Merge branch 'releases/Release_2_10_0_Branch'

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3a92e4b..6170b63 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -612,7 +612,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     boolean recalc = false;
     if (cs != null)
     {
-      cs.setConservationApplied(recalc = getConservationSelected());
+      recalc = getConservationSelected();
       if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
               || cs instanceof Blosum62ColourScheme)
       {
@@ -629,6 +629,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         cs.setConsensus(hconsensus);
         cs.setConservation(hconservation);
       }
+      cs.setConservationApplied(getConservationSelected());
       cs.alignmentChanged(alignment, hiddenRepSequences);
     }
     if (getColourAppliesToAllGroups())