*/
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.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.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.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.util.UrlConstants;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.params.ParamManager;
-import jalview.ws.utils.UrlDownloadClient;
+import java.util.Locale;
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.dnd.DropTargetListener;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
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.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Semaphore;
import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.ActionMap;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.DefaultDesktopManager;
import javax.swing.DesktopManager;
+import javax.swing.InputMap;
import javax.swing.JButton;
import javax.swing.JCheckBox;
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.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;
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";
+ protected 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 static MyDesktopPane desktop;
+ public static MyDesktopPane getDesktop()
+ {
+ // BH 2018 could use currentThread() here as a reference to a
+ // Hashtable<Thread, MyDesktopPane> in JavaScript
+ return desktop;
+ }
+
static int openFrameCount = 0;
static final int xOffset = 30;
*/
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.
*/
instance = this;
- 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);
+ 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())
+ {
+ 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));
+ }
+ }
+
+ /**
+ * APQHandlers sets handlers for About, Preferences and Quit actions
+ * peculiar to macOS's application menu. APQHandlers will check to see if a
+ * handler is supported before setting it.
+ */
+ try
+ {
+ APQHandlers.setAPQHandlers(this);
+ } catch (Exception e)
+ {
+ System.out.println("Cannot set APQHandlers");
+ // e.printStackTrace();
+ } catch (Throwable t)
+ {
+ jalview.bin.Console
+ .warn("Error setting APQHandlers: " + t.toString());
+ jalview.bin.Console.trace(Cache.getStackTraceString(t));
+ }
+ 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()
- ? new AquaInternalFrameManager(
- desktop.getDesktopManager())
- : desktop.getDesktopManager())));
+ desktop.setDesktopManager(new MyDesktopManager(
+ (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+ : Platform.isAMacAndNotJS()
+ ? new AquaInternalFrameManager(
+ desktop.getDesktopManager())
+ : desktop.getDesktopManager())));
Rectangle dims = getLastKnownDimensions("");
if (dims != null)
else
{
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2,
- 900, 650);
+ int xPos = Math.max(5, (screenSize.width - 900) / 2);
+ int yPos = Math.max(5, (screenSize.height - 650) / 2);
+ setBounds(xPos, yPos, 900, 650);
}
- 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);
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ jconsole = new Console(this, showjconsole);
+ jconsole.setHeader(Cache.getVersionDetailsForConsole());
+ showConsole(showjconsole);
+
+ showNews.setVisible(false);
- showNews.setVisible(false);
+ experimentalFeatures.setSelected(showExperimental());
+
+ getIdentifiersOrgData();
+
+ checkURLLinks();
+
+ // Spawn a thread that shows the splashscreen
+ if (!nosplash)
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ new SplashScreen(true);
+ }
+ });
+ }
- experimentalFeatures.setSelected(showExperimental());
+ // 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()
+ {
+ jalview.bin.Console.debug("Filechooser init thread started.");
+ String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+ fileFormat);
+ jalview.bin.Console.debug("Filechooser init thread finished.");
+ }
+ }).start();
+ // Add the service change listener
+ changeSupport.addJalviewPropertyChangeListener("services",
+ new PropertyChangeListener()
+ {
- getIdentifiersOrgData();
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ jalview.bin.Console
+ .debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
+ });
+ }
- checkURLLinks();
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
this.addWindowListener(new WindowAdapter()
{
}
});
desktop.addMouseListener(ma);
-
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
- // Spawn a thread that shows the splashscreen
- SwingUtilities.invokeLater(new Runnable()
- {
- @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()
- {
- 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.");
