*/
package jalview.gui;
-import static jalview.util.UrlConstants.SEQUENCE_ID;
-
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.gui.ImageExporter.ImageWriterI;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
-import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GSplitFrame;
-import jalview.jbgui.GStructureViewer;
-import jalview.structure.StructureSelectionManager;
-import jalview.urls.IdOrgSettings;
-import jalview.util.BrowserLauncher;
-import jalview.util.ImageMaker.TYPE;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.util.UrlConstants;
-import jalview.util.dialogrunner.RunResponse;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.params.ParamManager;
-import jalview.ws.utils.UrlDownloadClient;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.FontMetrics;
import java.awt.Graphics;
+import java.awt.Graphics2D;
import java.awt.GridLayout;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.event.MouseEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
+import java.awt.geom.AffineTransform;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
-import java.io.BufferedInputStream;
import java.io.File;
-import java.io.FileOutputStream;
+import java.io.FileWriter;
import java.io.IOException;
+import java.lang.reflect.Field;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.ListIterator;
-import java.util.StringTokenizer;
+import java.util.Locale;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDesktopPane;
-import javax.swing.JFrame;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.event.HyperlinkEvent.EventType;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
import org.stackoverflowusers.file.WindowsShortcut;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+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.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+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.BrowserLauncher;
+import jalview.util.ChannelProperties;
+import jalview.util.ImageMaker.TYPE;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.ShortcutKeyMaskExWrapper;
+import jalview.util.UrlConstants;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
+
/**
* Jalview Desktop
*
implements DropTargetListener, ClipboardOwner, IProgressIndicator,
jalview.api.StructureSelectionManagerProvider
{
+ private static final String CITATION;
+ static
+ {
+ URL bg_logo_url = ChannelProperties.getImageURL(
+ "bg_logo." + String.valueOf(SplashScreen.logoSize));
+ URL uod_logo_url = ChannelProperties.getImageURL(
+ "uod_banner." + String.valueOf(SplashScreen.logoSize));
+ boolean logo = (bg_logo_url != null || uod_logo_url != null);
+ StringBuilder sb = new StringBuilder();
+ sb.append(
+ "<br><br>Jalview is free software released under GPLv3.<br><br>Development is managed by The Barton Group, University of Dundee, Scotland, UK.");
+ if (logo)
+ {
+ sb.append("<br>");
+ }
+ sb.append(bg_logo_url == null ? ""
+ : "<img alt=\"Barton Group logo\" src=\""
+ + bg_logo_url.toString() + "\">");
+ sb.append(uod_logo_url == null ? ""
+ : " <img alt=\"University of Dundee shield\" src=\""
+ + uod_logo_url.toString() + "\">");
+ sb.append(
+ "<br><br>For help, see <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and join <a href=\"https://discourse.jalview.org\">discourse.jalview.org</a>");
+ sb.append("<br><br>If you use Jalview, please cite:"
+ + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "<br>Bioinformatics <a href=\"https://doi.org/10.1093/bioinformatics/btp033\">doi: 10.1093/bioinformatics/btp033</a>");
+ CITATION = sb.toString();
+ }
+
+ private static final String DEFAULT_AUTHORS = "The Jalview Authors (See AUTHORS file for current list)";
+
private static int DEFAULT_MIN_WIDTH = 300;
private static int DEFAULT_MIN_HEIGHT = 250;
private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
+ public static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
+
+ public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
+
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
+ public static boolean nosplash = false;
+
/**
* news reader - null if it was never started.
*/
*/
public Desktop()
{
+ super();
/**
- * 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.
+ * 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())
+
+ doConfigureStructurePrefs();
+ setTitle(ChannelProperties.getProperty("app_name") + " "
+ + Cache.getProperty("VERSION"));
+
+ /**
+ * Set taskbar "grouped windows" name for linux desktops (works in GNOME and
+ * KDE). This uses sun.awt.X11.XToolkit.awtAppClassName which is not
+ * officially documented or guaranteed to exist, so we access it via
+ * reflection. There appear to be unfathomable criteria about what this
+ * string can contain, and it if doesn't meet those criteria then "java"
+ * (KDE) or "jalview-bin-Jalview" (GNOME) is used. "Jalview", "Jalview
+ * Develop" and "Jalview Test" seem okay, but "Jalview non-release" does
+ * not. The reflection access may generate a warning: WARNING: An illegal
+ * reflective access operation has occurred WARNING: Illegal reflective
+ * access by jalview.gui.Desktop () to field
+ * sun.awt.X11.XToolkit.awtAppClassName which I don't think can be avoided.
+ */
+ if (Platform.isLinux())
{
- doVamsasClientCheck();
+ try
+ {
+ Toolkit xToolkit = Toolkit.getDefaultToolkit();
+ Field[] declaredFields = xToolkit.getClass().getDeclaredFields();
+ Field awtAppClassNameField = null;
+
+ if (Arrays.stream(declaredFields)
+ .anyMatch(f -> f.getName().equals("awtAppClassName")))
+ {
+ awtAppClassNameField = xToolkit.getClass()
+ .getDeclaredField("awtAppClassName");
+ }
+
+ String title = ChannelProperties.getProperty("app_name");
+ if (awtAppClassNameField != null)
+ {
+ awtAppClassNameField.setAccessible(true);
+ awtAppClassNameField.set(xToolkit, title);
+ }
+ else
+ {
+ jalview.bin.Console.debug("XToolkit: awtAppClassName not found");
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Console.debug("Error setting awtAppClassName");
+ jalview.bin.Console.trace(Cache.getStackTraceString(e));
+ }
}
- 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);
+ setIconImages(ChannelProperties.getIconList());
+
+ addWindowListener(new WindowAdapter()
+ {
+
+ @Override
+ public void windowClosing(WindowEvent ev)
+ {
+ quit();
+ }
+ });
+
+ boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false);
+
+ boolean showjconsole = 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);
+
+ // BH 2018 - just an experiment to try unclipped JInternalFrames.
