From b266a0f6122df2213d1cdcbdc609013287575deb Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 30 Oct 2014 15:26:11 +0000
Subject: [PATCH] patch for JAL-795 - use base secondary structure colour if
 no colour defined on annotation row element

---
 src/jalview/schemes/AnnotationColourGradient.java |    5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index e975884..3bca94b 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -244,7 +244,10 @@ public class AnnotationColourGradient extends FollowerColourScheme
         {
           if (predefinedColours)
           {
-            return currentColour;
+            return (annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
+                    : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
+                            : annotation.annotations[j].secondaryStructure != ' ' ? jalview.renderer.AnnotationRenderer.STEM_COLOUR
+                                    : currentColour);
           }
         }
         if (aboveAnnotationThreshold == NO_THRESHOLD
-- 
1.7.10.2