[Biojava-l] Is there setModeLazy()-like functionality forBlastParserFacade?

[Schreiber, Mark]

Hi -

The BlastXMLParserFacade is designed to look like the standard blast
parser, it doesn't actually parse anything other than BlastXML output.

- Mark


> -----Original Message-----
> From: DeAngelo Lampkin [mailto:dlampkin at xencor.com] 
> Sent: Wednesday, 16 July 2003 10:56 a.m.
> To: Biojava-L (E-mail)
> Subject: [Biojava-l] Is there setModeLazy()-like 
> functionality forBlastParserFacade?
> 
> 
> Hello, 
> 
> It's your favorite list spammer again!
> 
> I was wondering if there were something equivalent to 
> BlastLikeSAXPaser's setModeLazy() method inside of 
> BlastXMLParserFacade?
> 
> I get the following error when I try to parse a regular 
> (non-XML Blast report) with BlastXMLParserFacade:
> 
> --------------------------------------------------------------
> ---------------------------------------
> org.xml.sax.SAXParseException: Document root element is missing.
>         at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3182)
>         at org.apache.crimson.parser.Parser2.fatal(Parser2.java:3170)
>         at 
> org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:501)
>         at org.apache.crimson.parser.Parser2.parse(Parser2.java:305)
>         at 
> org.apache.crimson.parser.XMLReaderImpl.parse(XMLReaderImpl.java:442)
>         at 
> org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade.pars
> e(BlastXMLParserFacade.java:167)
>         at BlastParser.main(BlastParser.java:47)
> --------------------------------------------------------------
> ----------------------------------------------------
> 
> I *suspect* this may have something to do with the fact that 
> I'm using 2.2.6 (Mega)BLAST output.  I was able to get around 
> an error in the old  BlastLikeSaxParser by setting the lazy 
> mode which told the parser to ignore the version number.  I'm 
> not sure if this is exactly that same problem, but it seems 
> possible (assuming of course the Facade class actually pays 
> attention to version numbers).
> 
> Also FYI, when I parse MegaBlast 2.2.6 XML output (following 
> processing with David's sed script), inside the Annotations 
> object, the databaseId key is wrong.  It's the same as the 
> queryId. However, this may have something to do with the fact 
> that I'm parsing an "unapproved" BLAST format.
> 
> 
> Much appreciated!
> DeAngelo
> 
> _______________________________________________
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> http://biojava.org/mailman/listinfo/biojava-l
> 
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