+ if (Platform.isJS())
+ {
+ getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
+ }
+
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()
+ (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+ : Platform.isAMacAndNotJS()
? new AquaInternalFrameManager(
desktop.getDesktopManager())
: desktop.getDesktopManager())));
int yPos = Math.max(5, (screenSize.height - 650) / 2);
setBounds(xPos, yPos, 900, 650);
}
-
- boolean doFullLoad = /** @j2sNative ! */true;
-
- if (doFullLoad) {
-
- 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"));
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ jconsole = new Console(this, showjconsole);
+ jconsole.setHeader(Cache.getVersionDetailsForConsole());
showConsole(showjconsole);
showNews.setVisible(false);
checkURLLinks();
// Spawn a thread that shows the splashscreen
-
- SwingUtilities.invokeLater(new Runnable()
+ if (!nosplash)
{
- @Override
- public void run()
+ SwingUtilities.invokeLater(new Runnable()
{
- new SplashScreen();
- }
- });
+ @Override
+ public void run()
+ {
+ new SplashScreen(true);
+ }
+ });
+ }
- // Thread off a new instance of the file chooser - this reduces the time it
+ // 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.");
+ jalview.bin.Console.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.");
+ jalview.bin.Console.debug("Filechooser init thread finished.");
}
}).start();
// Add the service change listener
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- Cache.log.debug("Firing service changed event for "
- + evt.getNewValue());
+ jalview.bin.Console
+ .debug("Firing service changed event for "
+ + evt.getNewValue());
JalviewServicesChanged(evt);
}
-
});
-
- }
+ }
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
}
});
desktop.addMouseListener(ma);
-
}
/**
// configure services
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(this);
- if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
+ if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
{
- ssm.setAddTempFacAnnot(jalview.bin.Cache
- .getDefault(Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(jalview.bin.Cache
- .getDefault(Preferences.STRUCT_FROM_PDB, true));
+ ssm.setAddTempFacAnnot(
+ Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+ ssm.setProcessSecondaryStructure(
+ Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+ // JAL-3915 - RNAView is no longer an option so this has no effect
ssm.setSecStructServices(
- jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true));
+ Cache.getDefault(Preferences.USE_RNAVIEW, false));
}
else
{
@Override
public void run()
{
- Cache.log.debug("Starting news thread.");
+ jalview.bin.Console.debug("Starting news thread.");
jvnews = new BlogReader(me);
showNews.setVisible(true);
- Cache.log.debug("Completed news thread.");
+ jalview.bin.Console.debug("Completed news thread.");
}
}).start();
}
public void getIdentifiersOrgData()
{
- // Thread off the identifiers fetcher
- new Thread(new Runnable()
- {
- @Override
- public void run()
+ if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
+ {// Thread off the identifiers fetcher
+ new Thread(new Runnable()
{
- Cache.log.debug("Downloading data from identifiers.org");
- UrlDownloadClient client = new UrlDownloadClient();
- try
- {
- client.download(IdOrgSettings.getUrl(),
- IdOrgSettings.getDownloadLocation());
- } catch (IOException e)
+ @Override
+ public void run()
{
- Cache.log.debug("Exception downloading identifiers.org data"
- + e.getMessage());
+ jalview.bin.Console
+ .debug("Downloading data from identifiers.org");
+ try
+ {
+ UrlDownloadClient.download(IdOrgSettings.getUrl(),
+ IdOrgSettings.getDownloadLocation());
+ } catch (IOException e)
+ {
+ jalview.bin.Console
+ .debug("Exception downloading identifiers.org data"
+ + e.getMessage());
+ }
}
- }
- }).start();
- ;
+ }).start();
+ ;
+ }
}
@Override
void showNews(boolean visible)
{
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+ jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
if (visible && !jvnews.isVisible())
{
{
// TODO: lock aspect ratio for scaling desktop Bug #0058199
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
- String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
- String width = jalview.bin.Cache
- .getProperty(windowName + "SCREEN_WIDTH");
- String height = jalview.bin.Cache
- .getProperty(windowName + "SCREEN_HEIGHT");
+ String x = Cache.getProperty(windowName + "SCREEN_X");
+ String y = Cache.getProperty(windowName + "SCREEN_Y");
+ String width = Cache.getProperty(windowName + "SCREEN_WIDTH");
+ String height = Cache.getProperty(windowName + "SCREEN_HEIGHT");
if ((x != null) && (y != null) && (width != null) && (height != null))
{
int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
iw = Integer.parseInt(width), ih = Integer.parseInt(height);
- if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
+ if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
{
// attempt #1 - try to cope with change in screen geometry - this
// version doesn't preserve original jv aspect ratio.
// take ratio of current screen size vs original screen size.
- double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(
- jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
- double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(
- jalview.bin.Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
+ double sw = ((1f * screenSize.width) / (1f * Integer
+ .parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+ double sh = ((1f * screenSize.height) / (1f * Integer
+ .parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
// rescale the bounds depending upon the current screen geometry.
ix = (int) (ix * sw);
iw = (int) (iw * sw);
ih = (int) (ih * sh);
while (ix >= screenSize.width)
{
- jalview.bin.Cache.log.debug(
+ jalview.bin.Console.debug(
"Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
while (iy >= screenSize.height)
{
- jalview.bin.Cache.log.debug(
+ jalview.bin.Console.debug(
"Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- jalview.bin.Cache.log.debug(
+ jalview.bin.Console.debug(
"Got last known dimensions for " + windowName + ": x:" + ix
+ " y:" + iy + " width:" + iw + " height:" + ih);
}
return null;
}
- private void doVamsasClientCheck()
- {
- if (Cache.vamsasJarsPresent())
- {
- setupVamsasDisconnectedGui();
- VamsasMenu.setVisible(true);
- final Desktop us = this;
- VamsasMenu.addMenuListener(new MenuListener()
- {
- // this listener remembers when the menu was first selected, and
- // doesn't rebuild the session list until it has been cleared and
- // reselected again.
