JAL-3183 overwrite 'no colour' group colours

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 384635b..710ec2e 100644 (file)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -444,17 +444,21 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
     av.setGlobalColourScheme(acg);
 
-    if (av.getAlignment().getGroups() != null)
+    /*
+     * set this colour scheme on groups that have no colour scheme configured; 
+     * note we can skip this if 'apply to all groups' is selected,
+     *  as it will have been done by av.setGlobalColourScheme
+     */
+    if (!av.getColourAppliesToAllGroups()
+            && av.getAlignment().getGroups() != null)
     {
-
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        if (sg.cs == null)
+        if (sg.getColourScheme() == null)
         {
-          continue;
+          sg.setColourScheme(
+                  acg.getInstance(sg, ap.av.getHiddenRepSequences()));
         }
-        sg.setColourScheme(
-                acg.getInstance(sg, ap.av.getHiddenRepSequences()));
       }
     }
   }