[Bioperl-l] Alignment Blast parser

[Jason Stajich]

yes please - thanks Will!!

-jason
On Fri, 23 Jan 2004, Will Spooner wrote:

> Hi Jason,
>
> Having looked at the code, it does seem sensible to split the
> TextResultWriter->to_string method into component parts. This would allow
> users like me, with detached HSPI objects kicking about, to reuse the
> writer code, e.g:
>
>   my $writer = Bio::SearchIO::Writer::TextResultWriter->new();
>   my $hsp = Bio::Search::HSP::MyHSP->new(-id=>'foo');
>   print $writer->hsp_alignment_string( $hsp );
>
> This approach would also allow TextResultWriter subclasses to get a bit
> more granularity from the parent.
>
> I'm happy to do the necessary, and will post a patch to bugzilla once
> complete.
>
> Will
>
> On Fri, 23 Jan 2004, Jason Stajich wrote:
>
> > Currently the code to do this sort of thing is embedded in
> > SearchIO::Writer::TextResultWriter but generates a whole report.
> >
> > Someone can move the code out that part of the code to a separate function
> > so it can be used for situations like what Nathan is asking for.  Not sure
> > where it should go at this point other than in TextResultWriter - we don't
> > really have a class of 'HSP consumers' other than in there.
> >
> > Will's code is smarter as it figures out the multiplier from the start/end
> > while we code it up based on the alignment alg (TBLASTN, BLASTX, etc).
> >
> >
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu