[Biocorba-l] SeqFeature and Id

[Brad Chapman]

Hi Juha;
Nice to hear from you!

> One question which has been bothering us for some time is that should
> the SeqFeature has id? There are databases which have just features
> without sequences..
> 
> So, shall we make the SeqFeature (or even Annotation) inherit from the
> Identifiable? 

I'm indifferent about the change -- for me it doesn't make much
sense to have a sequence feature without a sequence (hey, the
sequence is the important part, right? :-). 

What I'd like to see is a concert IDL we can implement -- see how it
works and then adjust from there. This worked well for BioCorba: we
had an initial spec that worked good for us, then Alan came along
with the EMBL stuff and beefed it up for what he needed.

> BTW I have made (eh already sometime ago) IDLs and clickable UML
> documents out of the version we agreed during the BOSC. Those are on
> page: http://industry.ebi.ac.uk/BSANE

Cool. Thanks. I'm almost finished with a Biopython implementation of
the spec (hopefully after this weekend). I've got the Sequence and
Annotation stuff done, almost finished with SeqFeatures, and then
just collections to go. Yippee!

Since we're talking about the spec, I might as well bring up a few
snags I've got so far so people can comment on them:

--> The current idl won't compile with orbit-idl (so orbit-python
and orbit-perl won't work with it). There is a bug in the IDL
compiler (at least up to 0.5.8) and it can't handle recursive
structs. So the SeqFeatureLocation struct, which has a reference to
a list of SeqFeatureLocation sub_regions, will cause the compiler to
segfault. I'm not sure what the best thing to do about this is.
Suggestions from anyone?

--> The inclusion of CORBA.idl causes lots of problems for me.
First, CORBA.idl isn't included with any python ORB implementations
as far as I can tell -- I found some in a Java ORB, but it didn't
contain the definitions we are using (ObjectSeq, OctetSeq,
StringSeq, ULongSeq). My preference would be to just add these
definitions to the bsane.idl file and not worry about it -- what do
people think about this?

Other than that it's going okay. I'll post again here once I've
finished the python implementation so anyone interesting can play
with it.

Sorry for the long mail. Hope ya'll are having a good Friday.
Brad