I've encountered my first sequence which contains a "join" in a cds feature. I'm using the latest release version of biojava, with some code that looks like:
StreamReader
stream = new StreamReader(new BufferedReader(new InputStreamReader(inputStream)),
new GenbankFormat(),
DNATools.getDNA().getParser("token"),
new GenbankProcessor.Factory(SimpleSequenceBuilder.FACTORY));
and I get this exception:
[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)
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?
Thanks.
Mike
-- Michael A. Muratet Senior Software Engineer Bioinformatics ResGen, Invitrogen Corp. (800) 533-4363 x74431 (256) 539-4086 FAX
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