[Bioperl-l] SearchIO speed up

Sean Davis sdavis2 at mail.nih.gov
Thu Aug 10 12:41:08 EDT 2006

On 8/10/06 12:04 PM, "Sendu Bala" <bix at sendu.me.uk> wrote:

> Sean Davis wrote:
>> 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?
> That's what I've done actually, which is why performance varies between
> 5x and 1.5x (lower performance when the instantiation is forced).
> But, things like 'parsing and output' do need to force the instantiation
> unless, say, an output module knew about the hash structure of the thing
> stored inside a Result object. Which is too horrible a situation to
> comprehend. :O

I was just asking--I have no idea what is possible.  But what you have
already accomplished is QUITE impressive!


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