X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=85ec3aecf2c5b616c88a8e7e80522f6a69f42be2;hb=cb51e62fe2166b236ef488e0a8f35081fcd71388;hp=04487e0e521e3ae363f360f87e2b7ec4fd761265;hpb=81af7e9323594eee02a906091f4e5dd2140d2514;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 04487e0..85ec3aecf 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,12 +20,15 @@ */ package jalview.gui; -import static jalview.util.UrlConstants.SEQUENCE_ID; - 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; @@ -36,15 +39,19 @@ import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; +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.ImageMaker; +import jalview.util.BrowserLauncher; +import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.UrlConstants; import jalview.viewmodel.AlignmentViewport; +import jalview.ws.jws1.Discoverer; import jalview.ws.params.ParamManager; import jalview.ws.utils.UrlDownloadClient; @@ -69,6 +76,7 @@ import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.InputEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; @@ -85,17 +93,19 @@ import java.util.ArrayList; import java.util.Hashtable; import java.util.List; import java.util.ListIterator; -import java.util.StringTokenizer; import java.util.Vector; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; import javax.swing.AbstractAction; +import javax.swing.Action; +import javax.swing.ActionMap; import javax.swing.Box; import javax.swing.BoxLayout; import javax.swing.DefaultDesktopManager; import javax.swing.DesktopManager; +import javax.swing.InputMap; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JComboBox; @@ -108,6 +118,7 @@ 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; @@ -126,26 +137,28 @@ 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 int DEFAULT_MIN_WIDTH = 300; - private static int DEFAULT_MIN_HEIGHT = 250; + private final static int DEFAULT_MIN_WIDTH = 300; + + private final static int DEFAULT_MIN_HEIGHT = 250; - private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600; + private final static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600; - private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70; + private final static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70; - private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; + private final static String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); /** * news reader - null if it was never started. */ - private BlogReader jvnews = null; + BlogReader jvnews = null; private File projectFile; @@ -184,10 +197,17 @@ public class Desktop extends jalview.jbgui.GDesktop listener); } - /** Singleton Desktop instance */ - public static Desktop instance; + public static MyDesktopPane getDesktopPane() + { + Desktop desktop = Desktop.getInstance(); + return desktop == null ? null : desktop.desktopPane; + } - public static MyDesktopPane desktop; + public static StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager + .getStructureSelectionManager(getInstance()); + } static int openFrameCount = 0; @@ -195,13 +215,34 @@ public class Desktop extends jalview.jbgui.GDesktop static final int yOffset = 30; - public static jalview.ws.jws1.Discoverer discoverer; + public Discoverer discoverer; - public static Object[] jalviewClipboard; + public Object[] jalviewClipboard; - public static boolean internalCopy = false; + public boolean internalCopy = false; - static int fileLoadingCount = 0; + private static int fileLoadingCount = 0; + + public JInternalFrame conservationSlider; + + public JInternalFrame PIDSlider; + + /** + * just an instance (for testng, probably); no actual frames + * + * This flag, when set true, allows a headless-like operation, with a Desktop + * object but no actual frames. The issue has to do with the mess-up of the + * Windows JInternalFrame implementation, which surreptitiously and + * unforgivingly accesses a native peer class, preventing headless operation. + * + * It is set by invoking the Desktop(true) constructor. + * + * It is possible that we can remove this option now, since headless mode is + * finally working on Windows through careful attention to not creating any + * JInternalFrame objects when in that mode. + * + */ + private boolean instanceOnly; class MyDesktopManager implements DesktopManager { @@ -222,7 +263,7 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (NullPointerException npe) { Point p = getMousePosition(); - instance.showPasteMenu(p.x, p.y); + showPasteMenu(p.x, p.y); } } @@ -270,14 +311,14 @@ 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 @@ -326,154 +367,226 @@ public class Desktop extends jalview.jbgui.GDesktop } + public MyDesktopPane desktopPane; + /** - * Creates a new Desktop object. + * 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 Desktop() + public static Desktop getInstance() { - /** - * A note to implementors. It is ESSENTIAL that any activities that might - * block are spawned off as threads rather than waited for during this - * constructor. - */ - instance = this; - doVamsasClientCheck(); - - doConfigureStructurePrefs(); - setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); - setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); - boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE", - false); - boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE", - false); - 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 + return Jalview.isHeadlessMode() ? null + : (Desktop) ApplicationSingletonProvider + .getInstance(Desktop.class); + } + + /** + * For testing purposes, this constructor can be utilized to allow the creation + * of a singleton Desktop instance without the formation of frames. The Cache is + * initialized, but that is all. + * + * It is not currently used. + * + * @param forInstance + */ + public Desktop(boolean forInstance) + { + + Cache.initLogger(); + instanceOnly = true; + } + + /** + * Private constructor enforces singleton pattern. It is called by reflection + * from ApplicationSingletonProvider.getInstance(). + */ + @SuppressWarnings("unused") + private Desktop() + { + Cache.initLogger(); + try { - 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 Version: " + jalview.bin.Cache.getProperty("VERSION") - + "\n" + "Jalview Installation: " - + jalview.bin.Cache.getDefault("INSTALLATION", - "unknown") - + "\n" + "Build Date: " - + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") - + "\n" + "Java version: " - + System.getProperty("java.version") + "\n" - + System.getProperty("os.arch") + " " - + System.getProperty("os.name") + " " - + System.getProperty("os.version")); + /** + * 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. + */ + if (!Platform.isJS()) + { + doVamsasClientCheck(); + } - showConsole(showjconsole); + doConfigureStructurePrefs(); + setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); + setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); + boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE", + false); + boolean showjconsole = jalview.bin.Cache + .getDefault("SHOW_JAVA_CONSOLE", false); + desktopPane = new MyDesktopPane(selmemusage); - showNews.setVisible(false); + showMemusage.setSelected(selmemusage); + desktopPane.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); - 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 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()))); - this.addWindowListener(new WindowAdapter() - { - @Override - public void windowClosing(WindowEvent evt) + 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) + // Note that this next syntax, checking for Platform.isJS and also + // escaping the code using @j2sIgnore, serves two purposes. It gives + // us an easily findable tag, Platform.isJS(), to places in the code where + // there is something different about the SwingJS implementation. Second, + // it deletes the unneeded Java-only code form the JavaScript version + // completely (@j2sIgnore), since it will never be used there. + + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ { - if (evt.isPopupTrigger()) // Mac + + jconsole = new Console(this, showjconsole); + // add essential build information + jconsole.setHeader("Jalview Version: " + + jalview.bin.Cache.getProperty("VERSION") + "\n" + + "Jalview Installation: " + + jalview.bin.Cache.getDefault("INSTALLATION", "unknown") + + "\n" + "Build Date: " + + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + + "\n" + "Java version: " + + System.getProperty("java.version") + "\n" + + System.getProperty("os.arch") + " " + + System.getProperty("os.name") + " " + + System.getProperty("os.version")); + + showConsole(showjconsole); + + showNews.setVisible(false); + + experimentalFeatures.setSelected(showExperimental()); + + getIdentifiersOrgData(); + + checkURLLinks(); + + // Spawn a thread that shows the splashscreen + + SwingUtilities.invokeLater(new Runnable() { - showPasteMenu(evt.getX(), evt.getY()); - } + @Override + public void run() + { + new SplashScreen(); + } + }); + + // Thread off a new instance of the file chooser - this reduces the time + // it + // takes to open it later on. + new Thread(new Runnable() + { + @Override + public void run() + { + Cache.log.debug("Filechooser init thread started."); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), + fileFormat); + Cache.log.debug("Filechooser init thread finished."); + } + }).