Naming the modules; Mailing lists
Steven E. Brenner
Fri, 21 Feb 1997 21:32:02 +0900 ()
> > 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
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
>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.