[Biocorba-l] bioCORBA, BSANE SeqFeatures/Locations

[Jason Stajich]

Not sure where to start responding, so much traffic!

I assume we are to be looking at
http://corba.ebi.ac.uk/~muilu/uml/bsane_v3/idl/seqcore.idl to be the
merger between BSANE and biocorba core objects and when agreed upon, the
biocorba 0.3 spec?

Very happy to hear that Vectors may die!  I found I had to do very
stupid things in bioperl/ensembl corba bindings to comply with this
interface and then Alan told me he would just not implement methods he
thought were uncessary...  Gosh, I should have learned.

SeqFeatures:

I agree with Ewan's comments on what is missing for GFF.  I notice a lot
of "this is what biojava does", do we need to help explain what bioperl
does better to make sure all those views are at least heard?

SeqFeatureLocations:

Glad you put region_operator in there, that will help handle a set of
cases that were not possible with the existing biocorba spec.

I do think that 'sub_regions' or whatever we decide to name here will
be used to have Locations which contain locations even though we did not
really handle this in biocorba 0.2.  Implementations in bioperl and I know
biojava do support hierarchies of locations, it just didn't bubble to the
surface in time to be part of the 0.2 spec (Brad/Jeff I'm not sure if you
guys got to this yet). 

Additionally in bioperl we have a pluggable interface for how to
interpret locations, because it is a little unclear how you plan to
resolve the start() or end() calls on a SeqFeature with a set of
FuzzyLocations.  We have a coordinate policy object which one can plug
into the location object - Narrowest, Widest, and Average policies are
implemented so that when one calls start or end() on a Location which is
fuzzy or contains sub locations it can make a guess as to what you expect
here.

This may be over the top for what is desired in the seqcore proposal, but
at least explaining what we've done in bioperl.

-Jason

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