Hi Kevin,
I'm not familiar with the Ensembl schema or adapter (the code was written
by Steven Searle), but you might want to download the source code from
CVS and then step through the code to figure out what might be missing
in your data.
Cheers,
Ed
On Thu, 5 Mar 2009, Kevin Lam wrote:
Hi
I am pretty sure this is an error from my data.. but how do i find out more
info about what went wrong?
Exception in thread "Thread-6" java.lang.NullPointerException
at
org.ensembl.driver.impl.CoordinateSystemAdaptorImpl.getMappingPath(CoordinateSystemAdaptorImpl.java:217)
at
org.ensembl.driver.impl.AssemblyMapperAdaptorImpl.fetchByCoordSystems(AssemblyMapperAdaptorImpl.java:106)
at
org.ensembl.driver.impl.LocationConverterImpl.convert(LocationConverterImpl.java:353)
at
org.ensembl.driver.impl.LocationConverterImpl.convert(LocationConverterImpl.java:449)
at
org.ensembl.driver.impl.BaseFeatureAdaptorImpl.fetchAllByConstraint(BaseFeatureAdaptorImpl.java:733)
at
org.ensembl.driver.impl.BaseFeatureAdaptorImpl.fetchAllByConstraint(BaseFeatureAdaptorImpl.java:682)
at
org.ensembl.driver.impl.BaseFeatureAdaptorImpl.fetch(BaseFeatureAdaptorImpl.java:1360)
at org.ensembl.driver.impl.GeneAdaptorImpl.fetch(GeneAdaptorImpl.java:244)
at apollo.dataadapter.ensj.DataFetcher.addGenes(DataFetcher.java:74)
at apollo.dataadapter.ensj.EnsJAdapter.getResults(EnsJAdapter.java:420)
at
apollo.dataadapter.ensj.EnsJAdapter.getCurationSet(EnsJAdapter.java:149)
at
apollo.dataadapter.ensj.EnsJAdapterGUI.doOperation(EnsJAdapterGUI.java:52)
at
org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapterChooser.java:361)
at
apollo.main.DataLoader$ApolloAdapterChooser.doCommit(DataLoader.java:740)
at
org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChooser.java:136)
at java.lang.Thread.run(Unknown Source)
--
Kevin Lam
Bioinformatics Officer
Comparative Genomics Lab
Institute of Molecular and Cell Biology, A*STAR Singapore.
61 Biopolis Drive,Proteos,Singapore 138673
tel: 6586 9569
http://www.imcb.a-star.edu.sg/php/venkatesh.php
Note: This message may contain confidential information. If this Email/Fax
has been sent to you by mistake, please notify the sender and delete it
immediately. Thank you.
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