[Bioperl-l] Sequence IDs and Comment()s

[Hilmar Lapp]

Jason Eric Stajich wrote:
> >
> > So... What would people think of adding a type() (or class(),
> > category(), meta(), etc.) method to Comment to optionally qualify the
> > contents?
> >
> 
> I'm wary of this because it implies we are starting to interpret the data
> rather than just provide a mechanism for storing it and manipulating it,
> how would this work for a GenBank -> Seq -> BSML trip and back?
> 

For me this rather calls for a generic tag/value function. Hm. Do
we really want this? In an abstract sense, these to me looks like
structured annotation added to a Comment object. Will the
annotation overhaul support this?

(Sorry for providing more questions instead of answers.)

BTW as for the ID, normally you would create your own RichSeq
implementation or TitledSeq or whatever, and then have instances
of this returned by the SeqIO module. As soon as we'll have
migrated to using factories this will be easily possible (i.e.,
right now it is not).

	-hilmar
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Hilmar Lapp                              email: hilmarl@yahoo.com
San Diego, Ca. 92130                     phone: +1 858 812 1757
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