[Biojava-l] Bug in WuBlastSummaryLineHelper.java

[Matthew Muller]

I am using WU-BLAST version 2.0MP and am had some trouble using BlastLikeSaxParser
to parse the output.  A NoSuchElement exception is thrown from WuBlastSummaryLineHelper
and I think I've figured out why.  The exception occurs because the class
tries to parse out the reading frame from the summary line output of blastx.
 My version of blastx (2.0MP) does not print a reading frame and I don't
see how any version should.  I think this is a bug.

I have implemented a fix by modiifying the following section of code:

if ( (poVersion.getProgram() == BlastLikeVersionSupport.WU_BLASTN) ||
     (poVersion.getProgram() == BlastLikeVersionSupport.WU_BLASTP)
||
     (poVersion.getProgram() == BlastLikeVersionSupport.WU_BLASTX)
 ) { //ADDED THIS LINE
              iGrab = 3;
} else {
      //here if TBLASTN or TBLASTX
      iGrab = 4;
}

I suspect there is a comparable problem for parsing ncbi-blast but I haven't
checked.

Has anyone else experienced this?  Comments?

Matt