pax_global_header00006660000000000000000000000064122623441170014514gustar00rootroot0000000000000052 comment=1f03f41e7c4740164aae44570fa8d05c3f3e7ed6 libgtextutils-0.7/000077500000000000000000000000001226234411700142655ustar00rootroot00000000000000libgtextutils-0.7/.gitignore000066400000000000000000000013761226234411700162640ustar00rootroot00000000000000*~ .*.swp INSTALL Makefile Makefile.in */Makefile */Makefile.in */.deps/* src/gtextutils/.deps/ src/gtextutils/.libs/ src/gtextutils/*.o src/gtextutils/*.la src/gtextutils/*.lo tests/*.o tests/*.trs tests/*.log aclocal.m4 autom4te.cache/* config.h config.h.in config.log config.status config/* configure gtextutils.pc libtool m4/libtool.m4 m4/ltoptions.m4 m4/ltsugar.m4 m4/ltversion.m4 m4/lt~obsolete.m4 stamp-h1 libgtextutils-*.tar.bz2 libgtextutils-*.tar.gz tests/.libs tests/fdout.txt.gz tests/pipe_out.txt.gz tests/test_container_join tests/test_fd_inbuf tests/test_fd_outbuf tests/test_in_out_buf tests/test_input_stream_wrapper tests/test_natural_sort tests/test_pipe_fitter tests/test_string_tokenize tests/test_text_reader tests/test_text_reader_unget libgtextutils-0.7/AUTHORS000066400000000000000000000002161226234411700153340ustar00rootroot00000000000000Authors of Gordon-Text_utils-Library. See also the files THANKS and ChangeLog. A. Gordon designed and implemented Gordon-Text_utils-Library. libgtextutils-0.7/COPYING000066400000000000000000001033301226234411700153200ustar00rootroot00000000000000 GNU AFFERO GENERAL PUBLIC LICENSE Version 3, 19 November 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU Affero General Public License is a free, copyleft license for software and other kinds of works, specifically designed to ensure cooperation with the community in the case of network server software. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, our General Public Licenses are intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. 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For more information on this, and how to apply and follow the GNU AGPL, see . libgtextutils-0.7/ChangeLog000066400000000000000000000000001226234411700160250ustar00rootroot00000000000000libgtextutils-0.7/Makefile.am000066400000000000000000000013401226234411700163170ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. EXTRA_DIST = reconf configure SUBDIRS = m4 src doc tests ACLOCAL_AMFLAGS = -I m4 pkgconfigdir = $(libdir)/pkgconfig pkgconfig_DATA = gtextutils.pc distcleancheck_listfiles=\ ./tests/test.txt \ ./tests/fdout.txt.gz \ ./tests/pipe_out.txt.gz libgtextutils-0.7/NEWS000066400000000000000000000015731226234411700147720ustar00rootroot00000000000000Gordon-Text_utils-Library -- History of visible changes. Copyright (C) 2009-2013, A. Gordon See the end for copying conditions. Please send Gordon-Text_utils-Library bug reports to assafgordon@gmail.com . Version 0.1 * List your features here ------------------------------------------------------- Copying information: Copyright (C) 2009-2013, A. Gordon Permission is granted to anyone to make or distribute verbatim copies of this document as received, in any medium, provided that the copyright notice and this permission notice are preserved, thus giving the recipient permission to redistribute in turn. Permission is granted to distribute modified versions of this document, or of portions of it, under the above conditions, provided also that they carry prominent notices stating who last changed them. libgtextutils-0.7/README000066400000000000000000000004051226234411700151440ustar00rootroot00000000000000Welcome to Gordon-Text_utils-Library. Gordon-Text_utils-Library is free software. Please see the file COPYING for details. For documentation, please see the files in the doc subdirectory. For building and installation instructions please see the INSTALL file. libgtextutils-0.7/THANKS000066400000000000000000000004721226234411700152030ustar00rootroot00000000000000Gordon-Text_utils-Library THANKS file Gordon-Text_utils-Library has originally been written by A. Gordon. Many people have further contributed to FOO by reporting problems, suggesting various improvements, or submitting actual code. Here is a list of these people. Help me keep it complete and exempt of errors. libgtextutils-0.7/configure.ac000066400000000000000000000046451226234411700165640ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. AC_INIT([Gordon-Text_utils-Library], [0.7], [A. Gordon assafgordon@gmail.com], [libgtextutils]) AC_CONFIG_AUX_DIR(config) AC_CONFIG_MACRO_DIR([m4]) AM_CONFIG_HEADER(config.h) AM_INIT_AUTOMAKE([dist-bzip2]) # dynamic library version LIBGTU_CURRENT=0 LIBGTU_REVISION=0 LIBGTU_AGE=0 AC_PROG_CC AC_PROG_CXX AC_PROG_LIBTOOL dnl --enable-wall EXTRA_CHECKS="-Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror" AC_ARG_ENABLE(wall, [ --enable-wall Enable many common GCC warnings (-Wall,-Wextra, -Werror etc., default enabled)], [case "${enableval}" in yes) wall=true ;; no) wall=false ;; *) AC_MSG_ERROR(bad value ${enableval} for --enable-wall) ;; esac],[wall=true]) if test "$wall" = "true" then CFLAGS="${CFLAGS} ${EXTRA_CHECKS}" CXXFLAGS="${CXXFLAGS} ${EXTRA_CHECKS}" fi dnl --enable-debug AC_ARG_ENABLE(debug, [ --enable-debug Enable debug mode (default enabled)], [case "${enableval}" in yes) debug=true ;; no) debug=false ;; *) AC_MSG_ERROR(bad value ${enableval} for --enable-debug) ;; esac],[debug=true]) if test "$debug" = "true" then CFLAGS="${CFLAGS} -DDEBUG -g -O1" CXXFLAGS="${CFLAGS} -DDEBUG -g -O1" else CFLAGS="${CFLAGS} -O3" CXXFLAGS="${CFLAGS} -O3" fi dnl --enable-tuple-parser-check AC_ARG_ENABLE(tuple-parser-check, [ --enable-tuple-parser-check Enable Tuple Parser Check (default disabled, requires g++ > 4.3.2)], [case "${enableval}" in yes) tuple_parser_check=true ;; no) tuple_parser_check=false ;; *) AC_MSG_ERROR(bad value ${enableval} for --enable-tuple-parser-check) ;; esac],[tuple_parser_check=false]) AM_CONDITIONAL([TUPLE_PARSER_CHECK], [test x$tuple_parser_check = xtrue]) AC_SUBST(LIBGTU_CURRENT) AC_SUBST(LIBGTU_REVISION) AC_SUBST(LIBGTU_AGE) AC_CONFIG_FILES([ Makefile doc/Makefile m4/Makefile src/Makefile src/gtextutils/Makefile gtextutils.pc tests/Makefile ]) AC_OUTPUT libgtextutils-0.7/doc/000077500000000000000000000000001226234411700150325ustar00rootroot00000000000000libgtextutils-0.7/doc/Makefile.am000066400000000000000000000007431226234411700170720ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. libgtextutils-0.7/gtextutils.pc.in000066400000000000000000000003441226234411700174330ustar00rootroot00000000000000prefix=@prefix@ exec_prefix=@exec_prefix@ libdir=@libdir@ includedir=@includedir@ Name: gtextutils Description: Gordon's text-utility classes Version: @VERSION@ Libs: -L${libdir} -lgtextutils Cflags: -I${includedir}/gtextutils libgtextutils-0.7/m4/000077500000000000000000000000001226234411700146055ustar00rootroot00000000000000libgtextutils-0.7/m4/Makefile.am000066400000000000000000000012511226234411700166400ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # Install m4 macros in this directory m4datadir = $(datadir)/aclocal # List your m4 macros here m4macros = # The following is boilerplate m4data_DATA = $(m4macros) EXTRA_DIST = $(m4data_DATA) libgtextutils-0.7/reconf000077500000000000000000000012631226234411700154710ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. #!