X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=45a03faf204715afdcb1c8d435983cf971acf0fb;hb=5dd663636925f44c6f964fa32fed2f584223b295;hp=9f74e3e9d2e6e0aa4e4c7a39ffeea3ece74e5ded;hpb=a452823dc1f0f02a366ea432cb161a7e1b1570ca;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 9f74e3e9..45a03fa 100755
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -47,6 +47,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     public static jalview.ws.Discoverer discoverer;
 
     public static Object [] jalviewClipboard;
+    public static boolean internalCopy = false;
 
     static int fileLoadingCount= 0;
 
@@ -208,9 +209,11 @@ public class Desktop extends jalview.jbgui.GDesktop
 
               }
 
+
                 public void internalFrameClosed(
                     javax.swing.event.InternalFrameEvent evt)
                 {
+                    PaintRefresher.RemoveComponent(frame);
                     openFrameCount--;
                     windowMenu.remove(menuItem);
                     JInternalFrame itf = desktop.getSelectedFrame();
@@ -244,12 +247,15 @@ public class Desktop extends jalview.jbgui.GDesktop
           frame.setSelected(true);
           frame.requestFocus();
         }catch(java.beans.PropertyVetoException ve)
-        {}
+        {   }
     }
 
     public void lostOwnership(Clipboard clipboard, Transferable contents)
     {
-      Desktop.jalviewClipboard = null;
+      if (!internalCopy)
+        Desktop.jalviewClipboard = null;
+
+      internalCopy = false;
     }
 
     public void dragEnter(DropTargetDragEvent evt)
@@ -308,9 +314,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           }
         }
         catch (Exception e)
-        {
-          e.printStackTrace();
-        }
+        {      }
 
         if (files != null)
         {
@@ -339,9 +343,7 @@ public class Desktop extends jalview.jbgui.GDesktop
             }
           }
           catch (Exception ex)
-          {
-            ex.printStackTrace();
-          }
+          {      }
         }
     }
 
@@ -546,11 +548,93 @@ public class Desktop extends jalview.jbgui.GDesktop
             hb.setDisplayed(true);
         }
         catch (Exception ex)
+        {     }
+    }
+
+    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){}
+      }
+    }
+
+    public void raiseRelated_actionPerformed(ActionEvent e)
+    {
+      reorderAssociatedWindows(false, false);
+    }
+
+    public void minimizeAssociated_actionPerformed(ActionEvent e)
+    {
+      reorderAssociatedWindows(true, false);
+    }
+
+    void closeAssociatedWindows()
+    {
+      reorderAssociatedWindows(false, true);
+    }
+
+    void reorderAssociatedWindows(boolean minimize, boolean close)
+    {
+      JInternalFrame[] frames = desktop.getAllFrames();
+      if (frames == null || frames.length<1)
+        return;
+
+      AlignViewport source = null, target = null;
+      if (frames[0] instanceof AlignFrame)
+        source = ( (AlignFrame) frames[0]).getCurrentView();
+      else if (frames[0] instanceof TreePanel)
+        source = ( (TreePanel) frames[0]).getViewPort();
+      else if (frames[0] instanceof PCAPanel)
+        source = ( (PCAPanel) frames[0]).av;
+      else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
+        source = ((PairwiseAlignPanel)frames[0].getContentPane()).av;
+
+
+      if (source != null)
+        for (int i = 0; i < frames.length; i++)
         {
-            ex.printStackTrace();
+          target = null;
+          if(frames[i]==null)
+          {
+            continue;
+          }
+          if (frames[i] instanceof AlignFrame)
+            target = ( (AlignFrame) frames[i]).getCurrentView();
+          else if (frames[i] instanceof TreePanel)
+            target = ( (TreePanel) frames[i]).getViewPort();
+          else if (frames[i] instanceof PCAPanel)
+            target = ( (PCAPanel) frames[i]).av;
+          else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
+            target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av;
+
+          if (source == target)
+          {
+            try
+            {
+              if (close)
+                frames[i].setClosed(true);
+              else
+              {
+                frames[i].setIcon(minimize);
+                if (!minimize)
+                {
+                  frames[i].toFront();
+                }
+              }
+
+            }
+            catch (java.beans.PropertyVetoException ex)
+            {       }
+          }
         }
     }
 
+
+
     /**
      * DOCUMENT ME!
      *
@@ -699,7 +783,6 @@ 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 +793,21 @@ 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 +822,17 @@ 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);
+          }
         }
       }
 
@@ -801,5 +884,6 @@ public class Desktop extends jalview.jbgui.GDesktop
       vamsasStop.setVisible(!b);
 
     }
+
 }