[Biojava-l] Blast parser for ncbi blast version 2.2.13

[mark.schreiber at novartis.com]

Possibly some variation in this output is causing the problem

Can you post some blast output that replicates this error?

Thanks

- Mark





"Emily Wong" <emy_66 at hotmail.com>
Sent by: biojava-l-bounces at lists.open-bio.org
03/13/2006 01:39 PM

 
        To:     biojava-l at lists.open-bio.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Blast parser for ncbi blast version 2.2.13


Hi,

Is there a parser that takes into account ncbi blast version 2.2.13(on 
their 
website)? I am trying to use the code here to parse : 
http://www.biojava.org/docs/bj_in_anger/BlastParser.htm . If I set the 
parser from strict to lazy I get these comments :
Exception in thread "main" java.lang.NullPointerException
                 at 
org.biojava.bio.program.sax.BlastSAXParser.interpret(BlastSAXParser.java:215)
                 at 
org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:164)
                 at 
org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:311)
                 at 
org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:274)
                 at 
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160)
                 at BlastParser.main(BlastParser.java:46)

Thanks,

Emily


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