Khalil El Mazouari | 17 Nov 13:17 2014
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Re: Biojava-l Digest, Vol 141, Issue 11

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)
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> ----------------------------------------------------------------------
> 
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Khalil El Mazouari | 16 Nov 15:03 2014
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java 8 - Term cannot be null

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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Khalil El Mazouari | 8 Nov 18:30 2014
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Re: Biojava-l Digest, Vol 141, Issue 8

Hi,

I agree ;) It's fixed on 4.0.0-SNAPSHOT.

Any idea when biojava 4 will be released?

Thanks

kem

On 08 Nov 2014, at 13:00, biojava-l-request <at> mailman.open-bio.org wrote:

> Send Biojava-l mailing list submissions to
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> 
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> or, via email, send a message with subject or body 'help' to
> 	biojava-l-request <at> mailman.open-bio.org
> 
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> When replying, please edit your Subject line so it is more specific
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> Today's Topics:
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>   1. java 8 - Biojava3	java.util.concurrent.ExecutionException:
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Khalil El Mazouari | 7 Nov 21:56 2014
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java 8 - Biojava3 java.util.concurrent.ExecutionException: java.lang.ExceptionInInitializerError

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)
(Continue reading)

Fwd: Question about NiedlemanWunsch class

Thanks for answers!

I use 3.1. Today I checked results in SNAPSHOT version, but the problem remained.
Also I aligned sequences with themselves and recieved bad numbers  again.
As I understand it, score of alignment must be between minScore and maxScore , so similarity of sequences, which calculates according to formula

(score - minScore)/(maxScore - minScore)

must be
between 0.0 and 1.0.

Here is my code
and two sequences. Notice, that the output of "getMaxScore" method is negative.
Sorry for terrible appearance of letter, but all examples is too large.



public class NWSimilarity {

   public static void main (String[] args) {

      SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
      SimpleGapPenalty gap = new SimpleGapPenalty();

