X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=02643ec24eac93c59f2eb0bd8456f1423c3e652f;hb=5f4f772b4ce40f2ea987cb03dd2c06ec1f48ba67;hp=1b8dda7cef1fbfd753899f583dc7ba9782494c70;hpb=0d69df1fcdf53cd75eae383f8dcf62ea211edce6;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 1b8dda7..02643ec 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,39 +20,13 @@ */ package jalview.gui; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.bin.Jalview; -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.ImageMaker; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.util.UrlConstants; -import jalview.viewmodel.AlignmentViewport; -import jalview.ws.params.ParamManager; -import jalview.ws.utils.UrlDownloadClient; - +import java.util.Locale; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.FontMetrics; import java.awt.Graphics; +import java.awt.Graphics2D; import java.awt.GridLayout; import java.awt.Point; import java.awt.Rectangle; @@ -75,21 +49,26 @@ import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; +import java.awt.geom.AffineTransform; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; import java.io.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.StringTokenizer; import java.util.Vector; +import java.util.concurrent.ExecutionException; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; +import java.util.concurrent.Future; +import java.util.concurrent.FutureTask; import java.util.concurrent.Semaphore; import javax.swing.AbstractAction; @@ -111,6 +90,7 @@ import javax.swing.JMenuItem; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JProgressBar; +import javax.swing.JTextField; import javax.swing.KeyStroke; import javax.swing.SwingUtilities; import javax.swing.event.HyperlinkEvent; @@ -120,6 +100,44 @@ import javax.swing.event.InternalFrameEvent; import org.stackoverflowusers.file.WindowsShortcut; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.StructureSelectionManagerProvider; +import jalview.bin.ApplicationSingletonProvider; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +import jalview.bin.Cache; +import jalview.bin.Jalview; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.io.BackupFiles; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatException; +import jalview.io.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.APQHandlers; +import jalview.jbgui.GDesktop; +import jalview.jbgui.GSplitFrame; +import jalview.jbgui.GStructureViewer; +import jalview.project.Jalview2XML; +import jalview.structure.StructureSelectionManager; +import jalview.urls.IdOrgSettings; +import jalview.util.BrowserLauncher; +import jalview.util.ChannelProperties; +import jalview.util.ImageMaker.TYPE; +import jalview.util.LaunchUtils; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.UrlConstants; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.WSDiscovererI; +import jalview.ws.params.ParamManager; +import jalview.ws.utils.UrlDownloadClient; + /** * Jalview Desktop * @@ -127,10 +145,38 @@ import org.stackoverflowusers.file.WindowsShortcut; * @author $author$ * @version $Revision: 1.155 $ */ -public class Desktop extends jalview.jbgui.GDesktop +@SuppressWarnings("serial") +public class Desktop extends GDesktop implements DropTargetListener, ClipboardOwner, IProgressIndicator, - jalview.api.StructureSelectionManagerProvider + StructureSelectionManagerProvider, ApplicationSingletonI + { + private static 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( + "

Jalview is free software released under GPLv3.

Development is managed by The Barton Group, University of Dundee, Scotland, UK."); + if (logo) + { + sb.append("
"); + } + sb.append(bg_logo_url == null ? "" : "\"Barton"); + sb.append(uod_logo_url == null ? "" + : " \"University"); + sb.append( + "

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"); + 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; @@ -141,12 +187,15 @@ 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<>(); + public static HashMap savingFiles = new HashMap(); + @SuppressWarnings("deprecation") private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); + public static boolean nosplash = false; + /** * news reader - null if it was never started. */ @@ -158,6 +207,7 @@ public class Desktop extends jalview.jbgui.GDesktop * @param listener * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener) */ + @Deprecated public void addJalviewPropertyChangeListener( PropertyChangeListener listener) { @@ -170,6 +220,7 @@ public class Desktop extends jalview.jbgui.GDesktop * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String, * java.beans.PropertyChangeListener) */ + @Deprecated public void addJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) { @@ -182,6 +233,7 @@ public class Desktop extends jalview.jbgui.GDesktop * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String, * java.beans.PropertyChangeListener) */ + @Deprecated public void removeJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) { @@ -189,24 +241,46 @@ public class Desktop extends jalview.jbgui.GDesktop listener); } - /** Singleton Desktop instance */ - public static Desktop instance; + private MyDesktopPane desktopPane; - public static MyDesktopPane desktop; + public static MyDesktopPane getDesktopPane() + { + Desktop desktop = getInstance(); + return desktop == null ? null : desktop.desktopPane; + } - static int openFrameCount = 0; + /** + * Answers an 'application scope' singleton instance of this class. Separate + * SwingJS 'applets' running in the same browser page will each have a + * distinct instance of Desktop. + * + * @return + */ + public static Desktop getInstance() + { + return Jalview.isHeadlessMode() ? null + : ApplicationSingletonProvider.getInstance(Desktop.class); + } + + public static StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager + .getStructureSelectionManager(getInstance()); + } - static final int xOffset = 30; + int openFrameCount = 0; - static final int yOffset = 30; + final int xOffset = 30; - public static jalview.ws.jws1.Discoverer discoverer; + final int yOffset = 30; - public static Object[] jalviewClipboard; + public jalview.ws.jws1.Discoverer discoverer; - public static boolean internalCopy = false; + public Object[] jalviewClipboard; - static int fileLoadingCount = 0; + public boolean internalCopy = false; + + int fileLoadingCount = 0; class MyDesktopManager implements DesktopManager { @@ -227,7 +301,7 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (NullPointerException npe) { Point p = getMousePosition(); - instance.showPasteMenu(p.x, p.y); + showPasteMenu(p.x, p.y); } } @@ -275,14 +349,14 @@ public class Desktop extends jalview.jbgui.GDesktop public void endDraggingFrame(JComponent f) { delegate.endDraggingFrame(f); - desktop.repaint(); + desktopPane.repaint(); } @Override