X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=ace752973215601be7c9fd6c45a991af72a8394f;hb=72fb6df14f1ff426bbafa18dcc9a90450da93018;hp=88835c61af1ae22cc0ed74589c9fbae743973880;hpb=208f2c3de82e3327c4f930ab7d04f5b812ccd277;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 88835c6..ace7529 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -22,6 +22,9 @@ package jalview.gui;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.gui.ImageExporter.ImageWriterI;
@@ -36,6 +39,7 @@ import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
+import jalview.jbgui.GDesktop;
 import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
 import jalview.project.Jalview2XML;
@@ -47,6 +51,7 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.UrlConstants;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.jws1.Discoverer;
 import jalview.ws.params.ParamManager;
 import jalview.ws.utils.UrlDownloadClient;
 
@@ -133,10 +138,11 @@ import org.stackoverflowusers.file.WindowsShortcut;
  * @version $Revision: 1.155 $
  */
 @SuppressWarnings("serial")
-public class Desktop extends jalview.jbgui.GDesktop
+public class Desktop extends GDesktop
         implements DropTargetListener, ClipboardOwner, IProgressIndicator,
-        jalview.api.StructureSelectionManagerProvider
+        StructureSelectionManagerProvider, ApplicationSingletonI
 {
+
   private final static int DEFAULT_MIN_WIDTH = 300;
 
   private final static int DEFAULT_MIN_HEIGHT = 250;
@@ -191,47 +197,16 @@ public class Desktop extends jalview.jbgui.GDesktop
             listener);
   }
 
-  /**
-   * Singleton Desktop instance only in Java;
-   */
-  private static Desktop instance;
-
-  public static Desktop getInstance()
-  {
-    Desktop d;
-    @SuppressWarnings("unused")
-    ThreadGroup g = Thread.currentThread().getThreadGroup();
-    /**
-     * @j2sNative d = g._jalviewDesktopInstance;
-     */
-    {
-      d = instance;
-    }
-    return d;
-  }
-
-  private static void setInstance(Desktop d)
-  {
-    @SuppressWarnings("unused")
-    ThreadGroup g = Thread.currentThread().getThreadGroup();
-    /**
-     * @j2sNative g._jalviewDesktopInstance = d;
-     */
-    {
-      instance = d;
-    }
-  }
-
-  private MyDesktopPane desktopPane;
-
   public static MyDesktopPane getDesktopPane()
   {
-    return getInstance().desktopPane;
+    Desktop desktop = Desktop.getInstance();
+    return desktop == null ? null : desktop.desktopPane;
   }
 
-  private void setDesktopPane(MyDesktopPane pane)
+  public static StructureSelectionManager getStructureSelectionManager()
   {
-    getInstance().desktopPane = pane;
+    return StructureSelectionManager
+            .getStructureSelectionManager(getInstance());
   }
 
   static int openFrameCount = 0;
@@ -240,7 +215,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   static final int yOffset = 30;
 
-  public jalview.ws.jws1.Discoverer discoverer;
+  public Discoverer discoverer;
 
   public Object[] jalviewClipboard;
 
@@ -248,7 +223,14 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   private static int fileLoadingCount = 0;
 
-  public JInternalFrame conservationSlider, PIDSlider;
+  public JInternalFrame conservationSlider;
+
+  public JInternalFrame PIDSlider;
+
+  /**
+   * just an instance (for testng, probably); no actual frames
+   */
+  private boolean instanceOnly;
 
   class MyDesktopManager implements DesktopManager
   {
@@ -269,7 +251,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       } catch (NullPointerException npe)
       {
         Point p = getMousePosition();
-        getInstance().showPasteMenu(p.x, p.y);
+        showPasteMenu(p.x, p.y);
       }
     }
 
@@ -317,14 +299,14 @@ public class Desktop extends jalview.jbgui.GDesktop
     public void endDraggingFrame(JComponent f)
     {
       delegate.endDraggingFrame(f);
-      getDesktopPane().repaint();
+      desktopPane.repaint();
     }
 
     @Override
     public void endResizingFrame(JComponent f)
     {
       delegate.endResizingFrame(f);
-      getDesktopPane().repaint();
+      desktopPane.repaint();
     }
 
     @Override
@@ -373,23 +355,54 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   }
 
