Re: NullPointerException Exception While Creating DNA MultipleSequenceAlignment

Scooter Willis <[email protected]>
Newsgroups gmane.comp.java.bio.general
Message-ID <CA52EAC1.C085%[email protected]> 
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
lmpx.com only provides a reader for public news (NNTP) servers. It is not affiliated with the servers or forums shown here and is not responsible for the content of articles, which is written by their respective authors.