From d131f05c68757d57e5e4a1f440196ae1b70f3b8a Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 3 Sep 2015 21:20:13 +0100
Subject: [PATCH] JAL-1233 JAL-1576 copy constructor to propagate helix
 colours and applyTo implementation to clone colour scheme
 to subgroups

---
 src/jalview/schemes/RNAHelicesColour.java |   20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 57fcba5..2beb4cf 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -74,6 +74,19 @@ public class RNAHelicesColour extends ResidueColourScheme
     alignmentChanged(alignment, null);
   }
 
+  /**
+   * clones colour settings and annotation row data
+   * 
+   * @param rnaHelicesColour
+   */
+  public RNAHelicesColour(RNAHelicesColour rnaHelicesColour)
+  {
+    super(ResidueProperties.nucleotideIndex);
+    helixcolorhash = rnaHelicesColour.helixcolorhash;
+    annotation = rnaHelicesColour.annotation;
+    refresh();
+  }
+
   @Override
   public void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
@@ -193,4 +206,11 @@ public class RNAHelicesColour extends ResidueColourScheme
     // currentColour);
     return currentColour;
   }
+
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    return new RNAHelicesColour(this);
+  }
 }
-- 
1.7.10.2