[Biocorba-l] update on the ensembl/biocorba front

[Jason Stajich]

  So the ensembl CORBA bindings seem to work great.  I was able to use the
top_SeqFeatures method to pull in sequence features from a VirtualContig
so we do not need any extra methods for obtaining sequence feature
information.  I'm not totally clear where the hooks for pulling in
supporting evidence for transcripts is done, but we may want to think
about adding a method for that in the IDL.

  At some point we may also want an entry point which can specify which
external features should be loaded so choosing which objects to fetch
could be dynamic.

  What is next is dealing with Translations/Transcripts/Genes/Exons being
sequence features which needs changes to the Ensembl perl code to support
the more advanced location model.  I'm not 100% sure how this will get
done, but Ewan has suggested a possible plan of attack that I will try.

  The whole inheritance from Bio::Root::Object vs Bio::Root::RootI of
course complains for every object when using bioperl 0.7, but everything
seems to perform fine running under the 0.7 code.

-Jason
Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center
http://www.chg.duke.edu/