Naming the modules; Mailing lists

[Georg Fuellen]

> > > 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). 

Yep, I really do..

> However, if it's really universal, then shouldn't it be part of the
> Array:: hierarchy rather than Bio::?  :) :) 

It's got too much Bio in it :) Also, the idea of ``aligning'' is something
pretty biological.

> 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.

I agree. It's _Bio_::UnivAln... 

> To brainstorm for some more intuitive and useful names... let's see
> 
> SubAln - because of its power for finding sub-alignments (horizontally and
>          vertically)

It does much more, like mapping, consensus, variable sites, etc...

> 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 thought about GenAlign (generic alignment), but that would be very confusing
for some ppl :-):-):-)

> 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?

3D coordinate data can be dealt with, too. Etc, etc. 

> >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.

Agreed.

best wishes,
georg