debian/0000755000000000000000000000000012233514132007162 5ustar debian/control0000644000000000000000000000314312233514132010566 0ustar Source: loki Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Carleos Artime Section: science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/loki/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/loki/trunk/ Package: loki Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: loki-doc Description: MCMC linkage analysis on general pedigrees Performs Markov chain Monte Carlo multipoint linkage analysis on large, complex pedigrees. The current package supports analyses on quantitative traits only, although this restriction will be lifted in later versions. Joint estimation of QTL number, position and effects uses Reversible Jump MCMC. It is also possible to perform affected only IBD sharing analyses. Package: loki-doc Architecture: all Section: doc Depends: ${misc:Depends} Enhances: loki Description: MCMC linkage analysis on general pedigrees (PS manual) Performs Markov chain Monte Carlo multipoint linkage analysis on large, complex pedigrees. The current package supports analyses on quantitative traits only, although this restriction will be lifted in later versions. Joint estimation of QTL number, position and effects uses Reversible Jump MCMC. It is also possible to perform affected only IBD sharing analyses. . Documentation on how to use Simon Heath's "prep" and "loki" tools for MCMC genetic linkage and IBD analysis on general pedigrees. debian/loki.10000644000000000000000000000357411110210273010203 0ustar .\" Hey, EMACS: -*- nroff -*- .\" First parameter, NAME, should be all caps .\" Second parameter, SECTION, should be 1-8, maybe w/ subsection .\" other parameters are allowed: see man(7), man(1) .TH LOKI 1 "2004-09-24" .\" Please adjust this date whenever revising the manpage. .\" .\" Some roff macros, for reference: .\" .nh disable hyphenation .\" .hy enable hyphenation .\" .ad l left justify .\" .ad b justify to both left and right margins .\" .nf disable filling .\" .fi enable filling .\" .br insert line break .\" .sp insert n+1 empty lines .\" for manpage-specific macros, see man(7) .SH NAME loki \- Reversible jump MCMC linkage analysis in general pedigrees .SH SYNOPSIS .B prep .RI controlfile .br .B loki .RI -v .br .B loki .RI paramfile .SH DESCRIPTION This manual page documents briefly the .B prep and .B loki commands. Other post-hoc analysis scripts are available; please see the complete documentation. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. Instead, it has documentation in PostScript format; see below. .PP .\" TeX users may be more comfortable with the \fB\fP and .\" \fI\fP escape sequences to invode bold face and italics, .\" respectively. \fBloki\fP, written by Simon C. Heath, implements segregation and linkage analysis on possibly large and complex pedigrees, by means of a Reversible Jump Markov Chain Monte Carlo technique. \fBprep\fP performs previous data preparation. .SH OPTIONS .TP .B \-v Show version of the program. .SH SEE ALSO The programs are documented fully in .IR /usr/share/doc/loki-doc/ if you have installed the loki-doc package. .SH AUTHOR This manual page was written by Carleos Artime , for the Debian GNU/Linux system (but may be used by others). debian/loki.dirs0000644000000000000000000000005611110210273010774 0ustar usr/bin usr/share/doc/loki usr/share/man/man1 debian/loki.docs0000644000000000000000000000011111110210273010753 0ustar README README.known_systems README.multiple_records README.parallel_runs debian/rules0000755000000000000000000000113212233512437010245 0ustar #!/usr/bin/make -f # debian/rules for loki using dh # Andreas Tille , GPL pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') MANPAGES=check_het.1 \ hist.1 \ loki_count.1 \ loki_dist.1 \ loki_ext.1 \ loki_freq.1 \ loki_sort_error.1 \ prep.1 \ qavg.1 %: dh $@ override_dh_auto_install: for man in $(MANPAGES) ; do \ ln -s loki.1.gz debian/$(pkg)/usr/share/man/man1/$${man}.gz ; \ done make install prefix=$(CURDIR)/debian/loki/usr bindir=$(CURDIR)/debian/loki/usr/bin LDFLAGS="$(LDFLAGS)" debian/loki-doc.doc-base.lokimanual0000644000000000000000000000040511110210273014404 0ustar Document: lokimanual Title: Loki Manual Author: Simon C. Heath Abstract: This manual describes what loki is and how it can be used to perform genetic linkage analyses. Section: Science/Biology Format: postscript Files: /usr/share/doc/loki-doc/loki_doc.ps.gz debian/watch0000644000000000000000000000064512214301047010216 0ustar #Please note that loki is dead upstream, that means the development has #stopped and even the homepage http://loki.homeunix.net/ is not available any more. #You can read the content of the old homepage in the web archive at # http://web.archive.org/web/20051220050931/http://loki.homeunix.net/ #If you want to download the original source tarball, try the bzipped #version (the link to the gzipped version is broken). debian/upstream0000644000000000000000000000155311750436504010762 0ustar Reference: - Author: Simon C. Heath Title: Markov chain Monte Carlo segregation and linkage analysis for oligogenic models Journal: American Journal of Human Genetics Year: 1997 Volume: 61 Number: 3 Pages: 748-60 DOI: 10.1086/515506 PMID: 9326339 URL: http://www.cell.com/AJHG/abstract/S0002-9297%2807%2964337-7 eprint: http://download.cell.com/AJHG/pdf/PIIS0002929707643377.pdf - Author: E Warwick Daw and Simon C Heath and Yue Lu Title: Single-nucleotide polymorphism versus microsatellite markers in a combined linkage and segregation analysis of a quantitative trait Journal: BMC Genetics Year: 2005 Volume: 6 Number: Suppl 1 Pages: S32 DOI: 10.1186/1471-2156-6-S1-S32 PMID: 16451642 URL: http://www.biomedcentral.com/1471-2156/6/S1/S32 eprint: http://www.biomedcentral.com/content/pdf/1471-2156-6-S1-S32.pdf debian/copyright0000644000000000000000000000357311750741432011135 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Loki Upstream-Contact: Simon C. Heath Source: http://web.archive.org/web/20051220050931/http://loki.homeunix.net/ (web archive because original page vanished) Files: * Copyright: 1997-2004 Simon C. Heath License: BSD Files: debian/* Copyright: 2003-2004 Carleos Artime 2008-2012 Andreas Tille License: BSD License: BSD Loki source is available under a modified version of the BSD license: . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 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. The name of the author may not 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. debian/source/0000755000000000000000000000000011750567376010507 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000157611110210273011224 0ustar loki for Debian --------------- Please note that loki is dead upstream, that means the development has stopped and even the homepage http://loki.homeunix.net/ is not available any more. You can read the content of the old homepage in the web archive at http://web.archive.org/web/20051220050931/http://loki.homeunix.net/ If you want to download the original source tarball, try the bzipped version (the link to the gzipped version is broken). Notice that the Perl scripts ("utils") provided with Loki have been renamed as follows: count.pl -> loki_count dist.pl -> loki_dist freq.pl -> loki_freq loki_ext.pl -> loki_ext sort_error.pl -> loki_sort_error so please be aware when reading the documentation and using these programs. The package "loki-doc" contains full documentation for Loki. -- Carleos Artime , 2004-09-24 debian/loki-doc.docs0000644000000000000000000000001211110210273011516 0ustar docs/*.ps debian/loki.manpages0000644000000000000000000000001611110210273011622 0ustar debian/loki.1 debian/changelog0000644000000000000000000000750312233513657011054 0ustar loki (2.4.7.4-5) unstable; urgency=low * debian/upstream: added citation information * debian/control: - Standards-Version: 3.9.4 (no changes needed) - cme fix dpkg-control - Fixed Vcs fields - Depends: ${misc:Depends} - Canonical Vcs URLs - Removed Homepage field since homepage vanished from the net * debian/source/format: 3.0 (quilt) * debian/copyright: DEP5 * debian/rules: switch from cdbs to dh * debhelper 9 to enable hardening flags * debian/patches/hardening.patch -- Andreas Tille Mon, 28 Oct 2013 17:08:17 +0100 loki (2.4.7.4-4) unstable; urgency=low * Fixed lokisrc/param_lex.l and regenerated C file to solve problem with redefined __unused on 64 bit systems (Thanks to brian m. carlson ) Closes: #409370 -- Andreas Tille Tue, 25 Mar 2008 15:14:26 +0100 loki (2.4.7.4-3) unstable; urgency=low * Fixed install target to install to debian/tmp correctly Closes: #472320 -- Andreas Tille Sun, 23 Mar 2008 18:32:22 +0100 loki (2.4.7.4-2) unstable; urgency=low * Debhelper 5 * Standards-Version: 3.7.3 (no changes necessary) * Switch to cdbs * Use quilt and patches * Removed [Biology] from short description * Added hint to long description that the project is dead and homepage vanished * Group maintenance according to Debian-Med policy * Added Vcs-Fields * Added Homepage tag (with download page of latest upstream source, upstream seems to be dead since 1995) * Removed watch file because project is dead upstream so watch makes no sense * Use a single manpage and symlinks instead of several copies of the very same manpage file * Remove menu entry that just calls man loki * Fixed Section in doc-base files * Moced doc package to section doc (as suggested by lintian) -- Andreas Tille Thu, 20 Mar 2008 14:39:11 +0100 loki (2.4.7.4-1) unstable; urgency=low * New upstream release closes: #254166 * Added a hint about loki-doc package in README.Debian. * Standards-Version: 3.6.1 -- Carleos