[Biojava-l] ParseException when using interleaved Nexus file

[David Johnson]

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
>> --
>> David Johnson
>> School of Biological Sciences
>> University of Reading
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> 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: d.johnson at reading.ac.uk
web: http://www.rdg.ac.uk/~sis07dj
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Message ID org.biojava.bio.seq.io.ParseException

Complete Message

Found unexpected token interleave=yes in CHARACTERS block at org.biojavax.bio.phylo.io.nexus.CharactersBlockParser.parseToken(CharactersBlockParser.java:1177) at org.biojavax.bio.phylo.io.nexus.NexusFileListener$Abstract.parseToken(NexusFileListener.java:256) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat$TokenParser.parseToken(NexusFileFormat.java:345) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat$TokenParser.access$100(NexusFileFormat.java:296) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat.parse(NexusFileFormat.java:266) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat.parseReader(NexusFileFormat.java:117) at org.biojavax.bio.phylo.io.nexus.NexusFileFormat.parseFile(NexusFileFormat.java:79) at uk.ac.rdg.evo.portal.NexusUtil.parseFile(NexusUtil.java:24) at uk.ac.rdg.evo.portal.panels.BayesPhyloJobStep1Panel$UploadNexusForm.onSubmit(BayesPhyloJobStep1Panel.java:65) at org.apache.wicket.markup.html.form.Form.delegateSubmit(Form.java:1518) at org.apache.wicket.markup.html.form.Form.process(Form.java:914) at org.apache.wicket.markup.html.form.Form.onFormSubmitted(Form.java:876) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.wicket.RequestListenerInterface.invoke(RequestListenerInterface.java:182) at org.apache.wicket.request.target.component.listener.ListenerInterfaceRequestTarget.processEvents(ListenerInterfaceRequestTarget.java:73) at org.apache.wicket.request.AbstractRequestCycleProcessor.processEvents(AbstractRequestCycleProcessor.java:92) at org.apache.wicket.RequestCycle.processEventsAndRespond(RequestCycle.java:1241) at org.apache.wicket.RequestCycle.step(RequestCycle.java:1320) at org.apache.wicket.RequestCycle.steps(RequestCycle.java:1419) at org.apache.wicket.RequestCycle.request(RequestCycle.java:545) at org.apache.wicket.protocol.http.WicketFilter.doGet(WicketFilter.java:456) at org.apache.wicket.protocol.http.WicketFilter.doFilter(WicketFilter.java:289) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:230) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:198) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:288) at org.apache.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.java:271) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:202) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:632) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:577) at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:94) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:206) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:632) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:577) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:571) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:1080) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:150) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:632) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:577) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:571) at org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:1080) at org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:272) at com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.invokeAdapter(DefaultProcessorTask.java:637) at com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.doProcess(DefaultProcessorTask.java:568) at com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.process(DefaultProcessorTask.java:813) at com.sun.enterprise.web.connector.grizzly.DefaultReadTask.executeProcessorTask(DefaultReadTask.java:341) at com.sun.enterprise.web.connector.grizzly.DefaultReadTask.doTask(DefaultReadTask.java:263) at com.sun.enterprise.web.connector.grizzly.DefaultReadTask.doTask(DefaultReadTask.java:214) at com.sun.enterprise.web.connector.grizzly.TaskBase.run(TaskBase.java:265) at com.sun.enterprise.web.connector.grizzly.ssl.SSLWorkerThread.run(SSLWorkerThread.java:106)