Finnigan version 0.02
=====================

This module is part of the Unfinnigan project aimed at decoding
the proprietary data files used to acquire data from Thermo mass
spectrometers. These are are known as "raw" files and they were
intended to be read with proprietary software (Xcalibur) running
on the Windows operating system.

This module allows complete access to scan data without the need
to install any vendor software.

It can decode several recent file formats (versions 57, 62 and 63)
and it comes with a suite of command-line tools that can be used
to examine various elements of the data. One of the tools, uf-mzxml,
replaces ReAdW in the task of converting the Finnigan data to mzXML.

The module and the tools have been tested in an ongoing SILAC
proteomics project, where users are writing their own data analysis
scripts. 

For more details, go to 

  http://code.google.com/p/unfinnigan/

PLATFORM

Thermo software runs only on Intel platforms and therefore every
word in their files uses little-endian encoding. The (un)Finnigan
modules have also been tested only on Intel platforms.  

The decoder is built around Perl's unpack() function and there is
a chance that some of the templates may be incorrectly interpreted
on a big-endian platform. The tests should reveal that -- please
let me know if anything breaks.

INSTALLATION

To install this module type the following:

   perl Makefile.PL
   make
   make test
   make install

To install in user-space (without requiring root permissions),
run Makefile.PL like this:

   perl Makefile.PL PREFIX=/<your-home-dir>

Everything will work if your environment includes your home directory
in these variables:

PERL5LIB=...:<your-home-dir>/lib/perl5/site_perl
PATH=<your-home-dir>/bin:...
MANPATH=<your-home-dir>/man:...


DEPENDENCIES

This module requires these other modules:

   Data::Hexdumper
   DateTime::Format::WindowsFileTime
   Devel::Size (only in uf-mzxml, not essential)
   Encode
   File::Temp (only in uf-mzxml)
   Getopt::Declare
   Getopt::Long
   MIME::Base64 (in uf-mzxml and mzxml-unpack)
   Module::Find (not essential)
   Storable (only in uf-mzxml)
   XML::Generator (only in uf-mzxml)
   Tie::IxHash (only in uf-mzxml)

The non-essential dependencies can be removed by commenting out
the corresponding lines in the code. If you are not going to use
uf-mzxml, further dependencies can be removed by commenting them
out in Makefile.PL

COPYRIGHT AND LICENCE

Put the correct copyright and licence information here.

Copyright (C) 2010 by Gene Selkov

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.0 or,
at your option, any later version of Perl 5 you may have available.