Re: [Biojava-l] BlastXMLParserFacade

2004-03-12 Thread Thomas Down
On 12 Mar 2004, at 12:03, David Huen wrote: 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

Re: [Biojava-l] BlastXMLParserFacade

2004-03-12 Thread Dan Bolser
On Fri, 12 Mar 2004, 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. ! I have a perl module to 'cl

Re: [Biojava-l] BlastXMLParserFacade

2004-03-12 Thread 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

Re: [Biojava-l] BlastXMLParserFacade

2004-03-12 Thread Matthew Pocock
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. Matthew [EMAIL PROTECTED] wrote: I was wondering if anyone has successfully gotten B

[Biojava-l] BlastXMLParserFacade

2004-03-11 Thread DMGoodstein
I was wondering if anyone has successfully gotten BlastXMLParserFacade to work on an xml style NCBI blast output file (version 2.2.3)? I'm getting null pointer exceptions deep within the crimson parser implementation classes, but I now i'm correctly passing in the NCBI output file, since the dtd is