X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=45e39cc9d4837caac55c0cb3f47114edcdcacfa8;hb=8c0955545a1a10062467e2d6dc7feb1e855655c0;hp=6f83cec8935b78c4e6c9114a3433ce5f7a995fb7;hpb=9757315e2f66b72e669b6e7408ae8faedd1ae9b3;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 6f83cec..45e39cc 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -24,7 +24,6 @@ import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
-import jalview.bin.Cache;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -320,13 +319,14 @@ public class APopupMenu extends java.awt.PopupMenu implements
         urlLink = new UrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for URLLink '" + link + "'", foo);
+        System.err.println("Exception for URLLink '" + link + "': "
+                + foo.getMessage());
         continue;
       }
 
       if (!urlLink.isValid())
       {
-        Cache.log.error(urlLink.getInvalidMessage());
+        System.err.println(urlLink.getInvalidMessage());
         continue;
       }
 
@@ -335,17 +335,25 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     addshowLinks(linkMenu, linkset.values());
 
+    // disable link menu if there are no valid entries
     if (linkMenu.getItemCount() > 0)
     {
-      if (seq != null)
-      {
-        seqMenu.add(linkMenu);
-      }
-      else
-      {
-        add(linkMenu);
-      }
+      linkMenu.setEnabled(true);
     }
+    else
+    {
+      linkMenu.setEnabled(false);
+    }
+
+    if (seq != null)
+    {
+      seqMenu.add(linkMenu);
+    }
+    else
+    {
+      add(linkMenu);
+    }
+
   }
 
   private void addshowLinks(Menu linkMenu, Collection<List<String>> linkset)
@@ -1150,11 +1158,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     if (conservationMenuItem.getState())
     {
-
-      sg.cs.setConservation(Conservation.calculateConservation("Group", 3,
-              sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
-                      .getAlignment().getWidth(), false, ap.av
-                      .getConsPercGaps(), false));
+      sg.cs.setConservation(Conservation.calculateConservation("Group", sg
+              .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
+              .getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
+              false));
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }