X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=cf91b9cd9f7a240d2ebc0a7b9840b5f3364fa1ad;hb=1a751b8ddf0c8e7730dffced17cad4a1105da907;hp=c2eb598c3039b96fe4abb911e2ab4f44cea67fff;hpb=fba2298ae0ff5f3f737f7e14439b3211b0b1baf8;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index c2eb598..cf91b9c 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -24,6 +24,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
+import jalview.io.BackupFiles;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatException;
@@ -36,6 +37,7 @@ import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
+import jalview.project.Jalview2XML;
 import jalview.structure.StructureSelectionManager;
 import jalview.urls.IdOrgSettings;
 import jalview.util.ImageMaker;
@@ -60,14 +62,6 @@ import java.awt.datatransfer.Clipboard;
 import java.awt.datatransfer.ClipboardOwner;
 import java.awt.datatransfer.DataFlavor;
 import java.awt.datatransfer.Transferable;
-import java.awt.desktop.AboutEvent;
-import java.awt.desktop.AboutHandler;
-import java.awt.desktop.PreferencesEvent;
-import java.awt.desktop.PreferencesHandler;
-import java.awt.desktop.QuitEvent;
-import java.awt.desktop.QuitHandler;
-import java.awt.desktop.QuitResponse;
-import java.awt.desktop.QuitStrategy;
 import java.awt.dnd.DnDConstants;
 import java.awt.dnd.DropTargetDragEvent;
 import java.awt.dnd.DropTargetDropEvent;
@@ -116,7 +110,6 @@ import javax.swing.JDesktopPane;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JProgressBar;
@@ -152,6 +145,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
 
+  protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
+
   public static HashMap<String, FileWriter> savingFiles = new HashMap<>();
 
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
@@ -361,53 +356,24 @@ public class Desktop extends jalview.jbgui.GDesktop
       // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
     }
     else
+    {
+     this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+    }
     */
-    // {
-    // this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
-    java.awt.Desktop hdesktop = java.awt.Desktop.getDesktop();
 
-    hdesktop.setAboutHandler(new AboutHandler()
+    try
     {
-      @Override
-      public void handleAbout(AboutEvent e)
-      {
-        aboutMenuItem_actionPerformed(null);
-      }
-    });
-    hdesktop.setPreferencesHandler(new PreferencesHandler()
+      APQHandlers.setAPQHandlers(this);
+    } catch (Exception e)
     {
-      @Override
-      public void handlePreferences(PreferencesEvent e)
-      {
-        preferences_actionPerformed(null);
-      }
-    });
-    hdesktop.setQuitHandler(new QuitHandler()
+      System.out.println("Cannot set APQHandlers");
+      // e.printStackTrace();
+    } catch (Throwable t)
     {
-      @Override
-      public void handleQuitRequestWith(QuitEvent e, QuitResponse r)
-      {
-        int n = JOptionPane.showConfirmDialog(null,
-                MessageManager.getString("label.quit_jalview"),
-                MessageManager.getString("action.quit"),
-                JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE,
-                null);
-        if (n == JOptionPane.OK_OPTION)
-        {
-          System.out.println("Shortcut Quit confirmed by user");
-          quit();
-          r.performQuit(); // probably won't reach this line, but just in case
-        }
-        else
-        {
-          r.cancelQuit();
-          System.out.println("Shortcut Quit cancelled by user");
-        }
-      }
-    });
-    hdesktop.setQuitStrategy(QuitStrategy.CLOSE_ALL_WINDOWS);
+      System.out.println("Cannot set APQHandlers");
+      // t.printStackTrace();
+    }
 
