[Bioperl-l] Bio::Search::XXX::GenericXXX vs. Bio::Search::XXX::BlastXXX

[Steve Chervitz]

On Thursday, Mar 27, 2003, at 06:30 US/Pacific, Jason Stajich wrote:

> On Thu, 27 Mar 2003 Luc.Gauthier at aventis.com wrote:
>> <snip>
>>      "More likely than not the BlastXXX objects will be deprecated and
>> dismantled as their functionality is ported to the GenericXXX 
>> objects."
>
> I'm not lying here.  I'm waiting for Steve to finish his porting of
> psiblast parsing in (which means all of the functionality will be
> available in the GenericXX objects).  This didn't happen before 1.2 
> branch
> so they are still there.  It ought to happen before 1.4 release in the
> fall.

Yes, most of the functionality that's in the BlastXXX objects will 
migrate into the GenericXXX objects. The new SearchIO::blast will 
create BlastXXX result and hit objects, though they will look different 
than they do now. They will contain just some blast-specific things, 
such as stuff for dealing with PSI-BLAST iterations and PHI-BLAST 
patterns.

It makes sense to slate my new SearchIO::blast for the 1.3 developer 
release (using the convention is that odd-numbered releases have code 
that is newer and not as well-tested).

Steve

PS:  I had a near disaster last night: While biking in San Francisco, I 
collided with a car that took a surprise U-turn in the middle of the 
street. I somersaulted over the car landing squarely on my backpack, 
which saved me (no major injuries ;-). The backpack contained my laptop 
and it emerged unharmed. Good thing, since it contains some bioperl 
development code that hasn't been backed up for a while. The morals: 1) 
Backup early, backup often. 2) Always wear a helmet when you bike. 3) 
Apple powerbooks are tough! (Brenthaven backpacks are well-designed, 
too).