X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.java;h=9809fa9a0223f0bd3b030faad72e1bd963d6c6e5;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=90cc14f278529a224e0488e049826a6d8bc8f6b3;hpb=94379c810f9115b8564ee7bac46ed119218d5fd2;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index 90cc14f..9809fa9 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -58,12 +58,12 @@ public class RNAHelicesColourChooser
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
-      oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
+      oldgroupColours = new Hashtable<>();
       for (SequenceGroup sg : ap.getAlignment().getGroups())
       {
-        if (sg.cs != null)
+        if (sg.getColourScheme() != null)
         {
-          oldgroupColours.put(sg, sg.cs);
+          oldgroupColours.put(sg, sg.getColourScheme());
         }
       }
     }
@@ -71,7 +71,7 @@ public class RNAHelicesColourChooser
     this.ap = ap;
 
     adjusting = true;
-    Vector<String> list = new Vector<String>();
+    Vector<String> list = new Vector<>();
     int index = 1;
     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
     if (anns != null)
@@ -105,6 +105,6 @@ public class RNAHelicesColourChooser
 
     av.setGlobalColourScheme(rhc);
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 }