[Biojava-dev] ReadGenBank Problem

[David Maynard]

Dear BioJava Developers:

ReadGenBank seems to broken in the biojava-live tree.  
The following output results from running the ReadGB example from the BioJava In Anger website against the sample file AY069118.gb from the tests/files directory.

I am running Windows 2000 with Java version "1.4.2_01"
I have done a recent update -P -d against the biojava-live tree.

This used to work. Any suggestions?

Thank you,
David Maynard

ReadGB trying to read GenBank File AY069118.gb
org.biojava.bio.BioException: Couldn't realize feature
 at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147)
 at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97)
 at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217)
 at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223)
 at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:177)
 at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:91)
 at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99)
 at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102)
 at ReadGB.main(ReadGB.java:30)
Caused by: java.lang.NoClassDefFoundError: org/biojava/ontology/format/triples/node/Node
 at org.biojava.ontology.OntoTools.<clinit>(OntoTools.java:71)
 at org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:385)
 at org.biojava.bio.seq.impl.SimpleStrandedFeature.<init>(SimpleStrandedFeature.java:97)
 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
 at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
 at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
 at java.lang.reflect.Constructor.newInstance(Unknown Source)
 at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141)
 ... 8 more
org.biojava.bio.BioException: Couldn't realize feature
 at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147)
 at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97)
 at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217)
 at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223)
 at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:177)
 at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:91)
 at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99)
 at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102)
 at ReadGB.main(ReadGB.java:30)
Caused by: java.lang.NoClassDefFoundError
 at org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:385)
 at org.biojava.bio.seq.impl.SimpleStrandedFeature.<init>(SimpleStrandedFeature.java:97)
 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
 at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
 at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
 at java.lang.reflect.Constructor.newInstance(Unknown Source)
 at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141)
 ... 8 more
org.biojava.bio.BioException: Couldn't realize feature
 at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147)
 at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97)
 at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217)
 at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223)
 at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:177)
 at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:91)
 at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99)
 at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102)
 at ReadGB.main(ReadGB.java:30)
Caused by: java.lang.NoClassDefFoundError
 at org.biojava.bio.seq.impl.SimpleFeature.<init>(SimpleFeature.java:385)
 at org.biojava.bio.seq.impl.SimpleStrandedFeature.<init>(SimpleStrandedFeature.java:97)
 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
 at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
 at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
 at java.lang.reflect.Constructor.newInstance(Unknown Source)
 at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141)
 ... 8 more