while (token->type == OP_DUP_ASTERISK || token->type == OP_DUP_PLUS + || token->type == OP_DUP_QUESTION || token->type == OP_OPEN_DUP_NUM) + { + tree = parse_dup_op (tree, regexp, dfa, token, syntax, err); + if (BE (*err != REG_NOERROR && tree == NULL, 0)) + return NULL; + /* In BRE consecutive duplications are not allowed. */ + if ((syntax & RE_CONTEXT_INVALID_DUP) + && (token->type == OP_DUP_ASTERISK + || token->type == OP_OPEN_DUP_NUM)) + { + *err = REG_BADRPT; + return NULL; + } + } + + return tree; +} + +/* This function build the following tree, from regular expression + (): + SUBEXP + | + +*/ + +static bin_tree_t * +parse_sub_exp (re_string_t *regexp, regex_t *preg, re_token_t *token, + reg_syntax_t syntax, int nest, reg_errcode_t *err) +{ + re_dfa_t *dfa = (re_dfa_t *) preg->buffer; + bin_tree_t *tree; + size_t cur_nsub; + cur_nsub = preg->re_nsub++; + + fetch_token (token, regexp, syntax | RE_CARET_ANCHORS_HERE); + + /* The subexpression may be a null string. */ + if (token->type == OP_CLOSE_SUBEXP) + tree = NULL; + else + { + tree = parse_reg_exp (regexp, preg, token, syntax, nest, err); + if (BE (*err == REG_NOERROR && token->type != OP_CLOSE_SUBEXP, 0)) + *err = REG_EPAREN; + if (BE (*err != REG_NOERROR, 0)) + return NULL; + } + + if (cur_nsub <= '9' - '1') + dfa->completed_bkref_map |= 1 << cur_nsub; + + tree = create_tree (dfa, tree, NULL, SUBEXP); + if (BE (tree == NULL, 0)) + { + *err = REG_ESPACE; + return NULL; + } + tree->token.opr.idx = cur_nsub; + return tree; +} + +/* This function parse repetition operators like "*", "+", "{1,3}" etc. */ + +static bin_tree_t * +parse_dup_op (bin_tree_t *elem, re_string_t *regexp, re_dfa_t *dfa, + re_token_t *token, reg_syntax_t syntax, reg_errcode_t *err) +{ + bin_tree_t *tree = NULL, *old_tree = NULL; + int i, start, end, start_idx = re_string_cur_idx (regexp); + re_token_t start_token = *token; + + if (token->type == OP_OPEN_DUP_NUM) + { + end = 0; + start = fetch_number (regexp, token, syntax); + if (start == -1) + { + if (token->type == CHARACTER && token->opr.c == ',') + start = 0; /* We treat "{,m}" as "{0,m}". */ + else + { + *err = REG_BADBR; /* {} is invalid. */ + return NULL; + } + } + if (BE (start != -2, 1)) + { + /* We treat "{n}" as "{n,n}". */ + end = ((token->type == OP_CLOSE_DUP_NUM) ? start + : ((token->type == CHARACTER && token->opr.c == ',') + ? fetch_number (regexp, token, syntax) : -2)); + } + if (BE (start == -2 || end == -2, 0)) + { + /* Invalid sequence. */ + if (BE (!(syntax & RE_INVALID_INTERVAL_ORD), 0)) + { + if (token->type == END_OF_RE) + *err = REG_EBRACE; + else + *err = REG_BADBR; + + return NULL; + } + + /* If the syntax bit is set, rollback. */ + re_string_set_index (regexp, start_idx); + *token = start_token; + token->type = CHARACTER; + /* mb_partial and word_char bits should be already initialized by + peek_token. */ + return elem; + } + + if (BE (end != -1 && start > end, 0)) + { + /* First number greater than second. */ + *err = REG_BADBR; + return NULL; + } + } + else + { + start = (token->type == OP_DUP_PLUS) ? 1 : 0; + end = (token->type == OP_DUP_QUESTION) ? 1 : -1; + } + + fetch_token (token, regexp, syntax); + + if (BE (elem == NULL, 0)) + return NULL; + if (BE (start == 0 && end == 0, 0)) + { + postorder (elem, free_tree, NULL); + return NULL; + } + + /* Extract "{n,m}" to "...{0,}". */ + if (BE (start > 0, 0)) + { + tree = elem; + for (i = 2; i <= start; ++i) + { + elem = duplicate_tree (elem, dfa); + tree = create_tree (dfa, tree, elem, CONCAT); + if (BE (elem == NULL || tree == NULL, 0)) + goto parse_dup_op_espace; + } + + if (start == end) + return tree; + + /* Duplicate ELEM before it is marked optional. */ + elem = duplicate_tree (elem, dfa); + old_tree = tree; + } + else + old_tree = NULL; + + if (elem->token.type == SUBEXP) + postorder (elem, mark_opt_subexp, (void *) (long) elem->token.opr.idx); + + tree = create_tree (dfa, elem, NULL, (end == -1 ? OP_DUP_ASTERISK : OP_ALT)); + if (BE (tree == NULL, 0)) + goto parse_dup_op_espace; + + /* This loop is actually executed only when end != -1, + to rewrite {0,n} as ((...?)?)?... We have + already created the start+1-th copy. */ + for (i = start + 2; i <= end; ++i) + { + elem = duplicate_tree (elem, dfa); + tree = create_tree (dfa, tree, elem, CONCAT); + if (BE (elem == NULL || tree == NULL, 0)) + goto parse_dup_op_espace; + + tree = create_tree (dfa, tree, NULL, OP_ALT); + if (BE (tree == NULL, 0)) + goto parse_dup_op_espace; + } + + if (old_tree) + tree = create_tree (dfa, old_tree, tree, CONCAT); + + return tree; + + parse_dup_op_espace: + *err = REG_ESPACE; + return NULL; +} + +/* Size of the names for collating symbol/equivalence_class/character_class. + I'm not sure, but maybe enough. */ +#define BRACKET_NAME_BUF_SIZE 32 + +#ifndef _LIBC + /* Local function for parse_bracket_exp only used in case of NOT _LIBC. + Build the range expression which starts from START_ELEM, and ends + at END_ELEM. The result are written to MBCSET and SBCSET. + RANGE_ALLOC is the allocated size of mbcset->range_starts, and + mbcset->range_ends, is a pointer argument sinse we may + update it. */ + +static reg_errcode_t +internal_function +# ifdef RE_ENABLE_I18N +build_range_exp (bitset_t sbcset, re_charset_t *mbcset, int *range_alloc, + bracket_elem_t *start_elem, bracket_elem_t *end_elem) +# else /* not RE_ENABLE_I18N */ +build_range_exp (bitset_t sbcset, bracket_elem_t *start_elem, + bracket_elem_t *end_elem) +# endif /* not RE_ENABLE_I18N */ +{ + unsigned int start_ch, end_ch; + /* Equivalence Classes and Character Classes can't be a range start/end. */ + if (BE (start_elem->type == EQUIV_CLASS || start_elem->type == CHAR_CLASS + || end_elem->type == EQUIV_CLASS || end_elem->type == CHAR_CLASS, + 0)) + return REG_ERANGE; + + /* We can handle no multi character collating elements without libc + support. */ + if (BE ((start_elem->type == COLL_SYM + && strlen ((char *) start_elem->opr.name) > 1) + || (end_elem->type == COLL_SYM + && strlen ((char *) end_elem->opr.name) > 1), 0)) + return REG_ECOLLATE; + +# ifdef RE_ENABLE_I18N + { + wchar_t wc; + wint_t start_wc; + wint_t end_wc; + wchar_t cmp_buf[6] = {L'\0', L'\0', L'\0', L'\0', L'\0', L'\0'}; + + start_ch = ((start_elem->type == SB_CHAR) ? start_elem->opr.ch + : ((start_elem->type == COLL_SYM) ? start_elem->opr.name[0] + : 0)); + end_ch = ((end_elem->type == SB_CHAR) ? end_elem->opr.ch + : ((end_elem->type == COLL_SYM) ? end_elem->opr.name[0] + : 0)); + start_wc = ((start_elem->type == SB_CHAR || start_elem->type == COLL_SYM) + ? __btowc (start_ch) : start_elem->opr.wch); + end_wc = ((end_elem->type == SB_CHAR || end_elem->type == COLL_SYM) + ? __btowc (end_ch) : end_elem->opr.wch); + if (start_wc == WEOF || end_wc == WEOF) + return REG_ECOLLATE; + cmp_buf[0] = start_wc; + cmp_buf[4] = end_wc; + if (wcscoll (cmp_buf, cmp_buf + 4) > 0) + return REG_ERANGE; + + /* Got valid collation sequence values, add them as a new entry. + However, for !_LIBC we have no collation elements: if the + character set is single byte, the single byte character set + that we build below suffices. parse_bracket_exp passes + no MBCSET if dfa->mb_cur_max == 1. */ + if (mbcset) + { + /* Check the space of the arrays. */ + if (BE (*range_alloc == mbcset->nranges, 0)) + { + /* There is not enough space, need realloc. */ + wchar_t *new_array_start, *new_array_end; + int new_nranges; + + /* +1 in case of mbcset->nranges is 0. */ + new_nranges = 2 * mbcset->nranges + 1; + /* Use realloc since mbcset->range_starts and mbcset->range_ends + are NULL if *range_alloc == 0. */ + new_array_start = re_realloc (mbcset->range_starts, wchar_t, + new_nranges); + new_array_end = re_realloc (mbcset->range_ends, wchar_t, + new_nranges); + + if (BE (new_array_start == NULL || new_array_end == NULL, 0)) + return REG_ESPACE; + + mbcset->range_starts = new_array_start; + mbcset->range_ends = new_array_end; + *range_alloc = new_nranges; + } + + mbcset->range_starts[mbcset->nranges] = start_wc; + mbcset->range_ends[mbcset->nranges++] = end_wc; + } + + /* Build the table for single byte characters. */ + for (wc = 0; wc < SBC_MAX; ++wc) + { + cmp_buf[2] = wc; + if (wcscoll (cmp_buf, cmp_buf + 2) <= 0 + && wcscoll (cmp_buf + 2, cmp_buf + 4) <= 0) + bitset_set (sbcset, wc); + } + } +# else /* not RE_ENABLE_I18N */ + { + unsigned int ch; + start_ch = ((start_elem->type == SB_CHAR ) ? start_elem->opr.ch + : ((start_elem->type == COLL_SYM) ? start_elem->opr.name[0] + : 0)); + end_ch = ((end_elem->type == SB_CHAR ) ? end_elem->opr.ch + : ((end_elem->type == COLL_SYM) ? end_elem->opr.name[0] + : 0)); + if (start_ch > end_ch) + return REG_ERANGE; + /* Build the table for single byte characters. */ + for (ch = 0; ch < SBC_MAX; ++ch) + if (start_ch <= ch && ch <= end_ch) + bitset_set (sbcset, ch); + } +# endif /* not RE_ENABLE_I18N */ + return REG_NOERROR; +} +#endif /* not _LIBC */ + +#ifndef _LIBC +/* Helper function for parse_bracket_exp only used in case of NOT _LIBC.. + Build the collating element which is represented by NAME. + The result are written to MBCSET and SBCSET. + COLL_SYM_ALLOC is the allocated size of mbcset->coll_sym, is a + pointer argument since we may update it. */ + +static reg_errcode_t +internal_function +# ifdef RE_ENABLE_I18N +build_collating_symbol (bitset_t sbcset, re_charset_t *mbcset, + int *coll_sym_alloc, const unsigned char *name) +# else /* not RE_ENABLE_I18N */ +build_collating_symbol (bitset_t sbcset, const unsigned char *name) +# endif /* not RE_ENABLE_I18N */ +{ + size_t name_len = strlen ((const char *) name); + if (BE (name_len != 1, 0)) + return REG_ECOLLATE; + else + { + bitset_set (sbcset, name[0]); + return REG_NOERROR; + } +} +#endif /* not _LIBC */ + +/* This function parse bracket expression like "[abc]", "[a-c]", + "[[.a-a.]]" etc. */ + +static bin_tree_t * +parse_bracket_exp (re_string_t *regexp, re_dfa_t *dfa, re_token_t *token, + reg_syntax_t syntax, reg_errcode_t *err) +{ +#ifdef _LIBC + const unsigned char *collseqmb; + const char *collseqwc; + uint32_t nrules; + int32_t table_size; + const int32_t *symb_table; + const unsigned char *extra; + + /* Local function for parse_bracket_exp used in _LIBC environement. + Seek the collating symbol entry correspondings to NAME. + Return the index of the symbol in the SYMB_TABLE. */ + + auto inline int32_t + __attribute ((always_inline)) + seek_collating_symbol_entry (name, name_len) + const unsigned char *name; + size_t name_len; + { + int32_t hash = elem_hash ((const char *) name, name_len); + int32_t elem = hash % table_size; + if (symb_table[2 * elem] != 0) + { + int32_t second = hash % (table_size - 2) + 1; + + do + { + /* First compare the hashing value. */ + if (symb_table[2 * elem] == hash + /* Compare the length of the name. */ + && name_len == extra[symb_table[2 * elem + 1]] + /* Compare the name. */ + && memcmp (name, &extra[symb_table[2 * elem + 1] + 1], + name_len) == 0) + { + /* Yep, this is the entry. */ + break; + } + + /* Next entry. */ + elem += second; + } + while (symb_table[2 * elem] != 0); + } + return elem; + } + + /* Local function for parse_bracket_exp used in _LIBC environement. + Look up the collation sequence value of BR_ELEM. + Return the value if succeeded, UINT_MAX otherwise. */ + + auto inline unsigned int + __attribute ((always_inline)) + lookup_collation_sequence_value (br_elem) + bracket_elem_t *br_elem; + { + if (br_elem->type == SB_CHAR) + { + /* + if (MB_CUR_MAX == 1) + */ + if (nrules == 0) + return collseqmb[br_elem->opr.ch]; + else + { + wint_t wc = __btowc (br_elem->opr.ch); + return __collseq_table_lookup (collseqwc, wc); + } + } + else if (br_elem->type == MB_CHAR) + { + return __collseq_table_lookup (collseqwc, br_elem->opr.wch); + } + else if (br_elem->type == COLL_SYM) + { + size_t sym_name_len = strlen ((char *) br_elem->opr.name); + if (nrules != 0) + { + int32_t elem, idx; + elem = seek_collating_symbol_entry (br_elem->opr.name, + sym_name_len); + if (symb_table[2 * elem] != 0) + { + /* We found the entry. */ + idx = symb_table[2 * elem + 1]; + /* Skip the name of collating element name. */ + idx += 1 + extra[idx]; + /* Skip the byte sequence of the collating element. */ + idx += 1 + extra[idx]; + /* Adjust for the alignment. */ + idx = (idx + 3) & ~3; + /* Skip the multibyte collation sequence value. */ + idx += sizeof (unsigned int); + /* Skip the wide char sequence of the collating element. */ + idx += sizeof (unsigned int) * + (1 + *(unsigned int *) (extra + idx)); + /* Return the collation sequence value. */ + return *(unsigned int *) (extra + idx); + } + else if (symb_table[2 * elem] == 0 && sym_name_len == 1) + { + /* No valid character. Match it as a single byte + character. */ + return collseqmb[br_elem->opr.name[0]]; + } + } + else if (sym_name_len == 1) + return collseqmb[br_elem->opr.name[0]]; + } + return UINT_MAX; + } + + /* Local function for parse_bracket_exp used in _LIBC environement. + Build the range expression which starts from START_ELEM, and ends + at END_ELEM. The result are written to MBCSET and SBCSET. + RANGE_ALLOC is the allocated size of mbcset->range_starts, and + mbcset->range_ends, is a pointer argument sinse we may + update it. */ + + auto inline reg_errcode_t + __attribute ((always_inline)) + build_range_exp (sbcset, mbcset, range_alloc, start_elem, end_elem) + re_charset_t *mbcset; + int *range_alloc; + bitset_t sbcset; + bracket_elem_t *start_elem, *end_elem; + { + unsigned int ch; + uint32_t start_collseq; + uint32_t end_collseq; + + /* Equivalence Classes and Character Classes can't be a range + start/end. */ + if (BE (start_elem->type == EQUIV_CLASS || start_elem->type == CHAR_CLASS + || end_elem->type == EQUIV_CLASS || end_elem->type == CHAR_CLASS, + 0)) + return REG_ERANGE; + + start_collseq = lookup_collation_sequence_value (start_elem); + end_collseq = lookup_collation_sequence_value (end_elem); + /* Check start/end collation sequence values. */ + if (BE (start_collseq == UINT_MAX || end_collseq == UINT_MAX, 0)) + return REG_ECOLLATE; + if (BE ((syntax & RE_NO_EMPTY_RANGES) && start_collseq > end_collseq, 0)) + return REG_ERANGE; + + /* Got valid collation sequence values, add them as a new entry. + However, if we have no collation elements, and the character set + is single byte, the single byte character set that we + build below suffices. */ + if (nrules > 0 || dfa->mb_cur_max > 1) + { + /* Check the space of the arrays. */ + if (BE (*range_alloc == mbcset->nranges, 0)) + { + /* There is not enough space, need realloc. */ + uint32_t *new_array_start; + uint32_t *new_array_end; + int new_nranges; + + /* +1 in case of mbcset->nranges is 0. */ + new_nranges = 2 * mbcset->nranges + 1; + new_array_start = re_realloc (mbcset->range_starts, uint32_t, + new_nranges); + new_array_end = re_realloc (mbcset->range_ends, uint32_t, + new_nranges); + + if (BE (new_array_start == NULL || new_array_end == NULL, 0)) + return REG_ESPACE; + + mbcset->range_starts = new_array_start; + mbcset->range_ends = new_array_end; + *range_alloc = new_nranges; + } + + mbcset->range_starts[mbcset->nranges] = start_collseq; + mbcset->range_ends[mbcset->nranges++] = end_collseq; + } + + /* Build the table for single byte characters. */ + for (ch = 0; ch < SBC_MAX; ch++) + { + uint32_t ch_collseq; + /* + if (MB_CUR_MAX == 1) + */ + if (nrules == 0) + ch_collseq = collseqmb[ch]; + else + ch_collseq = __collseq_table_lookup (collseqwc, __btowc (ch)); + if (start_collseq <= ch_collseq && ch_collseq <= end_collseq) + bitset_set (sbcset, ch); + } + return REG_NOERROR; + } + + /* Local function for parse_bracket_exp used in _LIBC environement. + Build the collating element which is represented by NAME. + The result are written to MBCSET and SBCSET. + COLL_SYM_ALLOC is the allocated size of mbcset->coll_sym, is a + pointer argument sinse we may update it. */ + + auto inline reg_errcode_t + __attribute ((always_inline)) + build_collating_symbol (sbcset, mbcset, coll_sym_alloc, name) + re_charset_t *mbcset; + int *coll_sym_alloc; + bitset_t sbcset; + const unsigned char *name; + { + int32_t elem, idx; + size_t name_len = strlen ((const char *) name); + if (nrules != 0) + { + elem = seek_collating_symbol_entry (name, name_len); + if (symb_table[2 * elem] != 0) + { + /* We found the entry. */ + idx = symb_table[2 * elem + 1]; + /* Skip the name of collating element name. */ + idx += 1 + extra[idx]; + } + else if (symb_table[2 * elem] == 0 && name_len == 1) + { + /* No valid character, treat it as a normal + character. */ + bitset_set (sbcset, name[0]); + return REG_NOERROR; + } + else + return REG_ECOLLATE; + + /* Got valid collation sequence, add it as a new entry. */ + /* Check the space of the arrays. */ + if (BE (*coll_sym_alloc == mbcset->ncoll_syms, 0)) + { + /* Not enough, realloc it. */ + /* +1 in case of mbcset->ncoll_syms is 0. */ + int new_coll_sym_alloc = 2 * mbcset->ncoll_syms + 1; + /* Use realloc since mbcset->coll_syms is NULL + if *alloc == 0. */ + int32_t *new_coll_syms = re_realloc (mbcset->coll_syms, int32_t, + new_coll_sym_alloc); + if (BE (new_coll_syms == NULL, 0)) + return REG_ESPACE; + mbcset->coll_syms = new_coll_syms; + *coll_sym_alloc = new_coll_sym_alloc; + } + mbcset->coll_syms[mbcset->ncoll_syms++] = idx; + return REG_NOERROR; + } + else + { + if (BE (name_len != 1, 0)) + return REG_ECOLLATE; + else + { + bitset_set (sbcset, name[0]); + return REG_NOERROR; + } + } + } +#endif + + re_token_t br_token; + re_bitset_ptr_t sbcset; +#ifdef RE_ENABLE_I18N + re_charset_t *mbcset; + int coll_sym_alloc = 0, range_alloc = 0, mbchar_alloc = 0; + int equiv_class_alloc = 0, char_class_alloc = 0; +#endif /* not RE_ENABLE_I18N */ + int non_match = 0; + bin_tree_t *work_tree; + int token_len; + int first_round = 1; +#ifdef _LIBC + collseqmb = (const unsigned char *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_COLLSEQMB); + nrules = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES); + if (nrules) + { + /* + if (MB_CUR_MAX > 1) + */ + collseqwc = _NL_CURRENT (LC_COLLATE, _NL_COLLATE_COLLSEQWC); + table_size = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_SYMB_HASH_SIZEMB); + symb_table = (const int32_t *) _NL_CURRENT (LC_COLLATE, + _NL_COLLATE_SYMB_TABLEMB); + extra = (const unsigned char *) _NL_CURRENT (LC_COLLATE, + _NL_COLLATE_SYMB_EXTRAMB); + } +#endif + sbcset = (re_bitset_ptr_t) calloc (sizeof (bitset_t), 1); +#ifdef RE_ENABLE_I18N + mbcset = (re_charset_t *) calloc (sizeof (re_charset_t), 1); +#endif /* RE_ENABLE_I18N */ +#ifdef RE_ENABLE_I18N + if (BE (sbcset == NULL || mbcset == NULL, 0)) +#else + if (BE (sbcset == NULL, 0)) +#endif /* RE_ENABLE_I18N */ + { + *err = REG_ESPACE; + return NULL; + } + + token_len = peek_token_bracket (token, regexp, syntax); + if (BE (token->type == END_OF_RE, 0)) + { + *err = REG_BADPAT; + goto parse_bracket_exp_free_return; + } + if (token->type == OP_NON_MATCH_LIST) + { +#ifdef RE_ENABLE_I18N + mbcset->non_match = 1; +#endif /* not RE_ENABLE_I18N */ + non_match = 1; + if (syntax & RE_HAT_LISTS_NOT_NEWLINE) + bitset_set (sbcset, '\0'); + re_string_skip_bytes (regexp, token_len); /* Skip a token. */ + token_len = peek_token_bracket (token, regexp, syntax); + if (BE (token->type == END_OF_RE, 0)) + { + *err = REG_BADPAT; + goto parse_bracket_exp_free_return; + } + } + + /* We treat the first ']' as a normal character. */ + if (token->type == OP_CLOSE_BRACKET) + token->type = CHARACTER; + + while (1) + { + bracket_elem_t start_elem, end_elem; + unsigned char start_name_buf[BRACKET_NAME_BUF_SIZE]; + unsigned char end_name_buf[BRACKET_NAME_BUF_SIZE]; + reg_errcode_t ret; + int token_len2 = 0, is_range_exp = 0; + re_token_t token2; + + start_elem.opr.name = start_name_buf; + ret = parse_bracket_element (&start_elem, regexp, token, token_len, dfa, + syntax, first_round); + if (BE (ret != REG_NOERROR, 0)) + { + *err = ret; + goto parse_bracket_exp_free_return; + } + first_round = 0; + + /* Get information about the next token. We need it in any case. */ + token_len = peek_token_bracket (token, regexp, syntax); + + /* Do not check for ranges if we know they are not allowed. */ + if (start_elem.type != CHAR_CLASS && start_elem.type != EQUIV_CLASS) + { + if (BE (token->type == END_OF_RE, 0)) + { + *err = REG_EBRACK; + goto parse_bracket_exp_free_return; + } + if (token->type == OP_CHARSET_RANGE) + { + re_string_skip_bytes (regexp, token_len); /* Skip '-'. */ + token_len2 = peek_token_bracket (&token2, regexp, syntax); + if (BE (token2.type == END_OF_RE, 0)) + { + *err = REG_EBRACK; + goto parse_bracket_exp_free_return; + } + if (token2.type == OP_CLOSE_BRACKET) + { + /* We treat the last '-' as a normal character. */ + re_string_skip_bytes (regexp, -token_len); + token->type = CHARACTER; + } + else + is_range_exp = 1; + } + } + + if (is_range_exp == 1) + { + end_elem.opr.name = end_name_buf; + ret = parse_bracket_element (&end_elem, regexp, &token2, token_len2, + dfa, syntax, 1); + if (BE (ret != REG_NOERROR, 0)) + { + *err = ret; + goto parse_bracket_exp_free_return; + } + + token_len = peek_token_bracket (token, regexp, syntax); + +#ifdef _LIBC + *err = build_range_exp (sbcset, mbcset, &range_alloc, + &start_elem, &end_elem); +#else +# ifdef RE_ENABLE_I18N + *err = build_range_exp (sbcset, + dfa->mb_cur_max > 1 ? mbcset : NULL, + &range_alloc, &start_elem, &end_elem); +# else + *err = build_range_exp (sbcset, &start_elem, &end_elem); +# endif +#endif /* RE_ENABLE_I18N */ + if (BE (*err != REG_NOERROR, 0)) + goto parse_bracket_exp_free_return; + } + else + { + switch (start_elem.type) + { + case SB_CHAR: + bitset_set (sbcset, start_elem.opr.ch); + break; +#ifdef RE_ENABLE_I18N + case MB_CHAR: + /* Check whether the array has enough space. */ + if (BE (mbchar_alloc == mbcset->nmbchars, 0)) + { + wchar_t *new_mbchars; + /* Not enough, realloc it. */ + /* +1 in case of mbcset->nmbchars is 0. */ + mbchar_alloc = 2 * mbcset->nmbchars + 1; + /* Use realloc since array is NULL if *alloc == 0. */ + new_mbchars = re_realloc (mbcset->mbchars, wchar_t, + mbchar_alloc); + if (BE (new_mbchars == NULL, 0)) + goto parse_bracket_exp_espace; + mbcset->mbchars = new_mbchars; + } + mbcset->mbchars[mbcset->nmbchars++] = start_elem.opr.wch; + break; +#endif /* RE_ENABLE_I18N */ + case EQUIV_CLASS: + *err = build_equiv_class (sbcset, +#ifdef RE_ENABLE_I18N + mbcset, &equiv_class_alloc, +#endif /* RE_ENABLE_I18N */ + start_elem.opr.name); + if (BE (*err != REG_NOERROR, 0)) + goto parse_bracket_exp_free_return; + break; + case COLL_SYM: + *err = build_collating_symbol (sbcset, +#ifdef RE_ENABLE_I18N + mbcset, &coll_sym_alloc, +#endif /* RE_ENABLE_I18N */ + start_elem.opr.name); + if (BE (*err != REG_NOERROR, 0)) + goto parse_bracket_exp_free_return; + break; + case CHAR_CLASS: + *err = build_charclass (regexp->trans, sbcset, +#ifdef RE_ENABLE_I18N + mbcset, &char_class_alloc, +#endif /* RE_ENABLE_I18N */ + start_elem.opr.name, syntax); + if (BE (*err != REG_NOERROR, 0)) + goto parse_bracket_exp_free_return; + break; + default: + assert (0); + break; + } + } + if (BE (token->type == END_OF_RE, 0)) + { + *err = REG_EBRACK; + goto parse_bracket_exp_free_return; + } + if (token->type == OP_CLOSE_BRACKET) + break; + } + + re_string_skip_bytes (regexp, token_len); /* Skip a token. */ + + /* If it is non-matching list. */ + if (non_match) + bitset_not (sbcset); + +#ifdef RE_ENABLE_I18N + /* Ensure only single byte characters are set. */ + if (dfa->mb_cur_max > 1) + bitset_mask (sbcset, dfa->sb_char); + + if (mbcset->nmbchars || mbcset->ncoll_syms || mbcset->nequiv_classes + || mbcset->nranges || (dfa->mb_cur_max > 1 && (mbcset->nchar_classes + || mbcset->non_match))) + { + bin_tree_t *mbc_tree; + int sbc_idx; + /* Build a tree for complex bracket. */ + dfa->has_mb_node = 1; + br_token.type = COMPLEX_BRACKET; + br_token.opr.mbcset = mbcset; + mbc_tree = create_token_tree (dfa, NULL, NULL, &br_token); + if (BE (mbc_tree == NULL, 0)) + goto parse_bracket_exp_espace; + for (sbc_idx = 0; sbc_idx < BITSET_WORDS; ++sbc_idx) + if (sbcset[sbc_idx]) + break; + /* If there are no bits set in sbcset, there is no point + of having both SIMPLE_BRACKET and COMPLEX_BRACKET. */ + if (sbc_idx < BITSET_WORDS) + { + /* Build a tree for simple bracket. */ + br_token.type = SIMPLE_BRACKET; + br_token.opr.sbcset = sbcset; + work_tree = create_token_tree (dfa, NULL, NULL, &br_token); + if (BE (work_tree == NULL, 0)) + goto parse_bracket_exp_espace; + + /* Then join them by ALT node. */ + work_tree = create_tree (dfa, work_tree, mbc_tree, OP_ALT); + if (BE (work_tree == NULL, 0)) + goto parse_bracket_exp_espace; + } + else + { + re_free (sbcset); + work_tree = mbc_tree; + } + } + else +#endif /* not RE_ENABLE_I18N */ + { +#ifdef RE_ENABLE_I18N + free_charset (mbcset); +#endif + /* Build a tree for simple bracket. */ + br_token.type = SIMPLE_BRACKET; + br_token.opr.sbcset = sbcset; + work_tree = create_token_tree (dfa, NULL, NULL, &br_token); + if (BE (work_tree == NULL, 0)) + goto parse_bracket_exp_espace; + } + return work_tree; + + parse_bracket_exp_espace: + *err = REG_ESPACE; + parse_bracket_exp_free_return: + re_free (sbcset); +#ifdef RE_ENABLE_I18N + free_charset (mbcset); +#endif /* RE_ENABLE_I18N */ + return NULL; +} + +/* Parse an element in the bracket expression. */ + +static reg_errcode_t +parse_bracket_element (bracket_elem_t *elem, re_string_t *regexp, + re_token_t *token, int token_len, re_dfa_t *dfa, + reg_syntax_t syntax, int accept_hyphen) +{ +#ifdef RE_ENABLE_I18N + int cur_char_size; + cur_char_size = re_string_char_size_at (regexp, re_string_cur_idx (regexp)); + if (cur_char_size > 1) + { + elem->type = MB_CHAR; + elem->opr.wch = re_string_wchar_at (regexp, re_string_cur_idx (regexp)); + re_string_skip_bytes (regexp, cur_char_size); + return REG_NOERROR; + } +#endif /* RE_ENABLE_I18N */ + re_string_skip_bytes (regexp, token_len); /* Skip a token. */ + if (token->type == OP_OPEN_COLL_ELEM || token->type == OP_OPEN_CHAR_CLASS + || token->type == OP_OPEN_EQUIV_CLASS) + return parse_bracket_symbol (elem, regexp, token); + if (BE (token->type == OP_CHARSET_RANGE, 0) && !accept_hyphen) + { + /* A '-' must only appear as anything but a range indicator before + the closing bracket. Everything else is an error. */ + re_token_t token2; + (void) peek_token_bracket (&token2, regexp, syntax); + if (token2.type != OP_CLOSE_BRACKET) + /* The actual error value is not standardized since this whole + case is undefined. But ERANGE makes good sense. */ + return REG_ERANGE; + } + elem->type = SB_CHAR; + elem->opr.ch = token->opr.c; + return REG_NOERROR; +} + +/* Parse a bracket symbol in the bracket expression. Bracket symbols are + such as [::], [..], and + [==]. */ + +static reg_errcode_t +parse_bracket_symbol (bracket_elem_t *elem, re_string_t *regexp, + re_token_t *token) +{ + unsigned char ch, delim = token->opr.c; + int i = 0; + if (re_string_eoi(regexp)) + return REG_EBRACK; + for (;; ++i) + { + if (i >= BRACKET_NAME_BUF_SIZE) + return REG_EBRACK; + if (token->type == OP_OPEN_CHAR_CLASS) + ch = re_string_fetch_byte_case (regexp); + else + ch = re_string_fetch_byte (regexp); + if (re_string_eoi(regexp)) + return REG_EBRACK; + if (ch == delim && re_string_peek_byte (regexp, 0) == ']') + break; + elem->opr.name[i] = ch; + } + re_string_skip_bytes (regexp, 1); + elem->opr.name[i] = '\0'; + switch (token->type) + { + case OP_OPEN_COLL_ELEM: + elem->type = COLL_SYM; + break; + case OP_OPEN_EQUIV_CLASS: + elem->type = EQUIV_CLASS; + break; + case OP_OPEN_CHAR_CLASS: + elem->type = CHAR_CLASS; + break; + default: + break; + } + return REG_NOERROR; +} + + /* Helper function for parse_bracket_exp. + Build the equivalence class which is represented by NAME. + The result are written to MBCSET and SBCSET. + EQUIV_CLASS_ALLOC is the allocated size of mbcset->equiv_classes, + is a pointer argument sinse we may update it. */ + +static reg_errcode_t +#ifdef RE_ENABLE_I18N +build_equiv_class (bitset_t sbcset, re_charset_t *mbcset, + int *equiv_class_alloc, const unsigned char *name) +#else /* not RE_ENABLE_I18N */ +build_equiv_class (bitset_t sbcset, const unsigned char *name) +#endif /* not RE_ENABLE_I18N */ +{ +#ifdef _LIBC + uint32_t nrules = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES); + if (nrules != 0) + { + const int32_t *table, *indirect; + const unsigned char *weights, *extra, *cp; + unsigned char char_buf[2]; + int32_t idx1, idx2; + unsigned int ch; + size_t len; + /* This #include defines a local function! */ +# include + /* Calculate the index for equivalence class. */ + cp = name; + table = (const int32_t *) _NL_CURRENT (LC_COLLATE, _NL_COLLATE_TABLEMB); + weights = (const unsigned char *) _NL_CURRENT (LC_COLLATE, + _NL_COLLATE_WEIGHTMB); + extra = (const unsigned char *) _NL_CURRENT (LC_COLLATE, + _NL_COLLATE_EXTRAMB); + indirect = (const int32_t *) _NL_CURRENT (LC_COLLATE, + _NL_COLLATE_INDIRECTMB); + idx1 = findidx (&cp); + if (BE (idx1 == 0 || cp < name + strlen ((const char *) name), 0)) + /* This isn't a valid character. */ + return REG_ECOLLATE; + + /* Build single byte matcing table for this equivalence class. */ + char_buf[1] = (unsigned char) '\0'; + len = weights[idx1]; + for (ch = 0; ch < SBC_MAX; ++ch) + { + char_buf[0] = ch; + cp = char_buf; + idx2 = findidx (&cp); +/* + idx2 = table[ch]; +*/ + if (idx2 == 0) + /* This isn't a valid character. */ + continue; + if (len == weights[idx2]) + { + int cnt = 0; + while (cnt <= len && + weights[idx1 + 1 + cnt] == weights[idx2 + 1 + cnt]) + ++cnt; + + if (cnt > len) + bitset_set (sbcset, ch); + } + } + /* Check whether the array has enough space. */ + if (BE (*equiv_class_alloc == mbcset->nequiv_classes, 0)) + { + /* Not enough, realloc it. */ + /* +1 in case of mbcset->nequiv_classes is 0. */ + int new_equiv_class_alloc = 2 * mbcset->nequiv_classes + 1; + /* Use realloc since the array is NULL if *alloc == 0. */ + int32_t *new_equiv_classes = re_realloc (mbcset->equiv_classes, + int32_t, + new_equiv_class_alloc); + if (BE (new_equiv_classes == NULL, 0)) + return REG_ESPACE; + mbcset->equiv_classes = new_equiv_classes; + *equiv_class_alloc = new_equiv_class_alloc; + } + mbcset->equiv_classes[mbcset->nequiv_classes++] = idx1; + } + else +#endif /* _LIBC */ + { + if (BE (strlen ((const char *) name) != 1, 0)) + return REG_ECOLLATE; + bitset_set (sbcset, *name); + } + return REG_NOERROR; +} + + /* Helper function for parse_bracket_exp. + Build the character class which is represented by NAME. + The result are written to MBCSET and SBCSET. + CHAR_CLASS_ALLOC is the allocated size of mbcset->char_classes, + is a pointer argument sinse we may update it. */ + +static reg_errcode_t +#ifdef RE_ENABLE_I18N +build_charclass (RE_TRANSLATE_TYPE trans, bitset_t sbcset, + re_charset_t *mbcset, int *char_class_alloc, + const unsigned char *class_name, reg_syntax_t syntax) +#else /* not RE_ENABLE_I18N */ +build_charclass (RE_TRANSLATE_TYPE trans, bitset_t sbcset, + const unsigned char *class_name, reg_syntax_t syntax) +#endif /* not RE_ENABLE_I18N */ +{ + int i; + const char *name = (const char *) class_name; + + /* In case of REG_ICASE "upper" and "lower" match the both of + upper and lower cases. */ + if ((syntax & RE_ICASE) + && (strcmp (name, "upper") == 0 || strcmp (name, "lower") == 0)) + name = "alpha"; + +#ifdef RE_ENABLE_I18N + /* Check the space of the arrays. */ + if (BE (*char_class_alloc == mbcset->nchar_classes, 0)) + { + /* Not enough, realloc it. */ + /* +1 in case of mbcset->nchar_classes is 0. */ + int new_char_class_alloc = 2 * mbcset->nchar_classes + 1; + /* Use realloc since array is NULL if *alloc == 0. */ + wctype_t *new_char_classes = re_realloc (mbcset->char_classes, wctype_t, + new_char_class_alloc); + if (BE (new_char_classes == NULL, 0)) + return REG_ESPACE; + mbcset->char_classes = new_char_classes; + *char_class_alloc = new_char_class_alloc; + } + mbcset->char_classes[mbcset->nchar_classes++] = __wctype (name); +#endif /* RE_ENABLE_I18N */ + +#define BUILD_CHARCLASS_LOOP(ctype_func) \ + do { \ + if (BE (trans != NULL, 0)) \ + { \ + for (i = 0; i < SBC_MAX; ++i) \ + if (ctype_func (i)) \ + bitset_set (sbcset, trans[i]); \ + } \ + else \ + { \ + for (i = 0; i < SBC_MAX; ++i) \ + if (ctype_func (i)) \ + bitset_set (sbcset, i); \ + } \ + } while (0) + + if (strcmp (name, "alnum") == 0) + BUILD_CHARCLASS_LOOP (isalnum); + else if (strcmp (name, "cntrl") == 0) + BUILD_CHARCLASS_LOOP (iscntrl); + else if (strcmp (name, "lower") == 0) + BUILD_CHARCLASS_LOOP (islower); + else if (strcmp (name, "space") == 0) + BUILD_CHARCLASS_LOOP (isspace); + else if (strcmp (name, "alpha") == 0) + BUILD_CHARCLASS_LOOP (isalpha); + else if (strcmp (name, "digit") == 0) + BUILD_CHARCLASS_LOOP (isdigit); + else if (strcmp (name, "print") == 0) + BUILD_CHARCLASS_LOOP (isprint); + else if (strcmp (name, "upper") == 0) + BUILD_CHARCLASS_LOOP (isupper); + else if (strcmp (name, "blank") == 0) + BUILD_CHARCLASS_LOOP (isblank); + else if (strcmp (name, "graph") == 0) + BUILD_CHARCLASS_LOOP (isgraph); + else if (strcmp (name, "punct") == 0) + BUILD_CHARCLASS_LOOP (ispunct); + else if (strcmp (name, "xdigit") == 0) + BUILD_CHARCLASS_LOOP (isxdigit); + else + return REG_ECTYPE; + + return REG_NOERROR; +} + +static bin_tree_t * +build_charclass_op (re_dfa_t *dfa, RE_TRANSLATE_TYPE trans, + const unsigned char *class_name, + const unsigned char *extra, int non_match, + reg_errcode_t *err) +{ + re_bitset_ptr_t sbcset; +#ifdef RE_ENABLE_I18N + re_charset_t *mbcset; + int alloc = 0; +#endif /* not RE_ENABLE_I18N */ + reg_errcode_t ret; + re_token_t br_token; + bin_tree_t *tree; + + sbcset = (re_bitset_ptr_t) calloc (sizeof (bitset_t), 1); +#ifdef RE_ENABLE_I18N + mbcset = (re_charset_t *) calloc (sizeof (re_charset_t), 1); +#endif /* RE_ENABLE_I18N */ + +#ifdef RE_ENABLE_I18N + if (BE (sbcset == NULL || mbcset == NULL, 0)) +#else /* not RE_ENABLE_I18N */ + if (BE (sbcset == NULL, 0)) +#endif /* not RE_ENABLE_I18N */ + { + *err = REG_ESPACE; + return NULL; + } + + if (non_match) + { +#ifdef RE_ENABLE_I18N + /* + if (syntax & RE_HAT_LISTS_NOT_NEWLINE) + bitset_set(cset->sbcset, '\0'); + */ + mbcset->non_match = 1; +#endif /* not RE_ENABLE_I18N */ + } + + /* We don't care the syntax in this case. */ + ret = build_charclass (trans, sbcset, +#ifdef RE_ENABLE_I18N + mbcset, &alloc, +#endif /* RE_ENABLE_I18N */ + class_name, 0); + + if (BE (ret != REG_NOERROR, 0)) + { + re_free (sbcset); +#ifdef RE_ENABLE_I18N + free_charset (mbcset); +#endif /* RE_ENABLE_I18N */ + *err = ret; + return NULL; + } + /* \w match '_' also. */ + for (; *extra; extra++) + bitset_set (sbcset, *extra); + + /* If it is non-matching list. */ + if (non_match) + bitset_not (sbcset); + +#ifdef RE_ENABLE_I18N + /* Ensure only single byte characters are set. */ + if (dfa->mb_cur_max > 1) + bitset_mask (sbcset, dfa->sb_char); +#endif + + /* Build a tree for simple bracket. */ + br_token.type = SIMPLE_BRACKET; + br_token.opr.sbcset = sbcset; + tree = create_token_tree (dfa, NULL, NULL, &br_token); + if (BE (tree == NULL, 0)) + goto build_word_op_espace; + +#ifdef RE_ENABLE_I18N + if (dfa->mb_cur_max > 1) + { + bin_tree_t *mbc_tree; + /* Build a tree for complex bracket. */ + br_token.type = COMPLEX_BRACKET; + br_token.opr.mbcset = mbcset; + dfa->has_mb_node = 1; + mbc_tree = create_token_tree (dfa, NULL, NULL, &br_token); + if (BE (mbc_tree == NULL, 0)) + goto build_word_op_espace; + /* Then join them by ALT node. */ + tree = create_tree (dfa, tree, mbc_tree, OP_ALT); + if (BE (mbc_tree != NULL, 1)) + return tree; + } + else + { + free_charset (mbcset); + return tree; + } +#else /* not RE_ENABLE_I18N */ + return tree; +#endif /* not RE_ENABLE_I18N */ + + build_word_op_espace: + re_free (sbcset); +#ifdef RE_ENABLE_I18N + free_charset (mbcset); +#endif /* RE_ENABLE_I18N */ + *err = REG_ESPACE; + return NULL; +} + +/* This is intended for the expressions like "a{1,3}". + Fetch a number from `input', and return the number. + Return -1, if the number field is empty like "{,1}". + Return -2, If an error is occured. */ + +static int +fetch_number (re_string_t *input, re_token_t *token, reg_syntax_t syntax) +{ + int num = -1; + unsigned char c; + while (1) + { + fetch_token (token, input, syntax); + c = token->opr.c; + if (BE (token->type == END_OF_RE, 0)) + return -2; + if (token->type == OP_CLOSE_DUP_NUM || c == ',') + break; + num = ((token->type != CHARACTER || c < '0' || '9' < c || num == -2) + ? -2 : ((num == -1) ? c - '0' : num * 10 + c - '0')); + num = (num > RE_DUP_MAX) ? -2 : num; + } + return num; +} + +#ifdef RE_ENABLE_I18N +static void +free_charset (re_charset_t *cset) +{ + re_free (cset->mbchars); +# ifdef _LIBC + re_free (cset->coll_syms); + re_free (cset->equiv_classes); + re_free (cset->range_starts); + re_free (cset->range_ends); +# endif + re_free (cset->char_classes); + re_free (cset); +} +#endif /* RE_ENABLE_I18N */ + +/* Functions for binary tree operation. */ + +/* Create a tree node. */ + +static bin_tree_t * +create_tree (re_dfa_t *dfa, bin_tree_t *left, bin_tree_t *right, + re_token_type_t type) +{ + re_token_t t; + t.type = type; + return create_token_tree (dfa, left, right, &t); +} + +static bin_tree_t * +create_token_tree (re_dfa_t *dfa, bin_tree_t *left, bin_tree_t *right, + const re_token_t *token) +{ + bin_tree_t *tree; + if (BE (dfa->str_tree_storage_idx == BIN_TREE_STORAGE_SIZE, 0)) + { + bin_tree_storage_t *storage = re_malloc (bin_tree_storage_t, 1); + + if (storage == NULL) + return NULL; + storage->next = dfa->str_tree_storage; + dfa->str_tree_storage = storage; + dfa->str_tree_storage_idx = 0; + } + tree = &dfa->str_tree_storage->data[dfa->str_tree_storage_idx++]; + + tree->parent = NULL; + tree->left = left; + tree->right = right; + tree->token = *token; + tree->token.duplicated = 0; + tree->token.opt_subexp = 0; + tree->first = NULL; + tree->next = NULL; + tree->node_idx = -1; + + if (left != NULL) + left->parent = tree; + if (right != NULL) + right->parent = tree; + return tree; +} + +/* Mark the tree SRC as an optional subexpression. + To be called from preorder or postorder. */ + +static reg_errcode_t +mark_opt_subexp (void *extra, bin_tree_t *node) +{ + int idx = (int) (long) extra; + if (node->token.type == SUBEXP && node->token.opr.idx == idx) + node->token.opt_subexp = 1; + + return REG_NOERROR; +} + +/* Free the allocated memory inside NODE. */ + +static void +free_token (re_token_t *node) +{ +#ifdef RE_ENABLE_I18N + if (node->type == COMPLEX_BRACKET && node->duplicated == 0) + free_charset (node->opr.mbcset); + else +#endif /* RE_ENABLE_I18N */ + if (node->type == SIMPLE_BRACKET && node->duplicated == 0) + re_free (node->opr.sbcset); +} + +/* Worker function for tree walking. Free the allocated memory inside NODE + and its children. */ + +static reg_errcode_t +free_tree (void *extra, bin_tree_t *node) +{ + free_token (&node->token); + return REG_NOERROR; +} + + +/* Duplicate the node SRC, and return new node. This is a preorder + visit similar to the one implemented by the generic visitor, but + we need more infrastructure to maintain two parallel trees --- so, + it's easier to duplicate. */ + +static bin_tree_t * +duplicate_tree (const bin_tree_t *root, re_dfa_t *dfa) +{ + const bin_tree_t *node; + bin_tree_t *dup_root; + bin_tree_t **p_new = &dup_root, *dup_node = root->parent; + + for (node = root; ; ) + { + /* Create a new tree and link it back to the current parent. */ + *p_new = create_token_tree (dfa, NULL, NULL, &node->token); + if (*p_new == NULL) + return NULL; + (*p_new)->parent = dup_node; + (*p_new)->token.duplicated = 1; + dup_node = *p_new; + + /* Go to the left node, or up and to the right. */ + if (node->left) + { + node = node->left; + p_new = &dup_node->left; + } + else + { + const bin_tree_t *prev = NULL; + while (node->right == prev || node->right == NULL) + { + prev = node; + node = node->parent; + dup_node = dup_node->parent; + if (!node) + return dup_root; + } + node = node->right; + p_new = &dup_node->right; + } + } +} + +/******************************************************************************/ +/******************************************************************************/ +/******************************************************************************/ +/* GKINCLUDE #include "regexec.c" */ +/******************************************************************************/ +/******************************************************************************/ +/******************************************************************************/ +static reg_errcode_t match_ctx_init (re_match_context_t *cache, int eflags, + int n) internal_function; +static void match_ctx_clean (re_match_context_t *mctx) internal_function; +static void match_ctx_free (re_match_context_t *cache) internal_function; +static reg_errcode_t match_ctx_add_entry (re_match_context_t *cache, int node, + int str_idx, int from, int to) + internal_function; +static int search_cur_bkref_entry (const re_match_context_t *mctx, int str_idx) + internal_function; +static reg_errcode_t match_ctx_add_subtop (re_match_context_t *mctx, int node, + int str_idx) internal_function; +static re_sub_match_last_t * match_ctx_add_sublast (re_sub_match_top_t *subtop, + int node, int str_idx) + internal_function; +static void sift_ctx_init (re_sift_context_t *sctx, re_dfastate_t **sifted_sts, + re_dfastate_t **limited_sts, int last_node, + int last_str_idx) + internal_function; +static reg_errcode_t re_search_internal (const regex_t *preg, + const char *string, int length, + int start, int range, int stop, + size_t nmatch, regmatch_t pmatch[], + int eflags) internal_function; +static int re_search_2_stub (struct re_pattern_buffer *bufp, + const char *string1, int length1, + const char *string2, int length2, + int start, int range, struct re_registers *regs, + int stop, int ret_len) internal_function; +static int re_search_stub (struct re_pattern_buffer *bufp, + const char *string, int length, int start, + int range, int stop, struct re_registers *regs, + int ret_len) internal_function; +static unsigned re_copy_regs (struct re_registers *regs, regmatch_t *pmatch, + int nregs, int regs_allocated) internal_function; +static reg_errcode_t prune_impossible_nodes (re_match_context_t *mctx) + internal_function; +static int check_matching (re_match_context_t *mctx, int fl_longest_match, + int *p_match_first) internal_function; +static int check_halt_state_context (const re_match_context_t *mctx, + const re_dfastate_t *state, int idx) + internal_function; +static void update_regs (const re_dfa_t *dfa, regmatch_t *pmatch, + regmatch_t *prev_idx_match, int cur_node, + int cur_idx, int nmatch) internal_function; +static reg_errcode_t push_fail_stack (struct re_fail_stack_t *fs, + int str_idx, int dest_node, int nregs, + regmatch_t *regs, + re_node_set *eps_via_nodes) + internal_function; +static reg_errcode_t set_regs (const regex_t *preg, + const re_match_context_t *mctx, + size_t nmatch, regmatch_t *pmatch, + int fl_backtrack) internal_function; +static reg_errcode_t free_fail_stack_return (struct re_fail_stack_t *fs) + internal_function; + +#ifdef RE_ENABLE_I18N +static int sift_states_iter_mb (const re_match_context_t *mctx, + re_sift_context_t *sctx, + int node_idx, int str_idx, int max_str_idx) + internal_function; +#endif /* RE_ENABLE_I18N */ +static reg_errcode_t sift_states_backward (const re_match_context_t *mctx, + re_sift_context_t *sctx) + internal_function; +static reg_errcode_t build_sifted_states (const re_match_context_t *mctx, + re_sift_context_t *sctx, int str_idx, + re_node_set *cur_dest) + internal_function; +static reg_errcode_t update_cur_sifted_state (const re_match_context_t *mctx, + re_sift_context_t *sctx, + int str_idx, + re_node_set *dest_nodes) + internal_function; +static reg_errcode_t add_epsilon_src_nodes (const re_dfa_t *dfa, + re_node_set *dest_nodes, + const re_node_set *candidates) + internal_function; +static int check_dst_limits (const re_match_context_t *mctx, + re_node_set *limits, + int dst_node, int dst_idx, int src_node, + int src_idx) internal_function; +static int check_dst_limits_calc_pos_1 (const re_match_context_t *mctx, + int boundaries, int subexp_idx, + int from_node, int bkref_idx) + internal_function; +static int check_dst_limits_calc_pos (const re_match_context_t *mctx, + int limit, int subexp_idx, + int node, int str_idx, + int bkref_idx) internal_function; +static reg_errcode_t check_subexp_limits (const re_dfa_t *dfa, + re_node_set *dest_nodes, + const re_node_set *candidates, + re_node_set *limits, + struct re_backref_cache_entry *bkref_ents, + int str_idx) internal_function; +static reg_errcode_t sift_states_bkref (const re_match_context_t *mctx, + re_sift_context_t *sctx, + int str_idx, const re_node_set *candidates) + internal_function; +static reg_errcode_t merge_state_array (const re_dfa_t *dfa, + re_dfastate_t **dst, + re_dfastate_t **src, int num) + internal_function; +static re_dfastate_t *find_recover_state (reg_errcode_t *err, + re_match_context_t *mctx) internal_function; +static re_dfastate_t *transit_state (reg_errcode_t *err, + re_match_context_t *mctx, + re_dfastate_t *state) internal_function; +static re_dfastate_t *merge_state_with_log (reg_errcode_t *err, + re_match_context_t *mctx, + re_dfastate_t *next_state) + internal_function; +static reg_errcode_t check_subexp_matching_top (re_match_context_t *mctx, + re_node_set *cur_nodes, + int str_idx) internal_function; +#if 0 +static re_dfastate_t *transit_state_sb (reg_errcode_t *err, + re_match_context_t *mctx, + re_dfastate_t *pstate) + internal_function; +#endif +#ifdef RE_ENABLE_I18N +static reg_errcode_t transit_state_mb (re_match_context_t *mctx, + re_dfastate_t *pstate) + internal_function; +#endif /* RE_ENABLE_I18N */ +static reg_errcode_t transit_state_bkref (re_match_context_t *mctx, + const re_node_set *nodes) + internal_function; +static reg_errcode_t get_subexp (re_match_context_t *mctx, + int bkref_node, int bkref_str_idx) + internal_function; +static reg_errcode_t get_subexp_sub (re_match_context_t *mctx, + const re_sub_match_top_t *sub_top, + re_sub_match_last_t *sub_last, + int bkref_node, int bkref_str) + internal_function; +static int find_subexp_node (const re_dfa_t *dfa, const re_node_set *nodes, + int subexp_idx, int type) internal_function; +static reg_errcode_t check_arrival (re_match_context_t *mctx, + state_array_t *path, int top_node, + int top_str, int last_node, int last_str, + int type) internal_function; +static reg_errcode_t check_arrival_add_next_nodes (re_match_context_t *mctx, + int str_idx, + re_node_set *cur_nodes, + re_node_set *next_nodes) + internal_function; +static reg_errcode_t check_arrival_expand_ecl (const re_dfa_t *dfa, + re_node_set *cur_nodes, + int ex_subexp, int type) + internal_function; +static reg_errcode_t check_arrival_expand_ecl_sub (const re_dfa_t *dfa, + re_node_set *dst_nodes, + int target, int ex_subexp, + int type) internal_function; +static reg_errcode_t expand_bkref_cache (re_match_context_t *mctx, + re_node_set *cur_nodes, int cur_str, + int subexp_num, int type) + internal_function; +static int build_trtable (const re_dfa_t *dfa, + re_dfastate_t *state) internal_function; +#ifdef RE_ENABLE_I18N +static int check_node_accept_bytes (const re_dfa_t *dfa, int node_idx, + const re_string_t *input, int idx) + internal_function; +# ifdef _LIBC +static unsigned int find_collation_sequence_value (const unsigned char *mbs, + size_t name_len) + internal_function; +# endif /* _LIBC */ +#endif /* RE_ENABLE_I18N */ +static int group_nodes_into_DFAstates (const re_dfa_t *dfa, + const re_dfastate_t *state, + re_node_set *states_node, + bitset_t *states_ch) internal_function; +static int check_node_accept (const re_match_context_t *mctx, + const re_token_t *node, int idx) + internal_function; +static reg_errcode_t extend_buffers (re_match_context_t *mctx) + internal_function; + +/* Entry point for POSIX code. */ + +/* regexec searches for a given pattern, specified by PREG, in the + string STRING. + + If NMATCH is zero or REG_NOSUB was set in the cflags argument to + `regcomp', we ignore