Merge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index c605378..9a696e9 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -68,8 +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;
@@ -346,10 +344,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
             false);
     desktop = new MyDesktopPane(selmemusage);
-    if (Platform.isAMac())
-    {
-      desktop.setDoubleBuffered(false);
-    }
     showMemusage.setSelected(selmemusage);
     desktop.setBackground(Color.white);
     getContentPane().setLayout(new BorderLayout());
@@ -363,7 +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(new DefaultDesktopManager()));
+            new MyDesktopManager(
+                    (Platform.isWindows() ? new DefaultDesktopManager()
+                            : Platform.isAMac()
+                                    ? new AquaInternalFrameManager(
+                                            desktop.getDesktopManager())
+                                    : desktop.getDesktopManager())));
 
     Rectangle dims = getLastKnownDimensions("");
     if (dims != null)
@@ -433,24 +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()
@@ -868,13 +849,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     frame.setResizable(resizable);
     frame.setMaximizable(resizable);
     frame.setIconifiable(resizable);
-    if (Platform.isAMac())
-    {
-      frame.setIconifiable(false);
-      frame.setFrameIcon(null);
-      // frame.setDesktopIcon(null);
-      frame.setDoubleBuffered(false);
-    }
+    frame.setOpaque(false);
+
     if (frame.getX() < 1 && frame.getY() < 1)
     {
       frame.setLocation(xOffset * openFrameCount,
@@ -894,6 +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();
         }
       }
@@ -920,15 +900,7 @@ 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();
       };
     });
@@ -2367,7 +2339,7 @@ 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("|");
@@ -2456,6 +2428,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         Thread worker = new Thread(this);
         worker.start();
       }
+      repaint();
     }
 
     public boolean isShowMemoryUsage()
@@ -2519,14 +2492,6 @@ 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.
@@ -3434,4 +3399,41 @@ 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;
+  }
 }