public void endResizingFrame(JComponent f) { delegate.endResizingFrame(f); - desktop.repaint(); + desktopPane.repaint(); } @Override @@ -332,176 +406,242 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * Creates a new Desktop object. + * Private constructor enforces singleton pattern. It is called by reflection + * from ApplicationSingletonProvider.getInstance(). */ - public Desktop() + private Desktop() { + super(); + try + { + /** + * A note to implementors. It is ESSENTIAL that any activities that might + * block are spawned off as threads rather than waited for during this + * constructor. + */ + + doConfigureStructurePrefs(); + setTitle(ChannelProperties.getProperty("app_name") + " " + Cache.getProperty("VERSION")); + /** - * 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. + * 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. */ - instance = this; - - doConfigureStructurePrefs(); - setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); - /* - if (!Platform.isAMac()) - { - // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE); - } - else + if (Platform.isLinux()) { - this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE); + 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)); + } } - */ - try - { + /** + * 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) - { + } catch (Exception e) { System.out.println("Cannot set APQHandlers"); // e.printStackTrace(); - } catch (Throwable t) - { - System.out.println("Cannot set APQHandlers"); - // t.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() - { + addWindowListener(new WindowAdapter() { @Override - public void windowClosing(WindowEvent ev) - { + public void windowClosing(WindowEvent ev) { quit(); } }); - boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE", - false); - - boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE", - false); - desktop = new MyDesktopPane(selmemusage); - showMemusage.setSelected(selmemusage); - desktop.setBackground(Color.white); - - getContentPane().setLayout(new BorderLayout()); - // alternate config - have scrollbars - see notes in JAL-153 - // JScrollPane sp = new JScrollPane(); - // sp.getViewport().setView(desktop); - // getContentPane().add(sp, BorderLayout.CENTER); - getContentPane().add(desktop, BorderLayout.CENTER); - desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); - - // This line prevents Windows Look&Feel resizing all new windows to maximum - // if previous window was maximised - desktop.setDesktopManager(new MyDesktopManager( - (Platform.isWindows() ? new DefaultDesktopManager() - : Platform.isAMac() - ? new AquaInternalFrameManager( - desktop.getDesktopManager()) - : desktop.getDesktopManager()))); - - Rectangle dims = getLastKnownDimensions(""); - if (dims != null) - { - setBounds(dims); - } - else - { - Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); - setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2, - 900, 650); - } - jconsole = new Console(this, showjconsole); - // add essential build information - jconsole.setHeader(jalview.bin.Cache.getVersionDetailsForConsole()); + boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false); + + boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", false); + desktopPane = new MyDesktopPane(selmemusage); - showConsole(showjconsole); + showMemusage.setSelected(selmemusage); + desktopPane.setBackground(Color.white); - showNews.setVisible(false); + 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); - experimentalFeatures.setSelected(showExperimental()); + // BH 2018 - just an experiment to try unclipped JInternalFrames. + if (Platform.isJS()) + { + getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); + } - getIdentifiersOrgData(); + getContentPane().add(desktopPane, BorderLayout.CENTER); + desktopPane.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); - checkURLLinks(); - this.addWindowListener(new WindowAdapter() - { - @Override - public void windowClosing(WindowEvent evt) + // This line prevents Windows Look&Feel resizing all new windows to + // maximum + // if previous window was maximised + desktopPane.setDesktopManager(new MyDesktopManager( + (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager() + : Platform.isAMacAndNotJS() + ? new AquaInternalFrameManager( + desktopPane.getDesktopManager()) + : desktopPane.getDesktopManager()))); + + Rectangle dims = getLastKnownDimensions(""); + if (dims != null) { - quit(); + setBounds(dims); + } + else + { + Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); + int xPos = Math.max(5, (screenSize.width - 900) / 2); + int yPos = Math.max(5, (screenSize.height - 650) / 2); + setBounds(xPos, yPos, 900, 650); } - }); - MouseAdapter ma; - this.addMouseListener(ma = new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent evt) + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ { - if (evt.isPopupTrigger()) // Mac + jconsole = new Console(this, showjconsole); + jconsole.setHeader(Cache.getVersionDetailsForConsole()); + showConsole(showjconsole); + + showNews.setVisible(false); // not sure if we should only do this for interactive session? + + experimentalFeatures.setSelected(showExperimental()); + + getIdentifiersOrgData(); + + if (Jalview.isInteractive()) { - showPasteMenu(evt.getX(), evt.getY()); + // disabled for SeqCanvasTest + checkURLLinks(); + + // Spawn a thread that shows the splashscreen + if (!nosplash) { + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + new SplashScreen(true); + } + }); + } + + // Thread off a new instance of the file chooser - this reduces the + // time + // it + // takes to open it later on. + new Thread(new Runnable() + { + @Override + public void run() + { + jalview.bin.Console.debug("Filechooser init thread started."); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser.forRead( + Cache.getProperty("LAST_DIRECTORY"), fileFormat); + jalview.bin.Console.debug("Filechooser init thread finished."); + } + }).start(); + // Add the service change listener + changeSupport.addJalviewPropertyChangeListener("services", + new PropertyChangeListener() + { + + @Override + public void propertyChange(PropertyChangeEvent evt) + { + jalview.bin.Console.debug("Firing service changed event for " + + evt.getNewValue()); + JalviewServicesChanged(evt); + } + }); } } - @Override - public void mouseReleased(MouseEvent evt) + this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this)); + + this.addWindowListener(new WindowAdapter() { - if (evt.isPopupTrigger()) // Windows + @Override + public void windowClosing(WindowEvent evt) { - showPasteMenu(evt.getX(), evt.getY()); + quit(); } - } - }); - desktop.addMouseListener(ma); + }); - this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); - // Spawn