/bin/sh rm -f config.cache mkdir -p config echo "- libtoolize." libtoolize -i echo "- aclocal." aclocal -I m4 echo "- autoconf." autoconf echo "- autoheader." autoheader echo "- automake." automake -a exit libgtextutils-0.7/src/000077500000000000000000000000001226234411700150545ustar00rootroot00000000000000libgtextutils-0.7/src/Makefile.am000066400000000000000000000007701226234411700171140ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. SUBDIRS = gtextutils libgtextutils-0.7/src/gtextutils/000077500000000000000000000000001226234411700172705ustar00rootroot00000000000000libgtextutils-0.7/src/gtextutils/Makefile.am000066400000000000000000000023451226234411700213300ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. lib_LTLIBRARIES = libgtextutils.la libgtextutils_la_LDFLAGS = -version-info @LIBGTU_CURRENT@:@LIBGTU_REVISION@:@LIBGTU_AGE@ -release @VERSION@ libgtextutils_la_SOURCES = stream_wrapper.cpp stream_wrapper.h \ text_line_reader.cpp text_line_reader.h \ container_join.h \ natsort.h \ strnatcmp.c strnatcmp.h \ outbuf3.hpp \ tuple_parser.h \ exit_manip.h \ inbuf1.hpp \ pipe_fitter.c pipe_fitter.h libgtextutils_la_includedir = $(includedir)/gtextutils/gtextutils libgtextutils_la_include_HEADERS = container_join.h \ text_line_reader.h \ stream_wrapper.h \ natsort.h \ strnatcmp.h \ outbuf3.hpp \ inbuf1.hpp \ tuple_parser.h \ exit_manip.h \ string_tokenize.h \ pipe_fitter.h libgtextutils-0.7/src/gtextutils/container_join.h000066400000000000000000000136221226234411700224460ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #ifndef __LIBGTEXTUTILS_CONTAINER_JOIN_H__ #define __LIBGTEXTUTILS_CONTAINER_JOIN_H__ /* * Easily joins a container and outputs it to a stream. * * Tries to emulate Perl's join in an STL way. Usage: send container's elements into an output-stream: STD::OSTREAM << join ( CONTAINER, [DELIMITER] ) ; STD::OSTREAM << join ( BEGIN-ITERATOR, END-ITERATOR, [DELIMITER] ) ; send container's elements into a string: STD::STRING = join ( CONTAINER, [DELIMITER] ) ; STD::STRING = join ( BEGIN-ITERATOR, END-ITERATOR, [DELIMITER] ) ; [DELIMITER] = optional std::string, will be used as delimiter between two elements. defaults to a single tab. can contain multiple characters. Usage example: // A simple container (could also be a list/deque/stack/whatever): vector v; for (int i=0;i<10;++i) v.push_back(i); // Print the entire container: cout << join(v,",") << endl; // Will output: 0,1,2,3,4,5,6,7,8,9 // Print specific range, using begin/end iterators cout << join(v.begin(), v.end(),"-") << endl; // Will output: 0-1-2-3-4-5-6-7-8-9 // An std::pair<> based container // map/set/multimap/multiset/unorederd_map etc. // or // vector< pair > etc. map m; m[42] = "Don't Panic"; m[666]= "Beast" ; // Print the first values (of the pair) of the entire container: cout << "keys = " << join_firsts(m) << endl; // Will output: 42 666 // Print the first values (of the pair) of a specific range: cout << "keys = " << join_firsts(m.begin(), m.end(), ",") << endl; // Will output: 42,666 // Print the second values (of the pair) of the entire container: cout << "values= " << join_seconds(m) << endl; // Will output: Don't PanicBeast // Print the second values (of the pair) of a specific range: cout << "values= " << join_seconds(m.begin(), m.end(), ",") << endl; // Will output: Don't Panic,Beast // Store result in a string (instead of an output stream): string s = join_firsts(m); // 's' will contain: "42\t666"; */ #include #include #include #include #include template struct joiner { joiner ( ITERATOR _begin, ITERATOR _end, const std::string& _delimiter="\t" ) : begin(_begin), end(_end), delimiter(_delimiter) {} ITERATOR begin, end; std::string delimiter; OP op; operator std::string() const { std::ostringstream os; os << *this; return os.str(); } }; template inline std::ostream& operator<< ( std::ostream& strm, const joiner& j ) { ITERATOR it = j.begin; if (it != j.end) { //first element - doesn't need a delimiter strm << j.op(*it); it++; } for (; it != j.end ; ++it) { //print a delimiter before all other elements strm << j.delimiter ; strm << j.op(*it); } return strm; } template struct joiner_noop { const T& operator() (const T& t) const { return t; } }; template struct joiner_select1st { const FIRST& operator() ( const std::pair& pair ) const { return pair.first ; } }; template struct joiner_select2nd { const SECOND& operator() ( const std::pair& pair ) const { return pair.second; } }; template inline joiner< ITERATOR, joiner_noop > join(ITERATOR begin, ITERATOR end, const std::string& delimiter="\t") { return joiner< ITERATOR, joiner_noop > (begin, end, delimiter); } template inline joiner< ITERATOR, joiner_select1st > join_firsts(ITERATOR begin, ITERATOR end, const std::string& delimiter="\t") { return joiner< ITERATOR, joiner_select1st > (begin, end, delimiter); } template inline joiner< ITERATOR, joiner_select2nd > join_seconds(ITERATOR begin, ITERATOR end, const std::string& delimiter="\t") { return joiner< ITERATOR, joiner_select2nd > (begin, end, delimiter); } template inline joiner< typename CONTAINER::const_iterator, joiner_noop > join(const CONTAINER& a, const std::string& delimiter="\t") { return join(a.begin(), a.end(), delimiter); } template inline joiner< typename CONTAINER::const_iterator, joiner_select1st > join_firsts(const CONTAINER& a, const std::string& delimiter="\t") { return join_firsts(a.begin(), a.end(), delimiter); } template inline joiner< typename CONTAINER::const_iterator, joiner_select2nd > join_seconds(const CONTAINER& a, const std::string& delimiter="\t") { return join_seconds(a.begin(), a.end(), delimiter); } #endif libgtextutils-0.7/src/gtextutils/exit_manip.h000066400000000000000000000040711226234411700216000ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #ifndef __EXIT_MANIP__ #define __EXIT_MANIP__ /* Easily terminates a program while printing an error message. Tries to be an STL spirited version of errx(3) Usage: // from where ever in the code you wish to print message and terminate: // will print message to STDERR and exit with exit code 1 cerr << "Error: something failed. " << exit_program(1); // if you want file+list information, use: cerr << "Error: something failed. " << exit_program_with_source(1); */ struct exit_process_struct { int exitcode; bool show_source; const char* source_file; size_t source_file_line_number ; } ; #define exit_program_with_source(exitcode) exit_program((exitcode),__FILE__,__LINE__) inline exit_process_struct exit_program(int exitcode, const char* filename = NULL, const size_t line = 0 ) { exit_process_struct eps; eps.exitcode = exitcode ; if ( filename == NULL || line == 0 ) eps.show_source = false ; else { eps.show_source = true ; eps.source_file = filename ; eps.source_file_line_number = line ; } return eps; } inline std::ostream& operator<< ( std::ostream& strm, const exit_process_struct& eps ) { if (eps.show_source) strm << " [ " << eps.source_file << " : " << eps.source_file_line_number << " ]"; strm << std::endl; exit(eps.exitcode); return strm ; } #endif libgtextutils-0.7/src/gtextutils/inbuf1.hpp000066400000000000000000000101741226234411700211700ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #ifndef __JOSUTTIS_FD_INBUF_H__ #define __JOSUTTIS_FD_INBUF_H__ /* The following code example is taken from the book * "The C++ Standard Library - A Tutorial and Reference" * by Nicolai M. Josuttis, Addison-Wesley, 1999 * * (C) Copyright Nicolai M. Josuttis 1999. * Permission to copy, use, modify, sell and distribute this software * is granted provided this copyright notice appears in all copies. * This software is provided "as is" without express or implied * warranty, and with no claim as to its suitability for any purpose. * * Added by A. Gordon: * The file is available as "io/inbuf1.hpp" in the examples tarball at * http://www.josuttis.com/libbook/ * * And in the book at Chapter 13, Page 678. * * Modifications: * 1. Larger buffer, with vector * 2. Accepts input file descriptor in c'tor */ #include #include #include #include // for read(): #ifdef _MSC_VER # include #else # include #endif class josuttis_fd_inbuf : public std::streambuf { protected: /* data buffer: * - at most, four characters in putback area plus * - at most, six characters in ordinary read buffer */ static const int putBackSize = 4 ; static const int bufferSize = putBackSize + 32768; // size of the data buffer std::vector buffer_vector ; char* buffer; int input_fd; public: /* constructor * - initialize empty data buffer * - no putback area * => force underflow() */ josuttis_fd_inbuf( int _input_fd ) : buffer_vector(bufferSize), buffer(&buffer_vector[0]), input_fd(_input_fd) { setg (buffer+putBackSize, // beginning of putback area buffer+putBackSize, // read position buffer+putBackSize); // end position } protected: // insert new characters into the buffer virtual int_type underflow () { // is read position before end of buffer? if (gptr() < egptr()) { return traits_type::to_int_type(*gptr()); } /* process size of putback area * - use number of characters read * - but at most four */ int numPutback; numPutback = gptr() - eback(); if (numPutback > putBackSize) { numPutback = putBackSize; } /* copy up to four characters previously read into * the putback buffer (area of first four characters) */ std::memmove (buffer+(putBackSize-numPutback), gptr()-numPutback, numPutback); // read new characters int num; num = read (input_fd, buffer+putBackSize, bufferSize-putBackSize); if (num <= 0) { // ERROR or EOF return EOF; } // reset buffer pointers setg (buffer+(putBackSize-numPutback), // beginning of putback area buffer+putBackSize, // read position buffer+putBackSize+num); // end of buffer // return next character return traits_type::to_int_type(*gptr()); } }; /* * An output stream that uses the above inbuf * * Based on code example from page 673 (class fdostream) */ class josuttis_fdistream : public std::istream { private: josuttis_fd_inbuf buf ; public: josuttis_fdistream ( int fd ) : std::istream(0), buf(fd) { rdbuf(&buf) ; } }; #endif libgtextutils-0.7/src/gtextutils/natsort.h000066400000000000000000000056711226234411700211440ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #ifndef __NATURAL_SORT_STL_H__ #define __NATURAL_SORT_STL_H__ /* * natsort.h - * STL-compatible interface to Martin Pool's Natural-Order sorting routines. * * see http://sourcefrog.net/projects/natsort/ for more details * * Note 1: * There's a boost equivalent version of 'composable natural sort' * at http://www.boostcookbook.com/Recipe:/1235053 * But it requires the boost library (including the regex engine), * and I prefer not to use it for now. * * Note 2: * As of FSF GNU Coreutils version 7.1, the 'sort' progarm as a similar sorting order * called 'version' (with the -V command argument). * Coreutils's implementation is found in /src/filevercmp.{ch}. * The results are similar to Matrin Poo's NatSort, but not identical * if the sorted strings are more complex than . */ /* Usage: // sort an array in natural order vector v; v.push_back("chr20"); v.push_back("chr10"); v.push_back("chr5"); v.push_back("chr1"); v.push_back("chr2"); // "regular" sort sort(v.begin(), v.end() ); // order will be: // chr1 // chr10 // chr2 // chr20 // chr5 // "natural order" sort sort(v.begin(), v.end(), natural_sort_predicate() ); // order will be: // chr1 // chr2 // chr5 // chr10 // chr20 */ extern "C" { /* strnatcmp.{h,c} -- Perform 'natural order' comparisons of strings in C. Copyright (C) 2000, 2004 by Martin Pool */ #include "strnatcmp.h" } #include struct natural_sort_predicate : public std::binary_function { bool operator() ( const std::string& s1, const std::string& s2 ) { return strnatcmp(s1.c_str(), s2.c_str()) < 0 ; } }; struct natural_sort_ignore_case_predicate : public std::binary_function { bool operator() ( const std::string& s1, const std::string& s2 ) { return strnatcasecmp(s1.c_str(), s2.c_str()) < 0 ; } }; /* inline bool natural_sort_predicate(const std::string& s1, const std::string& s2) { return strnatcmp(s1.c_str(), s2.c_str()) < 0 ; } inline bool natural_sort_ignore_case_predicate(const std::string& s1, const std::string& s2) { return strnatcasecmp(s1.c_str(), s2.c_str()) < 0 ; }*/ #endif libgtextutils-0.7/src/gtextutils/outbuf3.hpp000066400000000000000000000075311226234411700213760ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #ifndef __JOSUTTIS_FD_OUTBUF_H__ #define __JOSUTTIS_FD_OUTBUF_H__ /* * The following code example is taken from the book * "The C++ Standard Library - A Tutorial and Reference" * by Nicolai M. Josuttis, Addison-Wesley, 1999 * * (C) Copyright Nicolai M. Josuttis 1999. * Permission to copy, use, modify, sell and distribute this software * is granted provided this copyright notice appears in all copies. * This software is provided "as is" without express or implied * warranty, and with no claim as to its suitability for any purpose. * * Added by A. Gordon: * The file is available as "io/outbuf3.hpp" in the examples tarball at * http://www.josuttis.com/libbook/ * * And in the book at Chapter 13, Page 673. * * Modifications: * 1. Larger buffer, with vector * 2. Accepts output file descriptor in c'tor */ #include #include #include // for write(): #ifdef _MSC_VER # include #else # include #endif class josuttis_fd_outbuf : public std::streambuf { protected: static const int bufferSize = 32768; // size of data buffer /* * Note: The vector is used simply because it will manage the memory * resource for us. The buffer is used as a regular C buffer. * see "Effective STL" By Scott Meyer, Page 77, * Item 17: "Know how to pass vector and string to legacy API" */ std::vector buffer_vector ; char* buffer ; int output_fd ; public: /* constructor * - initialize data buffer * - one character less to let the bufferSizeth character * cause a call of overflow() */ josuttis_fd_outbuf ( int _output_fd ) : buffer_vector(bufferSize), buffer ( &buffer_vector[0] ), output_fd ( _output_fd ) { setp (buffer, buffer+(bufferSize-1)); } /* destructor * - flush data buffer */ virtual ~josuttis_fd_outbuf () { sync(); } protected: // flush the characters in the buffer int flushBuffer () { int num = pptr()-pbase(); if (write (output_fd, buffer, num) != num) { return EOF; } pbump (-num); // reset put pointer accordingly return num; } /* buffer full * - write c and all previous characters */ virtual int_type overflow (int_type c) { if (c != EOF) { // insert character into the buffer *pptr() = c; pbump(1); } // flush the buffer if (flushBuffer() == EOF) { // ERROR return EOF; } return c; } /* synchronize data with file/destination * - flush the data in the buffer */ virtual int sync () { if (flushBuffer() == EOF) { // ERROR return -1; } return 0; } }; /* * An output stream that uses the above outbuf * * Based on code example from page 673 (class fdostream) */ class josuttis_fdostream : public std::ostream { private: josuttis_fd_outbuf buf ; public: josuttis_fdostream ( int fd ) : std::ostream(0), buf(fd) { rdbuf(&buf) ; } }; #endif libgtextutils-0.7/src/gtextutils/pipe_fitter.c000066400000000000000000000060521226234411700217510ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include #include #include #include "pipe_fitter.h" int pipe_close ( int fd, pid_t pid ) { int i, status ; pid_t p; int exit_code; i = close(fd); if ( i == -1 ) err(1,"close(in pipe_close) failed"); p = waitpid(pid, &status, 0); if (p==-1) err(1,"waitpid(in pipe_close) failed"); if (!WIFEXITED(status)) errx(1,"child process terminated abnormally (in pipe_close), status=%08x", status); exit_code = WEXITSTATUS(status); if (exit_code != 0) errx(1,"child process terminated with error code %d (in pipe_close)", exit_code); return 0; } static int pipe_open ( const char* executable, const char* filename, int pipe_input, pid_t* /*OUTPUT*/ child_pid ) { int file_fd=-1; pid_t pid; int parent_pipe[2]; //Create the pipe descriptoers if (pipe(parent_pipe)!=0) err(1,"pipe (for '%s') failed", executable); if (filename != NULL) { file_fd = open(filename, pipe_input?