JAL-952 refactor code to select annotation for colouring the alignment

[jalview.git] / src / jalview / schemes / RNAHelicesColourChooser.java

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index 1edca4b..bcac5c7 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -97,12 +97,9 @@ public class RNAHelicesColourChooser
     {
       return;
     }
-
-    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
     RNAHelicesColour rhc = null;
 
-    rhc = new RNAHelicesColour(currentAnnotation);
+    rhc = new RNAHelicesColour(av.getAlignment());
 
     av.setGlobalColourScheme(rhc);
 
@@ -115,7 +112,7 @@ public class RNAHelicesColourChooser
           continue;
         }
 
-        sg.cs = new RNAHelicesColour(currentAnnotation);
+        sg.cs = new RNAHelicesColour(sg);
 
       }
     }