Artime Fri, 24 Sep 2004 15:15:27 +0000 loki (2.4.6-1) unstable; urgency=low * First official release closes: #155071 * New upstream release. * Changed section in debian/control from "misc" to "science". * Added homepage to package description in debian/control. * Split up into two packages (loki, loki-doc). * Changes by Andreas Tille - Added "Suggests: loki-doc" to loki - Changed "Depends" to "Suggests: loki" in loki-doc to enable reading online documentation without installing the binary package - used debian/loki-doc.docs and dh_installdocs to install documentation - moved debian/lokifaq.doc-base to debian/loki-doc.doc-base.lokifaq and debian/lokimanual.doc-base debian/loki-doc.doc-base.lokimanual - Added debian/loci-doc.README.Debian to give a hint at the LaTeX source of the documentation. -- Carleos Artime Fri, 25 Apr 2003 18:56:57 +0200 loki (2.4.5-1) unstable; urgency=low * Initial Release. * Having read "man dh_installdocs", split "debian/doc-base" in two files. * Included a "menu" entry that simply shows loki's man page. * Renamed utils/loki_ext.in to utils/ext.in. * Modified utils/Makefile.in to rename executables: count.pl, dist.pl, freq.pl, loki_ext.pl, sort_error.pl, are now loki_count, loki_dist, loki_freq, loki_ext, and loki_sort_error. * Fixed copyright-lists-upstream-authors-with-dh_make-boilerplate bug by just removing (s) behind Author * Appended upstream COPYRIGHT to debian/copyright to get it included into the Debian package * Standards-Version: 3.5.9 -- Carleos Artime Sat, 5 Apr 2003 18:56:57 +0200 debian/patches/0000755000000000000000000000000012233513626010620 5ustar debian/patches/hardening.patch0000644000000000000000000000107512233513626013603 0ustar Author: Andreas Tille LastChanged: Mon, 28 Oct 2013 17:08:17 +0100 Description: Propagate hardening for linker also into subdirectory utils --- a/utils/Makefile.in +++ b/utils/Makefile.in @@ -12,7 +12,7 @@ bindir = @bindir@ INSTALL_PERM = 755 CFLAGS = $(MY_CFLAGS) -I../include -LDFLAGS = +LDFLAGS := $(LDFLAGS) LIBS = -lm ALL_LIBS = $(LIBS) @@ -26,7 +26,7 @@ qavg: qavg.c $(CC) $(CFLAGS) -o $@ qavg.c $(LDFLAGS) $(ALL_LIBS) hist: hist.c - $(CC) $(CFLAGS) -o $@ hist.c + $(CC) $(CFLAGS) -o $@ hist.c $(LDFLAGS) ../bin: mkdir ../bin debian/patches/10_lex0000644000000000000000000016067111110210273011627 0ustar --- loki.orig/lokisrc/param_lex.l +++ loki/lokisrc/param_lex.l @@ -127,7 +127,7 @@ void yy_cleanup(void) { - yy_delete_buffer(yy_current_buffer); + yy_delete_buffer(YY_CURRENT_BUFFER); } #ifdef FUNC_NAME --- loki.orig/lokisrc/param_lex.c +++ loki/lokisrc/param_lex.c @@ -1,74 +1,113 @@ -/* A lexical scanner generated by flex */ +#line 2 "param_lex.c" -/* Scanner skeleton version: - * $Header: /home/daffy/u0/vern/flex/RCS/flex.skl,v 2.91 96/09/10 16:58:48 vern Exp $ - * $FreeBSD: src/usr.bin/lex/flex.skl,v 1.8 2004/01/06 19:03:44 nectar Exp $ - */ +#line 4 "param_lex.c" -#if defined(__FreeBSD__) -#include -#else -#define __unused -#endif +#define YY_INT_ALIGNED short int + +/* A lexical scanner generated by flex */ #define FLEX_SCANNER #define YY_FLEX_MAJOR_VERSION 2 #define YY_FLEX_MINOR_VERSION 5 +#define YY_FLEX_SUBMINOR_VERSION 34 +#if YY_FLEX_SUBMINOR_VERSION > 0 +#define FLEX_BETA +#endif +/* First, we deal with platform-specific or compiler-specific issues. */ + +/* begin standard C headers. */ #include +#include +#include +#include +/* end standard C headers. */ -/* cfront 1.2 defines "c_plusplus" instead of "__cplusplus" */ -#ifdef c_plusplus -#ifndef __cplusplus -#define __cplusplus -#endif +/* flex integer type definitions */ + +#ifndef FLEXINT_H +#define FLEXINT_H + +/* C99 systems have . Non-C99 systems may or may not. */ + +#if defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + +/* C99 says to define __STDC_LIMIT_MACROS before including stdint.h, + * if you want the limit (max/min) macros for int types. + */ +#ifndef __STDC_LIMIT_MACROS +#define __STDC_LIMIT_MACROS 1 #endif +#include +typedef int8_t flex_int8_t; +typedef uint8_t flex_uint8_t; +typedef int16_t flex_int16_t; +typedef uint16_t flex_uint16_t; +typedef int32_t flex_int32_t; +typedef uint32_t flex_uint32_t; +#else +typedef signed char flex_int8_t; +typedef short int flex_int16_t; +typedef int flex_int32_t; +typedef unsigned char flex_uint8_t; +typedef unsigned short int flex_uint16_t; +typedef unsigned int flex_uint32_t; +#endif /* ! C99 */ -#ifdef __cplusplus +/* Limits of integral types. */ +#ifndef INT8_MIN +#define INT8_MIN (-128) +#endif +#ifndef INT16_MIN +#define INT16_MIN (-32767-1) +#endif +#ifndef INT32_MIN +#define INT32_MIN (-2147483647-1) +#endif +#ifndef INT8_MAX +#define INT8_MAX (127) +#endif +#ifndef INT16_MAX +#define INT16_MAX (32767) +#endif +#ifndef INT32_MAX +#define INT32_MAX (2147483647) +#endif +#ifndef UINT8_MAX +#define UINT8_MAX (255U) +#endif +#ifndef UINT16_MAX +#define UINT16_MAX (65535U) +#endif +#ifndef UINT32_MAX +#define UINT32_MAX (4294967295U) +#endif -#include -#include +#endif /* ! FLEXINT_H */ -/* Use prototypes in function declarations. */ -#define YY_USE_PROTOS +#ifdef __cplusplus /* The "const" storage-class-modifier is valid. */ #define YY_USE_CONST #else /* ! __cplusplus */ -#if __STDC__ +/* C99 requires __STDC__ to be defined as 1. */ +#if defined (__STDC__) -#define YY_USE_PROTOS #define YY_USE_CONST -#endif /* __STDC__ */ +#endif /* defined (__STDC__) */ #endif /* ! __cplusplus */ -#ifdef __TURBOC__ - #pragma warn -rch - #pragma warn -use -#include -#include -#define YY_USE_CONST -#define YY_USE_PROTOS -#endif - #ifdef YY_USE_CONST #define yyconst const #else #define yyconst #endif - -#ifdef YY_USE_PROTOS -#define YY_PROTO(proto) proto -#else -#define YY_PROTO(proto) () -#endif - /* Returned upon end-of-file. */ #define YY_NULL 0 @@ -83,71 +122,77 @@ * but we do it the disgusting crufty way forced on us by the ()-less * definition of BEGIN. */ -#define BEGIN yy_start = 1 + 2 * +#define BEGIN (yy_start) = 1 + 2 * /* Translate the current start state into a value that can be later handed * to BEGIN to return to the state. The YYSTATE alias is for lex * compatibility. */ -#define YY_START ((yy_start - 1) / 2) +#define YY_START (((yy_start) - 1) / 2) #define YYSTATE YY_START /* Action number for EOF rule of a given start state. */ #define YY_STATE_EOF(state) (YY_END_OF_BUFFER + state + 1) /* Special action meaning "start processing a new file". */ -#define YY_NEW_FILE yyrestart( yyin ) +#define YY_NEW_FILE yyrestart(yyin ) #define YY_END_OF_BUFFER_CHAR 0 /* Size of default input buffer. */ +#ifndef YY_BUF_SIZE #define YY_BUF_SIZE 16384 +#endif + +/* The state buf must be large enough to hold one state per character in the main buffer. + */ +#define YY_STATE_BUF_SIZE ((YY_BUF_SIZE + 2) * sizeof(yy_state_type)) +#ifndef YY_TYPEDEF_YY_BUFFER_STATE +#define YY_TYPEDEF_YY_BUFFER_STATE typedef struct yy_buffer_state *YY_BUFFER_STATE; +#endif extern int yyleng; + extern FILE *yyin, *yyout; #define EOB_ACT_CONTINUE_SCAN 0 #define EOB_ACT_END_OF_FILE 1 #define EOB_ACT_LAST_MATCH 2 -/* The funky do-while in the following #define is used to turn the definition - * int a single C statement (which needs a semi-colon terminator). This - * avoids problems with code like: - * - * if ( condition_holds ) - * yyless( 5 ); - * else - * do_something_else(); - * - * Prior to using the do-while the compiler would get upset at the - * "else" because it interpreted the "if" statement as being all - * done when it reached the ';' after the yyless() call. - */ - -/* Return all but the first 'n' matched characters back to the input stream. */ + #define YY_LESS_LINENO(n) +/* Return all but the first "n" matched characters back to the input stream. */ #define yyless(n) \ do \ { \ /* Undo effects of setting up yytext. */ \ - *yy_cp = yy_hold_char; \ + int yyless_macro_arg = (n); \ + YY_LESS_LINENO(yyless_macro_arg);\ + *yy_cp = (yy_hold_char); \ YY_RESTORE_YY_MORE_OFFSET \ - yy_c_buf_p = yy_cp = yy_bp + n - YY_MORE_ADJ; \ + (yy_c_buf_p) = yy_cp = yy_bp + yyless_macro_arg - YY_MORE_ADJ; \ YY_DO_BEFORE_ACTION; /* set up yytext again */ \ } \ while ( 0 ) -#define unput(c) yyunput( c, yytext_ptr ) +#define unput(c) yyunput( c, (yytext_ptr) ) /* The following is because we cannot portably get our hands on size_t * (without autoconf's help, which isn't available because we want * flex-generated scanners to compile on their own). + * Given that the standard has decreed that size_t exists since 1989, + * I guess we can afford to depend on it. Manoj. */ -typedef unsigned int yy_size_t; +#ifndef YY_TYPEDEF_YY_SIZE_T +#define YY_TYPEDEF_YY_SIZE_T +typedef size_t yy_size_t; +#endif +#ifndef YY_STRUCT_YY_BUFFER_STATE +#define YY_STRUCT_YY_BUFFER_STATE struct yy_buffer_state { FILE *yy_input_file; @@ -184,12 +229,16 @@ */ int yy_at_bol; + int yy_bs_lineno; /**< The line count. */ + int yy_bs_column; /**< The column count. */ + /* Whether to try to fill the input buffer when we reach the * end of it. */ int yy_fill_buffer; int yy_buffer_status; + #define YY_BUFFER_NEW 0 #define YY_BUFFER_NORMAL 1 /* When an EOF's been seen but there's still some text to process @@ -203,28 +252,38 @@ * just pointing yyin at a new input file. */ #define YY_BUFFER_EOF_PENDING 2 + }; +#endif /* !YY_STRUCT_YY_BUFFER_STATE */ -static YY_BUFFER_STATE yy_current_buffer = 0; +/* Stack of input buffers. */ +static size_t yy_buffer_stack_top = 0; /**< index of top of stack. */ +static size_t yy_buffer_stack_max = 0; /**< capacity of stack. */ +static YY_BUFFER_STATE * yy_buffer_stack = 0; /**< Stack as an array. */ /* We provide macros for accessing buffer states in case in the * future we want to put the buffer states in a more general * "scanner state". + * + * Returns