X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=03216624900fba740606837d8ca38241f04817ee;hb=8b844f70b97629d597be49cb6ac0d83c8da007c9;hp=e8d7ffd5975f644aa278af0640b5c5f047831a01;hpb=9194c4500128ee9d624c9a185770093c8620696a;p=jalview.git diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index e8d7ffd..0321662 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,6 +20,31 @@ */ package jalview.gui; +import static jalview.util.UrlConstants.EMBLEBI_STRING; +import static jalview.util.UrlConstants.SEQUENCE_ID; + +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.bin.Jalview; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatException; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; +import jalview.io.FileLoader; +import jalview.io.IdentifyFile; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.jbgui.GSplitFrame; +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; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -29,6 +54,7 @@ import java.awt.GridLayout; import java.awt.Point; import java.awt.Rectangle; import java.awt.Toolkit; +import java.awt.Window; import java.awt.datatransfer.Clipboard; import java.awt.datatransfer.ClipboardOwner; import java.awt.datatransfer.DataFlavor; @@ -42,31 +68,34 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusEvent; import java.awt.event.FocusListener; +import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; -import java.awt.event.MouseListener; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; -import java.beans.PropertyVetoException; import java.io.BufferedInputStream; import java.io.File; import java.io.FileOutputStream; -import java.lang.reflect.Constructor; import java.net.URL; import java.util.ArrayList; import java.util.Hashtable; import java.util.List; +import java.util.ListIterator; import java.util.StringTokenizer; import java.util.Vector; import java.util.concurrent.ExecutorService; import java.util.concurrent.Executors; import java.util.concurrent.Semaphore; +import javax.swing.AbstractAction; +import javax.swing.Box; +import javax.swing.BoxLayout; import javax.swing.DefaultDesktopManager; import javax.swing.DesktopManager; import javax.swing.JButton; +import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JComponent; import javax.swing.JDesktopPane; @@ -74,32 +103,18 @@ import javax.swing.JFrame; import javax.swing.JInternalFrame; import javax.swing.JLabel; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JProgressBar; +import javax.swing.KeyStroke; import javax.swing.SwingUtilities; import javax.swing.event.HyperlinkEvent; import javax.swing.event.HyperlinkEvent.EventType; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.io.FileLoader; -import jalview.io.FormatAdapter; -import jalview.io.IdentifyFile; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GSplitFrame; -import jalview.jbgui.GStructureViewer; -import jalview.structure.StructureSelectionManager; -import jalview.util.ImageMaker; -import jalview.util.MessageManager; -import jalview.viewmodel.AlignmentViewport; -import jalview.ws.params.ParamManager; - /** * Jalview Desktop * @@ -167,10 +182,6 @@ 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; public static Object[] jalviewClipboard; @@ -189,6 +200,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements this.delegate = delegate; } + @Override public void activateFrame(JInternalFrame f) { try @@ -201,31 +213,37 @@ 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 +253,46 @@ 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 +300,7 @@ 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) { @@ -298,7 +323,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ instance = this; doVamsasClientCheck(); - doGroovyCheck(); + + groovyShell = new JMenuItem(); + groovyShell.setText(MessageManager.getString("label.groovy_console")); + groovyShell.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + groovyShell_actionPerformed(); + } + }); + toolsMenu.add(groovyShell); + groovyShell.setVisible(true); + doConfigureStructurePrefs(); setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION")); setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); @@ -307,6 +345,10 @@ 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()); @@ -350,8 +392,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements showNews.setVisible(false); + checkURLLinks(); + this.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent evt) { quit(); @@ -361,9 +406,19 @@ 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)) + if (evt.isPopupTrigger()) // Mac + { + showPasteMenu(evt.getX(), evt.getY()); + } + } + + @Override + public void mouseReleased(MouseEvent evt) + { + if (evt.isPopupTrigger()) // Windows { showPasteMenu(evt.getX(), evt.getY()); } @@ -393,25 +448,24 @@ 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(); } }); - // displayed. // 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."); - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, - jalview.io.AppletFormatAdapter.READABLE_FNAMES, - jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), + fileFormat); Cache.log.debug("Filechooser init thread finished."); } }).start(); @@ -471,6 +525,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); } + @Override protected void showNews_actionPerformed(ActionEvent