X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=91ee3c100326bd61b9aa5f307031fe89677c318d;hb=80fa1ace4f6ce0cea9680fd8a6d683270c8b2944;hp=0f6d66be55d3bfec5c663e4b96d3b3d09660decc;hpb=63fe4d2b85bb9c1312a1313e27c899d1b30de4c0;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 0f6d66b..91ee3c1 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1420,11 +1420,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
   protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
           boolean visible)
   {
-    for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+    if (anns != null)
     {
-      if (ann.sequenceRef == sequenceI)
+      for (AlignmentAnnotation ann : anns)
       {
-        ann.visible = visible;
+        if (ann.sequenceRef == sequenceI)
+        {
+          ann.visible = visible;
+        }
       }
     }
   }