the top of the stack, or NULL. */ -#define YY_CURRENT_BUFFER yy_current_buffer +#define YY_CURRENT_BUFFER ( (yy_buffer_stack) \ + ? (yy_buffer_stack)[(yy_buffer_stack_top)] \ + : NULL) +/* Same as previous macro, but useful when we know that the buffer stack is not + * NULL or when we need an lvalue. For internal use only. + */ +#define YY_CURRENT_BUFFER_LVALUE (yy_buffer_stack)[(yy_buffer_stack_top)] /* yy_hold_char holds the character lost when yytext is formed. */ static char yy_hold_char; - static int yy_n_chars; /* number of characters read into yy_ch_buf */ - - int yyleng; /* Points to current character in buffer. */ static char *yy_c_buf_p = (char *) 0; -static int yy_init = 1; /* whether we need to initialize */ +static int yy_init = 0; /* whether we need to initialize */ static int yy_start = 0; /* start state number */ /* Flag which is used to allow yywrap()'s to do buffer switches @@ -232,66 +291,92 @@ */ static int yy_did_buffer_switch_on_eof; -void yyrestart YY_PROTO(( FILE *input_file )); - -void yy_switch_to_buffer YY_PROTO(( YY_BUFFER_STATE new_buffer )); -void yy_load_buffer_state YY_PROTO(( void )); -YY_BUFFER_STATE yy_create_buffer YY_PROTO(( FILE *file, int size )); -void yy_delete_buffer YY_PROTO(( YY_BUFFER_STATE b )); -void yy_init_buffer YY_PROTO(( YY_BUFFER_STATE b, FILE *file )); -void yy_flush_buffer YY_PROTO(( YY_BUFFER_STATE b )); -#define YY_FLUSH_BUFFER yy_flush_buffer( yy_current_buffer ) - -YY_BUFFER_STATE yy_scan_buffer YY_PROTO(( char *base, yy_size_t size )); -YY_BUFFER_STATE yy_scan_string YY_PROTO(( yyconst char *yy_str )); -YY_BUFFER_STATE yy_scan_bytes YY_PROTO(( yyconst char *bytes, int len )); - -static void *yy_flex_alloc YY_PROTO(( yy_size_t )); -static void *yy_flex_realloc YY_PROTO(( void *, yy_size_t )) __unused; -static void yy_flex_free YY_PROTO(( void * )); +void yyrestart (FILE *input_file ); +void yy_switch_to_buffer (YY_BUFFER_STATE new_buffer ); +YY_BUFFER_STATE yy_create_buffer (FILE *file,int size ); +void yy_delete_buffer (YY_BUFFER_STATE b ); +void yy_flush_buffer (YY_BUFFER_STATE b ); +void yypush_buffer_state (YY_BUFFER_STATE new_buffer ); +void yypop_buffer_state (void ); + +static void yyensure_buffer_stack (void ); +static void yy_load_buffer_state (void ); +static void yy_init_buffer (YY_BUFFER_STATE b,FILE *file ); + +#define YY_FLUSH_BUFFER yy_flush_buffer(YY_CURRENT_BUFFER ) + +YY_BUFFER_STATE yy_scan_buffer (char *base,yy_size_t size ); +YY_BUFFER_STATE yy_scan_string (yyconst char *yy_str ); +YY_BUFFER_STATE yy_scan_bytes (yyconst char *bytes,int len ); + +void *yyalloc (yy_size_t ); +void *yyrealloc (void *,yy_size_t ); +void yyfree (void * ); #define yy_new_buffer yy_create_buffer #define yy_set_interactive(is_interactive) \ { \ - if ( ! yy_current_buffer ) \ - yy_current_buffer = yy_create_buffer( yyin, YY_BUF_SIZE ); \ - yy_current_buffer->yy_is_interactive = is_interactive; \ + if ( ! YY_CURRENT_BUFFER ){ \ + yyensure_buffer_stack (); \ + YY_CURRENT_BUFFER_LVALUE = \ + yy_create_buffer(yyin,YY_BUF_SIZE ); \ + } \ + YY_CURRENT_BUFFER_LVALUE->yy_is_interactive = is_interactive; \ } #define yy_set_bol(at_bol) \ { \ - if ( ! yy_current_buffer ) \ - yy_current_buffer = yy_create_buffer( yyin, YY_BUF_SIZE ); \ - yy_current_buffer->yy_at_bol = at_bol; \ + if ( ! YY_CURRENT_BUFFER ){\ + yyensure_buffer_stack (); \ + YY_CURRENT_BUFFER_LVALUE = \ + yy_create_buffer(yyin,YY_BUF_SIZE ); \ + } \ + YY_CURRENT_BUFFER_LVALUE->yy_at_bol = at_bol; \ } -#define YY_AT_BOL() (yy_current_buffer->yy_at_bol) +#define YY_AT_BOL() (YY_CURRENT_BUFFER_LVALUE->yy_at_bol) + +/* Begin user sect3 */ typedef unsigned char YY_CHAR; + FILE *yyin = (FILE *) 0, *yyout = (FILE *) 0; + typedef int yy_state_type; + +extern int yylineno; + +int yylineno = 1; + extern char *yytext; #define yytext_ptr yytext -static yy_state_type yy_get_previous_state YY_PROTO(( void )); -static yy_state_type yy_try_NUL_trans YY_PROTO(( yy_state_type current_state )); -static int yy_get_next_buffer YY_PROTO(( void )); -static void yy_fatal_error YY_PROTO(( yyconst char msg[] )); +static yy_state_type yy_get_previous_state (void ); +static yy_state_type yy_try_NUL_trans (yy_state_type current_state ); +static int yy_get_next_buffer (void ); +static void yy_fatal_error (yyconst char msg[] ); /* Done after the current pattern has been matched and before the * corresponding action - sets up yytext. */ #define YY_DO_BEFORE_ACTION \ - yytext_ptr = yy_bp; \ - yyleng = (int) (yy_cp - yy_bp); \ - yy_hold_char = *yy_cp; \ + (yytext_ptr) = yy_bp; \ + yyleng = (size_t) (yy_cp - yy_bp); \ + (yy_hold_char) = *yy_cp; \ *yy_cp = '\0'; \ - yy_c_buf_p = yy_cp; + (yy_c_buf_p) = yy_cp; #define YY_NUM_RULES 15 #define YY_END_OF_BUFFER 16 -static yyconst short int yy_accept[74] = +/* This struct is not used in this scanner, + but its presence is necessary. */ +struct yy_trans_info + { + flex_int32_t yy_verify; + flex_int32_t yy_nxt; + }; +static yyconst flex_int16_t yy_accept[74] = { 0, 0, 0, 0, 0, 0, 0, 16, 14, 2, 1, 14, 14, 14, 14, 14, 14, 13, 11, 5, 6, @@ -303,7 +388,7 @@ 0, 12, 0 } ; -static yyconst int yy_ec[256] = +static yyconst flex_int32_t yy_ec[256] = { 0, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, @@ -335,13 +420,13 @@ 1, 1, 1, 1, 1 } ; -static yyconst int yy_meta[15] = +static yyconst flex_int32_t yy_meta[15] = { 0, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3 } ; -static yyconst short int yy_base[84] = +static yyconst flex_int16_t yy_base[84] = { 0, 0, 0, 12, 13, 20, 0, 133, 129, 128, 0, 14, 127, 32, 36, 33, 34, 39, 44, 134, 134, @@ -354,7 +439,7 @@ 116, 119, 37 } ; -static yyconst short int yy_def[84] = +static yyconst flex_int16_t yy_def[84] = { 0, 73, 1, 74, 74, 73, 5, 73, 75, 75, 76, 77, 78, 79, 75, 75, 75, 14, 14, 73, 73, @@ -367,7 +452,7 @@ 73, 73, 73 } ; -static yyconst short int yy_nxt[149] = +static yyconst flex_int16_t yy_nxt[149] = { 0, 8, 9, 10, 11, 12, 13, 8, 14, 15, 16, 17, 18, 18, 8, 20, 20, 37, 38, 21, 21, @@ -387,7 +472,7 @@ 73, 73, 73, 73, 73, 73, 73, 73 } ; -static yyconst short int yy_chk[149] = +static yyconst flex_int16_t yy_chk[149] = { 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 11, 11, 3, 4, @@ -410,6 +495,9 @@ static yy_state_type yy_last_accepting_state; static char *yy_last_accepting_cpos; +extern int yy_flex_debug; +int yy_flex_debug = 0; + /* The intent behind this definition is that it'll catch * any uses of REJECT which flex missed. */ @@ -419,7 +507,6 @@ #define YY_RESTORE_YY_MORE_OFFSET char *yytext; #line 1 "param_lex.l" -#define INITIAL 0 #line 2 "param_lex.l" /**************************************************************************** * * @@ -475,10 +562,27 @@ int list_ptr; static int ln_list[MAX_INCLUDE],ln1_list[MAX_INCLUDE]; -#define COMMENT 1 + +#line 568 "param_lex.c" + +#define INITIAL 0 +#define COMMENT 1 #define ISTATE 2 +#ifndef YY_NO_UNISTD_H +/* Special case for "unistd.h", since it is non-ANSI. We include it way + * down here because we want the user's section 1 to have been scanned first. + * The user has a chance to override it with an option. + */ +#include +#endif + +#ifndef YY_EXTRA_TYPE +#define YY_EXTRA_TYPE void * +#endif + +static int yy_init_globals (void ); /* Macros after this point can all be overridden by user definitions in * section 1. @@ -486,65 +590,30 @@ #ifndef YY_SKIP_YYWRAP #ifdef __cplusplus -extern "C" int yywrap YY_PROTO(( void )); +extern "C" int yywrap (void ); #else -extern int yywrap YY_PROTO(( void )); +extern int yywrap (void ); #endif #endif -#ifndef YY_NO_UNPUT -static void yyunput YY_PROTO(( int c, char *buf_ptr )); -#endif + static void yyunput (int c,char *buf_ptr ); #ifndef yytext_ptr -static void yy_flex_strncpy YY_PROTO(( char *, yyconst char *, int )); +static void yy_flex_strncpy (char *,yyconst char *,int ); #endif #ifdef YY_NEED_STRLEN -static int yy_flex_strlen YY_PROTO(( yyconst char * )); +static int yy_flex_strlen (yyconst char * ); #endif #ifndef YY_NO_INPUT + #ifdef __cplusplus -static int yyinput YY_PROTO(( void )); +static int yyinput (void ); #else -static int input YY_PROTO(( void )); -#endif +static int input (void ); #endif -#if YY_STACK_USED -static int yy_start_stack_ptr = 0; -static int yy_start_stack_depth = 0; -static int *yy_start_stack = 0; -#ifndef YY_NO_PUSH_STATE -static void yy_push_state YY_PROTO(( int new_state )); -#endif -#ifndef YY_NO_POP_STATE -static void yy_pop_state YY_PROTO(( void )); -#endif -#ifndef YY_NO_TOP_STATE -static int yy_top_state YY_PROTO(( void )); -#endif - -#else -#define YY_NO_PUSH_STATE 1 -#define YY_NO_POP_STATE 1 -#define YY_NO_TOP_STATE 1 -#endif - -#ifdef YY_MALLOC_DECL -YY_MALLOC_DECL -#else -#if __STDC__ -#ifndef __cplusplus -#include -#endif -#else -/* Just try to get by without declaring the routines. This will fail - * miserably on non-ANSI systems for which sizeof(size_t) != sizeof(int) - * or sizeof(void*) != sizeof(int). - */ -#endif #endif /* Amount of stuff to slurp up with each read. */ @@ -553,12 +622,11 @@ #endif /* Copy whatever the last rule matched to the standard output. */ - #ifndef ECHO /* This used to be an fputs(), but since the string might contain NUL's, * we now use fwrite(). */ -#define ECHO (void) fwrite( yytext, yyleng, 1, yyout ) +#define ECHO fwrite( yytext, yyleng, 1, yyout ) #endif /* Gets input and stuffs it into "buf". number of characters read, or YY_NULL, @@ -566,9 +634,10 @@ */ #ifndef YY_INPUT #define YY_INPUT(buf,result,max_size) \ - if ( yy_current_buffer->yy_is_interactive ) \ + if ( YY_CURRENT_BUFFER_LVALUE->yy_is_interactive ) \ { \ - int c = '*', n; \ + int c = '*'; \ + int n; \ for ( n = 0; n < max_size && \ (c = getc( yyin )) != EOF && c != '\n'; ++n ) \ buf[n] = (char) c; \ @@ -578,9 +647,22 @@ YY_FATAL_ERROR( "input in flex scanner failed" ); \ result = n; \ } \ - else if ( ((result = fread( buf, 1, max_size, yyin )) == 0) \ - && ferror( yyin ) ) \ - YY_FATAL_ERROR( "input in flex scanner failed" ); + else \ + { \ + errno=0; \ + while ( (result = fread(buf, 1, max_size, yyin))==0 && ferror(yyin)) \ + { \ + if( errno != EINTR) \ + { \ + YY_FATAL_ERROR( "input in flex scanner failed" ); \ + break; \ + } \ + errno=0; \ + clearerr(yyin); \ + } \ + }\ +\ + #endif /* No semi-colon after return; correct usage is to write "yyterminate();" - @@ -601,12 +683,18 @@ #define YY_FATAL_ERROR(msg) yy_fatal_error( msg ) #endif +/* end tables serialization structures and prototypes */ + /* Default declaration of generated scanner - a define so the user can * easily add parameters. */ #ifndef YY_DECL -#define YY_DECL int yylex YY_PROTO(( void )) -#endif +#define YY_DECL_IS_OURS 1 + +extern int yylex (void); + +#define YY_DECL int yylex (void) +#endif /* !YY_DECL */ /* Code executed at the beginning of each rule, after yytext and yyleng * have been set up. @@ -623,8 +711,10 @@ #define YY_RULE_SETUP \ YY_USER_ACTION +/** The main scanner function which does all the work. + */ YY_DECL - { +{ register yy_state_type yy_current_state; register char *yy_cp, *yy_bp; register int yy_act; @@ -632,17 +722,18 @@ #line 61 "param_lex.l" +#line 726 "param_lex.c" - if ( yy_init ) + if ( !