[Bioperl-l] pI and MW of seqs

[Hilmar Lapp]

We may want to put this back into the closet. Having direct attributes 
doesn't play very well with a Strategy pattern allowing for 
flexibility. OTOH the Strategy implementation could just be an argument 
to the attribute getter (with a default implementor if not supplied), 
and it would indeed be easier to use. I have no problems with either 
way.

Aaron commented out those columns in the schema (see rc3 of 
biosql-schema), so they are purely optional there.

	-hilmar

On Tuesday, February 18, 2003, at 11:24  PM, Aaron J Mackey wrote:

>
> one of the small changes to bioSQL that we're proposing is to add pI 
> and
> MW columns to biosequences ... this lead naturally to thinking about 
> how
> we handle these attributes in the various Bio::Seq objects.  We've
> previously batted around various Bio::Tools::pICalculator interfaces, 
> but
> what about a simpler:
>
> $seq = <get seq somehow>;
>
> $pI = $seq->pI();
> $MW = $seq->MW();
>
> where the pI and MW subs would see if the value had been already set 
> (via
> database load, or previously set/calculated) or needs to be calculated.
>
> I think I prefer this to:
>
> $calc = new Bio::Tools::pICalculator;
> $pI = $calc->pI($seq);
>
> Does anyone with a deeper understanding of proteomics want to comment 
> on
> the need to handle varying pIcalc parameters (e.g. different tables of
> pKa's vs. the canonical one Expasy uses?)
>
> -Aaron
>
> -- 
>  Aaron J Mackey
>  Pearson Laboratory
>  University of Virginia
>  (434) 924-2821
>  amackey at virginia.edu
>
>
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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