- boolean refresh = true;
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- refresh = true;
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- refresh = true;
- }
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- if (refresh)
- {
- us.buildVamsasStMenu();
- refresh = false;
- }
- }
- });
- vamsasStart.setVisible(true);
- }
- }
-
void showPasteMenu(int x, int y)
{
JPopupMenu popup = new JPopupMenu();
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)
{
}
/*
- * add an entry for the new frame in the Window menu
- * (and remove it when the frame is closed)
+ * 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);
frame.addInternalFrameListener(new InternalFrameAdapter()
PaintRefresher.RemoveComponent(frame);
/*
- * defensive check to prevent frames being
- * added half off the window
+ * defensive check to prevent frames being added half off the window
*/
if (openFrameCount > 0)
{
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
windowMenu.remove(menuItem);
- };
+ }
});
menuItem.addActionListener(new ActionListener()
frame.setIcon(false);
} catch (java.beans.PropertyVetoException ex)
{
- // System.err.println(ex.toString());
+
}
}
});
{
} catch (java.lang.ClassCastException cex)
{
- Cache.log.warn(
- "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+ jalview.bin.Console.warn(
+ "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
cex);
}
}
/**
- * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the
- * window
+ * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
+ * the window
*
* @param frame
*/
KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
InputEvent.CTRL_DOWN_MASK);
KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
+ ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
InputMap inputMap = frame
.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
{
format = new IdentifyFile().identify(file, protocol);
}
-
+ if (file instanceof File)
+ {
+ Platform.cacheFileData((File) file);
+ }
new FileLoader().LoadFile(null, file, protocol, format);
}
public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser chooser = JalviewFileChooser
- .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ JalviewFileChooser chooser = JalviewFileChooser.forRead(
+ Cache.getProperty("LAST_DIRECTORY"), fileFormat,
+ BackupFiles.getEnabled());
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()
{
/*
* Call IdentifyFile to verify the file contains what its extension implies.
- * Skip this step for dynamically added file formats, because
- * IdentifyFile does not know how to recognise them.
+ * Skip this step for dynamically added file formats, because IdentifyFile does
+ * not know how to recognise them.
*/
if (FileFormats.getInstance().isIdentifiable(format))
{
new FileLoader().LoadFile(viewport, selectedFile,
DataSourceType.FILE, format);
}
- }).openDialog(this);
+ });
+ chooser.showOpenDialog(this);
}
/**
JPanel panel = new JPanel(new GridLayout(2, 1));
panel.add(label);
-
+
/*
- * the URL to fetch is
- * Java: an editable combobox with history
- * JS: (pending JAL-3038) a plain text field
+ * the URL to fetch is input in Java: an editable combobox with history JS:
+ * (pending JAL-3038) a plain text field
*/
JComponent history;
- String urlBase = "http://www.";
- if (Jalview.isJS())
+ String urlBase = "https://www.";
+ if (Platform.isJS())
{
history = new JTextField(urlBase, 35);
}
else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
JComboBox<String> asCombo = new JComboBox<>();
asCombo.setPreferredSize(new Dimension(400, 20));
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
- RunResponse action = new RunResponse(JvOptionPane.OK_OPTION) {
+ Runnable action = new Runnable()
+ {
@Override
public void run()
{
- String url = Jalview.isJS() ? ((JTextField) history).getText()
- : ((JComboBox<String>) history).getSelectedItem()
- .toString();
+ @SuppressWarnings("unchecked")
+ String url = (history instanceof JTextField
+ ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getEditor().getItem()
+ .toString().trim());
- if (url.toLowerCase().endsWith(".jar"))
+ if (url.toLowerCase(Locale.ROOT).endsWith(".jar"))
{
if (viewport != null)
{
if (format == null)
{
- String msg = MessageManager.formatMessage("label.couldnt_locate", url);
+ String msg = MessageManager
+ .formatMessage("label.couldnt_locate", url);
JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
MessageManager.getString("label.url_not_found"),
JvOptionPane.WARNING_MESSAGE);
new FileLoader().LoadFile(url, DataSourceType.URL, format);
}
}
- }};
+ }
+ };
String dialogOption = MessageManager
.getString("label.input_alignment_from_url");
- JvOptionPane.newOptionDialog(desktop).response(action)
+ JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action)
.showInternalDialog(panel, dialogOption,
JvOptionPane.YES_NO_CANCEL_OPTION,
JvOptionPane.PLAIN_MESSAGE, null, options,
public void quit()
{
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
- screen.width + "");
- jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT",
- screen.height + "");
+ Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+ Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
getWidth(), getHeight()));
private void storeLastKnownDimensions(String string, Rectangle jc)
{
- jalview.bin.Cache.log.debug("Storing last known dimensions for "
- + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ jalview.bin.Console.debug("Storing last known dimensions for " + string
+ + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ " height:" + jc.height);
- jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
- jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
- jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
- jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
+ Cache.setProperty(string + "SCREEN_X", jc.x + "");
+ Cache.setProperty(string + "SCREEN_Y", jc.y + "");
+ Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
+ Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
}
/**
@Override
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
- // StringBuffer message = getAboutMessage(false);
- // JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- //
- // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
new Thread(new Runnable()
{
@Override
public void run()
{
- new SplashScreen(true);
+ new SplashScreen(false);
}
}).start();
}
- public StringBuffer getAboutMessage(boolean shortv)
+ /**
+ * Returns the html text for the About screen, including any available version
+ * number, build details, author details and citation reference, but without
+ * the enclosing {@code html} tags
+ *
+ * @return
+ */
+ public String getAboutMessage()
{
- StringBuffer message = new StringBuffer();
- message.append("<html>");
- if (shortv)
- {
- message.append("<h1><strong>Version: "
- + jalview.bin.Cache.getProperty("VERSION")
- + "</strong></h1>");
- message.append("<strong>Last Updated: <em>"
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "</em></strong>");
+ StringBuilder message = new StringBuilder(1024);
+ message.append("<div style=\"font-family: sans-serif;\">")
+ .append("<h1><strong>Version: ")
+ .append(Cache.getProperty("VERSION")).append("</strong></h1>")
+ .append("<strong>Built: <em>")
+ .append(Cache.getDefault("BUILD_DATE", "unknown"))
+ .append("</em> from ").append(Cache.getBuildDetailsForSplash())
+ .append("</strong>");
- }
- else
+ String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
+ if (latestVersion.equals("Checking"))
{
-
- message.append("<strong>Version "
- + jalview.bin.Cache.getProperty("VERSION")
- + "; last updated: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
- }
-
- 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")))
+ else if (!latestVersion.equals(Cache.getProperty("VERSION")))
{
boolean red = false;
- if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
+ if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT)
.indexOf("automated build") == -1)
{
red = true;
message.append("<div style=\"color: #FF0000;font-style: bold;\">");
}
- message.append("<br>!! Version "
- + jalview.bin.Cache.getDefault("LATEST_VERSION",
- "..Checking..")