(O_RDONLY):(O_CREAT|O_WRONLY), 0666 ) ; //create the file descriptor (input or output, based on function argument) if ( file_fd == -1 ) err(1,"failed to %s file '%s'", pipe_input?"open":"create", filename ) ; } pid = fork(); if (pid == -1) err(1,"Fork failed for '%s'", executable); if (pid>0) { /* The parent process */ *child_pid = pid; close(file_fd); //the parent process doesn't need the file handle. close(parent_pipe[ pipe_input?1:0 ]); return (parent_pipe[ pipe_input?0:1 ]); } /* The child process */ if (pipe_input) { dup2(parent_pipe[1], STDOUT_FILENO); close(parent_pipe[0]); if (file_fd != -1) dup2(file_fd, STDIN_FILENO); } else { dup2(parent_pipe[0], STDIN_FILENO); close(parent_pipe[1]); if (file_fd!=-1) dup2(file_fd, STDOUT_FILENO); } execlp(executable,executable,(char*)NULL); //Should never get here... err(1,"execlp(%s) failed",executable); return 0; //just to please gcc } int pipe_output_command ( const char* command, const char* output_filename, pid_t* /*OUTPUT*/ child_pid ) { return pipe_open ( command, output_filename, 0, child_pid ) ; } int pipe_input_command ( const char* command, const char* input_filename, pid_t* /*OUTPUT*/ child_pid ) { return pipe_open ( command, input_filename, 1, child_pid ) ; } libgtextutils-0.7/src/gtextutils/pipe_fitter.h000066400000000000000000000022021226234411700217470ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #ifndef __PIPE_FITTER_H__ #define __PIPE_FITTER_H__ #ifdef __cplusplus extern "C" { #endif int pipe_output_command ( const char* command, const char* output_filename, pid_t* /*OUTPUT*/ child_pid ); int pipe_input_command ( const char* command, const char* input_filename, pid_t* /*OUTPUT*/ child_pid ); int pipe_close ( int fd, pid_t pid ) ; #ifdef __cplusplus } #endif #endif libgtextutils-0.7/src/gtextutils/stream_wrapper.cpp000066400000000000000000000031461226234411700230330ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include #include "stream_wrapper.h" InputStreamWrapper::InputStreamWrapper(const std::string & filename) : use_stdin(filename.length()==0) { if (!use_stdin) { input_file.open(filename.c_str()) ; if (!input_file) err(1,"Failed to open input file (%s)", filename.c_str()) ; } }; OutputStreamWrapper::OutputStreamWrapper(const std::string & filename, bool _compressed ) : use_stdout(filename.length()==0), compressed(_compressed) { if (compressed) { /* compressed output stream: fork and run GZIP */ } else { /* normal (not-compressed) output file: just open the file (if needed) */ if (!use_stdout) { output_file.open(filename.c_str()) ; if (!output_file) err(1,"Failed to create output file (%s)", filename.c_str()) ; } } }; libgtextutils-0.7/src/gtextutils/stream_wrapper.h000066400000000000000000000027131226234411700224770ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #ifndef __STREAM_WRAPPER__ #define __STREAM_WRAPPER__ #include #include #include class InputStreamWrapper { private: std::ifstream input_file ; bool use_stdin; public: InputStreamWrapper(const std::string & filename = "") ; std::istream& stream() { return (use_stdin)?std::cin:input_file; } ; operator std::istream&() { return stream() ; } }; class OutputStreamWrapper { private: std::ofstream output_file ; bool use_stdout; bool compressed ; public: OutputStreamWrapper(const std::string & filename = "", bool _compressed = false) ; std::ostream& stream() { return (use_stdout)?std::cout:output_file; } ; operator std::ostream&() { return stream() ; } }; #endif libgtextutils-0.7/src/gtextutils/string_tokenize.h000066400000000000000000000037131226234411700226630ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #ifndef __STRING_TOKENIZE_H__ #define __STRING_TOKENIZE_H__ #include #include /* Splits a string into tokens, based on delimiter Heavily based on code from: C++ Programming HOW-TO Al Dev (Alavoor Vasudevan) alavoor[AT]yahoo.com http://oopweb.com/CPP/Documents/CPPHOWTO/Volume/C++Programming-HOWTO-7.html (Distributed under GPL) Usage Example: string input = "Hello|Token|World"; vector tokens; String_Tokenize ( input, back_inserter(tokens), "|" ); */ template void String_Tokenize(const std::string& str, OutputIterator output_iter, const std::string& delimiters = " ") { // Skip delimiters at beginning. std::string::size_type lastPos = str.find_first_not_of(delimiters, 0); // Find first "non-delimiter". std::string::size_type pos = str.find_first_of(delimiters, lastPos); while (std::string::npos != pos || std::string::npos != lastPos) { *output_iter = str.substr(lastPos, pos - lastPos); ++output_iter; // Skip delimiters. Note the "not_of" lastPos = str.find_first_not_of(delimiters, pos); // Find next "non-delimiter" pos = str.find_first_of(delimiters, lastPos); } } #endif libgtextutils-0.7/src/gtextutils/strnatcmp.c000066400000000000000000000102771226234411700214560ustar00rootroot00000000000000/* -*- mode: c; c-file-style: "k&r" -*- strnatcmp.c -- Perform 'natural order' comparisons of strings in C. Copyright (C) 2000, 2004 by Martin Pool This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. */ /* partial change history: * * 2004-10-10 mbp: Lift out character type dependencies into macros. * * Eric Sosman pointed out that ctype functions take a parameter whose * value must be that of an unsigned int, even on platforms that have * negative chars in their default char type. */ #include #include #include #include #include "strnatcmp.h" /* These are defined as macros to make it easier to adapt this code to * different characters types or comparison functions. */ static inline int nat_isdigit(nat_char a) { return isdigit((unsigned char) a); } static inline int nat_isspace(nat_char a) { return isspace((unsigned char) a); } static inline nat_char nat_toupper(nat_char a) { return toupper((unsigned char) a); } static int compare_right(nat_char const *a, nat_char const *b) { int bias = 0; /* The longest run of digits wins. That aside, the greatest value wins, but we can't know that it will until we've scanned both numbers to know that they have the same magnitude, so we remember it in BIAS. */ for (;; a++, b++) { if (!nat_isdigit(*a) && !nat_isdigit(*b)) return bias; else if (!nat_isdigit(*a)) return -1; else if (!nat_isdigit(*b)) return +1; else if (*a < *b) { if (!bias) bias = -1; } else if (*a > *b) { if (!bias) bias = +1; } else if (!*a && !*b) return bias; } return 0; } static int compare_left(nat_char const *a, nat_char const *b) { /* Compare two left-aligned numbers: the first to have a different value wins. */ for (;; a++, b++) { if (!nat_isdigit(*a) && !nat_isdigit(*b)) return 0; else if (!nat_isdigit(*a)) return -1; else if (!nat_isdigit(*b)) return +1; else if (*a < *b) return -1; else if (*a > *b) return +1; } return 0; } static int strnatcmp0(nat_char const *a, nat_char const *b, int fold_case) { int ai, bi; nat_char ca, cb; int fractional, result; assert(a && b); ai = bi = 0; while (1) { ca = a[ai]; cb = b[bi]; /* skip over leading spaces or zeros */ while (nat_isspace(ca)) ca = a[++ai]; while (nat_isspace(cb)) cb = b[++bi]; /* process run of digits */ if (nat_isdigit(ca) && nat_isdigit(cb)) { fractional = (ca == '0' || cb == '0'); if (fractional) { if ((result = compare_left(a+ai, b+bi)) != 0) return result; } else { if ((result = compare_right(a+ai, b+bi)) != 0) return result; } } if (!ca && !cb) { /* The strings compare the same. Perhaps the caller will want to call strcmp to break the tie. */ return 0; } if (fold_case) { ca = nat_toupper(ca); cb = nat_toupper(cb); } if (ca < cb) return -1; else if (ca > cb) return +1; ++ai; ++bi; } } int strnatcmp(nat_char const *a, nat_char const *b) { return strnatcmp0(a, b, 0); } /* Compare, recognizing numeric string and ignoring case. */ int strnatcasecmp(nat_char const *a, nat_char const *b) { return strnatcmp0(a, b, 