- }
- }, "InitFileChooser").start();
- // Add the service change listener
- changeSupport.addJalviewPropertyChangeListener("services",
- new PropertyChangeListener()
- {
-
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- Cache.log.debug("Firing service changed event for "
- + evt.getNewValue());
- JalviewServicesChanged(evt);
- }
-
- });
}
/**
// 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
{
{
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()
{
- 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
- addDialogThread(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();
+ ;
+ }
}
@Override
void showNews(boolean visible)
{
+ jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
+ showNews.setSelected(visible);
+ if (visible && !jvnews.isVisible())
{
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
- showNews.setSelected(visible);
- if (visible && !jvnews.isVisible())
+ new Thread(new Runnable()
{
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
- {
- long now = System.currentTimeMillis();
- Desktop.instance.setProgressBar(
- MessageManager.getString("status.refreshing_news"),
- now);
- jvnews.refreshNews();
- Desktop.instance.setProgressBar(null, now);
- jvnews.showNews();
- }
- }, "ShowNewsWindow").start();
- }
+ long now = System.currentTimeMillis();
+ Desktop.instance.setProgressBar(
+ MessageManager.getString("status.refreshing_news"), now);
+ jvnews.refreshNews();
+ Desktop.instance.setProgressBar(null, now);
+ jvnews.showNews();
+ }
+ }, "ShowNewsWindowThread").start();
}
}
{
// 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 (jalview.bin.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(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);
-
- System.gc();
- };
+ }
});
menuItem.addActionListener(new ActionListener()
}
});
+ setKeyBindings(frame);
+
desktop.add(frame);
windowMenu.add(menuItem);
{
} 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
+ *
+ * @param frame
+ */
+ private static void setKeyBindings(JInternalFrame frame)
+ {
+ @SuppressWarnings("serial")
+ final Action closeAction = new AbstractAction()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ frame.dispose();
+ }
+ };
+
+ /*
+ * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action
+ */
+ KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ InputEvent.CTRL_DOWN_MASK);
+ KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
+
+ InputMap inputMap = frame
+ .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
+ String ctrlW = ctrlWKey.toString();
+ inputMap.put(ctrlWKey, ctrlW);
+ inputMap.put(cmdWKey, ctrlW);
+
+ ActionMap actionMap = frame.getActionMap();
+ actionMap.put(ctrlW, closeAction);
+ }
+
@Override
public void lostOwnership(Clipboard clipboard, Transferable contents)
{
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
- List<String> files = new ArrayList<>();
+ List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
try
{
for (int i = 0; i < files.size(); i++)
{
- String file = files.get(i).toString();
+ // BH 2018 File or String
+ Object file = files.get(i);
+ String fileName = file.toString();
DataSourceType protocol = (protocols == null)
? DataSourceType.FILE
: protocols.get(i);
FileFormatI format = null;
- if (file.endsWith(".jar"))
+ if (fileName.endsWith(".jar"))
{
format = FileFormat.Jalview;
{
format = new IdentifyFile().identify(file, protocol);
}
-
- new FileLoader().LoadFile(file, protocol, format);
+ if (file instanceof File)
+ {
+ Platform.cacheFileData((File) file);
+ }
+ new FileLoader().LoadFile(null, file, protocol, format);
}
} catch (Exception ex)
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"));
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ @Override
+ public void run()
+ {
+ File selectedFile = chooser.getSelectedFile();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- FileFormatI format = chooser.getSelectedFormat();
+ FileFormatI format = chooser.getSelectedFormat();
- /*
- * 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.
- */
- if (FileFormats.getInstance().isIdentifiable(format))
- {
- try
- {
- format = new IdentifyFile().identify(choice, DataSourceType.FILE);
- } catch (FileFormatException e)
+ /*
+ * 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.
+ */
+ if (FileFormats.getInstance().isIdentifiable(format))
{
- // format = null; //??
+ try
+ {
+ format = new IdentifyFile().identify(selectedFile,
+ DataSourceType.FILE);
+ } catch (FileFormatException e)
+ {
+ // format = null; //??
