From b86014d3039eeb4a877d0e9e65bd4409065843f0 Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Wed, 16 Aug 2017 16:11:54 +0100
Subject: [PATCH] JAL-2599 HMM annotation now shows consensus characters at
 each column

---
 src/jalview/analysis/AAFrequency.java |    6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 046c589..82fca97 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -398,9 +398,9 @@ public class AAFrequency
       }
 
       String description = value + " bits";
-      
-      information.annotations[i] = new Annotation(" ", description,
-              ' ', value);
+      information.annotations[i] = new Annotation(
+              Character.toString(hmm.getConsensusAtAlignColumn(i)),
+              description, ' ', value);
     }
     information.graphMax = max;
     // long elapsed = System.currentTimeMillis() - now;
-- 
1.7.10.2