Group Menu level changed

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index eb62972..953b55c 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -136,7 +136,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         VamsasMenu.setVisible(true);
         vamsasLoad.setVisible(true);
       }
-      
+
     }
 
     /**
@@ -699,7 +699,6 @@ public class Desktop extends jalview.jbgui.GDesktop
       int size = af.alignPanels.size();
       if(size<2)
         return;
-      af.closeMenuItem_actionPerformed(null);
 
       for(int i=0; i<size; i++)
       {
@@ -710,17 +709,14 @@ public class Desktop extends jalview.jbgui.GDesktop
 
         ap.av.gatherViewsHere = false;
 
-        PaintRefresher.Register(ap.seqPanel.seqCanvas, ap.av.getSequenceSetId());
-        PaintRefresher.Register(ap.idPanel.idCanvas, ap.av.getSequenceSetId());
-        PaintRefresher.Register(ap, ap.av.getSequenceSetId());
-
-
-        newaf.viewport = ap.av;
         addInternalFrame(newaf, af.getTitle(),
                          AlignFrame.DEFAULT_WIDTH,
                          AlignFrame.DEFAULT_HEIGHT);
       }
 
+      af.alignPanels.clear();
+      af.closeMenuItem_actionPerformed(true);
+
     }
 
     public void gatherViews(AlignFrame source)
@@ -744,11 +740,15 @@ public class Desktop extends jalview.jbgui.GDesktop
               gatherThis = true;
               ap.av.gatherViewsHere = false;
               ap.av.explodedPosition = af.getBounds();
-              source.addAlignmentPanel(ap);
+              source.addAlignmentPanel(ap, false);
             }
           }
+
           if (gatherThis)
-            af.closeMenuItem_actionPerformed(null);
+          {
+            af.alignPanels.clear();
+            af.closeMenuItem_actionPerformed(true);
+          }
         }
       }
 
@@ -796,9 +796,9 @@ public class Desktop extends jalview.jbgui.GDesktop
      */
     public void setVamsasUpdate(boolean b) {
       jalview.bin.Cache.log.debug("Setting gui for Vamsas update "+(b ? "in progress" : "finished"));
-      vamsasLoad.setVisible(!b); 
+      vamsasLoad.setVisible(!b);
       vamsasStop.setVisible(!b);
-      
+
     }
 }