X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=2f77959611f9b741dba1bea97a585de7e8494c53;hb=3af9017e1f6c6d045c6c0d41245fcd7bfdae32a6;hp=2a7fb9f9c06e84dd0f695f04c3f0fcfe7f6ee86f;hpb=65740880573a48adc758bec3939ece9d9ae104dd;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2a7fb9f..2f77959 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -838,8 +838,13 @@ 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();