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); + } + + }); + } - @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(); - } - }); + @Override + public void mousePressed(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Mac + { + showPasteMenu(evt.getX(), evt.getY()); + } + } - // 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 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(); + } } /** @@ -515,33 +628,32 @@ public class Desktop extends jalview.jbgui.GDesktop { final Desktop me = this; // Thread off the news reader, in case there are connection problems. - addDialogThread(new Runnable() + new Thread(new Runnable() { @Override public void run() { Cache.log.debug("Starting news thread."); - jvnews = new BlogReader(me); showNews.setVisible(true); Cache.log.debug("Completed news thread."); } - }); + }).start(); } public void getIdentifiersOrgData() { // Thread off the identifiers fetcher - addDialogThread(new Runnable() + new Thread(new Runnable() { @Override public void run() { Cache.log.debug("Downloading data from identifiers.org"); - UrlDownloadClient client = new UrlDownloadClient(); + // UrlDownloadClient client = new UrlDownloadClient(); try { - client.download(IdOrgSettings.getUrl(), + UrlDownloadClient.download(IdOrgSettings.getUrl(), IdOrgSettings.getDownloadLocation()); } catch (IOException e) { @@ -549,7 +661,8 @@ public class Desktop extends jalview.jbgui.GDesktop + e.getMessage()); } } - }); + }).start(); + } @Override @@ -558,28 +671,25 @@ public class Desktop extends jalview.jbgui.GDesktop showNews(showNews.isSelected()); } - void showNews(boolean visible) + protected void showNews(boolean visible) { + Cache.log.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(); } } @@ -643,7 +753,7 @@ public class Desktop extends jalview.jbgui.GDesktop private void doVamsasClientCheck() { - if (jalview.bin.Cache.vamsasJarsPresent()) + if (Cache.vamsasJarsPresent()) { setupVamsasDisconnectedGui(); VamsasMenu.setVisible(true); @@ -681,7 +791,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } - void showPasteMenu(int x, int y) + protected void showPasteMenu(int x, int y) { JPopupMenu popup = new JPopupMenu(); JMenuItem item = new JMenuItem( @@ -714,7 +824,7 @@ public class Desktop extends jalview.jbgui.GDesktop FileFormatI format = new IdentifyFile().identify(file, DataSourceType.PASTE); - new FileLoader().LoadFile(file, DataSourceType.PASTE, format); + new FileLoader().loadFile(file, DataSourceType.PASTE, format); } } catch (Exception ex) @@ -809,13 +919,14 @@ public class Desktop extends jalview.jbgui.GDesktop int w, int h, boolean resizable, boolean ignoreMinSize) { + // TODO: allow callers to determine X and Y position of frame (eg. via // bounds object). // TODO: consider fixing method to update entries in the window submenu with // the current window title frame.setTitle(title); - if (frame.getWidth() < 1 || frame.getHeight() < 1) + if (w > 0 && (frame.getWidth() < 1 || frame.getHeight() < 1)) { frame.setSize(w, h); } @@ -823,8 +934,7 @@ public class Desktop extends jalview.jbgui.GDesktop // 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"))) + if (Jalview.isHeadlessMode() || Desktop.getInstance().instanceOnly) { return; } @@ -852,9 +962,10 @@ 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) + boolean isEmbedded = (Platform.getDimIfEmbedded(frame, -1, -1) != null); + if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1) { frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset); @@ -864,13 +975,13 @@ 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); + JMenuItem menuItem = new JMenuItem(title); 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) @@ -902,10 +1013,8 @@ public class Desktop extends jalview.jbgui.GDesktop { menuItem.removeActionListener(menuItem.getActionListeners()[0]); } - windowMenu.remove(menuItem); - - System.gc(); - }; + Desktop.getInstance().windowMenu.remove(menuItem); + } }); menuItem.addActionListener(new ActionListener() @@ -919,14 +1028,16 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setIcon(false); } catch (java.beans.PropertyVetoException ex) { - + // System.err.println(ex.toString()); } } }); - desktop.add(frame); + setKeyBindings(frame); + + getDesktopPane().add(frame); - windowMenu.add(menuItem); + Desktop.getInstance().windowMenu.add(menuItem); frame.toFront(); try @@ -943,12 +1054,47 @@ public class Desktop extends jalview.jbgui.GDesktop } } + /** + * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the + * window + * + * @param frame + */ + private static void setKeyBindings(JInternalFrame frame) + { + final Action closeAction = new AbstractAction() + { + @Override + public void actionPerformed(ActionEvent e) + { + frame.dispose(); + } + }; + + /* + * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action + */ + KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, + InputEvent.CTRL_DOWN_MASK); + KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()); + + InputMap inputMap = frame + .