[Biococoa-dev] Design question

John Timmer jtimmer at bellatlantic.net
Tue Aug 10 15:56:46 EDT 2004

> For the reference to other sequences we should come up with something
> like bundle identifiers that uniquely identify sequences inside a
> bundle, but this is of later problem while devising the file format we
> plan to use (I think BioJava uses URIs here, see link below).
I'd already thought about this.  I figure each sequence could have a list of
used indexes, and a reference to its parent bundle, which also has a list.
If the parent bundle exists, it hands out a new index to any sequence object
requesting it.  If it doesn't, the sequence object can choose its own.

If you add an existing sequence to a bundle, it should have a
rationalization mechanism - just reassign all indexes according to a range
provided by the bundle.

Sorry, sent the last message too soon, so you're getting two.



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