      String str1 =
      "AGATATATCTGAAGCTTAAAGGGCAGTGACAATGGCTGGCTCGGTTAACGGGAATCATAGTGCTGTAGGACCTGGTATAAATTATGAGACGGTGTCTCAAGTGGATGAGTTCTGTAAAGCACTTAGAGGGAAAAGGCCGATCCATAGTATTTTGATAGCTAACAATGGAATGGCGGCTGTGAAGTTTATACGTAGTGTCAGAACATGGGCTTATGAAACATTTGGTACGGAAAAAGCCATATTGTTGGTGGGGATGGCAACCCCTGAAGACATGCGGATCAATGCGGAGCATATCAGAATCGCTGATCAGTTTGTTGAGGTTCCCGGAGGAACCAACAATAACAATTATGCTAACGTTCAGCTGATTGTGGAGATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATATTTCTTGGTCCTCCAGCATCTTCAATGGCAGCACTGGGAGATAAGATTGGTTCTTCGTTGATTGCACAAGCTGCTGATGTACCCACTCTGCCATGGAGTGGTTCCCATGTTAAAATACCTCCTAATAGCAACTTGGTAACCATCCCAGAGGAGATCTACCGGCAAGCATGTGTCTACACAACTGAAGAAGCGATTGCTAGCTGTCAAGTTGTCGGTTACCCAGCAATGATCAAAGCATCGTGGGGTGGTGGTGGTAAAGGAATCAGGAAGGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAGGGTGAGGTCCCAGGCTCACCAATATTCATAATGAAGGTTGCGTCACAGAGTCGGCATCTAGAGGTCCAGCTGCTCTGTGACAAGCATGGAAATGTTTCAGCTCTGCATAGCCGTGATTGTAGCGTCCAGAGAAGACATCAAAAGATCATAGAGGAGGGTCCAATTACTGTGGCTCCGCCAGAAACTGTCAAGAAACTTGAACAAGCAGCTAGAAGGTTGGCTAAGAGTGTTAACTATGTTGGAGCTGCTACTGTTGAGTATCTCTACAGTATGGACACTGGGGAGTACTACTTCTTAGAGCTTAACCCTCGCTTACAGGTTGAGCATCCTGTCACTGAGTGGATTGCCGAGATAAATCTTCCTGCTGCCCAAGTTGCTGTGGGGATGGGAATTCCTCTCTGGCAAATCCCTGAGATAAGACGGTTCTATGGAATAGAACATGGTGGAGGTTATGATTCTTGGCGAAAAACATCTGTTGTAGCCTTCCCTTTTGATTTTGATAAAGCTCAATCTATAAGGCCAAAAGGTCATTGTGTGGCTGTACGTGTGACAAGTGAGGATCCTGATGACGGGTTCAAACCAACCAGCGGTAGAGTTCAGGAGTTGAGTTTTAAGAGCAAGCCAAATGTGTGGGCGTACTTCTCTGTCAAGTCTGGTGGAGGCATCCACGAGTTCTCGGATTCCCAGTTTGGACATGTTTTTGCATTTGGGGAATCCAGAGCCCTGGCGATAGCGAATATGGTTCTTGGGCTAAAAGAAATTCAGATCCGTGGAGAAATTAGGACTAACGTTGACTACACGATCGACCTTTTACATGCTTCTGATTACCGTGATAACAAAATTCACACTGGTTGGTTGGATAGTAGGATTGCTATGCGGGTCAGAGCTGAGAGGCCTCCATGGTATCTCTCTGTTGTCGGCGGAGCTCTCTATAAAGCATCAGCGACCAGTGCTGCTGTGGTTTCAGATTACGTTGGTTATCTGGAGAAGGGGCAAATCCCTCCAAAGCATATATCTCTTGTACATTCTCAAGTGTCTCTGAATATTGAAGGAAGTAAATATACGATTGATGTAGTCCGGGGTGGATCAGGAACCTACAGGCTAAGAATGAACAAGTCAGAAGTGGTAGCAGAAATACACACTCTACGTGATGGAGGTCTGTTGATGCAGTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAGAATGACCACGATCCATCAAAGTTAATGGCTGAGACACCGTGCAAGTTGATGAGGTATTTGATTTCCGACAACAGCAATATTGACGCTGATACGCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGGCTGGTGAACTTATAGCCAATCTTGATCTTGATGATCCTTCTGCTGTAAGAAAGGCCGAACCCTTCCATGGAAGTTTCCCAAGATTAGGGCTTCCAACTGCAATATCCGGTAGAGTTCATCAGAGATGTGCCGCAACATTAAATGCTGCACGCATGATTCTTGCTGGCTATGAGCATAAAGTAGATGAGGTTGTTCAAGACTTACTTAATTGCCTTGATAGCCCTGAACTCCCATTTCTTCAGTGGCAAGAGTGCTTTGCAGTTCTGGCGACACGACTACCTAAAAATCTCAGGAACATGCTAGAATCAAAGTATAGGGAATTTGAGAGTATTTCCAGAAACTCTTTGACCACCGATTTCCCTGCCAAACTTTTAAAAGGCATTCTTGAGGCACATTTATCTTCTTGTGATGAGAAAGAGAGAGGTGCCCTTGAAAGGCTCATTGAACCATTGATGAGCCTTGCAAAATCTTATGAAGGTGGTAGAGAAAGTCATGCCCGTGTTATTGTTCATTCTCTCTTTGAAGAATATCTATCAGTAGAAGAATTATTCAATGATAACATGCTGGCTGATGTTATAGAACGCATGCGTCAGCTATACAAGAAAGATCTGTTGAAAATTGTGGATATAGTGCTCTCACACCAGGGCATAAAAAACAAAAACAAACTCGTTCTCCGGCTCATGGAGCAGCTTGTTTACCCTAATCCTGCTGCTTACAGAGATAAACTTATTCGATTCTCAACACTTAACCATACTAACTACTCTGAGTTGGCGCTCAAGGCGAGTCAATTACTTGAACAGACCAAACTAAGTGAGCTTCGTTCAAACATTGCTAGAAGCCTTTCAGAGTTAGAAATGTTTACAGAGGACGGAGAAAATATGGATACTCCCAAGAGGAAAAGTGCCATTAATGAAAGAATAGAAGATCTTGTAAGCGCATCTTTAGCTGTTGAAGACGCTCTCGTGGGACTATTTGACCATAGCGATCACACACTTCAAAGACGGGTTGTTGAGACTTATATTCGCAGATTATACCAGCCCTACGTCGTTAAAGATAGCGTGAGGATGCAGTGGCACCGTTCTGGTCTTCTTGCTTCCTGGGAGTTCCTAGAGGAGCATATGGAAAGAAAAAACATTGGCTTAGACGATCCCGACACATCTGAAAAAGGATTGGTTGAGAAGCGTAGTAAGAGAAAATGGGGGGCTATGGTTATAATCAAATCTTTGCAGTTTCTTCCAAGTATAATAAGTGCAGCATTGAGAGAAACAAAGCACAACGACTATGAAACTGCCGGAGCTCCTTTATCTGGCAATATGATGCACATTGCTATTGTGGGCATCAACAACCAGATGAGTCTGCTTCAGGACAGTGGGGATGAAGACCAAGCTCAGGAAAGAGTAAACAAGTTGGCCAAAATTCTTAAAGAGGAAGAAGTGAGTTCAAGCCTCTGTTCTGCCGGTGTTGGTGTAATCAGCTGTATAATTCAGCGAGATGAAGGACGAACACCCATGAGACATTCTTTCCATTGGTCGTTGGAGAAACAGTATTATGTAGAAGAGCCGTTGCTGCGTCATCTTGAACCTCCTCTGTCCATTTACCTTGAGTTGGATAAGCTGAAAGGATACTCAAATATACAATATACGCCTTCTCGAGATCGTCAATGGCATCTGTATACTGTTACAGACAAGCCAGTGCCAATCAAGAGGATGTTCCTGAGATCTCTTGTTCGACAGGCTACAATGAACGATGGATTTATATTGCAGCAAGGGCAGGATAAGCAGCTTAGCCAAACACTGATCTCCATGGCGTTTACGTCGAAATGTGTTCTGAGGTCTTTGATGGATGCCATGGAGGAACTGGAACTGAATGCCCATAATGCTGCAATGAAACCAGATCACGCACATATGTTTCTTTGCATATTGCGTGAGCAGCAGATAGATGATCTTGTGCCTTTCCCCAGGAGAGTTGAAGTGAATGCGGAGGATGAAGAAACTACAGTTGAAATGATCTTAGAAGAAGCAGCACGAGAGATACATAGATCTGTTGGAGTGAGAATGCATAGGTTGGGCGTGTGCGAGTGGGAAGTGCGGCTGTGGTTGGTGTCCTCTGGACTGGCATGTGGTGCTTGGAGGGTTGTGGTTGCAAACGTGACAGGCCGTACATGCACTGTCCACATATACCGAGAAGTTGAAACTCCTGGAAGAAACAGTTTAATCTACCACTCAATAACCAAGAAGGGACCTTTGCATGAAACACCAATCAGTGATCAATATAAGCCCCTGGGATATCTCGACAGGCAACGTTTAGCAGCAAGGAGGAGTAACACTACTTATTGCTATGACTTCCCGTTGGCATTTGGGACAGCCTTGGAACTGTTGTGGGCATCACAACACCCAGGAGTTAAGAAACCATATAAGGATACTCTGATCAATGTTAAAGAGCTTGTATTCTCAAAACCAGAAGGTTCTTCGGGTACATCTCTAGATCTGGTTGAAAGACCACCCGGTCTCAACGACTTTGGAATGGTTGCCTGGTGCCTAGATATGTCGACCCCAGAGTTTCCTATGGGGCGGAAACTTCTCGTGATTGCGAATGATGTCACCTTCAAAGCTGGTTCTTTTGGTCCTAGAGAGGACGCGTTTTTCCTTGCTGTTACTGAACTCGCTTGTGCCAAGAAGCTTCCCTTGATTTACTTGGCAGCAAATTCTGGTGCCCGACTTGGGGTTGCTGAAGAAGTCAAAGCCTGCTTCAAAGTTGGATGGTCGGATGAAATTTCCCCTGAGAATGGTTTTCAGTATATATACCTAAGCCCTGAAGACCACGAAAGGATTGGATCATCTGTCATTGCCCATGAAGTAAAGCTCTCTAGTGGGGAAACTAGGTGGGTGATTGATACGATCGTTGGCAAAGAAGATGGTATTGGTGTAGAGAACTTAACAGGAAGTGGGGCCATAGCGGGTGCTTACTCAAAGGCATACAATGAAACTTTTACTTTAACCTTTGTTAGTGGAAGAACGGTTGGAATTGGTGCTTATCTTGCCCGCCTAGGTATGCGGTGCATACAGAGACTTGATCAGCCGATCATCTTGACTGGCTTCTCTACACTCAACAAGTTACTTGGGCGTGAGGTCTATAGCTCTCACATGCAACTGGGTGGCCCGAAAATCATGGGCACAAATGGTGTTGTTCATCTTACAGTCTCAGATGATCTTGAAGGCGTATCAGCAATTCTCAACTGGCTCAGCTACATTCCTGCTTACGTGGGTGGTCCTCTTCCTGTTCTTGCCCCTTTAGATCCACCGGAGAGAATTGTGGAGTATGTCCCAGAGAACTCTTGCGACCCACGAGCGGCTATAGCTGGGGTCAAAGACAATACCGGTAAATGGCTTGGAGGTATCTTTGATAAAAATAGTTTCATTGAGACTCTTGAAGGCTGGGCAAGGACGGTAGTGACTGGTAGAGCCAAGCTCGGGGGAATACCCGTTGGAGTTGTTGCAGTTGAGACACAGACTGTCATGCAGATCATCCCAGCCGATCCTGGACAGCTTGACTCTCATGAAAGAGTGGTTCCGCAAGCAGGGCAAGTCTGGTTTCCTGATTCAGCGGCCAAGACTGCTCAAGCGCTTATGGATTTCAACCGGGAAGAGCTTCCATTGTTTATCCTAGCGAACTGGAGAGGGTTTTCAGGTGGGCAGAGAGATCTTTTCGAAGGAATACTTCAGGCAGGTTCAACTATAGTAGAAAATCTGAGAACCTATCGTCAGCCAGTGTTTGTGTACATCCCAATGATGGGAGAGCTGCGCGGTGGAGCGTGGGTTGTTGTTGACAGCCAGATAAATTCGGATTATGTTGAAATGTATGCTGATGAAACAGCTCGTGGAAATGTGCTTGAGCCAGAAGGGACAATAGAGATAAAATTTAGAACAAAAGAGCTATTAGAGTGCATGGGAAGGTTGGACCAGAAGCTAATCAGTCTGAAAGCAAAACTGCAAGATGCCAAGCAAAGCGAGGCCTATGCAAACATCGAGCTTCTCCAGCAACAGATTAAAGCCCGAGAGAAACAGCTTTTACCAGTTTATATCCAAATCGCCACCAAATTTGCAGAACTTCATGACACTTCCATGAGAATGGCTGCAAAGGGAGTGATCAAAAGTGTTGTGGAATGGAGCGGCTCGCGGTCCTTCTTCTACAAAAAGCTCAATAGGAGAATCGCTGAGAGCTCTCTTGTGAAAAACGTAAGAGAAGCATCTGGAGACAACTTAGCATATAAATCTTCAATGCGTCTGATTCAGGATTGGTTCTGCAACTCTGATATTGCAAAGGGGAAAGAAGAAGCTTGGACAGACGACCAAGTGTTCTTTACATGGAAGGACAATGTTAGTAACTACGAGTTGAAGCTGAGCGAGTTGAGAGCGCAGAAACTACTGAACCAACTTGCAGAGATTGGGAATTCCTCAGATTTGCAAGCTCTGCCACAAGGACTTGCTAATCTTCTAAACAAGGTGGAGCCGTCGAAAAGAGAAGAGCTGGTGGCTGCTATTCGAAAGGTCTTGGGTTGACTGATATCGAAGACTTTAGCTTCTAATCCAAGAAAGATGGACATTTAAAGTTTGCTTGTGTCCGTTTGGATTGATAATTATATATTTGTTGGTCACAGTTGTAAATGTTGTTGTAGCTTTGTCATTTCCGTATAAACAAATACGCAATAATTCATTCAAC";

