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 static jalview.util.UrlConstants.SEQUENCE_ID;
25 import jalview.api.AlignViewportI;
26 import jalview.api.AlignmentViewPanel;
27 import jalview.bin.Cache;
28 import jalview.bin.Jalview;
29 import jalview.io.DataSourceType;
30 import jalview.io.FileFormat;
31 import jalview.io.FileFormatException;
32 import jalview.io.FileFormatI;
33 import jalview.io.FileFormats;
34 import jalview.io.FileLoader;
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.structure.StructureSelectionManager;
41 import jalview.urls.IdOrgSettings;
42 import jalview.util.ImageMaker;
43 import jalview.util.MessageManager;
44 import jalview.util.Platform;
45 import jalview.util.UrlConstants;
46 import jalview.viewmodel.AlignmentViewport;
47 import jalview.ws.params.ParamManager;
48 import jalview.ws.utils.UrlDownloadClient;
50 import java.awt.BorderLayout;
51 import java.awt.Color;
52 import java.awt.Dimension;
53 import java.awt.FontMetrics;
54 import java.awt.Graphics;
55 import java.awt.GridLayout;
56 import java.awt.Point;
57 import java.awt.Rectangle;
58 import java.awt.Toolkit;
59 import java.awt.Window;
60 import java.awt.datatransfer.Clipboard;
61 import java.awt.datatransfer.ClipboardOwner;
62 import java.awt.datatransfer.DataFlavor;
63 import java.awt.datatransfer.Transferable;
64 import java.awt.dnd.DnDConstants;
65 import java.awt.dnd.DropTargetDragEvent;
66 import java.awt.dnd.DropTargetDropEvent;
67 import java.awt.dnd.DropTargetEvent;
68 import java.awt.dnd.DropTargetListener;
69 import java.awt.event.ActionEvent;
70 import java.awt.event.ActionListener;
71 import java.awt.event.KeyEvent;
72 import java.awt.event.MouseAdapter;
73 import java.awt.event.MouseEvent;
74 import java.awt.event.WindowAdapter;
75 import java.awt.event.WindowEvent;
76 import java.beans.PropertyChangeEvent;
77 import java.beans.PropertyChangeListener;
78 import java.io.BufferedInputStream;
80 import java.io.FileOutputStream;
81 import java.io.IOException;
83 import java.util.ArrayList;
84 import java.util.Hashtable;
85 import java.util.List;
86 import java.util.ListIterator;
87 import java.util.StringTokenizer;
88 import java.util.Vector;
89 import java.util.concurrent.ExecutorService;
90 import java.util.concurrent.Executors;
91 import java.util.concurrent.Semaphore;
93 import javax.swing.AbstractAction;
94 import javax.swing.Box;
95 import javax.swing.BoxLayout;
96 import javax.swing.DefaultDesktopManager;
97 import javax.swing.DesktopManager;
98 import javax.swing.JButton;
99 import javax.swing.JCheckBox;
100 import javax.swing.JComboBox;
101 import javax.swing.JComponent;
102 import javax.swing.JDesktopPane;
103 import javax.swing.JFrame;
104 import javax.swing.JInternalFrame;
105 import javax.swing.JLabel;
106 import javax.swing.JMenuItem;
107 import javax.swing.JPanel;
108 import javax.swing.JPopupMenu;
109 import javax.swing.JProgressBar;
110 import javax.swing.KeyStroke;
111 import javax.swing.SwingUtilities;
112 import javax.swing.event.HyperlinkEvent;
113 import javax.swing.event.HyperlinkEvent.EventType;
114 import javax.swing.event.InternalFrameAdapter;
115 import javax.swing.event.InternalFrameEvent;
116 import javax.swing.event.MenuEvent;
117 import javax.swing.event.MenuListener;
124 * @version $Revision: 1.155 $
126 public class Desktop extends jalview.jbgui.GDesktop
127 implements DropTargetListener, ClipboardOwner, IProgressIndicator,
128 jalview.api.StructureSelectionManagerProvider
130 private static int DEFAULT_MIN_WIDTH = 300;
132 private static int DEFAULT_MIN_HEIGHT = 250;
134 private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600;
136 private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70;
138 private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
140 private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
143 * news reader - null if it was never started.
145 private BlogReader jvnews = null;
147 private File projectFile;
151 * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
153 public void addJalviewPropertyChangeListener(
154 PropertyChangeListener listener)
156 changeSupport.addJalviewPropertyChangeListener(listener);
160 * @param propertyName
162 * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
163 * java.beans.PropertyChangeListener)
165 public void addJalviewPropertyChangeListener(String propertyName,
166 PropertyChangeListener listener)
168 changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
172 * @param propertyName
174 * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
175 * java.beans.PropertyChangeListener)
177 public void removeJalviewPropertyChangeListener(String propertyName,
178 PropertyChangeListener listener)
180 changeSupport.removeJalviewPropertyChangeListener(propertyName,
184 /** Singleton Desktop instance */
185 public static Desktop instance;
187 public static MyDesktopPane desktop;
189 static int openFrameCount = 0;
191 static final int xOffset = 30;
193 static final int yOffset = 30;
195 public static jalview.ws.jws1.Discoverer discoverer;
197 public static Object[] jalviewClipboard;
199 public static boolean internalCopy = false;
201 static int fileLoadingCount = 0;
203 class MyDesktopManager implements DesktopManager
206 private DesktopManager delegate;
208 public MyDesktopManager(DesktopManager delegate)
210 this.delegate = delegate;
214 public void activateFrame(JInternalFrame f)
218 delegate.activateFrame(f);
219 } catch (NullPointerException npe)
221 Point p = getMousePosition();
222 instance.showPasteMenu(p.x, p.y);
227 public void beginDraggingFrame(JComponent f)
229 delegate.beginDraggingFrame(f);
233 public void beginResizingFrame(JComponent f, int direction)
235 delegate.beginResizingFrame(f, direction);
239 public void closeFrame(JInternalFrame f)
241 delegate.closeFrame(f);
245 public void deactivateFrame(JInternalFrame f)
247 delegate.deactivateFrame(f);
251 public void deiconifyFrame(JInternalFrame f)
253 delegate.deiconifyFrame(f);
257 public void dragFrame(JComponent f, int newX, int newY)
263 delegate.dragFrame(f, newX, newY);
267 public void endDraggingFrame(JComponent f)
269 delegate.endDraggingFrame(f);
274 public void endResizingFrame(JComponent f)
276 delegate.endResizingFrame(f);
281 public void iconifyFrame(JInternalFrame f)
283 delegate.iconifyFrame(f);
287 public void maximizeFrame(JInternalFrame f)
289 delegate.maximizeFrame(f);
293 public void minimizeFrame(JInternalFrame f)
295 delegate.minimizeFrame(f);
299 public void openFrame(JInternalFrame f)
301 delegate.openFrame(f);
305 public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
312 delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
316 public void setBoundsForFrame(JComponent f, int newX, int newY,
317 int newWidth, int newHeight)
319 delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
322 // All other methods, simply delegate
327 * Creates a new Desktop object.