+  public MyDesktopPane desktopPane;
+
   /**
-   * Creates a new Desktop object.
+   * Answers an 'application scope' singleton instance of this class. Separate
+   * SwingJS 'applets' running in the same browser page will each have a
+   * distinct instance of Desktop.
+   * 
+   * @return
    */
-  public Desktop()
+  public static Desktop getInstance()
+  {
+    return Jalview.isHeadlessMode() ? null
+            : (Desktop) ApplicationSingletonProvider
+                    .getInstance(Desktop.class);
+  }
+
+  /**
+   * For testing.
+   * 
+   * @param forInstance
+   */
+  public Desktop(boolean forInstance)
   {
-    super();
+
+    Cache.initLogger();
+    instanceOnly = true;
+  }
+  
+  /**
+   * Private constructor enforces singleton pattern. It is called by reflection
+   * from ApplicationSingletonProvider.getInstance().
+   */
+  @SuppressWarnings("unused")
+  private Desktop()
+  {
+    Cache.initLogger();
+    try
+    {
     /**
      * A note to implementors. It is ESSENTIAL that any activities that might
      * block are spawned off as threads rather than waited for during this
      * constructor.
      */
-    setInstance(this);
     if (!Platform.isJS())
     {
       doVamsasClientCheck();
     }
-
+    
     doConfigureStructurePrefs();
     setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
@@ -397,34 +410,34 @@ public class Desktop extends jalview.jbgui.GDesktop
             false);
     boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
             false);
-    setDesktopPane(new MyDesktopPane(selmemusage));
-
+    desktopPane = new MyDesktopPane(selmemusage);
+    
     showMemusage.setSelected(selmemusage);
-    getDesktopPane().setBackground(Color.white);
+    desktopPane.setBackground(Color.white);
     getContentPane().setLayout(new BorderLayout());
     // alternate config - have scrollbars - see notes in JAL-153
     // JScrollPane sp = new JScrollPane();
     // sp.getViewport().setView(desktop);
     // getContentPane().add(sp, BorderLayout.CENTER);
-
+    
     // BH 2018 - just an experiment to try unclipped JInternalFrames.
     if (Platform.isJS())
     {
       getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
     }
-
-    getContentPane().add(getDesktopPane(), BorderLayout.CENTER);
-    getDesktopPane().setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
-
+    
+    getContentPane().add(desktopPane, BorderLayout.CENTER);
+    desktopPane.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+    
     // This line prevents Windows Look&Feel resizing all new windows to maximum
     // if previous window was maximised
-    getDesktopPane().setDesktopManager(new MyDesktopManager(
+    desktopPane.setDesktopManager(new MyDesktopManager(
             (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
                     : Platform.isAMacAndNotJS()
                             ? new AquaInternalFrameManager(
-                                    getDesktopPane().getDesktopManager())
-                            : getDesktopPane().getDesktopManager())));
-
+                                    desktopPane.getDesktopManager())
+                            : desktopPane.getDesktopManager())));
+    
     Rectangle dims = getLastKnownDimensions("");
     if (dims != null)
     {
@@ -437,7 +450,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       int yPos = Math.max(5, (screenSize.height - 650) / 2);
       setBounds(xPos, yPos, 900, 650);
     }
-
+    
     if (!Platform.isJS())
     /**
      * Java only
@@ -445,7 +458,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      * @j2sIgnore
      */
     {
-
+    
       jconsole = new Console(this, showjconsole);
       // add essential build information
       jconsole.setHeader("Jalview Version: "
@@ -458,19 +471,19 @@ public class Desktop extends jalview.jbgui.GDesktop
               + System.getProperty("os.arch") + " "
               + System.getProperty("os.name") + " "
               + System.getProperty("os.version"));
-
+    
       showConsole(showjconsole);
-
+    
       showNews.setVisible(false);
-
+    
       experimentalFeatures.setSelected(showExperimental());
-
+    
       getIdentifiersOrgData();
-
+    
       checkURLLinks();
-
+    
       // Spawn a thread that shows the splashscreen
-
+    
       SwingUtilities.invokeLater(new Runnable()
       {
         @Override
@@ -479,7 +492,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           new SplashScreen();
         }
       });
-
+    
       // Thread off a new instance of the file chooser - this reduces the time
       // it
       // takes to open it later on.
@@ -499,7 +512,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       changeSupport.addJalviewPropertyChangeListener("services",
               new PropertyChangeListener()
               {
-
+    
                 @Override
                 public void propertyChange(PropertyChangeEvent evt)
                 {
@@ -507,13 +520,13 @@ public class Desktop extends jalview.jbgui.GDesktop
                           + evt.getNewValue());
                   JalviewServicesChanged(evt);
                 }
-
+    
               });
-
+    
     }
-
-    this.setDropTarget(new java.awt.dnd.DropTarget(getDesktopPane(), this));
-
+    
+    this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this));
+    
     this.addWindowListener(new WindowAdapter()
     {
       @Override
@@ -522,7 +535,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         quit();
       }
     });
-
+    
     MouseAdapter ma;
     this.addMouseListener(ma = new MouseAdapter()
     {
@@ -534,7 +547,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           showPasteMenu(evt.getX(), evt.getY());
         }
       }
-
+    
       @Override
       public void mouseReleased(MouseEvent evt)
       {
@@ -544,8 +557,11 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
       }
     });
-    getDesktopPane().addMouseListener(ma);
-
+    desktopPane.addMouseListener(ma);
+    } catch (Throwable t)
+    {
+      t.printStackTrace();
+    }
   }
 
