[Bioperl-l] Bio::SeqIO::game

[Ewan Birney]

On Fri, 1 Dec 2000, Bradley Marshall wrote:

> 
> How about this as a solution?
> 
> We'll add a top level attribute and/or tag describing
> whether or not the document is "chunkable".  Chris
> suggested we have a top level <flavor> element.  This
> can specify whether or not the document is chunkable. 
> A chunkable document would have this structure:
> 

;). 

I think all useful documents will be chunkable. I'd claim that were just
letting ourselves into trouble if we allow badly compacted XML to be
"valid"

This solution is ok, but I would argue that it is better to be strict
about these things otherwise implementations either will have to throw
exceptions on non chunkable documents or have other poorly defined
criteria....

 

> <game>
> <flavor>chunkable</flavor>
> <seq1/>
> < all features pertaining to seq1 />
> <seq2/>
> < all features pertaining to seq2 />
> <seq3/>
> < all features pertaining to seq3 />
> </game>
> 
> If a document is chunkable, we will read into memory a
> string from the first <seq> to the next <seq> and
> parse that in one pass when next_seq is called.  Then
> we'll move on to the next chunk.
> 
> If the document is not chunkable, we'll continue to
> parse it as we have been.  This allows us to keep GAME
> flexible and yet still be useful in the SeqIO system.
> 
> Brad
> 
> 
> 
> 
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