1); } libgtextutils-0.7/src/gtextutils/strnatcmp.h000066400000000000000000000024071226234411700214570ustar00rootroot00000000000000/* -*- mode: c; c-file-style: "k&r" -*- strnatcmp.c -- Perform 'natural order' comparisons of strings in C. Copyright (C) 2000, 2004 by Martin Pool This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. */ /* CUSTOMIZATION SECTION * * You can change this typedef, but must then also change the inline * functions in strnatcmp.c */ typedef char nat_char; int strnatcmp(nat_char const *a, nat_char const *b); int strnatcasecmp(nat_char const *a, nat_char const *b); libgtextutils-0.7/src/gtextutils/text_line_reader.cpp000066400000000000000000000025411226234411700233130ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include "text_line_reader.h" using namespace std; TextLineReader::TextLineReader(istream& _input_stream) : input_stream(_input_stream), current_line_number(0), unget_line_active(false) { } bool TextLineReader::next_line() { if (unget_line_active) { unget_line_active = false; } else { current_line_number++; getline(input_stream, current_line_string ) ; } current_line_stream.str( current_line_string ) ; current_line_stream.seekg(0, ios_base::beg ); current_line_stream.clear(); if (input_stream.eof()) return false; return input_stream ; } libgtextutils-0.7/src/gtextutils/text_line_reader.h000066400000000000000000000035071226234411700227630ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #ifndef __TEXT_FILE_READER__ #define __TEXT_FILE_READER__ #include #include #include class TextLineReader { private: std::istream& input_stream ; size_t current_line_number; std::string current_line_string ; std::istringstream current_line_stream ; bool unget_line_active ; TextLineReader(const TextLineReader&); TextLineReader& operator=(const TextLineReader&); public: TextLineReader(std::istream& _input_stream) ; size_t line_number() const { return current_line_number ; } bool next_line() ; void unget_line ( const std::string& line ) { unget_line_active = true ; current_line_string = line ; } void unget_current_line () { unget_line_active = true; } //explicit conversions const std::string& line_string() const { return current_line_string; } std::istringstream& line_stream() { return current_line_stream; } //implicit conversions operator const std::string& () const { return line_string() ; } operator std::string() const { return line_string(); } operator std::istream& () { return line_stream(); } }; #endif libgtextutils-0.7/src/gtextutils/tuple_parser.h000066400000000000000000000254511226234411700221550ustar00rootroot00000000000000#ifndef __TUPLE_PARSER_H__ #define __TUPLE_PARSER_H__ #include #include #include #include #include //This #pramga allows variadic templates //in a header file (imitating tr1/tuple) #pragma GCC system_header //#define TUPLE_PARSER_DEBUG /* The maximun valid number for a column. The value is used in a bitset to prevent duplicated columns. */ #ifndef TUPLE_PARSER_MAX_COLUMN_NUMBER #define TUPLE_PARSER_MAX_COLUMN_NUMBER (128) #endif /* Premature-end-of-line exception. Specialized exception class, which can report back the number of actual columns and expected columns. The what() still produces a user-friendly string, so if the exception is not caught, the report will still make some sense. */ class tuple_parser_premature_end_of_line : public std::runtime_error { private: std::string _what; size_t _expected_columns ; size_t _actual_columns; public: tuple_parser_premature_end_of_line(size_t expected_columns, size_t actual_columns) : std::runtime_error(""), _expected_columns(expected_columns), _actual_columns(actual_columns) { std::ostringstream os; os << "Error: premature end-of-line, expecting at least " << expected_columns << " columns, got only " << actual_columns << " columns" ; _what = os.str(); } size_t expected_columns() const { return _expected_columns ; } size_t actual_columns() const { return _actual_columns; } virtual const char* what() const throw() { return _what.c_str(); } virtual ~tuple_parser_premature_end_of_line() throw() { } }; /* Parse Error exception. Specialized exception class, which can report back the number of the failed column. The what() still produces a user-friendly string, so if the exception is not caught, the report will still make some sense. */ class tuple_parser_parsing_error: public std::runtime_error { private: std::string _what; size_t _column ; public: tuple_parser_parsing_error(size_t column) : std::runtime_error(""), _column(column) { std::ostringstream os; os << "Error: invalid input in column " << column ; _what = os.str(); } size_t column() const throw() { return _column; } virtual const char* what() const throw() { return _what.c_str(); } virtual ~tuple_parser_parsing_error() throw() { } }; /* Tiny hack to convert every type into a size_t. Used in the constructor of _Tuple_Parser_impl, so that for all lists of template types, the constructor will accept list of size_t as arguments. Usage Example: template class MyClass { public: //This 'regular' constructor accepts variables with the same //Type of the template arguments. MyClass ( _Elements... vars ) ; //This constructor accepts variables of type size_t, //regardless of the actual type of the //template arguments. MyClass ( typename __column_index<_Elements>::type... vars ) ; }; The outcome: A class with the following four template arguments: MyClass will have a constructor accepting four 'size_t' arguments: MyClass::MyClass(size_t, size_t, size_t, size_t) Modeled after tr1/tuple's __add_c_ref helper structs. */ template struct __column_index { typedef size_t type; }; /* Tuple-Parser starts here. */ template class _Tuple_Parser_impl; /* Zero-element tuple implementation. This is the basis case for the inheritance recursion. used_column_bitset is used (during runtime) do make sure there are no duplicates in column numbers. max_column_number is used (during runtime) do deduce the maximum required column number. Since column assignment is done in runtime (not during compile-time), this can not be inlined or meta-programmed. Inherited sub-classes should call 'update_used_column()' in their constructor to add a new column number. */ template class _Tuple_Parser_impl<_Idx> { private: size_t max_column_number ; std::bitset used_column_bitset; public: _Tuple_Parser_impl() : max_column_number(0) { #ifdef TUPLE_PARSER_DEBUG std::cerr << "At base, _Idx = " << _Idx << std::endl; #endif } void update_max_column_number(size_t num) { max_column_number = std::max(max_column_number,num); } void update_used_column ( size_t column ) { if ( column >= TUPLE_PARSER_MAX_COLUMN_NUMBER ) { std::ostringstream os; os << "Internal error: Invalid column number (" << column << "). maximum allowed value is " << TUPLE_PARSER_MAX_COLUMN_NUMBER << ". To change this value, re-define TUPLE_PARSER_MAX_COLUMN_NUMBER in " \ __FILE__ " and re-compile the program. "; throw std::length_error ( os.str() ) ; } if ( used_column_bitset.test ( column ) ) { std::ostringstream os; os << "Error: column number " << column << " is used more than once." ; throw std::invalid_argument( os.str() ) ; } used_column_bitset.set(column); update_max_column_number(column) ; } size_t max_column() const { return max_column_number ; } #ifdef TUPLE_PARSER_DEBUG void print() const {} #endif bool consume_input ( size_t , std::istream& ) { return false; } }; /* The heart of the Tuple Parser recursive implementation. Modeled after GCC-4.3.2's . At compile time, the types of the fields is recursively set (just like in a tuple). At run time, the constructor accepts the column number for each field, and the 'read_from_stream()' method extract the fields from the given input stream (according to the column numbers). Users should use a Tuple_Parser<> instead of _Tuple_Parser_impl<>. Usage exmaple: //Define a parser that extracts three fields from an input stream: //an int, a string and a double. typedef Tuple_Parser MyParser ; //Create a parser object, that will expect //the int field to be on the 8th column, //the string field to be the 4th column, //and the double field to be on the 2nd column. //the other columns will be skipped and ignored. MyParser p(8,4,2); //Extract the columns from the input stream. istringstream is ( "DUMMY1 3.14 DUMMY3 HELLO DUMMY5 DUMMY6 DUMMY7 42 DUMMY9" ) ; is >> p ; //Get the extracted values. int a = get<0>(p); string s = get<1>(p); double d = get<2>(p); */ template struct _Tuple_Parser_impl<_Idx, _Head, _Tail...