JAL-3725 restrict mapped virtual feature location to mapped region

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 568f7f1..abe9835 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -832,9 +832,21 @@ 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];
+      int[] localRange = mf.getMappedPositions(start, end);
+      if (localRange == null)
+      {
+        return;
+      }
+      start = localRange[0];
+      end = localRange[localRange.length - 1];
     }
     StringBuilder desc = new StringBuilder();
     desc.append(sf.getType()).append(" ").append(String.valueOf(start));