X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;fp=src%2Fjalview%2Fgui%2FDesktop.java;h=f35a6a890366d42e77854fac5452aa0906ed6e4d;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=0f80dd52f4b9f47cebcd7b87c920b52cc62e0ab7;hpb=61ff8fb4efa315c35149c9d11850d99e3d00c441;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 0f80dd5..f35a6a8 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -21,7 +21,6 @@ package jalview.gui; import java.util.Locale; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -65,8 +64,11 @@ import java.util.Hashtable; import java.util.List; import java.util.ListIterator; import java.util.Vector; +import java.util.concurrent.ExecutionException; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; +import java.util.concurrent.Future; +import java.util.concurrent.FutureTask; import java.util.concurrent.Semaphore; import javax.swing.AbstractAction; @@ -100,6 +102,9 @@ import org.stackoverflowusers.file.WindowsShortcut; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.StructureSelectionManagerProvider; +import jalview.bin.ApplicationSingletonProvider; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.gui.ImageExporter.ImageWriterI; @@ -114,6 +119,7 @@ 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; @@ -127,6 +133,7 @@ import jalview.util.Platform; import jalview.util.ShortcutKeyMaskExWrapper; import jalview.util.UrlConstants; import jalview.viewmodel.AlignmentViewport; +import jalview.ws.WSDiscovererI; import jalview.ws.params.ParamManager; import jalview.ws.utils.UrlDownloadClient; @@ -137,8 +144,12 @@ import jalview.ws.utils.UrlDownloadClient; * @author $author$ * @version $Revision: 1.155 $ */ -public class Desktop extends jalview.jbgui.GDesktop - implements DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider { +@SuppressWarnings("serial") +public class Desktop extends GDesktop + implements DropTargetListener, ClipboardOwner, IProgressIndicator, + StructureSelectionManagerProvider, ApplicationSingletonI + +{ private static final String CITATION; static { URL bg_logo_url = ChannelProperties.getImageURL("bg_logo." + String.valueOf(SplashScreen.logoSize)); @@ -177,10 +188,10 @@ public class Desktop extends jalview.jbgui.GDesktop public static HashMap savingFiles = new HashMap(); + @SuppressWarnings("deprecation") private JalviewChangeSupport changeSupport = new JalviewChangeSupport(); public static boolean nosplash = false; - /** * news reader - null if it was never started. */ @@ -192,7 +203,10 @@ public class Desktop extends jalview.jbgui.GDesktop * @param listener * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener) */ - public void addJalviewPropertyChangeListener(PropertyChangeListener listener) { + @Deprecated + public void addJalviewPropertyChangeListener( + PropertyChangeListener listener) + { changeSupport.addJalviewPropertyChangeListener(listener); } @@ -202,7 +216,10 @@ public class Desktop extends jalview.jbgui.GDesktop * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String, * java.beans.PropertyChangeListener) */ - public void addJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) { + @Deprecated + public void addJalviewPropertyChangeListener(String propertyName, + PropertyChangeListener listener) + { changeSupport.addJalviewPropertyChangeListener(propertyName, listener); } @@ -212,128 +229,172 @@ public class Desktop extends jalview.jbgui.GDesktop * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String, * java.beans.PropertyChangeListener) */ - public void removeJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) { - changeSupport.removeJalviewPropertyChangeListener(propertyName, listener); + @Deprecated + public void removeJalviewPropertyChangeListener(String propertyName, + PropertyChangeListener listener) + { + changeSupport.removeJalviewPropertyChangeListener(propertyName, + listener); } - /** Singleton Desktop instance */ - public static Desktop instance; + private MyDesktopPane desktopPane; - public static MyDesktopPane desktop; + public static MyDesktopPane getDesktopPane() + { + Desktop desktop = getInstance(); + return desktop == null ? null : desktop.desktopPane; + } - public static MyDesktopPane getDesktop() { - // BH 2018 could use currentThread() here as a reference to a - // Hashtable in JavaScript - return desktop; + /** + * Answers an 'application scope' singleton instance of this class. Separate + * SwingJS 'applets' running in the same browser page will each have a + * distinct instance of Desktop. + * + * @return + */ + public static Desktop getInstance() + { + return Jalview.isHeadlessMode() ? null + : (Desktop) ApplicationSingletonProvider + .getInstance(Desktop.class); } - static int openFrameCount = 0; + public static StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager + .getStructureSelectionManager(getInstance()); + } + + int openFrameCount = 0; - static final int xOffset = 30; + final int xOffset = 30; - static final int yOffset = 30; + final int yOffset = 30; - public static jalview.ws.jws1.Discoverer discoverer; + public jalview.ws.jws1.Discoverer discoverer; - public static Object[] jalviewClipboard; + public Object[] jalviewClipboard; - public static boolean internalCopy = false; + public boolean internalCopy = false; - static int fileLoadingCount = 0; + int fileLoadingCount = 0; - class MyDesktopManager implements DesktopManager { + class MyDesktopManager implements DesktopManager + { private DesktopManager delegate; - public MyDesktopManager(DesktopManager delegate) { + public MyDesktopManager(DesktopManager delegate) + { this.delegate = delegate; } @Override - public void activateFrame(JInternalFrame f) { - try { + public void activateFrame(JInternalFrame f) + { + try + { delegate.activateFrame(f); - } catch (NullPointerException npe) { + } catch (NullPointerException npe) + { Point p = getMousePosition(); - instance.showPasteMenu(p.x, p.y); + showPasteMenu(p.x, p.y); } } @Override - public void beginDraggingFrame(JComponent f) { + public void beginDraggingFrame(JComponent f) + { delegate.beginDraggingFrame(f); } @Override - public void beginResizingFrame(JComponent f, int direction) { + public void beginResizingFrame(JComponent f, int direction) + { delegate.beginResizingFrame(f, direction); } @Override - public void closeFrame(JInternalFrame f) { + public void closeFrame(JInternalFrame f) + { delegate.closeFrame(f); } @Override - public void deactivateFrame(JInternalFrame f) { + public void deactivateFrame(JInternalFrame f) + { delegate.deactivateFrame(f); } @Override - public void deiconifyFrame(JInternalFrame f) { + public void deiconifyFrame(JInternalFrame f) + { delegate.deiconifyFrame(f); } @Override - public void dragFrame(JComponent f, int newX, int newY) { - if (newY < 0) { + public void dragFrame(JComponent f, int newX, int newY) + { + if (newY < 0) + { newY = 0; } delegate.dragFrame(f, newX, newY); } @Override - public void endDraggingFrame(JComponent f) { + public void endDraggingFrame(JComponent f) + { delegate.endDraggingFrame(f); - desktop.repaint(); + desktopPane.repaint(); } @Override - public void endResizingFrame(JComponent f) { + public void endResizingFrame(JComponent f) + { delegate.endResizingFrame(f); - desktop.repaint(); + desktopPane.repaint(); } @Override - public void iconifyFrame(JInternalFrame f) { + public void iconifyFrame(JInternalFrame f) + { delegate.iconifyFrame(f); } @Override - public void maximizeFrame(JInternalFrame f) { + public void maximizeFrame(JInternalFrame f) + { delegate.maximizeFrame(f); } @Override - public void minimizeFrame(JInternalFrame f) { + public void minimizeFrame(JInternalFrame f) + { delegate.minimizeFrame(f); } @Override - public void openFrame(JInternalFrame f) { + public void openFrame(JInternalFrame f) + { delegate.openFrame(f); } @Override - public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { - if (newY < 0) { + public void resizeFrame(JComponent f, int newX, int newY, int newWidth, + int newHeight) + { + if (newY < 0) + { newY = 0; } delegate.resizeFrame(f, newX, newY, newWidth, newHeight); } @Override - public void setBoundsForFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { + public void setBoundsForFrame(JComponent f, int newX, int newY, + int newWidth, int newHeight) + { delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight); } @@ -342,17 +403,22 @@ public class Desktop extends jalview.jbgui.GDesktop } /** - * Creates a new Desktop object. + * Private constructor enforces singleton pattern. It is called by reflection + * from ApplicationSingletonProvider.getInstance(). */ - public Desktop() { + private Desktop() + { super(); - /** - * 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; + Cache.initLogger(); + try + { + /** + * A note to implementors. It is ESSENTIAL that any activities that might + * block are spawned off as threads rather than waited for during this + * constructor. + */ - doConfigureStructurePrefs(); + doConfigureStructurePrefs(); setTitle(ChannelProperties.getProperty("app_name") + " " + Cache.getProperty("VERSION")); /** @@ -414,124 +480,156 @@ public class Desktop extends jalview.jbgui.GDesktop } }); - boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false); + boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false); - boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", false); - desktop = new MyDesktopPane(selmemusage); + boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", false); + desktopPane = new MyDesktopPane(selmemusage); - showMemusage.setSelected(selmemusage); - desktop.setBackground(Color.white); + 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); + getContentPane().setLayout(new BorderLayout()); + // alternate config - have scrollbars - see notes in JAL-153 + // JScrollPane sp = new JScrollPane(); + // sp.getViewport().setView(desktop); + // getContentPane().add(sp, BorderLayout.CENTER); - // BH 2018 - just an experiment to try unclipped JInternalFrames. - if (Platform.isJS()) { - getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); - } + // BH 2018 - just an experiment to try unclipped JInternalFrames. + if (Platform.isJS()) + { + getRootPane().putClientProperty("swingjs.overflow.hidden", "false"); + } - getContentPane().add(desktop, BorderLayout.CENTER); - desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); + getContentPane().add(desktopPane, BorderLayout.CENTER); + desktopPane.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.isWindowsAndNotJS() ? new DefaultDesktopManager() - : Platform.isAMacAndNotJS() ? new AquaInternalFrameManager(desktop.getDesktopManager()) - : desktop.getDesktopManager()))); - Rectangle dims = getLastKnownDimensions(""); - if (dims != null) { - 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); - } + // 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()))); - if (!Platform.isJS()) - /** - * Java only - * - * @j2sIgnore - */ - { - jconsole = new Console(this, showjconsole); - jconsole.setHeader(Cache.getVersionDetailsForConsole()); - showConsole(showjconsole); + Rectangle dims = getLastKnownDimensions(""); + if (dims != null) + { + 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); + } - showNews.setVisible(false); + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { + jconsole = new Console(this, showjconsole); + jconsole.setHeader(Cache.getVersionDetailsForConsole()); + showConsole(showjconsole); - experimentalFeatures.setSelected(showExperimental()); + showNews.setVisible(false); // not sure if we should only do this for interactive session? - getIdentifiersOrgData(); + experimentalFeatures.setSelected(showExperimental()); - checkURLLinks(); + getIdentifiersOrgData(); - // Spawn a thread that shows the splashscreen - if (!nosplash) { - SwingUtilities.invokeLater(new Runnable() { - @Override - public void run() { - new SplashScreen(true); + if (Jalview.isInteractive()) + { + // disabled for SeqCanvasTest + checkURLLinks(); + + // Spawn a thread that shows the splashscreen + if (!nosplash) { + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + new SplashScreen(true); + } + }); } - }); - } - // Thread off a new instance of the file chooser - this reduces the time - // it - // takes to open it later on. - new Thread(new Runnable() { - @Override - public void run() { - 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."); + // 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); + } + }); } - }).start(); - // Add