*/
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.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.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 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
*
* @version $Revision: 1.155 $
*/
public class Desktop extends jalview.jbgui.GDesktop
- implements DropTargetListener, ClipboardOwner, IProgressIndicator,
- jalview.api.StructureSelectionManagerProvider
-{
+ 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>Development 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 the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list");
+ 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 doi: 10.1093/bioinformatics/btp033");
+ 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.
*/
* @param listener
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
*/
- public void addJalviewPropertyChangeListener(
- PropertyChangeListener listener)
- {
+ public void addJalviewPropertyChangeListener(PropertyChangeListener listener) {
changeSupport.addJalviewPropertyChangeListener(listener);
}
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
* java.beans.PropertyChangeListener)
*/
- public void addJalviewPropertyChangeListener(String propertyName,
- PropertyChangeListener listener)
- {
+ public void addJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) {
changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
}
* @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
* java.beans.PropertyChangeListener)
*/
- public void removeJalviewPropertyChangeListener(String propertyName,
- PropertyChangeListener listener)
- {
- changeSupport.removeJalviewPropertyChangeListener(propertyName,
- listener);
+ public void removeJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) {
+ changeSupport.removeJalviewPropertyChangeListener(propertyName, listener);
}
/** Singleton Desktop instance */
public static MyDesktopPane desktop;
- public static MyDesktopPane getDesktop()
- {
+ public static MyDesktopPane getDesktop() {
// BH 2018 could use currentThread() here as a reference to a
// Hashtable<Thread, MyDesktopPane> in JavaScript
return desktop;
static int fileLoadingCount = 0;
- class MyDesktopManager implements DesktopManager
- {
+ class MyDesktopManager implements DesktopManager {
private DesktopManager delegate;
- public MyDesktopManager(DesktopManager delegate)
- {
+ public MyDesktopManager(DesktopManager delegate) {
this.delegate = delegate;
}
@Override
- public void activateFrame(JInternalFrame f)
- {
- try
- {
+ public void activateFrame(JInternalFrame f) {
+ try {
delegate.activateFrame(f);
- } catch (NullPointerException npe)
- {
+ } catch (NullPointerException npe) {
Point p = getMousePosition();
instance.showPasteMenu(p.x, p.y);
}
}
@Override
- public void beginDraggingFrame(JComponent f)
- {
+ public void beginDraggingFrame(JComponent f) {
delegate.beginDraggingFrame(f);
}
@Override
- public void beginResizingFrame(JComponent f, int direction)
- {
+ public void beginResizingFrame(JComponent f, int direction) {
delegate.beginResizingFrame(f, direction);
}
@Override
- public void closeFrame(JInternalFrame f)
- {
+ public void closeFrame(JInternalFrame f) {
delegate.closeFrame(f);
}
@Override
- public void deactivateFrame(JInternalFrame f)
- {
+ public void deactivateFrame(JInternalFrame f) {
delegate.deactivateFrame(f);
}
@Override
- public void deiconifyFrame(JInternalFrame f)
- {
+ public void deiconifyFrame(JInternalFrame f) {
delegate.deiconifyFrame(f);
}
@Override
- public void dragFrame(JComponent f, int newX, int newY)
- {
- if (newY < 0)
- {
+ public void dragFrame(JComponent f, int newX, int newY) {
+ if (newY < 0) {
newY = 0;
}
delegate.dragFrame(f, newX, newY);
}
@Override
- public void endDraggingFrame(JComponent f)
- {
+ public void endDraggingFrame(JComponent f) {
delegate.endDraggingFrame(f);
desktop.repaint();
}
@Override
- public void endResizingFrame(JComponent f)
- {
+ public void endResizingFrame(JComponent f) {
delegate.endResizingFrame(f);
desktop.repaint();
}
@Override
- public void iconifyFrame(JInternalFrame f)
- {
+ public void iconifyFrame(JInternalFrame f) {
delegate.iconifyFrame(f);
}
@Override
- public void maximizeFrame(JInternalFrame f)
- {
+ public void maximizeFrame(JInternalFrame f) {
delegate.maximizeFrame(f);
}
@Override
- public void minimizeFrame(JInternalFrame f)
- {
+ public void minimizeFrame(JInternalFrame f) {
delegate.minimizeFrame(f);
}
@Override
- public void openFrame(JInternalFrame f)
- {
+ public void openFrame(JInternalFrame f) {
delegate.openFrame(f);
}
@Override
- public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
- int newHeight)
- {
- if (newY < 0)
- {
+ public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) {
+ if (newY < 0) {
newY = 0;
}
delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
}
@Override
- public void setBoundsForFrame(JComponent f, int newX, int newY,
- int newWidth, int newHeight)
- {
+ public void setBoundsForFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) {
delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
}
/**
* Creates a new Desktop object.
*/
- public Desktop()
- {
+ 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;
- if (!Jalview.isJS())
- {
- doVamsasClientCheck();
- }
doConfigureStructurePrefs();
- setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
- false);
- boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
- false);
+ 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.
- // Must set for all three to be active:
- if (Jalview.isJS())
- {
- getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
- ((JComponent) getContentPane()).putClientProperty("swingjs.overflow.hidden", "false");
- desktop.putClientProperty("swingjs.overflow.hidden", "false");
- }
-
+
+ // 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)
- {
+ if (dims != null) {
setBounds(dims);
- }
- else
- {
+ } else {
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
int xPos = Math.max(5, (screenSize.width - 900) / 2);
int yPos = Math.max(5, (screenSize.height - 650) / 2);
setBounds(xPos, yPos, 900, 650);
}
-
- 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
+ if (!nosplash) {
+ SwingUtilities.invokeLater(new Runnable() {
+ @Override
+ public void run() {
+ new SplashScreen(true);
+ }
+ });
+ }
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- new SplashScreen();
- }
- });
-
- // 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()
- {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
- Cache.log.debug("Filechooser init thread started.");
+ 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);
- Cache.log.debug("Filechooser init thread finished.");
+ 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()
- {
+ changeSupport.addJalviewPropertyChangeListener("services", new PropertyChangeListener() {
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- Cache.log.debug("Firing service changed event for "
- + evt.getNewValue());
- JalviewServicesChanged(evt);
- }
-
- });
-
- }
+ @Override
+ public void propertyChange(PropertyChangeEvent evt) {
+ jalview.bin.Console.debug("Firing service changed event for " + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
+ });
+ }
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
- this.addWindowListener(new WindowAdapter()
- {
+ this.addWindowListener(new WindowAdapter() {
@Override
- public void windowClosing(WindowEvent evt)
- {
+ public void windowClosing(WindowEvent evt) {
quit();
}
});
MouseAdapter ma;
- this.addMouseListener(ma = new MouseAdapter()
- {
+ this.addMouseListener(ma = new MouseAdapter() {
@Override
- public void mousePressed(MouseEvent evt)
- {
+ public void mousePressed(MouseEvent evt) {
if (evt.isPopupTrigger()) // Mac
{
showPasteMenu(evt.getX(), evt.getY());
}
@Override
- public void mouseReleased(MouseEvent evt)
- {
+ public void mouseReleased(MouseEvent evt) {
if (evt.isPopupTrigger()) // Windows
{
showPasteMenu(evt.getX(), evt.getY());
}
});
desktop.addMouseListener(ma);
-
}
/**
*
* @return
*/
- public boolean showExperimental()
- {
- String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
- Boolean.FALSE.toString());
+ public boolean showExperimental() {
+ String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, Boolean.FALSE.toString());
return Boolean.valueOf(experimental).booleanValue();
}
- public void doConfigureStructurePrefs()
- {
+ public void doConfigureStructurePrefs() {
// configure services
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(this);
- if (jalview.bin.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.setSecStructServices(
- jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true));
- }
- else
- {
+ StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(this);
+ if (Cache.getDefault(Preferences.ADD_SS_ANN, 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(Cache.getDefault(Preferences.USE_RNAVIEW, false));
+ } else {
ssm.setAddTempFacAnnot(false);
ssm.setProcessSecondaryStructure(false);
ssm.setSecStructServices(false);
}
}
- public void checkForNews()
- {
+ public void checkForNews() {
final Desktop me = this;
// Thread off the news reader, in case there are connection problems.
