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 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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