[Biojava-l] Experimental DAS 1.900 implementation

[Lincoln Stein]

Hi Thomas, et al.,

I've moved the biodas repository to cvs.biodas.org (physically the
same machine as biojava.org, I think).  Shall we move the CVS
repository there and integrate the biodas.org and biojava.org/das web
pages? (I'll do the stitching together).

Lincoln

Thomas Down writes:
 > Hi...
 > 
 > I've started working on an experimental Java implementation of
 > the DAS 1.900 proposal, so that we've got something to play
 > with as the specification develops.  At the moment there's
 > just a Sequence service (vaguely equivalent to refererence
 > servers in DAS1).  I've got most of the pieces of a Features
 > service, and should be able to check that in in the next day
 > or so.
 > 
 > For anyone who's interested in tracking development, there's
 > code in the BioJava CVS repository (http://cvs.biojava.org/
 > for more info).  Checkout the module `xdas'.
 > 
 > What you get:
 > 
 >   - Prototype DAS sequence service
 > 
 >   - The SOAP toolkit it relies on.
 > 
 >   - An obligatory stock-quote demo ;)
 > 
 > To preempt the inevitable question, yes I have looked at other
 > SOAP toolkits (especially the IBM/Apache one).  While they're good
 > a lot of the time, they tend to use DOM to represent the SOAP messages
 > in-memory.  I know from past experience that this really isn't a good
 > idea where DAS is concerned -- sometimes you want to shift quite
 > serious amounts of data around (especially feature-tables), and I've
 > seen OutOfMemoryErrors (as well as poor performance) when the BioJava
 > DAS client was using a DOM based solution.
 > 
 > The new SOAP toolkit is based on S[t]AX event-based XML parsing,
 > so that should help scalability.
 > 
 > 
 > I'd be interested to hear any comments about this code...
 > 
 > 
 >    Thomas.

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY

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