- new Thread(new Runnable()
- {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
- Cache.log.debug("Starting news thread.");
+ public void run() {
+ 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()
- {
- Cache.log.debug("Downloading data from identifiers.org");
- UrlDownloadClient client = new UrlDownloadClient();
- try
- {
- client.download(IdOrgSettings.getUrl(),
- IdOrgSettings.getDownloadLocation());
- } catch (IOException e)
- {
- Cache.log.debug("Exception downloading identifiers.org data"
- + e.getMessage());
+ public void getIdentifiersOrgData() {
+ if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) {
+ // Thread off the identifiers fetcher
+ new Thread(new Runnable() {
+ @Override
+ public void run() {
+ 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
- protected void showNews_actionPerformed(ActionEvent e)
- {
+ protected void showNews_actionPerformed(ActionEvent e) {
showNews(showNews.isSelected());
}
- void showNews(boolean visible)
- {
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+ void showNews(boolean visible) {
+ jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
- if (visible && !jvnews.isVisible())
- {
- new Thread(new Runnable()
- {
+ if (visible && !jvnews.isVisible()) {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
+ public void run() {
long now = System.currentTimeMillis();
- Desktop.instance.setProgressBar(
- MessageManager.getString("status.refreshing_news"), now);
+ Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), now);
jvnews.refreshNews();
Desktop.instance.setProgressBar(null, now);
jvnews.showNews();
/**
* recover the last known dimensions for a jalview window
*
- * @param windowName
- * - empty string is desktop, all other windows have unique prefix
+ * @param windowName - empty string is desktop, all other windows have unique
+ * prefix
* @return null or last known dimensions scaled to current geometry (if last
* window geom was known)
*/
- Rectangle getLastKnownDimensions(String windowName)
- {
+ Rectangle getLastKnownDimensions(String windowName) {
// 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");
- 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)
- {
+ 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 (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);
iy = (int) (iy * sh);
ih = (int) (ih * sh);
- while (ix >= screenSize.width)
- {
- jalview.bin.Cache.log.debug(
- "Window geometry location recall error: shifting horizontal to within screenbounds.");
+ while (ix >= screenSize.width) {
+ 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(
- "Window geometry location recall error: shifting vertical to within screenbounds.");
+ while (iy >= screenSize.height) {
+ jalview.bin.Console.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- jalview.bin.Cache.log.debug(
- "Got last known dimensions for " + windowName + ": x:" + ix
- + " y:" + iy + " width:" + iw + " height:" + ih);
+ jalview.bin.Console.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
+ + " height:" + ih);
}
// return dimensions for new instance
return new Rectangle(ix, iy, iw, 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)
- {
+ void showPasteMenu(int x, int y) {
JPopupMenu popup = new JPopupMenu();
- JMenuItem item = new JMenuItem(
- MessageManager.getString("label.paste_new_window"));
- item.addActionListener(new ActionListener()
- {
+ JMenuItem item = new JMenuItem(MessageManager.getString("label.paste_new_window"));
+ item.addActionListener(new ActionListener() {
@Override
- public void actionPerformed(ActionEvent evt)
- {
+ public void actionPerformed(ActionEvent evt) {
paste();
}
});
popup.show(this, x, y);
}
- public void paste()
- {
- try
- {
+ public void paste() {
+ try {
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
Transferable contents = c.getContents(this);
- if (contents != null)
- {
- String file = (String) contents
- .getTransferData(DataFlavor.stringFlavor);
+ if (contents != null) {
+ String file = (String) contents.getTransferData(DataFlavor.stringFlavor);
- FileFormatI format = new IdentifyFile().identify(file,
- DataSourceType.PASTE);
+ FileFormatI format = new IdentifyFile().identify(file, DataSourceType.PASTE);
new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
}
- } catch (Exception ex)
- {
- System.out.println(
- "Unable to paste alignment from system clipboard:\n" + ex);
+ } catch (Exception ex) {
+ System.out.println("Unable to paste alignment from system clipboard:\n" + ex);
}
}
/**
* Adds and opens the given frame to the desktop
*
- * @param frame
- * Frame to show
- * @param title
- * Visible Title
- * @param w
- * width
- * @param h
- * height
- */
- public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, int w, int h)
- {
+ * @param frame Frame to show
+ * @param title Visible Title
+ * @param w width
+ * @param h height
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame, String title, int w, int h) {
addInternalFrame(frame, title, true, w, h, true, false);
}
/**
* Add an internal frame to the Jalview desktop
*
- * @param frame
- * Frame to show
- * @param title
- * Visible Title
- * @param makeVisible
- * When true, display frame immediately, otherwise, caller must call
- * setVisible themselves.
- * @param w
- * width
- * @param h
- * height
- */
- public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, boolean makeVisible,
- int w, int h)
- {
+ * @param frame Frame to show
+ * @param title Visible Title
+ * @param makeVisible When true, display frame immediately, otherwise, caller
+ * must call setVisible themselves.
+ * @param w width
+ * @param h height
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame, String title, boolean makeVisible, int w,
+ int h) {
addInternalFrame(frame, title, makeVisible, w, h, true, false);
}
/**
* Add an internal frame to the Jalview desktop and make it visible
*
- * @param frame
- * Frame to show
- * @param title
- * Visible Title
- * @param w
- * width
- * @param h
- * height
- * @param resizable
- * Allow resize
- */
- public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, int w, int h,
- boolean resizable)
- {
+ * @param frame Frame to show
+ * @param title Visible Title
+ * @param w width
+ * @param h height
+ * @param resizable Allow resize
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame, String title, int w, int h,
+ boolean resizable) {
addInternalFrame(frame, title, true, w, h, resizable, false);
}
/**
* Add an internal frame to the Jalview desktop
*
- * @param frame
- * Frame to show
- * @param title
- * Visible Title
- * @param makeVisible
- * When true, display frame immediately, otherwise, caller must call
- * setVisible themselves.
- * @param w
- * width
- * @param h
- * height
- * @param resizable
- * Allow resize
- * @param ignoreMinSize
- * Do not set the default minimum size for frame
- */
- public static synchronized void addInternalFrame(
- final JInternalFrame frame, String title, boolean makeVisible,
- int w, int h, boolean resizable, boolean ignoreMinSize)
- {
+ * @param frame Frame to show
+ * @param title Visible Title
+ * @param makeVisible When true, display frame immediately, otherwise, caller
+ * must call setVisible themselves.
+ * @param w width
+ * @param h height
+ * @param resizable Allow resize
+ * @param ignoreMinSize Do not set the default minimum size for frame
+ */
+ public static synchronized void addInternalFrame(final JInternalFrame frame, String title, boolean makeVisible, int w,
+ int h, boolean resizable, boolean ignoreMinSize) {
// TODO: allow callers to determine X and Y position of frame (eg. via
// bounds object).
// the current window title
frame.setTitle(title);
- if (frame.getWidth() < 1 || frame.getHeight() < 1)
- {
+ if (frame.getWidth() < 1 || frame.getHeight() < 1) {
frame.setSize(w, h);
}
// THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
if (instance == null || (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true")))
- {
+ && System.getProperty("java.awt.headless").equals("true"))) {
return;
}
openFrameCount++;
- if (!ignoreMinSize)
- {
- frame.setMinimumSize(
- new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
+ if (!ignoreMinSize) {
+ frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
// Set default dimension for Alignment Frame window.
// The Alignment Frame window could be added from a number of places,
// hence,
// I did this here in order not to miss out on any Alignment frame.
- if (frame instanceof AlignFrame)
- {
- frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH,
- ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
+ if (frame instanceof AlignFrame) {
+ frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
}
}
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)
- {
- frame.setLocation(xOffset * openFrameCount,
- yOffset * ((openFrameCount - 1) % 10) + yOffset);
+ if (frame.getX() < 1 && frame.getY() < 1) {
+ frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset);
}
/*
- * add an entry for the new frame in the Window menu
- * (and remove it when the frame is closed)
+ * 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()
- {
+ frame.addInternalFrameListener(new InternalFrameAdapter() {
@Override
- public void internalFrameActivated(InternalFrameEvent evt)
- {
+ public void internalFrameActivated(InternalFrameEvent evt) {
JInternalFrame itf = desktop.getSelectedFrame();
- if (itf != null)
- {
- if (itf instanceof AlignFrame)
- {
+ if (itf != null) {
+ if (itf instanceof AlignFrame) {
Jalview.setCurrentAlignFrame((AlignFrame) itf);
}
itf.requestFocus();
}
@Override
- public void internalFrameClosed(InternalFrameEvent evt)
- {
+ public void internalFrameClosed(InternalFrameEvent evt) {
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)
- {
+ if (openFrameCount > 0) {
openFrameCount--;
}
/*
* ensure no reference to alignFrame retained by menu item listener
*/
- if (menuItem.getActionListeners().length > 0)
- {
+ if (menuItem.getActionListeners().length > 0) {
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
windowMenu.remove(menuItem);
- };
+ }
});
- menuItem.addActionListener(new ActionListener()
- {
+ menuItem.addActionListener(new ActionListener() {
@Override
- public void actionPerformed(ActionEvent e)
- {
- try
- {
+ public void actionPerformed(ActionEvent e) {
+ try {
frame.setSelected(true);
frame.setIcon(false);
- } catch (java.beans.PropertyVetoException ex)
- {
- // System.err.println(ex.toString());
+ } catch (java.beans.PropertyVetoException ex) {
+
}
}
});
windowMenu.add(menuItem);
frame.toFront();
- try
- {
+ try {
frame.setSelected(true);
frame.requestFocus();
- } catch (java.beans.PropertyVetoException ve)
- {
- } 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",
- cex);
+ } catch (java.beans.PropertyVetoException ve) {
+ } catch (java.lang.ClassCastException cex) {
+ 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);
}
}
*
* @param frame
*/
- private static void setKeyBindings(JInternalFrame frame)
- {
+ private static void setKeyBindings(JInternalFrame frame) {
@SuppressWarnings("serial")
- final Action closeAction = new AbstractAction()
- {
+ final Action closeAction = new AbstractAction() {
@Override
- public void actionPerformed(ActionEvent e)
- {
+ 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,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
+ 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);
+ InputMap inputMap = frame.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
String ctrlW = ctrlWKey.toString();
inputMap.put(ctrlWKey, ctrlW);
inputMap.put(cmdWKey, ctrlW);
}
@Override
- public void lostOwnership(Clipboard clipboard, Transferable contents)
- {
- if (!internalCopy)
- {
+ public void lostOwnership(Clipboard clipboard, Transferable contents) {
+ if (!internalCopy) {
Desktop.jalviewClipboard = null;
}
}
@Override
- public void dragEnter(DropTargetDragEvent evt)
- {
+ public void dragEnter(DropTargetDragEvent evt) {
}
@Override
- public void dragExit(DropTargetEvent evt)
- {
+ public void dragExit(DropTargetEvent evt) {
}
@Override
- public void dragOver(DropTargetDragEvent evt)
- {
+ public void dragOver(DropTargetDragEvent evt) {
}
@Override
- public void dropActionChanged(DropTargetDragEvent evt)
- {
+ public void dropActionChanged(DropTargetDragEvent evt) {
}
/**
* DOCUMENT ME!
*
- * @param evt
- * DOCUMENT ME!
+ * @param evt DOCUMENT ME!
*/
@Override
- public void drop(DropTargetDropEvent evt)
- {
+ public void drop(DropTargetDropEvent evt) {
boolean success = true;
// JAL-1552 - acceptDrop required before getTransferable call for
// Java's Transferable for native dnd
List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
- try
- {
+ try {
Desktop.transferFromDropTarget(files, protocols, evt, t);
- } catch (Exception e)
- {
+ } catch (Exception e) {
e.printStackTrace();
success = false;
}
- if (files != null)
- {
- try
- {
- for (int i = 0; i < files.size(); i++)
- {
+ if (files != null) {
+ try {
+ for (int i = 0; i < files.size(); i++) {
// BH 2018 File or String
Object file = files.get(i);
String fileName = file.toString();
- DataSourceType protocol = (protocols == null)
- ? DataSourceType.FILE
- : protocols.get(i);
+ DataSourceType protocol = (protocols == null) ? DataSourceType.FILE : protocols.get(i);
FileFormatI format = null;
- if (fileName.endsWith(".jar"))
- {
+ if (fileName.endsWith(".jar")) {
format = FileFormat.Jalview;
- }
- else
- {
+ } else {
format = new IdentifyFile().identify(file, protocol);
}
-
+ if (file instanceof File) {
+ Platform.cacheFileData((File) file);
+ }
new FileLoader().LoadFile(null, file, protocol, format);
}
- } catch (Exception ex)
- {
+ } catch (Exception ex) {
success = false;
}
}
/**
* DOCUMENT ME!
*
- * @param e
- * DOCUMENT ME!
+ * @param e DOCUMENT ME!
*/
@Override
- public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
- {
+ 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.setDialogTitle(MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
- chooser.addResponse(0, new RunResponse(JalviewFileChooser.APPROVE_OPTION)
- {
+ chooser.setResponseHandler(0, new Runnable() {
@Override
- public void run()
- {
+ public void run() {
File selectedFile = chooser.getSelectedFile();
Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
/*
* 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))
- {
- try
- {
- format = new IdentifyFile().identify(selectedFile,
- DataSourceType.FILE);
- } catch (FileFormatException e)
- {
+ if (FileFormats.getInstance().isIdentifiable(format)) {
+ try {
+ format = new IdentifyFile().identify(selectedFile, DataSourceType.FILE);
+ } catch (FileFormatException e) {
// format = null; //??
}
}
- new FileLoader().LoadFile(viewport, selectedFile,
- DataSourceType.FILE, format);
+ new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, format);
}
});
chooser.showOpenDialog(this);
* @param viewport
*/
@Override
- public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
- {
+ public void inputURLMenuItem_actionPerformed(AlignViewport viewport) {
// This construct allows us to have a wider textfield
// for viewing
- JLabel label = new JLabel(
- MessageManager.getString("label.input_file_url"));
+ JLabel label = new JLabel(MessageManager.getString("label.input_file_url"));
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
+ } else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
JComboBox<String> asCombo = new JComboBox<>();
asCombo.setPreferredSize(new Dimension(400, 20));
asCombo.setEditable(true);
asCombo.addItem(urlBase);
String historyItems = Cache.getProperty("RECENT_URL");
- if (historyItems != null)
- {
- for (String token : historyItems.split("\\t"))
- {
+ if (historyItems != null) {
+ for (String token : historyItems.split("\\t")) {
asCombo.addItem(token);
}
}
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();
-
- if (url.toLowerCase().endsWith(".jar"))
- {
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- FileFormat.Jalview);
+ public void run() {
+ @SuppressWarnings("unchecked")
+ String url = (history instanceof JTextField ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getEditor().getItem().toString().trim());
+
+ 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
- {
- new FileLoader().LoadFile(url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- }
- else
- {
+ } else {
FileFormatI format = null;
- try
- {
+ try {
format = new IdentifyFile().identify(url, DataSourceType.URL);
- } catch (FileFormatException e)
- {
+ } catch (FileFormatException e) {
// TODO revise error handling, distinguish between
// URL not found and response not valid
}
- if (format == null)
- {
+ 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);
+ MessageManager.getString("label.url_not_found"), JvOptionPane.WARNING_MESSAGE);
return;
}
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- format);
- }
- else
- {
+ 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).addResponse(0, action)
- .showInternalDialog(panel, dialogOption,
- JvOptionPane.YES_NO_CANCEL_OPTION,
- JvOptionPane.PLAIN_MESSAGE, null, options,
- MessageManager.getString("action.ok"));
+ }
+ };
+ 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"));
}
/**
* Opens the CutAndPaste window for the user to paste an alignment in to
*
- * @param viewPanel
- * - if not null, the pasted alignment is added to the current
- * alignment; if null, to a new alignment window
+ * @param viewPanel - if not null, the pasted alignment is added to the current
+ * alignment; if null, to a new alignment window
*/
@Override
- public void inputTextboxMenuItem_actionPerformed(
- AlignmentViewPanel viewPanel)
- {
+ public void inputTextboxMenuItem_actionPerformed(AlignmentViewPanel viewPanel) {
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(viewPanel);
- Desktop.addInternalFrame(cap,
- MessageManager.getString("label.cut_paste_alignmen_file"), true,
- 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), true, 600, 500);
}
/*
* Exit the program
*/
@Override
- public void quit()
- {
+ public void quit() {
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
- screen.width + "");
- jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT",
- screen.height + "");
- storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
- getWidth(), getHeight()));
-
- if (jconsole != null)
- {
+ Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+ Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
+ storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, getWidth(), getHeight()));
+
+ if (jconsole != null) {
storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
jconsole.stopConsole();
}
- if (jvnews != null)
- {
+ if (jvnews != null) {
storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
}
- if (dialogExecutor != null)
- {
+ if (dialogExecutor != null) {
dialogExecutor.shutdownNow();
}
closeAll_actionPerformed(null);
- if (groovyConsole != null)
- {
+ if (groovyConsole != null) {
// suppress a possible repeat prompt to save script
groovyConsole.setDirty(false);
groovyConsole.exit();
System.exit(0);
}
- 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
- + " height:" + jc.height);
+ private void storeLastKnownDimensions(String string, Rectangle jc) {
+ 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 + "");
}
/**
* DOCUMENT ME!
*
- * @param e
- * DOCUMENT ME!
+ * @param e DOCUMENT ME!