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); + String ctrlW = ctrlWKey.toString(); + inputMap.put(ctrlWKey, ctrlW); + inputMap.put(cmdWKey, ctrlW); + + ActionMap actionMap = frame.getActionMap(); + actionMap.put(ctrlW, closeAction); + } + @Override public void lostOwnership(Clipboard clipboard, Transferable contents) { if (!internalCopy) { - Desktop.jalviewClipboard = null; + Desktop.getInstance().jalviewClipboard = null; } internalCopy = false; @@ -988,7 +1134,7 @@ 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 @@ -1006,13 +1152,15 @@ 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; @@ -1021,8 +1169,11 @@ 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) @@ -1045,56 +1196,51 @@ public class Desktop extends jalview.jbgui.GDesktop { String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); JalviewFileChooser chooser = JalviewFileChooser - .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); + .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, true); 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); + new FileLoader().loadFile(viewport, selectedFile, + DataSourceType.FILE, format); } - else - { - new FileLoader().LoadFile(choice, 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) @@ -1103,87 +1249,114 @@ 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 = "http://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).getSelectedItem() + .toString()); - 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().endsWith(".jar")) + { + if (viewport != null) + { + new FileLoader().loadFile(viewport, url, DataSourceType.URL, + FileFormat.Jalview); + } + else + { + new FileLoader().loadFile(url, DataSourceType.URL, + FileFormat.Jalview); + } + } + else + { + FileFormatI format = null; + try + { + format = new IdentifyFile().identify(url, DataSourceType.URL); + } catch (FileFormatException e) + { + // TODO revise error handling, distinguish between + // URL not found and response not valid + } - return; - } + if (format == null) + { + String msg = MessageManager + .formatMessage("label.couldnt_locate", url); + JvOptionPane.showInternalMessageDialog(Desktop.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(getDesktopPane()) + .setResponseHandler(0, action) + .showInternalDialog(panel, dialogOption, + JvOptionPane.YES_NO_CANCEL_OPTION, + JvOptionPane.PLAIN_MESSAGE, null, options, + MessageManager.getString("action.ok")); } /** @@ -1265,7 +1438,7 @@ public class Desktop extends jalview.jbgui.GDesktop public void aboutMenuItem_actionPerformed(ActionEvent e) { // StringBuffer message = getAboutMessage(false); - // JvOptionPane.showInternalMessageDialog(Desktop.desktop, + // JvOptionPane.showInternalMessageDialog(Desktop.getDesktop(), // // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE); new Thread(new Runnable() @@ -1345,27 +1518,41 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on requesting Help documentation */ @Override - public void documentationMenuItem_actionPerformed(ActionEvent e) + public void documentationMenuItem_actionPerformed() { try { - Help.showHelpWindow(); + if (Platform.isJS()) + { + BrowserLauncher.openURL("http://www.jalview.org/help.html"); + } + else + /** + * Java only + * + * @j2sIgnore + */ + { + Help.showHelpWindow(); + } } catch (Exception ex) { + System.err.println("Error opening help: " + ex.getMessage()); } } @Override public void closeAll_actionPerformed(ActionEvent e) { + if (desktopPane == null) + { + return; + } // TODO show a progress bar while closing? - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); for (int i = 0; i < frames.length; i++) { try @@ -1386,13 +1573,7 @@ public class Desktop extends jalview.jbgui.GDesktop * reset state of singleton objects as appropriate (clear down session state * when all windows are closed) */ - StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(this); - if (ssm != null) - { - ssm.resetAll(); - } - System.gc(); + getStructureSelectionManager().resetAll(); } @Override @@ -1437,7 +1618,7 @@ public class Desktop extends jalview.jbgui.GDesktop @Override protected void showMemusage_actionPerformed(ActionEvent e) { - desktop.showMemoryUsage(showMemusage.isSelected()); + getDesktopPane().showMemoryUsage(showMemusage.isSelected()); } /* @@ -1462,16 +1643,19 @@ 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 = getDesktopPane().getAllFrames(); if (frames == null || frames.length < 1) { return; @@ -1559,28 +1743,49 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Prompts the user to choose a file and then saves the Jalview state as a + * Jalview project file */ @Override - public void saveState_actionPerformed(ActionEvent e) + public void saveState_actionPerformed() { - JalviewFileChooser chooser = new JalviewFileChooser("jvp", - "Jalview Project"); + saveState_actionPerformed(false); + } - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_state")); + public void saveState_actionPerformed(boolean saveAs) + { + java.io.File projectFile = getProjectFile(); + // autoSave indicates we already have a file and don't need to ask + boolean autoSave = projectFile != null && !saveAs + && BackupFiles.getEnabled(); - int value = chooser.showSaveDialog(this); + // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"', + // saveAs="+saveAs+", Backups + // "+(BackupFiles.getEnabled()?"enabled":"disabled")); - if (value == JalviewFileChooser.APPROVE_OPTION) + boolean approveSave = false; + if (!autoSave) { - final Desktop me = this; - final java.io.File choice = chooser.getSelectedFile(); - setProjectFile(choice); + JalviewFileChooser chooser = new JalviewFileChooser("jvp", + "Jalview Project"); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager.getString("label.save_state")); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + projectFile = chooser.getSelectedFile(); + setProjectFile(projectFile); + approveSave = true; + } + } + + if (approveSave || autoSave) + { + final Desktop me = this; + final java.io.File chosenFile = projectFile; new Thread(new Runnable() { @Override @@ -1589,39 +1794,52 @@ public class Desktop extends jalview.jbgui.GDesktop // TODO: refactor to Jalview desktop session controller action. setProgressBar(MessageManager.formatMessage( "label.saving_jalview_project", new Object[] - { choice.getName() }), choice.hashCode()); + { chosenFile.getName() }), chosenFile.hashCode()); jalview.bin.Cache.setProperty("LAST_DIRECTORY", - choice.getParent()); + chosenFile.getParent()); // TODO catch and handle errors for savestate // TODO prevent user from messing with the Desktop whilst we're saving try { - new Jalview2XML().saveState(choice); + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null; + + new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile); + + if (doBackup) + { + backupfiles.setWriteSuccess(true); + backupfiles.rollBackupsAndRenameTempFile(); + } } catch (OutOfMemoryError oom) { - new OOMWarning( - "Whilst saving current state to " + choice.getName(), - oom); + new OOMWarning("Whilst saving current state to " + + chosenFile.getName(), oom); } catch (Exception ex) { - Cache.log.error( - "Problems whilst trying to save to " + choice.getName(), - ex); + Cache.log.error("Problems whilst trying to save to " + + chosenFile.getName(), ex); JvOptionPane.showMessageDialog(me, MessageManager.formatMessage( "label.error_whilst_saving_current_state_to", new Object[] - { choice.getName() }), + { chosenFile.getName() }), MessageManager.getString("label.couldnt_save_project"), JvOptionPane.WARNING_MESSAGE); } - setProgressBar(null, choice.hashCode()); + setProgressBar(null, chosenFile.hashCode()); } }).start(); - } + } + } + + @Override + public void saveAsState_actionPerformed(ActionEvent e) + { + saveState_actionPerformed(true); } - private void setProjectFile(File choice) + protected void setProjectFile(File choice) { this.projectFile = choice; } @@ -1632,61 +1850,59 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a file chooser dialog and tries to read in the selected file as a + * Jalview project */ @Override - public void loadState_actionPerformed(ActionEvent e) + public void loadState_actionPerformed() { + final String[] suffix = new String[] { "jvp", "jar" }; + final String[] desc = new String[] { "Jalview Project", + "Jalview Project (old)" }; JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jvp", "jar" }, - new String[] - { "Jalview Project", "Jalview Project (old)" }, - "Jalview Project"); + Cache.getProperty("LAST_DIRECTORY"), suffix, desc, + "Jalview Project", true, true); // 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(choice); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Whilst loading project from " + choice, oom); + } catch (Exception ex) + { + Cache.log.error( + "Problems whilst loading project from " + choice, ex); + JvOptionPane.showMessageDialog(Desktop.