+ }
}
- }
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE,
- format);
- }
- else
- {
- new FileLoader().LoadFile(choice, DataSourceType.FILE, format);
+ new FileLoader().LoadFile(viewport, selectedFile,
+ DataSourceType.FILE, format);
}
- }
+ });
+ 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)
// for viewing
JLabel label = new JLabel(
MessageManager.getString("label.input_file_url"));
- final 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 input in Java: an editable combobox with history JS:
+ * (pending JAL-3038) a plain text field
+ */
+ JComponent history;
+ String urlBase = "https://www.";
+ if (Platform.isJS())
{
- st = new StringTokenizer(historyItems, "\t");
-
- while (st.hasMoreTokens())
- {
- history.addItem(st.nextElement());
- }
- }
-
- int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel,
- MessageManager.getString("label.input_alignment_from_url"),
- JvOptionPane.OK_CANCEL_OPTION);
-
- if (reply != JvOptionPane.OK_OPTION)
- {
- return;
+ history = new JTextField(urlBase, 35);
}
-
- String url = history.getSelectedItem().toString();
-
- if (url.toLowerCase().endsWith(".jar"))
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- if (viewport != null)
+ 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)
{
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL,
- FileFormat.Jalview);
+ for (String token : historyItems.split("\\t"))
+ {
+ asCombo.addItem(token);
+ }
}
+ history = asCombo;
}
- else
+ panel.add(history);
+
+ Object[] options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ Runnable action = new Runnable()
{
- FileFormatI format = null;
- try
- {
- format = new IdentifyFile().identify(url, DataSourceType.URL);
- } catch (FileFormatException e)
+ @Override
+ public void run()
{
- // TODO revise error handling, distinguish between
- // URL not found and response not valid
- }
+ @SuppressWarnings("unchecked")
+ String url = (history instanceof JTextField
+ ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getEditor().getItem()
+ .toString().trim());
- if (format == null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.couldnt_locate",
- new String[]
- { url }),
- MessageManager.getString("label.url_not_found"),
- JvOptionPane.WARNING_MESSAGE);
+ if (url.toLowerCase(Locale.ROOT).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
+ }
- return;
- }
+ if (format == null)
+ {
+ String msg = MessageManager
+ .formatMessage("label.couldnt_locate", url);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ MessageManager.getString("label.url_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- format);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL, format);
+ 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(desktop).setResponseHandler(0, action)
+ .showInternalDialog(panel, dialogOption,
+ JvOptionPane.YES_NO_CANCEL_OPTION,
+ JvOptionPane.PLAIN_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
}
/**
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);
}
}, "ShowAboutMenu").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>");
-
- }
- else
- {
-
- message.append("<strong>Version "
- + jalview.bin.Cache.getProperty("VERSION")
- + "; last updated: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
- }
+ 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>");
- if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
- .equals("Checking"))
+ String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
+ if (latestVersion.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();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on requesting Help documentation
*/
@Override
- public void documentationMenuItem_actionPerformed(ActionEvent e)
+ public void documentationMenuItem_actionPerformed()
{
try
{
- Help.showHelpWindow();
+ if (Platform.isJS())
+ {
+ BrowserLauncher.openURL("https://www.jalview.org/help.html");
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ Help.showHelpWindow();
+ }
} catch (Exception ex)
{
+ System.err.println("Error opening help: " + ex.getMessage());
}
}
}
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
{
ssm.resetAll();
}
- System.gc();
}
@Override
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)
*/
void showConsole(boolean selected)
{
- showConsole.setSelected(selected);
// TODO: decide if we should update properties file
- Cache.setProperty("SHOW_JAVA_CONSOLE",
- Boolean.valueOf(selected).toString());
- jconsole.setVisible(selected);
+ if (jconsole != null) // BH 2018
+ {
+ showConsole.setSelected(selected);
+ Cache.setProperty("SHOW_JAVA_CONSOLE",
+ Boolean.valueOf(selected).toString());
+ jconsole.setVisible(selected);
+ }
}
void reorderAssociatedWindows(boolean minimize, boolean close)
@Override
protected void preferences_actionPerformed(ActionEvent e)
{
- new Preferences();
+ Preferences.openPreferences();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Prompts the user to choose a file and then saves the Jalview state as a
+ * Jalview project file
*/
@Override
- public void saveState_actionPerformed(ActionEvent e)
+ public void saveState_actionPerformed()
{
- JalviewFileChooser chooser = new JalviewFileChooser("jvp",
- "Jalview Project");
+ saveState_actionPerformed(false);
+ }
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+ public void saveState_actionPerformed(boolean saveAs)
+ {
+ java.io.File projectFile = getProjectFile();
+ // autoSave indicates we already have a file and don't need to ask
+ boolean autoSave = projectFile != null && !saveAs
+ && BackupFiles.getEnabled();
- int value = chooser.showSaveDialog(this);
+ // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+ // saveAs="+saveAs+", Backups
+ // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ boolean approveSave = false;
+ if (!autoSave)
{
- final Desktop me = this;
- final java.io.File choice = chooser.getSelectedFile();
- setProjectFile(choice);
+ JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+ "Jalview Project");
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ projectFile = chooser.getSelectedFile();
+ setProjectFile(projectFile);
+ approveSave = true;
+ }
+ }
+
+ if (approveSave || autoSave)
+ {
+ final Desktop me = this;
+ final java.io.File chosenFile = projectFile;
new Thread(new Runnable()
{
@Override
// TODO: refactor to Jalview desktop session controller action.
