[Open-bio-l] RE: seqfeature

[Thomas Down]

On Wed, May 01, 2002 at 10:58:42AM -0700, Hilmar Lapp wrote:
> I guess I should have said seqfeature (and there is a StrandedFeature or something in BioJava isn't there?). Also, I cared much more about the frame, which is absent too. Wouldn't you want to know the frame for a translation feature?

Yes, frame is kind-of useful occasionally, if you're dealing
with partial CDS.  It's also, of course, important if you're
writing an ensembl-style `gene builder'.  My point was that
for an everything other than coding exons (or DNA-protein 
alignment results, which amount to almost the same thing), it
seems to be a meaningless concept.  Perhaps I misunderstood
your original post, but it sounded as though you wanted frame
added as an extra column somewhere in the schema.  I just think
it should be an optional property (in the qualifier_value table)
for those types of feature where it's meaningful.

Does this make sense?

     Thomas.


PS.  BioJava also allows you to represent features with
     frames, when necesary (the FramedFeature interface).