*/
package jalview.gui;
-import static jalview.util.UrlConstants.SEQUENCE_ID;
-
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;
+import jalview.io.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
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;
import jalview.structure.StructureSelectionManager;
import jalview.urls.IdOrgSettings;
import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.UrlConstants;
-import jalview.util.dialogrunner.RunResponse;
import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.jws1.Discoverer;
import jalview.ws.params.ParamManager;
import jalview.ws.utils.UrlDownloadClient;
import java.util.Hashtable;
import java.util.List;
import java.util.ListIterator;
-import java.util.StringTokenizer;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
+import javax.swing.JTextField;
import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
import javax.swing.event.HyperlinkEvent;
* @author $author$
* @version $Revision: 1.155 $
*/
-public class Desktop extends jalview.jbgui.GDesktop
+@SuppressWarnings("serial")
+public class Desktop extends GDesktop
implements DropTargetListener, ClipboardOwner, IProgressIndicator,
- jalview.api.StructureSelectionManagerProvider
+ StructureSelectionManagerProvider, ApplicationSingletonI
{
- private static int DEFAULT_MIN_WIDTH = 300;
- private static int DEFAULT_MIN_HEIGHT = 250;
+ private final static int DEFAULT_MIN_WIDTH = 300;
+
+ private final static int DEFAULT_MIN_HEIGHT = 250;
- private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600;
+ private final static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600;
- private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70;
+ private final static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70;
- private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
+ private final static String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
/**
* news reader - null if it was never started.
*/
- private BlogReader jvnews = null;
+ BlogReader jvnews = null;
private File projectFile;
listener);
}
- /** Singleton Desktop instance */
- public static Desktop instance;
-
- public static MyDesktopPane desktop;
+ public static MyDesktopPane getDesktopPane()
+ {
+ Desktop desktop = Desktop.getInstance();
+ return desktop == null ? null : desktop.desktopPane;
+ }
- public static MyDesktopPane getDesktop()
+ public static StructureSelectionManager getStructureSelectionManager()
{
- // BH 2018 could use currentThread() here as a reference to a
- // Hashtable<Thread, MyDesktopPane> in JavaScript
- return desktop;
+ return StructureSelectionManager
+ .getStructureSelectionManager(getInstance());
}
static int openFrameCount = 0;
static final int yOffset = 30;
- public static jalview.ws.jws1.Discoverer discoverer;
+ public Discoverer discoverer;
- public static Object[] jalviewClipboard;
+ public Object[] jalviewClipboard;
- public static boolean internalCopy = false;
+ public boolean internalCopy = false;
- static int fileLoadingCount = 0;
+ private static int fileLoadingCount = 0;
+
+ public JInternalFrame conservationSlider;
+
+ public JInternalFrame PIDSlider;
class MyDesktopManager implements DesktopManager
{
} catch (NullPointerException npe)
{
Point p = getMousePosition();
- instance.showPasteMenu(p.x, p.y);
+ showPasteMenu(p.x, p.y);
}
}
public void endDraggingFrame(JComponent f)
{
delegate.endDraggingFrame(f);
- desktop.repaint();
+ desktopPane.repaint();
}
@Override
public void endResizingFrame(JComponent f)
{
delegate.endResizingFrame(f);
- desktop.repaint();
+ desktopPane.repaint();
}
@Override
}
+ 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()
{
- /**
- * 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.
- */
- instance = this;
- if (!Jalview.isJS())
- {
- doVamsasClientCheck();
- }
-
- doConfigureStructurePrefs();
- setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
- false);
- boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
- false);
- desktop = new MyDesktopPane(selmemusage);
- showMemusage.setSelected(selmemusage);
- desktop.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);
- getContentPane().add(desktop, BorderLayout.CENTER);
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
-
- // This line prevents Windows Look&Feel resizing all new windows to maximum
- // if previous window was maximised
- desktop.setDesktopManager(new MyDesktopManager(
- (Platform.isWindows() ? new DefaultDesktopManager()
- : Platform.isAMac()
- ? new AquaInternalFrameManager(
- desktop.getDesktopManager())
- : desktop.getDesktopManager())));
-
- Rectangle dims = getLastKnownDimensions("");
- if (dims != null)
- {
- setBounds(dims);
- }
- else
- {
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- int xPos = Math.max(5, (screenSize.width - 900) / 2);
- int yPos = Math.max(5, (screenSize.height - 650) / 2);
- setBounds(xPos, yPos, 900, 650);
- }
- /**
- * BH 2018
- *
- * @j2sNative
- */
+ return Jalview.isHeadlessMode() ? null
+ : (Desktop) ApplicationSingletonProvider
+ .getInstance(Desktop.class);
+ }
+
+ /**
+ * Private constructor enforces singleton pattern. It is called by reflection
+ * from ApplicationSingletonProvider.getInstance().
