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:[EMAIL PROTECTED] > 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 > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
