[Biojava-l] FramedFeature files

[Thomas Down]

On Mon, Sep 10, 2001 at 11:00:27AM +1200, Mark Schreiber wrote:
> Hi -
> 
> The attached file contains biojava source files updated to allow the use
> of the FramedFeature. I have updated GFFEntrySet but I stoped short of
> making the frame property of a GFFRecord into a FramedFeature cause I'm
> not sure what this will break in other classes.
> 
> I have done testing myself and things appear to work.

Great!

One query, though, which I think ought to be discussed
a little bit before this goes in for final: FramedFeature
extends StrandedFeature, but it also includes forward/reverse
strand information in the ReadingFrame, a duplication which
worries me a little.  You recognize this problem in the
template class (which doesn't have a strand field).  However,
this introduces another (probably very minor) issue:  when
realizing new features, the idea is that implemetations will
search for the most specific feature implementation which matches
the supplied template.  So if a sequence implementation has
a StrandedFeature implemetation but not a FramedFeature implementation,
right now you'll end up losing the strand information too, which
seems kind-of unfortunate to me.

Do you have a specific reason why you don't want to handle
strand and frame as separate properties, in much the same way
GFF does?


(By the way, would you like a CVS read/write account so
you can check this in yourself?  If so, just drop me
a suggested user name and an SSH public key)

   Thomas.