X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=28442a9a1c28d67a642381687dd0f2100bf9dede;hb=3ff37e4f45063555989ff1cdf308938daeaaa84c;hp=50ec7e018b1175e7c68cc37278af44a02954140d;hpb=db098429f712e3cda729b937cd3f635482f96b52;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 50ec7e0..28442a9 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -930,12 +930,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     boolean showForAlignment = showAlignmentAnnotations.getState();
     boolean showForSequences = showSequenceAnnotations.getState();
-    for (AlignmentAnnotation aa : alignPanel.getAlignment()
+    if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
+    {
+      for (AlignmentAnnotation aa : alignPanel.getAlignment()
             .getAlignmentAnnotation())
     {
       boolean visible = (aa.sequenceRef == null ? showForAlignment
               : showForSequences);
       aa.visible = visible;
+      }
     }
     alignPanel.validateAnnotationDimensions(true);
     validate();