From 1ab4723a0134d9301c4547d3a7fb9116f6aa376e Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 17 Oct 2013 11:09:24 +0100
Subject: [PATCH] JAL-1397 propagate any consensus/conservation colourscheme
 state changes to the background colourscheme being
 thresholded by annotation colourscheme

---
 src/jalview/schemes/AnnotationColourGradient.java |   26 +++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 17af427..9c5512c 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -17,6 +17,7 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.GraphLine;
@@ -24,6 +25,7 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
+import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Map;
 
@@ -289,4 +291,28 @@ public class AnnotationColourGradient extends ResidueColourScheme
   {
     seqAssociated = sassoc;
   }
+  @Override
+  public void setConsensus(Hashtable[] consensus)
+  {
+    if (colourScheme!=null)
+    {
+      colourScheme.setConsensus(consensus);
+    }
+  }
+  @Override
+  public void setConservation(Conservation cons)
+  {
+    if (colourScheme!=null)
+    {
+      colourScheme.setConservation(cons);
+    }
+  }
+  @Override
+  public void setConservationInc(int i)
+  {
+    if (colourScheme!=null)
+    {
+      colourScheme.setConservationInc(i);
+    }
+  }
 }
-- 
1.7.10.2