[BioRuby] Codeml parser

[Pjotr Prins]

The writeup is pretty much done, as well as the implementation.

  http://bioruby.open-bio.org/wiki/BIORUBY_PAML

All unit tests pass:

  Running tests for PAML
  Loaded suite .
  Started
  ....................
  Finished in 0.398394 seconds.
  20 tests, 37 assertions, 0 failures, 0 errors

It is compatible with the old version. I have added 41 assertions
in the doctest (the header of report.rb).

  === Testing 'mydoc.test'...
  1.   OK  | Default Test
  41 comparisons, 1 doctests, 0 failures, 0 errors

You can view the tests and implementation at

  http://github.com/pjotrp/bioruby/blob/PAML/lib/bio/appl/paml/codeml/report.rb
See also 

The branch is:

  http://github.com/pjotrp/bioruby/tree/PAML

(don't you love github).

Pj.