+ */
+ 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.
+ */
+ if (!Platform.isJS())
+ {
+ doVamsasClientCheck();
+ }
- 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"));
+ doConfigureStructurePrefs();
+ setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
+ setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
+ false);
+ boolean showjconsole = jalview.bin.Cache
+ .getDefault("SHOW_JAVA_CONSOLE", false);
+ desktopPane = new MyDesktopPane(selmemusage);
- showConsole(showjconsole);
+ showMemusage.setSelected(selmemusage);
+ 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);
- showNews.setVisible(false);
+ // BH 2018 - just an experiment to try unclipped JInternalFrames.
+ if (Platform.isJS())
+ {
+ getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
+ }
- experimentalFeatures.setSelected(showExperimental());
+ getContentPane().add(desktopPane, BorderLayout.CENTER);
+ desktopPane.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
- getIdentifiersOrgData();
+ // This line prevents Windows Look&Feel resizing all new windows to
+ // maximum
+ // if previous window was maximised
+ desktopPane.setDesktopManager(new MyDesktopManager(
+ (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+ : Platform.isAMacAndNotJS()
+ ? new AquaInternalFrameManager(
+ desktopPane.getDesktopManager())
+ : desktopPane.getDesktopManager())));
- checkURLLinks();
+ Rectangle dims = getLastKnownDimensions("");
+ if (dims != null)
+ {
+ setBounds(dims);
+ }
+ else
+ {
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+ int xPos = Math.max(5, (screenSize.width - 900) / 2);
+ int yPos = Math.max(5, (screenSize.height - 650) / 2);
+ setBounds(xPos, yPos, 900, 650);
+ }
- // Spawn a thread that shows the splashscreen
+ // Note that this next syntax, checking for Platform.isJS and also
+ // escaping the code using @j2sIgnore, serves two purposes. It gives
+ // us an easily findable tag, Platform.isJS(), to places in the code where
+ // there is something different about the SwingJS implementation. Second,
+ // it deletes the unneeded Java-only code form the JavaScript version
+ // completely (@j2sIgnore), since it will never be used there.
- SwingUtilities.invokeLater(new Runnable()
+ if (!Platform.isJS() && !Jalview.isSynchronous())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- @Override
- public void run()
- {
- new SplashScreen();
- }
- });
- // Thread off a new instance of the file chooser - this reduces the time it
- // takes to open it later on.
- new Thread(new Runnable()
- {
- @Override
- public void run()
+ 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"));
+
+ showConsole(showjconsole);
+
+ showNews.setVisible(false);
+
+ experimentalFeatures.setSelected(showExperimental());
+
+ getIdentifiersOrgData();
+
+ checkURLLinks();
+
+ // Spawn a thread that shows the splashscreen
+
+ SwingUtilities.invokeLater(new Runnable()
{
- Cache.log.debug("Filechooser init thread started.");
- String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
- fileFormat);
- Cache.log.debug("Filechooser init thread finished.");
- }
- }).start();
- // Add the service change listener
- changeSupport.addJalviewPropertyChangeListener("services",
- new PropertyChangeListener()
- {
+ @Override
+ public void run()
+ {
+ new SplashScreen();
+ }
+ });
- @Override
- public void propertyChange(PropertyChangeEvent evt)
+ // Thread off a new instance of the file chooser - this reduces the time
+ // it
+ // takes to open it later on.
