Not sure if this is an issue with the MultipleSequenceAlignment code versus the way you are doing pairwise is simply throwing a concurrency exception. Can you complete all pairwise comparisons independently to rule out a problem related to the code and the sequences you are trying to align?
From: Muhammad Tariq Pervez <[email protected]<mailto:[email protected]>> Date: Mon, 25 Jul 2011 06:27:02 -0400 To: Scooter Willis <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: [Biojava-l] NullPointerException Exception While Creating DNA MultipleSequenceAlignment Following is tmpLst filled with two DNA sequences. Scorers object is displayed from inside the object of Alignments (getMultipleSequenceAlignment method). All==1 is displayed from inside the method of public static <S extends Sequence<C>, C extends Compound> int[] runPairwiseScorers( List<PairwiseSequenceScorer<S, C>> scorers) { (class is Alignments) as follows all = scorers.size(); But the line System.out.println("futures==="+futures.get(0).get()); causes NullPointer Exception. List<Future<Integer>> futures = new ArrayList<Future<Integer>>(); for (PairwiseSequenceScorer<S, C> scorer : scorers) { futures.add(ConcurrencyTools.submit(new CallablePairwiseSequenceScorer<S, C>(scorer), String.format("Scoring pair %d of %d", n++, all))); } try{ // perhaps this code is not working fine. System.out.println("futures==="+futures.get(0).get()); tmpLst==[GAATCTATAGGGCGATTGGGCCTCTAGATGCATGCTCGAGCGGCCGCCAGTGTGATGGATATCTGCAGAATTCAGGTAGTCGACTCAGATTCTTGTAGTGGCTCTCATCTGATCAAGGGTATTATTCCCAAGCCATAGTAAGGTCTTCTGTTGTGCCTTTTGCTTATACATCAGGTAACATGATAGAACTAGGCTAAGTG, ATGGGCTCCAAACCTTCTACCAGGATCCCAGCACCTCTAATGCTGATCACTCGGACTATGCTGATATTGAGCTGTATCCGTCTGACAAGCTCTCTTGACGGCAGGCCCCTTGCAGCTGCAGGAATTGTAGTAACAGGAGATAAGGCAGTCAATGTATACACCTCGTCTCAGACAGGGTCAATCATAGTCAAGTTGCTCCCGAATATGCCCAGAGATAAGGAGGCATGTGCAAAAGCCCCATTGGAGGCATATAACAGAACACTGACTACTCTGCTCACTC] sequences=== [GAATCTATAGGGCGATTGGGCCTCTAGATGCATGCTCGAGCGGCCGCCAGTGTGATGGATATCTGCAGAATTCAGGTAGTCGACTCAGATTCTTGTAGTGGCTCTCATCTGATCAAGGGTATTATTCCCAAGCCATAGTAAGGTCTTCTGTTGTGCCTTTTGCTTATACATCAGGTAACATGATAGAACTAGGCTAAGTG, ATGGGCTCCAAACCTTCTACCAGGATCCCAGCACCTCTAATGCTGATCACTCGGACTATGCTGATATTGAGCTGTATCCGTCTGACAAGCTCTCTTGACGGCAGGCCCCTTGCAGCTGCAGGAATTGTAGTAACAGGAGATAAGGCAGTCAATGTATACACCTCGTCTCAGACAGGGTCAATCATAGTCAAGTTGCTCCCGAATATGCCCAGAGATAAGGAGGCATGTGCAAAAGCCCCATTGGAGGCATATAACAGAACACTGACTACTCTGCTCACTC] scorers=== [org.biojava3.alignment.FractionalIdentityScorer@d337d3] all===1 scorers===org.biojava3.alignment.FractionalIdentityScorer@d337d3 java.util.concurrent.ExecutionException: java.lang.NullPointerException at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222) at java.util.concurrent.FutureTask.get(FutureTask.java:83) at pakjalphiew.Alignments.getListFromFutures(Alignments.java:304) at pakjalphiew.Alignments.runPairwiseScorers(Alignments.java:631) at pakjalphiew.Alignments.getMultipleSequenceAlignment(Alignments.java:194) at pakjalphiew.MSA.msaDNAFromFiles(MSA.java:109) at pakjalphiew.MSACalculation.calculateDNAMSAFromFiles(MSACalculation.java:42) at pakjalphiew.MSAInterFrame.<init>(MSAInterFrame.java:60) at pakjalphiew.LaunchingFrame.newDNAFromFileActionPerformed(LaunchingFrame.java:265) at pakjalphiew.LaunchingFrame.access$000(LaunchingFrame.java:26) at pakjalphiew.LaunchingFrame$1.actionPerformed(LaunchingFrame.java:83) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.AbstractButton.doClick(AbstractButton.java:357) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850) at java.awt.Component.processMouseEvent(Component.java:6288) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6053) at java.awt.Container.processEvent(Container.java:2041) at java.awt.Component.dispatchEventImpl(Component.java:4651) at java.awt.Container.dispatchEventImpl(Container.java:2099) at java.awt.Component.dispatchEvent(Component.java:4481) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168) at java.awt.Container.dispatchEventImpl(Container.java:2085) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4481) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:643) at java.awt.EventQueue.access$000(EventQueue.java:84) at java.awt.EventQueue$1.run(EventQueue.java:602) at java.awt.EventQueue$1.run(EventQueue.java:600) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$2.run(EventQueue.java:616) at java.awt.EventQueue$2.run(EventQueue.java:614) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:613) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) Caused by: java.lang.NullPointerException at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112) at org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105) at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53) at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:662) Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at pakjalphiew.AlignmentRuler.getRuler(AlignmentRuler.java:34) at pakjalphiew.AlignmentRuler.<init>(AlignmentRuler.java:26) at pakjalphiew.MSAInterFrame.initComponents(MSAInterFrame.java:81) at pakjalphiew.MSAInterFrame.<init>(MSAInterFrame.java:62) at pakjalphiew.LaunchingFrame.newDNAFromFileActionPerformed(LaunchingFrame.java:265) at pakjalphiew.LaunchingFrame.access$000(LaunchingFrame.java:26) at pakjalphiew.LaunchingFrame$1.actionPerformed(LaunchingFrame.java:83) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.AbstractButton.doClick(AbstractButton.java:357) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850) at java.awt.Component.processMouseEvent(Component.java:6288) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6053) at java.awt.Container.processEvent(Container.java:2041) at java.awt.Component.dispatchEventImpl(Component.java:4651) at java.awt.Container.dispatchEventImpl(Container.java:2099) at java.awt.Component.dispatchEvent(Component.java:4481) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168) at java.awt.Container.dispatchEventImpl(Container.java:2085) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4481) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:643) at java.awt.EventQueue.access$000(EventQueue.java:84) at java.awt.EventQueue$1.run(EventQueue.java:602) at java.awt.EventQueue$1.run(EventQueue.java:600) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$2.run(EventQueue.java:616) at java.awt.EventQueue$2.run(EventQueue.java:614) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:613) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) Muhammad Tariq Pervez Assistant Professor, Department of Computer Science Virtual University of Pakistan, Lahore Tel: (042) 9203114-7 URL: www.vu.edu.pk Mobile: +923364120541, +923214602694 > From: [email protected]<mailto:[email protected]> > To: [email protected]<mailto:[email protected]>; > [email protected]<mailto:[email protected]> > Date: Fri, 22 Jul 2011 08:11:34 -0400 > Subject: Re: [Biojava-l] NullPointerException Exception While Creating DNA > MultipleSequenceAlignment > > Can you include the output of the stack trace as well as a small working > example that causes the exception? > > On 7/22/11 7:56 AM, "Muhammad Tariq Pervez" > <[email protected]<mailto:[email protected]>> wrote: > > > > > > > > >Dear all, > > > >I faced the NullPointerException exception while creating the DNA > >MultipleSequenceAlignment. The same goes right with protein sequence. > >Exception is thrown at the following line > > > >dnaProfile = Alignments.getMultipleSequenceAlignment(tmpLst); > > > >tmpLst is list of DNA sequences created/declared as follows > >List<DNASequence> tmpLst=new ArrayList<DNASequence>(); > > > >Note: the tmpLst is filled/populated with two or more two sequences. > > > >I traced the exception by going into > >Alignments.getMultipleSequenceAlignmen method of the Alignments class and > >found the following line of code the cause of exception. > > > >static <E> List<E> getListFromFutures(List<Future<E>> futures) { > > List<E> list = new ArrayList<E>(); > > for (Future<E> f : futures) { > > // TODO when added to ConcurrencyTools, log completions and > >exceptions instead of printing stack traces > > try { > > > > list.add(f.get());** > > } catch (InterruptedException e) { > > e.printStackTrace(); > > } catch (ExecutionException e) { > > e.printStackTrace(); > > } > > } > > return list; > > } > >** is the cause of exception. All is right with the protein sequences. > >Can any body help/guide me regarding the problem. > > > >Best Regards. > > > > > > > >Tariq, PhD Scholar > > > >_______________________________________________ > >Biojava-l mailing list - > >[email protected]<mailto:[email protected]> > >http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