- + " is available for download from "
- + jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
- + " !!");
+ message.append("<br>!! Version ")
+ .append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
+ .append(" is available for download from ")
+ .append(Cache.getDefault("www.jalview.org",
+ "https://www.jalview.org"))
+ .append(" !!");
if (red)
{
message.append("</div>");
}
}
- message.append("<br>Authors: " + jalview.bin.Cache.getDefault(
- "AUTHORFNAMES",
- "The Jalview Authors (See AUTHORS file for current list)")
- + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
- + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
- + "<br><br>If you use Jalview, please cite:"
- + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
- + "</html>");
- return message;
+ message.append("<br>Authors: ");
+ message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
+ message.append(CITATION);
+
+ message.append("</div>");
+
+ return message.toString();
}
/**
{
try
{
- if (Jalview.isJS())
+ if (Platform.isJS())
{
- BrowserLauncher.openURL("http://www.jalview.org/help.html");
+ BrowserLauncher.openURL("https://www.jalview.org/help.html");
}
else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
Help.showHelpWindow();
}
}
Jalview.setCurrentAlignFrame(null);
System.out.println("ALL CLOSED");
- if (v_client != null)
- {
- // TODO clear binding to vamsas document objects on close_all
- }
/*
* reset state of singleton objects as appropriate (clear down session state
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
- jalview.bin.Cache.log.debug("Collecting garbage...");
+ jalview.bin.Console.debug("Collecting garbage...");
System.gc();
- jalview.bin.Cache.log.debug("Finished garbage collection.");
+ jalview.bin.Console.debug("Finished garbage collection.");
}
/*
* (non-Javadoc)
*
- * @see
- * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
- * )
+ * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.
+ * ActionEvent )
*/
@Override
protected void showMemusage_actionPerformed(ActionEvent e)
@Override
protected void preferences_actionPerformed(ActionEvent e)
{
- new Preferences();
+ Preferences.openPreferences();
}
/**
* Jalview project file
*/
@Override
- public void saveState_actionPerformed(boolean asCastor)
+ public void saveState_actionPerformed()
{
- JalviewFileChooser chooser = new JalviewFileChooser(
- asCastor ? "jvp" : "jvx",
- "Jalview Project");
+ saveState_actionPerformed(false);
+ }
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_state"));
- int option = chooser.showSaveDialog(this);
- if (option == JalviewFileChooser.APPROVE_OPTION)
+ 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();
+
+ // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+ // saveAs="+saveAs+", Backups
+ // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
+
+ boolean approveSave = false;
+ if (!autoSave)
{
- 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());
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- choice.getParent());
+ { chosenFile.getName() }), chosenFile.hashCode());
+ Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- if (asCastor)
- {
- new Jalview2XML().saveState(choice);
- }
- else
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile)
+ : null;
+
+ new Jalview2XML().saveState(
+ doBackup ? backupfiles.getTempFile() : chosenFile);
+
+ if (doBackup)
{
- new jalview.project.Jalview2XML().saveState(choice);
+ 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);
- JvOptionPane.showMessageDialog(Desktop.this,
+ jalview.bin.Console.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();
- }
+ }
}
- void setProjectFile(File choice)
+ @Override
+ public void saveAsState_actionPerformed(ActionEvent e)
+ {
+ saveState_actionPerformed(true);
+ }
+
+ private 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(boolean asCastor)
- {
- // TODO: GET RID OF .JVX BEFORE RELEASE JIM!
- final String[] suffix = asCastor ? new String[] { "jvp", "jar" }
- : new String[]
- { "jvx" };
- final String[] desc = asCastor
- ? new String[]
- { "Jalview Project", "Jalview Project (old)" }
- : new String[]
- { "Jalview Project" };
+ 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"), suffix,
- desc,
- "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"));
- chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
@Override
public void run()
{
File selectedFile = chooser.getSelectedFile();
setProjectFile(selectedFile);
- final String choice = selectedFile.getAbsolutePath();
+ String choice = selectedFile.getAbsolutePath();
Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
new Thread(new Runnable()
{
@Override
public void run()
{
- try {
- if (asCastor)
- {
- new Jalview2XML().loadJalviewAlign(choice);
- }
- else
- {
- new jalview.project.Jalview2XML().loadJalviewAlign(choice);
- }
+ try
+ {
+ new Jalview2XML().loadJalviewAlign(selectedFile);
} catch (OutOfMemoryError oom)
{
- new OOMWarning("Whilst loading project from " + choice, 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);
+ jalview.bin.Console.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);
}
}
- }).start();
+ }, "Project Loader").start();
}
});
-
+
chooser.showOpenDialog(this);
}
return;
}
+ // FIXME: ideally should use UI interface API
+ FeatureSettings viewFeatureSettings = (af.featureSettings != null
+ && af.featureSettings.isOpen()) ? af.featureSettings : null;
+ Rectangle fsBounds = af.getFeatureSettingsGeometry();
for (int i = 0; i < size; i++)
{
AlignmentPanel ap = af.alignPanels.get(i);
+
AlignFrame newaf = new AlignFrame(ap);
+ // transfer reference for existing feature settings to new alignFrame
+ if (ap == af.alignPanel)
+ {
+ if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
+ {
+ newaf.featureSettings = viewFeatureSettings;
+ }
+ newaf.setFeatureSettingsGeometry(fsBounds);
+ }
+
/*
- * Restore the view's last exploded frame geometry if known. Multiple
- * views from one exploded frame share and restore the same (frame)
- * position and size.
+ * Restore the view's last exploded frame geometry if known. Multiple views from
+ * one exploded frame share and restore the same (frame) position and size.
