X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=653c071579c754563068095bb0a0a2bf3e985c82;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=36980f8d7616facc6103e358bc8d308b98136966;hpb=f3392c352962c6827674ada5948500725e4eed1e;p=jalview.git

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 36980f8..653c071 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -735,6 +735,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   @Override
   public void configureForView(AlignmentViewPanel avpanel)
   {
+    if (avpanel == null)
+    {
+      return;
+    }
     super.configureForView(avpanel);
     AlignViewportI viewport = avpanel.getAlignViewport();
     AlignmentI alignment = viewport.getAlignment();
@@ -744,11 +748,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     fr = avpanel.cloneFeatureRenderer();
 
     // Add non auto calculated annotation to AlignFile
-    for (AlignmentAnnotation annot : annots)
+    if (annots != null)
     {
-      if (annot != null && !annot.autoCalculated)
+      for (AlignmentAnnotation annot : annots)
       {
-        annotations.add(annot);
+        if (annot != null && !annot.autoCalculated)
+        {
+          annotations.add(annot);
+        }
       }
     }
     globalColourScheme = ColourSchemeProperty.getColourName(viewport