PMATCH. Otherwise, we assume PMATCH has at + least NMATCH elements, and we set them to the offsets of the + corresponding matched substrings. + + EFLAGS specifies `execution flags' which affect matching: if + REG_NOTBOL is set, then ^ does not match at the beginning of the + string; if REG_NOTEOL is set, then $ does not match at the end. + + We return 0 if we find a match and REG_NOMATCH if not. */ + +int +regexec (preg, string, nmatch, pmatch, eflags) + const regex_t *__restrict preg; + const char *__restrict string; + size_t nmatch; + regmatch_t pmatch[]; + int eflags; +{ + reg_errcode_t err; + int start, length; + re_dfa_t *dfa = (re_dfa_t *) preg->buffer; + + if (eflags & ~(REG_NOTBOL | REG_NOTEOL | REG_STARTEND)) + return REG_BADPAT; + + if (eflags & REG_STARTEND) + { + start = pmatch[0].rm_so; + length = pmatch[0].rm_eo; + } + else + { + start = 0; + length = strlen (string); + } + + __libc_lock_lock (dfa->lock); + if (preg->no_sub) + err = re_search_internal (preg, string, length, start, length - start, + length, 0, NULL, eflags); + else + err = re_search_internal (preg, string, length, start, length - start, + length, nmatch, pmatch, eflags); + __libc_lock_unlock (dfa->lock); + return err != REG_NOERROR; +} + +#ifdef _LIBC +# include +versioned_symbol (libc, __regexec, regexec, GLIBC_2_3_4); + +# if SHLIB_COMPAT (libc, GLIBC_2_0, GLIBC_2_3_4) +__typeof__ (__regexec) __compat_regexec; + +int +attribute_compat_text_section +__compat_regexec (const regex_t *__restrict preg, + const char *__restrict string, size_t nmatch, + regmatch_t pmatch[], int eflags) +{ + return regexec (preg, string, nmatch, pmatch, + eflags & (REG_NOTBOL | REG_NOTEOL)); +} +compat_symbol (libc, __compat_regexec, regexec, GLIBC_2_0); +# endif +#endif + +/* Entry points for GNU code. */ + +/* re_match, re_search, re_match_2, re_search_2 + + The former two functions operate on STRING with length LENGTH, + while the later two operate on concatenation of STRING1 and STRING2 + with lengths LENGTH1 and LENGTH2, respectively. + + re_match() matches the compiled pattern in BUFP against the string, + starting at index START. + + re_search() first tries matching at index START, then it tries to match + starting from index START + 1, and so on. The last start position tried + is START + RANGE. (Thus RANGE = 0 forces re_search to operate the same + way as re_match().) + + The parameter STOP of re_{match,search}_2 specifies that no match exceeding + the first STOP characters of the concatenation of the strings should be + concerned. + + If REGS is not NULL, and BUFP->no_sub is not set, the offsets of the match + and all groups is stroed in REGS. (For the "_2" variants, the offsets are + computed relative to the concatenation, not relative to the individual + strings.) + + On success, re_match* functions return the length of the match, re_search* + return the position of the start of the match. Return value -1 means no + match was found and -2 indicates an internal error. */ + +int +re_match (bufp, string, length, start, regs) + struct re_pattern_buffer *bufp; + const char *string; + int length, start; + struct re_registers *regs; +{ + return re_search_stub (bufp, string, length, start, 0, length, regs, 1); +} +#ifdef _LIBC +weak_alias (__re_match, re_match) +#endif + +int +re_search (bufp, string, length, start, range, regs) + struct re_pattern_buffer *bufp; + const char *string; + int length, start, range; + struct re_registers *regs; +{ + return re_search_stub (bufp, string, length, start, range, length, regs, 0); +} +#ifdef _LIBC +weak_alias (__re_search, re_search) +#endif + +int +re_match_2 (bufp, string1, length1, string2, length2, start, regs, stop) + struct re_pattern_buffer *bufp; + const char *string1, *string2; + int length1, length2, start, stop; + struct re_registers *regs; +{ + return re_search_2_stub (bufp, string1, length1, string2, length2, + start, 0, regs, stop, 1); +} +#ifdef _LIBC +weak_alias (__re_match_2, re_match_2) +#endif + +int +re_search_2 (bufp, string1, length1, string2, length2, start, range, regs, stop) + struct re_pattern_buffer *bufp; + const char *string1, *string2; + int length1, length2, start, range, stop; + struct re_registers *regs; +{ + return re_search_2_stub (bufp, string1, length1, string2, length2, + start, range, regs, stop, 0); +} +#ifdef _LIBC +weak_alias (__re_search_2, re_search_2) +#endif + +static int +re_search_2_stub (bufp, string1, length1, string2, length2, start, range, regs, + stop, ret_len) + struct re_pattern_buffer *bufp; + const char *string1, *string2; + int length1, length2, start, range, stop, ret_len; + struct re_registers *regs; +{ + const char *str; + int rval; + int len = length1 + length2; + int free_str = 0; + + if (BE (length1 < 0 || length2 < 0 || stop < 0, 0)) + return -2; + + /* Concatenate the strings. */ + if (length2 > 0) + if (length1 > 0) + { + char *s = re_malloc (char, len); + + if (BE (s == NULL, 0)) + return -2; +#ifdef _LIBC + memcpy (__mempcpy (s, string1, length1), string2, length2); +#else + memcpy (s, string1, length1); + memcpy (s + length1, string2, length2); +#endif + str = s; + free_str = 1; + } + else + str = string2; + else + str = string1; + + rval = re_search_stub (bufp, str, len, start, range, stop, regs, + ret_len); + if (free_str) + re_free ((char *) str); + return rval; +} + +/* The parameters have the same meaning as those of re_search. + Additional parameters: + If RET_LEN is nonzero the length of the match is returned (re_match style); + otherwise the position of the match is returned. */ + +static int +re_search_stub (bufp, string, length, start, range, stop, regs, ret_len) + struct re_pattern_buffer *bufp; + const char *string; + int length, start, range, stop, ret_len; + struct re_registers *regs; +{ + reg_errcode_t result; + regmatch_t *pmatch; + int nregs, rval; + int eflags = 0; + re_dfa_t *dfa = (re_dfa_t *) bufp->buffer; + + /* Check for out-of-range. */ + if (BE (start < 0 || start > length, 0)) + return -1; + if (BE (start + range > length, 0)) + range = length - start; + else if (BE (start + range < 0, 0)) + range = -start; + + __libc_lock_lock (dfa->lock); + + eflags |= (bufp->not_bol) ? REG_NOTBOL : 0; + eflags |= (bufp->not_eol) ? REG_NOTEOL : 0; + + /* Compile fastmap if we haven't yet. */ + if (range > 0 && bufp->fastmap != NULL && !bufp->fastmap_accurate) + re_compile_fastmap (bufp); + + if (BE (bufp->no_sub, 0)) + regs = NULL; + + /* We need at least 1 register. */ + if (regs == NULL) + nregs = 1; + else if (BE (bufp->regs_allocated == REGS_FIXED && + regs->num_regs < bufp->re_nsub + 1, 0)) + { + nregs = regs->num_regs; + if (BE (nregs < 1, 0)) + { + /* Nothing can be copied to regs. */ + regs = NULL; + nregs = 1; + } + } + else + nregs = bufp->re_nsub + 1; + pmatch = re_malloc (regmatch_t, nregs); + if (BE (pmatch == NULL, 0)) + { + rval = -2; + goto out; + } + + result = re_search_internal (bufp, string, length, start, range, stop, + nregs, pmatch, eflags); + + rval = 0; + + /* I hope we needn't fill ther regs with -1's when no match was found. */ + if (result != REG_NOERROR) + rval = -1; + else if (regs != NULL) + { + /* If caller wants register contents data back, copy them. */ + bufp->regs_allocated = re_copy_regs (regs, pmatch, nregs, + bufp->regs_allocated); + if (BE (bufp->regs_allocated == REGS_UNALLOCATED, 0)) + rval = -2; + } + + if (BE (rval == 0, 1)) + { + if (ret_len) + { + assert (pmatch[0].rm_so == start); + rval = pmatch[0].rm_eo - start; + } + else + rval = pmatch[0].rm_so; + } + re_free (pmatch); + out: + __libc_lock_unlock (dfa->lock); + return rval; +} + +static unsigned +re_copy_regs (regs, pmatch, nregs, regs_allocated) + struct re_registers *regs; + regmatch_t *pmatch; + int nregs, regs_allocated; +{ + int rval = REGS_REALLOCATE; + int i; + int need_regs = nregs + 1; + /* We need one extra element beyond `num_regs' for the `-1' marker GNU code + uses. */ + + /* Have the register data arrays been allocated? */ + if (regs_allocated == REGS_UNALLOCATED) + { /* No. So allocate them with malloc. */ + regs->start = re_malloc (regoff_t, need_regs); + regs->end = re_malloc (regoff_t, need_regs); + if (BE (regs->start == NULL, 0) || BE (regs->end == NULL, 0)) + return REGS_UNALLOCATED; + regs->num_regs = need_regs; + } + else if (regs_allocated == REGS_REALLOCATE) + { /* Yes. If we need more elements than were already + allocated, reallocate them. If we need fewer, just + leave it alone. */ + if (BE (need_regs > regs->num_regs, 0)) + { + regoff_t *new_start = re_realloc (regs->start, regoff_t, need_regs); + regoff_t *new_end = re_realloc (regs->end, regoff_t, need_regs); + if (BE (new_start == NULL, 0) || BE (new_end == NULL, 0)) + return REGS_UNALLOCATED; + regs->start = new_start; + regs->end = new_end; + regs->num_regs = need_regs; + } + } + else + { + assert (regs_allocated == REGS_FIXED); + /* This function may not be called with REGS_FIXED and nregs too big. */ + assert (regs->num_regs >= nregs); + rval = REGS_FIXED; + } + + /* Copy the regs. */ + for (i = 0; i < nregs; ++i) + { + regs->start[i] = pmatch[i].rm_so; + regs->end[i] = pmatch[i].rm_eo; + } + for ( ; i < regs->num_regs; ++i) + regs->start[i] = regs->end[i] = -1; + + return rval; +} + +/* Set REGS to hold NUM_REGS registers, storing them in STARTS and + ENDS. Subsequent matches using PATTERN_BUFFER and REGS will use + this memory for recording register information. STARTS and ENDS + must be allocated using the malloc library routine, and must each + be at least NUM_REGS * sizeof (regoff_t) bytes long. + + If NUM_REGS == 0, then subsequent matches should allocate their own + register data. + + Unless this function is called, the first search or match using + PATTERN_BUFFER will allocate its own register data, without + freeing the old data. */ + +void +re_set_registers (bufp, regs, num_regs, starts, ends) + struct re_pattern_buffer *bufp; + struct re_registers *regs; + unsigned num_regs; + regoff_t *starts, *ends; +{ + if (num_regs) + { + bufp->regs_allocated = REGS_REALLOCATE; + regs->num_regs = num_regs; + regs->start = starts; + regs->end = ends; + } + else + { + bufp->regs_allocated = REGS_UNALLOCATED; + regs->num_regs = 0; + regs->start = regs->end = (regoff_t *) 0; + } +} +#ifdef _LIBC +weak_alias (__re_set_registers, re_set_registers) +#endif + +/* Entry points compatible with 4.2 BSD regex library. We don't define + them unless specifically requested. */ + +#if defined _REGEX_RE_COMP || defined _LIBC +int +# ifdef _LIBC +weak_function +# endif +re_exec (s) + const char *s; +{ + return 0 == regexec (&re_comp_buf, s, 0, NULL, 0); +} +#endif /* _REGEX_RE_COMP */ + +/* Internal entry point. */ + +/* Searches for a compiled pattern PREG in the string STRING, whose + length is LENGTH. NMATCH, PMATCH, and EFLAGS have the same + mingings with regexec. START, and RANGE have the same meanings + with re_search. + Return REG_NOERROR if we find a match, and REG_NOMATCH if not, + otherwise return the error code. + Note: We assume front end functions already check ranges. + (START + RANGE >= 0 && START + RANGE <= LENGTH) */ + +static reg_errcode_t +re_search_internal (preg, string, length, start, range, stop, nmatch, pmatch, + eflags) + const regex_t *preg; + const char *string; + int length, start, range, stop, eflags; + size_t nmatch; + regmatch_t pmatch[]; +{ + reg_errcode_t err; + const re_dfa_t *dfa = (const re_dfa_t *) preg->buffer; + int left_lim, right_lim, incr; + int fl_longest_match, match_first, match_kind, match_last = -1; + int extra_nmatch; + int sb, ch; +#if defined _LIBC || (defined __STDC_VERSION__ && __STDC_VERSION__ >= 199901L) + re_match_context_t mctx = { .dfa = dfa }; +#else + re_match_context_t mctx; +#endif + char *fastmap = (preg->fastmap != NULL && preg->fastmap_accurate + && range && !preg->can_be_null) ? preg->fastmap : NULL; + RE_TRANSLATE_TYPE t = preg->translate; + +#if !(defined _LIBC || (defined __STDC_VERSION__ && __STDC_VERSION__ >= 199901L)) + memset (&mctx, '\0', sizeof (re_match_context_t)); + mctx.dfa = dfa; +#endif + + extra_nmatch = (nmatch > preg->re_nsub) ? nmatch - (preg->re_nsub + 1) : 0; + nmatch -= extra_nmatch; + + /* Check if the DFA haven't been compiled. */ + if (BE (preg->used == 0 || dfa->init_state == NULL + || dfa->init_state_word == NULL || dfa->init_state_nl == NULL + || dfa->init_state_begbuf == NULL, 0)) + return REG_NOMATCH; + +#ifdef DEBUG + /* We assume front-end functions already check them. */ + assert (start + range >= 0 && start + range <= length); +#endif + + /* If initial states with non-begbuf contexts have no elements, + the regex must be anchored. If preg->newline_anchor is set, + we'll never use init_state_nl, so do not check it. */ + if (dfa->init_state->nodes.nelem == 0 + && dfa->init_state_word->nodes.nelem == 0 + && (dfa->init_state_nl->nodes.nelem == 0 + || !preg->newline_anchor)) + { + if (start != 0 && start + range != 0) + return REG_NOMATCH; + start = range = 0; + } + + /* We must check the longest matching, if nmatch > 0. */ + fl_longest_match = (nmatch != 0 || dfa->nbackref); + + err = re_string_allocate (&mctx.input, string, length, dfa->nodes_len + 1, + preg->translate, preg->syntax & RE_ICASE, dfa); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + mctx.input.stop = stop; + mctx.input.raw_stop = stop; + mctx.input.newline_anchor = preg->newline_anchor; + + err = match_ctx_init (&mctx, eflags, dfa->nbackref * 2); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + + /* We will log all the DFA states through which the dfa pass, + if nmatch > 1, or this dfa has "multibyte node", which is a + back-reference or a node which can accept multibyte character or + multi character collating element. */ + if (nmatch > 1 || dfa->has_mb_node) + { + mctx.state_log = re_malloc (re_dfastate_t *, mctx.input.bufs_len + 1); + if (BE (mctx.state_log == NULL, 0)) + { + err = REG_ESPACE; + goto free_return; + } + } + else + mctx.state_log = NULL; + + match_first = start; + mctx.input.tip_context = (eflags & REG_NOTBOL) ? CONTEXT_BEGBUF + : CONTEXT_NEWLINE | CONTEXT_BEGBUF; + + /* Check incrementally whether of not the input string match. */ + incr = (range < 0) ? -1 : 1; + left_lim = (range < 0) ? start + range : start; + right_lim = (range < 0) ? start : start + range; + sb = dfa->mb_cur_max == 1; + match_kind = + (fastmap + ? ((sb || !(preg->syntax & RE_ICASE || t) ? 4 : 0) + | (range >= 0 ? 2 : 0) + | (t != NULL ? 1 : 0)) + : 8); + + for (;; match_first += incr) + { + err = REG_NOMATCH; + if (match_first < left_lim || right_lim < match_first) + goto free_return; + + /* Advance as rapidly as possible through the string, until we + find a plausible place to start matching. This may be done + with varying efficiency, so there are various possibilities: + only the most common of them are specialized, in order to + save on code size. We use a switch statement for speed. */ + switch (match_kind) + { + case 8: + /* No fastmap. */ + break; + + case 7: + /* Fastmap with single-byte translation, match forward. */ + while (BE (match_first < right_lim, 1) + && !fastmap[t[(unsigned char) string[match_first]]]) + ++match_first; + goto forward_match_found_start_or_reached_end; + + case 6: + /* Fastmap without translation, match forward. */ + while (BE (match_first < right_lim, 1) + && !fastmap[(unsigned char) string[match_first]]) + ++match_first; + + forward_match_found_start_or_reached_end: + if (BE (match_first == right_lim, 0)) + { + ch = match_first >= length + ? 0 : (unsigned char) string[match_first]; + if (!fastmap[t ? t[ch] : ch]) + goto free_return; + } + break; + + case 4: + case 5: + /* Fastmap without multi-byte translation, match backwards. */ + while (match_first >= left_lim) + { + ch = match_first >= length + ? 0 : (unsigned char) string[match_first]; + if (fastmap[t ? t[ch] : ch]) + break; + --match_first; + } + if (match_first < left_lim) + goto free_return; + break; + + default: + /* In this case, we can't determine easily the current byte, + since it might be a component byte of a multibyte + character. Then we use the constructed buffer instead. */ + for (;;) + { + /* If MATCH_FIRST is out of the valid range, reconstruct the + buffers. */ + unsigned int offset = match_first - mctx.input.raw_mbs_idx; + if (BE (offset >= (unsigned int) mctx.input.valid_raw_len, 0)) + { + err = re_string_reconstruct (&mctx.input, match_first, + eflags); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + + offset = match_first - mctx.input.raw_mbs_idx; + } + /* If MATCH_FIRST is out of the buffer, leave it as '\0'. + Note that MATCH_FIRST must not be smaller than 0. */ + ch = (match_first >= length + ? 0 : re_string_byte_at (&mctx.input, offset)); + if (fastmap[ch]) + break; + match_first += incr; + if (match_first < left_lim || match_first > right_lim) + { + err = REG_NOMATCH; + goto free_return; + } + } + break; + } + + /* Reconstruct the buffers so that the matcher can assume that + the matching starts from the beginning of the buffer. */ + err = re_string_reconstruct (&mctx.input, match_first, eflags); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + +#ifdef RE_ENABLE_I18N + /* Don't consider this char as a possible match start if it part, + yet isn't the head, of a multibyte character. */ + if (!sb && !re_string_first_byte (&mctx.input, 0)) + continue; +#endif + + /* It seems to be appropriate one, then use the matcher. */ + /* We assume that the matching starts from 0. */ + mctx.state_log_top = mctx.nbkref_ents = mctx.max_mb_elem_len = 0; + match_last = check_matching (&mctx, fl_longest_match, + range >= 0 ? &match_first : NULL); + if (match_last != -1) + { + if (BE (match_last == -2, 0)) + { + err = REG_ESPACE; + goto free_return; + } + else + { + mctx.match_last = match_last; + if ((!preg->no_sub && nmatch > 1) || dfa->nbackref) + { + re_dfastate_t *pstate = mctx.state_log[match_last]; + mctx.last_node = check_halt_state_context (&mctx, pstate, + match_last); + } + if ((!preg->no_sub && nmatch > 1 && dfa->has_plural_match) + || dfa->nbackref) + { + err = prune_impossible_nodes (&mctx); + if (err == REG_NOERROR) + break; + if (BE (err != REG_NOMATCH, 0)) + goto free_return; + match_last = -1; + } + else + break; /* We found a match. */ + } + } + + match_ctx_clean (&mctx); + } + +#ifdef DEBUG + assert (match_last != -1); + assert (err == REG_NOERROR); +#endif + + /* Set pmatch[] if we need. */ + if (nmatch > 0) + { + int reg_idx; + + /* Initialize registers. */ + for (reg_idx = 1; reg_idx < nmatch; ++reg_idx) + pmatch[reg_idx].rm_so = pmatch[reg_idx].rm_eo = -1; + + /* Set the points where matching start/end. */ + pmatch[0].rm_so = 0; + pmatch[0].rm_eo = mctx.match_last; + + if (!preg->no_sub && nmatch > 1) + { + err = set_regs (preg, &mctx, nmatch, pmatch, + dfa->has_plural_match && dfa->nbackref > 0); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + } + + /* At last, add the offset to the each registers, since we slided + the buffers so that we could assume that the matching starts + from 0. */ + for (reg_idx = 0; reg_idx < nmatch; ++reg_idx) + if (pmatch[reg_idx].rm_so != -1) + { +#ifdef RE_ENABLE_I18N + if (BE (mctx.input.offsets_needed != 0, 0)) + { + pmatch[reg_idx].rm_so = + (pmatch[reg_idx].rm_so == mctx.input.valid_len + ? mctx.input.valid_raw_len + : mctx.input.offsets[pmatch[reg_idx].rm_so]); + pmatch[reg_idx].rm_eo = + (pmatch[reg_idx].rm_eo == mctx.input.valid_len + ? mctx.input.valid_raw_len + : mctx.input.offsets[pmatch[reg_idx].rm_eo]); + } +#else + assert (mctx.input.offsets_needed == 0); +#endif + pmatch[reg_idx].rm_so += match_first; + pmatch[reg_idx].rm_eo += match_first; + } + for (reg_idx = 0; reg_idx < extra_nmatch; ++reg_idx) + { + pmatch[nmatch + reg_idx].rm_so = -1; + pmatch[nmatch + reg_idx].rm_eo = -1; + } + + if (dfa->subexp_map) + for (reg_idx = 0; reg_idx + 1 < nmatch; reg_idx++) + if (dfa->subexp_map[reg_idx] != reg_idx) + { + pmatch[reg_idx + 1].rm_so + = pmatch[dfa->subexp_map[reg_idx] + 1].rm_so; + pmatch[reg_idx + 1].rm_eo + = pmatch[dfa->subexp_map[reg_idx] + 1].rm_eo; + } + } + + free_return: + re_free (mctx.state_log); + if (dfa->nbackref) + match_ctx_free (&mctx); + re_string_destruct (&mctx.input); + return err; +} + +static reg_errcode_t +prune_impossible_nodes (mctx) + re_match_context_t *mctx; +{ + const re_dfa_t *const dfa = mctx->dfa; + int halt_node, match_last; + reg_errcode_t ret; + re_dfastate_t **sifted_states; + re_dfastate_t **lim_states = NULL; + re_sift_context_t sctx; +#ifdef DEBUG + assert (mctx->state_log != NULL); +#endif + match_last = mctx->match_last; + halt_node = mctx->last_node; + sifted_states = re_malloc (re_dfastate_t *, match_last + 1); + if (BE (sifted_states == NULL, 0)) + { + ret = REG_ESPACE; + goto free_return; + } + if (dfa->nbackref) + { + lim_states = re_malloc (re_dfastate_t *, match_last + 1); + if (BE (lim_states == NULL, 0)) + { + ret = REG_ESPACE; + goto free_return; + } + while (1) + { + memset (lim_states, '\0', + sizeof (re_dfastate_t *) * (match_last + 1)); + sift_ctx_init (&sctx, sifted_states, lim_states, halt_node, + match_last); + ret = sift_states_backward (mctx, &sctx); + re_node_set_free (&sctx.limits); + if (BE (ret != REG_NOERROR, 0)) + goto free_return; + if (sifted_states[0] != NULL || lim_states[0] != NULL) + break; + do + { + --match_last; + if (match_last < 0) + { + ret = REG_NOMATCH; + goto free_return; + } + } while (mctx->state_log[match_last] == NULL + || !mctx->state_log[match_last]->halt); + halt_node = check_halt_state_context (mctx, + mctx->state_log[match_last], + match_last); + } + ret = merge_state_array (dfa, sifted_states, lim_states, + match_last + 1); + re_free (lim_states); + lim_states = NULL; + if (BE (ret != REG_NOERROR, 0)) + goto free_return; + } + else + { + sift_ctx_init (&sctx, sifted_states, lim_states, halt_node, match_last); + ret = sift_states_backward (mctx, &sctx); + re_node_set_free (&sctx.limits); + if (BE (ret != REG_NOERROR, 0)) + goto free_return; + } + re_free (mctx->state_log); + mctx->state_log = sifted_states; + sifted_states = NULL; + mctx->last_node = halt_node; + mctx->match_last = match_last; + ret = REG_NOERROR; + free_return: + re_free (sifted_states); + re_free (lim_states); + return ret; +} + +/* Acquire an initial state and return it. + We must select appropriate initial state depending on the context, + since initial states may have constraints like "\<", "^", etc.. */ + +static inline re_dfastate_t * +__attribute ((always_inline)) internal_function +acquire_init_state_context (reg_errcode_t *err, const re_match_context_t *mctx, + int idx) +{ + const re_dfa_t *const dfa = mctx->dfa; + if (dfa->init_state->has_constraint) + { + unsigned int context; + context = re_string_context_at (&mctx->input, idx - 1, mctx->eflags); + if (IS_WORD_CONTEXT (context)) + return dfa->init_state_word; + else if (IS_ORDINARY_CONTEXT (context)) + return dfa->init_state; + else if (IS_BEGBUF_CONTEXT (context) && IS_NEWLINE_CONTEXT (context)) + return dfa->init_state_begbuf; + else if (IS_NEWLINE_CONTEXT (context)) + return dfa->init_state_nl; + else if (IS_BEGBUF_CONTEXT (context)) + { + /* It is relatively rare case, then calculate on demand. */ + return re_acquire_state_context (err, dfa, + dfa->init_state->entrance_nodes, + context); + } + else + /* Must not happen? */ + return dfa->init_state; + } + else + return dfa->init_state; +} + +/* Check whether the regular expression match input string INPUT or not, + and return the index where the matching end, return -1 if not match, + or return -2 in case of an error. + FL_LONGEST_MATCH means we want the POSIX longest matching. + If P_MATCH_FIRST is not NULL, and the match fails, it is set to the + next place where we may want to try matching. + Note that the matcher assume that the maching starts from the current + index of the buffer. */ + +static int +internal_function +check_matching (re_match_context_t *mctx, int fl_longest_match, + int *p_match_first) +{ + const re_dfa_t *const dfa = mctx->dfa; + reg_errcode_t err; + int match = 0; + int match_last = -1; + int cur_str_idx = re_string_cur_idx (&mctx->input); + re_dfastate_t *cur_state; + int at_init_state = p_match_first != NULL; + int next_start_idx = cur_str_idx; + + err = REG_NOERROR; + cur_state = acquire_init_state_context (&err, mctx, cur_str_idx); + /* An initial state must not be NULL (invalid). */ + if (BE (cur_state == NULL, 0)) + { + assert (err == REG_ESPACE); + return -2; + } + + if (mctx->state_log != NULL) + { + mctx->state_log[cur_str_idx] = cur_state; + + /* Check OP_OPEN_SUBEXP in the initial state in case that we use them + later. E.g. Processing back references. */ + if (BE (dfa->nbackref, 0)) + { + at_init_state = 0; + err = check_subexp_matching_top (mctx, &cur_state->nodes, 0); + if (BE (err != REG_NOERROR, 0)) + return err; + + if (cur_state->has_backref) + { + err = transit_state_bkref (mctx, &cur_state->nodes); + if (BE (err != REG_NOERROR, 0)) + return err; + } + } + } + + /* If the RE accepts NULL string. */ + if (BE (cur_state->halt, 0)) + { + if (!cur_state->has_constraint + || check_halt_state_context (mctx, cur_state, cur_str_idx)) + { + if (!fl_longest_match) + return cur_str_idx; + else + { + match_last = cur_str_idx; + match = 1; + } + } + } + + while (!re_string_eoi (&mctx->input)) + { + re_dfastate_t *old_state = cur_state; + int next_char_idx = re_string_cur_idx (&mctx->input) + 1; + + if (BE (next_char_idx >= mctx->input.bufs_len, 0) + || (BE (next_char_idx >= mctx->input.valid_len, 0) + && mctx->input.valid_len < mctx->input.len)) + { + err = extend_buffers (mctx); + if (BE (err != REG_NOERROR, 0)) + { + assert (err == REG_ESPACE); + return -2; + } + } + + cur_state = transit_state (&err, mctx, cur_state); + if (mctx->state_log != NULL) + cur_state = merge_state_with_log (&err, mctx, cur_state); + + if (cur_state == NULL) + { + /* Reached the invalid state or an error. Try to recover a valid + state using the state log, if available and if we have not + already found a valid (even if not the longest) match. */ + if (BE (err != REG_NOERROR, 0)) + return -2; + + if (mctx->state_log == NULL + || (match && !fl_longest_match) + || (cur_state = find_recover_state (&err, mctx)) == NULL) + break; + } + + if (BE (at_init_state, 0)) + { + if (old_state == cur_state) + next_start_idx = next_char_idx; + else + at_init_state = 0; + } + + if (cur_state->halt) + { + /* Reached a halt state. + Check the halt state can satisfy the current context. */ + if (!cur_state->has_constraint + || check_halt_state_context (mctx, cur_state, + re_string_cur_idx (&mctx->input))) + { + /* We found an appropriate halt state. */ + match_last = re_string_cur_idx (&mctx->input); + match = 1; + + /* We found a match, do not modify match_first below. */ + p_match_first = NULL; + if (!fl_longest_match) + break; + } + } + } + + if (p_match_first) + *p_match_first += next_start_idx; + + return match_last; +} + +/* Check NODE match the current context. */ + +static int +internal_function +check_halt_node_context (const re_dfa_t *dfa, int node, unsigned int context) +{ + re_token_type_t type = dfa->nodes[node].type; + unsigned int constraint = dfa->nodes[node].constraint; + if (type != END_OF_RE) + return 0; + if (!constraint) + return 1; + if (NOT_SATISFY_NEXT_CONSTRAINT (constraint, context)) + return 0; + return 1; +} + +/* Check the halt state STATE match the current context. + Return 0 if not match, if the node, STATE has, is a halt node and + match the context, return the node. */ + +static int +internal_function +check_halt_state_context (const re_match_context_t *mctx, + const re_dfastate_t *state, int idx) +{ + int i; + unsigned int context; +#ifdef DEBUG + assert (state->halt); +#endif + context = re_string_context_at (&mctx->input, idx, mctx->eflags); + for (i = 0; i < state->nodes.nelem; ++i) + if (check_halt_node_context (mctx->dfa, state->nodes.elems[i], context)) + return state->nodes.elems[i]; + return 0; +} + +/* Compute the next node to which "NFA" transit from NODE("NFA" is a NFA + corresponding to the DFA). + Return the destination node, and update EPS_VIA_NODES, return -1 in case + of errors. */ + +static int +internal_function +proceed_next_node (const re_match_context_t *mctx, int nregs, regmatch_t *regs, + int *pidx, int node, re_node_set *eps_via_nodes, + struct re_fail_stack_t *fs) +{ + const re_dfa_t *const dfa = mctx->dfa; + int i, err; + if (IS_EPSILON_NODE (dfa->nodes[node].type)) + { + re_node_set *cur_nodes = &mctx->state_log[*pidx]->nodes; + re_node_set *edests = &dfa->edests[node]; + int dest_node; + err = re_node_set_insert (eps_via_nodes, node); + if (BE (err < 0, 0)) + return -2; + /* Pick up a valid destination, or return -1 if none is found. */ + for (dest_node = -1, i = 0; i < edests->nelem; ++i) + { + int candidate = edests->elems[i]; + if (!re_node_set_contains (cur_nodes, candidate)) + continue; + if (dest_node == -1) + dest_node = candidate; + + else + { + /* In order to avoid infinite loop like "(a*)*", return the second + epsilon-transition if the first was already considered. */ + if (re_node_set_contains (eps_via_nodes, dest_node)) + return candidate; + + /* Otherwise, push the second epsilon-transition on the fail stack. */ + else if (fs != NULL + && push_fail_stack (fs, *pidx, candidate, nregs, regs, + eps_via_nodes)) + return -2; + + /* We know we are going to exit. */ + break; + } + } + return dest_node; + } + else + { + int naccepted = 0; + re_token_type_t type = dfa->nodes[node].type; + +#ifdef RE_ENABLE_I18N + if (dfa->nodes[node].accept_mb) + naccepted = check_node_accept_bytes (dfa, node, &mctx->input, *pidx); + else +#endif /* RE_ENABLE_I18N */ + if (type == OP_BACK_REF) + { + int subexp_idx = dfa->nodes[node].opr.idx + 1; + naccepted = regs[subexp_idx].rm_eo - regs[subexp_idx].rm_so; + if (fs != NULL) + { + if (regs[subexp_idx].rm_so == -1 || regs[subexp_idx].rm_eo == -1) + return -1; + else if (naccepted) + { + char *buf = (char *) re_string_get_buffer (&mctx->input); + if (memcmp (buf + regs[subexp_idx].rm_so, buf + *pidx, + naccepted) != 0) + return -1; + } + } + + if (naccepted == 0) + { + int dest_node; + err = re_node_set_insert (eps_via_nodes, node); + if (BE (err < 0, 0)) + return -2; + dest_node = dfa->edests[node].elems[0]; + if (re_node_set_contains (&mctx->state_log[*pidx]->nodes, + dest_node)) + return dest_node; + } + } + + if (naccepted != 0 + || check_node_accept (mctx, dfa->nodes + node, *pidx)) + { + int dest_node = dfa->nexts[node]; + *pidx = (naccepted == 0) ? *pidx + 1 : *pidx + naccepted; + if (fs && (*pidx > mctx->match_last || mctx->state_log[*pidx] == NULL + || !re_node_set_contains (&mctx->state_log[*pidx]->nodes, + dest_node))) + return -1; + re_node_set_empty (eps_via_nodes); + return dest_node; + } + } + return -1; +} + +static reg_errcode_t +internal_function +push_fail_stack (struct re_fail_stack_t *fs, int str_idx, int dest_node, + int nregs, regmatch_t *regs, re_node_set *eps_via_nodes) +{ + reg_errcode_t err; + int num = fs->num++; + if (fs->num == fs->alloc) + { + struct re_fail_stack_ent_t *new_array; + new_array = realloc (fs->stack, (sizeof (struct re_fail_stack_ent_t) + * fs->alloc * 2)); + if (new_array == NULL) + return REG_ESPACE; + fs->alloc *= 2; + fs->stack = new_array; + } + fs->stack[num].idx = str_idx; + fs->stack[num].node = dest_node; + fs->stack[num].regs = re_malloc (regmatch_t, nregs); + if (fs->stack[num].regs == NULL) + return REG_ESPACE; + memcpy (fs->stack[num].regs, regs, sizeof (regmatch_t) * nregs); + err = re_node_set_init_copy (&fs->stack[num].eps_via_nodes, eps_via_nodes); + return err; +} + +static int +internal_function +pop_fail_stack (struct re_fail_stack_t *fs, int *pidx, int nregs, + regmatch_t *regs, re_node_set *eps_via_nodes) +{ + int num = --fs->num; + assert (num >= 0); + *pidx = fs->stack[num].idx; + memcpy (regs, fs->stack[num].regs, sizeof (regmatch_t) * nregs); + re_node_set_free (eps_via_nodes); + re_free (fs->stack[num].regs); + *eps_via_nodes = fs->stack[num].eps_via_nodes; + return fs->stack[num].node; +} + +/* Set the positions where the subexpressions are starts/ends to registers + PMATCH. + Note: We assume that pmatch[0] is already set, and + pmatch[i].rm_so == pmatch[i].rm_eo == -1 for 0 < i < nmatch. */ + +static reg_errcode_t +internal_function +set_regs (const regex_t *preg, const re_match_context_t *mctx, size_t nmatch, + regmatch_t *pmatch, int fl_backtrack) +{ + const re_dfa_t *dfa = (const re_dfa_t *) preg->buffer; + int idx, cur_node; + re_node_set eps_via_nodes; + struct re_fail_stack_t *fs; + struct re_fail_stack_t fs_body = { 0, 2, NULL }; + regmatch_t *prev_idx_match; + int prev_idx_match_malloced = 0; + +#ifdef DEBUG + assert (nmatch > 1); + assert (mctx->state_log != NULL); +#endif + if (fl_backtrack) + { + fs = &fs_body; + fs->stack = re_malloc (struct re_fail_stack_ent_t, fs->alloc); + if (fs->stack == NULL) + return REG_ESPACE; + } + else + fs = NULL; + + cur_node = dfa->init_node; + re_node_set_init_empty (&eps_via_nodes); + + if (__libc_use_alloca (nmatch * sizeof (regmatch_t))) + prev_idx_match = (regmatch_t *) alloca (nmatch * sizeof (regmatch_t)); + else + { + prev_idx_match = re_malloc (regmatch_t, nmatch); + if (prev_idx_match == NULL) + { + free_fail_stack_return (fs); + return REG_ESPACE; + } + prev_idx_match_malloced = 1; + } + memcpy (prev_idx_match, pmatch, sizeof (regmatch_t) * nmatch); + + for (idx = pmatch[0].rm_so; idx <= pmatch[0].rm_eo ;) + { + update_regs (dfa, pmatch, prev_idx_match, cur_node, idx, nmatch); + + if (idx == pmatch[0].rm_eo && cur_node == mctx->last_node) + { + int reg_idx; + if (fs) + { + for (reg_idx = 0; reg_idx < nmatch; ++reg_idx) + if (pmatch[reg_idx].rm_so > -1 && pmatch[reg_idx].rm_eo == -1) + break; + if (reg_idx == nmatch) + { + re_node_set_free (&eps_via_nodes); + if (prev_idx_match_malloced) + re_free (prev_idx_match); + return free_fail_stack_return (fs); + } + cur_node = pop_fail_stack (fs, &idx, nmatch, pmatch, + &eps_via_nodes); + } + else + { + re_node_set_free (&eps_via_nodes); + if (prev_idx_match_malloced) + re_free (prev_idx_match); + return REG_NOERROR; + } + } + + /* Proceed to next node. */ + cur_node = proceed_next_node (mctx, nmatch, pmatch, &idx, cur_node, + &eps_via_nodes, fs); + + if (BE (cur_node < 0, 0)) + { + if (BE (cur_node == -2, 0)) + { + re_node_set_free (&eps_via_nodes); + if (prev_idx_match_malloced) + re_free (prev_idx_match); + free_fail_stack_return (fs); + return REG_ESPACE; + } + if (fs) + cur_node = pop_fail_stack (fs, &idx, nmatch, pmatch, + &eps_via_nodes); + else + { + re_node_set_free (&eps_via_nodes); + if (prev_idx_match_malloced) + re_free (prev_idx_match); + return REG_NOMATCH; + } + } + } + re_node_set_free (&eps_via_nodes); + if (prev_idx_match_malloced) + re_free (prev_idx_match); + return free_fail_stack_return (fs); +} + +static reg_errcode_t +internal_function +free_fail_stack_return (struct re_fail_stack_t *fs) +{ + if (fs) + { + int fs_idx; + for (fs_idx = 0; fs_idx < fs->num; ++fs_idx) + { + re_node_set_free (&fs->stack[fs_idx].eps_via_nodes); + re_free (fs->stack[fs_idx].regs); + } + re_free (fs->stack); + } + return REG_NOERROR; +} + +static void +internal_function +update_regs (const re_dfa_t *dfa, regmatch_t *pmatch, + regmatch_t *prev_idx_match, int cur_node, int cur_idx, int nmatch) +{ + int type = dfa->nodes[cur_node].type; + if (type == OP_OPEN_SUBEXP) + { + int reg_num = dfa->nodes[cur_node].opr.idx + 1; + + /* We are at the first node of this sub expression. */ + if (reg_num < nmatch) + { + pmatch[reg_num].rm_so = cur_idx; + pmatch[reg_num].rm_eo = -1; + } + } + else if (type == OP_CLOSE_SUBEXP) + { + int reg_num = dfa->nodes[cur_node].opr.idx + 1; + if (reg_num < nmatch) + { + /* We are at the last node of this sub expression. */ + if (pmatch[reg_num].rm_so < cur_idx) + { + pmatch[reg_num].rm_eo = cur_idx; + /* This is a non-empty match or we are not inside an optional + subexpression. Accept this right away. */ + memcpy (prev_idx_match, pmatch, sizeof (regmatch_t) * nmatch); + } + else + { + if (dfa->nodes[cur_node].opt_subexp + && prev_idx_match[reg_num].rm_so != -1) + /* We transited through an empty match for an optional + subexpression, like (a?)*, and this is not the subexp's + first match. Copy back the old content of the registers + so that matches of an inner subexpression are undone as + well, like in ((a?))*. */ + memcpy (pmatch, prev_idx_match, sizeof (regmatch_t) * nmatch); + else + /* We completed a subexpression, but it may be part of + an optional one, so do not update PREV_IDX_MATCH. */ + pmatch[reg_num].rm_eo = cur_idx; + } + } + } +} + +/* This function checks the STATE_LOG from the SCTX->last_str_idx to 0 + and sift the nodes in each states according to the following rules. + Updated state_log will be wrote to STATE_LOG. + + Rules: We throw away the Node `a' in the STATE_LOG[STR_IDX] if... + 1. When STR_IDX == MATCH_LAST(the last index in the state_log): + If `a' isn't the LAST_NODE and `a' can't epsilon transit to + the LAST_NODE, we throw away the node `a'. + 2. When 0 <= STR_IDX < MATCH_LAST and `a' accepts + string `s' and transit to `b': + i. If 'b' isn't in the STATE_LOG[STR_IDX+strlen('s')], we throw + away the node `a'. + ii. If 'b' is in the STATE_LOG[STR_IDX+strlen('s')] but 'b' is + thrown away, we throw away the node `a'. + 3. When 0 <= STR_IDX < MATCH_LAST and 'a' epsilon transit to 'b': + i. If 'b' isn't in the STATE_LOG[STR_IDX], we throw away the + node `a'. + ii. If 'b' is in the STATE_LOG[STR_IDX] but 'b' is thrown away, + we throw away the node `a'. */ + +#define STATE_NODE_CONTAINS(state,node) \ + ((state) != NULL && re_node_set_contains (&(state)->nodes, node)) + +static reg_errcode_t +internal_function +sift_states_backward (const re_match_context_t *mctx, re_sift_context_t *sctx) +{ + reg_errcode_t err; + int null_cnt = 0; + int str_idx = sctx->last_str_idx; + re_node_set cur_dest; + +#ifdef DEBUG + assert (mctx->state_log != NULL && mctx->state_log[str_idx] != NULL); +#endif + + /* Build sifted state_log[str_idx]. It has the nodes which can epsilon + transit to the last_node and the last_node itself. */ + err = re_node_set_init_1 (&cur_dest, sctx->last_node); + if (BE (err != REG_NOERROR, 0)) + return err; + err = update_cur_sifted_state (mctx, sctx, str_idx, &cur_dest); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + + /* Then check each states in the state_log. */ + while (str_idx > 0) + { + /* Update counters. */ + null_cnt = (sctx->sifted_states[str_idx] == NULL) ? null_cnt + 1 : 0; + if (null_cnt > mctx->max_mb_elem_len) + { + memset (sctx->sifted_states, '\0', + sizeof (re_dfastate_t *) * str_idx); + re_node_set_free (&cur_dest); + return REG_NOERROR; + } + re_node_set_empty (&cur_dest); + --str_idx; + + if (mctx->state_log[str_idx]) + { + err = build_sifted_states (mctx, sctx, str_idx, &cur_dest); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + } + + /* Add all the nodes which satisfy the following conditions: + - It can epsilon transit to a node in CUR_DEST. + - It is in CUR_SRC. + And update state_log. */ + err = update_cur_sifted_state (mctx, sctx, str_idx, &cur_dest); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + } + err = REG_NOERROR; + free_return: + re_node_set_free (&cur_dest); + return err; +} + +static reg_errcode_t +internal_function +build_sifted_states (const re_match_context_t *mctx, re_sift_context_t *sctx, + int str_idx, re_node_set *cur_dest) +{ + const re_dfa_t *const dfa = mctx->dfa; + const re_node_set *cur_src = &mctx->state_log[str_idx]->non_eps_nodes; + int i; + + /* Then build the next sifted state. + We build the next sifted state on `cur_dest', and update + `sifted_states[str_idx]' with `cur_dest'. + Note: + `cur_dest' is the sifted state from `state_log[str_idx + 1]'. + `cur_src' points the node_set of the old `state_log[str_idx]' + (with the epsilon nodes pre-filtered out). */ + for (i = 0; i < cur_src->nelem; i++) + { + int prev_node = cur_src->elems[i]; + int naccepted = 0; + int ret; + +#ifdef DEBUG + re_token_type_t type = dfa->nodes[prev_node].type; + assert (!IS_EPSILON_NODE (type)); +#endif +#ifdef RE_ENABLE_I18N + /* If the node may accept `multi byte'. */ + if (dfa->nodes[prev_node].accept_mb) + naccepted = sift_states_iter_mb (mctx, sctx, prev_node, + str_idx, sctx->last_str_idx); +#endif /* RE_ENABLE_I18N */ + + /* We don't check backreferences here. + See update_cur_sifted_state(). */ + if (!naccepted + && check_node_accept (mctx, dfa->nodes + prev_node, str_idx) + && STATE_NODE_CONTAINS (sctx->sifted_states[str_idx + 1], + dfa->nexts[prev_node])) + naccepted = 1; + + if (naccepted == 0) + continue; + + if (sctx->limits.nelem) + { + int to_idx = str_idx + naccepted; + if (check_dst_limits (mctx, &sctx->limits, + dfa->nexts[prev_node], to_idx, + prev_node, str_idx)) + continue; + } + ret = re_node_set_insert (cur_dest, prev_node); + if (BE (ret == -1, 0)) + return REG_ESPACE; + } + + return REG_NOERROR; +} + +/* Helper functions. */ + +static reg_errcode_t +internal_function +clean_state_log_if_needed (re_match_context_t *mctx, int next_state_log_idx) +{ + int top = mctx->state_log_top; + + if (next_state_log_idx >= mctx->input.bufs_len + || (next_state_log_idx >= mctx->input.valid_len + && mctx->input.valid_len < mctx->input.len)) + { + reg_errcode_t err; + err = extend_buffers (mctx); + if (BE (err != REG_NOERROR, 0)) + return err; + } + + if (top < next_state_log_idx) + { + memset (mctx->state_log + top + 1, '\0', + sizeof (re_dfastate_t *) * (next_state_log_idx - top)); + mctx->state_log_top = next_state_log_idx; + } + return REG_NOERROR; +} + +static reg_errcode_t +internal_function +merge_state_array (const re_dfa_t *dfa, re_dfastate_t **dst, + re_dfastate_t **src, int num) +{ + int st_idx; + reg_errcode_t err; + for (st_idx = 0; st_idx < num; ++st_idx) + { + if (dst[st_idx] == NULL) + dst[st_idx] = src[st_idx]; + else if (src[st_idx] != NULL) + { + re_node_set merged_set; + err = re_node_set_init_union (&merged_set, &dst[st_idx]->nodes, + &src[st_idx]->nodes); + if (BE (err != REG_NOERROR, 0)) + return err; + dst[st_idx] = re_acquire_state (&err, dfa, &merged_set); + re_node_set_free (&merged_set); + if (BE (err != REG_NOERROR, 0)) + return err; + } + } + return REG_NOERROR; +} + +static reg_errcode_t +internal_function +update_cur_sifted_state (const re_match_context_t *mctx, + re_sift_context_t *sctx, int str_idx, + re_node_set *dest_nodes) +{ + const re_dfa_t *const dfa = mctx->dfa; + reg_errcode_t err = REG_NOERROR; + const re_node_set *candidates; + candidates = ((mctx->state_log[str_idx] == NULL) ? NULL + : &mctx->state_log[str_idx]->nodes); + + if (dest_nodes->nelem == 0) + sctx->sifted_states[str_idx] = NULL; + else + { + if (candidates) + { + /* At first, add the nodes which can epsilon transit to a node in + DEST_NODE. */ + err = add_epsilon_src_nodes (dfa, dest_nodes, candidates); + if (BE (err != REG_NOERROR, 0)) + return err; + + /* Then, check the limitations in the current sift_context. */ + if (sctx->limits.nelem) + { + err = check_subexp_limits (dfa, dest_nodes, candidates, &sctx->limits, + mctx->bkref_ents, str_idx); + if (BE (err != REG_NOERROR, 0)) + return err; + } + } + + sctx->sifted_states[str_idx] = re_acquire_state (&err, dfa, dest_nodes); + if (BE (err != REG_NOERROR, 0)) + return err; + } + + if (candidates && mctx->state_log[str_idx]->has_backref) + { + err = sift_states_bkref (mctx, sctx, str_idx, candidates); + if (BE (err != REG_NOERROR, 0)) + return err; + } + return REG_NOERROR; +} + +static reg_errcode_t +internal_function +add_epsilon_src_nodes (const re_dfa_t *dfa, re_node_set *dest_nodes, + const re_node_set *candidates) +{ + reg_errcode_t err = REG_NOERROR; + int i; + + re_dfastate_t *state = re_acquire_state (&err, dfa, dest_nodes); + if (BE (err != REG_NOERROR, 0)) + return err; + + if (!state->inveclosure.alloc) + { + err = re_node_set_alloc (&state->inveclosure, dest_nodes->nelem); + if (BE (err != REG_NOERROR, 0)) + return REG_ESPACE; + for (i = 0; i < dest_nodes->nelem; i++) + re_node_set_merge (&state->inveclosure, + dfa->inveclosures + dest_nodes->elems[i]); + } + return re_node_set_add_intersect (dest_nodes, candidates, + &state->inveclosure); +} + +static reg_errcode_t +internal_function +sub_epsilon_src_nodes (const re_dfa_t *dfa, int node, re_node_set *dest_nodes, + const re_node_set *candidates) +{ + int ecl_idx; + reg_errcode_t err; + re_node_set *inv_eclosure = dfa->inveclosures + node; + re_node_set except_nodes; + re_node_set_init_empty (&except_nodes); + for (ecl_idx = 0; ecl_idx < inv_eclosure->nelem; ++ecl_idx) + { + int cur_node = inv_eclosure->elems[ecl_idx]; + if (cur_node == node) + continue; + if (IS_EPSILON_NODE (dfa->nodes[cur_node].type)) + { + int edst1 = dfa->edests[cur_node].elems[0]; + int edst2 = ((dfa->edests[cur_node].nelem > 1) + ? dfa->edests[cur_node].elems[1] : -1); + if ((!re_node_set_contains (inv_eclosure, edst1) + && re_node_set_contains (dest_nodes, edst1)) + || (edst2 > 0 + && !re_node_set_contains (inv_eclosure, edst2) + && re_node_set_contains (dest_nodes, edst2))) + { + err = re_node_set_add_intersect (&except_nodes, candidates, + dfa->inveclosures + cur_node); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&except_nodes); + return err; + } + } + } + } + for (ecl_idx = 0; ecl_idx < inv_eclosure->nelem; ++ecl_idx) + { + int cur_node = inv_eclosure->elems[ecl_idx]; + if (!re_node_set_contains (&except_nodes, cur_node)) + { + int idx = re_node_set_contains (dest_nodes, cur_node) - 1; + re_node_set_remove_at (dest_nodes, idx); + } + } + re_node_set_free (&except_nodes); + return REG_NOERROR; +} + +static int +internal_function +check_dst_limits (const re_match_context_t *mctx, re_node_set *limits, + int dst_node, int dst_idx, int src_node, int src_idx) +{ + const re_dfa_t *const dfa = mctx->dfa; + int lim_idx, src_pos, dst_pos; + + int dst_bkref_idx = search_cur_bkref_entry (mctx, dst_idx); + int src_bkref_idx = search_cur_bkref_entry (mctx, src_idx); + for (lim_idx = 0; lim_idx < limits->nelem; ++lim_idx) + { + int subexp_idx; + struct re_backref_cache_entry *ent; + ent = mctx->bkref_ents + limits->elems[lim_idx]; + subexp_idx = dfa->nodes[ent->node].opr.idx; + + dst_pos = check_dst_limits_calc_pos (mctx, limits->elems[lim_idx], + subexp_idx, dst_node, dst_idx, + dst_bkref_idx); + src_pos = check_dst_limits_calc_pos (mctx, limits->elems[lim_idx], + subexp_idx, src_node, src_idx, + src_bkref_idx); + + /* In case of: + ( ) + ( ) + ( ) */ + if (src_pos == dst_pos) + continue; /* This is unrelated limitation. */ + else + return 1; + } + return 0; +} + +static int +internal_function +check_dst_limits_calc_pos_1 (const re_match_context_t *mctx, int boundaries, + int subexp_idx, int from_node, int bkref_idx) +{ + const re_dfa_t *const dfa = mctx->dfa; + const re_node_set *eclosures = dfa->eclosures + from_node; + int node_idx; + + /* Else, we are on the boundary: examine the nodes on the epsilon + closure. */ + for (node_idx = 0; node_idx < eclosures->nelem; ++node_idx) + { + int node = eclosures->elems[node_idx]; + switch (dfa->nodes[node].type) + { + case OP_BACK_REF: + if (bkref_idx != -1) + { + struct re_backref_cache_entry *ent = mctx->bkref_ents + bkref_idx; + do + { + int dst, cpos; + + if (ent->node != node) + continue; + + if (subexp_idx < BITSET_WORD_BITS + && !(ent->eps_reachable_subexps_map + & ((bitset_word_t) 1 << subexp_idx))) + continue; + + /* Recurse trying to reach the OP_OPEN_SUBEXP and + OP_CLOSE_SUBEXP cases below. But, if the + destination node is the same node as the source + node, don't recurse because it would cause an + infinite loop: a regex that exhibits this behavior + is ()\1*\1* */ + dst = dfa->edests[node].elems[0]; + if (dst == from_node) + { + if (boundaries & 1) + return -1; + else /* if (boundaries & 2) */ + return 0; + } + + cpos = + check_dst_limits_calc_pos_1 (mctx, boundaries, subexp_idx, + dst, bkref_idx); + if (cpos == -1 /* && (boundaries & 1) */) + return -1; + if (cpos == 0 && (boundaries & 2)) + return 0; + + if (subexp_idx < BITSET_WORD_BITS) + ent->eps_reachable_subexps_map + &= ~((bitset_word_t) 1 << subexp_idx); + } + while (ent++->more); + } + break; + + case OP_OPEN_SUBEXP: + if ((boundaries & 1) && subexp_idx == dfa->nodes[node].opr.idx) + return -1; + break; + + case OP_CLOSE_SUBEXP: + if ((boundaries & 2) && subexp_idx == dfa->nodes[node].opr.idx) + return 0; + break; + + default: + break; + } + } + + return (boundaries & 2) ? 