[Bioperl-l] Re: Bio::DasI

[Jason Stajich]

Does it make sense to think about a new Bio::SeqI implementation which
implements the DasI interface by storing features in a Collection rather
than as the current hash/array.

All of the DAS interface methods seem useful to integrating into Sequence
objects at some point, how about I get it working in an independent
implementation and then we see if we should consider building a new Seq
object that has all of this functionality.

I'm not sure the Collection object by itself can handle these requests.
I think that if the features were created on top of a sequence object then
they will have references to the sequence object and can then pull in the
underlying seq.

-j

On Tue, 21 May 2002, Lincoln Stein wrote:

> Hi Jason,
>
> I've just checked in revisions to Bio::DasI and Bio::Das::SegmentI.
> These provide the interface methods needed to run generic genome
> browser on top of a feature collection.  I don't think the interface
> is particularly onerous to implement and I'm really excited by the
> prospect of being able to run gbrowse on top of your new feature
> Collection classes.
>
> Despite the name, DasI is not quite at the point where it encapsulates
> all functionality from the Bio::Das module.  What's missing is calls
> to fetch DNA and stylesheets.
>
> Lincoln
>
>
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu