[Biojava-l] fileToBiojava question

[Richard Holland]

Your classpath is missing bytecode.jar. It's available in the same location as the main biojava jars.

cheers,
Richard

On 23 Sep 2010, at 15:40, Bernd Jagla wrote:

> Hello again,...
> 
> I am still struggling with my little problem. I am getting closer I think...
> I made some minor modifications to some biojava files and would like to compile it under 1.6. Is this possible?
> 
> When I compare version 1.7.1 with mine the only difference seems to be the java version. And the sample code runs with your but not with mine... ;(
> 
> I get the following error message:
> 
> Exception in thread "main" java.lang.NoClassDefFoundError: org/biojava/utils/bytecode/CodeException
>    at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(FeatureFilter.java:1273)
>    at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1817)
>    at org.biojava.bio.seq.SimpleFeatureHolder.<init>(SimpleFeatureHolder.java:54)
>    at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(RichFeature.java:167)
>    at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java:61)
>    at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(SimpleRichSequenceBuilder.java:100)
>    at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(SimpleRichSequenceBuilder.java:81)
>    at org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder(SimpleRichSequenceBuilderFactory.java:68)
>    at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
>    at org.pasteur.pf2.biojava.biojavaIO.execute(biojavaIO.java:54)
>    at org.pasteur.pf2.biojava.biojavaIO.main(biojavaIO.java:29)
> Caused by: java.lang.ClassNotFoundException: org.biojava.utils.bytecode.CodeException
>    at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
>    at java.security.AccessController.doPrivileged(Native Method)
>    at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
>    at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>    at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
>    at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
>    ... 11 more
> 
> 
> Do you think this problem can be due to the compiler???
> 
> Reading through some of the information on the web about NoClassDefFoundError it should be something like or my class path is messed or something like that...
> 
> Thanks for any tip/hint and how to identify and solve this problem
> 
> Best,
> 
> Bernd
> 
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--
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/