[Biojava-l] BlastXMLParserFacade

[Matthew Pocock]

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 at lbl.gov 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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