[Biojava-l] Biojava-l Digest, Vol 141, Issue 11

[Khalil El Mazouari]

Hi,

Fixed. parallelStream from lambda was calling non synchronized method. 

Best


On 17 Nov 2014, at 13:00, biojava-l-request at mailman.open-bio.org wrote:

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>   1. java 8 - Term cannot be null (Khalil El Mazouari)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 16 Nov 2014 15:03:30 +0100
> From: Khalil El Mazouari <khalil.elmazouari at gmail.com>
> To: biojava-l at mailman.open-bio.org
> Subject: [Biojava-l] java 8 - Term cannot be null
> Message-ID: <C9286623-43D5-4230-AC37-50C79BFF989F at gmail.com>
> Content-Type: text/plain; charset=windows-1252
> 
> Hi,
> 
> I am porting my java/BioJava project to BioJava 1.9.1/java 8, in order to use lambda expressions.
> 
> IllegalArgumentException: Term cannot be null exception is sometimes raised. Can?t trace it back as it?s not raised at every run. It seems to be Thread-Related? and it?s not raised if I use BioJava 1.8.2/Java 7. 
> 
> Best
> 
> 
> Exception in thread "main" java.lang.IllegalArgumentException: Term cannot be null
> 	at org.biojavax.bio.seq.SimpleRichFeature.setTypeTerm(SimpleRichFeature.java:330)
> 	at org.biojavax.bio.seq.SimpleRichFeature.setType(SimpleRichFeature.java:315)
> 	?.
> 	at com.kem.ae.core.AnnotationManager.lambda$annotate$5(AnnotationManager.java:122)
> 	at com.kem.ae.core.AnnotationManager$$Lambda$1/10347942.accept(Unknown Source)
> 	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
> 	at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
> 	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:512)
> 	at java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:290)
> 	at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)
> 	at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
> 	at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:902)
> 	at java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1689)
> 	at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1644)
> 	at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)
> 
> 
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> End of Biojava-l Digest, Vol 141, Issue 11
> ******************************************