X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;fp=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=9fa98ee3e8bdd66651e6e6754e4bd221da4bf210;hb=8e1be43e250107a4d86898bd554cf03098fa5957;hp=8ad5699d1801d11e5a73eee76da8eaeec3042cdd;hpb=8b55eedb9d76a8c65b80f756c4412bf029906bf7;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 8ad5699..9fa98ee 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1002,13 +1002,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                           .getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
-        if (cs != null)
-        {
-          cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.isIgnoreGapsConsensus());
-        }
+        // if (cs != null)
+        // {
+        // cs.setThreshold(av.getViewportColourScheme().getThreshold(),
+        // av.isIgnoreGapsConsensus());
+        // }
       }
-      sg.cs = cs;
+      sg.setColourScheme(cs);
+      sg.getGroupColourScheme().setThreshold(
+              av.getViewportColourScheme().getThreshold(),
+              av.isIgnoreGapsConsensus());
       // sg.recalcConservation();
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
@@ -1016,7 +1019,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       for (int a = 0; a < aps.length; a++)
       {
         if (aps[a].av.getGlobalColourScheme() != null
-                && aps[a].av.getGlobalColourScheme().conservationApplied())
+                && aps[a].av.getViewportColourScheme()
+                        .conservationApplied())
         {
           Conservation c = new Conservation("Group", sg.getSequences(null),
                   sg.getStartRes(), sg.getEndRes());