a thread that shows the splashscreen - SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() + MouseAdapter ma; + this.addMouseListener(ma = new MouseAdapter() { - new SplashScreen(); - } - }); - - // Thread off a new instance of the file chooser - this reduces the time it - // takes to open it later on. - new Thread(new Runnable() + @Override + public void mousePressed(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Mac + { + showPasteMenu(evt.getX(), evt.getY()); + } + } + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Windows + { + showPasteMenu(evt.getX(), evt.getY()); + } + } + }); + desktopPane.addMouseListener(ma); + } catch (Throwable t) { - @Override - public void run() - { - Cache.log.debug("Filechooser init thread started."); - String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); - JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), - fileFormat); - Cache.log.debug("Filechooser init thread finished."); - } - }).start(); - // Add the service change listener - changeSupport.addJalviewPropertyChangeListener("services", - new PropertyChangeListener() - { - - @Override - public void propertyChange(PropertyChangeEvent evt) - { - Cache.log.debug("Firing service changed event for " - + evt.getNewValue()); - JalviewServicesChanged(evt); - } - - }); + t.printStackTrace(); + } } /** @@ -520,95 +660,80 @@ public class Desktop extends jalview.jbgui.GDesktop 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."); - + 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) + public void getIdentifiersOrgData() { + if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) { + // Thread off the identifiers fetcher + new Thread(new Runnable() { + @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 - protected void showNews_actionPerformed(ActionEvent e) - { + protected void showNews_actionPerformed(ActionEvent e) { showNews(showNews.isSelected()); } void showNews(boolean visible) { + jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news."); + showNews.setSelected(visible); + if (visible && !jvnews.isVisible()) { - Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); - showNews.setSelected(visible); - if (visible && !jvnews.isVisible()) + new Thread(new Runnable() { - new Thread(new Runnable() + @Override + public void run() { - @Override - public void run() - { - long now = System.currentTimeMillis(); - Desktop.instance.setProgressBar( - MessageManager.getString("status.refreshing_news"), - now); - jvnews.refreshNews(); - Desktop.instance.setProgressBar(null, now); - jvnews.showNews(); - } - }).start(); - } + long now = System.currentTimeMillis(); + setProgressBar(MessageManager.getString("status.refreshing_news"), + now); + jvnews.refreshNews(); + setProgressBar(null, now); + jvnews.showNews(); + } + }).start(); } } @@ -624,25 +749,19 @@ public class Desktop extends jalview.jbgui.GDesktop { // 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); @@ -650,17 +769,17 @@ public class Desktop extends jalview.jbgui.GDesktop ih = (int) (ih * sh); while (ix >= screenSize.width) { - jalview.bin.Cache.log.debug( + jalview.bin.Console.debug( "Window geometry location recall error: shifting horizontal to within screenbounds."); ix -= screenSize.width; } while (iy >= screenSize.height) { - jalview.bin.Cache.log.debug( + jalview.bin.Console.debug( "Window geometry location recall error: shifting vertical to within screenbounds."); iy -= screenSize.height; } - jalview.bin.Cache.log.debug( + jalview.bin.Console.debug( "Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw + " height:" + ih); } @@ -713,48 +832,11 @@ public class Desktop extends jalview.jbgui.GDesktop } } - /** - * 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) - { - 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) - { - addInternalFrame(frame, title, makeVisible, w, h, true, false); - } /** - * Add an internal frame to the Jalview desktop and make it visible + * Adds and opens the given frame to the desktop that is visible, allowed to + * resize, and has a 300px minimum width. * * @param frame * Frame to show @@ -764,18 +846,19 @@ public class Desktop extends jalview.jbgui.GDesktop * width * @param h * height - * @param resizable - * Allow resize */ public static synchronized void addInternalFrame( - final JInternalFrame frame, String title, int w, int h, - boolean resizable) + final JInternalFrame frame, String title, int w, int h) { - addInternalFrame(frame, title, true, w, h, resizable, false); + // 58 classes + + addInternalFrame(frame, title, Desktop.FRAME_MAKE_VISIBLE, w, h, + FRAME_ALLOW_RESIZE, FRAME_SET_MIN_SIZE_300); } /** - * Add an internal frame to the Jalview desktop + * Add an internal frame to the Jalview desktop that may optionally be + * visible, resizable, and allowed to be any size * * @param frame * Frame to show @@ -797,6 +880,8 @@ public class Desktop extends jalview.jbgui.GDesktop final JInternalFrame frame, String title, boolean makeVisible, int w, int h, boolean resizable, boolean ignoreMinSize) { + // 15 classes call this method directly. + // TODO: allow callers to determine X and Y position of frame (eg. via // bounds object). @@ -808,22 +893,40 @@ public class Desktop extends jalview.jbgui.GDesktop { frame.setSize(w, h); } - // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN - // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN - // IF JALVIEW IS RUNNING HEADLESS - // /////////////////////////////////////////////// - if (instance == null || (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true"))) - { - return; - } + if (getInstance() != null) + getInstance().addFrame(frame, makeVisible, resizable, + ignoreMinSize); + } + + // These can now by put into a single int flag, if desired: + + public final static boolean FRAME_MAKE_VISIBLE = true; + + public final static boolean FRAME_NOT_VISIBLE = false; + + public final static boolean FRAME_ALLOW_RESIZE = true; + + public final static boolean FRAME_NOT_RESIZABLE = false; + + public final static boolean FRAME_ALLOW_ANY_SIZE = true; + + public final static boolean FRAME_SET_MIN_SIZE_300 = false; + + private void addFrame(JInternalFrame frame, + boolean makeVisible, boolean resizable, + boolean ignoreMinSize) + { openFrameCount++; + + boolean isEmbedded = (Platform.getEmbeddedAttribute(frame, "id") != null); + boolean hasEmbeddedSize = (Platform.getDimIfEmbedded(frame, -1, -1) != null); + // Web page embedding allows us to ignore minimum size + ignoreMinSize |= hasEmbeddedSize; + 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, @@ -833,6 +936,10 @@ public class Desktop extends jalview.jbgui.GDesktop { frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, ALIGN_FRAME_DEFAULT_MIN_HEIGHT)); + } else { + frame.setMinimumSize( + new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT)); + } } @@ -841,9 +948,9 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setResizable(resizable); frame.setMaximizable(resizable); frame.setIconifiable(resizable); - frame.setOpaque(false); + frame.setOpaque(Platform.isJS()); - if (frame.getX() < 1 && frame.getY() < 1) + if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1) { frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset); @@ -853,13 +960,13 @@ 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) */ - final JMenuItem menuItem = new JMenuItem(title); + final JMenuItem menuItem = new JMenuItem(frame.getTitle()); frame.addInternalFrameListener(new InternalFrameAdapter() { @Override public void internalFrameActivated(InternalFrameEvent evt) { - JInternalFrame itf = desktop.getSelectedFrame(); + JInternalFrame itf = getDesktopPane().getSelectedFrame(); if (itf != null) { if (itf instanceof AlignFrame) @@ -891,8 +998,8 @@ public class Desktop extends jalview.jbgui.GDesktop { menuItem.removeActionListener(menuItem.getActionListeners()[0]); } - windowMenu.remove(menuItem); - }; + getInstance().windowMenu.remove(menuItem); + } }); menuItem.addActionListener(new ActionListener() @@ -906,6 +1013,7 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setIcon(false); } catch (java.beans.PropertyVetoException ex) { + // System.err.println(ex.toString()); } } @@ -913,9 +1021,9 @@ public class Desktop extends jalview.jbgui.GDesktop setKeyBindings(frame); - desktop.add(frame); + getDesktopPane().add(frame); - windowMenu.add(menuItem); + getInstance().windowMenu.add(menuItem); frame.toFront(); try @@ -926,8 +1034,8 @@ public class Desktop extends jalview.jbgui.GDesktop { } catch (java.lang.ClassCastException cex) { - Cache.log.warn( - "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869", + jalview.bin.Console.warn( + "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869", cex); } } @@ -953,10 +1061,8 @@ public class Desktop extends jalview.jbgui.GDesktop /* * 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, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()); + KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, InputEvent.CTRL_DOWN_MASK); + KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK); InputMap inputMap = frame .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); @@ -973,7 +1079,7 @@ public class Desktop extends jalview.jbgui.GDesktop { if (!internalCopy) { - Desktop.jalviewClipboard = null; + jalviewClipboard = null; } internalCopy = false; @@ -1013,12 +1119,12 @@ public class Desktop extends jalview.jbgui.GDesktop // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - List files = new ArrayList<>(); + List files = new ArrayList<>(); List protocols = new ArrayList<>(); try { - Desktop.transferFromDropTarget(files, protocols, evt, t); + transferFromDropTarget(files, protocols, evt, t); } catch (Exception e) { e.printStackTrace(); @@ -1031,13 +1137,15 @@ public class Desktop extends jalview.jbgui.GDesktop { for (int i = 0; i < files.size(); i++) { - String file = files.get(i).toString(); + // BH 2018 File or String + Object file = files.get(i); + String fileName = file.toString(); DataSourceType protocol = (protocols == null) ? DataSourceType.FILE : protocols.get(i); FileFormatI format = null; - if (file.endsWith(".jar")) + if (fileName.endsWith(".jar")) { format = FileFormat.Jalview; @@ -1046,8 +1154,11 @@ public class Desktop extends jalview.jbgui.GDesktop { format = new IdentifyFile().identify(file, protocol); } - - new FileLoader().LoadFile(file, protocol, format); + if (file instanceof File) + { + Platform.cacheFileData((File) file); + } + new FileLoader().LoadFile(null, file, protocol, format); } } catch (Exception ex) @@ -1069,57 +1180,53 @@ public class Desktop extends jalview.jbgui.GDesktop public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); - JalviewFileChooser chooser = JalviewFileChooser - .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled()); + JalviewFileChooser chooser = JalviewFileChooser.forRead( + Cache.getProperty("LAST_DIRECTORY"), fileFormat, + BackupFiles.getEnabled()); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.open_local_file")); chooser.setToolTipText(MessageManager.getString("action.open")); - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + chooser.setResponseHandler(0, new Runnable() { - String choice = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); + @Override + public void run() + { + File selectedFile = chooser.getSelectedFile(); + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); - FileFormatI format = chooser.getSelectedFormat(); + FileFormatI format = chooser.getSelectedFormat(); - /* - * Call IdentifyFile to verify the file contains what its extension implies. - * Skip this step for dynamically added file formats, because - * IdentifyFile does not know how to recognise them. - */ - if (FileFormats.getInstance().isIdentifiable(format)) - { - try - { - format = new IdentifyFile().identify(choice, DataSourceType.FILE); - } catch (FileFormatException e) + /* + * Call IdentifyFile to verify the file contains what its extension implies. + * Skip this step for dynamically added file formats, because + * IdentifyFile does not know how to recognise them. + */ + if (FileFormats.getInstance().isIdentifiable(format)) { - // format = null; //?? + try + { + format = new IdentifyFile().identify(selectedFile, + DataSourceType.FILE); + } catch (FileFormatException e) + { + // format = null; //?? + } } - } - if (viewport != null) - { - new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE, - format); - } - else - { - new FileLoader().LoadFile(choice, DataSourceType.FILE, format); + new FileLoader().LoadFile(viewport, selectedFile, + DataSourceType.FILE, format); } - } + }); + chooser.showOpenDialog(this); } /** - * DOCUMENT ME! + * Shows a dialog for input of a URL at which to retrieve alignment data * - * @param e - * DOCUMENT ME! + * @param viewport */ @Override public void inputURLMenuItem_actionPerformed(AlignViewport viewport) @@ -1128,87 +1235,102 @@ public class Desktop extends jalview.jbgui.GDesktop // for viewing JLabel label = new JLabel( MessageManager.getString("label.input_file_url")); - final JComboBox history = new JComboBox(); JPanel panel = new JPanel(new GridLayout(2, 1)); panel.add(label); - panel.add(history); - history.setPreferredSize(new Dimension(400, 20)); - history.setEditable(true); - history.addItem("http://www."); - - String historyItems = jalview.bin.Cache.getProperty("RECENT_URL"); - - StringTokenizer st; - - if (historyItems != null) - { - st = new StringTokenizer(historyItems, "\t"); - while (st.hasMoreTokens()) - { - history.addItem(st.nextElement()); - } - } - - int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel, - MessageManager.getString("label.input_alignment_from_url"), - JvOptionPane.OK_CANCEL_OPTION); - - if (reply != JvOptionPane.OK_OPTION) + /* + * the URL to fetch is + * Java: an editable combobox with history + * JS: (pending JAL-3038) a plain text field + */ + JComponent history; + String urlBase = "https://www."; + if (Platform.isJS()) { - return; + history = new JTextField(urlBase, 35); } - - String url = history.getSelectedItem().toString(); - - if (url.toLowerCase().endsWith(".jar")) + else + /** + * Java only + * + * @j2sIgnore + */ { - if (viewport != null) - { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, - FileFormat.Jalview); - } - else + JComboBox asCombo = new JComboBox<>(); + asCombo.setPreferredSize(new Dimension(400, 20)); + asCombo.setEditable(true); + asCombo.addItem(urlBase); + String historyItems = Cache.getProperty("RECENT_URL"); + if (historyItems != null) { - new FileLoader().LoadFile(url, DataSourceType.URL, - FileFormat.Jalview); + for (String token : historyItems.split("\\t")) + { + asCombo.addItem(token); + } } + history = asCombo; } - else + panel.add(history); + + Object[] options = new Object[] { MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }; + Runnable action = new Runnable() { - FileFormatI format = null; - try - { - format = new IdentifyFile().identify(url, DataSourceType.URL); - } catch (FileFormatException e) + @Override + public void run() { - // TODO revise error handling, distinguish between - // URL not found and response not valid - } + @SuppressWarnings("unchecked") + String url = (history instanceof JTextField ? ((JTextField) history).getText() + : ((JComboBox) history).getEditor().getItem().toString().trim()); - if (format == null) - { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.couldnt_locate", - new Object[] - { url }), - MessageManager.getString("label.url_not_found"), - JvOptionPane.WARNING_MESSAGE); + if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) { + if (viewport != null) { + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, FileFormat.Jalview); + } else { + new FileLoader().LoadFile(url, DataSourceType.URL, FileFormat.Jalview); + } + } else { + FileFormatI format = null; + try + { + format = new IdentifyFile().identify(url, DataSourceType.URL); + } catch (FileFormatException e) + { + // TODO revise error handling, distinguish between + // URL not found and response not valid + } - return; - } + if (format == null) + { + String msg = MessageManager + .formatMessage("label.couldnt_locate", url); + JvOptionPane.showInternalMessageDialog(getDesktopPane(), msg, + MessageManager.getString("label.url_not_found"), + JvOptionPane.WARNING_MESSAGE); - if (viewport != null) - { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, - format); - } - else - { - new FileLoader().LoadFile(url, DataSourceType.URL, format); + return; + } + + if (viewport != null) + { + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + format); + } + else + { + new FileLoader().LoadFile(url, DataSourceType.URL, format); + } + } } - } + }; + String dialogOption = MessageManager + .getString("label.input_alignment_from_url"); + JvOptionPane.newOptionDialog(desktopPane).setResponseHandler(0, action) + .showInternalDialog(panel, dialogOption, + JvOptionPane.YES_NO_CANCEL_OPTION, + JvOptionPane.PLAIN_MESSAGE, null, options, + MessageManager.getString("action.ok")); } /** @@ -1224,9 +1346,10 @@ public class Desktop extends jalview.jbgui.GDesktop { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(viewPanel); - Desktop.addInternalFrame(cap, - MessageManager.getString("label.cut_paste_alignmen_file"), true, - 600, 500); + addInternalFrame(cap, + MessageManager.getString("label.cut_paste_alignmen_file"), + FRAME_MAKE_VISIBLE, 600, 500, FRAME_ALLOW_RESIZE, + FRAME_SET_MIN_SIZE_300); } /* @@ -1236,10 +1359,8 @@ public class Desktop extends jalview.jbgui.GDesktop public void quit() { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); - jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH", - screen.width + ""); - jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", - screen.height + ""); + Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); + Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, getWidth(), getHeight())); @@ -1270,14 +1391,14 @@ public class Desktop extends jalview.jbgui.GDesktop private void storeLastKnownDimensions(String string, Rectangle jc) { - jalview.bin.Cache.log.debug("Storing last known dimensions for " - + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width + jalview.bin.Console.debug("Storing last known dimensions for " + string + + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width + " height:" + jc.height); - jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + ""); - jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + ""); - jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + ""); - jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + ""); + Cache.setProperty(string + "SCREEN_X", jc.x + ""); + Cache.setProperty(string + "SCREEN_Y", jc.y + ""); + Cache.setProperty(string + "SCREEN_WIDTH", jc.width + ""); + Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + ""); } /** @@ -1289,102 +1410,79 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void aboutMenuItem_actionPerformed(ActionEvent e) { - // StringBuffer message = getAboutMessage(false); - // JvOptionPane.showInternalMessageDialog(Desktop.desktop, - // - // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE); new Thread(new Runnable() { @Override public void run() { - new SplashScreen(true); + new SplashScreen(false); } }).start(); } - public StringBuffer getAboutMessage(boolean shortv) + /** + * Returns the html text for the About screen, including any available version + * number, build details, author details and citation reference, but without + * the enclosing {@code html} tags + * + * @return + */ + public String getAboutMessage() { - StringBuffer message = new StringBuffer(); - message.append(""); - if (shortv) - { - message.append("

Version: " - + jalview.bin.Cache.getProperty("VERSION") - + "

"); - message.append("Built: " - + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") - + " from " + jalview.bin.Cache.getBuildDetailsForSplash() - + ""); + StringBuilder message = new StringBuilder(1024); + message.append("
").append("

Version: ") + .append(Cache.getProperty("VERSION")).append("

").append("Built: ") + .append(Cache.getDefault("BUILD_DATE", "unknown")).append(" from ") + .append(Cache.getBuildDetailsForSplash()).append(""); - } - else - { - - message.append("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")) - { + 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("
...Checking latest version...