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Filechooser init thread started.");
+ String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+ fileFormat);
+ Cache.log.debug("Filechooser init thread finished.");
+ }
+ }).start();
+ // Add the service change listener
+ changeSupport.addJalviewPropertyChangeListener("services",
+ new PropertyChangeListener()
{
- Cache.log.debug("Firing service changed event for "
- + evt.getNewValue());
- JalviewServicesChanged(evt);
- }
- });
-
- } // end BH 2018 ignore
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ Cache.log.debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
+ });
- this.addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowClosing(WindowEvent evt)
- {
- quit();
}
- });
- MouseAdapter ma;
- this.addMouseListener(ma = new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
+ if (!Jalview.isSynchronous())
{
- if (evt.isPopupTrigger()) // Mac
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this));
+
+ this.addWindowListener(new WindowAdapter()
{
- showPasteMenu(evt.getX(), evt.getY());
- }
- }
+ @Override
+ public void windowClosing(WindowEvent evt)
+ {
+ quit();
+ }
+ });
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
+ MouseAdapter ma;
+ this.addMouseListener(ma = new MouseAdapter()
{
- showPasteMenu(evt.getX(), evt.getY());
- }
- }
- });
- desktop.addMouseListener(ma);
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Mac
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
+ {
+ showPasteMenu(evt.getX(), evt.getY());
+ }
+ }
+ });
+ desktopPane.addMouseListener(ma);
+ }
+ } catch (Throwable t)
+ {
+ t.printStackTrace();
+ }
}
/**
{
final Desktop me = this;
// Thread off the news reader, in case there are connection problems.
- addDialogThread(new Runnable()
+ new Thread(new Runnable()
{
@Override
public void run()
showNews.setVisible(true);
Cache.log.debug("Completed news thread.");
}
- });
+ }).start();
}
public void getIdentifiersOrgData()
{
// Thread off the identifiers fetcher
- addDialogThread(new Runnable()
+ new Thread(new Runnable()
{
@Override
public void run()
{
Cache.log.debug("Downloading data from identifiers.org");
- UrlDownloadClient client = new UrlDownloadClient();
+ // UrlDownloadClient client = new UrlDownloadClient();
try
{
- client.download(IdOrgSettings.getUrl(),
+ UrlDownloadClient.download(IdOrgSettings.getUrl(),
IdOrgSettings.getDownloadLocation());
} catch (IOException e)
{
+ e.getMessage());
}
}
- });
+ }).start();
+
}
@Override
showNews(showNews.isSelected());
}
- void showNews(boolean visible)
+ protected void showNews(boolean visible)
{
Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
public void run()
{
long now = System.currentTimeMillis();
- Desktop.instance.setProgressBar(
+ setProgressBar(
MessageManager.getString("status.refreshing_news"), now);
jvnews.refreshNews();
- Desktop.instance.setProgressBar(null, now);
+ setProgressBar(null, now);
jvnews.showNews();
}
}).start();
}
}
- void showPasteMenu(int x, int y)
+ protected void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
JMenuItem item = new JMenuItem(
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)
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);
}
// A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
- if (instance == null || (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true")))
+ if (Jalview.isHeadlessMode())
{
return;
}
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
- frame.setOpaque(/** @j2sNative true || */
- false);
+ frame.setOpaque(Platform.isJS());
- if (frame.getX() < 1 && frame.getY() < 1)
+ boolean isEmbedded = (Platform.getDimIfEmbedded(frame, -1, -1) != null);
+ if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1)
{
frame.setLocation(xOffset * openFrameCount,
yOffset * ((openFrameCount - 1) % 10) + yOffset);
* add an entry for the new frame in the Window menu
* (and remove it when the frame is closed)
*/
- final JMenuItem menuItem = new JMenuItem(title);
+ JMenuItem menuItem = new JMenuItem(title);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
public void internalFrameActivated(InternalFrameEvent evt)
{
- JInternalFrame itf = desktop.getSelectedFrame();
+ JInternalFrame itf = getDesktopPane().getSelectedFrame();
if (itf != null)
{
if (itf instanceof AlignFrame)
{
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
- windowMenu.remove(menuItem);
- };
+ Desktop.getInstance().windowMenu.remove(menuItem);
+ }
});
menuItem.addActionListener(new ActionListener()
setKeyBindings(frame);
- desktop.add(frame);
+ getDesktopPane().add(frame);
- windowMenu.add(menuItem);
+ Desktop.getInstance().windowMenu.add(menuItem);
frame.toFront();
try
*/
private static void setKeyBindings(JInternalFrame frame)
{
- @SuppressWarnings("serial")
final Action closeAction = new AbstractAction()
{
@Override
{
if (!internalCopy)
{
- Desktop.jalviewClipboard = null;
+ Desktop.getInstance().jalviewClipboard = null;
}
internalCopy = false;
{
format = new IdentifyFile().identify(file, protocol);
}
-
- new FileLoader().LoadFile(null, file, protocol, format);
+ if (file instanceof File)
+ {
+ Platform.cacheFileData((File) file);
+ }
+ new FileLoader().loadFile(null, file, protocol, format);
}
} catch (Exception ex)
{
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(
MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
- chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
-
@Override
public void run()
{
}
}
- new FileLoader().LoadFile(viewport, selectedFile,
+ new FileLoader().loadFile(viewport, selectedFile,
DataSourceType.FILE, format);
}
- }).openDialog(this);
+ });
+ chooser.showOpenDialog(this);
}
/**
- * DOCUMENT ME!
