X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;fp=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=b00f27ddcff599b5339baf0248ec895020b3e64d;hb=5935396709349dbe2926fa1ad0dd24995712b77b;hp=01926dcc84f0b58a48fc07cb45942543f4a02648;hpb=fd9428e5dcaee143c17ce93054db6698bbd9fb99;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 01926dc..b00f27d 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -980,18 +980,20 @@ public class AlignmentAnnotation
     int position;
     Annotation[] temp = new Annotation[aSize];
     Integer index;
-
-    for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
+    if (sequenceMapping != null)
     {
-      index = new Integer(a);
-      if (sequenceMapping != null && sequenceMapping.containsKey(index))
+      for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
       {
-        position = sequenceRef.findIndex(a) - 1;
+        index = new Integer(a);
+        Annotation annot = sequenceMapping.get(index);
+        if (annot != null)
+        {
+          position = sequenceRef.findIndex(a) - 1;
 
-        temp[position] = sequenceMapping.get(index);
+          temp[position] = annot;
+        }
       }
     }
-
     annotations = temp;
   }