[Bioperl-l] SearchIO speed up

Sendu Bala bix at sendu.me.uk
Fri Aug 18 09:11:10 EDT 2006


Chris Fields wrote:
> On Aug 18, 2006, at 2:00 AM, Sendu Bala wrote:
>
>>> So far, sorry to say, it's debatable whether a 1.5-fold increase
>>> in speed along with even small API changes is worth all the
>>> effort you are putting into it.
 >
>> To be fair, no API change is required, and it only took a few 
>> minutes to implement and try the idea out :)
> 
> Maybe I'm missing something here; didn't you say it failed tests 
> somewhere?  That's suggestive of API problems.

The alternate suggestion using
my $self = $class->Bio::Root::Root::new(@args);
doesn't cause any test failures because it doesn't involve any API 
change, only a harmless implementation change. Hilmar wasn't happy with 
that because of 'loss of standard constructor implementation and 
behavior'. To be honest, the current implementation of GenericHSP and 
SimilarityPair&ancestors is a bit of a messy kludge with lots of wasted 
work, which is why we get the speed up in the first place by going 
straight to Root.

My PullParser modules solve the problem in a much better way (read: 
Hilmar would have no objections), but I was hoping for something that 
would work for all existing SearchIO modules as well.

It doesn't matter in the end: it was easy to suggest it, and just as 
easy to not use it if people are unhappy with it.


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