1 : 0; +} + +static int +internal_function +check_dst_limits_calc_pos (const re_match_context_t *mctx, int limit, + int subexp_idx, int from_node, int str_idx, + int bkref_idx) +{ + struct re_backref_cache_entry *lim = mctx->bkref_ents + limit; + int boundaries; + + /* If we are outside the range of the subexpression, return -1 or 1. */ + if (str_idx < lim->subexp_from) + return -1; + + if (lim->subexp_to < str_idx) + return 1; + + /* If we are within the subexpression, return 0. */ + boundaries = (str_idx == lim->subexp_from); + boundaries |= (str_idx == lim->subexp_to) << 1; + if (boundaries == 0) + return 0; + + /* Else, examine epsilon closure. */ + return check_dst_limits_calc_pos_1 (mctx, boundaries, subexp_idx, + from_node, bkref_idx); +} + +/* Check the limitations of sub expressions LIMITS, and remove the nodes + which are against limitations from DEST_NODES. */ + +static reg_errcode_t +internal_function +check_subexp_limits (const re_dfa_t *dfa, re_node_set *dest_nodes, + const re_node_set *candidates, re_node_set *limits, + struct re_backref_cache_entry *bkref_ents, int str_idx) +{ + reg_errcode_t err; + int node_idx, lim_idx; + + for (lim_idx = 0; lim_idx < limits->nelem; ++lim_idx) + { + int subexp_idx; + struct re_backref_cache_entry *ent; + ent = bkref_ents + limits->elems[lim_idx]; + + if (str_idx <= ent->subexp_from || ent->str_idx < str_idx) + continue; /* This is unrelated limitation. */ + + subexp_idx = dfa->nodes[ent->node].opr.idx; + if (ent->subexp_to == str_idx) + { + int ops_node = -1; + int cls_node = -1; + for (node_idx = 0; node_idx < dest_nodes->nelem; ++node_idx) + { + int node = dest_nodes->elems[node_idx]; + re_token_type_t type = dfa->nodes[node].type; + if (type == OP_OPEN_SUBEXP + && subexp_idx == dfa->nodes[node].opr.idx) + ops_node = node; + else if (type == OP_CLOSE_SUBEXP + && subexp_idx == dfa->nodes[node].opr.idx) + cls_node = node; + } + + /* Check the limitation of the open subexpression. */ + /* Note that (ent->subexp_to = str_idx != ent->subexp_from). */ + if (ops_node >= 0) + { + err = sub_epsilon_src_nodes (dfa, ops_node, dest_nodes, + candidates); + if (BE (err != REG_NOERROR, 0)) + return err; + } + + /* Check the limitation of the close subexpression. */ + if (cls_node >= 0) + for (node_idx = 0; node_idx < dest_nodes->nelem; ++node_idx) + { + int node = dest_nodes->elems[node_idx]; + if (!re_node_set_contains (dfa->inveclosures + node, + cls_node) + && !re_node_set_contains (dfa->eclosures + node, + cls_node)) + { + /* It is against this limitation. + Remove it form the current sifted state. */ + err = sub_epsilon_src_nodes (dfa, node, dest_nodes, + candidates); + if (BE (err != REG_NOERROR, 0)) + return err; + --node_idx; + } + } + } + else /* (ent->subexp_to != str_idx) */ + { + for (node_idx = 0; node_idx < dest_nodes->nelem; ++node_idx) + { + int node = dest_nodes->elems[node_idx]; + re_token_type_t type = dfa->nodes[node].type; + if (type == OP_CLOSE_SUBEXP || type == OP_OPEN_SUBEXP) + { + if (subexp_idx != dfa->nodes[node].opr.idx) + continue; + /* It is against this limitation. + Remove it form the current sifted state. */ + err = sub_epsilon_src_nodes (dfa, node, dest_nodes, + candidates); + if (BE (err != REG_NOERROR, 0)) + return err; + } + } + } + } + return REG_NOERROR; +} + +static reg_errcode_t +internal_function +sift_states_bkref (const re_match_context_t *mctx, re_sift_context_t *sctx, + int str_idx, const re_node_set *candidates) +{ + const re_dfa_t *const dfa = mctx->dfa; + reg_errcode_t err; + int node_idx, node; + re_sift_context_t local_sctx; + int first_idx = search_cur_bkref_entry (mctx, str_idx); + + if (first_idx == -1) + return REG_NOERROR; + + local_sctx.sifted_states = NULL; /* Mark that it hasn't been initialized. */ + + for (node_idx = 0; node_idx < candidates->nelem; ++node_idx) + { + int enabled_idx; + re_token_type_t type; + struct re_backref_cache_entry *entry; + node = candidates->elems[node_idx]; + type = dfa->nodes[node].type; + /* Avoid infinite loop for the REs like "()\1+". */ + if (node == sctx->last_node && str_idx == sctx->last_str_idx) + continue; + if (type != OP_BACK_REF) + continue; + + entry = mctx->bkref_ents + first_idx; + enabled_idx = first_idx; + do + { + int subexp_len; + int to_idx; + int dst_node; + int ret; + re_dfastate_t *cur_state; + + if (entry->node != node) + continue; + subexp_len = entry->subexp_to - entry->subexp_from; + to_idx = str_idx + subexp_len; + dst_node = (subexp_len ? dfa->nexts[node] + : dfa->edests[node].elems[0]); + + if (to_idx > sctx->last_str_idx + || sctx->sifted_states[to_idx] == NULL + || !STATE_NODE_CONTAINS (sctx->sifted_states[to_idx], dst_node) + || check_dst_limits (mctx, &sctx->limits, node, + str_idx, dst_node, to_idx)) + continue; + + if (local_sctx.sifted_states == NULL) + { + local_sctx = *sctx; + err = re_node_set_init_copy (&local_sctx.limits, &sctx->limits); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + } + local_sctx.last_node = node; + local_sctx.last_str_idx = str_idx; + ret = re_node_set_insert (&local_sctx.limits, enabled_idx); + if (BE (ret < 0, 0)) + { + err = REG_ESPACE; + goto free_return; + } + cur_state = local_sctx.sifted_states[str_idx]; + err = sift_states_backward (mctx, &local_sctx); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + if (sctx->limited_states != NULL) + { + err = merge_state_array (dfa, sctx->limited_states, + local_sctx.sifted_states, + str_idx + 1); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + } + local_sctx.sifted_states[str_idx] = cur_state; + re_node_set_remove (&local_sctx.limits, enabled_idx); + + /* mctx->bkref_ents may have changed, reload the pointer. */ + entry = mctx->bkref_ents + enabled_idx; + } + while (enabled_idx++, entry++->more); + } + err = REG_NOERROR; + free_return: + if (local_sctx.sifted_states != NULL) + { + re_node_set_free (&local_sctx.limits); + } + + return err; +} + + +#ifdef RE_ENABLE_I18N +static int +internal_function +sift_states_iter_mb (const re_match_context_t *mctx, re_sift_context_t *sctx, + int node_idx, int str_idx, int max_str_idx) +{ + const re_dfa_t *const dfa = mctx->dfa; + int naccepted; + /* Check the node can accept `multi byte'. */ + naccepted = check_node_accept_bytes (dfa, node_idx, &mctx->input, str_idx); + if (naccepted > 0 && str_idx + naccepted <= max_str_idx && + !STATE_NODE_CONTAINS (sctx->sifted_states[str_idx + naccepted], + dfa->nexts[node_idx])) + /* The node can't accept the `multi byte', or the + destination was already thrown away, then the node + could't accept the current input `multi byte'. */ + naccepted = 0; + /* Otherwise, it is sure that the node could accept + `naccepted' bytes input. */ + return naccepted; +} +#endif /* RE_ENABLE_I18N */ + + +/* Functions for state transition. */ + +/* Return the next state to which the current state STATE will transit by + accepting the current input byte, and update STATE_LOG if necessary. + If STATE can accept a multibyte char/collating element/back reference + update the destination of STATE_LOG. */ + +static re_dfastate_t * +internal_function +transit_state (reg_errcode_t *err, re_match_context_t *mctx, + re_dfastate_t *state) +{ + re_dfastate_t **trtable; + unsigned char ch; + +#ifdef RE_ENABLE_I18N + /* If the current state can accept multibyte. */ + if (BE (state->accept_mb, 0)) + { + *err = transit_state_mb (mctx, state); + if (BE (*err != REG_NOERROR, 0)) + return NULL; + } +#endif /* RE_ENABLE_I18N */ + + /* Then decide the next state with the single byte. */ +#if 0 + if (0) + /* don't use transition table */ + return transit_state_sb (err, mctx, state); +#endif + + /* Use transition table */ + ch = re_string_fetch_byte (&mctx->input); + for (;;) + { + trtable = state->trtable; + if (BE (trtable != NULL, 1)) + return trtable[ch]; + + trtable = state->word_trtable; + if (BE (trtable != NULL, 1)) + { + unsigned int context; + context + = re_string_context_at (&mctx->input, + re_string_cur_idx (&mctx->input) - 1, + mctx->eflags); + if (IS_WORD_CONTEXT (context)) + return trtable[ch + SBC_MAX]; + else + return trtable[ch]; + } + + if (!build_trtable (mctx->dfa, state)) + { + *err = REG_ESPACE; + return NULL; + } + + /* Retry, we now have a transition table. */ + } +} + +/* Update the state_log if we need */ +re_dfastate_t * +internal_function +merge_state_with_log (reg_errcode_t *err, re_match_context_t *mctx, + re_dfastate_t *next_state) +{ + const re_dfa_t *const dfa = mctx->dfa; + int cur_idx = re_string_cur_idx (&mctx->input); + + if (cur_idx > mctx->state_log_top) + { + mctx->state_log[cur_idx] = next_state; + mctx->state_log_top = cur_idx; + } + else if (mctx->state_log[cur_idx] == 0) + { + mctx->state_log[cur_idx] = next_state; + } + else + { + re_dfastate_t *pstate; + unsigned int context; + re_node_set next_nodes, *log_nodes, *table_nodes = NULL; + /* If (state_log[cur_idx] != 0), it implies that cur_idx is + the destination of a multibyte char/collating element/ + back reference. Then the next state is the union set of + these destinations and the results of the transition table. */ + pstate = mctx->state_log[cur_idx]; + log_nodes = pstate->entrance_nodes; + if (next_state != NULL) + { + table_nodes = next_state->entrance_nodes; + *err = re_node_set_init_union (&next_nodes, table_nodes, + log_nodes); + if (BE (*err != REG_NOERROR, 0)) + return NULL; + } + else + next_nodes = *log_nodes; + /* Note: We already add the nodes of the initial state, + then we don't need to add them here. */ + + context = re_string_context_at (&mctx->input, + re_string_cur_idx (&mctx->input) - 1, + mctx->eflags); + next_state = mctx->state_log[cur_idx] + = re_acquire_state_context (err, dfa, &next_nodes, context); + /* We don't need to check errors here, since the return value of + this function is next_state and ERR is already set. */ + + if (table_nodes != NULL) + re_node_set_free (&next_nodes); + } + + if (BE (dfa->nbackref, 0) && next_state != NULL) + { + /* Check OP_OPEN_SUBEXP in the current state in case that we use them + later. We must check them here, since the back references in the + next state might use them. */ + *err = check_subexp_matching_top (mctx, &next_state->nodes, + cur_idx); + if (BE (*err != REG_NOERROR, 0)) + return NULL; + + /* If the next state has back references. */ + if (next_state->has_backref) + { + *err = transit_state_bkref (mctx, &next_state->nodes); + if (BE (*err != REG_NOERROR, 0)) + return NULL; + next_state = mctx->state_log[cur_idx]; + } + } + + return next_state; +} + +/* Skip bytes in the input that correspond to part of a + multi-byte match, then look in the log for a state + from which to restart matching. */ +re_dfastate_t * +internal_function +find_recover_state (reg_errcode_t *err, re_match_context_t *mctx) +{ + re_dfastate_t *cur_state; + do + { + int max = mctx->state_log_top; + int cur_str_idx = re_string_cur_idx (&mctx->input); + + do + { + if (++cur_str_idx > max) + return NULL; + re_string_skip_bytes (&mctx->input, 1); + } + while (mctx->state_log[cur_str_idx] == NULL); + + cur_state = merge_state_with_log (err, mctx, NULL); + } + while (*err == REG_NOERROR && cur_state == NULL); + return cur_state; +} + +/* Helper functions for transit_state. */ + +/* From the node set CUR_NODES, pick up the nodes whose types are + OP_OPEN_SUBEXP and which have corresponding back references in the regular + expression. And register them to use them later for evaluating the + correspoding back references. */ + +static reg_errcode_t +internal_function +check_subexp_matching_top (re_match_context_t *mctx, re_node_set *cur_nodes, + int str_idx) +{ + const re_dfa_t *const dfa = mctx->dfa; + int node_idx; + reg_errcode_t err; + + /* TODO: This isn't efficient. + Because there might be more than one nodes whose types are + OP_OPEN_SUBEXP and whose index is SUBEXP_IDX, we must check all + nodes. + E.g. RE: (a){2} */ + for (node_idx = 0; node_idx < cur_nodes->nelem; ++node_idx) + { + int node = cur_nodes->elems[node_idx]; + if (dfa->nodes[node].type == OP_OPEN_SUBEXP + && dfa->nodes[node].opr.idx < BITSET_WORD_BITS + && (dfa->used_bkref_map + & ((bitset_word_t) 1 << dfa->nodes[node].opr.idx))) + { + err = match_ctx_add_subtop (mctx, node, str_idx); + if (BE (err != REG_NOERROR, 0)) + return err; + } + } + return REG_NOERROR; +} + +#if 0 +/* Return the next state to which the current state STATE will transit by + accepting the current input byte. */ + +static re_dfastate_t * +transit_state_sb (reg_errcode_t *err, re_match_context_t *mctx, + re_dfastate_t *state) +{ + const re_dfa_t *const dfa = mctx->dfa; + re_node_set next_nodes; + re_dfastate_t *next_state; + int node_cnt, cur_str_idx = re_string_cur_idx (&mctx->input); + unsigned int context; + + *err = re_node_set_alloc (&next_nodes, state->nodes.nelem + 1); + if (BE (*err != REG_NOERROR, 0)) + return NULL; + for (node_cnt = 0; node_cnt < state->nodes.nelem; ++node_cnt) + { + int cur_node = state->nodes.elems[node_cnt]; + if (check_node_accept (mctx, dfa->nodes + cur_node, cur_str_idx)) + { + *err = re_node_set_merge (&next_nodes, + dfa->eclosures + dfa->nexts[cur_node]); + if (BE (*err != REG_NOERROR, 0)) + { + re_node_set_free (&next_nodes); + return NULL; + } + } + } + context = re_string_context_at (&mctx->input, cur_str_idx, mctx->eflags); + next_state = re_acquire_state_context (err, dfa, &next_nodes, context); + /* We don't need to check errors here, since the return value of + this function is next_state and ERR is already set. */ + + re_node_set_free (&next_nodes); + re_string_skip_bytes (&mctx->input, 1); + return next_state; +} +#endif + +#ifdef RE_ENABLE_I18N +static reg_errcode_t +internal_function +transit_state_mb (re_match_context_t *mctx, re_dfastate_t *pstate) +{ + const re_dfa_t *const dfa = mctx->dfa; + reg_errcode_t err; + int i; + + for (i = 0; i < pstate->nodes.nelem; ++i) + { + re_node_set dest_nodes, *new_nodes; + int cur_node_idx = pstate->nodes.elems[i]; + int naccepted, dest_idx; + unsigned int context; + re_dfastate_t *dest_state; + + if (!dfa->nodes[cur_node_idx].accept_mb) + continue; + + if (dfa->nodes[cur_node_idx].constraint) + { + context = re_string_context_at (&mctx->input, + re_string_cur_idx (&mctx->input), + mctx->eflags); + if (NOT_SATISFY_NEXT_CONSTRAINT (dfa->nodes[cur_node_idx].constraint, + context)) + continue; + } + + /* How many bytes the node can accept? */ + naccepted = check_node_accept_bytes (dfa, cur_node_idx, &mctx->input, + re_string_cur_idx (&mctx->input)); + if (naccepted == 0) + continue; + + /* The node can accepts `naccepted' bytes. */ + dest_idx = re_string_cur_idx (&mctx->input) + naccepted; + mctx->max_mb_elem_len = ((mctx->max_mb_elem_len < naccepted) ? naccepted + : mctx->max_mb_elem_len); + err = clean_state_log_if_needed (mctx, dest_idx); + if (BE (err != REG_NOERROR, 0)) + return err; +#ifdef DEBUG + assert (dfa->nexts[cur_node_idx] != -1); +#endif + new_nodes = dfa->eclosures + dfa->nexts[cur_node_idx]; + + dest_state = mctx->state_log[dest_idx]; + if (dest_state == NULL) + dest_nodes = *new_nodes; + else + { + err = re_node_set_init_union (&dest_nodes, + dest_state->entrance_nodes, new_nodes); + if (BE (err != REG_NOERROR, 0)) + return err; + } + context = re_string_context_at (&mctx->input, dest_idx - 1, + mctx->eflags); + mctx->state_log[dest_idx] + = re_acquire_state_context (&err, dfa, &dest_nodes, context); + if (dest_state != NULL) + re_node_set_free (&dest_nodes); + if (BE (mctx->state_log[dest_idx] == NULL && err != REG_NOERROR, 0)) + return err; + } + return REG_NOERROR; +} +#endif /* RE_ENABLE_I18N */ + +static reg_errcode_t +internal_function +transit_state_bkref (re_match_context_t *mctx, const re_node_set *nodes) +{ + const re_dfa_t *const dfa = mctx->dfa; + reg_errcode_t err; + int i; + int cur_str_idx = re_string_cur_idx (&mctx->input); + + for (i = 0; i < nodes->nelem; ++i) + { + int dest_str_idx, prev_nelem, bkc_idx; + int node_idx = nodes->elems[i]; + unsigned int context; + const re_token_t *node = dfa->nodes + node_idx; + re_node_set *new_dest_nodes; + + /* Check whether `node' is a backreference or not. */ + if (node->type != OP_BACK_REF) + continue; + + if (node->constraint) + { + context = re_string_context_at (&mctx->input, cur_str_idx, + mctx->eflags); + if (NOT_SATISFY_NEXT_CONSTRAINT (node->constraint, context)) + continue; + } + + /* `node' is a backreference. + Check the substring which the substring matched. */ + bkc_idx = mctx->nbkref_ents; + err = get_subexp (mctx, node_idx, cur_str_idx); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + + /* And add the epsilon closures (which is `new_dest_nodes') of + the backreference to appropriate state_log. */ +#ifdef DEBUG + assert (dfa->nexts[node_idx] != -1); +#endif + for (; bkc_idx < mctx->nbkref_ents; ++bkc_idx) + { + int subexp_len; + re_dfastate_t *dest_state; + struct re_backref_cache_entry *bkref_ent; + bkref_ent = mctx->bkref_ents + bkc_idx; + if (bkref_ent->node != node_idx || bkref_ent->str_idx != cur_str_idx) + continue; + subexp_len = bkref_ent->subexp_to - bkref_ent->subexp_from; + new_dest_nodes = (subexp_len == 0 + ? dfa->eclosures + dfa->edests[node_idx].elems[0] + : dfa->eclosures + dfa->nexts[node_idx]); + dest_str_idx = (cur_str_idx + bkref_ent->subexp_to + - bkref_ent->subexp_from); + context = re_string_context_at (&mctx->input, dest_str_idx - 1, + mctx->eflags); + dest_state = mctx->state_log[dest_str_idx]; + prev_nelem = ((mctx->state_log[cur_str_idx] == NULL) ? 0 + : mctx->state_log[cur_str_idx]->nodes.nelem); + /* Add `new_dest_node' to state_log. */ + if (dest_state == NULL) + { + mctx->state_log[dest_str_idx] + = re_acquire_state_context (&err, dfa, new_dest_nodes, + context); + if (BE (mctx->state_log[dest_str_idx] == NULL + && err != REG_NOERROR, 0)) + goto free_return; + } + else + { + re_node_set dest_nodes; + err = re_node_set_init_union (&dest_nodes, + dest_state->entrance_nodes, + new_dest_nodes); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&dest_nodes); + goto free_return; + } + mctx->state_log[dest_str_idx] + = re_acquire_state_context (&err, dfa, &dest_nodes, context); + re_node_set_free (&dest_nodes); + if (BE (mctx->state_log[dest_str_idx] == NULL + && err != REG_NOERROR, 0)) + goto free_return; + } + /* We need to check recursively if the backreference can epsilon + transit. */ + if (subexp_len == 0 + && mctx->state_log[cur_str_idx]->nodes.nelem > prev_nelem) + { + err = check_subexp_matching_top (mctx, new_dest_nodes, + cur_str_idx); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + err = transit_state_bkref (mctx, new_dest_nodes); + if (BE (err != REG_NOERROR, 0)) + goto free_return; + } + } + } + err = REG_NOERROR; + free_return: + return err; +} + +/* Enumerate all the candidates which the backreference BKREF_NODE can match + at BKREF_STR_IDX, and register them by match_ctx_add_entry(). + Note that we might collect inappropriate candidates here. + However, the cost of checking them strictly here is too high, then we + delay these checking for prune_impossible_nodes(). */ + +static reg_errcode_t +internal_function +get_subexp (re_match_context_t *mctx, int bkref_node, int bkref_str_idx) +{ + const re_dfa_t *const dfa = mctx->dfa; + int subexp_num, sub_top_idx; + const char *buf = (const char *) re_string_get_buffer (&mctx->input); + /* Return if we have already checked BKREF_NODE at BKREF_STR_IDX. */ + int cache_idx = search_cur_bkref_entry (mctx, bkref_str_idx); + if (cache_idx != -1) + { + const struct re_backref_cache_entry *entry + = mctx->bkref_ents + cache_idx; + do + if (entry->node == bkref_node) + return REG_NOERROR; /* We already checked it. */ + while (entry++->more); + } + + subexp_num = dfa->nodes[bkref_node].opr.idx; + + /* For each sub expression */ + for (sub_top_idx = 0; sub_top_idx < mctx->nsub_tops; ++sub_top_idx) + { + reg_errcode_t err; + re_sub_match_top_t *sub_top = mctx->sub_tops[sub_top_idx]; + re_sub_match_last_t *sub_last; + int sub_last_idx, sl_str, bkref_str_off; + + if (dfa->nodes[sub_top->node].opr.idx != subexp_num) + continue; /* It isn't related. */ + + sl_str = sub_top->str_idx; + bkref_str_off = bkref_str_idx; + /* At first, check the last node of sub expressions we already + evaluated. */ + for (sub_last_idx = 0; sub_last_idx < sub_top->nlasts; ++sub_last_idx) + { + int sl_str_diff; + sub_last = sub_top->lasts[sub_last_idx]; + sl_str_diff = sub_last->str_idx - sl_str; + /* The matched string by the sub expression match with the substring + at the back reference? */ + if (sl_str_diff > 0) + { + if (BE (bkref_str_off + sl_str_diff > mctx->input.valid_len, 0)) + { + /* Not enough chars for a successful match. */ + if (bkref_str_off + sl_str_diff > mctx->input.len) + break; + + err = clean_state_log_if_needed (mctx, + bkref_str_off + + sl_str_diff); + if (BE (err != REG_NOERROR, 0)) + return err; + buf = (const char *) re_string_get_buffer (&mctx->input); + } + if (memcmp (buf + bkref_str_off, buf + sl_str, sl_str_diff) != 0) + /* We don't need to search this sub expression any more. */ + break; + } + bkref_str_off += sl_str_diff; + sl_str += sl_str_diff; + err = get_subexp_sub (mctx, sub_top, sub_last, bkref_node, + bkref_str_idx); + + /* Reload buf, since the preceding call might have reallocated + the buffer. */ + buf = (const char *) re_string_get_buffer (&mctx->input); + + if (err == REG_NOMATCH) + continue; + if (BE (err != REG_NOERROR, 0)) + return err; + } + + if (sub_last_idx < sub_top->nlasts) + continue; + if (sub_last_idx > 0) + ++sl_str; + /* Then, search for the other last nodes of the sub expression. */ + for (; sl_str <= bkref_str_idx; ++sl_str) + { + int cls_node, sl_str_off; + const re_node_set *nodes; + sl_str_off = sl_str - sub_top->str_idx; + /* The matched string by the sub expression match with the substring + at the back reference? */ + if (sl_str_off > 0) + { + if (BE (bkref_str_off >= mctx->input.valid_len, 0)) + { + /* If we are at the end of the input, we cannot match. */ + if (bkref_str_off >= mctx->input.len) + break; + + err = extend_buffers (mctx); + if (BE (err != REG_NOERROR, 0)) + return err; + + buf = (const char *) re_string_get_buffer (&mctx->input); + } + if (buf [bkref_str_off++] != buf[sl_str - 1]) + break; /* We don't need to search this sub expression + any more. */ + } + if (mctx->state_log[sl_str] == NULL) + continue; + /* Does this state have a ')' of the sub expression? */ + nodes = &mctx->state_log[sl_str]->nodes; + cls_node = find_subexp_node (dfa, nodes, subexp_num, + OP_CLOSE_SUBEXP); + if (cls_node == -1) + continue; /* No. */ + if (sub_top->path == NULL) + { + sub_top->path = calloc (sizeof (state_array_t), + sl_str - sub_top->str_idx + 1); + if (sub_top->path == NULL) + return REG_ESPACE; + } + /* Can the OP_OPEN_SUBEXP node arrive the OP_CLOSE_SUBEXP node + in the current context? */ + err = check_arrival (mctx, sub_top->path, sub_top->node, + sub_top->str_idx, cls_node, sl_str, + OP_CLOSE_SUBEXP); + if (err == REG_NOMATCH) + continue; + if (BE (err != REG_NOERROR, 0)) + return err; + sub_last = match_ctx_add_sublast (sub_top, cls_node, sl_str); + if (BE (sub_last == NULL, 0)) + return REG_ESPACE; + err = get_subexp_sub (mctx, sub_top, sub_last, bkref_node, + bkref_str_idx); + if (err == REG_NOMATCH) + continue; + } + } + return REG_NOERROR; +} + +/* Helper functions for get_subexp(). */ + +/* Check SUB_LAST can arrive to the back reference BKREF_NODE at BKREF_STR. + If it can arrive, register the sub expression expressed with SUB_TOP + and SUB_LAST. */ + +static reg_errcode_t +internal_function +get_subexp_sub (re_match_context_t *mctx, const re_sub_match_top_t *sub_top, + re_sub_match_last_t *sub_last, int bkref_node, int bkref_str) +{ + reg_errcode_t err; + int to_idx; + /* Can the subexpression arrive the back reference? */ + err = check_arrival (mctx, &sub_last->path, sub_last->node, + sub_last->str_idx, bkref_node, bkref_str, + OP_OPEN_SUBEXP); + if (err != REG_NOERROR) + return err; + err = match_ctx_add_entry (mctx, bkref_node, bkref_str, sub_top->str_idx, + sub_last->str_idx); + if (BE (err != REG_NOERROR, 0)) + return err; + to_idx = bkref_str + sub_last->str_idx - sub_top->str_idx; + return clean_state_log_if_needed (mctx, to_idx); +} + +/* Find the first node which is '(' or ')' and whose index is SUBEXP_IDX. + Search '(' if FL_OPEN, or search ')' otherwise. + TODO: This function isn't efficient... + Because there might be more than one nodes whose types are + OP_OPEN_SUBEXP and whose index is SUBEXP_IDX, we must check all + nodes. + E.g. RE: (a){2} */ + +static int +internal_function +find_subexp_node (const re_dfa_t *dfa, const re_node_set *nodes, + int subexp_idx, int type) +{ + int cls_idx; + for (cls_idx = 0; cls_idx < nodes->nelem; ++cls_idx) + { + int cls_node = nodes->elems[cls_idx]; + const re_token_t *node = dfa->nodes + cls_node; + if (node->type == type + && node->opr.idx == subexp_idx) + return cls_node; + } + return -1; +} + +/* Check whether the node TOP_NODE at TOP_STR can arrive to the node + LAST_NODE at LAST_STR. We record the path onto PATH since it will be + heavily reused. + Return REG_NOERROR if it can arrive, or REG_NOMATCH otherwise. */ + +static reg_errcode_t +internal_function +check_arrival (re_match_context_t *mctx, state_array_t *path, int top_node, + int top_str, int last_node, int last_str, int type) +{ + const re_dfa_t *const dfa = mctx->dfa; + reg_errcode_t err = REG_NOERROR; + int subexp_num, backup_cur_idx, str_idx, null_cnt; + re_dfastate_t *cur_state = NULL; + re_node_set *cur_nodes, next_nodes; + re_dfastate_t **backup_state_log; + unsigned int context; + + subexp_num = dfa->nodes[top_node].opr.idx; + /* Extend the buffer if we need. */ + if (BE (path->alloc < last_str + mctx->max_mb_elem_len + 1, 0)) + { + re_dfastate_t **new_array; + int old_alloc = path->alloc; + path->alloc += last_str + mctx->max_mb_elem_len + 1; + new_array = re_realloc (path->array, re_dfastate_t *, path->alloc); + if (BE (new_array == NULL, 0)) + { + path->alloc = old_alloc; + return REG_ESPACE; + } + path->array = new_array; + memset (new_array + old_alloc, '\0', + sizeof (re_dfastate_t *) * (path->alloc - old_alloc)); + } + + str_idx = path->next_idx ? path->next_idx : top_str; + + /* Temporary modify MCTX. */ + backup_state_log = mctx->state_log; + backup_cur_idx = mctx->input.cur_idx; + mctx->state_log = path->array; + mctx->input.cur_idx = str_idx; + + /* Setup initial node set. */ + context = re_string_context_at (&mctx->input, str_idx - 1, mctx->eflags); + if (str_idx == top_str) + { + err = re_node_set_init_1 (&next_nodes, top_node); + if (BE (err != REG_NOERROR, 0)) + return err; + err = check_arrival_expand_ecl (dfa, &next_nodes, subexp_num, type); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&next_nodes); + return err; + } + } + else + { + cur_state = mctx->state_log[str_idx]; + if (cur_state && cur_state->has_backref) + { + err = re_node_set_init_copy (&next_nodes, &cur_state->nodes); + if (BE (err != REG_NOERROR, 0)) + return err; + } + else + re_node_set_init_empty (&next_nodes); + } + if (str_idx == top_str || (cur_state && cur_state->has_backref)) + { + if (next_nodes.nelem) + { + err = expand_bkref_cache (mctx, &next_nodes, str_idx, + subexp_num, type); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&next_nodes); + return err; + } + } + cur_state = re_acquire_state_context (&err, dfa, &next_nodes, context); + if (BE (cur_state == NULL && err != REG_NOERROR, 0)) + { + re_node_set_free (&next_nodes); + return err; + } + mctx->state_log[str_idx] = cur_state; + } + + for (null_cnt = 0; str_idx < last_str && null_cnt <= mctx->max_mb_elem_len;) + { + re_node_set_empty (&next_nodes); + if (mctx->state_log[str_idx + 1]) + { + err = re_node_set_merge (&next_nodes, + &mctx->state_log[str_idx + 1]->nodes); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&next_nodes); + return err; + } + } + if (cur_state) + { + err = check_arrival_add_next_nodes (mctx, str_idx, + &cur_state->non_eps_nodes, + &next_nodes); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&next_nodes); + return err; + } + } + ++str_idx; + if (next_nodes.nelem) + { + err = check_arrival_expand_ecl (dfa, &next_nodes, subexp_num, type); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&next_nodes); + return err; + } + err = expand_bkref_cache (mctx, &next_nodes, str_idx, + subexp_num, type); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&next_nodes); + return err; + } + } + context = re_string_context_at (&mctx->input, str_idx - 1, mctx->eflags); + cur_state = re_acquire_state_context (&err, dfa, &next_nodes, context); + if (BE (cur_state == NULL && err != REG_NOERROR, 0)) + { + re_node_set_free (&next_nodes); + return err; + } + mctx->state_log[str_idx] = cur_state; + null_cnt = cur_state == NULL ? null_cnt + 1 : 0; + } + re_node_set_free (&next_nodes); + cur_nodes = (mctx->state_log[last_str] == NULL ? NULL + : &mctx->state_log[last_str]->nodes); + path->next_idx = str_idx; + + /* Fix MCTX. */ + mctx->state_log = backup_state_log; + mctx->input.cur_idx = backup_cur_idx; + + /* Then check the current node set has the node LAST_NODE. */ + if (cur_nodes != NULL && re_node_set_contains (cur_nodes, last_node)) + return REG_NOERROR; + + return REG_NOMATCH; +} + +/* Helper functions for check_arrival. */ + +/* Calculate the destination nodes of CUR_NODES at STR_IDX, and append them + to NEXT_NODES. + TODO: This function is similar to the functions transit_state*(), + however this function has many additional works. + Can't we unify them? */ + +static reg_errcode_t +internal_function +check_arrival_add_next_nodes (re_match_context_t *mctx, int str_idx, + re_node_set *cur_nodes, re_node_set *next_nodes) +{ + const re_dfa_t *const dfa = mctx->dfa; + int result; + int cur_idx; + reg_errcode_t err = REG_NOERROR; + re_node_set union_set; + re_node_set_init_empty (&union_set); + for (cur_idx = 0; cur_idx < cur_nodes->nelem; ++cur_idx) + { + int naccepted = 0; + int cur_node = cur_nodes->elems[cur_idx]; +#ifdef DEBUG + re_token_type_t type = dfa->nodes[cur_node].type; + assert (!IS_EPSILON_NODE (type)); +#endif +#ifdef RE_ENABLE_I18N + /* If the node may accept `multi byte'. */ + if (dfa->nodes[cur_node].accept_mb) + { + naccepted = check_node_accept_bytes (dfa, cur_node, &mctx->input, + str_idx); + if (naccepted > 1) + { + re_dfastate_t *dest_state; + int next_node = dfa->nexts[cur_node]; + int next_idx = str_idx + naccepted; + dest_state = mctx->state_log[next_idx]; + re_node_set_empty (&union_set); + if (dest_state) + { + err = re_node_set_merge (&union_set, &dest_state->nodes); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&union_set); + return err; + } + } + result = re_node_set_insert (&union_set, next_node); + if (BE (result < 0, 0)) + { + re_node_set_free (&union_set); + return REG_ESPACE; + } + mctx->state_log[next_idx] = re_acquire_state (&err, dfa, + &union_set); + if (BE (mctx->state_log[next_idx] == NULL + && err != REG_NOERROR, 0)) + { + re_node_set_free (&union_set); + return err; + } + } + } +#endif /* RE_ENABLE_I18N */ + if (naccepted + || check_node_accept (mctx, dfa->nodes + cur_node, str_idx)) + { + result = re_node_set_insert (next_nodes, dfa->nexts[cur_node]); + if (BE (result < 0, 0)) + { + re_node_set_free (&union_set); + return REG_ESPACE; + } + } + } + re_node_set_free (&union_set); + return REG_NOERROR; +} + +/* For all the nodes in CUR_NODES, add the epsilon closures of them to + CUR_NODES, however exclude the nodes which are: + - inside the sub expression whose number is EX_SUBEXP, if FL_OPEN. + - out of the sub expression whose number is EX_SUBEXP, if !FL_OPEN. +*/ + +static reg_errcode_t +internal_function +check_arrival_expand_ecl (const re_dfa_t *dfa, re_node_set *cur_nodes, + int ex_subexp, int type) +{ + reg_errcode_t err; + int idx, outside_node; + re_node_set new_nodes; +#ifdef DEBUG + assert (cur_nodes->nelem); +#endif + err = re_node_set_alloc (&new_nodes, cur_nodes->nelem); + if (BE (err != REG_NOERROR, 0)) + return err; + /* Create a new node set NEW_NODES with the nodes which are epsilon + closures of the node in CUR_NODES. */ + + for (idx = 0; idx < cur_nodes->nelem; ++idx) + { + int cur_node = cur_nodes->elems[idx]; + const re_node_set *eclosure = dfa->eclosures + cur_node; + outside_node = find_subexp_node (dfa, eclosure, ex_subexp, type); + if (outside_node == -1) + { + /* There are no problematic nodes, just merge them. */ + err = re_node_set_merge (&new_nodes, eclosure); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&new_nodes); + return err; + } + } + else + { + /* There are problematic nodes, re-calculate incrementally. */ + err = check_arrival_expand_ecl_sub (dfa, &new_nodes, cur_node, + ex_subexp, type); + if (BE (err != REG_NOERROR, 0)) + { + re_node_set_free (&new_nodes); + return err; + } + } + } + re_node_set_free (cur_nodes); + *cur_nodes = new_nodes; + return REG_NOERROR; +} + +/* Helper function for check_arrival_expand_ecl. + Check incrementally the epsilon closure of TARGET, and if it isn't + problematic append it to DST_NODES. */ + +static reg_errcode_t +internal_function +check_arrival_expand_ecl_sub (const re_dfa_t *dfa, re_node_set *dst_nodes, + int target, int ex_subexp, int type) +{ + int cur_node; + for (cur_node = target; !re_node_set_contains (dst_nodes, cur_node);) + { + int err; + + if (dfa->nodes[cur_node].type == type + && dfa->nodes[cur_node].opr.idx == ex_subexp) + { + if (type == OP_CLOSE_SUBEXP) + { + err = re_node_set_insert (dst_nodes, cur_node); + if (BE (err == -1, 0)) + return REG_ESPACE; + } + break; + } + err = re_node_set_insert (dst_nodes, cur_node); + if (BE (err == -1, 0)) + return REG_ESPACE; + if (dfa->edests[cur_node].nelem == 0) + break; + if (dfa->edests[cur_node].nelem == 2) + { + err = check_arrival_expand_ecl_sub (dfa, dst_nodes, + dfa->edests[cur_node].elems[1], + ex_subexp, type); + if (BE (err != REG_NOERROR, 0)) + return err; + } + cur_node = dfa->edests[cur_node].elems[0]; + } + return REG_NOERROR; +} + + +/* For all the back references in the current state, calculate the + destination of the back references by the appropriate entry + in MCTX->BKREF_ENTS. */ + +static reg_errcode_t +internal_function +expand_bkref_cache (re_match_context_t *mctx, re_node_set *cur_nodes, + int cur_str, int subexp_num, int type) +{ + const re_dfa_t *const dfa = mctx->dfa; + reg_errcode_t err; + int cache_idx_start = search_cur_bkref_entry (mctx, cur_str); + struct re_backref_cache_entry *ent; + + if (cache_idx_start == -1) + return REG_NOERROR; + + restart: + ent = mctx->bkref_ents + cache_idx_start; + do + { + int to_idx, next_node; + + /* Is this entry ENT is appropriate? */ + if (!re_node_set_contains (cur_nodes, ent->node)) + continue; /* No. */ + + to_idx = cur_str + ent->subexp_to - ent->subexp_from; + /* Calculate the destination of the back reference, and append it + to MCTX->STATE_LOG. */ + if (to_idx == cur_str) + { + /* The backreference did epsilon transit, we must re-check all the + node in the current state. */ + re_node_set new_dests; + reg_errcode_t err2, err3; + next_node = dfa->edests[ent->node].elems[0]; + if (re_node_set_contains (cur_nodes, next_node)) + continue; + err = re_node_set_init_1 (&new_dests, next_node); + err2 = check_arrival_expand_ecl (dfa, &new_dests, subexp_num, type); + err3 = re_node_set_merge (cur_nodes, &new_dests); + re_node_set_free (&new_dests); + if (BE (err != REG_NOERROR || err2 != REG_NOERROR + || err3 != REG_NOERROR, 0)) + { + err = (err != REG_NOERROR ? err + : (err2 != REG_NOERROR ? err2 : err3)); + return err; + } + /* TODO: It is still inefficient... */ + goto restart; + } + else + { + re_node_set union_set; + next_node = dfa->nexts[ent->node]; + if (mctx->state_log[to_idx]) + { + int ret; + if (re_node_set_contains (&mctx->state_log[to_idx]->nodes, + next_node)) + continue; + err = re_node_set_init_copy (&union_set, + &mctx->state_log[to_idx]->nodes); + ret = re_node_set_insert (&union_set, next_node); + if (BE (err != REG_NOERROR || ret < 0, 0)) + { + re_node_set_free (&union_set); + err = err != REG_NOERROR ? err : REG_ESPACE; + return err; + } + } + else + { + err = re_node_set_init_1 (&union_set, next_node); + if (BE (err != REG_NOERROR, 0)) + return err; + } + mctx->state_log[to_idx] = re_acquire_state (&err, dfa, &union_set); + re_node_set_free (&union_set); + if (BE (mctx->state_log[to_idx] == NULL + && err != REG_NOERROR, 0)) + return err; + } + } + while (ent++->more); + return REG_NOERROR; +} + +/* Build transition table for the state. + Return 1 if succeeded, otherwise return NULL. */ + +static int +internal_function +build_trtable (const re_dfa_t *dfa, re_dfastate_t *state) +{ + reg_errcode_t err; + int i, j, ch, need_word_trtable = 0; + bitset_word_t elem, mask; + bool dests_node_malloced = false; + bool dest_states_malloced = false; + int ndests; /* Number of the destination states from `state'. */ + re_dfastate_t **trtable; + re_dfastate_t **dest_states = NULL, **dest_states_word, **dest_states_nl; + re_node_set follows, *dests_node; + bitset_t *dests_ch; + bitset_t acceptable; + + struct dests_alloc + { + re_node_set dests_node[SBC_MAX]; + bitset_t dests_ch[SBC_MAX]; + } *dests_alloc; + + /* We build DFA states which corresponds to the destination nodes + from `state'. `dests_node[i]' represents the nodes which i-th + destination state contains, and `dests_ch[i]' represents the + characters which i-th destination state accepts. */ + if (__libc_use_alloca (sizeof (struct dests_alloc))) + dests_alloc = (struct dests_alloc *) alloca (sizeof (struct dests_alloc)); + else + { + dests_alloc = re_malloc (struct dests_alloc, 1); + if (BE (dests_alloc == NULL, 0)) + return 0; + dests_node_malloced = true; + } + dests_node = dests_alloc->dests_node; + dests_ch = dests_alloc->dests_ch; + + /* Initialize transiton table. */ + state->word_trtable = state->trtable = NULL; + + /* At first, group all nodes belonging to `state' into several + destinations. */ + ndests = group_nodes_into_DFAstates (dfa, state, dests_node, dests_ch); + if (BE (ndests <= 0, 0)) + { + if (dests_node_malloced) + free (dests_alloc); + /* Return 0 in case of an error, 1 otherwise. */ + if (ndests == 0) + { + state->trtable = (re_dfastate_t **) + calloc (sizeof (re_dfastate_t *), SBC_MAX); + return 1; + } + return 0; + } + + err = re_node_set_alloc (&follows, ndests + 1); + if (BE (err != REG_NOERROR, 0)) + goto out_free; + + if (__libc_use_alloca ((sizeof (re_node_set) + sizeof (bitset_t)) * SBC_MAX + + ndests * 3 * sizeof (re_dfastate_t *))) + dest_states = (re_dfastate_t **) + alloca (ndests * 3 * sizeof (re_dfastate_t *)); + else + { + dest_states = (re_dfastate_t **) + malloc (ndests * 3 * sizeof (re_dfastate_t *)); + if (BE (dest_states == NULL, 0)) + { +out_free: + if (dest_states_malloced) + free (dest_states); + re_node_set_free (&follows); + for (i = 0; i < ndests; ++i) + re_node_set_free (dests_node + i); + if (dests_node_malloced) + free (dests_alloc); + return 0; + } + dest_states_malloced = true; + } + dest_states_word = dest_states + ndests; + dest_states_nl = dest_states_word + ndests; + bitset_empty (acceptable); + + /* Then build the states for all destinations. */ + for (i = 0; i < ndests; ++i) + { + int next_node; + re_node_set_empty (&follows); + /* Merge the follows of this destination states. */ + for (j = 0; j < dests_node[i].nelem; ++j) + { + next_node = dfa->nexts[dests_node[i].elems[j]]; + if (next_node != -1) + { + err = re_node_set_merge (&follows, dfa->eclosures + next_node); + if (BE (err != REG_NOERROR, 0)) + goto out_free; + } + } + dest_states[i] = re_acquire_state_context (&err, dfa, &follows, 0); + if (BE (dest_states[i] == NULL && err != REG_NOERROR, 0)) + goto out_free; + /* If the new state has context constraint, + build appropriate states for these contexts. */ + if (dest_states[i]->has_constraint) + { + dest_states_word[i] = re_acquire_state_context (&err, dfa, &follows, + CONTEXT_WORD); + if (BE (dest_states_word[i] == NULL && err != REG_NOERROR, 0)) + goto out_free; + + if (dest_states[i] != dest_states_word[i] && dfa->mb_cur_max > 1) + need_word_trtable = 1; + + dest_states_nl[i] = re_acquire_state_context (&err, dfa, &follows, + CONTEXT_NEWLINE); + if (BE (dest_states_nl[i] == NULL && err != REG_NOERROR, 0)) + goto out_free; + } + else + { + dest_states_word[i] = dest_states[i]; + dest_states_nl[i] = dest_states[i]; + } + bitset_merge (acceptable, dests_ch[i]); + } + + if (!BE (need_word_trtable, 0)) + { + /* We don't care about whether the following character is a word + character, or we are in a single-byte character set so we can + discern by looking at the character code: allocate a + 256-entry transition table. */ + trtable = state->trtable = + (re_dfastate_t **) calloc (sizeof (re_dfastate_t *), SBC_MAX); + if (BE (trtable == NULL, 0)) + goto out_free; + + /* For all characters ch...: */ + for (i = 0; i < BITSET_WORDS; ++i) + for (ch = i * BITSET_WORD_BITS, elem = acceptable[i], mask = 1; + elem; + mask <<= 1, elem >>= 1, ++ch) + if (BE (elem & 1, 0)) + { + /* There must be exactly one destination which accepts + character ch. See group_nodes_into_DFAstates. */ + for (j = 0; (dests_ch[j][i] & mask) == 0; ++j) + ; + + /* j-th destination accepts the word character ch. */ + if (dfa->word_char[i] & mask) + trtable[ch] = dest_states_word[j]; + else + trtable[ch] = dest_states[j]; + } + } + else + { + /* We care about whether the following character is a word + character, and we are in a multi-byte character set: discern + by looking at the character code: build two 256-entry + transition tables, one starting at trtable[0] and one + starting at trtable[SBC_MAX]. */ + trtable = state->word_trtable = + (re_dfastate_t **) calloc (sizeof (re_dfastate_t *), 2 * SBC_MAX); + if (BE (trtable == NULL, 0)) + goto out_free; + + /* For all characters ch...: */ + for (i = 0; i < BITSET_WORDS; ++i) + for (ch = i * BITSET_WORD_BITS, elem = acceptable[i], mask = 1; + elem; + mask <<= 1, elem >>= 1, ++ch) + if (BE (elem & 1, 0)) + { + /* There must be exactly one destination which accepts + character ch. See group_nodes_into_DFAstates. */ + for (j = 0; (dests_ch[j][i] & mask) == 0; ++j) + ; + + /* j-th destination accepts the word character ch. */ + trtable[ch] = dest_states[j]; + trtable[ch + SBC_MAX] = dest_states_word[j]; + } + } + + /* new line */ + if (bitset_contain (acceptable, NEWLINE_CHAR)) + { + /* The current state accepts newline character. */ + for (j = 0; j < ndests; ++j) + if (bitset_contain (dests_ch[j], NEWLINE_CHAR)) + { + /* k-th destination accepts newline character. */ + trtable[NEWLINE_CHAR] = dest_states_nl[j]; + if (need_word_trtable) + trtable[NEWLINE_CHAR + SBC_MAX] = dest_states_nl[j]; + /* There must be only one destination which accepts + newline. See group_nodes_into_DFAstates. */ + break; + } + } + + if (dest_states_malloced) + free (dest_states); + + re_node_set_free (&follows); + for (i = 0; i < ndests; ++i) + re_node_set_free (dests_node + i); + + if (dests_node_malloced) + free (dests_alloc); + + return 1; +} + +/* Group all nodes belonging to STATE into several destinations. + Then for all destinations, set the nodes belonging to the destination + to DESTS_NODE[i] and set the characters accepted by the destination + to DEST_CH[i]. This function return the number of destinations. */ + +static int +internal_function +group_nodes_into_DFAstates (const re_dfa_t *dfa, const re_dfastate_t *state, + re_node_set *dests_node, bitset_t *dests_ch) +{ + reg_errcode_t err; + int result; + int i, j, k; + int ndests; /* Number of the destinations from `state'. */ + bitset_t accepts; /* Characters a node can accept. */ + const re_node_set *cur_nodes = &state->nodes; + bitset_empty (accepts); + ndests = 0; + + /* For all the nodes belonging to `state', */ + for (i = 0; i < cur_nodes->nelem; ++i) + { + re_token_t *node = &dfa->nodes[cur_nodes->elems[i]]; + re_token_type_t type = node->type; + unsigned int constraint = node->constraint; + + /* Enumerate all single byte character this node can accept. */ + if (type == CHARACTER) + bitset_set (accepts, node->opr.c); + else if (type == SIMPLE_BRACKET) + { + bitset_merge (accepts, node->opr.sbcset); + } + else if (type == OP_PERIOD) + { +#ifdef RE_ENABLE_I18N + if (dfa->mb_cur_max > 1) + bitset_merge (accepts, dfa->sb_char); + else +#endif + bitset_set_all (accepts); + if (!(dfa->syntax & RE_DOT_NEWLINE)) + bitset_clear (accepts, '\n'); + if (dfa->syntax & RE_DOT_NOT_NULL) + bitset_clear (accepts, '\0'); + } +#ifdef RE_ENABLE_I18N + else if (type == OP_UTF8_PERIOD) + { + memset (accepts, '\xff', sizeof (bitset_t) / 2); + if (!(dfa->syntax & RE_DOT_NEWLINE)) + bitset_clear (accepts, '\n'); + if (dfa->syntax & RE_DOT_NOT_NULL) + bitset_clear (accepts, '\0'); + } +#endif + else + continue; + + /* Check the `accepts' and sift the characters which are not + match it the context. */ + if (constraint) + { + if (constraint & NEXT_NEWLINE_CONSTRAINT) + { + bool accepts_newline = bitset_contain (accepts, NEWLINE_CHAR); + bitset_empty (accepts); + if (accepts_newline) + bitset_set (accepts, NEWLINE_CHAR); + else + continue; + } + if (constraint & NEXT_ENDBUF_CONSTRAINT) + { + bitset_empty (accepts); + continue; + } + + if (constraint & NEXT_WORD_CONSTRAINT) + { + bitset_word_t any_set = 0; + if (type == CHARACTER && !node->word_char) + { + bitset_empty (accepts); + continue; + } +#ifdef RE_ENABLE_I18N + if (dfa->mb_cur_max > 1) + for (j = 0; j < BITSET_WORDS; ++j) + any_set |= (accepts[j] &= (dfa->word_char[j] | ~dfa->sb_char[j])); + else +#endif + for (j = 0; j < BITSET_WORDS; ++j) + any_set |= (accepts[j] &= dfa->word_char[j]); + if (!any_set) + continue; + } + if (constraint & NEXT_NOTWORD_CONSTRAINT) + { + bitset_word_t any_set = 0; + if (type == CHARACTER && node->word_char) + { + bitset_empty (accepts); + continue; + } +#ifdef RE_ENABLE_I18N + if (dfa->mb_cur_max > 1) + for (j = 0; j < BITSET_WORDS; ++j) + any_set |= (accepts[j] &= ~(dfa->word_char[j] & dfa->sb_char[j])); + else +#endif + for (j = 0; j < BITSET_WORDS; ++j) + any_set |= (accepts[j] &= ~dfa->word_char[j]); + if (!any_set) + continue; + } + } + + /* Then divide `accepts' into DFA states, or create a new + state. Above, we make sure that accepts is not empty. */ + for (j = 0; j < ndests; ++j) + { + bitset_t intersec; /* Intersection sets, see below. */ + bitset_t remains; + /* Flags, see below. */ + bitset_word_t has_intersec, not_subset, not_consumed; + + /* Optimization, skip if this state doesn't accept the character. */ + if (type == CHARACTER && !bitset_contain (dests_ch[j], node->opr.c)) + continue; + + /* Enumerate the intersection set of this state and `accepts'. */ + has_intersec = 0; + for (k = 0; k < BITSET_WORDS; ++k) + has_intersec |= intersec[k] = accepts[k] & dests_ch[j][k]; + /* And skip if the intersection set is empty. */ + if (!has_intersec) + continue; + + /* Then check if this state is a subset of `accepts'. */ + not_subset = not_consumed = 0; + for (k = 0; k < BITSET_WORDS; ++k) + { + not_subset |= remains[k] = ~accepts[k] & dests_ch[j][k]; + not_consumed |= accepts[k] = accepts[k] & ~dests_ch[j][k]; + } + + /* If this state isn't a subset of `accepts', create a + new group state, which has the `remains'. */ + if (not_subset) + { + bitset_copy (dests_ch[ndests], remains); + bitset_copy (dests_ch[j], intersec); + err = re_node_set_init_copy (dests_node + ndests, &dests_node[j]); + if (BE (err != REG_NOERROR, 0)) + goto error_return; + ++ndests; + } + + /* Put the position in the current group. */ + result = re_node_set_insert (&dests_node[j], cur_nodes->elems[i]); + if (BE (result < 0, 0)) + goto error_return; + + /* If all characters are consumed, go to next node. */ + if (!not_consumed) + break; + } + /* Some characters remain, create a new group. */ + if (j == ndests) + { + bitset_copy (dests_ch[ndests], accepts); + err = re_node_set_init_1 (dests_node + ndests, cur_nodes->elems[i]); + if (BE (err != REG_NOERROR, 0)) + goto error_return; + ++ndests; + bitset_empty (accepts); + } + } + return ndests; + error_return: + for (j = 0; j < ndests; ++j) + re_node_set_free (dests_node + j); + return -1; +} + +#ifdef RE_ENABLE_I18N +/* Check how many bytes the node `dfa->nodes[node_idx]' accepts. + Return the number of the bytes the node accepts. + STR_IDX is the current index of the input string. + + This function handles the nodes which can accept one character, or + one collating element like '.', '[a-z]', opposite to the other nodes + can only accept one byte. */ + +static int +internal_function +check_node_accept_bytes (const re_dfa_t *dfa, int node_idx, + const re_string_t *input, int str_idx) +{ + const re_token_t *node = dfa->nodes + node_idx; + int char_len, elem_len; + int i; + + if (BE (node->type == OP_UTF8_PERIOD, 0)) + { + unsigned char c = re_string_byte_at (input, str_idx), d; + if (BE (c < 0xc2, 1)) + return 0; + + if (str_idx + 2 > input->len) + return 0; + + d = re_string_byte_at (input, str_idx + 1); + if (c < 0xe0) + return (d < 0x80 || d > 0xbf) ? 