332 * A note to implementors. It is ESSENTIAL that any activities that might
333 * block are spawned off as threads rather than waited for during this
337 doVamsasClientCheck();
339 doConfigureStructurePrefs();
340 setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
341 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
342 boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
344 boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
346 desktop = new MyDesktopPane(selmemusage);
347 showMemusage.setSelected(selmemusage);
348 desktop.setBackground(Color.white);
349 getContentPane().setLayout(new BorderLayout());
350 // alternate config - have scrollbars - see notes in JAL-153
351 // JScrollPane sp = new JScrollPane();
352 // sp.getViewport().setView(desktop);
353 // getContentPane().add(sp, BorderLayout.CENTER);
354 getContentPane().add(desktop, BorderLayout.CENTER);
355 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
357 // This line prevents Windows Look&Feel resizing all new windows to maximum
358 // if previous window was maximised
359 desktop.setDesktopManager(
360 new MyDesktopManager(
361 (Platform.isWindows() ? new DefaultDesktopManager()
363 ? new AquaInternalFrameManager(
364 desktop.getDesktopManager())
365 : desktop.getDesktopManager())));
367 Rectangle dims = getLastKnownDimensions("");
374 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
375 setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2,
378 jconsole = new Console(this, showjconsole);
379 // add essential build information
381 "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
382 + "\n" + "Jalview Installation: "
383 + jalview.bin.Cache.getDefault("INSTALLATION",
385 + "\n" + "Build Date: "
386 + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
387 + "\n" + "Java version: "
388 + System.getProperty("java.version") + "\n"
389 + System.getProperty("os.arch") + " "
390 + System.getProperty("os.name") + " "
391 + System.getProperty("os.version"));
393 showConsole(showjconsole);
395 showNews.setVisible(false);
397 experimentalFeatures.setSelected(showExperimental());
399 getIdentifiersOrgData();
403 this.addWindowListener(new WindowAdapter()
406 public void windowClosing(WindowEvent evt)
413 this.addMouseListener(ma = new MouseAdapter()
416 public void mousePressed(MouseEvent evt)
418 if (evt.isPopupTrigger()) // Mac
420 showPasteMenu(evt.getX(), evt.getY());
425 public void mouseReleased(MouseEvent evt)
427 if (evt.isPopupTrigger()) // Windows
429 showPasteMenu(evt.getX(), evt.getY());
433 desktop.addMouseListener(ma);
435 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
436 // Spawn a thread that shows the splashscreen
437 SwingUtilities.invokeLater(new Runnable()
446 // Thread off a new instance of the file chooser - this reduces the time it
447 // takes to open it later on.
448 new Thread(new Runnable()
453 Cache.log.debug("Filechooser init thread started.");
454 String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
455 JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
457 Cache.log.debug("Filechooser init thread finished.");
460 // Add the service change listener
461 changeSupport.addJalviewPropertyChangeListener("services",
462 new PropertyChangeListener()
466 public void propertyChange(PropertyChangeEvent evt)
468 Cache.log.debug("Firing service changed event for "
469 + evt.getNewValue());
470 JalviewServicesChanged(evt);
477 * Answers true if user preferences to enable experimental features is True
482 public boolean showExperimental()
484 String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
485 Boolean.FALSE.toString());
486 return Boolean.valueOf(experimental).booleanValue();
489 public void doConfigureStructurePrefs()
491 // configure services
492 StructureSelectionManager ssm = StructureSelectionManager
493 .getStructureSelectionManager(this);
494 if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
496 ssm.setAddTempFacAnnot(jalview.bin.Cache
497 .getDefault(Preferences.ADD_TEMPFACT_ANN, true));
498 ssm.setProcessSecondaryStructure(jalview.bin.Cache
499 .getDefault(Preferences.STRUCT_FROM_PDB, true));
500 ssm.setSecStructServices(
501 jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true));
505 ssm.setAddTempFacAnnot(false);
506 ssm.setProcessSecondaryStructure(false);
507 ssm.setSecStructServices(false);
511 public void checkForNews()
513 final Desktop me = this;
514 // Thread off the news reader, in case there are connection problems.
515 addDialogThread(new Runnable()
520 Cache.log.debug("Starting news thread.");
522 jvnews = new BlogReader(me);
523 showNews.setVisible(true);
524 Cache.log.debug("Completed news thread.");
529 public void getIdentifiersOrgData()
531 // Thread off the identifiers fetcher
532 addDialogThread(new Runnable()
537 Cache.log.debug("Downloading data from identifiers.org");
538 UrlDownloadClient client = new UrlDownloadClient();
541 client.download(IdOrgSettings.getUrl(),
542 IdOrgSettings.getDownloadLocation());
543 } catch (IOException e)
545 Cache.log.debug("Exception downloading identifiers.org data"
553 protected void showNews_actionPerformed(ActionEvent e)
555 showNews(showNews.isSelected());
558 void showNews(boolean visible)
561 Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
562 showNews.setSelected(visible);
563 if (visible && !jvnews.isVisible())
565 new Thread(new Runnable()
570 long now = System.currentTimeMillis();
571 Desktop.instance.setProgressBar(
572 MessageManager.getString("status.refreshing_news"),
574 jvnews.refreshNews();
575 Desktop.instance.setProgressBar(null, now);
584 * recover the last known dimensions for a jalview window
587 * - empty string is desktop, all other windows have unique prefix
588 * @return null or last known dimensions scaled to current geometry (if last
589 * window geom was known)
591 Rectangle getLastKnownDimensions(String windowName)
593 // TODO: lock aspect ratio for scaling desktop Bug #0058199
594 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
595 String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
596 String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
597 String width = jalview.bin.Cache
598 .getProperty(windowName + "SCREEN_WIDTH");
599 String height = jalview.bin.Cache
600 .getProperty(windowName + "SCREEN_HEIGHT");
601 if ((x != null) && (y != null) && (width != null) && (height != null))
603 int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
604 iw = Integer.parseInt(width), ih = Integer.parseInt(height);
605 if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
607 // attempt #1 - try to cope with change in screen geometry - this
608 // version doesn't preserve original jv aspect ratio.
609 // take ratio of current screen size vs original screen size.
610 double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(
611 jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
612 double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(
613 jalview.bin.Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
614 // rescale the bounds depending upon the current screen geometry.
615 ix = (int) (ix * sw);
616 iw = (int) (iw * sw);
617 iy = (int) (iy * sh);
618 ih = (int) (ih * sh);
619 while (ix >= screenSize.width)
621 jalview.bin.Cache.log.debug(
622 "Window geometry location recall error: shifting horizontal to within screenbounds.");
623 ix -= screenSize.width;
625 while (iy >= screenSize.height)
627 jalview.bin.Cache.log.debug(
628 "Window geometry location recall error: shifting vertical to within screenbounds.");
629 iy -= screenSize.height;
631 jalview.bin.Cache.log.debug(
632 "Got last known dimensions for " + windowName + ": x:" + ix
633 + " y:" + iy + " width:" + iw + " height:" + ih);
635 // return dimensions for new instance
636 return new Rectangle(ix, iy, iw, ih);
641 private void doVamsasClientCheck()
643 if (jalview.bin.Cache.vamsasJarsPresent())
645 setupVamsasDisconnectedGui();
646 VamsasMenu.setVisible(true);
647 final Desktop us = this;
648 VamsasMenu.addMenuListener(new MenuListener()
650 // this listener remembers when the menu was first selected, and
651 // doesn't rebuild the session list until it has been cleared and
653 boolean refresh = true;
656 public void menuCanceled(MenuEvent e)
662 public void menuDeselected(MenuEvent e)
668 public void menuSelected(MenuEvent e)
672 us.buildVamsasStMenu();
677 vamsasStart.setVisible(true);
681 void showPasteMenu(int x, int y)
683 JPopupMenu popup = new JPopupMenu();
684 JMenuItem item = new JMenuItem(
685 MessageManager.getString("label.paste_new_window"));
686 item.addActionListener(new ActionListener()
689 public void actionPerformed(ActionEvent evt)
696 popup.show(this, x, y);
703 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
704 Transferable contents = c.getContents(this);
706 if (contents != null)
708 String file = (String) contents
709 .getTransferData(DataFlavor.stringFlavor);
711 FileFormatI format = new IdentifyFile().identify(file,
712 DataSourceType.PASTE);
714 new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
717 } catch (Exception ex)
720 "Unable to paste alignment from system clipboard:\n" + ex);
725 * Adds and opens the given frame to the desktop
736 public static synchronized void addInternalFrame(
737 final JInternalFrame frame, String title, int w, int h)
739 addInternalFrame(frame, title, true, w, h, true, false);
743 * Add an internal frame to the Jalview desktop
750 * When true, display frame immediately, otherwise, caller must call
751 * setVisible themselves.
