X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=8ba21e5a08bab761334ccb73b059b9a8f3e802c1;hb=e1767448d422ab26a6920bae2173804eda662e31;hp=cc9daa13eaa100f338c3dd8fb8bb6c1b72f62443;hpb=6dd554fdbf34db6b79595d5027159d20225f4894;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index cc9daa1..8ba21e5 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -23,6 +23,7 @@ package jalview.gui; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.IdentifyFile; @@ -33,6 +34,7 @@ import jalview.jbgui.GStructureViewer; import jalview.structure.StructureSelectionManager; import jalview.util.ImageMaker; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.ParamManager; @@ -167,8 +169,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements static final int yOffset = 30; - private static final int THREE = 3; - private static AlignFrame currentAlignFrame; public static jalview.ws.jws1.Discoverer discoverer; @@ -189,6 +189,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements this.delegate = delegate; } + @Override public void activateFrame(JInternalFrame f) { try @@ -201,31 +202,37 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void beginDraggingFrame(JComponent f) { delegate.beginDraggingFrame(f); } + @Override public void beginResizingFrame(JComponent f, int direction) { delegate.beginResizingFrame(f, direction); } + @Override public void closeFrame(JInternalFrame f) { delegate.closeFrame(f); } + @Override public void deactivateFrame(JInternalFrame f) { delegate.deactivateFrame(f); } + @Override public void deiconifyFrame(JInternalFrame f) { delegate.deiconifyFrame(f); } + @Override public void dragFrame(JComponent f, int newX, int newY) { if (newY < 0) @@ -235,40 +242,46 @@ public class Desktop extends jalview.jbgui.GDesktop implements delegate.dragFrame(f, newX, newY); } + @Override public void endDraggingFrame(JComponent f) { delegate.endDraggingFrame(f); } + @Override public void endResizingFrame(JComponent f) { delegate.endResizingFrame(f); } + @Override public void iconifyFrame(JInternalFrame f) { delegate.iconifyFrame(f); } + @Override public void maximizeFrame(JInternalFrame f) { delegate.maximizeFrame(f); } + @Override public void minimizeFrame(JInternalFrame f) { delegate.minimizeFrame(f); } + @Override public void openFrame(JInternalFrame f) { delegate.openFrame(f); } + @Override public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { - Rectangle b = desktop.getBounds(); if (newY < 0) { newY = 0; @@ -276,6 +289,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements delegate.resizeFrame(f, newX, newY, newWidth, newHeight); } + @Override public void setBoundsForFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) { @@ -307,6 +321,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements boolean showjconsole = jalview.bin.Cache.getDefault( "SHOW_JAVA_CONSOLE", false); desktop = new MyDesktopPane(selmemusage); + if (Platform.isAMac()) + { + desktop.setDoubleBuffered(false); + } showMemusage.setSelected(selmemusage); desktop.setBackground(Color.white); getContentPane().setLayout(new BorderLayout()); @@ -352,6 +370,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements this.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent evt) { quit(); @@ -361,6 +380,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements MouseAdapter ma; this.addMouseListener(ma = new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { if (SwingUtilities.isRightMouseButton(evt)) @@ -393,6 +413,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements // Spawn a thread that shows the splashscreen SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { new SplashScreen(); @@ -404,10 +425,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements // takes to open it later on. new Thread(new Runnable() { + @Override public void run() { Cache.log.debug("Filechooser init thread started."); - JalviewFileChooser chooser = new JalviewFileChooser( + new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, jalview.io.AppletFormatAdapter.READABLE_FNAMES, @@ -471,6 +493,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); } + @Override protected void showNews_actionPerformed(ActionEvent e) { showNews(showNews.isSelected()); @@ -488,12 +511,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements @Override public void run() { - long instance = System.currentTimeMillis(); + long now = System.currentTimeMillis(); Desktop.instance.setProgressBar( - MessageManager.getString("status.refreshing_news"), - instance); + MessageManager.getString("status.refreshing_news"), now); jvnews.refreshNews(); - Desktop.instance.setProgressBar(null, instance); + Desktop.instance.setProgressBar(null, now); jvnews.showNews(); } }).start(); @@ -575,16 +597,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements // reselected again. boolean refresh = true; + @Override public void menuCanceled(MenuEvent e) { refresh = true; } + @Override public void menuDeselected(MenuEvent e) { refresh = true; } + @Override public void menuSelected(MenuEvent e) { if (refresh) @@ -605,6 +630,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements MessageManager.getString("label.paste_new_window")); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { paste(); @@ -752,8 +778,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements frame.setResizable(resizable); frame.setMaximizable(resizable); frame.setIconifiable(resizable); - frame.setFrameIcon(null); - + if (Platform.isAMac()) + { + frame.setIconifiable(false); + frame.setFrameIcon(null); + // frame.setDesktopIcon(null); + frame.setDoubleBuffered(false); + } if (frame.getX() < 1 && frame.getY() < 1) { frame.setLocation(xOffset * openFrameCount, yOffset @@ -763,6 +794,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements final JMenuItem menuItem = new JMenuItem(title); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameActivated( javax.swing.event.InternalFrameEvent evt) { @@ -774,6 +806,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -791,6 +824,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { try @@ -863,6 +897,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void lostOwnership(Clipboard clipboard, Transferable contents) { if (!internalCopy) @@ -873,18 +908,22 @@ public class Desktop extends jalview.jbgui.GDesktop implements internalCopy = false; } + @Override public void dragEnter(DropTargetDragEvent evt) { } + @Override public void dragExit(DropTargetEvent evt) { } + @Override public void dragOver(DropTargetDragEvent evt) { } + @Override public void dropActionChanged(DropTargetDragEvent evt) { } @@ -895,6 +934,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param evt * DOCUMENT ME! */ + @Override public void drop(DropTargetDropEvent evt) { boolean success = true; @@ -988,6 +1028,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -1045,6 +1086,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void inputURLMenuItem_actionPerformed(AlignViewport viewport) { // This construct allows us to have a wider textfield @@ -1105,8 +1147,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage("label.couldnt_locate", - new Object[] - { url }), MessageManager + new Object[] { url }), MessageManager .getString("label.url_not_found"), JOptionPane.WARNING_MESSAGE); @@ -1125,15 +1166,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * DOCUMENT ME! + * Opens the CutAndPaste window for the user to paste an alignment in to * - * @param e - * DOCUMENT ME! + * @param viewPanel + * - if not null, the pasted alignment is added to the current + * alignment; if null, to a new alignment window */ - public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport) + @Override + public void inputTextboxMenuItem_actionPerformed( + AlignmentViewPanel viewPanel) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(viewport.getAlignPanel()); + cap.setForInput(viewPanel); Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), true, 600, 500); @@ -1142,6 +1186,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /* * Exit the program */ + @Override public void quit() { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); @@ -1188,6 +1233,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void aboutMenuItem_actionPerformed(ActionEvent e) { // StringBuffer message = getAboutMessage(false); @@ -1196,6 +1242,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); new Thread(new Runnable() { + @Override public void run() { new SplashScreen(true); @@ -1274,6 +1321,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void documentationMenuItem_actionPerformed(ActionEvent e) { try @@ -1284,6 +1332,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void closeAll_actionPerformed(ActionEvent e) { JInternalFrame[] frames = desktop.getAllFrames(); @@ -1300,15 +1349,27 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (v_client != null) { // TODO clear binding to vamsas document objects on close_all + } + /* + * reset state of singleton objects as appropriate (clear down session state + * when all windows are closed) + */ + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(this); + if (ssm != null) + { + ssm.resetAll(); } } + @Override public void raiseRelated_actionPerformed(ActionEvent e) { reorderAssociatedWindows(false, false); } + @Override public void minimizeAssociated_actionPerformed(ActionEvent e) { reorderAssociatedWindows(true, false); @@ -1325,6 +1386,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event. * ActionEvent) */ + @Override protected void garbageCollect_actionPerformed(ActionEvent e) { // We simply collect the garbage @@ -1340,6 +1402,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void showMemusage_actionPerformed(ActionEvent e) { desktop.showMemoryUsage(showMemusage.isSelected()); @@ -1352,6 +1415,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void showConsole_actionPerformed(ActionEvent e) { showConsole(showConsole.isSelected()); @@ -1456,6 +1520,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override protected void preferences_actionPerformed(ActionEvent e) { new Preferences(); @@ -1467,12 +1532,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void saveState_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jvp" }, new String[] - { "Jalview Project" }, "Jalview Project"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), + new String[] { "jvp" }, new String[] { "Jalview Project" }, + "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.save_state")); @@ -1487,12 +1553,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements new Thread(new Runnable() { + @Override public void