0 : 2; + else if (c < 0xf0) + { + char_len = 3; + if (c == 0xe0 && d < 0xa0) + return 0; + } + else if (c < 0xf8) + { + char_len = 4; + if (c == 0xf0 && d < 0x90) + return 0; + } + else if (c < 0xfc) + { + char_len = 5; + if (c == 0xf8 && d < 0x88) + return 0; + } + else if (c < 0xfe) + { + char_len = 6; + if (c == 0xfc && d < 0x84) + return 0; + } + else + return 0; + + if (str_idx + char_len > input->len) + return 0; + + for (i = 1; i < char_len; ++i) + { + d = re_string_byte_at (input, str_idx + i); + if (d < 0x80 || d > 0xbf) + return 0; + } + return char_len; + } + + char_len = re_string_char_size_at (input, str_idx); + if (node->type == OP_PERIOD) + { + if (char_len <= 1) + return 0; + /* FIXME: I don't think this if is needed, as both '\n' + and '\0' are char_len == 1. */ + /* '.' accepts any one character except the following two cases. */ + if ((!(dfa->syntax & RE_DOT_NEWLINE) && + re_string_byte_at (input, str_idx) == '\n') || + ((dfa->syntax & RE_DOT_NOT_NULL) && + re_string_byte_at (input, str_idx) == '\0')) + return 0; + return char_len; + } + + elem_len = re_string_elem_size_at (input, str_idx); + if ((elem_len <= 1 && char_len <= 1) || char_len == 0) + return 0; + + if (node->type == COMPLEX_BRACKET) + { + const re_charset_t *cset = node->opr.mbcset; +# ifdef _LIBC + const unsigned char *pin + = ((const unsigned char *) re_string_get_buffer (input) + str_idx); + int j; + uint32_t nrules; +# endif /* _LIBC */ + int match_len = 0; + wchar_t wc = ((cset->nranges || cset->nchar_classes || cset->nmbchars) + ? re_string_wchar_at (input, str_idx) : 0); + + /* match with multibyte character? */ + for (i = 0; i < cset->nmbchars; ++i) + if (wc == cset->mbchars[i]) + { + match_len = char_len; + goto check_node_accept_bytes_match; + } + /* match with character_class? */ + for (i = 0; i < cset->nchar_classes; ++i) + { + wctype_t wt = cset->char_classes[i]; + if (__iswctype (wc, wt)) + { + match_len = char_len; + goto check_node_accept_bytes_match; + } + } + +# ifdef _LIBC + nrules = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES); + if (nrules != 0) + { + unsigned int in_collseq = 0; + const int32_t *table, *indirect; + const unsigned char *weights, *extra; + const char *collseqwc; + int32_t idx; + /* This #include defines a local function! */ +# include + + /* match with collating_symbol? */ + if (cset->ncoll_syms) + extra = (const unsigned char *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_SYMB_EXTRAMB); + for (i = 0; i < cset->ncoll_syms; ++i) + { + const unsigned char *coll_sym = extra + cset->coll_syms[i]; + /* Compare the length of input collating element and + the length of current collating element. */ + if (*coll_sym != elem_len) + continue; + /* Compare each bytes. */ + for (j = 0; j < *coll_sym; j++) + if (pin[j] != coll_sym[1 + j]) + break; + if (j == *coll_sym) + { + /* Match if every bytes is equal. */ + match_len = j; + goto check_node_accept_bytes_match; + } + } + + if (cset->nranges) + { + if (elem_len <= char_len) + { + collseqwc = _NL_CURRENT (LC_COLLATE, _NL_COLLATE_COLLSEQWC); + in_collseq = __collseq_table_lookup (collseqwc, wc); + } + else + in_collseq = find_collation_sequence_value (pin, elem_len); + } + /* match with range expression? */ + for (i = 0; i < cset->nranges; ++i) + if (cset->range_starts[i] <= in_collseq + && in_collseq <= cset->range_ends[i]) + { + match_len = elem_len; + goto check_node_accept_bytes_match; + } + + /* match with equivalence_class? */ + if (cset->nequiv_classes) + { + const unsigned char *cp = pin; + table = (const int32_t *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_TABLEMB); + weights = (const unsigned char *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_WEIGHTMB); + extra = (const unsigned char *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_EXTRAMB); + indirect = (const int32_t *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_INDIRECTMB); + idx = findidx (&cp); + if (idx > 0) + for (i = 0; i < cset->nequiv_classes; ++i) + { + int32_t equiv_class_idx = cset->equiv_classes[i]; + size_t weight_len = weights[idx]; + if (weight_len == weights[equiv_class_idx]) + { + int cnt = 0; + while (cnt <= weight_len + && (weights[equiv_class_idx + 1 + cnt] + == weights[idx + 1 + cnt])) + ++cnt; + if (cnt > weight_len) + { + match_len = elem_len; + goto check_node_accept_bytes_match; + } + } + } + } + } + else +# endif /* _LIBC */ + { + /* match with range expression? */ +#if __GNUC__ >= 2 + wchar_t cmp_buf[] = {L'\0', L'\0', wc, L'\0', L'\0', L'\0'}; +#else + wchar_t cmp_buf[] = {L'\0', L'\0', L'\0', L'\0', L'\0', L'\0'}; + cmp_buf[2] = wc; +#endif + for (i = 0; i < cset->nranges; ++i) + { + cmp_buf[0] = cset->range_starts[i]; + cmp_buf[4] = cset->range_ends[i]; + if (wcscoll (cmp_buf, cmp_buf + 2) <= 0 + && wcscoll (cmp_buf + 2, cmp_buf + 4) <= 0) + { + match_len = char_len; + goto check_node_accept_bytes_match; + } + } + } + check_node_accept_bytes_match: + if (!cset->non_match) + return match_len; + else + { + if (match_len > 0) + return 0; + else + return (elem_len > char_len) ? elem_len : char_len; + } + } + return 0; +} + +# ifdef _LIBC +static unsigned int +internal_function +find_collation_sequence_value (const unsigned char *mbs, size_t mbs_len) +{ + uint32_t nrules = _NL_CURRENT_WORD (LC_COLLATE, _NL_COLLATE_NRULES); + if (nrules == 0) + { + if (mbs_len == 1) + { + /* No valid character. Match it as a single byte character. */ + const unsigned char *collseq = (const unsigned char *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_COLLSEQMB); + return collseq[mbs[0]]; + } + return UINT_MAX; + } + else + { + int32_t idx; + const unsigned char *extra = (const unsigned char *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_SYMB_EXTRAMB); + int32_t extrasize = (const unsigned char *) + _NL_CURRENT (LC_COLLATE, _NL_COLLATE_SYMB_EXTRAMB + 1) - extra; + + for (idx = 0; idx < extrasize;) + { + int mbs_cnt, found = 0; + int32_t elem_mbs_len; + /* Skip the name of collating element name. */ + idx = idx + extra[idx] + 1; + elem_mbs_len = extra[idx++]; + if (mbs_len == elem_mbs_len) + { + for (mbs_cnt = 0; mbs_cnt < elem_mbs_len; ++mbs_cnt) + if (extra[idx + mbs_cnt] != mbs[mbs_cnt]) + break; + if (mbs_cnt == elem_mbs_len) + /* Found the entry. */ + found = 1; + } + /* Skip the byte sequence of the collating element. */ + idx += elem_mbs_len; + /* Adjust for the alignment. */ + idx = (idx + 3) & ~3; + /* Skip the collation sequence value. */ + idx += sizeof (uint32_t); + /* Skip the wide char sequence of the collating element. */ + idx = idx + sizeof (uint32_t) * (extra[idx] + 1); + /* If we found the entry, return the sequence value. */ + if (found) + return *(uint32_t *) (extra + idx); + /* Skip the collation sequence value. */ + idx += sizeof (uint32_t); + } + return UINT_MAX; + } +} +# endif /* _LIBC */ +#endif /* RE_ENABLE_I18N */ + +/* Check whether the node accepts the byte which is IDX-th + byte of the INPUT. */ + +static int +internal_function +check_node_accept (const re_match_context_t *mctx, const re_token_t *node, + int idx) +{ + unsigned char ch; + ch = re_string_byte_at (&mctx->input, idx); + switch (node->type) + { + case CHARACTER: + if (node->opr.c != ch) + return 0; + break; + + case SIMPLE_BRACKET: + if (!bitset_contain (node->opr.sbcset, ch)) + return 0; + break; + +#ifdef RE_ENABLE_I18N + case OP_UTF8_PERIOD: + if (ch >= 0x80) + return 0; + /* FALLTHROUGH */ +#endif + case OP_PERIOD: + if ((ch == '\n' && !(mctx->dfa->syntax & RE_DOT_NEWLINE)) + || (ch == '\0' && (mctx->dfa->syntax & RE_DOT_NOT_NULL))) + return 0; + break; + + default: + return 0; + } + + if (node->constraint) + { + /* The node has constraints. Check whether the current context + satisfies the constraints. */ + unsigned int context = re_string_context_at (&mctx->input, idx, + mctx->eflags); + if (NOT_SATISFY_NEXT_CONSTRAINT (node->constraint, context)) + return 0; + } + + return 1; +} + +/* Extend the buffers, if the buffers have run out. */ + +static reg_errcode_t +internal_function +extend_buffers (re_match_context_t *mctx) +{ + reg_errcode_t ret; + re_string_t *pstr = &mctx->input; + + /* Double the lengthes of the buffers. */ + ret = re_string_realloc_buffers (pstr, pstr->bufs_len * 2); + if (BE (ret != REG_NOERROR, 0)) + return ret; + + if (mctx->state_log != NULL) + { + /* And double the length of state_log. */ + /* XXX We have no indication of the size of this buffer. If this + allocation fail we have no indication that the state_log array + does not have the right size. */ + re_dfastate_t **new_array = re_realloc (mctx->state_log, re_dfastate_t *, + pstr->bufs_len + 1); + if (BE (new_array == NULL, 0)) + return REG_ESPACE; + mctx->state_log = new_array; + } + + /* Then reconstruct the buffers. */ + if (pstr->icase) + { +#ifdef RE_ENABLE_I18N + if (pstr->mb_cur_max > 1) + { + ret = build_wcs_upper_buffer (pstr); + if (BE (ret != REG_NOERROR, 0)) + return ret; + } + else +#endif /* RE_ENABLE_I18N */ + build_upper_buffer (pstr); + } + else + { +#ifdef RE_ENABLE_I18N + if (pstr->mb_cur_max > 1) + build_wcs_buffer (pstr); + else +#endif /* RE_ENABLE_I18N */ + { + if (pstr->trans != NULL) + re_string_translate_buffer (pstr); + } + } + return REG_NOERROR; +} + + +/* Functions for matching context. */ + +/* Initialize MCTX. */ + +static reg_errcode_t +internal_function +match_ctx_init (re_match_context_t *mctx, int eflags, int n) +{ + mctx->eflags = eflags; + mctx->match_last = -1; + if (n > 0) + { + mctx->bkref_ents = re_malloc (struct re_backref_cache_entry, n); + mctx->sub_tops = re_malloc (re_sub_match_top_t *, n); + if (BE (mctx->bkref_ents == NULL || mctx->sub_tops == NULL, 0)) + return REG_ESPACE; + } + /* Already zero-ed by the caller. + else + mctx->bkref_ents = NULL; + mctx->nbkref_ents = 0; + mctx->nsub_tops = 0; */ + mctx->abkref_ents = n; + mctx->max_mb_elem_len = 1; + mctx->asub_tops = n; + return REG_NOERROR; +} + +/* Clean the entries which depend on the current input in MCTX. + This function must be invoked when the matcher changes the start index + of the input, or changes the input string. */ + +static void +internal_function +match_ctx_clean (re_match_context_t *mctx) +{ + int st_idx; + for (st_idx = 0; st_idx < mctx->nsub_tops; ++st_idx) + { + int sl_idx; + re_sub_match_top_t *top = mctx->sub_tops[st_idx]; + for (sl_idx = 0; sl_idx < top->nlasts; ++sl_idx) + { + re_sub_match_last_t *last = top->lasts[sl_idx]; + re_free (last->path.array); + re_free (last); + } + re_free (top->lasts); + if (top->path) + { + re_free (top->path->array); + re_free (top->path); + } + free (top); + } + + mctx->nsub_tops = 0; + mctx->nbkref_ents = 0; +} + +/* Free all the memory associated with MCTX. */ + +static void +internal_function +match_ctx_free (re_match_context_t *mctx) +{ + /* First, free all the memory associated with MCTX->SUB_TOPS. */ + match_ctx_clean (mctx); + re_free (mctx->sub_tops); + re_free (mctx->bkref_ents); +} + +/* Add a new backreference entry to MCTX. + Note that we assume that caller never call this function with duplicate + entry, and call with STR_IDX which isn't smaller than any existing entry. +*/ + +static reg_errcode_t +internal_function +match_ctx_add_entry (re_match_context_t *mctx, int node, int str_idx, int from, + int to) +{ + if (mctx->nbkref_ents >= mctx->abkref_ents) + { + struct re_backref_cache_entry* new_entry; + new_entry = re_realloc (mctx->bkref_ents, struct re_backref_cache_entry, + mctx->abkref_ents * 2); + if (BE (new_entry == NULL, 0)) + { + re_free (mctx->bkref_ents); + return REG_ESPACE; + } + mctx->bkref_ents = new_entry; + memset (mctx->bkref_ents + mctx->nbkref_ents, '\0', + sizeof (struct re_backref_cache_entry) * mctx->abkref_ents); + mctx->abkref_ents *= 2; + } + if (mctx->nbkref_ents > 0 + && mctx->bkref_ents[mctx->nbkref_ents - 1].str_idx == str_idx) + mctx->bkref_ents[mctx->nbkref_ents - 1].more = 1; + + mctx->bkref_ents[mctx->nbkref_ents].node = node; + mctx->bkref_ents[mctx->nbkref_ents].str_idx = str_idx; + mctx->bkref_ents[mctx->nbkref_ents].subexp_from = from; + mctx->bkref_ents[mctx->nbkref_ents].subexp_to = to; + + /* This is a cache that saves negative results of check_dst_limits_calc_pos. + If bit N is clear, means that this entry won't epsilon-transition to + an OP_OPEN_SUBEXP or OP_CLOSE_SUBEXP for the N+1-th subexpression. If + it is set, check_dst_limits_calc_pos_1 will recurse and try to find one + such node. + + A backreference does not epsilon-transition unless it is empty, so set + to all zeros if FROM != TO. */ + mctx->bkref_ents[mctx->nbkref_ents].eps_reachable_subexps_map + = (from == to ? ~0 : 0); + + mctx->bkref_ents[mctx->nbkref_ents++].more = 0; + if (mctx->max_mb_elem_len < to - from) + mctx->max_mb_elem_len = to - from; + return REG_NOERROR; +} + +/* Search for the first entry which has the same str_idx, or -1 if none is + found. Note that MCTX->BKREF_ENTS is already sorted by MCTX->STR_IDX. */ + +static int +internal_function +search_cur_bkref_entry (const re_match_context_t *mctx, int str_idx) +{ + int left, right, mid, last; + last = right = mctx->nbkref_ents; + for (left = 0; left < right;) + { + mid = (left + right) / 2; + if (mctx->bkref_ents[mid].str_idx < str_idx) + left = mid + 1; + else + right = mid; + } + if (left < last && mctx->bkref_ents[left].str_idx == str_idx) + return left; + else + return -1; +} + +/* Register the node NODE, whose type is OP_OPEN_SUBEXP, and which matches + at STR_IDX. */ + +static reg_errcode_t +internal_function +match_ctx_add_subtop (re_match_context_t *mctx, int node, int str_idx) +{ +#ifdef DEBUG + assert (mctx->sub_tops != NULL); + assert (mctx->asub_tops > 0); +#endif + if (BE (mctx->nsub_tops == mctx->asub_tops, 0)) + { + int new_asub_tops = mctx->asub_tops * 2; + re_sub_match_top_t **new_array = re_realloc (mctx->sub_tops, + re_sub_match_top_t *, + new_asub_tops); + if (BE (new_array == NULL, 0)) + return REG_ESPACE; + mctx->sub_tops = new_array; + mctx->asub_tops = new_asub_tops; + } + mctx->sub_tops[mctx->nsub_tops] = calloc (1, sizeof (re_sub_match_top_t)); + if (BE (mctx->sub_tops[mctx->nsub_tops] == NULL, 0)) + return REG_ESPACE; + mctx->sub_tops[mctx->nsub_tops]->node = node; + mctx->sub_tops[mctx->nsub_tops++]->str_idx = str_idx; + return REG_NOERROR; +} + +/* Register the node NODE, whose type is OP_CLOSE_SUBEXP, and which matches + at STR_IDX, whose corresponding OP_OPEN_SUBEXP is SUB_TOP. */ + +static re_sub_match_last_t * +internal_function +match_ctx_add_sublast (re_sub_match_top_t *subtop, int node, int str_idx) +{ + re_sub_match_last_t *new_entry; + if (BE (subtop->nlasts == subtop->alasts, 0)) + { + int new_alasts = 2 * subtop->alasts + 1; + re_sub_match_last_t **new_array = re_realloc (subtop->lasts, + re_sub_match_last_t *, + new_alasts); + if (BE (new_array == NULL, 0)) + return NULL; + subtop->lasts = new_array; + subtop->alasts = new_alasts; + } + new_entry = calloc (1, sizeof (re_sub_match_last_t)); + if (BE (new_entry != NULL, 1)) + { + subtop->lasts[subtop->nlasts] = new_entry; + new_entry->node = node; + new_entry->str_idx = str_idx; + ++subtop->nlasts; + } + return new_entry; +} + +static void +internal_function +sift_ctx_init (re_sift_context_t *sctx, re_dfastate_t **sifted_sts, + re_dfastate_t **limited_sts, int last_node, int last_str_idx) +{ + sctx->sifted_states = sifted_sts; + sctx->limited_states = limited_sts; + sctx->last_node = last_node; + sctx->last_str_idx = last_str_idx; + re_node_set_init_empty (&sctx->limits); +} + + +/* Binary backward compatibility. */ +#if _LIBC +# include +# if SHLIB_COMPAT (libc, GLIBC_2_0, GLIBC_2_3) +link_warning (re_max_failures, "the 're_max_failures' variable is obsolete and will go away.") +int re_max_failures = 2000; +# endif +#endif +#endif diff --git a/gkregex.h b/gkregex.h new file mode 100644 index 0000000..807c404 --- /dev/null +++ b/gkregex.h @@ -0,0 +1,556 @@ +/* Definitions for data structures and routines for the regular + expression library. + Copyright (C) 1985,1989-93,1995-98,2000,2001,2002,2003,2005,2006 + Free Software Foundation, Inc. + This file is part of the GNU C Library. + + The GNU C Library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2.1 of the License, or (at your option) any later version. + + The GNU C Library 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 + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with the GNU C Library; if not, write to the Free + Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA + 02111-1307 USA. */ + +#ifndef _REGEX_H +#define _REGEX_H 1 + +#include + +/* Allow the use in C++ code. */ +#ifdef __cplusplus +extern "C" { +#endif + +/* The following two types have to be signed and unsigned integer type + wide enough to hold a value of a pointer. For most ANSI compilers + ptrdiff_t and size_t should be likely OK. Still size of these two + types is 2 for Microsoft C. Ugh... */ +typedef long int s_reg_t; +typedef unsigned long int active_reg_t; + +/* The following bits are used to determine the regexp syntax we + recognize. The set/not-set meanings are chosen so that Emacs syntax + remains the value 0. The bits are given in alphabetical order, and + the definitions shifted by one from the previous bit; thus, when we + add or remove a bit, only one other definition need change. */ +typedef unsigned long int reg_syntax_t; + +/* If this bit is not set, then \ inside a bracket expression is literal. + If set, then such a \ quotes the following character. */ +#define RE_BACKSLASH_ESCAPE_IN_LISTS ((unsigned long int) 1) + +/* If this bit is not set, then + and ? are operators, and \+ and \? are + literals. + If set, then \+ and \? are operators and + and ? are literals. */ +#define RE_BK_PLUS_QM (RE_BACKSLASH_ESCAPE_IN_LISTS << 1) + +/* If this bit is set, then character classes are supported. They are: + [:alpha:], [:upper:], [:lower:], [:digit:], [:alnum:], [:xdigit:], + [:space:], [:print:], [:punct:], [:graph:], and [:cntrl:]. + If not set, then character classes are not supported. */ +#define RE_CHAR_CLASSES (RE_BK_PLUS_QM << 1) + +/* If this bit is set, then ^ and $ are always anchors (outside bracket + expressions, of course). + If this bit is not set, then it depends: + ^ is an anchor if it is at the beginning of a regular + expression or after an open-group or an alternation operator; + $ is an anchor if it is at the end of a regular expression, or + before a close-group or an alternation operator. + + This bit could be (re)combined with RE_CONTEXT_INDEP_OPS, because + POSIX draft 11.2 says that * etc. in leading positions is undefined. + We already implemented a previous draft which made those constructs + invalid, though, so we haven't changed the code back. */ +#define RE_CONTEXT_INDEP_ANCHORS (RE_CHAR_CLASSES << 1) + +/* If this bit is set, then special characters are always special + regardless of where they are in the pattern. + If this bit is not set, then special characters are special only in + some contexts; otherwise they are ordinary. Specifically, + * + ? and intervals are only special when not after the beginning, + open-group, or alternation operator. */ +#define RE_CONTEXT_INDEP_OPS (RE_CONTEXT_INDEP_ANCHORS << 1) + +/* If this bit is set, then *, +, ?, and { cannot be first in an re or + immediately after an alternation or begin-group operator. */ +#define RE_CONTEXT_INVALID_OPS (RE_CONTEXT_INDEP_OPS << 1) + +/* If this bit is set, then . matches newline. + If not set, then it doesn't. */ +#define RE_DOT_NEWLINE (RE_CONTEXT_INVALID_OPS << 1) + +/* If this bit is set, then . doesn't match NUL. + If not set, then it does. */ +#define RE_DOT_NOT_NULL (RE_DOT_NEWLINE << 1) + +/* If this bit is set, nonmatching lists [^...] do not match newline. + If not set, they do. */ +#define RE_HAT_LISTS_NOT_NEWLINE (RE_DOT_NOT_NULL << 1) + +/* If this bit is set, either \{...\} or {...} defines an + interval, depending on RE_NO_BK_BRACES. + If not set, \{, \}, {, and } are literals. */ +#define RE_INTERVALS (RE_HAT_LISTS_NOT_NEWLINE << 1) + +/* If this bit is set, +, ? and | aren't recognized as operators. + If not set, they are. */ +#define RE_LIMITED_OPS (RE_INTERVALS << 1) + +/* If this bit is set, newline is an alternation operator. + If not set, newline is literal. */ +#define RE_NEWLINE_ALT (RE_LIMITED_OPS << 1) + +/* If this bit is set, then `{...}' defines an interval, and \{ and \} + are literals. + If not set, then `\{...\}' defines an interval. */ +#define RE_NO_BK_BRACES (RE_NEWLINE_ALT << 1) + +/* If this bit is set, (...) defines a group, and \( and \) are literals. + If not set, \(...\) defines a group, and ( and ) are literals. */ +#define RE_NO_BK_PARENS (RE_NO_BK_BRACES << 1) + +/* If this bit is set, then \ matches . + If not set, then \ is a back-reference. */ +#define RE_NO_BK_REFS (RE_NO_BK_PARENS << 1) + +/* If this bit is set, then | is an alternation operator, and \| is literal. + If not set, then \| is an alternation operator, and | is literal. */ +#define RE_NO_BK_VBAR (RE_NO_BK_REFS << 1) + +/* If this bit is set, then an ending range point collating higher + than the starting range point, as in [z-a], is invalid. + If not set, then when ending range point collates higher than the + starting range point, the range is ignored. */ +#define RE_NO_EMPTY_RANGES (RE_NO_BK_VBAR << 1) + +/* If this bit is set, then an unmatched ) is ordinary. + If not set, then an unmatched ) is invalid. */ +#define RE_UNMATCHED_RIGHT_PAREN_ORD (RE_NO_EMPTY_RANGES << 1) + +/* If this bit is set, succeed as soon as we match the whole pattern, + without further backtracking. */ +#define RE_NO_POSIX_BACKTRACKING (RE_UNMATCHED_RIGHT_PAREN_ORD << 1) + +/* If this bit is set, do not process the GNU regex operators. + If not set, then the GNU regex operators are recognized. */ +#define RE_NO_GNU_OPS (RE_NO_POSIX_BACKTRACKING << 1) + +/* If this bit is set, turn on internal regex debugging. + If not set, and debugging was on, turn it off. + This only works if regex.c is compiled -DDEBUG. + We define this bit always, so that all that's needed to turn on + debugging is to recompile regex.c; the calling code can always have + this bit set, and it won't affect anything in the normal case. */ +#define RE_DEBUG (RE_NO_GNU_OPS << 1) + +/* If this bit is set, a syntactically invalid interval is treated as + a string of ordinary characters. For example, the ERE 'a{1' is + treated as 'a\{1'. */ +#define RE_INVALID_INTERVAL_ORD (RE_DEBUG << 1) + +/* If this bit is set, then ignore case when matching. + If not set, then case is significant. */ +#define RE_ICASE (RE_INVALID_INTERVAL_ORD << 1) + +/* This bit is used internally like RE_CONTEXT_INDEP_ANCHORS but only + for ^, because it is difficult to scan the regex backwards to find + whether ^ should be special. */ +#define RE_CARET_ANCHORS_HERE (RE_ICASE << 1) + +/* If this bit is set, then \{ cannot be first in an bre or + immediately after an alternation or begin-group operator. */ +#define RE_CONTEXT_INVALID_DUP (RE_CARET_ANCHORS_HERE << 1) + +/* If this bit is set, then no_sub will be set to 1 during + re_compile_pattern. */ +#define RE_NO_SUB (RE_CONTEXT_INVALID_DUP << 1) + +/* This global variable defines the particular regexp syntax to use (for + some interfaces). When a regexp is compiled, the syntax used is + stored in the pattern buffer, so changing this does not affect + already-compiled regexps. */ +extern reg_syntax_t re_syntax_options; + +/* Define combinations of the above bits for the standard possibilities. + (The [[[ comments delimit what gets put into the Texinfo file, so + don't delete them!) */ +/* [[[begin syntaxes]]] */ +#define RE_SYNTAX_EMACS 0 + +#define RE_SYNTAX_AWK \ + (RE_BACKSLASH_ESCAPE_IN_LISTS | RE_DOT_NOT_NULL \ + | RE_NO_BK_PARENS | RE_NO_BK_REFS \ + | RE_NO_BK_VBAR | RE_NO_EMPTY_RANGES \ + | RE_DOT_NEWLINE | RE_CONTEXT_INDEP_ANCHORS \ + | RE_UNMATCHED_RIGHT_PAREN_ORD | RE_NO_GNU_OPS) + +#define RE_SYNTAX_GNU_AWK \ + ((RE_SYNTAX_POSIX_EXTENDED | RE_BACKSLASH_ESCAPE_IN_LISTS | RE_DEBUG) \ + & ~(RE_DOT_NOT_NULL | RE_INTERVALS | RE_CONTEXT_INDEP_OPS \ + | RE_CONTEXT_INVALID_OPS )) + +#define RE_SYNTAX_POSIX_AWK \ + (RE_SYNTAX_POSIX_EXTENDED | RE_BACKSLASH_ESCAPE_IN_LISTS \ + | RE_INTERVALS | RE_NO_GNU_OPS) + +#define RE_SYNTAX_GREP \ + (RE_BK_PLUS_QM | RE_CHAR_CLASSES \ + | RE_HAT_LISTS_NOT_NEWLINE | RE_INTERVALS \ + | RE_NEWLINE_ALT) + +#define RE_SYNTAX_EGREP \ + (RE_CHAR_CLASSES | RE_CONTEXT_INDEP_ANCHORS \ + | RE_CONTEXT_INDEP_OPS | RE_HAT_LISTS_NOT_NEWLINE \ + | RE_NEWLINE_ALT | RE_NO_BK_PARENS \ + | RE_NO_BK_VBAR) + +#define RE_SYNTAX_POSIX_EGREP \ + (RE_SYNTAX_EGREP | RE_INTERVALS | RE_NO_BK_BRACES \ + | RE_INVALID_INTERVAL_ORD) + +/* P1003.2/D11.2, section 4.20.7.1, lines 5078ff. */ +#define RE_SYNTAX_ED RE_SYNTAX_POSIX_BASIC + +#define RE_SYNTAX_SED RE_SYNTAX_POSIX_BASIC + +/* Syntax bits common to both basic and extended POSIX regex syntax. */ +#define _RE_SYNTAX_POSIX_COMMON \ + (RE_CHAR_CLASSES | RE_DOT_NEWLINE | RE_DOT_NOT_NULL \ + | RE_INTERVALS | RE_NO_EMPTY_RANGES) + +#define RE_SYNTAX_POSIX_BASIC \ + (_RE_SYNTAX_POSIX_COMMON | RE_BK_PLUS_QM | RE_CONTEXT_INVALID_DUP) + +/* Differs from ..._POSIX_BASIC only in that RE_BK_PLUS_QM becomes + RE_LIMITED_OPS, i.e., \? \+ \| are not recognized. Actually, this + isn't minimal, since other operators, such as \`, aren't disabled. */ +#define RE_SYNTAX_POSIX_MINIMAL_BASIC \ + (_RE_SYNTAX_POSIX_COMMON | RE_LIMITED_OPS) + +#define RE_SYNTAX_POSIX_EXTENDED \ + (_RE_SYNTAX_POSIX_COMMON | RE_CONTEXT_INDEP_ANCHORS \ + | RE_CONTEXT_INDEP_OPS | RE_NO_BK_BRACES \ + | RE_NO_BK_PARENS | RE_NO_BK_VBAR \ + | RE_CONTEXT_INVALID_OPS | RE_UNMATCHED_RIGHT_PAREN_ORD) + +/* Differs from ..._POSIX_EXTENDED in that RE_CONTEXT_INDEP_OPS is + removed and RE_NO_BK_REFS is added. */ +#define RE_SYNTAX_POSIX_MINIMAL_EXTENDED \ + (_RE_SYNTAX_POSIX_COMMON | RE_CONTEXT_INDEP_ANCHORS \ + | RE_CONTEXT_INVALID_OPS | RE_NO_BK_BRACES \ + | RE_NO_BK_PARENS | RE_NO_BK_REFS \ + | RE_NO_BK_VBAR | RE_UNMATCHED_RIGHT_PAREN_ORD) +/* [[[end syntaxes]]] */ + +/* Maximum number of duplicates an interval can allow. Some systems + (erroneously) define this in other header files, but we want our + value, so remove any previous define. */ +#ifdef RE_DUP_MAX +# undef RE_DUP_MAX +#endif +/* If sizeof(int) == 2, then ((1 << 15) - 1) overflows. */ +#define RE_DUP_MAX (0x7fff) + + +/* POSIX `cflags' bits (i.e., information for `regcomp'). */ + +/* If this bit is set, then use extended regular expression syntax. + If not set, then use basic regular expression syntax. */ +#define REG_EXTENDED 1 + +/* If this bit is set, then ignore case when matching. + If not set, then case is significant. */ +#define REG_ICASE (REG_EXTENDED << 1) + +/* If this bit is set, then anchors do not match at newline + characters in the string. + If not set, then anchors do match at newlines. */ +#define REG_NEWLINE (REG_ICASE << 1) + +/* If this bit is set, then report only success or fail in regexec. + If not set, then returns differ between not matching and errors. */ +#define REG_NOSUB (REG_NEWLINE << 1) + + +/* POSIX `eflags' bits (i.e., information for regexec). */ + +/* If this bit is set, then the beginning-of-line operator doesn't match + the beginning of the string (presumably because it's not the + beginning of a line). + If not set, then the beginning-of-line operator does match the + beginning of the string. */ +#define REG_NOTBOL 1 + +/* Like REG_NOTBOL, except for the end-of-line. */ +#define REG_NOTEOL (1 << 1) + +/* Use PMATCH[0] to delimit the start and end of the search in the + buffer. */ +#define REG_STARTEND (1 << 2) + + +/* If any error codes are removed, changed, or added, update the + `re_error_msg' table in regex.c. */ +typedef enum +{ +#ifdef _XOPEN_SOURCE + REG_ENOSYS = -1, /* This will never happen for this implementation. */ +#endif + + REG_NOERROR = 0, /* Success. */ + REG_NOMATCH, /* Didn't find a match (for regexec). */ + + /* POSIX regcomp return error codes. (In the order listed in the + standard.) */ + REG_BADPAT, /* Invalid pattern. */ + REG_ECOLLATE, /* Inalid collating element. */ + REG_ECTYPE, /* Invalid character class name. */ + REG_EESCAPE, /* Trailing backslash. */ + REG_ESUBREG, /* Invalid back reference. */ + REG_EBRACK, /* Unmatched left bracket. */ + REG_EPAREN, /* Parenthesis imbalance. */ + REG_EBRACE, /* Unmatched \{. */ + REG_BADBR, /* Invalid contents of \{\}. */ + REG_ERANGE, /* Invalid range end. */ + REG_ESPACE, /* Ran out of memory. */ + REG_BADRPT, /* No preceding re for repetition op. */ + + /* Error codes we've added. */ + REG_EEND, /* Premature end. */ + REG_ESIZE, /* Compiled pattern bigger than 2^16 bytes. */ + REG_ERPAREN /* Unmatched ) or \); not returned from regcomp. */ +} reg_errcode_t; + +/* This data structure represents a compiled pattern. Before calling + the pattern compiler, the fields `buffer', `allocated', `fastmap', + `translate', and `no_sub' can be set. After the pattern has been + compiled, the `re_nsub' field is available. All other fields are + private to the regex routines. */ + +#ifndef RE_TRANSLATE_TYPE +# define RE_TRANSLATE_TYPE unsigned char * +#endif + +struct re_pattern_buffer +{ + /* Space that holds the compiled pattern. It is declared as + `unsigned char *' because its elements are sometimes used as + array indexes. */ + unsigned char *buffer; + + /* Number of bytes to which `buffer' points. */ + unsigned long int allocated; + + /* Number of bytes actually used in `buffer'. */ + unsigned long int used; + + /* Syntax setting with which the pattern was compiled. */ + reg_syntax_t syntax; + + /* Pointer to a fastmap, if any, otherwise zero. re_search uses the + fastmap, if there is one, to skip over impossible starting points + for matches. */ + char *fastmap; + + /* Either a translate table to apply to all characters before + comparing them, or zero for no translation. The translation is + applied to a pattern when it is compiled and to a string when it + is matched. */ + RE_TRANSLATE_TYPE translate; + + /* Number of subexpressions found by the compiler. */ + size_t re_nsub; + + /* Zero if this pattern cannot match the empty string, one else. + Well, in truth it's used only in `re_search_2', to see whether or + not we should use the fastmap, so we don't set this absolutely + perfectly; see `re_compile_fastmap' (the `duplicate' case). */ + unsigned can_be_null : 1; + + /* If REGS_UNALLOCATED, allocate space in the `regs' structure + for `max (RE_NREGS, re_nsub + 1)' groups. + If REGS_REALLOCATE, reallocate space if necessary. + If REGS_FIXED, use what's there. */ +#define REGS_UNALLOCATED 0 +#define REGS_REALLOCATE 1 +#define REGS_FIXED 2 + unsigned regs_allocated : 2; + + /* Set to zero when `regex_compile' compiles a pattern; set to one + by `re_compile_fastmap' if it updates the fastmap. */ + unsigned fastmap_accurate : 1; + + /* If set, `re_match_2' does not return information about + subexpressions. */ + unsigned no_sub : 1; + + /* If set, a beginning-of-line anchor doesn't match at the beginning + of the string. */ + unsigned not_bol : 1; + + /* Similarly for an end-of-line anchor. */ + unsigned not_eol : 1; + + /* If true, an anchor at a newline matches. */ + unsigned newline_anchor : 1; +}; + +typedef struct re_pattern_buffer regex_t; + +/* Type for byte offsets within the string. POSIX mandates this. */ +typedef int regoff_t; + + +/* This is the structure we store register match data in. See + regex.texinfo for a full description of what registers match. */ +struct re_registers +{ + unsigned num_regs; + regoff_t *start; + regoff_t *end; +}; + + +/* If `regs_allocated' is REGS_UNALLOCATED in the pattern buffer, + `re_match_2' returns information about at least this many registers + the first time a `regs' structure is passed. */ +#ifndef RE_NREGS +# define RE_NREGS 30 +#endif + + +/* POSIX specification for registers. Aside from the different names than + `re_registers', POSIX uses an array of structures, instead of a + structure of arrays. */ +typedef struct +{ + regoff_t rm_so; /* Byte offset from string's start to substring's start. */ + regoff_t rm_eo; /* Byte offset from string's start to substring's end. */ +} regmatch_t; + +/* Declarations for routines. */ + +/* Sets the current default syntax to SYNTAX, and return the old syntax. + You can also simply assign to the `re_syntax_options' variable. */ +extern reg_syntax_t re_set_syntax (reg_syntax_t __syntax); + +/* Compile the regular expression PATTERN, with length LENGTH + and syntax given by the global `re_syntax_options', into the buffer + BUFFER. Return NULL if successful, and an error string if not. */ +extern const char *re_compile_pattern (const char *__pattern, size_t __length, + struct re_pattern_buffer *__buffer); + + +/* Compile a fastmap for the compiled pattern in BUFFER; used to + accelerate searches. Return 0 if successful and -2 if was an + internal error. */ +extern int re_compile_fastmap (struct re_pattern_buffer *__buffer); + + +/* Search in the string STRING (with length LENGTH) for the pattern + compiled into BUFFER. Start searching at position START, for RANGE + characters. Return the starting position of the match, -1 for no + match, or -2 for an internal error. Also return register + information in REGS (if REGS and BUFFER->no_sub are nonzero). */ +extern int re_search (struct re_pattern_buffer *__buffer, const char *__string, + int __length, int __start, int __range, + struct re_registers *__regs); + + +/* Like `re_search', but search in the concatenation of STRING1 and + STRING2. Also, stop searching at index START + STOP. */ +extern int re_search_2 (struct re_pattern_buffer *__buffer, + const char *__string1, int __length1, + const char *__string2, int __length2, int __start, + int __range, struct re_registers *__regs, int __stop); + + +/* Like `re_search', but return how many characters in STRING the regexp + in BUFFER matched, starting at position START. */ +extern int re_match (struct re_pattern_buffer *__buffer, const char *__string, + int __length, int __start, struct re_registers *__regs); + + +/* Relates to `re_match' as `re_search_2' relates to `re_search'. */ +extern int re_match_2 (struct re_pattern_buffer *__buffer, + const char *__string1, int __length1, + const char *__string2, int __length2, int __start, + struct re_registers *__regs, int __stop); + + +/* Set REGS to hold NUM_REGS registers, storing them in STARTS and + ENDS. Subsequent matches using BUFFER and REGS will use this memory + for recording register information. STARTS and ENDS must be + allocated with malloc, and must each be at least `NUM_REGS * sizeof + (regoff_t)' bytes long. + + If NUM_REGS == 0, then subsequent matches should allocate their own + register data. + + Unless this function is called, the first search or match using + PATTERN_BUFFER will allocate its own register data, without + freeing the old data. */ +extern void re_set_registers (struct re_pattern_buffer *__buffer, + struct re_registers *__regs, + unsigned int __num_regs, + regoff_t *__starts, regoff_t *__ends); + +#if defined _REGEX_RE_COMP || defined _LIBC +# ifndef _CRAY +/* 4.2 bsd compatibility. */ +extern char *re_comp (const char *); +extern int re_exec (const char *); +# endif +#endif + +/* GCC 2.95 and later have "__restrict"; C99 compilers have + "restrict", and "configure" may have defined "restrict". */ +#ifndef __restrict +# if ! (2 < __GNUC__ || (2 == __GNUC__ && 95 <= __GNUC_MINOR__)) +# if defined restrict || 199901L <= __STDC_VERSION__ +# define __restrict restrict +# else +# define __restrict +# endif +# endif +#endif +/* gcc 3.1 and up support the [restrict] syntax. */ +#ifndef __restrict_arr +# if (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 1)) \ + && !defined __GNUG__ +# define __restrict_arr __restrict +# else +# define __restrict_arr +# endif +#endif + +/* POSIX compatibility. */ +extern int regcomp (regex_t *__restrict __preg, + const char *__restrict __pattern, + int __cflags); + +extern int regexec (const regex_t *__restrict __preg, + const char *__restrict __string, size_t __nmatch, + regmatch_t __pmatch[__restrict_arr], + int __eflags); + +extern size_t regerror (int __errcode, const regex_t *__restrict __preg, + char *__restrict __errbuf, size_t __errbuf_size); + +extern void regfree (regex_t *__preg); + + +#ifdef __cplusplus +} +#endif /* C++ */ + +#endif /* regex.h */ diff --git a/graph.c b/graph.c new file mode 100644 index 0000000..fa40f07 --- /dev/null +++ b/graph.c @@ -0,0 +1,1940 @@ +/*! + * \file + * + * \brief Various routines with dealing with sparse graphs + * + * \author George Karypis + * \version\verbatim $Id: graph.c 22415 2019-09-05 16:55:00Z karypis $ \endverbatim + */ + +#include + +#define OMPMINOPS 50000 + +/*************************************************************************/ +/*! Allocate memory for a graph and initializes it + \returns the allocated graph. The various fields are set to NULL. +*/ +/**************************************************************************/ +gk_graph_t *gk_graph_Create() +{ + gk_graph_t *graph; + + graph = (gk_graph_t *)gk_malloc(sizeof(gk_graph_t), "gk_graph_Create: graph"); + + gk_graph_Init(graph); + + return graph; +} + + +/*************************************************************************/ +/*! Initializes the graph. + \param graph is the graph to be initialized. +*/ +/*************************************************************************/ +void gk_graph_Init(gk_graph_t *graph) +{ + memset(graph, 0, sizeof(gk_graph_t)); + graph->nvtxs = -1; +} + + +/*************************************************************************/ +/*! Frees all the memory allocated for a graph. + \param graph is the graph to be freed. +*/ +/*************************************************************************/ +void gk_graph_Free(gk_graph_t **graph) +{ + if (*graph == NULL) + return; + gk_graph_FreeContents(*graph); + gk_free((void **)graph, LTERM); +} + + +/*************************************************************************/ +/*! Frees only the memory allocated for the graph's different fields and + sets them to NULL. + \param graph is the graph whose contents will be freed. +*/ +/*************************************************************************/ +void gk_graph_FreeContents(gk_graph_t *graph) +{ + gk_free((void *)&graph->xadj, &graph->adjncy, + &graph->iadjwgt, &graph->fadjwgt, + &graph->ivwgts, &graph->fvwgts, + &graph->ivsizes, &graph->fvsizes, + &graph->vlabels, + LTERM); +} + + +/**************************************************************************/ +/*! Reads a sparse graph from the supplied file + \param filename is the file that stores the data. + \param format is the graph format. The supported values are: + GK_GRAPH_FMT_METIS, GK_GRAPH_FMT_IJV. + \param hasvals is 1 if the input file has values + \param numbering is 1 if the input file numbering starts from one + \param isfewgts is 1 if the edge-weights should be read as floats + \param isfvwgts is 1 if the vertex-weights should be read as floats + \param isfvsizes is 1 if the vertex-sizes should be read as floats + \returns the graph that was read. +*/ +/**************************************************************************/ +gk_graph_t *gk_graph_Read(char *filename, int format, int hasvals, + int numbering, int isfewgts, int isfvwgts, int isfvsizes) +{ + ssize_t i, k, l; + size_t nfields, nvtxs, nedges, fmt, ncon, lnlen; + ssize_t *xadj; + int32_t ival, *iinds=NULL, *jinds=NULL, *ivals=NULL, *adjncy, *iadjwgt; + float fval, *fvals=NULL, *fadjwgt; + int readsizes=0, readwgts=0, readvals=0; + char *line=NULL, *head, *tail, fmtstr[256]; + FILE *fpin=NULL; + gk_graph_t *graph=NULL; + + + if (!gk_fexists(filename)) + gk_errexit(SIGERR, "File %s does not exist!\n", filename); + + switch (format) { + case GK_GRAPH_FMT_METIS: + fpin = gk_fopen(filename, "r", "gk_graph_Read: fpin"); + do { + if (gk_getline(&line, &lnlen, fpin) <= 0) + gk_errexit(SIGERR, "Premature end of input file: file:%s\n", filename); + } while (line[0] == '%'); + + fmt = ncon = 0; + nfields = sscanf(line, "%zu %zu %zu %zu", &nvtxs, &nedges, &fmt, &ncon); + if (nfields < 2) + gk_errexit(SIGERR, "Header line must contain at least 2 integers (#vtxs and #edges).\n"); + + nedges *= 2; + + if (fmt > 111) + gk_errexit(SIGERR, "Cannot read this type of file format [fmt=%zu]!\n", fmt); + + sprintf(fmtstr, "%03zu", fmt%1000); + readsizes = (fmtstr[0] == '1'); + readwgts = (fmtstr[1] == '1'); + readvals = (fmtstr[2] == '1'); + numbering = 1; + ncon = (ncon == 0 ? 1 : ncon); + + graph = gk_graph_Create(); + + graph->nvtxs = nvtxs; + + graph->xadj = gk_zmalloc(nvtxs+1, "gk_graph_Read: xadj"); + graph->adjncy = gk_i32malloc(nedges, "gk_graph_Read: adjncy"); + if (readvals) { + if (isfewgts) + graph->fadjwgt = gk_fmalloc(nedges, "gk_graph_Read: fadjwgt"); + else + graph->iadjwgt = gk_i32malloc(nedges, "gk_graph_Read: iadjwgt"); + } + + if (readsizes) { + if (isfvsizes) + graph->fvsizes = gk_fmalloc(nvtxs, "gk_graph_Read: fvsizes"); + else + graph->ivsizes = gk_i32malloc(nvtxs, "gk_graph_Read: ivsizes"); + } + + if (readwgts) { + if (isfvwgts) + graph->fvwgts = gk_fmalloc(nvtxs*ncon, "gk_graph_Read: fvwgts"); + else + graph->ivwgts = gk_i32malloc(nvtxs*ncon, "gk_graph_Read: ivwgts"); + } + + + /*---------------------------------------------------------------------- + * Read the sparse graph file + *---------------------------------------------------------------------*/ + numbering = (numbering ? - 1 : 0); + for (graph->xadj[0]=0, k=0, i=0; ifvsizes[i] = (float)strtod(head, &tail); +#else + graph->fvsizes[i] = strtof(head, &tail); +#endif + if (tail == head) + gk_errexit(SIGERR, "The line for vertex %zd does not have size information\n", i+1); + if (graph->fvsizes[i] < 0) + gk_errexit(SIGERR, "The size for vertex %zd must be >= 0\n", i+1); + } + else { + graph->ivsizes[i] = strtol(head, &tail, 0); + if (tail == head) + gk_errexit(SIGERR, "The line for vertex %zd does not have size information\n", i+1); + if (graph->ivsizes[i] < 0) + gk_errexit(SIGERR, "The size for vertex %zd must be >= 0\n", i+1); + } + head = tail; + } + + /* Read vertex weights */ + if (readwgts) { + for (l=0; lfvwgts[i*ncon+l] = (float)strtod(head, &tail); +#else + graph->fvwgts[i*ncon+l] = strtof(head, &tail); +#endif + if (tail == head) + gk_errexit(SIGERR, "The line for vertex %zd does not have enough weights " + "for the %d constraints.\n", i+1, ncon); + if (graph->fvwgts[i*ncon+l] < 0) + gk_errexit(SIGERR, "The weight vertex %zd and constraint %zd must be >= 0\n", i+1, l); + } + else { + graph->ivwgts[i*ncon+l] = strtol(head, &tail, 0); + if (tail == head) + gk_errexit(SIGERR, "The line for vertex %zd does not have enough weights " + "for the %d constraints.\n", i+1, ncon); + if (graph->ivwgts[i*ncon+l] < 0) + gk_errexit(SIGERR, "The weight vertex %zd and constraint %zd must be >= 0\n", i+1, l); + } + head = tail; + } + } + + + /* Read the rest of the row */ + while (1) { + ival = (int)strtol(head, &tail, 0); + if (tail == head) + break; + head = tail; + + if ((graph->adjncy[k] = ival + numbering) < 0) + gk_errexit(SIGERR, "Error: Invalid column number %d at row %zd.\n", ival, i); + + if (readvals) { + if (isfewgts) { +#ifdef __MSC__ + fval = (float)strtod(head, &tail); +#else + fval = strtof(head, &tail); +#endif + if (tail == head) + gk_errexit(SIGERR, "Value could not be found for edge! Vertex:%zd, NNZ:%zd\n", i, k); + + graph->fadjwgt[k] = fval; + } + else { + ival = strtol(head, &tail, 0); + if (tail == head) + gk_errexit(SIGERR, "Value could not be found for edge! Vertex:%zd, NNZ:%zd\n", i, k); + + graph->iadjwgt[k] = ival; + } + head = tail; + } + k++; + } + graph->xadj[i+1] = k; + } + + if (k != nedges) + gk_errexit(SIGERR, "gk_graph_Read: Something wrong with the number of edges in " + "the input file. nedges=%zd, Actualnedges=%zd.\n", nedges, k); + + gk_fclose(fpin); + + gk_free((void **)&line, LTERM); + + break; + + case GK_GRAPH_FMT_IJV: + case GK_GRAPH_FMT_HIJV: + gk_getfilestats(filename, &nvtxs, &nedges, NULL, NULL); + + if (format == GK_GRAPH_FMT_HIJV) { /* remove the #rows/#cols values and row */ + nedges -= 2; + nvtxs -= 1; + } + + if (hasvals == 1 && 3*nvtxs != nedges) + gk_errexit(SIGERR, "Error: The number of numbers (%zd %d) in the input file is not a multiple of 3.\n", nedges, hasvals); + if (hasvals == 0 && 2*nvtxs != nedges) + gk_errexit(SIGERR, "Error: The number of numbers (%zd %d) in the input file is not a multiple of 2.\n", nedges, hasvals); + + nedges = nvtxs; + numbering = (numbering ? -1 : 0); + + /* read the data into three arrays */ + iinds = gk_i32malloc(nedges, "iinds"); + jinds = gk_i32malloc(nedges, "jinds"); + if (hasvals) { + if (isfewgts) + fvals = gk_fmalloc(nedges, "fvals"); + else + ivals = gk_i32malloc(nedges, "ivals"); + } + + fpin = gk_fopen(filename, "r", "gk_graph_Read: fpin"); + + if (format == GK_GRAPH_FMT_HIJV) { /* read and ignore the #rows/#cols values */ + if (fscanf(fpin, "%zd %zd", &i, &i) != 2) + gk_errexit(SIGERR, "Error: Failed to read the header line.