JAL-3436 save filePath from fileObject, tidy updateRecentlyOpened

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

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 46e5f14..dadf25a 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -246,7 +246,7 @@ 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);
@@ -273,6 +273,7 @@ public class IdPanel extends JPanel
     if (scrollThread != null)
     {
       scrollThread.stopScrolling();
+      scrollThread = null;
     }
   }
 
@@ -317,14 +318,7 @@ 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
@@ -348,13 +342,22 @@ public class IdPanel extends JPanel
         {
           if (scrollThread == null)
           {
-            // finished and nulled itself
+            // IdPanel.stopScrolling called
             t.stop();
           }
         }
       });
       t.start();
     }
+    else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      scrollThread.start();
+    }
   }
 
   /**
@@ -453,7 +456,8 @@ public class IdPanel extends JPanel
     }
 
     PopupMenu pop = new PopupMenu(alignPanel, sq, features,
-            Preferences.getGroupURLLinks());
+            Preferences.getGroupURLLinks() // empty list; not implemented
+    );
     pop.show(this, e.getX(), e.getY());
   }
 
@@ -549,7 +553,7 @@ public class IdPanel extends JPanel
   {
     if (scrollThread != null)
     {
-      scrollThread.stopScrolling();
+      stopScrolling();
     }
     MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
 
@@ -618,7 +622,6 @@ public class IdPanel extends JPanel
     {
       this.up = up;
       setName("IdPanel$ScrollThread$" + String.valueOf(up));
-      start();
     }
 
     /**