Mon, 12 Oct 1998 15:56:46 +0200 (METDST)
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
> > 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.
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
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.
Univ. Bielefeld, Research Group in Practical Comp. Science
> Lincoln D. Stein Cold Spring Harbor Laboratory
> email@example.com Cold Spring Harbor, NY
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