Thanks David. One more quick question - is this the exact file that is
throwing the exception? I haven't tested it yet - but if I could test
against the real file that is throwing the problem, that would help me
find out exactly what's going wrong.
For what it's worth, the exception is normally thrown when more than
one interleave=yes/no token is found in the header of the Data or
Characters block, or when the interleave token appears in a line other
than the Format line of the header.
cheers,
Richard
On 7 Aug 2009, at 10:28, David Johnson wrote:
Hi Richard,
Thanks for your mail. An example of an interleaved file can be found
here:
http://www.molecularevolution.org/si/resources/fileformats/files/dna.nex
where the link pointing to the example file is from
http://www.molecularevolution.org/si/resources/fileformats/ and under
the NEXUS section.
The specific error message is: "org.biojava.bio.seq.io.ParseException:
Found unexpected token interleave=yes in CHARACTERS block"
So it looks like the error is thrown reading the "interleave"
parameter in the top of the data block, and before reaching the actual
interleaved matrix data. Full stacktrace in attached .txt.
Cheers,
-David
2009/8/7 Richard Holland <[email protected]>:
Could you point me to an example of an interleaved file?
And also the full stack trace of the exception that gets thrown?
cheers,
Richard
On 6 Aug 2009, at 18:03, David Johnson wrote:
Hi everyone,
A quick question about the BioJava Nexus parser. I've been trying to
use the Nexus file parser, simply by doing something like:
NexusFileBuilder builder = new NexusFileBuilder();
NexusFileFormat.parseFile(builder, f);
However, when parsing Nexus files that are interleaved, I get a
ParseException.
Is there a way to setup the parser provided by BioJava to handle
interleaved Nexus files?
Thanks,
-David
--
David Johnson
School of Biological Sciences
University of Reading
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--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [email protected]
http://www.eaglegenomics.com/
--
David Johnson
Post-doc Research Assistant
School of Biological Sciences
506, Philip Lyle Research Building
University of Reading
Whiteknights
Reading, RG6 6BX
UK
Tel: +44 (0) 118 378 4415
email: [email protected]
web: http://www.rdg.ac.uk/~sis07dj
<nexusInterleavedParseException_stacktrace.txt>
--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [email protected]
http://www.eaglegenomics.com/
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