[Bioperl-l] general coordinate transformation in LocatableSeq

Mark A. Jensen maj at fortinbras.us
Fri Nov 28 16:54:56 EST 2008

Dave- this was an excellent trial run. Have uploaded patches to #2476 
that seem to eliminate the problem there. Will need to explore other 
issues (length_aln, particularly) further. MAJ
----- Original Message ----- 
From: "Dave Messina" <David.Messina at sbc.su.se>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>; "Chris Fields" 
<cjfields at illinois.edu>
Sent: Friday, November 28, 2008 3:33 AM
Subject: Re: [Bioperl-l] general coordinate transformation in 

>I wonder if this would be useful for sorting out the subsequence 
>issues that
> we've seen
> in Bio::Search::SearchUtils::tile_hsps,
> Bio::Search::Hit::GenericHit::length_aln,
> et al. (e.g. Bug 2476 
> <http://bugzilla.open-bio.org/show_bug.cgi?id=2476> ).
> Not for release 1.6, but a 1.6.x point release perhaps.
> Dave
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