ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/owl/trunk/src/owl/tests/core/sequence/data/Q8WZ42.fasta
Links to HEAD: (view) (annotate)
Sticky Revision:
Sort logs by:
Revision 1647 - (view) (annotate) - [select for diffs]
Added Thu Jul 4 08:39:06 2013 UTC (6 years, 3 months ago) by jmduarteg
File length: 34985 byte(s)
Fixing bug in jaligner: the NeedlemanWunschGotoh method used by owl.core.sequence.PairwiseSequenceAlignment had a bug causing infinite hanging when using very long sequences. The issue would happen when either of the 2 sequences to align was longer than 32768 (16 bit) and the other sequence would match it after the 32768 region, a test case is included in this commit to demonstrate it. The problem was an overflow: an array used for the traceback procedure was declared as short[] (16 bit), changing it to int[] (32 bit) the issue disappears. 
As the development in jaligner seems to be stopped I've simply downloaded the source, fixed the issue there (plus removing the loggers) and repackaged in a jar (jaligner-bugfixed.jar) that includes the sources.

This form allows you to request diffs between any two revisions of this file. For each of the two "sides" of the diff, enter a numeric revision.

  Diffs between and
  Type of Diff should be a