[Biojava-l] fileToBiojava question

[Bernd Jagla]

  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