[Biojava-l] Remote location exception

Michael Muratet michael.muratet@invitrogen.com
Tue, 21 Aug 2001 17:09:18 -0500 

<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
Greetings All
<p>I've encountered my first sequence which contains a "join" in a cds
feature.&nbsp; I'm using the latest release version of biojava, with some
code that looks like:
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; StreamReader
stream = new StreamReader(new BufferedReader(new InputStreamReader(inputStream)),
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
new GenbankFormat(),
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
DNATools.getDNA().getParser("token"),
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
new GenbankProcessor.Factory(SimpleSequenceBuilder.FACTORY));
<br>and I get this exception:
<p>&nbsp;&nbsp;&nbsp;&nbsp; [java] org.biojava.bio.BioException: Remote
locations are not supported: join(M77176.1:1149..2925,M77177.1:1..370,M77178.1:1..377,M77179.1:1..386,M77180.1:1..378,1..946)
<p>I can live with this, but I would like to catch the exception in my
code so that I can skip further calculations. The exception is apparently
caught somewhere in biojava. I've tried working backwards from the EmblLikeLocationParser
class, but I can't find it. Does anyone have any clues?
<p>Thanks.
<p>Mike
<pre>--&nbsp;
Michael A. Muratet
Senior Software Engineer
Bioinformatics
ResGen, Invitrogen Corp.
(800) 533-4363 x74431
(256) 539-4086 FAX</pre>
&nbsp;</html>