(yy_init) ) { - yy_init = 0; + (yy_init) = 1; #ifdef YY_USER_INIT YY_USER_INIT; #endif - if ( ! yy_start ) - yy_start = 1; /* first start state */ + if ( ! (yy_start) ) + (yy_start) = 1; /* first start state */ if ( ! yyin ) yyin = stdin; @@ -650,34 +741,36 @@ if ( ! yyout ) yyout = stdout; - if ( ! yy_current_buffer ) - yy_current_buffer = - yy_create_buffer( yyin, YY_BUF_SIZE ); + if ( ! YY_CURRENT_BUFFER ) { + yyensure_buffer_stack (); + YY_CURRENT_BUFFER_LVALUE = + yy_create_buffer(yyin,YY_BUF_SIZE ); + } - yy_load_buffer_state(); + yy_load_buffer_state( ); } while ( 1 ) /* loops until end-of-file is reached */ { - yy_cp = yy_c_buf_p; + yy_cp = (yy_c_buf_p); /* Support of yytext. */ - *yy_cp = yy_hold_char; + *yy_cp = (yy_hold_char); /* yy_bp points to the position in yy_ch_buf of the start of * the current run. */ yy_bp = yy_cp; - yy_current_state = yy_start; + yy_current_state = (yy_start); yy_match: do { register YY_CHAR yy_c = yy_ec[YY_SC_TO_UI(*yy_cp)]; if ( yy_accept[yy_current_state] ) { - yy_last_accepting_state = yy_current_state; - yy_last_accepting_cpos = yy_cp; + (yy_last_accepting_state) = yy_current_state; + (yy_last_accepting_cpos) = yy_cp; } while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state ) { @@ -694,27 +787,26 @@ yy_act = yy_accept[yy_current_state]; if ( yy_act == 0 ) { /* have to back up */ - yy_cp = yy_last_accepting_cpos; - yy_current_state = yy_last_accepting_state; + yy_cp = (yy_last_accepting_cpos); + yy_current_state = (yy_last_accepting_state); yy_act = yy_accept[yy_current_state]; } YY_DO_BEFORE_ACTION; - do_action: /* This label is used only to access EOF actions. */ - switch ( yy_act ) { /* beginning of action switch */ case 0: /* must back up */ /* undo the effects of YY_DO_BEFORE_ACTION */ - *yy_cp = yy_hold_char; - yy_cp = yy_last_accepting_cpos; - yy_current_state = yy_last_accepting_state; + *yy_cp = (yy_hold_char); + yy_cp = (yy_last_accepting_cpos); + yy_current_state = (yy_last_accepting_state); goto yy_find_action; case 1: +/* rule 1 can match eol */ YY_RULE_SETUP #line 63 "param_lex.l" { @@ -750,9 +842,10 @@ {tokenpos+=yyleng;} YY_BREAK case 3: +/* rule 3 can match eol */ YY_RULE_SETUP #line 88 "param_lex.l" -{ +{ lineno++; tokenpos=0; (void)strncpy(linebuf,yytext+1,512); @@ -770,6 +863,7 @@ {tokenpos+=yyleng;} YY_BREAK case 6: +/* rule 6 can match eol */ YY_RULE_SETUP #line 97 "param_lex.l" {lineno++; tokenpos=0;} @@ -780,14 +874,15 @@ {BEGIN(ISTATE); tokenpos+=yyleng;} YY_BREAK case 8: -*yy_cp = yy_hold_char; /* undo effects of setting up yytext */ -yy_c_buf_p = yy_cp -= 1; +*yy_cp = (yy_hold_char); /* undo effects of setting up yytext */ +(yy_c_buf_p) = yy_cp -= 1; YY_DO_BEFORE_ACTION; /* set up yytext again */ YY_RULE_SETUP #line 100 "param_lex.l" ; YY_BREAK case 9: +/* rule 9 can match eol */ YY_RULE_SETUP #line 102 "param_lex.l" { tokenpos+=yyleng; @@ -797,6 +892,7 @@ return STRING; } YY_BREAK case 10: +/* rule 10 can match eol */ YY_RULE_SETUP #line 108 "param_lex.l" { tokenpos+=yyleng; @@ -834,30 +930,31 @@ #line 126 "param_lex.l" ECHO; YY_BREAK +#line 934 "param_lex.c" case YY_END_OF_BUFFER: { /* Amount of text matched not including the EOB char. */ - int yy_amount_of_matched_text = (int) (yy_cp - yytext_ptr) - 1; + int yy_amount_of_matched_text = (int) (yy_cp - (yytext_ptr)) - 1; /* Undo the effects of YY_DO_BEFORE_ACTION. */ - *yy_cp = yy_hold_char; + *yy_cp = (yy_hold_char); YY_RESTORE_YY_MORE_OFFSET - if ( yy_current_buffer->yy_buffer_status == YY_BUFFER_NEW ) + if ( YY_CURRENT_BUFFER_LVALUE->yy_buffer_status == YY_BUFFER_NEW ) { /* We're scanning a new file or input source. It's * possible that this happened because the user * just pointed yyin at a new source and called * yylex(). If so, then we have to assure - * consistency between yy_current_buffer and our + * consistency between YY_CURRENT_BUFFER and our * globals. Here is the right place to do so, because * this is the first action (other than possibly a * back-up) that will match for the new input source. */ - yy_n_chars = yy_current_buffer->yy_n_chars; - yy_current_buffer->yy_input_file = yyin; - yy_current_buffer->yy_buffer_status = YY_BUFFER_NORMAL; + (yy_n_chars) = YY_CURRENT_BUFFER_LVALUE->yy_n_chars; + YY_CURRENT_BUFFER_LVALUE->yy_input_file = yyin; + YY_CURRENT_BUFFER_LVALUE->yy_buffer_status = YY_BUFFER_NORMAL; } /* Note that here we test for yy_c_buf_p "<=" to the position @@ -867,13 +964,13 @@ * end-of-buffer state). Contrast this with the test * in input(). */ - if ( yy_c_buf_p <= &yy_current_buffer->yy_ch_buf[yy_n_chars] ) + if ( (yy_c_buf_p) <= &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars)] ) { /* This was really a NUL. */ yy_state_type yy_next_state; - yy_c_buf_p = yytext_ptr + yy_amount_of_matched_text; + (yy_c_buf_p) = (yytext_ptr) + yy_amount_of_matched_text; - yy_current_state = yy_get_previous_state(); + yy_current_state = yy_get_previous_state( ); /* Okay, we're now positioned to make the NUL * transition. We couldn't have @@ -886,30 +983,30 @@ yy_next_state = yy_try_NUL_trans( yy_current_state ); - yy_bp = yytext_ptr + YY_MORE_ADJ; + yy_bp = (yytext_ptr) + YY_MORE_ADJ; if ( yy_next_state ) { /* Consume the NUL. */ - yy_cp = ++yy_c_buf_p; + yy_cp = ++(yy_c_buf_p); yy_current_state = yy_next_state; goto yy_match; } else { - yy_cp = yy_c_buf_p; + yy_cp = (yy_c_buf_p); goto yy_find_action; } } - else switch ( yy_get_next_buffer() ) + else switch ( yy_get_next_buffer( ) ) { case EOB_ACT_END_OF_FILE: { - yy_did_buffer_switch_on_eof = 0; + (yy_did_buffer_switch_on_eof) = 0; - if ( yywrap() ) + if ( yywrap( ) ) { /* Note: because we've taken care in * yy_get_next_buffer() to have set up @@ -920,7 +1017,7 @@ * YY_NULL, it'll still work - another * YY_NULL will get returned. */ - yy_c_buf_p = yytext_ptr + YY_MORE_ADJ; + (yy_c_buf_p) = (yytext_ptr) + YY_MORE_ADJ; yy_act = YY_STATE_EOF(YY_START); goto do_action; @@ -928,30 +1025,30 @@ else { - if ( ! yy_did_buffer_switch_on_eof ) + if ( ! (yy_did_buffer_switch_on_eof) ) YY_NEW_FILE; } break; } case EOB_ACT_CONTINUE_SCAN: - yy_c_buf_p = - yytext_ptr + yy_amount_of_matched_text; + (yy_c_buf_p) = + (yytext_ptr) + yy_amount_of_matched_text; - yy_current_state = yy_get_previous_state(); + yy_current_state = yy_get_previous_state( ); - yy_cp = yy_c_buf_p; - yy_bp = yytext_ptr + YY_MORE_ADJ; + yy_cp = (yy_c_buf_p); + yy_bp = (yytext_ptr) + YY_MORE_ADJ; goto yy_match; case EOB_ACT_LAST_MATCH: - yy_c_buf_p = - &yy_current_buffer->yy_ch_buf[yy_n_chars]; + (yy_c_buf_p) = + &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars)]; - yy_current_state = yy_get_previous_state(); + yy_current_state = yy_get_previous_state( ); - yy_cp = yy_c_buf_p; - yy_bp = yytext_ptr + YY_MORE_ADJ; + yy_cp = (yy_c_buf_p); + yy_bp = (yytext_ptr) + YY_MORE_ADJ; goto yy_find_action; } break; @@ -962,8 +1059,7 @@ "fatal flex scanner internal error--no action found" ); } /* end of action switch */ } /* end of scanning one token */ - } /* end of yylex */ - +} /* end of yylex */ /* yy_get_next_buffer - try to read in a new buffer * @@ -972,21 +1068,20 @@ * EOB_ACT_CONTINUE_SCAN - continue scanning from current position * EOB_ACT_END_OF_FILE - end of file */ - -static int yy_get_next_buffer() - { - register char *dest = yy_current_buffer->yy_ch_buf; - register char *source = yytext_ptr; +static int yy_get_next_buffer (void) +{ + register char *dest = YY_CURRENT_BUFFER_LVALUE->yy_ch_buf; + register char *source = (yytext_ptr); register int number_to_move, i; int ret_val; - if ( yy_c_buf_p > &yy_current_buffer->yy_ch_buf[yy_n_chars + 1] ) + if ( (yy_c_buf_p) > &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars) + 1] ) YY_FATAL_ERROR( "fatal flex scanner internal error--end of buffer missed" ); - if ( yy_current_buffer->yy_fill_buffer == 0 ) + if ( YY_CURRENT_BUFFER_LVALUE->yy_fill_buffer == 0 ) { /* Don't try to fill the buffer, so this is an EOF. */ - if ( yy_c_buf_p - yytext_ptr - YY_MORE_ADJ == 1 ) + if ( (yy_c_buf_p) - (yytext_ptr) - YY_MORE_ADJ == 1 ) { /* We matched a single character, the EOB, so * treat this as a final EOF. @@ -1006,34 +1101,30 @@ /* Try to read more data. */ /* First move last chars to start of buffer. */ - number_to_move = (int) (yy_c_buf_p - yytext_ptr) - 1; + number_to_move = (int) ((yy_c_buf_p) - (yytext_ptr)) - 1; for ( i = 0; i < number_to_move; ++i ) *(dest++) = *(source++); - if ( yy_current_buffer->yy_buffer_status == YY_BUFFER_EOF_PENDING ) + if ( YY_CURRENT_BUFFER_LVALUE->yy_buffer_status == YY_BUFFER_EOF_PENDING ) /* don't do the read, it's not guaranteed to return an EOF, * just force an EOF */ - yy_current_buffer->yy_n_chars = yy_n_chars = 0; + YY_CURRENT_BUFFER_LVALUE->yy_n_chars = (yy_n_chars) = 0; else { - int num_to_read = - yy_current_buffer->yy_buf_size - number_to_move - 1; + int num_to_read = + YY_CURRENT_BUFFER_LVALUE->yy_buf_size - number_to_move - 1; while ( num_to_read <= 0 ) { /* Not enough room in the buffer - grow it. */ -#ifdef YY_USES_REJECT - YY_FATAL_ERROR( -"input buffer overflow, can't enlarge buffer because scanner uses REJECT" ); -#else /* just a shorter name for the current buffer */ - YY_BUFFER_STATE b = yy_current_buffer; + YY_BUFFER_STATE b = YY_CURRENT_BUFFER; int yy_c_buf_p_offset = - (int) (yy_c_buf_p - b->yy_ch_buf); + (int) ((yy_c_buf_p) - b->yy_ch_buf); if ( b->yy_is_our_buffer ) { @@ -1046,8 +1137,7 @@ b->yy_ch_buf = (char *) /* Include room in for 2 EOB chars. */ - yy_flex_realloc( (void *) b->yy_ch_buf, - b->yy_buf_size + 2 ); + yyrealloc((void *) b->yy_ch_buf,b->yy_buf_size + 2 ); } else /* Can't grow it, we don't own it. */ @@ -1057,35 +1147,35 @@ YY_FATAL_ERROR( "fatal error - scanner input buffer overflow" ); - yy_c_buf_p = &b->yy_ch_buf[yy_c_buf_p_offset]; + (yy_c_buf_p) = &b->yy_ch_buf[yy_c_buf_p_offset]; - num_to_read = yy_current_buffer->yy_buf_size - + num_to_read = YY_CURRENT_BUFFER_LVALUE->yy_buf_size - number_to_move - 1; -#endif + } if ( num_to_read > YY_READ_BUF_SIZE ) num_to_read = YY_READ_BUF_SIZE; /* Read in more data. */ - YY_INPUT( (&yy_current_buffer->yy_ch_buf[number_to_move]), - yy_n_chars, num_to_read ); + YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]), + (yy_n_chars), (size_t) num_to_read ); - yy_current_buffer->yy_n_chars = yy_n_chars; + YY_CURRENT_BUFFER_LVALUE->yy_n_chars = (yy_n_chars); } - if ( yy_n_chars == 0 ) + if ( (yy_n_chars) == 0 ) { if ( number_to_move == YY_MORE_ADJ ) { ret_val = EOB_ACT_END_OF_FILE; - yyrestart( yyin ); + yyrestart(yyin ); } else { ret_val = EOB_ACT_LAST_MATCH; - yy_current_buffer->yy_buffer_status = + YY_CURRENT_BUFFER_LVALUE->yy_buffer_status = YY_BUFFER_EOF_PENDING; } } @@ -1093,32 +1183,39 @@ else ret_val = EOB_ACT_CONTINUE_SCAN; - yy_n_chars += number_to_move; - yy_current_buffer->yy_ch_buf[yy_n_chars] = YY_END_OF_BUFFER_CHAR; - yy_current_buffer->yy_ch_buf[yy_n_chars + 1] = YY_END_OF_BUFFER_CHAR; + if ((yy_size_t) ((yy_n_chars) + number_to_move) > YY_CURRENT_BUFFER_LVALUE->yy_buf_size) { + /* Extend the array by 50%, plus the number we really need. */ + yy_size_t new_size = (yy_n_chars) + number_to_move + ((yy_n_chars) >> 1); + YY_CURRENT_BUFFER_LVALUE->yy_ch_buf = (char *) yyrealloc((void *) YY_CURRENT_BUFFER_LVALUE->yy_ch_buf,new_size ); + if ( ! YY_CURRENT_BUFFER_LVALUE->yy_ch_buf ) + YY_FATAL_ERROR( "out of dynamic memory in yy_get_next_buffer()" ); + } - yytext_ptr = &yy_current_buffer->yy_ch_buf[0]; + (yy_n_chars) += number_to_move; + YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars)] = YY_END_OF_BUFFER_CHAR; + YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars) + 1] = YY_END_OF_BUFFER_CHAR; - return ret_val; - } + (yytext_ptr) = &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[0]; + return ret_val; +} /* yy_get_previous_state - get the state just before the EOB char was reached */ -static yy_state_type yy_get_previous_state() - { + static yy_state_type yy_get_previous_state (void) +{ register yy_state_type yy_current_state; register char *yy_cp; - yy_current_state = yy_start; + yy_current_state = (yy_start); - for ( yy_cp = yytext_ptr + YY_MORE_ADJ; yy_cp < yy_c_buf_p; ++yy_cp ) + for ( yy_cp = (yytext_ptr) + YY_MORE_ADJ; yy_cp < (yy_c_buf_p); ++yy_cp ) { register YY_CHAR yy_c = (*yy_cp ? yy_ec[YY_SC_TO_UI(*yy_cp)] : 1); if ( yy_accept[yy_current_state] ) { - yy_last_accepting_state = yy_current_state; - yy_last_accepting_cpos = yy_cp; + (yy_last_accepting_state) = yy_current_state; + (yy_last_accepting_cpos) = yy_cp; } while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state ) { @@ -1130,30 +1227,23 @@ } return yy_current_state; - } - +} /* yy_try_NUL_trans - try to make a transition on the NUL character * * synopsis * next_state = yy_try_NUL_trans( current_state ); */ - -#ifdef YY_USE_PROTOS -static yy_state_type yy_try_NUL_trans( yy_state_type yy_current_state ) -#else -static yy_state_type yy_try_NUL_trans( yy_current_state ) -yy_state_type yy_current_state; -#endif - { + static yy_state_type yy_try_NUL_trans (yy_state_type yy_current_state ) +{ register int yy_is_jam; - register char *yy_cp = yy_c_buf_p; + register char *yy_cp = (yy_c_buf_p); register YY_CHAR yy_c = 1; if ( yy_accept[yy_current_state] ) { - yy_last_accepting_state = yy_current_state; - yy_last_accepting_cpos = yy_cp; + (yy_last_accepting_state) = yy_current_state; + (yy_last_accepting_cpos) = yy_cp; } while ( yy_chk[yy_base[yy_current_state] + yy_c] != yy_current_state ) { @@ -1165,80 +1255,73 @@ yy_is_jam = (yy_current_state == 73); return yy_is_jam ? 0 : yy_current_state; - } +} + static void yyunput (int c, register char * yy_bp ) +{ + register char *yy_cp; -#ifndef YY_NO_UNPUT -#ifdef YY_USE_PROTOS -static void yyunput( int c, register char *yy_bp ) -#else -static void yyunput( c, yy_bp ) -int c; -register char *yy_bp; -#endif - { - register char *yy_cp = yy_c_buf_p; + yy_cp = (yy_c_buf_p); /* undo effects of setting up yytext */ - *yy_cp = yy_hold_char; + *yy_cp = (yy_hold_char); - if ( yy_cp < yy_current_buffer->yy_ch_buf + 2 ) + if ( yy_cp < YY_CURRENT_BUFFER_LVALUE->yy_ch_buf + 2 ) { /* need to shift things up to make room */ /* +2 for EOB chars. */ - register int number_to_move = yy_n_chars + 2; - register char *dest = &yy_current_buffer->yy_ch_buf[ - yy_current_buffer->yy_buf_size + 2]; + register int number_to_move = (yy_n_chars) + 2; + register char *dest = &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[ + YY_CURRENT_BUFFER_LVALUE->yy_buf_size + 2]; register char *source = - &yy_current_buffer->yy_ch_buf[number_to_move]; + &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]; - while ( source > yy_current_buffer->yy_ch_buf ) + while ( source > YY_CURRENT_BUFFER_LVALUE->yy_ch_buf ) *--dest = *--source; yy_cp += (int) (dest - source); yy_bp += (int) (dest - source); - yy_current_buffer->yy_n_chars = - yy_n_chars = yy_current_buffer->yy_buf_size; + YY_CURRENT_BUFFER_LVALUE->yy_n_chars = + (yy_n_chars) = YY_CURRENT_BUFFER_LVALUE->yy_buf_size; - if ( yy_cp < yy_current_buffer->yy_ch_buf + 2 ) + if ( yy_cp < YY_CURRENT_BUFFER_LVALUE->yy_ch_buf + 2 ) YY_FATAL_ERROR( "flex scanner push-back overflow" ); } *--yy_cp = (char) c; + (yytext_ptr) = yy_bp; + (yy_hold_char) = *yy_cp; + (yy_c_buf_p) = yy_cp; +} - yytext_ptr = yy_bp; - yy_hold_char = *yy_cp; - yy_c_buf_p = yy_cp; - } -#endif /* ifndef YY_NO_UNPUT */ - - +#ifndef YY_NO_INPUT #ifdef __cplusplus -static int yyinput() + static int yyinput (void) #else -static int input() + static int input (void) #endif - { + +{ int c; - *yy_c_buf_p = yy_hold_char; + *(yy_c_buf_p) = (yy_hold_char); - if ( *yy_c_buf_p == YY_END_OF_BUFFER_CHAR ) + if ( *(yy_c_buf_p) == YY_END_OF_BUFFER_CHAR ) { /* yy_c_buf_p now points to the character we want to return. * If this occurs *before* the EOB characters, then it's a * valid NUL; if not, then we've hit the end of the buffer. */ - if ( yy_c_buf_p < &yy_current_buffer->yy_ch_buf[yy_n_chars] ) + if ( (yy_c_buf_p) < &YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[(yy_n_chars)] ) /* This was really a NUL. */ - *yy_c_buf_p = '\0'; + *(yy_c_buf_p) = '\0'; else { /* need more input */ - int offset = yy_c_buf_p - yytext_ptr; - ++yy_c_buf_p; + int offset = (yy_c_buf_p) - (yytext_ptr); + ++(yy_c_buf_p); - switch ( yy_get_next_buffer() ) + switch ( yy_get_next_buffer( ) ) { case EOB_ACT_LAST_MATCH: /* This happens because yy_g_n_b() @@ -1252,16 +1335,16 @@ */ /* Reset buffer status. */ - yyrestart( yyin ); + yyrestart(yyin ); - /* fall through */ + /*FALLTHROUGH*/ case EOB_ACT_END_OF_FILE: { - if ( yywrap() ) + if ( yywrap( ) ) return EOF; - if ( ! yy_did_buffer_switch_on_eof ) + if ( ! (yy_did_buffer_switch_on_eof) ) YY_NEW_FILE; #ifdef __cplusplus return yyinput(); @@ -1271,90 +1354,92 @@ } case EOB_ACT_CONTINUE_SCAN: - yy_c_buf_p = yytext_ptr + offset; + (yy_c_buf_p) = (yytext_ptr) + offset; break; } } } - c = *(unsigned char *) yy_c_buf_p; /* cast for 8-bit char's */ - *yy_c_buf_p = '\0'; /* preserve yytext */ - yy_hold_char = *++yy_c_buf_p; - + c = *(unsigned char *) (yy_c_buf_p); /* cast for 8-bit char's */ + *(yy_c_buf_p) = '\0'; /* preserve yytext */ + (yy_hold_char) = *++(yy_c_buf_p); return c; - } - +} +#endif /* ifndef YY_NO_INPUT */ -#ifdef YY_USE_PROTOS -void yyrestart( FILE *input_file ) -#else -void yyrestart( input_file ) -FILE *input_file; -#endif - { - if ( ! yy_current_buffer ) - yy_current_buffer = yy_create_buffer( yyin, YY_BUF_SIZE ); +/** Immediately switch to a different input stream. + * @param input_file A readable stream. + * + * @note This function does not reset the start condition to @c INITIAL . + */ + void yyrestart (FILE * input_file ) +{ - yy_init_buffer( yy_current_buffer, input_file ); - yy_load_buffer_state(); + if ( ! YY_CURRENT_BUFFER ){ + yyensure_buffer_stack (); + YY_CURRENT_BUFFER_LVALUE = + yy_create_buffer(yyin,YY_BUF_SIZE ); } + yy_init_buffer(YY_CURRENT_BUFFER,input_file ); + yy_load_buffer_state( ); +} -#ifdef YY_USE_PROTOS -void yy_switch_to_buffer( YY_BUFFER_STATE new_buffer ) -#else -void