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(); - } + }).start(); + } + }); + + chooser.showOpenDialog(this); } @Override @@ -1699,7 +1915,7 @@ 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) { @@ -1716,7 +1932,7 @@ 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(); @@ -1729,7 +1945,7 @@ public class Desktop extends jalview.jbgui.GDesktop ((GridLayout) progressPanel.getLayout()).setRows( ((GridLayout) progressPanel.getLayout()).getRows() + 1); ++totalProgressCount; - instance.validate(); + validate(); return thisprogress; } @@ -1783,7 +1999,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public static AlignmentPanel[] getAlignmentPanels(String alignmentId) { - if (Desktop.desktop == null) + if (Desktop.getDesktopPane() == null) { // no frames created and in headless mode // TODO: verify that frames are recoverable when in headless mode @@ -1825,7 +2041,7 @@ 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(); @@ -1901,9 +2117,9 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Gather expanded views (separate AlignFrame's) with the same sequence set - * identifier back in to this frame as additional views, and close the - * expanded views. Note the expanded frames may themselves have multiple - * views. We take the lot. + * identifier back in to this frame as additional views, and close the expanded + * views. Note the expanded frames may themselves have multiple views. We take + * the lot. * * @param source */ @@ -1911,7 +2127,7 @@ public class Desktop extends jalview.jbgui.GDesktop { source.viewport.setGatherViewsHere(true); source.viewport.setExplodedGeometry(source.getBounds()); - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = getAllFrames(); String viewId = source.viewport.getSequenceSetId(); for (int t = 0; t < frames.length; t++) @@ -1947,6 +2163,8 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void vamsasImport_actionPerformed(ActionEvent e) { + // TODO: JAL-3048 not needed for Jalview-JS + if (v_client == null) { // Load and try to start a session. @@ -1966,7 +2184,7 @@ public class Desktop extends jalview.jbgui.GDesktop String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.formatMessage( "label.couldnt_import_as_vamsas_session", new Object[] @@ -2198,7 +2416,7 @@ public class Desktop extends jalview.jbgui.GDesktop }); rthr.start(); } - }; + } }); VamsasStMenu.add(sessit); } @@ -2223,6 +2441,8 @@ public class Desktop extends jalview.jbgui.GDesktop @Override public void vamsasSave_actionPerformed(ActionEvent e) { + // TODO: JAL-3048 not needed for Jalview-JS + if (v_client != null) { // TODO: VAMSAS DOCUMENT EXTENSION is VDJ @@ -2265,7 +2485,7 @@ public class Desktop extends jalview.jbgui.GDesktop removeProgressPanel(progpanel); if (warnmsg != null) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); } @@ -2302,7 +2522,7 @@ public class Desktop extends jalview.jbgui.GDesktop public JInternalFrame[] getAllFrames() { - return desktop.getAllFrames(); + return desktopPane.getAllFrames(); } /** @@ -2341,7 +2561,7 @@ public class Desktop extends jalview.jbgui.GDesktop while (li.hasNext()) { String link = li.next(); - if (link.contains(SEQUENCE_ID) + if (link.contains(UrlConstants.SEQUENCE_ID) && !UrlConstants.isDefaultString(link)) { check = true; @@ -2388,7 +2608,7 @@ 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); @@ -2399,14 +2619,13 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Proxy class for JDesktopPane which optionally displays the current memory - * usage and highlights the desktop area with a red bar if free memory runs - * low. + * usage and highlights the desktop area with a red bar if free memory runs low. * * @author AMW */ - public class MyDesktopPane extends JDesktopPane implements Runnable + public class MyDesktopPane extends JDesktopPane + implements Runnable { - private static final float ONE_MB = 1048576f; boolean showMemoryUsage = false; @@ -2495,7 +2714,6 @@ public class Desktop extends jalview.jbgui.GDesktop } } - /** * Accessor method to quickly get all the AlignmentFrames loaded. * @@ -2505,11 +2723,11 @@ public class Desktop extends jalview.jbgui.GDesktop { if (Jalview.isHeadlessMode()) { - // Desktop.desktop is null in headless mode - return new AlignFrame[] { Jalview.currentAlignFrame }; + // Desktop.getDesktop() is null in headless mode + return new AlignFrame[] { Jalview.getCurrentAlignFrame() }; } - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); if (frames == null) { @@ -2554,7 +2772,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public GStructureViewer[] getJmols() { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); if (frames == null) { @@ -2590,7 +2808,7 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (Exception