From 5161aef05fe56b2fc188fe069396d0f15e5968a8 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 24 May 2012 18:52:03 +0100
Subject: [PATCH] JAL-1065 per sequence and per-alignment scores added to
 annotation

---
 src/jalview/io/TCoffeeScoreFile.java |    3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 0da4628..cf33671 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -490,6 +490,7 @@ public class TCoffeeScoreFile extends AlignFile {
 	      aa.annotations=annotations;
 	      aa.visible=false;
 	      aa.belowAlignment=false;
+	      aa.setScore(header.getScoreFor(id.getKey()));
               aa.createSequenceMapping(s, s.getStart(),true);
               s.addAlignmentAnnotation(aa);
               aa.adjustForAlignment();
@@ -500,11 +501,13 @@ public class TCoffeeScoreFile extends AlignFile {
 	      aa.annotations=annotations;
               aa.belowAlignment=true;
 	      aa.visible=true;
+	      aa.setScore(header.getScoreAvg());
 	    }
 	    aa.showAllColLabels=true;
 	    aa.validateRangeAndDisplay();
 	    added=true;
 	  }
+	  
 	  return added;
 	}
 
-- 
1.7.10.2