-
- Conservation cons = Conservation.calculateConservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alWidth - 1, false, ConsPercGaps, quality!=null);
- cons.completeAnnotations(conservation,
- quality, 0, alWidth);
+ try
+ {
+ cons = Conservation.calculateConservation("All",
+ jalview.schemes.ResidueProperties.propHash, 3,
+ alignment.getSequences(), 0, alWidth - 1, false,
+ ConsPercGaps, quality != null);
+ } catch (IndexOutOfBoundsException x)
+ {
+ // probable race condition. just finish and return without any fuss.
+ calcMan.workerComplete(this);
+ return;
+ }
+ updateResultAnnotation(true);