[Bioperl-l] v1.0.1 BLAST SearchIO woes

[Jason Stajich]

On the trunk:
$hsp->subject()
is no longer deprecated - this is identical to $hsp->hit() call


>       - Add a score() method to HSPI ... unless someone can fill me if it was
>         left out intentionally
$hsp->score should exist and is inherited from SeqFeature::Similarity

>
>       - Add an implementing method to BlastHSP to return scores from HSPs
>         pulled from reports
>                   (this way it won't matter if a newbie uses blast.pm or
> psiblast.pm)
>
>       - Fix the strand('query') access method in GenericHSP which currently
>                    returns the word  'query' or 'sbjct' instead of a strand
> ID.
I've fixed this by adding code in the HSPI interface which delegates the
appropriate call to $hsp->query->strand or $hsp->hit->strand

Additionally I changed the code for $hsp->length('hit') to delegate to
$hsp->hit->length

We will need to add
$hsp->seq_str('hsp') to delegate to $hsp->homology_string() and
$hsp->seq_str('hit') to delegate to $hsp->hit_string(), etc...


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