> : public _Tuple_Parser_impl<_Idx + 1, _Tail...> { typedef _Tuple_Parser_impl<_Idx + 1, _Tail...> _Inherited; typedef _Head _M_head_type; _M_head_type _M_head ; size_t _M_head_column ; _Inherited& _M_tail() { return *this; } const _Inherited& _M_tail() const { return *this; } _Tuple_Parser_impl() : _Inherited(), _M_head_column(_Idx+1),_M_head() { } _Tuple_Parser_impl( size_t _head_column, typename __column_index<_Tail>::type... __tail) : _Inherited(__tail...), _M_head_column(_head_column) { update_used_column ( _M_head_column ) ; #ifdef TUPLE_PARSER_DEBUG std::cerr << "At Ctor, _Idx = " << _Idx << " Max-Column-Number = " << _M_tail().max_column() << std::endl; #endif } #ifdef TUPLE_PARSER_DEBUG void print() const { std::cout << "_Idx=" << _Idx << " " << "typeid(head)=" << typeid(_M_head).name() << " column = " << _M_head_column << " value = " << _M_head << std::endl ; _M_tail().print() ; } #endif void read_from_stream(std::istream& strm) { size_t current_column = 0 ; while ( strm && !strm.eof() ) { current_column++; if ( ! consume_input ( current_column, strm ) ) { //consume input with dummy variable std::string dummy ; strm >> dummy ; #ifdef TUPLE_PARSER_DEBUG std::cout << "skipping column " << current_column << std::endl; #endif } } if (current_column<_M_tail().max_column()) { throw tuple_parser_premature_end_of_line ( _M_tail().max_column(), current_column ) ; } } bool consume_input ( size_t column_number, std::istream& strm ) { if ( column_number == _M_head_column ) { #ifdef TUPLE_PARSER_DEBUG std::cout << "consuming column " << column_number << ", _Idx = " << _Idx << std::endl; #endif strm >> _M_head; if (!strm) throw tuple_parser_parsing_error(column_number); return true; } return _M_tail().consume_input ( column_number, strm ) ; } void update_used_column (size_t num) { _M_tail().update_used_column(num); } size_t max_column() const { return _M_tail().max_column() ; } }; /* Tuple_Parser - The user-friendly version of _Tuple_Parser_impl. See comments of _Tuple_Parser_impl for details. */ template struct Tuple_Parser : public _Tuple_Parser_impl<0,_Elements...> { Tuple_Parser ( typename __column_index<_Elements>::type... _UElements) : _Tuple_Parser_impl<0, _Elements...>(_UElements...) { } }; /* Template to get the type of the Nth element in a tuple parser. copied from 'tr1/tuple', based on tuple_element<> template. Usage Example: typedef Tuple_Parser MyParser ; // 'MyVariable' will have type std::string, // which is the third (index=2) element in MyParser ) tuple_parser_element<2, MyParser>::type MyVariable ; */ /// Gives the type of the ith element of a given tuple type. template struct tuple_parser_element; /** * Recursive case for tuple_element: strip off the first element in * the tuple and retrieve the (i-1)th element of the remaining tuple. */ template struct tuple_parser_element<__i, Tuple_Parser<_Head, _Tail...> > : tuple_parser_element<__i - 1, Tuple_Parser<_Tail...> > { }; /** * Basis case for tuple_element: The first element is the one we're seeking. */ template struct tuple_parser_element<0, Tuple_Parser<_Head, _Tail...> > { typedef _Head type; }; /* Get the value of the Nth element in a Tuple_Parser. Copied almost verbatim from . See comments of _Tuple_Parser_impl for usage example. */ // Adds a const reference to a non-reference type. template inline typename std::tr1::__add_c_ref<_Head>::type __get_helper(const _Tuple_Parser_impl<__i, _Head, _Tail...>& __t) { return __t._M_head; } template inline typename std::tr1::__add_c_ref< typename tuple_parser_element<__i, Tuple_Parser<_Elements...> >::type >::type get(const Tuple_Parser<_Elements...>& __t) { return __get_helper<__i>(__t); } /* Input Stream operator for Tuple_Parser See comments of _Tuple_Parser_impl for usage example. */ template std::istream& operator>> ( std::istream& strm, _Tuple_Parser_impl<0, _Elements... > &parser ) { parser.read_from_stream(strm); return strm; } #endif libgtextutils-0.7/tests/000077500000000000000000000000001226234411700154275ustar00rootroot00000000000000libgtextutils-0.7/tests/Makefile.am000066400000000000000000000035751226234411700174750ustar00rootroot00000000000000# Copyright (C) 2008-2013 Assaf Gordon # # This file is free software; as a special exception the author gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY, to the extent permitted by law; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. if TUPLE_PARSER_CHECK TUPLE_PROG = test_tuple_parser \ test_tuple_parser_file else TUPLE_PROG = endif AM_TESTS_ENVIRONMENT=\ printf "first line\nsecond line\nthird line\nfourth line\n" > test.txt; check_PROGRAMS = test_container_join \ test_natural_sort \ test_input_stream_wrapper \ test_text_reader \ test_text_reader_unget \ test_fd_outbuf \ test_fd_inbuf \ test_in_out_buf \ test_pipe_fitter \ test_string_tokenize \ $(TUPLE_PROG) TESTS = $(check_PROGRAMS) LDADD = $(top_builddir)/src/gtextutils/libgtextutils.la AM_CPPFLAGS = -I$(top_srcdir)/src test_container_join_SOURCES = test_container_join.cpp tests_assertion.h test_natural_sort_SOURCES = test_natural_sort.cpp tests_assertion.h test_input_stream_wrapper_SOURCES = test_input_stream_wrapper.cpp tests_assertion.h test_text_reader_SOURCES = test_text_reader.cpp tests_assertion.h test_text_reader_unget_SOURCES = test_text_reader_unget.cpp tests_assertion.h test_fd_outbuf_SOURCES = test_fd_outbuf.cpp tests_assertion.h test_fd_inbuf_SOURCES = test_fd_inbuf.cpp tests_assertion.h test_in_out_buf_SOURCES = test_in_out_buf.cpp tests_assertion.h test_pipe_fitter_SOURCES = test_pipe_fitter.c tests_assertion.h test_tuple_parser_SOURCES = test_tuple_parser.cpp tests_assertion.h test_tuple_parser_file_SOURCES = test_tuple_parser_file.cpp tests_assertion.h test_string_tokenize_SOURCES = test_string_tokenize.cpp tests_assertion.h libgtextutils-0.7/tests/test_container_join.cpp000066400000000000000000000042511226234411700221750ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include /* * Tiny test suite for container-join templates */ using namespace std; int main() { vector v; for (int i=0;i<10;++i) v.push_back(i); // Print the entire container: cout << join(v,",") << endl; // Will output: 0,1,2,3,4,5,6,7,8,9 // Print specific range, using begin/end iterators cout << join(v.begin(), v.end(),"-") << endl; // Will output: 0-1-2-3-4-5-6-7-8-9 // An std::pair<> based container // map/set/multimap/multiset/unorederd_map etc. // or // vector< pair > etc. map m; m[42] = "Don't Panic"; m[666]= "Beast" ; // Print the first values (of the pair) of the entire container: cout << "keys = " << join_firsts(m) << endl; // Will output: 42 666 // Print the first values (of the pair) of a specific range: cout << "keys = " << join_firsts(m.begin(), m.end(), ",") << endl; // Will output: 42,666 // Print the second values (of the pair) of the entire container: cout << "values= " << join_seconds(m) << endl; // Will output: Don't PanicBeast // Print the second values (of the pair) of a specific range: cout << "values= " << join_seconds(m.begin(), m.end(), ",") << endl; // Will output: Don't Panic,Beast // Store result in a string (instead of an output stream): string s = join_firsts(m); // 's' will contain: "42\t666"; return 0; } libgtextutils-0.7/tests/test_fd_inbuf.cpp000066400000000000000000000033301226234411700207450ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include #include #include #include #include #include #include #include #include "tests_assertion.h" /* * Test for File-Descriptor-based input buffer. */ using namespace std; const char* filename = "test.txt" ; int main() { //Open a file using C API int fd = open(filename, O_RDONLY); if (fd == -1) perror ("Failed to open test file 'test.txt'"); //Connect the file-descriptor to an input stream josuttis_fdistream in1(fd); string s; //Read and verify the file content in1 >> s ; ASSERT ( s == "first" ) ; in1 >> s ; ASSERT ( s == "line" ) ; in1 >> s ; ASSERT ( s == "second" ) ; in1 >> s ; ASSERT ( s == "line" ) ; in1 >> s ; ASSERT ( s == "third" ) ; in1 >> s ; ASSERT ( s == "line" ) ; in1 >> s ; ASSERT ( s == "fourth" ) ; in1 >> s ; ASSERT ( s == "line" ) ; close(fd); } libgtextutils-0.7/tests/test_fd_outbuf.cpp000066400000000000000000000041201226234411700211440ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include #include #include #include #include #include #include #include #include "tests_assertion.h" /* * Test for File-Descriptor-based output buffer. */ using namespace std; const char* filename = "fdout.tmp" ; void create_file() { //Create a File (using C API), //then connect an output stream to it int fd = open("fdout.tmp", O_CREAT | O_WRONLY | O_TRUNC, S_IRUSR|S_IWUSR ) ; if ( fd == -1 ) perror("Failed to create file 'fdout.tmp'"); josuttis_fdostream out2(fd); out2 << "first line" << endl ; out2 << "second line" << endl ; out2 << "third line" << endl; close(fd); } void verify_file() { //To verify - use only STL classes, //no home made libgtextutils classes. ifstream ifs(filename); string s; ifs >> s ; ASSERT ( s == "first" ) ; ifs >> s ; ASSERT ( s == "line" ) ; ifs >> s ; ASSERT ( s == "second" ) ; ifs >> s ; ASSERT ( s == "line" ) ; ifs >> s ; ASSERT ( s == "third" ) ; ifs >> s ; ASSERT ( s == "line" ) ; } int main() { //Use file-descriptor 1 = STDOUT josuttis_fdostream out1(1); out1 << "Hello World from File-Descriptor Output Stream (josuttifs_fdostream)!" << endl; create_file(); verify_file(); unlink(filename); } libgtextutils-0.7/tests/test_in_out_buf.cpp000066400000000000000000000044001226234411700213210ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include "tests_assertion.h" /* * Test for File-Descriptor-based input and output buffers, through a system pipe. */ using namespace std; int fork_pipe_command ( const char* program, const char* output_filename) { int fd; pid_t child_pid; int parent_pipe[2]; if (pipe(parent_pipe)!=0) err(1,"pipe (for gzip) failed"); child_pid = fork(); if (child_pid>0) { /* The parent process */ fd = parent_pipe[1]; close(parent_pipe[0]); return fd; } /* The child process */ //the compressor's STDIN is the pipe from the parent dup2(parent_pipe[0], STDIN_FILENO); close(parent_pipe[1]); //the compressor's STDOUT is the output file //(which can be the parent's STDOUT, too) fd = open(output_filename, O_WRONLY | O_CREAT, 0666 ); if (fd==-1) err(1,"Failed to open output '%s'", output_filename); dup2(fd, STDOUT_FILENO); //Run GZIP execlp(program,program,"-f",NULL); //Should never get here... err(1,"execlp(%s) failed",program); } void test_compress_output() { int pipe_out_fd = fork_pipe_command ( "gzip", "fdout.txt.gz" ) ; josuttis_fdostream out(pipe_out_fd); out << "first line" << endl; out << "second line" << endl; out << "third line" << endl; close(pipe_out_fd); } int main() { test_compress_output(); } libgtextutils-0.7/tests/test_input_stream_wrapper.cpp000066400000000000000000000025161226234411700234500ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include "tests_assertion.h" /* * Simple unit test - InputStreamWrapper * * Read the first word out of a test file (whose content we know), */ using namespace std; int main() { //The object will create a 'ifstream' file with this file, //or exit if there was an error InputStreamWrapper input("test.txt"); // InputStreamWrapper can be used as 'istream&' // with it's conversion operator istream& is ( input ) ; std::string s; is >> s ; ASSERT ( s == "first" ) ; return 0; } libgtextutils-0.7/tests/test_natural_sort.cpp000066400000000000000000000030041226234411700217040ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include /* * Tiny test suite for natural sort */ using namespace std; int main() { vector v; v.push_back("chr4"); v.push_back("chr2"); v.push_back("chr10"); v.push_back("chr11"); v.push_back("chr1"); v.push_back("chrX"); v.push_back("chr20"); v.push_back("ChR13"); sort(v.begin(), v.end()); cout << "Regular sort: " << join(v) << endl; sort(v.begin(), v.end(), natural_sort_predicate() ); cout << "Natural sort (case sensitive): " << join(v) << endl; sort(v.begin(), v.end(), natural_sort_ignore_case_predicate() ); cout << "Natural sort (case-insensitive): " << join(v) << endl; return 0; } libgtextutils-0.7/tests/test_pipe_fitter.c000066400000000000000000000037021226234411700211460ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include #include #include #include #include #include #include "tests_assertion.h" const char* text = "Hello World\n"; int main() { int fd; int pid; char temp[1000]; char str[1000]; int n ; int i ; //Pipe output through a GZIP program fd = pipe_output_command ( "gzip", "pipe_out.txt.gz", &pid ) ; i = write ( fd, text, strlen(text)) ; if ( i == -1 ) err(1,"write failed"); pipe_close(fd, pid); //Read input through a GUNZIP program fd = pipe_input_command ( "gunzip", "pipe_out.txt.gz", &pid ); //Read entire input from the pipe. //Note: // 'read' doesn't have to return the entire input in one read - so // we loop until the end of the file and concatnate the input. strcat(str,""); while (1) { n = read ( fd, temp, sizeof(temp)-1) ; if (n==-1) err(1,"Read from GZIP input pipe failed"); if (n==0) break; //End-Of-File //Ensure proper NULL termination temp[n] = 0 ; strncpy ( str, temp, sizeof(str)-1); } pipe_close(fd,pid); //Validate the input ASSERT ( strcmp(str, text)==0 ) ; return 0 ; } libgtextutils-0.7/tests/test_string_tokenize.cpp000066400000000000000000000031211226234411700224050ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include #include #include "tests_assertion.h" #include /* * Tiny test suite for string tokenize */ using namespace std; //Test tokenize by single delimiter character void test_token1() { string test1 = "Hello|Token|World"; vector v; String_Tokenize ( test1, back_inserter(v), "|" ) ; ASSERT ( v[0] == "Hello" ) ; ASSERT ( v[1] == "Token" ) ; ASSERT ( v[2] == "World" ) ; } //Test tokenize by multiple delimiters void test_token2() { string test1 = "Hello Token|World"; vector v; String_Tokenize ( test1, back_inserter(v), "| " ) ; ASSERT ( v[0] == "Hello" ) ; ASSERT ( v[1] == "Token" ) ; ASSERT ( v[2] == "World" ) ; } int main() { test_token1(); test_token2(); return 0; } libgtextutils-0.7/tests/test_text_reader.cpp000066400000000000000000000044541226234411700215070ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include #include "tests_assertion.h" /* * Testing the TextLineReader class * * Read four lines from a known file, * using different methods */ using namespace std; int main() { InputStreamWrapper input("test.txt"); TextLineReader reader ( input.stream() ); string line ; ASSERT ( reader.next_line() ); line = reader.line_string() ; //first line - with explicit method to get the string ASSERT( line == "first line" ) ; ASSERT ( reader.next_line() ); line = reader ; //second line - with implicit conversion to std::string ASSERT( line == "second line" ) ; ASSERT ( reader.next_line() ); istream &is1 ( reader.line_stream() ); //third