[Bioperl-l] SeqIO profiling

[Jason Stajich]

oops - was working on seqfeature collection for my own stuff - meant to
say annotation collection.

Speaking of Seqfeature::Collection - my idea is to eventually shoehorn
this more robust object for feature collections into the Bio::Seq system -
this would allow Bio::Seq to be-a Bio::DasI compliant and essentially do
Das from a genbank file.  But one could use the original array-based
methods to not pay any more performance costs.  Since you can't really
store objects in DB_File structures, what I do instead is store array
locations in a DB_Tree B-TREE which can then be used to extract certain
features from the feature array.

The interface for SeqFeature::Collection should be hammered into Bio::DasI
shape before 1.2 IMHO.  Something I meant to do this summer but never got
around to....

-jason

On Sun, 22 Sep 2002, Hilmar Lapp wrote:

>
> On Sunday, September 22, 2002, at 02:23 PM, Ewan Birney wrote:
>
> > On Sun, 22 Sep 2002, Jason Stajich wrote:
> >
> >
> >
> >>
> >> Additionally I just made the seqfeature collection instantiation
> >> lazy so
> >> it is only built when requested in Bio::Seq.  Don't think we'll
> >> see much
> >> improvement but would be good to test how much effect it had on fasta
> >> format sequence parsing.
> >>
> >
> >
> > I wanted to do the same thing with the Bio::AnnotationCollection
> > instantion as well...
>
> That's what Jason did -- Bio::Seq doesn't use SeqFeature::Collection
> yet ... (hmm ... should it do so?)
>
> 	-hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>

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