2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.bin.Cache;
26 import jalview.bin.Jalview;
27 import jalview.io.BackupFiles;
28 import jalview.io.DataSourceType;
29 import jalview.io.FileFormat;
30 import jalview.io.FileFormatException;
31 import jalview.io.FileFormatI;
32 import jalview.io.FileFormats;
33 import jalview.io.FileLoader;
34 import jalview.io.FormatAdapter;
35 import jalview.io.IdentifyFile;
36 import jalview.io.JalviewFileChooser;
37 import jalview.io.JalviewFileView;
38 import jalview.jbgui.GSplitFrame;
39 import jalview.jbgui.GStructureViewer;
40 import jalview.project.Jalview2XML;
41 import jalview.structure.StructureSelectionManager;
42 import jalview.urls.IdOrgSettings;
43 import jalview.util.ImageMaker;
44 import jalview.util.MessageManager;
45 import jalview.util.Platform;
46 import jalview.util.UrlConstants;
47 import jalview.viewmodel.AlignmentViewport;
48 import jalview.ws.params.ParamManager;
49 import jalview.ws.utils.UrlDownloadClient;
51 import java.awt.BorderLayout;
52 import java.awt.Color;
53 import java.awt.Dimension;
54 import java.awt.FontMetrics;
55 import java.awt.Graphics;
56 import java.awt.GridLayout;
57 import java.awt.Point;
58 import java.awt.Rectangle;
59 import java.awt.Toolkit;
60 import java.awt.Window;
61 import java.awt.datatransfer.Clipboard;
62 import java.awt.datatransfer.ClipboardOwner;
63 import java.awt.datatransfer.DataFlavor;
64 import java.awt.datatransfer.Transferable;
65 import java.awt.dnd.DnDConstants;
66 import java.awt.dnd.DropTargetDragEvent;
67 import java.awt.dnd.DropTargetDropEvent;
68 import java.awt.dnd.DropTargetEvent;
69 import java.awt.dnd.DropTargetListener;
70 import java.awt.event.ActionEvent;
71 import java.awt.event.ActionListener;
72 import java.awt.event.InputEvent;
73 import java.awt.event.KeyEvent;
74 import java.awt.event.MouseAdapter;
75 import java.awt.event.MouseEvent;
76 import java.awt.event.WindowAdapter;
77 import java.awt.event.WindowEvent;
78 import java.beans.PropertyChangeEvent;
79 import java.beans.PropertyChangeListener;
81 import java.io.FileWriter;
82 import java.io.IOException;
84 import java.util.ArrayList;
85 import java.util.HashMap;
86 import java.util.Hashtable;
87 import java.util.List;
88 import java.util.ListIterator;
89 import java.util.StringTokenizer;
90 import java.util.Vector;
91 import java.util.concurrent.ExecutorService;
92 import java.util.concurrent.Executors;
93 import java.util.concurrent.Semaphore;
95 import javax.swing.AbstractAction;
96 import javax.swing.Action;
97 import javax.swing.ActionMap;
98 import javax.swing.Box;
99 import javax.swing.BoxLayout;
100 import javax.swing.DefaultDesktopManager;
101 import javax.swing.DesktopManager;
102 import javax.swing.InputMap;
103 import javax.swing.JButton;
104 import javax.swing.JCheckBox;
105 import javax.swing.JComboBox;
106 import javax.swing.JComponent;
107 import javax.swing.JDesktopPane;
108 import javax.swing.JInternalFrame;
109 import javax.swing.JLabel;
110 import javax.swing.JMenuItem;
111 import javax.swing.JPanel;
112 import javax.swing.JPopupMenu;
113 import javax.swing.JProgressBar;
114 import javax.swing.KeyStroke;
115 import javax.swing.SwingUtilities;
116 import javax.swing.event.HyperlinkEvent;
117 import javax.swing.event.HyperlinkEvent.EventType;
118 import javax.swing.event.InternalFrameAdapter;
119 import javax.swing.event.InternalFrameEvent;
121 import org.stackoverflowusers.file.WindowsShortcut;
128 * @version $Revision: 1.155 $
130 public class Desktop extends jalview.jbgui.GDesktop
131 implements DropTargetListener, ClipboardOwner, IProgressIndicator,
132 jalview.api.StructureSelectionManagerProvider
134 private static int DEFAULT_MIN_WIDTH = 300;
136 private static int DEFAULT_MIN_HEIGHT = 250;
138 private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600;
140 private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70;
142 private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
144 protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
146 public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
148 private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
151 * news reader - null if it was never started.
153 private BlogReader jvnews = null;
155 private File projectFile;
159 * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
161 public void addJalviewPropertyChangeListener(
162 PropertyChangeListener listener)
164 changeSupport.addJalviewPropertyChangeListener(listener);
168 * @param propertyName
170 * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
171 * java.beans.PropertyChangeListener)
173 public void addJalviewPropertyChangeListener(String propertyName,
174 PropertyChangeListener listener)
176 changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
180 * @param propertyName
182 * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
183 * java.beans.PropertyChangeListener)
185 public void removeJalviewPropertyChangeListener(String propertyName,
186 PropertyChangeListener listener)
188 changeSupport.removeJalviewPropertyChangeListener(propertyName,
192 /** Singleton Desktop instance */
193 public static Desktop instance;
195 public static MyDesktopPane desktop;
197 static int openFrameCount = 0;
199 static final int xOffset = 30;
201 static final int yOffset = 30;
203 public static jalview.ws.jws1.Discoverer discoverer;
205 public static Object[] jalviewClipboard;
207 public static boolean internalCopy = false;
209 static int fileLoadingCount = 0;
211 class MyDesktopManager implements DesktopManager
214 private DesktopManager delegate;
216 public MyDesktopManager(DesktopManager delegate)
218 this.delegate = delegate;
222 public void activateFrame(JInternalFrame f)
226 delegate.activateFrame(f);
227 } catch (NullPointerException npe)
229 Point p = getMousePosition();
230 instance.showPasteMenu(p.x, p.y);
235 public void beginDraggingFrame(JComponent f)
237 delegate.beginDraggingFrame(f);
241 public void beginResizingFrame(JComponent f, int direction)
243 delegate.beginResizingFrame(f, direction);
247 public void closeFrame(JInternalFrame f)
249 delegate.closeFrame(f);
253 public void deactivateFrame(JInternalFrame f)
255 delegate.deactivateFrame(f);
259 public void deiconifyFrame(JInternalFrame f)
261 delegate.deiconifyFrame(f);
265 public void dragFrame(JComponent f, int newX, int newY)
271 delegate.dragFrame(f, newX, newY);
275 public void endDraggingFrame(JComponent f)
277 delegate.endDraggingFrame(f);
282 public void endResizingFrame(JComponent f)
284 delegate.endResizingFrame(f);
289 public void iconifyFrame(JInternalFrame f)
291 delegate.iconifyFrame(f);
295 public void maximizeFrame(JInternalFrame f)
297 delegate.maximizeFrame(f);
301 public void minimizeFrame(JInternalFrame f)
303 delegate.minimizeFrame(f);
307 public void openFrame(JInternalFrame f)
309 delegate.openFrame(f);
313 public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
320 delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
324 public void setBoundsForFrame(JComponent f, int newX, int newY,
325 int newWidth, int newHeight)
327 delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
330 // All other methods, simply delegate
335 * Creates a new Desktop object.
340 * A note to implementors. It is ESSENTIAL that any activities that might
341 * block are spawned off as threads rather than waited for during this
346 doConfigureStructurePrefs();
347 setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
349 if (!Platform.isAMac())
351 // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
355 this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
361 APQHandlers.setAPQHandlers(this);
362 } catch (Exception e)
364 System.out.println("Cannot set APQHandlers");
365 // e.printStackTrace();
366 } catch (Throwable t)
368 System.out.println("Cannot set APQHandlers");
369 // t.printStackTrace();
373 addWindowListener(new WindowAdapter()
377 public void windowClosing(WindowEvent ev)
383 boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
386 boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
388 desktop = new MyDesktopPane(selmemusage);
389 showMemusage.setSelected(selmemusage);
390 desktop.setBackground(Color.white);
392 getContentPane().setLayout(new BorderLayout());
393 // alternate config - have scrollbars - see notes in JAL-153
394 // JScrollPane sp = new JScrollPane();
395 // sp.getViewport().setView(desktop);
396 // getContentPane().add(sp, BorderLayout.CENTER);
397 getContentPane().add(desktop, BorderLayout.CENTER);
398 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
400 // This line prevents Windows Look&Feel resizing all new windows to maximum
401 // if previous window was maximised
402 desktop.setDesktopManager(new MyDesktopManager(
403 (Platform.isWindows() ? new DefaultDesktopManager()
405 ? new AquaInternalFrameManager(
406 desktop.getDesktopManager())
407 : desktop.getDesktopManager())));
409 Rectangle dims = getLastKnownDimensions("");
416 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
417 setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2,
420 jconsole = new Console(this, showjconsole);
421 // add essential build information
422 jconsole.setHeader(jalview.bin.Cache.getVersionDetailsForConsole());
424 showConsole(showjconsole);
426 showNews.setVisible(false);
428 experimentalFeatures.setSelected(showExperimental());
430 getIdentifiersOrgData();
434 this.addWindowListener(new WindowAdapter()
437 public void windowClosing(WindowEvent evt)
444 this.addMouseListener(ma = new MouseAdapter()
447 public void mousePressed(MouseEvent evt)
449 if (evt.isPopupTrigger()) // Mac
451 showPasteMenu(evt.getX(), evt.getY());
456 public void mouseReleased(MouseEvent evt)
458 if (evt.isPopupTrigger()) // Windows
460 showPasteMenu(evt.getX(), evt.getY());
464 desktop.addMouseListener(ma);
466 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
467 // Spawn a thread that shows the splashscreen
468 SwingUtilities.invokeLater(new Runnable()
477 // Thread off a new instance of the file chooser - this reduces the time it
478 // takes to open it later on.
