[Biojava-l] Dazzle server-client bottlenecks

David Huen smh1008@cus.cam.ac.uk
Mon, 23 Jul 2001 13:04:31 +0100 (BST)

On Mon, 23 Jul 2001, Thomas Down wrote:

> I have a horrible feeling I know exactly what the problem is
> here :(.  The DNA fetching code is still building a full DOM
> tree, then walking over all the Text nodes in this to build
> the BioJava symbolList (David, if you're still in a benchmark-y
> mood you could probably test this quite easily).
OK, I'll do that tonight.  It should be simple to check.

> Anyway, there's a very simple fix: extract the symbol data
> directly from SAX (or StAX) events.  I'm pretty confident that
> the limiting factor will then be the BioJava SymbolParsers
> (which have already been optimized to some extent anyway).
> This should have been done a while back, but I've kept
> putting it back, probably because I hardly ever have the
> symbols display turned on in DAS.  I'll have a go this afternoon,
> once I've caught up with my mails from BOSC...
If this turns out to be the problem I might recode the parsing
eventually if you haven't done it by then already.

David H.