[Bioperl-l] Bio::Tools::Blast update

[Ewan Birney]

I think you are the only person who is actively working on that.


We also want to extend this area into running interface, borrowing heavily
from Martin Senger's novella ideas (basically BSA written in a perl
friendly way). Conceptually I think we need the following interfaces

(stealing novella names for these)

AnalysisServiceFactoryI - where we get "services" which we can run
 - has get_AnalysisService('blast')


AnalysisServiceI - A service (like BLAST) where we get probe metadata to
understand what it wants
  - has a input mechanism for getting a particular AnalysisInstanceI


AnalysisInstanceI - a particular BLAST run where you will get the results
eventually
  - has the method 'run'

JobControlI - you get this from AnalysisInstanceI and allows you to
monitor or poll or listen for the job to finish


Along with this, we need interfaces for the results which all produce
sequence features, like


Bio::Tools::SeqFeatureProducerI which isd what analysisparserI is at the
moment but I think it is a crap name.

(this would defined next_feature)




Not sure what we have already and what needs to go/needs to get rewritten.


Does this make sense to people? let's thrash this out a while.... ;)



PS BOSC - much fun!









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