Repost: Naming the modules; Mailing lists
Fri, 21 Feb 1997 11:10:15 +0000 (GMT)
[The following message was not redistributed, so I'm posting it again.
Apologies if the first copy sent yesterday is just stuck somewhere and
we end up with two copies.]
SteveBr wrote -re- Bio::Aln
> Let's start refering to the package as Bio::Seq::NucAln (or just NucAln),
> to avoid confusion.
I've got a strong interest to keep the package name Bio::Aln;
but I would feel bound to your ultimate decision.
However, please consider:
I'm using Bio::Aln for the phylogenetic analysis of protein sequences
as well, and IMO there's nothing in there that is nucleotide-only.
I even consider Bio::Aln to be sufficiently general to
process alignments of numeric data, linguistic data, etc !
I'd suggest to have Bio::Aln and Bio::ProtAln, where ProtAln has
special features needed for protein data, incl. speed enhancements
where necessary. See also my post from Monday, in particular,
> Moreover, it seems that the internal design of the code makes
> implementation of [protein-processing] features extremely difficult.
I'm really not sure. Do you mean that storing the alignment as an
array of array references is already problematic ?
If no, what is problematic ?
I think array of array references is the most efficient if you need
rapid access to the data (using strings or Bio::Seq's would slow this
down considerably). Unless, of course, you move towards PerlDL / C plug-ins.
Note that it's a two-liner to add $aln->column($col_number) to the current
Bio::Aln code. I'll do that for the final release, since
$aln->seqs(,$col_number) is kinda clumsy.
I hope I can convince you to agree to a co-existence of
Bio::Aln and Bio::ProtAln :-)
> > > Also, I most likly solved the Q. at the end of the Bio::Aln code, i.e.
> > > OO Qu.: Methods taking functions as arguments, how ? (repost,modified)
> > > Newsgroups: comp.lang.perl.misc,de.comp.lang.perl,comp.lang.perl.modules
> I didn't understand the question anyway! (See the package I've sent you).
I'm looking forward to it !!
now has Bio::Aln 1.001 beta using Perl closures for the utility
functions, and a small fix to _rowbounds()/_colbounds() which
showed incorrect behaviour if the first row/column index was 0.
> > vsns-bcd-perl-announce is enabled.
> Could you send me a draft of your "announcement of the change of list
I'll prepare a draft early next week at the latest.
> address" message? I will have a look at it and see if I have any
> > > There's also, **for later**,
> > > * vsns-bcd-perl-guts like vsns-bcd-perl, incl. subscribers
> > > * vsns-bcd-perl-talk like vsns-bcd-perl, incl. subscribers
> "including subscribers" What's the difference between -guts and -perl
These lists are indeed ``for later''. E.g. -guts could be used for topics
that are too boring for the more general list vsns-bcd-perl, once
vsns-bcd-perl has many subscribers. This could e.g. be a special topic
like using Perl Data Language stuff, or GUI development (note that my
belief is that we don't need a GUI; WWW/CGI can do the job.) (They've just
split the PerlDL list in a similar way). (Let's not worry about this now.:)