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Re: BlastXMLParserFacade: msg#00025

java.bio.general

Subject: Re: BlastXMLParserFacade

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

DMGoodstein@xxxxxxx wrote:

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
getting read.

--David Goodstein
Joint Genome Institute

/usr/java/j2sdk1.4.1_02/bin/java2/bin/java
-classpath .:./biojava-1.3.1
.1.jar BlastParser fred.xml
a/j2sdk1.4.1_02/bin/javac -classpath .:./biojava-1.3.
java.lang.NullPointerException
at
org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:524)
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:172)
at BlastParser.main(BlastParser.java:44)
1.jar BlastParser
./fred.xmlava/j2sdk1.4.1_02/bin/java -classpath
.:./biojava-1.3.1
java.lang.NullPointerException
at
org.apache.crimson.parser.Parser2.parseInternal(Parser2.java:524)
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:172)
at BlastParser.main(BlastParser.java:44)

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