479 new Thread(new Runnable()
484 Cache.log.debug("Filechooser init thread started.");
485 String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
486 JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
488 Cache.log.debug("Filechooser init thread finished.");
491 // Add the service change listener
492 changeSupport.addJalviewPropertyChangeListener("services",
493 new PropertyChangeListener()
497 public void propertyChange(PropertyChangeEvent evt)
499 Cache.log.debug("Firing service changed event for "
500 + evt.getNewValue());
501 JalviewServicesChanged(evt);
508 * Answers true if user preferences to enable experimental features is True
513 public boolean showExperimental()
515 String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
516 Boolean.FALSE.toString());
517 return Boolean.valueOf(experimental).booleanValue();
520 public void doConfigureStructurePrefs()
522 // configure services
523 StructureSelectionManager ssm = StructureSelectionManager
524 .getStructureSelectionManager(this);
525 if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
527 ssm.setAddTempFacAnnot(jalview.bin.Cache
528 .getDefault(Preferences.ADD_TEMPFACT_ANN, true));
529 ssm.setProcessSecondaryStructure(jalview.bin.Cache
530 .getDefault(Preferences.STRUCT_FROM_PDB, true));
531 ssm.setSecStructServices(
532 jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true));
536 ssm.setAddTempFacAnnot(false);
537 ssm.setProcessSecondaryStructure(false);
538 ssm.setSecStructServices(false);
542 public void checkForNews()
544 final Desktop me = this;
545 // Thread off the news reader, in case there are connection problems.
546 new Thread(new Runnable()
551 Cache.log.debug("Starting news thread.");
553 jvnews = new BlogReader(me);
554 showNews.setVisible(true);
555 Cache.log.debug("Completed news thread.");
560 public void getIdentifiersOrgData()
562 // Thread off the identifiers fetcher
563 new Thread(new Runnable()
568 Cache.log.debug("Downloading data from identifiers.org");
569 UrlDownloadClient client = new UrlDownloadClient();
572 client.download(IdOrgSettings.getUrl(),
573 IdOrgSettings.getDownloadLocation());
574 } catch (IOException e)
576 Cache.log.debug("Exception downloading identifiers.org data"
585 protected void showNews_actionPerformed(ActionEvent e)
587 showNews(showNews.isSelected());
590 void showNews(boolean visible)
593 Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
594 showNews.setSelected(visible);
595 if (visible && !jvnews.isVisible())
597 new Thread(new Runnable()
602 long now = System.currentTimeMillis();
603 Desktop.instance.setProgressBar(
604 MessageManager.getString("status.refreshing_news"),
606 jvnews.refreshNews();
607 Desktop.instance.setProgressBar(null, now);
616 * recover the last known dimensions for a jalview window
619 * - empty string is desktop, all other windows have unique prefix
620 * @return null or last known dimensions scaled to current geometry (if last
621 * window geom was known)
623 Rectangle getLastKnownDimensions(String windowName)
625 // TODO: lock aspect ratio for scaling desktop Bug #0058199
626 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
627 String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
628 String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
629 String width = jalview.bin.Cache
630 .getProperty(windowName + "SCREEN_WIDTH");
631 String height = jalview.bin.Cache
632 .getProperty(windowName + "SCREEN_HEIGHT");
633 if ((x != null) && (y != null) && (width != null) && (height != null))
635 int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
636 iw = Integer.parseInt(width), ih = Integer.parseInt(height);
637 if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
639 // attempt #1 - try to cope with change in screen geometry - this
640 // version doesn't preserve original jv aspect ratio.
641 // take ratio of current screen size vs original screen size.
642 double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(
643 jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
644 double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(
645 jalview.bin.Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
646 // rescale the bounds depending upon the current screen geometry.
647 ix = (int) (ix * sw);
648 iw = (int) (iw * sw);
649 iy = (int) (iy * sh);
650 ih = (int) (ih * sh);
651 while (ix >= screenSize.width)
653 jalview.bin.Cache.log.debug(
654 "Window geometry location recall error: shifting horizontal to within screenbounds.");
655 ix -= screenSize.width;
657 while (iy >= screenSize.height)
659 jalview.bin.Cache.log.debug(
660 "Window geometry location recall error: shifting vertical to within screenbounds.");
661 iy -= screenSize.height;
663 jalview.bin.Cache.log.debug(
664 "Got last known dimensions for " + windowName + ": x:" + ix
665 + " y:" + iy + " width:" + iw + " height:" + ih);
667 // return dimensions for new instance
668 return new Rectangle(ix, iy, iw, ih);
673 void showPasteMenu(int x, int y)
675 JPopupMenu popup = new JPopupMenu();
676 JMenuItem item = new JMenuItem(
677 MessageManager.getString("label.paste_new_window"));
678 item.addActionListener(new ActionListener()
681 public void actionPerformed(ActionEvent evt)
688 popup.show(this, x, y);
695 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
696 Transferable contents = c.getContents(this);
698 if (contents != null)
700 String file = (String) contents
701 .getTransferData(DataFlavor.stringFlavor);
703 FileFormatI format = new IdentifyFile().identify(file,
704 DataSourceType.PASTE);
706 new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
709 } catch (Exception ex)
712 "Unable to paste alignment from system clipboard:\n" + ex);
717 * Adds and opens the given frame to the desktop
728 public static synchronized void addInternalFrame(
729 final JInternalFrame frame, String title, int w, int h)
731 addInternalFrame(frame, title, true, w, h, true, false);
735 * Add an internal frame to the Jalview desktop
742 * When true, display frame immediately, otherwise, caller must call
743 * setVisible themselves.
749 public static synchronized void addInternalFrame(
750 final JInternalFrame frame, String title, boolean makeVisible,
753 addInternalFrame(frame, title, makeVisible, w, h, true, false);
757 * Add an internal frame to the Jalview desktop and make it visible
770 public static synchronized void addInternalFrame(
771 final JInternalFrame frame, String title, int w, int h,
774 addInternalFrame(frame, title, true, w, h, resizable, false);
778 * Add an internal frame to the Jalview desktop
785 * When true, display frame immediately, otherwise, caller must call
786 * setVisible themselves.
793 * @param ignoreMinSize
794 * Do not set the default minimum size for frame
796 public static synchronized void addInternalFrame(
797 final JInternalFrame frame, String title, boolean makeVisible,
798 int w, int h, boolean resizable, boolean ignoreMinSize)
801 // TODO: allow callers to determine X and Y position of frame (eg. via
803 // TODO: consider fixing method to update entries in the window submenu with
804 // the current window title
806 frame.setTitle(title);
807 if (frame.getWidth() < 1 || frame.getHeight() < 1)
811 // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
812 // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
813 // IF JALVIEW IS RUNNING HEADLESS
814 // ///////////////////////////////////////////////
815 if (instance == null || (System.getProperty("java.awt.headless") != null
816 && System.getProperty("java.awt.headless").equals("true")))
825 frame.setMinimumSize(
826 new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
828 // Set default dimension for Alignment Frame window.
829 // The Alignment Frame window could be added from a number of places,
831 // I did this here in order not to miss out on any Alignment frame.
