+
+ if (alignment == null || (alWidth = alignment.getWidth()) < 0)
+ {
+ calcMan.workerComplete(this);
+ // .updatingConservation = false;
+ // AlignViewport.UPDATING_CONSERVATION = false;
+
+ return;
+ }
+ try
+ {
+ cons = Conservation.calculateConservation("All",
+ jalview.schemes.ResidueProperties.propHash, 3,
+ alignment.getSequences(), 0, alWidth - 1, false,
+ ConsPercGaps, quality != null);
+ } catch (IndexOutOfBoundsException x)