*/
@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()
- {
+ public void aboutMenuItem_actionPerformed(ActionEvent e) {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
- new SplashScreen(true);
+ public void run() {
+ new SplashScreen(false);
}
}).start();
}
- public StringBuffer getAboutMessage(boolean shortv)
- {
- 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"));
- }
-
- if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
- .equals("Checking"))
- {
- message.append("<br>...Checking latest version...</br>");
- }
- else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
- .equals(jalview.bin.Cache.getProperty("VERSION")))
- {
+ /**
+ * 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() {
+ 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>");
+
+ String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
+ if (latestVersion.equals("Checking")) {
+ // JBP removed this message for 2.11: May be reinstated in future version
+ // message.append("<br>...Checking latest version...</br>");
+ } else if (!latestVersion.equals(Cache.getProperty("VERSION"))) {
boolean red = false;
- if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
- .indexOf("automated build") == -1)
- {
+ if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT).indexOf("automated build") == -1) {
red = true;
// Displayed when code version and jnlp version do not match and code
// version is not a development build
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")
- + " !!");
- if (red)
- {
+ 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();
}
/**
* Action on requesting Help documentation
*/
@Override
- public void documentationMenuItem_actionPerformed()
- {
- try
- {
- if (Jalview.isJS())
- {
- BrowserLauncher.openURL("http://www.jalview.org/help.html");
- }
- else
+ public void documentationMenuItem_actionPerformed() {
+ try {
+ if (Platform.isJS()) {
+ BrowserLauncher.openURL("https://www.jalview.org/help.html");
+ } else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
Help.showHelpWindow();
}
- } catch (Exception ex)
- {
+ } catch (Exception ex) {
System.err.println("Error opening help: " + ex.getMessage());
}
}
@Override
- public void closeAll_actionPerformed(ActionEvent e)
- {
+ public void closeAll_actionPerformed(ActionEvent e) {
// TODO show a progress bar while closing?
JInternalFrame[] frames = desktop.getAllFrames();
- for (int i = 0; i < frames.length; i++)
- {
- try
- {
+ for (int i = 0; i < frames.length; i++) {
+ try {
frames[i].setClosed(true);
- } catch (java.beans.PropertyVetoException ex)
- {
+ } catch (java.beans.PropertyVetoException ex) {
}
}
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
* when all windows are closed)
*/
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(this);
- if (ssm != null)
- {
+ StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(this);
+ if (ssm != null) {
ssm.resetAll();
}
}
@Override
- public void raiseRelated_actionPerformed(ActionEvent e)
- {
+ public void raiseRelated_actionPerformed(ActionEvent e) {
reorderAssociatedWindows(false, false);
}
@Override
- public void minimizeAssociated_actionPerformed(ActionEvent e)
- {
+ public void minimizeAssociated_actionPerformed(ActionEvent e) {
reorderAssociatedWindows(true, false);
}
- void closeAssociatedWindows()
- {
+ void closeAssociatedWindows() {
reorderAssociatedWindows(false, true);
}
* ActionEvent)
*/
@Override
- protected void garbageCollect_actionPerformed(ActionEvent e)
- {
+ 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)
- {
+ protected void showMemusage_actionPerformed(ActionEvent e) {
desktop.showMemoryUsage(showMemusage.isSelected());
}
* )
*/
@Override
- protected void showConsole_actionPerformed(ActionEvent e)
- {
+ protected void showConsole_actionPerformed(ActionEvent e) {
showConsole(showConsole.isSelected());
}
*
* @param selected
*/
- void showConsole(boolean selected)
- {
+ void showConsole(boolean selected) {
// TODO: decide if we should update properties file
if (jconsole != null) // BH 2018
{
showConsole.setSelected(selected);
- Cache.setProperty("SHOW_JAVA_CONSOLE",
- Boolean.valueOf(selected).toString());
+ Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected).toString());
jconsole.setVisible(selected);
}
}
- void reorderAssociatedWindows(boolean minimize, boolean close)
- {
+ void reorderAssociatedWindows(boolean minimize, boolean close) {
JInternalFrame[] frames = desktop.getAllFrames();
- if (frames == null || frames.length < 1)
- {
+ if (frames == null || frames.length < 1) {
return;
}
AlignmentViewport source = null, target = null;
- if (frames[0] instanceof AlignFrame)
- {
+ if (frames[0] instanceof AlignFrame) {
source = ((AlignFrame) frames[0]).getCurrentView();
- }
- else if (frames[0] instanceof TreePanel)
- {
+ } else if (frames[0] instanceof TreePanel) {
source = ((TreePanel) frames[0]).getViewPort();
- }
- else if (frames[0] instanceof PCAPanel)
- {
+ } else if (frames[0] instanceof PCAPanel) {
source = ((PCAPanel) frames[0]).av;
- }
- else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
- {
+ } else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) {
source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
}
- if (source != null)
- {
- for (int i = 0; i < frames.length; i++)
- {
+ if (source != null) {
+ for (int i = 0; i < frames.length; i++) {
target = null;
- if (frames[i] == null)
- {
+ if (frames[i] == null) {
continue;
}
- if (frames[i] instanceof AlignFrame)
- {
+ if (frames[i] instanceof AlignFrame) {
target = ((AlignFrame) frames[i]).getCurrentView();
- }
- else if (frames[i] instanceof TreePanel)
- {
+ } else if (frames[i] instanceof TreePanel) {
target = ((TreePanel) frames[i]).getViewPort();
- }
- else if (frames[i] instanceof PCAPanel)
- {
+ } else if (frames[i] instanceof PCAPanel) {
target = ((PCAPanel) frames[i]).av;
- }
- else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
- {
+ } else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) {
target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
}
- if (source == target)
- {
- try
- {
- if (close)
- {
+ if (source == target) {
+ try {
+ if (close) {
frames[i].setClosed(true);
- }
- else
- {
+ } else {
frames[i].setIcon(minimize);
- if (!minimize)
- {
+ if (!minimize) {
frames[i].toFront();
}
}
- } catch (java.beans.PropertyVetoException ex)
- {
+ } catch (java.beans.PropertyVetoException ex) {
}
}
}
/**
* DOCUMENT ME!
*
- * @param e
- * DOCUMENT ME!
+ * @param e DOCUMENT ME!
*/
@Override
- protected void preferences_actionPerformed(ActionEvent e)
- {
- new Preferences();
+ protected void preferences_actionPerformed(ActionEvent e) {
+ Preferences.openPreferences();
}
/**
* Jalview project file
*/
@Override
- public void saveState_actionPerformed(boolean asCastor)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- asCastor ? "jvp" : "jvx",
- "Jalview Project");
+ public void saveState_actionPerformed() {
+ saveState_actionPerformed(false);
+ }
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_state"));
- int option = chooser.showSaveDialog(this);
- if (option == JalviewFileChooser.APPROVE_OPTION)
- {
- File choice = chooser.getSelectedFile();
- setProjectFile(choice);
+ 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();
- new Thread(new Runnable()
- {
+ // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+ // saveAs="+saveAs+", Backups
+ // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
+
+ boolean approveSave = false;
+ if (!autoSave) {
+ 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
- public void run()
- {
+ public void run() {
// 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());
+ setProgressBar(
+ MessageManager.formatMessage("label.saving_jalview_project", new Object[] { 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
- {
- new jalview.project.Jalview2XML().saveState(choice);
+ try {
+ 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);
- } catch (Exception ex)
- {
- Cache.log.error(
- "Problems whilst trying to save to " + choice.getName(),
- ex);
- JvOptionPane.showMessageDialog(Desktop.this,
- MessageManager.formatMessage(
- "label.error_whilst_saving_current_state_to",
- new Object[]
- { choice.getName() }),
- MessageManager.getString("label.couldnt_save_project"),
- JvOptionPane.WARNING_MESSAGE);
+ } catch (OutOfMemoryError oom) {
+ new OOMWarning("Whilst saving current state to " + chosenFile.getName(), oom);
+ } catch (Exception 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[] { 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;
}
- public File getProjectFile()
- {
+ public File getProjectFile() {
return this.projectFile;
}
/**
- * 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" };
- JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), suffix,
- desc,
- "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", true, BackupFiles.getEnabled()); // last two
+ // booleans:
+ // allFiles,
+ // allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
- chooser.addResponse(0, new RunResponse(JalviewFileChooser.APPROVE_OPTION)
- {
+ chooser.setResponseHandler(0, new Runnable() {
@Override
- public void run()
- {
+ 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()
- {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
- try {
- if (asCastor)
- {
- new Jalview2XML().loadJalviewAlign(choice);
- }
- else
- {
- new jalview.project.Jalview2XML().loadJalviewAlign(choice);
- }
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
- {
- Cache.log.error(
- "Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager.getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
+ public void run() {
+ 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);
}
}
- }).start();
+ }, "Project Loader").start();
}
});
-
+
chooser.showOpenDialog(this);
}
@Override
- public void inputSequence_actionPerformed(ActionEvent e)
- {
+ public void inputSequence_actionPerformed(ActionEvent e) {
new SequenceFetcher(this);
}
ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
- public void startLoading(final Object fileName)
- {
- if (fileLoadingCount == 0)