*/
Rectangle geometry = ap.av.getExplodedGeometry();
if (geometry != null)
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
+ // and materialise a new feature settings dialog instance for the new
+ // alignframe
+ // (closes the old as if 'OK' was pressed)
+ if (ap == af.alignPanel && newaf.featureSettings != null
+ && newaf.featureSettings.isOpen()
+ && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
+ {
+ newaf.showFeatureSettingsUI();
+ }
}
+ af.featureSettings = null;
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
/**
* Gather expanded views (separate AlignFrame's) with the same sequence set
- * identifier back in to this frame as additional views, and close the expanded
- * views. Note the expanded frames may themselves have multiple views. We take
- * the lot.
+ * identifier back in to this frame as additional views, and close the
+ * expanded views. Note the expanded frames may themselves have multiple
+ * views. We take the lot.
*
* @param source
*/
source.viewport.setExplodedGeometry(source.getBounds());
JInternalFrame[] frames = desktop.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
-
for (int t = 0; t < frames.length; t++)
{
if (frames[t] instanceof AlignFrame && frames[t] != source)
if (gatherThis)
{
- af.alignPanels.clear();
- af.closeMenuItem_actionPerformed(true);
- }
- }
- }
-
- }
-
- jalview.gui.VamsasApplication v_client = null;
-
- @Override
- public void vamsasImport_actionPerformed(ActionEvent e)
- {
- // TODO: JAL-3048 not needed for Jalview-JS
-
- if (v_client == null)
- {
- // Load and try to start a session.
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.open_saved_vamsas_session"));
- chooser.setToolTipText(MessageManager.getString(
- "label.select_vamsas_session_opened_as_new_vamsas_session"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String fle = chooser.getSelectedFile().toString();
- if (!vamsasImport(chooser.getSelectedFile()))
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.couldnt_import_as_vamsas_session",
- new Object[]
- { fle }),
- MessageManager
- .getString("label.vamsas_document_import_failed"),
- JvOptionPane.ERROR_MESSAGE);
- }
- }
- }
- else
- {
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- }
- }
-
- /**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- *
- * @param file
- * @return true if import was a success and a session was started.
- */
- public boolean vamsasImport(URL url)
- {
- // TODO: create progress bar
- if (v_client != null)
- {
-
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- return false;
- }
-
- try
- {
- // copy the URL content to a temporary local file
- // TODO: be a bit cleverer here with nio (?!)
- File file = File.createTempFile("vdocfromurl", ".vdj");
- FileOutputStream fos = new FileOutputStream(file);
- BufferedInputStream bis = new BufferedInputStream(url.openStream());
- byte[] buffer = new byte[2048];
- int ln;
- while ((ln = bis.read(buffer)) > -1)
- {
- fos.write(buffer, 0, ln);
- }
- bis.close();
- fos.close();
- v_client = new jalview.gui.VamsasApplication(this, file,
- url.toExternalForm());
- } catch (Exception ex)
- {
- jalview.bin.Cache.log.error(
- "Failed to create new vamsas session from contents of URL "
- + url,
- ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- return v_client.inSession();
- }
-
- /**
- * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
- *
- * @param file
- * @return true if import was a success and a session was started.
- */
- public boolean vamsasImport(File file)
- {
- if (v_client != null)
- {
-
- jalview.bin.Cache.log.error(
- "Implementation error - load session from a running session is not supported.");
- return false;
- }
-
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- try
- {
- v_client = new jalview.gui.VamsasApplication(this, file, null);
- } catch (Exception ex)
- {
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- jalview.bin.Cache.log.error(
- "New vamsas session from existing session file failed:", ex);
- return false;
- }
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- setProgressBar(MessageManager.formatMessage(
- "status.importing_vamsas_session_from", new Object[]
- { file.getName() }), file.hashCode());
- return v_client.inSession();
- }
-
- public boolean joinVamsasSession(String mysesid)
- {
- if (v_client != null)
- {
- throw new Error(MessageManager
- .getString("error.try_join_vamsas_session_another"));
- }
- if (mysesid == null)
- {
- throw new Error(
- MessageManager.getString("error.invalid_vamsas_session_id"));
- }
- v_client = new VamsasApplication(this, mysesid);
- setupVamsasConnectedGui();
- v_client.initial_update();
- return (v_client.inSession());
- }
-
- @Override
- public void vamsasStart_actionPerformed(ActionEvent e)
- {
- if (v_client == null)
- {
- // Start a session.
- // we just start a default session for moment.
- /*
- * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- * getProperty("LAST_DIRECTORY"));
- *
- * chooser.setFileView(new JalviewFileView());
- * chooser.setDialogTitle("Load Vamsas file");
- * chooser.setToolTipText("Import");
- *
- * int value = chooser.showOpenDialog(this);
- *
- * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
- * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
- */
- v_client = new VamsasApplication(this);
- setupVamsasConnectedGui();
- v_client.initial_update(); // TODO: thread ?
- }
- else
- {
- // store current data in session.
- v_client.push_update(); // TODO: thread
- }
- }
-
- protected void setupVamsasConnectedGui()
- {
- vamsasStart.setText(MessageManager.getString("label.session_update"));
- vamsasSave.setVisible(true);
- vamsasStop.setVisible(true);
- vamsasImport.setVisible(false); // Document import to existing session is
- // not possible for vamsas-client-1.0.