e) { showNews(showNews.isSelected()); @@ -488,12 +543,11 @@ 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 +629,19 @@ 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 +662,7 @@ 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(); @@ -627,10 +685,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements String file = (String) contents .getTransferData(DataFlavor.stringFlavor); - String format = new IdentifyFile().Identify(file, - FormatAdapter.PASTE); + FileFormatI format = new IdentifyFile().identify(file, + DataSourceType.PASTE); - new FileLoader().LoadFile(file, FormatAdapter.PASTE, format); + new FileLoader().LoadFile(file, DataSourceType.PASTE, format); } } catch (Exception ex) @@ -752,38 +810,66 @@ 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 * ((openFrameCount - 1) % 10) + yOffset); } + /* + * 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 javax.swing.event.InternalFrameAdapter() + frame.addInternalFrameListener(new InternalFrameAdapter() { - public void internalFrameActivated( - javax.swing.event.InternalFrameEvent evt) + @Override + public void internalFrameActivated(InternalFrameEvent evt) { JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { itf.requestFocus(); } - } - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) + @Override + public void internalFrameClosed(InternalFrameEvent evt) { PaintRefresher.RemoveComponent(frame); - openFrameCount--; + + /* + * defensive check to prevent frames being + * added half off the window + */ + if (openFrameCount > 0) + { + openFrameCount--; + } + + /* + * ensure no reference to alignFrame retained by menu item listener + */ + if (menuItem.getActionListeners().length > 0) + { + menuItem.removeActionListener(menuItem.getActionListeners()[0]); + } windowMenu.remove(menuItem); JInternalFrame itf = desktop.getSelectedFrame(); if (itf != null) { itf.requestFocus(); + if (itf instanceof AlignFrame) + { + Jalview.setCurrentAlignFrame((AlignFrame) itf); + } } System.gc(); }; @@ -791,6 +877,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { try @@ -803,51 +890,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } }); - menuItem.addMouseListener(new MouseListener() - { - - @Override - public void mouseReleased(MouseEvent e) - { - } - - @Override - public void mousePressed(MouseEvent e) - { - } - - @Override - public void mouseExited(MouseEvent e) - { - try - { - frame.setSelected(false); - } catch (PropertyVetoException e1) - { - } - } - - @Override - public void mouseEntered(MouseEvent e) - { - try - { - frame.setSelected(true); - } catch (PropertyVetoException e1) - { - } - } - @Override - public void mouseClicked(MouseEvent e) - { - - } - }); + desktop.add(frame); windowMenu.add(menuItem); - desktop.add(frame); frame.toFront(); try { @@ -863,6 +910,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void lostOwnership(Clipboard clipboard, Transferable contents) { if (!internalCopy) @@ -873,18 +921,22 @@ 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) { } @@ -895,57 +947,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param evt * DOCUMENT ME! */ + @Override public void drop(DropTargetDropEvent evt) { boolean success = true; + // JAL-1552 - acceptDrop required before getTransferable call for + // Java's Transferable for native dnd + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - java.util.List files = null; - java.util.List protocols = null; + List files = new ArrayList(); + List protocols = new ArrayList(); try { - DataFlavor uriListFlavor = new DataFlavor( - "text/uri-list;class=java.lang.String"); - if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) - { - // Works on Windows and MacOSX - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - files = (java.util.List) t - .getTransferData(DataFlavor.javaFileListFlavor); - } - else if (t.isDataFlavorSupported(uriListFlavor)) - { - // This is used by Unix drag system - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - String data = (String) t.getTransferData(uriListFlavor); - files = new java.util.ArrayList(1); - protocols = new java.util.ArrayList(1); - for (java.util.StringTokenizer st = new java.util.StringTokenizer( - data, "\r\n"); st.hasMoreTokens();) - { - String s = st.nextToken(); - if (s.startsWith("#")) - { - // the line is a comment (as per the RFC 2483) - continue; - } - java.net.URI uri = new java.net.URI(s); - if (uri.getScheme().toLowerCase().startsWith("http")) - { - protocols.add(FormatAdapter.URL); - files.add(uri.toString()); - } - else - { - // otherwise preserve old behaviour: catch all for file objects - java.io.File file = new java.io.File(uri); - protocols.add(FormatAdapter.FILE); - files.add(file.toString()); - } - } - } + Desktop.transferFromDropTarget(files, protocols, evt, t); } catch (Exception e) { + e.printStackTrace(); success = false; } @@ -956,18 +974,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements for (int i = 0; i < files.size(); i++) { String file = files.get(i).toString(); - String protocol = (protocols == null) ? FormatAdapter.FILE - : (String) protocols.get(i); - String format = null; + DataSourceType protocol = (protocols == null) ? DataSourceType.FILE + : protocols.get(i); + FileFormatI format = null; if (file.endsWith(".jar")) { - format = "Jalview"; + format = FileFormat.Jalview; } else { - format = new IdentifyFile().Identify(file, protocol); + format = new IdentifyFile().identify(file, protocol); } new FileLoader().LoadFile(file, protocol, format); @@ -988,13 +1006,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS, - jalview.io.AppletFormatAdapter.READABLE_FNAMES, - jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); + String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT"); + JalviewFileChooser chooser = JalviewFileChooser.forRead( + Cache.getProperty("LAST_DIRECTORY"), fileFormat); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -1006,35 +1023,35 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (value == JalviewFileChooser.APPROVE_OPTION) { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser + Cache.setProperty("LAST_DIRECTORY", chooser .getSelectedFile().getParent()); - String format = null; - if (chooser.getSelectedFormat() != null - && chooser.getSelectedFormat().equals("Jalview")) - { - format = "Jalview"; - } - else + FileFormatI format = chooser.getSelectedFormat(); + + /* + * Call IdentifyFile to verify the file contains what its extension implies. + * Skip this step for dynamically added file formats, because + * IdentifyFile does not know how to recognise them. + */ + if (FileFormats.getInstance().isIdentifiable(format)) { - format = new IdentifyFile().Identify(choice, FormatAdapter.FILE); + try + { + format = new IdentifyFile().identify(choice, DataSourceType.FILE); + } catch (FileFormatException e) + { + // format = null; //?? + } } if (viewport != null) { - new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, + new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE, format); - // viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled()); - // AlignFrame af = viewport.getAlignPanel().alignFrame; - // if (af != null) - // { - // af.changeColour(JSONFile.getColourScheme()); - // af.setMenusForViewport(); - // } } else { - new FileLoader().LoadFile(choice, FormatAdapter.FILE, format); + new FileLoader().LoadFile(choice, DataSourceType.FILE, format); } } } @@ -1045,6 +1062,7 @@ 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 @@ -1074,11 +1092,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } - int reply = JOptionPane.showInternalConfirmDialog(desktop, panel, + int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel, MessageManager.getString("label.input_alignment_from_url"), - JOptionPane.OK_CANCEL_OPTION); + JvOptionPane.OK_CANCEL_OPTION); - if (reply != JOptionPane.OK_OPTION) + if (reply != JvOptionPane.OK_OPTION) { return; } @@ -1089,51 +1107,63 @@ public class Desktop extends jalview.jbgui.GDesktop implements { if (viewport != null) { - new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, - "Jalview"); + new FileLoader().LoadFile(viewport, url, DataSourceType.URL, + FileFormat.Jalview); } else { - new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview"); + new FileLoader().LoadFile(url, DataSourceType.URL, + FileFormat.Jalview); } } else { - String format = new IdentifyFile().Identify(url, FormatAdapter.URL); + FileFormatI format = null; + try + { + format = new IdentifyFile().identify(url, DataSourceType.URL); + } catch (FileFormatException e) + { + // TODO revise error handling, distinguish between + // URL not found and response not valid + } - if (format.equals("URL NOT FOUND")) + if (format == null) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage("label.couldnt_locate", - new Object[] - { url }), MessageManager + new Object[] { url }), MessageManager .getString("label.url_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } if (viewport != null) { - new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format); + new FileLoader() + .LoadFile(viewport, url, DataSourceType.URL, format); } else { - new FileLoader().LoadFile(url, FormatAdapter.URL, format); + new FileLoader().LoadFile(url, DataSourceType.URL, format); } } } /** - * 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); + cap.setForInput(viewPanel); Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), true, 600, 500); @@ -1142,6 +1172,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements /* * Exit the program */ + @Override public void quit() { Dimension screen = Toolkit.getDefaultToolkit().getScreenSize(); @@ -1167,6 +1198,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements dialogExecutor.shutdownNow(); } closeAll_actionPerformed(null); + + if (groovyConsole != null) + { + // suppress a possible repeat prompt to save script + groovyConsole.setDirty(false); + groovyConsole.exit(); + } System.exit(0); } @@ -1188,14 +1226,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void aboutMenuItem_actionPerformed(ActionEvent e) { // StringBuffer message = getAboutMessage(false); - // JOptionPane.showInternalMessageDialog(Desktop.desktop, + // JvOptionPane.showInternalMessageDialog(Desktop.desktop, // - // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); + // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE); new Thread(new Runnable() { + @Override public void run() { new SplashScreen(true); @@ -1274,6 +1314,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override public void documentationMenuItem_actionPerformed(ActionEvent