the service change listener - changeSupport.addJalviewPropertyChangeListener("services", new PropertyChangeListener() { + } + this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this)); + + this.addWindowListener(new WindowAdapter() + { @Override - public void propertyChange(PropertyChangeEvent evt) { - Cache.log.debug("Firing service changed event for " + evt.getNewValue()); - JalviewServicesChanged(evt); + public void windowClosing(WindowEvent evt) + { + quit(); } }); - } - - this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); - this.addWindowListener(new WindowAdapter() { - @Override - public void windowClosing(WindowEvent evt) { - quit(); - } - }); - - MouseAdapter ma; - this.addMouseListener(ma = new MouseAdapter() { - @Override - public void mousePressed(MouseEvent evt) { - if (evt.isPopupTrigger()) // Mac + MouseAdapter ma; + this.addMouseListener(ma = new MouseAdapter() + { + @Override + public void mousePressed(MouseEvent evt) { - showPasteMenu(evt.getX(), evt.getY()); + if (evt.isPopupTrigger()) // Mac + { + showPasteMenu(evt.getX(), evt.getY()); + } } - } - - @Override - public void mouseReleased(MouseEvent evt) { - if (evt.isPopupTrigger()) // Windows + @Override + public void mouseReleased(MouseEvent evt) { - showPasteMenu(evt.getX(), evt.getY()); + if (evt.isPopupTrigger()) // Windows + { + showPasteMenu(evt.getX(), evt.getY()); + } } - } - }); - desktop.addMouseListener(ma); + }); + desktopPane.addMouseListener(ma); + } catch (Throwable t) + { + t.printStackTrace(); + } + } /** @@ -540,12 +638,15 @@ public class Desktop extends jalview.jbgui.GDesktop * * @return */ - public boolean showExperimental() { - String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, Boolean.FALSE.toString()); + public boolean showExperimental() + { + String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, + Boolean.FALSE.toString()); return Boolean.valueOf(experimental).booleanValue(); } - public void doConfigureStructurePrefs() { + public void doConfigureStructurePrefs() + { // configure services StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(this); if (Cache.getDefault(Preferences.ADD_SS_ANN, true)) { @@ -596,17 +697,22 @@ public class Desktop extends jalview.jbgui.GDesktop showNews(showNews.isSelected()); } - void showNews(boolean visible) { + void showNews(boolean visible) + { Cache.log.debug((visible ? "Showing" : "Hiding") + " news."); showNews.setSelected(visible); - if (visible && !jvnews.isVisible()) { - new Thread(new Runnable() { + if (visible && !jvnews.isVisible()) + { + new Thread(new Runnable() + { @Override - public void run() { + public void run() + { long now = System.currentTimeMillis(); - Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), now); + setProgressBar(MessageManager.getString("status.refreshing_news"), + now); jvnews.refreshNews(); - Desktop.instance.setProgressBar(null, now); + setProgressBar(null, now); jvnews.showNews(); } }).start(); @@ -616,12 +722,13 @@ public class Desktop extends jalview.jbgui.GDesktop /** * recover the last known dimensions for a jalview window * - * @param windowName - empty string is desktop, all other windows have unique - * prefix + * @param windowName + * - empty string is desktop, all other windows have unique prefix * @return null or last known dimensions scaled to current geometry (if last * window geom was known) */ - Rectangle getLastKnownDimensions(String windowName) { + Rectangle getLastKnownDimensions(String windowName) + { // TODO: lock aspect ratio for scaling desktop Bug #0058199 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); String x = Cache.getProperty(windowName + "SCREEN_X"); @@ -659,12 +766,16 @@ public class Desktop extends jalview.jbgui.GDesktop return null; } - void showPasteMenu(int x, int y) { + void showPasteMenu(int x, int y) + { JPopupMenu popup = new JPopupMenu(); - JMenuItem item = new JMenuItem(MessageManager.getString("label.paste_new_window")); - item.addActionListener(new ActionListener() { + JMenuItem item = new JMenuItem( + MessageManager.getString("label.paste_new_window")); + item.addActionListener(new ActionListener() + { @Override - public void actionPerformed(ActionEvent evt) { + public void actionPerformed(ActionEvent evt) + { paste(); } }); @@ -673,79 +784,81 @@ public class Desktop extends jalview.jbgui.GDesktop popup.show(this, x, y); } - public void paste() { - try { + public void paste() + { + try + { Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); Transferable contents = c.getContents(this); - if (contents != null) { - String file = (String) contents.getTransferData(DataFlavor.stringFlavor); + if (contents != null) + { + String file = (String) contents + .getTransferData(DataFlavor.stringFlavor); - FileFormatI format = new IdentifyFile().identify(file, DataSourceType.PASTE); + FileFormatI format = new IdentifyFile().identify(file, + DataSourceType.PASTE); new FileLoader().LoadFile(file, DataSourceType.PASTE, format); } - } catch (Exception ex) { - System.out.println("Unable to paste alignment from system clipboard:\n" + ex); + } catch (Exception ex) + { + System.out.println( + "Unable to paste alignment from system clipboard:\n" + ex); } } - /** - * Adds and opens the given frame to the desktop - * - * @param frame Frame to show - * @param title Visible Title - * @param w width - * @param h height - */ - public static synchronized void addInternalFrame(final JInternalFrame frame, String title, int w, int h) { - addInternalFrame(frame, title, true, w, h, true, false); - } - /** - * Add an internal frame to the Jalview desktop - * - * @param frame Frame to show - * @param title Visible Title - * @param makeVisible When true, display frame immediately, otherwise, caller - * must call setVisible themselves. - * @param w width - * @param h height - */ - public static synchronized void addInternalFrame(final JInternalFrame frame, String title, boolean makeVisible, int w, - int h) { - addInternalFrame(frame, title, makeVisible, w, h, true, false); - } /** - * Add an internal frame to the Jalview desktop and make it visible + * Adds and opens the given frame to the desktop that is visible, allowed to + * resize, and has a 300px minimum width. * - * @param frame Frame to show - * @param title Visible Title - * @param w width - * @param h height - * @param resizable Allow resize - */ - public static synchronized void addInternalFrame(final JInternalFrame frame, String title, int w, int h, - boolean resizable) { - addInternalFrame(frame, title, true, w, h, resizable, false); + * @param frame + * Frame to show + * @param title + * Visible Title + * @param w + * width + * @param h + * height + */ + public static synchronized void addInternalFrame( + final JInternalFrame frame, String title, int w, int h) + { + // 58 classes + + addInternalFrame(frame, title, Desktop.FRAME_MAKE_VISIBLE, w, h, + FRAME_ALLOW_RESIZE, FRAME_SET_MIN_SIZE_300); } /** - * Add an internal frame to the Jalview desktop + * Add an internal frame to the Jalview desktop that may optionally be + * visible, resizable, and allowed to be any size * - * @param frame Frame to show - * @param title Visible Title - * @param makeVisible When true, display frame immediately, otherwise, caller - * must call setVisible themselves. - * @param w width - * @param h height - * @param resizable Allow resize - * @param ignoreMinSize Do not set the default minimum size for frame - */ - public static synchronized void addInternalFrame(final JInternalFrame frame, String title, boolean makeVisible, int w, - int h, boolean resizable, boolean ignoreMinSize) { + * @param frame + * Frame to show + * @param title + * Visible Title + * @param makeVisible + * When true, display frame immediately, otherwise, caller must call + * setVisible themselves. + * @param w + * width + * @param h + * height + * @param resizable + * Allow resize + * @param ignoreMinSize + * Do not set the default minimum size for frame + */ + public static synchronized void addInternalFrame( + final JInternalFrame frame, String title, boolean makeVisible, + int w, int h, boolean resizable, boolean ignoreMinSize) + { + // 15 classes call this method directly. + // TODO: allow callers to determine X and Y position of frame (eg. via // bounds object). @@ -753,29 +866,57 @@ public class Desktop extends jalview.jbgui.GDesktop // the current window title frame.setTitle(title); - if (frame.getWidth() < 1 || frame.getHeight() < 1) { + if (frame.getWidth() < 1 || frame.getHeight() < 1) + { frame.setSize(w, h); } - // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN - // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN - // IF JALVIEW IS RUNNING HEADLESS - // /////////////////////////////////////////////// - if (instance == null || (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true"))) { - return; - } + if (getInstance() != null) + getInstance().addFrame(frame, makeVisible, resizable, + ignoreMinSize); + } + + // These can now by put into a single int flag, if desired: + + public final static boolean FRAME_MAKE_VISIBLE = true; + + public final static boolean FRAME_NOT_VISIBLE = false; + + public final static boolean FRAME_ALLOW_RESIZE = true; + + public final static boolean FRAME_NOT_RESIZABLE = false; + + public final static boolean FRAME_ALLOW_ANY_SIZE = true; + + public final static boolean FRAME_SET_MIN_SIZE_300 = false; + + private void addFrame(JInternalFrame frame, + boolean makeVisible, boolean resizable, + boolean ignoreMinSize) + { openFrameCount++; - if (!ignoreMinSize) { - frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT)); + + boolean isEmbedded = (Platform.getEmbeddedAttribute(frame, "id") != null); + boolean hasEmbeddedSize = (Platform.getDimIfEmbedded(frame, -1, -1) != null); + // Web page embedding allows us to ignore minimum size + ignoreMinSize |= hasEmbeddedSize; + + if (!ignoreMinSize) + { // Set default dimension for Alignment Frame window. // The Alignment Frame window could be added from a number of places, // hence, // I did this here in order not to miss out on any Alignment frame. - if (frame instanceof AlignFrame) { - frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, ALIGN_FRAME_DEFAULT_MIN_HEIGHT)); + if (frame instanceof AlignFrame) + { + frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, + ALIGN_FRAME_DEFAULT_MIN_HEIGHT)); + } else { + frame.setMinimumSize( + new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT)); + } } @@ -786,21 +927,27 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setIconifiable(resizable); frame.setOpaque(Platform.isJS()); - if (frame.getX() < 1 && frame.getY() < 1) { - frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset); + if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1) + { + frame.setLocation(xOffset * openFrameCount, + yOffset * ((openFrameCount - 1) % 10) + yOffset); } /* - * add an entry for the new frame in the Window menu (and remove it when the - * frame is closed) + * add an entry for the new frame in the Window menu + * (and remove it when the frame is closed) */ - final JMenuItem menuItem = new JMenuItem(title); - frame.addInternalFrameListener(new InternalFrameAdapter() { + final JMenuItem menuItem = new JMenuItem(frame.getTitle()); + frame.addInternalFrameListener(new InternalFrameAdapter() + { @Override - public void internalFrameActivated(InternalFrameEvent evt) { - JInternalFrame itf = desktop.getSelectedFrame(); - if (itf != null) { - if (itf instanceof AlignFrame) { + public void internalFrameActivated(InternalFrameEvent evt) + { + JInternalFrame itf = getDesktopPane().getSelectedFrame(); + if (itf != null) + { + if (itf instanceof AlignFrame) + { Jalview.setCurrentAlignFrame((AlignFrame) itf); } itf.requestFocus(); @@ -808,67 +955,80 @@ public class Desktop extends jalview.jbgui.GDesktop } @Override - public void internalFrameClosed(InternalFrameEvent evt) { + public void internalFrameClosed(InternalFrameEvent evt) + { PaintRefresher.RemoveComponent(frame); /* - * defensive check to prevent frames being added half off the window + * defensive check to prevent frames being + * added half off the window */ - if (openFrameCount > 0) { + if (openFrameCount > 0) + { openFrameCount--; } /* * ensure no reference to alignFrame retained by menu item listener */ - if (menuItem.getActionListeners().length > 0) { + if (menuItem.getActionListeners().length > 0) + { menuItem.removeActionListener(menuItem.getActionListeners()[0]); } - windowMenu.remove(menuItem); + getInstance().windowMenu.remove(menuItem); } }); - menuItem.addActionListener(new ActionListener() { + menuItem.addActionListener(new ActionListener() + { @Override - public void actionPerformed(ActionEvent e) { - try { + public void actionPerformed(ActionEvent e) + { + try + { frame.setSelected(true); frame.setIcon(false); - } catch (java.beans.PropertyVetoException ex) { - + } catch (java.beans.PropertyVetoException ex) + { + // System.err.println(ex.toString()); } } }); setKeyBindings(frame); - desktop.add(frame); + getDesktopPane().add(frame); - windowMenu.add(menuItem); + getInstance().windowMenu.add(menuItem); frame.toFront(); - try { + try + { frame.setSelected(true); frame.requestFocus(); - } catch (java.beans.PropertyVetoException ve) { - } catch (java.lang.ClassCastException cex) { + } catch (java.beans.PropertyVetoException ve) + { + } catch (java.lang.ClassCastException cex) + { Cache.log.warn( - "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869", - cex); + "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 + * 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() { + private static void setKeyBindings(JInternalFrame frame) + { + final Action closeAction = new AbstractAction() + { @Override - public void actionPerformed(ActionEvent e) { + public void actionPerformed(ActionEvent e) + { frame.dispose(); } }; @@ -879,7 +1039,8 @@ public class Desktop extends jalview.jbgui.GDesktop KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, InputEvent.CTRL_DOWN_MASK); KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()); - InputMap inputMap = frame.