+ * Shows a dialog for input of a URL at which to retrieve alignment data
*
- * @param e
- * DOCUMENT ME!
+ * @param viewport
*/
@Override
public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
JLabel label = new JLabel(
MessageManager.getString("label.input_file_url"));
- JComboBox history = new JComboBox();
JPanel panel = new JPanel(new GridLayout(2, 1));
panel.add(label);
- panel.add(history);
- history.setPreferredSize(new Dimension(400, 20));
- history.setEditable(true);
- history.addItem("http://www.");
-
- String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
- StringTokenizer st;
-
- if (historyItems != null)
+ /*
+ * the URL to fetch is
+ * Java: an editable combobox with history
+ * JS: (pending JAL-3038) a plain text field
+ */
+ JComponent history;
+ String urlBase = "http://www.";
+ if (Platform.isJS())
{
- st = new StringTokenizer(historyItems, "\t");
-
- while (st.hasMoreTokens())
+ history = new JTextField(urlBase, 35);
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ JComboBox<String> asCombo = new JComboBox<>();
+ asCombo.setPreferredSize(new Dimension(400, 20));
+ asCombo.setEditable(true);
+ asCombo.addItem(urlBase);
+ String historyItems = Cache.getProperty("RECENT_URL");
+ if (historyItems != null)
{
- history.addItem(st.nextElement());
+ for (String token : historyItems.split("\\t"))
+ {
+ asCombo.addItem(token);
+ }
}
+ history = asCombo;
}
+ panel.add(history);
- // BH 2018 -- providing a callback for SwingJS
- // dialogOption is just a simple way to provide
- // context for the modal-like response.
- // The only requirement is that desktop implement
- // PropertyChangeListener, which is used already in Java
- // for changes in input value and such within the dialogs.
+ Object[] options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ Runnable action = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ @SuppressWarnings("unchecked")
+ String url = (history instanceof JTextField
+ ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getSelectedItem()
+ .toString());
- String dialogOption = "label.input_alignment_from_url";
- desktop.dialogData = new Object[] { dialogOption, viewport, history };
- desktop.onDialogReturn(JvOptionPane.showInternalConfirmDialog(desktop,
- panel, MessageManager.getString(dialogOption),
- JvOptionPane.OK_CANCEL_OPTION));
+ if (url.toLowerCase().endsWith(".jar"))
+ {
+ if (viewport != null)
+ {
+ new FileLoader().loadFile(viewport, url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ else
+ {
+ new FileLoader().loadFile(url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ }
+ else
+ {
+ FileFormatI format = null;
+ try
+ {
+ format = new IdentifyFile().identify(url, DataSourceType.URL);
+ } catch (FileFormatException e)
+ {
+ // TODO revise error handling, distinguish between
+ // URL not found and response not valid
+ }
- // no code may follow this, as SwingJS will not block
- // callback in JavaScript comes via a property change event,
- // thus going into desktop.onDialogReturn(int) just the same as
- // in Java.
