[Bioperl-l] SearchIO speed up

Hilmar Lapp hlapp at gmx.net
Thu Aug 17 16:20:23 EDT 2006


On Aug 17, 2006, at 4:07 PM, Sendu Bala wrote:

> The entire test suite is happy except for t/SimilarityPair (it tests
> that a HSP is a SimilarityPair, which it obviously isn't anymore)

This is a sure sign that the change should not be made. There are  
numerous possible applications that may need to rely on this being a  
SeqFeature::SimilarityPair, for instance OR mappers.

A change like this is pretty drastic. Making it in a well-traveled  
interface like SearchIO and friends would need to be justified by the  
previous design being clearly very poor or too limiting (or both), or  
by an at least equally drastic speed-up. Any speed-up would have to  
be more than an order of magnitude to count as drastic.

	-hilmar

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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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