\n"); + } + + for (nvtxs=0, i=0; invtxs = ++nvtxs; + xadj = graph->xadj = gk_zsmalloc(nvtxs+1, 0, "xadj"); + adjncy = graph->adjncy = gk_i32malloc(nedges, "adjncy"); + if (hasvals) { + if (isfewgts) + fadjwgt = graph->fadjwgt = gk_fmalloc(nedges, "fadjwgt"); + else + iadjwgt = graph->iadjwgt = gk_i32malloc(nedges, "iadjwgt"); + } + + for (i=0; iiadjwgt || graph->fadjwgt); + hasvwgts = (graph->ivwgts || graph->fvwgts); + hasvsizes = (graph->ivsizes || graph->fvsizes); + + switch (format) { + case GK_GRAPH_FMT_METIS: + /* write the header line */ + fprintf(fpout, "%d %zd", graph->nvtxs, graph->xadj[graph->nvtxs]/2); + if (hasvwgts || hasvsizes || hasewgts) + fprintf(fpout, " %d%d%d", hasvsizes, hasvwgts, hasewgts); + fprintf(fpout, "\n"); + + + for (i=0; invtxs; i++) { + if (hasvsizes) { + if (graph->ivsizes) + fprintf(fpout, " %d", graph->ivsizes[i]); + else + fprintf(fpout, " %f", graph->fvsizes[i]); + } + + if (hasvwgts) { + if (graph->ivwgts) + fprintf(fpout, " %d", graph->ivwgts[i]); + else + fprintf(fpout, " %f", graph->fvwgts[i]); + } + + for (j=graph->xadj[i]; jxadj[i+1]; j++) { + fprintf(fpout, " %d", graph->adjncy[j]+1); + if (hasewgts) { + if (graph->iadjwgt) + fprintf(fpout, " %d", graph->iadjwgt[j]); + else + fprintf(fpout, " %f", graph->fadjwgt[j]); + } + } + fprintf(fpout, "\n"); + } + break; + + case GK_GRAPH_FMT_IJV: + for (i=0; invtxs; i++) { + for (j=graph->xadj[i]; jxadj[i+1]; j++) { + fprintf(fpout, "%d %d ", i+numbering, graph->adjncy[j]+numbering); + if (hasewgts) { + if (graph->iadjwgt) + fprintf(fpout, " %d\n", graph->iadjwgt[j]); + else + fprintf(fpout, " %f\n", graph->fadjwgt[j]); + } + else { + fprintf(fpout, " 1\n"); + } + } + } + break; + + default: + gk_errexit(SIGERR, "Unknown file format. %d\n", format); + } + + if (filename) + gk_fclose(fpout); +} + + +/*************************************************************************/ +/*! Returns a copy of a graph. + \param graph is the graph to be duplicated. + \returns the newly created copy of the graph. +*/ +/**************************************************************************/ +gk_graph_t *gk_graph_Dup(gk_graph_t *graph) +{ + gk_graph_t *ngraph; + + ngraph = gk_graph_Create(); + + ngraph->nvtxs = graph->nvtxs; + + /* copy the adjacency structure */ + if (graph->xadj) + ngraph->xadj = gk_zcopy(graph->nvtxs+1, graph->xadj, + gk_zmalloc(graph->nvtxs+1, "gk_graph_Dup: xadj")); + if (graph->ivwgts) + ngraph->ivwgts = gk_i32copy(graph->nvtxs, graph->ivwgts, + gk_i32malloc(graph->nvtxs, "gk_graph_Dup: ivwgts")); + if (graph->ivsizes) + ngraph->ivsizes = gk_i32copy(graph->nvtxs, graph->ivsizes, + gk_i32malloc(graph->nvtxs, "gk_graph_Dup: ivsizes")); + if (graph->vlabels) + ngraph->vlabels = gk_i32copy(graph->nvtxs, graph->vlabels, + gk_i32malloc(graph->nvtxs, "gk_graph_Dup: ivlabels")); + if (graph->fvwgts) + ngraph->fvwgts = gk_fcopy(graph->nvtxs, graph->fvwgts, + gk_fmalloc(graph->nvtxs, "gk_graph_Dup: fvwgts")); + if (graph->fvsizes) + ngraph->fvsizes = gk_fcopy(graph->nvtxs, graph->fvsizes, + gk_fmalloc(graph->nvtxs, "gk_graph_Dup: fvsizes")); + + + if (graph->adjncy) + ngraph->adjncy = gk_i32copy(graph->xadj[graph->nvtxs], graph->adjncy, + gk_i32malloc(graph->xadj[graph->nvtxs], "gk_graph_Dup: adjncy")); + if (graph->iadjwgt) + ngraph->iadjwgt = gk_i32copy(graph->xadj[graph->nvtxs], graph->iadjwgt, + gk_i32malloc(graph->xadj[graph->nvtxs], "gk_graph_Dup: iadjwgt")); + if (graph->fadjwgt) + ngraph->fadjwgt = gk_fcopy(graph->xadj[graph->nvtxs], graph->fadjwgt, + gk_fmalloc(graph->xadj[graph->nvtxs], "gk_graph_Dup: fadjwgt")); + + return ngraph; +} + + +/*************************************************************************/ +/*! Returns the transpose of a graph. + \param graph is the graph to be transposed. + \returns the newly created copy of the graph. +*/ +/**************************************************************************/ +gk_graph_t *gk_graph_Transpose(gk_graph_t *graph) +{ + int32_t vi, vj; + ssize_t ei; + + gk_graph_t *ngraph; + + ngraph = gk_graph_Create(); + + ngraph->nvtxs = graph->nvtxs; + ngraph->xadj = gk_zsmalloc(graph->nvtxs+1, 0, "gk_graph_Transpose: xadj"); + ngraph->adjncy = gk_i32malloc(graph->xadj[graph->nvtxs], "gk_graph_Transpose: adjncy"); + + if (graph->iadjwgt) + ngraph->iadjwgt = gk_i32malloc(graph->xadj[graph->nvtxs], "gk_graph_Transpose: iadjwgt"); + if (graph->fadjwgt) + ngraph->fadjwgt = gk_fmalloc(graph->xadj[graph->nvtxs], "gk_graph_Transpose: fadjwgt"); + + for (vi=0; vinvtxs; vi++) { + for (ei=graph->xadj[vi]; eixadj[vi+1]; ei++) + ngraph->xadj[graph->adjncy[ei]]++; + } + MAKECSR(vi, ngraph->nvtxs, ngraph->xadj); + + for (vi=0; vinvtxs; vi++) { + for (ei=graph->xadj[vi]; eixadj[vi+1]; ei++) { + vj = graph->adjncy[ei]; + ngraph->adjncy[ngraph->xadj[vj]] = vi; + if (ngraph->iadjwgt) + ngraph->iadjwgt[ngraph->xadj[vj]] = graph->iadjwgt[ei]; + if (ngraph->fadjwgt) + ngraph->fadjwgt[ngraph->xadj[vj]] = graph->fadjwgt[ei]; + ngraph->xadj[vj]++; + } + } + SHIFTCSR(vi, ngraph->nvtxs, ngraph->xadj); + + /* copy vertex attributes */ + if (graph->ivwgts) + ngraph->ivwgts = gk_i32copy(graph->nvtxs, graph->ivwgts, + gk_i32malloc(graph->nvtxs, "gk_graph_Transpose: ivwgts")); + if (graph->ivsizes) + ngraph->ivsizes = gk_i32copy(graph->nvtxs, graph->ivsizes, + gk_i32malloc(graph->nvtxs, "gk_graph_Transpose: ivsizes")); + if (graph->vlabels) + ngraph->vlabels = gk_i32copy(graph->nvtxs, graph->vlabels, + gk_i32malloc(graph->nvtxs, "gk_graph_Transpose: ivlabels")); + if (graph->fvwgts) + ngraph->fvwgts = gk_fcopy(graph->nvtxs, graph->fvwgts, + gk_fmalloc(graph->nvtxs, "gk_graph_Transpose: fvwgts")); + if (graph->fvsizes) + ngraph->fvsizes = gk_fcopy(graph->nvtxs, graph->fvsizes, + gk_fmalloc(graph->nvtxs, "gk_graph_Transpose: fvsizes")); + + + return ngraph; +} + + +/*************************************************************************/ +/*! Returns a subgraph containing a set of consecutive vertices. + \param graph is the original graph. + \param vstart is the starting vertex. + \param nvtxs is the number of vertices from vstart to extract. + \returns the newly created subgraph. +*/ +/**************************************************************************/ +gk_graph_t *gk_graph_ExtractSubgraph(gk_graph_t *graph, int vstart, int nvtxs) +{ + ssize_t i; + gk_graph_t *ngraph; + + if (vstart+nvtxs > graph->nvtxs) + return NULL; + + ngraph = gk_graph_Create(); + + ngraph->nvtxs = nvtxs; + + /* copy the adjancy structure */ + if (graph->xadj) + ngraph->xadj = gk_zcopy(nvtxs+1, graph->xadj+vstart, + gk_zmalloc(nvtxs+1, "gk_graph_ExtractSubgraph: xadj")); + for (i=nvtxs; i>=0; i--) + ngraph->xadj[i] -= ngraph->xadj[0]; + ASSERT(ngraph->xadj[0] == 0); + + if (graph->ivwgts) + ngraph->ivwgts = gk_i32copy(nvtxs, graph->ivwgts+vstart, + gk_i32malloc(nvtxs, "gk_graph_ExtractSubgraph: ivwgts")); + if (graph->ivsizes) + ngraph->ivsizes = gk_i32copy(nvtxs, graph->ivsizes+vstart, + gk_i32malloc(nvtxs, "gk_graph_ExtractSubgraph: ivsizes")); + if (graph->vlabels) + ngraph->vlabels = gk_i32copy(nvtxs, graph->vlabels+vstart, + gk_i32malloc(nvtxs, "gk_graph_ExtractSubgraph: vlabels")); + + if (graph->fvwgts) + ngraph->fvwgts = gk_fcopy(nvtxs, graph->fvwgts+vstart, + gk_fmalloc(nvtxs, "gk_graph_ExtractSubgraph: fvwgts")); + if (graph->fvsizes) + ngraph->fvsizes = gk_fcopy(nvtxs, graph->fvsizes+vstart, + gk_fmalloc(nvtxs, "gk_graph_ExtractSubgraph: fvsizes")); + + + ASSERT(ngraph->xadj[nvtxs] == graph->xadj[vstart+nvtxs]-graph->xadj[vstart]); + if (graph->adjncy) + ngraph->adjncy = gk_i32copy(graph->xadj[vstart+nvtxs]-graph->xadj[vstart], + graph->adjncy+graph->xadj[vstart], + gk_i32malloc(graph->xadj[vstart+nvtxs]-graph->xadj[vstart], + "gk_graph_ExtractSubgraph: adjncy")); + if (graph->iadjwgt) + ngraph->iadjwgt = gk_i32copy(graph->xadj[vstart+nvtxs]-graph->xadj[vstart], + graph->iadjwgt+graph->xadj[vstart], + gk_i32malloc(graph->xadj[vstart+nvtxs]-graph->xadj[vstart], + "gk_graph_ExtractSubgraph: iadjwgt")); + if (graph->fadjwgt) + ngraph->fadjwgt = gk_fcopy(graph->xadj[vstart+nvtxs]-graph->xadj[vstart], + graph->fadjwgt+graph->xadj[vstart], + gk_fmalloc(graph->xadj[vstart+nvtxs]-graph->xadj[vstart], + "gk_graph_ExtractSubgraph: fadjwgt")); + + return ngraph; +} + + +/*************************************************************************/ +/*! Returns a graph that has been reordered according to the permutation. + \param[IN] graph is the graph to be re-ordered. + \param[IN] perm is the new ordering of the graph's vertices + \param[IN] iperm is the original ordering of the re-ordered graph's vertices + \returns the newly created copy of the graph. + + \note Either perm or iperm can be NULL but not both. +*/ +/**************************************************************************/ +gk_graph_t *gk_graph_Reorder(gk_graph_t *graph, int32_t *perm, int32_t *iperm) +{ + ssize_t j, jj, *xadj; + int i, k, u, v, nvtxs; + int freeperm=0, freeiperm=0; + int32_t *adjncy; + gk_graph_t *ngraph; + + if (perm == NULL && iperm == NULL) + return NULL; + + ngraph = gk_graph_Create(); + + ngraph->nvtxs = nvtxs = graph->nvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + /* allocate memory for the different structures that are present in graph */ + if (graph->xadj) + ngraph->xadj = gk_zmalloc(nvtxs+1, "gk_graph_Reorder: xadj"); + + if (graph->ivwgts) + ngraph->ivwgts = gk_i32malloc(nvtxs, "gk_graph_Reorder: ivwgts"); + + if (graph->ivsizes) + ngraph->ivsizes = gk_i32malloc(nvtxs, "gk_graph_Reorder: ivsizes"); + + if (graph->vlabels) + ngraph->vlabels = gk_i32malloc(nvtxs, "gk_graph_Reorder: ivlabels"); + + if (graph->fvwgts) + ngraph->fvwgts = gk_fmalloc(nvtxs, "gk_graph_Reorder: fvwgts"); + + if (graph->fvsizes) + ngraph->fvsizes = gk_fmalloc(nvtxs, "gk_graph_Reorder: fvsizes"); + + + if (graph->adjncy) + ngraph->adjncy = gk_i32malloc(graph->xadj[nvtxs], "gk_graph_Reorder: adjncy"); + + if (graph->iadjwgt) + ngraph->iadjwgt = gk_i32malloc(graph->xadj[nvtxs], "gk_graph_Reorder: iadjwgt"); + + if (graph->fadjwgt) + ngraph->fadjwgt = gk_fmalloc(graph->xadj[nvtxs], "gk_graph_Reorder: fadjwgt"); + + + /* create perm/iperm if not provided */ + if (perm == NULL) { + freeperm = 1; + perm = gk_i32malloc(nvtxs, "gk_graph_Reorder: perm"); + for (i=0; ixadj[0] = jj = 0; + for (v=0; vadjncy[jj] = perm[adjncy[j]]; + if (graph->iadjwgt) + ngraph->iadjwgt[jj] = graph->iadjwgt[j]; + if (graph->fadjwgt) + ngraph->fadjwgt[jj] = graph->fadjwgt[j]; + } + if (graph->ivwgts) + ngraph->ivwgts[v] = graph->ivwgts[u]; + if (graph->fvwgts) + ngraph->fvwgts[v] = graph->fvwgts[u]; + if (graph->ivsizes) + ngraph->ivsizes[v] = graph->ivsizes[u]; + if (graph->fvsizes) + ngraph->fvsizes[v] = graph->fvsizes[u]; + if (graph->vlabels) + ngraph->vlabels[v] = graph->vlabels[u]; + + ngraph->xadj[v+1] = jj; + } + + + /* free memory */ + if (freeperm) + gk_free((void **)&perm, LTERM); + if (freeiperm) + gk_free((void **)&iperm, LTERM); + + return ngraph; +} + + +/*************************************************************************/ +/*! This function finds the connected components in a graph. + + \param graph is the graph structure + \param cptr is the ptr structure of the CSR representation of the + components. The length of this vector must be graph->nvtxs+1. + \param cind is the indices structure of the CSR representation of + the components. The length of this vector must be graph->nvtxs. + + \returns the number of components that it found. + + \note The cptr and cind parameters can be NULL, in which case only the + number of connected components is returned. +*/ +/*************************************************************************/ +int gk_graph_FindComponents(gk_graph_t *graph, int32_t *cptr, int32_t *cind) +{ + ssize_t i, ii, j, jj, k, nvtxs, first, last, ntodo, ncmps; + ssize_t *xadj; + int32_t *adjncy, *pos, *todo; + int32_t mustfree_ccsr=0; + + nvtxs = graph->nvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + /* Deal with NULL supplied cptr/cind vectors */ + if (cptr == NULL) { + cptr = gk_i32malloc(nvtxs+1, "gk_graph_FindComponents: cptr"); + cind = gk_i32malloc(nvtxs, "gk_graph_FindComponents: cind"); + mustfree_ccsr = 1; + } + + /* The list of vertices that have not been touched yet. + The valid entries are from [0..ntodo). */ + todo = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_FindComponents: todo")); + + /* For a vertex that has not been visited, pos[i] is the position in the + todo list that this vertex is stored. + If a vertex has been visited, pos[i] = -1. */ + pos = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_FindComponents: pos")); + + + /* Find the connected componends */ + ncmps = -1; + ntodo = nvtxs; /* All vertices have not been visited */ + first = last = 0; /* Point to the first and last vertices that have been touched + but not explored. + These vertices are stored in cind[first]...cind[last-1]. */ + while (1) { + if (first == last) { /* Find another starting vertex */ + cptr[++ncmps] = first; /* Mark the end of the current CC */ + + if (ntodo > 0) { + /* put the first vertex in the todo list as the start of the new CC */ + GKASSERT(pos[todo[0]] != -1); + cind[last++] = todo[0]; + + pos[todo[0]] = -1; + todo[0] = todo[--ntodo]; + pos[todo[0]] = 0; + } + else { + break; + } + } + + i = cind[first++]; /* Get the first visited but unexplored vertex */ + + for (j=xadj[i]; jnvtxs <= 0) + return; + + nvtxs = graph->nvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + /* This array will function like pos + touched of the CC method */ + pos = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_ComputeBFSOrdering: pos")); + + /* This array ([C]losed[O]pen[T]odo => cot) serves three purposes. + Positions from [0...first) is the current iperm[] vector of the explored vertices; + Positions from [first...last) is the OPEN list (i.e., visited vertices); + Positions from [last...nvtxs) is the todo list. */ + cot = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_ComputeBFSOrdering: cot")); + + + /* put v at the front of the todo list */ + pos[0] = cot[0] = v; + pos[v] = cot[v] = 0; + + /* compute a BFS ordering from the seed vertex */ + first = last = 0; + while (first < nvtxs) { + if (first == last) { /* Find another starting vertex */ + k = cot[last]; + ASSERT(pos[k] != -1); + pos[k] = -1; /* mark node as being visited */ + last++; + } + + i = cot[first++]; /* the ++ advances the explored vertices */ + for (j=xadj[i]; jnvtxs <= 0) + return; + + nvtxs = graph->nvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + /* the degree of the vertices in the closed list */ + degrees = gk_i32smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: degrees"); + + /* the minimum vertex ID of an open vertex to the closed list */ + minIDs = gk_i32smalloc(nvtxs, nvtxs+1, "gk_graph_ComputeBestFOrdering: minIDs"); + + /* the open list */ + open = gk_i32malloc(nvtxs, "gk_graph_ComputeBestFOrdering: open"); + + /* if perm[i] >= 0, then perm[i] is the order of vertex i; + otherwise perm[i] == -1. + */ + perm = gk_i32smalloc(nvtxs, -1, "gk_graph_ComputeBestFOrdering: perm"); + + /* create the queue and put everything in it */ + queue = gk_i32pqCreate(nvtxs); + for (i=0; invtxs <= 0) + return; + + nvtxs = graph->nvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + /* the degree of the vertices in the closed list */ + degrees = gk_i32smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: degrees"); + + /* the weighted degree of the vertices in the closed list for type==3 */ + wdegrees = gk_i64smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: wdegrees"); + + /* the sum of differences for type==4 */ + sod = gk_i32smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: sod"); + + /* the encountering level of a vertex type==5 */ + level = gk_i32smalloc(nvtxs, 0, "gk_graph_ComputeBestFOrdering: level"); + + /* The open+todo list of vertices. + The vertices from [0..nopen] are the open vertices. + The vertices from [nopen..ntodo) are the todo vertices. + */ + ot = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_FindComponents: ot")); + + /* For a vertex that has not been explored, pos[i] is the position in the ot list. */ + pos = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "gk_graph_FindComponents: pos")); + + /* if perm[i] >= 0, then perm[i] is the order of vertex i; otherwise perm[i] == -1. */ + perm = gk_i32smalloc(nvtxs, -1, "gk_graph_ComputeBestFOrdering: perm"); + + /* create the queue and put the starting vertex in it */ + queue = gk_i32pqCreate(nvtxs); + gk_i32pqInsert(queue, v, 1); + + /* put v at the front of the open list */ + pos[0] = ot[0] = v; + pos[v] = ot[v] = 0; + nopen = 1; + ntodo = nvtxs; + + /* start processing the nodes */ + for (i=0; i= nopen) + gk_errexit(SIGERR, "The position of v is not in open list. pos[%d]=%d is >=%d.\n", v, pos[v], nopen); + + /* remove v from the open list and re-arrange the todo part of the list */ + ot[pos[v]] = ot[nopen-1]; + pos[ot[nopen-1]] = pos[v]; + if (ntodo > nopen) { + ot[nopen-1] = ot[ntodo-1]; + pos[ot[ntodo-1]] = nopen-1; + } + nopen--; + ntodo--; + + for (j=xadj[v]; jnvtxs <= 0) + return; + + nvtxs = graph->nvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + inqueue = gk_i32smalloc(nvtxs, 0, "gk_graph_SingleSourceShortestPaths: inqueue"); + + /* determine if you will be computing using int32_t or float and proceed from there */ + if (graph->iadjwgt != NULL) { + gk_i32pq_t *queue; + int32_t *adjwgt; + int32_t *sps; + + adjwgt = graph->iadjwgt; + + queue = gk_i32pqCreate(nvtxs); + gk_i32pqInsert(queue, v, 0); + inqueue[v] = 1; + + sps = gk_i32smalloc(nvtxs, -1, "gk_graph_SingleSourceShortestPaths: sps"); + sps[v] = 0; + + /* start processing the nodes */ + while ((v = gk_i32pqGetTop(queue)) != -1) { + inqueue[v] = 2; + + /* relax the adjacent edges */ + for (i=xadj[v]; ifadjwgt; + + queue = gk_fpqCreate(nvtxs); + gk_fpqInsert(queue, v, 0); + inqueue[v] = 1; + + sps = gk_fsmalloc(nvtxs, -1, "gk_graph_SingleSourceShortestPaths: sps"); + sps[v] = 0; + + /* start processing the nodes */ + while ((v = gk_fpqGetTop(queue)) != -1) { + inqueue[v] = 2; + + /* relax the adjacent edges */ + for (i=xadj[v]; invtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + iadjwgt = graph->iadjwgt; + fadjwgt = graph->fadjwgt; + + #pragma omp parallel if (nvtxs > 100) + { + ssize_t i, j, k; + gk_ikv_t *cand; + int32_t *itwgts=NULL; + float *ftwgts=NULL; + + #pragma omp single + for (i=0; i xadj[i] && adjncy[j] < adjncy[j-1]) + k = 1; /* an inversion */ + cand[j-xadj[i]].val = (int32_t)(j-xadj[i]); + cand[j-xadj[i]].key = adjncy[j]; + if (itwgts) + itwgts[j-xadj[i]] = iadjwgt[j]; + if (ftwgts) + ftwgts[j-xadj[i]] = fadjwgt[j]; + } + if (k) { + gk_ikvsorti(xadj[i+1]-xadj[i], cand); + for (j=xadj[i]; jiadjwgt != NULL || graph->fadjwgt != NULL); + + nrows = graph->nvtxs; + rowptr = graph->xadj; + rowind = graph->adjncy; + if (hasvals) { + irowval = graph->iadjwgt; + rowval = graph->fadjwgt; + } + + /* create the column view for efficient processing */ + colptr = gk_zsmalloc(nrows+1, 0, "colptr"); + colind = gk_i32malloc(rowptr[nrows], "colind"); + if (hasvals) { + if (rowval) + colval = gk_fmalloc(rowptr[nrows], "colval"); + if (irowval) + icolval = gk_i32malloc(rowptr[nrows], "icolval"); + } + + for (i=0; invtxs = graph->nvtxs; + + nrowptr = ngraph->xadj = gk_zmalloc(nrows+1, "gk_csr_MakeSymmetric: nrowptr"); + nrowind = ngraph->adjncy = gk_imalloc(2*rowptr[nrows], "gk_csr_MakeSymmetric: nrowind"); + if (hasvals) { + if (rowval) + nrowval = graph->fadjwgt = gk_fmalloc(2*rowptr[nrows], "gk_csr_MakeSymmetric: nrowval"); + if (irowval) + nirowval = graph->iadjwgt = gk_i32malloc(2*rowptr[nrows], "gk_csr_MakeSymmetric: nrowval"); + } + + marker = gk_ismalloc(nrows, -1, "marker"); + ids = gk_imalloc(nrows, "ids"); + if (hasvals) { + if (rowval) + wgts = gk_fmalloc(nrows, "wgts"); + if (irowval) + iwgts = gk_i32malloc(nrows, "wgts"); + } + + nrowptr[0] = nnz = 0; + for (i=0; inrows = nrows; + ngraph->ncols = graph->ncols; + + for (nnz=0, i=0; irowptr[rind[i]+1]-graph->rowptr[rind[i]]; + + ngraph->rowptr = gk_zmalloc(ngraph->nrows+1, "gk_graph_ExtractPartition: rowptr"); + ngraph->rowind = gk_imalloc(nnz, "gk_graph_ExtractPartition: rowind"); + ngraph->rowval = gk_fmalloc(nnz, "gk_graph_ExtractPartition: rowval"); + + ngraph->rowptr[0] = 0; + for (nnz=0, j=0, ii=0; iirowptr[i+1]-graph->rowptr[i], graph->rowind+graph->rowptr[i], ngraph->rowind+nnz); + gk_fcopy(graph->rowptr[i+1]-graph->rowptr[i], graph->rowval+graph->rowptr[i], ngraph->rowval+nnz); + nnz += graph->rowptr[i+1]-graph->rowptr[i]; + ngraph->rowptr[++j] = nnz; + } + ASSERT(j == ngraph->nrows); + + return ngraph; +} + + +/*************************************************************************/ +/*! Returns a subgraphrix corresponding to a specified partitioning of rows. + \param graph is the original graphrix. + \param part is the partitioning vector of the rows. + \param pid is the partition ID that will be extracted. + \returns the row structure of the newly created subgraphrix. +*/ +/**************************************************************************/ +gk_graph_t *gk_graph_ExtractPartition(gk_graph_t *graph, int *part, int pid) +{ + ssize_t i, j, nnz; + gk_graph_t *ngraph; + + ngraph = gk_graph_Create(); + + ngraph->nrows = 0; + ngraph->ncols = graph->ncols; + + for (nnz=0, i=0; inrows; i++) { + if (part[i] == pid) { + ngraph->nrows++; + nnz += graph->rowptr[i+1]-graph->rowptr[i]; + } + } + + ngraph->rowptr = gk_zmalloc(ngraph->nrows+1, "gk_graph_ExtractPartition: rowptr"); + ngraph->rowind = gk_imalloc(nnz, "gk_graph_ExtractPartition: rowind"); + ngraph->rowval = gk_fmalloc(nnz, "gk_graph_ExtractPartition: rowval"); + + ngraph->rowptr[0] = 0; + for (nnz=0, j=0, i=0; inrows; i++) { + if (part[i] == pid) { + gk_icopy(graph->rowptr[i+1]-graph->rowptr[i], graph->rowind+graph->rowptr[i], ngraph->rowind+nnz); + gk_fcopy(graph->rowptr[i+1]-graph->rowptr[i], graph->rowval+graph->rowptr[i], ngraph->rowval+nnz); + nnz += graph->rowptr[i+1]-graph->rowptr[i]; + ngraph->rowptr[++j] = nnz; + } + } + ASSERT(j == ngraph->nrows); + + return ngraph; +} + + +/*************************************************************************/ +/*! Splits the graphrix into multiple sub-graphrices based on the provided + color array. + \param graph is the original graphrix. + \param color is an array of size equal to the number of non-zeros + in the graphrix (row-wise structure). The graphrix is split into + as many parts as the number of colors. For meaningfull results, + the colors should be numbered consecutively starting from 0. + \returns an array of graphrices for each supplied color number. +*/ +/**************************************************************************/ +gk_graph_t **gk_graph_Split(gk_graph_t *graph, int *color) +{ + ssize_t i, j; + int nrows, ncolors; + ssize_t *rowptr; + int *rowind; + float *rowval; + gk_graph_t **sgraphs; + + nrows = graph->nrows; + rowptr = graph->rowptr; + rowind = graph->rowind; + rowval = graph->rowval; + + ncolors = gk_imax(rowptr[nrows], color)+1; + + sgraphs = (gk_graph_t **)gk_malloc(sizeof(gk_graph_t *)*ncolors, "gk_graph_Split: sgraphs"); + for (i=0; inrows = graph->nrows; + sgraphs[i]->ncols = graph->ncols; + sgraphs[i]->rowptr = gk_zsmalloc(nrows+1, 0, "gk_graph_Split: sgraphs[i]->rowptr"); + } + + for (i=0; irowptr[i]++; + } + for (i=0; irowptr); + + for (i=0; irowind = gk_imalloc(sgraphs[i]->rowptr[nrows], "gk_graph_Split: sgraphs[i]->rowind"); + sgraphs[i]->rowval = gk_fmalloc(sgraphs[i]->rowptr[nrows], "gk_graph_Split: sgraphs[i]->rowval"); + } + + for (i=0; irowind[sgraphs[color[j]]->rowptr[i]] = rowind[j]; + sgraphs[color[j]]->rowval[sgraphs[color[j]]->rowptr[i]] = rowval[j]; + sgraphs[color[j]]->rowptr[i]++; + } + } + + for (i=0; irowptr); + + return sgraphs; +} + + +/*************************************************************************/ +/*! Prunes certain rows/columns of the graphrix. The prunning takes place + by analyzing the row structure of the graphrix. The prunning takes place + by removing rows/columns but it does not affect the numbering of the + remaining rows/columns. + + \param graph the graphrix to be prunned, + \param what indicates if the rows (GK_CSR_ROW) or the columns (GK_CSR_COL) + of the graphrix will be prunned, + \param minf is the minimum number of rows (columns) that a column (row) must + be present in order to be kept, + \param maxf is the maximum number of rows (columns) that a column (row) must + be present at in order to be kept. + \returns the prunned graphrix consisting only of its row-based structure. + The input graphrix is not modified. +*/ +/**************************************************************************/ +gk_graph_t *gk_graph_Prune(gk_graph_t *graph, int what, int minf, int maxf) +{ + ssize_t i, j, nnz; + int nrows, ncols; + ssize_t *rowptr, *nrowptr; + int *rowind, *nrowind, *collen; + float *rowval, *nrowval; + gk_graph_t *ngraph; + + ngraph = gk_graph_Create(); + + nrows = ngraph->nrows = graph->nrows; + ncols = ngraph->ncols = graph->ncols; + + rowptr = graph->rowptr; + rowind = graph->rowind; + rowval = graph->rowval; + + nrowptr = ngraph->rowptr = gk_zmalloc(nrows+1, "gk_graph_Prune: nrowptr"); + nrowind = ngraph->rowind = gk_imalloc(rowptr[nrows], "gk_graph_Prune: nrowind"); + nrowval = ngraph->rowval = gk_fmalloc(rowptr[nrows], "gk_graph_Prune: nrowval"); + + + switch (what) { + case GK_CSR_COL: + collen = gk_ismalloc(ncols, 0, "gk_graph_Prune: collen"); + + for (i=0; i= minf && collen[i] <= maxf ? 1 : 0); + + nrowptr[0] = 0; + for (nnz=0, i=0; i= minf && rowptr[i+1]-rowptr[i] <= maxf) { + for (j=rowptr[i]; jrowval) { + n = graph->nrows; + ptr = graph->rowptr; + val = graph->rowval; + + #pragma omp parallel if (ptr[n] > OMPMINOPS) + { + #pragma omp for private(j,sum) schedule(static) + for (i=0; i 0 */ + } + if (sum > 0) { + if (norm == 2) + sum=1.0/sqrt(sum); + else if (norm == 1) + sum=1.0/sum; + for (j=ptr[i]; jcolval) { + n = graph->ncols; + ptr = graph->colptr; + val = graph->colval; + + #pragma omp parallel if (ptr[n] > OMPMINOPS) + { + #pragma omp for private(j,sum) schedule(static) + for (i=0; i 0) { + if (norm == 2) + sum=1.0/sqrt(sum); + else if (norm == 1) + sum=1.0/sum; + for (j=ptr[i]; j + +/****************************************************************************** +* This function creates the hash-table +*******************************************************************************/ +gk_HTable_t *HTable_Create(int nelements) +{ + gk_HTable_t *htable; + + htable = gk_malloc(sizeof(gk_HTable_t), "HTable_Create: htable"); + htable->harray = gk_ikvmalloc(nelements, "HTable_Create: harray"); + htable->nelements = nelements; + + HTable_Reset(htable); + + return htable; +} + + +/****************************************************************************** +* This function resets the data-structures associated with the hash-table +*******************************************************************************/ +void HTable_Reset(gk_HTable_t *htable) +{ + int i; + + for (i=0; inelements; i++) + htable->harray[i].key = HTABLE_EMPTY; + htable->htsize = 0; + +} + +/****************************************************************************** +* This function resizes the hash-table +*******************************************************************************/ +void HTable_Resize(gk_HTable_t *htable, int nelements) +{ + int i, old_nelements; + gk_ikv_t *old_harray; + + old_nelements = htable->nelements; + old_harray = htable->harray; + + /* prepare larger hash */ + htable->nelements = nelements; + htable->htsize = 0; + htable->harray = gk_ikvmalloc(nelements, "HTable_Resize: harray"); + for (i=0; iharray[i].key = HTABLE_EMPTY; + + /* reassign the values */ + for (i=0; ihtsize > htable->nelements/2) + HTable_Resize(htable, 2*htable->nelements); + + first = HTable_HFunction(htable->nelements, key); + + for (i=first; inelements; i++) { + if (htable->harray[i].key == HTABLE_EMPTY || htable->harray[i].key == HTABLE_DELETED) { + htable->harray[i].key = key; + htable->harray[i].val = val; + htable->htsize++; + return; + } + } + + for (i=0; iharray[i].key == HTABLE_EMPTY || htable->harray[i].key == HTABLE_DELETED) { + htable->harray[i].key = key; + htable->harray[i].val = val; + htable->htsize++; + return; + } + } + +} + + +/****************************************************************************** +* This function deletes key from the htable +*******************************************************************************/ +void HTable_Delete(gk_HTable_t *htable, int key) +{ + int i, first; + + first = HTable_HFunction(htable->nelements, key); + + for (i=first; inelements; i++) { + if (htable->harray[i].key == key) { + htable->harray[i].key = HTABLE_DELETED; + htable->htsize--; + return; + } + } + + for (i=0; iharray[i].key == key) { + htable->harray[i].key = HTABLE_DELETED; + htable->htsize--; + return; + } + } + +} + + +/****************************************************************************** +* This function returns the data associated with the key in the hastable +*******************************************************************************/ +int HTable_Search(gk_HTable_t *htable, int key) +{ + int i, first; + + first = HTable_HFunction(htable->nelements, key); + + for (i=first; inelements; i++) { + if (htable->harray[i].key == key) + return htable->harray[i].val; + else if (htable->harray[i].key == HTABLE_EMPTY) + return -1; + } + + for (i=0; iharray[i].key == key) + return htable->harray[i].val; + else if (htable->harray[i].key == HTABLE_EMPTY) + return -1; + } + + return -1; +} + + +/****************************************************************************** +* This function returns the next key/val +*******************************************************************************/ +int HTable_GetNext(gk_HTable_t *htable, int key, int *r_val, int type) +{ + int i; + static int first, last; + + if (type == HTABLE_FIRST) + first = last = HTable_HFunction(htable->nelements, key); + + if (first > last) { + for (i=first; inelements; i++) { + if (htable->harray[i].key == key) { + *r_val = htable->harray[i].val; + first = i+1; + return 1; + } + else if (htable->harray[i].key == HTABLE_EMPTY) + return -1; + } + first = 0; + } + + for (i=first; iharray[i].key == key) { + *r_val = htable->harray[i].val; + first = i+1; + return 1; + } + else if (htable->harray[i].key == HTABLE_EMPTY) + return -1; + } + + return -1; +} + + +/****************************************************************************** +* This function returns the data associated with the key in the hastable +*******************************************************************************/ +int HTable_SearchAndDelete(gk_HTable_t *htable, int key) +{ + int i, first; + + first = HTable_HFunction(htable->nelements, key); + + for (i=first; inelements; i++) { + if (htable->harray[i].key == key) { + htable->harray[i].key = HTABLE_DELETED; + htable->htsize--; + return htable->harray[i].val; + } + else if (htable->harray[i].key == HTABLE_EMPTY) + gk_errexit(SIGERR, "HTable_SearchAndDelete: Failed to find the key!\n"); + } + + for (i=0; iharray[i].key == key) { + htable->harray[i].key = HTABLE_DELETED; + htable->htsize--; + return htable->harray[i].val; + } + else if (htable->harray[i].key == HTABLE_EMPTY) + gk_errexit(SIGERR, "HTable_SearchAndDelete: Failed to find the key!\n"); + } + + return -1; + +} + + + +/****************************************************************************** +* This function destroys the data structures associated with the hash-table +*******************************************************************************/ +void HTable_Destroy(gk_HTable_t *htable) +{ + gk_free((void **)&htable->harray, &htable, LTERM); +} + + +/****************************************************************************** +* This is the hash-function. Based on multiplication +*******************************************************************************/ +int HTable_HFunction(int nelements, int key) +{ + return (int)(key%nelements); +} diff --git a/io.c b/io.c new file mode 100644 index 0000000..289b401 --- /dev/null +++ b/io.c @@ -0,0 +1,681 @@ +/*! +\file io.c +\brief Various file I/O functions. + +This file contains various functions that perform I/O. + +\date Started 4/10/95 +\author George +\version\verbatim $Id: io.c 18951 2015-08-08 20:10:46Z karypis $ \endverbatim +*/ + +#ifdef HAVE_GETLINE +/* Get getline to be defined. */ +#define _GNU_SOURCE +#include +#undef _GNU_SOURCE +#endif + +#include + +/************************************************************************* +* This function opens a file +**************************************************************************/ +FILE *gk_fopen(char *fname, char *mode, const char *msg) +{ + FILE *fp; + char errmsg[8192]; + + fp = fopen(fname, mode); + if (fp != NULL) + return fp; + + sprintf(errmsg,"file: %s, mode: %s, [%s]", fname, mode, msg); + perror(errmsg); + errexit("Failed on gk_fopen()\n"); + + return NULL; +} + + +/************************************************************************* +* This function closes a file +**************************************************************************/ +void gk_fclose(FILE *fp) +{ + fclose(fp); +} + + +/*************************************************************************/ +/*! This function is a wrapper around the read() function that ensures + that all data is been read, by issuing multiple read requests. + The only time when not 'count' items are read is when the EOF has been + reached. +*/ +/*************************************************************************/ +ssize_t gk_read(int fd, void *vbuf, size_t count) +{ + char *buf = (char *)vbuf; + ssize_t rsize, tsize=count; + + do { + if ((rsize = read(fd, buf, tsize)) == -1) + return -1; + buf += rsize; + tsize -= rsize; + } while (tsize > 0 && rsize > 0); + + return count-tsize; +} + + +/*************************************************************************/ +/*! This function is a wrapper around the write() function that ensures + that all data is been written, by issueing multiple write requests. +*/ +/*************************************************************************/ +ssize_t gk_write(int fd, void *vbuf, size_t count) +{ + char *buf = (char *)vbuf; + ssize_t size, tsize=count; + + do { + if ((size = write(fd, buf, tsize)) == -1) + return -1; + buf += size; + tsize -= size; + } while (tsize > 0); + + return count; +} + + +/*************************************************************************/ +/*! This function is the GKlib implementation of glibc's getline() + function. + \returns -1 if the EOF has been reached, otherwise it returns the + number of bytes read. +*/ +/*************************************************************************/ +ssize_t gk_getline(char **lineptr, size_t *n, FILE *stream) +{ +#ifdef HAVE_GETLINE + return getline(lineptr, n, stream); +#else + size_t i; + int ch; + + if (feof(stream)) + return -1; + + /* Initial memory allocation if *lineptr is NULL */ + if (*lineptr == NULL || *n == 0) { + *n = 1024; + *lineptr = gk_malloc((*n)*sizeof(char), "gk_getline: lineptr"); + } + + /* get into the main loop */ + i = 0; + while ((ch = getc(stream)) != EOF) { + (*lineptr)[i++] = (char)ch; + + /* reallocate memory if reached at the end of the buffer. The +1 is for '\0' */ + if (i+1 == *n) { + *n = 2*(*n); + *lineptr = gk_realloc(*lineptr, (*n)*sizeof(char), "gk_getline: lineptr"); + } + + if (ch == '\n') + break; + } + (*lineptr)[i] = '\0'; + + return (i == 0 ? -1 : i); +#endif +} + + +/*************************************************************************/ +/*! This function reads the contents of a text file and returns it in the + form of an array of strings. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +char **gk_readfile(char *fname, size_t *r_nlines) +{ + size_t lnlen, nlines=0; + char *line=NULL, **lines=NULL; + FILE *fpin; + + gk_getfilestats(fname, &nlines, NULL, NULL, NULL); + if (nlines > 0) { + lines = (char **)gk_malloc(nlines*sizeof(char *), "gk_readfile: lines"); + + fpin = gk_fopen(fname, "r", "gk_readfile"); + nlines = 0; + while (gk_getline(&line, &lnlen, fpin) != -1) { + gk_strtprune(line, "\n\r"); + lines[nlines++] = gk_strdup(line); + } + gk_fclose(fpin); + } + + gk_free((void **)&line, LTERM); + + if (r_nlines != NULL) + *r_nlines = nlines; + + return lines; +} + + +/*************************************************************************/ +/*! This function reads the contents of a file and returns it in the + form of an array of int32_t. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +int32_t *gk_i32readfile(char *fname, size_t *r_nlines) +{ + size_t lnlen, nlines=0; + char *line=NULL; + int32_t *array=NULL; + FILE *fpin; + + gk_getfilestats(fname, &nlines, NULL, NULL, NULL); + if (nlines > 0) { + array = gk_i32malloc(nlines, "gk_i32readfile: array"); + + fpin = gk_fopen(fname, "r", "gk_readfile"); + nlines = 0; + + while (gk_getline(&line, &lnlen, fpin) != -1) { + sscanf(line, "%"SCNd32, &array[nlines++]); + } + + gk_fclose(fpin); + } + + gk_free((void **)&line, LTERM); + + if (r_nlines != NULL) + *r_nlines = nlines; + + return array; +} + +/*************************************************************************/ +/*! This function reads the contents of a file and returns it in the + form of an array of int64_t. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +int64_t *gk_i64readfile(char *fname, size_t *r_nlines) +{ + size_t lnlen, nlines=0; + char *line=NULL; + int64_t *array=NULL; + FILE *fpin; + + gk_getfilestats(fname, &nlines, NULL, NULL, NULL); + if (nlines > 0) { + array = gk_i64malloc(nlines, "gk_i64readfile: array"); + + fpin = gk_fopen(fname, "r", "gk_readfile"); + nlines = 0; + + while (gk_getline(&line, &lnlen, fpin) != -1) { + sscanf(line, "%"SCNd64, &array[nlines++]); + } + + gk_fclose(fpin); + } + + gk_free((void **)&line, LTERM); + + if (r_nlines != NULL) + *r_nlines = nlines; + + return array; +} + +/*************************************************************************/ +/*! This function reads the contents of a file and returns it in the + form of an array of ssize_t. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +ssize_t *gk_zreadfile(char *fname, size_t *r_nlines) +{ + size_t lnlen, nlines=0; + char *line=NULL; + ssize_t *array=NULL; + FILE *fpin; + + gk_getfilestats(fname, &nlines, NULL, NULL, NULL); + if (nlines > 0) { + array = gk_zmalloc(nlines, "gk_zreadfile: array"); + + fpin = gk_fopen(fname, "r", "gk_readfile"); + nlines = 0; + + while (gk_getline(&line, &lnlen, fpin) != -1) { + sscanf(line, "%zd", &array[nlines++]); + } + + gk_fclose(fpin); + } + + gk_free((void **)&line, LTERM); + + if (r_nlines != NULL) + *r_nlines = nlines; + + return array; +} + +/*************************************************************************/ +/*! This function reads the contents of a binary file and returns it in the + form of an array of char. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +char *gk_creadfilebin(char *fname, size_t *r_nelmnts) +{ + size_t nelmnts; + ssize_t fsize; + char *array=NULL; + FILE *fpin; + + *r_nelmnts = 0; + + fsize = gk_getfsize(fname); + + if (fsize == -1) { + gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); + return NULL; + } + + nelmnts = fsize; + array = gk_cmalloc(nelmnts, "gk_creadfilebin: array"); + + fpin = gk_fopen(fname, "rb", "gk_creadfilebin"); + if (fread(array, sizeof(char), nelmnts, fpin) != nelmnts) { + gk_errexit(SIGERR, "Failed to read the number of words requested. %zu\n", nelmnts); + gk_free((void **)&array, LTERM); + return NULL; + } + gk_fclose(fpin); + + *r_nelmnts = nelmnts; + + return array; +} + +/*************************************************************************/ +/*! This function writes the contents of an array into a binary file. + \param fname is the name of the file + \param n the number of elements in the array. + \param a the array to be written out. +*/ +/*************************************************************************/ +size_t gk_cwritefilebin(char *fname, size_t n, char *a) +{ + size_t fsize; + FILE *fp; + + fp = gk_fopen(fname, "wb", "gk_writefilebin"); + + fsize = fwrite(a, sizeof(char), n, fp); + + gk_fclose(fp); + + return fsize; +} + +/*************************************************************************/ +/*! This function reads the contents of a binary file and returns it in the + form of an array of int32_t. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +int32_t *gk_i32readfilebin(char *fname, size_t *r_nelmnts) +{ + size_t nelmnts; + ssize_t fsize; + int32_t *array=NULL; + FILE *fpin; + + *r_nelmnts = 0; + + fsize = gk_getfsize(fname); + + if (fsize == -1) { + gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); + return NULL; + } + + if (fsize%sizeof(int32_t) != 0) { + gk_errexit(SIGERR, "The size [%zd] of the file [%s] is not in multiples of sizeof(int32_t).\n", fsize, fname); + return NULL; + } + + nelmnts = fsize/sizeof(int32_t); + array = gk_i32malloc(nelmnts, "gk_i32readfilebin: array"); + + fpin = gk_fopen(fname, "rb", "gk_i32readfilebin"); + + if (fread(array, sizeof(int32_t), nelmnts, fpin) != nelmnts) { + gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts); + gk_free((void **)&array, LTERM); + return NULL; + } + gk_fclose(fpin); + + *r_nelmnts = nelmnts; + + return array; +} + +/*************************************************************************/ +/*! This function writes the contents of an array into a binary file. + \param fname is the name of the file + \param n the number of elements in the array. + \param a the array to be written out. +*/ +/*************************************************************************/ +size_t gk_i32writefilebin(char *fname, size_t n, int32_t *a) +{ + size_t fsize; + FILE *fp; + + fp = gk_fopen(fname, "wb", "gk_writefilebin"); + + fsize = fwrite(a, sizeof(int32_t), n, fp); + + gk_fclose(fp); + + return fsize; +} + +/*************************************************************************/ +/*! This function reads the contents of a binary file and returns it in the + form of an array of int64_t. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +int64_t *gk_i64readfilebin(char *fname, size_t *r_nelmnts) +{ + size_t nelmnts; + ssize_t fsize; + int64_t *array=NULL; + FILE *fpin; + + *r_nelmnts = 0; + + fsize = gk_getfsize(fname); + + if (fsize == -1) { + gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); + return NULL; + } + + if (fsize%sizeof(int64_t) != 0) { + gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(int64_t).\n"); + return NULL; + } + + nelmnts = fsize/sizeof(int64_t); + array = gk_i64malloc(nelmnts, "gk_i64readfilebin: array"); + + fpin = gk_fopen(fname, "rb", "gk_i64readfilebin"); + + if (fread(array, sizeof(int64_t), nelmnts, fpin) != nelmnts) { + gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts); + gk_free((void **)&array, LTERM); + return NULL; + } + gk_fclose(fpin); + + *r_nelmnts = nelmnts; + + return array; +} + +/*************************************************************************/ +/*! This function writes the contents of an array into a binary file. + \param fname is the name of the file + \param n the number of elements in the array. + \param a the array to be written out. +*/ +/*************************************************************************/ +size_t gk_i64writefilebin(char *fname, size_t n, int64_t *a) +{ + size_t fsize; + FILE *fp; + + fp = gk_fopen(fname, "wb", "gk_writefilebin"); + + fsize = fwrite(a, sizeof(int64_t), n, fp); + + gk_fclose(fp); + + return fsize; +} + +/*************************************************************************/ +/*! This function reads the contents of a binary file and returns it in the + form of an array of ssize_t. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +ssize_t *gk_zreadfilebin(char *fname, size_t *r_nelmnts) +{ + size_t nelmnts; + ssize_t fsize; + ssize_t *array=NULL; + FILE *fpin; + + *r_nelmnts = 0; + + fsize = gk_getfsize(fname); + + if (fsize == -1) { + gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); + return NULL; + } + + if (fsize%sizeof(ssize_t) != 0) { + gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(ssize_t).\n"); + return NULL; + } + + nelmnts = fsize/sizeof(ssize_t); + array = gk_zmalloc(nelmnts, "gk_zreadfilebin: array"); + + fpin = gk_fopen(fname, "rb", "gk_zreadfilebin"); + + if (fread(array, sizeof(ssize_t), nelmnts, fpin) != nelmnts) { + gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts); + gk_free((void **)&array, LTERM); + return NULL; + } + gk_fclose(fpin); + + *r_nelmnts = nelmnts; + + return array; +} + +/*************************************************************************/ +/*! This function writes the contents of an array into a binary file. + \param fname is the name of the file + \param n the number of elements in the array. + \param a the array to be written out. +*/ +/*************************************************************************/ +size_t gk_zwritefilebin(char *fname, size_t n, ssize_t *a) +{ + size_t fsize; + FILE *fp; + + fp = gk_fopen(fname, "wb", "gk_writefilebin"); + + fsize = fwrite(a, sizeof(ssize_t), n, fp); + + gk_fclose(fp); + + return fsize; +} + +/*************************************************************************/ +/*! This function reads the contents of a binary file and returns it in the + form of an array of float. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +float *gk_freadfilebin(char *fname, size_t *r_nelmnts) +{ + size_t nelmnts; + ssize_t fsize; + float *array=NULL; + FILE *fpin; + + *r_nelmnts = 0; + + fsize = gk_getfsize(fname); + + if (fsize == -1) { + gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); + return NULL; + } + + if (fsize%sizeof(float) != 0) { + gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(float).\n"); + return NULL; + } + + nelmnts = fsize/sizeof(float); + array = gk_fmalloc(nelmnts, "gk_freadfilebin: array"); + + fpin = gk_fopen(fname, "rb", "gk_freadfilebin"); + + if (fread(array, sizeof(float), nelmnts, fpin) != nelmnts) { + gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts); + gk_free((void **)&array, LTERM); + return NULL; + } + gk_fclose(fpin); + + *r_nelmnts = nelmnts; + + return array; +} + +/*************************************************************************/ +/*! This function writes the contents of an array into a binary file. + \param fname is the name of the file + \param n the number of elements in the array. + \param a the array to be written out. +*/ +/*************************************************************************/ +size_t gk_fwritefilebin(char *fname, size_t n, float *a) +{ + size_t fsize; + FILE *fp; + + fp = gk_fopen(fname, "wb", "gk_fwritefilebin"); + + fsize = fwrite(a, sizeof(float), n, fp); + + gk_fclose(fp); + + return fsize; +} + +/*************************************************************************/ +/*! This function reads the contents of a binary file and returns it in the + form of an array of double. + \param fname is the name of the file + \param r_nlines is the number of lines in the file. If it is NULL, + this information is not returned. +*/ +/*************************************************************************/ +double *gk_dreadfilebin(char *fname, size_t *r_nelmnts) +{ + size_t nelmnts; + ssize_t fsize; + double *array=NULL; + FILE *fpin; + + *r_nelmnts = 0; + + fsize = gk_getfsize(fname); + + if (fsize == -1) { + gk_errexit(SIGERR, "Failed to fstat(%s).\n", fname); + return NULL; + } + + if (fsize%sizeof(double) != 0) { + gk_errexit(SIGERR, "The size of the file is not in multiples of sizeof(double).