   /**
@@ -621,7 +637,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
       }
     }).start();
-    ;
+    
   }
 
   @Override
@@ -642,10 +658,10 @@ public class Desktop extends jalview.jbgui.GDesktop
         public void run()
         {
           long now = System.currentTimeMillis();
-          Desktop.getInstance().setProgressBar(
+          setProgressBar(
                   MessageManager.getString("status.refreshing_news"), now);
           jvnews.refreshNews();
-          Desktop.getInstance().setProgressBar(null, now);
+          setProgressBar(null, now);
           jvnews.showNews();
         }
       }).start();
@@ -783,7 +799,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         FileFormatI format = new IdentifyFile().identify(file,
                 DataSourceType.PASTE);
 
-        new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
+        new FileLoader().loadFile(file, DataSourceType.PASTE, format);
 
       }
     } catch (Exception ex)
@@ -878,13 +894,14 @@ public class Desktop extends jalview.jbgui.GDesktop
           int w, int h, boolean resizable, boolean ignoreMinSize)
   {
 
+
     // TODO: allow callers to determine X and Y position of frame (eg. via
     // bounds object).
     // TODO: consider fixing method to update entries in the window submenu with
     // the current window title
 
     frame.setTitle(title);
-    if (frame.getWidth() < 1 || frame.getHeight() < 1)
+    if (w > 0 && (frame.getWidth() < 1 || frame.getHeight() < 1))
     {
       frame.setSize(w, h);
     }
@@ -892,7 +909,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
-    if (getInstance() == null || Jalview.isHeadlessMode())
+    if (Jalview.isHeadlessMode() || Desktop.getInstance().instanceOnly)
     {
       return;
     }
@@ -970,8 +987,8 @@ public class Desktop extends jalview.jbgui.GDesktop
         {
           menuItem.removeActionListener(menuItem.getActionListeners()[0]);
         }
-        getInstance().windowMenu.remove(menuItem);
-      };
+        Desktop.getInstance().windowMenu.remove(menuItem);
+      }
     });
 
     menuItem.addActionListener(new ActionListener()
@@ -994,7 +1011,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     getDesktopPane().add(frame);
 
-    getInstance().windowMenu.add(menuItem);
+    Desktop.getInstance().windowMenu.add(menuItem);
 
     frame.toFront();
     try
@@ -1130,7 +1147,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           {
             Platform.cacheFileData((File) file);
           }
-          new FileLoader().LoadFile(null, file, protocol, format);
+          new FileLoader().loadFile(null, file, protocol, format);
 
         }
       } catch (Exception ex)
@@ -1187,7 +1204,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           }
         }
 
-        new FileLoader().LoadFile(viewport, selectedFile,
+        new FileLoader().loadFile(viewport, selectedFile,
                 DataSourceType.FILE, format);
       }
     });
@@ -1261,12 +1278,12 @@ public class Desktop extends jalview.jbgui.GDesktop
         {
           if (viewport != null)
           {
-            new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+            new FileLoader().loadFile(viewport, url, DataSourceType.URL,
                     FileFormat.Jalview);
           }
           else
           {
-            new FileLoader().LoadFile(url, DataSourceType.URL,
+            new FileLoader().loadFile(url, DataSourceType.URL,
                     FileFormat.Jalview);
           }
         }
@@ -1296,12 +1313,12 @@ public class Desktop extends jalview.jbgui.GDesktop
 
           if (viewport != null)
           {
-            new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+            new FileLoader().loadFile(viewport, url, DataSourceType.URL,
                     format);
           }
           else
           {
-            new FileLoader().LoadFile(url, DataSourceType.URL, format);
+            new FileLoader().loadFile(url, DataSourceType.URL, format);
           }
         }
       }
@@ -1504,8 +1521,12 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void closeAll_actionPerformed(ActionEvent e)
   {
+    if (desktopPane == null)
+    {
+      return;
+    }
     // TODO show a progress bar while closing?
-    JInternalFrame[] frames = getDesktopPane().getAllFrames();
+    JInternalFrame[] frames = desktopPane.getAllFrames();
     for (int i = 0; i < frames.length; i++)
     {
       try
@@ -1526,12 +1547,7 @@ public class Desktop extends jalview.jbgui.GDesktop
      * reset state of singleton objects as appropriate (clear down session state
      * when all windows are closed)
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(this);
-    if (ssm != null)
-    {
-      ssm.resetAll();
-    }
+    getStructureSelectionManager().resetAll();
   }
 
