[Bioperl-l] Re: [BioXML-dev] Bio::SeqIO::game

[Bradley Marshall]

--- Hilmar Lapp <hlapp@gmx.net> wrote:
> Bradley Marshall wrote:
> > [...] 
> > do it in chunks, but...).  In addition, due to the
> > game format, there is no guarantee that all of the
> > features that go with one seq will be between that
> > sequence definition and the next one.  So it can
> be:
> > 
> > Seq 1
> > features on seq 1
> > Seq 2
> > features on Seq 1
> > 
> 
> What is (was?) the rationale behind such a design?

Basically it comes down to a decision whether or not
to show relationships as embedded tags or using ID's
and ID ref's.  In GAME the decision was made to use ID
ref's to reduce data duplication.  Any time you have a
data structure that's a DAG, with embedding, you
introduce data duplication.  Once this decision was
made, there's really nothing you can do in a DTD to
specify which order to put things in.  This may change
if we move to XML Schema, but it'll stick for now.

Brad


> 
> 	Hilmar
> -- 
>
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> Hilmar Lapp                                email:
> hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1
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