X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=ea13922c13e1602da45d59a057fa163da415b9f8;hb=08c9327201cdf77a77bf884f3c5fa45cdaf8bc7f;hp=2f5f2704b8842a15d824c2b00c1eb4a60a74172c;hpb=27e20b88d0c73ced06e9c20a6e0fa14e27fed179;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 2f5f270..ea13922 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -516,7 +516,7 @@ public class AlignmentAnnotation
     float min = graphMin;
     float max = graphMax;
     boolean drawValues = true;
-    _linecolour=null;
+    _linecolour = null;
     if (min == max)
     {
       min = 999999999;
@@ -621,7 +621,14 @@ public class AlignmentAnnotation
       this.annotations = new Annotation[ann.length];
       for (int i = 0; i < ann.length; i++)
       {
-        annotations[i] = new Annotation(ann[i]);
+        if (ann[i] != null)
+        {
+          annotations[i] = new Annotation(ann[i]);
+          if (_linecolour != null)
+          {
+            _linecolour = annotations[i].colour;
+          }
+        }
       }
       ;
       if (annotation.sequenceRef != null)