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

[Hilmar Lapp]

Hilmar Lapp wrote:
> 
> 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 forgot the following:
6) Method rp() is probably specific to certain flat-file formats
(SwissProt?). If so, it should go into its own sub-class. (main trunk
only!)
7) start() and end(): why not simply inherit from Bio::Range, too? Would
add all the comparison methods provided there, and it refers to sequence
ranges anyway.

	Hilmar

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Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
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