832 if (frame instanceof AlignFrame)
834 frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH,
835 ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
839 frame.setVisible(makeVisible);
840 frame.setClosable(true);
841 frame.setResizable(resizable);
842 frame.setMaximizable(resizable);
843 frame.setIconifiable(resizable);
844 frame.setOpaque(false);
846 if (frame.getX() < 1 && frame.getY() < 1)
848 frame.setLocation(xOffset * openFrameCount,
849 yOffset * ((openFrameCount - 1) % 10) + yOffset);
853 * add an entry for the new frame in the Window menu
854 * (and remove it when the frame is closed)
856 final JMenuItem menuItem = new JMenuItem(title);
857 frame.addInternalFrameListener(new InternalFrameAdapter()
860 public void internalFrameActivated(InternalFrameEvent evt)
862 JInternalFrame itf = desktop.getSelectedFrame();
865 if (itf instanceof AlignFrame)
867 Jalview.setCurrentAlignFrame((AlignFrame) itf);
874 public void internalFrameClosed(InternalFrameEvent evt)
876 PaintRefresher.RemoveComponent(frame);
879 * defensive check to prevent frames being
880 * added half off the window
882 if (openFrameCount > 0)
888 * ensure no reference to alignFrame retained by menu item listener
890 if (menuItem.getActionListeners().length > 0)
892 menuItem.removeActionListener(menuItem.getActionListeners()[0]);
894 windowMenu.remove(menuItem);
898 menuItem.addActionListener(new ActionListener()
901 public void actionPerformed(ActionEvent e)
905 frame.setSelected(true);
906 frame.setIcon(false);
907 } catch (java.beans.PropertyVetoException ex)
914 setKeyBindings(frame);
918 windowMenu.add(menuItem);
923 frame.setSelected(true);
924 frame.requestFocus();
925 } catch (java.beans.PropertyVetoException ve)
927 } catch (java.lang.ClassCastException cex)
930 "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
936 * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
941 private static void setKeyBindings(JInternalFrame frame)
943 @SuppressWarnings("serial")
944 final Action closeAction = new AbstractAction()
947 public void actionPerformed(ActionEvent e)
954 * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action
956 KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
957 InputEvent.CTRL_DOWN_MASK);
958 KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
959 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
961 InputMap inputMap = frame
962 .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
963 String ctrlW = ctrlWKey.toString();
964 inputMap.put(ctrlWKey, ctrlW);
965 inputMap.put(cmdWKey, ctrlW);
967 ActionMap actionMap = frame.getActionMap();
968 actionMap.put(ctrlW, closeAction);
972 public void lostOwnership(Clipboard clipboard, Transferable contents)
976 Desktop.jalviewClipboard = null;
979 internalCopy = false;
983 public void dragEnter(DropTargetDragEvent evt)
988 public void dragExit(DropTargetEvent evt)
993 public void dragOver(DropTargetDragEvent evt)
998 public void dropActionChanged(DropTargetDragEvent evt)
1009 public void drop(DropTargetDropEvent evt)
1011 boolean success = true;
1012 // JAL-1552 - acceptDrop required before getTransferable call for
1013 // Java's Transferable for native dnd
1014 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
1015 Transferable t = evt.getTransferable();
1016 List<String> files = new ArrayList<>();
1017 List<DataSourceType> protocols = new ArrayList<>();
1021 Desktop.transferFromDropTarget(files, protocols, evt, t);
1022 } catch (Exception e)
1024 e.printStackTrace();
1032 for (int i = 0; i < files.size(); i++)
1034 String file = files.get(i).toString();
1035 DataSourceType protocol = (protocols == null)
1036 ? DataSourceType.FILE
1038 FileFormatI format = null;
1040 if (file.endsWith(".jar"))
1042 format = FileFormat.Jalview;
1047 format = new IdentifyFile().identify(file, protocol);
1050 new FileLoader().LoadFile(file, protocol, format);
1053 } catch (Exception ex)
1058 evt.dropComplete(success); // need this to ensure input focus is properly
1059 // transfered to any new windows created
1069 public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
1071 String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1072 JalviewFileChooser chooser = JalviewFileChooser
1073 .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat, BackupFiles.getEnabled());
1075 chooser.setFileView(new JalviewFileView());
1076 chooser.setDialogTitle(
1077 MessageManager.getString("label.open_local_file"));
1078 chooser.setToolTipText(MessageManager.getString("action.open"));
1080 int value = chooser.showOpenDialog(this);
1082 if (value == JalviewFileChooser.APPROVE_OPTION)
1084 String choice = chooser.getSelectedFile().getPath();
1085 Cache.setProperty("LAST_DIRECTORY",
1086 chooser.getSelectedFile().getParent());
1088 FileFormatI format = chooser.getSelectedFormat();
1091 * Call IdentifyFile to verify the file contains what its extension implies.
1092 * Skip this step for dynamically added file formats, because
1093 * IdentifyFile does not know how to recognise them.
1095 if (FileFormats.getInstance().isIdentifiable(format))
1099 format = new IdentifyFile().identify(choice, DataSourceType.FILE);
1100 } catch (FileFormatException e)
1102 // format = null; //??
1106 if (viewport != null)
1108 new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE,
1113 new FileLoader().LoadFile(choice, DataSourceType.FILE, format);
1125 public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
1127 // This construct allows us to have a wider textfield
1129 JLabel label = new JLabel(
1130 MessageManager.getString("label.input_file_url"));
1131 final JComboBox history = new JComboBox();
1133 JPanel panel = new JPanel(new GridLayout(2, 1));
1136 history.setPreferredSize(new Dimension(400, 20));
1137 history.setEditable(true);
1138 history.addItem("http://www.");
1140 String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
1144 if (historyItems != null)
1146 st = new StringTokenizer(historyItems, "\t");
1148 while (st.hasMoreTokens())
1150 history.addItem(st.nextElement());
1154 int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel,
1155 MessageManager.getString("label.input_alignment_from_url"),
1156 JvOptionPane.OK_CANCEL_OPTION);
1158 if (reply != JvOptionPane.OK_OPTION)
1163 String url = history.getSelectedItem().toString();
1165 if (url.toLowerCase().endsWith(".jar"))
1167 if (viewport != null)
1169 new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
1170 FileFormat.Jalview);
1174 new FileLoader().LoadFile(url, DataSourceType.URL,
1175 FileFormat.Jalview);
1180 FileFormatI format = null;
1183 format = new IdentifyFile().identify(url, DataSourceType.URL);
1184 } catch (FileFormatException e)
1186 // TODO revise error handling, distinguish between
1187 // URL not found and response not valid
1192 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1193 MessageManager.formatMessage("label.couldnt_locate",
1196 MessageManager.getString("label.url_not_found"),
1197 JvOptionPane.WARNING_MESSAGE);
1202 if (viewport != null)
1204 new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
1209 new FileLoader().LoadFile(url, DataSourceType.URL, format);
1215 * Opens the CutAndPaste window for the user to paste an alignment in to
1218 * - if not null, the pasted alignment is added to the current
1219 * alignment; if null, to a new alignment window
1222 public void inputTextboxMenuItem_actionPerformed(
1223 AlignmentViewPanel viewPanel)
1225 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1226 cap.setForInput(viewPanel);
1227 Desktop.addInternalFrame(cap,
1228 MessageManager.getString("label.cut_paste_alignmen_file"), true,
1238 Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
1239 jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
1241 jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT",
1242 screen.height + "");
1243 storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
1244 getWidth(), getHeight()));
1246 if (jconsole != null)
1248 storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
1249 jconsole.stopConsole();
1253 storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
1256 if (dialogExecutor != null)
1258 dialogExecutor.shutdownNow();
1260 closeAll_actionPerformed(null);
1262 if (groovyConsole != null)
1264 // suppress a possible repeat prompt to save script
1265 groovyConsole.setDirty(false);
1266 groovyConsole.exit();
1271 private void storeLastKnownDimensions(String string, Rectangle jc)
1273 jalview.bin.Cache.log.debug("Storing last known dimensions for "
1274 + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
1275 + " height:" + jc.height);
1277 jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
1278 jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
1279 jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
1280 jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
1290 public void aboutMenuItem_actionPerformed(ActionEvent e)
1292 // StringBuffer message = getAboutMessage(false);
1293 // JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1295 // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
1296 new Thread(new Runnable()
1301 new SplashScreen(true);
1306 public StringBuffer getAboutMessage(boolean shortv)
1308 StringBuffer message = new StringBuffer();
1309 message.append("<html>");
1312 message.append("<h1><strong>Version: "
1313 + jalview.bin.Cache.getProperty("VERSION")
1314 + "</strong></h1>");
1315 message.append("<strong>Built: <em>"
1316 + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
1317 + "</em> from " + jalview.bin.Cache.getBuildDetailsForSplash()
1324 message.append("<strong>Version "
1325 + jalview.bin.Cache.getProperty("VERSION")
1326 + "; last updated: "
1327 + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1330 if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
1331 .equals("Checking"))
1333 // JBP removed this message for 2.11: May be reinstated in future version
1334 // message.append("<br>...Checking latest version...</br>");
1336 else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
1337 .equals(jalview.bin.Cache.getProperty("VERSION")))
1339 boolean red = false;
1340 if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
1341 .indexOf("automated build") == -1)
1344 // Displayed when code version and jnlp version do not match and code
1345 // version is not a development build
1346 message.append("<div style=\"color: #FF0000;font-style: bold;\">");
1349 message.append("<br>!! Version "
1350 + jalview.bin.Cache.getDefault("LATEST_VERSION",
1352 + " is available for download from "
1353 + jalview.bin.Cache.getDefault("www.jalview.org",
1354 "http://www.jalview.org")
1358 message.append("</div>");
1361 message.append("<br>Authors: " + jalview.bin.Cache.getDefault(
1363 "The Jalview Authors (See AUTHORS file for current list)")
1364 + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
1365 + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
1366 + "<br><br>If you use Jalview, please cite:"
1367 + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
1368 + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
1369 + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
1381 public void documentationMenuItem_actionPerformed(ActionEvent e)
1385 Help.showHelpWindow();
1386 } catch (Exception ex)
1392 public void closeAll_actionPerformed(ActionEvent e)
1394 // TODO show a progress bar while closing?
