[Bioperl-l] SearchIO speed up

Sendu Bala 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?

More information about the Bioperl-l mailing list