Naming the modules; Mailing lists

[Steven E. Brenner]

> > GF> I even consider Bio::Aln to be sufficiently general to
> > GF> process alignments of numeric data, linguistic data, etc !
> >   Indeed, right now it can hold any sort of data -- but that is perhaps a
> > weakness!  This is a bioperl object and it should have features for
> > supporting biological sequences.  Right now, the object lacks support
> > for many types of operations that people would want to do on proteins.
> 
> Ok, Let's call the module Bio::UnivAln, for it's universality. :-)
> And let's call the module you're envisioning Bio::Seq::ProtAln.

If you _really_ want to call it UnivAln, then I won't argue (much). 
However, if it's really universal, then shouldn't it be part of the
Array:: hierarchy rather than Bio::?  :) :) 

Seriously, you should carefully consider whether you want the alignment
object to be general for any sort of data or specfic for biological
sequences.  I would think that making optimizations and assumptions based
on biological sequences would be a good thing.

To brainstorm for some more intuitive and useful names... let's see

SubAln - because of its power for finding sub-alignments (horizontally and
         vertically)

PhyAln - because of its utility for phylogeny.  (but it's really more
         more general than this)


I sort of like SubAln; what do you think?  

I think it should be Bio::Seq::SubAln, but I'm open to persuasion
otherwise.  Do you see the module aligning any biological "things" other
than sequences?



>Maybe the fact that Bio::UnivAln can hold any sort of data can be put to
> use here ? I mean, you can perhaps put the additional data into the >
zeroeth column / zeroeth row ?! 

That sounds like a pretty severe kludge to me!



> Agreed; I hope PerlDL will be easy to install in a year or so 
> (I've spent many hours trying to install it, with limited success,
> so I can relate to this :-)

Even if it is "easy to install," so long as it requires non-Perl code,
most people won't have it and won't be willing to get it.