[Bioperl-l] SearchIO speed up
bix at sendu.me.uk
Thu Aug 17 18:05:10 EDT 2006
Chris Fields wrote:
> I suppose you could do it that way. What I was thinking would be having
> hit() and query() methods directly in HSPI (no inheritance)
Hilmar already suggested HSPIs would be best left as SimilarityPairs, so
inheritance is required.
> They would return Bio::SeqFeature::Similarity objects directly. Though I
> don't really know if it's possible, and also don't really see the purpose
> here if the speedup is marginal.
It's the rate-limiting step after all my other speedups (not considered
in the present discussion). And if we can have a 50% speedup for 'free',
why would we say no?
My changes in experimental branch already do something similar: new()
calls SUPER but just doesn't pass it any args. That's a little slower
than this (calling Bio::Root::Root::new directly), and you miss out on
passing -verbose et al.
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