[Biojava-dev] NullPointerException from BlastSAXParser.java

[W. Eric Trull]

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