      String str2 =
      "TAAAGTCTTCGATATCAGTCAACCCAAGACCTTTCGAATAGCAGCCACCAGCTCTTCTCTTTTCGACGGCTCCACCTTGTTTAGAAGATTAGCAAGTCCTTGTGGCAGAGCTTGCAAATCTGAGGAATTCCCAATCTCTGCAAGTTGGTTCAGTAGTTTCTGCGCTCTCAACTCGCTCAGCTTCAACTCGTAGTTACTAACATTGTCCTTCCATGTAAAGAACACTTGGTCGTCTGTCCAAGCTTCTTCTTTCCCCTTTGCAATATCAGAGTTGCAGAACCAATCCTGAATCAGACGCATTGAAGATTTATATGCTAAGTTGTCTCCAGATGCTTCTCTTACGTTTTTTACAAGAGAGCTCTCAGCGATTCTCCTATTGAGCTTTTTGTAGAAGAAGGACCGCGAGCCGCTCCATTCCACAACACTTTTGATCACTCCCTTTGCAGCCATTCTCATGGAAGTGTCATGAAGTTCTGCAAATTTGGTGGCGATTTGGATATAAACTGGTAAAAGCTGTTTCTCTCGGGCTTTAATCTGTTGCTGGAGAAGCTCGATGTTTGCATAGGCCTCGCTTTGCTTGGCATCTTGCAGTTTTGCTTTCAGACTGATTAGCTTCTGGTCCAACCTTCCCATGCACTCTAATAGCTCTTTTGTTCTAAATTTTATCTCTATTGTCCCTTCTGGCTCGAGCACATTTCCACGAGCTGTTTCATCAGCATACATTTCAACATAATCCGAATTTATCTGGCTGTCAACAACAACCCACGCTCCACCGCGCAGCTCTCCCATCATTGGGATGTACACAAACACTGGCTGACGATAGGTTCTCAGATTTTCTACTATAGTTGAACCTGCCTGAAGTATTCCTTCGAAAAGATCTCTCTGCCCACCTGAAAACCCTCTCCAGTTCGCTAGGATAAACAATGGAAGCTCTTCCCGGTTGAAATCCATAAGTGCTTGAGCAGTCTTGGCCGCTGAATCAGGAAACCAGACTTGCCCTGCTTGCGGAACCACTCTTTCATGAGAGTCAAGCTGTCCAGGATCGGCTGGGATGATCTGCATGACAGTCTGTGTCTCAACTGCAACAACTCCAACGGGTATTCCCCCGAGCTTGGCTCTACCAGTCACTACCGTCCTTGCCCAGCCTTCAAGAGTCTCAATGAAACTATTTTTATCAAAGATACCTCCAAGCCATTTACCGGTATTGTCTTTGACCCCAGCTATAGCCGCTCGTGGGTCGCAAGAGTTCTCTGGGACATACTCCACAATTCTCTCCGGTGGATCTAAAGGGGCAAGAACAGGAAGAGGACCACCCACGTAAGCAGGAATGTAGCTGAGCCAGTTGAGAATTGCTGATACGCCTTCAAGATCATCTGAGACTGTAAGATGAACAACACCATTTGTGCCCATGATTTTCGGGCCACCCAGTTGCATGTGAGAGCTATAGACCTCACGCCCAAGTAACTTGTTGAGTGTAGAGAAGCCAGTCAAGATGATCGGCTGATCAAGTCTCTGTATGCACCGCATACCTAGGCGGGCAAGATAAGCACCAATTCCAACCGTTCTTCCACTAACAAAGGTTAAAGTAAAAGTTTCATTGTATGCCTTTGAGTAAGCACCCGCTATGGCCCCACTTCCTGTTAAGTTCTCTACACCAATACCATCTTCTTTGCCAACGATCGTATCAATCACCCACCTAGTTTCCCCACTAGGGAGCTTTACTTCATGGGCAATGACAGATGATCCAATCCTTTCGTGGTCTTCAGGGCTTAGGTATATATACTGAAAACCATTCTCAGGGGAAATTTCATCCGACCATCCAACTTTGAAGCAGGCTTTGACTTCTTCAGCAACCCCAAGTCGGGCACCAGAATTTGCTGCCAAGTAAATCAAGGGAAGCTTCTTGGCACAAGCGAGTTCAGTAACAGCAAGGAAAAACGCGTCCTCTCTAGGACCAAAAGAACCAGCTTTGAAGGTGACATCATTCGCAATCACGAGAAGTTTCCGCCCCATAGGAAACTCTGGGGTCGACATATCTAGGCACCAGGCAACCATTCCAAAGTCGTTGAGACCGGGTGGTCTTTCAACCAGATCTAGAGATGTACCCGAAGAACCTTCTGGTTTTGAGAATACAAGCTCTTTAACATTGATCAGAGTATCCTTATATGGTTTCTTAACTCCTGGGTGTTGTGATGCCCACAACAGTTCCAAGGCTGTCCCAAATGCCAACGGGAAGTCATAGCAATAAGTAGTGTTACTCCTCCTTGCTGCTAAACGTTGCCTGTCGAGATATCCCAGGGGCTTATATTGATCACTGATTGGGGTTTCATGCAAAGGTCCCTTCTTGGTTATTGAGTGGTAGATTAAACTGTTTCTTCCAGGAGTTTCAACTTCTCGGTATATGTGGACAGTGCATGTACGGCCTGTCACGTTTGCAACCACAACCCTCCAAGCACCACATGCCAGTCCAGAGGACACCAACCACAGCCGCACTTCCCACTCGCACACGCCCAACCTATGCATTCTCACTCCAACAGATCTATGTATCTCTCGTGCTGCTTCTTCTAAGATCATTTCAACTGTAGTTTCTTCATCCTCCGCATTCACTTCAACTCTCCTGGGGAAAGGCACAAGATCATCTATCTGCTGCTCACGCAATATGCAAAGAAACATATGTGCGTGATCTGGTTTCATTGCAGCATTATGGGCATTCAGTTCCAGTTCCTCCATGGCATCCATCAAAGACCTCAGAACACATTTCGACGTAAACGCCATGGAGATCAGTGTTTGGCTAAGCTGCTTATCCTGCCCTTGCTGCAATATAAATCCATCGTTCATTGTAGCCTGTCGAACAAGAGATCTCAGGAACATCCTCTTGATTGGCACTGGCTTGTCTGTAACAGTATACAGATGCCATTGACGATCTCGAGAAGGCGTATATTGTATATTTGAGTATCCTTTCAGCTTATCCAACTCAAGGTAAATGGACAGAGGAGGTTCAAGATGACGCAGCAACGGCTCTTCTACATAATACTGTTTCTCCAACGACCAATGGAAAGAATGTCTCATGGGTGTTCGTCCTTCATCTCGCTGAATTATACAGCTGATTACACCAACACCGGCAGAACAGAGGCTTGAACTCACTTCTTCCTCTTTAAGAATTTTGGCCAACTTGTTTACTCTTTCCTGAGCTTGGTCTTCATCCCCACTGTCCTGAAGCAGACTCATCTGGTTGTTGATGCCCACAATAGCAATGTGCATCATATTGCCAGATAAAGGAGCTCCGGCAGTTTCATAGTCGTTGTGCTTTGTTTCTCTCAATGCTGCACTTATTATACTTGGAAGAAACTGCAAAGATTTGATTATAACCATAGCCCCCCATTTTCTCTTACTACGCTTCTCAACCAATCCTTTTTCAGATGTGTCGTGATCGTCTAAGCCAATGTTTTTTCTTTCCATATGCTCCTCTAGGAAATCCCAGGAAGCAAGAAGACCAGAACGGTGCCACTGCATCCTCACGCTATCTTTAACGACGTAGGGCTGGTATAATCTGCGAATATAAGTCTCAACAACCCGTCTTTGAAGTGTGTGATCGCTATGGTCAAATAGTCCCACGAGAGCGTCTTCAACAGCTAAAGATGCGCTTACAAGATCTTCTATTCTTTCATTAATGGCACTTTTCCTCTTGGGAGTATCCATATTTTCTCCGTCCTCTGTAAACATTTCTAACTCTGAAAGGCTTCTAGCAATGTTTGAACGAAGCTCACTTAGTTTGGTCTGTTCAAGTAATTGACTCGCCTTGAGCGCCAACTCAGAGTAGTTAGTATGGTTAAGTGTTGAGAATCGAATAAGTTTATCTCTGTAAGCAGCAGGATTAGGGTAAACAAGCTGCTCCATGAGCCGGAGAACGAGTTTGTTTTTGTTTTTTATGCCCTGGTGTGAGAGCACTATATCCACAATTTTCAACAGATCTTTCTTGTATAGCTGACGCATGCGTTCTATAACATCAGCCAGCATGTTATCATTGAATAATTCTTCTACTGATAGATATTCTTCAAAGAGAGAATGAACAATAACACGGGCATGACTTTCTCTACCACCTTCATAAGATTTTGCAAGGCTCATCAATGGTTCAATGAGCCTTTCAAGGGCACCTCTCTCTTTCTCATCACAAGAAGATAAATGTGCCTCAAGAATGCCTTTTAAAAGTTTGGCAGGGAAATCGGTGGTCAAAGAGTTTCTGGAAATACTCTCAAATTCCCTATACTTTGATTCTAGCATGTTCCTGAGATTTTTAGGTAGTCGTGTCGCCAGAACTGCAAAGCACTCTTGCCACTGAAGAAATGGGAGTTCAGGGCTATCAAGGCAATTAAGTAAGTCTTGAACAACCTCATCTACTTTATGCTCATAGCCAGCAAGAATCATGCGTGCAGCATTTAATGTTGCGGCACATCTCTGATGAACTCTACCGGATATTGCAGTTGGAAGCCCTAATCTTGGGAAACTTCCATGGAAGGGTTCGGCCTTTCTTACAGCAGAAGGATCATCAAGATCAAGATTGGCGATAAGTTCACCAGCCTGCATGGCTTGTCCTTCAGACATTTTAAAATGGATAACTCCTGAAGCAGGTGAAAGAAGTGGCATGCACATCTTCATGACCTCAACTTCGGCATAAGGCGTATCAGCGTCAATATTGCTGTTGTCAGAAACCAAATACCTCATCAACTTGCACGGTGTCTCAGCCATTAACTTTGATGGATCATGGTCATTCTGTAGCAAACAAGTTCTTCCATCAATGAGAAGACGAGTTCCTGCAGCTTCTTCCTCTGCATATATCACATGGCTTTTGCCATCCAACTGCATCAACAGACCTCCATCACGTAGAGTGTGTATTTCTGCTACCACTTCTGACTTGTTCATTCTTAGCCTGTAGGTTCCTGATCCACCCCGGACTACATCAATCGTATATTTACTTCCTTCAATATTCAGAGACACTTGAGAATGCACAAGAGATATATGCTTTGGGGGAATTTGCCCCTTTTCTAGATAGCCAACGTAATCCGAAACTACAGCAGAACTGGTCGTAGATGCTTTATAAAGAGCCCCACCGACTACAGAGAGATACCATGGAGGTCTCTCTGCTCTGACCCGCATAGCAATCCTACTGTCCAACCAACCAGTGTGTATTTTGTTTTCCCGGTAATCAGAAGCATGTAGAAGGTCGATCGTGTAGTCAACGTTAGTCCTAATTTCTCCACGGATCTGAATTTCTTTTAGCCCAAGAACCATATTCGCTATCGCCAGGGCTCTGGATTCCCCAAATGCAAAAACATGTCCAAACTGGGAATCCGAGAACTCGTGGATGCCTCCACCAGACTTGACAGAGAAGTACGCCCACACATTTGGCTTGCTCTTAAAACTCAACTCCTGAACTCTACCGCTGGTTGGTTTGAACCCGTCATCAGGATCCTCACTTGTCACACGTACAGCCACACAATGACCTTTTGGCCTTATAGATTGAGCTTTATCAAAATCAAAAGGGAAGGCTACAACAGATGTTTTTCGCCAAGAATCATAACCTCCACCATGTTCTATTCCATAGAACCGTCTTATCTCAGGGATTTGCCAGAGAGGAATTCCCATCCCCACAGCAACTTGGGCAGCAGGAAGATTTATCTCGGCAATCCACTCAGTGACAGGATGCTCAACCTGTAAGCGAGGGTTAAGCTCTAAGAAGTAGTACTCCCCAGTGTCCATACTGTAGAGATACTCAACAGTAGCAGCTCCAACATAGTTAACACTCTTAGCCAACCTTCTAGCTGCTTGTTCAAGTTTCTTGACAGTTTCTGGCGGAGCCACAGTAATTGGACCCTCCTCTATGATCTTTTGATGTCTTCTCTGGACGCTACAATCACGGCTATGCAGAGCTGAAACATTTCCATGCTTGTCACAGAGCAGCTGGACCTCTAGATGCCGACTCTGTGACGCAACCTTCATTATGAATATTGGTGAGCCTGGGACCTCACCCTGAACTTGCTTGAATAGAGCCCTAACCTCATCATCATTATGAACCTTCCTGATTCCTTTACCACCACCACCCCACGATGCTTTGATCATTGCTGGGTAACCGACAACTTGACAGCTAGCAATCGCTTCTTCAGTTGTGTAGACACATGCTTGCCGGTAGATCTCCTCTGGGATGGTTACCAAGTTGCTATTAGGAGGTATTTTAACATGGGAACCACTCCATGGCAGAGTGGGTACATCAGCAGCTTGTGCAATCAACGAAGAACCAATCTTATCTCCCAGTGCTGCCATTGAAGATGCTGGAGGACCAAGAAATATGATTCCTTTTGCATCTAGGGCATCAGGTAATTCGGGGTTTTCAGATGCATGACCCCAACCAGGCCAAACTGCATCCACGCGTGTTACTTCAGCCATCTCCACAATCAGCTGAACGTTAGCATAATTGTTATTGTTAGTTCCTCCGGGAACCTCAACAAACTGATCAGCGATTCTGATATGCTCCGCATTGATCCGCATGTCTTCAGGGGTTGCCATCCCCACCAACAATATGGCTTTTTCCGTACCAAATGTTTCATAAGCCCATGTTCTGACACTACGTATAAACTTCACAGCCGCCATTCCATTGTTAGCTATCAAAATACTATGGATCGGCCTTTTCCCTCTAAGTGCTTTACAGAACTCATCCACTTGAGACACCGTCTCATAATTTATACCAGGTCCTACAGCACTATGATTCCCGTTAACCGAGCCAGCCATTGTCACTGCCCTTTAATCTTCAGATATATCTTGTAAGGAAGCAGA";

