X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=701d778723fdeffa3a1d0e033f23a97ad1cc329c;hb=8a5e515191927f18f4d06b261888c011798ff506;hp=7d0eb7f0fe562638ebbac244c8346c1f7db35fef;hpb=c355d0f7a994d0d064078d363e612eb8c89581f1;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 7d0eb7f..701d778 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -26,12 +26,14 @@ import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.bin.Jalview; +import jalview.gui.ImageExporter.ImageWriterI; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatException; import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FileLoader; +import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; @@ -39,10 +41,12 @@ import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; 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.util.dialogrunner.RunResponse; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.ParamManager; import jalview.ws.utils.UrlDownloadClient; @@ -68,8 +72,7 @@ import java.awt.dnd.DropTargetEvent; import java.awt.dnd.DropTargetListener; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.awt.event.FocusEvent; -import java.awt.event.FocusListener; +import java.awt.event.InputEvent; import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; @@ -93,10 +96,13 @@ 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; @@ -109,6 +115,7 @@ 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; @@ -118,6 +125,8 @@ import javax.swing.event.InternalFrameEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; +import org.stackoverflowusers.file.WindowsShortcut; + /** * Jalview Desktop * @@ -125,10 +134,19 @@ import javax.swing.event.MenuListener; * @author $author$ * @version $Revision: 1.155 $ */ -public class Desktop extends jalview.jbgui.GDesktop implements - DropTargetListener, ClipboardOwner, IProgressIndicator, +public class Desktop extends jalview.jbgui.GDesktop + implements DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider { + private static int DEFAULT_MIN_WIDTH = 300; + + private static int DEFAULT_MIN_HEIGHT = 250; + + private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600; + + private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70; + + private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES"; private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); @@ -179,6 +197,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements public static MyDesktopPane desktop; + public static MyDesktopPane getDesktop() + { + // BH 2018 could use currentThread() here as a reference to a + // Hashtable in JavaScript + return desktop; + } + static int openFrameCount = 0; static final int xOffset = 30; @@ -260,12 +285,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void endDraggingFrame(JComponent f) { delegate.endDraggingFrame(f); + desktop.repaint(); } @Override public void endResizingFrame(JComponent f) { delegate.endResizingFrame(f); + desktop.repaint(); } @Override @@ -320,38 +347,25 @@ public class Desktop extends jalview.jbgui.GDesktop implements public Desktop() { /** - * 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. + * 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(); - - groovyShell = new JMenuItem(); - groovyShell.setText(MessageManager.getString("label.groovy_console")); - groovyShell.addActionListener(new ActionListener() + if (!Jalview.isJS()) { - @Override - public void actionPerformed(ActionEvent e) - { - groovyShell_actionPerformed(); - } - }); - toolsMenu.add(groovyShell); - groovyShell.setVisible(true); + 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); + boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE", + false); desktop = new MyDesktopPane(selmemusage); - if (Platform.isAMac()) - { - desktop.setDoubleBuffered(false); - } + + showMemusage.setSelected(selmemusage); desktop.setBackground(Color.white); getContentPane().setLayout(new BorderLayout()); @@ -359,13 +373,27 @@ public class Desktop extends jalview.jbgui.GDesktop implements // JScrollPane sp = new JScrollPane(); // sp.getViewport().setView(desktop); // getContentPane().add(sp, BorderLayout.CENTER); + + // BH 2018 - just an experiment to try unclipped JInternalFrames. + // Must set for all three to be active: + if (Jalview.isJS()) + { + getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); + ((JComponent) getContentPane()).putClientProperty("swingjs.overflow.hidden", "false"); + desktop.putClientProperty("swingjs.overflow.hidden", "false"); + } + 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( - new DefaultDesktopManager())); + (Platform.isWindows() ? new DefaultDesktopManager() + : Platform.isAMac() + ? new AquaInternalFrameManager( + desktop.getDesktopManager()) + : desktop.getDesktopManager()))); Rectangle dims = getLastKnownDimensions(""); if (dims != null) @@ -375,29 +403,81 @@ public class Desktop extends jalview.jbgui.GDesktop implements else { Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); - setBounds((screenSize.width - 900) / 2, - (screenSize.height - 650) / 2, 900, 650); + int xPos = Math.max(5, (screenSize.width - 900) / 2); + int yPos = Math.max(5, (screenSize.height - 650) / 2); + setBounds(xPos, yPos, 900, 650); } - jconsole = new Console(this, showjconsole); - // add essential build information - jconsole.setHeader("Jalview Version: " - + jalview.bin.Cache.getProperty("VERSION") + "\n" - + "Jalview Installation: " - + jalview.bin.Cache.getDefault("INSTALLATION", "unknown") - + "\n" + "Build Date: " - + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n" - + "Java version: " + System.getProperty("java.version") + "\n" - + System.getProperty("os.arch") + " " - + System.getProperty("os.name") + " " - + System.getProperty("os.version")); + + boolean doFullLoad = /** @j2sNative ! */true; + + if (doFullLoad) { + + jconsole = new Console(this, showjconsole); + // add essential build information + jconsole.setHeader("Jalview Version: " + + jalview.bin.Cache.getProperty("VERSION") + "\n" + + "Jalview Installation: " + + jalview.bin.Cache.getDefault("INSTALLATION", "unknown") + + "\n" + "Build Date: " + + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n" + + "Java version: " + System.getProperty("java.version") + "\n" + + System.getProperty("os.arch") + " " + + System.getProperty("os.name") + " " + + System.getProperty("os.version")); + + showConsole(showjconsole); + + showNews.setVisible(false); - showConsole(showjconsole); + experimentalFeatures.setSelected(showExperimental()); - showNews.setVisible(false); + getIdentifiersOrgData(); - getIdentifiersOrgData(); + checkURLLinks(); - checkURLLinks(); + // Spawn a thread that shows the splashscreen + + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + new SplashScreen(); + } + }); + + // Thread off a new instance of the file chooser - this reduces the time it + // takes to open it later on. + new Thread(new Runnable() + { + @Override + public void run() + { + Cache.log.debug("Filechooser init thread started."); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), + fileFormat); + Cache.log.debug("Filechooser init thread finished."); + } + }).