757 public static synchronized void addInternalFrame(
758 final JInternalFrame frame, String title, boolean makeVisible,
761 addInternalFrame(frame, title, makeVisible, w, h, true, false);
765 * Add an internal frame to the Jalview desktop and make it visible
778 public static synchronized void addInternalFrame(
779 final JInternalFrame frame, String title, int w, int h,
782 addInternalFrame(frame, title, true, w, h, resizable, false);
786 * Add an internal frame to the Jalview desktop
793 * When true, display frame immediately, otherwise, caller must call
794 * setVisible themselves.
801 * @param ignoreMinSize
802 * Do not set the default minimum size for frame
804 public static synchronized void addInternalFrame(
805 final JInternalFrame frame, String title, boolean makeVisible,
806 int w, int h, boolean resizable, boolean ignoreMinSize)
809 // TODO: allow callers to determine X and Y position of frame (eg. via
811 // TODO: consider fixing method to update entries in the window submenu with
812 // the current window title
814 frame.setTitle(title);
815 if (frame.getWidth() < 1 || frame.getHeight() < 1)
819 // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
820 // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
821 // IF JALVIEW IS RUNNING HEADLESS
822 // ///////////////////////////////////////////////
823 if (instance == null || (System.getProperty("java.awt.headless") != null
824 && System.getProperty("java.awt.headless").equals("true")))
833 frame.setMinimumSize(
834 new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
836 // Set default dimension for Alignment Frame window.
837 // The Alignment Frame window could be added from a number of places,
839 // I did this here in order not to miss out on any Alignment frame.
840 if (frame instanceof AlignFrame)
842 frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH,
843 ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
847 frame.setVisible(makeVisible);
848 frame.setClosable(true);
849 frame.setResizable(resizable);
850 frame.setMaximizable(resizable);
851 frame.setIconifiable(resizable);
852 frame.setOpaque(false);
854 if (frame.getX() < 1 && frame.getY() < 1)
856 frame.setLocation(xOffset * openFrameCount,
857 yOffset * ((openFrameCount - 1) % 10) + yOffset);
861 * add an entry for the new frame in the Window menu
862 * (and remove it when the frame is closed)
864 final JMenuItem menuItem = new JMenuItem(title);
865 frame.addInternalFrameListener(new InternalFrameAdapter()
868 public void internalFrameActivated(InternalFrameEvent evt)
870 JInternalFrame itf = desktop.getSelectedFrame();
873 if (itf instanceof AlignFrame)
875 Jalview.setCurrentAlignFrame((AlignFrame) itf);
882 public void internalFrameClosed(InternalFrameEvent evt)
884 PaintRefresher.RemoveComponent(frame);
887 * defensive check to prevent frames being
888 * added half off the window
890 if (openFrameCount > 0)
896 * ensure no reference to alignFrame retained by menu item listener
898 if (menuItem.getActionListeners().length > 0)
900 menuItem.removeActionListener(menuItem.getActionListeners()[0]);
902 windowMenu.remove(menuItem);
906 menuItem.addActionListener(new ActionListener()
909 public void actionPerformed(ActionEvent e)
913 frame.setSelected(true);
914 frame.setIcon(false);
915 } catch (java.beans.PropertyVetoException ex)
924 windowMenu.add(menuItem);
929 frame.setSelected(true);
930 frame.requestFocus();
931 } catch (java.beans.PropertyVetoException ve)
933 } catch (java.lang.ClassCastException cex)
936 "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
942 public void lostOwnership(Clipboard clipboard, Transferable contents)
946 Desktop.jalviewClipboard = null;
949 internalCopy = false;
953 public void dragEnter(DropTargetDragEvent evt)
958 public void dragExit(DropTargetEvent evt)
963 public void dragOver(DropTargetDragEvent evt)
968 public void dropActionChanged(DropTargetDragEvent evt)
979 public void drop(DropTargetDropEvent evt)
981 boolean success = true;
982 // JAL-1552 - acceptDrop required before getTransferable call for
983 // Java's Transferable for native dnd
984 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
985 Transferable t = evt.getTransferable();
986 List<String> files = new ArrayList<>();
987 List<DataSourceType> protocols = new ArrayList<>();
991 Desktop.transferFromDropTarget(files, protocols, evt, t);
992 } catch (Exception e)
1002 for (int i = 0; i < files.size(); i++)
1004 String file = files.get(i).toString();
1005 DataSourceType protocol = (protocols == null)
1006 ? DataSourceType.FILE
1008 FileFormatI format = null;
1010 if (file.endsWith(".jar"))
1012 format = FileFormat.Jalview;
1017 format = new IdentifyFile().identify(file, protocol);
1020 new FileLoader().LoadFile(file, protocol, format);
1023 } catch (Exception ex)
1028 evt.dropComplete(success); // need this to ensure input focus is properly
1029 // transfered to any new windows created
1039 public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
1041 String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
1042 JalviewFileChooser chooser = JalviewFileChooser
1043 .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
1045 chooser.setFileView(new JalviewFileView());
1046 chooser.setDialogTitle(
1047 MessageManager.getString("label.open_local_file"));
1048 chooser.setToolTipText(MessageManager.getString("action.open"));
1050 int value = chooser.showOpenDialog(this);
1052 if (value == JalviewFileChooser.APPROVE_OPTION)
1054 String choice = chooser.getSelectedFile().getPath();
1055 Cache.setProperty("LAST_DIRECTORY",
1056 chooser.getSelectedFile().getParent());
1058 FileFormatI format = chooser.getSelectedFormat();
1061 * Call IdentifyFile to verify the file contains what its extension implies.
1062 * Skip this step for dynamically added file formats, because
1063 * IdentifyFile does not know how to recognise them.
1065 if (FileFormats.getInstance().isIdentifiable(format))
1069 format = new IdentifyFile().identify(choice, DataSourceType.FILE);
1070 } catch (FileFormatException e)
1072 // format = null; //??
