JAL-3148 pull up getSequenceRenderer to AlignmentViewPanel

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9de9e3b..764ba54 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -5305,6 +5305,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (avc.createGroup())
     {
+      if (applyAutoAnnotationSettings.isSelected())
+      {
+        alignPanel.updateAnnotation(true, false);
+      }
       alignPanel.alignmentChanged();
     }
   }
@@ -5564,8 +5568,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(textColour);
     colourMenu.addSeparator();
 
-    ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
-            false);
+       ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment());
 
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);