yy_switch_to_buffer( new_buffer ) -YY_BUFFER_STATE new_buffer; -#endif - { - if ( yy_current_buffer == new_buffer ) +/** Switch to a different input buffer. + * @param new_buffer The new input buffer. + * + */ + void yy_switch_to_buffer (YY_BUFFER_STATE new_buffer ) +{ + + /* TODO. We should be able to replace this entire function body + * with + * yypop_buffer_state(); + * yypush_buffer_state(new_buffer); + */ + yyensure_buffer_stack (); + if ( YY_CURRENT_BUFFER == new_buffer ) return; - if ( yy_current_buffer ) + if ( YY_CURRENT_BUFFER ) { /* Flush out information for old buffer. */ - *yy_c_buf_p = yy_hold_char; - yy_current_buffer->yy_buf_pos = yy_c_buf_p; - yy_current_buffer->yy_n_chars = yy_n_chars; + *(yy_c_buf_p) = (yy_hold_char); + YY_CURRENT_BUFFER_LVALUE->yy_buf_pos = (yy_c_buf_p); + YY_CURRENT_BUFFER_LVALUE->yy_n_chars = (yy_n_chars); } - yy_current_buffer = new_buffer; - yy_load_buffer_state(); + YY_CURRENT_BUFFER_LVALUE = new_buffer; + yy_load_buffer_state( ); /* We don't actually know whether we did this switch during * EOF (yywrap()) processing, but the only time this flag * is looked at is after yywrap() is called, so it's safe * to go ahead and always set it. */ - yy_did_buffer_switch_on_eof = 1; - } - - -#ifdef YY_USE_PROTOS -void yy_load_buffer_state( void ) -#else -void yy_load_buffer_state() -#endif - { - yy_n_chars = yy_current_buffer->yy_n_chars; - yytext_ptr = yy_c_buf_p = yy_current_buffer->yy_buf_pos; - yyin = yy_current_buffer->yy_input_file; - yy_hold_char = *yy_c_buf_p; - } + (yy_did_buffer_switch_on_eof) = 1; +} +static void yy_load_buffer_state (void) +{ + (yy_n_chars) = YY_CURRENT_BUFFER_LVALUE->yy_n_chars; + (yytext_ptr) = (yy_c_buf_p) = YY_CURRENT_BUFFER_LVALUE->yy_buf_pos; + yyin = YY_CURRENT_BUFFER_LVALUE->yy_input_file; + (yy_hold_char) = *(yy_c_buf_p); +} -#ifdef YY_USE_PROTOS -YY_BUFFER_STATE yy_create_buffer( FILE *file, int size ) -#else -YY_BUFFER_STATE yy_create_buffer( file, size ) -FILE *file; -int size; -#endif - { +/** Allocate and initialize an input buffer state. + * @param file A readable stream. + * @param size The character buffer size in bytes. When in doubt, use @c YY_BUF_SIZE. + * + * @return the allocated buffer state. + */ + YY_BUFFER_STATE yy_create_buffer (FILE * file, int size ) +{ YY_BUFFER_STATE b; - b = (YY_BUFFER_STATE) yy_flex_alloc( sizeof( struct yy_buffer_state ) ); + b = (YY_BUFFER_STATE) yyalloc(sizeof( struct yy_buffer_state ) ); if ( ! b ) YY_FATAL_ERROR( "out of dynamic memory in yy_create_buffer()" ); @@ -1363,80 +1448,75 @@ /* yy_ch_buf has to be 2 characters longer than the size given because * we need to put in 2 end-of-buffer characters. */ - b->yy_ch_buf = (char *) yy_flex_alloc( b->yy_buf_size + 2 ); + b->yy_ch_buf = (char *) yyalloc(b->yy_buf_size + 2 ); if ( ! b->yy_ch_buf ) YY_FATAL_ERROR( "out of dynamic memory in yy_create_buffer()" ); b->yy_is_our_buffer = 1; - yy_init_buffer( b, file ); + yy_init_buffer(b,file ); return b; - } +} +/** Destroy the buffer. + * @param b a buffer created with yy_create_buffer() + * + */ + void yy_delete_buffer (YY_BUFFER_STATE b ) +{ -#ifdef YY_USE_PROTOS -void yy_delete_buffer( YY_BUFFER_STATE b ) -#else -void yy_delete_buffer( b ) -YY_BUFFER_STATE b; -#endif - { if ( ! b ) return; - if ( b == yy_current_buffer ) - yy_current_buffer = (YY_BUFFER_STATE) 0; + if ( b == YY_CURRENT_BUFFER ) /* Not sure if we should pop here. */ + YY_CURRENT_BUFFER_LVALUE = (YY_BUFFER_STATE) 0; if ( b->yy_is_our_buffer ) - yy_flex_free( (void *) b->yy_ch_buf ); + yyfree((void *) b->yy_ch_buf ); - yy_flex_free( (void *) b ); - } + yyfree((void *) b ); +} +#ifndef __cplusplus +extern int isatty (int ); +#endif /* __cplusplus */ -#ifndef YY_ALWAYS_INTERACTIVE -#ifndef YY_NEVER_INTERACTIVE -extern int isatty YY_PROTO(( int )); -#endif -#endif +/* Initializes or reinitializes a buffer. + * This function is sometimes called more than once on the same buffer, + * such as during a yyrestart() or at EOF. + */ + static void yy_init_buffer (YY_BUFFER_STATE b, FILE * file ) -#ifdef YY_USE_PROTOS -void yy_init_buffer( YY_BUFFER_STATE b, FILE *file ) -#else -void yy_init_buffer( b, file ) -YY_BUFFER_STATE b; -FILE *file; -#endif +{ + int oerrno = errno; - - { - yy_flush_buffer( b ); + yy_flush_buffer(b ); b->yy_input_file = file; b->yy_fill_buffer = 1; -#if YY_ALWAYS_INTERACTIVE - b->yy_is_interactive = 1; -#else -#if YY_NEVER_INTERACTIVE - b->yy_is_interactive = 0; -#else - b->yy_is_interactive = file ? (isatty( fileno(file) ) > 0) : 0; -#endif -#endif - } + /* If b is the current buffer, then yy_init_buffer was _probably_ + * called from yyrestart() or through yy_get_next_buffer. + * In that case, we don't want to reset the lineno or column. + */ + if (b != YY_CURRENT_BUFFER){ + b->yy_bs_lineno = 1; + b->yy_bs_column = 0; + } + b->yy_is_interactive = file ? (isatty( fileno(file) ) > 0) : 0; -#ifdef YY_USE_PROTOS -void yy_flush_buffer( YY_BUFFER_STATE b ) -#else -void yy_flush_buffer( b ) -YY_BUFFER_STATE b; -#endif + errno = oerrno; +} - { - if ( ! b ) +/** Discard all buffered characters. On the next scan, YY_INPUT will be called. + * @param b the buffer state to be flushed, usually @c YY_CURRENT_BUFFER. + * + */ + void yy_flush_buffer (YY_BUFFER_STATE b ) +{ + if ( ! b ) return; b->yy_n_chars = 0; @@ -1453,20 +1533,116 @@ b->yy_at_bol = 1; b->yy_buffer_status = YY_BUFFER_NEW; - if ( b == yy_current_buffer ) - yy_load_buffer_state(); + if ( b == YY_CURRENT_BUFFER ) + yy_load_buffer_state( ); +} + +/** Pushes the new state onto the stack. The new state becomes + * the current state. This function will allocate the stack + * if necessary. + * @param new_buffer The new state. + * + */ +void yypush_buffer_state (YY_BUFFER_STATE new_buffer ) +{ + if (new_buffer == NULL) + return; + + yyensure_buffer_stack(); + + /* This block is copied from yy_switch_to_buffer. */ + if ( YY_CURRENT_BUFFER ) + { + /* Flush out information for old buffer. */ + *(yy_c_buf_p) = (yy_hold_char); + YY_CURRENT_BUFFER_LVALUE->yy_buf_pos = (yy_c_buf_p); + YY_CURRENT_BUFFER_LVALUE->yy_n_chars = (yy_n_chars); + } + + /* Only push if top exists. Otherwise, replace top. */ + if (YY_CURRENT_BUFFER) + (yy_buffer_stack_top)++; + YY_CURRENT_BUFFER_LVALUE = new_buffer; + + /* copied from yy_switch_to_buffer. */ + yy_load_buffer_state( ); + (yy_did_buffer_switch_on_eof) = 1; +} + +/** Removes and deletes the top of the stack, if present. + * The next element becomes the new top. + * + */ +void yypop_buffer_state (void) +{ + if (!YY_CURRENT_BUFFER) + return; + + yy_delete_buffer(YY_CURRENT_BUFFER ); + YY_CURRENT_BUFFER_LVALUE = NULL; + if ((yy_buffer_stack_top) > 0) + --(yy_buffer_stack_top); + + if (YY_CURRENT_BUFFER) { + yy_load_buffer_state( ); + (yy_did_buffer_switch_on_eof) = 1; } +} +/* Allocates the stack if it does not exist. + * Guarantees space for at least one push. + */ +static void yyensure_buffer_stack (void) +{ + int num_to_alloc; -#ifndef YY_NO_SCAN_BUFFER -#ifdef YY_USE_PROTOS -YY_BUFFER_STATE yy_scan_buffer( char *base, yy_size_t size ) -#else -YY_BUFFER_STATE yy_scan_buffer( base, size ) -char *base; -yy_size_t size; -#endif - { + if (!(yy_buffer_stack)) { + + /* First allocation is just for 2 elements, since we don't know if this + * scanner will even need a stack. We use 2 instead of 1 to avoid an + * immediate realloc on the next call. + */ + num_to_alloc = 1; + (yy_buffer_stack) = (struct yy_buffer_state**)yyalloc + (num_to_alloc * sizeof(struct yy_buffer_state*) + ); + if ( ! (yy_buffer_stack) ) + YY_FATAL_ERROR( "out of dynamic memory in yyensure_buffer_stack()" ); + + memset((yy_buffer_stack), 0, num_to_alloc * sizeof(struct yy_buffer_state*)); + + (yy_buffer_stack_max) = num_to_alloc; + (yy_buffer_stack_top) = 0; + return; + } + + if ((yy_buffer_stack_top) >= ((yy_buffer_stack_max)) - 1){ + + /* Increase the buffer to prepare for a possible push. */ + int grow_size = 8 /* arbitrary grow size */; + + num_to_alloc = (yy_buffer_stack_max) + grow_size; + (yy_buffer_stack) = (struct yy_buffer_state**)yyrealloc + ((yy_buffer_stack), + num_to_alloc * sizeof(struct yy_buffer_state*) + ); + if ( ! (yy_buffer_stack) ) + YY_FATAL_ERROR( "out of dynamic memory in yyensure_buffer_stack()" ); + + /* zero only the new slots.