   @Override
@@ -1890,7 +1906,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     {
       progressPanel = new JPanel(new GridLayout(1, 1));
       totalProgressCount = 0;
-      getInstance().getContentPane().add(progressPanel, BorderLayout.SOUTH);
+      getContentPane().add(progressPanel, BorderLayout.SOUTH);
     }
     JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
     JProgressBar progressBar = new JProgressBar();
@@ -1903,7 +1919,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     ((GridLayout) progressPanel.getLayout()).setRows(
             ((GridLayout) progressPanel.getLayout()).getRows() + 1);
     ++totalProgressCount;
-    getInstance().validate();
+    validate();
     return thisprogress;
   }
 
@@ -2085,7 +2101,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     source.viewport.setGatherViewsHere(true);
     source.viewport.setExplodedGeometry(source.getBounds());
-    JInternalFrame[] frames = getDesktopPane().getAllFrames();
+    JInternalFrame[] frames = getAllFrames();
     String viewId = source.viewport.getSequenceSetId();
 
     for (int t = 0; t < frames.length; t++)
@@ -2374,7 +2390,7 @@ public class Desktop extends jalview.jbgui.GDesktop
                 });
                 rthr.start();
               }
-            };
+            }
           });
           VamsasStMenu.add(sessit);
         }
@@ -2480,7 +2496,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public JInternalFrame[] getAllFrames()
   {
-    return getDesktopPane().getAllFrames();
+    return desktopPane.getAllFrames();
   }
 
   /**
@@ -2566,7 +2582,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           });
           msgPanel.add(jcb);
 
-          JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msgPanel,
+          JvOptionPane.showMessageDialog(desktopPane, msgPanel,
                   MessageManager
                           .getString("label.SEQUENCE_ID_no_longer_used"),
                   JvOptionPane.WARNING_MESSAGE);
@@ -2766,7 +2782,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     } catch (Exception ex)
     {
       jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
-      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+      JvOptionPane.showInternalMessageDialog(desktopPane,
 
               MessageManager.getString("label.couldnt_create_groovy_shell"),
               MessageManager.getString("label.groovy_support_failed"),
@@ -3024,7 +3040,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       // todo: changesupport handlers need to be transferred
       if (discoverer == null)
       {
-        discoverer = new jalview.ws.jws1.Discoverer();
+        discoverer = Discoverer.getInstance();
         // register PCS handler for getDesktop().
         discoverer.addPropertyChangeListener(changeSupport);
       }
@@ -3035,7 +3051,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
-      t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+      t2 = jalview.ws.jws2.Jws2Discoverer.getInstance()
               .startDiscoverer(changeSupport);
     }
     Thread t3 = null;
@@ -3068,7 +3084,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
     {
-      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance()
               .getErrorMessages();
       if (ermsg != null)
       {
@@ -3193,7 +3209,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public static ParamManager getUserParameterStore()
   {
-    Desktop d = getInstance();
+    Desktop d = Desktop.getInstance();
     if (d.wsparamManager == null)
     {
       d.wsparamManager = new WsParamSetManager();
@@ -3274,9 +3290,8 @@ public class Desktop extends jalview.jbgui.GDesktop
           } catch (InterruptedException x)
           {
           }
-          ;
         }
-        if (getInstance() == null)
+        if (instanceOnly)
         {
           return;
         }
@@ -3440,7 +3455,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     String topViewId = myTopFrame.viewport.getSequenceSetId();
     String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
 
-    JInternalFrame[] frames = getDesktopPane().getAllFrames();
+    JInternalFrame[] frames = desktopPane.getAllFrames();
     for (JInternalFrame frame : frames)
     {
       if (frame instanceof SplitFrame && frame != source)
@@ -3485,7 +3500,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public static groovy.ui.Console getGroovyConsole()
   {
-    return getInstance().groovyConsole;
+    Desktop desktop = Desktop.getInstance();
+    return desktop == null ? null : desktop.groovyConsole;
   }
 
   /**
@@ -3563,7 +3579,6 @@ public class Desktop extends jalview.jbgui.GDesktop
             System.err.println(
                     "Please ignore plist error - occurs due to problem with java 8 on OSX");
           }
-          ;
         }
       } catch (Throwable ex)
       {
@@ -3738,7 +3753,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           Class<? extends StructureViewerBase> structureViewerClass)
   {
     List<StructureViewerBase> result = new ArrayList<>();
-    JInternalFrame[] frames = Desktop.getInstance().getAllFrames();
+    JInternalFrame[] frames = getAllFrames();
 
     for (JInternalFrame frame : frames)
     {