[Bioperl-l] SeqIO::swiss.pm and Annotation::Reference

L.Pollak lorenz@ist.org
Mon, 18 Sep 2000 00:10:43 +0200

> So, after inspecting Annotation::Reference I noticed / did the following:
> 1) Removed comment() because it only duplicated the inherited method.
> 2) Changed database() to allow for changing the hard-coded default of
> MEDLINE (code shouldn't just silently ignore wrong calling attempts, and
> if someone wants to have something else as MEDLINE here, why not).
> 3) added pubmed()
> 4) overrode optional_id() to become an alias for pubmed()
> 5) Fixed a bug in primary_id() that did not pass on the argument for set.

ok, i've just commited some code for swiss.pm using your new methods!

now i really see no more differences between read and written swissprot
files besides that nasty line break position in entries that have more
than one line but that should be of no great importance...

for peter who has to look at swiss.pm:
this actual version (1.25) depends on Annotation/Reference version 1.9
but my earlier changes had no particular dependencies. 
yes, we were talking about having a comment subclass for swissprot but
then i thought that it was working fine as it was and did not change

sorry for not being uptodate but there's another thing regarding cvs
is dubious to me: i commited those changes in the main trunk, but how 
can they come into the branch?

thx, Lorenz