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

Bradley Marshall bradmars@yahoo.com
Fri, 1 Dec 2000 14:26:15 -0800 (PST)

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:

< all features pertaining to seq1 />
< all features pertaining to seq2 />
< all features pertaining to seq3 />

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.


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