X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=75033f34b2f1203a840a6e23b68ec131023b1e05;hb=9b8a7cae41e5d0e2dfcd806319ca2d301dd133c5;hp=5d8248b3e210b1e7c585f792d73107c6e651119f;hpb=379357f76f6c8f973c145ed94a69225f358f4d0c;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 5d8248b..75033f3 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -41,6 +41,7 @@ import jalview.structure.StructureSelectionManager;
 import jalview.urls.IdOrgSettings;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.util.UrlConstants;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.ParamManager;
@@ -67,8 +68,6 @@ import java.awt.dnd.DropTargetEvent;
 import java.awt.dnd.DropTargetListener;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
@@ -94,6 +93,7 @@ import java.util.concurrent.Semaphore;
 import javax.swing.AbstractAction;
 import javax.swing.Box;
 import javax.swing.BoxLayout;
+import javax.swing.DefaultDesktopManager;
 import javax.swing.DesktopManager;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
@@ -357,7 +357,12 @@ public class Desktop extends jalview.jbgui.GDesktop
     // This line prevents Windows Look&Feel resizing all new windows to maximum
     // if previous window was maximised
     desktop.setDesktopManager(
-            new MyDesktopManager(desktop.getDesktopManager()));
+            new MyDesktopManager(
+                    (Platform.isWindows() ? new DefaultDesktopManager()
+                            : Platform.isAMac()
+                                    ? new AquaInternalFrameManager(
+                                            desktop.getDesktopManager())
+                                    : desktop.getDesktopManager())));
 
     Rectangle dims = getLastKnownDimensions("");
     if (dims != null)
@@ -427,24 +432,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     });
     desktop.addMouseListener(ma);
 
-    this.addFocusListener(new FocusListener()
-    {
-
-      @Override
-      public void focusLost(FocusEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
-
-      @Override
-      public void focusGained(FocusEvent e)
-      {
-        Cache.log.debug("Relaying windows after focus gain");
-        // make sure that we sort windows properly after we gain focus
-        instance.relayerWindows();
-      }
-    });
     this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
     // Spawn a thread that shows the splashscreen
     SwingUtilities.invokeLater(new Runnable()
@@ -862,6 +849,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     frame.setResizable(resizable);
     frame.setMaximizable(resizable);
     frame.setIconifiable(resizable);
+    frame.setOpaque(false);
 
     if (frame.getX() < 1 && frame.getY() < 1)
     {
@@ -882,6 +870,10 @@ public class Desktop extends jalview.jbgui.GDesktop
         JInternalFrame itf = desktop.getSelectedFrame();
         if (itf != null)
         {
+          if (itf instanceof AlignFrame)
+          {
+            Jalview.setCurrentAlignFrame((AlignFrame) itf);
+          }
           itf.requestFocus();
         }
       }
@@ -908,16 +900,6 @@ public class Desktop extends jalview.jbgui.GDesktop
           menuItem.removeActionListener(menuItem.getActionListeners()[0]);
         }
         windowMenu.remove(menuItem);
-        JInternalFrame itf = desktop.getSelectedFrame();
-        if (itf != null)
-        {
-          itf.requestFocus();
-          if (itf instanceof AlignFrame)
-          {
-            Jalview.setCurrentAlignFrame((AlignFrame) itf);
-          }
-        }
-        System.gc();
       };
     });
 
@@ -1405,7 +1387,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     {
       ssm.resetAll();
     }
-    System.gc();
   }
 
   @Override
@@ -2355,7 +2336,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           {
             String link = li.next();
             if (link.contains(SEQUENCE_ID)
-                    && !link.equals(UrlConstants.DEFAULT_STRING))
+                    && !UrlConstants.isDefaultString(link))
             {
               check = true;
               int barPos = link.indexOf("|");
@@ -2444,6 +2425,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         Thread worker = new Thread(this);
         worker.start();
       }
+      repaint();
     }
 
     public boolean isShowMemoryUsage()
@@ -2507,14 +2489,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
   }
 
-  /**
-   * fixes stacking order after a modal dialog to ensure windows that should be
-   * on top actually are
-   */
-  public void relayerWindows()
-  {
-
-  }
 
   /**
    * Accessor method to quickly get all the AlignmentFrames loaded.
@@ -3422,4 +3396,41 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
   }
+
+  /**
+   * Answers a (possibly empty) list of any structure viewer frames (currently
+   * for either Jmol or Chimera) which are currently open. This may optionally
+   * be restricted to viewers of a specified class, or viewers linked to a
+   * specified alignment panel.
+   * 
+   * @param apanel
+   *          if not null, only return viewers linked to this panel
+   * @param structureViewerClass
+   *          if not null, only return viewers of this class
+   * @return
+   */
+  public List<StructureViewerBase> getStructureViewers(
+          AlignmentPanel apanel,
+          Class<? extends StructureViewerBase> structureViewerClass)
+  {
+    List<StructureViewerBase> result = new ArrayList<>();
+    JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+    for (JInternalFrame frame : frames)
+    {
+      if (frame instanceof StructureViewerBase)
+      {
+        if (structureViewerClass == null
+                || structureViewerClass.isInstance(frame))
+        {
+          if (apanel == null
+                  || ((StructureViewerBase) frame).isLinkedWith(apanel))
+          {
+            result.add((StructureViewerBase) frame);
+          }
+        }
+      }
+    }
+    return result;
+  }
 }