[Bioperl-l] SearchIO::blast, was Bio::SearchIO::hmmer hsp behaviour

Chris Fields cjfields at uiuc.edu
Thu Jun 29 23:53:22 EDT 2006


If we can work around the listener/handler that'll definitely speed  
things up.  I was thinking about tackling the SearchIO::blast parser  
next, refactoring it to use hashes as a separate plugin module; if I  
don't need the handler for that then it'll speed things up a bit.

Chris

On Jun 29, 2006, at 1:04 PM, Jason Stajich wrote:

> however you want - the idea of listeners at the time was to make it
> more SAX like so we could throw away events we didn't want and speed
> up the whole system when there was some idea of how you wanted the
> data filtered.  That may have been too much wishful thinking and I
> just couldn't do it alone.
>
>
> On Jun 29, 2006, at 3:54 AM, Sendu Bala wrote:
>
>> Jason Stajich wrote:
>>>
>>> Feel free to propose an alternative implement for parser as you see
>>> fit as long as the API is preserved.  you can contibute a new
>>> SearchIO plugin and HMMERSearchResultListener to deal with it - or
>>> [snip]
>>
>> What's the thinking behind the way SearchIOs work? Is it necessary or
>> desirable to always do it with events and listeners? Or is it
>> enough to
>> simply return a ResultI regardless of how you made it?
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>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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