New Bio::Seq and Bio::Seq::Parse (.025 BETA)

[Steven E. Brenner]

Georg Fuellen wrote:
> I agree w/ all the comments you made, and I hope you'll respond to the other
> issues in a week..

Glad to hear that we're (at last) in agreement.


During my trip, I gave some thought to the future developments needed
by the Bio::Seq module.  I think that it is a great piece of code, though
it has a few rough spots, especially:

  * consistency/validity
  * alphabet support
  * parsing
  * numeration

All of these are implemented, but not necessarily in a way which is
extensible or efficient.  Since these affect the interface, I think we
can't release the module as-is.

On the other hand, correctly rewritting the code for all these features
could take a long time.  Since the code is certainly usable and important
as it is, I think that there is great value in just getting it to the
community. 

Therefore, I suggest that we release the module as "Bio::PreSeq".  By
analagy with what's being done with Bio::UnivAln, we will release and
support Bio::PreSeq for the community.  However, as we better figure out
how to construct the interface, especially to deal with the items
mentioned above (and possibly to incorporate other issues), changes to the
interface will be rolled into a Bio::Seq.


Do people think this is a good idea?