"); - } - else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") - .equals(jalview.bin.Cache.getProperty("VERSION"))) - { + } else if (!latestVersion.equals(Cache.getProperty("VERSION"))) { boolean red = false; - if (jalview.bin.Cache.getProperty("VERSION").toLowerCase() - .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("
"); } - message.append("
!! 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("
!! 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("
"); } } - message.append("
Authors: " + jalview.bin.Cache.getDefault( - "AUTHORFNAMES", - "The Jalview Authors (See AUTHORS file for current list)") - + "

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

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

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" - + ""); - return message; + message.append("
Authors: "); + message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS)); + message.append(CITATION); + + message.append("
"); + + return message.toString(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on requesting Help documentation */ @Override - public void documentationMenuItem_actionPerformed(ActionEvent e) - { - try - { - Help.showHelpWindow(); - } catch (Exception ex) - { + 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) { + System.err.println("Error opening help: " + ex.getMessage()); } } @@ -1392,7 +1490,7 @@ public class Desktop extends jalview.jbgui.GDesktop public void closeAll_actionPerformed(ActionEvent e) { // TODO show a progress bar while closing? - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); for (int i = 0; i < frames.length; i++) { try @@ -1444,9 +1542,9 @@ public class Desktop extends jalview.jbgui.GDesktop 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."); } /* @@ -1459,7 +1557,7 @@ public class Desktop extends jalview.jbgui.GDesktop @Override protected void showMemusage_actionPerformed(ActionEvent e) { - desktop.showMemoryUsage(showMemusage.isSelected()); + desktopPane.showMemoryUsage(showMemusage.isSelected()); } /* @@ -1484,22 +1582,26 @@ public class Desktop extends jalview.jbgui.GDesktop */ void showConsole(boolean selected) { - showConsole.setSelected(selected); // TODO: decide if we should update properties file - Cache.setProperty("SHOW_JAVA_CONSOLE", - Boolean.valueOf(selected).toString()); - jconsole.setVisible(selected); + if (jconsole != null) // BH 2018 + { + showConsole.setSelected(selected); + Cache.setProperty("SHOW_JAVA_CONSOLE", + Boolean.valueOf(selected).toString()); + jconsole.setVisible(selected); + } } void reorderAssociatedWindows(boolean minimize, boolean close) { - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); if (frames == null || frames.length < 1) { return; } - AlignmentViewport source = null, target = null; + AlignViewportI source = null; + AlignViewportI target = null; if (frames[0] instanceof AlignFrame) { source = ((AlignFrame) frames[0]).getCurrentView(); @@ -1575,14 +1677,13 @@ public class Desktop extends jalview.jbgui.GDesktop * DOCUMENT ME! */ @Override - protected void preferences_actionPerformed(ActionEvent e) - { - new Preferences(); + protected void preferences_actionPerformed(ActionEvent e) { + Preferences.openPreferences(); } /** - * Shows a file chooser dialog and writes out the current session as a Jalview - * project file + * Prompts the user to choose a file and then saves the Jalview state as a + * Jalview project file */ @Override public void saveState_actionPerformed() @@ -1620,8 +1721,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } - if (approveSave || autoSave) - { + if (approveSave || autoSave) { final Desktop me = this; final java.io.File chosenFile = projectFile; new Thread(new Runnable() @@ -1633,25 +1733,30 @@ public class Desktop extends jalview.jbgui.GDesktop setProgressBar(MessageManager.formatMessage( "label.saving_jalview_project", new Object[] { chosenFile.getName() }), chosenFile.hashCode()); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chosenFile.getParent()); + 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 { - BackupFiles backupfiles = new BackupFiles(chosenFile); + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) + : null; - new Jalview2XML().saveState(backupfiles.getTempFile()); + new Jalview2XML().saveState( + doBackup ? backupfiles.getTempFile() : chosenFile); - backupfiles.setWriteSuccess(true); - backupfiles.rollBackupsAndRenameTempFile(); + if (doBackup) + { + backupfiles.setWriteSuccess(true); + backupfiles.rollBackupsAndRenameTempFile(); + } } catch (OutOfMemoryError oom) { new OOMWarning("Whilst saving current state to " + 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( @@ -1695,49 +1800,51 @@ public class Desktop extends jalview.jbgui.GDesktop "Jalview Project (old)" }; JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY"), suffix, desc, - "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles, - // allowBackupFiles + "Jalview Project", true, BackupFiles.getEnabled()); // last two + // booleans: + // allFiles, + // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + chooser.setResponseHandler(0, new Runnable() { - final File selectedFile = chooser.getSelectedFile(); - setProjectFile(selectedFile); - final String choice = selectedFile.getAbsolutePath(); - Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); - new Thread(new Runnable() + @Override + public void run() { - @Override - public void run() + File selectedFile = chooser.getSelectedFile(); + setProjectFile(selectedFile); + String choice = selectedFile.getAbsolutePath(); + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); + new Thread(new Runnable() { - setProgressBar(MessageManager.formatMessage( - "label.loading_jalview_project", new Object[] - { choice }), choice.hashCode()); - try - { - new Jalview2XML().loadJalviewAlign(choice); - } catch (OutOfMemoryError oom) - { - new OOMWarning("Whilst loading project from " + choice, oom); - } catch (Exception ex) + @Override + public void run() { - Cache.log.error( - "Problems whilst loading project from " + choice, ex); - JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.error_whilst_loading_project_from", - new Object[] - { choice }), - MessageManager.getString("label.couldnt_load_project"), - JvOptionPane.WARNING_MESSAGE); + 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(getDesktopPane(), + MessageManager.formatMessage( + "label.error_whilst_loading_project_from", + new Object[] + { choice }), + MessageManager + .getString("label.couldnt_load_project"), + JvOptionPane.WARNING_MESSAGE); + } } - setProgressBar(null, choice.hashCode()); - } - }).start(); - } + }, "Project Loader").start(); + } + }); + + chooser.showOpenDialog(this); } @Override @@ -1750,7 +1857,7 @@ public class Desktop extends jalview.jbgui.GDesktop ArrayList fileLoadingPanels = new ArrayList<>(); - public void startLoading(final String fileName) + public void startLoading(final Object fileName) { if (fileLoadingCount == 0) { @@ -1767,7 +1874,7 @@ public class Desktop extends jalview.jbgui.GDesktop { progressPanel = new JPanel(new GridLayout(1, 1)); totalProgressCount = 0; - instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); + getContentPane().add(progressPanel, BorderLayout.SOUTH); } JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); JProgressBar progressBar = new JProgressBar(); @@ -1780,7 +1887,7 @@ public class Desktop extends jalview.jbgui.GDesktop ((GridLayout) progressPanel.getLayout()).setRows( ((GridLayout) progressPanel.getLayout()).getRows() + 1); ++totalProgressCount; - instance.validate(); + validate(); return thisprogress; } @@ -1834,7 +1941,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public static AlignmentPanel[] getAlignmentPanels(String alignmentId) { - if (Desktop.desktop == null) + if (getDesktopPane() == null) { // no frames created and in headless mode // TODO: verify that frames are recoverable when in headless mode @@ -1876,9 +1983,9 @@ public class Desktop extends jalview.jbgui.GDesktop public static AlignmentViewport[] getViewports(String sequenceSetId) { List viewp = new ArrayList<>(); - if (desktop != null) + if (getDesktopPane() != null) { - AlignFrame[] frames = Desktop.getAlignFrames(); + AlignFrame[] frames = getAlignFrames(); for (AlignFrame afr : frames) { @@ -1925,9 +2032,7 @@ public class Desktop extends jalview.jbgui.GDesktop // FIXME: ideally should use UI interface API FeatureSettings viewFeatureSettings = (af.featureSettings != null - && af.featureSettings.isOpen()) - ? af.featureSettings - : null; + && af.featureSettings.isOpen()) ? af.featureSettings : null; Rectangle fsBounds = af.getFeatureSettingsGeometry(); for (int i = 0; i < size; i++) { @@ -1960,7 +2065,8 @@ public class Desktop extends jalview.jbgui.GDesktop addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - // and materialise a new feature settings dialog instance for the new alignframe + // 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() @@ -1988,7 +2094,7 @@ public class Desktop extends jalview.jbgui.GDesktop { source.viewport.setGatherViewsHere(true); source.viewport.setExplodedGeometry(source.getBounds()); - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); String viewId = source.viewport.getSequenceSetId(); for (int t = 0; t < frames.length; t++) { @@ -2030,9 +2136,9 @@ public class Desktop extends jalview.jbgui.GDesktop } } } + // refresh the feature setting UI for the source frame if it exists - if (source.featureSettings != null - && source.featureSettings.isOpen()) + if (source.featureSettings != null && source.featureSettings.isOpen()) { source.showFeatureSettingsUI(); } @@ -2041,7 +2147,7 @@ public class Desktop extends jalview.jbgui.GDesktop public JInternalFrame[] getAllFrames() { - return desktop.getAllFrames(); + return desktopPane.getAllFrames(); } /** @@ -2127,7 +2233,7 @@ public class Desktop extends jalview.jbgui.GDesktop }); msgPanel.add(jcb); - JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, + JvOptionPane.showMessageDialog(desktopPane, msgPanel, MessageManager .getString("label.SEQUENCE_ID_no_longer_used"), JvOptionPane.WARNING_MESSAGE); @@ -2145,7 +2251,6 @@ public class Desktop extends jalview.jbgui.GDesktop */ public class MyDesktopPane extends JDesktopPane implements Runnable { - private static final float ONE_MB = 1048576f; boolean showMemoryUsage = false; @@ -2231,6 +2336,9 @@ public class Desktop extends jalview.jbgui.GDesktop 10, getHeight() - fm.getHeight()); } } + + // output debug scale message. Important for jalview.bin.HiDPISettingTest2 + Desktop.debugScaleMessage(Desktop.getDesktopPane().getGraphics()); } } @@ -2243,11 +2351,10 @@ public class Desktop extends jalview.jbgui.GDesktop { if (Jalview.isHeadlessMode()) { - // Desktop.desktop is null in headless mode - return new AlignFrame[] { Jalview.currentAlignFrame }; + return new AlignFrame[] { Jalview.getInstance().currentAlignFrame }; } - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = getDesktopPane().getAllFrames(); if (frames == null) { @@ -2292,7 +2399,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public GStructureViewer[] getJmols() { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); if (frames == null) { @@ -2327,8 +2434,8 @@ public class Desktop extends jalview.jbgui.GDesktop openGroovyConsole(); } catch (Exception ex) { - jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + jalview.bin.Console.error("Groovy Shell Creation failed.", ex); + JvOptionPane.showInternalMessageDialog(desktopPane, MessageManager.getString("label.couldnt_create_groovy_shell"), MessageManager.getString("label.groovy_support_failed"), @@ -2386,9 +2493,10 @@ public class Desktop extends jalview.jbgui.GDesktop */ protected void addQuitHandler() { + getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW) .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q, - jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()), + Platform.SHORTCUT_KEY_MASK), "Quit"); getRootPane().getActionMap().put("Quit", new AbstractAction() { @@ -2439,6 +2547,8 @@ 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<>(); @@ -2459,6 +2569,20 @@ public class Desktop extends jalview.jbgui.GDesktop progressBars.put(Long.valueOf(id), addProgressPanel(message)); } } + + @Override + public void addProgressBar(long id, String message) + { + // TODO + throw new UnsupportedOperationException("not implemented"); + } + + @Override + public void removeProgressBar(long id) + { + //TODO + throw new UnsupportedOperationException("not implemented"); + } /* * (non-Javadoc) @@ -2524,7 +2648,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public static AlignFrame getAlignFrameFor(AlignViewportI viewport) { - if (desktop != null) + if (getDesktopPane() != null) { AlignmentPanel[] aps = getAlignmentPanels( viewport.getSequenceSetId()); @@ -2571,52 +2695,69 @@ 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) { - boolean alive = true; - Thread t0 = null, t1 = null, t2 = null; + jalview.bin.Console.debug("Starting service discovery"); + + var tasks = new ArrayList>(); // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release - if (true) + + System.out.println("loading services"); + + /** @j2sIgnore */ { // todo: changesupport handlers need to be transferred if (discoverer == null) { - discoverer = new jalview.ws.jws1.Discoverer(); + discoverer = jalview.ws.jws1.Discoverer.getInstance(); // register PCS handler for desktop. discoverer.addPropertyChangeListener(changeSupport); } // JAL-940 - disabled JWS1 service configuration - always start discoverer // until we phase out completely - (t0 = new Thread(discoverer)).start(); + var f = new FutureTask(discoverer, null); + new Thread(f).start(); + tasks.add(f); } if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { - t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() - .startDiscoverer(changeSupport); + tasks.add(jalview.ws.jws2.Jws2Discoverer.getInstance().startDiscoverer()); } - Thread t3 = null; + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { - // TODO: do rest service discovery + tasks.add(jalview.ws2.client.slivka.SlivkaWSDiscoverer + .getInstance().startDiscoverer()); + } + if (Cache.getDefault("SHOW_EBI_SERVICES", true)) + { + tasks.add(jalview.ws2.client.ebi.JobDispatcherWSDiscoverer + .getInstance().startDiscoverer()); } if (blocking) { - while (alive) - { + for (Future task : tasks) { try { - Thread.sleep(15); + // block until all discovery tasks are done + task.get(); } catch (Exception e) { + e.printStackTrace(); } - alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) - || (t3 != null && t3.isAlive()) - || (t0 != null && t0.isAlive()); } } } @@ -2630,8 +2771,10 @@ public class Desktop extends jalview.jbgui.GDesktop { if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) { - final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() - .getErrorMessages(); + final WSDiscovererI discoverer = jalview.ws.jws2.Jws2Discoverer + .getInstance(); + final String ermsg = discoverer.getErrorMessages(); + // CONFLICT:ALT:? final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance() if (ermsg != null) { if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) @@ -2669,7 +2812,7 @@ public class Desktop extends jalview.jbgui.GDesktop * * jd.waitForInput(); */ - JvOptionPane.showConfirmDialog(Desktop.desktop, + JvOptionPane.showConfirmDialog(desktopPane, new JLabel("