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); + InputMap inputMap = frame + .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW); String ctrlW = ctrlWKey.toString(); inputMap.put(ctrlWKey, ctrlW); inputMap.put(cmdWKey, ctrlW); @@ -889,37 +1050,45 @@ public class Desktop extends jalview.jbgui.GDesktop } @Override - public void lostOwnership(Clipboard clipboard, Transferable contents) { - if (!internalCopy) { - Desktop.jalviewClipboard = null; + public void lostOwnership(Clipboard clipboard, Transferable contents) + { + if (!internalCopy) + { + jalviewClipboard = null; } internalCopy = false; } @Override - public void dragEnter(DropTargetDragEvent evt) { + public void dragEnter(DropTargetDragEvent evt) + { } @Override - public void dragExit(DropTargetEvent evt) { + public void dragExit(DropTargetEvent evt) + { } @Override - public void dragOver(DropTargetDragEvent evt) { + public void dragOver(DropTargetDragEvent evt) + { } @Override - public void dropActionChanged(DropTargetDragEvent evt) { + public void dropActionChanged(DropTargetDragEvent evt) + { } /** * DOCUMENT ME! * - * @param evt DOCUMENT ME! + * @param evt + * DOCUMENT ME! */ @Override - public void drop(DropTargetDropEvent evt) { + public void drop(DropTargetDropEvent evt) + { boolean success = true; // JAL-1552 - acceptDrop required before getTransferable call for // Java's Transferable for native dnd @@ -928,35 +1097,47 @@ public class Desktop extends jalview.jbgui.GDesktop List files = new ArrayList<>(); List protocols = new ArrayList<>(); - try { - Desktop.transferFromDropTarget(files, protocols, evt, t); - } catch (Exception e) { + try + { + transferFromDropTarget(files, protocols, evt, t); + } catch (Exception e) + { e.printStackTrace(); success = false; } - if (files != null) { - try { - for (int i = 0; i < files.size(); i++) { + if (files != null) + { + try + { + for (int i = 0; i < files.size(); i++) + { // BH 2018 File or String Object file = files.get(i); String fileName = file.toString(); - DataSourceType protocol = (protocols == null) ? DataSourceType.FILE : protocols.get(i); + DataSourceType protocol = (protocols == null) + ? DataSourceType.FILE + : protocols.get(i); FileFormatI format = null; - if (fileName.endsWith(".jar")) { + if (fileName.endsWith(".jar")) + { format = FileFormat.Jalview; - } else { + } + else + { format = new IdentifyFile().identify(file, protocol); } - if (file instanceof File) { + if (file instanceof File) + { Platform.cacheFileData((File) file); } new FileLoader().LoadFile(null, file, protocol, format); } - } catch (Exception ex) { + } catch (Exception ex) + { success = false; } } @@ -967,21 +1148,27 @@ public class Desktop extends jalview.jbgui.GDesktop /** * DOCUMENT ME! * - * @param e DOCUMENT ME! + * @param e + * DOCUMENT ME! */ @Override - public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { + public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) + { String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); - JalviewFileChooser chooser = JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, - BackupFiles.getEnabled()); + JalviewFileChooser chooser = JalviewFileChooser.forRead( + Cache.getProperty("LAST_DIRECTORY"), fileFormat, + BackupFiles.getEnabled()); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.open_local_file")); + chooser.setDialogTitle( + MessageManager.getString("label.open_local_file")); chooser.setToolTipText(MessageManager.getString("action.open")); - chooser.setResponseHandler(0, new Runnable() { + chooser.setResponseHandler(0, new Runnable() + { @Override - public void run() { + public void run() + { File selectedFile = chooser.getSelectedFile(); Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); @@ -989,18 +1176,23 @@ public class Desktop extends jalview.jbgui.GDesktop /* * Call IdentifyFile to verify the file contains what its extension implies. - * Skip this step for dynamically added file formats, because IdentifyFile does - * not know how to recognise them. + * Skip this step for dynamically added file formats, because + * IdentifyFile does not know how to recognise them. */ - if (FileFormats.getInstance().isIdentifiable(format)) { - try { - format = new IdentifyFile().identify(selectedFile, DataSourceType.FILE); - } catch (FileFormatException e) { + if (FileFormats.getInstance().isIdentifiable(format)) + { + try + { + format = new IdentifyFile().identify(selectedFile, + DataSourceType.FILE); + } catch (FileFormatException e) + { // format = null; //?? } } - new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, format); + new FileLoader().LoadFile(viewport, selectedFile, + DataSourceType.FILE, format); } }); chooser.showOpenDialog(this); @@ -1012,23 +1204,28 @@ public class Desktop extends jalview.jbgui.GDesktop * @param viewport */ @Override - public void inputURLMenuItem_actionPerformed(AlignViewport viewport) { + public void inputURLMenuItem_actionPerformed(AlignViewport viewport) + { // This construct allows us to have a wider textfield // for viewing - JLabel label = new JLabel(MessageManager.getString("label.input_file_url")); + JLabel label = new JLabel( + MessageManager.getString("label.input_file_url")); JPanel panel = new JPanel(new GridLayout(2, 1)); panel.add(label); /* - * the URL to fetch is input in Java: an editable combobox with history JS: - * (pending JAL-3038) a plain text field + * the URL to fetch is + * Java: an editable combobox with history + * JS: (pending JAL-3038) a plain text field */ JComponent history; - String urlBase = "https://www."; - if (Platform.isJS()) { + String urlBase = "http://www."; + if (Platform.isJS()) + { history = new JTextField(urlBase, 35); - } else + } + else /** * Java only * @@ -1040,8 +1237,10 @@ public class Desktop extends jalview.jbgui.GDesktop asCombo.setEditable(true); asCombo.addItem(urlBase); String historyItems = Cache.getProperty("RECENT_URL"); - if (historyItems != null) { - for (String token : historyItems.split("\\t")) { + if (historyItems != null) + { + for (String token : historyItems.split("\\t")) + { asCombo.addItem(token); } } @@ -1051,9 +1250,11 @@ public class Desktop extends jalview.jbgui.GDesktop Object[] options = new Object[] { MessageManager.getString("action.ok"), MessageManager.getString("action.cancel") }; - Runnable action = new Runnable() { + Runnable action = new Runnable() + { @Override - public void run() { + public void run() + { @SuppressWarnings("unchecked") String url = (history instanceof JTextField ? ((JTextField) history).getText() : ((JComboBox) history).getEditor().getItem().toString().trim()); @@ -1066,72 +1267,96 @@ public class Desktop extends jalview.jbgui.GDesktop } } else { FileFormatI format = null; - try { + try + { format = new IdentifyFile().identify(url, DataSourceType.URL); - } catch (FileFormatException e) { + } catch (FileFormatException e) + { // TODO revise error handling, distinguish between // URL not found and response not valid } - if (format == null) { - String msg = MessageManager.formatMessage("label.couldnt_locate", url); - JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg, - MessageManager.getString("label.url_not_found"), JvOptionPane.WARNING_MESSAGE); + if (format == null) + { + String msg = MessageManager + .formatMessage("label.couldnt_locate", url); + JvOptionPane.showInternalMessageDialog(getDesktopPane(), msg, + MessageManager.getString("label.url_not_found"), + JvOptionPane.WARNING_MESSAGE); return; } - if (viewport != null) { - new FileLoader().LoadFile(viewport, url, DataSourceType.URL, format); - } else { + if (viewport != null) + { + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + format); + } + else + { new FileLoader().LoadFile(url, DataSourceType.URL, format); } } } }; - String dialogOption = MessageManager.getString("label.input_alignment_from_url"); - JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action).showInternalDialog(panel, dialogOption, - JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, - MessageManager.getString("action.ok")); + String dialogOption = MessageManager + .getString("label.input_alignment_from_url"); + JvOptionPane.newOptionDialog(desktopPane).setResponseHandler(0, action) + .showInternalDialog(panel, dialogOption, + JvOptionPane.YES_NO_CANCEL_OPTION, + JvOptionPane.PLAIN_MESSAGE, null, options, + MessageManager.getString("action.ok")); } /** * Opens the CutAndPaste window for the user to paste an alignment in to * - * @param viewPanel - if not null, the pasted alignment is added to the current - * alignment; if null, to a new alignment window + * @param viewPanel + * - if not null, the pasted alignment is added to the current + * alignment; if null, to a new alignment window */ @Override - public void inputTextboxMenuItem_actionPerformed(AlignmentViewPanel viewPanel) { + public void inputTextboxMenuItem_actionPerformed( + AlignmentViewPanel viewPanel) + { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(viewPanel); - Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), true, 600, 500); + addInternalFrame(cap, + MessageManager.getString("label.cut_paste_alignmen_file"), + FRAME_MAKE_VISIBLE, 600, 500, FRAME_ALLOW_RESIZE, + FRAME_SET_MIN_SIZE_300); } /* * Exit the program */ @Override - public void quit() { + public void quit() + { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + ""); Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + ""); - storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, getWidth(), getHeight())); + storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, + getWidth(), getHeight())); - if (jconsole != null) { + if (jconsole != null) + { storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds()); jconsole.stopConsole(); } - if (jvnews != null) { + if (jvnews != null) + { storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds()); } - if (dialogExecutor != null) { + if (dialogExecutor != null) + { dialogExecutor.shutdownNow(); } closeAll_actionPerformed(null); - if (groovyConsole != null) { + if (groovyConsole != null) + { // suppress a possible repeat prompt to save script groovyConsole.setDirty(false); groovyConsole.exit(); @@ -1139,9 +1364,11 @@ public class Desktop extends jalview.jbgui.GDesktop System.exit(0); } - private void storeLastKnownDimensions(String string, Rectangle jc) { - Cache.log.debug("Storing last known dimensions for " + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width - + " height:" + jc.height); + private void storeLastKnownDimensions(String string, Rectangle jc) + { + Cache.log.debug("Storing last known dimensions for " + string + ": x:" + + jc.x + " y:" + jc.y + " width:" + jc.width + " height:" + + jc.height); Cache.setProperty(string + "SCREEN_X", jc.x + ""); Cache.setProperty(string + "SCREEN_Y", jc.y + ""); @@ -1152,13 +1379,17 @@ public class Desktop extends jalview.jbgui.GDesktop /** * DOCUMENT ME! * - * @param e DOCUMENT ME! + * @param e + * DOCUMENT ME! */ @Override - public void aboutMenuItem_actionPerformed(ActionEvent e) { - new Thread(new Runnable() { + public void aboutMenuItem_actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { @Override - public void run() { + public void run() + { new SplashScreen(false); } }).start(); @@ -1166,12 +1397,13 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Returns the html text for the About screen, including any available version - * number, build details, author details and citation reference, but without the - * enclosing {@code html} tags + * number, build details, author details and citation reference, but without + * the enclosing {@code html} tags * * @return */ - public String getAboutMessage() { + public String getAboutMessage() + { StringBuilder message = new StringBuilder(1024); message.append("