- {
- fileLoadingPanels.add(addProgressPanel(MessageManager
- .formatMessage("label.loading_file", new Object[]
- { fileName })));
+ public void startLoading(final Object fileName) {
+ if (fileLoadingCount == 0) {
+ fileLoadingPanels
+ .add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new Object[] { fileName })));
}
fileLoadingCount++;
}
- private JPanel addProgressPanel(String string)
- {
- if (progressPanel == null)
- {
+ private JPanel addProgressPanel(String string) {
+ if (progressPanel == null) {
progressPanel = new JPanel(new GridLayout(1, 1));
totalProgressCount = 0;
instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
thisprogress.add(progressBar, BorderLayout.CENTER);
progressPanel.add(thisprogress);
- ((GridLayout) progressPanel.getLayout()).setRows(
- ((GridLayout) progressPanel.getLayout()).getRows() + 1);
+ ((GridLayout) progressPanel.getLayout()).setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
instance.validate();
return thisprogress;
int totalProgressCount = 0;
- private void removeProgressPanel(JPanel progbar)
- {
- if (progressPanel != null)
- {
- synchronized (progressPanel)
- {
+ private void removeProgressPanel(JPanel progbar) {
+ if (progressPanel != null) {
+ synchronized (progressPanel) {
progressPanel.remove(progbar);
GridLayout gl = (GridLayout) progressPanel.getLayout();
gl.setRows(gl.getRows() - 1);
- if (--totalProgressCount < 1)
- {
+ if (--totalProgressCount < 1) {
this.getContentPane().remove(progressPanel);
progressPanel = null;
}
validate();
}
- public void stopLoading()
- {
+ public void stopLoading() {
fileLoadingCount--;
- if (fileLoadingCount < 1)
- {
- while (fileLoadingPanels.size() > 0)
- {
+ if (fileLoadingCount < 1) {
+ while (fileLoadingPanels.size() > 0) {
removeProgressPanel(fileLoadingPanels.remove(0));
}
fileLoadingPanels.clear();
validate();
}
- public static int getViewCount(String alignmentId)
- {
+ public static int getViewCount(String alignmentId) {
AlignmentViewport[] aps = getViewports(alignmentId);
return (aps == null) ? 0 : aps.length;
}
/**
*
- * @param alignmentId
- * - if null, all sets are returned
+ * @param alignmentId - if null, all sets are returned
* @return all AlignmentPanels concerning the alignmentId sequence set
*/
- public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
- {
- if (Desktop.desktop == null)
- {
+ public static AlignmentPanel[] getAlignmentPanels(String alignmentId) {
+ if (Desktop.desktop == null) {
// no frames created and in headless mode
// TODO: verify that frames are recoverable when in headless mode
return null;
}
List<AlignmentPanel> aps = new ArrayList<>();
AlignFrame[] frames = getAlignFrames();
- if (frames == null)
- {
+ if (frames == null) {
return null;
}
- for (AlignFrame af : frames)
- {
- for (AlignmentPanel ap : af.alignPanels)
- {
- if (alignmentId == null
- || alignmentId.equals(ap.av.getSequenceSetId()))
- {
+ for (AlignFrame af : frames) {
+ for (AlignmentPanel ap : af.alignPanels) {
+ if (alignmentId == null || alignmentId.equals(ap.av.getSequenceSetId())) {
aps.add(ap);
}
}
}
- if (aps.size() == 0)
- {
- return null;
- }
- AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
- return vap;
- }
-
- /**
- * get all the viewports on an alignment.
- *
- * @param sequenceSetId
- * unique alignment id (may be null - all viewports returned in that
- * case)
- * @return all viewports on the alignment bound to sequenceSetId
- */
- public static AlignmentViewport[] getViewports(String sequenceSetId)
- {
- List<AlignmentViewport> viewp = new ArrayList<>();
- 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)
- {
- // 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();
+ if (aps.size() == 0) {
+ return null;
}
+ AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
+ return vap;
}
- 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()
- {
+ /**
+ * get all the viewports on an alignment.
+ *
+ * @param sequenceSetId unique alignment id (may be null - all viewports
+ * returned in that case)
+ * @return all viewports on the alignment bound to sequenceSetId
+ */
+ public static AlignmentViewport[] getViewports(String sequenceSetId) {
+ List<AlignmentViewport> viewp = new ArrayList<>();
+ if (desktop != null) {
+ AlignFrame[] frames = Desktop.getAlignFrames();
- @Override
- public void actionPerformed(ActionEvent e)
- {
- 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();
+ 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);
}
- };
- });
- VamsasStMenu.add(sessit);
+ }
+ } else {
+ viewp.add(afr.getViewport());
+ }
}
- // 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);
+ if (viewp.size() > 0) {
+ 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)
- {
- // TODO: JAL-3048 not needed for Jalview-JS
-
- if (v_client != null)
- {
- // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
- JalviewFileChooser chooser = new JalviewFileChooser("vdj",
- "Vamsas Document");
+ /**
+ * 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;
+ }
- 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)
- {
- 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);
+ // 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);
+ }
- } 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)
- {
- Cache.log.debug("Setting gui for Vamsas update "
- + (b ? "in progress" : "finished"));
+ 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 (vamUpdate != null)
- {
- this.removeProgressPanel(vamUpdate);
+ 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)
- {
- vamUpdate = this.addProgressPanel(
- MessageManager.getString("label.updating_vamsas_session"));
+
+ // refresh the feature setting UI for the source frame if it exists
+ if (source.featureSettings != null && source.featureSettings.isOpen()) {
+ source.showFeatureSettingsUI();
}
- vamsasStart.setVisible(!b);
- vamsasStop.setVisible(!b);
- vamsasSave.setVisible(!b);
+
}
- public JInternalFrame[] getAllFrames()
- {
+ public JInternalFrame[] getAllFrames() {
return desktop.getAllFrames();
}
*
* @param url
*/
- public void checkForQuestionnaire(String url)
- {
+ public void checkForQuestionnaire(String url) {
UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
// javax.swing.SwingUtilities.invokeLater(jvq);
new Thread(jvq).start();
}
- public void checkURLLinks()
- {
+ public void checkURLLinks() {
// Thread off the URL link checker
- addDialogThread(new Runnable()
- {
+ addDialogThread(new Runnable() {
@Override
- public void run()
- {
- if (Cache.getDefault("CHECKURLLINKS", true))
- {
+ public void run() {
+ if (Cache.getDefault("CHECKURLLINKS", true)) {
// check what the actual links are - if it's just the default don't
// bother with the warning
- List<String> links = Preferences.sequenceUrlLinks
- .getLinksForMenu();
+ List<String> links = Preferences.sequenceUrlLinks.getLinksForMenu();
// only need to check links if there is one with a
// SEQUENCE_ID which is not the default EMBL_EBI link
ListIterator<String> li = links.listIterator();
boolean check = false;
List<JLabel> urls = new ArrayList<>();
- while (li.hasNext())
- {
+ while (li.hasNext()) {
String link = li.next();
- if (link.contains(SEQUENCE_ID)
- && !UrlConstants.isDefaultString(link))
- {
+ if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) && !UrlConstants.isDefaultString(link)) {
check = true;
int barPos = link.indexOf("|");
- String urlMsg = barPos == -1 ? link
- : link.substring(0, barPos) + ": "
- + link.substring(barPos + 1);
+ String urlMsg = barPos == -1 ? link : link.substring(0, barPos) + ": " + link.substring(barPos + 1);
urls.add(new JLabel(urlMsg));
}
}
- if (!check)
- {
+ if (!check) {
return;
}
JPanel msgPanel = new JPanel();
msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
msgPanel.add(Box.createVerticalGlue());
- JLabel msg = new JLabel(MessageManager
- .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
- JLabel msg2 = new JLabel(MessageManager
- .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+ JLabel msg = new JLabel(MessageManager.getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+ JLabel msg2 = new JLabel(MessageManager.getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
msgPanel.add(msg);
- for (JLabel url : urls)
- {
+ for (JLabel url : urls) {
msgPanel.add(url);
}
msgPanel.add(msg2);
- final JCheckBox jcb = new JCheckBox(
- MessageManager.getString("label.do_not_display_again"));
- jcb.addActionListener(new ActionListener()
- {
+ final JCheckBox jcb = new JCheckBox(MessageManager.getString("label.do_not_display_again"));
+ jcb.addActionListener(new ActionListener() {
@Override
- public void actionPerformed(ActionEvent e)
- {
+ public void actionPerformed(ActionEvent e) {
// update Cache settings for "don't show this again"
boolean showWarningAgain = !jcb.isSelected();
- Cache.setProperty("CHECKURLLINKS",
- Boolean.valueOf(showWarningAgain).toString());
+ Cache.setProperty("CHECKURLLINKS", Boolean.valueOf(showWarningAgain).toString());
}
});
msgPanel.add(jcb);
JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
- MessageManager
- .getString("label.SEQUENCE_ID_no_longer_used"),
- JvOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.SEQUENCE_ID_no_longer_used"), JvOptionPane.WARNING_MESSAGE);
}
}
});
*
* @author AMW
*/
- public class MyDesktopPane extends JDesktopPane
- implements Runnable
- {
+ public class MyDesktopPane extends JDesktopPane implements Runnable {
private static final float ONE_MB = 1048576f;
boolean showMemoryUsage = false;
java.text.NumberFormat df;
- float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
- percentUsage;
+ float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage;
- public MyDesktopPane(boolean showMemoryUsage)
- {
+ public MyDesktopPane(boolean showMemoryUsage) {
showMemoryUsage(showMemoryUsage);
}
- public void showMemoryUsage(boolean showMemory)
- {
+ public void showMemoryUsage(boolean showMemory) {
this.showMemoryUsage = showMemory;
- if (showMemory)
- {
+ if (showMemory) {
Thread worker = new Thread(this);
worker.start();
}
repaint();
}
- public boolean isShowMemoryUsage()
- {
+ public boolean isShowMemoryUsage() {