*/ + memset((yy_buffer_stack) + (yy_buffer_stack_max), 0, grow_size * sizeof(struct yy_buffer_state*)); + (yy_buffer_stack_max) = num_to_alloc; + } +} + +/** Setup the input buffer state to scan directly from a user-specified character buffer. + * @param base the character buffer + * @param size the size in bytes of the character buffer + * + * @return the newly allocated buffer state object. + */ +YY_BUFFER_STATE yy_scan_buffer (char * base, yy_size_t size ) +{ YY_BUFFER_STATE b; if ( size < 2 || @@ -1475,7 +1651,7 @@ /* They forgot to leave room for the EOB's. */ return 0; - b = (YY_BUFFER_STATE) yy_flex_alloc( sizeof( struct yy_buffer_state ) ); + b = (YY_BUFFER_STATE) yyalloc(sizeof( struct yy_buffer_state ) ); if ( ! b ) YY_FATAL_ERROR( "out of dynamic memory in yy_scan_buffer()" ); @@ -1489,56 +1665,51 @@ b->yy_fill_buffer = 0; b->yy_buffer_status = YY_BUFFER_NEW; - yy_switch_to_buffer( b ); + yy_switch_to_buffer(b ); return b; - } -#endif - - -#ifndef YY_NO_SCAN_STRING -#ifdef YY_USE_PROTOS -YY_BUFFER_STATE yy_scan_string( yyconst char *yy_str ) -#else -YY_BUFFER_STATE yy_scan_string( yy_str ) -yyconst char *yy_str; -#endif - { - int len; - for ( len = 0; yy_str[len]; ++len ) - ; +} - return yy_scan_bytes( yy_str, len ); - } -#endif +/** Setup the input buffer state to scan a string. The next call to yylex() will + * scan from a @e copy of @a str. + * @param yystr a NUL-terminated string to scan + * + * @return the newly allocated buffer state object. + * @note If you want to scan bytes that may contain NUL values, then use + * yy_scan_bytes() instead. + */ +YY_BUFFER_STATE yy_scan_string (yyconst char * yystr ) +{ + return yy_scan_bytes(yystr,strlen(yystr) ); +} -#ifndef YY_NO_SCAN_BYTES -#ifdef YY_USE_PROTOS -YY_BUFFER_STATE yy_scan_bytes( yyconst char *bytes, int len ) -#else -YY_BUFFER_STATE yy_scan_bytes( bytes, len ) -yyconst char *bytes; -int len; -#endif - { +/** Setup the input buffer state to scan the given bytes. The next call to yylex() will + * scan from a @e copy of @a bytes. + * @param bytes the byte buffer to scan + * @param len the number of bytes in the buffer pointed to by @a bytes. + * + * @return the newly allocated buffer state object. + */ +YY_BUFFER_STATE yy_scan_bytes (yyconst char * yybytes, int _yybytes_len ) +{ YY_BUFFER_STATE b; char *buf; yy_size_t n; int i; /* Get memory for full buffer, including space for trailing EOB's. */ - n = len + 2; - buf = (char *) yy_flex_alloc( n ); + n = _yybytes_len + 2; + buf = (char *) yyalloc(n ); if ( ! buf ) YY_FATAL_ERROR( "out of dynamic memory in yy_scan_bytes()" ); - for ( i = 0; i < len; ++i ) - buf[i] = bytes[i]; + for ( i = 0; i < _yybytes_len; ++i ) + buf[i] = yybytes[i]; - buf[len] = buf[len+1] = YY_END_OF_BUFFER_CHAR; + buf[_yybytes_len] = buf[_yybytes_len+1] = YY_END_OF_BUFFER_CHAR; - b = yy_scan_buffer( buf, n ); + b = yy_scan_buffer(buf,n ); if ( ! b ) YY_FATAL_ERROR( "bad buffer in yy_scan_bytes()" ); @@ -1548,148 +1719,196 @@ b->yy_is_our_buffer = 1; return b; - } +} + +#ifndef YY_EXIT_FAILURE +#define YY_EXIT_FAILURE 2 #endif +static void yy_fatal_error (yyconst char* msg ) +{ + (void) fprintf( stderr, "%s\n", msg ); + exit( YY_EXIT_FAILURE ); +} -#ifndef YY_NO_PUSH_STATE -#ifdef YY_USE_PROTOS -static void yy_push_state( int new_state ) -#else -static void yy_push_state( new_state ) -int new_state; -#endif - { - if ( yy_start_stack_ptr >= yy_start_stack_depth ) - { - yy_size_t new_size; +/* Redefine yyless() so it works in section 3 code. */ - yy_start_stack_depth += YY_START_STACK_INCR; - new_size = yy_start_stack_depth * sizeof( int ); +#undef yyless +#define yyless(n) \ + do \ + { \ + /* Undo effects of setting up yytext. */ \ + int yyless_macro_arg = (n); \ + YY_LESS_LINENO(yyless_macro_arg);\ + yytext[yyleng] = (yy_hold_char); \ + (yy_c_buf_p) = yytext + yyless_macro_arg; \ + (yy_hold_char) = *(yy_c_buf_p); \ + *(yy_c_buf_p) = '\0'; \ + yyleng = yyless_macro_arg; \ + } \ + while ( 0 ) - if ( ! yy_start_stack ) - yy_start_stack = (int *) yy_flex_alloc( new_size ); +/* Accessor methods (get/set functions) to struct members. */ - else - yy_start_stack = (int *) yy_flex_realloc( - (void *) yy_start_stack, new_size ); +/** Get the current line number. + * + */ +int yyget_lineno (void) +{ - if ( ! yy_start_stack ) - YY_FATAL_ERROR( - "out of memory expanding start-condition stack" ); - } + return yylineno; +} - yy_start_stack[yy_start_stack_ptr++] = YY_START; +/** Get the input stream. + * + */ +FILE *yyget_in (void) +{ + return yyin; +} - BEGIN(new_state); - } -#endif +/** Get the output stream. + * + */ +FILE *yyget_out (void) +{ + return yyout; +} +/** Get the length of the current token. + * + */ +int yyget_leng (void) +{ + return yyleng; +} -#ifndef YY_NO_POP_STATE -static void yy_pop_state() - { - if ( --yy_start_stack_ptr < 0 ) - YY_FATAL_ERROR( "start-condition stack underflow" ); +/** Get the current token. + * + */ - BEGIN(yy_start_stack[yy_start_stack_ptr]); - } -#endif +char *yyget_text (void) +{ + return yytext; +} +/** Set the current line number. + * @param line_number + * + */ +void yyset_lineno (int line_number ) +{ -#ifndef YY_NO_TOP_STATE -static int yy_top_state() - { - return yy_start_stack[yy_start_stack_ptr - 1]; - } -#endif + yylineno = line_number; +} -#ifndef YY_EXIT_FAILURE -#define YY_EXIT_FAILURE 2 -#endif +/** Set the input stream. This does not discard the current + * input buffer. + * @param in_str A readable stream. + * + * @see yy_switch_to_buffer + */ +void yyset_in (FILE * in_str ) +{ + yyin = in_str ; +} -#ifdef YY_USE_PROTOS -static void yy_fatal_error( yyconst char msg[] ) -#else -static void yy_fatal_error( msg ) -char msg[]; -#endif - { - (void) fprintf( stderr, "%s\n", msg ); - exit( YY_EXIT_FAILURE ); - } +void yyset_out (FILE * out_str ) +{ + yyout = out_str ; +} +int yyget_debug (void) +{ + return yy_flex_debug; +} +void yyset_debug (int bdebug ) +{ + yy_flex_debug = bdebug ; +} -/* Redefine yyless() so it works in section 3 code. */ +static int yy_init_globals (void) +{ + /* Initialization is the same as for the non-reentrant scanner. + * This function is called from yylex_destroy(), so don't allocate here. + */ + + (yy_buffer_stack) = 0; + (yy_buffer_stack_top) = 0; + (yy_buffer_stack_max) = 0; + (yy_c_buf_p) = (char *) 0; + (yy_init) = 0; + (yy_start) = 0; + +/* Defined in main.c */ +#ifdef YY_STDINIT + yyin = stdin; + yyout = stdout; +#else + yyin = (FILE *) 0; + yyout = (FILE *) 0; +#endif + + /* For future reference: Set errno on error, since we are called by + * yylex_init() + */ + return 0; +} -#undef yyless -#define yyless(n) \ - do \ - { \ - /* Undo effects of setting up yytext. */ \ - yytext[yyleng] = yy_hold_char; \ - yy_c_buf_p = yytext + n; \ - yy_hold_char = *yy_c_buf_p; \ - *yy_c_buf_p = '\0'; \ - yyleng = n; \ - } \ - while ( 0 ) +/* yylex_destroy is for both reentrant and non-reentrant scanners. */ +int yylex_destroy (void) +{ + + /* Pop the buffer stack, destroying each element. */ + while(YY_CURRENT_BUFFER){ + yy_delete_buffer(YY_CURRENT_BUFFER ); + YY_CURRENT_BUFFER_LVALUE = NULL; + yypop_buffer_state(); + } + + /* Destroy the stack itself. */ + yyfree((yy_buffer_stack) ); + (yy_buffer_stack) = NULL; + + /* Reset the globals. This is important in a non-reentrant scanner so the next time + * yylex() is called, initialization will occur. */ + yy_init_globals( ); + return 0; +} -/* Internal utility routines. */ +/* + * Internal utility routines. + */ #ifndef yytext_ptr -#ifdef YY_USE_PROTOS -static void yy_flex_strncpy( char *s1, yyconst char *s2, int n ) -#else -static void yy_flex_strncpy( s1, s2, n ) -char *s1; -yyconst char *s2; -int n; -#endif - { +static void yy_flex_strncpy (char* s1, yyconst char * s2, int n ) +{ register int i; for ( i = 0; i < n; ++i ) s1[i] = s2[i]; - } +} #endif #ifdef YY_NEED_STRLEN -#ifdef YY_USE_PROTOS -static int yy_flex_strlen( yyconst char *s ) -#else -static int yy_flex_strlen( s ) -yyconst char *s; -#endif - { +static int yy_flex_strlen (yyconst char * s ) +{ register int n; for ( n = 0; s[n]; ++n ) ; return n; - } +} #endif - -#ifdef YY_USE_PROTOS -static void *yy_flex_alloc( yy_size_t size ) -#else -static void *yy_flex_alloc( size ) -yy_size_t size; -#endif - { +void *yyalloc (yy_size_t size ) +{ return (void *) malloc( size ); - } +} -#ifdef YY_USE_PROTOS -static void *yy_flex_realloc( void *ptr, yy_size_t size ) -#else -static void *yy_flex_realloc( ptr, size ) -void *ptr; -yy_size_t size; -#endif - { +void *yyrealloc (void * ptr, yy_size_t size ) +{ /* The cast to (char *) in the following accommodates both * implementations that use char* generic pointers, and those * that use void* generic pointers. It works with the latter @@ -1698,31 +1917,22 @@ * as though doing an assignment. */ return (void *) realloc( (char *) ptr, size ); - } +} -#ifdef YY_USE_PROTOS -static void yy_flex_free( void *ptr ) -#else -static void yy_flex_free( ptr ) -void *ptr; -#endif - { - free( ptr ); - } +void yyfree (void * ptr ) +{ + free( (char *) ptr ); /* see yyrealloc() for (char *) cast */ +} + +#define YYTABLES_NAME "yytables" -#if YY_MAIN -int main() - { - yylex(); - return 0; - } -#endif #line 126 "param_lex.l" + void yy_cleanup(void) { - yy_delete_buffer(yy_current_buffer); + yy_delete_buffer(YY_CURRENT_BUFFER); } #ifdef FUNC_NAME @@ -1790,7 +2000,7 @@ YY_BUFFER_STATE ystate; int i,j; struct stat st1,st2; - + if(fname) { if(!fname[0]) yyerror("Null filename from INCLUDE command\n"); if(stat(fname,&st1)) { @@ -1833,3 +2043,4 @@ } else yyerror("Too many nested includes\n"); } } + debian/patches/series0000644000000000000000000000004612233513365012035 0ustar 10_utils.patch 10_lex hardening.patch debian/patches/10_utils.patch0000644000000000000000000002604311110210273013267 0ustar --- loki.orig/utils/Makefile.in +++ loki/utils/Makefile.in @@ -18,7 +18,7 @@ SRC = qavg.c hist.c PROGS = qavg hist -SCRIPTS = loki_ext count dist freq sort_error +SCRIPTS = ext count dist freq sort_error all: qavg hist @@ -30,11 +30,11 @@ ../bin: mkdir ../bin - + scripts: ../bin for file in $(SCRIPTS); do \ - $(SED) 's!+PERLPROG+!$(PERL)!' $$file.in > $(bindir)/$$file.pl; \ - $(CHMOD) $(INSTALL_PERM) $(bindir)/$$file.pl; \ + $(SED) 's!+PERLPROG+!$(PERL)!' $$file.in > $(bindir)/loki_$$file; \ + $(CHMOD) $(INSTALL_PERM) $(bindir)/loki_$$file; \ done install: $(PROGS) scripts @@ -42,16 +42,16 @@ $(CP) $$file $(bindir)/; \ $(CHMOD) $(INSTALL_PERM) $(bindir)/$$file ; \ done - + clean: rm -f *~ *.o *.a *.bak a.out core seedfile depend distclean: clean - rm -f Makefile *.pl $(PROGS) + rm -f Makefile loki_* $(PROGS) rm -rf ../bin - + depend: $(SRC) ../include/config.h @MAKEDEPEND@ -I../include $(DMALLOC_INC) $(SRC) touch depend - + # DO NOT DELETE THIS LINE -- make depend depends on it. --- /dev/null +++ loki/utils/ext.in @@ -0,0 +1,373 @@ +#!