[Biojava-l] NullPointerException Exception While Creating DNA MultipleSequenceAlignment

[Muhammad Tariq Pervez]

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