1076 if (viewport != null)
1078 new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE,
1083 new FileLoader().LoadFile(choice, DataSourceType.FILE, format);
1095 public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
1097 // This construct allows us to have a wider textfield
1099 JLabel label = new JLabel(
1100 MessageManager.getString("label.input_file_url"));
1101 final JComboBox history = new JComboBox();
1103 JPanel panel = new JPanel(new GridLayout(2, 1));
1106 history.setPreferredSize(new Dimension(400, 20));
1107 history.setEditable(true);
1108 history.addItem("http://www.");
1110 String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
1114 if (historyItems != null)
1116 st = new StringTokenizer(historyItems, "\t");
1118 while (st.hasMoreTokens())
1120 history.addItem(st.nextElement());
1124 int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel,
1125 MessageManager.getString("label.input_alignment_from_url"),
1126 JvOptionPane.OK_CANCEL_OPTION);
1128 if (reply != JvOptionPane.OK_OPTION)
1133 String url = history.getSelectedItem().toString();
1135 if (url.toLowerCase().endsWith(".jar"))
1137 if (viewport != null)
1139 new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
1140 FileFormat.Jalview);
1144 new FileLoader().LoadFile(url, DataSourceType.URL,
1145 FileFormat.Jalview);
1150 FileFormatI format = null;
1153 format = new IdentifyFile().identify(url, DataSourceType.URL);
1154 } catch (FileFormatException e)
1156 // TODO revise error handling, distinguish between
1157 // URL not found and response not valid
1162 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1163 MessageManager.formatMessage("label.couldnt_locate",
1166 MessageManager.getString("label.url_not_found"),
1167 JvOptionPane.WARNING_MESSAGE);
1172 if (viewport != null)
1174 new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
1179 new FileLoader().LoadFile(url, DataSourceType.URL, format);
1185 * Opens the CutAndPaste window for the user to paste an alignment in to
1188 * - if not null, the pasted alignment is added to the current
1189 * alignment; if null, to a new alignment window
1192 public void inputTextboxMenuItem_actionPerformed(
1193 AlignmentViewPanel viewPanel)
1195 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1196 cap.setForInput(viewPanel);
1197 Desktop.addInternalFrame(cap,
1198 MessageManager.getString("label.cut_paste_alignmen_file"), true,
1208 Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
1209 jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
1211 jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT",
1212 screen.height + "");
1213 storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
1214 getWidth(), getHeight()));
1216 if (jconsole != null)
1218 storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
1219 jconsole.stopConsole();
1223 storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
1226 if (dialogExecutor != null)
1228 dialogExecutor.shutdownNow();
1230 closeAll_actionPerformed(null);
1232 if (groovyConsole != null)
1234 // suppress a possible repeat prompt to save script
1235 groovyConsole.setDirty(false);
1236 groovyConsole.exit();
1241 private void storeLastKnownDimensions(String string, Rectangle jc)
1243 jalview.bin.Cache.log.debug("Storing last known dimensions for "
1244 + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
1245 + " height:" + jc.height);
1247 jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
1248 jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
1249 jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
1250 jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
1260 public void aboutMenuItem_actionPerformed(ActionEvent e)
1262 // StringBuffer message = getAboutMessage(false);
1263 // JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1265 // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
1266 new Thread(new Runnable()
1271 new SplashScreen(true);
1276 public StringBuffer getAboutMessage(boolean shortv)
1278 StringBuffer message = new StringBuffer();
1279 message.append("<html>");
1282 message.append("<h1><strong>Version: "
1283 + jalview.bin.Cache.getProperty("VERSION")
1284 + "</strong></h1>");
1285 message.append("<strong>Last Updated: <em>"
1286 + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
1287 + "</em></strong>");
1293 message.append("<strong>Version "
1294 + jalview.bin.Cache.getProperty("VERSION")
1295 + "; last updated: "
1296 + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1299 if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
1300 .equals("Checking"))
1302 message.append("<br>...Checking latest version...</br>");
1304 else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
1305 .equals(jalview.bin.Cache.getProperty("VERSION")))
1307 boolean red = false;
1308 if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
1309 .indexOf("automated build") == -1)
1312 // Displayed when code version and jnlp version do not match and code
1313 // version is not a development build
1314 message.append("<div style=\"color: #FF0000;font-style: bold;\">");
1317 message.append("<br>!! Version "
1318 + jalview.bin.Cache.getDefault("LATEST_VERSION",
1320 + " is available for download from "
1321 + jalview.bin.Cache.getDefault("www.jalview.org",
1322 "http://www.jalview.org")
1326 message.append("</div>");
1329 message.append("<br>Authors: " + jalview.bin.Cache.getDefault(
1331 "The Jalview Authors (See AUTHORS file for current list)")
1332 + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
1333 + "<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"
1334 + "<br><br>If you use Jalview, please cite:"
1335 + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
1336 + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
1337 + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
1349 public void documentationMenuItem_actionPerformed(ActionEvent e)
1353 Help.showHelpWindow();
1354 } catch (Exception ex)
1360 public void closeAll_actionPerformed(ActionEvent e)
1362 // TODO show a progress bar while closing?
1363 JInternalFrame[] frames = desktop.getAllFrames();
1364 for (int i = 0; i < frames.length; i++)
1368 frames[i].setClosed(true);
1369 } catch (java.beans.PropertyVetoException ex)
1373 Jalview.setCurrentAlignFrame(null);
1374 System.out.println("ALL CLOSED");
1375 if (v_client != null)
1377 // TODO clear binding to vamsas document objects on close_all
1381 * reset state of singleton objects as appropriate (clear down session state
1382 * when all windows are closed)
1384 StructureSelectionManager ssm = StructureSelectionManager
1385 .getStructureSelectionManager(this);
1393 public void raiseRelated_actionPerformed(ActionEvent e)
1395 reorderAssociatedWindows(false, false);
1399 public void minimizeAssociated_actionPerformed(ActionEvent e)
1401 reorderAssociatedWindows(true, false);
1404 void closeAssociatedWindows()
1406 reorderAssociatedWindows(false, true);
1412 * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
1416 protected void garbageCollect_actionPerformed(ActionEvent e)
1418 // We simply collect the garbage
1419 jalview.bin.Cache.log.debug("Collecting garbage...");
1421 jalview.bin.Cache.log.debug("Finished garbage collection.");
1428 * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
1432 protected void showMemusage_actionPerformed(ActionEvent e)
1434 desktop.showMemoryUsage(showMemusage.isSelected());
1441 * jalview.jbgui.GDesktop#showConsole_actionPerformed(java.awt.event.ActionEvent
1445 protected void showConsole_actionPerformed(ActionEvent e)
1447 showConsole(showConsole.isSelected());
1450 Console jconsole = null;
1453 * control whether the java console is visible or not
1457 void showConsole(boolean selected)
1459 showConsole.setSelected(selected);
1460 // TODO: decide if we should update properties file
1461 Cache.setProperty("SHOW_JAVA_CONSOLE",
1462 Boolean.valueOf(selected).toString());
1463 jconsole.setVisible(selected);
1466 void reorderAssociatedWindows(boolean minimize, boolean close)
1468 JInternalFrame[] frames = desktop.getAllFrames();
1469 if (frames == null || frames.length < 1)
1474 AlignViewportI source = null;
1475 AlignViewportI target = null;
1476 if (frames[0] instanceof AlignFrame)
1478 source = ((AlignFrame) frames[0]).getCurrentView();
1480 else if (frames[0] instanceof TreePanel)
1482 source = ((TreePanel) frames[0]).getViewPort();
1484 else if (frames[0] instanceof PCAPanel)
1486 source = ((PCAPanel) frames[0]).av;
1488 else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
1490 source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
1495 for (int i = 0; i < frames.length; i++)
1498 if (frames[i] == null)
1502 if (frames[i] instanceof AlignFrame)
1504 target = ((AlignFrame) frames[i]).getCurrentView();
1506 else if (frames[i] instanceof TreePanel)
1508 target = ((TreePanel) frames[i]).getViewPort();
1510 else if (frames[i] instanceof PCAPanel)
1512 target = ((PCAPanel) frames[i]).av;
1514 else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
1516 target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
1519 if (source == target)
1525 frames[i].setClosed(true);
1529 frames[i].setIcon(minimize);
1532 frames[i].toFront();
1536 } catch (java.beans.PropertyVetoException ex)
1551 protected void preferences_actionPerformed(ActionEvent e)
1563 public void saveState_actionPerformed(ActionEvent e)
1565 JalviewFileChooser chooser = new JalviewFileChooser("jvp",
1568 chooser.setFileView(new JalviewFileView());
1569 chooser.setDialogTitle(MessageManager.getString("label.save_state"));
1571 int value = chooser.showSaveDialog(this);
1573 if (value == JalviewFileChooser.APPROVE_OPTION)
1575 final Desktop me = this;
1576 final java.io.File choice = chooser.getSelectedFile();
1577 setProjectFile(choice);
1579 new Thread(new Runnable()
1584 // TODO: refactor to Jalview desktop session controller action.