+ if (format == null)
+ {
+ String msg = MessageManager
+ .formatMessage("label.couldnt_locate", url);
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ msg,
+ MessageManager.getString("label.url_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ if (viewport != null)
+ {
+ new FileLoader().loadFile(viewport, url, DataSourceType.URL,
+ format);
+ }
+ else
+ {
+ new FileLoader().loadFile(url, DataSourceType.URL, format);
+ }
+ }
+ }
+ };
+ String dialogOption = MessageManager
+ .getString("label.input_alignment_from_url");
+ JvOptionPane.newOptionDialog(getDesktopPane())
+ .setResponseHandler(0, action)
+ .showInternalDialog(panel, dialogOption,
+ JvOptionPane.YES_NO_CANCEL_OPTION,
+ JvOptionPane.PLAIN_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
}
/**
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
// StringBuffer message = getAboutMessage(false);
- // JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ // JvOptionPane.showInternalMessageDialog(Desktop.getDesktop(),
//
// message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
new Thread(new Runnable()
{
try
{
- if (Jalview.isJS())
+ if (Platform.isJS())
{
BrowserLauncher.openURL("http://www.jalview.org/help.html");
}
else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
Help.showHelpWindow();
}
@Override
public void closeAll_actionPerformed(ActionEvent e)
{
+ if (desktopPane == null)
+ {
+ return;
+ }
// TODO show a progress bar while closing?
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
for (int i = 0; i < frames.length; i++)
{
try
* 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
@Override
protected void showMemusage_actionPerformed(ActionEvent e)
{
- desktop.showMemoryUsage(showMemusage.isSelected());
+ getDesktopPane().showMemoryUsage(showMemusage.isSelected());
}
/*
void reorderAssociatedWindows(boolean minimize, boolean close)
{
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = getDesktopPane().getAllFrames();
if (frames == null || frames.length < 1)
{
return;
@Override
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);
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null;
+
+ new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile);
+
+ if (doBackup)
+ {
+ 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)
+ protected void setProjectFile(File choice)
{
this.projectFile = choice;
}
}
/**
- * Prompts the user to choose a file and loads in as a Jalview project file
+ * Shows a file chooser dialog and tries to read in the selected file as a
+ * Jalview project
*/
@Override
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"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- final File selectedFile = chooser.getSelectedFile();
- setProjectFile(selectedFile);
- final String choice = selectedFile.getAbsolutePath();
- Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
+ File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ String choice = selectedFile.getAbsolutePath();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+ new Thread(new Runnable()
{
- setProgressBar(MessageManager.formatMessage(
- "label.loading_jalview_project", new Object[]
- { choice }), choice.hashCode());
- try
+ @Override
+ public void run()
{
- new Jalview2XML().loadJalviewAlign(choice);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
- {
- Cache.log.error(
- "Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager.getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
+ try
+ {
+ new Jalview2XML().loadJalviewAlign(selectedFile);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager.getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
}
- setProgressBar(null, choice.hashCode());
- }
- }).start();
- }
+ }).start();
+ }
+ });
+
+ chooser.showOpenDialog(this);
}
@Override
{
progressPanel = new JPanel(new GridLayout(1, 1));
totalProgressCount = 0;
- instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+ getContentPane().add(progressPanel, BorderLayout.SOUTH);
}
JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
JProgressBar progressBar = new JProgressBar();
((GridLayout) progressPanel.getLayout()).setRows(
((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
- instance.validate();
+ validate();
return thisprogress;
}
*/
public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
{
- if (Desktop.desktop == null)
+ if (Desktop.getDesktopPane() == null)
{
// no frames created and in headless mode
// TODO: verify that frames are recoverable when in headless mode
public static AlignmentViewport[] getViewports(String sequenceSetId)
{
List<AlignmentViewport> viewp = new ArrayList<>();
- if (desktop != null)
+ if (getDesktopPane() != null)
{
AlignFrame[] frames = Desktop.getAlignFrames();
{
source.viewport.setGatherViewsHere(true);
source.viewport.setExplodedGeometry(source.getBounds());
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = getAllFrames();
String viewId = source.viewport.getSequenceSetId();
for (int t = 0; t < frames.length; t++)
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.couldnt_import_as_vamsas_session",
new Object[]
});
rthr.start();
}
- };
+ }
});
VamsasStMenu.add(sessit);
}
removeProgressPanel(progpanel);
if (warnmsg != null)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
}
public JInternalFrame[] getAllFrames()
{
- return desktop.getAllFrames();
+ return desktopPane.getAllFrames();
}
/**
while (li.hasNext())
{
String link = li.next();
- if (link.contains(SEQUENCE_ID)
+ if (link.contains(UrlConstants.SEQUENCE_ID)
&& !UrlConstants.isDefaultString(link))
{
check = true;
});
msgPanel.add(jcb);
- JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
+ JvOptionPane.showMessageDialog(desktopPane, msgPanel,
MessageManager
.getString("label.SEQUENCE_ID_no_longer_used"),
JvOptionPane.WARNING_MESSAGE);
* @author AMW
*/
public class MyDesktopPane extends JDesktopPane
- implements Runnable, PropertyChangeListener
+ implements Runnable
{
-
- public Object[] dialogData;
-
- // @Override
- @Override
- public void propertyChange(PropertyChangeEvent event)
- {
- // TODO this is obsolete with JAL-3048 - delete?
