protein-ms Files

Hi user,

Free software is software without documentation and reading documentation
is very uncool.

But to help you before you're getting too frustrated, we added some notes that
have been kept short.

0) If you use it or find it useful, please cite the correspondig publication as
   follows:
   Florian Grosse-Coosmann , Andreas M. Boehm and Albert Sickmann
   Efficient Analysis and Extraction of MS/MS Result Data from Mascot(TM) 
   Result Files, BMC Bioinformatics 2005, 6:290.
   doi:10.1186/1471-2105-6-290
   http://www.biomedcentral.com/1471-2105/6/290/abstract

1) Compilation
   Tested on Linux/386/gcc and on W2K/386/VC. It should run on arbitrary
   unices and on every NT/W2K/XP. 64 bit support should work.

   unix: Use "make", a makefile called "Makefile" exists. So give it a try.
         Some more informations, esp. for usage, are at the begin of the file.

         For flex problems see below.

         You need a c99 compatible compiler. (At least) gcc 3.3.1 works.

   WIN32: An nmake-compatible makefile called "vcwin32.mak" exists. Use it as
          a template for compilers other than MSVC 6+. With MSVC you have
          to use a command line session, call "vcvars32.bat" somewhere in your
          compiler tree and do a "nmake -f vcwin32.mak".

          For flex problems see below.

          Support is limited to MSVC. Other compilers may need some adaptions
          of mascot.h and sysdep.c.

   flex: We're using flex, a tool which builds lexical parsers. The
         description file lexer.l is compiled by flex into lexer.c which
         should be compiled by the C compiler.
         Not everybody has a perfectly running flex. So we added a skeleton
         file for flex (don't bother about it if you don't know I'm talking
         about) and a completely compiled file lexer.c which works on my
         machine.
         For unix: flex support is needed. If you don't have flex, please,
                   copy the makefile and change the lines regarding lexer.l.
                   A comment there helps.
         For WIN32: flex support is not needed. The current makefile doesn't
                    use it. If you really want to use it, feel free to reenable
                    it. The standard distribution uses lexer.c of the contrib
                    directory.

   still problems?
   a) ask your admin (no joke)
   b) reread the above once more, but more carefully
   c) OK, drop us an email

2) Corrections in the code
   Did you find something interesting? Feel free to contribute it. We'll
   merge the changes and put it on sourceforge.
   Don't forget to document it!

3) Documentation of the program
   Use your favorite browser for reading Overview.html.
   My favorite settings are
        -d filename -o tab -f mascotdir/*.dat

4) Documentation of the format
   Only the tabular format is described. Use your favorite browser for reading
   Tabformat.html.

5) Legal stuff
   This program and its parts are published under der GPL.

6) Acknowledgements
   You should thank Andreas Boehm and Albert Sickmann, too.

6) Contact
   mailto:florian.coosmann@virchow.uni-wuerzburg.de
   mailto:andreas.boehm@virchow.uni-wuerzburg.de
   mailto:albert.sickmann@virchow.uni-wuerzburg.de


Best wishes for good results,

Florian Grosse-Coosmann