-    // }
 
     addWindowListener(new WindowAdapter()
     {
@@ -458,18 +424,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
     jconsole = new Console(this, showjconsole);
     // add essential build information
-    jconsole.setHeader(
-            "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
-                    + "\n" + "Jalview Installation: "
-                    + jalview.bin.Cache.getDefault("INSTALLATION",
-                            "unknown")
-                    + "\n" + "Build Date: "
-                    + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
-                    + "\n" + "Java version: "
-                    + System.getProperty("java.version") + "\n"
-                    + System.getProperty("os.arch") + " "
-                    + System.getProperty("os.name") + " "
-                    + System.getProperty("os.version"));
+    jconsole.setHeader(jalview.bin.Cache.getVersionDetailsForConsole());
 
     showConsole(showjconsole);
 
@@ -1046,7 +1001,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
             InputEvent.CTRL_DOWN_MASK);
     KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
 
     InputMap inputMap = frame
             .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
@@ -1160,7 +1115,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
     JalviewFileChooser chooser = JalviewFileChooser
-            .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+            .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled());
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
@@ -1325,8 +1280,6 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void quit()
   {
-    System.out.println("********** Desktop.quit()");
-    System.out.println(savingFiles.toString());
     Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
     jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
             screen.width + "");
@@ -1404,9 +1357,10 @@ public class Desktop extends jalview.jbgui.GDesktop
       message.append("<h1><strong>Version: "
               + jalview.bin.Cache.getProperty("VERSION")
               + "</strong></h1>");
-      message.append("<strong>Last Updated: <em>"
+      message.append("<strong>Built: <em>"
               + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
-              + "</em></strong>");
+              + "</em> from " + jalview.bin.Cache.getBuildDetailsForSplash()
+              + "</strong>");
 
     }
     else
@@ -1421,7 +1375,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
             .equals("Checking"))
     {
-      message.append("<br>...Checking latest version...</br>");
+      // JBP removed this message for 2.11: May be reinstated in future version
+      // message.append("<br>...Checking latest version...</br>");
     }
     else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
             .equals(jalview.bin.Cache.getProperty("VERSION")))
@@ -1675,28 +1630,49 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Shows a file chooser dialog and writes out the current session as a Jalview
+   * project file
    */
   @Override
-  public void saveState_actionPerformed(ActionEvent e)
+  public void saveState_actionPerformed()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser("jvp",
-            "Jalview Project");
+    saveState_actionPerformed(false);
+  }
 
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+  public void saveState_actionPerformed(boolean saveAs)
+  {
+    java.io.File projectFile = getProjectFile();
+    // autoSave indicates we already have a file and don't need to ask
+    boolean autoSave = projectFile != null && !saveAs
+            && BackupFiles.getEnabled();
 
-    int value = chooser.showSaveDialog(this);
+    // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+    // saveAs="+saveAs+", Backups
+    // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    boolean approveSave = false;
+    if (!autoSave)
     {
-      final Desktop me = this;
-      final java.io.File choice = chooser.getSelectedFile();
-      setProjectFile(choice);
+      JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+              "Jalview Project");
+
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+
+      int value = chooser.showSaveDialog(this);
 
