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

Chervitz, Steve Steve_Chervitz@affymetrix.com
Mon, 13 Aug 2001 14:13:48 -0700

Hilmar Lapp wrote:
> "Chervitz, Steve" wrote:
> > 
> > Before I go checking in large modifications within 
> Bio::Search::*, is there
> > anyone else who has been working on these modules lately 
> that has any input
> > here? Aaron?
> > 
> What I remember is that Aaron basically had to cease working on
> the Bio::Search:: stuff. Let us know if you want to revitalize
> them, because there were already discussions whether we should
> prune the whole hierarchy (it is already pruned from releases).

Yes, I'd like to pick up the ball on the Bio::Search hierarchy. It's a nice
framework that can accomodate sequence database searches generically.
Aaron's Fasta-parsing code will require some modifications to make it
equivalent to what I'm doing with Blast. 

> This was also one of the reasons I did not make the
> AnalysisResult.pm dependent on one of the Bio::Search interfaces,
> and I didn't want to work on them.

Perhaps we can factor out some commonality into a basic result interface
module from which Bio::Search::Result::ResultI and
Bio::Tools::AnalysisResult could derive. The problem I have with
AnalysisResult is that it mixes in parsing behavior, which I'd like to keep
separate. But I'd like the Bio::Search::* objects to be able to work with
the existing SeqAnalysisParserI/AnalysisResult system. 

> As for the general design directions and discussions, Ewan
> summarized that already in his response.

which looked fine by me.