").append("

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

").append("Built: ") @@ -1203,7 +1435,6 @@ public class Desktop extends jalview.jbgui.GDesktop message.append(CITATION); message.append("
"); - return message.toString(); } @@ -1230,13 +1461,17 @@ public class Desktop extends jalview.jbgui.GDesktop } @Override - public void closeAll_actionPerformed(ActionEvent e) { + public void closeAll_actionPerformed(ActionEvent e) + { // TODO show a progress bar while closing? - JInternalFrame[] frames = desktop.getAllFrames(); - for (int i = 0; i < frames.length; i++) { - try { + JInternalFrame[] frames = desktopPane.getAllFrames(); + for (int i = 0; i < frames.length; i++) + { + try + { frames[i].setClosed(true); - } catch (java.beans.PropertyVetoException ex) { + } catch (java.beans.PropertyVetoException ex) + { } } Jalview.setCurrentAlignFrame(null); @@ -1246,23 +1481,28 @@ 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) { + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(this); + if (ssm != null) + { ssm.resetAll(); } } @Override - public void raiseRelated_actionPerformed(ActionEvent e) { + public void raiseRelated_actionPerformed(ActionEvent e) + { reorderAssociatedWindows(false, false); } @Override - public void minimizeAssociated_actionPerformed(ActionEvent e) { + public void minimizeAssociated_actionPerformed(ActionEvent e) + { reorderAssociatedWindows(true, false); } - void closeAssociatedWindows() { + void closeAssociatedWindows() + { reorderAssociatedWindows(false, true); } @@ -1273,7 +1513,8 @@ public class Desktop extends jalview.jbgui.GDesktop * ActionEvent) */ @Override - protected void garbageCollect_actionPerformed(ActionEvent e) { + protected void garbageCollect_actionPerformed(ActionEvent e) + { // We simply collect the garbage Cache.log.debug("Collecting garbage..."); System.gc(); @@ -1283,12 +1524,14 @@ public class Desktop extends jalview.jbgui.GDesktop /* * (non-Javadoc) * - * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event. - * ActionEvent ) + * @see + * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent + * ) */ @Override - protected void showMemusage_actionPerformed(ActionEvent e) { - desktop.showMemoryUsage(showMemusage.isSelected()); + protected void showMemusage_actionPerformed(ActionEvent e) + { + desktopPane.showMemoryUsage(showMemusage.isSelected()); } /* @@ -1299,7 +1542,8 @@ public class Desktop extends jalview.jbgui.GDesktop * ) */ @Override - protected void showConsole_actionPerformed(ActionEvent e) { + protected void showConsole_actionPerformed(ActionEvent e) + { showConsole(showConsole.isSelected()); } @@ -1310,61 +1554,90 @@ public class Desktop extends jalview.jbgui.GDesktop * * @param selected */ - void showConsole(boolean selected) { + void showConsole(boolean selected) + { // TODO: decide if we should update properties file if (jconsole != null) // BH 2018 { showConsole.setSelected(selected); - Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected).toString()); + Cache.setProperty("SHOW_JAVA_CONSOLE", + Boolean.valueOf(selected).toString()); jconsole.setVisible(selected); } } - void reorderAssociatedWindows(boolean minimize, boolean close) { - JInternalFrame[] frames = desktop.getAllFrames(); - if (frames == null || frames.length < 1) { + void reorderAssociatedWindows(boolean minimize, boolean close) + { + JInternalFrame[] frames = desktopPane.getAllFrames(); + if (frames == null || frames.length < 1) + { return; } - AlignmentViewport source = null, target = null; - if (frames[0] instanceof AlignFrame) { + AlignViewportI source = null; + AlignViewportI target = null; + if (frames[0] instanceof AlignFrame) + { source = ((AlignFrame) frames[0]).getCurrentView(); - } else if (frames[0] instanceof TreePanel) { + } + else if (frames[0] instanceof TreePanel) + { source = ((TreePanel) frames[0]).getViewPort(); - } else if (frames[0] instanceof PCAPanel) { + } + else if (frames[0] instanceof PCAPanel) + { source = ((PCAPanel) frames[0]).av; - } else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) { + } + else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) + { source = ((PairwiseAlignPanel) frames[0].getContentPane()).av; } - if (source != null) { - for (int i = 0; i < frames.length; i++) { + if (source != null) + { + for (int i = 0; i < frames.length; i++) + { target = null; - if (frames[i] == null) { + if (frames[i] == null) + { continue; } - if (frames[i] instanceof AlignFrame) { + if (frames[i] instanceof AlignFrame) + { target = ((AlignFrame) frames[i]).getCurrentView(); - } else if (frames[i] instanceof TreePanel) { + } + else if (frames[i] instanceof TreePanel) + { target = ((TreePanel) frames[i]).getViewPort(); - } else if (frames[i] instanceof PCAPanel) { + } + else if (frames[i] instanceof PCAPanel) + { target = ((PCAPanel) frames[i]).av; - } else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) { + } + else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) + { target = ((PairwiseAlignPanel) frames[i].getContentPane()).av; } - if (source == target) { - try { - if (close) { + if (source == target) + { + try + { + if (close) + { frames[i].setClosed(true); - } else { + } + else + { frames[i].setIcon(minimize); - if (!minimize) { + if (!minimize) + { frames[i].toFront(); } } - } catch (java.beans.PropertyVetoException ex) { + } catch (java.beans.PropertyVetoException ex) + { } } } @@ -1374,7 +1647,8 @@ public class Desktop extends jalview.jbgui.GDesktop /** * DOCUMENT ME! * - * @param e DOCUMENT ME! + * @param e + * DOCUMENT ME! */ @Override protected void preferences_actionPerformed(ActionEvent e) { @@ -1386,66 +1660,84 @@ public class Desktop extends jalview.jbgui.GDesktop * Jalview project file */ @Override - public void saveState_actionPerformed() { + public void saveState_actionPerformed() + { saveState_actionPerformed(false); } - public void saveState_actionPerformed(boolean saveAs) { + 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(); + boolean autoSave = projectFile != null && !saveAs + && BackupFiles.getEnabled(); // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"', // saveAs="+saveAs+", Backups // "+(BackupFiles.getEnabled()?"enabled":"disabled")); boolean approveSave = false; - if (!autoSave) { - JalviewFileChooser chooser = new JalviewFileChooser("jvp", "Jalview Project"); + if (!autoSave) + { + JalviewFileChooser chooser = new JalviewFileChooser("jvp", + "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.save_state")); int value = chooser.showSaveDialog(this); - if (value == JalviewFileChooser.APPROVE_OPTION) { + 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() { + new Thread(new Runnable() + { @Override - public void run() { + public void run() + { // TODO: refactor to Jalview desktop session controller action. - setProgressBar( - MessageManager.formatMessage("label.saving_jalview_project", new Object[] { chosenFile.getName() }), - chosenFile.hashCode()); + setProgressBar(MessageManager.formatMessage( + "label.saving_jalview_project", new Object[] + { chosenFile.getName() }), chosenFile.hashCode()); Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent()); // TODO catch and handle errors for savestate // TODO prevent user from messing with the Desktop whilst we're saving - try { + try + { boolean doBackup = BackupFiles.getEnabled(); - BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null; + BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) + : null; - new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile); + new Jalview2XML().saveState( + doBackup ? backupfiles.getTempFile() : chosenFile); - if (doBackup) { + if (doBackup) + { backupfiles.setWriteSuccess(true); backupfiles.rollBackupsAndRenameTempFile(); } - } catch (OutOfMemoryError oom) { - new OOMWarning("Whilst saving current state to " + chosenFile.getName(), oom); - } catch (Exception ex) { - Cache.log.error("Problems whilst trying to save to " + chosenFile.getName(), ex); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Whilst saving current state to " + + chosenFile.getName(), oom); + } catch (Exception ex) + { + Cache.log.error("Problems whilst trying to save to " + + chosenFile.getName(), ex); JvOptionPane.showMessageDialog(me, - MessageManager.formatMessage("label.error_whilst_saving_current_state_to", - new Object[] { chosenFile.getName() }), - MessageManager.getString("label.couldnt_save_project"), JvOptionPane.WARNING_MESSAGE); + MessageManager.formatMessage( + "label.error_whilst_saving_current_state_to", + new Object[] + { chosenFile.getName() }), + MessageManager.getString("label.couldnt_save_project"), + JvOptionPane.WARNING_MESSAGE); } setProgressBar(null, chosenFile.hashCode()); } @@ -1454,15 +1746,18 @@ public class Desktop extends jalview.jbgui.GDesktop } @Override - public void saveAsState_actionPerformed(ActionEvent e) { + public void saveAsState_actionPerformed(ActionEvent e) + { saveState_actionPerformed(true); } - private void setProjectFile(File choice) { + private void setProjectFile(File choice) + { this.projectFile = choice; } - public File getProjectFile() { + public File getProjectFile() + { return this.projectFile; } @@ -1471,46 +1766,62 @@ public class Desktop extends jalview.jbgui.GDesktop * Jalview project */ @Override - public void loadState_actionPerformed() { + public void loadState_actionPerformed() + { final String[] suffix = new String[] { "jvp", "jar" }; - final String[] desc = new String[] { "Jalview Project", "Jalview Project (old)" }; - JalviewFileChooser chooser = new JalviewFileChooser(Cache.getProperty("LAST_DIRECTORY"), suffix, desc, - "Jalview Project", true, BackupFiles.getEnabled()); // last two - // booleans: - // allFiles, + final String[] desc = new String[] { "Jalview Project", + "Jalview Project (old)" }; + JalviewFileChooser chooser = new JalviewFileChooser( + Cache.getProperty("LAST_DIRECTORY"), suffix, desc, + "Jalview Project", true, BackupFiles.getEnabled()); // last two + // booleans: + // allFiles, // allowBackupFiles chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); - chooser.setResponseHandler(0, new Runnable() { + chooser.setResponseHandler(0, new Runnable() + { @Override - public void run() { + public void run() + { File selectedFile = chooser.getSelectedFile(); setProjectFile(selectedFile); String choice = selectedFile.getAbsolutePath(); Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent()); - new Thread(new Runnable() { + new Thread(new Runnable() + { @Override - public void run() { - try { + public void run() + { + try + { new Jalview2XML().loadJalviewAlign(selectedFile); - } catch (OutOfMemoryError oom) { + } catch (OutOfMemoryError oom) + { new OOMWarning("Whilst loading project from " + choice, oom); - } catch (Exception ex) { - Cache.log.error("Problems whilst loading project from " + choice, ex); - JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.formatMessage("label.error_whilst_loading_project_from", new Object[] { choice }), - MessageManager.getString("label.couldnt_load_project"), JvOptionPane.WARNING_MESSAGE); + } catch (Exception ex) + { + Cache.log.error( + "Problems whilst loading project from " + choice, ex); + JvOptionPane.showMessageDialog(getDesktopPane(), + MessageManager.formatMessage( + "label.error_whilst_loading_project_from", + new Object[] + { choice }), + MessageManager + .getString("label.couldnt_load_project"), + JvOptionPane.WARNING_MESSAGE); } } }, "Project