JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-neede...

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6b32efa..1c3ab8f 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -56,7 +56,7 @@ import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
 import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -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);
+        Console.error("Exception for URLLink '" + link + "'", foo);
         continue;
       }
 
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        Console.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);
+        Console.error("Exception for GroupURLLink '" + link + "'", foo);
         continue;
       }
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        Console.error(urlLink.getInvalidMessage());
         continue;
       }
       final String label = urlLink.getLabel();