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 <[email protected]>: > 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 >>>> -- >>>> _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