return showMemoryUsage;
}
@Override
- public void run()
- {
+ public void run() {
df = java.text.NumberFormat.getNumberInstance();
df.setMaximumFractionDigits(2);
runtime = Runtime.getRuntime();
- while (showMemoryUsage)
- {
- try
- {
+ while (showMemoryUsage) {
+ try {
maxMemory = runtime.maxMemory() / ONE_MB;
allocatedMemory = runtime.totalMemory() / ONE_MB;
freeMemory = runtime.freeMemory() / ONE_MB;
repaint();
// sleep after showing usage
Thread.sleep(3000);
- } catch (Exception ex)
- {
+ } catch (Exception ex) {
ex.printStackTrace();
}
}
}
@Override
- public void paintComponent(Graphics g)
- {
- if (showMemoryUsage && g != null && df != null)
- {
- if (percentUsage < 20)
- {
+ public void paintComponent(Graphics g) {
+ if (showMemoryUsage && g != null && df != null) {
+ if (percentUsage < 20) {
g.setColor(Color.red);
}
FontMetrics fm = g.getFontMetrics();
- if (fm != null)
- {
- g.drawString(MessageManager.formatMessage("label.memory_stats",
- new Object[]
- { df.format(totalFreeMemory), df.format(maxMemory),
- df.format(percentUsage) }),
- 10, getHeight() - fm.getHeight());
+ if (fm != null) {
+ g.drawString(
+ MessageManager.formatMessage("label.memory_stats",
+ new Object[] { df.format(totalFreeMemory), df.format(maxMemory), df.format(percentUsage) }),
+ 10, getHeight() - fm.getHeight());
}
}
+
+ // output debug scale message. Important for jalview.bin.HiDPISettingTest2
+ Desktop.debugScaleMessage(Desktop.getDesktop().getGraphics());
}
}
*
* @return an array of AlignFrame, or null if none found
*/
- public static AlignFrame[] getAlignFrames()
- {
- if (Jalview.isHeadlessMode())
- {
+ public static AlignFrame[] getAlignFrames() {
+ if (Jalview.isHeadlessMode()) {
// Desktop.desktop is null in headless mode
return new AlignFrame[] { Jalview.currentAlignFrame };
}
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- if (frames == null)
- {
+ if (frames == null) {
return null;
}
List<AlignFrame> avp = new ArrayList<>();
// REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
- {
- if (frames[i] instanceof AlignFrame)
- {
+ for (int i = frames.length - 1; i > -1; i--) {
+ if (frames[i] instanceof AlignFrame) {
avp.add((AlignFrame) frames[i]);
- }
- else if (frames[i] instanceof SplitFrame)
- {
+ } else if (frames[i] instanceof SplitFrame) {
/*
* Also check for a split frame containing an AlignFrame
*/
GSplitFrame sf = (GSplitFrame) frames[i];
- if (sf.getTopFrame() instanceof AlignFrame)
- {
+ if (sf.getTopFrame() instanceof AlignFrame) {
avp.add((AlignFrame) sf.getTopFrame());
}
- if (sf.getBottomFrame() instanceof AlignFrame)
- {
+ if (sf.getBottomFrame() instanceof AlignFrame) {
avp.add((AlignFrame) sf.getBottomFrame());
}
}
}
- if (avp.size() == 0)
- {
+ if (avp.size() == 0) {
return null;
}
AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]);
*
* @return
*/
- public GStructureViewer[] getJmols()
- {
+ public GStructureViewer[] getJmols() {
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- if (frames == null)
- {
+ if (frames == null) {
return null;
}
List<GStructureViewer> avp = new ArrayList<>();
// REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--)
- {
- if (frames[i] instanceof AppJmol)
- {
+ for (int i = frames.length - 1; i > -1; i--) {
+ if (frames[i] instanceof AppJmol) {
GStructureViewer af = (GStructureViewer) frames[i];
avp.add(af);
}
}
- if (avp.size() == 0)
- {
+ if (avp.size() == 0) {
return null;
}
GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]);
* Add Groovy Support to Jalview
*/
@Override
- public void groovyShell_actionPerformed()
- {
- try
- {
+ public void groovyShell_actionPerformed() {
+ try {
openGroovyConsole();
- } catch (Exception ex)
- {
- jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+ } catch (Exception ex) {
+ jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.couldnt_create_groovy_shell"),
- MessageManager.getString("label.groovy_support_failed"),
- JvOptionPane.ERROR_MESSAGE);
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE);
}
}
/**
* Open the Groovy console
*/
- void openGroovyConsole()
- {
- if (groovyConsole == null)
- {
+ void openGroovyConsole() {
+ if (groovyConsole == null) {
groovyConsole = new groovy.ui.Console();
groovyConsole.setVariable("Jalview", this);
groovyConsole.run();
/*
* 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.addWindowListener(new WindowAdapter() {
@Override
- public void windowClosed(WindowEvent e)
- {
+ public void windowClosed(WindowEvent e) {
/*
* rebind CMD-Q from Groovy Console to Jalview Quit
*/
((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
*/
- protected void addQuitHandler()
- {
- getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
- .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()),
- "Quit");
- getRootPane().getActionMap().put("Quit", new AbstractAction()
- {
+ protected void addQuitHandler() {
+ getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke.getKeyStroke(KeyEvent.VK_Q, jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
+ "Quit");
+ getRootPane().getActionMap().put("Quit", new AbstractAction() {
@Override
- public void actionPerformed(ActionEvent e)
- {
+ public void actionPerformed(ActionEvent e) {
quit();
}
});
/**
* Enable or disable 'Run Groovy script' in AlignFrame calculate menus
*
- * @param enabled
- * true if Groovy console is open
+ * @param enabled true if Groovy console is open
*/
- public void enableExecuteGroovy(boolean enabled)
- {
+ 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);
AlignFrame[] alignFrames = getAlignFrames();
- if (alignFrames != null)
- {
- for (AlignFrame af : alignFrames)
- {
+ if (alignFrames != null) {
+ for (AlignFrame af : alignFrames) {
af.setGroovyEnabled(enabled);
}
}
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
@Override
- public void setProgressBar(String message, long id)
- {
- if (progressBars == null)
- {
+ public void setProgressBar(String message, long id) {
+ if (progressBars == null) {
progressBars = new Hashtable<>();
progressBarHandlers = new Hashtable<>();
}
- if (progressBars.get(new Long(id)) != null)
- {
- JPanel panel = progressBars.remove(new Long(id));
- if (progressBarHandlers.contains(new Long(id)))
- {
- progressBarHandlers.remove(new Long(id));
+ if (progressBars.get(Long.valueOf(id)) != null) {
+ JPanel panel = progressBars.remove(Long.valueOf(id));
+ if (progressBarHandlers.contains(Long.valueOf(id))) {
+ progressBarHandlers.remove(Long.valueOf(id));
}
removeProgressPanel(panel);
- }
- else
- {
- progressBars.put(new Long(id), addProgressPanel(message));
+ } else {
+ progressBars.put(Long.valueOf(id), addProgressPanel(message));
}
}
* jalview.gui.IProgressIndicatorHandler)
*/
@Override
- public void registerHandler(final long id,
- final IProgressIndicatorHandler handler)
- {
- if (progressBarHandlers == null
- || !progressBars.containsKey(new Long(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));
- if (handler.canCancel())
- {
- JButton cancel = new JButton(
- MessageManager.getString("action.cancel"));
+ public void registerHandler(final long id, final IProgressIndicatorHandler handler) {
+ if (progressBarHandlers == null || !progressBars.containsKey(Long.valueOf(id))) {
+ throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
+ }
+ progressBarHandlers.put(Long.valueOf(id), handler);
+ final JPanel progressPanel = progressBars.get(Long.valueOf(id));
+ if (handler.canCancel()) {
+ JButton cancel = new JButton(MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
- cancel.addActionListener(new ActionListener()
- {
+ cancel.addActionListener(new ActionListener() {
@Override
- public void actionPerformed(ActionEvent e)
- {
+ public void actionPerformed(ActionEvent e) {
handler.cancelActivity(id);
- us.setProgressBar(MessageManager
- .formatMessage("label.cancelled_params", new Object[]
- { ((JLabel) progressPanel.getComponent(0)).getText() }),
- id);
+ us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
+ new Object[] { ((JLabel) progressPanel.getComponent(0)).getText() }), id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
* @return true if any progress bars are still active
*/
@Override
- public boolean operationInProgress()
- {
- if (progressBars != null && progressBars.size() > 0)
- {
+ public boolean operationInProgress() {
+ if (progressBars != null && progressBars.size() > 0) {
return true;
}
return false;
* @param viewport
* @return alignFrame for viewport
*/
- public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
- {
- if (desktop != null)
- {
- AlignmentPanel[] aps = getAlignmentPanels(
- viewport.getSequenceSetId());
- for (int panel = 0; aps != null && panel < aps.length; panel++)
- {
- if (aps[panel] != null && aps[panel].av == viewport)
- {
+ public static AlignFrame getAlignFrameFor(AlignViewportI viewport) {
+ if (desktop != null) {
+ AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
+ for (int panel = 0; aps != null && panel < aps.length; panel++) {
+ if (aps[panel] != null && aps[panel].av == viewport) {
return aps[panel].alignFrame;
}
}
return null;
}
- public VamsasApplication getVamsasApplication()
- {
- return v_client;
+ public VamsasApplication getVamsasApplication() {
+ // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
+ return null;
}
*
* @return inBatchMode
*/
- public boolean isInBatchMode()
- {
+ public boolean isInBatchMode() {
return inBatchMode;
}
*
* @param inBatchMode
*/
- public void setInBatchMode(boolean inBatchMode)
- {
+ public void setInBatchMode(boolean inBatchMode) {
this.inBatchMode = inBatchMode;
}
- public void startServiceDiscovery()
- {
+ /**
+ * start service discovery and wait till it is done
+ */
+ public void startServiceDiscovery() {
startServiceDiscovery(false);
}
- public void startServiceDiscovery(boolean blocking)
- {
+ /**
+ * 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
- if (true)
- {
+ if (true) {
// todo: changesupport handlers need to be transferred
- if (discoverer == null)
- {
+ if (discoverer == null) {
discoverer = new jalview.ws.jws1.Discoverer();
// register PCS handler for desktop.
