[Bioperl-l] SimpleAlign - get_seq_by_id

[Hilmar Lapp]

On Oct 25, 2008, at 8:47 AM, Jason Stajich wrote:

> We have a real problem with each vs get for our API mixture. I think  
> there had been some logic there at one point but I think it is  
> confusingly mixed now.


The each_XXX is (supposed to be) old-style. I started cleaning this up  
to use get_XXX a long time ago but didn't get much beyond Bio::SeqI  
and Bio::SeqFeatureI.

> you're right - it should be rolled back. I guess each_seq_xxx gets  
> the job done.

Well, couldn't it be that for some implementations iterating over all  
sequences is way more expensive that possible using an indexed access?

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