- }
-
- protected void setupVamsasDisconnectedGui()
- {
- vamsasSave.setVisible(false);
- vamsasStop.setVisible(false);
- vamsasImport.setVisible(true);
- vamsasStart
- .setText(MessageManager.getString("label.new_vamsas_session"));
- }
-
- @Override
- public void vamsasStop_actionPerformed(ActionEvent e)
- {
- if (v_client != null)
- {
- v_client.end_session();
- v_client = null;
- setupVamsasDisconnectedGui();
- }
- }
-
- protected void buildVamsasStMenu()
- {
- if (v_client == null)
- {
- String[] sess = null;
- try
- {
- sess = VamsasApplication.getSessionList();
- } catch (Exception e)
- {
- jalview.bin.Cache.log.warn("Problem getting current sessions list.",
- e);
- sess = null;
- }
- if (sess != null)
- {
- jalview.bin.Cache.log.debug(
- "Got current sessions list: " + sess.length + " entries.");
- VamsasStMenu.removeAll();
- for (int i = 0; i < sess.length; i++)
- {
- JMenuItem sessit = new JMenuItem();
- sessit.setText(sess[i]);
- sessit.setToolTipText(MessageManager
- .formatMessage("label.connect_to_session", new Object[]
- { sess[i] }));
- final Desktop dsktp = this;
- final String mysesid = sess[i];
- sessit.addActionListener(new ActionListener()
+ if (af.featureSettings != null && af.featureSettings.isOpen())
{
-
- @Override
- public void actionPerformed(ActionEvent e)
+ if (source.featureSettings == null)
{
- if (dsktp.v_client == null)
- {
- Thread rthr = new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- dsktp.v_client = new VamsasApplication(dsktp, mysesid);
- dsktp.setupVamsasConnectedGui();
- dsktp.v_client.initial_update();
- }
-
- });
- rthr.start();
- }
- };
- });
- VamsasStMenu.add(sessit);
+ // preserve the feature settings geometry for this frame
+ source.featureSettings = af.featureSettings;
+ source.setFeatureSettingsGeometry(
+ af.getFeatureSettingsGeometry());
+ }
+ else
+ {
+ // close it and forget
+ af.featureSettings.close();
+ }
+ }
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
}
- // don't show an empty menu.
- VamsasStMenu.setVisible(sess.length > 0);
-
- }
- else
- {
- jalview.bin.Cache.log.debug("No current vamsas sessions.");
- VamsasStMenu.removeAll();
- VamsasStMenu.setVisible(false);
}
}
- else
- {
- // Not interested in the content. Just hide ourselves.
- VamsasStMenu.setVisible(false);
- }
- }
-
- @Override
- public void vamsasSave_actionPerformed(ActionEvent e)
- {
- // TODO: JAL-3048 not needed for Jalview-JS
- if (v_client != null)
+ // refresh the feature setting UI for the source frame if it exists
+ if (source.featureSettings != null && source.featureSettings.isOpen())
{
- // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- JalviewFileChooser chooser = new JalviewFileChooser("vdj",
- "Vamsas Document");
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_vamsas_document_archive"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- java.io.File choice = chooser.getSelectedFile();
- JPanel progpanel = addProgressPanel(MessageManager
- .formatMessage("label.saving_vamsas_doc", new Object[]
- { choice.getName() }));
- Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- String warnmsg = null;
- String warnttl = null;
- try
- {
- v_client.vclient.storeDocument(choice);
- } catch (Error ex)
- {
- warnttl = "Serious Problem saving Vamsas Document";
- warnmsg = ex.toString();
- jalview.bin.Cache.log
- .error("Error Whilst saving document to " + choice, ex);
-
- } catch (Exception ex)
- {
- warnttl = "Problem saving Vamsas Document.";
- warnmsg = ex.toString();
- jalview.bin.Cache.log.warn(
- "Exception Whilst saving document to " + choice, ex);
-
- }
- removeProgressPanel(progpanel);
- if (warnmsg != null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-
- warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
- }
- }
+ source.showFeatureSettingsUI();
}
- }
-
- JPanel vamUpdate = null;
-
- /**
- * hide vamsas user gui bits when a vamsas document event is being handled.
- *
- * @param b
- * true to hide gui, false to reveal gui
- */
- public void setVamsasUpdate(boolean b)
- {
- Cache.log.debug("Setting gui for Vamsas update "
- + (b ? "in progress" : "finished"));
- if (vamUpdate != null)
- {
- this.removeProgressPanel(vamUpdate);
- }
- if (b)
- {
- vamUpdate = this.addProgressPanel(
- MessageManager.getString("label.updating_vamsas_session"));
- }
- vamsasStart.setVisible(!b);
- vamsasStop.setVisible(!b);
- vamsasSave.setVisible(!b);
}
public JInternalFrame[] getAllFrames()
while (li.hasNext())
{
String link = li.next();
- if (link.contains(SEQUENCE_ID)
+ if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID)
&& !UrlConstants.isDefaultString(link))
{
check = true;
/**
* Proxy class for JDesktopPane which optionally displays the current memory
- * usage and highlights the desktop area with a red bar if free memory runs low.
+ * usage and highlights the desktop area with a red bar if free memory runs
+ * low.
*
* @author AMW
*/
- public class MyDesktopPane extends JDesktopPane
- implements Runnable
+ public class MyDesktopPane extends JDesktopPane implements Runnable
{
private static final float ONE_MB = 1048576f;
10, getHeight() - fm.getHeight());
}
}
+
+ // output debug scale message. Important for jalview.bin.HiDPISettingTest2
+ Desktop.debugScaleMessage(Desktop.getDesktop().getGraphics());
}
}
openGroovyConsole();
} catch (Exception ex)
{
- jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+ jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
/*
* We allow only one console at a time, so that AlignFrame menu option
- * 'Calculate | Run Groovy script' is unambiguous.
- * Disable 'Groovy Console', and enable 'Run script', when the console is
- * opened, and the reverse when it is closed
+ * 'Calculate | Run Groovy script' is unambiguous. Disable 'Groovy Console', and
+ * enable 'Run script', when the console is opened, and the reverse when it is
+ * closed
*/
Window window = (Window) groovyConsole.getFrame();
window.addWindowListener(new WindowAdapter()
((Window) groovyConsole.getFrame()).setVisible(true);
/*
- * if we got this far, enable 'Run Groovy' in AlignFrame menus
- * and disable opening a second console
+ * if we got this far, enable 'Run Groovy' in AlignFrame menus and disable
+ * opening a second console
*/
enableExecuteGroovy(true);
}
/**
- * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding
- * when opened
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
+ * binding when opened
*/
protected void addQuitHandler()
{
- getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
- .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()),
+ getRootPane()
+ .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke
+ .getKeyStroke(KeyEvent.VK_Q,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx()),
"Quit");
getRootPane().getActionMap().put("Quit", new AbstractAction()
{
public void enableExecuteGroovy(boolean enabled)
{
/*
- * disable opening a second Groovy console
- * (or re-enable when the console is closed)
+ * disable opening a second Groovy console (or re-enable when the console is
+ * closed)
*/
groovyShell.setEnabled(!enabled);
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(
}
/**
- * This will return the first AlignFrame holding the given viewport instance. It
- * will break if there are more than one AlignFrames viewing a particular av.
