Close all added

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 9f74e3e..caa3f5e 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -551,6 +551,18 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
     }
 
+    public void closeAll_actionPerformed(ActionEvent e)
+    {
+      JInternalFrame [] frames = desktop.getAllFrames();
+      for(int i=0; i<frames.length; i++)
+      {
+        try{
+        frames[i].setClosed(true);
+      }catch(java.beans.PropertyVetoException ex){}
+      }
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -699,7 +711,6 @@ 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++)
       {
@@ -710,24 +721,21 @@ 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)
     {
       source.viewport.gatherViewsHere = true;
       source.viewport.explodedPosition = source.getBounds();
-      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+      JInternalFrame[] frames = desktop.getAllFrames();
       String viewId = source.viewport.sequenceSetID;
 
       for (int t = 0; t < frames.length; t++)
@@ -742,14 +750,17 @@ 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.closeMenuItem_actionPerformed(null);
+          {
+            af.alignPanels.clear();
+            af.closeMenuItem_actionPerformed(true);
+          }
         }
       }