1585 setProgressBar(MessageManager.formatMessage(
1586 "label.saving_jalview_project", new Object[]
1587 { choice.getName() }), choice.hashCode());
1588 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
1589 choice.getParent());
1590 // TODO catch and handle errors for savestate
1591 // TODO prevent user from messing with the Desktop whilst we're saving
1594 new Jalview2XML().saveState(choice);
1595 } catch (OutOfMemoryError oom)
1598 "Whilst saving current state to " + choice.getName(),
1600 } catch (Exception ex)
1603 "Problems whilst trying to save to " + choice.getName(),
1605 JvOptionPane.showMessageDialog(me,
1606 MessageManager.formatMessage(
1607 "label.error_whilst_saving_current_state_to",
1609 { choice.getName() }),
1610 MessageManager.getString("label.couldnt_save_project"),
1611 JvOptionPane.WARNING_MESSAGE);
1613 setProgressBar(null, choice.hashCode());
1619 private void setProjectFile(File choice)
1621 this.projectFile = choice;
1624 public File getProjectFile()
1626 return this.projectFile;
1636 public void loadState_actionPerformed(ActionEvent e)
1638 JalviewFileChooser chooser = new JalviewFileChooser(
1639 Cache.getProperty("LAST_DIRECTORY"), new String[]
1642 { "Jalview Project", "Jalview Project (old)" },
1644 chooser.setFileView(new JalviewFileView());
1645 chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
1647 int value = chooser.showOpenDialog(this);
1649 if (value == JalviewFileChooser.APPROVE_OPTION)
1651 final File selectedFile = chooser.getSelectedFile();
1652 setProjectFile(selectedFile);
1653 final String choice = selectedFile.getAbsolutePath();
1654 Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
1655 new Thread(new Runnable()
1660 setProgressBar(MessageManager.formatMessage(
1661 "label.loading_jalview_project", new Object[]
1662 { choice }), choice.hashCode());
1665 new Jalview2XML().loadJalviewAlign(choice);
1666 } catch (OutOfMemoryError oom)
1668 new OOMWarning("Whilst loading project from " + choice, oom);
1669 } catch (Exception ex)
1672 "Problems whilst loading project from " + choice, ex);
1673 JvOptionPane.showMessageDialog(Desktop.desktop,
1674 MessageManager.formatMessage(
1675 "label.error_whilst_loading_project_from",
1678 MessageManager.getString("label.couldnt_load_project"),
1679 JvOptionPane.WARNING_MESSAGE);
1681 setProgressBar(null, choice.hashCode());
1688 public void inputSequence_actionPerformed(ActionEvent e)
1690 new SequenceFetcher(this);
1693 JPanel progressPanel;
1695 ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
1697 public void startLoading(final String fileName)
1699 if (fileLoadingCount == 0)
1701 fileLoadingPanels.add(addProgressPanel(MessageManager
1702 .formatMessage("label.loading_file", new Object[]
1708 private JPanel addProgressPanel(String string)
1710 if (progressPanel == null)
1712 progressPanel = new JPanel(new GridLayout(1, 1));
1713 totalProgressCount = 0;
1714 instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
1716 JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
1717 JProgressBar progressBar = new JProgressBar();
1718 progressBar.setIndeterminate(true);
1720 thisprogress.add(new JLabel(string), BorderLayout.WEST);
1722 thisprogress.add(progressBar, BorderLayout.CENTER);
1723 progressPanel.add(thisprogress);
1724 ((GridLayout) progressPanel.getLayout()).setRows(
1725 ((GridLayout) progressPanel.getLayout()).getRows() + 1);
1726 ++totalProgressCount;
1727 instance.validate();
1728 return thisprogress;
1731 int totalProgressCount = 0;
1733 private void removeProgressPanel(JPanel progbar)
1735 if (progressPanel != null)
1737 synchronized (progressPanel)
1739 progressPanel.remove(progbar);
1740 GridLayout gl = (GridLayout) progressPanel.getLayout();
1741 gl.setRows(gl.getRows() - 1);
1742 if (--totalProgressCount < 1)
1744 this.getContentPane().remove(progressPanel);
1745 progressPanel = null;
1752 public void stopLoading()
1755 if (fileLoadingCount < 1)
1757 while (fileLoadingPanels.size() > 0)
1759 removeProgressPanel(fileLoadingPanels.remove(0));
1761 fileLoadingPanels.clear();
1762 fileLoadingCount = 0;
1767 public static int getViewCount(String alignmentId)
1769 AlignmentViewport[] aps = getViewports(alignmentId);
1770 return (aps == null) ? 0 : aps.length;
1775 * @param alignmentId
1776 * - if null, all sets are returned
1777 * @return all AlignmentPanels concerning the alignmentId sequence set
1779 public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
1781 if (Desktop.desktop == null)
1783 // no frames created and in headless mode
1784 // TODO: verify that frames are recoverable when in headless mode
1787 List<AlignmentPanel> aps = new ArrayList<>();
1788 AlignFrame[] frames = getAlignFrames();
1793 for (AlignFrame af : frames)
1795 for (AlignmentPanel ap : af.alignPanels)
1797 if (alignmentId == null
1798 || alignmentId.equals(ap.av.getSequenceSetId()))
1804 if (aps.size() == 0)
1808 AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
1813 * get all the viewports on an alignment.
1815 * @param sequenceSetId
1816 * unique alignment id (may be null - all viewports returned in that
1818 * @return all viewports on the alignment bound to sequenceSetId
1820 public static AlignmentViewport[] getViewports(String sequenceSetId)
1822 List<AlignmentViewport> viewp = new ArrayList<>();
1823 if (desktop != null)
1825 AlignFrame[] frames = Desktop.getAlignFrames();
1827 for (AlignFrame afr : frames)
1829 if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
1830 .equals(sequenceSetId))
1832 if (afr.alignPanels != null)
1834 for (AlignmentPanel ap : afr.alignPanels)
1836 if (sequenceSetId == null
1837 || sequenceSetId.equals(ap.av.getSequenceSetId()))
1845 viewp.add(afr.getViewport());
1849 if (viewp.size() > 0)
1851 return viewp.toArray(new AlignmentViewport[viewp.size()]);
1858 * Explode the views in the given frame into separate AlignFrame
1862 public static void explodeViews(AlignFrame af)
1864 int size = af.alignPanels.size();
1870 for (int i = 0; i < size; i++)
1872 AlignmentPanel ap = af.alignPanels.get(i);
1873 AlignFrame newaf = new AlignFrame(ap);
1876 * Restore the view's last exploded frame geometry if known. Multiple
1877 * views from one exploded frame share and restore the same (frame)
1878 * position and size.