\n"); + return NULL; + } + + nelmnts = fsize/sizeof(double); + array = gk_dmalloc(nelmnts, "gk_dreadfilebin: array"); + + fpin = gk_fopen(fname, "rb", "gk_dreadfilebin"); + + if (fread(array, sizeof(double), nelmnts, fpin) != nelmnts) { + gk_errexit(SIGERR, "Failed to read the number of words requested. %zd\n", nelmnts); + gk_free((void **)&array, LTERM); + return NULL; + } + gk_fclose(fpin); + + *r_nelmnts = nelmnts; + + return array; +} + +/*************************************************************************/ +/*! This function writes the contents of an array into a binary file. + \param fname is the name of the file + \param n the number of elements in the array. + \param a the array to be written out. +*/ +/*************************************************************************/ +size_t gk_dwritefilebin(char *fname, size_t n, double *a) +{ + size_t fsize; + FILE *fp; + + fp = gk_fopen(fname, "wb", "gk_writefilebin"); + + fsize = fwrite(a, sizeof(double), n, fp); + + gk_fclose(fp); + + return fsize; +} + diff --git a/itemsets.c b/itemsets.c new file mode 100644 index 0000000..beb58ae --- /dev/null +++ b/itemsets.c @@ -0,0 +1,210 @@ +/*! + * \file + * \brief Frequent/Closed itemset discovery routines + * + * This file contains the code for finding frequent/closed itemests. These routines + * are implemented using a call-back mechanism to deal with the discovered itemsets. + * + * \date 6/13/2008 + * \author George Karypis + * \version\verbatim $Id: itemsets.c 19240 2015-10-22 12:41:19Z karypis $ \endverbatim + */ + +#include + +/*-------------------------------------------------------------*/ +/*! Data structures for use within this module */ +/*-------------------------------------------------------------*/ +typedef struct { + int minfreq; /* the minimum frequency of a pattern */ + int maxfreq; /* the maximum frequency of a pattern */ + int minlen; /* the minimum length of the requested pattern */ + int maxlen; /* the maximum length of the requested pattern */ + int tnitems; /* the initial range of the item space */ + + /* the call-back function */ + void (*callback)(void *stateptr, int nitems, int *itemids, int ntrans, int *transids); + void *stateptr; /* the user-supplied pointer to pass to the callback */ + + /* workspace variables */ + int *rmarker; + gk_ikv_t *cand; +} isparams_t; + + +/*-------------------------------------------------------------*/ +/*! Prototypes for this module */ +/*-------------------------------------------------------------*/ +void itemsets_find_frequent_itemsets(isparams_t *params, gk_csr_t *mat, + int preflen, int *prefix); +gk_csr_t *itemsets_project_matrix(isparams_t *param, gk_csr_t *mat, int cid); + + + +/*************************************************************************/ +/*! The entry point of the frequent itemset discovery code */ +/*************************************************************************/ +void gk_find_frequent_itemsets(int ntrans, ssize_t *tranptr, int *tranind, + int minfreq, int maxfreq, int minlen, int maxlen, + void (*process_itemset)(void *stateptr, int nitems, int *itemids, + int ntrans, int *transids), + void *stateptr) +{ + ssize_t i; + gk_csr_t *mat, *pmat; + isparams_t params; + int *pattern; + + /* Create the matrix */ + mat = gk_csr_Create(); + mat->nrows = ntrans; + mat->ncols = tranind[gk_iargmax(tranptr[ntrans], tranind, 1)]+1; + mat->rowptr = gk_zcopy(ntrans+1, tranptr, gk_zmalloc(ntrans+1, "gk_find_frequent_itemsets: mat.rowptr")); + mat->rowind = gk_icopy(tranptr[ntrans], tranind, gk_imalloc(tranptr[ntrans], "gk_find_frequent_itemsets: mat.rowind")); + mat->colids = gk_iincset(mat->ncols, 0, gk_imalloc(mat->ncols, "gk_find_frequent_itemsets: mat.colids")); + + /* Setup the parameters */ + params.minfreq = minfreq; + params.maxfreq = (maxfreq == -1 ? mat->nrows : maxfreq); + params.minlen = minlen; + params.maxlen = (maxlen == -1 ? mat->ncols : maxlen); + params.tnitems = mat->ncols; + params.callback = process_itemset; + params.stateptr = stateptr; + params.rmarker = gk_ismalloc(mat->nrows, 0, "gk_find_frequent_itemsets: rmarker"); + params.cand = gk_ikvmalloc(mat->ncols, "gk_find_frequent_itemsets: cand"); + + /* Perform the initial projection */ + gk_csr_CreateIndex(mat, GK_CSR_COL); + pmat = itemsets_project_matrix(¶ms, mat, -1); + gk_csr_Free(&mat); + + pattern = gk_imalloc(pmat->ncols, "gk_find_frequent_itemsets: pattern"); + itemsets_find_frequent_itemsets(¶ms, pmat, 0, pattern); + + gk_csr_Free(&pmat); + gk_free((void **)&pattern, ¶ms.rmarker, ¶ms.cand, LTERM); + +} + + + +/*************************************************************************/ +/*! The recursive routine for DFS-based frequent pattern discovery */ +/*************************************************************************/ +void itemsets_find_frequent_itemsets(isparams_t *params, gk_csr_t *mat, + int preflen, int *prefix) +{ + ssize_t i; + gk_csr_t *cmat; + + /* Project each frequent column */ + for (i=0; incols; i++) { + prefix[preflen] = mat->colids[i]; + + if (preflen+1 >= params->minlen) + (*params->callback)(params->stateptr, preflen+1, prefix, + mat->colptr[i+1]-mat->colptr[i], mat->colind+mat->colptr[i]); + + if (preflen+1 < params->maxlen) { + cmat = itemsets_project_matrix(params, mat, i); + itemsets_find_frequent_itemsets(params, cmat, preflen+1, prefix); + gk_csr_Free(&cmat); + } + } + +} + + +/******************************************************************************/ +/*! This function projects a matrix w.r.t. to a particular column. + It performs the following steps: + - Determines the length of each column that is remaining. + - Sorts the columns in increasing length. + - Creates a column-based version of the matrix with the proper + column ordering. + */ +/*******************************************************************************/ +gk_csr_t *itemsets_project_matrix(isparams_t *params, gk_csr_t *mat, int cid) +{ + ssize_t i, j, k, ii, pnnz; + int nrows, ncols, pnrows, pncols; + ssize_t *colptr, *pcolptr; + int *colind, *colids, *pcolind, *pcolids, *rmarker; + gk_csr_t *pmat; + gk_ikv_t *cand; + + nrows = mat->nrows; + ncols = mat->ncols; + colptr = mat->colptr; + colind = mat->colind; + colids = mat->colids; + + rmarker = params->rmarker; + cand = params->cand; + + + /* Allocate space for the projected matrix based on what you know thus far */ + pmat = gk_csr_Create(); + pmat->nrows = pnrows = (cid == -1 ? nrows : colptr[cid+1]-colptr[cid]); + + + /* Mark the rows that will be kept and determine the prowids */ + if (cid == -1) { /* Initial projection */ + gk_iset(nrows, 1, rmarker); + } + else { /* The other projections */ + for (i=colptr[cid]; i= params->minfreq && k <= params->maxfreq) { + cand[pncols].val = i; + cand[pncols++].key = k; + pnnz += k; + } + } + + /* Sort the columns in increasing order */ + gk_ikvsorti(pncols, cand); + + + /* Allocate space for the remaining fields of the projected matrix */ + pmat->ncols = pncols; + pmat->colids = pcolids = gk_imalloc(pncols, "itemsets_project_matrix: pcolids"); + pmat->colptr = pcolptr = gk_zmalloc(pncols+1, "itemsets_project_matrix: pcolptr"); + pmat->colind = pcolind = gk_imalloc(pnnz, "itemsets_project_matrix: pcolind"); + + + /* Populate the projected matrix */ + pcolptr[0] = 0; + for (pnnz=0, ii=0; ii + + +/*************************************************************************/ +/*! This function creates an mcore + */ +/*************************************************************************/ +gk_mcore_t *gk_mcoreCreate(size_t coresize) +{ + gk_mcore_t *mcore; + + mcore = (gk_mcore_t *)gk_malloc(sizeof(gk_mcore_t), "gk_mcoreCreate: mcore"); + memset(mcore, 0, sizeof(gk_mcore_t)); + + mcore->coresize = coresize; + mcore->corecpos = 0; + + mcore->core = (coresize == 0 ? NULL : gk_malloc(mcore->coresize, "gk_mcoreCreate: core")); + + /* allocate the memory for keeping track of malloc ops */ + mcore->nmops = 2048; + mcore->cmop = 0; + mcore->mops = (gk_mop_t *)gk_malloc(mcore->nmops*sizeof(gk_mop_t), "gk_mcoreCreate: mcore->mops"); + + return mcore; +} + + +/*************************************************************************/ +/*! This function creates an mcore. This version is used for gkmcore. + */ +/*************************************************************************/ +gk_mcore_t *gk_gkmcoreCreate() +{ + gk_mcore_t *mcore; + + if ((mcore = (gk_mcore_t *)malloc(sizeof(gk_mcore_t))) == NULL) + return NULL; + memset(mcore, 0, sizeof(gk_mcore_t)); + + /* allocate the memory for keeping track of malloc ops */ + mcore->nmops = 2048; + mcore->cmop = 0; + if ((mcore->mops = (gk_mop_t *)malloc(mcore->nmops*sizeof(gk_mop_t))) == NULL) { + free(mcore); + return NULL; + } + + return mcore; +} + + +/*************************************************************************/ +/*! This function destroys an mcore. + */ +/*************************************************************************/ +void gk_mcoreDestroy(gk_mcore_t **r_mcore, int showstats) +{ + gk_mcore_t *mcore = *r_mcore; + + if (mcore == NULL) + return; + + if (showstats) + printf("\n gk_mcore statistics\n" + " coresize: %12zu nmops: %12zu cmop: %6zu\n" + " num_callocs: %12zu num_hallocs: %12zu\n" + " size_callocs: %12zu size_hallocs: %12zu\n" + " cur_callocs: %12zu cur_hallocs: %12zu\n" + " max_callocs: %12zu max_hallocs: %12zu\n", + mcore->coresize, mcore->nmops, mcore->cmop, + mcore->num_callocs, mcore->num_hallocs, + mcore->size_callocs, mcore->size_hallocs, + mcore->cur_callocs, mcore->cur_hallocs, + mcore->max_callocs, mcore->max_hallocs); + + if (mcore->cur_callocs != 0 || mcore->cur_hallocs != 0 || mcore->cmop != 0) { + printf("***Warning: mcore memory was not fully freed when destroyed.\n" + " cur_callocs: %6zu cur_hallocs: %6zu cmop: %6zu\n", + mcore->cur_callocs, mcore->cur_hallocs, mcore->cmop); + } + + gk_free((void **)&mcore->core, &mcore->mops, &mcore, LTERM); + + *r_mcore = NULL; +} + + +/*************************************************************************/ +/*! This function destroys an mcore. This version is for gkmcore. + */ +/*************************************************************************/ +void gk_gkmcoreDestroy(gk_mcore_t **r_mcore, int showstats) +{ + gk_mcore_t *mcore = *r_mcore; + + if (mcore == NULL) + return; + + if (showstats) + printf("\n gk_mcore statistics\n" + " nmops: %12zu cmop: %6zu\n" + " num_hallocs: %12zu\n" + " size_hallocs: %12zu\n" + " cur_hallocs: %12zu\n" + " max_hallocs: %12zu\n", + mcore->nmops, mcore->cmop, + mcore->num_hallocs, + mcore->size_hallocs, + mcore->cur_hallocs, + mcore->max_hallocs); + + if (mcore->cur_hallocs != 0 || mcore->cmop != 0) { + printf("***Warning: mcore memory was not fully freed when destroyed.\n" + " cur_hallocs: %6zu cmop: %6zu\n", + mcore->cur_hallocs, mcore->cmop); + } + + free(mcore->mops); + free(mcore); + + *r_mcore = NULL; +} + + +/*************************************************************************/ +/*! This function allocate space from the core/heap + */ +/*************************************************************************/ +void *gk_mcoreMalloc(gk_mcore_t *mcore, size_t nbytes) +{ + void *ptr; + + /* pad to make pointers 8-byte aligned */ + nbytes += (nbytes%8 == 0 ? 0 : 8 - nbytes%8); + + if (mcore->corecpos + nbytes < mcore->coresize) { + /* service this request from the core */ + ptr = ((char *)mcore->core)+mcore->corecpos; + mcore->corecpos += nbytes; + + gk_mcoreAdd(mcore, GK_MOPT_CORE, nbytes, ptr); + } + else { + /* service this request from the heap */ + ptr = gk_malloc(nbytes, "gk_mcoremalloc: ptr"); + + gk_mcoreAdd(mcore, GK_MOPT_HEAP, nbytes, ptr); + } + + /* + printf("MCMALLOC: %zu %d %8zu\n", mcore->cmop-1, + mcore->mops[mcore->cmop-1].type, mcore->mops[mcore->cmop-1].nbytes); + */ + + return ptr; +} + + +/*************************************************************************/ +/*! This function sets a marker in the stack of malloc ops to be used + subsequently for freeing purposes + */ +/*************************************************************************/ +void gk_mcorePush(gk_mcore_t *mcore) +{ + gk_mcoreAdd(mcore, GK_MOPT_MARK, 0, NULL); + /* printf("MCPPUSH: %zu\n", mcore->cmop-1); */ +} + + +/*************************************************************************/ +/*! This function sets a marker in the stack of malloc ops to be used + subsequently for freeing purposes. This is the gkmcore version. + */ +/*************************************************************************/ +void gk_gkmcorePush(gk_mcore_t *mcore) +{ + gk_gkmcoreAdd(mcore, GK_MOPT_MARK, 0, NULL); + /* printf("MCPPUSH: %zu\n", mcore->cmop-1); */ +} + + +/*************************************************************************/ +/*! This function frees all mops since the last push + */ +/*************************************************************************/ +void gk_mcorePop(gk_mcore_t *mcore) +{ + while (mcore->cmop > 0) { + mcore->cmop--; + switch (mcore->mops[mcore->cmop].type) { + case GK_MOPT_MARK: /* push marker */ + goto DONE; + break; + + case GK_MOPT_CORE: /* core free */ + if (mcore->corecpos < mcore->mops[mcore->cmop].nbytes) + errexit("Internal Error: wspace's core is about to be over-freed [%zu, %zu, %zd]\n", + mcore->coresize, mcore->corecpos, mcore->mops[mcore->cmop].nbytes); + + mcore->corecpos -= mcore->mops[mcore->cmop].nbytes; + mcore->cur_callocs -= mcore->mops[mcore->cmop].nbytes; + break; + + case GK_MOPT_HEAP: /* heap free */ + gk_free((void **)&mcore->mops[mcore->cmop].ptr, LTERM); + mcore->cur_hallocs -= mcore->mops[mcore->cmop].nbytes; + break; + + default: + gk_errexit(SIGMEM, "Unknown mop type of %d\n", mcore->mops[mcore->cmop].type); + } + } + +DONE: + ; + /*printf("MCPPOP: %zu\n", mcore->cmop); */ +} + + +/*************************************************************************/ +/*! This function frees all mops since the last push. This version is + for poping the gkmcore and it uses free instead of gk_free. + */ +/*************************************************************************/ +void gk_gkmcorePop(gk_mcore_t *mcore) +{ + while (mcore->cmop > 0) { + mcore->cmop--; + switch (mcore->mops[mcore->cmop].type) { + case GK_MOPT_MARK: /* push marker */ + goto DONE; + break; + + case GK_MOPT_HEAP: /* heap free */ + free(mcore->mops[mcore->cmop].ptr); + mcore->cur_hallocs -= mcore->mops[mcore->cmop].nbytes; + break; + + default: + gk_errexit(SIGMEM, "Unknown mop type of %d\n", mcore->mops[mcore->cmop].type); + } + } + +DONE: + ; +} + + +/*************************************************************************/ +/*! Adds a memory allocation at the end of the list. + */ +/*************************************************************************/ +void gk_mcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr) +{ + if (mcore->cmop == mcore->nmops) { + mcore->nmops *= 2; + mcore->mops = realloc(mcore->mops, mcore->nmops*sizeof(gk_mop_t)); + if (mcore->mops == NULL) + gk_errexit(SIGMEM, "***Memory allocation for gkmcore failed.\n"); + } + + mcore->mops[mcore->cmop].type = type; + mcore->mops[mcore->cmop].nbytes = nbytes; + mcore->mops[mcore->cmop].ptr = ptr; + mcore->cmop++; + + switch (type) { + case GK_MOPT_MARK: + break; + + case GK_MOPT_CORE: + mcore->num_callocs++; + mcore->size_callocs += nbytes; + mcore->cur_callocs += nbytes; + if (mcore->max_callocs < mcore->cur_callocs) + mcore->max_callocs = mcore->cur_callocs; + break; + + case GK_MOPT_HEAP: + mcore->num_hallocs++; + mcore->size_hallocs += nbytes; + mcore->cur_hallocs += nbytes; + if (mcore->max_hallocs < mcore->cur_hallocs) + mcore->max_hallocs = mcore->cur_hallocs; + break; + default: + gk_errexit(SIGMEM, "Incorrect mcore type operation.\n"); + } +} + + +/*************************************************************************/ +/*! Adds a memory allocation at the end of the list. This is the gkmcore + version. + */ +/*************************************************************************/ +void gk_gkmcoreAdd(gk_mcore_t *mcore, int type, size_t nbytes, void *ptr) +{ + if (mcore->cmop == mcore->nmops) { + mcore->nmops *= 2; + mcore->mops = realloc(mcore->mops, mcore->nmops*sizeof(gk_mop_t)); + if (mcore->mops == NULL) + gk_errexit(SIGMEM, "***Memory allocation for gkmcore failed.\n"); + } + + mcore->mops[mcore->cmop].type = type; + mcore->mops[mcore->cmop].nbytes = nbytes; + mcore->mops[mcore->cmop].ptr = ptr; + mcore->cmop++; + + switch (type) { + case GK_MOPT_MARK: + break; + + case GK_MOPT_HEAP: + mcore->num_hallocs++; + mcore->size_hallocs += nbytes; + mcore->cur_hallocs += nbytes; + if (mcore->max_hallocs < mcore->cur_hallocs) + mcore->max_hallocs = mcore->cur_hallocs; + break; + default: + gk_errexit(SIGMEM, "Incorrect mcore type operation.\n"); + } +} + + +/*************************************************************************/ +/*! This function deletes the mop associated with the supplied pointer. + The mop has to be a heap allocation, otherwise it fails violently. + */ +/*************************************************************************/ +void gk_mcoreDel(gk_mcore_t *mcore, void *ptr) +{ + int i; + + for (i=mcore->cmop-1; i>=0; i--) { + if (mcore->mops[i].type == GK_MOPT_MARK) + gk_errexit(SIGMEM, "Could not find pointer %p in mcore\n", ptr); + + if (mcore->mops[i].ptr == ptr) { + if (mcore->mops[i].type != GK_MOPT_HEAP) + gk_errexit(SIGMEM, "Trying to delete a non-HEAP mop.\n"); + + mcore->cur_hallocs -= mcore->mops[i].nbytes; + mcore->mops[i] = mcore->mops[--mcore->cmop]; + return; + } + } + + gk_errexit(SIGMEM, "mcoreDel should never have been here!\n"); +} + + +/*************************************************************************/ +/*! This function deletes the mop associated with the supplied pointer. + The mop has to be a heap allocation, otherwise it fails violently. + This is the gkmcore version. + */ +/*************************************************************************/ +void gk_gkmcoreDel(gk_mcore_t *mcore, void *ptr) +{ + int i; + + for (i=mcore->cmop-1; i>=0; i--) { + if (mcore->mops[i].type == GK_MOPT_MARK) + gk_errexit(SIGMEM, "Could not find pointer %p in mcore\n", ptr); + + if (mcore->mops[i].ptr == ptr) { + if (mcore->mops[i].type != GK_MOPT_HEAP) + gk_errexit(SIGMEM, "Trying to delete a non-HEAP mop.\n"); + + mcore->cur_hallocs -= mcore->mops[i].nbytes; + mcore->mops[i] = mcore->mops[--mcore->cmop]; + return; + } + } + + gk_errexit(SIGMEM, "gkmcoreDel should never have been here!\n"); +} + diff --git a/memory.c b/memory.c new file mode 100644 index 0000000..e6dc99c --- /dev/null +++ b/memory.c @@ -0,0 +1,307 @@ +/*! +\file memory.c +\brief This file contains various allocation routines + +The allocation routines included are for 1D and 2D arrays of the +most datatypes that GKlib support. Many of these routines are +defined with the help of the macros in gk_memory.h. These macros +can be used to define other memory allocation routines. + +\date Started 4/3/2007 +\author George +\version\verbatim $Id: memory.c 21050 2017-05-25 03:53:58Z karypis $ \endverbatim +*/ + + +#include + +/* This is for the global mcore that tracks all heap allocations */ +static __thread gk_mcore_t *gkmcore = NULL; + + +/*************************************************************************/ +/*! Define the set of memory allocation routines for each data type */ +/**************************************************************************/ +GK_MKALLOC(gk_c, char) +GK_MKALLOC(gk_i, int) +GK_MKALLOC(gk_i8, int8_t) +GK_MKALLOC(gk_i16, int16_t) +GK_MKALLOC(gk_i32, int32_t) +GK_MKALLOC(gk_i64, int64_t) +GK_MKALLOC(gk_ui8, uint8_t) +GK_MKALLOC(gk_ui16, uint16_t) +GK_MKALLOC(gk_ui32, uint32_t) +GK_MKALLOC(gk_ui64, uint64_t) +GK_MKALLOC(gk_z, ssize_t) +GK_MKALLOC(gk_zu, size_t) +GK_MKALLOC(gk_f, float) +GK_MKALLOC(gk_d, double) +GK_MKALLOC(gk_idx, gk_idx_t) + +GK_MKALLOC(gk_ckv, gk_ckv_t) +GK_MKALLOC(gk_ikv, gk_ikv_t) +GK_MKALLOC(gk_i8kv, gk_i8kv_t) +GK_MKALLOC(gk_i16kv, gk_i16kv_t) +GK_MKALLOC(gk_i32kv, gk_i32kv_t) +GK_MKALLOC(gk_i64kv, gk_i64kv_t) +GK_MKALLOC(gk_zkv, gk_zkv_t) +GK_MKALLOC(gk_zukv, gk_zukv_t) +GK_MKALLOC(gk_fkv, gk_fkv_t) +GK_MKALLOC(gk_dkv, gk_dkv_t) +GK_MKALLOC(gk_skv, gk_skv_t) +GK_MKALLOC(gk_idxkv, gk_idxkv_t) + + + + + + +/*************************************************************************/ +/*! This function allocates a two-dimensional matrix. + */ +/*************************************************************************/ +void gk_AllocMatrix(void ***r_matrix, size_t elmlen, size_t ndim1, size_t ndim2) +{ + size_t i, j; + void **matrix; + + *r_matrix = NULL; + + if ((matrix = (void **)gk_malloc(ndim1*sizeof(void *), "gk_AllocMatrix: matrix")) == NULL) + return; + + for (i=0; icmop == 0) { + gk_gkmcoreDestroy(&gkmcore, showstats); + gkmcore = NULL; + } + } +} + + +/*************************************************************************/ +/*! This function is my wrapper around malloc that provides the following + enhancements over malloc: + * It always allocates one byte of memory, even if 0 bytes are requested. + This is to ensure that checks of returned values do not lead to NULL + due to 0 bytes requested. + * It zeros-out the memory that is allocated. This is for a quick init + of the underlying datastructures. +*/ +/**************************************************************************/ +void *gk_malloc(size_t nbytes, char *msg) +{ + void *ptr=NULL; + + if (nbytes == 0) + nbytes++; /* Force mallocs to actually allocate some memory */ + + ptr = (void *)malloc(nbytes); + + if (ptr == NULL) { + fprintf(stderr, " Current memory used: %10zu bytes\n", gk_GetCurMemoryUsed()); + fprintf(stderr, " Maximum memory used: %10zu bytes\n", gk_GetMaxMemoryUsed()); + gk_errexit(SIGMEM, "***Memory allocation failed for %s. Requested size: %zu bytes", + msg, nbytes); + return NULL; + } + + /* add this memory allocation */ + if (gkmcore != NULL) gk_gkmcoreAdd(gkmcore, GK_MOPT_HEAP, nbytes, ptr); + + return ptr; +} + + +/************************************************************************* +* This function is my wrapper around realloc +**************************************************************************/ +void *gk_realloc(void *oldptr, size_t nbytes, char *msg) +{ + void *ptr=NULL; + + if (nbytes == 0) + nbytes++; /* Force mallocs to actually allocate some memory */ + + /* remove this memory de-allocation */ + if (gkmcore != NULL && oldptr != NULL) gk_gkmcoreDel(gkmcore, oldptr); + + ptr = (void *)realloc(oldptr, nbytes); + + if (ptr == NULL) { + fprintf(stderr, " Maximum memory used: %10zu bytes\n", gk_GetMaxMemoryUsed()); + fprintf(stderr, " Current memory used: %10zu bytes\n", gk_GetCurMemoryUsed()); + gk_errexit(SIGMEM, "***Memory realloc failed for %s. " "Requested size: %zu bytes", + msg, nbytes); + return NULL; + } + + /* add this memory allocation */ + if (gkmcore != NULL) gk_gkmcoreAdd(gkmcore, GK_MOPT_HEAP, nbytes, ptr); + + return ptr; +} + + +/************************************************************************* +* This function is my wrapper around free, allows multiple pointers +**************************************************************************/ +void gk_free(void **ptr1,...) +{ + va_list plist; + void **ptr; + + if (*ptr1 != NULL) { + free(*ptr1); + + /* remove this memory de-allocation */ + if (gkmcore != NULL) + gk_gkmcoreDel(gkmcore, *ptr1); + } + *ptr1 = NULL; + + va_start(plist, ptr1); + while ((ptr = va_arg(plist, void **)) != LTERM) { + if (*ptr != NULL) { + free(*ptr); + + /* remove this memory de-allocation */ + if (gkmcore != NULL) + gk_gkmcoreDel(gkmcore, *ptr); + } + *ptr = NULL; + } + va_end(plist); +} + + +/************************************************************************* +* This function returns the current ammount of dynamically allocated +* memory that is used by the system +**************************************************************************/ +size_t gk_GetCurMemoryUsed() +{ + if (gkmcore == NULL) + return 0; + else + return gkmcore->cur_hallocs; +} + + +/************************************************************************* +* This function returns the maximum ammount of dynamically allocated +* memory that was used by the system +**************************************************************************/ +size_t gk_GetMaxMemoryUsed() +{ + if (gkmcore == NULL) + return 0; + else + return gkmcore->max_hallocs; +} + + +/*************************************************************************/ +/*! This function returns the VmSize and VmRSS of the calling process. */ +/*************************************************************************/ +void gk_GetVMInfo(size_t *vmsize, size_t *vmrss) +{ + FILE *fp; + char fname[1024]; + + sprintf(fname, "/proc/%d/statm", getpid()); + fp = gk_fopen(fname, "r", "proc/pid/statm"); + if (fscanf(fp, "%zu %zu", vmsize, vmrss) != 2) + errexit("Failed to read to values from %s\n", fname); + gk_fclose(fp); + + /* + *vmsize *= sysconf(_SC_PAGESIZE); + *vmrss *= sysconf(_SC_PAGESIZE); + */ + + return; +} + + +/*************************************************************************/ +/*! This function returns the peak virtual memory of the calling process + by reading the VmPeak field in /proc/self/status . */ +/*************************************************************************/ +size_t gk_GetProcVmPeak() +{ + FILE *fp; + char line[128]; + size_t vmpeak=0; + + if (gk_fexists("/proc/self/status")) { + fp = gk_fopen("/proc/self/status", "r", "proc/self/status"); + while (fgets(line, 128, fp) != NULL) { + if (strncmp(line, "VmPeak:", 7) == 0) { + vmpeak = atoll(line+8)*1024; + break; + } + } + gk_fclose(fp); + } + + return vmpeak; +} diff --git a/pqueue.c b/pqueue.c new file mode 100644 index 0000000..2fb8515 --- /dev/null +++ b/pqueue.c @@ -0,0 +1,25 @@ +/*! +\file pqueue.c +\brief This file implements various max-priority queues. + +The priority queues are generated using the GK_MKPQUEUE macro. + +\date Started 3/27/2007 +\author George +\version\verbatim $Id: pqueue.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim +*/ + +#include + + +/*************************************************************************/ +/*! Create the various max priority queues */ +/*************************************************************************/ +#define key_gt(a, b) ((a) > (b)) +GK_MKPQUEUE(gk_ipq, gk_ipq_t, gk_ikv_t, int, gk_idx_t, gk_ikvmalloc, INT_MAX, key_gt) +GK_MKPQUEUE(gk_i32pq, gk_i32pq_t, gk_i32kv_t, int32_t, gk_idx_t, gk_i32kvmalloc, INT32_MAX, key_gt) +GK_MKPQUEUE(gk_i64pq, gk_i64pq_t, gk_i64kv_t, int64_t, gk_idx_t, gk_i64kvmalloc, INT64_MAX, key_gt) +GK_MKPQUEUE(gk_fpq, gk_fpq_t, gk_fkv_t, float, gk_idx_t, gk_fkvmalloc, FLT_MAX, key_gt) +GK_MKPQUEUE(gk_dpq, gk_dpq_t, gk_dkv_t, double, gk_idx_t, gk_dkvmalloc, DBL_MAX, key_gt) +GK_MKPQUEUE(gk_idxpq, gk_idxpq_t, gk_idxkv_t, gk_idx_t, gk_idx_t, gk_idxkvmalloc, GK_IDX_MAX, key_gt) +#undef key_gt diff --git a/random.c b/random.c new file mode 100644 index 0000000..3698614 --- /dev/null +++ b/random.c @@ -0,0 +1,136 @@ +/*! +\file +\brief Various routines for providing portable 32 and 64 bit random number + generators. + +\date Started 5/17/2007 +\author George +\version\verbatim $Id: random.c 18796 2015-06-02 11:39:45Z karypis $ \endverbatim +*/ + +#include + + +/*************************************************************************/ +/*! Create the various random number functions */ +/*************************************************************************/ +GK_MKRANDOM(gk_c, size_t, char) +GK_MKRANDOM(gk_i, size_t, int) +GK_MKRANDOM(gk_i32, size_t, int32_t) +GK_MKRANDOM(gk_f, size_t, float) +GK_MKRANDOM(gk_d, size_t, double) +GK_MKRANDOM(gk_idx, size_t, gk_idx_t) +GK_MKRANDOM(gk_z, size_t, ssize_t) +GK_MKRANDOM(gk_zu, size_t, size_t) + + + +/*************************************************************************/ +/*! GKlib's built in random number generator for portability across + different architectures */ +/*************************************************************************/ +#ifdef USE_GKRAND +/* + A C-program for MT19937-64 (2004/9/29 version). + Coded by Takuji Nishimura and Makoto Matsumoto. + + This is a 64-bit version of Mersenne Twister pseudorandom number + generator. + + Before using, initialize the state by using init_genrand64(seed) + or init_by_array64(init_key, key_length). + + Copyright (C) 2004, Makoto Matsumoto and Takuji Nishimura, + All rights reserved. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, + EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, + PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR + PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF + LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +*/ + +#define NN 312 +#define MM 156 +#define MATRIX_A 0xB5026F5AA96619E9ULL +#define UM 0xFFFFFFFF80000000ULL /* Most significant 33 bits */ +#define LM 0x7FFFFFFFULL /* Least significant 31 bits */ + + +/* The array for the state vector */ +static uint64_t mt[NN]; +/* mti==NN+1 means mt[NN] is not initialized */ +static int mti=NN+1; +#endif /* USE_GKRAND */ + +/* initializes mt[NN] with a seed */ +void gk_randinit(uint64_t seed) +{ +#ifdef USE_GKRAND + mt[0] = seed; + for (mti=1; mti> 62)) + mti); +#else + srand((unsigned int) seed); +#endif +} + + +/* generates a random number on [0, 2^64-1]-interval */ +uint64_t gk_randint64(void) +{ +#ifdef USE_GKRAND + int i; + unsigned long long x; + static uint64_t mag01[2]={0ULL, MATRIX_A}; + + if (mti >= NN) { /* generate NN words at one time */ + /* if init_genrand64() has not been called, */ + /* a default initial seed is used */ + if (mti == NN+1) + gk_randinit(5489ULL); + + for (i=0; i>1) ^ mag01[(int)(x&1ULL)]; + } + for (; i>1) ^ mag01[(int)(x&1ULL)]; + } + x = (mt[NN-1]&UM)|(mt[0]&LM); + mt[NN-1] = mt[MM-1] ^ (x>>1) ^ mag01[(int)(x&1ULL)]; + + mti = 0; + } + + x = mt[mti++]; + + x ^= (x >> 29) & 0x5555555555555555ULL; + x ^= (x << 17) & 0x71D67FFFEDA60000ULL; + x ^= (x << 37) & 0xFFF7EEE000000000ULL; + x ^= (x >> 43); + + return x & 0x7FFFFFFFFFFFFFFF; +#else + return (uint64_t)(((uint64_t) rand()) << 32 | ((uint64_t) rand())); +#endif +} + +/* generates a random number on [0, 2^32-1]-interval */ +uint32_t gk_randint32(void) +{ +#ifdef USE_GKRAND + return (uint32_t)(gk_randint64() & 0x7FFFFFFF); +#else + return (uint32_t)rand(); +#endif +} + + diff --git a/rw.c b/rw.c new file mode 100644 index 0000000..7cd4391 --- /dev/null +++ b/rw.c @@ -0,0 +1,103 @@ +/*! + * \file + * + * \brief Various routines that perform random-walk based operations + on graphs stored as gk_csr_t matrices. + * + * \author George Karypis + * \version\verbatim $Id: rw.c 11078 2011-11-12 00:20:44Z karypis $ \endverbatim + */ + +#include + + +/*************************************************************************/ +/*! Computes the (personalized) page-rank of the vertices in a graph. + + \param mat is the matrix storing the graph. + \param lamda is the restart probability. + \param eps is the error tolerance for convergance. + \param max_niter is the maximum number of allowed iterations. + \param pr on entry stores the restart distribution of the vertices. + This allows for the computation of personalized page-rank scores + by appropriately setting that parameter. + On return, pr stores the computed page ranks. + + \returns the number of iterations that were performed. +*/ +/**************************************************************************/ +int gk_rw_PageRank(gk_csr_t *mat, float lamda, float eps, int max_niter, float *pr) +{ + ssize_t i, j, k, iter, nrows; + double *rscale, *prold, *prnew, *prtmp; + double fromsinks, error; + ssize_t *rowptr; + int *rowind; + float *rowval; + + nrows = mat->nrows; + rowptr = mat->rowptr; + rowind = mat->rowind; + rowval = mat->rowval; + + prold = gk_dsmalloc(nrows, 0, "gk_rw_PageRank: prnew"); + prnew = gk_dsmalloc(nrows, 0, "gk_rw_PageRank: prold"); + rscale = gk_dsmalloc(nrows, 0, "gk_rw_PageRank: rscale"); + + /* compute the scaling factors to get adjacency weights into transition + probabilities */ + for (i=0; i 0) + rscale[i] = 1.0/rscale[i]; + } + + /* the restart distribution is the initial pr scores */ + for (i=0; i error ? fabs(prnew[i]-prold[i]) : error); + + //printf("nrm1: %le maxfabserr: %le\n", gk_dsum(nrows, prnew, 1), error); + + if (error < eps) + break; + } + + /* store the computed pr scores into pr for output */ + for (i=0; i \n" unless @ARGV == 2; + +$filein = shift(@ARGV); +$ncopies = shift(@ARGV); + +open(FPIN, "<$filein") or die "Could not open $filein. $!\n"; + +$_ = ; +chomp($_); +($nvtxs, $nedges) = split(' ', $_); + +#print "nvtxs: $nvtxs, nedges: $nedges\n"; + +$u = 1; +while () { + chomp($_); + @edges = split(' ', $_); + + # put the within layer edges + foreach $v (@edges) { + next if $v < $u; + for ($i=0; $i<$ncopies; $i++) { + printf("%d %d\n", $i*$nvtxs+$u-1, $i*$nvtxs+$v-1); + printf("%d %d\n", $i*$nvtxs+$v-1, $i*$nvtxs+$u-1); + } + } + + # put the vertex across layer edges + for ($i=0; $i<$ncopies-1; $i++) { + printf("%d %d\n", $i*$nvtxs+$u-1, ($i+1)*$nvtxs+$u-1); + printf("%d %d\n", ($i+1)*$nvtxs+$u-1, $i*$nvtxs+$u-1); + } + + # put the adjacent across layer edges + for ($i=0; $i<$ncopies-1; $i++) { + $j=0; + foreach $v (@edges) { + $j++; + next if (($j+$i)%2 == 0); + printf("%d %d\n", $i*$nvtxs+$u-1, ($i+1)*$nvtxs+$v-1); + printf("%d %d\n", ($i+1)*$nvtxs+$v-1, $i*$nvtxs+$u-1); + } + } + + goto DONE; + +DONE: + $u++; +} + +close(FPIN); diff --git a/seq.c b/seq.c new file mode 100644 index 0000000..f267a3e --- /dev/null +++ b/seq.c @@ -0,0 +1,174 @@ +/* + * + * Sequence handler library by Huzefa Rangwala + * Date : 03.01.2007 + * + * + * + */ + + +#include + + + + +/*********************************************************/ +/* ! \brief Initializes the gk_seq_t variable + + + + +\param A pointer to gk_seq_t itself +\returns null +*/ +/***********************************************************************/ + +void gk_seq_init(gk_seq_t *seq) +{ + + seq->len = 0; + seq->sequence = NULL; + + seq->pssm = NULL; + seq->psfm = NULL; + + seq->name = NULL; + +} + +/***********************************************************************/ +/*! \brief This function creates the localizations for the various sequences + +\param string i.e amino acids, nucleotides, sequences +\returns gk_i2cc2i_t variable +*/ +/*********************************************************************/ + +gk_i2cc2i_t *gk_i2cc2i_create_common(char *alphabet) +{ + + + int nsymbols; + gk_idx_t i; + gk_i2cc2i_t *t; + + nsymbols = strlen(alphabet); + t = gk_malloc(sizeof(gk_i2cc2i_t),"gk_i2c_create_common"); + t->n = nsymbols; + t->i2c = gk_cmalloc(256, "gk_i2c_create_common"); + t->c2i = gk_imalloc(256, "gk_i2c_create_common"); + + + gk_cset(256, -1, t->i2c); + gk_iset(256, -1, t->c2i); + + for(i=0;ii2c[i] = alphabet[i]; + t->c2i[(int)alphabet[i]] = i; + } + + return t; + +} + + +/*********************************************************************/ +/*! \brief This function reads a pssm in the format of gkmod pssm + +\param file_name is the name of the pssm file +\returns gk_seq_t +*/ +/********************************************************************/ +gk_seq_t *gk_seq_ReadGKMODPSSM(char *filename) +{ + gk_seq_t *seq; + gk_idx_t i, j, ii; + size_t ntokens, nbytes, len; + FILE *fpin; + + + gk_Tokens_t tokens; + static char *AAORDER = "ARNDCQEGHILKMFPSTWYVBZX*"; + static int PSSMWIDTH = 20; + char *header, line[MAXLINELEN]; + gk_i2cc2i_t *converter; + + header = gk_cmalloc(PSSMWIDTH, "gk_seq_ReadGKMODPSSM: header"); + + converter = gk_i2cc2i_create_common(AAORDER); + + gk_getfilestats(filename, &len, &ntokens, NULL, &nbytes); + len --; + + seq = gk_malloc(sizeof(gk_seq_t),"gk_seq_ReadGKMODPSSM"); + gk_seq_init(seq); + + seq->len = len; + seq->sequence = gk_imalloc(len, "gk_seq_ReadGKMODPSSM"); + seq->pssm = gk_iAllocMatrix(len, PSSMWIDTH, 0, "gk_seq_ReadGKMODPSSM"); + seq->psfm = gk_iAllocMatrix(len, PSSMWIDTH, 0, "gk_seq_ReadGKMODPSSM"); + + seq->nsymbols = PSSMWIDTH; + seq->name = gk_getbasename(filename); + + fpin = gk_fopen(filename,"r","gk_seq_ReadGKMODPSSM"); + + + /* Read the header line */ + if (fgets(line, MAXLINELEN-1, fpin) == NULL) + errexit("Unexpected end of file: %s\n", filename); + gk_strtoupper(line); + gk_strtokenize(line, " \t\n", &tokens); + + for (i=0; isequence[i] = converter->c2i[(int)tokens.list[1][0]]; + + for (j=0; jpssm[i][converter->c2i[(int)header[j]]] = atoi(tokens.list[2+j]); + seq->psfm[i][converter->c2i[(int)header[j]]] = atoi(tokens.list[2+PSSMWIDTH+j]); + } + + + + gk_freetokenslist(&tokens); + i++; + } + + seq->len = i; /* Reset the length if certain characters were skipped */ + + gk_free((void **)&header, LTERM); + gk_fclose(fpin); + + return seq; +} + + +/**************************************************************************/ +/*! \brief This function frees the memory allocated to the seq structure. + +\param gk_seq_t +\returns nothing +*/ +/**************************************************************************/ +void gk_seq_free(gk_seq_t *seq) +{ + gk_iFreeMatrix(&seq->pssm, seq->len, seq->nsymbols); + gk_iFreeMatrix(&seq->psfm, seq->len, seq->nsymbols); + gk_free((void **)&seq->name, &seq->sequence, LTERM); + //gk_free((void **)&seq, LTERM); + gk_free((void **) &seq, LTERM); + +} diff --git a/sort.c b/sort.c new file mode 100644 index 0000000..f0144ae --- /dev/null +++ b/sort.c @@ -0,0 +1,437 @@ +/*! +\file sort.c +\brief This file contains GKlib's various sorting routines + +These routines are implemented using the GKSORT macro that is defined +in gk_qsort.h and is based on GNU's GLIBC qsort() implementation. + +Additional sorting routines can be created using the same way that +these routines where defined. + +\date Started 4/4/07 +\author George +\version\verbatim $Id: sort.c 21050 2017-05-25 03:53:58Z karypis $ \endverbatim +*/ + +#include + + + +/*************************************************************************/ +/*! Sorts an array of chars in increasing order */ +/*************************************************************************/ +void gk_csorti(size_t n, char *base) +{ +#define char_lt(a, b) ((*a) < (*b)) + GK_MKQSORT(char, base, n, char_lt); +#undef char_lt +} + + +/*************************************************************************/ +/*! Sorts an array of chars in decreasing order */ +/*************************************************************************/ +void gk_csortd(size_t n, char *base) +{ +#define char_gt(a, b) ((*a) > (*b)) + GK_MKQSORT(char, base, n, char_gt); +#undef char_gt +} + + +/*************************************************************************/ +/*! Sorts an array of integers in increasing order */ +/*************************************************************************/ +void gk_isorti(size_t n, int *base) +{ +#define int_lt(a, b) ((*a) < (*b)) + GK_MKQSORT(int, base, n, int_lt); +#undef int_lt +} + + +/*************************************************************************/ +/*! Sorts an array of integers in decreasing order */ +/*************************************************************************/ +void gk_isortd(size_t n, int *base) +{ +#define int_gt(a, b) ((*a) > (*b)) + GK_MKQSORT(int, base, n, int_gt); +#undef int_gt +} + + +/*************************************************************************/ +/*! Sorts an array of integers in increasing order */ +/*************************************************************************/ +void gk_i32sorti(size_t n, int32_t *base) +{ +#define int_lt(a, b) ((*a) < (*b)) + GK_MKQSORT(int32_t, base, n, int_lt); +#undef int_lt +} + + +/*************************************************************************/ +/*! Sorts an array of integers in decreasing order */ +/*************************************************************************/ +void gk_i32sortd(size_t n, int32_t *base) +{ +#define int_gt(a, b) ((*a) > (*b)) + GK_MKQSORT(int32_t, base, n, int_gt); +#undef int_gt +} + + +/*************************************************************************/ +/*! Sorts an array of integers in increasing order */ +/*************************************************************************/ +void gk_i64sorti(size_t n, int64_t *base) +{ +#define int_lt(a, b) ((*a) < (*b)) + GK_MKQSORT(int64_t, base, n, int_lt); +#undef int_lt +} + + +/*************************************************************************/ +/*! Sorts an array of integers in increasing order */ +/*************************************************************************/ +void gk_ui32sorti(size_t n, uint32_t *base) +{ +#define int_lt(a, b) ((*a) < (*b)) + GK_MKQSORT(uint32_t, base, n, int_lt); +#undef int_lt +} + + +/*************************************************************************/ +/*! Sorts an array of integers in decreasing order */ +/*************************************************************************/ +void gk_ui32sortd(size_t n, uint32_t *base) +{ +#define int_gt(a, b) ((*a) > (*b)) + GK_MKQSORT(uint32_t, base, n, int_gt); +#undef int_gt +} + + +/*************************************************************************/ +/*! Sorts an array of integers in increasing order */ +/*************************************************************************/ +void gk_ui64sorti(size_t n, uint64_t *base) +{ +#define int_lt(a, b) ((*a) < (*b)) + GK_MKQSORT(uint64_t, base, n, int_lt); +#undef int_lt +} + + +/*************************************************************************/ +/*! Sorts an array of integers in decreasing order */ +/*************************************************************************/ +void gk_ui64sortd(size_t n, uint64_t *base) +{ +#define int_gt(a, b) ((*a) > (*b)) + GK_MKQSORT(uint64_t, base, n, int_gt); +#undef int_gt +} + + +/*************************************************************************/ +/*! Sorts an array of integers in decreasing order */ +/*************************************************************************/ +void gk_i64sortd(size_t n, int64_t *base) +{ +#define int_gt(a, b) ((*a) > (*b)) + GK_MKQSORT(int64_t, base, n, int_gt); +#undef int_gt +} + + +/*************************************************************************/ +/*! Sorts an array of floats in increasing order */ +/*************************************************************************/ +void gk_fsorti(size_t n, float *base) +{ +#define float_lt(a, b) ((*a) < (*b)) + GK_MKQSORT(float, base, n, float_lt); +#undef float_lt +} + + +/*************************************************************************/ +/*! Sorts an array of floats in decreasing order */ +/*************************************************************************/ +void gk_fsortd(size_t n, float *base) +{ +#define float_gt(a, b) ((*a) > (*b)) + GK_MKQSORT(float, base, n, float_gt); +#undef float_gt +} + + +/*************************************************************************/ +/*! Sorts an array of doubles in increasing order */ +/*************************************************************************/ +void gk_dsorti(size_t n, double *base) +{ +#define double_lt(a, b) ((*a) < (*b)) + GK_MKQSORT(double, base, n, double_lt); +#undef double_lt +} + + +/*************************************************************************/ +/*! Sorts an array of doubles in decreasing order */ +/*************************************************************************/ +void gk_dsortd(size_t n, double *base) +{ +#define double_gt(a, b) ((*a) > (*b)) + GK_MKQSORT(double, base, n, double_gt); +#undef double_gt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_idx_t in increasing order */ +/*************************************************************************/ +void gk_idxsorti(size_t n, gk_idx_t *base) +{ +#define idx_lt(a, b) ((*a) < (*b)) + GK_MKQSORT(gk_idx_t, base, n, idx_lt); +#undef idx_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_idx_t in decreasing order */ +/*************************************************************************/ +void gk_idxsortd(size_t n, gk_idx_t *base) +{ +#define idx_gt(a, b) ((*a) > (*b)) + GK_MKQSORT(gk_idx_t, base, n, idx_gt); +#undef idx_gt +} + + + + +/*************************************************************************/ +/*! Sorts an array of gk_ckv_t in increasing order */ +/*************************************************************************/ +void gk_ckvsorti(size_t n, gk_ckv_t *base) +{ +#define ckey_lt(a, b) ((a)->key < (b)->key) + GK_MKQSORT(gk_ckv_t, base, n, ckey_lt); +#undef ckey_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_ckv_t in decreasing order */ +/*************************************************************************/ +void gk_ckvsortd(size_t n, gk_ckv_t *base) +{ +#define ckey_gt(a, b) ((a)->key > (b)->key) + GK_MKQSORT(gk_ckv_t, base, n, ckey_gt); +#undef ckey_gt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_ikv_t in increasing order */ +/*************************************************************************/ +void gk_ikvsorti(size_t n, gk_ikv_t *base) +{ +#define ikey_lt(a, b) ((a)->key < (b)->key) + GK_MKQSORT(gk_ikv_t, base, n, ikey_lt); +#undef ikey_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_ikv_t in decreasing order */ +/*************************************************************************/ +void gk_ikvsortd(size_t n, gk_ikv_t *base) +{ +#define ikey_gt(a, b) ((a)->key > (b)->key) + GK_MKQSORT(gk_ikv_t, base, n, ikey_gt); +#undef ikey_gt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_i32kv_t in increasing order */ +/*************************************************************************/ +void gk_i32kvsorti(size_t n, gk_i32kv_t *base) +{ +#define ikey_lt(a, b) ((a)->key < (b)->key) + GK_MKQSORT(gk_i32kv_t, base, n, ikey_lt); +#undef ikey_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_i32kv_t in decreasing order */ +/*************************************************************************/ +void gk_i32kvsortd(size_t n, gk_i32kv_t *base) +{ +#define ikey_gt(a, b) ((a)->key > (b)->key) + GK_MKQSORT(gk_i32kv_t, base, n, ikey_gt); +#undef ikey_gt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_i64kv_t in increasing order */ +/*************************************************************************/ +void gk_i64kvsorti(size_t n, gk_i64kv_t *base) +{ +#define ikey_lt(a, b) ((a)->key < (b)->key) + GK_MKQSORT(gk_i64kv_t, base, n, ikey_lt); +#undef ikey_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_i64kv_t in decreasing order */ +/*************************************************************************/ +void gk_i64kvsortd(size_t n, gk_i64kv_t *base) +{ +#define ikey_gt(a, b) ((a)->key > (b)->key) + GK_MKQSORT(gk_i64kv_t, base, n, ikey_gt); +#undef ikey_gt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_zkv_t in increasing order */ +/*************************************************************************/ +void gk_zkvsorti(size_t n, gk_zkv_t *base) +{ +#define zkey_lt(a, b) ((a)->key < (b)->key) + GK_MKQSORT(gk_zkv_t, base, n, zkey_lt); +#undef zkey_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_zkv_t in decreasing order */ +/*************************************************************************/ +void gk_zkvsortd(size_t n, gk_zkv_t *base) +{ +#define zkey_gt(a, b) ((a)->key > (b)->key) + GK_MKQSORT(gk_zkv_t, base, n, zkey_gt); +#undef zkey_gt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_zukv_t in increasing order */ +/*************************************************************************/ +void gk_zukvsorti(size_t n, gk_zukv_t *base) +{ +#define zukey_lt(a, b) ((a)->key < (b)->key) + GK_MKQSORT(gk_zukv_t, base, n, zukey_lt); +#undef zukey_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_zukv_t in decreasing order */ +/*************************************************************************/ +void gk_zukvsortd(size_t n, gk_zukv_t *base) +{ +#define zukey_gt(a, b) ((a)->key > (b)->key) + GK_MKQSORT(gk_zukv_t, base, n, zukey_gt); +#undef zukey_gt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_fkv_t in increasing order */ +/*************************************************************************/ +void gk_fkvsorti(size_t n, gk_fkv_t *base) +{ +#define fkey_lt(a, b) ((a)->key < (b)->key) + GK_MKQSORT(gk_fkv_t, base, n, fkey_lt); +#undef fkey_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_fkv_t in decreasing order */ +/*************************************************************************/ +void gk_fkvsortd(size_t n, gk_fkv_t *base) +{ +#define fkey_gt(a, b) ((a)->key > (b)->key) + GK_MKQSORT(gk_fkv_t, base, n, fkey_gt); +#undef fkey_gt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_dkv_t in increasing order */ +/*************************************************************************/ +void gk_dkvsorti(size_t n, gk_dkv_t *base) +{ +#define dkey_lt(a, b) ((a)->key < (b)->key) + GK_MKQSORT(gk_dkv_t, base, n, dkey_lt); +#undef dkey_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_fkv_t in decreasing order */ +/*************************************************************************/ +void gk_dkvsortd(size_t n, gk_dkv_t *base) +{ +#define dkey_gt(a, b) ((a)->key > (b)->key) + GK_MKQSORT(gk_dkv_t, base, n, dkey_gt); +#undef dkey_gt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_skv_t in increasing order */ +/*************************************************************************/ +void gk_skvsorti(size_t n, gk_skv_t *base) +{ +#define skey_lt(a, b) (strcmp((a)->key, (b)->key) < 0) + GK_MKQSORT(gk_skv_t, base, n, skey_lt); +#undef skey_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_skv_t in decreasing order */ +/*************************************************************************/ +void gk_skvsortd(size_t n, gk_skv_t *base) +{ +#define skey_gt(a, b) (strcmp((a)->key, (b)->key) > 0) + GK_MKQSORT(gk_skv_t, base, n, skey_gt); +#undef skey_gt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_idxkv_t in increasing order */ +/*************************************************************************/ +void gk_idxkvsorti(size_t n, gk_idxkv_t *base) +{ +#define idxkey_lt(a, b) ((a)->key < (b)->key) + GK_MKQSORT(gk_idxkv_t, base, n, idxkey_lt); +#undef idxkey_lt +} + + +/*************************************************************************/ +/*! Sorts an array of gk_idxkv_t in decreasing order */ +/*************************************************************************/ +void gk_idxkvsortd(size_t n, gk_idxkv_t *base) +{ +#define idxkey_gt(a, b) ((a)->key > (b)->key) + GK_MKQSORT(gk_idxkv_t, base, n, idxkey_gt); +#undef idxkey_gt +} diff --git a/string.c b/string.c new file mode 100644 index 0000000..4a3fb14 --- /dev/null +++ b/string.c @@ -0,0 +1,530 @@ +/************************************************************************/ +/*! \file + +\brief Functions for manipulating strings. + +Various functions for manipulating strings. Some of these functions +provide new functionality, whereas others are drop-in replacements +of standard functions (but with enhanced functionality). + +\date Started 11/1/99 +\author George +\version $Id: string.c 14330 2013-05-18 12:15:15Z karypis $ +*/ +/************************************************************************/ + +/* the following is for strptime() */ +#define _XOPEN_SOURCE +#include +#undef _XOPEN_SOURCE + +#include + + + +/************************************************************************/ +/*! \brief Replaces certain characters in a string. + +This function takes a string and replaces all the characters in the +\c fromlist with the corresponding characters from the \c tolist. +That is, each occurence of fromlist[i] is replaced by +tolist[i]. +If the \c tolist is shorter than \c fromlist, then the corresponding +characters are deleted. The modifications on \c str are done in place. +It tries to provide a functionality similar to Perl's \b tr// function. + +\param str is the string whose characters will be replaced. +\param fromlist is the set of characters to be replaced. +\param tolist is the set of replacement characters . +\returns A pointer to \c str itself. +*/ +/************************************************************************/ +char *gk_strchr_replace(char *str, char *fromlist, char *tolist) +{ + ssize_t i, j, k, len, fromlen, tolen; + + len = strlen(str); + fromlen = strlen(fromlist); + tolen = strlen(tolist); + + for (i=j=0; i s// regular-expression +based substitution function. + +\param str + is the input string on which the operation will be performed. +\param pattern + is the regular expression for the pattern to be matched for substitution. +\param replacement + is the replacement string, in which the possible captured pattern substrings + are referred to as $1, $2, ..., $9. The entire matched pattern is refered + to as $0. +\param options + is a string specified options for the substitution operation. Currently the + "i" (case insensitive) and "g" (global substitution) are + supported. +\param new_str + is a reference to a pointer that will store a pointer to the newly created + string that results from the substitutions. This string is allocated via + gk_malloc() and needs to be freed using gk_free(). The string is returned + even if no substitutions were performed. +\returns + If successful, it returns 1 + the number of substitutions that were performed. + Thus, if no substitutions were performed, the returned value will be 1. + Otherwise it returns 0. In case of error, a meaningful error message is + returned in newstr, which also needs to be freed afterwards. +*/ +/************************************************************************/ +int gk_strstr_replace(char *str, char *pattern, char *replacement, char *options, + char **new_str) +{ + ssize_t i, len, rlen, nlen, offset, noffset; + int j, rc, flags, global, nmatches; + regex_t re; + regmatch_t matches[10]; + + + /* Parse the options */ + flags = REG_EXTENDED; + if (strchr(options, 'i') != NULL) + flags = flags | REG_ICASE; + global = (strchr(options, 'g') != NULL ? 