[Bioperl-l] SearchIO speed up
bix at sendu.me.uk
Fri Aug 18 03:00:57 EDT 2006
Chris Fields wrote:
> On Aug 17, 2006, at 4:53 PM, Sendu Bala wrote:
> I don't think it's worth that much effort really. There are other
> ways to go about this, such as your and Aaron's suggested pull
> parser, the hash-based approach, etc., which may be better.
Doing multiple things gives a better final result. Every penny counts,
so to speak.
> 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 :)
> That being said, the nice thing about SearchIO is that you could
> introduce new SearchIO::* modules using your own custom handler/
> Search class combinations to work alongside the current ones; that
> way everybody has an option (use the old slow more OO ones vs. the
> new fast hash-based ones). There, they may choose to use a new API
> for the speed advantages. Make it easier for them to make the right
> choice i.e. Damian Conway's affordances.
Even if you were making a new SearchIO module, I think you'd want to
have it return HSPI objects for the hsps. Otherwise to what extent is it
a bioperl or searchio module? To what extent will people be able to
easily use the new module with existing code that expects a SearchIO to
eventually provide HSPI objects?
Maybe I'm wrong about that - is it reasonable to just come up with a
whole new system for returning the results, and have users learn to use
the new system?
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