      DNASequence target = new DNASequence(str1,
                    AmbiguityDNACompoundSet.getDNACompoundSet());

      DNASequence query = new DNASequence(str2,
                        AmbiguityDNACompoundSet.getDNACompoundSet());

      NeedlemanWunsch aligner = new NeedlemanWunsch(query, target, gap, matrix);

      System.out.println("getScore: " + aligner.getScore());
      System.out.println("getMaxScore: " + aligner.getMaxScore());
      System.out.println("getMinScore: " + aligner.getMinScore());
      System.out.println("getSimilarity: " + aligner.getSimilarity());
   }            
}



Regards,
Alexander Beskrovnyy
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Question about NiedlemanWunsch class

Hello!
I have a problem with aligning the sequences with the help of NiedlemanWunsch class. The problem is following: I found the sequences, where method "getSimilarity" got negative numbers, but the description said: "It returns score as a similarity between 0.0 and 1.0"
I looked at the output of methods "getMaxScore", "getMinScore" and "getScore", which are involved in calculations of method "getSimilarity", and I have noticed, that "getMinScore" and "getMaxScore" got strange numbers (maxScore was less than minScore or both were negative), but output of "getScore" seemed adequate.
I used SimpleGapPenalty and SubstitutionMatrixHelper.getNuc4_4() as a parameters of constructor of NiedlemanWunsch class.
According to rules, i can’t attach file with sequences to my letter. But in case it is possible, I would kindly ask you to explain me, how to do it correctly,and then i'll send you the sequences. They are too long to be send like a text in a letter.

Thanks for your attention!

--
Regards,
Alexander Beskrovnyy
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Pola Kyzioł | 31 Oct 18:17 2014
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Parser for MrBayes output

Hello,

my name is Pola and I'm currently a third year student in the Theoretical Computer Science
at Jagiellonian University. I have also interest in biology, especially in the field of genetics.
I've been searching a project connected with bioinformatics which I could develop
and next use to writing my bachelor's thesis. I've found BioJava and looked at its issues -
parser for MrBayes output seems for me to be interesting to code.
I would like to know some details about it: 
- what data you want extracted from MrBayes' output files;
- how the created model should look like and if appropriate modules already exist.

Thanks for your help,
Pola
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Andreas Prlic | 7 Oct 20:52 2014
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The NIH Software Discovery Index | We invite your comments -- a system for linking software, publications and users in the research community.

Greetings Everyone,

 

On behalf of a number of software developers, end-users, publishers associated with the scientific analysis community, we would like to invite all of you to review a document generated as a result of a NIH BD2K supported meeting that focused on the opportunities and challenges of developing a software management ecosystem that could be valuable for finding and linking software, publications and users in the research community. You may be also be aware of a related project, the Data Discovery Index, which will be fully integrated with the software system.

The product of this workshop and the subsequent discussion is a document which details the opportunities and challenges of developing a Software Discovery Index that would enable researchers to find, cite, and link software and analysis tools publications and researchers. To ensure that the opportunities, challenges, and recommendations detailed in the document reflect the breadth of experience from the community, we are seeking your input.  In conjunction with related efforts already under way at NIH, including the development of a Data Discovery Index, the final document will be used by the NIH Office of the Associate Director (ADDS) to inform a strategy for the development of a Software Discovery Index and a commons ecosystem for data, software, and resources.