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
- { choice.getName() }), choice.hashCode());
- 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
{
- 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);
+ 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());
}
}, "SaveJalviewProject").start();
}
}
+ @Override
+ public void saveAsState_actionPerformed(ActionEvent e)
+ {
+ saveState_actionPerformed(true);
+ }
+
private void setProjectFile(File choice)
{
this.projectFile = choice;
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Shows a file chooser dialog and tries to read in the selected file as a
+ * Jalview project
*/
@Override
- public void loadState_actionPerformed(ActionEvent e)
+ public void loadState_actionPerformed()
{
+ final String[] suffix = new String[] { "jvp", "jar" };
+ final String[] desc = new String[] { "Jalview Project",
+ "Jalview Project (old)" };
JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jvp", "jar" },
- new String[]
- { "Jalview Project", "Jalview Project (old)" },
- "Jalview Project");
+ Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
+ "Jalview Project", true, BackupFiles.getEnabled()); // 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);
+ final 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
- {
- new Jalview2XML().loadJalviewAlign(choice);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
+ @Override
+ public void run()
{
- 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);
- }
+ setProgressBar(MessageManager.formatMessage(
+ "label.loading_jalview_project", new Object[]
+ { choice }), choice.hashCode());
+
+ try
+ {
+ new Jalview2XML().loadJalviewAlign(selectedFile);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ 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);
+ }
setProgressBar(null, choice.hashCode());
- }
- }, "LoadJalviewProject").start();
- }
+ }
+ }, "Project Loader").start();
+ }
+ });
+
+ chooser.showOpenDialog(this);
}
@Override
ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
- public void startLoading(final String fileName)
+ public void startLoading(final Object fileName)
{
if (fileLoadingCount == 0)
{
if (desktop != null)
{
AlignFrame[] frames = Desktop.getAlignFrames();
-
- for (AlignFrame afr : frames)
- {
- if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
- .equals(sequenceSetId))
- {
- if (afr.alignPanels != null)
- {
- for (AlignmentPanel ap : afr.alignPanels)
- {
- if (sequenceSetId == null
- || sequenceSetId.equals(ap.av.getSequenceSetId()))
- {
- viewp.add(ap.av);
- }
- }
- }
- else
- {
- viewp.add(afr.getViewport());
- }
- }
- }
- if (viewp.size() > 0)
- {
- return viewp.toArray(new AlignmentViewport[viewp.size()]);
- }
- }
- return null;
- }
-
- /**
- * Explode the views in the given frame into separate AlignFrame
- *
- * @param af
- */
- public static void explodeViews(AlignFrame af)
- {
- int size = af.alignPanels.size();
- if (size < 2)
- {
- return;
- }
-
- for (int i = 0; i < size; i++)
- {
- AlignmentPanel ap = af.alignPanels.get(i);
- AlignFrame newaf = new AlignFrame(ap);
-
- /*
- * 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)
- {
- newaf.setBounds(geometry);
- }
-
- ap.av.setGatherViewsHere(false);
-
- addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- }
-
- 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.
- *
- * @param source
- */
- public void gatherViews(AlignFrame source)
- {
- source.viewport.setGatherViewsHere(true);
- 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)
- {
- AlignFrame af = (AlignFrame) frames[t];
- boolean gatherThis = false;
- for (int a = 0; a < af.alignPanels.size(); a++)
- {
- AlignmentPanel ap = af.alignPanels.get(a);
- if (viewId.equals(ap.av.getSequenceSetId()))
- {
- gatherThis = true;
- ap.av.setGatherViewsHere(false);
- ap.av.setExplodedGeometry(af.getBounds());
- source.addAlignmentPanel(ap, false);
- }
- }
-
- if (gatherThis)
- {
- af.alignPanels.clear();
- af.closeMenuItem_actionPerformed(true);
- }
- }
- }
-
- }
-
- jalview.gui.VamsasApplication v_client = null;
-
- @Override
- public void vamsasImport_actionPerformed(ActionEvent e)
- {
- 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)
+
+ for (AlignFrame afr : frames)
{
- 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 (sequenceSetId == null || afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
+ {
+ if (afr.alignPanels != null)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
+ for (AlignmentPanel ap : afr.alignPanels)
{
- if (dsktp.v_client == null)
+ if (sequenceSetId == null
+ || sequenceSetId.equals(ap.av.getSequenceSetId()))
{
- Thread rthr = new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- dsktp.v_client = new VamsasApplication(dsktp, mysesid);
- dsktp.setupVamsasConnectedGui();
- dsktp.v_client.initial_update();
- }
-
- }, "VamsasSession");
- rthr.start();
+ viewp.add(ap.av);
}
- };
- });
- VamsasStMenu.add(sessit);
+ }
+ }
+ else
+ {
+ viewp.add(afr.getViewport());
+ }
}
- // don't show an empty menu.
