Re: java 8 - Biojava3 java.util.concurrent.ExecutionException: java.lang.ExceptionInInitializerError

Are you using Biojava 3.1? This indeed seems to be a problem in 3.1 and 
before.

However I've tried with the current 4.0.0-SNAPSHOT and it seems to work 
fine.

Jose



On 07.11.2014 21:56, Khalil El Mazouari wrote:
> Hi
>
> I am porting my code from java 7 to java 8.
>
> Biojava3.alignment is not working on java 8! While it was OK on java 7
>
> All jars are in the classpath.
>
> Thanks
>
> Khalil
>
> java.util.concurrent.ExecutionException: java.lang.ExceptionInInitializerError
> 	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
> 	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
> 	at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:289)
> 	at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:612)
> 	at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:180)
> ...
> Caused by: java.lang.ExceptionInInitializerError
> 	at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358)
> 	at org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88)
> 	at org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118)
> 	at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86)
> 	at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:69)
> 	at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71)
> 	at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342)
> 	at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112)
> 	at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112)
> 	at org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105)
> 	at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53)
> 	at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38)
> 	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> 	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> 	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> 	at java.lang.Thread.run(Thread.java:745)
> Caused by: java.lang.NullPointerException
> 	at java.util.Collections$UnmodifiableCollection.<init>(Collections.java:1026)
> 	at java.util.Collections$UnmodifiableList.<init>(Collections.java:1302)
> 	at java.util.Collections.unmodifiableList(Collections.java:1287)
> 	at org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:111)
> 	at org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:85)
> 	at org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:57)
> 	at org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:53)
> 	at org.biojava3.core.sequence.location.template.Location.<clinit>(Location.java:48)
> 	... 16 more
> java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation
>
> ….
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