No subject

[fuellen@dali.Mathematik.Uni-Bielefeld.DE]

Lincoln Stein writes,
> Ewan Birney writes:
>  > It's a very nice article. 

I agree... I'd almost say-- don't cut anything, but submit the article
somewhere else;-)

...
>  > Two content points:
>  > 
>  > a) I think the bio.perl.org site is the better site to reference about
>  > bioperl.

Definitely-- The Bielefeld addresses are mostly historical except
for the UnivAln-related stuff.

Minor comments:
>>>>>>
The method first checks whether the new sequence is an object by
calling the Perl built-in ref(), which returns the class name for
objects, and the undefined value for non-objects.
<<<<<<
I believe ref() returns the empty string for non-objects.

>>>>>>
     croak "Doesn't look like sequence data"
       unless $sequence=~/^[gactnu ]+$/i;
<<<<<<
At least in this case, I'd prefer carp() to croak(). I'm always very 
unhappy if some Perl module stops a long script although it could just
as well have proceeded along after issuing a warning. Perl itself 
usually tries to issue warnings instead of dying.

>>>>>>>
   my $seq = $self->SUPER::seq;
<<<<<<
The extra code listing for sub seq has a different statement here.

>>>>>>>
well as Perl classes for proteins, genes, genetic maps, phylogenetic
trees and 3D protein structures.
<<<<<<<
I've not yet released my phylogenetics code; only multiple alignment
is available.

As an aside, I'm currently waiting for PDL 2.0 to come out
and stabilize; my plan is to use PDL for UnivAln.pm -- I hope to
be very fast in this way, without touching XS at all.

best wishes,
Georg Fuellen,
Univ. Bielefeld, Research Group in Practical Comp. Science
http://www.techfak.uni-bielefeld.de/bcd/welcome.html

> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
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