Eventaully, I succeeded in finding the exact location of exception and fixes it
as well. The problem is with that in getMultipleSequenceAlignment Method of
Alignments class there are two 'if' statements as follows:
if (cs == AminoAcidCompoundSet.getAminoAcidCompoundSet()) {
@SuppressWarnings("unchecked") // compound types must be equal
since compound sets are equal
SubstitutionMatrix<C> temp = (SubstitutionMatrix<C>)
SubstitutionMatrixHelper.getBlosum62();
subMatrix = temp;
}else if (cs == AmbiguityDNACompoundSet.getDNACompoundSet()) {
@SuppressWarnings("unchecked") // compound types must be equal
since compound sets are equal
SubstitutionMatrix<C> temp = (SubstitutionMatrix<C>)
SubstitutionMatrixHelper.getNuc4_4();
subMatrix = temp;
System.out.println("Inside getMSA===" +subMatrix);
}
and 'subMatrix' remains null when we try to DNA sequences. But when i added the
third 'if' statement as follows the problem fixes and DNA sequences are aligned
correctly.
if (cs == AminoAcidCompoundSet.getAminoAcidCompoundSet()) {
@SuppressWarnings("unchecked") // compound types must be equal
since compound sets are equal
SubstitutionMatrix<C> temp = (SubstitutionMatrix<C>)
SubstitutionMatrixHelper.getBlosum62();
subMatrix = temp;
} else if (cs == DNACompoundSet.getDNACompoundSet()) {
@SuppressWarnings("unchecked") // compound types must be equal
since compound sets are equal
SubstitutionMatrix<C> temp = (SubstitutionMatrix<C>)
SubstitutionMatrixHelper.getNuc4_4();
subMatrix = temp;
System.out.println("Inside getMSA===" +subMatrix);
}
else if (cs == AmbiguityDNACompoundSet.getDNACompoundSet()) {
@SuppressWarnings("unchecked") // compound types must be equal
since compound sets are equal
SubstitutionMatrix<C> temp = (SubstitutionMatrix<C>)
SubstitutionMatrixHelper.getNuc4_4();
subMatrix = temp;
System.out.println("Inside getMSA===" +subMatrix);
}
Tariq, Phd Scholar
From: [email protected]
To: [email protected]; [email protected]
Date: Mon, 25 Jul 2011 09:44:23 -0400
Subject: Re: [Biojava-l] NullPointerException Exception While Creating DNA
MultipleSequenceAlignment
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]>
Date: Mon, 25 Jul 2011 06:27:02 -0400
To: Scooter Willis <[email protected]>, "[email protected]"
<[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]
> To: [email protected]; [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]> 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]
> >http://lists.open-bio.org/mailman/listinfo/biojava-l
>
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