1880 Rectangle geometry = ap.av.getExplodedGeometry();
1881 if (geometry != null)
1883 newaf.setBounds(geometry);
1886 ap.av.setGatherViewsHere(false);
1888 addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
1889 AlignFrame.DEFAULT_HEIGHT);
1892 af.alignPanels.clear();
1893 af.closeMenuItem_actionPerformed(true);
1898 * Gather expanded views (separate AlignFrame's) with the same sequence set
1899 * identifier back in to this frame as additional views, and close the
1900 * expanded views. Note the expanded frames may themselves have multiple
1901 * views. We take the lot.
1905 public void gatherViews(AlignFrame source)
1907 source.viewport.setGatherViewsHere(true);
1908 source.viewport.setExplodedGeometry(source.getBounds());
1909 JInternalFrame[] frames = desktop.getAllFrames();
1910 String viewId = source.viewport.getSequenceSetId();
1912 for (int t = 0; t < frames.length; t++)
1914 if (frames[t] instanceof AlignFrame && frames[t] != source)
1916 AlignFrame af = (AlignFrame) frames[t];
1917 boolean gatherThis = false;
1918 for (int a = 0; a < af.alignPanels.size(); a++)
1920 AlignmentPanel ap = af.alignPanels.get(a);
1921 if (viewId.equals(ap.av.getSequenceSetId()))
1924 ap.av.setGatherViewsHere(false);
1925 ap.av.setExplodedGeometry(af.getBounds());
1926 source.addAlignmentPanel(ap, false);
1932 af.alignPanels.clear();
1933 af.closeMenuItem_actionPerformed(true);
1940 jalview.gui.VamsasApplication v_client = null;
1943 public void vamsasImport_actionPerformed(ActionEvent e)
1945 if (v_client == null)
1947 // Load and try to start a session.
1948 JalviewFileChooser chooser = new JalviewFileChooser(
1949 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1951 chooser.setFileView(new JalviewFileView());
1952 chooser.setDialogTitle(
1953 MessageManager.getString("label.open_saved_vamsas_session"));
1954 chooser.setToolTipText(MessageManager.getString(
1955 "label.select_vamsas_session_opened_as_new_vamsas_session"));
1957 int value = chooser.showOpenDialog(this);
1959 if (value == JalviewFileChooser.APPROVE_OPTION)
1961 String fle = chooser.getSelectedFile().toString();
1962 if (!vamsasImport(chooser.getSelectedFile()))
1964 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1965 MessageManager.formatMessage(
1966 "label.couldnt_import_as_vamsas_session",
1970 .getString("label.vamsas_document_import_failed"),
1971 JvOptionPane.ERROR_MESSAGE);
1977 jalview.bin.Cache.log.error(
1978 "Implementation error - load session from a running session is not supported.");
1983 * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
1986 * @return true if import was a success and a session was started.
1988 public boolean vamsasImport(URL url)
1990 // TODO: create progress bar
1991 if (v_client != null)
1994 jalview.bin.Cache.log.error(
1995 "Implementation error - load session from a running session is not supported.");
2001 // copy the URL content to a temporary local file
2002 // TODO: be a bit cleverer here with nio (?!)
2003 File file = File.createTempFile("vdocfromurl", ".vdj");
2004 FileOutputStream fos = new FileOutputStream(file);
2005 BufferedInputStream bis = new BufferedInputStream(url.openStream());
2006 byte[] buffer = new byte[2048];
2008 while ((ln = bis.read(buffer)) > -1)
2010 fos.write(buffer, 0, ln);
2014 v_client = new jalview.gui.VamsasApplication(this, file,
2015 url.toExternalForm());
2016 } catch (Exception ex)
2018 jalview.bin.Cache.log.error(
2019 "Failed to create new vamsas session from contents of URL "
2024 setupVamsasConnectedGui();
2025 v_client.initial_update(); // TODO: thread ?
2026 return v_client.inSession();
2030 * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
2033 * @return true if import was a success and a session was started.
2035 public boolean vamsasImport(File file)
2037 if (v_client != null)
2040 jalview.bin.Cache.log.error(
2041 "Implementation error - load session from a running session is not supported.");
2045 setProgressBar(MessageManager.formatMessage(
2046 "status.importing_vamsas_session_from", new Object[]
2047 { file.getName() }), file.hashCode());
2050 v_client = new jalview.gui.VamsasApplication(this, file, null);
2051 } catch (Exception ex)
2053 setProgressBar(MessageManager.formatMessage(
2054 "status.importing_vamsas_session_from", new Object[]
2055 { file.getName() }), file.hashCode());
2056 jalview.bin.Cache.log.error(
2057 "New vamsas session from existing session file failed:", ex);
2060 setupVamsasConnectedGui();
2061 v_client.initial_update(); // TODO: thread ?
2062 setProgressBar(MessageManager.formatMessage(
2063 "status.importing_vamsas_session_from", new Object[]
2064 { file.getName() }), file.hashCode());
2065 return v_client.inSession();
2068 public boolean joinVamsasSession(String mysesid)
2070 if (v_client != null)
2072 throw new Error(MessageManager
2073 .getString("error.try_join_vamsas_session_another"));
2075 if (mysesid == null)
2078 MessageManager.getString("error.invalid_vamsas_session_id"));
2080 v_client = new VamsasApplication(this, mysesid);
2081 setupVamsasConnectedGui();
2082 v_client.initial_update();
2083 return (v_client.inSession());
2087 public void vamsasStart_actionPerformed(ActionEvent e)
2089 if (v_client == null)
2092 // we just start a default session for moment.
2094 * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
2095 * getProperty("LAST_DIRECTORY"));
2097 * chooser.setFileView(new JalviewFileView());
2098 * chooser.setDialogTitle("Load Vamsas file");
2099 * chooser.setToolTipText("Import");
2101 * int value = chooser.showOpenDialog(this);
2103 * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
2104 * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
2106 v_client = new VamsasApplication(this);
2107 setupVamsasConnectedGui();
2108 v_client.initial_update(); // TODO: thread ?
2112 // store current data in session.
2113 v_client.push_update(); // TODO: thread
2117 protected void setupVamsasConnectedGui()
2119 vamsasStart.setText(MessageManager.getString("label.session_update"));
2120 vamsasSave.setVisible(true);
2121 vamsasStop.setVisible(true);
2122 vamsasImport.setVisible(false); // Document import to existing session is
2123 // not possible for vamsas-client-1.0.