- VamsasStMenu.setVisible(sess.length > 0);
-
}
- else
+ if (viewp.size() > 0)
{
- jalview.bin.Cache.log.debug("No current vamsas sessions.");
- VamsasStMenu.removeAll();
- VamsasStMenu.setVisible(false);
+ return viewp.toArray(new AlignmentViewport[viewp.size()]);
}
}
- else
- {
- // Not interested in the content. Just hide ourselves.
- VamsasStMenu.setVisible(false);
- }
+ return null;
}
- @Override
- public void vamsasSave_actionPerformed(ActionEvent e)
+ /**
+ * Explode the views in the given frame into separate AlignFrame
+ *
+ * @param af
+ */
+ public static void explodeViews(AlignFrame af)
{
- if (v_client != null)
+ int size = af.alignPanels.size();
+ if (size < 2)
{
- // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- JalviewFileChooser chooser = new JalviewFileChooser("vdj",
- "Vamsas Document");
+ return;
+ }
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager
- .getString("label.save_vamsas_document_archive"));
+ // 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);
- int value = chooser.showSaveDialog(this);
+ AlignFrame newaf = new AlignFrame(ap);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ // transfer reference for existing feature settings to new alignFrame
+ if (ap == af.alignPanel)
{
- 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
+ if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
{
- 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);
+ newaf.featureSettings = viewFeatureSettings;
+ }
+ newaf.setFeatureSettingsGeometry(fsBounds);
+ }
- } catch (Exception ex)
- {
- warnttl = "Problem saving Vamsas Document.";
- warnmsg = ex.toString();
- jalview.bin.Cache.log.warn(
- "Exception Whilst saving document to " + choice, ex);
+ /*
+ * 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)
+ {
+ newaf.setBounds(geometry);
+ }
- }
- removeProgressPanel(progpanel);
- if (warnmsg != null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ ap.av.setGatherViewsHere(false);
- warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
- }
+ 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();
}
}
- }
- JPanel vamUpdate = null;
+ af.featureSettings = null;
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+
+ }
/**
- * hide vamsas user gui bits when a vamsas document event is being handled.
+ * 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.
*
- * @param b
- * true to hide gui, false to reveal gui
+ * @param source
*/
- public void setVamsasUpdate(boolean b)
+ public void gatherViews(AlignFrame source)
{
- Cache.log.debug("Setting gui for Vamsas update "
- + (b ? "in progress" : "finished"));
-
- if (vamUpdate != null)
+ source.viewport.setGatherViewsHere(true);
+ source.viewport.setExplodedGeometry(source.getBounds());
+ JInternalFrame[] frames = desktop.getAllFrames();
+ String viewId = source.viewport.getSequenceSetId();
+ for (int t = 0; t < frames.length; t++)
{
- this.removeProgressPanel(vamUpdate);
+ if (frames[t] instanceof AlignFrame && frames[t] != source)
+ {
+ AlignFrame af = (AlignFrame) frames[t];
+ boolean gatherThis = false;
+ for (int a = 0; a < af.alignPanels.size(); a++)
+ {
+ AlignmentPanel ap = af.alignPanels.get(a);
+ if (viewId.equals(ap.av.getSequenceSetId()))
+ {
+ gatherThis = true;
+ ap.av.setGatherViewsHere(false);
+ ap.av.setExplodedGeometry(af.getBounds());
+ source.addAlignmentPanel(ap, false);
+ }
+ }
+
+ if (gatherThis)
+ {
+ if (af.featureSettings != null && af.featureSettings.isOpen())
+ {
+ if (source.featureSettings == null)
+ {
+ // 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);
+ }
+ }
}
- if (b)
+
+ // refresh the feature setting UI for the source frame if it exists
+ if (source.featureSettings != null && source.featureSettings.isOpen())
{
- vamUpdate = this.addProgressPanel(
- MessageManager.getString("label.updating_vamsas_session"));
+ source.showFeatureSettingsUI();
}
- 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;
*/
public class MyDesktopPane extends JDesktopPane implements Runnable
{
-
private static final float ONE_MB = 1048576f;
boolean showMemoryUsage = false;
10, getHeight() - fm.getHeight());
}
}
+
+ // output debug scale message. Important for jalview.bin.HiDPISettingTest2
+ Desktop.debugScaleMessage(Desktop.getDesktop().getGraphics());
}
}
-
/**
* Accessor method to quickly get all the AlignmentFrames loaded.
