X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FDesktop.java;h=9b1bef3047dae85856bf6f1ea5f656445b41b590;hb=1a56a24b084eadd78387eabf71dc7114e356bd00;hp=9f74e3e9d2e6e0aa4e4c7a39ffeea3ece74e5ded;hpb=a452823dc1f0f02a366ea432cb161a7e1b1570ca;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 9f74e3e9..9b1bef3 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -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(null);
+
     }
 
     public void gatherViews(AlignFrame source)
@@ -742,14 +738,17 @@ public class Desktop extends jalview.jbgui.GDesktop
             if (viewId.equals(ap.av.getSequenceSetId()))
             {
               gatherThis = true;
-              ap.alignFrame = source;
               ap.av.gatherViewsHere = false;
               ap.av.explodedPosition = af.getBounds();
-              source.addAlignmentPanel(ap);
+              source.addAlignmentPanel(ap, false);
             }
           }
+
           if (gatherThis)
+          {
+            af.alignPanels.clear();
             af.closeMenuItem_actionPerformed(null);
+          }
         }
       }