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;
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;
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.dnd.DnDConstants;
import java.awt.dnd.DropTargetDragEvent;
import java.awt.dnd.DropTargetDropEvent;
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;
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();
doConfigureStructurePrefs();
setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
- // setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- /* comments
- * galore
- * to
- * change the line numbers
- */
-
+ /*
if (!Platform.isAMac())
{
// this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
}
else
{
- // this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
- java.awt.Desktop desktop = java.awt.Desktop.getDesktop();
+ this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+ }
+ */
- desktop.setAboutHandler(new AboutHandler()
- {
- @Override
- public void handleAbout(AboutEvent e)
- {
- aboutMenuItem_actionPerformed(null);
- }
- });
- desktop.setPreferencesHandler(new PreferencesHandler()
- {
- @Override
- public void handlePreferences(PreferencesEvent e)
- {
- preferences_actionPerformed(null);
- }
- });
- desktop.setQuitHandler(new QuitHandler()
- {
- @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();
- }
- else
- {
- System.out.println("Shortcut Quit cancelled by user");
- }
- }
- });
+ try
+ {
+ APQHandlers.setAPQHandlers(this);
+ } catch (Exception e)
+ {
+ System.out.println("Exception when trying to set APQHandlers");
+ e.printStackTrace();
+ } catch (Throwable t)
+ {
+ System.out.println("Throwable when trying to set APQHandlers");
+ t.printStackTrace();
+ }
- addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowClosing(WindowEvent ev)
- {
- quit();
- }
- });
- }
+ addWindowListener(new WindowAdapter()
+ {
+
+ @Override
+ public void windowClosing(WindowEvent ev)
+ {
+ quit();
+ }
+ });
boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
false);
+ System.getProperty("java.version") + "\n"
+ System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
- + System.getProperty("os.version"));
+ + System.getProperty("os.version")
+ + (jalview.bin.Cache.getProperty("VERSION").equals("DEVELOPMENT")
+ ? "\nJava path:"
+ + System.getProperty(
+ "java.home")
+ + File.separator + "bin"
+ + File.separator + "java"
+ : "")
+ );
showConsole(showjconsole);
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);
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser chooser = JalviewFileChooser
- .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, true);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
@Override
public void quit()
{
- System.out.println("********** Desktop.quit()");
- System.out.println(savingFiles.toString());
+ //System.out.println("********** Desktop.quit()");
+ //System.out.println(savingFiles.toString());
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
screen.width + "");
}
/**
- * 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
// 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;
}
/**
- * 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, true); // last two booleans: allFiles,
+ // allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
{
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()
{
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));
}
}
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(
git://source.jalview.org / jalview.git / blobdiff