discoverer.addPropertyChangeListener(changeSupport);
(t0 = new Thread(discoverer)).start();
}
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
- {
- t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .startDiscoverer(changeSupport);
+ if (ignore_SHOW_JWS2_SERVICES_preference || Cache.getDefault("SHOW_JWS2_SERVICES", true)) {
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(changeSupport);
}
Thread t3 = null;
{
// TODO: do rest service discovery
}
- if (blocking)
- {
- while (alive)
- {
- try
- {
+ if (blocking) {
+ while (alive) {
+ try {
Thread.sleep(15);
- } catch (Exception e)
- {
+ } catch (Exception e) {
}
- alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
- || (t3 != null && t3.isAlive())
- || (t0 != null && t0.isAlive());
+ alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) || (t3 != null && t3.isAlive())
+ || (t0 != null && t0.isAlive());
}
}
}
*
* @param evt
*/
- protected void JalviewServicesChanged(PropertyChangeEvent evt)
- {
- if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
- {
- final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .getErrorMessages();
- if (ermsg != null)
- {
- if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
- {
- if (serviceChangedDialog == null)
- {
+ protected void JalviewServicesChanged(PropertyChangeEvent evt) {
+ if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) {
+ final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().getErrorMessages();
+ if (ermsg != null) {
+ if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) {
+ if (serviceChangedDialog == null) {
// only run if we aren't already displaying one of these.
- addDialogThread(serviceChangedDialog = new Runnable()
- {
+ addDialogThread(serviceChangedDialog = new Runnable() {
@Override
- public void run()
- {
+ public void run() {
/*
* 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();
*/
JvOptionPane.showConfirmDialog(Desktop.desktop,
- new JLabel("<html><table width=\"450\"><tr><td>"
- + ermsg + "</td></tr></table>"
- + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
- + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
- + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
- + " Tools->Preferences dialog box to change them.</p></html>"),
- "Web Service Configuration Problem",
- JvOptionPane.DEFAULT_OPTION,
- JvOptionPane.ERROR_MESSAGE);
+ new JLabel("<html><table width=\"450\"><tr><td>" + ermsg + "</td></tr></table>"
+ + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
+ + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
+ + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+ + " Tools->Preferences dialog box to change them.</p></html>"),
+ "Web Service Configuration Problem", JvOptionPane.DEFAULT_OPTION, JvOptionPane.ERROR_MESSAGE);
serviceChangedDialog = null;
}
});
}
- }
- else
- {
- Cache.log.error(
- "Errors reported by JABA discovery service. Check web services preferences.\n"
- + ermsg);
+ } else {
+ jalview.bin.Console.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg);
}
}
}
*
* @param url
*/
- public static void showUrl(final String url)
- {
+ public static void showUrl(final String url) {
showUrl(url, Desktop.instance);
}
* Like showUrl but allows progress handler to be specified
*
* @param url
- * @param progress
- * (null) or object implementing IProgressIndicator
+ * @param progress (null) or object implementing IProgressIndicator
*/
- public static void showUrl(final String url,
- final IProgressIndicator progress)
- {
- new Thread(new Runnable()
- {
+ public static void showUrl(final String url, final IProgressIndicator progress) {
+ new Thread(new Runnable() {
@Override
- public void run()
- {
- try
- {
- if (progress != null)
- {
- progress.setProgressBar(MessageManager
- .formatMessage("status.opening_params", new Object[]
- { url }), this.hashCode());
+ public void run() {
+ try {
+ if (progress != null) {
+ progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new Object[] { url }),
+ this.hashCode());
}
jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception ex)
- {
+ } catch (Exception ex) {
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager
- .getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"),
- JvOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"), JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
- if (progress != null)
- {
+ if (progress != null) {
progress.setProgressBar(null, this.hashCode());
}
}
public static WsParamSetManager wsparamManager = null;
- public static ParamManager getUserParameterStore()
- {
- if (wsparamManager == null)
- {
+ public static ParamManager getUserParameterStore() {
+ if (wsparamManager == null) {
wsparamManager = new WsParamSetManager();
}
return wsparamManager;
*
* @param e
*/
- public static void hyperlinkUpdate(HyperlinkEvent e)
- {
- if (e.getEventType() == EventType.ACTIVATED)
- {
+ public static void hyperlinkUpdate(HyperlinkEvent e) {
+ if (e.getEventType() == EventType.ACTIVATED) {
String url = null;
- try
- {
+ try {
url = e.getURL().toString();
Desktop.showUrl(url);
- } catch (Exception x)
- {
- 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.");
- }
+ } catch (Exception x) {
+ if (url != null) {
+ jalview.bin.Console.error("Couldn't handle string " + url + " as a URL.");
}
// ignore any exceptions due to dud links.
}
*
* @param prompter
*/
- public void addDialogThread(final Runnable prompter)
- {
- dialogExecutor.submit(new Runnable()
- {
+ public void addDialogThread(final Runnable prompter) {
+ dialogExecutor.submit(new Runnable() {
@Override
- public void run()
- {
- if (dialogPause)
- {
- try
- {
+ public void run() {
+ if (dialogPause) {
+ try {
block.acquire();
- } catch (InterruptedException x)
- {
+ } catch (InterruptedException x) {
}
- ;
}
- if (instance == null)
- {
+ if (instance == null) {
return;
}
- try
- {
+ try {
SwingUtilities.invokeAndWait(prompter);
- } catch (Exception q)
- {
- Cache.log.warn("Unexpected Exception in dialog thread.", q);
+ } catch (Exception q) {
+ jalview.bin.Console.warn("Unexpected Exception in dialog thread.", q);
}
}
});
}
- public void startDialogQueue()
- {
+ public void startDialogQueue() {
// set the flag so we don't pause waiting for another permit and semaphore
// the current task to begin
dialogPause = false;
* </pre>
*/
@Override
- protected void snapShotWindow_actionPerformed(ActionEvent e)
- {
+ protected void snapShotWindow_actionPerformed(ActionEvent e) {
// currently the menu option to do this is not shown
invalidate();
int width = getWidth();
int height = getHeight();
- File of = new File(
- "Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
- ImageWriterI writer = new ImageWriterI()
- {
+ File of = new File("Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
+ ImageWriterI writer = new ImageWriterI() {
@Override
- public void exportImage(Graphics g) throws Exception
- {
+ public void exportImage(Graphics g) throws Exception {
paintAll(g);
- Cache.log.info("Successfully written snapshot to file "
- + of.getAbsolutePath());
+ 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);
+ ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, title);
exporter.doExport(of, this, width, height, title);
}
*
* @param sf
*/
- public void explodeViews(SplitFrame sf)
- {
+ public void explodeViews(SplitFrame sf) {
AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame();
AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame();
- List<? extends AlignmentViewPanel> topPanels = oldTopFrame
- .getAlignPanels();
- List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame
- .getAlignPanels();
+ List<? extends AlignmentViewPanel> topPanels = oldTopFrame.getAlignPanels();
+ List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame.getAlignPanels();
int viewCount = topPanels.size();
- if (viewCount < 2)
- {
+ if (viewCount < 2) {
return;
}
/*
- * 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--)
- {
+ 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
AlignFrame newTopFrame = new AlignFrame(topPanel);
newTopFrame.setSize(oldTopFrame.getSize());
newTopFrame.setVisible(true);
- Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
- .getExplodedGeometry();
- if (geometry != null)
- {
+ Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()).getExplodedGeometry();
+ if (geometry != null) {
newTopFrame.setSize(geometry.getSize());
}
AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
newBottomFrame.setSize(oldBottomFrame.getSize());
newBottomFrame.setVisible(true);
- geometry = ((AlignViewport) bottomPanel.getAlignViewport())
- .getExplodedGeometry();
- if (geometry != null)
- {
+ geometry = ((AlignViewport) bottomPanel.getAlignViewport()).getExplodedGeometry();
+ if (geometry != null) {
newBottomFrame.setSize(geometry.getSize());
}
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- JInternalFrame splitFrame = new SplitFrame(newTopFrame,
- newBottomFrame);
- if (geometry != null)
- {
+ JInternalFrame splitFrame = new SplitFrame(newTopFrame, newBottomFrame);
+ if (geometry != null) {
splitFrame.setLocation(geometry.getLocation());
}
Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
}
/*
- * 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();
*
* @param source
*/
- public void gatherViews(GSplitFrame source)
- {
+ public void gatherViews(GSplitFrame source) {
/*
* special handling of explodedGeometry for a view within a SplitFrame: - it
* holds the (x, y) position of the enclosing SplitFrame, and the (width,
*/
AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
- myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
- source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
- myBottomFrame.viewport
- .setExplodedGeometry(new Rectangle(source.getX(), source.getY(),
- myBottomFrame.getWidth(), myBottomFrame.getHeight()));
+ myTopFrame.viewport.setExplodedGeometry(
+ new Rectangle(source.getX(), source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
+ myBottomFrame.viewport.setExplodedGeometry(
+ new Rectangle(source.getX(), source.getY(), myBottomFrame.getWidth(), myBottomFrame.getHeight()));
myTopFrame.viewport.setGatherViewsHere(true);
myBottomFrame.viewport.setGatherViewsHere(true);
String topViewId = myTopFrame.viewport.getSequenceSetId();
String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
JInternalFrame[] frames = desktop.getAllFrames();
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof SplitFrame && frame != source)
- {
+ for (JInternalFrame frame : frames) {
+ if (frame instanceof SplitFrame && frame != source) {
SplitFrame sf = (SplitFrame) frame;
AlignFrame topFrame = (AlignFrame) sf.getTopFrame();
AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame();
boolean gatherThis = false;
- for (int a = 0; a < topFrame.alignPanels.size(); a++)
- {
+ for (int a = 0; a < topFrame.alignPanels.size(); a++) {
AlignmentPanel topPanel = topFrame.alignPanels.get(a);
AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a);
if (topViewId.equals(topPanel.av.getSequenceSetId())
- && bottomViewId.equals(bottomPanel.av.getSequenceSetId()))
- {
+ && bottomViewId.equals(bottomPanel.av.getSequenceSetId())) {
gatherThis = true;
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- topPanel.av.setExplodedGeometry(
- new Rectangle(sf.getLocation(), topFrame.getSize()));
- bottomPanel.av.setExplodedGeometry(
- new Rectangle(sf.getLocation(), bottomFrame.getSize()));
+ topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), topFrame.getSize()));
+ bottomPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), bottomFrame.getSize()));
myTopFrame.addAlignmentPanel(topPanel, false);
myBottomFrame.addAlignmentPanel(bottomPanel, false);
}
}
- if (gatherThis)
- {
+ if (gatherThis) {
topFrame.getAlignPanels().clear();
bottomFrame.getAlignPanels().clear();
sf.close();
myTopFrame.setDisplayedView(myTopFrame.alignPanel);
}
- public static groovy.ui.Console getGroovyConsole()
- {
+ public static groovy.ui.Console getGroovyConsole() {
return groovyConsole;
}
*
* 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
+ * @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
- {
-
- // 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
- {
- urlFlavour = new DataFlavor(
- "application/x-java-url; class=java.net.URL");
- } catch (ClassNotFoundException cfe)
- {
- Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ 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"), 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))
- {
+ if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) {
- try
- {
+ 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)
- {
+ if (url != null) {
protocols.add(DataSourceType.URL);
files.add(url.toString());
- Cache.log.debug("Drop handled as URL dataflavor "
- + files.get(files.size() - 1));
+ jalview.bin.Console.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1));
return;
- }
- else
- {
- if (Platform.isAMac())
- {
- System.err.println(
- "Please ignore plist error - occurs due to problem with java 8 on OSX");
+ } else {
+ 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);
+ } catch (Throwable ex) {
+ jalview.bin.Console.debug("URL drop handler failed.", ex);
}
}
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
- {
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) {
// Works on Windows and MacOSX
- Cache.log.debug("Drop handled as javaFileListFlavor");
- for (Object file : (List) t
- .getTransferData(DataFlavor.javaFileListFlavor))
- {
+ jalview.bin.Console.debug("Drop handled as javaFileListFlavor");
+ for (Object file : (List) t.getTransferData(DataFlavor.javaFileListFlavor)) {
files.add(file);
protocols.add(DataSourceType.FILE);
}
- }
- else
- {
+ } else {
// Unix like behaviour
boolean added = false;
String data = null;
- if (t.isDataFlavorSupported(uriListFlavor))
- {
- Cache.log.debug("Drop handled as uriListFlavor");
+ if (t.isDataFlavorSupported(uriListFlavor)) {
+ jalview.bin.Console.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
data = (String) t.getTransferData(uriListFlavor);
}
- if (data == null)
- {
+ 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");
- if (t.isDataFlavorSupported(textDf))
- {
+ DataFlavor textDf = new DataFlavor("text/plain;class=java.lang.String");
+ if (t.isDataFlavorSupported(textDf)) {
data = (String) t.getTransferData(textDf);
}
- Cache.log.debug("Plain text drop content returned "
- + (data == null ? "Null - failed" : data));
+ jalview.bin.Console.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data));
}
- if (data != null)
- {
- while (protocols.size() < files.size())
- {
- Cache.log.debug("Adding missing FILE protocol for "
- + files.get(protocols.size()));
+ if (data != null) {
+ while (protocols.size() < files.size()) {
+ jalview.bin.Console.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();)
- {
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(data, "\r\n"); st.hasMoreTokens();) {
added = true;
String s = st.nextToken();
- if (s.startsWith("#"))
- {
+ 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"))
- {
+ if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http")) {
protocols.add(DataSourceType.URL);
files.add(uri.toString());
- }
- else
- {
+ } else {
// otherwise preserve old behaviour: catch all for file objects
java.io.File file = new java.io.File(uri);
protocols.add(DataSourceType.FILE);
}
}
- if (Cache.log.isDebugEnabled())
- {
- if (data == null || !added)
- {
+ if (jalview.bin.Console.isDebugEnabled()) {
+ if (data == null || !added) {
- if (t.getTransferDataFlavors() != null
- && t.getTransferDataFlavors().length > 0)
- {
- Cache.log.debug(
- "Couldn't resolve drop data. Here are the supported flavors:");
- for (DataFlavor fl : t.getTransferDataFlavors())
- {
- Cache.log.debug(
- "Supported transfer dataflavor: " + fl.toString());
+ if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) {
+ jalview.bin.Console.debug("Couldn't resolve drop data. Here are the supported flavors:");
+ for (DataFlavor fl : t.getTransferDataFlavors()) {
+ jalview.bin.Console.debug("Supported transfer dataflavor: " + fl.toString());
Object df = t.getTransferData(fl);
- if (df != null)
- {
- Cache.log.debug("Retrieves: " + df);
- }
- else
- {
- Cache.log.debug("Retrieved nothing");
+ if (df != null) {
+ jalview.bin.Console.debug("Retrieves: " + df);
+ } else {
+ jalview.bin.Console.debug("Retrieved nothing");
}
}
- }
- else
- {
- Cache.log.debug("Couldn't resolve dataflavor for drop: "
- + t.toString());
+ } else {
+ jalview.bin.Console.debug("Couldn't resolve dataflavor for drop: " + t.toString());
}
}
}
}
- if (Platform.isWindows())
-
- {
- Cache.log.debug("Scanning dropped content for Windows Link Files");
+ 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();
+ 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
- {
+ && (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));
+ 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
- + " to extract protocol: " + protocols.get(f));
- } catch (Exception ex)
- {
- Cache.log.error(
- "Couldn't parse " + files.get(f) + " as a link file.",
- ex);
+ 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);
}
}
}
* depending on the state of the controlling menu item
*/
@Override
- protected void showExperimental_actionPerformed(boolean selected)
- {
+ protected void showExperimental_actionPerformed(boolean selected) {
Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
}
* 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
+ * @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)
- {
+ 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))
- {
+ 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