line - with explicit method to get the istream is1 >> line ; // read each word from the line ASSERT( line == "third" ) ; is1 >> line ; ASSERT ( line == "line" ) ; is1 >> line ; // read past the end of the line - this should fail (and not read the next word from the next line, as it would have happened with a normal istream; ASSERT ( ! is1 ) ; ASSERT ( reader.next_line() ); istream &is2 ( reader ) ; // fourth line - with implicit conversion to std::istream is2 >> line ; ASSERT( line == "fourth" ) ; is2 >> line ; ASSERT( line == "line" ) ; is1 >> line ; // read past the end of the line - this should fail (and not read the next word from the next line ASSERT ( !is2 ) ; //read past the end of the file - make sure it fails. ASSERT ( !reader.next_line() ) ; return 0; } libgtextutils-0.7/tests/test_text_reader_unget.cpp000066400000000000000000000046661226234411700227160ustar00rootroot00000000000000/* Gordon's Text-Utilities Library Copyright (C) 2009-2013 Assaf Gordon (assafgordon@gmail.com) This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. You should have received a copy of the GNU Affero General Public License along with this program. If not, see */ #include #include #include #include #include #include "tests_assertion.h" using namespace std; int main() { InputStreamWrapper input("test.txt"); TextLineReader reader ( input.stream() ); string line ; //Read first line ASSERT ( reader.next_line() ); line = reader; ASSERT( line == "first line" ) ; //Unget the current line - //The next call to 'reader.next_line' should return this SAME line //instead of actually reading the next line from the file. reader.unget_current_line(); //Read the next line - //but because of the 'unget' it should still return the first line ASSERT ( reader.next_line() ) ; line = reader ; ASSERT( line == "first line" ) ; ASSERT ( reader.line_number() == 1 ) ; //we should still be on line 1 //Read the next line - //This should be the real second line from the file. ASSERT ( reader.next_line() ) ; line = reader; ASSERT ( line == "second line" ); ASSERT ( reader.line_number() == 2 ) ; //Test multiple consecutive ungets for ( int i=0 ; i < 10; ++i ) { reader.unget_current_line(); ASSERT ( reader.next_line() ) ; line = reader; ASSERT ( line == "second line" ); ASSERT ( reader.line_number() == 2 ) ; } //Read the next line - //This should be the real third line from the file. ASSERT ( reader.next_line() ) ; line = reader; ASSERT ( line == "third line" ); ASSERT ( reader.line_number() == 3 ) ; //Unget a custom line string reader.unget_line("hello world"); //Read the next line - this should return the ungot text ("hello world") ASSERT ( reader.next_line() ) ; line = reader; ASSERT ( line == "hello world" ); return 0; } libgtextutils-0.7/tests/test_tuple_parser.cpp000066400000000000000000000064071226234411700217060ustar00rootroot00000000000000#include #include #include #include #include #include #include #include #include #include "gtextutils/tuple_parser.h" #include "tests_assertion.h" using namespace std; using namespace std::tr1; // Helper function to safely compare doubles bool doubles_are_equal ( double a, double b ) { return std::abs(a-b) <= numeric_limits::epsilon() ; } /* Test most basic TupleParser usage. Parser expects three values: int, string, double. The int is expected to be on column 4. The string is expected on column 3, The double is expected on column 1. After parsing, validate extracted values. */ void test_parser1() { Tuple_Parser parser(4,3,1); istringstream is ( "3.14 DUMMY HELLOWORLD 42" ) ; is >> parser ; int a = get<0>(parser); ASSERT ( a == 42 ) ; std::string b = get<1>(parser); ASSERT ( b == "HELLOWORLD" ) ; double c = get<2>(parser); ASSERT ( doubles_are_equal (c, 3.14) ) ; } /* Test column collusion detection. Parser expects three values: int, string, double. Two fields use the same column number. An exception should be thrown. */ void test_parser_column_collusion() { try { Tuple_Parser parser(1,3,1); //We should not get here ASSERT ( ! "Column collusion (1) not detected." ) ; } catch ( std::invalid_argument &ex ) { //fine, exception was thrown. we can continue } } /* Test max. column number overflow */ void test_parser_column_number_overflow() { try { Tuple_Parser parser(1,20000,1); //We should not get here ASSERT ( ! "Max. Column number overflow not detected." ) ; } catch ( std::length_error &ex ) { //fine, exception was thrown. we can continue } } /* Test parsing error Parser expects three values: int, string, double. The int is expected to be on column 4. The string is expected on column 3, The double is expected on column 1. The 4th column doesn't contain a valid integer, and should fail. */ void test_parser_parsing_error() { Tuple_Parser parser(4,3,1); istringstream is ( "3.14 DUMMY HELLOWORLD i42" ) ; try { is >> parser ; //We should not get here ASSERT ( ! "Invalid input not detected." ) ; } catch ( tuple_parser_parsing_error &ex ) { //exception was thrown. valid reported errornous columns ASSERT ( ex.column() == 4 ) ; } } /* Test premature-end-of-line Parser expects three values: int, string, double. The int is expected to be on column 4. The string is expected on column 3, The double is expected on column 1. The input contains only 2 columns (instead of expected 4) */ void test_parser_premature_eol() { Tuple_Parser parser(4,3,1); istringstream is ( "3.14 DUMMY" ) ; try { is >> parser ; //We should not get here ASSERT ( ! "premature-end-of-line not detected." ) ; } catch ( tuple_parser_premature_end_of_line &ex ) { //exception was thrown. valid reported errornous columns ASSERT ( ex.expected_columns() == 4 ) ; ASSERT ( ex.actual_columns() == 2 ) ; } } int main() { test_parser1(); test_parser_column_collusion(); test_parser_column_number_overflow(); test_parser_parsing_error(); test_parser_premature_eol(); return 0; } libgtextutils-0.7/tests/test_tuple_parser_file.cpp000066400000000000000000000036221226234411700227010ustar00rootroot00000000000000#include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "tests_assertion.h" using namespace std; using namespace std::tr1; std::string input_filename = "test.bed"; size_t chrom_column = 1 ; size_t start_column = 2 ; size_t end_column = 3 ; bool verbose = false ; void read_and_parse_file() { InputStreamWrapper input(input_filename); TextLineReader reader ( input.stream() ); Tuple_Parser parser( chrom_column, start_column, end_column); while ( reader.next_line() ) { reader.line_stream() >> parser ; } } void usage() { exit(0); } void parse_command_line(int argc, char* argv[]) { int opt; while ((opt=getopt(argc, argv,"hi:c:s:ev")) != -1) { switch(opt) { case 'h': usage(); case 'i': input_filename = optarg ; break; case 'c': if ( sscanf(optarg, "%zu", &chrom_column ) != 1 ) errx(1,"Error: invalid chromosome column (%s)", optarg ) ; if ( chrom_column <= 0 ) errx(1,"Error: invalid chromosome column (%s)", optarg ) ; break; case 's': if ( sscanf(optarg, "%zu", &start_column ) != 1 ) errx(1,"Error: invalid start column (%s)", optarg ) ; if ( start_column <= 0 ) errx(1,"Error: invalid start column (%s)", optarg ) ; break; case 'e': if ( sscanf(optarg, "%zu", &end_column ) != 1 ) errx(1,"Error: invalid end column (%s)", optarg ) ; if ( end_column <= 0 ) errx(1,"Error: invalid end column (%s)", optarg ) ; break; case 'v': verbose=true; break ; default: exit(1); } } } int main(int argc, char* argv[]) { parse_command_line(argc, argv) ; read_and_parse_file(); return 0; } libgtextutils-0.7/tests/tests_assertion.h000066400000000000000000000003311226234411700210260ustar00rootroot00000000000000#ifndef __UNIT_TESTS_ASSERTION_H__ #define __UNIT_TESTS_ASSERTION_H__ #define ASSERT(x) \ do { \ if (!(x)) { \ errx(1,"ASSERTION FAILED (%s:%d): "#x, \ __FILE__, __LINE__ ) ; \ } \ } while (0) #endif