[Biojava-dev] NullPointerException from BlastSAXParser.java

[mark.schreiber at novartis.com]

Hello -

This is very odd.

The JUnit tests currently pass using the files in 
/tests/files/org/biojava/bio/programs/ssbind  These BLAST files all have 
the string "Searching....". Maybe there is a variation in the windows 
output?

Can you post at least the header of your output to the list (preferably an 
entire example output)?

- Mark





"W. Eric Trull" <wetrull at yahoo.com>
Sent by: biojava-dev-bounces at portal.open-bio.org
10/06/2005 06:11 AM

 
        To:     biojava-dev at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] NullPointerException from BlastSAXParser.java


Hello all,

I'm new to the list, but have done as much archive searching, Google
searching, and debugging as I can on the problem I describe here.

I'm trying to parse NCBI BLAST output (as shown in BioJava in Anger), but
keep getting a NullPointerException.  One of my searches turned up using
BlastEcho to debug the problem, but that also throws the
NullPointerException:

startSearch
                 SearchProp:             program: ncbi-blastp
                 SearchProp:             version: 2.0.11
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 
com.pfizer.search.sequence.BlastEcho.echo(BlastEcho.java:42)
                 at 
com.pfizer.search.sequence.BlastEcho.main(BlastEcho.java:88)
Exception in thread "main" 

Stepping through the code in a debugger shows that the while loop added in
revision 1.13 of
/biojava-live/src/org/biojava/bio/program/sax/BlastSAXParser.java (fixed
truncation of database id) reads all the lines without ever matching the
"Searching" string.  At first I thought it was because I was using a later
version of BLAST, but then I tried 2.0.11 and 2.2.3 (supported version) 
but
they also result in a NullPointerException.  In the BLAST output for the
various versions I never see a "Searching" string anywhere.  I've tried 
all
the -m options as well, without success.

Is there a NCBI BLAST option that I need to be using?  I'm running on 
Windows
XP (during development) - is the UNIX version output different? 

Thanks.

-Eric Trull


_______________________________________________
biojava-dev mailing list
biojava-dev at biojava.org
http://biojava.org/mailman/listinfo/biojava-dev