1395 JInternalFrame[] frames = desktop.getAllFrames();
1396 for (int i = 0; i < frames.length; i++)
1400 frames[i].setClosed(true);
1401 } catch (java.beans.PropertyVetoException ex)
1405 Jalview.setCurrentAlignFrame(null);
1406 System.out.println("ALL CLOSED");
1409 * reset state of singleton objects as appropriate (clear down session state
1410 * when all windows are closed)
1412 StructureSelectionManager ssm = StructureSelectionManager
1413 .getStructureSelectionManager(this);
1421 public void raiseRelated_actionPerformed(ActionEvent e)
1423 reorderAssociatedWindows(false, false);
1427 public void minimizeAssociated_actionPerformed(ActionEvent e)
1429 reorderAssociatedWindows(true, false);
1432 void closeAssociatedWindows()
1434 reorderAssociatedWindows(false, true);
1440 * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
1444 protected void garbageCollect_actionPerformed(ActionEvent e)
1446 // We simply collect the garbage
1447 jalview.bin.Cache.log.debug("Collecting garbage...");
1449 jalview.bin.Cache.log.debug("Finished garbage collection.");
1456 * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
1460 protected void showMemusage_actionPerformed(ActionEvent e)
1462 desktop.showMemoryUsage(showMemusage.isSelected());
1469 * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
1473 protected void showConsole_actionPerformed(ActionEvent e)
1475 showConsole(showConsole.isSelected());
1478 Console jconsole = null;
1481 * control whether the java console is visible or not
1485 void showConsole(boolean selected)
1487 showConsole.setSelected(selected);
1488 // TODO: decide if we should update properties file
1489 Cache.setProperty("SHOW_JAVA_CONSOLE",
1490 Boolean.valueOf(selected).toString());
1491 jconsole.setVisible(selected);
1494 void reorderAssociatedWindows(boolean minimize, boolean close)
1496 JInternalFrame[] frames = desktop.getAllFrames();
1497 if (frames == null || frames.length < 1)
1502 AlignViewportI source = null;
1503 AlignViewportI target = null;
1504 if (frames[0] instanceof AlignFrame)
1506 source = ((AlignFrame) frames[0]).getCurrentView();
1508 else if (frames[0] instanceof TreePanel)
1510 source = ((TreePanel) frames[0]).getViewPort();
1512 else if (frames[0] instanceof PCAPanel)
1514 source = ((PCAPanel) frames[0]).av;
1516 else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
1518 source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
1523 for (int i = 0; i < frames.length; i++)
1526 if (frames[i] == null)
1530 if (frames[i] instanceof AlignFrame)
1532 target = ((AlignFrame) frames[i]).getCurrentView();
1534 else if (frames[i] instanceof TreePanel)
1536 target = ((TreePanel) frames[i]).getViewPort();
1538 else if (frames[i] instanceof PCAPanel)
1540 target = ((PCAPanel) frames[i]).av;
1542 else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
1544 target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
1547 if (source == target)
1553 frames[i].setClosed(true);
1557 frames[i].setIcon(minimize);
1560 frames[i].toFront();
1564 } catch (java.beans.PropertyVetoException ex)
1579 protected void preferences_actionPerformed(ActionEvent e)
1585 * Shows a file chooser dialog and writes out the current session as a Jalview
1589 public void saveState_actionPerformed()
1591 saveState_actionPerformed(false);
1594 public void saveState_actionPerformed(boolean saveAs)
1596 java.io.File projectFile = getProjectFile();
1597 // autoSave indicates we already have a file and don't need to ask
1598 boolean autoSave = projectFile != null && !saveAs
1599 && BackupFiles.getEnabled();
1601 // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
1602 // saveAs="+saveAs+", Backups
1603 // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
1605 boolean approveSave = false;
1608 JalviewFileChooser chooser = new JalviewFileChooser("jvp",
1611 chooser.setFileView(new JalviewFileView());
1612 chooser.setDialogTitle(MessageManager.getString("label.save_state"));
1614 int value = chooser.showSaveDialog(this);
1616 if (value == JalviewFileChooser.APPROVE_OPTION)
1618 projectFile = chooser.getSelectedFile();
1619 setProjectFile(projectFile);
1624 if (approveSave || autoSave)
1626 final Desktop me = this;
1627 final java.io.File chosenFile = projectFile;
1628 new Thread(new Runnable()
1633 // TODO: refactor to Jalview desktop session controller action.
1634 setProgressBar(MessageManager.formatMessage(
1635 "label.saving_jalview_project", new Object[]
1636 { chosenFile.getName() }), chosenFile.hashCode());
1637 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
1638 chosenFile.getParent());
1639 // TODO catch and handle errors for savestate
1640 // TODO prevent user from messing with the Desktop whilst we're saving
1643 BackupFiles backupfiles = new BackupFiles(chosenFile);
1645 new Jalview2XML().saveState(backupfiles.getTempFile());
1647 backupfiles.setWriteSuccess(true);
1648 backupfiles.rollBackupsAndRenameTempFile();
1649 } catch (OutOfMemoryError oom)
1651 new OOMWarning("Whilst saving current state to "
1652 + chosenFile.getName(), oom);
1653 } catch (Exception ex)
1655 Cache.log.error("Problems whilst trying to save to "
1656 + chosenFile.getName(), ex);
1657 JvOptionPane.showMessageDialog(me,
1658 MessageManager.formatMessage(
1659 "label.error_whilst_saving_current_state_to",
1661 { chosenFile.getName() }),
1662 MessageManager.getString("label.couldnt_save_project"),
1663 JvOptionPane.WARNING_MESSAGE);
1665 setProgressBar(null, chosenFile.hashCode());
1672 public void saveAsState_actionPerformed(ActionEvent e)
1674 saveState_actionPerformed(true);
1677 private void setProjectFile(File choice)
1679 this.projectFile = choice;
1682 public File getProjectFile()
1684 return this.projectFile;
1688 * Shows a file chooser dialog and tries to read in the selected file as a
1692 public void loadState_actionPerformed()
1694 final String[] suffix = new String[] { "jvp", "jar" };
1695 final String[] desc = new String[] { "Jalview Project",
1696 "Jalview Project (old)" };
1697 JalviewFileChooser chooser = new JalviewFileChooser(
1698 Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
1699 "Jalview Project", true, BackupFiles.getEnabled()); // last two booleans: allFiles,
1701 chooser.setFileView(new JalviewFileView());
1702 chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
1704 int value = chooser.showOpenDialog(this);
1706 if (value == JalviewFileChooser.APPROVE_OPTION)
1708 final File selectedFile = chooser.getSelectedFile();
1709 setProjectFile(selectedFile);
1710 final String choice = selectedFile.getAbsolutePath();
1711 Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
1712 new Thread(new Runnable()
1717 setProgressBar(MessageManager.formatMessage(
1718 "label.loading_jalview_project", new Object[]
1719 { choice }), choice.hashCode());
1722 new Jalview2XML().loadJalviewAlign(choice);
1723 } catch (OutOfMemoryError oom)
1725 new OOMWarning("Whilst loading project from " + choice, oom);
1726 } catch (Exception ex)
1729 "Problems whilst loading project from " + choice, ex);
1730 JvOptionPane.showMessageDialog(Desktop.desktop,
1731 MessageManager.formatMessage(
