[BioRuby] Codeml parser

[Michael Barton]

Hi Pjotr,

The expand report.rb looks like an excellent and substantial
improvement to the previous version. You could add a depreciated tag
to the old interface methods and these could then be removed in a
later bioruby version to decrease clutter in the API.

Mike

2010/1/4 Pjotr Prins <pjotr.public14 at thebird.nl>:
> 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.
>
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