X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=2ef1c766fd3603ec72fdfbb6845b9d56c1a17fdd;hb=fd235cc7542d6e308e054a8a76580a6c511ae631;hp=307a06fa7e728beff858393adb92c98a6f140521;hpb=99b68710784bd85a781b5d157f34691fc7beacce;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 307a06f..2ef1c76 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -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()));
           }
         }
       }