1 : 0); + + + /* Compile the regex */ + if ((rc = regcomp(&re, pattern, flags)) != 0) { + len = regerror(rc, &re, NULL, 0); + *new_str = gk_cmalloc(len, "gk_strstr_replace: new_str"); + regerror(rc, &re, *new_str, len); + return 0; + } + + /* Prepare the output string */ + len = strlen(str); + nlen = 2*len; + noffset = 0; + *new_str = gk_cmalloc(nlen+1, "gk_strstr_replace: new_str"); + + + /* Get into the matching-replacing loop */ + rlen = strlen(replacement); + offset = 0; + nmatches = 0; + do { + rc = regexec(&re, str+offset, 10, matches, 0); + + if (rc == REG_ESPACE) { + gk_free((void **)new_str, LTERM); + *new_str = gk_strdup("regexec ran out of memory."); + regfree(&re); + return 0; + } + else if (rc == REG_NOMATCH) { + if (nlen-noffset < len-offset) { + nlen += (len-offset) - (nlen-noffset); + *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); + } + strcpy(*new_str+noffset, str+offset); + noffset += (len-offset); + break; + } + else { /* A match was found! */ + nmatches++; + + /* Copy the left unmatched portion of the string */ + if (matches[0].rm_so > 0) { + if (nlen-noffset < matches[0].rm_so) { + nlen += matches[0].rm_so - (nlen-noffset); + *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); + } + strncpy(*new_str+noffset, str+offset, matches[0].rm_so); + noffset += matches[0].rm_so; + } + + /* Go and append the replacement string */ + for (i=0; i 9) { + gk_free((void **)new_str, LTERM); + *new_str = gk_strdup("Error in captured subexpression specification."); + regfree(&re); + return 0; + } + + if (nlen-noffset < matches[j].rm_eo-matches[j].rm_so) { + nlen += nlen + (matches[j].rm_eo-matches[j].rm_so); + *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); + } + + strncpy(*new_str+noffset, str+offset+matches[j].rm_so, matches[j].rm_eo); + noffset += matches[j].rm_eo-matches[j].rm_so; + } + else { + gk_free((void **)new_str, LTERM); + *new_str = gk_strdup("Error in replacement string. Missing subexpression number folloing '$'."); + regfree(&re); + return 0; + } + break; + + default: + if (nlen-noffset < 1) { + nlen += nlen + 1; + *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); + } + (*new_str)[noffset++] = replacement[i]; + } + } + + /* Update the offset of str for the next match */ + offset += matches[0].rm_eo; + + if (!global) { + /* Copy the right portion of the string if no 'g' option */ + if (nlen-noffset < len-offset) { + nlen += (len-offset) - (nlen-noffset); + *new_str = (char *)gk_realloc(*new_str, (nlen+1)*sizeof(char), "gk_strstr_replace: new_str"); + } + strcpy(*new_str+noffset, str+offset); + noffset += (len-offset); + } + } + } while (global); + + (*new_str)[noffset] = '\0'; + + regfree(&re); + return nmatches + 1; + +} + + + +/************************************************************************/ +/*! \brief Prunes characters from the end of the string. + +This function removes any trailing characters that are included in the +\c rmlist. The trimming stops at the last character (i.e., first character +from the end) that is not in \c rmlist. +This function can be used to removed trailing spaces, newlines, etc. +This is a distructive operation as it modifies the string. + +\param str is the string that will be trimmed. +\param rmlist contains the set of characters that will be removed. +\returns A pointer to \c str itself. +\sa gk_strhprune() +*/ +/*************************************************************************/ +char *gk_strtprune(char *str, char *rmlist) +{ + ssize_t i, j, len; + + len = strlen(rmlist); + + for (i=strlen(str)-1; i>=0; i--) { + for (j=0; j0) { /* If something needs to be removed */ + for (j=0; str[i]; i++, j++) + str[j] = str[i]; + str[j] = '\0'; + } + + return str; +} + + +/************************************************************************/ +/*! \brief Converts a string to upper case. + +This function converts a string to upper case. This operation modifies the +string itself. + +\param str is the string whose case will be changed. +\returns A pointer to \c str itself. +\sa gk_strtolower() +*/ +/*************************************************************************/ +char *gk_strtoupper(char *str) +{ + int i; + + for (i=0; str[i]!='\0'; str[i]=toupper(str[i]), i++); + return str; +} + + +/************************************************************************/ +/*! \brief Converts a string to lower case. + +This function converts a string to lower case. This operation modifies the +string itself. + +\param str is the string whose case will be changed. +\returns A pointer to \c str itself. +\sa gk_strtoupper() +*/ +/*************************************************************************/ +char *gk_strtolower(char *str) +{ + int i; + + for (i=0; str[i]!='\0'; str[i]=tolower(str[i]), i++); + return str; +} + + +/************************************************************************/ +/*! \brief Duplicates a string + +This function is a replacement for C's standard strdup() function. +The key differences between the two are that gk_strdup(): + - uses the dynamic memory allocation routines of \e GKlib. + - it correctly handles NULL input strings. + +The string that is returned must be freed by gk_free(). + +\param orgstr is the string that will be duplicated. +\returns A pointer to the newly created string. +\sa gk_free() +*/ +/*************************************************************************/ +char *gk_strdup(char *orgstr) +{ + int len; + char *str=NULL; + + if (orgstr != NULL) { + len = strlen(orgstr)+1; + str = gk_malloc(len*sizeof(char), "gk_strdup: str"); + strcpy(str, orgstr); + } + + return str; +} + + +/************************************************************************/ +/*! \brief Case insensitive string comparison. + +This function compares two strings for equality by ignoring the case of the +strings. + +\warning This function is \b not equivalent to a case-insensitive + strcmp() function, as it does not return ordering + information. + +\todo Remove the above warning. + +\param s1 is the first string to be compared. +\param s2 is the second string to be compared. +\retval 1 if the strings are identical, +\retval 0 otherwise. +*/ +/*************************************************************************/ +int gk_strcasecmp(char *s1, char *s2) +{ + int i=0; + + if (strlen(s1) != strlen(s2)) + return 0; + + while (s1[i] != '\0') { + if (tolower(s1[i]) != tolower(s2[i])) + return 0; + i++; + } + + return 1; +} + + +/************************************************************************/ +/*! \brief Compare two strings in revere order + +This function is similar to strcmp but it performs the comparison as +if the two strings were reversed. + +\param s1 is the first string to be compared. +\param s2 is the second string to be compared. +\retval -1, 0, 1, if the s1 < s2, s1 == s2, or s1 > s2. +*/ +/*************************************************************************/ +int gk_strrcmp(char *s1, char *s2) +{ + int i1 = strlen(s1)-1; + int i2 = strlen(s2)-1; + + while ((i1 >= 0) && (i2 >= 0)) { + if (s1[i1] != s2[i2]) + return (s1[i1] - s2[i2]); + i1--; + i2--; + } + + /* i1 == -1 and/or i2 == -1 */ + + if (i1 < i2) + return -1; + if (i1 > i2) + return 1; + return 0; +} + + + +/************************************************************************/ +/*! \brief Converts a time_t time into a string + +This function takes a time_t-specified time and returns a string-formated +representation of the corresponding time. The format of the string is +mm/dd/yyyy hh:mm:ss, in which the hours are in military time. + +\param time is the time to be converted. +\return It returns a pointer to a statically allocated string that is + over-written in successive calls of this function. If the + conversion failed, it returns NULL. + +*/ +/*************************************************************************/ +char *gk_time2str(time_t time) +{ + static char datestr[128]; + struct tm *tm; + + tm = localtime(&time); + + if (strftime(datestr, 128, "%m/%d/%Y %H:%M:%S", tm) == 0) + return NULL; + else + return datestr; +} + + + +#if !defined(WIN32) && !defined(__MINGW32__) +/************************************************************************/ +/*! \brief Converts a date/time string into its equivalent time_t value + +This function takes date and/or time specification and converts it in +the equivalent time_t representation. The conversion is done using the +strptime() function. The format that gk_str2time() understands is +mm/dd/yyyy hh:mm:ss, in which the hours are in military time. + +\param str is the date/time string to be converted. +\return If the conversion was successful it returns the time, otherwise + it returns -1. +*/ +/*************************************************************************/ +time_t gk_str2time(char *str) +{ + struct tm time; + time_t rtime; + + memset(&time, '\0', sizeof(time)); + + if (strptime(str, "%m/%d/%Y %H:%M:%S", &time) == NULL) + return -1; + + rtime = mktime(&time); + return (rtime < 0 ? 0 : rtime); +} +#endif + + +/************************************************************************* +* This function returns the ID of a particular string based on the +* supplied StringMap array +**************************************************************************/ +int gk_GetStringID(gk_StringMap_t *strmap, char *key) +{ + int i; + + for (i=0; strmap[i].name; i++) { + if (gk_strcasecmp(key, strmap[i].name)) + return strmap[i].id; + } + + return -1; +} diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt new file mode 100644 index 0000000..8584820 --- /dev/null +++ b/test/CMakeLists.txt @@ -0,0 +1,19 @@ +# Build program. +add_executable(strings strings.c) +add_executable(gksort gksort.c) +add_executable(fis fis.c) +add_executable(gkrw rw.c) +add_executable(gkgraph gkgraph.c) +add_executable(csrcnv csrcnv.c) +add_executable(grKx grKx.c) +add_executable(m2mnbrs m2mnbrs.c) +add_executable(cmpnbrs cmpnbrs.c) +add_executable(splatt2svd splatt2svd.c) +add_executable(gkuniq gkuniq.c) + +foreach(prog strings gksort fis gkrw gkgraph csrcnv grKx m2mnbrs cmpnbrs splatt2svd gkuniq) + target_link_libraries(${prog} GKlib) +endforeach(prog) + +# Install a subset of them +install(TARGETS csrcnv RUNTIME DESTINATION bin) diff --git a/test/cmpnbrs.c b/test/cmpnbrs.c new file mode 100644 index 0000000..6e3ace8 --- /dev/null +++ b/test/cmpnbrs.c @@ -0,0 +1,301 @@ +/*! +\file +\brief It takes as input two CSR matrices A and B and computes how + similar AA' and A'A are to BB' and B'B, respectively in terms + of the cosine similarity of the corresponding rows. + +\date 11/09/2015 +\author George +\version \verbatim $Id: m2mnbrs.c 17699 2014-09-27 18:05:31Z karypis $ \endverbatim +*/ + +#include + +/*************************************************************************/ +/*! Data structures for the code */ +/*************************************************************************/ +typedef struct { + int simtype; /*!< The similarity type to use */ + int verbosity; /*!< The reporting verbosity level */ + + char *afile; /*!< The file storing the query documents */ + char *bfile; /*!< The file storing the collection documents */ + + /* timers */ + double timer_global; +} params_t; + + +/*************************************************************************/ +/*! Constants */ +/*************************************************************************/ +/* Versions */ +#define VER_MAJOR 0 +#define VER_MINOR 1 +#define VER_SUBMINOR 0 + +/* Command-line option codes */ +#define CMD_SIMTYPE 10 +#define CMD_VERBOSITY 70 +#define CMD_HELP 100 + +/* The text labels for the different simtypes */ +static char simtypenames[][10] = {"", "dotp", "cos", "jac", ""}; + + +/*************************************************************************/ +/*! Local variables */ +/*************************************************************************/ +static struct gk_option long_options[] = { + {"simtype", 1, 0, CMD_SIMTYPE}, + {"verbosity", 1, 0, CMD_VERBOSITY}, + + {"help", 0, 0, CMD_HELP}, + {0, 0, 0, 0} +}; + +static gk_StringMap_t simtype_options[] = { + {"dotp", GK_CSR_DOTP}, + {"cos", GK_CSR_COS}, + {"jac", GK_CSR_JAC}, + {NULL, 0} +}; + + +/*------------------------------------------------------------------- + * Mini help + *-------------------------------------------------------------------*/ +static char helpstr[][100] = +{ +" ", +"Usage: cmpnbrs [options] afile bfile", +" ", +" Options", +" -simtype=string", +" Specifies the type of similarity to use. Possible values are:", +" dotp - Dot-product similarity [default]", +" cos - Cosine similarity", +" jac - Jacquard similarity", +" ", +" -verbosity=int", +" Specifies the level of debugging information to be displayed.", +" Default value is 0.", +" ", +" -help", +" Prints this message.", +"" +}; + + + +/*************************************************************************/ +/*! Function prototypes */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]); +double ComputeNeighborhoodSimilarity(params_t *params, gk_csr_t *amat, gk_csr_t *bmat); + + +/*************************************************************************/ +/*! This is the entry point of the command-line argument parser */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]) +{ + int i; + int c, option_index; + params_t *params; + + params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); + + /* initialize the params data structure */ + params->simtype = GK_CSR_DOTP; + params->verbosity = -1; + params->afile = NULL; + params->bfile = NULL; + + + /* Parse the command line arguments */ + while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { + switch (c) { + case CMD_SIMTYPE: + if (gk_optarg) { + if ((params->simtype = gk_GetStringID(simtype_options, gk_optarg)) == -1) + errexit("Invalid simtype of %s.\n", gk_optarg); + } + break; + + case CMD_VERBOSITY: + if (gk_optarg) params->verbosity = atoi(gk_optarg); + break; + + case CMD_HELP: + for (i=0; strlen(helpstr[i]) > 0; i++) + printf("%s\n", helpstr[i]); + exit(EXIT_SUCCESS); + break; + + case '?': + default: + printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); + exit(EXIT_FAILURE); + } + } + + /* Get the input/output file info */ + if (argc-gk_optind != 2) { + printf("Missing input file info.\n Use %s -help for a summary of the options.\n", argv[0]); + exit(EXIT_FAILURE); + } + + params->afile = gk_strdup(argv[gk_optind++]); + params->bfile = gk_strdup(argv[gk_optind++]); + + if (!gk_fexists(params->afile)) + errexit("input file %s does not exist.\n", params->afile); + if (!gk_fexists(params->bfile)) + errexit("input file %s does not exist.\n", params->bfile); + + return params; +} + + +/*************************************************************************/ +/*! This is the entry point of the program */ +/**************************************************************************/ +int main(int argc, char *argv[]) +{ + params_t *params; + gk_csr_t *amat, *bmat, *amatt, *bmatt; + int rc = EXIT_SUCCESS; + + params = parse_cmdline(argc, argv); + + amat = gk_csr_Read(params->afile, GK_CSR_FMT_CSR, 1, 0); + bmat = gk_csr_Read(params->bfile, GK_CSR_FMT_CSR, 1, 0); + + /* make the matrices of similar dimensions (if neccessary) */ + GKASSERT(amat->nrows == bmat->nrows); + amat->ncols = gk_max(amat->ncols, bmat->ncols); + bmat->ncols = amat->ncols; + + /* create the transpose matrices */ + amatt = gk_csr_Transpose(amat); + bmatt = gk_csr_Transpose(bmat); + + printf("********************************************************************************\n"); + printf("cmpnbrs (%d.%d.%d) Copyright 2015, GK.\n", VER_MAJOR, VER_MINOR, VER_SUBMINOR); + printf(" simtype=%s\n", + simtypenames[params->simtype]); + printf(" afile=%s, nrows=%d, ncols=%d, nnz=%zd\n", + params->afile, amat->nrows, amat->ncols, amat->rowptr[amat->nrows]); + printf(" bfile=%s, nrows=%d, ncols=%d, nnz=%zd\n", + params->bfile, bmat->nrows, bmat->ncols, bmat->rowptr[bmat->nrows]); + + gk_clearwctimer(params->timer_global); + gk_startwctimer(params->timer_global); + + printf("SIM(AA', BB'): %.5lf\t", ComputeNeighborhoodSimilarity(params, amat, bmat)); + printf("SIM(A'A, B'B): %.5lf\n", ComputeNeighborhoodSimilarity(params, amatt, bmatt)); + + gk_stopwctimer(params->timer_global); + + printf(" wclock: %.2lfs\n", gk_getwctimer(params->timer_global)); + printf("********************************************************************************\n"); + + gk_csr_Free(&amat); + gk_csr_Free(&bmat); + gk_csr_Free(&amatt); + gk_csr_Free(&bmatt); + + exit(rc); +} + + +/*************************************************************************/ +/*! Compares the neighbors of AA' vs BB' */ +/**************************************************************************/ +double ComputeNeighborhoodSimilarity(params_t *params, gk_csr_t *amat, + gk_csr_t *bmat) +{ + int iR, iH, nahits, nbhits, ncmps; + int32_t *marker; + gk_fkv_t *ahits, *bhits, *cand; + double tabsim, abdot, anorm2, bnorm2, *avec, *bvec; + + /* if cosine, make rows unit length */ + if (params->simtype == GK_CSR_COS) { + gk_csr_Normalize(amat, GK_CSR_ROW, 2); + gk_csr_Normalize(bmat, GK_CSR_ROW, 2); + } + + /* create the inverted index */ + gk_csr_CreateIndex(amat, GK_CSR_COL); + gk_csr_CreateIndex(bmat, GK_CSR_COL); + + /* compute the row squared norms */ + gk_csr_ComputeSquaredNorms(amat, GK_CSR_ROW); + gk_csr_ComputeSquaredNorms(bmat, GK_CSR_ROW); + + + /* allocate memory for the necessary working arrays */ + ahits = gk_fkvmalloc(amat->nrows, "ComputeNeighborhoodSimilarity: ahits"); + bhits = gk_fkvmalloc(bmat->nrows, "ComputeNeighborhoodSimilarity: bhits"); + marker = gk_i32smalloc(amat->nrows, -1, "ComputeNeighborhoodSimilarity: marker"); + cand = gk_fkvmalloc(amat->nrows, "ComputeNeighborhoodSimilarity: cand"); + avec = gk_dsmalloc(amat->nrows, 0.0, "ComputeNeighborhoodSimilarity: avec"); + bvec = gk_dsmalloc(bmat->nrows, 0.0, "ComputeNeighborhoodSimilarity: bvec"); + + + /* find the best neighbors for each row in the two matrices and compute + the cosine similarity between them. */ + tabsim = 0.0; + ncmps = 0; + for (iR=0; iRnrows; iR++) { + if (params->verbosity > 1) + printf("Working on row %7d\n", iR); + + if (amat->rowptr[iR+1]-amat->rowptr[iR] == 0 || + bmat->rowptr[iR+1]-bmat->rowptr[iR] == 0) + continue; + + nahits = gk_csr_GetSimilarRows(amat, + amat->rowptr[iR+1]-amat->rowptr[iR], + amat->rowind+amat->rowptr[iR], + amat->rowval+amat->rowptr[iR], + params->simtype, amat->nrows, 0.0, + ahits, marker, cand); + + nbhits = gk_csr_GetSimilarRows(bmat, + bmat->rowptr[iR+1]-bmat->rowptr[iR], + bmat->rowind+bmat->rowptr[iR], + bmat->rowval+bmat->rowptr[iR], + params->simtype, bmat->nrows, 0.0, + bhits, marker, cand); + + if (params->verbosity > 0) + printf("Row %7d %7d %7d %8zd %8zd\n", iR, nahits, nbhits, + amat->rowptr[iR+1]-amat->rowptr[iR], bmat->rowptr[iR+1]-bmat->rowptr[iR]); + + for (iH=0; iHnrows; iH++) { + abdot += avec[iH]*bvec[iH]; + anorm2 += avec[iH]*avec[iH]; + bnorm2 += bvec[iH]*bvec[iH]; + } + tabsim += (abdot > 0 ? abdot/sqrt(anorm2*bnorm2) : 0.0); + ncmps++; + + for (iH=0; iH + +/*************************************************************************/ +/*! Data structures for the code */ +/*************************************************************************/ +typedef struct { + int inf, outf; /* input/output format */ + int numbering; /* input numbering (output when applicable) */ + int readvals; /* input values (output when applicable) */ + int writevals; /* output values */ + int rshuf, cshuf; /* random shuffle of rows/columns */ + int symmetric; /* a symmetric shuffle */ + int mincolfreq; /* column prunning */ + int maxcolfreq; /* column prunning */ + int minrowfreq; /* row prunning */ + int maxrowfreq; /* row prunning */ + float rownrmfltr; /* row-lowfilter threshold */ + int compactcols; /* if to renumber columns to eliminate empty ones */ + int transpose; /* transpose the output matrix */ + char *srenumber; /* the iperm file for the symmetric renumbering */ + char *infile; /* input file */ + char *outfile; /* output file */ +} params_t; + + +/*************************************************************************/ +/*! Constants */ +/*************************************************************************/ +#define CMD_NUMONE 1 +#define CMD_NOREADVALS 2 +#define CMD_NOWRITEVALS 3 +#define CMD_RSHUF 4 +#define CMD_CSHUF 5 +#define CMD_SYMMETRIC 6 +#define CMD_MINCOLFREQ 7 +#define CMD_MAXCOLFREQ 8 +#define CMD_MINROWFREQ 9 +#define CMD_MAXROWFREQ 10 +#define CMD_ROWNRMFLTR 11 +#define CMD_COMPACTCOLS 12 +#define CMD_TRANSPOSE 13 +#define CMD_SRENUMBER 14 +#define CMD_HELP 100 + + +/*************************************************************************/ +/*! Local variables */ +/*************************************************************************/ +static struct gk_option long_options[] = { + {"numone", 0, 0, CMD_NUMONE}, + {"noreadvals", 0, 0, CMD_NOREADVALS}, + {"nowritevals", 0, 0, CMD_NOWRITEVALS}, + {"rshuf", 0, 0, CMD_RSHUF}, + {"cshuf", 0, 0, CMD_CSHUF}, + {"symmetric", 0, 0, CMD_SYMMETRIC}, + {"mincolfreq", 1, 0, CMD_MINCOLFREQ}, + {"maxcolfreq", 1, 0, CMD_MAXCOLFREQ}, + {"minrowfreq", 1, 0, CMD_MINROWFREQ}, + {"maxrowfreq", 1, 0, CMD_MAXROWFREQ}, + {"rownrmfltr", 1, 0, CMD_ROWNRMFLTR}, + {"compactcols", 0, 0, CMD_COMPACTCOLS}, + {"transpose", 0, 0, CMD_TRANSPOSE}, + {"srenumber", 1, 0, CMD_SRENUMBER}, + {"help", 0, 0, CMD_HELP}, + {0, 0, 0, 0} +}; + + +/*-------------------------------------------------------------------*/ +/* Mini help */ +/*-------------------------------------------------------------------*/ +static char helpstr[][100] = { +" ", +"Usage: csrconv [options] ", +" ", +" Required parameters", +" infile, outfile", +" The name of the input/output CSR file.", +" ", +" inf/outf", +" The format of the input/output file.", +" Supported values are:", +" 1 GK_CSR_FMT_CLUTO", +" 2 GK_CSR_FMT_CSR", +" 3 GK_CSR_FMT_METIS", +" 4 GK_CSR_FMT_BINROW", +" 6 GK_CSR_FMT_IJV", +" 7 GK_CSR_FMT_BIJV", +" ", +" Optional parameters", +" -numone", +" Specifies that the numbering of the input file starts from 1. ", +" It only applies to CSR/IJV formats.", +" ", +" -nowritevals", +" Specifies that no values will be output.", +" ", +" -noreadvals", +" Specifies that the values will not be read when applicable.", +" ", +" -rshuf", +" Specifies that the rows will be randmly shuffled prior to output.", +" ", +" -cshuf", +" Specifies that the columns will be randmly shuffled prior to output.", +" ", +" -symmetric", +" Specifies that the row+column shuffling will be symmetric.", +" ", +" -mincolfreq=int", +" Used to prune infrequent columns.", +" ", +" -maxcolfreq=int", +" Used to prune frequent columns.", +" ", +" -minrowfreq=int", +" Used to prune infrequent rows.", +" ", +" -maxrowfreq=int", +" Used to prune frequent.", +" ", +" -rownrmfltr=float", +" The parameter to use for the row-wise low filter.", +" ", +" -compactcols", +" Specifies if empty columns will be removed and the columns renumbered.", +" ", +" -transpose", +" Specifies that the transposed matrix will be written.", +" ", +" -srenumber=iperm-file", +" Performs a symmetric renumbering based on the provided iperm file.", +" ", +" -help", +" Prints this message.", +"" +}; + +static char shorthelpstr[][100] = { +" ", +" Usage: csrconv [options] ", +" use 'csrconv -help' for a summary of the options.", +"" +}; + + +/*************************************************************************/ +/*! This is the entry point of the command-line argument parser */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]) +{ + int i; + int c, option_index; + params_t *params; + + params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); + + /* initialize the params data structure */ + params->numbering = 0; + params->readvals = 1; + params->writevals = 1; + params->rshuf = 0; + params->cshuf = 0; + params->symmetric = 0; + params->transpose = 0; + params->srenumber = NULL; + + params->mincolfreq = -1; + params->minrowfreq = -1; + params->maxcolfreq = -1; + params->maxrowfreq = -1; + params->rownrmfltr = -1; + params->compactcols = 0; + + params->inf = -1; + params->outf = -1; + params->infile = NULL; + params->outfile = NULL; + + + /* Parse the command line arguments */ + while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { + switch (c) { + case CMD_NUMONE: + params->numbering = 1; + break; + case CMD_NOREADVALS: + params->readvals = 0; + break; + case CMD_NOWRITEVALS: + params->writevals = 0; + break; + case CMD_RSHUF: + params->rshuf = 1; + break; + case CMD_CSHUF: + params->cshuf = 1; + break; + case CMD_SYMMETRIC: + params->symmetric = 1; + break; + case CMD_TRANSPOSE: + params->transpose = 1; + break; + + + case CMD_MINCOLFREQ: + if (gk_optarg) params->mincolfreq = atoi(gk_optarg); + break; + case CMD_MINROWFREQ: + if (gk_optarg) params->minrowfreq = atoi(gk_optarg); + break; + case CMD_MAXCOLFREQ: + if (gk_optarg) params->maxcolfreq = atoi(gk_optarg); + break; + case CMD_MAXROWFREQ: + if (gk_optarg) params->maxrowfreq = atoi(gk_optarg); + break; + case CMD_ROWNRMFLTR: + if (gk_optarg) params->rownrmfltr = atof(gk_optarg); + break; + case CMD_COMPACTCOLS: + params->compactcols = 1; + break; + + case CMD_SRENUMBER: + if (gk_optarg) { + params->srenumber = gk_strdup(gk_optarg); + if (!gk_fexists(params->srenumber)) + errexit("srenumber file %s does not exist.\n", params->srenumber); + } + break; + + case CMD_HELP: + for (i=0; strlen(helpstr[i]) > 0; i++) + printf("%s\n", helpstr[i]); + exit(0); + break; + case '?': + default: + printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); + exit(0); + } + } + + if (argc-gk_optind != 4) { + printf("Unrecognized parameters."); + for (i=0; strlen(shorthelpstr[i]) > 0; i++) + printf("%s\n", shorthelpstr[i]); + exit(0); + } + + params->infile = gk_strdup(argv[gk_optind++]); + params->inf = atoi(argv[gk_optind++]); + params->outfile = gk_strdup(argv[gk_optind++]); + params->outf = atoi(argv[gk_optind++]); + + if (!gk_fexists(params->infile)) + errexit("input file %s does not exist.\n", params->infile); + + return params; +} + + +/*************************************************************************/ +/*! the entry point */ +/**************************************************************************/ +int main(int argc, char *argv[]) +{ + int what; + params_t *params; + gk_csr_t *mat, *mat1, *smat; + + /* get command-line options */ + params = parse_cmdline(argc, argv); + + /* read the data */ + mat = gk_csr_Read(params->infile, params->inf, params->readvals, params->numbering); + + /* deal with weird transformations */ + if (params->mincolfreq != -1 || params->maxcolfreq != -1) { + params->mincolfreq = (params->mincolfreq == -1 ? 0 : params->mincolfreq); + params->maxcolfreq = (params->maxcolfreq == -1 ? mat->nrows : params->maxcolfreq); + + printf("Column prune: %d %d; nnz: %zd => ", + params->mincolfreq, params->maxcolfreq, mat->rowptr[mat->nrows]); + mat1 = gk_csr_Prune(mat, GK_CSR_COL, params->mincolfreq, params->maxcolfreq); + gk_csr_Free(&mat); + mat = mat1; + mat1 = NULL; + + printf("%zd\n", mat->rowptr[mat->nrows]); + } + + if (params->minrowfreq != -1 || params->maxrowfreq != -1) { + params->minrowfreq = (params->minrowfreq == -1 ? 0 : params->minrowfreq); + params->maxrowfreq = (params->maxrowfreq == -1 ? mat->ncols : params->maxrowfreq); + + printf("Row prune: %d %d; nnz: %zd => ", + params->minrowfreq, params->maxrowfreq, mat->rowptr[mat->nrows]); + mat1 = gk_csr_Prune(mat, GK_CSR_ROW, params->minrowfreq, params->maxrowfreq); + gk_csr_Free(&mat); + mat = mat1; + mat1 = NULL; + + printf("%zd\n", mat->rowptr[mat->nrows]); + } + + if (params->rownrmfltr >= 0.0) { + //gk_csr_Scale(mat, GK_CSR_LOG); + //gk_csr_Scale(mat, GK_CSR_IDF2); + + printf("Row low filter: %f; nnz: %zd => ", params->rownrmfltr, mat->rowptr[mat->nrows]); + mat1 = gk_csr_LowFilter(mat, GK_CSR_ROW, 2, params->rownrmfltr); + gk_csr_Normalize(mat1, GK_CSR_ROW, 2); + + gk_csr_Free(&mat); + mat = mat1; + mat1 = NULL; + + printf("%zd\n", mat->rowptr[mat->nrows]); + } + + if (params->compactcols) { + printf("Compacting columns: %d => ", mat->ncols); + gk_csr_CompactColumns(mat); + printf("%d\n", mat->ncols); + } + + + if (params->rshuf || params->cshuf) { + if (params->rshuf && params->cshuf) + what = GK_CSR_ROWCOL; + else if (params->rshuf) + what = GK_CSR_ROW; + else + what = GK_CSR_COL; + + smat = gk_csr_Shuffle(mat, what, params->symmetric); + gk_csr_Free(&mat); + mat = smat; + } + + + if (params->srenumber) { + int32_t i; + size_t nlines; + int32_t *iperm; + gk_csr_t *smat; + + iperm = gk_i32readfile(params->srenumber, &nlines); + if (nlines != mat->nrows && nlines != mat->ncols) + errexit("The nlines=%zud of srenumber file does not match nrows: %d, ncols: %d\n", nlines, mat->nrows, mat->ncols); + + if (gk_i32max(nlines, iperm, 1) >= nlines && gk_i32min(nlines, iperm, 1) <= 0) + errexit("The srenumber iperm seems to be wrong.\n"); + + if (gk_i32max(nlines, iperm, 1) == nlines) { /* need to renumber */ + for (i=0; iwritevals && mat->rowval == NULL) + mat->rowval = gk_fsmalloc(mat->rowptr[mat->nrows], 1.0, "mat->rowval"); + + if (params->transpose) { + mat1 = gk_csr_Transpose(mat); + gk_csr_Free(&mat); + mat = mat1; + mat1 = NULL; + } + + + + gk_csr_Write(mat, params->outfile, params->outf, params->writevals, 0); + + gk_csr_Free(&mat); + +} + diff --git a/test/fis.c b/test/fis.c new file mode 100644 index 0000000..084a4b6 --- /dev/null +++ b/test/fis.c @@ -0,0 +1,286 @@ +/*! +\file +\brief A simple frequent itemset discovery program to test GKlib's routines + +\date 6/12/2008 +\author George +\version \verbatim $Id: fis.c 11075 2011-11-11 22:31:52Z karypis $ \endverbatim +*/ + +#include + +/*************************************************************************/ +/*! Data structures for the code */ +/*************************************************************************/ +typedef struct { + ssize_t minlen, maxlen; + ssize_t minfreq, maxfreq; + char *filename; + int silent; + ssize_t nitemsets; + char *clabelfile; + char **clabels; +} params_t; + +/*************************************************************************/ +/*! Constants */ +/*************************************************************************/ +#define CMD_MINLEN 1 +#define CMD_MAXLEN 2 +#define CMD_MINFREQ 3 +#define CMD_MAXFREQ 4 +#define CMD_SILENT 5 +#define CMD_CLABELFILE 6 +#define CMD_HELP 10 + + +/*************************************************************************/ +/*! Local variables */ +/*************************************************************************/ +static struct gk_option long_options[] = { + {"minlen", 1, 0, CMD_MINLEN}, + {"maxlen", 1, 0, CMD_MAXLEN}, + {"minfreq", 1, 0, CMD_MINFREQ}, + {"maxfreq", 1, 0, CMD_MAXFREQ}, + {"silent", 0, 0, CMD_SILENT}, + {"clabels", 1, 0, CMD_CLABELFILE}, + {"help", 0, 0, CMD_HELP}, + {0, 0, 0, 0} +}; + + +/*-------------------------------------------------------------------*/ +/* Mini help */ +/*-------------------------------------------------------------------*/ +static char helpstr[][100] = { +" ", +"Usage: fis [options] ", +" ", +" Required parameters", +" mat-file", +" The name of the file storing the transactions. The file is in ", +" Cluto's .mat format.", +" ", +" Optional parameters", +" -minlen=int", +" Specifies the minimum length of the patterns. [default: 1]", +" ", +" -maxlen=int", +" Specifies the maximum length of the patterns. [default: none]", +" ", +" -minfreq=int", +" Specifies the minimum frequency of the patterns. [default: 10]", +" ", +" -maxfreq=int", +" Specifies the maximum frequency of the patterns. [default: none]", +" ", +" -silent", +" Does not print the discovered itemsets.", +" ", +" -clabels=filename", +" Specifies the name of the file that stores the column labels.", +" ", +" -help", +" Prints this message.", +"" +}; + +static char shorthelpstr[][100] = { +" ", +" Usage: fis [options] ", +" use 'fis -help' for a summary of the options.", +"" +}; + + + +/*************************************************************************/ +/*! Function prototypes */ +/*************************************************************************/ +void print_init_info(params_t *params, gk_csr_t *mat); +void print_final_info(params_t *params); +params_t *parse_cmdline(int argc, char *argv[]); +void print_an_itemset(void *stateptr, int nitems, int *itemind, + int ntrans, int *tranind); + + +/*************************************************************************/ +/*! the entry point */ +/**************************************************************************/ +int main(int argc, char *argv[]) +{ + ssize_t i; + char line[8192]; + FILE *fpin; + params_t *params; + gk_csr_t *mat; + + params = parse_cmdline(argc, argv); + params->nitemsets = 0; + + /* read the data */ + mat = gk_csr_Read(params->filename, GK_CSR_FMT_CLUTO, 1, 1); + gk_csr_CreateIndex(mat, GK_CSR_COL); + + /* read the column labels */ + params->clabels = (char **)gk_malloc(mat->ncols*sizeof(char *), "main: clabels"); + if (params->clabelfile == NULL) { + for (i=0; incols; i++) { + sprintf(line, "%zd", i); + params->clabels[i] = gk_strdup(line); + } + } + else { + fpin = gk_fopen(params->clabelfile, "r", "main: fpin"); + for (i=0; incols; i++) { + if (fgets(line, 8192, fpin) == NULL) + errexit("Failed on fgets.\n"); + params->clabels[i] = gk_strdup(gk_strtprune(line, " \n\t")); + } + gk_fclose(fpin); + } + + + print_init_info(params, mat); + + gk_find_frequent_itemsets(mat->nrows, mat->rowptr, mat->rowind, + params->minfreq, params->maxfreq, params->minlen, params->maxlen, + &print_an_itemset, (void *)params); + + printf("Total itemsets found: %zd\n", params->nitemsets); + + print_final_info(params); +} + + + +/*************************************************************************/ +/*! This function prints run parameters */ +/*************************************************************************/ +void print_init_info(params_t *params, gk_csr_t *mat) +{ + printf("*******************************************************************************\n"); + printf(" fis\n\n"); + printf("Matrix Information ---------------------------------------------------------\n"); + printf(" input file=%s, [%d, %d, %zd]\n", + params->filename, mat->nrows, mat->ncols, mat->rowptr[mat->nrows]); + + printf("\n"); + printf("Options --------------------------------------------------------------------\n"); + printf(" minlen=%zd, maxlen=%zd, minfeq=%zd, maxfreq=%zd\n", + params->minlen, params->maxlen, params->minfreq, params->maxfreq); + + printf("\n"); + printf("Finding patterns... -----------------------------------------------------\n"); +} + + +/*************************************************************************/ +/*! This function prints final statistics */ +/*************************************************************************/ +void print_final_info(params_t *params) +{ + printf("\n"); + printf("Memory Usage Information -----------------------------------------------------\n"); + printf(" Maximum memory used: %10zd bytes\n", (ssize_t) gk_GetMaxMemoryUsed()); + printf(" Current memory used: %10zd bytes\n", (ssize_t) gk_GetCurMemoryUsed()); + printf("********************************************************************************\n"); +} + + +/*************************************************************************/ +/*! This is the entry point of the command-line argument parser */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]) +{ + int i; + int c, option_index; + params_t *params; + + params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); + + /* initialize the params data structure */ + params->minlen = 1; + params->maxlen = -1; + params->minfreq = 10; + params->maxfreq = -1; + params->silent = 0; + params->filename = NULL; + params->clabelfile = NULL; + + + /* Parse the command line arguments */ + while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { + switch (c) { + case CMD_MINLEN: + if (gk_optarg) params->minlen = atoi(gk_optarg); + break; + case CMD_MAXLEN: + if (gk_optarg) params->maxlen = atoi(gk_optarg); + break; + case CMD_MINFREQ: + if (gk_optarg) params->minfreq = atoi(gk_optarg); + break; + case CMD_MAXFREQ: + if (gk_optarg) params->maxfreq = atoi(gk_optarg); + break; + + case CMD_SILENT: + params->silent = 1; + break; + + case CMD_CLABELFILE: + if (gk_optarg) params->clabelfile = gk_strdup(gk_optarg); + break; + + case CMD_HELP: + for (i=0; strlen(helpstr[i]) > 0; i++) + printf("%s\n", helpstr[i]); + exit(0); + break; + case '?': + default: + printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); + exit(0); + } + } + + if (argc-gk_optind != 1) { + printf("Unrecognized parameters."); + for (i=0; strlen(shorthelpstr[i]) > 0; i++) + printf("%s\n", shorthelpstr[i]); + exit(0); + } + + params->filename = gk_strdup(argv[gk_optind++]); + + if (!gk_fexists(params->filename)) + errexit("input file %s does not exist.\n", params->filename); + + return params; +} + + + +/*************************************************************************/ +/*! This is the callback function for the itemset discovery routine */ +/*************************************************************************/ +void print_an_itemset(void *stateptr, int nitems, int *itemids, int ntrans, + int *transids) +{ + ssize_t i; + params_t *params; + + params = (params_t *)stateptr; + params->nitemsets++; + + if (!params->silent) { + printf("%4zd %4d %4d => ", params->nitemsets, nitems, ntrans); + for (i=0; iclabels[itemids[i]]); + printf("\n"); + for (i=0; i + + +/*************************************************************************/ +/*! Data structures for the code */ +/*************************************************************************/ +typedef struct { + int lnbits; + int cnbits; + int type; + int niter; + float eps; + float lamda; + int nosort; + int write; + + char *infile; + char *outfile; +} params_t; + +/*************************************************************************/ +/*! Constants */ +/*************************************************************************/ +#define CMD_NITER 1 +#define CMD_EPS 2 +#define CMD_LAMDA 3 +#define CMD_TYPE 4 +#define CMD_NOSORT 5 +#define CMD_WRITE 6 +#define CMD_LNBITS 7 +#define CMD_CNBITS 8 +#define CMD_HELP 10 + +#define CLINE32 16 +#define CLINE64 8 +#define MAXRCLOCKSPAN (1<<20) + +/*************************************************************************/ +/*! Local variables */ +/*************************************************************************/ +static struct gk_option long_options[] = { + {"lnbits", 1, 0, CMD_LNBITS}, + {"cnbits", 1, 0, CMD_CNBITS}, + {"type", 1, 0, CMD_TYPE}, + {"niter", 1, 0, CMD_NITER}, + {"lamda", 1, 0, CMD_LAMDA}, + {"eps", 1, 0, CMD_EPS}, + {"nosort", 0, 0, CMD_NOSORT}, + {"write", 0, 0, CMD_WRITE}, + {"help", 0, 0, CMD_HELP}, + {0, 0, 0, 0} +}; + + +/*-------------------------------------------------------------------*/ +/* Mini help */ +/*-------------------------------------------------------------------*/ +static char helpstr[][100] = { +" ", +"Usage: gkgraph [options] []", +" ", +" Required parameters", +" graph-file", +" The name of the file storing the graph. The file is in ", +" Metis' graph format.", +" ", +" Optional parameters", +" -niter=int", +" Specifies the maximum number of iterations. [default: 100]", +" ", +" -lnbits=int", +" Specifies the number of address bits indexing the cacheline. [default: 6]", +" ", +" -cnbits=int", +" Specifies the number of address bits indexing the cache. [default: 13]", +" ", +" -lamda=float", +" Specifies the follow-the-adjacent-links probability. [default: 0.80]", +" ", +" -eps=float", +" Specifies the error tollerance. [default: 1e-10]", +" ", +" -nosort", +" Does not sort the adjacency lists.", +" ", +" -write", +" Output the reordered graphs.", +" ", +" -help", +" Prints this message.", +"" +}; + +static char shorthelpstr[][100] = { +" ", +" Usage: gkgraph [options] []", +" use 'gkgraph -help' for a summary of the options.", +"" +}; + + + +/*************************************************************************/ +/*! Function prototypes */ +/*************************************************************************/ +void test_spmv(params_t *params); +void test_tc(params_t *params); +void sort_adjacencies(params_t *params, gk_graph_t *graph); +double compute_spmvstats(params_t *params, gk_graph_t *graph); +double compute_tcstats(params_t *params, gk_graph_t *graph, int32_t *iperm); +int32_t *reorder_degrees(params_t *params, gk_graph_t *graph); +int32_t *reorder_freqlpn(params_t *params, gk_graph_t *graph); +int32_t *reorder_freqlpn_db(params_t *params, gk_graph_t *graph); +int32_t *reorder_minlpn(params_t *params, gk_graph_t *graph); +int32_t *reorder_minlpn_db(params_t *params, gk_graph_t *graph); +void print_init_info(params_t *params, gk_graph_t *graph); +void print_final_info(params_t *params); +params_t *parse_cmdline(int argc, char *argv[]); + + +/*************************************************************************/ +/*! the entry point */ +/**************************************************************************/ +int main(int argc, char *argv[]) +{ + params_t *params; + + /* get command-line options */ + params = parse_cmdline(argc, argv); + + test_tc(params); +} + + +/*************************************************************************/ +/*! various spmv-related tests */ +/**************************************************************************/ +void test_spmv(params_t *params) +{ + ssize_t i, j, v; + gk_graph_t *graph, *pgraph; + int32_t *perm; + + /* read the data */ + graph = gk_graph_Read(params->infile, GK_GRAPH_FMT_METIS, -1, -1, 0, 0, 0); + + /* display some basic stats */ + print_init_info(params, graph); + + sort_adjacencies(params, graph); + if (params->write) gk_graph_Write(graph, "original.ijv", GK_GRAPH_FMT_IJV, 1); + printf("Input SPMV HitRate: %.4lf\n", compute_spmvstats(params, graph)); + + + v = RandomInRange(graph->nvtxs); + gk_graph_ComputeBFSOrdering(graph, v, &perm, NULL); + pgraph = gk_graph_Reorder(graph, perm, NULL); + sort_adjacencies(params, pgraph); + if (params->write) gk_graph_Write(pgraph, "bfs.ijv", GK_GRAPH_FMT_IJV, 1); + printf("BFS SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); + gk_graph_Free(&pgraph); + gk_free((void **)&perm, LTERM); + + + perm = reorder_degrees(params, graph); + pgraph = gk_graph_Reorder(graph, perm, NULL); + sort_adjacencies(params, pgraph); + if (params->write) gk_graph_Write(pgraph, "degrees.ijv", GK_GRAPH_FMT_IJV, 1); + printf("Degrees SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); + gk_graph_Free(&pgraph); + gk_free((void **)&perm, LTERM); + + + perm = reorder_freqlpn(params, graph); + pgraph = gk_graph_Reorder(graph, perm, NULL); + sort_adjacencies(params, pgraph); + if (params->write) gk_graph_Write(pgraph, "freqlpn.ijv", GK_GRAPH_FMT_IJV, 1); + printf("FreqLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); + gk_graph_Free(&pgraph); + gk_free((void **)&perm, LTERM); + + perm = reorder_freqlpn_db(params, graph); + pgraph = gk_graph_Reorder(graph, perm, NULL); + sort_adjacencies(params, pgraph); + if (params->write) gk_graph_Write(pgraph, "freqlpn-db.ijv", GK_GRAPH_FMT_IJV, 1); + printf("DBFreqLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); + gk_graph_Free(&pgraph); + gk_free((void **)&perm, LTERM); + + perm = reorder_minlpn(params, graph); + pgraph = gk_graph_Reorder(graph, perm, NULL); + sort_adjacencies(params, pgraph); + if (params->write) gk_graph_Write(pgraph, "minlpn.ijv", GK_GRAPH_FMT_IJV, 1); + printf("MinLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); + gk_graph_Free(&pgraph); + gk_free((void **)&perm, LTERM); + + perm = reorder_minlpn_db(params, graph); + pgraph = gk_graph_Reorder(graph, perm, NULL); + sort_adjacencies(params, pgraph); + if (params->write) gk_graph_Write(pgraph, "minlpn-db.ijv", GK_GRAPH_FMT_IJV, 1); + printf("DBMinLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); + gk_graph_Free(&pgraph); + gk_free((void **)&perm, LTERM); + + gk_graph_Free(&graph); + + print_final_info(params); + + return; +} + + +/*************************************************************************/ +/*! various tc-related tests */ +/**************************************************************************/ +void test_tc(params_t *params) +{ + ssize_t i, j, v; + gk_graph_t *graph, *pgraph; + int32_t *perm, *iperm; + + /* read the data */ + graph = gk_graph_Read(params->infile, GK_GRAPH_FMT_METIS, -1, -1, 0, 0, 0); + + /* display some basic stats */ + print_init_info(params, graph); + + perm = reorder_degrees(params, graph); + pgraph = gk_graph_Reorder(graph, perm, NULL); + gk_free((void **)&perm, LTERM); + sort_adjacencies(params, pgraph); + iperm = gk_i32incset(graph->nvtxs, 0, gk_i32malloc(graph->nvtxs, "iperm")); + printf("Degrees TC HitRate: %.4lf\n", compute_tcstats(params, pgraph, iperm)); + + + sort_adjacencies(params, pgraph); + v = RandomInRange(pgraph->nvtxs); + gk_graph_ComputeBFSOrdering(pgraph, v, &perm, NULL); + for (i=0; invtxs; i++) iperm[perm[i]] = i; + gk_free((void **)&perm, LTERM); + printf("BFS TC HitRate: %.4lf\n", compute_tcstats(params, pgraph, iperm)); + + + sort_adjacencies(params, pgraph); + perm = reorder_freqlpn(params, pgraph); + for (i=0; invtxs; i++) iperm[perm[i]] = i; + gk_free((void **)&perm, LTERM); + printf("FreqLabelPropN TC HitRate: %.4lf\n", compute_tcstats(params, pgraph, iperm)); + + sort_adjacencies(params, pgraph); + perm = reorder_freqlpn_db(params, pgraph); + for (i=0; invtxs; i++) iperm[perm[i]] = i; + gk_free((void **)&perm, LTERM); + printf("DBFreqLabelPropN TC HitRate: %.4lf\n", compute_tcstats(params, pgraph, iperm)); + + +#ifdef XXX + perm = reorder_minlpn(params, graph); + pgraph = gk_graph_Reorder(graph, perm, NULL); + sort_adjacencies(params, pgraph); + if (params->write) gk_graph_Write(pgraph, "minlpn.ijv", GK_GRAPH_FMT_IJV, 1); + printf("MinLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); + gk_graph_Free(&pgraph); + gk_free((void **)&perm, LTERM); + + perm = reorder_minlpn_db(params, graph); + pgraph = gk_graph_Reorder(graph, perm, NULL); + sort_adjacencies(params, pgraph); + if (params->write) gk_graph_Write(pgraph, "minlpn-db.ijv", GK_GRAPH_FMT_IJV, 1); + printf("DBMinLabelPropN SPMV HitRate: %.4lf\n", compute_spmvstats(params, pgraph)); + gk_graph_Free(&pgraph); + gk_free((void **)&perm, LTERM); +#endif + + gk_free((void **)&iperm, LTERM); + gk_graph_Free(&graph); + + print_final_info(params); + + return; +} + + +/*************************************************************************/ +/*! This function sorts the adjacency lists of the vertices in increasing + order. +*/ +/*************************************************************************/ +void sort_adjacencies(params_t *params, gk_graph_t *graph) +{ + uint64_t i, nvtxs; + ssize_t *xadj; + int32_t *adjncy; + + if (params->nosort) + return; + + nvtxs = graph->nvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + for (i=0; ilnbits, params->cnbits); /* 8MB total; i7 spec */ + + nvtxs = graph->nvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + vec = gk_i32malloc(nvtxs, "vec"); + for (i=0; ilnbits, params->cnbits); + + nvtxs = graph->nvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + /* determine the starting location of the upper trianglular part */ + uxadj = gk_zmalloc(nvtxs, "uxadj"); + for (vi=0; vi(1<vj; ei++) { + vk = adjncy[ei]; + for (l=vk&hmsize; + gk_cacheLoad(cache, (size_t)(&hmap[l])) && hmap[l]!