-
- cons = Conservation.calculateConservation("All",
- jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alWidth - 1, false, ConsPercGaps, quality!=null);
+ try
+ {
+ // TODO - TDI is there a conservation measure ?
+ cons = Conservation.calculateConservation("All",
+ alignment.getSequences(), 0, alWidth - 1, false,
+ ConsPercGaps, quality != null, alignViewport.is3di() ? ScoreModels.getInstance().getFOLDSEEK3DI():ScoreModels.getInstance().getDefaultModel(true));
+ } catch (IndexOutOfBoundsException x)
+ {
+ // probable race condition. just finish and return without any fuss.
+ calcMan.workerComplete(this);
+ return;
+ }