e) { try @@ -1284,8 +1325,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override 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++) { @@ -1296,19 +1339,33 @@ public class Desktop extends jalview.jbgui.GDesktop implements { } } + Jalview.setCurrentAlignFrame(null); System.out.println("ALL CLOSED"); 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(); } + System.gc(); } + @Override public void raiseRelated_actionPerformed(ActionEvent e) { reorderAssociatedWindows(false, false); } + @Override public void minimizeAssociated_actionPerformed(ActionEvent e) { reorderAssociatedWindows(true, false); @@ -1325,6 +1382,7 @@ 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 +1398,7 @@ 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 +1411,7 @@ 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 +1516,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * @param e * DOCUMENT ME! */ + @Override protected void preferences_actionPerformed(ActionEvent e) { new Preferences(); @@ -1467,12 +1528,11 @@ 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"); + JalviewFileChooser chooser = new JalviewFileChooser("jvp", + "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.save_state")); @@ -1485,17 +1545,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements final java.io.File choice = chooser.getSelectedFile(); setProjectFile(choice); - // TODO or move inside the new Thread? - saveChimeraSessions(choice.getAbsolutePath()); - 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 @@ -1512,12 +1570,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.log.error( "Problems whilst trying to save to " + choice.getName(), ex); - JOptionPane.showMessageDialog(me, MessageManager.formatMessage( + JvOptionPane.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); + JvOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } @@ -1525,32 +1582,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } - /** - * Request any open, linked Chimera sessions to save their state. - * - * @param jalviewProjectFilename - * the filename of the Jalview project; Chimera session files should - * be given distinct, but obviously related, names. - */ - public void saveChimeraSessions(String jalviewProjectFilename) - { - int i = 0; - for (JInternalFrame frame : getAllFrames()) - { - if (frame instanceof ChimeraViewFrame) - { - /* - * Construct a filename for the Chimera session by append _chimera.py - * to the Jalview project file name. - */ - String chimeraPath = jalviewProjectFilename + "_chimera_" + i - + ".py"; - ((ChimeraViewFrame) frame).saveSession(chimeraPath); - i++; - } - } - } - private void setProjectFile(File choice) { this.projectFile = choice; @@ -1567,13 +1598,13 @@ 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"); + 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")); @@ -1584,15 +1615,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements final File selectedFile = chooser.getSelectedFile(); setProjectFile(selectedFile); final String choice = selectedFile.getAbsolutePath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", + Cache.setProperty("LAST_DIRECTORY", 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); @@ -1603,13 +1636,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements { Cache.log.error("Problems whilst loading project from " + choice, ex); - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.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); + JvOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } @@ -1617,6 +1649,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void inputSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); @@ -1631,8 +1664,7 @@ 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++; } @@ -1726,7 +1758,8 @@ 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); } @@ -1757,7 +1790,9 @@ 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) { @@ -1789,7 +1824,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * @param af */ - public void explodeViews(AlignFrame af) + public static void explodeViews(AlignFrame af) { int size = af.alignPanels.size(); if (size < 2) @@ -1869,6 +1904,7 @@ 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) @@ -1890,16 +1926,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { - JOptionPane + JvOptionPane .showInternalMessageDialog( 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); + JvOptionPane.ERROR_MESSAGE); } } } @@ -1973,16 +2008,16 @@ 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; @@ -1990,8 +2025,8 @@ 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(); } @@ -2014,6 +2049,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements return (v_client.inSession()); } + @Override public void vamsasStart_actionPerformed(ActionEvent e) { if (v_client == null) @@ -2062,6 +2098,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements .getString("label.new_vamsas_session")); } + @Override public void vamsasStop_actionPerformed(ActionEvent e) { if (v_client != null) @@ -2096,13 +2133,13 @@ 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) @@ -2110,6 +2147,7 @@ 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); @@ -2142,15 +2180,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void