X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=c01be4ef28deb1c5b2bd402447bf1eff0fca0a73;hb=c9e34d0b5eb6aff1938ee5488c313beb5abc5d06;hp=49f537d412951209a6da02a306ef03c0bb4b40a7;hpb=b7c6fbe6d47b510f7ac845eb5c29e971ffb41cfb;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 49f537d..c01be4e 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -613,7 +613,7 @@ 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)
       {
@@ -630,6 +630,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         cs.setConsensus(hconsensus);
         cs.setConservation(hconservation);
       }
+      cs.setConservationApplied(getConservationSelected());
       cs.alignmentChanged(alignment, hiddenRepSequences);
     }
     if (getColourAppliesToAllGroups())
@@ -939,7 +940,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
     groupConservation = null;
     hconsensus = null;
     hcomplementConsensus = null;
-    // TODO removed listeners from changeSupport?
+    // colour scheme may hold reference to consensus
+    globalColourScheme = null;
+    // TODO remove listeners from changeSupport?
     changeSupport = null;
     setAlignment(null);
   }