run() { - + // TODO: refactor to Jalview desktop session controller action. setProgressBar(MessageManager.formatMessage( - "label.saving_jalview_project", new Object[] - { choice.getName() }), choice.hashCode()); + "label.saving_jalview_project", + new Object[] { choice.getName() }), choice.hashCode()); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); // TODO catch and handle errors for savestate @@ -1511,8 +1578,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements ex); JOptionPane.showMessageDialog(me, MessageManager.formatMessage( "label.error_whilst_saving_current_state_to", - new Object[] - { choice.getName() }), MessageManager + new Object[] { choice.getName() }), MessageManager .getString("label.couldnt_save_project"), JOptionPane.WARNING_MESSAGE); } @@ -1538,13 +1604,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void loadState_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] - { "jvp", "jar" }, new String[] - { "Jalview Project", "Jalview Project (old)" }, - "Jalview Project"); + jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { + "jvp", "jar" }, new String[] { "Jalview Project", + "Jalview Project (old)" }, "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); @@ -1559,11 +1625,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements selectedFile.getParent()); new Thread(new Runnable() { + @Override public void run() { - setProgressBar(MessageManager.formatMessage( - "label.loading_jalview_project", new Object[] - { choice }), choice.hashCode()); + setProgressBar( + MessageManager.formatMessage( + "label.loading_jalview_project", + new Object[] { choice }), choice.hashCode()); try { new Jalview2XML().loadJalviewAlign(choice); @@ -1577,8 +1645,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage( "label.error_whilst_loading_project_from", - new Object[] - { choice }), MessageManager + new Object[] { choice }), MessageManager .getString("label.couldnt_load_project"), JOptionPane.WARNING_MESSAGE); } @@ -1588,6 +1655,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void inputSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); @@ -1602,8 +1670,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (fileLoadingCount == 0) { fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage( - "label.loading_file", new Object[] - { fileName }))); + "label.loading_file", new Object[] { fileName }))); } fileLoadingCount++; } @@ -1697,7 +1764,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { for (AlignmentPanel ap : af.alignPanels) { - if (alignmentId==null || alignmentId.equals(ap.av.getSequenceSetId())) + if (alignmentId == null + || alignmentId.equals(ap.av.getSequenceSetId())) { aps.add(ap); } @@ -1728,7 +1796,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements for (AlignFrame afr : frames) { - if (sequenceSetId==null || afr.getViewport().getSequenceSetId().equals(sequenceSetId)) + if (sequenceSetId == null + || afr.getViewport().getSequenceSetId() + .equals(sequenceSetId)) { if (afr.alignPanels != null) { @@ -1840,6 +1910,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements jalview.gui.VamsasApplication v_client = null; + @Override public void vamsasImport_actionPerformed(ActionEvent e) { if (v_client == null) @@ -1866,8 +1937,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements Desktop.desktop, MessageManager.formatMessage( "label.couldnt_import_as_vamsas_session", - new Object[] - { fle }), + new Object[] { fle }), MessageManager .getString("label.vamsas_document_import_failed"), JOptionPane.ERROR_MESSAGE); @@ -1944,16 +2014,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements } setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", + new Object[] { file.getName() }), file.hashCode()); try { v_client = new jalview.gui.VamsasApplication(this, file, null); } catch (Exception ex) { setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", + new Object[] { file.getName() }), file.hashCode()); jalview.bin.Cache.log.error( "New vamsas session from existing session file failed:", ex); return false; @@ -1961,8 +2031,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements setupVamsasConnectedGui(); v_client.initial_update(); // TODO: thread ? setProgressBar(MessageManager.formatMessage( - "status.importing_vamsas_session_from", new Object[] - { file.getName() }), file.hashCode()); + "status.importing_vamsas_session_from", + new Object[] { file.getName() }), file.hashCode()); return v_client.inSession(); } @@ -1985,6 +2055,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements return (v_client.inSession()); } + @Override public void vamsasStart_actionPerformed(ActionEvent e) { if (v_client == null) @@ -2033,6 +2104,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements .getString("label.new_vamsas_session")); } + @Override public void vamsasStop_actionPerformed(ActionEvent e) { if (v_client != null) @@ -2067,13 +2139,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements JMenuItem sessit = new JMenuItem(); sessit.setText(sess[i]); sessit.setToolTipText(MessageManager.formatMessage( - "label.connect_to_session", new Object[] - { sess[i] })); + "label.connect_to_session", new Object[] { sess[i] })); final Desktop dsktp = this; final String mysesid = sess[i]; sessit.