*
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);
}
*/
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(
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, "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);
}
}
});
block.release();
}
+ /**
+ * Outputs an image of the desktop to file in EPS format, after prompting the
+ * user for choice of Text or Lineart character rendering (unless a preference
+ * has been set). The file name is generated as
+ *
+ * <pre>
+ * Jalview_snapshot_nnnnn.eps where nnnnn is the current timestamp in milliseconds
+ * </pre>
+ */
@Override
protected void snapShotWindow_actionPerformed(ActionEvent e)
{
+ // currently the menu option to do this is not shown
invalidate();
- File of;
- ImageMaker im = new jalview.util.ImageMaker(
- this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(),
- getHeight(), of = new File("Jalview_snapshot"
- + System.currentTimeMillis() + ".eps"),
- "View of desktop", null, 0, false);
- try
- {
- paintAll(im.getGraphics());
- im.writeImage();
- } catch (Exception q)
+
+ int width = getWidth();
+ int height = getHeight();
+ File of = new File(
+ "Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
+ ImageWriterI writer = new ImageWriterI()
{
- Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
- q);
- return;
- }
- Cache.log.info("Successfully written snapshot to file "
- + of.getAbsolutePath());
+ @Override
+ public void exportImage(Graphics g) throws Exception
+ {
+ paintAll(g);
+ jalview.bin.Console.info("Successfully written snapshot to file "
+ + of.getAbsolutePath());
+ }
+ };
+ String title = "View of desktop";
+ ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
+ title);
+ exporter.doExport(of, this, width, height, title);
}
/**
}
/*
- * 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();
return groovyConsole;
}
- public static void transferFromDropTarget(List<String> files,
+ /**
+ * handles the payload of a drag and drop event.
+ *
+ * TODO refactor to desktop utilities class
+ *
+ * @param files
+ * - Data source strings extracted from the drop event
+ * @param protocols
+ * - protocol for each data source extracted from the drop event
+ * @param evt
+ * - the drop event
+ * @param t
+ * - the payload from the drop event
+ * @throws Exception
+ */
+ public static void transferFromDropTarget(List<Object> files,
List<DataSourceType> protocols, DropTargetDropEvent evt,
Transferable t) throws Exception
{
DataFlavor uriListFlavor = new DataFlavor(
- "text/uri-list;class=java.lang.String");
+ "text/uri-list;class=java.lang.String"), urlFlavour = null;
+ try
+ {
+ urlFlavour = new DataFlavor(
+ "application/x-java-url; class=java.net.URL");
+ } catch (ClassNotFoundException cfe)
+ {
+ jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.",
+ cfe);
+ }
+
+ if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
+ {
+
+ try
+ {
+ java.net.URL url = (URL) t.getTransferData(urlFlavour);
+ // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
+ // means url may be null.