2126 protected void setupVamsasDisconnectedGui()
2128 vamsasSave.setVisible(false);
2129 vamsasStop.setVisible(false);
2130 vamsasImport.setVisible(true);
2132 .setText(MessageManager.getString("label.new_vamsas_session"));
2136 public void vamsasStop_actionPerformed(ActionEvent e)
2138 if (v_client != null)
2140 v_client.end_session();
2142 setupVamsasDisconnectedGui();
2146 protected void buildVamsasStMenu()
2148 if (v_client == null)
2150 String[] sess = null;
2153 sess = VamsasApplication.getSessionList();
2154 } catch (Exception e)
2156 jalview.bin.Cache.log.warn("Problem getting current sessions list.",
2162 jalview.bin.Cache.log.debug(
2163 "Got current sessions list: " + sess.length + " entries.");
2164 VamsasStMenu.removeAll();
2165 for (int i = 0; i < sess.length; i++)
2167 JMenuItem sessit = new JMenuItem();
2168 sessit.setText(sess[i]);
2169 sessit.setToolTipText(MessageManager
2170 .formatMessage("label.connect_to_session", new Object[]
2172 final Desktop dsktp = this;
2173 final String mysesid = sess[i];
2174 sessit.addActionListener(new ActionListener()
2178 public void actionPerformed(ActionEvent e)
2180 if (dsktp.v_client == null)
2182 Thread rthr = new Thread(new Runnable()
2188 dsktp.v_client = new VamsasApplication(dsktp, mysesid);
2189 dsktp.setupVamsasConnectedGui();
2190 dsktp.v_client.initial_update();
2198 VamsasStMenu.add(sessit);
2200 // don't show an empty menu.
2201 VamsasStMenu.setVisible(sess.length > 0);
2206 jalview.bin.Cache.log.debug("No current vamsas sessions.");
2207 VamsasStMenu.removeAll();
2208 VamsasStMenu.setVisible(false);
2213 // Not interested in the content. Just hide ourselves.
2214 VamsasStMenu.setVisible(false);
2219 public void vamsasSave_actionPerformed(ActionEvent e)
2221 if (v_client != null)
2223 // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
2224 JalviewFileChooser chooser = new JalviewFileChooser("vdj",
2227 chooser.setFileView(new JalviewFileView());
2228 chooser.setDialogTitle(MessageManager
2229 .getString("label.save_vamsas_document_archive"));
2231 int value = chooser.showSaveDialog(this);
2233 if (value == JalviewFileChooser.APPROVE_OPTION)
2235 java.io.File choice = chooser.getSelectedFile();
2236 JPanel progpanel = addProgressPanel(MessageManager
2237 .formatMessage("label.saving_vamsas_doc", new Object[]
2238 { choice.getName() }));
2239 Cache.setProperty("LAST_DIRECTORY", choice.getParent());
2240 String warnmsg = null;
2241 String warnttl = null;
2244 v_client.vclient.storeDocument(choice);
2247 warnttl = "Serious Problem saving Vamsas Document";
2248 warnmsg = ex.toString();
2249 jalview.bin.Cache.log
2250 .error("Error Whilst saving document to " + choice, ex);
2252 } catch (Exception ex)
2254 warnttl = "Problem saving Vamsas Document.";
2255 warnmsg = ex.toString();
2256 jalview.bin.Cache.log.warn(
2257 "Exception Whilst saving document to " + choice, ex);
2260 removeProgressPanel(progpanel);
2261 if (warnmsg != null)
2263 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
2265 warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
2271 JPanel vamUpdate = null;
2274 * hide vamsas user gui bits when a vamsas document event is being handled.
2277 * true to hide gui, false to reveal gui
2279 public void setVamsasUpdate(boolean b)
2281 Cache.log.debug("Setting gui for Vamsas update "
2282 + (b ? "in progress" : "finished"));
2284 if (vamUpdate != null)
2286 this.removeProgressPanel(vamUpdate);
2290 vamUpdate = this.addProgressPanel(
2291 MessageManager.getString("label.updating_vamsas_session"));
2293 vamsasStart.setVisible(!b);
2294 vamsasStop.setVisible(!b);
2295 vamsasSave.setVisible(!b);
2298 public JInternalFrame[] getAllFrames()
2300 return desktop.getAllFrames();
2304 * Checks the given url to see if it gives a response indicating that the user
2305 * should be informed of a new questionnaire.
2309 public void checkForQuestionnaire(String url)
2311 UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
2312 // javax.swing.SwingUtilities.invokeLater(jvq);
2313 new Thread(jvq).start();
2316 public void checkURLLinks()
2318 // Thread off the URL link checker
2319 addDialogThread(new Runnable()
2324 if (Cache.getDefault("CHECKURLLINKS", true))
2326 // check what the actual links are - if it's just the default don't
2327 // bother with the warning
2328 List<String> links = Preferences.sequenceUrlLinks
2331 // only need to check links if there is one with a
2332 // SEQUENCE_ID which is not the default EMBL_EBI link
2333 ListIterator<String> li = links.listIterator();
2334 boolean check = false;
2335 List<JLabel> urls = new ArrayList<>();
2336 while (li.hasNext())
2338 String link = li.next();
2339 if (link.contains(SEQUENCE_ID)
2340 && !UrlConstants.isDefaultString(link))
2343 int barPos = link.indexOf("|");
2344 String urlMsg = barPos == -1 ? link
2345 : link.substring(0, barPos) + ": "
2346 + link.substring(barPos + 1);
2347 urls.add(new JLabel(urlMsg));
2355 // ask user to check in case URL links use old style tokens
2356 // ($SEQUENCE_ID$ for sequence id _or_ accession id)
2357 JPanel msgPanel = new JPanel();
2358 msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
2359 msgPanel.add(Box.createVerticalGlue());
2360 JLabel msg = new JLabel(MessageManager
2361 .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
2362 JLabel msg2 = new JLabel(MessageManager
2363 .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
2365 for (JLabel url : urls)
2371 final JCheckBox jcb = new JCheckBox(
2372 MessageManager.getString("label.do_not_display_again"));
2373 jcb.addActionListener(new ActionListener()
2376 public void actionPerformed(ActionEvent e)
2378 // update Cache settings for "don't show this again"
2379 boolean showWarningAgain = !jcb.isSelected();
2380 Cache.setProperty("CHECKURLLINKS",
2381 Boolean.valueOf(showWarningAgain).toString());
2386 JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
2388 .getString("label.SEQUENCE_ID_no_longer_used"),
2389 JvOptionPane.WARNING_MESSAGE);
2396 * Proxy class for JDesktopPane which optionally displays the current memory
2397 * usage and highlights the desktop area with a red bar if free memory runs
2402 public class MyDesktopPane extends JDesktopPane implements Runnable
2405 private static final float ONE_MB = 1048576f;
2407 boolean showMemoryUsage = false;
2411 java.text.NumberFormat df;
2413 float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
2416 public MyDesktopPane(boolean showMemoryUsage)
2418 showMemoryUsage(showMemoryUsage);
2421 public void showMemoryUsage(boolean showMemory)
2423 this.showMemoryUsage = showMemory;
2426 Thread worker = new Thread(this);
2432 public boolean isShowMemoryUsage()
2434 return showMemoryUsage;
2440 df = java.text.NumberFormat.getNumberInstance();
2441 df.setMaximumFractionDigits(2);
2442 runtime = Runtime.getRuntime();
2444 while (showMemoryUsage)
2448 maxMemory = runtime.maxMemory() / ONE_MB;
2449 allocatedMemory = runtime.totalMemory() / ONE_MB;
2450 freeMemory = runtime.freeMemory() / ONE_MB;
2451 totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
2453 percentUsage = (totalFreeMemory / maxMemory) * 100;
2455 // if (percentUsage < 20)
2457 // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12,
2459 // instance.set.setBorder(border1);
2462 // sleep after showing usage
2464 } catch (Exception ex)
2466 ex.printStackTrace();
2472 public void paintComponent(Graphics g)
2474 if (showMemoryUsage && g != null && df != null)
2476 if (percentUsage < 20)
2478 g.setColor(Color.red);
2480 FontMetrics fm = g.getFontMetrics();
2483 g.drawString(MessageManager.formatMessage("label.memory_stats",
2485 { df.format(totalFreeMemory), df.format(maxMemory),
2486 df.format(percentUsage) }),
2487 10, getHeight() - fm.getHeight());
2495 * Accessor method to quickly get all the AlignmentFrames loaded.