+ * This will return the first AlignFrame holding the given viewport instance.
+ * It will break if there are more than one AlignFrames viewing a particular
+ * av.
*
* @param viewport
* @return alignFrame for viewport
public VamsasApplication getVamsasApplication()
{
- return v_client;
+ // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
+ return null;
}
this.inBatchMode = inBatchMode;
}
+ /**
+ * start service discovery and wait till it is done
+ */
public void startServiceDiscovery()
{
startServiceDiscovery(false);
}
+ /**
+ * start service discovery threads - blocking or non-blocking
+ *
+ * @param blocking
+ */
public void startServiceDiscovery(boolean blocking)
{
+ startServiceDiscovery(blocking, false);
+ }
+
+ /**
+ * start service discovery threads
+ *
+ * @param blocking
+ * - false means call returns immediately
+ * @param ignore_SHOW_JWS2_SERVICES_preference
+ * - when true JABA services are discovered regardless of user's JWS2
+ * discovery preference setting
+ */
+ public void startServiceDiscovery(boolean blocking,
+ boolean ignore_SHOW_JWS2_SERVICES_preference)
+ {
boolean alive = true;
Thread t0 = null, t1 = null, t2 = null;
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
(t0 = new Thread(discoverer)).start();
}
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ if (ignore_SHOW_JWS2_SERVICES_preference
+ || Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
.startDiscoverer(changeSupport);
/*
* JalviewDialog jd =new JalviewDialog() {
*
- * @Override protected void cancelPressed() { // TODO
- * Auto-generated method stub
+ * @Override protected void cancelPressed() { // TODO Auto-generated method stub
*
- * }@Override protected void okPressed() { // TODO
- * Auto-generated method stub
+ * }@Override protected void okPressed() { // TODO Auto-generated method stub
*
- * }@Override protected void raiseClosed() { // TODO
- * Auto-generated method stub
+ * }@Override protected void raiseClosed() { // TODO Auto-generated method stub
*
- * } }; jd.initDialogFrame(new
- * JLabel("<html><table width=\"450\"><tr><td>" + ermsg +
+ * } }; jd.initDialogFrame(new JLabel("<html><table width=\"450\"><tr><td>" +
+ * ermsg +
* "<br/>It may be that you have invalid JABA URLs in your web service preferences,"
* + " or mis-configured HTTP proxy settings.<br/>" +
- * "Check the <em>Connections</em> and <em>Web services</em> tab of the"
- * +
- * " Tools->Preferences dialog box to change them.</td></tr></table></html>"
- * ), true, true, "Web Service Configuration Problem", 450,
- * 400);
+ * "Check the <em>Connections</em> and <em>Web services</em> tab of the" +
+ * " Tools->Preferences dialog box to change them.</td></tr></table></html>" ),
+ * true, true, "Web Service Configuration Problem", 450, 400);
*
* jd.waitForInput();
*/
}
else
{
- Cache.log.error(
+ jalview.bin.Console.error(
"Errors reported by JABA discovery service. Check web services preferences.\n"
+ ermsg);
}
{
if (url != null)
{
- if (Cache.log != null)
- {
- Cache.log.error("Couldn't handle string " + url + " as a URL.");
- }
- else
- {
- System.err.println(
- "Couldn't handle string " + url + " as a URL.");
- }
+ jalview.bin.Console
+ .error("Couldn't handle string " + url + " as a URL.");
}
// ignore any exceptions due to dud links.
}
} catch (InterruptedException x)
{
}
- ;
}
if (instance == null)
{
SwingUtilities.invokeAndWait(prompter);
} catch (Exception q)
{
- Cache.log.warn("Unexpected Exception in dialog thread.", q);
+ jalview.bin.Console.warn("Unexpected Exception in dialog thread.",
+ q);
}
}
});
public void exportImage(Graphics g) throws Exception
{
paintAll(g);
- Cache.log.info("Successfully written snapshot to file "
+ jalview.bin.Console.info("Successfully written snapshot to file "
+ of.getAbsolutePath());
}
};
/**
* Explode the views in the given SplitFrame into separate SplitFrame windows.
- * This respects (remembers) any previous 'exploded geometry' i.e. the size and
- * location last time the view was expanded (if any). However it does not
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size
+ * and location last time the view was expanded (if any). However it does not
* remember the split pane divider location - this is set to match the
* 'exploding' frame.
*
}
/*
- * Processing in reverse order works, forwards order leaves the first panels
- * not visible. I don't know why!
+ * Processing in reverse order works, forwards order leaves the first panels not
+ * visible. I don't know why!
*/
for (int i = viewCount - 1; i >= 0; i--)
{
/*
- * Make new top and bottom frames. These take over the respective
- * AlignmentPanel objects, including their AlignmentViewports, so the
- * cdna/protein relationships between the viewports is carried over to the
- * new split frames.
+ * Make new top and bottom frames. These take over the respective AlignmentPanel
+ * objects, including their AlignmentViewports, so the cdna/protein
+ * relationships between the viewports is carried over to the new split frames.
*
* explodedGeometry holds the (x, y) position of the previously exploded
* SplitFrame, and the (width, height) of the AlignFrame component
}
/*
- * Clear references to the panels (now relocated in the new SplitFrames)
- * before closing the old SplitFrame.
+ * Clear references to the panels (now relocated in the new SplitFrames) before
+ * closing the old SplitFrame.
