To get a brief summary of the important command-line options, invoke lutefisk
with the '-h' option. (On the Macintosh, command-line options are entered on
the 'Argurments:' line of the initial dialog box. To use command-line options
under Win32 the executable must be invoked from a DOS prompt such as by using
the Command Prompt program.)
USAGE: lutefisk [options] [CID file pathname]
-o = output file pathname
-q = quiet mode ON (default OFF)
-m = precursor ion mass
-d = details file pathname
-p = params file pathname
-r = residues file pathname
-s = pathnane of file with database sequences to score
-v = verbose mode ON (default OFF)
-h = print this help text
LUTEFISK SOURCE CODE ARCHIVE CONTENTS:
(The Lutefisk_src.tar.gz archive is a tar archive that has been gzipped.)
* Example Lutefisk input file, "QTof_ETYGDMADCCEK.dta"
* Example Lutefisk output file, "QTof_ETYGDMADCCEK.lut"
* This README file, "README"
* The copright file, "COPYRIGHT"
* The version history, "HISTORY"
* The lutefisk accessory files:
* C Source code files for Lutefisk:
Makefile.XXX - Makefiles for compiling Lutefisk for
AIX, IRIX, LINUX, OSF, OSX, or SUN
LutefiskGlobalDeclarations.c Declaration of global variables.
LutefiskMain.c Reads parameter, edman, and detail files.
Also contains the function main.
LutefiskGetAutoTag.c Finds peptide sequence tags automatically.
LutefiskGetCID.c Loads data file and performs peak detection.
LutefiskMakeGraph.c Produces N and C terminal sequence graphs.
LutefiskSummedNode.c Combines N and C terminal sequence graphs
into a single graph.
LutefiskHaggis.c Finds candidate sequences by searching for
contiguous series of ions that do not necessarily
connect with either N- or C-termini.
LutefiskSubseqMaker.c Uses the sequence graph to determine
LutefiskScore.c Assigns score and rank to sequence candidates.
LutefiskXCorr.c Performs cross-correlation scoring.
LutefiskFourier.c Used for cross-correlation scoring.
ListRoutines.c Handles lists.
getopt.c Interprets line commands when starting the
program (Needed by the Mac and Win32 versions).
Lutefisk.rsrc Resources needed by the Mac version.
LutefiskDefinitions.h Contains #defines and struct definitions.
LutefiskPrototypes.h Contains function prototypes.
getopt.h Needed by the Mac and Win32 versions.
* Compiling on the Macintosh
Current Metrowerks Projects are included in the "Macintosh" folder (provided as a self-
extracting archive to maintain fidelity). If you have an older compiler you will need to
create a new "Std C Console PPC" project and add the source files as specified above. Set
the preferred heap size to 16M, the minimum heap size to 8M, and the stack size to 512k. You
may have to change the files to creator 'CWIE' and type 'TEXT' to get Codewarrior to like
them. Note that in MacOS X the apps can be compiled using the UNIX directions if desired.
* Compiling under Win32
Current Metrowerks Projects are included in the "Win32" folder. If you have an older
compiler you will need to create a new "C Console App" project and add the source files
as specified above.
* Compiling on UNIX
After untarring the archive, copy the makefile for your system to "Makefile".
Use the "make lutefisk" command.
Richard S. Johnson