[Biojava-l] Bug in WuBlastSummaryLineHelper.java

Matthew Muller mullermw@sbh.com
Mon, 10 Sep 2001 17:06:13 -0700 

--------------080807080104060104000409
Content-Type: text/plain; charset=us-ascii; format=flowed
Content-Transfer-Encoding: 7bit

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
  


--------------080807080104060104000409
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<html>
<head>
</head>
<body>
I am using WU-BLAST version 2.0MP and am had some trouble using BlastLikeSaxParser
to parse the output. &nbsp;A NoSuchElement exception is thrown from WuBlastSummaryLineHelper
and I think I've figured out why. &nbsp;The exception occurs because the class
tries to parse out the reading frame from the summary line output of blastx.
&nbsp;My version of blastx (2.0MP) does not print a reading frame and I don't
see how any version should. &nbsp;I think this is a bug.<br>
<br>
I have implemented a fix by modiifying the following section of code:<br>
<br>
<tt>if ( (poVersion.getProgram() == BlastLikeVersionSupport.WU_BLASTN) ||</tt><tt><br>
</tt><tt>&nbsp; &nbsp;&nbsp; (poVersion.getProgram() == BlastLikeVersionSupport.WU_BLASTP)
||<br>
&nbsp; &nbsp; &nbsp;</tt><font color="#ff0000"><tt>(poVersion.getProgram() == BlastLikeVersionSupport.WU_BLASTX)</tt></font><font color="#ff0000"><tt>
 ) {</tt></font><font color="#ff0000"><tt> //ADDED THIS LINE</tt></font>
<tt>&nbsp; &nbsp;&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; iGrab = 3;</tt><tt><br>
</tt><tt>} else {</tt><tt><br>
</tt><tt>&nbsp; &nbsp;&nbsp;&nbsp; //here if TBLASTN or TBLASTX</tt><tt><br>
</tt><tt>&nbsp; &nbsp;&nbsp;&nbsp; iGrab = 4;</tt><tt><br>
</tt><tt>}</tt><tt><br>
</tt><br>
I suspect there is a comparable problem for parsing ncbi-blast but I haven't
checked.<br>
<br>
Has anyone else experienced this? &nbsp;Comments?<br>
<br>
Matt<br>
&nbsp;&nbsp;<br>
<br>
</body>
</html>

--------------080807080104060104000409--