Loader").start(); } }); - chooser.showOpenDialog(this); } @Override - public void inputSequence_actionPerformed(ActionEvent e) { + public void inputSequence_actionPerformed(ActionEvent e) + { new SequenceFetcher(this); } @@ -1518,19 +1829,24 @@ public class Desktop extends jalview.jbgui.GDesktop ArrayList fileLoadingPanels = new ArrayList<>(); - public void startLoading(final Object fileName) { - if (fileLoadingCount == 0) { - fileLoadingPanels - .add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new Object[] { fileName }))); + public void startLoading(final Object fileName) + { + if (fileLoadingCount == 0) + { + fileLoadingPanels.add(addProgressPanel(MessageManager + .formatMessage("label.loading_file", new Object[] + { fileName }))); } fileLoadingCount++; } - private JPanel addProgressPanel(String string) { - if (progressPanel == null) { + private JPanel addProgressPanel(String string) + { + if (progressPanel == null) + { progressPanel = new JPanel(new GridLayout(1, 1)); totalProgressCount = 0; - instance.getContentPane().add(progressPanel, BorderLayout.SOUTH); + getContentPane().add(progressPanel, BorderLayout.SOUTH); } JPanel thisprogress = new JPanel(new BorderLayout(10, 5)); JProgressBar progressBar = new JProgressBar(); @@ -1540,21 +1856,26 @@ public class Desktop extends jalview.jbgui.GDesktop 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(); + validate(); return thisprogress; } int totalProgressCount = 0; - private void removeProgressPanel(JPanel progbar) { - if (progressPanel != null) { - synchronized (progressPanel) { + private void removeProgressPanel(JPanel progbar) + { + if (progressPanel != null) + { + synchronized (progressPanel) + { progressPanel.remove(progbar); GridLayout gl = (GridLayout) progressPanel.getLayout(); gl.setRows(gl.getRows() - 1); - if (--totalProgressCount < 1) { + if (--totalProgressCount < 1) + { this.getContentPane().remove(progressPanel); progressPanel = null; } @@ -1563,10 +1884,13 @@ public class Desktop extends jalview.jbgui.GDesktop validate(); } - public void stopLoading() { + public void stopLoading() + { fileLoadingCount--; - if (fileLoadingCount < 1) { - while (fileLoadingPanels.size() > 0) { + if (fileLoadingCount < 1) + { + while (fileLoadingPanels.size() > 0) + { removeProgressPanel(fileLoadingPanels.remove(0)); } fileLoadingPanels.clear(); @@ -1575,35 +1899,45 @@ public class Desktop extends jalview.jbgui.GDesktop validate(); } - public static int getViewCount(String alignmentId) { + public static int getViewCount(String alignmentId) + { AlignmentViewport[] aps = getViewports(alignmentId); return (aps == null) ? 0 : aps.length; } /** * - * @param alignmentId - if null, all sets are returned + * @param alignmentId + * - if null, all sets are returned * @return all AlignmentPanels concerning the alignmentId sequence set */ - public static AlignmentPanel[] getAlignmentPanels(String alignmentId) { - if (Desktop.desktop == null) { + public static AlignmentPanel[] getAlignmentPanels(String alignmentId) + { + if (getDesktopPane() == null) + { // no frames created and in headless mode // TODO: verify that frames are recoverable when in headless mode return null; } List aps = new ArrayList<>(); AlignFrame[] frames = getAlignFrames(); - if (frames == null) { + if (frames == null) + { return null; } - for (AlignFrame af : frames) { - for (AlignmentPanel ap : af.alignPanels) { - if (alignmentId == null || alignmentId.equals(ap.av.getSequenceSetId())) { + for (AlignFrame af : frames) + { + for (AlignmentPanel ap : af.alignPanels) + { + if (alignmentId == null + || alignmentId.equals(ap.av.getSequenceSetId())) + { aps.add(ap); } } } - if (aps.size() == 0) { + if (aps.size() == 0) + { return null; } AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]); @@ -1613,29 +1947,42 @@ public class Desktop extends jalview.jbgui.GDesktop /** * get all the viewports on an alignment. * - * @param sequenceSetId unique alignment id (may be null - all viewports - * returned in that case) + * @param sequenceSetId + * unique alignment id (may be null - all viewports returned in that + * case) * @return all viewports on the alignment bound to sequenceSetId */ - public static AlignmentViewport[] getViewports(String sequenceSetId) { + public static AlignmentViewport[] getViewports(String sequenceSetId) + { List viewp = new ArrayList<>(); - if (desktop != null) { - AlignFrame[] frames = Desktop.getAlignFrames(); - - for (AlignFrame afr : frames) { - if (sequenceSetId == null || afr.getViewport().getSequenceSetId().equals(sequenceSetId)) { - if (afr.alignPanels != null) { - for (AlignmentPanel ap : afr.alignPanels) { - if (sequenceSetId == null || sequenceSetId.equals(ap.av.getSequenceSetId())) { + if (getDesktopPane() != null) + { + AlignFrame[] frames = getAlignFrames(); + + for (AlignFrame afr : frames) + { + if (sequenceSetId == null || afr.getViewport().getSequenceSetId() + .equals(sequenceSetId)) + { + if (afr.alignPanels != null) + { + for (AlignmentPanel ap : afr.alignPanels) + { + if (sequenceSetId == null + || sequenceSetId.equals(ap.av.getSequenceSetId())) + { viewp.add(ap.av); } } - } else { + } + else + { viewp.add(afr.getViewport()); } } } - if (viewp.size() > 0) { + if (viewp.size() > 0) + { return viewp.toArray(new AlignmentViewport[viewp.size()]); } } @@ -1647,47 +1994,56 @@ public class Desktop extends jalview.jbgui.GDesktop * * @param af */ - public static void explodeViews(AlignFrame af) { + public static void explodeViews(AlignFrame af) + { int size = af.alignPanels.size(); - if (size < 2) { + if (size < 2) + { return; } // FIXME: ideally should use UI interface API - FeatureSettings viewFeatureSettings = (af.featureSettings != null && af.featureSettings.isOpen()) - ? af.featureSettings - : null; + FeatureSettings viewFeatureSettings = (af.featureSettings != null + && af.featureSettings.isOpen()) ? af.featureSettings : null; Rectangle fsBounds = af.getFeatureSettingsGeometry(); - for (int i = 0; i < size; i++) { + for (int i = 0; i < size; i++) + { AlignmentPanel ap = af.alignPanels.get(i); AlignFrame newaf = new AlignFrame(ap); // transfer reference for existing feature settings to new alignFrame - if (ap == af.alignPanel) { - if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap) { + if (ap == af.alignPanel) + { + if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap) + { newaf.featureSettings = viewFeatureSettings; } newaf.setFeatureSettingsGeometry(fsBounds); } /* - * Restore the view's last exploded frame geometry if known. Multiple views from - * one exploded frame share and restore the same (frame) position and size. + * Restore the view's last exploded frame geometry if known. Multiple + * views from one exploded frame share and restore the same (frame) + * position and size. */ Rectangle geometry = ap.av.getExplodedGeometry(); - if (geometry != null) { + if (geometry != null) + { newaf.setBounds(geometry); } ap.av.setGatherViewsHere(false); - addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); // and materialise a new feature settings dialog instance for the new // alignframe // (closes the old as if 'OK' was pressed) - if (ap == af.alignPanel && newaf.featureSettings != null && newaf.featureSettings.isOpen() - && af.alignPanel.getAlignViewport().isShowSequenceFeatures()) { + if (ap == af.alignPanel && newaf.featureSettings != null + && newaf.featureSettings.isOpen() + && af.alignPanel.getAlignViewport().isShowSequenceFeatures()) + { newaf.showFeatureSettingsUI(); } } @@ -1700,24 +2056,29 @@ 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 */ - public void gatherViews(AlignFrame source) { + public void gatherViews(AlignFrame source) + { source.viewport.setGatherViewsHere(true); source.viewport.setExplodedGeometry(source.getBounds()); - JInternalFrame[] frames = desktop.getAllFrames(); + JInternalFrame[] frames = desktopPane.getAllFrames(); String viewId = source.viewport.getSequenceSetId(); - for (int t = 0; t < frames.length; t++) { - if (frames[t] instanceof AlignFrame && frames[t] != source) { + for (int t = 0; t < frames.length; t++) + { + if (frames[t] instanceof AlignFrame && frames[t] != source) + { AlignFrame af = (AlignFrame) frames[t]; boolean gatherThis = false; - for (int a = 0; a < af.alignPanels.size(); a++) { + for (int a = 0; a < af.alignPanels.size(); a++) + { AlignmentPanel ap = af.alignPanels.get(a); - if (viewId.equals(ap.av.getSequenceSetId())) { + if (viewId.equals(ap.av.getSequenceSetId())) + { gatherThis = true; ap.av.setGatherViewsHere(false); ap.av.setExplodedGeometry(af.getBounds()); @@ -1725,13 +2086,19 @@ public class Desktop extends jalview.jbgui.GDesktop } } - if (gatherThis) { - if (af.featureSettings != null && af.featureSettings.isOpen()) { - if (source.featureSettings == null) { + if (gatherThis) + { + if (af.featureSettings != null && af.featureSettings.isOpen()) + { + if (source.featureSettings == null) + { // preserve the feature settings geometry for this frame source.featureSettings = af.featureSettings; - source.setFeatureSettingsGeometry(af.getFeatureSettingsGeometry()); - } else { + source.setFeatureSettingsGeometry( + af.getFeatureSettingsGeometry()); + } + else + { // close it and forget af.featureSettings.close(); } @@ -1743,14 +2110,15 @@ public class Desktop extends jalview.jbgui.GDesktop } // refresh the feature setting UI for the source frame if it exists - if (source.featureSettings != null && source.featureSettings.isOpen()) { + if (source.featureSettings != null && source.featureSettings.isOpen()) + { source.showFeatureSettingsUI(); } - } - public JInternalFrame[] getAllFrames() { - return desktop.getAllFrames(); + public JInternalFrame[] getAllFrames() + { + return desktopPane.getAllFrames(); } /** @@ -1759,37 +2127,49 @@ public class Desktop extends jalview.jbgui.GDesktop * * @param url */ - public void checkForQuestionnaire(String url) { + public void checkForQuestionnaire(String url) + { UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url); // javax.swing.SwingUtilities.invokeLater(jvq); new Thread(jvq).start(); } - public void checkURLLinks() { + public void checkURLLinks() + { // Thread off the URL link checker - addDialogThread(new Runnable() { + addDialogThread(new Runnable() + { @Override - public void run() { - if (Cache.getDefault("CHECKURLLINKS", true)) { + public void run() + { + if (Cache.getDefault("CHECKURLLINKS", true)) + { // check what the actual links are - if it's just the default don't // bother with the warning - List links = Preferences.sequenceUrlLinks.getLinksForMenu(); + List links = Preferences.sequenceUrlLinks + .getLinksForMenu(); // only need to check links if there is one with a // SEQUENCE_ID which is not the default EMBL_EBI link ListIterator li = links.listIterator(); boolean check = false; List urls = new ArrayList<>(); - while (li.hasNext()) { + while (li.hasNext()) + { String link = li.next(); - if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) && !UrlConstants.isDefaultString(link)) { + if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) + && !UrlConstants.isDefaultString(link)) + { check = true; int barPos = link.indexOf("|"); - String urlMsg = barPos == -1 ? link : link.substring(0, barPos) + ": " + link.substring(barPos + 1); + String urlMsg = barPos == -1 ? link + : link.substring(0, barPos) + ": " + + link.substring(barPos + 1); urls.add(new JLabel(urlMsg)); } } - if (!check) { + if (!check) + { return; } @@ -1798,27 +2178,36 @@ public class Desktop extends jalview.jbgui.GDesktop JPanel msgPanel = new JPanel(); msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS)); msgPanel.add(Box.createVerticalGlue()); - JLabel msg = new JLabel(MessageManager.getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); - JLabel msg2 = new JLabel(MessageManager.getString("label.SEQUENCE_ID_for_DB_ACCESSION2")); + JLabel msg = new JLabel(MessageManager + .getString("label.SEQUENCE_ID_for_DB_ACCESSION1")); + JLabel msg2 = new JLabel(MessageManager + .getString("label.SEQUENCE_ID_for_DB_ACCESSION2")); msgPanel.add(msg); - for (JLabel url : urls) { + for (JLabel url : urls) + { msgPanel.add(url); } msgPanel.add(msg2); - final JCheckBox jcb = new JCheckBox(MessageManager.getString("label.do_not_display_again")); - jcb.addActionListener(new ActionListener() { + final JCheckBox jcb = new JCheckBox( + MessageManager.getString("label.do_not_display_again")); + jcb.addActionListener(new ActionListener() + { @Override - public void