X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=54eed1a73c9dcf6b049a5e872c85f97ad072061a;hb=532f84b54e9039d831af69f394d72dd6ffbcee15;hp=7acae98b3e9a4e4236feea5f29ad23d97a6f6c69;hpb=b0cee3aaf7d8873910939f97b6acb217d518968d;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 7acae98..54eed1a 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -997,18 +997,21 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sg,
+          cs = ColourSchemeProperty.getColourScheme(sg,
                   ColourSchemeProperty.getColourName(av
                           .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.getResidueShading().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.getResidueShading()
+                        .conservationApplied())
         {
           Conservation c = new Conservation("Group", sg.getSequences(null),
                   sg.getStartRes(), sg.getEndRes());