1732 "label.error_whilst_loading_project_from",
1735 MessageManager.getString("label.couldnt_load_project"),
1736 JvOptionPane.WARNING_MESSAGE);
1738 setProgressBar(null, choice.hashCode());
1745 public void inputSequence_actionPerformed(ActionEvent e)
1747 new SequenceFetcher(this);
1750 JPanel progressPanel;
1752 ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
1754 public void startLoading(final String fileName)
1756 if (fileLoadingCount == 0)
1758 fileLoadingPanels.add(addProgressPanel(MessageManager
1759 .formatMessage("label.loading_file", new Object[]
1765 private JPanel addProgressPanel(String string)
1767 if (progressPanel == null)
1769 progressPanel = new JPanel(new GridLayout(1, 1));
1770 totalProgressCount = 0;
1771 instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
1773 JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
1774 JProgressBar progressBar = new JProgressBar();
1775 progressBar.setIndeterminate(true);
1777 thisprogress.add(new JLabel(string), BorderLayout.WEST);
1779 thisprogress.add(progressBar, BorderLayout.CENTER);
1780 progressPanel.add(thisprogress);
1781 ((GridLayout) progressPanel.getLayout()).setRows(
1782 ((GridLayout) progressPanel.getLayout()).getRows() + 1);
1783 ++totalProgressCount;
1784 instance.validate();
1785 return thisprogress;
1788 int totalProgressCount = 0;
1790 private void removeProgressPanel(JPanel progbar)
1792 if (progressPanel != null)
1794 synchronized (progressPanel)
1796 progressPanel.remove(progbar);
1797 GridLayout gl = (GridLayout) progressPanel.getLayout();
1798 gl.setRows(gl.getRows() - 1);
1799 if (--totalProgressCount < 1)
1801 this.getContentPane().remove(progressPanel);
1802 progressPanel = null;
1809 public void stopLoading()
1812 if (fileLoadingCount < 1)
1814 while (fileLoadingPanels.size() > 0)
1816 removeProgressPanel(fileLoadingPanels.remove(0));
1818 fileLoadingPanels.clear();
1819 fileLoadingCount = 0;
1824 public static int getViewCount(String alignmentId)
1826 AlignmentViewport[] aps = getViewports(alignmentId);
1827 return (aps == null) ? 0 : aps.length;
1832 * @param alignmentId
1833 * - if null, all sets are returned
1834 * @return all AlignmentPanels concerning the alignmentId sequence set
1836 public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
1838 if (Desktop.desktop == null)
1840 // no frames created and in headless mode
1841 // TODO: verify that frames are recoverable when in headless mode
1844 List<AlignmentPanel> aps = new ArrayList<>();
1845 AlignFrame[] frames = getAlignFrames();
1850 for (AlignFrame af : frames)
1852 for (AlignmentPanel ap : af.alignPanels)
1854 if (alignmentId == null
1855 || alignmentId.equals(ap.av.getSequenceSetId()))
1861 if (aps.size() == 0)
1865 AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
1870 * get all the viewports on an alignment.
1872 * @param sequenceSetId
1873 * unique alignment id (may be null - all viewports returned in that
1875 * @return all viewports on the alignment bound to sequenceSetId
1877 public static AlignmentViewport[] getViewports(String sequenceSetId)
1879 List<AlignmentViewport> viewp = new ArrayList<>();
1880 if (desktop != null)
1882 AlignFrame[] frames = Desktop.getAlignFrames();
1884 for (AlignFrame afr : frames)
1886 if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
1887 .equals(sequenceSetId))
1889 if (afr.alignPanels != null)
1891 for (AlignmentPanel ap : afr.alignPanels)
1893 if (sequenceSetId == null
1894 || sequenceSetId.equals(ap.av.getSequenceSetId()))
1902 viewp.add(afr.getViewport());
1906 if (viewp.size() > 0)
1908 return viewp.toArray(new AlignmentViewport[viewp.size()]);
1915 * Explode the views in the given frame into separate AlignFrame
1919 public static void explodeViews(AlignFrame af)
1921 int size = af.alignPanels.size();
1927 // FIXME: ideally should use UI interface API
1928 FeatureSettings viewFeatureSettings = (af.featureSettings != null
1929 && af.featureSettings.isOpen())
1930 ? af.featureSettings
1932 Rectangle fsBounds = af.getFeatureSettingsGeometry();
1933 for (int i = 0; i < size; i++)
1935 AlignmentPanel ap = af.alignPanels.get(i);
1937 AlignFrame newaf = new AlignFrame(ap);
1939 // transfer reference for existing feature settings to new alignFrame
1940 if (ap == af.alignPanel)
1942 if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
1944 newaf.featureSettings = viewFeatureSettings;
1946 newaf.setFeatureSettingsGeometry(fsBounds);
1950 * Restore the view's last exploded frame geometry if known. Multiple
1951 * views from one exploded frame share and restore the same (frame)
1952 * position and size.
1954 Rectangle geometry = ap.av.getExplodedGeometry();
1955 if (geometry != null)
1957 newaf.setBounds(geometry);
1960 ap.av.setGatherViewsHere(false);
1962 addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
1963 AlignFrame.DEFAULT_HEIGHT);
1964 // and materialise a new feature settings dialog instance for the new alignframe
1965 // (closes the old as if 'OK' was pressed)
1966 if (ap == af.alignPanel && newaf.featureSettings != null
1967 && newaf.featureSettings.isOpen()
1968 && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
1970 newaf.showFeatureSettingsUI();
1974 af.featureSettings = null;
1975 af.alignPanels.clear();
1976 af.closeMenuItem_actionPerformed(true);
1981 * Gather expanded views (separate AlignFrame's) with the same sequence set
1982 * identifier back in to this frame as additional views, and close the
1983 * expanded views. Note the expanded frames may themselves have multiple
1984 * views. We take the lot.
1988 public void gatherViews(AlignFrame source)
1990 source.viewport.setGatherViewsHere(true);
1991 source.viewport.setExplodedGeometry(source.getBounds());
1992 JInternalFrame[] frames = desktop.getAllFrames();
1993 String viewId = source.viewport.getSequenceSetId();
1994 for (int t = 0; t < frames.length; t++)
1996 if (frames[t] instanceof AlignFrame && frames[t] != source)
1998 AlignFrame af = (AlignFrame) frames[t];
1999 boolean gatherThis = false;
2000 for (int a = 0; a < af.alignPanels.size(); a++)
2002 AlignmentPanel ap = af.alignPanels.get(a);
2003 if (viewId.equals(ap.av.getSequenceSetId()))
2006 ap.av.setGatherViewsHere(false);
2007 ap.av.setExplodedGeometry(af.getBounds());
2008 source.addAlignmentPanel(ap, false);
2014 if (af.featureSettings != null && af.featureSettings.isOpen())
2016 if (source.featureSettings == null)
2018 // preserve the feature settings geometry for this frame
2019 source.featureSettings = af.featureSettings;
2020 source.setFeatureSettingsGeometry(
2021 af.getFeatureSettingsGeometry());
2025 // close it and forget
2026 af.featureSettings.close();
2029 af.alignPanels.clear();
2030 af.closeMenuItem_actionPerformed(true);
2034 // refresh the feature setting UI for the source frame if it exists
2035 if (source.featureSettings != null
2036 && source.featureSettings.isOpen())
2038 source.showFeatureSettingsUI();
2043 public JInternalFrame[] getAllFrames()
2045 return desktop.getAllFrames();
2049 * Checks the given url to see if it gives a response indicating that the user
2050 * should be informed of a new questionnaire.