actionPerformed(ActionEvent e) { + public void actionPerformed(ActionEvent e) + { // update Cache settings for "don't show this again" boolean showWarningAgain = !jcb.isSelected(); - Cache.setProperty("CHECKURLLINKS", Boolean.valueOf(showWarningAgain).toString()); + Cache.setProperty("CHECKURLLINKS", + Boolean.valueOf(showWarningAgain).toString()); } }); msgPanel.add(jcb); - JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, - MessageManager.getString("label.SEQUENCE_ID_no_longer_used"), JvOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(desktopPane, msgPanel, + MessageManager + .getString("label.SEQUENCE_ID_no_longer_used"), + JvOptionPane.WARNING_MESSAGE); } } }); @@ -1826,11 +2215,13 @@ 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; @@ -1839,33 +2230,41 @@ public class Desktop extends jalview.jbgui.GDesktop java.text.NumberFormat df; - float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage; + float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, + percentUsage; - public MyDesktopPane(boolean showMemoryUsage) { + public MyDesktopPane(boolean showMemoryUsage) + { showMemoryUsage(showMemoryUsage); } - public void showMemoryUsage(boolean showMemory) { + public void showMemoryUsage(boolean showMemory) + { this.showMemoryUsage = showMemory; - if (showMemory) { + if (showMemory) + { Thread worker = new Thread(this); worker.start(); } repaint(); } - public boolean isShowMemoryUsage() { + public boolean isShowMemoryUsage() + { return showMemoryUsage; } @Override - public void run() { + public void run() + { df = java.text.NumberFormat.getNumberInstance(); df.setMaximumFractionDigits(2); runtime = Runtime.getRuntime(); - while (showMemoryUsage) { - try { + while (showMemoryUsage) + { + try + { maxMemory = runtime.maxMemory() / ONE_MB; allocatedMemory = runtime.totalMemory() / ONE_MB; freeMemory = runtime.freeMemory() / ONE_MB; @@ -1882,27 +2281,32 @@ public class Desktop extends jalview.jbgui.GDesktop repaint(); // sleep after showing usage Thread.sleep(3000); - } catch (Exception ex) { + } catch (Exception ex) + { ex.printStackTrace(); } } } @Override - public void paintComponent(Graphics g) { - if (showMemoryUsage && g != null && df != null) { - if (percentUsage < 20) { + public void paintComponent(Graphics g) + { + if (showMemoryUsage && g != null && df != null) + { + if (percentUsage < 20) + { g.setColor(Color.red); } FontMetrics fm = g.getFontMetrics(); - if (fm != null) { - g.drawString( - MessageManager.formatMessage("label.memory_stats", - new Object[] { df.format(totalFreeMemory), df.format(maxMemory), df.format(percentUsage) }), - 10, getHeight() - fm.getHeight()); + if (fm != null) + { + g.drawString(MessageManager.formatMessage("label.memory_stats", + new Object[] + { df.format(totalFreeMemory), df.format(maxMemory), + df.format(percentUsage) }), + 10, getHeight() - fm.getHeight()); } } - // output debug scale message. Important for jalview.bin.HiDPISettingTest2 Desktop.debugScaleMessage(Desktop.getDesktop().getGraphics()); } @@ -1913,36 +2317,45 @@ public class Desktop extends jalview.jbgui.GDesktop * * @return an array of AlignFrame, or null if none found */ - public static AlignFrame[] getAlignFrames() { - if (Jalview.isHeadlessMode()) { - // Desktop.desktop is null in headless mode - return new AlignFrame[] { Jalview.currentAlignFrame }; + public static AlignFrame[] getAlignFrames() + { + if (Jalview.isHeadlessMode()) + { + return new AlignFrame[] { Jalview.getInstance().currentAlignFrame }; } - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = getDesktopPane().getAllFrames(); - if (frames == null) { + if (frames == null) + { return null; } List avp = new ArrayList<>(); // REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) { - if (frames[i] instanceof AlignFrame) { + for (int i = frames.length - 1; i > -1; i--) + { + if (frames[i] instanceof AlignFrame) + { avp.add((AlignFrame) frames[i]); - } else if (frames[i] instanceof SplitFrame) { + } + else if (frames[i] instanceof SplitFrame) + { /* * Also check for a split frame containing an AlignFrame */ GSplitFrame sf = (GSplitFrame) frames[i]; - if (sf.getTopFrame() instanceof AlignFrame) { + if (sf.getTopFrame() instanceof AlignFrame) + { avp.add((AlignFrame) sf.getTopFrame()); } - if (sf.getBottomFrame() instanceof AlignFrame) { + if (sf.getBottomFrame() instanceof AlignFrame) + { avp.add((AlignFrame) sf.getBottomFrame()); } } } - if (avp.size() == 0) { + if (avp.size() == 0) + { return null; } AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]); @@ -1954,21 +2367,26 @@ public class Desktop extends jalview.jbgui.GDesktop * * @return */ - public GStructureViewer[] getJmols() { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + public GStructureViewer[] getJmols() + { + JInternalFrame[] frames = desktopPane.getAllFrames(); - if (frames == null) { + if (frames == null) + { return null; } List avp = new ArrayList<>(); // REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) { - if (frames[i] instanceof AppJmol) { + for (int i = frames.length - 1; i > -1; i--) + { + if (frames[i] instanceof AppJmol) + { GStructureViewer af = (GStructureViewer) frames[i]; avp.add(af); } } - if (avp.size() == 0) { + if (avp.size() == 0) + { return null; } GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]); @@ -1979,37 +2397,45 @@ public class Desktop extends jalview.jbgui.GDesktop * Add Groovy Support to Jalview */ @Override - public void groovyShell_actionPerformed() { - try { + public void groovyShell_actionPerformed() + { + try + { openGroovyConsole(); - } catch (Exception ex) { + } catch (Exception ex) + { 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"), JvOptionPane.ERROR_MESSAGE); + MessageManager.getString("label.couldnt_create_groovy_shell"), + MessageManager.getString("label.groovy_support_failed"), + JvOptionPane.ERROR_MESSAGE); } } /** * Open the Groovy console */ - void openGroovyConsole() { - if (groovyConsole == null) { + void openGroovyConsole() + { + if (groovyConsole == null) + { groovyConsole = new groovy.ui.Console(); groovyConsole.setVariable("Jalview", this); groovyConsole.run(); /* * We allow only one console at a time, so that AlignFrame menu option - * 'Calculate | Run Groovy script' is unambiguous. Disable 'Groovy Console', and - * enable 'Run script', when the console is opened, and the reverse when it is - * closed + * 'Calculate | Run Groovy script' is unambiguous. + * Disable 'Groovy Console', and enable 'Run script', when the console is + * opened, and the reverse when it is closed */ Window window = (Window) groovyConsole.getFrame(); - window.addWindowListener(new WindowAdapter() { + window.addWindowListener(new WindowAdapter() + { @Override - public void windowClosed(WindowEvent e) { + public void windowClosed(WindowEvent e) + { /* * rebind CMD-Q from Groovy Console to Jalview Quit */ @@ -2025,23 +2451,28 @@ public class Desktop extends jalview.jbgui.GDesktop ((Window) groovyConsole.getFrame()).setVisible(true); /* - * if we got this far, enable 'Run Groovy' in AlignFrame menus and disable - * opening a second console + * if we got this far, enable 'Run Groovy' in AlignFrame menus + * and disable opening a second console */ enableExecuteGroovy(true); } /** - * 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, jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()), - "Quit"); - getRootPane().getActionMap().put("Quit", new AbstractAction() { + protected void addQuitHandler() + { + + getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW) + .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q, + Platform.SHORTCUT_KEY_MASK), + "Quit"); + getRootPane().getActionMap().put("Quit", new AbstractAction() + { @Override - public void actionPerformed(ActionEvent e) { + public void actionPerformed(ActionEvent e) + { quit(); } }); @@ -2050,18 +2481,22 @@ public class Desktop extends jalview.jbgui.GDesktop /** * Enable or disable 'Run Groovy script' in AlignFrame calculate menus * - * @param enabled true if Groovy console is open + * @param enabled + * true if Groovy console is open */ - public void enableExecuteGroovy(boolean enabled) { + public void enableExecuteGroovy(boolean enabled) + { /* - * disable opening a second Groovy console (or re-enable when the console is - * closed) + * disable opening a second Groovy console + * (or re-enable when the console is closed) */ groovyShell.setEnabled(!enabled); AlignFrame[] alignFrames = getAlignFrames(); - if (alignFrames != null) { - for (AlignFrame af : alignFrames) { + if (alignFrames != null) + { + for (AlignFrame af : alignFrames) + { af.setGroovyEnabled(enabled); } } @@ -2080,22 +2515,37 @@ public class Desktop extends jalview.jbgui.GDesktop * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ @Override - public void setProgressBar(String message, long id) { - if (progressBars == null) { + public void setProgressBar(String message, long id) + { + // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK); + + if (progressBars == null) + { progressBars = new Hashtable<>(); progressBarHandlers = new Hashtable<>(); } - if (progressBars.get(Long.valueOf(id)) != null) { + if (progressBars.get(Long.valueOf(id)) != null) + { JPanel panel = progressBars.remove(Long.valueOf(id)); - if (progressBarHandlers.contains(Long.valueOf(id))) { + if (progressBarHandlers.contains(Long.valueOf(id))) + { progressBarHandlers.remove(Long.valueOf(id)); } removeProgressPanel(panel); - } else { + } + else + { progressBars.put(Long.valueOf(id), addProgressPanel(message)); } } + + @Override + public void removeProgressBar(long id) + { + //TODO + throw new UnsupportedOperationException("not implemented"); + } /* * (non-Javadoc) @@ -2104,22 +2554,33 @@ public class Desktop extends jalview.jbgui.GDesktop * jalview.gui.IProgressIndicatorHandler) */ @Override - public void registerHandler(final long id, final IProgressIndicatorHandler handler) { - if (progressBarHandlers == null || !progressBars.containsKey(Long.valueOf(id))) { - throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler")); + public void registerHandler(final long id, + final IProgressIndicatorHandler handler) + { + if (progressBarHandlers == null + || !progressBars.containsKey(Long.valueOf(id))) + { + throw new Error(MessageManager.getString( + "error.call_setprogressbar_before_registering_handler")); } progressBarHandlers.put(Long.valueOf(id), handler); final JPanel progressPanel = progressBars.get(Long.valueOf(id)); - if (handler.canCancel()) { - JButton cancel = new JButton(MessageManager.getString("action.cancel")); + if (handler.canCancel()) + { + JButton cancel = new JButton( + MessageManager.getString("action.cancel")); final IProgressIndicator us = this; - cancel.addActionListener(new ActionListener() { + cancel.addActionListener(new ActionListener() + { @Override - public void actionPerformed(ActionEvent e) { + public void actionPerformed(ActionEvent e) + { handler.cancelActivity(id); - us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", - new Object[] { ((JLabel) progressPanel.getComponent(0)).getText() }), id); + us.setProgressBar(MessageManager + .formatMessage("label.cancelled_params", new Object[] + { ((JLabel) progressPanel.getComponent(0)).getText() }), + id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -2131,25 +2592,33 @@ public class Desktop extends jalview.jbgui.GDesktop * @return true if any progress bars are still active */ @Override - public boolean operationInProgress() { - if (progressBars != null && progressBars.size() > 0) { + public boolean operationInProgress() + { + if (progressBars != null && progressBars.size() > 0) + { return true; } return false; } /** - * 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) { - AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId()); - for (int panel = 0; aps != null && panel < aps.length; panel++) { - if (aps[panel] != null && aps[panel].av == viewport) { + public static AlignFrame getAlignFrameFor(AlignViewportI viewport) + { + if (getDesktopPane() != null) + { + AlignmentPanel[] aps = getAlignmentPanels( + viewport.getSequenceSetId()); + for (int panel = 0; aps != null && panel < aps.length; panel++) + { + if (aps[panel] != null && aps[panel].av == viewport) + { return aps[panel].alignFrame; } } @@ -2157,7 +2626,8 @@ public class Desktop extends jalview.jbgui.GDesktop return null; } - public VamsasApplication getVamsasApplication() { + public VamsasApplication