[Biojava-l] BlastXMLParserFacade

[David Huen]

On Friday 12 Mar 2004 11:17 am, Matthew Pocock wrote:
> Hi,
>
> The parser shouldn't be throwing a NPE. However, the NCBI blast xml
> output didn't used to be well-formed XML, so was not parseable by any
> XML parser. I don't know if this has since been fixed by the NCBI.
>
In this case, that's not the problem.  The problem started when we switched 
from the Xerces parsers to Sun's own and no attempt on my part was 
successful in getting it it use the NCBI's DTD.  Part of the problem is 
that DTD from NCBI refers to other DTDs and those references are not 
complete so my code used to explicitly resolve them but with Sun's parser, 
I could never convince it to use the provided DTDs.

I don't have time to return to that problem for a while so perhaps someone 
else more familiar with Crimson could figure it out.  Alternatively, we 
could hack it to not use DTDs at all (totally non-validating).

Regards,
David