Compid
======

  Copyright 2009 Lari Natri <lari.natri@gmail.com>


Starting Compid:
================

  Compid doesn't work by clicking compid.jar file, because the
  default memory heap settings are usually too small. Please
  use the startup scripts provided.

  - On Windows machines, click file:
      
        compid.cmd

  - On Linux machines, run:

        compid.sh


Requirements
============
  Compid requires Java Version 6 or newer.


Importing Mascot DAT files
==========================

  Compid supports using the freely available Mascot Parser plugin from
  Matrix Science to import DAT files created by Mascot. To enable this
  functionality, obtain the correct Mascot Parser version for your platform
  from:

    http://www.matrixscience.com/parser_support.html

  Unarchive the file and place the two files in java subdirectory
  to Compid's lib subdirectory from where Compid will implicitly
  find and utilize them. An alternative placement is ".compid"
  directory in your home folder. The files are named msparser.jar
  and [msparserj.dll (for Windows) or libmsparserj.so (for Linux)].
  It is imperative to get both files from the same archive.

  Note that C++ Standard Library must be installed on the target
  machine (which it usually is). At least Mascot Parser versions
  2.2.x require the Standard Library to be of version 5.


Concerning Memory
=================

  Compid uses quite a lot of memory for some operations.

  If memory runs out (you see OutOfHeapSpace exceptions), edit
  the startup script file (compid.cmd or compid.sh) and increase
  the -Xmx parameter. A good idea would be to do it in 50 MiB
  increments. 

  If you use Mascot Parser plugin and it crashes the software with
  ACCESS_VIOLATION errors, it is usually because too much memory
  is allocated. To fix this, lower the -Xmx and -Xms parameters in
  startup scripts.

  Default values for -Xms and -Xmx Java parameters, which seem to
  work well for most computers with at least 1 GiB of memory are:
  -Xms128m -Xmx850m

  Remember to start Compid with the script in question and not by
  running compid.jar.


License
=======
  
  Compid itself is licensed with GNU General Public License version
  3 or later (at your option). For information on licenses of other
  software included in Compid, see NOTICE file.