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); + } + + }); + + } + + this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); this.addWindowListener(new WindowAdapter() { @@ -431,63 +511,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); desktop.addMouseListener(ma); - this.addFocusListener(new FocusListener() - { - - @Override - public void focusLost(FocusEvent e) - { - // TODO Auto-generated method stub - - } - - @Override - public void focusGained(FocusEvent e) - { - Cache.log.debug("Relaying windows after focus gain"); - // make sure that we sort windows properly after we gain focus - instance.relayerWindows(); - } - }); - this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); - // Spawn a thread that shows the splashscreen - SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - new SplashScreen(); - } - }); - - // Thread off a new instance of the file chooser - this reduces the time it - // takes to open it later on. - new Thread(new Runnable() - { - @Override - public void run() - { - Cache.log.debug("Filechooser init thread started."); - String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); - JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), - fileFormat); - Cache.log.debug("Filechooser init thread finished."); - } - }).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); - } + } - }); + /** + * Answers true if user preferences to enable experimental features is True + * (on), else false + * + * @return + */ + public boolean showExperimental() + { + String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, + Boolean.FALSE.toString()); + return Boolean.valueOf(experimental).booleanValue(); } public void doConfigureStructurePrefs() @@ -497,12 +533,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements .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)); + 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 { @@ -516,24 +552,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements { 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() @@ -550,7 +585,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements + e.getMessage()); } } - }); + }).start(); + ; } @Override @@ -561,25 +597,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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(); + Desktop.instance.setProgressBar( + MessageManager.getString("status.refreshing_news"), now); + jvnews.refreshNews(); + Desktop.instance.setProgressBar(null, now); + jvnews.showNews(); + } + }).start(); } } @@ -597,25 +631,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X"); String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y"); - String width = jalview.bin.Cache.getProperty(windowName - + "SCREEN_WIDTH"); - String height = jalview.bin.Cache.getProperty(windowName - + "SCREEN_HEIGHT"); + String 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); + 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) { // 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( + jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH")))); + double sh = ((1f * screenSize.height) / (1f * Integer.parseInt( + jalview.bin.Cache.getProperty("SCREENGEOMETRY_HEIGHT")))); // rescale the bounds depending upon the current screen geometry. ix = (int) (ix * sw); iw = (int) (iw * sw); @@ -623,19 +655,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements ih = (int) (ih * sh); while (ix >= screenSize.width) { - jalview.bin.Cache.log - .debug("Window geometry location recall error: shifting horizontal to within screenbounds."); + jalview.bin.Cache.log.debug( + "Window geometry location recall error: shifting horizontal to within screenbounds."); ix -= screenSize.width; } while (iy >= screenSize.height) { - jalview.bin.Cache.log - .debug("Window geometry location recall error: shifting vertical to within screenbounds."); + jalview.bin.Cache.log.debug( + "Window geometry location recall error: shifting vertical to within screenbounds."); iy -= screenSize.height; } - jalview.bin.Cache.log.debug("Got last known dimensions for " - + windowName + ": x:" + ix + " y:" + iy + " width:" + iw - + " height:" + ih); + jalview.bin.Cache.log.debug( + "Got last known dimensions for " + windowName + ": x:" + ix + + " y:" + iy + " width:" + iw + " height:" + ih); } // return dimensions for new instance return new Rectangle(ix, iy, iw, ih); @@ -645,7 +677,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements private void doVamsasClientCheck() { - if (jalview.bin.Cache.vamsasJarsPresent()) + if (Cache.vamsasJarsPresent()) { setupVamsasDisconnectedGui(); VamsasMenu.setVisible(true); @@ -721,9 +753,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } catch (Exception ex) { - System.out - .println("Unable to paste alignment from system clipboard:\n" - + ex); + System.out.println( + "Unable to paste alignment from system clipboard:\n" + ex); } } @@ -742,7 +773,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements public static synchronized void addInternalFrame( final JInternalFrame frame, String title, int w, int h) { - addInternalFrame(frame, title, true, w, h, true); + addInternalFrame(frame, title, true, w, h, true, false); } /** @@ -764,7 +795,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements final JInternalFrame frame, String title, boolean makeVisible, int w, int h) { - addInternalFrame(frame, title, makeVisible, w, h, true); + addInternalFrame(frame, title, makeVisible, w, h, true, false); } /** @@ -785,7 +816,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements final JInternalFrame frame, String title, int w, int h, boolean resizable) { - addInternalFrame(frame, title, true, w, h, resizable); + addInternalFrame(frame, title, true, w, h, resizable, false); } /** @@ -804,10 +835,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements * height * @param resizable * Allow resize + * @param ignoreMinSize + * Do not set the default minimum size for frame */ public static synchronized void addInternalFrame( final JInternalFrame frame, String title, boolean makeVisible, - int w, int h, boolean resizable) + int w, int h, boolean resizable, boolean ignoreMinSize) { // TODO: allow callers to determine X and Y position of frame (eg. via @@ -824,31 +857,42 @@ public class Desktop extends jalview.jbgui.GDesktop implements // 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 (instance == null || (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true"))) { return; } openFrameCount++; + if (!ignoreMinSize) + { + frame.setMinimumSize( + new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT)); + + // Set default dimension for Alignment Frame window. + // The Alignment Frame window could be added from a number of places, + // hence, + // I did this here in order not to miss out on any Alignment frame. + if (frame instanceof AlignFrame) + { + frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, + ALIGN_FRAME_DEFAULT_MIN_HEIGHT)); + } + } + frame.setVisible(makeVisible); frame.setClosable(true); frame.setResizable(resizable); frame.setMaximizable(resizable); frame.setIconifiable(resizable); - if (Platform.isAMac()) - { - frame.setIconifiable(false); - frame.setFrameIcon(null); - // frame.setDesktopIcon(null); - frame.setDoubleBuffered(false); - } + frame.setOpaque(/** @j2sNative true || */ + false); + if (frame.getX() < 1 && frame.getY() < 1) { - frame.setLocation(xOffset * openFrameCount, yOffset - * ((openFrameCount - 1) % 10) + yOffset); + frame.setLocation(xOffset * openFrameCount, + yOffset * ((openFrameCount - 1) % 10) + yOffset); } /* @@ -864,6 +908,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { + if (itf instanceof AlignFrame) + { + Jalview.setCurrentAlignFrame((AlignFrame) itf); + } itf.requestFocus(); } } @@ -890,16 +938,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements menuItem.removeActionListener(menuItem.getActionListeners()[0]); } windowMenu.remove(menuItem); - JInternalFrame itf = desktop.getSelectedFrame(); - if (itf != null) - { - itf.requestFocus(); - if (itf instanceof AlignFrame) - { - Jalview.setCurrentAlignFrame((AlignFrame) itf); - } - } - System.gc(); }; }); @@ -914,11 +952,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements frame.setIcon(false); } catch (java.beans.PropertyVetoException ex) { - + // System.err.println(ex.toString()); } } }); + setKeyBindings(frame); + desktop.add(frame); windowMenu.add(menuItem); @@ -932,12 +972,48 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } catch (java.lang.ClassCastException cex) { - Cache.log - .warn("Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869", - cex); + Cache.log.warn( + "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869", + cex); } } + /** + * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the + * window + * + * @param frame + */ + private static void setKeyBindings(JInternalFrame frame) + { + @SuppressWarnings("serial") + final Action closeAction = new AbstractAction() + { + @Override + public void actionPerformed(ActionEvent e) + { + frame.dispose(); + } + }; + + /* + * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action + */ + KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, + InputEvent.CTRL_DOWN_MASK); + KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, + 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) { @@ -983,8 +1059,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - List files = new ArrayList(); - List protocols = new ArrayList(); + List files = new ArrayList<>(); + List protocols = new ArrayList<>(); try { @@ -1001,12 +1077,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements { for (int i = 0; i < files.size(); i++) { - String file = files.get(i).toString(); - DataSourceType protocol = (protocols == null) ? DataSourceType.FILE + // 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; @@ -1016,7 +1095,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements format = new IdentifyFile().identify(file, protocol); } - new FileLoader().LoadFile(file, protocol, format); + new FileLoader().LoadFile(null, file, protocol, format); } } catch (Exception ex) @@ -1038,57 +1117,52 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); - JalviewFileChooser chooser = JalviewFileChooser.forRead( - Cache.getProperty("LAST_DIRECTORY"), fileFormat); + JalviewFileChooser chooser = JalviewFileChooser + .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.open_local_file")); + chooser.setDialogTitle( + MessageManager.getString("label.open_local_file")); chooser.setToolTipText(MessageManager.getString("action.open")); - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", chooser - .getSelectedFile().getParent()); - - 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)) + @Override + public void run() { - try - { - format = new IdentifyFile().identify(choice, DataSourceType.FILE); - } catch (FileFormatException e) + File selectedFile = chooser.getSelectedFile(); + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); + + 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)) { - // 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); - } - } + }).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) @@ -1097,86 +1171,102 @@ public class Desktop extends jalview.jbgui.GDesktop implements // 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) - { - return; - } - - String url = history.getSelectedItem().toString(); - - if (url.toLowerCase().endsWith(".jar")) + + /* + * 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 (Jalview.isJS()) { - if (viewport != null) - { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, - FileFormat.Jalview); - } - else - { - new FileLoader().LoadFile(url, DataSourceType.URL, - FileFormat.Jalview); - } + history = new JTextField(urlBase, 35); } else { - FileFormatI format = null; - try - { - format = new IdentifyFile().identify(url, DataSourceType.URL); - } catch (FileFormatException e) + 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) { - // TODO revise error handling, distinguish between - // URL not found and response not valid + for (String token : historyItems.split("\\t")) + { + asCombo.addItem(token); + } } + history = asCombo; + } + panel.add(history); - if (format == null) + Object[] options = new Object[] { MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }; + RunResponse action = new RunResponse(JvOptionPane.OK_OPTION) { + @Override + public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.couldnt_locate", - new Object[] { url }), MessageManager - .getString("label.url_not_found"), - JvOptionPane.WARNING_MESSAGE); + String url = Jalview.isJS() ? ((JTextField) history).getText() + : ((JComboBox) history).getSelectedItem() + .toString(); - return; - } + 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 + } - if (viewport != null) - { - new FileLoader() - .LoadFile(viewport, url, DataSourceType.URL, format); - } - else - { - new FileLoader().LoadFile(url, DataSourceType.URL, format); - } - } + if (format == null) + { + String msg = MessageManager.formatMessage("label.couldnt_locate", url); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, + MessageManager.getString("label.url_not_found"), + JvOptionPane.WARNING_MESSAGE); + + return; + } + + if (viewport != null) + { + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + format); + } + else + { + new FileLoader().LoadFile(url, DataSourceType.URL, format); + } + } + }}; + String dialogOption = MessageManager + .getString("label.input_alignment_from_url"); + JvOptionPane.newOptionDialog(desktop).response(action) + .showInternalDialog(panel, dialogOption, + JvOptionPane.YES_NO_CANCEL_OPTION, + JvOptionPane.PLAIN_MESSAGE, null, options, + MessageManager.getString("action.ok")); } /** @@ -1193,8 +1283,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(viewPanel); Desktop.addInternalFrame(cap, - MessageManager.getString("label.cut_paste_alignmen_file"), - true, 600, 500); + MessageManager.getString("label.cut_paste_alignmen_file"), true, + 600, 500); } /* @@ -1204,12 +1294,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void quit() { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); - jalview.bin.Cache - .setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); - jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height - + ""); - storeLastKnownDimensions("", new Rectangle(getBounds().x, - getBounds().y, getWidth(), getHeight())); + jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH", + screen.width + ""); + jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", + screen.height + ""); + storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, + getWidth(), getHeight())); if (jconsole != null) { @@ -1278,7 +1368,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (shortv) { message.append("

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

"); + + jalview.bin.Cache.getProperty("VERSION") + + ""); message.append("Last Updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + ""); @@ -1293,8 +1384,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); } - if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals( - "Checking")) + if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking") + .equals("Checking")) { message.append("
...Checking latest version...