2054 public void checkForQuestionnaire(String url)
2056 UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
2057 // javax.swing.SwingUtilities.invokeLater(jvq);
2058 new Thread(jvq).start();
2061 public void checkURLLinks()
2063 // Thread off the URL link checker
2064 addDialogThread(new Runnable()
2069 if (Cache.getDefault("CHECKURLLINKS", true))
2071 // check what the actual links are - if it's just the default don't
2072 // bother with the warning
2073 List<String> links = Preferences.sequenceUrlLinks
2076 // only need to check links if there is one with a
2077 // SEQUENCE_ID which is not the default EMBL_EBI link
2078 ListIterator<String> li = links.listIterator();
2079 boolean check = false;
2080 List<JLabel> urls = new ArrayList<>();
2081 while (li.hasNext())
2083 String link = li.next();
2084 if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID)
2085 && !UrlConstants.isDefaultString(link))
2088 int barPos = link.indexOf("|");
2089 String urlMsg = barPos == -1 ? link
2090 : link.substring(0, barPos) + ": "
2091 + link.substring(barPos + 1);
2092 urls.add(new JLabel(urlMsg));
2100 // ask user to check in case URL links use old style tokens
2101 // ($SEQUENCE_ID$ for sequence id _or_ accession id)
2102 JPanel msgPanel = new JPanel();
2103 msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
2104 msgPanel.add(Box.createVerticalGlue());
2105 JLabel msg = new JLabel(MessageManager
2106 .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
2107 JLabel msg2 = new JLabel(MessageManager
2108 .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
2110 for (JLabel url : urls)
2116 final JCheckBox jcb = new JCheckBox(
2117 MessageManager.getString("label.do_not_display_again"));
2118 jcb.addActionListener(new ActionListener()
2121 public void actionPerformed(ActionEvent e)
2123 // update Cache settings for "don't show this again"
2124 boolean showWarningAgain = !jcb.isSelected();
2125 Cache.setProperty("CHECKURLLINKS",
2126 Boolean.valueOf(showWarningAgain).toString());
2131 JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
2133 .getString("label.SEQUENCE_ID_no_longer_used"),
2134 JvOptionPane.WARNING_MESSAGE);
2141 * Proxy class for JDesktopPane which optionally displays the current memory
2142 * usage and highlights the desktop area with a red bar if free memory runs
2147 public class MyDesktopPane extends JDesktopPane implements Runnable
2150 private static final float ONE_MB = 1048576f;
2152 boolean showMemoryUsage = false;
2156 java.text.NumberFormat df;
2158 float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
2161 public MyDesktopPane(boolean showMemoryUsage)
2163 showMemoryUsage(showMemoryUsage);
2166 public void showMemoryUsage(boolean showMemory)
2168 this.showMemoryUsage = showMemory;
2171 Thread worker = new Thread(this);
2177 public boolean isShowMemoryUsage()
2179 return showMemoryUsage;
2185 df = java.text.NumberFormat.getNumberInstance();
2186 df.setMaximumFractionDigits(2);
2187 runtime = Runtime.getRuntime();
2189 while (showMemoryUsage)
2193 maxMemory = runtime.maxMemory() / ONE_MB;
2194 allocatedMemory = runtime.totalMemory() / ONE_MB;
2195 freeMemory = runtime.freeMemory() / ONE_MB;
2196 totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
2198 percentUsage = (totalFreeMemory / maxMemory) * 100;
2200 // if (percentUsage < 20)
2202 // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12,
2204 // instance.set.setBorder(border1);
2207 // sleep after showing usage
2209 } catch (Exception ex)
2211 ex.printStackTrace();
2217 public void paintComponent(Graphics g)
2219 if (showMemoryUsage && g != null && df != null)
2221 if (percentUsage < 20)
2223 g.setColor(Color.red);
2225 FontMetrics fm = g.getFontMetrics();
2228 g.drawString(MessageManager.formatMessage("label.memory_stats",
2230 { df.format(totalFreeMemory), df.format(maxMemory),
2231 df.format(percentUsage) }),
2232 10, getHeight() - fm.getHeight());
2239 * Accessor method to quickly get all the AlignmentFrames loaded.
2241 * @return an array of AlignFrame, or null if none found
2243 public static AlignFrame[] getAlignFrames()
2245 if (Jalview.isHeadlessMode())
2247 // Desktop.desktop is null in headless mode
2248 return new AlignFrame[] { Jalview.currentAlignFrame };
2251 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
2257 List<AlignFrame> avp = new ArrayList<>();
2259 for (int i = frames.length - 1; i > -1; i--)
2261 if (frames[i] instanceof AlignFrame)
2263 avp.add((AlignFrame) frames[i]);
2265 else if (frames[i] instanceof SplitFrame)
2268 * Also check for a split frame containing an AlignFrame
2270 GSplitFrame sf = (GSplitFrame) frames[i];
2271 if (sf.getTopFrame() instanceof AlignFrame)
2273 avp.add((AlignFrame) sf.getTopFrame());
2275 if (sf.getBottomFrame() instanceof AlignFrame)
2277 avp.add((AlignFrame) sf.getBottomFrame());
2281 if (avp.size() == 0)
2285 AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]);
2290 * Returns an array of any AppJmol frames in the Desktop (or null if none).
2294 public GStructureViewer[] getJmols()
2296 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
2302 List<GStructureViewer> avp = new ArrayList<>();
2304 for (int i = frames.length - 1; i > -1; i--)
2306 if (frames[i] instanceof AppJmol)
2308 GStructureViewer af = (GStructureViewer) frames[i];
2312 if (avp.size() == 0)
2316 GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]);
2321 * Add Groovy Support to Jalview
2324 public void groovyShell_actionPerformed()
2328 openGroovyConsole();
2329 } catch (Exception ex)
2331 jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
2332 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
2334 MessageManager.getString("label.couldnt_create_groovy_shell"),
2335 MessageManager.getString("label.groovy_support_failed"),
2336 JvOptionPane.ERROR_MESSAGE);
2341 * Open the Groovy console
2343 void openGroovyConsole()
2345 if (groovyConsole == null)
2347 groovyConsole = new groovy.ui.Console();
2348 groovyConsole.setVariable("Jalview", this);
2349 groovyConsole.run();
2352 * We allow only one console at a time, so that AlignFrame menu option
2353 * 'Calculate | Run Groovy script' is unambiguous.
2354 * Disable 'Groovy Console', and enable 'Run script', when the console is
2355 * opened, and the reverse when it is closed
2357 Window window = (Window) groovyConsole.getFrame();
2358 window.addWindowListener(new WindowAdapter()
2361 public void windowClosed(WindowEvent e)
2364 * rebind CMD-Q from Groovy Console to Jalview Quit
2367 enableExecuteGroovy(false);
2373 * show Groovy console window (after close and reopen)
2375 ((Window) groovyConsole.getFrame()).setVisible(true);
2378 * if we got this far, enable 'Run Groovy' in AlignFrame menus
2379 * and disable opening a second console
2381 enableExecuteGroovy(true);
2385 * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
2386 * binding when opened
2388 protected void addQuitHandler()
2390 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
2391 .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
2392 jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
2394 getRootPane().getActionMap().put("Quit", new AbstractAction()
2397 public void actionPerformed(ActionEvent e)
2405 * Enable or disable 'Run Groovy script' in AlignFrame calculate menus
2408 * true if Groovy console is open
2410 public void enableExecuteGroovy(boolean enabled)
2413 * disable opening a second Groovy console
2414 * (or re-enable when the console is closed)
2416 groovyShell.setEnabled(!enabled);
2418 AlignFrame[] alignFrames = getAlignFrames();
2419 if (alignFrames != null)
2421 for (AlignFrame af : alignFrames)
2423 af.setGroovyEnabled(enabled);
2429 * Progress bars managed by the IProgressIndicator method.
2431 private Hashtable<Long, JPanel> progressBars;
2433 private Hashtable<Long, IProgressIndicatorHandler> progressBarHandlers;
2438 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
2441 public void setProgressBar(String message, long id)
2443 if (progressBars == null)
2445 progressBars = new Hashtable<>();
2446 progressBarHandlers = new Hashtable<>();
2449 if (progressBars.get(Long.valueOf(id)) != null)
2451 JPanel panel = progressBars.remove(Long.valueOf(id));
2452 if (progressBarHandlers.contains(Long.valueOf(id)))
2454 progressBarHandlers.remove(Long.valueOf(id));
2456 removeProgressPanel(panel);
2460 progressBars.put(Long.valueOf(id), addProgressPanel(message));
2467 * @see jalview.gui.IProgressIndicator#registerHandler(long,
2468 * jalview.gui.IProgressIndicatorHandler)
2471 public void registerHandler(final long id,
2472 final IProgressIndicatorHandler handler)
2474 if (progressBarHandlers == null
2475 || !progressBars.containsKey(Long.valueOf(id)))
2477 throw new Error(MessageManager.getString(
2478 "error.call_setprogressbar_before_registering_handler"));
2480 progressBarHandlers.put(Long.valueOf(id), handler);
2481 final JPanel progressPanel = progressBars.get(Long.valueOf(id));
2482 if (handler.canCancel())
2484 JButton cancel = new JButton(
2485 MessageManager.getString("action.cancel"));
2486 final IProgressIndicator us = this;
2487 cancel.addActionListener(new ActionListener()
2491 public void actionPerformed(ActionEvent e)
2493 handler.cancelActivity(id);
2494 us.setProgressBar(MessageManager
2495 .formatMessage("label.cancelled_params", new Object[]
2496 { ((JLabel) progressPanel.getComponent(0)).getText() }),
2500 progressPanel.add(cancel, BorderLayout.EAST);
2506 * @return true if any progress bars are still active
2509 public boolean operationInProgress()
2511 if (progressBars != null && progressBars.size() > 0)
2519 * This will return the first AlignFrame holding the given viewport instance.