*/
topPanels.clear();
bottomPanels.clear();
Transferable t) throws Exception
{
- // BH 2018 changed List<String> to List<Object> to allow for File from SwingJS
-
- // DataFlavor[] flavors = t.getTransferDataFlavors();
- // for (int i = 0; i < flavors.length; i++) {
- // if (flavors[i].isFlavorJavaFileListType()) {
- // evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- // List<File> list = (List<File>) t.getTransferData(flavors[i]);
- // for (int j = 0; j < list.size(); j++) {
- // File file = (File) list.get(j);
- // byte[] data = getDroppedFileBytes(file);
- // fileName.setText(file.getName() + " - " + data.length + " " +
- // evt.getLocation());
- // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent();
- // target.setText(new String(data));
- // }
- // dtde.dropComplete(true);
- // return;
- // }
- //
-
DataFlavor uriListFlavor = new DataFlavor(
"text/uri-list;class=java.lang.String"), urlFlavour = null;
try
"application/x-java-url; class=java.net.URL");
} catch (ClassNotFoundException cfe)
{
- Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.",
+ cfe);
}
if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
{
protocols.add(DataSourceType.URL);
files.add(url.toString());
- Cache.log.debug("Drop handled as URL dataflavor "
+ jalview.bin.Console.debug("Drop handled as URL dataflavor "
+ files.get(files.size() - 1));
return;
}
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)
{
- Cache.log.debug("URL drop handler failed.", ex);
+ jalview.bin.Console.debug("URL drop handler failed.", ex);
}
}
if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
{
// Works on Windows and MacOSX
- Cache.log.debug("Drop handled as javaFileListFlavor");
+ jalview.bin.Console.debug("Drop handled as javaFileListFlavor");
for (Object file : (List) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
String data = null;
if (t.isDataFlavorSupported(uriListFlavor))
{
- Cache.log.debug("Drop handled as uriListFlavor");
+ jalview.bin.Console.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
data = (String) t.getTransferData(uriListFlavor);
}
if (data == null)
{
// fallback to text: workaround - on OSX where there's a JVM bug
- Cache.log.debug("standard URIListFlavor failed. Trying text");
+ jalview.bin.Console
+ .debug("standard URIListFlavor failed. Trying text");
// try text fallback
DataFlavor textDf = new DataFlavor(
"text/plain;class=java.lang.String");
data = (String) t.getTransferData(textDf);
}
- Cache.log.debug("Plain text drop content returned "
+ jalview.bin.Console.debug("Plain text drop content returned "
+ (data == null ? "Null - failed" : data));
}
{
while (protocols.size() < files.size())
{
- Cache.log.debug("Adding missing FILE protocol for "
+ jalview.bin.Console.debug("Adding missing FILE protocol for "
+ files.get(protocols.size()));
protocols.add(DataSourceType.FILE);
}
continue;
}
java.net.URI uri = new java.net.URI(s);
- if (uri.getScheme().toLowerCase().startsWith("http"))
+ if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http"))
{
protocols.add(DataSourceType.URL);
files.add(uri.toString());
}
}
- if (Cache.log.isDebugEnabled())
+ if (jalview.bin.Console.isDebugEnabled())
{
if (data == null || !added)
{
if (t.getTransferDataFlavors() != null
&& t.getTransferDataFlavors().length > 0)
{
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Couldn't resolve drop data. Here are the supported flavors:");
for (DataFlavor fl : t.getTransferDataFlavors())
{
- Cache.log.debug(
+ jalview.bin.Console.debug(
"Supported transfer dataflavor: " + fl.toString());
Object df = t.getTransferData(fl);
if (df != null)
{
- Cache.log.debug("Retrieves: " + df);
+ jalview.bin.Console.debug("Retrieves: " + df);
}
else
{
- Cache.log.debug("Retrieved nothing");
+ jalview.bin.Console.debug("Retrieved nothing");
}
}
}
else
{
- Cache.log.debug("Couldn't resolve dataflavor for drop: "
- + t.toString());
+ jalview.bin.Console
+ .debug("Couldn't resolve dataflavor for drop: "
+ + t.toString());
}
}
}
}
- if (Platform.isWindows())
-
+ if (Platform.isWindowsAndNotJS())
{
- Cache.log.debug("Scanning dropped content for Windows Link Files");
+ jalview.bin.Console
+ .debug("Scanning dropped content for Windows Link Files");
// resolve any .lnk files in the file drop
for (int f = 0; f < files.size(); f++)
{
- String source = files.get(f).toString().toLowerCase();
+ String source = files.get(f).toString().toLowerCase(Locale.ROOT);
if (protocols.get(f).equals(DataSourceType.FILE)
&& (source.endsWith(".lnk") || source.endsWith(".url")
|| source.endsWith(".site")))
File lf = (obj instanceof File ? (File) obj
: new File((String) obj));
// process link file to get a URL
- Cache.log.debug("Found potential link file: " + lf);
+ jalview.bin.Console.debug("Found potential link file: " + lf);
WindowsShortcut wscfile = new WindowsShortcut(lf);
String fullname = wscfile.getRealFilename();
protocols.set(f, FormatAdapter.checkProtocol(fullname));
files.set(f, fullname);
- Cache.log.debug("Parsed real filename " + fullname
+ jalview.bin.Console.debug("Parsed real filename " + fullname
+ " to extract protocol: " + protocols.get(f));
} catch (Exception ex)
{
- Cache.log.error(
+ jalview.bin.Console.error(
"Couldn't parse " + files.get(f) + " as a link file.",
ex);
}
}
/**
- * 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.
+ * 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
}
return result;
}
+
+ public static final String debugScaleMessage = "Desktop graphics transform scale=";
+
+ private static boolean debugScaleMessageDone = false;
+
+ public static void debugScaleMessage(Graphics g)
+ {
+ if (debugScaleMessageDone)
+ {
+ return;
+ }
+ // output used by tests to check HiDPI scaling settings in action
+ try
+ {
+ Graphics2D gg = (Graphics2D) g;
+ if (gg != null)
+ {
+ AffineTransform t = gg.getTransform();
+ double scaleX = t.getScaleX();
+ double scaleY = t.getScaleY();
+ jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)");
+ jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)");
+ debugScaleMessageDone = true;
+ }
+ else
+ {
+ jalview.bin.Console.debug("Desktop graphics null");
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Console.debug(Cache.getStackTraceString(e));
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff