X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=94145bdc61a964a2a957d412e8d308af4e038f13;hb=4c007a518fc7e2fdaa863f16cb715f8e45e6cfbf;hp=39c68a0eb2c283a46d6681a6613cbce575762d22;hpb=04e2d97b71fad3d9d02abbe292ea1fa9ba6d1438;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 39c68a0..94145bd 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -54,13 +54,17 @@ import java.beans.PropertyChangeListener; import java.io.File; 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.Locale; import java.util.Vector; +import java.util.concurrent.Callable; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; @@ -78,6 +82,7 @@ import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JComponent; import javax.swing.JDesktopPane; +import javax.swing.JFrame; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JMenuItem; @@ -87,6 +92,7 @@ import javax.swing.JProgressBar; import javax.swing.JTextField; import javax.swing.KeyStroke; import javax.swing.SwingUtilities; +import javax.swing.WindowConstants; import javax.swing.event.HyperlinkEvent; import javax.swing.event.HyperlinkEvent.EventType; import javax.swing.event.InternalFrameAdapter; @@ -99,6 +105,7 @@ import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.gui.ImageExporter.ImageWriterI; +import jalview.gui.QuitHandler.QResponse; import jalview.io.BackupFiles; import jalview.io.DataSourceType; import jalview.io.FileFormat; @@ -118,6 +125,7 @@ import jalview.urls.IdOrgSettings; import jalview.util.BrowserLauncher; import jalview.util.ChannelProperties; import jalview.util.ImageMaker.TYPE; +import jalview.util.LaunchUtils; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.ShortcutKeyMaskExWrapper; @@ -147,7 +155,7 @@ public class Desktop extends jalview.jbgui.GDesktop boolean logo = (bg_logo_url != null || uod_logo_url != null); StringBuilder sb = new StringBuilder(); sb.append( - "

Development managed by The Barton Group, University of Dundee, Scotland, UK."); + "

Jalview is free software released under GPLv3.

Development is managed by The Barton Group, University of Dundee, Scotland, UK."); if (logo) { sb.append("
"); @@ -159,11 +167,11 @@ public class Desktop extends jalview.jbgui.GDesktop : " \"University"); sb.append( - "

For help, see the FAQ at www.jalview.org/faq and/or join the jalview-discuss@jalview.org mailing list"); + "

For help, see www.jalview.org/faq and join discourse.jalview.org"); sb.append("

If you use Jalview, please cite:" + "
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" + "
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench" - + "
Bioinformatics doi: 10.1093/bioinformatics/btp033"); + + "
Bioinformatics doi: 10.1093/bioinformatics/btp033"); CITATION = sb.toString(); } @@ -179,7 +187,7 @@ public class Desktop extends jalview.jbgui.GDesktop private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; - protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT"; + public static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT"; public static HashMap savingFiles = new HashMap(); @@ -394,34 +402,67 @@ public class Desktop extends jalview.jbgui.GDesktop doConfigureStructurePrefs(); setTitle(ChannelProperties.getProperty("app_name") + " " + Cache.getProperty("VERSION")); - /* - if (!Platform.isAMac()) - { - // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE); - } - else - { - this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); - } - */ - try - { - APQHandlers.setAPQHandlers(this); - } catch (Throwable t) + /** + * 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()) { - System.out.println("Error setting APQHandlers: " + t.toString()); - // t.printStackTrace(); + if (LaunchUtils.getJavaVersion() >= 11) + { + jalview.bin.Console.info( + "Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that."); + } + 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)); + } } + setIconImages(ChannelProperties.getIconList()); + // override quit handling when GUI OS close [X] button pressed + this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); addWindowListener(new WindowAdapter() { - @Override public void windowClosing(WindowEvent ev) { - quit(); + QuitHandler.QResponse ret = desktopQuit(true, true); // ui, disposeFlag } }); @@ -433,8 +474,6 @@ public class Desktop extends jalview.jbgui.GDesktop showMemusage.setSelected(selmemusage); desktop.setBackground(Color.white); - this.setIconImages(ChannelProperties.getIconList()); - getContentPane().setLayout(new BorderLayout()); // alternate config - have scrollbars - see notes in JAL-153 // JScrollPane sp = new JScrollPane(); @@ -512,11 +551,11 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void run() { - Cache.log.debug("Filechooser init thread started."); + jalview.bin.Console.debug("Filechooser init thread started."); String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); - Cache.log.debug("Filechooser init thread finished."); + jalview.bin.Console.debug("Filechooser init thread finished."); } }).start(); // Add the service change listener @@ -527,8 +566,9 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void propertyChange(PropertyChangeEvent evt) { - Cache.log.debug("Firing service changed event for " - + evt.getNewValue()); + jalview.bin.Console + .debug("Firing service changed event for " + + evt.getNewValue()); JalviewServicesChanged(evt); } }); @@ -536,15 +576,6 @@ public class Desktop extends jalview.jbgui.GDesktop this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); - this.addWindowListener(new WindowAdapter() - { - @Override - public void windowClosing(WindowEvent evt) - { - quit(); - } - }); - MouseAdapter ma; this.addMouseListener(ma = new MouseAdapter() { @@ -593,8 +624,9 @@ public class Desktop extends jalview.jbgui.GDesktop 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, true)); + Cache.getDefault(Preferences.USE_RNAVIEW, false)); } else { @@ -613,35 +645,39 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void run() { - Cache.log.debug("Starting news thread."); + jalview.bin.Console.debug("Starting news thread."); jvnews = new BlogReader(me); showNews.setVisible(true); - Cache.log.debug("Completed news thread."); + jalview.bin.Console.debug("Completed news thread."); } }).start(); } public void getIdentifiersOrgData() { - // Thread off the identifiers fetcher - new Thread(new Runnable() - { - @Override - public void run() + if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) + {// Thread off the identifiers fetcher + new Thread(new Runnable() { - Cache.log.debug("Downloading data from identifiers.org"); - try - { - UrlDownloadClient.download(IdOrgSettings.getUrl(), - IdOrgSettings.getDownloadLocation()); - } catch (IOException e) + @Override + public void run() { - Cache.log.debug("Exception downloading identifiers.org data" - + e.getMessage()); + jalview.bin.Console + .debug("Downloading data from identifiers.org"); + try + { + UrlDownloadClient.download(IdOrgSettings.getUrl(), + IdOrgSettings.getDownloadLocation()); + } catch (IOException e) + { + jalview.bin.Console + .debug("Exception downloading identifiers.org data" + + e.getMessage()); + } } - } - }).start(); - + }).start(); + ; + } } @Override @@ -652,7 +688,7 @@ public class Desktop extends jalview.jbgui.GDesktop void showNews(boolean visible) { - Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); + jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news."); showNews.setSelected(visible); if (visible && !jvnews.isVisible()) { @@ -708,17 +744,17 @@ public class Desktop extends jalview.jbgui.GDesktop ih = (int) (ih * sh); while (ix >= screenSize.width) { - Cache.log.debug( + jalview.bin.Console.debug( "Window geometry location recall error: shifting horizontal to within screenbounds."); ix -= screenSize.width; } while (iy >= screenSize.height) { - Cache.log.debug( + jalview.bin.Console.debug( "Window geometry location recall error: shifting vertical to within screenbounds."); iy -= screenSize.height; } - Cache.log.debug( + jalview.bin.Console.debug( "Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw + " height:" + ih); } @@ -908,8 +944,8 @@ public class Desktop extends jalview.jbgui.GDesktop } /* - * 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() @@ -934,8 +970,7 @@ public class Desktop extends jalview.jbgui.GDesktop 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) { @@ -964,7 +999,7 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setIcon(false); } catch (java.beans.PropertyVetoException ex) { - // System.err.println(ex.toString()); + } } }); @@ -984,7 +1019,7 @@ public class Desktop extends jalview.jbgui.GDesktop { } catch (java.lang.ClassCastException cex) { - Cache.log.warn( + 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); } @@ -1141,36 +1176,32 @@ public class Desktop extends jalview.jbgui.GDesktop MessageManager.getString("label.open_local_file")); chooser.setToolTipText(MessageManager.getString("action.open")); - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() - { - File selectedFile = chooser.getSelectedFile(); - Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); + chooser.setResponseHandler(0, () -> { + File selectedFile = chooser.getSelectedFile(); + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); - FileFormatI format = chooser.getSelectedFormat(); + FileFormatI format = chooser.getSelectedFormat(); - /* - * Call IdentifyFile to verify the file contains what its extension implies. - * Skip this step for dynamically added file formats, because - * IdentifyFile does not know how to recognise them. - */ - if (FileFormats.getInstance().isIdentifiable(format)) + /* + * Call IdentifyFile to verify the file contains what its extension implies. + * Skip this step for dynamically added file formats, because IdentifyFile does + * not know how to recognise them. + */ + if (FileFormats.getInstance().isIdentifiable(format)) + { + try { - try - { - format = new IdentifyFile().identify(selectedFile, - DataSourceType.FILE); - } catch (FileFormatException e) - { - // format = null; //?? - } + 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); + return null; }); chooser.showOpenDialog(this); } @@ -1192,9 +1223,8 @@ public class Desktop extends jalview.jbgui.GDesktop 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 = "https://www."; @@ -1227,64 +1257,60 @@ public class Desktop extends jalview.jbgui.GDesktop Object[] options = new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }; - Runnable action = new Runnable() - { - @Override - public void run() - { - @SuppressWarnings("unchecked") - String url = (history instanceof JTextField - ? ((JTextField) history).getText() - : ((JComboBox) history).getSelectedItem() - .toString()); + Callable action = () -> { + @SuppressWarnings("unchecked") + String url = (history instanceof JTextField + ? ((JTextField) history).getText() + : ((JComboBox) history).getEditor().getItem() + .toString().trim()); - if (url.toLowerCase().endsWith(".jar")) + if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) + { + if (viewport != null) { - if (viewport != null) - { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, - FileFormat.Jalview); - } - else - { - new FileLoader().LoadFile(url, DataSourceType.URL, - FileFormat.Jalview); - } + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + FileFormat.Jalview); } else { - FileFormatI format = null; - try - { - format = new IdentifyFile().identify(url, DataSourceType.URL); - } catch (FileFormatException e) - { - // TODO revise error handling, distinguish between - // URL not found and response not valid - } + new FileLoader().LoadFile(url, DataSourceType.URL, + FileFormat.Jalview); + } + } + else + { + FileFormatI format = null; + try + { + format = new IdentifyFile().identify(url, DataSourceType.URL); + } catch (FileFormatException e) + { + // TODO revise error handling, distinguish between + // URL not found and response not valid + } - if (format == null) - { - String msg = MessageManager - .formatMessage("label.couldnt_locate", url); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, - MessageManager.getString("label.url_not_found"), - JvOptionPane.WARNING_MESSAGE); + 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); - return; - } + return null; // Void + } - if (viewport != null) - { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, - format); - } - else - { - new FileLoader().LoadFile(url, DataSourceType.URL, format); - } + if (viewport != null) + { + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + format); + } + else + { + new FileLoader().LoadFile(url, DataSourceType.URL, format); } } + return null; // Void }; String dialogOption = MessageManager .getString("label.input_alignment_from_url"); @@ -1314,47 +1340,87 @@ public class Desktop extends jalview.jbgui.GDesktop } /* - * Exit the program + * Check with user and saving files before actually quitting */ - @Override - public void quit() + public void desktopQuit() { - Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); - Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); - Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); - storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, - getWidth(), getHeight())); + desktopQuit(true, false); + } - if (jconsole != null) - { - storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); - jconsole.stopConsole(); - } - if (jvnews != null) - { - storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); + public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag) + { + final Callable doDesktopQuit = () -> { + Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); + Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); + Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); + storeLastKnownDimensions("", new Rectangle(getBounds().x, + getBounds().y, getWidth(), getHeight())); - } - if (dialogExecutor != null) - { - dialogExecutor.shutdownNow(); - } - closeAll_actionPerformed(null); + if (jconsole != null) + { + storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); + jconsole.stopConsole(); + } - if (groovyConsole != null) - { - // suppress a possible repeat prompt to save script - groovyConsole.setDirty(false); - groovyConsole.exit(); - } + if (jvnews != null) + { + storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); + + } + + if (dialogExecutor != null) + { + dialogExecutor.shutdownNow(); + } + + closeAll_actionPerformed(null); + + if (groovyConsole != null) + { + // suppress a possible repeat prompt to save script + groovyConsole.setDirty(false); + groovyConsole.exit(); + } + + if (QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT) + { + // note that shutdown hook will not be run + jalview.bin.Console.debug("Force Quit selected by user"); + Runtime.getRuntime().halt(0); + } + + jalview.bin.Console.debug("Quit selected by user"); + if (disposeFlag) + { + instance.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); + // instance.dispose(); + } + instance.quit(); + + return QuitHandler.gotQuitResponse(); + }; + + return QuitHandler.getQuitResponse(ui, doDesktopQuit, doDesktopQuit, + QuitHandler.defaultCancelQuit); + } + + /** + * Don't call this directly, use desktopQuit() above. Exits the program. + */ + @Override + public void quit() + { + // this will run the shutdownHook but QuitHandler.getQuitResponse() should + // not run a second time if gotQuitResponse flag has been set (i.e. user + // confirmed quit of some kind). System.exit(0); } private void storeLastKnownDimensions(String string, Rectangle jc) { - Cache.log.debug("Storing last known dimensions for " + string + ": x:" - + jc.x + " y:" + jc.y + " width:" + jc.width + " height:" - + jc.height); + jalview.bin.Console.debug("Storing last known dimensions for " + string + + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width + + " height:" + jc.height); Cache.setProperty(string + "SCREEN_X", jc.x + ""); Cache.setProperty(string + "SCREEN_Y", jc.y + ""); @@ -1408,7 +1474,7 @@ public class Desktop extends jalview.jbgui.GDesktop else if (!latestVersion.equals(Cache.getProperty("VERSION"))) { boolean red = false; - if (Cache.getProperty("VERSION").toLowerCase() + if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT) .indexOf("automated build") == -1) { red = true; @@ -1520,17 +1586,16 @@ public class Desktop extends jalview.jbgui.GDesktop protected void garbageCollect_actionPerformed(ActionEvent e) { // We simply collect the garbage - Cache.log.debug("Collecting garbage..."); + jalview.bin.Console.debug("Collecting garbage..."); System.gc(); - 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) @@ -1735,7 +1800,7 @@ public class Desktop extends jalview.jbgui.GDesktop + chosenFile.getName(), oom); } catch (Exception ex) { - Cache.log.error("Problems whilst trying to save to " + jalview.bin.Console.error("Problems whilst trying to save to " + chosenFile.getName(), ex); JvOptionPane.showMessageDialog(me, MessageManager.formatMessage( @@ -1785,42 +1850,37 @@ public class Desktop extends jalview.jbgui.GDesktop // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() + chooser.setResponseHandler(0, () -> { + File selectedFile = chooser.getSelectedFile(); + setProjectFile(selectedFile); + String choice = selectedFile.getAbsolutePath(); + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); + new Thread(new Runnable() { - File selectedFile = chooser.getSelectedFile(); - setProjectFile(selectedFile); - String choice = selectedFile.getAbsolutePath(); - Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); - new Thread(new Runnable() + @Override + public void run() { - @Override - public void run() + try { - try - { - new Jalview2XML().loadJalviewAlign(selectedFile); - } catch (OutOfMemoryError oom) - { - new OOMWarning("Whilst loading project from " + choice, oom); - } catch (Exception ex) - { - Cache.log.error( - "Problems whilst loading project from " + choice, ex); - JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.error_whilst_loading_project_from", - new Object[] - { choice }), - MessageManager - .getString("label.couldnt_load_project"), - JvOptionPane.WARNING_MESSAGE); - } + 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); } - }, "Project Loader").start(); - } + } + }, "Project Loader").start(); + return null; }); chooser.showOpenDialog(this); @@ -2030,9 +2090,8 @@ public class Desktop extends jalview.jbgui.GDesktop } /* - * Restore the view's last exploded frame geometry if known. Multiple - * views from one exploded frame share and restore the same (frame) - * position and size. + * Restore the view's last exploded frame geometry if known. Multiple views from + * one exploded frame share and restore the same (frame) position and size. */ Rectangle geometry = ap.av.getExplodedGeometry(); if (geometry != null) @@ -2121,6 +2180,7 @@ public class Desktop extends jalview.jbgui.GDesktop { source.showFeatureSettingsUI(); } + } public JInternalFrame[] getAllFrames() @@ -2413,7 +2473,7 @@ public class Desktop extends jalview.jbgui.GDesktop openGroovyConsole(); } catch (Exception ex) { - Cache.log.error("Groovy Shell Creation failed.", ex); + jalview.bin.Console.error("Groovy Shell Creation failed.", ex); JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_create_groovy_shell"), @@ -2435,9 +2495,9 @@ public class Desktop extends jalview.jbgui.GDesktop /* * 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() @@ -2460,8 +2520,8 @@ public class Desktop extends jalview.jbgui.GDesktop ((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); } @@ -2484,7 +2544,7 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void actionPerformed(ActionEvent e) { - quit(); + desktopQuit(); } }); } @@ -2498,8 +2558,8 @@ public class Desktop extends jalview.jbgui.GDesktop 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); @@ -2528,8 +2588,6 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void setProgressBar(String message, long id) { - // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK); - if (progressBars == null) { progressBars = new Hashtable<>(); @@ -2662,13 +2720,36 @@ public class Desktop extends jalview.jbgui.GDesktop this.inBatchMode = inBatchMode; } + /** + * start service discovery and wait till it is done + */ public void startServiceDiscovery() { startServiceDiscovery(false); } + /** + * start service discovery threads - blocking or non-blocking + * + * @param blocking + */ public void startServiceDiscovery(boolean blocking) { + startServiceDiscovery(blocking, false); + } + + /** + * start service discovery threads + * + * @param blocking + * - false means call returns immediately + * @param ignore_SHOW_JWS2_SERVICES_preference + * - when true JABA services are discovered regardless of user's JWS2 + * discovery preference setting + */ + public void startServiceDiscovery(boolean blocking, + boolean ignore_SHOW_JWS2_SERVICES_preference) + { boolean alive = true; Thread t0 = null, t1 = null, t2 = null; // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release @@ -2686,7 +2767,8 @@ public class Desktop extends jalview.jbgui.GDesktop (t0 = new Thread(discoverer)).start(); } - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + if (ignore_SHOW_JWS2_SERVICES_preference + || Cache.getDefault("SHOW_JWS2_SERVICES", true)) { t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() .startDiscoverer(changeSupport); @@ -2739,24 +2821,19 @@ public class Desktop extends jalview.jbgui.GDesktop /* * 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("
" + ermsg + + * } }; jd.initDialogFrame(new JLabel("
" + + * ermsg + * "
It may be that you have invalid JABA URLs in your web service preferences," * + " or mis-configured HTTP proxy settings.
" + - * "Check the Connections and Web services tab of the" - * + - * " Tools->Preferences dialog box to change them.
" - * ), true, true, "Web Service Configuration Problem", 450, - * 400); + * "Check the Connections and Web services tab of the" + + * " Tools->Preferences dialog box to change them.
" ), + * true, true, "Web Service Configuration Problem", 450, 400); * * jd.waitForInput(); */ @@ -2778,7 +2855,7 @@ public class Desktop extends jalview.jbgui.GDesktop } else { - Cache.log.error( + jalview.bin.Console.error( "Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg); } @@ -2871,15 +2948,8 @@ public class Desktop extends jalview.jbgui.GDesktop { if (url != null) { - if (Cache.log != null) - { - Cache.log.error("Couldn't handle string " + url + " as a URL."); - } - else - { - System.err.println( - "Couldn't handle string " + url + " as a URL."); - } + jalview.bin.Console + .error("Couldn't handle string " + url + " as a URL."); } // ignore any exceptions due to dud links. } @@ -2934,7 +3004,8 @@ public class Desktop extends jalview.jbgui.GDesktop SwingUtilities.invokeAndWait(prompter); } catch (Exception q) { - Cache.log.warn("Unexpected Exception in dialog thread.", q); + jalview.bin.Console.warn("Unexpected Exception in dialog thread.", + q); } } }); @@ -2973,7 +3044,7 @@ public class Desktop extends jalview.jbgui.GDesktop public void exportImage(Graphics g) throws Exception { paintAll(g); - Cache.log.info("Successfully written snapshot to file " + jalview.bin.Console.info("Successfully written snapshot to file " + of.getAbsolutePath()); } }; @@ -3007,16 +3078,15 @@ public class Desktop extends jalview.jbgui.GDesktop } /* - * Processing in reverse order works, forwards order leaves the first panels - * not visible. I don't know why! + * Processing in reverse order works, forwards order leaves the first panels not + * visible. I don't know why! */ for (int i = viewCount - 1; i >= 0; i--) { /* - * Make new top and bottom frames. These take over the respective - * AlignmentPanel objects, including their AlignmentViewports, so the - * cdna/protein relationships between the viewports is carried over to the - * new split frames. + * Make new top and bottom frames. These take over the respective AlignmentPanel + * objects, including their AlignmentViewports, so the cdna/protein + * relationships between the viewports is carried over to the new split frames. * * explodedGeometry holds the (x, y) position of the previously exploded * SplitFrame, and the (width, height) of the AlignFrame component @@ -3055,8 +3125,8 @@ public class Desktop extends jalview.jbgui.GDesktop } /* - * 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(); @@ -3157,28 +3227,6 @@ public class Desktop extends jalview.jbgui.GDesktop Transferable t) throws Exception { - // BH 2018 changed List to List 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 list = (List) 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 @@ -3187,7 +3235,8 @@ public class Desktop extends jalview.jbgui.GDesktop "application/x-java-url; class=java.net.URL"); } catch (ClassNotFoundException cfe) { - Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe); + jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.", + cfe); } if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) @@ -3202,7 +3251,7 @@ public class Desktop extends jalview.jbgui.GDesktop { protocols.add(DataSourceType.URL); files.add(url.toString()); - Cache.log.debug("Drop handled as URL dataflavor " + jalview.bin.Console.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1)); return; } @@ -3216,13 +3265,13 @@ public class Desktop extends jalview.jbgui.GDesktop } } catch (Throwable ex) { - Cache.log.debug("URL drop handler failed.", ex); + jalview.bin.Console.debug("URL drop handler failed.", ex); } } if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) { // Works on Windows and MacOSX - Cache.log.debug("Drop handled as javaFileListFlavor"); + jalview.bin.Console.debug("Drop handled as javaFileListFlavor"); for (Object file : (List) t .getTransferData(DataFlavor.javaFileListFlavor)) { @@ -3237,14 +3286,15 @@ public class Desktop extends jalview.jbgui.GDesktop String data = null; if (t.isDataFlavorSupported(uriListFlavor)) { - Cache.log.debug("Drop handled as uriListFlavor"); + jalview.bin.Console.debug("Drop handled as uriListFlavor"); // This is used by Unix drag system data = (String) t.getTransferData(uriListFlavor); } if (data == null) { // fallback to text: workaround - on OSX where there's a JVM bug - Cache.log.debug("standard URIListFlavor failed. Trying text"); + jalview.bin.Console + .debug("standard URIListFlavor failed. Trying text"); // try text fallback DataFlavor textDf = new DataFlavor( "text/plain;class=java.lang.String"); @@ -3253,7 +3303,7 @@ public class Desktop extends jalview.jbgui.GDesktop data = (String) t.getTransferData(textDf); } - Cache.log.debug("Plain text drop content returned " + jalview.bin.Console.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data)); } @@ -3261,7 +3311,7 @@ public class Desktop extends jalview.jbgui.GDesktop { while (protocols.size() < files.size()) { - Cache.log.debug("Adding missing FILE protocol for " + jalview.bin.Console.debug("Adding missing FILE protocol for " + files.get(protocols.size())); protocols.add(DataSourceType.FILE); } @@ -3276,7 +3326,7 @@ public class Desktop extends jalview.jbgui.GDesktop 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()); @@ -3291,7 +3341,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } - if (Cache.log.isDebugEnabled()) + if (jalview.bin.Console.isDebugEnabled()) { if (data == null || !added) { @@ -3299,39 +3349,41 @@ public class Desktop extends jalview.jbgui.GDesktop if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) { - Cache.log.debug( + jalview.bin.Console.debug( "Couldn't resolve drop data. Here are the supported flavors:"); for (DataFlavor fl : t.getTransferDataFlavors()) { - Cache.log.debug( + jalview.bin.Console.debug( "Supported transfer dataflavor: " + fl.toString()); Object df = t.getTransferData(fl); if (df != null) { - Cache.log.debug("Retrieves: " + df); + jalview.bin.Console.debug("Retrieves: " + df); } else { - Cache.log.debug("Retrieved nothing"); + jalview.bin.Console.debug("Retrieved nothing"); } } } else { - Cache.log.debug("Couldn't resolve dataflavor for drop: " - + t.toString()); + jalview.bin.Console + .debug("Couldn't resolve dataflavor for drop: " + + t.toString()); } } } } if (Platform.isWindowsAndNotJS()) { - Cache.log.debug("Scanning dropped content for Windows Link Files"); + jalview.bin.Console + .debug("Scanning dropped content for Windows Link Files"); // resolve any .lnk files in the file drop for (int f = 0; f < files.size(); f++) { - String source = files.get(f).toString().toLowerCase(); + String source = files.get(f).toString().toLowerCase(Locale.ROOT); if (protocols.get(f).equals(DataSourceType.FILE) && (source.endsWith(".lnk") || source.endsWith(".url") || source.endsWith(".site"))) @@ -3342,16 +3394,16 @@ public class Desktop extends jalview.jbgui.GDesktop File lf = (obj instanceof File ? (File) obj : new File((String) obj)); // process link file to get a URL - Cache.log.debug("Found potential link file: " + lf); + jalview.bin.Console.debug("Found potential link file: " + lf); WindowsShortcut wscfile = new WindowsShortcut(lf); String fullname = wscfile.getRealFilename(); protocols.set(f, FormatAdapter.checkProtocol(fullname)); files.set(f, fullname); - Cache.log.debug("Parsed real filename " + fullname + jalview.bin.Console.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f)); } catch (Exception ex) { - Cache.log.error( + jalview.bin.Console.error( "Couldn't parse " + files.get(f) + " as a link file.", ex); } @@ -3426,17 +3478,17 @@ public class Desktop extends jalview.jbgui.GDesktop AffineTransform t = gg.getTransform(); double scaleX = t.getScaleX(); double scaleY = t.getScaleY(); - Cache.debug(debugScaleMessage + scaleX + " (X)"); - Cache.debug(debugScaleMessage + scaleY + " (Y)"); + jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)"); + jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)"); debugScaleMessageDone = true; } else { - Cache.debug("Desktop graphics null"); + jalview.bin.Console.debug("Desktop graphics null"); } } catch (Exception e) { - Cache.debug(Cache.getStackTraceString(e)); + jalview.bin.Console.debug(Cache.getStackTraceString(e)); } } }