X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=a587ac3aad757e2ac97ac23a1f72cb78fe1cc892;hp=8dd6d0cc5645218457849c85ca77cb0f8004dc54;hb=16d109024847af92482237e43f99b82fd997451a;hpb=7091ed4ecff294623230f96ed93f9a5689ea5938

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8dd6d0c..a587ac3 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3352,6 +3352,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * otherwise set the chosen colour scheme (or null for 'None')
      */
     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+            viewport,
             viewport.getAlignment(), viewport.getHiddenRepSequences());
     changeColour(cs);
   }
@@ -5308,7 +5309,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true, true);
+      alignPanel.paintAlignment(true,
+              viewport.needToUpdateStructureViews());
     }
   }