[Bioperl-l] SearchIO speed up

Sean Davis sdavis2 at mail.nih.gov
Thu Aug 10 11:59:04 EDT 2006




On 8/10/06 11:19 AM, "Sendu Bala" <bix at sendu.me.uk> wrote:


> ...Except I need to know if the community considers the speed problem
> solved or not. More radical changes will make SearchIO even faster, eg.
> Chris Fields and Jason (if I interpret the Project priority list item
> correctly) have suggested an end to individual Hit and HSP objects,
> which become just data members of a Result-like object. Ideally I don't
> want to go down that route because we lose quite a bit of OO power; HSP
> objects in particular make important use of inheritance and we'd end up
> stuffing tens of duplicated-code methods into the Result object
> replacement. Ugh. Or having the Result-like object implement 4 different
> interfaces. Ugh. That said, judging by the results below, having hsps as
> pure hashes would result in a ~5x speedup all the time instead of only a
> 1.5x speedup in worst case.

Just curious, but is there a possibility of making "lazy" instantiation of
objects like HSP and HIT objects?  Things like parsing and output could be
accomplished without these objects?

Sean



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