=0 && hmap[l]!=vk; + l=((l+1)&hmsize)); + gk_cacheLoad(cache, (size_t)(&hmap[l])); + if (hmap[l] == vk) + ntriangles++; + } + } + + /* reset hash */ + gk_cacheLoad(cache, (size_t)(&uxadj[vj])); + gk_cacheLoad(cache, (size_t)(&xadj[vj+1])); + for (ej=uxadj[vj], ejend=xadj[vj+1]; ejnhits, (ssize_t)cache->clock); + + double hitrate = gk_cacheGetHitRate(cache); + gk_cacheDestroy(&cache); + + return hitrate; +} + + +/*************************************************************************/ +/*! This function computes an increasing degree ordering +*/ +/*************************************************************************/ +int32_t *reorder_degrees(params_t *params, gk_graph_t *graph) +{ + int i, v, u, nvtxs, range; + ssize_t j, *xadj; + int32_t *counts, *perm; + + nvtxs = graph->nvtxs; + xadj = graph->xadj; + + for (range=0, i=0; invtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + labels = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "labels")); + freq = gk_i32smalloc(nvtxs, 0, "freq"); + perm = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "perm")); + + for (k=0; kniter; k++) { + gk_i32randArrayPermuteFine(nvtxs, perm, 0); + for (ii=0; iinvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + labels = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "labels")); + freq = gk_i32smalloc(nvtxs, 0, "freq"); + perm = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "perm")); + dbucket = gk_i32malloc(nvtxs, "dbucket"); + + for (i=0; i>3); + + for (k=0; kniter; k++) { + gk_i32randArrayPermuteFine(nvtxs, perm, 0); + for (ii=0; iinvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + labels = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "labels")); + perm = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "perm")); + + for (k=0; kniter; k++) { + for (i=0; i labels[adjncy[j]]) + minlbl = labels[adjncy[j]]; + } + labels[i] = minlbl; + } + } + + cand = gk_i32kvmalloc(nvtxs, "cand"); + for (i=0; i0 && cand[i].key != cand[i-1].key) + // printf("%10d %10d\n", i-1, cand[i-1].key); + } + //printf("%10d %10d\n", i-1, cand[i-1].key); + + gk_free((void **)&labels, &cand, LTERM); + + return perm; +} + + +/*************************************************************************/ +/*! This function re-orders the graph by: + - performing a fixed number of min-label propagation iterations + - restricts that propagation to take place within similar degree buckets + of vertices + - locally renumbers the vertices with the same label +*/ +/*************************************************************************/ +int32_t *reorder_minlpn_db(params_t *params, gk_graph_t *graph) +{ + int32_t i, ii, k, nvtxs, minlbl; + ssize_t j, *xadj; + int32_t *adjncy, *labels, *perm, *dbucket; + gk_i32kv_t *cand; + + nvtxs = graph->nvtxs; + xadj = graph->xadj; + adjncy = graph->adjncy; + + labels = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "labels")); + perm = gk_i32incset(nvtxs, 0, gk_i32malloc(nvtxs, "perm")); + dbucket = gk_i32malloc(nvtxs, "dbucket"); + + for (i=0; i>3); + + for (k=0; kniter; k++) { + for (i=0; i labels[adjncy[j]]) + minlbl = labels[adjncy[j]]; + } + labels[i] = minlbl; + } + } + + cand = gk_i32kvmalloc(nvtxs, "cand"); + for (i=0; i0 && cand[i].key != cand[i-1].key) + // printf("%10d %10d\n", i-1, cand[i-1].key); + } + //printf("%10d %10d\n", i-1, cand[i-1].key); + + gk_free((void **)&labels, &dbucket, &cand, LTERM); + + return perm; +} + + +/*************************************************************************/ +/*! This function prints run parameters */ +/*************************************************************************/ +void print_init_info(params_t *params, gk_graph_t *graph) +{ + printf("*******************************************************************************\n"); + printf(" gkgraph\n\n"); + printf("Graph Information ----------------------------------------------------------\n"); + printf(" input file=%s, [%d, %zd]\n", + params->infile, graph->nvtxs, graph->xadj[graph->nvtxs]); + + printf("\n"); + printf("Options --------------------------------------------------------------------\n"); + printf(" lnbits=%d, cnbits=%d, type=%d, niter=%d, lamda=%f, eps=%e\n", + params->lnbits, params->cnbits, params->type, params->niter, + params->lamda, params->eps); + + printf("\n"); + printf("Working... -----------------------------------------------------------------\n"); +} + + +/*************************************************************************/ +/*! This function prints final statistics */ +/*************************************************************************/ +void print_final_info(params_t *params) +{ + printf("\n"); + printf("Memory Usage Information -----------------------------------------------------\n"); + printf(" Maximum memory used: %10zd bytes\n", (ssize_t) gk_GetMaxMemoryUsed()); + printf(" Current memory used: %10zd bytes\n", (ssize_t) gk_GetCurMemoryUsed()); + printf("********************************************************************************\n"); +} + + +/*************************************************************************/ +/*! This is the entry point of the command-line argument parser */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]) +{ + int i; + int c, option_index; + params_t *params; + + params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); + + /* initialize the params data structure */ + params->lnbits = 6; + params->cnbits = 13; + params->type = 1; + params->niter = 1; + params->eps = 1e-10; + params->lamda = 0.20; + params->nosort = 0; + params->write = 0; + params->infile = NULL; + + + /* Parse the command line arguments */ + while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { + switch (c) { + case CMD_LNBITS: + if (gk_optarg) params->lnbits = atoi(gk_optarg); + break; + case CMD_CNBITS: + if (gk_optarg) params->cnbits = atoi(gk_optarg); + break; + case CMD_TYPE: + if (gk_optarg) params->type = atoi(gk_optarg); + break; + case CMD_NITER: + if (gk_optarg) params->niter = atoi(gk_optarg); + break; + case CMD_EPS: + if (gk_optarg) params->eps = atof(gk_optarg); + break; + case CMD_LAMDA: + if (gk_optarg) params->lamda = atof(gk_optarg); + break; + case CMD_NOSORT: + params->nosort = 1; + break; + case CMD_WRITE: + params->write = 1; + break; + + case CMD_HELP: + for (i=0; strlen(helpstr[i]) > 0; i++) + printf("%s\n", helpstr[i]); + exit(0); + break; + case '?': + default: + printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); + exit(0); + } + } + + if (argc-gk_optind != 1) { + printf("Unrecognized parameters."); + for (i=0; strlen(shorthelpstr[i]) > 0; i++) + printf("%s\n", shorthelpstr[i]); + exit(0); + } + + params->infile = gk_strdup(argv[gk_optind++]); + + if (argc-gk_optind > 0) + params->outfile = gk_strdup(argv[gk_optind++]); + else + params->outfile = gk_strdup("gkgraph.out"); + + if (!gk_fexists(params->infile)) + errexit("input file %s does not exist.\n", params->infile); + + return params; +} + diff --git a/test/gksort.c b/test/gksort.c new file mode 100644 index 0000000..6543836 --- /dev/null +++ b/test/gksort.c @@ -0,0 +1,346 @@ +/*! +\file gksort.c +\brief Testing module for the various sorting routines in GKlib + +\date Started 4/4/2007 +\author George +\version\verbatim $Id: gksort.c 11058 2011-11-10 00:02:50Z karypis $ \endverbatim +*/ + +#include + +#define N 10000 + +/*************************************************************************/ +/*! Testing module for gk_?isort() routine */ +/*************************************************************************/ +void test_isort() +{ + gk_idx_t i; + int array[N]; + + /* test the increasing sort */ + printf("Testing iisort...\n"); + for (i=0; i array[i+1]) + printf("gk_isorti error at index %jd [%d %d]\n", (intmax_t)i, array[i], array[i+1]); + } + + + /* test the decreasing sort */ + printf("Testing disort...\n"); + for (i=0; i array[i+1]) + printf("gk_fsorti error at index %jd [%f %f]\n", (intmax_t)i, array[i], array[i+1]); + } + + + /* test the decreasing sort */ + printf("Testing dfsort...\n"); + for (i=0; i array[i+1]) + printf("gk_idxsorti error at index %zd [%zd %zd]\n", (ssize_t)i, (ssize_t)array[i], (ssize_t)array[i+1]); + } + + + /* test the decreasing sort */ + printf("Testing idxsortd...\n"); + for (i=0; i array[i+1].key) + printf("gk_ikvsorti error at index %jd [%d %d] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); + } + + + /* test the decreasing sort */ + printf("Testing ikvsortd...\n"); + for (i=0; i array[i+1].key) + printf("gk_fkvsorti error at index %jd [%f %f] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); + } + + + /* test the decreasing sort */ + printf("Testing fkvsortd...\n"); + for (i=0; i array[i+1].key) + printf("gk_dkvsorti error at index %jd [%lf %lf] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); + } + + + /* test the decreasing sort */ + printf("Testing dkvsortd...\n"); + for (i=0; i 0) + printf("gk_skvsorti error at index %jd [%s %s] [%jd %jd]\n", (intmax_t)i, array[i].key, array[i+1].key, (intmax_t)array[i].val, (intmax_t)array[i+1].val); + } + + + /* test the decreasing sort */ + printf("Testing skvsortd...\n"); + for (i=0; i array[i+1].key) + printf("gk_idxkvsorti error at index %zd [%zd %zd] [%zd %zd]\n", + (ssize_t)i, (ssize_t)array[i].key, (ssize_t)array[i+1].key, + (ssize_t)array[i].val, (ssize_t)array[i+1].val); + } + + + /* test the decreasing sort */ + printf("Testing idxkvsortd...\n"); + for (i=0; i + +/*************************************************************************/ +/*! Data structures for the code */ +/*************************************************************************/ +typedef struct { + ssize_t length, dupfactor; +} params_t; + +/*************************************************************************/ +/*! Constants */ +/*************************************************************************/ +#define CMD_HELP 10 + + +/*************************************************************************/ +/*! Local variables */ +/*************************************************************************/ +static struct gk_option long_options[] = { + {"help", 0, 0, CMD_HELP}, + {0, 0, 0, 0} +}; + + +/*-------------------------------------------------------------------*/ +/* Mini help */ +/*-------------------------------------------------------------------*/ +static char helpstr[][100] = { +" ", +"Usage: gkuniq length dupfactor", +" ", +" Required parameters", +" length", +" The length of the base array.", +" ", +" dupfactor", +" The number of times the initial array is replicated.", +" ", +" Optional parameters", +" -help", +" Prints this message.", +"" +}; + + + +/*************************************************************************/ +/*! Function prototypes */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]); +int unique_v1(int n, int *input, int *output); +int unique_v2(int n, int *input, int *output); +int unique_v3(int n, int *input, int *output, int *r_maxsize, int **r_hmap); +void mem_flush(const void *p, unsigned int allocation_size); + +/*************************************************************************/ +/*! A function to flush the cache associated with an array */ +/**************************************************************************/ +void mem_flush(const void *p, unsigned int allocation_size) +{ +#ifndef NO_X86 + const size_t cache_line = 64; + const char *cp = (const char *)p; + size_t i = 0; + + if (p == NULL || allocation_size <= 0) + return; + + for (i = 0; i < allocation_size; i += cache_line) { + __asm__ volatile("clflush (%0)\n\t" + : + : "r"(&cp[i]) + : "memory"); + } + + __asm__ volatile("sfence\n\t" + : + : + : "memory"); +#endif +} + +/*************************************************************************/ +/*! the entry point */ +/**************************************************************************/ +int main(int argc, char *argv[]) +{ + int i, j, k; + params_t *params; + double tmr; + int n, nunique, *input, *output; + int maxsize=0, *hmap=NULL; + + params = parse_cmdline(argc, argv); + + /* create the input data */ + n = params->length*params->dupfactor; + input = gk_imalloc(n, "input"); + output = gk_imalloc(n, "output"); + for (i=0; ilength; i++) { + k = RandomInRange(n); + for (j=0; jdupfactor; j++) + input[j*params->length+i] = k; + } + + gk_clearwctimer(tmr); + gk_startwctimer(tmr); + mem_flush(input, n*sizeof(int)); + mem_flush(output, n*sizeof(int)); + nunique = unique_v1(n, input, output); + gk_stopwctimer(tmr); + printf(" V1: nunique: %d, timer: %.5lf\n", nunique, gk_getwctimer(tmr)); + + gk_clearwctimer(tmr); + gk_startwctimer(tmr); + mem_flush(input, n*sizeof(int)); + mem_flush(output, n*sizeof(int)); + nunique = unique_v2(n, input, output); + gk_stopwctimer(tmr); + printf(" V2: nunique: %d, timer: %.5lf\n", nunique, gk_getwctimer(tmr)); + + gk_clearwctimer(tmr); + gk_startwctimer(tmr); + mem_flush(input, n*sizeof(int)); + mem_flush(output, n*sizeof(int)); + nunique = unique_v3(n, input, output, &maxsize, &hmap); + gk_stopwctimer(tmr); + printf("V3c: nunique: %d, timer: %.5lf\n", nunique, gk_getwctimer(tmr)); + + gk_clearwctimer(tmr); + gk_startwctimer(tmr); + mem_flush(input, n*sizeof(int)); + mem_flush(output, n*sizeof(int)); + nunique = unique_v3(n, input, output, &maxsize, &hmap); + gk_stopwctimer(tmr); + printf("V3w: nunique: %d, timer: %.5lf\n", nunique, gk_getwctimer(tmr)); + + gk_free((void **)&input, &output, &hmap, LTERM); + +} + + + +/*************************************************************************/ +/*! This is the entry point of the command-line argument parser */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]) +{ + int i; + int c, option_index; + params_t *params; + + params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); + + /* Parse the command line arguments */ + while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { + switch (c) { + case CMD_HELP: + for (i=0; strlen(helpstr[i]) > 0; i++) + printf("%s\n", helpstr[i]); + exit(0); + break; + case '?': + default: + printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); + exit(0); + } + } + + if (argc-gk_optind != 2) { + printf("Unrecognized parameters."); + for (i=0; strlen(helpstr[i]) > 0; i++) + printf("%s\n", helpstr[i]); + exit(0); + } + + params->length = atoi(argv[gk_optind++]); + params->dupfactor = atoi(argv[gk_optind++]); + + return params; +} + + +/*************************************************************************/ +/*! gklib-sort based approach */ +/*************************************************************************/ +int unique_v1(int n, int *input, int *output) +{ + int i, j; + + gk_isorti(n, input); + + output[0] = input[0]; + for (j=0, i=1; i *r_maxsize) { + gk_free((void **)r_hmap, LTERM); + hmap = *r_hmap = gk_ismalloc(size, -1, "hmap"); + *r_maxsize = size; + } + else { + hmap = *r_hmap; + gk_iset(size, -1, hmap); + } + + for (nuniq=0, i=0; i + +/*************************************************************************/ +/*! Data structures for the code */ +/*************************************************************************/ +typedef struct { + int inf, outf; + int numbering; /* input numbering (output when applicable) */ + int readvals; /* input values (output when applicable) */ + int writevals; /* output values */ + int rshuf, cshuf; /* random shuffle of rows/columns */ + int symmetric; /* a symmetric shuffle */ + int ncopies; /* the copies of the graph to create */ + char *infile; /* input file */ + char *outfile; /* output file */ +} params_t; + + +/*************************************************************************/ +/*! Constants */ +/*************************************************************************/ +#define CMD_NUMONE 1 +#define CMD_NOREADVALS 2 +#define CMD_NOWRITEVALS 3 +#define CMD_RSHUF 4 +#define CMD_CSHUF 5 +#define CMD_SYMMETRIC 6 +#define CMD_HELP 100 + + +/*************************************************************************/ +/*! Local variables */ +/*************************************************************************/ +static struct gk_option long_options[] = { + {"numone", 0, 0, CMD_NUMONE}, + {"noreadvals", 0, 0, CMD_NOREADVALS}, + {"nowritevals", 0, 0, CMD_NOWRITEVALS}, + {"rshuf", 0, 0, CMD_RSHUF}, + {"cshuf", 0, 0, CMD_CSHUF}, + {"symmetric", 0, 0, CMD_SYMMETRIC}, + {"help", 0, 0, CMD_HELP}, + {0, 0, 0, 0} +}; + + +/*-------------------------------------------------------------------*/ +/* Mini help */ +/*-------------------------------------------------------------------*/ +static char helpstr[][100] = { +" ", +"Usage: grKx [options] ", +" ", +" Required parameters", +" infile, outfile", +" The name of the input/output CSR file.", +" ", +" inf/outf", +" The format of the input/output file.", +" Supported values are:", +" 1 GK_CSR_FMT_CLUTO", +" 2 GK_CSR_FMT_CSR", +" 3 GK_CSR_FMT_METIS", +" 4 GK_CSR_FMT_BINROW", +" 6 GK_CSR_FMT_IJV", +" 7 GK_CSR_FMT_BIJV", +" ", +" Optional parameters", +" -numone", +" Specifies that the numbering of the input file starts from 1. ", +" It only applies to CSR/IJV formats.", +" ", +" -nowritevals", +" Specifies that no values will be output.", +" ", +" -noreadvals", +" Specifies that the values will not be read when applicable.", +" ", +" -rshuf", +" Specifies that the rows will be randmly shuffled prior to output.", +" ", +" -cshuf", +" Specifies that the columns will be randmly shuffled prior to output.", +" ", +" -symmetric", +" Specifies that the row+column shuffling will be symmetric.", +" ", +" -help", +" Prints this message.", +"" +}; + +static char shorthelpstr[][100] = { +" ", +" Usage: grKx [options] ", +" use 'csrconv -help' for a summary of the options.", +"" +}; + + +/*************************************************************************/ +/*! This is the entry point of the command-line argument parser */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]) +{ + int i; + int c, option_index; + params_t *params; + + params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); + + /* initialize the params data structure */ + params->numbering = 0; + params->readvals = 1; + params->writevals = 1; + params->rshuf = 0; + params->cshuf = 0; + params->symmetric = 0; + + params->inf = -1; + params->outf = -1; + params->infile = NULL; + params->outfile = NULL; + + + /* Parse the command line arguments */ + while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { + switch (c) { + case CMD_NUMONE: + params->numbering = 1; + break; + case CMD_NOREADVALS: + params->readvals = 0; + break; + case CMD_NOWRITEVALS: + params->writevals = 0; + break; + case CMD_RSHUF: + params->rshuf = 1; + break; + case CMD_CSHUF: + params->cshuf = 1; + break; + case CMD_SYMMETRIC: + params->symmetric = 1; + break; + + case CMD_HELP: + for (i=0; strlen(helpstr[i]) > 0; i++) + printf("%s\n", helpstr[i]); + exit(0); + break; + case '?': + default: + printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); + exit(0); + } + } + + if (argc-gk_optind != 5) { + printf("Unrecognized parameters."); + for (i=0; strlen(shorthelpstr[i]) > 0; i++) + printf("%s\n", shorthelpstr[i]); + exit(0); + } + + params->infile = gk_strdup(argv[gk_optind++]); + params->inf = atoi(argv[gk_optind++]); + params->outfile = gk_strdup(argv[gk_optind++]); + params->outf = atoi(argv[gk_optind++]); + params->ncopies = atoi(argv[gk_optind++]); + + if (!gk_fexists(params->infile)) + errexit("input file %s does not exist.\n", params->infile); + + return params; +} + + +/*************************************************************************/ +/*! the entry point */ +/**************************************************************************/ +int main(int argc, char *argv[]) +{ + ssize_t i, j, k, knnz, nrows, ncols, ncopies; + int what; + params_t *params; + gk_csr_t *mat, *kmat, *smat; + + /* get command-line options */ + params = parse_cmdline(argc, argv); + + /* read the data */ + mat = gk_csr_Read(params->infile, params->inf, params->readvals, params->numbering); + + /* create the copies */ + ncopies = params->ncopies; + + nrows = mat->nrows; + ncols = mat->ncols; + knnz = mat->rowptr[nrows]*ncopies; + + kmat = gk_csr_Create(); + kmat->nrows = nrows*ncopies; + kmat->ncols = ncols*ncopies; + kmat->rowptr = gk_zmalloc(kmat->nrows+1, "rowptr"); + kmat->rowind = gk_imalloc(knnz, "rowind"); + if (mat->rowval) + kmat->rowval = gk_fmalloc(knnz, "rowval"); + + kmat->rowptr[0] = knnz = 0; + for (k=0; krowptr[i]; jrowptr[i+1]; j++, knnz++) { + kmat->rowind[knnz] = mat->rowind[j] + k*ncols; + if (mat->rowval) + kmat->rowval[knnz] = mat->rowval[j]; + } + kmat->rowptr[k*nrows+i+1] = knnz; + } + } + + gk_csr_Free(&mat); + mat = kmat; + + + if (params->rshuf || params->cshuf) { + if (params->rshuf && params->cshuf) + what = GK_CSR_ROWCOL; + else if (params->rshuf) + what = GK_CSR_ROW; + else + what = GK_CSR_COL; + + smat = gk_csr_Shuffle(mat, what, params->symmetric); + gk_csr_Free(&mat); + mat = smat; + } + + if (params->writevals && mat->rowval == NULL) + mat->rowval = gk_fsmalloc(mat->rowptr[mat->nrows], 1.0, "mat->rowval"); + + gk_csr_Write(mat, params->outfile, params->outf, params->writevals, 0); + + gk_csr_Free(&mat); + +} + diff --git a/test/m2mnbrs.c b/test/m2mnbrs.c new file mode 100644 index 0000000..53f35ca --- /dev/null +++ b/test/m2mnbrs.c @@ -0,0 +1,304 @@ +/*! +\file +\brief It takes as input two CSR matrices and finds for each row of the + first matrix the most similar rows in the second matrix. + +\date 9/27/2014 +\author George +\version \verbatim $Id: m2mnbrs.c 17699 2014-09-27 18:05:31Z karypis $ \endverbatim +*/ + +#include + +/*************************************************************************/ +/*! Data structures for the code */ +/*************************************************************************/ +typedef struct { + int simtype; /*!< The similarity type to use */ + int nnbrs; /*!< The maximum number of nearest neighbots to output */ + float minsim; /*!< The minimum similarity to use for keeping neighbors */ + + int verbosity; /*!< The reporting verbosity level */ + + char *qfile; /*!< The file storing the query documents */ + char *cfile; /*!< The file storing the collection documents */ + char *outfile; /*!< The file where the output will be stored */ + + /* timers */ + double timer_global; + double timer_1; + double timer_2; + double timer_3; + double timer_4; +} params_t; + + +/*************************************************************************/ +/*! Constants */ +/*************************************************************************/ +/* Versions */ +#define VER_MAJOR 0 +#define VER_MINOR 1 +#define VER_SUBMINOR 0 + +/* Command-line option codes */ +#define CMD_SIMTYPE 10 +#define CMD_NNBRS 20 +#define CMD_MINSIM 22 +#define CMD_VERBOSITY 70 +#define CMD_HELP 100 + +/* The text labels for the different simtypes */ +static char simtypenames[][10] = {"", "dotp", "cos", "jac", ""}; + + + +/*************************************************************************/ +/*! Local variables */ +/*************************************************************************/ +static struct gk_option long_options[] = { + {"simtype", 1, 0, CMD_SIMTYPE}, + {"nnbrs", 1, 0, CMD_NNBRS}, + {"minsim", 1, 0, CMD_MINSIM}, + {"verbosity", 1, 0, CMD_VERBOSITY}, + + {"help", 0, 0, CMD_HELP}, + {0, 0, 0, 0} +}; + +static gk_StringMap_t simtype_options[] = { + {"cos", GK_CSR_COS}, + {"jac", GK_CSR_JAC}, + {NULL, 0} +}; + + +/*------------------------------------------------------------------- + * Mini help + *-------------------------------------------------------------------*/ +static char helpstr[][100] = +{ +" ", +"Usage: m2mnbrs [options] qfile cfile [outfile]", +" ", +" Options", +" -simtype=string", +" Specifies the type of similarity to use. Possible values are:", +" cos - Cosine similarity", +" jac - Jacquard similarity [default]", +" ", +" -nnbrs=int", +" Specifies the maximum number of nearest neighbors.", +" A value of -1 indicates that all neighbors will be considered.", +" Default value is 100.", +" ", +" -minsim=float", +" The minimum allowed similarity between neighbors. ", +" Default value is .25.", +" ", +" -verbosity=int", +" Specifies the level of debugging information to be displayed.", +" Default value is 0.", +" ", +" -help", +" Prints this message.", +"" +}; + + + +/*************************************************************************/ +/*! Function prototypes */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]); +void FindNeighbors(params_t *params, gk_csr_t *qmat, gk_csr_t *cmat); + + +/*************************************************************************/ +/*! This is the entry point of the command-line argument parser */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]) +{ + int i; + int c, option_index; + params_t *params; + + params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); + + /* initialize the params data structure */ + params->simtype = GK_CSR_JAC; + params->nnbrs = 100; + params->minsim = .25; + params->verbosity = -1; + params->qfile = NULL; + params->cfile = NULL; + params->outfile = NULL; + + + /* Parse the command line arguments */ + while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { + switch (c) { + case CMD_SIMTYPE: + if (gk_optarg) { + if ((params->simtype = gk_GetStringID(simtype_options, gk_optarg)) == -1) + errexit("Invalid simtype of %s.\n", gk_optarg); + } + break; + + case CMD_NNBRS: + if (gk_optarg) params->nnbrs = atoi(gk_optarg); + break; + + case CMD_MINSIM: + if (gk_optarg) params->minsim = atof(gk_optarg); + break; + + case CMD_VERBOSITY: + if (gk_optarg) params->verbosity = atoi(gk_optarg); + break; + + case CMD_HELP: + for (i=0; strlen(helpstr[i]) > 0; i++) + printf("%s\n", helpstr[i]); + exit(EXIT_SUCCESS); + break; + + case '?': + default: + printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); + exit(EXIT_FAILURE); + } + } + + /* Get the input/output file info */ + if (argc-gk_optind < 1) { + printf("Missing input/output file info.\n Use %s -help for a summary of the options.\n", argv[0]); + exit(EXIT_FAILURE); + } + + params->qfile = gk_strdup(argv[gk_optind++]); + params->cfile = gk_strdup(argv[gk_optind++]); + params->outfile = (gk_optind < argc ? gk_strdup(argv[gk_optind++]) : NULL); + + if (!gk_fexists(params->qfile)) + errexit("input file %s does not exist.\n", params->qfile); + if (!gk_fexists(params->cfile)) + errexit("input file %s does not exist.\n", params->cfile); + + return params; +} + + +/*************************************************************************/ +/*! This is the entry point of the program */ +/**************************************************************************/ +int main(int argc, char *argv[]) +{ + params_t *params; + gk_csr_t *qmat, *cmat; + int rc = EXIT_SUCCESS; + + params = parse_cmdline(argc, argv); + + qmat = gk_csr_Read(params->qfile, GK_CSR_FMT_CSR, 1, 0); + cmat = gk_csr_Read(params->cfile, GK_CSR_FMT_CSR, 1, 0); + + + printf("********************************************************************************\n"); + printf("sd (%d.%d.%d) Copyright 2014, GK.\n", VER_MAJOR, VER_MINOR, VER_SUBMINOR); + printf(" simtype=%s, nnbrs=%d, minsim=%.2f\n", + simtypenames[params->simtype], params->nnbrs, params->minsim); + printf(" qfile=%s, nrows=%d, ncols=%d, nnz=%zd\n", + params->qfile, qmat->nrows, qmat->ncols, qmat->rowptr[qmat->nrows]); + printf(" cfile=%s, nrows=%d, ncols=%d, nnz=%zd\n", + params->cfile, cmat->nrows, cmat->ncols, cmat->rowptr[cmat->nrows]); + + gk_clearwctimer(params->timer_global); + gk_clearwctimer(params->timer_1); + gk_clearwctimer(params->timer_2); + gk_clearwctimer(params->timer_3); + gk_clearwctimer(params->timer_4); + + gk_startwctimer(params->timer_global); + + FindNeighbors(params, qmat, cmat); + + gk_stopwctimer(params->timer_global); + + printf(" wclock: %.2lfs\n", gk_getwctimer(params->timer_global)); + printf(" timer1: %.2lfs\n", gk_getwctimer(params->timer_1)); + printf(" timer2: %.2lfs\n", gk_getwctimer(params->timer_2)); + printf(" timer3: %.2lfs\n", gk_getwctimer(params->timer_3)); + printf(" timer4: %.2lfs\n", gk_getwctimer(params->timer_4)); + printf("********************************************************************************\n"); + + gk_csr_Free(&qmat); + gk_csr_Free(&cmat); + + exit(rc); +} + + +/*************************************************************************/ +/*! Reads and computes the neighbors of each query document against the + collection of documents */ +/**************************************************************************/ +void FindNeighbors(params_t *params, gk_csr_t *qmat, gk_csr_t *cmat) +{ + int iQ, iH, nhits; + int32_t *marker; + gk_fkv_t *hits, *cand; + FILE *fpout; + + GKASSERT(qmat->ncols <= cmat->ncols); + + /* if cosine, make rows unit length */ + if (params->simtype == GK_CSR_COS) { + gk_csr_Normalize(qmat, GK_CSR_ROW, 2); + gk_csr_Normalize(cmat, GK_CSR_ROW, 2); + } + + /* create the inverted index */ + gk_csr_CreateIndex(cmat, GK_CSR_COL); + + /* compute the row norms */ + gk_csr_ComputeSquaredNorms(cmat, GK_CSR_ROW); + + /* create the output file */ + fpout = (params->outfile ? gk_fopen(params->outfile, "w", "FindNeighbors: fpout") : NULL); + + /* allocate memory for the necessary working arrays */ + hits = gk_fkvmalloc(cmat->nrows, "FindNeighbors: hits"); + marker = gk_i32smalloc(cmat->nrows, -1, "FindNeighbors: marker"); + cand = gk_fkvmalloc(cmat->nrows, "FindNeighbors: cand"); + + + /* find the best neighbors for each query document */ + gk_startwctimer(params->timer_1); + for (iQ=0; iQnrows; iQ++) { + if (params->verbosity > 0) + printf("Working on query %7d\n", iQ); + + /* find the neighbors of the ith document */ + nhits = gk_csr_GetSimilarRows(cmat, + qmat->rowptr[iQ+1]-qmat->rowptr[iQ], + qmat->rowind+qmat->rowptr[iQ], + qmat->rowval+qmat->rowptr[iQ], + params->simtype, params->nnbrs, params->minsim, + hits, marker, cand); + + /* write the results in the file */ + if (fpout) { + for (iH=0; iHtimer_1); + + + /* cleanup and exit */ + if (fpout) gk_fclose(fpout); + + gk_free((void **)&hits, &marker, &cand, LTERM); +} + diff --git a/test/rw.c b/test/rw.c new file mode 100644 index 0000000..1a3295e --- /dev/null +++ b/test/rw.c @@ -0,0 +1,306 @@ +/*! +\file +\brief A simple (personalized) random walk program to test GKlib's routines + +\date 6/12/2008 +\author George +\version \verbatim $Id$ \endverbatim +*/ + +#include + +/*************************************************************************/ +/*! Data structures for the code */ +/*************************************************************************/ +typedef struct { + int niter; + int ntvs; + int ppr; + float eps; + float lamda; + char *infile; + char *outfile; +} params_t; + +/*************************************************************************/ +/*! Constants */ +/*************************************************************************/ +#define CMD_NITER 1 +#define CMD_EPS 2 +#define CMD_LAMDA 3 +#define CMD_PPR 4 +#define CMD_NTVS 5 +#define CMD_HELP 10 + + +/*************************************************************************/ +/*! Local variables */ +/*************************************************************************/ +static struct gk_option long_options[] = { + {"niter", 1, 0, CMD_NITER}, + {"lamda", 1, 0, CMD_LAMDA}, + {"eps", 1, 0, CMD_EPS}, + {"ppr", 1, 0, CMD_PPR}, + {"ntvs", 1, 0, CMD_NTVS}, + {"help", 0, 0, CMD_HELP}, + {0, 0, 0, 0} +}; + + +/*-------------------------------------------------------------------*/ +/* Mini help */ +/*-------------------------------------------------------------------*/ +static char helpstr[][100] = { +" ", +"Usage: rw [options] ", +" ", +" Required parameters", +" graph-file", +" The name of the file storing the transactions. The file is in ", +" Metis' graph format.", +" ", +" Optional parameters", +" -niter=int", +" Specifies the maximum number of iterations. [default: 100]", +" ", +" -lamda=float", +" Specifies the follow-the-adjacent-links probability. [default: 0.80]", +" ", +" -eps=float", +" Specifies the error tollerance. [default: 1e-10]", +" ", +" -ppr=int", +" Specifies the source of the personalized PR. [default: -1]", +" ", +" -ntvs=int", +" Specifies the number of test-vectors to compute. [default: -1]", +" ", +" -help", +" Prints this message.", +"" +}; + +static char shorthelpstr[][100] = { +" ", +" Usage: rw [options] ", +" use 'rw -help' for a summary of the options.", +"" +}; + + + +/*************************************************************************/ +/*! Function prototypes */ +/*************************************************************************/ +void print_init_info(params_t *params, gk_csr_t *mat); +void print_final_info(params_t *params); +params_t *parse_cmdline(int argc, char *argv[]); + + +/*************************************************************************/ +/*! the entry point */ +/**************************************************************************/ +int main(int argc, char *argv[]) +{ + ssize_t i, j, niter; + params_t *params; + gk_csr_t *mat; + FILE *fpout; + + /* get command-line options */ + params = parse_cmdline(argc, argv); + + /* read the data */ + mat = gk_csr_Read(params->infile, GK_CSR_FMT_METIS, 1, 1); + + /* display some basic stats */ + print_init_info(params, mat); + + + if (params->ntvs != -1) { + /* compute the pr for different randomly generated restart-distribution vectors */ + float **prs; + + prs = gk_fAllocMatrix(params->ntvs, mat->nrows, 0.0, "main: prs"); + + /* generate the random restart vectors */ + for (j=0; jntvs; j++) { + for (i=0; inrows; i++) + prs[j][i] = RandomInRange(931); + gk_fscale(mat->nrows, 1.0/gk_fsum(mat->nrows, prs[j], 1), prs[j], 1); + + niter = gk_rw_PageRank(mat, params->lamda, params->eps, params->niter, prs[j]); + printf("tvs#: %zd; niters: %zd\n", j, niter); + } + + /* output the computed pr scores */ + fpout = gk_fopen(params->outfile, "w", "main: outfile"); + for (i=0; inrows; i++) { + for (j=0; jntvs; j++) + fprintf(fpout, "%.4e ", prs[j][i]); + fprintf(fpout, "\n"); + } + gk_fclose(fpout); + + gk_fFreeMatrix(&prs, params->ntvs, mat->nrows); + } + else if (params->ppr != -1) { + /* compute the personalized pr from the specified vertex */ + float *pr; + + pr = gk_fsmalloc(mat->nrows, 0.0, "main: pr"); + + pr[params->ppr-1] = 1.0; + + niter = gk_rw_PageRank(mat, params->lamda, params->eps, params->niter, pr); + printf("ppr: %d; niters: %zd\n", params->ppr, niter); + + /* output the computed pr scores */ + fpout = gk_fopen(params->outfile, "w", "main: outfile"); + for (i=0; inrows; i++) + fprintf(fpout, "%.4e\n", pr[i]); + gk_fclose(fpout); + + gk_free((void **)&pr, LTERM); + } + else { + /* compute the standard pr */ + int jmax; + float diff, maxdiff; + float *pr; + + pr = gk_fsmalloc(mat->nrows, 1.0/mat->nrows, "main: pr"); + + niter = gk_rw_PageRank(mat, params->lamda, params->eps, params->niter, pr); + printf("pr; niters: %zd\n", niter); + + /* output the computed pr scores */ + fpout = gk_fopen(params->outfile, "w", "main: outfile"); + for (i=0; inrows; i++) { + for (jmax=i, maxdiff=0.0, j=mat->rowptr[i]; jrowptr[i+1]; j++) { + if ((diff = fabs(pr[i]-pr[mat->rowind[j]])) > maxdiff) { + maxdiff = diff; + jmax = mat->rowind[j]; + } + } + fprintf(fpout, "%.4e %10zd %.4e %10d\n", pr[i], + mat->rowptr[i+1]-mat->rowptr[i], maxdiff, jmax+1); + } + gk_fclose(fpout); + + gk_free((void **)&pr, LTERM); + } + + gk_csr_Free(&mat); + + /* display some final stats */ + print_final_info(params); +} + + + +/*************************************************************************/ +/*! This function prints run parameters */ +/*************************************************************************/ +void print_init_info(params_t *params, gk_csr_t *mat) +{ + printf("*******************************************************************************\n"); + printf(" fis\n\n"); + printf("Matrix Information ---------------------------------------------------------\n"); + printf(" input file=%s, [%d, %d, %zd]\n", + params->infile, mat->nrows, mat->ncols, mat->rowptr[mat->nrows]); + + printf("\n"); + printf("Options --------------------------------------------------------------------\n"); + printf(" niter=%d, ntvs=%d, ppr=%d, lamda=%f, eps=%e\n", + params->niter, params->ntvs, params->ppr, params->lamda, params->eps); + + printf("\n"); + printf("Performing random walks... ----------------------------------------------\n"); +} + + +/*************************************************************************/ +/*! This function prints final statistics */ +/*************************************************************************/ +void print_final_info(params_t *params) +{ + printf("\n"); + printf("Memory Usage Information -----------------------------------------------------\n"); + printf(" Maximum memory used: %10zd bytes\n", (ssize_t) gk_GetMaxMemoryUsed()); + printf(" Current memory used: %10zd bytes\n", (ssize_t) gk_GetCurMemoryUsed()); + printf("********************************************************************************\n"); +} + + +/*************************************************************************/ +/*! This is the entry point of the command-line argument parser */ +/*************************************************************************/ +params_t *parse_cmdline(int argc, char *argv[]) +{ + int i; + int c, option_index; + params_t *params; + + params = (params_t *)gk_malloc(sizeof(params_t), "parse_cmdline: params"); + + /* initialize the params data structure */ + params->niter = 100; + params->ppr = -1; + params->ntvs = -1; + params->eps = 1e-10; + params->lamda = 0.80; + params->infile = NULL; + params->outfile = NULL; + + + /* Parse the command line arguments */ + while ((c = gk_getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) { + switch (c) { + case CMD_NITER: + if (gk_optarg) params->niter = atoi(gk_optarg); + break; + case CMD_NTVS: + if (gk_optarg) params->ntvs = atoi(gk_optarg); + break; + case CMD_PPR: + if (gk_optarg) params->ppr = atoi(gk_optarg); + break; + case CMD_EPS: + if (gk_optarg) params->eps = atof(gk_optarg); + break; + case CMD_LAMDA: + if (gk_optarg) params->lamda = atof(gk_optarg); + break; + + case CMD_HELP: + for (i=0; strlen(helpstr[i]) > 0; i++) + printf("%s\n", helpstr[i]); + exit(0); + break; + case '?': + default: + printf("Illegal command-line option(s)\nUse %s -help for a summary of the options.\n", argv[0]); + exit(0); + } + } + + if (argc-gk_optind != 2) { + printf("Unrecognized parameters."); + for (i=0; strlen(shorthelpstr[i]) > 0; i++) + printf("%s\n", shorthelpstr[i]); + exit(0); + } + + params->infile = gk_strdup(argv[gk_optind++]); + params->outfile = gk_strdup(argv[gk_optind++]); + + if (!gk_fexists(params->infile)) + errexit("input file %s does not exist.\n", params->infile); + + if (params->ppr != -1 && params->ntvs != -1) + errexit("Only one of the -ppr and -ntvs options can be specified.\n"); + + return params; +} + diff --git a/test/splatt2svd.c b/test/splatt2svd.c new file mode 100644 index 0000000..111d31c --- /dev/null +++ b/test/splatt2svd.c @@ -0,0 +1,98 @@ +/*! +\file +\brief A simple program to convert a tensor in coordinate format into an unfolded + matrix + +\author George +*/ + +#include + + +int main(int argc, char *argv[]) +{ + size_t nnz, i, j, k, nI, nJ, nK, nrows, ncols; + int32_t *I, *J, *K, *rowind, *colind; + ssize_t *rowptr, *colptr; + float *V, *rowval, *colval; + + if (argc != 2) + errexit("Usage %s [%d]\n", argv[0], argc); + + if (!gk_fexists(argv[1])) + errexit("File %s does not exist.\n", argv[1]); + + gk_getfilestats(argv[1], &nnz, NULL, NULL, NULL); + I = gk_i32malloc(nnz, "I"); + J = gk_i32malloc(nnz, "J"); + K = gk_i32malloc(nnz, "K"); + V = gk_fmalloc(nnz, "V"); + + fprintf(stderr, "Input nnz: %zd\n", nnz); + + FILE *fpin = gk_fopen(argv[1], "r", "infile"); + for (i=0; i + + +/*************************************************************************/ +/*! Testing module for gk_strstr_replace() */ +/*************************************************************************/ +void test_strstr_replace() +{ + char *new_str; + int rc; + + rc = gk_strstr_replace("This is a simple string", "s", "S", "", &new_str); + printf("%d, %s.\n", rc, new_str); + gk_free((void **)&new_str, LTERM); + + + rc = gk_strstr_replace("This is a simple string", "s", "S", "g", &new_str); + printf("%d, %s.\n", rc, new_str); + gk_free((void **)&new_str, LTERM); + + + rc = gk_strstr_replace("This is a simple SS & ss string", "s", "T", "g", &new_str); + printf("%d, %s.\n", rc, new_str); + gk_free((void **)&new_str, LTERM); + + + rc = gk_strstr_replace("This is a simple SS & ss string", "s", "T", "ig", &new_str); + printf("%d, %s.\n", rc, new_str); + gk_free((void **)&new_str, LTERM); + + rc = gk_strstr_replace("This is a simple SS & ss string", "\\b\\w(\\w+)\\w\\b", "$1", "ig", &new_str); + printf("%d, %s.\n", rc, new_str); + gk_free((void **)&new_str, LTERM); + + rc = gk_strstr_replace("This is a simple SS & ss string", "\\b\\w+\\b", "word", "ig", &new_str); + printf("%d, %s.\n", rc, new_str); + gk_free((void **)&new_str, LTERM); + + rc = gk_strstr_replace("http://www.cs.umn.edu/This-is-something-T12323?pp=20&page=4", + "(http://www\\.cs\\.umn\\.edu/)(.*)-T(\\d+)", "$1$2-P$3", "g", &new_str); + printf("%d, %s.\n", rc, new_str); + gk_free((void **)&new_str, LTERM); + + rc = gk_strstr_replace("http://www.cs.umn.edu/This-is-something-T12323?pp=20&page=4", + "(\\d+)", "number:$1", "ig", &new_str); + printf("%d, %s.\n", rc, new_str); + gk_free((void **)&new_str, LTERM); + + + rc = gk_strstr_replace("http://www.cs.umn.edu/This-is-something-T12323?pp=20&page=4", + "(http://www\\.cs\\.umn\\.edu/)", "[$1]", "g", &new_str); + printf("%d, %s.\n", rc, new_str); + gk_free((void **)&new_str, LTERM); + + + +} + + + +int main() +{ + test_strstr_replace(); + +/* + { + int i; + for (i=0; i<1000; i++) + printf("%d\n", RandomInRange(3)); + } +*/ +} + diff --git a/timers.c b/timers.c new file mode 100644 index 0000000..bb8f296 --- /dev/null +++ b/timers.c @@ -0,0 +1,52 @@ +/*! +\file timers.c +\brief Various timing functions + +\date Started 4/12/2007 +\author George +\version\verbatim $Id: timers.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim +*/ + + +#include + + + + +/************************************************************************* +* This function returns the CPU seconds +**************************************************************************/ +double gk_WClockSeconds(void) +{ +#ifdef __GNUC__ + struct timeval ctime; + + gettimeofday(&ctime, NULL); + + return (double)ctime.tv_sec + (double).000001*ctime.tv_usec; +#else + return (double)time(NULL); +#endif +} + + +/************************************************************************* +* This function returns the CPU seconds +**************************************************************************/ +double gk_CPUSeconds(void) +{ +//#ifdef __OPENMP__ +#ifdef __OPENMPXXXX__ + return omp_get_wtime(); +#else + #if defined(WIN32) || defined(__MINGW32__) + return((double) clock()/CLOCKS_PER_SEC); + #else + struct rusage r; + + getrusage(RUSAGE_SELF, &r); + return ((r.ru_utime.tv_sec + r.ru_stime.tv_sec) + 1.0e-6*(r.ru_utime.tv_usec + r.ru_stime.tv_usec)); + #endif +#endif +} + diff --git a/tokenizer.c b/tokenizer.c new file mode 100644 index 0000000..5efd262 --- /dev/null +++ b/tokenizer.c @@ -0,0 +1,77 @@ +/*! +\file tokenizer.c +\brief String tokenization routines + +This file contains various routines for splitting an input string into +tokens and returning them in form of a list. The goal is to mimic perl's +split function. + +\date Started 11/23/04 +\author George +\version\verbatim $Id: tokenizer.c 10711 2011-08-31 22:23:04Z karypis $ \endverbatim +*/ + + +#include + + +/************************************************************************ +* This function tokenizes a string based on the user-supplied delimiters +* list. The resulting tokens are returned into an array of strings. +*************************************************************************/ +void gk_strtokenize(char *str, char *delim, gk_Tokens_t *tokens) +{ + int i, ntoks, slen; + + tokens->strbuf = gk_strdup(str); + + slen = strlen(str); + str = tokens->strbuf; + + /* Scan once to determine the number of tokens */ + for (ntoks=0, i=0; intoks = ntoks; + tokens->list = (char **)gk_malloc(ntoks*sizeof(char *), "strtokenize: tokens->list"); + + + /* Scan a second time to mark and link the tokens */ + for (ntoks=0, i=0; ilist[ntoks++] = str+i; + + /* Consume all the consecutive characters from the token */ + while (ilist, &tokens->strbuf, LTERM); +} + diff --git a/win32/adapt.c b/win32/adapt.c new file mode 100644 index 0000000..546857c --- /dev/null +++ b/win32/adapt.c @@ -0,0 +1,11 @@ +/* +\file win32/adapt.c +\brief Implementation of Win32 adaptation of libc functions +*/ + +#include "adapt.h" + +pid_t getpid(void) +{ + return GetCurrentProcessId(); +} diff --git a/win32/adapt.h b/win32/adapt.h new file mode 100644 index 0000000..35e60ed --- /dev/null +++ b/win32/adapt.h @@ -0,0 +1,14 @@ +/* +\file win32/adapt.h +\brief Declaration of Win32 adaptation of POSIX functions and types +*/ +#ifndef _WIN32_ADAPT_H_ +#define _WIN32_ADAPT_H_ + +#include + +typedef DWORD pid_t; + +pid_t getpid(void); + +#endif /* _WIN32_ADAPT_H_ */