X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=96c9b72219d39dcc665f987e80374bc89c488feb;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=307a06fa7e728beff858393adb92c98a6f140521;hpb=99b68710784bd85a781b5d157f34691fc7beacce;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 307a06f..96c9b72 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -1153,9 +1153,10 @@ public class AlignSeq
               ap++;
             }
           }
-          if (sq.getAnnotation() != null)
+          if (sq.getAnnotation() != null && sq.getAnnotation().length > 0)
           {
-            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+            annotations.addAll(inspos == -1 ? annotations.size() : inspos,
+                    Arrays.asList(sq.getAnnotation()));
           }
         }
       }