vamsasSave_actionPerformed(ActionEvent e) { if (v_client != null) { - 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"); + // TODO: VAMSAS DOCUMENT EXTENSION is VDJ + JalviewFileChooser chooser = new JalviewFileChooser("vdj", + "Vamsas Document"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -2162,9 +2199,9 @@ 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() })); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); + "label.saving_vamsas_doc", + new Object[] { choice.getName() })); + Cache.setProperty("LAST_DIRECTORY", choice.getParent()); String warnmsg = null; String warnttl = null; try @@ -2188,9 +2225,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements removeProgressPanel(progpanel); if (warnmsg != null) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, - warnmsg, warnttl, JOptionPane.ERROR_MESSAGE); + warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); } } } @@ -2206,7 +2243,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ public void setVamsasUpdate(boolean b) { - jalview.bin.Cache.log.debug("Setting gui for Vamsas update " + Cache.log.debug("Setting gui for Vamsas update " + (b ? "in progress" : "finished")); if (vamUpdate != null) @@ -2241,6 +2278,84 @@ public class Desktop extends jalview.jbgui.GDesktop implements new Thread(jvq).start(); } + public void checkURLLinks() + { + // Thread off the URL link checker + addDialogThread(new Runnable() + { + @Override + 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 + Vector links = Preferences.sequenceURLLinks; + + // 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()) + { + String link = li.next(); + if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING)) + { + check = true; + int barPos = link.indexOf("|"); + String urlMsg = barPos == -1 ? link : link.substring(0, + barPos) + ": " + link.substring(barPos + 1); + urls.add(new JLabel(urlMsg)); + } + } + if (!check) + { + return; + } + + // ask user to check in case URL links use old style tokens + // ($SEQUENCE_ID$ for sequence id _or_ accession id) + 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")); + msgPanel.add(msg); + 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() + { + @Override + 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()); + } + }); + msgPanel.add(jcb); + + JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, + MessageManager + .getString("label.SEQUENCE_ID_no_longer_used"), + JvOptionPane.WARNING_MESSAGE); + } + } + }); + } + /** * Proxy class for JDesktopPane which optionally displays the current memory * usage and highlights the desktop area with a red bar if free memory runs @@ -2267,10 +2382,10 @@ 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(); @@ -2282,6 +2397,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements return showMemoryUsage; } + @Override public void run() { df = java.text.NumberFormat.getNumberInstance(); @@ -2315,6 +2431,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } + @Override public void paintComponent(Graphics g) { if (showMemoryUsage && g != null && df != null) @@ -2328,9 +2445,8 @@ 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()); } } @@ -2348,24 +2464,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements protected JMenuItem groovyShell; - public void doGroovyCheck() - { - if (jalview.bin.Cache.groovyJarsPresent()) - { - groovyShell = new JMenuItem(); - groovyShell.setText(MessageManager.getString("label.groovy_console")); - groovyShell.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groovyShell_actionPerformed(e); - } - }); - toolsMenu.add(groovyShell); - groovyShell.setVisible(true); - } - } - /** * Accessor method to quickly get all the AlignmentFrames loaded. * @@ -2373,6 +2471,12 @@ 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[] { Jalview.currentAlignFrame }; + } + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) @@ -2445,36 +2549,106 @@ 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()) - { - throw new Error( - MessageManager - .getString("error.implementation_error_cannot_create_groovyshell")); - } try { - Class gcClass = Desktop.class.getClassLoader().loadClass( - "groovy.ui.Console"); - Constructor gccons = gcClass.getConstructor(); - java.lang.reflect.Method setvar = gcClass.getMethod("setVariable", - 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 }); - run.invoke(gc); + openGroovyConsole(); } catch (Exception ex) { jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_create_groovy_shell"), MessageManager.getString("label.groovy_support_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); + } + } + + /** + * Open the Groovy console + */ + 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 + */ + Window window = (Window) groovyConsole.getFrame(); + window.addWindowListener(new WindowAdapter() + { + @Override + public void windowClosed(WindowEvent e) + { + /* + * rebind CMD-Q from Groovy Console to Jalview Quit + */ + addQuitHandler(); + enableExecuteGroovy(false); + } + }); + } + + /* + * show Groovy console window (after close and reopen) + */ + ((Window) groovyConsole.getFrame()).setVisible(true); + + /* + * 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 + */ + protected void addQuitHandler() + { + getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( + KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit + .getDefaultToolkit().getMenuShortcutKeyMask()), "Quit"); + getRootPane().getActionMap().put("Quit", new AbstractAction() + { + @Override + public void actionPerformed(ActionEvent e) + { + quit(); + } + }); + } + + /** + * Enable or disable 'Run Groovy script' in AlignFrame calculate menus + * + * @param enabled + * true if Groovy console is open + */ + public void enableExecuteGroovy(boolean enabled) + { + /* + * 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) + { + af.setGroovyEnabled(enabled); + } } } @@ -2490,6 +2664,7 @@ 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) @@ -2500,12 +2675,12 @@ 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 { @@ -2519,6 +2694,7 @@ 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) { @@ -2539,13 +2715,14 @@ 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); @@ -2567,8 +2744,9 @@ 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 @@ -2577,8 +2755,7 @@ 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) @@ -2645,28 +2822,6 @@ 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()) @@ -2719,6 +2874,7 @@ 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() { @@ -2746,7 +2902,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * jd.waitForInput(); */ - JOptionPane + JvOptionPane .showConfirmDialog( Desktop.desktop, new JLabel( @@ -2758,8 +2914,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements + "

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

"), "Web Service Configuration Problem", - JOptionPane.DEFAULT_OPTION, - JOptionPane.ERROR_MESSAGE); + JvOptionPane.DEFAULT_OPTION, + JvOptionPane.ERROR_MESSAGE); serviceChangedDialog = null; } @@ -2802,6 +2958,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { new Thread(new Runnable() { + @Override public void run() { try @@ -2809,17 +2966,17 @@ 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) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -2891,6 +3048,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements */ private java.util.concurrent.Semaphore block = new Semaphore(0); + private static groovy.ui.Console groovyConsole; + /** * add another dialog thread to the queue * @@ -2900,6 +3059,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements { dialogExecutor.submit(new Runnable() { + @Override public void run() { if (dialogPause) @@ -2943,7 +3103,7 @@ 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()); @@ -2959,7 +3119,11 @@ 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 */ @@ -2988,27 +3152,39 @@ 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); } @@ -3031,15 +3207,23 @@ 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) { @@ -3059,15 +3243,15 @@ 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(); @@ -3081,18 +3265,107 @@ public class Desktop extends jalview.jbgui.GDesktop implements * The dust settles...give focus to the tab we did this from. */ myTopFrame.setDisplayedView(myTopFrame.alignPanel); - } - // public static AlignFrame getCurrentAlignFrame() - // { - // return currentAlignFrame; - // } - // - // public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) - // { - // Desktop.currentAlignFrame = currentAlignFrame; - // } + public static groovy.ui.Console getGroovyConsole() + { + return groovyConsole; + } + 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"); + 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)) + { + files.add(((File) file).toString()); + protocols.add(DataSourceType.FILE); + } + } + else + { + // Unix like behaviour + boolean added = false; + String data = null; + 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) + { + // fallback to text: workaround - on OSX where there's a JVM bug + Cache.log.debug("standard URIListFlavor failed. Trying text"); + // try text fallback + data = (String) t.getTransferData(new DataFlavor( + "text/plain;class=java.lang.String")); + if (Cache.log.isDebugEnabled()) + { + Cache.log.debug("fallback returned " + data); + } + } + while (protocols.size() < files.size()) + { + Cache.log.debug("Adding missing FILE protocol for " + + files.get(protocols.size())); + protocols.add(DataSourceType.FILE); + } + for (java.util.StringTokenizer st = new java.util.StringTokenizer( + data, "\r\n"); st.hasMoreTokens();) + { + added = true; + String s = st.nextToken(); + if (s.startsWith("#")) + { + // the line is a comment (as per the RFC 2483) + continue; + } + java.net.URI uri = new java.net.URI(s); + if (uri.getScheme().toLowerCase().startsWith("http")) + { + protocols.add(DataSourceType.URL); + files.add(uri.toString()); + } + else + { + // otherwise preserve old behaviour: catch all for file objects + java.io.File file = new java.io.File(uri); + protocols.add(DataSourceType.FILE); + files.add(file.toString()); + } + } + if (Cache.log.isDebugEnabled()) + { + if (data == null || !added) + { + Cache.log + .debug("Couldn't resolve drop data. Here are the supported flavors:"); + for (DataFlavor fl : t.getTransferDataFlavors()) + { + Cache.log.debug("Supported transfer dataflavor: " + + fl.toString()); + Object df = t.getTransferData(fl); + if (df != null) + { + Cache.log.debug("Retrieves: " + df); + } + else + { + Cache.log.debug("Retrieved nothing"); + } + } + } + } + } + } }