- Object val = event.getNewValue();
- String name = event.getPropertyName();
- System.out.println(name);
- switch (event.getSource().getClass().getName())
- {
- case "javax.swing.JOptionPane":
- switch (name)
- {
- case "inputValue":
- onDialogReturn(val);
- return;
- case "value":
- if (val instanceof Integer)
- {
- onDialogReturn(((Integer) val).intValue());
- }
- else
- {
- onDialogReturn(val);
- }
- return;
- }
- break;
- case "javax.swing.JFileChooser":
- switch (name)
- {
- case "SelectedFile":
- // in JavaScript, this File object will have a _bytes property,
- // because the file data has already been loaded
- onDialogReturn(new Object[] { (File) val });
- return;
- }
- break;
- }
- System.out.println(event.getSource().getClass().getName() + " "
- + event.getPropertyName() + ": " + event.getNewValue());
- }
-
- // JSCOmponent.DialogCaller interface
- void onDialogReturn(Object value)
- {
- switch ((String) dialogData[0])
- {
- case "SelectedFile":
- case "runnable":
- dialogData[0] = value;
- ((Runnable) dialogData[1]).run();
- break;
- default:
- }
- }
-
- // JSCOmponent.DialogCaller interface
- void onDialogReturn(int value)
- {
- if (value != Math.floor(value))
- {
- // in JavaScript, this will be NaN, oddly enough
- return;
- }
-
- switch ((String) dialogData[0])
- {
- case "runnable":
- dialogData[0] = Integer.valueOf(value);
- ((Runnable) dialogData[1]).run();
- break;
- case "label.input_alignment_from_url":
- // reconstruct the parameter data
- int reply = value;
- AlignViewport viewport = (AlignViewport) dialogData[1];
- JComboBox history = (JComboBox) dialogData[2];
- // the rest of this is unchangaed
- if (reply != JvOptionPane.OK_OPTION)
- {
- return;
- }
-
- String url = history.getSelectedItem().toString();
-
- if (url.toLowerCase().endsWith(".jar"))
- {
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- }
- else
- {
- FileFormatI format = null;
- try
- {
- format = new IdentifyFile().identify(url, DataSourceType.URL);
- } catch (FileFormatException e)
- {
- // TODO revise error handling, distinguish between
- // URL not found and response not valid
- }
-
- if (format == null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.couldnt_locate",
- new Object[]
- { url }),
- MessageManager.getString("label.url_not_found"),
- JvOptionPane.WARNING_MESSAGE);
-
- return;
- }
-
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- format);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL, format);
- }
- }
-
- break;
- }
-
- }
-
private static final float ONE_MB = 1048576f;
boolean showMemoryUsage = false;
{
if (Jalview.isHeadlessMode())
{
- // Desktop.desktop is null in headless mode
- return new AlignFrame[] { Jalview.currentAlignFrame };
+ // Desktop.getDesktop() is null in headless mode
+ return new AlignFrame[] { Jalview.getCurrentAlignFrame() };
}
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
if (frames == null)
{
*/
public GStructureViewer[] getJmols()
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
if (frames == null)
{
} catch (Exception ex)
{
jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(desktopPane,
MessageManager.getString("label.couldnt_create_groovy_shell"),
MessageManager.getString("label.groovy_support_failed"),
/**
* Open the Groovy console
*/
- void openGroovyConsole()
+ private void openGroovyConsole()
{
if (groovyConsole == null)
{
@Override
public void setProgressBar(String message, long id)
{
+ Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
+
if (progressBars == null)
{
progressBars = new Hashtable<>();
*/
public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
{
- if (desktop != null)
+ if (getDesktopPane() != null)
{
AlignmentPanel[] aps = getAlignmentPanels(
viewport.getSequenceSetId());
// todo: changesupport handlers need to be transferred
if (discoverer == null)
{
- discoverer = new jalview.ws.jws1.Discoverer();
- // register PCS handler for desktop.