ex) { jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(desktopPane, MessageManager.getString("label.couldnt_create_groovy_shell"), MessageManager.getString("label.groovy_support_failed"), @@ -2601,7 +2819,7 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Open the Groovy console */ - void openGroovyConsole() + private void openGroovyConsole() { if (groovyConsole == null) { @@ -2643,8 +2861,8 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this - * binding when opened + * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding + * when opened */ protected void addQuitHandler() { @@ -2701,6 +2919,8 @@ 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<>(); @@ -2777,16 +2997,15 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * This will return the first AlignFrame holding the given viewport instance. - * It will break if there are more than one AlignFrames viewing a particular - * av. + * This will return the first AlignFrame holding the given viewport instance. It + * will break if there are more than one AlignFrames viewing a particular av. * * @param viewport * @return alignFrame for viewport */ public static AlignFrame getAlignFrameFor(AlignViewportI viewport) { - if (desktop != null) + if (getDesktopPane() != null) { AlignmentPanel[] aps = getAlignmentPanels( viewport.getSequenceSetId()); @@ -2847,8 +3066,8 @@ public class Desktop extends jalview.jbgui.GDesktop // todo: changesupport handlers need to be transferred if (discoverer == null) { - discoverer = new jalview.ws.jws1.Discoverer(); - // register PCS handler for desktop. + discoverer = Discoverer.getInstance(); + // register PCS handler for getDesktop(). discoverer.addPropertyChangeListener(changeSupport); } // JAL-940 - disabled JWS1 service configuration - always start discoverer @@ -2858,7 +3077,7 @@ public class Desktop extends jalview.jbgui.GDesktop if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { - t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() + t2 = jalview.ws.jws2.Jws2Discoverer.getInstance() .startDiscoverer(changeSupport); } Thread t3 = null; @@ -2891,7 +3110,7 @@ public class Desktop extends jalview.jbgui.GDesktop { if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) { - final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() + final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance() .getErrorMessages(); if (ermsg != null) { @@ -2930,7 +3149,7 @@ public class Desktop extends jalview.jbgui.GDesktop * * jd.waitForInput(); */ - JvOptionPane.showConfirmDialog(Desktop.desktop, + JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(), new JLabel("
" + ermsg + "
" + "

It may be that you have invalid JABA URLs
in your web service preferences," @@ -2956,7 +3175,7 @@ public class Desktop extends jalview.jbgui.GDesktop } } - private Runnable serviceChangedDialog = null; + Runnable serviceChangedDialog = null; /** * start a thread to open a URL in the configured browser. Pops up a warning @@ -2967,7 +3186,7 @@ public class Desktop extends jalview.jbgui.GDesktop */ public static void showUrl(final String url) { - showUrl(url, Desktop.instance); + showUrl(url, Desktop.getInstance()); } /** @@ -2993,10 +3212,10 @@ public class Desktop extends jalview.jbgui.GDesktop .formatMessage("status.opening_params", new Object[] { url }), this.hashCode()); } - jalview.util.BrowserLauncher.openURL(url); + BrowserLauncher.openURL(url); } catch (Exception ex) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager .getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), @@ -3012,15 +3231,16 @@ public class Desktop extends jalview.jbgui.GDesktop }).start(); } - public static WsParamSetManager wsparamManager = null; + private WsParamSetManager wsparamManager = null; public static ParamManager getUserParameterStore() { - if (wsparamManager == null) + Desktop d = Desktop.getInstance(); + if (d.wsparamManager == null) { - wsparamManager = new WsParamSetManager(); + d.wsparamManager = new WsParamSetManager(); } - return wsparamManager; + return d.wsparamManager; } /** @@ -3065,14 +3285,16 @@ public class Desktop extends jalview.jbgui.GDesktop /** * flag indicating if dialogExecutor should try to acquire a permit */ - private volatile boolean dialogPause = true; + volatile boolean dialogPause = true; /** * pause the queue */ - private java.util.concurrent.Semaphore block = new Semaphore(0); + java.util.concurrent.Semaphore block = new Semaphore(0); + + private groovy.ui.Console groovyConsole; - private static groovy.ui.Console groovyConsole; + public StructureViewer lastTargetedView; /** * add another dialog thread to the queue @@ -3094,9 +3316,8 @@ public class Desktop extends jalview.jbgui.GDesktop } catch (InterruptedException x) { } - ; } - if (instance == null) + if (instanceOnly) { return; } @@ -3119,34 +3340,45 @@ 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); + Cache.log.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); } /** * Explode the views in the given SplitFrame into separate SplitFrame windows. - * This respects (remembers) any previous 'exploded geometry' i.e. the size - * and location last time the view was expanded (if any). However it does not + * This respects (remembers) any previous 'exploded geometry' i.e. the size and + * location last time the view was expanded (if any). However it does not * remember the split pane divider location - this is set to match the * 'exploding' frame. * @@ -3249,7 +3481,7 @@ 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) @@ -3294,14 +3526,51 @@ public class Desktop extends jalview.jbgui.GDesktop public static groovy.ui.Console getGroovyConsole() { - return groovyConsole; + Desktop desktop = Desktop.getInstance(); + return desktop == null ? null : desktop.groovyConsole; } - public static void transferFromDropTarget(List files, + /** + * handles the payload of a drag and drop event. + * + * TODO refactor to desktop utilities class + * + * @param files + * - Data source strings extracted from the drop event + * @param protocols + * - protocol for each data source extracted from the drop event + * @param evt + * - the drop event + * @param t + * - the payload from the drop event + * @throws Exception + */ + @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 @@ -3318,26 +3587,25 @@ public class Desktop extends jalview.jbgui.GDesktop try { - java.net.URL url = (URL) t.getTransferData(urlFlavour); + java.net.URL url = (URL) t.getTransferData(urlFlavour); // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099 // means url may be null. - if (url != null) - { - protocols.add(DataSourceType.URL); - files.add(url.toString()); - Cache.log.debug("Drop handled as URL dataflavor " - + files.get(files.size() - 1)); + if (url != null) + { + protocols.add(DataSourceType.URL); + files.add(url.toString()); + Cache.log.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); @@ -3347,10 +3615,10 @@ public class Desktop extends jalview.jbgui.GDesktop { // Works on Windows and MacOSX Cache.log.debug("Drop handled as javaFileListFlavor"); - for (Object file : (List) t + for (Object file : (List) t .getTransferData(DataFlavor.javaFileListFlavor)) { - files.add(((File) file).toString()); + files.add(file); protocols.add(DataSourceType.FILE); } } @@ -3448,18 +3716,23 @@ public class Desktop extends jalview.jbgui.GDesktop } } } - if (Platform.isWindows()) - + if (Platform.isWindowsAndNotJS()) { Cache.log.debug("Scanning dropped content for Windows Link Files"); // resolve any .lnk files in the file drop for (int f = 0; f < files.size(); f++) { - if (protocols.get(f).equals(DataSourceType.FILE) && files.get(f).toLowerCase().endsWith(".lnk") || files.get(f).toLowerCase().endsWith(".url")|| files.get(f).toLowerCase().endsWith(".site")) + String source = files.get(f).toString().toLowerCase(); + if (protocols.get(f).equals(DataSourceType.FILE) + && (source.endsWith(".lnk") || source.endsWith(".url") + || source.endsWith(".site"))) { - try { - File lf = new File(files.get(f)); + try + { + 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); WindowsShortcut wscfile = new WindowsShortcut(lf); @@ -3468,10 +3741,11 @@ public class Desktop extends jalview.jbgui.GDesktop files.set(f, fullname); Cache.log.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f)); - } - catch (Exception ex) + } catch (Exception ex) { - Cache.log.error("Couldn't parse "+files.get(f)+" as a link file.",ex); + Cache.log.error( + "Couldn't parse " + files.get(f) + " as a link file.", + ex); } } } @@ -3489,10 +3763,10 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * Answers a (possibly empty) list of any structure viewer frames (currently - * for either Jmol or Chimera) which are currently open. This may optionally - * be restricted to viewers of a specified class, or viewers linked to a - * specified alignment panel. + * Answers a (possibly empty) list of any structure viewer frames (currently for + * either Jmol or Chimera) which are currently open. This may optionally be + * restricted to viewers of a specified class, or viewers linked to a specified + * alignment panel. * * @param apanel * if not null, only return viewers linked to this panel @@ -3505,7 +3779,7 @@ 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) { @@ -3524,4 +3798,5 @@ public class Desktop extends jalview.jbgui.GDesktop } return result; } + }