getVamsasApplication() + { // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS return null; @@ -2173,7 +2643,8 @@ public class Desktop extends jalview.jbgui.GDesktop * * @return inBatchMode */ - public boolean isInBatchMode() { + public boolean isInBatchMode() + { return inBatchMode; } @@ -2182,66 +2653,59 @@ public class Desktop extends jalview.jbgui.GDesktop * * @param inBatchMode */ - public void setInBatchMode(boolean inBatchMode) { + public void setInBatchMode(boolean inBatchMode) + { this.inBatchMode = inBatchMode; } - /** - * start service discovery and wait till it is done - */ - public void startServiceDiscovery() { + public void startServiceDiscovery() + { startServiceDiscovery(false); } - /** - * start service discovery threads - blocking or non-blocking - * - * @param blocking - */ - public void startServiceDiscovery(boolean blocking) { - startServiceDiscovery(blocking, false); - } - - /** - * start service discovery threads - * - * @param blocking - false means call returns - * immediately - * @param ignore_SHOW_JWS2_SERVICES_preference - when true JABA services are - * discovered regardless of user's - * JWS2 discovery preference setting - */ - public void startServiceDiscovery(boolean blocking, boolean ignore_SHOW_JWS2_SERVICES_preference) { - boolean alive = true; - Thread t0 = null, t1 = null, t2 = null; + public void startServiceDiscovery(boolean blocking) + { + System.out.println("Starting service discovery"); + var tasks = new ArrayList>(); // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release - if (true) { + + System.out.println("loading services"); + + /** @j2sIgnore */ + { // todo: changesupport handlers need to be transferred - if (discoverer == null) { - discoverer = new jalview.ws.jws1.Discoverer(); + if (discoverer == null) + { + discoverer = jalview.ws.jws1.Discoverer.getInstance(); // register PCS handler for desktop. discoverer.addPropertyChangeListener(changeSupport); } // JAL-940 - disabled JWS1 service configuration - always start discoverer // until we phase out completely - (t0 = new Thread(discoverer)).start(); + var f = new FutureTask(discoverer, null); + new Thread(f).start(); + tasks.add(f); } - if (ignore_SHOW_JWS2_SERVICES_preference || Cache.getDefault("SHOW_JWS2_SERVICES", true)) { - t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(changeSupport); + if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) + { + tasks.add(jalview.ws.jws2.Jws2Discoverer.getInstance().startDiscoverer()); } - Thread t3 = null; + if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true)) { - // TODO: do rest service discovery + tasks.add(jalview.ws.slivkaws.SlivkaWSDiscoverer.getInstance().startDiscoverer()); } - if (blocking) { - while (alive) { - try { - Thread.sleep(15); - } catch (Exception e) { + if (blocking) + { + for (Future task : tasks) { + try + { + // block until all discovery tasks are done + task.get(); + } catch (Exception e) + { + e.printStackTrace(); } - alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) || (t3 != null && t3.isAlive()) - || (t0 != null && t0.isAlive()); } } } @@ -2251,50 +2715,72 @@ public class Desktop extends jalview.jbgui.GDesktop * * @param evt */ - protected void JalviewServicesChanged(PropertyChangeEvent evt) { - if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) { - final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().getErrorMessages(); - if (ermsg != null) { - if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) { - if (serviceChangedDialog == null) { + protected void JalviewServicesChanged(PropertyChangeEvent evt) + { + if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) + { + final WSDiscovererI discoverer = jalview.ws.jws2.Jws2Discoverer + .getInstance(); + final String ermsg = discoverer.getErrorMessages(); + // CONFLICT:ALT:? final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance() + if (ermsg != null) + { + if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) + { + if (serviceChangedDialog == null) + { // only run if we aren't already displaying one of these. - addDialogThread(serviceChangedDialog = new Runnable() { + addDialogThread(serviceChangedDialog = new Runnable() + { @Override - public void run() { + public void run() + { /* * JalviewDialog jd =new JalviewDialog() { * - * @Override protected void cancelPressed() { // TODO Auto-generated method stub + * @Override protected void cancelPressed() { // TODO + * Auto-generated method stub * - * }@Override protected void okPressed() { // TODO Auto-generated method stub + * }@Override protected void okPressed() { // TODO + * Auto-generated method stub * - * }@Override protected void raiseClosed() { // TODO Auto-generated method stub + * }@Override protected void raiseClosed() { // TODO + * Auto-generated method stub * - * } }; jd.initDialogFrame(new JLabel("
" + - * ermsg + + * } }; jd.initDialogFrame(new + * JLabel("
" + ermsg + * "
It may be that you have invalid JABA URLs in your web service preferences," * + " or mis-configured HTTP proxy settings.
" + - * "Check the Connections and Web services tab of the" + - * " Tools->Preferences dialog box to change them.
" ), - * true, true, "Web Service Configuration Problem", 450, 400); + * "Check the Connections and Web services tab of the" + * + + * " Tools->Preferences dialog box to change them.
" + * ), true, true, "Web Service Configuration Problem", 450, + * 400); * * jd.waitForInput(); */ - 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(desktopPane, + 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; } }); } - } else { - Cache.log.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg); + } + else + { + Cache.log.error( + "Errors reported by JABA discovery service. Check web services preferences.\n" + + ermsg); } } } @@ -2309,34 +2795,47 @@ public class Desktop extends jalview.jbgui.GDesktop * * @param url */ - public static void showUrl(final String url) { - showUrl(url, Desktop.instance); + public static void showUrl(final String url) + { + showUrl(url, getInstance()); } /** * Like showUrl but allows progress handler to be specified * * @param url - * @param progress (null) or object implementing IProgressIndicator + * @param progress + * (null) or object implementing IProgressIndicator */ - public static void showUrl(final String url, final IProgressIndicator progress) { - new Thread(new Runnable() { + public static void showUrl(final String url, + final IProgressIndicator progress) + { + new Thread(new Runnable() + { @Override - public void run() { - try { - if (progress != null) { - progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new Object[] { url }), - this.hashCode()); + public void run() + { + try + { + if (progress != null) + { + progress.setProgressBar(MessageManager + .formatMessage("status.opening_params", new Object[] + { url }), this.hashCode()); } jalview.util.BrowserLauncher.openURL(url); - } catch (Exception ex) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.web_browser_not_found_unix"), - MessageManager.getString("label.web_browser_not_found"), JvOptionPane.WARNING_MESSAGE); + } catch (Exception ex) + { + JvOptionPane.showInternalMessageDialog(getDesktopPane(), + MessageManager + .getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } - if (progress != null) { + if (progress != null) + { progress.setProgressBar(null, this.hashCode()); } } @@ -2345,8 +2844,10 @@ public class Desktop extends jalview.jbgui.GDesktop public static WsParamSetManager wsparamManager = null; - public static ParamManager getUserParameterStore() { - if (wsparamManager == null) { + public static ParamManager getUserParameterStore() + { + if (wsparamManager == null) + { wsparamManager = new WsParamSetManager(); } return wsparamManager; @@ -2357,18 +2858,27 @@ public class Desktop extends jalview.jbgui.GDesktop * * @param e */ - public static void hyperlinkUpdate(HyperlinkEvent e) { - if (e.getEventType() == EventType.ACTIVATED) { + public static void hyperlinkUpdate(HyperlinkEvent e) + { + if (e.getEventType() == EventType.ACTIVATED) + { String url = null; - try { + try + { url = e.getURL().toString(); - Desktop.showUrl(url); - } catch (Exception x) { - if (url != null) { - if (Cache.log != null) { + showUrl(url); + } catch (Exception x) + { + if (url != null) + { + if (Cache.log != null) + { Cache.log.error("Couldn't handle string " + url + " as a URL."); - } else { - System.err.println("Couldn't handle string " + url + " as a URL."); + } + else + { + System.err.println( + "Couldn't handle string " + url + " as a URL."); } } // ignore any exceptions due to dud links. @@ -2399,29 +2909,39 @@ public class Desktop extends jalview.jbgui.GDesktop * * @param prompter */ - public void addDialogThread(final Runnable prompter) { - dialogExecutor.submit(new Runnable() { + public void addDialogThread(final Runnable prompter) + { + dialogExecutor.submit(new Runnable() + { @Override - public void run() { - if (dialogPause) { - try { + public void run() + { + if (dialogPause) + { + try + { block.acquire(); - } catch (InterruptedException x) { + } catch (InterruptedException x) + { } } - if (instance == null) { + if (Jalview.isHeadlessMode()) + { return; } - try { + try + { SwingUtilities.invokeAndWait(prompter); - } catch (Exception q) { + } catch (Exception q) + { Cache.log.warn("Unexpected Exception in dialog thread.", q); } } }); } - public void startDialogQueue() { + public void startDialogQueue() + { // set the flag so we don't pause waiting for another permit and semaphore // the current task to begin dialogPause = false; @@ -2438,53 +2958,65 @@ public class Desktop extends jalview.jbgui.GDesktop * */ @Override - protected void snapShotWindow_actionPerformed(ActionEvent e) { + protected void snapShotWindow_actionPerformed(ActionEvent e) + { // currently the menu option to do this is not shown invalidate(); int width = getWidth(); int height = getHeight(); - File of = new File("Jalview_snapshot_" + System.currentTimeMillis() + ".eps"); - ImageWriterI writer = new ImageWriterI() { + File of = new File( + "Jalview_snapshot_" + System.currentTimeMillis() + ".eps"); + ImageWriterI writer = new ImageWriterI() + { @Override - public void exportImage(Graphics g) throws Exception { + public void exportImage(Graphics g) throws Exception + { paintAll(g); - Cache.log.info("Successfully written snapshot to file " + of.getAbsolutePath()); + Cache.log.info("Successfully written snapshot to file " + + of.getAbsolutePath()); } }; String title = "View of desktop"; - ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, title); + ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, + title); exporter.doExport(of, this, width, height, title); } /** * 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. * * @param sf */ - public void explodeViews(SplitFrame sf) { + public void explodeViews(SplitFrame sf) + { AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame(); AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame(); - List topPanels = oldTopFrame.getAlignPanels(); - List bottomPanels = oldBottomFrame.getAlignPanels(); + List topPanels = oldTopFrame + .getAlignPanels(); + List bottomPanels = oldBottomFrame + .getAlignPanels(); int viewCount = topPanels.size(); - if (viewCount < 2) { + if (viewCount < 2) + { return; } /* - * Processing in reverse order works, forwards order leaves the first panels not - * visible. I don't know why! + * Processing in reverse order works, forwards order leaves the first panels + * not visible. I don't know why! */ - for (int i = viewCount - 1; i >= 0; i--) { + for (int i = viewCount - 1; i >= 0; i--) + { /* - * Make new top and bottom frames. These take over the respective AlignmentPanel - * objects, including their AlignmentViewports, so the cdna/protein - * relationships between the viewports is carried over to the new split frames. + * Make new top and bottom frames. These take over the respective + * AlignmentPanel objects, including their AlignmentViewports, so the + * cdna/protein relationships between the viewports is carried over to the + * new split frames. * * explodedGeometry holds the (x, y) position of the previously exploded * SplitFrame, and the (width, height) of the AlignFrame component @@ -2493,8 +3025,10 @@ public class Desktop extends jalview.jbgui.GDesktop AlignFrame newTopFrame = new AlignFrame(topPanel); newTopFrame.setSize(oldTopFrame.getSize()); newTopFrame.setVisible(true); - Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()).getExplodedGeometry(); - if (geometry != null) { + Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()) + .getExplodedGeometry(); + if (geometry != null) + { newTopFrame.setSize(geometry.getSize()); } @@ -2502,23 +3036,27 @@ public class Desktop extends jalview.jbgui.GDesktop AlignFrame newBottomFrame = new AlignFrame(bottomPanel); newBottomFrame.setSize(oldBottomFrame.getSize()); newBottomFrame.setVisible(true); - geometry = ((AlignViewport) bottomPanel.getAlignViewport()).getExplodedGeometry(); - if (geometry != null) { + geometry = ((AlignViewport) bottomPanel.getAlignViewport()) + .getExplodedGeometry(); + if (geometry != null) + { newBottomFrame.setSize(geometry.getSize()); } topPanel.av.setGatherViewsHere(false); bottomPanel.av.setGatherViewsHere(false); - JInternalFrame splitFrame = new SplitFrame(newTopFrame, newBottomFrame); - if (geometry != null) { + JInternalFrame splitFrame = new SplitFrame(newTopFrame, + newBottomFrame); + if (geometry != null) + { splitFrame.setLocation(geometry.getLocation()); } - Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1); + addInternalFrame(splitFrame, sf.getTitle(), -1, -1); } /* - * Clear references to the panels (now relocated in the new SplitFrames) before - * closing the old SplitFrame. + * Clear references to the panels (now relocated in the new SplitFrames) + * before closing the old SplitFrame. */ topPanels.clear(); bottomPanels.clear(); @@ -2532,7 +3070,8 @@ public class Desktop extends jalview.jbgui.GDesktop * * @param source */ - public void gatherViews(GSplitFrame source) { + public void gatherViews(GSplitFrame source) + { /* * special handling of explodedGeometry for a view within a SplitFrame: - it * holds the (x, y) position of the enclosing SplitFrame, and the (width, @@ -2540,38 +3079,46 @@ public class Desktop extends jalview.jbgui.GDesktop */ AlignFrame myTopFrame = (AlignFrame) source.getTopFrame(); AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame(); - myTopFrame.viewport.setExplodedGeometry( - new Rectangle(source.getX(), source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight())); - myBottomFrame.viewport.setExplodedGeometry( - new Rectangle(source.getX(), source.getY(), myBottomFrame.getWidth(), myBottomFrame.getHeight())); + myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(), + source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight())); + myBottomFrame.viewport + .setExplodedGeometry(new Rectangle(source.getX(), source.getY(), + myBottomFrame.getWidth(), myBottomFrame.getHeight())); myTopFrame.viewport.setGatherViewsHere(true); myBottomFrame.viewport.setGatherViewsHere(true); String topViewId = myTopFrame.viewport.getSequenceSetId(); String bottomViewId = myBottomFrame.viewport.getSequenceSetId(); - JInternalFrame[] frames = desktop.getAllFrames(); - for (JInternalFrame frame : frames) { - if (frame instanceof SplitFrame && frame != source) { + JInternalFrame[] frames = desktopPane.getAllFrames(); + for (JInternalFrame frame : frames) + { + if (frame instanceof SplitFrame && frame != source) + { SplitFrame sf = (SplitFrame) frame; AlignFrame topFrame = (AlignFrame) sf.getTopFrame(); AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame(); boolean gatherThis = false; - for (int a = 0; a < topFrame.alignPanels.size(); a++) { + for (int a = 0; a < topFrame.alignPanels.size(); a++) + { AlignmentPanel topPanel = topFrame.alignPanels.get(a); AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a); if (topViewId.equals(topPanel.av.getSequenceSetId()) - && bottomViewId.equals(bottomPanel.av.getSequenceSetId())) { + && bottomViewId.equals(bottomPanel.av.getSequenceSetId())) + { gatherThis = true; topPanel.av.setGatherViewsHere(false); bottomPanel.av.setGatherViewsHere(false); - topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), topFrame.getSize())); - bottomPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), bottomFrame.getSize())); + topPanel.av.setExplodedGeometry( + new Rectangle(sf.getLocation(), topFrame.getSize())); + bottomPanel.av.setExplodedGeometry( + new Rectangle(sf.getLocation(), bottomFrame.getSize())); myTopFrame.addAlignmentPanel(topPanel, false); myBottomFrame.addAlignmentPanel(bottomPanel, false); } } - if (gatherThis) { + if (gatherThis) + { topFrame.getAlignPanels().clear(); bottomFrame.getAlignPanels().clear(); sf.close(); @@ -2585,7 +3132,8 @@ public class Desktop extends jalview.jbgui.GDesktop myTopFrame.setDisplayedView(myTopFrame.alignPanel); } - public static groovy.ui.Console getGroovyConsole() { + public static groovy.ui.Console getGroovyConsole() + { return groovyConsole; } @@ -2594,88 +3142,148 @@ public class Desktop extends jalview.jbgui.GDesktop * * TODO refactor to desktop utilities class * - * @param files - Data source strings extracted from the drop event - * @param protocols - protocol for each data source extracted from the drop - * event - * @param evt - the drop event - * @param t - the payload from the drop event + * @param files + * - Data source strings extracted from the drop event + * @param protocols + * - protocol for each data source extracted from the drop event + * @param evt + * - the drop event + * @param t + * - the payload from the drop event * @throws Exception */ - public static void transferFromDropTarget(List files, List protocols, DropTargetDropEvent evt, - Transferable t) throws Exception { - - DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String"), urlFlavour = null; - try { - urlFlavour = new DataFlavor("application/x-java-url; class=java.net.URL"); - } catch (ClassNotFoundException cfe) { + @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 + { + 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)) { + if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) + { - try { + try + { java.net.URL url = (URL) t.getTransferData(urlFlavour); // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099 // means url may be null. - if (url != null) { + if (url != null) + { protocols.add(DataSourceType.URL); files.add(url.toString()); - Cache.log.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1)); + Cache.log.debug("Drop handled as URL dataflavor " + + files.get(files.size() - 1)); return; - } else { - if (Platform.isAMacAndNotJS()) { - System.err.println("Please ignore plist error - occurs due to problem with java 8 on OSX"); + } + else + { + if (Platform.isAMacAndNotJS()) + { + System.err.println( + "Please ignore plist error - occurs due to problem with java 8 on OSX"); } } - } catch (Throwable ex) { + } catch (Throwable ex) + { Cache.log.debug("URL drop handler failed.", ex); } } - if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) { + if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) + { // Works on Windows and MacOSX Cache.log.debug("Drop handled as javaFileListFlavor"); - for (Object file : (List) t.getTransferData(DataFlavor.javaFileListFlavor)) { + for (File file : (List) t + .getTransferData(DataFlavor.javaFileListFlavor)) + { files.add(file); protocols.add(DataSourceType.FILE); } - } else { + } + else + { // Unix like behaviour boolean added = false; String data = null; - if (t.isDataFlavorSupported(uriListFlavor)) { + if (t.isDataFlavorSupported(uriListFlavor)) + { Cache.log.debug("Drop handled as uriListFlavor"); // This is used by Unix drag system data = (String) t.getTransferData(uriListFlavor); } - if (data == null) { + if (data == null) + { // fallback to text: workaround - on OSX where there's a JVM bug Cache.log.debug("standard URIListFlavor failed. Trying text"); // try text fallback - DataFlavor textDf = new DataFlavor("text/plain;class=java.lang.String"); - if (t.isDataFlavorSupported(textDf)) { + DataFlavor textDf = new DataFlavor( + "text/plain;class=java.lang.String"); + if (t.isDataFlavorSupported(textDf)) + { data = (String) t.getTransferData(textDf); } - Cache.log.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data)); + Cache.log.debug("Plain text drop content returned " + + (data == null ? "Null - failed" : data)); } - if (data != null) { - while (protocols.size() < files.size()) { - Cache.log.debug("Adding missing FILE protocol for " + files.get(protocols.size())); + if (data != null) + { + while (protocols.size() < files.size()) + { + 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();) { + for (java.util.StringTokenizer st = new java.util.StringTokenizer( + data, "\r\n"); st.hasMoreTokens();) + { added = true; String s = st.nextToken(); - if (s.startsWith("#")) { + if (s.startsWith("#")) + { // the line is a comment (as per the RFC 2483) continue; } java.net.URI uri = new java.net.URI(s); - if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http")) { + if (uri.getScheme().toLowerCase().startsWith("http")) + { protocols.add(DataSourceType.URL); files.add(uri.toString()); - } else { + } + else + { // otherwise preserve old behaviour: catch all for file objects java.io.File file = new java.io.File(uri); protocols.add(DataSourceType.FILE); @@ -2684,46 +3292,69 @@ public class Desktop extends jalview.jbgui.GDesktop } } - if (Cache.log.isDebugEnabled()) { - if (data == null || !added) { + if (Cache.log.isDebugEnabled()) + { + if (data == null || !added) + { - if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) { - Cache.log.debug("Couldn't resolve drop data. Here are the supported flavors:"); - for (DataFlavor fl : t.getTransferDataFlavors()) { - Cache.log.debug("Supported transfer dataflavor: " + fl.toString()); + if (t.getTransferDataFlavors() != null + && t.getTransferDataFlavors().length > 0) + { + Cache.log.debug( + "Couldn't resolve drop data. Here are the supported flavors:"); + for (DataFlavor fl : t.getTransferDataFlavors()) + { + Cache.log.debug( + "Supported transfer dataflavor: " + fl.toString()); Object df = t.getTransferData(fl); - if (df != null) { + if (df != null) + { Cache.log.debug("Retrieves: " + df); - } else { + } + else + { Cache.log.debug("Retrieved nothing"); } } - } else { - Cache.log.debug("Couldn't resolve dataflavor for drop: " + t.toString()); + } + else + { + Cache.log.debug("Couldn't resolve dataflavor for drop: " + + t.toString()); } } } } - if (Platform.isWindowsAndNotJS()) { + 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++) { - String source = files.get(f).toString().toLowerCase(Locale.ROOT); + 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 { + && (source.endsWith(".lnk") || source.endsWith(".url") + || source.endsWith(".site"))) + { + try + { Object obj = files.get(f); - File lf = (obj instanceof File ? (File) obj : new File((String) obj)); + File lf = (obj instanceof File ? (File) obj + : new File((String) obj)); // process link file to get a URL Cache.log.debug("Found potential link file: " + lf); 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); + 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); } } } @@ -2735,30 +3366,40 @@ public class Desktop extends jalview.jbgui.GDesktop * depending on the state of the controlling menu item */ @Override - protected void showExperimental_actionPerformed(boolean selected) { + protected void showExperimental_actionPerformed(boolean selected) + { Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected)); } /** - * 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 - * @param structureViewerClass if not null, only return viewers of this class + * @param apanel + * if not null, only return viewers linked to this panel + * @param structureViewerClass + * if not null, only return viewers of this class * @return */ - public List getStructureViewers(AlignmentPanel apanel, - Class structureViewerClass) { + public List getStructureViewers( + AlignmentPanel apanel, + Class structureViewerClass) + { List result = new ArrayList<>(); - JInternalFrame[] frames = Desktop.instance.getAllFrames(); + JInternalFrame[] frames = getAllFrames(); - for (JInternalFrame frame : frames) { - if (frame instanceof StructureViewerBase) { - if (structureViewerClass == null || structureViewerClass.isInstance(frame)) { - if (apanel == null || ((StructureViewerBase) frame).isLinkedWith(apanel)) { + for (JInternalFrame frame : frames) + { + if (frame instanceof StructureViewerBase) + { + if (structureViewerClass == null + || structureViewerClass.isInstance(frame)) + { + if (apanel == null + || ((StructureViewerBase) frame).isLinkedWith(apanel)) + { result.add((StructureViewerBase) frame); } }