+ if (url != null)
+ {
+ protocols.add(DataSourceType.URL);
+ files.add(url.toString());
+ jalview.bin.Console.debug("Drop handled as URL dataflavor "
+ + files.get(files.size() - 1));
+ return;
+ }
+ else
+ {
+ if (Platform.isAMacAndNotJS())
+ {
+ System.err.println(
+ "Please ignore plist error - occurs due to problem with java 8 on OSX");
+ }
+ }
+ } catch (Throwable 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))
{
- files.add(((File) file).toString());
+ files.add(file);
protocols.add(DataSourceType.FILE);
}
}
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
- data = (String) t.getTransferData(
- new DataFlavor("text/plain;class=java.lang.String"));
- if (Cache.log.isDebugEnabled())
+ DataFlavor textDf = new DataFlavor(
+ "text/plain;class=java.lang.String");
+ if (t.isDataFlavorSupported(textDf))
{
- Cache.log.debug("fallback returned " + data);
+ data = (String) t.getTransferData(textDf);
}
+
+ 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 "
- + files.get(protocols.size()));
- protocols.add(DataSourceType.FILE);
- }
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(
- data, "\r\n"); st.hasMoreTokens();)
+ if (data != null)
{
- added = true;
- String s = st.nextToken();
- if (s.startsWith("#"))
- {
- // the line is a comment (as per the RFC 2483)
- continue;
- }
- java.net.URI uri = new java.net.URI(s);
- if (uri.getScheme().toLowerCase().startsWith("http"))
+ while (protocols.size() < files.size())
{
- protocols.add(DataSourceType.URL);
- files.add(uri.toString());
+ jalview.bin.Console.debug("Adding missing FILE protocol for "
+ + files.get(protocols.size()));
+ protocols.add(DataSourceType.FILE);
}
- else
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data, "\r\n"); st.hasMoreTokens();)
{
- // otherwise preserve old behaviour: catch all for file objects
- java.io.File file = new java.io.File(uri);
- protocols.add(DataSourceType.FILE);
- files.add(file.toString());
+ added = true;
+ String s = st.nextToken();
+ if (s.startsWith("#"))
+ {
+ // the line is a comment (as per the RFC 2483)
+ continue;
+ }
+ java.net.URI uri = new java.net.URI(s);
+ if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http"))
+ {
+ protocols.add(DataSourceType.URL);
+ files.add(uri.toString());
+ }
+ else
+ {
+ // otherwise preserve old behaviour: catch all for file objects
+ java.io.File file = new java.io.File(uri);
+ protocols.add(DataSourceType.FILE);
+ files.add(file.toString());
+ }
}
}
- if (Cache.log.isDebugEnabled())
+
+ if (jalview.bin.Console.isDebugEnabled())
{
if (data == null || !added)
{
- Cache.log.debug(
- "Couldn't resolve drop data. Here are the supported flavors:");
- for (DataFlavor fl : t.getTransferDataFlavors())
+
+ if (t.getTransferDataFlavors() != null
+ && t.getTransferDataFlavors().length > 0)
{
- Cache.log.debug(
- "Supported transfer dataflavor: " + fl.toString());
- Object df = t.getTransferData(fl);
- if (df != null)
- {
- Cache.log.debug("Retrieves: " + df);
- }
- else
+ jalview.bin.Console.debug(
+ "Couldn't resolve drop data. Here are the supported flavors:");
+ for (DataFlavor fl : t.getTransferDataFlavors())
{
- Cache.log.debug("Retrieved nothing");
+ jalview.bin.Console.debug(
+ "Supported transfer dataflavor: " + fl.toString());
+ Object df = t.getTransferData(fl);
+ if (df != null)
+ {
+ jalview.bin.Console.debug("Retrieves: " + df);
+ }
+ else
+ {
+ jalview.bin.Console.debug("Retrieved nothing");
+ }
}
}
+ else
+ {
+ jalview.bin.Console
+ .debug("Couldn't resolve dataflavor for drop: "
+ + t.toString());
+ }
+ }
+ }
+ }
+ if (Platform.isWindowsAndNotJS())
+ {
+ 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(Locale.ROOT);
+ if (protocols.get(f).equals(DataSourceType.FILE)
+ && (source.endsWith(".lnk") || source.endsWith(".url")
+ || source.endsWith(".site")))
+ {
+ try
+ {
+ Object obj = files.get(f);
+ File lf = (obj instanceof File ? (File) obj
+ : new File((String) obj));
+ // process link file to get a URL
+ 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);
+ jalview.bin.Console.debug("Parsed real filename " + fullname
+ + " to extract protocol: " + protocols.get(f));
+ } catch (Exception ex)
+ {
+ jalview.bin.Console.error(
+ "Couldn't parse " + files.get(f) + " as a link file.",
+ ex);
+ }
}
}
}
{
Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
}
+
+ /**
+ * 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
+ * @param structureViewerClass
+ * if not null, only return viewers of this class
+ * @return
+ */
+ public List<StructureViewerBase> getStructureViewers(
+ AlignmentPanel apanel,
+ Class<? extends StructureViewerBase> structureViewerClass)
+ {
+ List<StructureViewerBase> result = new ArrayList<>();
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof StructureViewerBase)
+ {
+ if (structureViewerClass == null
+ || structureViewerClass.isInstance(frame))
+ {
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
+ {
+ result.add((StructureViewerBase) frame);
+ }
+ }
+ }
+ }
+ 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