" + ermsg + "
" + "

It may be that you have invalid JABA URLs
in your web service preferences," @@ -2687,7 +2830,7 @@ 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); } @@ -2706,7 +2849,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public static void showUrl(final String url) { - showUrl(url, Desktop.instance); + showUrl(url, getInstance()); } /** @@ -2735,7 +2878,7 @@ public class Desktop extends jalview.jbgui.GDesktop jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(getDesktopPane(), MessageManager .getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), @@ -2775,20 +2918,13 @@ public class Desktop extends jalview.jbgui.GDesktop try { url = e.getURL().toString(); - Desktop.showUrl(url); + 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."); - } + // TODO does error send to stderr if no log exists ? + jalview.bin.Console.error("Couldn't handle string " + url + " as a URL."); } // ignore any exceptions due to dud links. } @@ -2833,9 +2969,8 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (InterruptedException x) { } - ; } - if (instance == null) + if (Jalview.isHeadlessMode()) { return; } @@ -2844,7 +2979,7 @@ 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); } } }); @@ -2858,28 +2993,39 @@ public class Desktop extends jalview.jbgui.GDesktop block.release(); } + /** + * Outputs an image of the desktop to file in EPS format, after prompting the + * user for choice of Text or Lineart character rendering (unless a preference + * has been set). The file name is generated as + * + *

+   * Jalview_snapshot_nnnnn.eps where nnnnn is the current timestamp in milliseconds
+   * 
+ */ @Override protected void snapShotWindow_actionPerformed(ActionEvent e) { + // currently the menu option to do this is not shown invalidate(); - File of; - ImageMaker im = new jalview.util.ImageMaker( - this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(), - getHeight(), of = new File("Jalview_snapshot" - + System.currentTimeMillis() + ".eps"), - "View of desktop", null, 0, false); - try - { - paintAll(im.getGraphics()); - im.writeImage(); - } catch (Exception q) + + int width = getWidth(); + int height = getHeight(); + File of = new File( + "Jalview_snapshot_" + System.currentTimeMillis() + ".eps"); + ImageWriterI writer = new ImageWriterI() { - Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(), - q); - return; - } - Cache.log.info("Successfully written snapshot to file " - + of.getAbsolutePath()); + @Override + public void exportImage(Graphics g) throws Exception + { + paintAll(g); + jalview.bin.Console.info("Successfully written snapshot to file " + + of.getAbsolutePath()); + } + }; + String title = "View of desktop"; + ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, + title); + exporter.doExport(of, this, width, height, title); } /** @@ -2950,7 +3096,7 @@ public class Desktop extends jalview.jbgui.GDesktop { splitFrame.setLocation(geometry.getLocation()); } - Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1); + addInternalFrame(splitFrame, sf.getTitle(), -1, -1); } /* @@ -2988,7 +3134,7 @@ public class Desktop extends jalview.jbgui.GDesktop String topViewId = myTopFrame.viewport.getSequenceSetId(); String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); for (JInternalFrame frame : frames) { if (frame instanceof SplitFrame && frame != source) @@ -3051,11 +3197,34 @@ public class Desktop extends jalview.jbgui.GDesktop * - the payload from the drop event * @throws Exception */ - public static void transferFromDropTarget(List files, + @SuppressWarnings("unchecked") + public static void transferFromDropTarget(List files, List protocols, DropTargetDropEvent evt, 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 @@ -3064,7 +3233,8 @@ 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)) @@ -3079,32 +3249,31 @@ 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; } else { - if (Platform.isAMac()) + if (Platform.isAMacAndNotJS()) { System.err.println( "Please ignore plist error - occurs due to problem with java 8 on OSX"); } - ; } } catch (Throwable ex) { - Cache.log.debug("URL drop handler failed.", ex); + jalview.bin.Console.debug("URL drop handler failed.", ex); } } if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) { // Works on Windows and MacOSX - Cache.log.debug("Drop handled as javaFileListFlavor"); - for (Object file : (List) t + jalview.bin.Console.debug("Drop handled as javaFileListFlavor"); + for (File file : (List) t .getTransferData(DataFlavor.javaFileListFlavor)) { - files.add(((File) file).toString()); + files.add(file); protocols.add(DataSourceType.FILE); } } @@ -3115,14 +3284,15 @@ 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"); @@ -3131,7 +3301,7 @@ 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)); } @@ -3139,7 +3309,7 @@ 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); } @@ -3154,7 +3324,7 @@ 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()); @@ -3169,7 +3339,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } - if (Cache.log.isDebugEnabled()) + if (jalview.bin.Console.isDebugEnabled()) { if (data == null || !added) { @@ -3177,58 +3347,59 @@ 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.isWindows()) - + if (Platform.isWindowsAndNotJS()) { - Cache.log.debug("Scanning dropped content for Windows Link Files"); + jalview.bin.Console.debug("Scanning dropped content for Windows Link Files"); // resolve any .lnk files in the file drop for (int f = 0; f < files.size(); f++) { - String source = files.get(f).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"))) { try { - File lf = new File(files.get(f)); + Object obj = files.get(f); + 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); } @@ -3264,7 +3435,7 @@ public class Desktop extends jalview.jbgui.GDesktop Class structureViewerClass) { List result = new ArrayList<>(); - JInternalFrame[] frames = Desktop.instance.getAllFrames(); + JInternalFrame[] frames = getAllFrames(); for (JInternalFrame frame : frames) { @@ -3283,4 +3454,33 @@ public class Desktop extends jalview.jbgui.GDesktop } 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)); + } + } }