X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=fc3c3422b64824409ac184c63655c6505362fef6;hb=b59e6ecc36fb98f4285213a685d0546e98ebd556;hp=568f7f1fe28e71fa66236d04cd9e51b9a72691f4;hpb=5a631296dd1dcc1df7b50487a647c27333696c74;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 568f7f1..fc3c342 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -832,8 +832,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
        * show local rather than linked feature coordinates
        */
       int[] beginRange = mf.getMappedPositions(start, start);
-      start = beginRange[0];
       int[] endRange = mf.getMappedPositions(end, end);
+      if (beginRange == null || endRange == null)
+      {
+        // e.g. variant extending to stop codon so not mappable
+        return;
+      }
+      start = beginRange[0];
       end = endRange[endRange.length - 1];
     }
     StringBuilder desc = new StringBuilder();