+PERLPROG+ +# +# Script to extract columns from loki.out +# +# Should work with output from all versions of Loki (up to loki_2.3) +# +# Simon Heath - September 2000 +# +use Getopt::Std; +use IO::File; +use POSIX qw(tmpnam); +use strict; +my($i,$j,$k,%opt,$file,$hi,$lo,$flag,$out_type,$version,$link_fg,$start,$stop); +my($lg,%chrom,@map_start,@map_end,@map_length,$sex_map,$model); +my(@mkchrom,@mkpos,@mkname,$nmk,@col,$n_cov,$max_col,$ngroup); +my($it_col,$tv_col,$resvar_col,$mean_col,$addvar_col); +my($mean_set,$mean,$resvar_set,$resvar,$max_col1,$tau_col,$tau_beta,$tau,$tau_mode); +my($nc,$nqtl,$nqtl1,$line,$iter,$tv,$tv1,$sz,$nrand,@rand_col,@rand_fg,$tmp); +my(@no_output,$out_col_flag,$adj); +my($x1,$x2); +# Chromsome extracted defaults to the first one +$opt{c}=1; +getopts('xc:CDf:r:o:i:',\%opt); +# -r option sets a range of positions on the chromosome to look at +if($opt{r}) { + $tmp=$opt{r}; + if($tmp=~/^([+-]?(?:(?:[0-9]*\.[0-9]+)|(?:[0-9]+))(?:[eE][-+]?[0-9]+)?)(.*)/) { + $lo=$1; + $tmp=$2; + } + if($tmp=~/^[,-:](.*)/) { + $tmp=$1; + if($tmp=~/^([+-]?(?:(?:[0-9]*\.[0-9]+)|(?:[0-9]+))(?:[eE][-+]?[0-9]+)?)/) { + $hi=$1; + } + } + die "Bad -r option\n" if(!defined($hi) && !defined($lo)); + if(defined($lo) && defined($hi) && $lo>$hi) { + $tmp=$lo; + $lo=$hi; + $hi=$tmp; + } +} +# -i option sets a range of iterations to consider +if($opt{i}) { + $tmp=$opt{i}; + if($tmp=~/^([1-9][0-9]*)(.*)/) { + $start=$1; + $tmp=$2; + } + if($tmp=~/^[,-:](.*)/) { + $tmp=$1; + if($tmp=~/^([1-9][0-9]*)/) { + $stop=$1; + } + } + die "Bad -i option\n" if(!defined($start) && !defined($stop)); + if(defined($start) && defined($stop) && $start>$stop) { + $tmp=$start; + $start=$stop; + $stop=$tmp; + } + $start=1 if(!defined($start)); +} + +# Set default number of genetic groups +$ngroup=1; +# Used to store columns where to find interesting quantitities +# -1 means not known +$it_col=-1; # Iteration count +$tv_col=-1; # Total genetic variance +$resvar_col=-1; # Residual variance +$mean_col=-1; # Grand mean +$max_col=-1; # No. fixed output columns +$n_cov=-1; # No. covariate columns +$ngroup=1; # No. genetic groups +$tau_col=-1; +$tau_mode=-1; +$out_type=-1; # Output type +# Open output file if specified, otherwise we use STDOUT +if($opt{o}) { + open OFILE,">".$opt{o} or die "Couldn't open output file ",$opt{o},"\n"; +} else { + open OFILE,">&STDOUT" or die "Couldn't dup STDOUT\n"; +} +$sex_map=0; +$i=$opt{x}+$opt{C}+$opt{D}; +die "Can not specify more that 1 of the options C,D,x at once.\n" if($i>1); +$opt{x}=1 unless $i; +$file=$opt{f}?$opt{f}:"loki.out"; +open FILE,$file or die "Could not open file '$file'\n"; +# Go though file +while() { + $line++; + if($flag) { # Parse the data portion of the file + split; + # Iteration number + $iter=$_[0]; + if($opt{i}) { + next if($iter<$start); + last if(defined($stop) && $iter>$stop); + } + $nc=@_; + next if($nc<$max_col); + if($version==-1) { + $i=$max_col+$_[6]; + last if($nc<$max_col); + $ngroup=$_[7]; + } else {$i=$max_col;} + $max_col1=$i; + if($opt{C}) { + for($i=0;$i<$max_col1;$i++) {print OFILE " $_[$i]";} + print OFILE "\n"; + next; + } + # Total variance + $tv1=0; #first get non-genetic variance + for($j=0;$j<$nrand;$j++) { + if($rand_fg[$j]==2) { + $sz=$_[$rand_col[$j]]; + $tv1+=$sz; + } + } + # Now get genetic variance + if($tv_col>=0) {$tv=$_[$tv_col];} + else { # Not specified, must calculate + $tv=0; + for($j=0;$j<$nrand;$j++) { + $sz=$_[$rand_col[$j]]; + $sz*=$sz if($rand_fg[$j]==1); + if($rand_fg[$j]!=2) {$tv+=$sz;} + } + } + # Count QTL's + $nqtl=0; + $nqtl1=0; + while($i<$nc) { + $lg=$_[$i]; + die "Illegal linkage group $lg at line $line column ",$i+1,"\n" if($lg && !$chrom{$lg}); + $i+=1+$sex_map if($lg || !$out_type); + $i+=4+$ngroup; + if($tv_col<0) { + $sz=$_[$i-1]; + $tv+=$sz*$sz; + } + $nqtl++; + if($lg) { + $nqtl1++; + } + } + # If QTL numbers are given, check against what we found + if($out_type<2) { + die "Mismatch in QTL numbers ($nqtl,$_[1]) at line $line\n" if($nqtl!=$_[1]); + die "Mismatch in linked QTL numbers ($nqtl1,$_[2]) at line $line\n" if($nqtl1!=$_[2]); + } + # Get residual variance + if(!$resvar_set) { + # Do we know where it is ? + if($resvar_col>=0) {$resvar=$_[$resvar_col];} + # if not, guess + elsif($out_type<2) {$resvar=$_[4];} + else {$resvar=$_[2];} + } + # Total non-genetic variance + $tv1+=$resvar; + # Print out a 'standard' (across output types) set of columns + if($opt{D}) { + # Get Mean + if(!$mean_set) { + if($mean_col>=0) {$mean=$_[$mean_col];} + elsif($out_type<2) {$mean=$_[3];} + else {$mean=$_[1];} + } + # get Tau + if($tau_col>=0) {$tau=$_[$tau_col];} + elsif($tau_mode>=0) { + if($tau_mode==2) {$tau=$resvar*$tau_beta;} + else {$tau=$tau_beta;} + } else { + # Must be a very early version, assume that we know where tau is... + $tau=$_[5]; + } + print OFILE "$iter $nqtl $nqtl1 $mean $resvar $tau "; + printf OFILE "%g",$tv; + # Are we on a recent version with all column info? + if($out_col_flag) { + for($i=1;$i<$max_col1;$i++) { + print OFILE " $_[$i]" if(!$no_output[$i]); + } + # This is more complicated + } else { + if(!$out_type) {$i=8;} + elsif($out_type<2) {$i=6;} + else {$i=3}; + for(;$i<$max_col1;$i++) { + print OFILE " $_[$i]"; + } + } + print OFILE "\n"; + # Extract information about linked QTL's + } elsif($opt{x} && $nqtl) { + # Go through QTL's + $i=$max_col1; + while($i<$nc) { + $lg=$_[$i]; + if($lg eq $opt{c}) { + $j=$i+1; + if($lg) { + $x1=$_[$j++]; + $x2=$_[$j++] if($sex_map); + } + # Select QTL based on linkage group and range + if(!$lg || !$opt{r} || ((!defined($lo) || $x1>=$lo) && (!defined($hi) || $x1<=$hi))) { + print OFILE $iter; + # Print position if linked + if($lg) { + print OFILE " $x1"; + print OFILE " $x2" if($sex_map); + } + for($k=0;$k<2+$ngroup;$k++) {print OFILE " ",$_[$j++];} + $sz=$_[$j]; + print OFILE " $sz"; + $sz*=$sz; + if($tv>0.0) {printf OFILE " %g",$sz/$tv;} + else {print OFILE " 0.0";} + if(($tv1+$tv)>0.0) {printf OFILE " %g\n",$sz/($tv+$tv1)} + else {print OFILE " 0.0\n";} + } + } + $i+=1+$sex_map if($lg || !$out_type); + $i+=4+$ngroup; + } + } + # We've reached the end of the header + } elsif(/^--*/) { + $flag=1; + # $max_col will not be set if working with an earlier version + if($max_col<0) { + # but $n_cov should be set unless ... + if($n_cov>=0) { + if($out_type<0) {$out_type=1;} + $max_col=3+$n_cov; + $version=1; + if(!$out_type) {$max_col+=5;} + elsif($out_type==1) {$max_col+=3;} + } else { # ... we are working with a genuine v2.0 copy + $out_type=0; + $max_col=8; + $version=-1; + } + } + } elsif(!$flag) { # First parse the header + if(/^Output format: (\d+)/) { + $out_type=$1; + next; + } + if(/^Created by loki (\d+).(\d+).(\d+).*:/) { + $version=2 if($1>2 || ($1==2 && $2>=3)); + next; + } + # Pull out linkage group information if it is there + if(/^Linkage groups:$/) { + $link_fg=1; + next; + } + if($link_fg==1) { + # Check for linkage group names and map lengths + if(/(\d+): (.*)$/) { + $lg=$1; + if($2=~/^(.*) Map range: (.*)/) { + $chrom{$lg}=$1; + if($2=~/\((-?[0-9.]+)cM to (-?[0-9.]+)cM\)(.*)/) { + $map_start[$lg][0]=$1; + $map_end[$lg][0]=$1; + if($3=~/\((-?[0-9.]+)cM to (-?[0-9.]+)cM\)/) { + $map_start[$lg][1]=$1; + $map_end[$lg][1]=$1; + $sex_map=1; + } + } else { die "Error reading linkage group map range\n"; } + } else {$chrom{$lg}=$1;} + } elsif(/^\s+(.+) - ([\d\.]+)\s*([\d\.]*)/) { + if(!$opt{c} || $lg eq $opt{c}) { + $mkchrom[$nmk]=$lg; + $mkpos[$nmk][0]=$2; + $mkpos[$nmk][1]=$3; + $mkname[$nmk++]=$1; + } + } else { + # Check for total map length + if(/^Total Map Length: (.*)$/) { + if($1=~/(\d\d*\.?\d*)cM(.*)/) { + $map_length[0]=$1; + if($2=~/(\d\d*\.?\d*)cM$/) { + $map_length[1]=$1; + $sex_map=1; + } + } else { die "Error reading map lengths\n"; } + $link_fg=2; + next; + } + } + } + $model=$1 if(/^Model: (.+)/); + if($link_fg<3) { + if(/^Output columns:$/) { + $link_fg=3; + $out_col_flag=1; + next; + } elsif(/Output covariate data:$/) { + $link_fg=4; + } + } elsif($link_fg>2) { + if(/(\d+): (.*)/) { + $col[$1]=$2; + $tmp=$1-1; + if($link_fg==4) { + $link_fg=3; + if(!$tmp) {$adj=6;} + } + $tmp+=$adj; + if($2 eq "Total genetic variance") { + $tv_col=$tmp; + $no_output[$tmp]=1; + } elsif($2 eq "Additive variance") { + $rand_fg[$nrand]=0; + $rand_col[$nrand++]=$tmp; + } elsif($2=~/^Additional random variance for/) { + $rand_fg[$nrand]=2; + $rand_col[$nrand++]=$tmp; + } elsif($2=~/\S+ size$/) { + $rand_fg[$nrand]=1; + $rand_col[$nrand++]=$tmp; + } elsif($2 eq "Residual variance") { + $resvar_col=$tmp; + $no_output[$tmp]=1; + } elsif($2 eq "Grand mean") { + $mean_col=$tmp; + $no_output[$tmp]=1; + } elsif($2 eq "Tau") { + $tau_col=$tmp; + $no_output[$tmp]=1; + } elsif($2 eq "No. QTL's in model") { + $no_output[$tmp]=1; + } elsif($2 eq "No. linked QTL's") { + $no_output[$tmp]=1; + } elsif($2 eq "No. covariate columns") { + $no_output[$tmp]=1; + } elsif($2 eq "No. genetic groups") { + $no_output[$tmp]=1; + } + } elsif(/No. covariate columns: (\d+)/) { + $n_cov=$1; + } elsif(/No. fixed output columns: (\d+)/) { + $max_col=$1; + } elsif(/No. genetic groups: (\d+)/) { + $ngroup=$1; + } elsif(/^Sex specific map$/) { + $sex_map=1; + } elsif(/^Residual variance: ([0-9-.]+)/) { + $resvar_set=1; + $resvar=$1; + } elsif(/^Grand mean: ([0-9-.]+)/) { + $mean_set=1; + $mean=$1; + } elsif(/^Tau Mode: ([0-9]+)/) { + $tau_mode=$1; + } elsif(/^Tau Beta: ([0-9.]+)/) { + $tau_beta=$1; + } + } + } +} debian/compat0000644000000000000000000000000211750760421010367 0ustar 9 debian/loki-doc.doc-base.lokifaq0000644000000000000000000000033711110210273013702 0ustar Document: lokifaq Title: Loki Manual Author: Simon C. Heath Abstract: This document answers frequently asked questions about Loki. Section: Science/Biology Format: postscript Files: /usr/share/doc/loki-doc/loki_faq.ps.gz debian/loki-doc.README.Debian0000644000000000000000000000020711110210273012712 0ustar This is the documentation for the loki package. The source package of loki also contains the LaTeX source of these PostScript files.