From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 24 May 2012 17:52:03 +0000 (+0100)
Subject: JAL-1065 per sequence and per-alignment scores added to annotation
X-Git-Tag: Jalview_2_9~503
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5161aef05fe56b2fc188fe069396d0f15e5968a8;hp=642d5e474b3ab4c98837cfe8eb2d354d2733133e;p=jalview.git

JAL-1065 per sequence and per-alignment scores added to annotation
---

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;
 	}