BLAST DTD (was RE: [Biojava-l] SeqSimilaritySearchSubHit -Str and information)

[Bobick, Stephen]

Mark writes:
>I suspect you hit the nail on the head when you asked how it was designed
and under what 
>standards. My guess at the answers would be, it wasn't and none,
respectively.

That's too bad.  Merely submitting an RFC to a wider audience (like this one
for example) could have caught these issues quickly, and resulted in a
better-designed DTD.

>It's pretty funny if you put the DTD into a tool that automatically makes
JAXB style bindings. 
>You end up with millions of objects each of which contain a single piece of
data. It would have
>been better to do it the way you suggested.

I would even go further at this point at suggest encoding the validation
rules in an XML schema...

>For a long time the DTD didn't actually validate what was being produced
either so I guess we 
>should be glad it actually works now.

Since the parser validates XML... do you mean that the DTD did not agree
with the emitted XML period?  Ouch.

Stephen Bobick