"); } @@ -1316,16 +1407,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements "..Checking..") + " is available for download from " + jalview.bin.Cache.getDefault("www.jalview.org", - "http://www.jalview.org") + " !!"); + "http://www.jalview.org") + + " !!"); if (red) { message.append(""); } } - message.append("
Authors: " - + jalview.bin.Cache - .getDefault("AUTHORFNAMES", - "The Jalview Authors (See AUTHORS file for current list)") + 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:" @@ -1337,19 +1428,24 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * 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 (Jalview.isJS()) + { + BrowserLauncher.openURL("http://www.jalview.org/help.html"); + } + else + { + Help.showHelpWindow(); + } } catch (Exception ex) { + System.err.println("Error opening help: " + ex.getMessage()); } } @@ -1384,7 +1480,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements { ssm.resetAll(); } - System.gc(); } @Override @@ -1454,11 +1549,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ 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) @@ -1551,26 +1649,22 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * 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(boolean asCastor) { - JalviewFileChooser chooser = new JalviewFileChooser("jvp", + JalviewFileChooser chooser = new JalviewFileChooser( + asCastor ? "jvp" : "jvx", "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.save_state")); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + int option = chooser.showSaveDialog(this); + if (option == JalviewFileChooser.APPROVE_OPTION) { - final Desktop me = this; - final java.io.File choice = chooser.getSelectedFile(); + File choice = chooser.getSelectedFile(); setProjectFile(choice); new Thread(new Runnable() @@ -1580,37 +1674,47 @@ public class Desktop extends jalview.jbgui.GDesktop implements { // TODO: refactor to Jalview desktop session controller action. setProgressBar(MessageManager.formatMessage( - "label.saving_jalview_project", - new Object[] { choice.getName() }), choice.hashCode()); + "label.saving_jalview_project", new Object[] + { choice.getName() }), choice.hashCode()); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.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); + if (asCastor) + { + new Jalview2XML().saveState(choice); + } + else + { + new jalview.project.Jalview2XML().saveState(choice); + } } catch (OutOfMemoryError oom) { - new OOMWarning("Whilst saving current state to " - + choice.getName(), oom); + new OOMWarning( + "Whilst saving current state to " + choice.getName(), + oom); } catch (Exception ex) { Cache.log.error( "Problems whilst trying to save to " + choice.getName(), ex); - JvOptionPane.showMessageDialog(me, MessageManager.formatMessage( - "label.error_whilst_saving_current_state_to", - new Object[] { choice.getName() }), MessageManager - .getString("label.couldnt_save_project"), + JvOptionPane.showMessageDialog(Desktop.this, + MessageManager.formatMessage( + "label.error_whilst_saving_current_state_to", + new Object[] + { choice.getName() }), + MessageManager.getString("label.couldnt_save_project"), JvOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } }).start(); - } + } } - private void setProjectFile(File choice) + void setProjectFile(File choice) { this.projectFile = choice; } @@ -1621,60 +1725,70 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Prompts the user to choose a file and loads in as a Jalview project file */ @Override - public void loadState_actionPerformed(ActionEvent e) - { + public void loadState_actionPerformed(boolean asCastor) + { + // TODO: GET RID OF .JVX BEFORE RELEASE JIM! + final String[] suffix = asCastor ? new String[] { "jvp", "jar" } + : new String[] + { "jvx" }; + final String[] desc = asCastor + ? new String[] + { "Jalview Project", "Jalview Project (old)" } + : new String[] + { "Jalview Project" }; JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), new String[] { - "jvp", "jar" }, new String[] { "Jalview Project", - "Jalview Project (old)" }, "Jalview Project"); + Cache.getProperty("LAST_DIRECTORY"), suffix, + desc, + "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) + chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION) { - final File selectedFile = chooser.getSelectedFile(); - setProjectFile(selectedFile); - final String choice = selectedFile.getAbsolutePath(); - Cache.setProperty("LAST_DIRECTORY", - selectedFile.getParent()); - new Thread(new Runnable() + @Override + public void run() { - @Override - public void run() + File selectedFile = chooser.getSelectedFile(); + setProjectFile(selectedFile); + final String choice = selectedFile.getAbsolutePath(); + Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); + new Thread(new Runnable() { - setProgressBar( - MessageManager.formatMessage( - "label.loading_jalview_project", - new Object[] { choice }), choice.hashCode()); - try - { - new Jalview2XML().loadJalviewAlign(choice); - } catch (OutOfMemoryError oom) + @Override + public void run() { + try { + if (asCastor) + { + new Jalview2XML().loadJalviewAlign(choice); + } + else + { + new jalview.project.Jalview2XML().loadJalviewAlign(choice); + } + } catch (OutOfMemoryError oom) + { new OOMWarning("Whilst loading project from " + choice, oom); - } catch (Exception ex) - { - Cache.log.error("Problems whilst loading project from " - + choice, ex); - JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager - .formatMessage( + } catch (Exception ex) + { + Cache.log.error( + "Problems whilst loading project from " + choice, ex); + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.formatMessage( "label.error_whilst_loading_project_from", - new Object[] { choice }), MessageManager - .getString("label.couldnt_load_project"), + new Object[] + { choice }), + MessageManager.getString("label.couldnt_load_project"), JvOptionPane.WARNING_MESSAGE); + } } - setProgressBar(null, choice.hashCode()); - } - }).start(); - } + }).start(); + } + }); + + chooser.showOpenDialog(this); } @Override @@ -1685,14 +1799,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements JPanel progressPanel; - ArrayList fileLoadingPanels = new ArrayList(); + ArrayList fileLoadingPanels = new ArrayList<>(); - public void startLoading(final String fileName) + public