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)
_______________________________________________
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
