Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

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

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 6448898..056a167 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -55,6 +55,14 @@ public class RNAHelicesColour extends ResidueColourScheme
   public AlignmentAnnotation annotation;
 
   /**
+   * Default constructor (required for ColourSchemes cache)
+   */
+  public RNAHelicesColour()
+  {
+
+  }
+
+  /**
    * Creates a new RNAHelicesColour object.
    */
   public RNAHelicesColour(AlignmentAnnotation annotation)
@@ -198,10 +206,10 @@ public class RNAHelicesColour extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    return new RNAHelicesColour(this);
+    return new RNAHelicesColour(sg);
   }
 
   @Override
@@ -216,15 +224,14 @@ public class RNAHelicesColour extends ResidueColourScheme
   @Override
   public boolean isApplicableTo(AnnotatedCollectionI ac)
   {
-    AnnotatedCollectionI context = ac.getContext();
-    if (context == null)
-    {
-      context = ac;
-    }
-    if (context instanceof AlignmentI)
+    if (ac instanceof AlignmentI && ((AlignmentI) ac).hasRNAStructure())
     {
-      return ((AlignmentI) context).hasRNAStructure();
+      return true;
     }
+
+    /*
+     * not currently supporting this option for group annotation / colouring
+     */
     return false;
   }
 
@@ -233,4 +240,10 @@ public class RNAHelicesColour extends ResidueColourScheme
   {
     return JalviewColourScheme.RNAHelices.toString();
   }
+
+  @Override
+  public boolean isSimple()
+  {
+    return false;
+  }
 }