void startLoading(final Object fileName) { if (fileLoadingCount == 0) { - fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage( - "label.loading_file", new Object[] { fileName }))); + fileLoadingPanels.add(addProgressPanel(MessageManager + .formatMessage("label.loading_file", new Object[] + { fileName }))); } fileLoadingCount++; } @@ -1713,8 +1828,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements thisprogress.add(progressBar, BorderLayout.CENTER); progressPanel.add(thisprogress); - ((GridLayout) progressPanel.getLayout()) - .setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1); + ((GridLayout) progressPanel.getLayout()).setRows( + ((GridLayout) progressPanel.getLayout()).getRows() + 1); ++totalProgressCount; instance.validate(); return thisprogress; @@ -1776,7 +1891,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements // TODO: verify that frames are recoverable when in headless mode return null; } - List aps = new ArrayList(); + List aps = new ArrayList<>(); AlignFrame[] frames = getAlignFrames(); if (frames == null) { @@ -1811,16 +1926,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public static AlignmentViewport[] getViewports(String sequenceSetId) { - List viewp = new ArrayList(); + List viewp = new ArrayList<>(); if (desktop != null) { AlignFrame[] frames = Desktop.getAlignFrames(); for (AlignFrame afr : frames) { - if (sequenceSetId == null - || afr.getViewport().getSequenceSetId() - .equals(sequenceSetId)) + if (sequenceSetId == null || afr.getViewport().getSequenceSetId() + .equals(sequenceSetId)) { if (afr.alignPanels != null) { @@ -1889,9 +2003,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * 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 */ @@ -1935,6 +2049,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements @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. @@ -1942,10 +2058,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.open_saved_vamsas_session")); - chooser.setToolTipText(MessageManager - .getString("label.select_vamsas_session_opened_as_new_vamsas_session")); + chooser.setDialogTitle( + MessageManager.getString("label.open_saved_vamsas_session")); + chooser.setToolTipText(MessageManager.getString( + "label.select_vamsas_session_opened_as_new_vamsas_session")); int value = chooser.showOpenDialog(this); @@ -1954,22 +2070,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { - JvOptionPane - .showInternalMessageDialog( - Desktop.desktop, - MessageManager.formatMessage( - "label.couldnt_import_as_vamsas_session", - new Object[] { fle }), - MessageManager - .getString("label.vamsas_document_import_failed"), - JvOptionPane.ERROR_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.couldnt_import_as_vamsas_session", + new Object[] + { fle }), + MessageManager + .getString("label.vamsas_document_import_failed"), + JvOptionPane.ERROR_MESSAGE); } } } else { - jalview.bin.Cache.log - .error("Implementation error - load session from a running session is not supported."); + jalview.bin.Cache.log.error( + "Implementation error - load session from a running session is not supported."); } } @@ -1985,8 +2100,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (v_client != null) { - jalview.bin.Cache.log - .error("Implementation error - load session from a running session is not supported."); + jalview.bin.Cache.log.error( + "Implementation error - load session from a running session is not supported."); return false; } @@ -2011,7 +2126,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { jalview.bin.Cache.log.error( "Failed to create new vamsas session from contents of URL " - + url, ex); + + url, + ex); return false; } setupVamsasConnectedGui(); @@ -2030,22 +2146,22 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (v_client != null) { - jalview.bin.Cache.log - .error("Implementation error - load session from a running session is not supported."); + jalview.bin.Cache.log.error( + "Implementation error - load session from a running session is not supported."); return false; } setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", - new Object[] { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", new Object[] + { file.getName() }), file.hashCode()); try { v_client = new jalview.gui.VamsasApplication(this, file, null); } catch (Exception ex) { setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", - new Object[] { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", new Object[] + { file.getName() }), file.hashCode()); jalview.bin.Cache.log.error( "New vamsas session from existing session file failed:", ex); return false; @@ -2053,8 +2169,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements setupVamsasConnectedGui(); v_client.initial_update(); // TODO: thread ? setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", - new Object[] { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", new Object[] + { file.getName() }), file.hashCode()); return v_client.inSession(); } @@ -2062,9 +2178,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (v_client != null) { - throw new Error( - MessageManager - .getString("error.try_join_vamsas_session_another")); + throw new Error(MessageManager + .getString("error.try_join_vamsas_session_another")); } if (mysesid == null) { @@ -2122,8 +2237,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements vamsasSave.setVisible(false); vamsasStop.setVisible(false); vamsasImport.setVisible(true); - vamsasStart.setText(MessageManager - .getString("label.new_vamsas_session")); + vamsasStart + .setText(MessageManager.getString("label.new_vamsas_session")); } @Override @@ -2147,21 +2262,22 @@ public class Desktop extends jalview.jbgui.GDesktop implements sess = VamsasApplication.getSessionList(); } catch (Exception e) { - jalview.bin.Cache.log.warn( - "Problem getting current sessions list.", e); + jalview.bin.Cache.log.warn("Problem getting current sessions list.", + e); sess = null; } if (sess != null) { - jalview.bin.Cache.log.debug("Got current sessions list: " - + sess.length + " entries."); + jalview.bin.Cache.log.debug( + "Got current sessions list: " + sess.length + " entries."); VamsasStMenu.removeAll(); for (int i = 0; i < sess.length; i++) { JMenuItem sessit = new JMenuItem(); sessit.setText(sess[i]); - sessit.setToolTipText(MessageManager.formatMessage( - "label.connect_to_session", new