[Bioperl-l] SearchIO speed up

Hilmar Lapp hlapp at gmx.net
Thu Aug 17 17:16:44 EDT 2006


You mean you maintain inheritance but re-implement the methods to  
override the inherited ones?

On Aug 17, 2006, at 4:49 PM, Chris Fields wrote:

> I have to agree.  If there was a way to get around this by having  
> the change
> behind the scenes in HSPI then I wouldn't see a problem.
>
> Hence my suggestion of implementing hit() and other
> SeqFeature::SimilarityPair methods directly in  
> Bio::Search::HSP::HSPI (i.e.
> no SimilarityPair inheritance) to return  
> Bio::SeqFeature::Similarity objects
> directly.
>
> Chris
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
>> Sent: Thursday, August 17, 2006 3:20 PM
>> To: Sendu Bala
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] SearchIO speed up
>>
>>
>> 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
>>
>> --
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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