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { if (dsktp.v_client == null) @@ -2081,6 +2153,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements Thread rthr = new Thread(new Runnable() { + @Override public void run() { dsktp.v_client = new VamsasApplication(dsktp, mysesid); @@ -2113,6 +2186,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void vamsasSave_actionPerformed(ActionEvent e) { if (v_client != null) @@ -2120,8 +2194,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ - new String[] - { "Vamsas Document" }, "Vamsas Document"); + new String[] { "Vamsas Document" }, "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -2133,8 +2206,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { java.io.File choice = chooser.getSelectedFile(); JPanel progpanel = addProgressPanel(MessageManager.formatMessage( - "label.saving_vamsas_doc", new Object[] - { choice.getName() })); + "label.saving_vamsas_doc", + new Object[] { choice.getName() })); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); String warnmsg = null; String warnttl = null; @@ -2238,10 +2311,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements showMemoryUsage(showMemoryUsage); } - public void showMemoryUsage(boolean showMemoryUsage) + public void showMemoryUsage(boolean showMemory) { - this.showMemoryUsage = showMemoryUsage; - if (showMemoryUsage) + this.showMemoryUsage = showMemory; + if (showMemory) { Thread worker = new Thread(this); worker.start(); @@ -2253,6 +2326,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements return showMemoryUsage; } + @Override public void run() { df = java.text.NumberFormat.getNumberInstance(); @@ -2286,6 +2360,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void paintComponent(Graphics g) { if (showMemoryUsage && g != null && df != null) @@ -2299,9 +2374,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { g.drawString(MessageManager.formatMessage( "label.memory_stats", - new Object[] - { df.format(totalFreeMemory), df.format(maxMemory), - df.format(percentUsage) }), 10, + new Object[] { df.format(totalFreeMemory), + df.format(maxMemory), df.format(percentUsage) }), 10, getHeight() - fm.getHeight()); } } @@ -2327,9 +2401,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements groovyShell.setText(MessageManager.getString("label.groovy_console")); groovyShell.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { - groovyShell_actionPerformed(e); + groovyShell_actionPerformed(); } }); toolsMenu.add(groovyShell); @@ -2344,6 +2419,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public static AlignFrame[] getAlignFrames() { + if (Jalview.isHeadlessMode()) + { + // Desktop.desktop is null in headless mode + return new AlignFrame[] { currentAlignFrame }; + } + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) @@ -2416,7 +2497,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /** * Add Groovy Support to Jalview */ - public void groovyShell_actionPerformed(ActionEvent e) + public void groovyShell_actionPerformed() { // use reflection to avoid creating compilation dependency. if (!jalview.bin.Cache.groovyJarsPresent()) @@ -2431,12 +2512,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements "groovy.ui.Console"); Constructor gccons = gcClass.getConstructor(); java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", - new Class[] - { String.class, Object.class }); + new Class[] { String.class, Object.class }); java.lang.reflect.Method run = gcClass.getMethod("run"); Object gc = gccons.newInstance(); - setvar.invoke(gc, new Object[] - { "Jalview", this }); + setvar.invoke(gc, new Object[] { "Jalview", this }); run.invoke(gc); } catch (Exception ex) { @@ -2461,6 +2540,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ + @Override public void setProgressBar(String message, long id) { if (progressBars == null) @@ -2471,12 +2551,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (progressBars.get(new Long(id)) != null) { - JPanel progressPanel = progressBars.remove(new Long(id)); + JPanel panel = progressBars.remove(new Long(id)); if (progressBarHandlers.contains(new Long(id))) { progressBarHandlers.remove(new Long(id)); } - removeProgressPanel(progressPanel); + removeProgressPanel(panel); } else { @@ -2490,6 +2570,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @see jalview.gui.IProgressIndicator#registerHandler(long, * jalview.gui.IProgressIndicatorHandler) */ + @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { @@ -2510,13 +2591,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); us.setProgressBar(MessageManager.formatMessage( - "label.cancelled_params", new Object[] - { ((JLabel) progressPanel.getComponent(0)).getText() }), - id); + "label.cancelled_params", + new Object[] { ((JLabel) progressPanel.getComponent(0)) + .getText() }), id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -2538,8 +2620,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * This will return the first AlignFrame holding the given viewport instance. It - * will break if there are more than one AlignFrames viewing a particular av. + * This will return the first AlignFrame holding the given viewport instance. + * It will break if there are more than one AlignFrames viewing a particular + * av. * * @param viewport * @return alignFrame for viewport @@ -2548,8 +2631,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (desktop != null) { - AlignmentPanel[] aps = getAlignmentPanels(viewport - .getSequenceSetId()); + AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId()); for (int panel = 0; aps != null && panel < aps.length; panel++) { if (aps[panel] != null && aps[panel].av == viewport) @@ -2616,28 +2698,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements (t0 = new Thread(discoverer)).start(); } - // ENFIN services are EOLed as of Jalview 2.8.1 release - if (false) - { - try - { - if (Cache.getDefault("SHOW_ENFIN_SERVICES", true)) - { - // EnfinEnvision web service menu entries are rebuild every time the - // menu is shown, so no changeSupport events are needed. - jalview.ws.EnfinEnvision2OneWay.getInstance(); - (t1 = new Thread(jalview.ws.EnfinEnvision2OneWay.getInstance())) - .start(); - } - } catch (Exception e) - { - Cache.log - .info("Exception when trying to launch Envision2 workflow discovery.", - e); - Cache.log.info(e.getStackTrace()); - } - } - if (Cache.getDefault("SHOW_JWS2_SERVICES", true)) { if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning()) @@ -2690,6 +2750,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements // only run if we aren't already displaying one of these. addDialogThread(serviceChangedDialog = new Runnable() { + @Override public void run() { @@ -2773,6 +2834,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { new Thread(new Runnable() { + @Override public void run() { try @@ -2780,8 +2842,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (progress != null) { progress.setProgressBar(MessageManager.formatMessage( - "status.opening_params", new Object[] - { url }), this.hashCode()); + "status.opening_params", new Object[] { url }), this + .hashCode()); } jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) @@ -2871,6 +2933,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { dialogExecutor.submit(new Runnable() { + @Override public void run() { if (dialogPause) @@ -2914,7 +2977,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(), getHeight(), of = new File( "Jalview_snapshot" + System.currentTimeMillis() - + ".eps"), "View of desktop"); + + ".eps"), "View of desktop", null, 0, false); try { paintAll(im.getGraphics()); @@ -2930,7 +2993,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } /** - * Explode the views in the given frame into separate AlignFrame windows. + * 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 + * remember the split pane divider location - this is set to match the + * 'exploding' frame. * * @param sf */ @@ -2959,27 +3026,39 @@ public class Desktop extends jalview.jbgui.GDesktop implements * 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 */ AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i); AlignFrame newTopFrame = new AlignFrame(topPanel); - newTopFrame.setSize(new Dimension(AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT)); + newTopFrame.setSize(oldTopFrame.getSize()); newTopFrame.setVisible(true); + Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()) + .getExplodedGeometry(); + if (geometry != null) + { + newTopFrame.setSize(geometry.getSize()); + } + AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i); AlignFrame newBottomFrame = new AlignFrame(bottomPanel); - newBottomFrame.setSize(new Dimension(AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT)); + newBottomFrame.setSize(oldBottomFrame.getSize()); newBottomFrame.setVisible(true); + 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); - // either panel may hold previous exploded frame geometry - Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()) - .getExplodedGeometry(); if (geometry != null) { - splitFrame.setBounds(geometry); + splitFrame.setLocation(geometry.getLocation()); } Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1); } @@ -3002,15 +3081,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ 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, + * height) of the AlignFrame component + */ AlignFrame myTopFrame = (AlignFrame) source.getTopFrame(); AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame(); - myTopFrame.viewport.setExplodedGeometry(source.getBounds()); - myBottomFrame.viewport.setExplodedGeometry(source.getBounds()); + 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) { @@ -3030,15 +3117,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements gatherThis = true; topPanel.av.setGatherViewsHere(false); bottomPanel.av.setGatherViewsHere(false); - // both panels refer to the same split frame geometry - Rectangle position = sf.getBounds(); - topPanel.av.setExplodedGeometry(position); - bottomPanel.av.setExplodedGeometry(position); + 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) { topFrame.getAlignPanels().clear(); @@ -3055,15 +3142,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements } - // public static AlignFrame getCurrentAlignFrame() - // { - // return currentAlignFrame; - // } - // - // public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) - // { - // Desktop.currentAlignFrame = currentAlignFrame; - // } + public static AlignFrame getCurrentAlignFrame() + { + return currentAlignFrame; + } + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + { + Desktop.currentAlignFrame = currentAlignFrame; + } }