Repost: Naming the modules; Mailing lists

[Georg Fuellen]

[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 !!
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/welcome.html
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
> comments. 
...
> > > 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.:)

> Steve

best wishes,
georg