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 >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> 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: [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
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)
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