[Biojava-dev] ReadGenBank Problem

[Schreiber, Mark]

Hi David -
 
You need to put  the grammars.jar on your class path. This is a new jar built by biojava that contains all the ontology stuff that is new in biojava-live.
 
Let me know if that doesn't work.
 
- Mark
 

	-----Original Message----- 
	From: David Maynard [mailto:davidmaynard at pacbell.net] 
	Sent: Mon 3/11/2003 3:43 p.m. 
	To: biojava-dev at biojava.org 
	Cc: 
	Subject: [Biojava-dev] ReadGenBank Problem
	
	

	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 


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