 

We need your help to ensure that this critical task is achieved: to guide the development of a community based system that gives credit and acknowledgment to the builder and maintainers of the software we all depend on! We invite all users, software developers, publishers, and software repository administrators to review our report prior to its submission to the NIH. Please complete your review and post comments by November 1, 2014.

 

The link to the report is here: http://softwarediscoveryindex.org

 

On behalf of the organizing committee, thank you for your assistance!

 

Organizing Committee

 

Owen White

Director of Bioinformatics, University of Maryland, Baltimore, School of Medicine

Co-Chair of NIH BD2K  Software Index Workshop

 

Asif Dhar

Principal & Chief Medical Informatics Officer

Co-Chair of NIH BD2K  Software Index Workshop

 

Vivien Bonazzi

Senior Advisor for Data Science Technologies (ADDS)

Co-Chair of BD2K Software and Methods Group

 

Jennifer Couch

Chief, Structural Biology and Molecular Applications Branch

NCI Co-Chair of BD2K Software and Methods Group

 

Chris Wellington

Program Director (NHGRI)

 

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Mike Noseworthy | 19 Sep 21:33 2014
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NoClassDefFoundError

Hi there,

I recently started working on a project the uses BioJava 3.0.4 and am encountering a   NoClassDefFound exception when I try to run it. This leads me to believe something is wrong with the classpath. However all the biojava jars are included. Has anyone had a similar problem or have any insight into where I should look next? Are there any other jars that biojava depends on other than the biojava jars from the downloads page. Any help would be greatly appreciated!

Here are the errors:
Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation
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(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation
at java.util.concurrent.FutureTask.report(Unknown Source)
at java.util.concurrent.FutureTask.get(Unknown Source)
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)
at externalcalcs.BLASTRunner.writeBlast(BLASTRunner.java:143)
at externalcalcs.Conservation.runConservation(Conservation.java:31)
at externalcalcs.ExternalCalculations.runExternalCalcs(ExternalCalculations.java:58)
at runtime.PACE.externalCalcs(PACE.java:298)
at runtime.PACE.main(PACE.java:168)

Thanks!

Michael Noseworthy
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Michael Heuer | 3 Sep 04:11 2014
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BioJava Legacy 1.9.1 released

== BioJava Legacy 1.9.1 released ==

BioJava Legacy 1.9.1 was released on September 2nd 2014 and is
available from http://biojava.org/wiki/BioJava:Download_1.9.1 as well
as from the Maven Central repository.

To use BioJava Legacy in your Maven-based JVM project, just include
module dependencies such as

  <dependencies>
    <dependency>
      <groupId>org.biojava</groupId>
      <artifactId>core</artifactId>
      <version>1.9.1</version>
    </dependency>
  </dependencies>

and you are ready to go.  For a list of modules, see
http://search.maven.org/#search%7Cga%7C1%7Cg%3A%22org.biojava%22

For a detailed comparison see here:
https://github.com/biojava/biojava-legacy/compare/biojava-legacy-1.9.0...biojava-legacy-1.9.1

About BioJava:

BioJava is a mature open-source project that provides a framework for
processing of biological data. BioJava contains powerful analysis and
statistical routines, tools for parsing common file formats, and
packages for manipulating sequences and 3D structures. It enables
rapid bioinformatics application development in the Java programming
language.

On behalf of all the BioJava developers,

   michael
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Spencer Bliven | 26 Aug 11:45 2014

New Release of BioJava 3.1.0

== BioJava 3.1.0 released ==

BioJava 3.1.0 was released on August 25th 2014 and is available from
http://biojava.org/wiki/BioJava:Download as well as from the
BioJava maven repository at http://www.biojava.org/download/maven/

While most development is going towards the upcoming 4.0.0 release, this release provides bug fixes and a few new features:

* CE-CP version 1.4, with additional parameters
* Update to SCOPe 2.04
* Improvements in FASTQ parsing
* Fix bugs in PDB parsing
* Minor fixes in structure alignments

For a detailed comparison see here:
https://github.com/biojava/biojava/compare/biojava-3.0.8...biojava-3.1.0

This version is compatible with Java 6 and 7. If you're using Java 8, please use the latest snapshot build. Snapshots are now available from Maven central just by setting your pom.xml file to version '4.0.0-SNAPSHOT'!

Thanks to the contributors who submitted code to this release–heuermh, Elinow, Siarhei, sbliven and andreasprlic–and to those who contributed to the 4.0.0 branch!


About BioJava:

BioJava is a mature open-source project that provides a framework for
processing of biological data. BioJava contains powerful analysis and
statistical routines, tools for parsing common file formats, and
packages for manipulating sequences and 3D structures. It enables
rapid bioinformatics application development in the Java programming
language.


Cheers,

Spencer
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Gmane