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

[DeAngelo Lampkin]

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:

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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.parse(BlastXMLParserFacade.java:167)
        at BlastParser.main(BlastParser.java:47)
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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