[Bioperl-l] moltype/molecule

[Heikki Lehvaslaiho]

Having slept over the problem and talked with Ewan I propose to do the
following:

- revert to previous genbank.pm behaviour on HEAD

- fix embl.pm to show moltype=dna on RNA entries on HEAD and BRANCH

- molecule() remains as it is; values are database dependent

- add new method into PrimarySeqI: is_circular (HEAD)
  -- values (from ID/LOCUS line): undef/false, true
  -- update genbank.pm and embl.pm to parse in circularity
  -- update genbank.pm and embl.pm to write out circularity

- change moltype() into alphabet(), keep moltype() as a depreciated method
  (HEAD only) Opinions?

We really should start putting into HEAD all API changes we can think of  so
that we do not have to change things immediately after 1.0.

If you think you'll be hit badly by these changes, say so now. 
I will not commit anything until Friday (European time).

	-Heikki


Ewan Birney wrote:
> 
> On Wed, 17 Oct 2001, Heikki Lehvaslaiho wrote:
> 
> > Sounds like breaking a good old system.
> >
> > Why not :
> > moltype() eq alphabet()
> >
> > molecule() could be a shortcut into source/sequenced_mol
> >     and is it is not defined use the value from ID/Locus line
> >
> > I am being difficult?
> 
> So moltype() ne molecule() - aren't we setting ourselves up for confusion
> here?
> 
> I appreciate the need for backward compatibility.
> 
> What about
> 
>   ->biological_molecule()

	->source_molecule() RichSeqI 
	   ->molecule() depreciated

	->moltype() meaning alphabet
	-- revert to old genbank behaviour
	-- fix embl.pm



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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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