Object[] { sess[i] })); + sessit.setToolTipText(MessageManager + .formatMessage("label.connect_to_session", new Object[] + { sess[i] })); final Desktop dsktp = this; final String mysesid = sess[i]; sessit.addActionListener(new ActionListener() @@ -2211,9 +2327,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements @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 + // TODO: VAMSAS DOCUMENT EXTENSION is VDJ JalviewFileChooser chooser = new JalviewFileChooser("vdj", "Vamsas Document"); @@ -2226,9 +2344,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (value == JalviewFileChooser.APPROVE_OPTION) { java.io.File choice = chooser.getSelectedFile(); - JPanel progpanel = addProgressPanel(MessageManager.formatMessage( - "label.saving_vamsas_doc", - new Object[] { choice.getName() })); + JPanel progpanel = addProgressPanel(MessageManager + .formatMessage("label.saving_vamsas_doc", new Object[] + { choice.getName() })); Cache.setProperty("LAST_DIRECTORY", choice.getParent()); String warnmsg = null; String warnttl = null; @@ -2239,15 +2357,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements { warnttl = "Serious Problem saving Vamsas Document"; warnmsg = ex.toString(); - jalview.bin.Cache.log.error("Error Whilst saving document to " - + choice, ex); + jalview.bin.Cache.log + .error("Error Whilst saving document to " + choice, ex); } catch (Exception ex) { warnttl = "Problem saving Vamsas Document."; warnmsg = ex.toString(); - jalview.bin.Cache.log.warn("Exception Whilst saving document to " - + choice, ex); + jalview.bin.Cache.log.warn( + "Exception Whilst saving document to " + choice, ex); } removeProgressPanel(progpanel); @@ -2255,7 +2373,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); + warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); } } } @@ -2280,8 +2398,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } if (b) { - vamUpdate = this.addProgressPanel(MessageManager - .getString("label.updating_vamsas_session")); + vamUpdate = this.addProgressPanel( + MessageManager.getString("label.updating_vamsas_session")); } vamsasStart.setVisible(!b); vamsasStop.setVisible(!b); @@ -2325,17 +2443,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements // SEQUENCE_ID which is not the default EMBL_EBI link ListIterator li = links.listIterator(); boolean check = false; - List urls = new ArrayList(); + List urls = new ArrayList<>(); while (li.hasNext()) { String link = li.next(); if (link.contains(SEQUENCE_ID) - && !link.equals(UrlConstants.DEFAULT_STRING)) + && !UrlConstants.isDefaultString(link)) { check = true; int barPos = link.indexOf("|"); - String urlMsg = barPos == -1 ? link : link.substring(0, - barPos) + ": " + link.substring(barPos + 1); + String urlMsg = barPos == -1 ? link + : link.substring(0, barPos) + ": " + + link.substring(barPos + 1); urls.add(new JLabel(urlMsg)); } } @@ -2349,12 +2468,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements JPanel msgPanel = new JPanel(); msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS)); msgPanel.add(Box.createVerticalGlue()); - JLabel msg = new JLabel( - MessageManager - .getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); - JLabel msg2 = new JLabel( - MessageManager - .getString("label.SEQUENCE_ID_for_DB_ACCESSION2")); + JLabel msg = new JLabel(MessageManager + .getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); + JLabel msg2 = new JLabel(MessageManager + .getString("label.SEQUENCE_ID_for_DB_ACCESSION2")); msgPanel.add(msg); for (JLabel url : urls) { @@ -2384,18 +2501,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } }); - } + } /** * 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; @@ -2420,6 +2536,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements Thread worker = new Thread(this); worker.start(); } + repaint(); } public boolean isShowMemoryUsage() @@ -2473,28 +2590,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements FontMetrics fm = g.getFontMetrics(); if (fm != null) { - g.drawString(MessageManager.formatMessage( - "label.memory_stats", - new Object[] { df.format(totalFreeMemory), - df.format(maxMemory), df.format(percentUsage) }), 10, - getHeight() - fm.getHeight()); + g.drawString(MessageManager.formatMessage("label.memory_stats", + new Object[] + { df.format(totalFreeMemory), df.format(maxMemory), + df.format(percentUsage) }), + 10, getHeight() - fm.getHeight()); } } } } /** - * fixes stacking order after a modal dialog to ensure windows that should be - * on top actually are - */ - public void relayerWindows() - { - - } - - protected JMenuItem groovyShell; - - /** * Accessor method to quickly get all the AlignmentFrames loaded. * * @return an array of AlignFrame, or null if none found @@ -2513,7 +2619,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { return null; } - List avp = new ArrayList(); + List avp = new ArrayList<>(); // REVERSE ORDER for (int i = frames.length - 1; i > -1; i--) { @@ -2558,7 +2664,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { return null; } - List avp = new ArrayList(); + List avp = new ArrayList<>(); // REVERSE ORDER for (int i = frames.length - 1; i > -1; i--) { @@ -2579,6 +2685,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * Add Groovy Support to Jalview */ + @Override public void groovyShell_actionPerformed() { try @@ -2589,7 +2696,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.couldnt_create_groovy_shell"), + MessageManager.getString("label.couldnt_create_groovy_shell"), MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE); } @@ -2640,14 +2747,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * 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() { - getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( - KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit - .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit"); + getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW) + .