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

[Ewan Birney]

On Sun, 17 Sep 2000, Hilmar Lapp wrote:

> Well, first I notice that the RX line is dropped from output, may be
> because it hasn't been recognized as such during parse due to the deviant
> syntax.
> 
> Second, I don't really have a problem with adding a pubmed() method to
> Annotation::Reference.
> 
> 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.

I like these fixes hilmar. Whether we should think up more intricate
models for this sort of multiple id for one database thing is open, or
should a refrence have two dblinks - medline and pubmed (?).


> 
> 	Hilmar
> 
> -- 
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> Hilmar Lapp                                email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
> A-1235 Vienna                                fax: +43 1 86634 727
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