+ discoverer = Discoverer.getInstance();
+ // register PCS handler for getDesktop().
discoverer.addPropertyChangeListener(changeSupport);
}
// JAL-940 - disabled JWS1 service configuration - always start discoverer
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ t2 = jalview.ws.jws2.Jws2Discoverer.getInstance()
.startDiscoverer(changeSupport);
}
Thread t3 = null;
{
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)
{
*
* jd.waitForInput();
*/
- JvOptionPane.showConfirmDialog(Desktop.desktop,
+ JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
new JLabel("<html><table width=\"450\"><tr><td>"
+ ermsg + "</td></tr></table>"
+ "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
}
}
- private Runnable serviceChangedDialog = null;
+ Runnable serviceChangedDialog = null;
/**
* start a thread to open a URL in the configured browser. Pops up a warning
*/
public static void showUrl(final String url)
{
- showUrl(url, Desktop.instance);
+ showUrl(url, Desktop.getInstance());
}
/**
.formatMessage("status.opening_params", new Object[]
{ url }), this.hashCode());
}
- jalview.util.BrowserLauncher.openURL(url);
+ BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager
.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
}).start();
}
- public static WsParamSetManager wsparamManager = null;
+ private WsParamSetManager wsparamManager = null;
public static ParamManager getUserParameterStore()
{
- if (wsparamManager == null)
+ Desktop d = Desktop.getInstance();
+ if (d.wsparamManager == null)
{
- wsparamManager = new WsParamSetManager();
+ d.wsparamManager = new WsParamSetManager();
}
- return wsparamManager;
+ return d.wsparamManager;
}
/**
/**
* flag indicating if dialogExecutor should try to acquire a permit
*/
- private volatile boolean dialogPause = true;
+ volatile boolean dialogPause = true;
/**
* pause the queue
*/
- private java.util.concurrent.Semaphore block = new Semaphore(0);
+ java.util.concurrent.Semaphore block = new Semaphore(0);
+
+ private groovy.ui.Console groovyConsole;
- private static groovy.ui.Console groovyConsole;
+ public StructureViewer lastTargetedView;
/**
* add another dialog thread to the queue
} catch (InterruptedException x)
{
}
- ;
}
- if (instance == null)
+ if (Jalview.isHeadlessMode())
{
return;
}
String topViewId = myTopFrame.viewport.getSequenceSetId();
String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
- JInternalFrame[] frames = desktop.getAllFrames();
+ JInternalFrame[] frames = desktopPane.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof SplitFrame && frame != source)
public static groovy.ui.Console getGroovyConsole()
{
- return groovyConsole;
+ Desktop desktop = Desktop.getInstance();
+ return desktop == null ? null : desktop.groovyConsole;
}
/**
* - the payload from the drop event
* @throws Exception
*/
+ @SuppressWarnings("unchecked")
public static void transferFromDropTarget(List<Object> files,
List<DataSourceType> protocols, DropTargetDropEvent evt,
Transferable t) throws Exception
}
else
{
- if (Platform.isAMac())
+ if (Platform.isAMacAndNotJS())
{
System.err.println(
"Please ignore plist error - occurs due to problem with java 8 on OSX");
}
- ;
}
} catch (Throwable ex)
{
{
// Works on Windows and MacOSX
Cache.log.debug("Drop handled as javaFileListFlavor");
- for (Object file : (List) t
+ for (Object file : (List<Object>) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
files.add(file);
}
}
}
- if (Platform.isWindows())
-
+ if (Platform.isWindowsAndNotJS())
{
Cache.log.debug("Scanning dropped content for Windows Link Files");
Class<? extends StructureViewerBase> structureViewerClass)
{
List<StructureViewerBase> result = new ArrayList<>();
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ JInternalFrame[] frames = getAllFrames();
for (JInternalFrame frame : frames)
{
}
return result;
}
+
}
git://source.jalview.org / jalview.git / blobdiff