[Biojava-l] ParseException when using interleaved Nexus file

[David Johnson]

Hi Richard,

Actually the original exception was thrown in a different file that my
supervisor tried uploading to a Web app I'm developing that uses the
BioJava Nexus parser, but can't get hold of that particular file
today. So the one I provided the link for was just another example of
an interleaved Nexus file I Googled for when I got your first email
this morning, as I figured they'd probably be the same formatting. But
I remember it's definitely the same exception in both cases.

I had a quick look in the example I provided today, and the
interleave=yes token is definitely in the header of the data block,
and is also definitely in the Format line.

Oh, just FYI, I'm using the BioJava 1.7 binary distribution
(http://www.biojava.org/download/bj17/bin/biojava.jar).

Cheers,
-David

2009/8/7 Richard Holland <holland at eaglegenomics.com>:
> 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 <holland at eaglegenomics.com>:
>>>
>>> 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
>>>> --
>>>>