2520 * It will break if there are more than one AlignFrames viewing a particular
2524 * @return alignFrame for viewport
2526 public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
2528 if (desktop != null)
2530 AlignmentPanel[] aps = getAlignmentPanels(
2531 viewport.getSequenceSetId());
2532 for (int panel = 0; aps != null && panel < aps.length; panel++)
2534 if (aps[panel] != null && aps[panel].av == viewport)
2536 return aps[panel].alignFrame;
2543 public VamsasApplication getVamsasApplication()
2545 // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
2551 * flag set if jalview GUI is being operated programmatically
2553 private boolean inBatchMode = false;
2556 * check if jalview GUI is being operated programmatically
2558 * @return inBatchMode
2560 public boolean isInBatchMode()
2566 * set flag if jalview GUI is being operated programmatically
2568 * @param inBatchMode
2570 public void setInBatchMode(boolean inBatchMode)
2572 this.inBatchMode = inBatchMode;
2575 public void startServiceDiscovery()
2577 startServiceDiscovery(false);
2580 public void startServiceDiscovery(boolean blocking)
2582 boolean alive = true;
2583 Thread t0 = null, t1 = null, t2 = null;
2584 // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
2587 // todo: changesupport handlers need to be transferred
2588 if (discoverer == null)
2590 discoverer = new jalview.ws.jws1.Discoverer();
2591 // register PCS handler for desktop.
2592 discoverer.addPropertyChangeListener(changeSupport);
2594 // JAL-940 - disabled JWS1 service configuration - always start discoverer
2595 // until we phase out completely
2596 (t0 = new Thread(discoverer)).start();
2599 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
2601 t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
2602 .startDiscoverer(changeSupport);
2606 // start slivka discovery
2607 t3 = new Thread(jalview.ws.slivkaws.SlivkaWSDiscoverer.getInstance());
2617 } catch (Exception e)
2620 alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
2621 || (t3 != null && t3.isAlive())
2622 || (t0 != null && t0.isAlive());
2628 * called to check if the service discovery process completed successfully.
2632 protected void JalviewServicesChanged(PropertyChangeEvent evt)
2634 if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
2636 final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
2637 .getErrorMessages();
2640 if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
2642 if (serviceChangedDialog == null)
2644 // only run if we aren't already displaying one of these.
2645 addDialogThread(serviceChangedDialog = new Runnable()
2652 * JalviewDialog jd =new JalviewDialog() {
2654 * @Override protected void cancelPressed() { // TODO
2655 * Auto-generated method stub
2657 * }@Override protected void okPressed() { // TODO
2658 * Auto-generated method stub
2660 * }@Override protected void raiseClosed() { // TODO
2661 * Auto-generated method stub
2663 * } }; jd.initDialogFrame(new
2664 * JLabel("<html><table width=\"450\"><tr><td>" + ermsg +
2665 * "<br/>It may be that you have invalid JABA URLs in your web service preferences,"
2666 * + " or mis-configured HTTP proxy settings.<br/>" +
2667 * "Check the <em>Connections</em> and <em>Web services</em> tab of the"
2669 * " Tools->Preferences dialog box to change them.</td></tr></table></html>"
2670 * ), true, true, "Web Service Configuration Problem", 450,
2673 * jd.waitForInput();
2675 JvOptionPane.showConfirmDialog(Desktop.desktop,
2676 new JLabel("<html><table width=\"450\"><tr><td>"
2677 + ermsg + "</td></tr></table>"
2678 + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
2679 + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
2680 + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
2681 + " Tools->Preferences dialog box to change them.</p></html>"),
2682 "Web Service Configuration Problem",
2683 JvOptionPane.DEFAULT_OPTION,
2684 JvOptionPane.ERROR_MESSAGE);
2685 serviceChangedDialog = null;
2694 "Errors reported by JABA discovery service. Check web services preferences.\n"
2701 private Runnable serviceChangedDialog = null;
2704 * start a thread to open a URL in the configured browser. Pops up a warning
2705 * dialog to the user if there is an exception when calling out to the browser
2710 public static void showUrl(final String url)
2712 showUrl(url, Desktop.instance);
2716 * Like showUrl but allows progress handler to be specified
2720 * (null) or object implementing IProgressIndicator
2722 public static void showUrl(final String url,
2723 final IProgressIndicator progress)
2725 new Thread(new Runnable()
2732 if (progress != null)
2734 progress.setProgressBar(MessageManager
2735 .formatMessage("status.opening_params", new Object[]
2736 { url }), this.hashCode());
2738 jalview.util.BrowserLauncher.openURL(url);
2739 } catch (Exception ex)
2741 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
2743 .getString("label.web_browser_not_found_unix"),
2744 MessageManager.getString("label.web_browser_not_found"),
2745 JvOptionPane.WARNING_MESSAGE);
2747 ex.printStackTrace();
2749 if (progress != null)
2751 progress.setProgressBar(null, this.hashCode());
2757 public static WsParamSetManager wsparamManager = null;
2759 public static ParamManager getUserParameterStore()
2761 if (wsparamManager == null)
2763 wsparamManager = new WsParamSetManager();
2765 return wsparamManager;
2769 * static hyperlink handler proxy method for use by Jalview's internal windows
2773 public static void hyperlinkUpdate(HyperlinkEvent e)
2775 if (e.getEventType() == EventType.ACTIVATED)
2780 url = e.getURL().toString();
2781 Desktop.showUrl(url);
2782 } catch (Exception x)
2786 if (Cache.log != null)
2788 Cache.log.error("Couldn't handle string " + url + " as a URL.");
2793 "Couldn't handle string " + url + " as a URL.");
2796 // ignore any exceptions due to dud links.
2803 * single thread that handles display of dialogs to user.
2805 ExecutorService dialogExecutor = Executors.newSingleThreadExecutor();
2808 * flag indicating if dialogExecutor should try to acquire a permit
2810 private volatile boolean dialogPause = true;
2815 private java.util.concurrent.Semaphore block = new Semaphore(0);
2817 private static groovy.ui.Console groovyConsole;
2820 * add another dialog thread to the queue
2824 public void addDialogThread(final Runnable prompter)
2826 dialogExecutor.submit(new Runnable()
2836 } catch (InterruptedException x)
2841 if (instance == null)
2847 SwingUtilities.invokeAndWait(prompter);
2848 } catch (Exception q)
2850 Cache.log.warn("Unexpected Exception in dialog thread.", q);
2856 public void startDialogQueue()
2858 // set the flag so we don't pause waiting for another permit and semaphore
2859 // the current task to begin
2860 dialogPause = false;
2865 protected void snapShotWindow_actionPerformed(ActionEvent e)
2869 ImageMaker im = new jalview.util.ImageMaker(
2870 this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(),
2871 getHeight(), of = new File("Jalview_snapshot"
2872 + System.currentTimeMillis() + ".eps"),
2873 "View of desktop", null, 0, false);
2876 paintAll(im.getGraphics());
2878 } catch (Exception q)
2880 Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
2884 Cache.log.info("Successfully written snapshot to file "
2885 + of.getAbsolutePath());
2889 * Explode the views in the given SplitFrame into separate SplitFrame windows.
2890 * This respects (remembers) any previous 'exploded geometry' i.e. the size
2891 * and location last time the view was expanded (if any). However it does not
2892 * remember the split pane divider location - this is set to match the
2893 * 'exploding' frame.
2897 public void explodeViews(SplitFrame sf)
2899 AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame();
2900 AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame();
2901 List<? extends AlignmentViewPanel> topPanels = oldTopFrame
2903 List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame
2905 int viewCount = topPanels.size();
2912 * Processing in reverse order works, forwards order leaves the first panels
2913 * not visible. I don't know why!
2915 for (int i = viewCount - 1; i >= 0; i--)
2918 * Make new top and bottom frames. These take over the respective
2919 * AlignmentPanel objects, including their AlignmentViewports, so the
2920 * cdna/protein relationships between the viewports is carried over to the
2923 * explodedGeometry holds the (x, y) position of the previously exploded
2924 * SplitFrame, and the (width, height) of the AlignFrame component
2926 AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i);
2927 AlignFrame newTopFrame = new AlignFrame(topPanel);
2928 newTopFrame.setSize(oldTopFrame.getSize());
2929 newTopFrame.setVisible(true);
2930 Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
2931 .getExplodedGeometry();
2932 if (geometry != null)
2934 newTopFrame.setSize(geometry.getSize());
2937 AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i);
2938 AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
2939 newBottomFrame.setSize(oldBottomFrame.getSize());
2940 newBottomFrame.setVisible(true);
2941 geometry = ((AlignViewport) bottomPanel.getAlignViewport())
2942 .getExplodedGeometry();
2943 if (geometry != null)
2945 newBottomFrame.setSize(geometry.getSize());
2948 topPanel.av.setGatherViewsHere(false);
2949 bottomPanel.av.setGatherViewsHere(false);
2950 JInternalFrame splitFrame = new SplitFrame(newTopFrame,
2952 if (geometry != null)
2954 splitFrame.setLocation(geometry.getLocation());
2956 Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
2960 * Clear references to the panels (now relocated in the new SplitFrames)
2961 * before closing the old SplitFrame.