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        projectFile = chooser.getSelectedFile();
+        setProjectFile(projectFile);
+        approveSave = true;
+      }
+    }
+
+    if (approveSave || autoSave)
+    {
+      final Desktop me = this;
+      final java.io.File chosenFile = projectFile;
       new Thread(new Runnable()
       {
         @Override
@@ -1705,38 +1681,47 @@ public class Desktop extends jalview.jbgui.GDesktop
           // TODO: refactor to Jalview desktop session controller action.
           setProgressBar(MessageManager.formatMessage(
                   "label.saving_jalview_project", new Object[]
-                  { choice.getName() }), choice.hashCode());
+                  { chosenFile.getName() }), chosenFile.hashCode());
           jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                  choice.getParent());
+                  chosenFile.getParent());
           // TODO catch and handle errors for savestate
           // TODO prevent user from messing with the Desktop whilst we're saving
           try
           {
-            new Jalview2XML().saveState(choice);
+            BackupFiles backupfiles = new BackupFiles(chosenFile);
+
+            new Jalview2XML().saveState(backupfiles.getTempFile());
+
+            backupfiles.setWriteSuccess(true);
+            backupfiles.rollBackupsAndRenameTempFile();
           } catch (OutOfMemoryError oom)
           {
-            new OOMWarning(
-                    "Whilst saving current state to " + choice.getName(),
-                    oom);
+            new OOMWarning("Whilst saving current state to "
+                    + chosenFile.getName(), oom);
           } catch (Exception ex)
           {
-            Cache.log.error(
-                    "Problems whilst trying to save to " + choice.getName(),
-                    ex);
+            Cache.log.error("Problems whilst trying to save to "
+                    + chosenFile.getName(), ex);
             JvOptionPane.showMessageDialog(me,
                     MessageManager.formatMessage(
                             "label.error_whilst_saving_current_state_to",
                             new Object[]
-                            { choice.getName() }),
+                            { chosenFile.getName() }),
                     MessageManager.getString("label.couldnt_save_project"),
                     JvOptionPane.WARNING_MESSAGE);
           }
-          setProgressBar(null, choice.hashCode());
+          setProgressBar(null, chosenFile.hashCode());
         }
       }).start();
     }
   }
 
+  @Override
+  public void saveAsState_actionPerformed(ActionEvent e)
+  {
+    saveState_actionPerformed(true);
+  }
+
   private void setProjectFile(File choice)
   {
     this.projectFile = choice;
@@ -1748,20 +1733,19 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Shows a file chooser dialog and tries to read in the selected file as a
+   * Jalview project
    */
   @Override
-  public void loadState_actionPerformed(ActionEvent e)
+  public void loadState_actionPerformed()
   {
+    final String[] suffix = new String[] { "jvp", "jar" };
+    final String[] desc = new String[] { "Jalview Project",
+        "Jalview Project (old)" };
     JalviewFileChooser chooser = new JalviewFileChooser(
-            Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "jvp", "jar" },
-            new String[]
-            { "Jalview Project", "Jalview Project (old)" },
-            "Jalview Project");
+            Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
+            "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
+                                            // allowBackupFiles
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
 
@@ -2765,7 +2749,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
             .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
-                    Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()),
+                    jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
                     "Quit");
     getRootPane().getActionMap().put("Quit", new AbstractAction()
     {
@@ -2822,18 +2806,18 @@ public class Desktop extends jalview.jbgui.GDesktop
       progressBarHandlers = new Hashtable<>();
     }
 
-    if (progressBars.get(new Long(id)) != null)
+    if (progressBars.get(Long.valueOf(id)) != null)
     {
-      JPanel panel = progressBars.remove(new Long(id));
-      if (progressBarHandlers.contains(new Long(id)))
+      JPanel panel = progressBars.remove(Long.valueOf(id));
+      if (progressBarHandlers.contains(Long.valueOf(id)))
       {
-        progressBarHandlers.remove(new Long(id));
+        progressBarHandlers.remove(Long.valueOf(id));
       }
       removeProgressPanel(panel);
     }
     else
     {
-      progressBars.put(new Long(id), addProgressPanel(message));
+      progressBars.put(Long.valueOf(id), addProgressPanel(message));
     }
   }
 
@@ -2848,13 +2832,13 @@ public class Desktop extends jalview.jbgui.GDesktop
           final IProgressIndicatorHandler handler)
   {
     if (progressBarHandlers == null
-            || !progressBars.containsKey(new Long(id)))
+            || !progressBars.containsKey(Long.valueOf(id)))
     {
       throw new Error(MessageManager.getString(
               "error.call_setprogressbar_before_registering_handler"));
     }
-    progressBarHandlers.put(new Long(id), handler);
-    final JPanel progressPanel = progressBars.get(new Long(id));
+    progressBarHandlers.put(Long.valueOf(id), handler);
+    final JPanel progressPanel = progressBars.get(Long.valueOf(id));
     if (handler.canCancel())
     {
       JButton cancel = new JButton(