From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Wed, 16 Aug 2017 15:11:54 +0000 (+0100)
Subject: JAL-2599 HMM annotation now shows consensus characters at each column
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b86014d3039eeb4a877d0e9e65bd4409065843f0;p=jalview.git

JAL-2599 HMM annotation now shows consensus characters at each column
---

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;