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q, + Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()), + "Quit"); getRootPane().getActionMap().put("Quit", new AbstractAction() { @Override @@ -2699,8 +2807,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (progressBars == null) { - progressBars = new Hashtable(); - progressBarHandlers = new Hashtable(); + progressBars = new Hashtable<>(); + progressBarHandlers = new Hashtable<>(); } if (progressBars.get(new Long(id)) != null) @@ -2731,9 +2839,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (progressBarHandlers == null || !progressBars.containsKey(new Long(id))) { - throw new Error( - MessageManager - .getString("error.call_setprogressbar_before_registering_handler")); + throw new Error(MessageManager.getString( + "error.call_setprogressbar_before_registering_handler")); } progressBarHandlers.put(new Long(id), handler); final JPanel progressPanel = progressBars.get(new Long(id)); @@ -2749,10 +2856,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); - us.setProgressBar(MessageManager.formatMessage( - "label.cancelled_params", - new Object[] { ((JLabel) progressPanel.getComponent(0)) - .getText() }), id); + us.setProgressBar(MessageManager + .formatMessage("label.cancelled_params", new Object[] + { ((JLabel) progressPanel.getComponent(0)).getText() }), + id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -2774,9 +2881,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * 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 @@ -2785,7 +2891,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (desktop != null) { - AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId()); + AlignmentPanel[] aps = getAlignmentPanels( + viewport.getSequenceSetId()); for (int panel = 0; aps != null && panel < aps.length; panel++) { if (aps[panel] != null && aps[panel].av == viewport) @@ -2854,8 +2961,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { - t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer( - changeSupport); + t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer() + .startDiscoverer(changeSupport); } Thread t3 = null; { @@ -2871,8 +2978,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } catch (Exception e) { } - alive = (t1 != null && t1.isAlive()) - || (t2 != null && t2.isAlive()) + alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) || (t3 != null && t3.isAlive()) || (t0 != null && t0.isAlive()); } @@ -2927,20 +3033,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * jd.waitForInput(); */ - JvOptionPane - .showConfirmDialog( - Desktop.desktop, - new JLabel( - "
" - + ermsg - + "
" - + "

It may be that you have invalid JABA URLs
in your web service preferences," - + "
or as a command-line argument, or mis-configured HTTP proxy settings.

" - + "

Check the Connections and Web services tab
of the" - + " Tools->Preferences dialog box to change them.

"), - "Web Service Configuration Problem", - JvOptionPane.DEFAULT_OPTION, - JvOptionPane.ERROR_MESSAGE); + JvOptionPane.showConfirmDialog(Desktop.desktop, + new JLabel("
" + + ermsg + "
" + + "

It may be that you have invalid JABA URLs
in your web service preferences," + + "
or as a command-line argument, or mis-configured HTTP proxy settings.

" + + "

Check the Connections and Web services tab
of the" + + " Tools->Preferences dialog box to change them.

"), + "Web Service Configuration Problem", + JvOptionPane.DEFAULT_OPTION, + JvOptionPane.ERROR_MESSAGE); serviceChangedDialog = null; } @@ -2949,8 +3051,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } else { - Cache.log - .error("Errors reported by JABA discovery service. Check web services preferences.\n" + Cache.log.error( + "Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg); } } @@ -2990,9 +3092,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (progress != null) { - progress.setProgressBar(MessageManager.formatMessage( - "status.opening_params", new Object[] { url }), this - .hashCode()); + progress.setProgressBar(MessageManager + .formatMessage("status.opening_params", new Object[] + { url }), this.hashCode()); } jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) @@ -3048,8 +3150,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements } else { - System.err.println("Couldn't handle string " + url - + " as a URL."); + System.err.println( + "Couldn't handle string " + url + " as a URL."); } } // ignore any exceptions due to dud links. @@ -3120,33 +3222,45 @@ public class Desktop extends jalview.jbgui.GDesktop implements 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. * @@ -3241,9 +3355,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame(); myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(), source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight())); - myBottomFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(), - source.getY(), myBottomFrame.getWidth(), myBottomFrame - .getHeight())); + myBottomFrame.viewport + .setExplodedGeometry(new Rectangle(source.getX(), source.getY(), + myBottomFrame.getWidth(), myBottomFrame.getHeight())); myTopFrame.viewport.setGatherViewsHere(true); myBottomFrame.viewport.setGatherViewsHere(true); String topViewId = myTopFrame.viewport.getSequenceSetId(); @@ -3268,10 +3382,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements gatherThis = true; topPanel.av.setGatherViewsHere(false); bottomPanel.av.setGatherViewsHere(false); - topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), - topFrame.getSize())); - bottomPanel.av.setExplodedGeometry(new Rectangle(sf - .getLocation(), bottomFrame.getSize())); + topPanel.av.setExplodedGeometry( + new Rectangle(sf.getLocation(), topFrame.getSize())); + bottomPanel.av.setExplodedGeometry( + new Rectangle(sf.getLocation(), bottomFrame.getSize())); myTopFrame.addAlignmentPanel(topPanel, false); myBottomFrame.addAlignmentPanel(bottomPanel, false); } @@ -3297,14 +3411,87 @@ public class Desktop extends jalview.jbgui.GDesktop implements return 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 + */ + public static void transferFromDropTarget(List files, List protocols, DropTargetDropEvent evt, - Transferable t) - throws Exception - { + 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"); + "text/uri-list;class=java.lang.String"), urlFlavour = null; + try + { + urlFlavour = new DataFlavor( + "application/x-java-url; class=java.net.URL"); + } catch (ClassNotFoundException cfe) + { + Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe); + } + + if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) + { + + try + { + java.net.URL url = (URL) t.getTransferData(urlFlavour); + // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099 + // means url may be null. + if (url != null) + { + protocols.add(DataSourceType.URL); + files.add(url.toString()); + Cache.log.debug("Drop handled as URL dataflavor " + + files.get(files.size() - 1)); + return; + } + else + { + if (Platform.isAMac()) + { + System.err.println( + "Please ignore plist error - occurs due to problem with java 8 on OSX"); + } + ; + } + } catch (Throwable ex) + { + Cache.log.debug("URL drop handler failed.", ex); + } + } if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) { // Works on Windows and MacOSX @@ -3312,7 +3499,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements for (Object file : (List) t .getTransferData(DataFlavor.javaFileListFlavor)) { - files.add(((File) file).toString()); + files.add(file); protocols.add(DataSourceType.FILE); } } @@ -3332,65 +3519,165 @@ public class Desktop extends jalview.jbgui.GDesktop implements // fallback to text: workaround - on OSX where there's a JVM bug Cache.log.debug("standard URIListFlavor failed. Trying text"); // try text fallback - data = (String) t.getTransferData(new DataFlavor( - "text/plain;class=java.lang.String")); - if (Cache.log.isDebugEnabled()) + DataFlavor textDf = new DataFlavor( + "text/plain;class=java.lang.String"); + if (t.isDataFlavorSupported(textDf)) { - Cache.log.debug("fallback returned " + data); + data = (String) t.getTransferData(textDf); } + + Cache.log.debug("Plain text drop content returned " + + (data == null ? "Null - failed" : data)); + } - while (protocols.size() < files.size()) - { - Cache.log.debug("Adding missing FILE protocol for " - + files.get(protocols.size())); - protocols.add(DataSourceType.FILE); - } - for (java.util.StringTokenizer st = new java.util.StringTokenizer( - data, "\r\n"); st.hasMoreTokens();) + if (data != null) { - added = true; - String s = st.nextToken(); - if (s.startsWith("#")) + while (protocols.size() < files.size()) { - // the line is a comment (as per the RFC 2483) - continue; - } - java.net.URI uri = new java.net.URI(s); - if (uri.getScheme().toLowerCase().startsWith("http")) - { - protocols.add(DataSourceType.URL); - files.add(uri.toString()); + Cache.log.debug("Adding missing FILE protocol for " + + files.get(protocols.size())); + protocols.add(DataSourceType.FILE); } - else + for (java.util.StringTokenizer st = new java.util.StringTokenizer( + data, "\r\n"); st.hasMoreTokens();) { - // otherwise preserve old behaviour: catch all for file objects - java.io.File file = new java.io.File(uri); - protocols.add(DataSourceType.FILE); - files.add(file.toString()); + added = true; + String s = st.nextToken(); + if (s.startsWith("#")) + { + // the line is a comment (as per the RFC 2483) + continue; + } + java.net.URI uri = new java.net.URI(s); + if (uri.getScheme().toLowerCase().startsWith("http")) + { + protocols.add(DataSourceType.URL); + files.add(uri.toString()); + } + else + { + // otherwise preserve old behaviour: catch all for file objects + java.io.File file = new java.io.File(uri); + protocols.add(DataSourceType.FILE); + files.add(file.toString()); + } } } + if (Cache.log.isDebugEnabled()) { if (data == null || !added) { - Cache.log - .debug("Couldn't resolve drop data. Here are the supported flavors:"); - for (DataFlavor fl : t.getTransferDataFlavors()) + + if (t.getTransferDataFlavors() != null + && t.getTransferDataFlavors().length > 0) { - Cache.log.debug("Supported transfer dataflavor: " - + fl.toString()); - Object df = t.getTransferData(fl); - if (df != null) - { - Cache.log.debug("Retrieves: " + df); - } - else + Cache.log.debug( + "Couldn't resolve drop data. Here are the supported flavors:"); + for (DataFlavor fl : t.getTransferDataFlavors()) { - Cache.log.debug("Retrieved nothing"); + Cache.log.debug( + "Supported transfer dataflavor: " + fl.toString()); + Object df = t.getTransferData(fl); + if (df != null) + { + Cache.log.debug("Retrieves: " + df); + } + else + { + Cache.log.debug("Retrieved nothing"); + } } } + else + { + Cache.log.debug("Couldn't resolve dataflavor for drop: " + + t.toString()); + } + } + } + } + if (Platform.isWindows()) + + { + 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++) + { + String source = files.get(f).toString().toLowerCase(); + if (protocols.get(f).equals(DataSourceType.FILE) + && (source.endsWith(".lnk") || source.endsWith(".url") + || source.endsWith(".site"))) + { + try + { + Object obj = files.get(f); + File lf = (obj instanceof File ? (File) obj + : new File((String) obj)); + // process link file to get a URL + Cache.log.debug("Found potential link file: " + lf); + WindowsShortcut wscfile = new WindowsShortcut(lf); + String fullname = wscfile.getRealFilename(); + protocols.set(f, FormatAdapter.checkProtocol(fullname)); + files.set(f, fullname); + Cache.log.debug("Parsed real filename " + fullname + + " to extract protocol: " + protocols.get(f)); + } catch (Exception ex) + { + Cache.log.error( + "Couldn't parse " + files.get(f) + " as a link file.", + ex); + } + } + } + } + } + + /** + * Sets the Preferences property for experimental features to True or False + * depending on the state of the controlling menu item + */ + @Override + protected void showExperimental_actionPerformed(boolean selected) + { + Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected)); + } + + /** + * Answers a (possibly empty) list of any structure viewer frames (currently for + * either Jmol or Chimera) which are currently open. This may optionally be + * restricted to viewers of a specified class, or viewers linked to a specified + * alignment panel. + * + * @param apanel + * if not null, only return viewers linked to this panel + * @param structureViewerClass + * if not null, only return viewers of this class + * @return + */ + public List getStructureViewers( + AlignmentPanel apanel, + Class structureViewerClass) + { + List result = new ArrayList<>(); + JInternalFrame[] frames = Desktop.instance.getAllFrames(); + + for (JInternalFrame frame : frames) + { + if (frame instanceof StructureViewerBase) + { + if (structureViewerClass == null + || structureViewerClass.isInstance(frame)) + { + if (apanel == null + || ((StructureViewerBase) frame).isLinkedWith(apanel)) + { + result.add((StructureViewerBase) frame); + } } } } + return result; } }