3253-omnibus save

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

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 5908810..10641eb 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.SeqPanel.MousePos;
@@ -246,7 +245,7 @@ public class IdPanel extends JPanel
       jalview.util.BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
               MessageManager.getString("label.web_browser_not_found_unix"),
               MessageManager.getString("label.web_browser_not_found"),
               JvOptionPane.WARNING_MESSAGE);
@@ -318,14 +317,7 @@ public class IdPanel extends JPanel
   void startScrolling(boolean up)
   {
     scrollThread = new ScrollThread(up);
-    if (!Platform.isJS())
-    {
-      /*
-       * Java - run in a new thread
-       */
-      scrollThread.start();
-    }
-    else
+    if (Platform.isJS())
     {
       /*
        * for JalviewJS using Swing Timer
@@ -356,6 +348,15 @@ public class IdPanel extends JPanel
       });
       t.start();
     }
+    else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      scrollThread.start();
+    }
   }
 
   /**
@@ -434,29 +435,13 @@ public class IdPanel extends JPanel
     }
 
     Sequence sq = (Sequence) av.getAlignment().getSequenceAt(pos.seqIndex);
-
-    /*
-     *  build a new links menu based on the current links
-     *  and any non-positional features
-     */
-    List<SequenceFeature> features = null;
     if (sq != null)
     {
-    List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
-      features = sq.getFeatures().getNonPositionalFeatures();
-    for (SequenceFeature sf : features)
-    {
-      if (sf.links != null)
-      {
-        nlinks.addAll(sf.links);
+      PopupMenu pop = new PopupMenu(alignPanel, sq,
+              Preferences.getGroupURLLinks());
+      pop.show(this, e.getX(), e.getY());
       }
     }
-    }
-
-    PopupMenu pop = new PopupMenu(alignPanel, sq, features,
-            Preferences.getGroupURLLinks());
-    pop.show(this, e.getX(), e.getY());
-  }
 
   /**
    * On right mouse click on a Consensus annotation label, shows a limited popup