Naming the modules; Mailing lists

Georg Fuellen fuellen@dali.Mathematik.Uni-Bielefeld.DE
Fri, 28 Feb 1997 11:10:30 +0000 (GMT)

> On Thu, 27 Feb 1997, Georg Fuellen wrote:
> > Steve wrote,
> > > > > * Alphabets.  See the notes in Bio::Seq.  My idea is that there should be
> ... 
> > What if I don't mention any alphabet support in Bio::UnivAln ?
> Ok!

I'm now writing 
Checking an alignment for characters that should not be there according
to the Alignment Type is currently not well-supported; see alphabet_check()
for a _preliminary_ way of doing manual checkup, though.

> > > Again, interface issues can NOT be put off for non-beta releases.  This is
> > > not so much an issue of changing code so much as just making a decision
> > > (which will affect code dependencies later).  We should make the decision
> > > before the beta release.
> > 
> > What's your suggestion about the issue, then ?
> > Copy everything in the object recursively, except X ? What is X ?
> I think we're talking at cross-purposes.  My question is about defining
> the data inside the UnivAln object. What do we allow as data types for
> names and other parameters passed in?  If it is anything (scalars or
> references), then we have problems of copying.  If it is free-text, then
> we have the problem that things we may define in the future may clash with
> user-named items.

Can this be postponed if we mention in the POD that copy() 
currently copies everything in the object, but that this may be
subject to change ?

Currently I just write, in the POD for new(),
            $names: A reference to a hash which stores {loc,name} pairs of 
                    other database locations and corresponding names where 
                    the alignment is located. Also, $names->{'seqs'}[$i]{'id'}
                    and $names->{'seqs'}[$i]{'desc'} may hold the ids and 
                    descriptions of the sequence number $i. They are currently
                    just set if Fasta format is read, or if Bio::Seq objects
                    are passed to the constructor, and they're included if
                    Fasta format is written. More support is planned.
best wishes,