[BioRuby] BioRuby and log4r

[Pjotr Prins]

I propose we start using 

  http://log4r.rubyforge.org/manual.html

which has the standard logging features one would expect. I
particularly like the lazy evaluation (deferred block).

What it does fall short on, as well as most other loggers, is
usage use cases. A logger has to behave differently when a tool is
used by:

- developer: fail early and often (on warnings!)
- user: fail on normal error
- library: fail on serious error
- web server: fail on serious error
- fault tolerant system: never fail, try to resume
 
Essentially, I see three or four error handlers.

We can create a default logger for BioRuby = user

But I like to have more options. It would be nice to have several
levels within 'info', 'warn' or 'error', to be displayed/logged on
user needs.

Also, with the plugins we should have standardized switches for CLI
utilities. 

Are we interested in making this core BioRuby, or should I
incorporate it as a bio-plugin? I am thinking of writing a front-end
of log4r.

Pj.