2964 bottomPanels.clear();
2969 * Gather expanded split frames, sharing the same pairs of sequence set ids,
2970 * back into the given SplitFrame as additional views. Note that the gathered
2971 * frames may themselves have multiple views.
2975 public void gatherViews(GSplitFrame source)
2978 * special handling of explodedGeometry for a view within a SplitFrame: - it
2979 * holds the (x, y) position of the enclosing SplitFrame, and the (width,
2980 * height) of the AlignFrame component
2982 AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
2983 AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
2984 myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
2985 source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
2986 myBottomFrame.viewport
2987 .setExplodedGeometry(new Rectangle(source.getX(), source.getY(),
2988 myBottomFrame.getWidth(), myBottomFrame.getHeight()));
2989 myTopFrame.viewport.setGatherViewsHere(true);
2990 myBottomFrame.viewport.setGatherViewsHere(true);
2991 String topViewId = myTopFrame.viewport.getSequenceSetId();
2992 String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
2994 JInternalFrame[] frames = desktop.getAllFrames();
2995 for (JInternalFrame frame : frames)
2997 if (frame instanceof SplitFrame && frame != source)
2999 SplitFrame sf = (SplitFrame) frame;
3000 AlignFrame topFrame = (AlignFrame) sf.getTopFrame();
3001 AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame();
3002 boolean gatherThis = false;
3003 for (int a = 0; a < topFrame.alignPanels.size(); a++)
3005 AlignmentPanel topPanel = topFrame.alignPanels.get(a);
3006 AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a);
3007 if (topViewId.equals(topPanel.av.getSequenceSetId())
3008 && bottomViewId.equals(bottomPanel.av.getSequenceSetId()))
3011 topPanel.av.setGatherViewsHere(false);
3012 bottomPanel.av.setGatherViewsHere(false);
3013 topPanel.av.setExplodedGeometry(
3014 new Rectangle(sf.getLocation(), topFrame.getSize()));
3015 bottomPanel.av.setExplodedGeometry(
3016 new Rectangle(sf.getLocation(), bottomFrame.getSize()));
3017 myTopFrame.addAlignmentPanel(topPanel, false);
3018 myBottomFrame.addAlignmentPanel(bottomPanel, false);
3024 topFrame.getAlignPanels().clear();
3025 bottomFrame.getAlignPanels().clear();
3032 * The dust settles...give focus to the tab we did this from.
3034 myTopFrame.setDisplayedView(myTopFrame.alignPanel);
3037 public static groovy.ui.Console getGroovyConsole()
3039 return groovyConsole;
3043 * handles the payload of a drag and drop event.
3045 * TODO refactor to desktop utilities class
3048 * - Data source strings extracted from the drop event
3050 * - protocol for each data source extracted from the drop event
3054 * - the payload from the drop event
3057 public static void transferFromDropTarget(List<String> files,
3058 List<DataSourceType> protocols, DropTargetDropEvent evt,
3059 Transferable t) throws Exception
3062 DataFlavor uriListFlavor = new DataFlavor(
3063 "text/uri-list;class=java.lang.String"), urlFlavour = null;
3066 urlFlavour = new DataFlavor(
3067 "application/x-java-url; class=java.net.URL");
3068 } catch (ClassNotFoundException cfe)
3070 Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
3073 if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
3078 java.net.URL url = (URL) t.getTransferData(urlFlavour);
3079 // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
3080 // means url may be null.
3083 protocols.add(DataSourceType.URL);
3084 files.add(url.toString());
3085 Cache.log.debug("Drop handled as URL dataflavor "
3086 + files.get(files.size() - 1));
3091 if (Platform.isAMac())
3094 "Please ignore plist error - occurs due to problem with java 8 on OSX");
3098 } catch (Throwable ex)
3100 Cache.log.debug("URL drop handler failed.", ex);
3103 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3105 // Works on Windows and MacOSX
3106 Cache.log.debug("Drop handled as javaFileListFlavor");
3107 for (Object file : (List) t
3108 .getTransferData(DataFlavor.javaFileListFlavor))
3110 files.add(((File) file).toString());
3111 protocols.add(DataSourceType.FILE);
3116 // Unix like behaviour
3117 boolean added = false;
3119 if (t.isDataFlavorSupported(uriListFlavor))
3121 Cache.log.debug("Drop handled as uriListFlavor");
3122 // This is used by Unix drag system
3123 data = (String) t.getTransferData(uriListFlavor);
3127 // fallback to text: workaround - on OSX where there's a JVM bug
3128 Cache.log.debug("standard URIListFlavor failed. Trying text");
3129 // try text fallback
3130 DataFlavor textDf = new DataFlavor(
3131 "text/plain;class=java.lang.String");
3132 if (t.isDataFlavorSupported(textDf))
3134 data = (String) t.getTransferData(textDf);
3137 Cache.log.debug("Plain text drop content returned "
3138 + (data == null ? "Null - failed" : data));
3143 while (protocols.size() < files.size())
3145 Cache.log.debug("Adding missing FILE protocol for "
3146 + files.get(protocols.size()));
3147 protocols.add(DataSourceType.FILE);
3149 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3150 data, "\r\n"); st.hasMoreTokens();)
3153 String s = st.nextToken();
3154 if (s.startsWith("#"))
3156 // the line is a comment (as per the RFC 2483)
3159 java.net.URI uri = new java.net.URI(s);
3160 if (uri.getScheme().toLowerCase().startsWith("http"))
3162 protocols.add(DataSourceType.URL);
3163 files.add(uri.toString());
3167 // otherwise preserve old behaviour: catch all for file objects
3168 java.io.File file = new java.io.File(uri);
3169 protocols.add(DataSourceType.FILE);
3170 files.add(file.toString());
3175 if (Cache.log.isDebugEnabled())
3177 if (data == null || !added)
3180 if (t.getTransferDataFlavors() != null
3181 && t.getTransferDataFlavors().length > 0)
3184 "Couldn't resolve drop data. Here are the supported flavors:");
3185 for (DataFlavor fl : t.getTransferDataFlavors())
3188 "Supported transfer dataflavor: " + fl.toString());
3189 Object df = t.getTransferData(fl);
3192 Cache.log.debug("Retrieves: " + df);
3196 Cache.log.debug("Retrieved nothing");
3202 Cache.log.debug("Couldn't resolve dataflavor for drop: "
3208 if (Platform.isWindows())
3211 Cache.log.debug("Scanning dropped content for Windows Link Files");
3213 // resolve any .lnk files in the file drop
3214 for (int f = 0; f < files.size(); f++)
3216 String source = files.get(f).toLowerCase();
3217 if (protocols.get(f).equals(DataSourceType.FILE)
3218 && (source.endsWith(".lnk") || source.endsWith(".url")
3219 || source.endsWith(".site")))
3223 File lf = new File(files.get(f));
3224 // process link file to get a URL
3225 Cache.log.debug("Found potential link file: " + lf);
3226 WindowsShortcut wscfile = new WindowsShortcut(lf);
3227 String fullname = wscfile.getRealFilename();
3228 protocols.set(f, FormatAdapter.checkProtocol(fullname));
3229 files.set(f, fullname);
3230 Cache.log.debug("Parsed real filename " + fullname
3231 + " to extract protocol: " + protocols.get(f));
3232 } catch (Exception ex)
3235 "Couldn't parse " + files.get(f) + " as a link file.",
3244 * Sets the Preferences property for experimental features to True or False
3245 * depending on the state of the controlling menu item
3248 protected void showExperimental_actionPerformed(boolean selected)
3250 Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
3254 * Answers a (possibly empty) list of any structure viewer frames (currently
3255 * for either Jmol or Chimera) which are currently open. This may optionally
3256 * be restricted to viewers of a specified class, or viewers linked to a
3257 * specified alignment panel.
3260 * if not null, only return viewers linked to this panel
3261 * @param structureViewerClass
3262 * if not null, only return viewers of this class
3265 public List<StructureViewerBase> getStructureViewers(
3266 AlignmentPanel apanel,
3267 Class<? extends StructureViewerBase> structureViewerClass)
3269 List<StructureViewerBase> result = new ArrayList<>();
3270 JInternalFrame[] frames = Desktop.instance.getAllFrames();
3272 for (JInternalFrame frame : frames)
3274 if (frame instanceof StructureViewerBase)
3276 if (structureViewerClass == null
3277 || structureViewerClass.isInstance(frame))
3280 || ((StructureViewerBase) frame).isLinkedWith(apanel))
3282 result.add((StructureViewerBase) frame);