[Biojava-dev] [BioJava - Bug #3272] (New) NullPointerException Exception While Creating DNA Multiple Sequence Alignment

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Issue #3272 has been reported by Muhammad Tariq Pervez.

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Bug #3272: NullPointerException Exception While Creating DNA Multiple Sequence Alignment
https://redmine.open-bio.org/issues/3272

Author: Muhammad Tariq Pervez
Status: New
Priority: High
Assignee: biojava-dev list
Category: alignment
Target version: live (SVN source)
URL: 


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.



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