X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=6db90118ccdcfff7bda451709484d17c6a8bc638;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=6b32efafb54ea04a8981fe4b8c068904cf25c8aa;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6b32efa..6db9011 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -230,13 +230,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         urlLink = new UrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for URLLink '" + link + "'", foo);
+        Cache.error("Exception for URLLink '" + link + "'", foo);
         continue;
       }
 
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        Cache.error(urlLink.getInvalidMessage());
         continue;
       }
 
@@ -839,10 +839,14 @@ 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);
-      end = endRange[endRange.length - 1];
+      int[] localRange = mf.getMappedPositions(start, end);
+      if (localRange == null)
+      {
+        // e.g. variant extending to stop codon so not mappable
+        return;
+      }
+      start = localRange[0];
+      end = localRange[localRange.length - 1];
     }
     StringBuilder desc = new StringBuilder();
     desc.append(sf.getType()).append(" ").append(String.valueOf(start));
@@ -1161,12 +1165,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         urlLink = new GroupUrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
+        Cache.error("Exception for GroupURLLink '" + link + "'", foo);
         continue;
       }
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        Cache.error(urlLink.getInvalidMessage());
         continue;
       }
       final String label = urlLink.getLabel();