2497 * @return an array of AlignFrame, or null if none found
2499 public static AlignFrame[] getAlignFrames()
2501 if (Jalview.isHeadlessMode())
2503 // Desktop.desktop is null in headless mode
2504 return new AlignFrame[] { Jalview.currentAlignFrame };
2507 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
2513 List<AlignFrame> avp = new ArrayList<>();
2515 for (int i = frames.length - 1; i > -1; i--)
2517 if (frames[i] instanceof AlignFrame)
2519 avp.add((AlignFrame) frames[i]);
2521 else if (frames[i] instanceof SplitFrame)
2524 * Also check for a split frame containing an AlignFrame
2526 GSplitFrame sf = (GSplitFrame) frames[i];
2527 if (sf.getTopFrame() instanceof AlignFrame)
2529 avp.add((AlignFrame) sf.getTopFrame());
2531 if (sf.getBottomFrame() instanceof AlignFrame)
2533 avp.add((AlignFrame) sf.getBottomFrame());
2537 if (avp.size() == 0)
2541 AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]);
2546 * Returns an array of any AppJmol frames in the Desktop (or null if none).
2550 public GStructureViewer[] getJmols()
2552 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
2558 List<GStructureViewer> avp = new ArrayList<>();
2560 for (int i = frames.length - 1; i > -1; i--)
2562 if (frames[i] instanceof AppJmol)
2564 GStructureViewer af = (GStructureViewer) frames[i];
2568 if (avp.size() == 0)
2572 GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]);
2577 * Add Groovy Support to Jalview
2580 public void groovyShell_actionPerformed()
2584 openGroovyConsole();
2585 } catch (Exception ex)
2587 jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
2588 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
2590 MessageManager.getString("label.couldnt_create_groovy_shell"),
2591 MessageManager.getString("label.groovy_support_failed"),
2592 JvOptionPane.ERROR_MESSAGE);
2597 * Open the Groovy console
2599 void openGroovyConsole()
2601 if (groovyConsole == null)
2603 groovyConsole = new groovy.ui.Console();
2604 groovyConsole.setVariable("Jalview", this);
2605 groovyConsole.run();
2608 * We allow only one console at a time, so that AlignFrame menu option
2609 * 'Calculate | Run Groovy script' is unambiguous.
2610 * Disable 'Groovy Console', and enable 'Run script', when the console is
2611 * opened, and the reverse when it is closed
2613 Window window = (Window) groovyConsole.getFrame();
2614 window.addWindowListener(new WindowAdapter()
2617 public void windowClosed(WindowEvent e)
2620 * rebind CMD-Q from Groovy Console to Jalview Quit
2623 enableExecuteGroovy(false);
2629 * show Groovy console window (after close and reopen)
2631 ((Window) groovyConsole.getFrame()).setVisible(true);
2634 * if we got this far, enable 'Run Groovy' in AlignFrame menus
2635 * and disable opening a second console
2637 enableExecuteGroovy(true);
2641 * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
2642 * binding when opened
2644 protected void addQuitHandler()
2646 getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
2647 .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
2648 Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()),
2650 getRootPane().getActionMap().put("Quit", new AbstractAction()
2653 public void actionPerformed(ActionEvent e)
2661 * Enable or disable 'Run Groovy script' in AlignFrame calculate menus
2664 * true if Groovy console is open
2666 public void enableExecuteGroovy(boolean enabled)
2669 * disable opening a second Groovy console
2670 * (or re-enable when the console is closed)
2672 groovyShell.setEnabled(!enabled);
2674 AlignFrame[] alignFrames = getAlignFrames();
2675 if (alignFrames != null)
2677 for (AlignFrame af : alignFrames)
2679 af.setGroovyEnabled(enabled);
2685 * Progress bars managed by the IProgressIndicator method.
2687 private Hashtable<Long, JPanel> progressBars;
2689 private Hashtable<Long, IProgressIndicatorHandler> progressBarHandlers;
2694 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
2697 public void setProgressBar(String message, long id)
2699 if (progressBars == null)
2701 progressBars = new Hashtable<>();
2702 progressBarHandlers = new Hashtable<>();
2705 if (progressBars.get(new Long(id)) != null)
2707 JPanel panel = progressBars.remove(new Long(id));
2708 if (progressBarHandlers.contains(new Long(id)))
2710 progressBarHandlers.remove(new Long(id));
2712 removeProgressPanel(panel);
2716 progressBars.put(new Long(id), addProgressPanel(message));
2723 * @see jalview.gui.IProgressIndicator#registerHandler(long,
2724 * jalview.gui.IProgressIndicatorHandler)
2727 public void registerHandler(final long id,
2728 final IProgressIndicatorHandler handler)
2730 if (progressBarHandlers == null
2731 || !progressBars.containsKey(new Long(id)))
2733 throw new Error(MessageManager.getString(
2734 "error.call_setprogressbar_before_registering_handler"));
2736 progressBarHandlers.put(new Long(id), handler);
2737 final JPanel progressPanel = progressBars.get(new Long(id));
2738 if (handler.canCancel())
2740 JButton cancel = new JButton(
2741 MessageManager.getString("action.cancel"));
2742 final IProgressIndicator us = this;
2743 cancel.addActionListener(new ActionListener()
2747 public void actionPerformed(ActionEvent e)
2749 handler.cancelActivity(id);
2750 us.setProgressBar(MessageManager
2751 .formatMessage("label.cancelled_params", new Object[]
2752 { ((JLabel) progressPanel.getComponent(0)).getText() }),
2756 progressPanel.add(cancel, BorderLayout.EAST);
2762 * @return true if any progress bars are still active
2765 public boolean operationInProgress()
2767 if (progressBars != null && progressBars.size() > 0)
2775 * This will return the first AlignFrame holding the given viewport instance.
2776 * It will break if there are more than one AlignFrames viewing a particular
2780 * @return alignFrame for viewport
2782 public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
2784 if (desktop != null)
2786 AlignmentPanel[] aps = getAlignmentPanels(
2787 viewport.getSequenceSetId());
2788 for (int panel = 0; aps != null && panel < aps.length; panel++)
2790 if (aps[panel] != null && aps[panel].av == viewport)
2792 return aps[panel].alignFrame;
2799 public VamsasApplication getVamsasApplication()
2806 * flag set if jalview GUI is being operated programmatically
2808 private boolean inBatchMode = false;
2811 * check if jalview GUI is being operated programmatically
2813 * @return inBatchMode
2815 public boolean isInBatchMode()
2821 * set flag if jalview GUI is being operated programmatically
2823 * @param inBatchMode
2825 public void setInBatchMode(boolean inBatchMode)
2827 this.inBatchMode = inBatchMode;
2830 public void startServiceDiscovery()
2832 startServiceDiscovery(false);
2835 public void startServiceDiscovery(boolean blocking)
2837 boolean alive = true;
2838 Thread t0 = null, t1 = null, t2 = null;
2839 // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
2842 // todo: changesupport handlers need to be transferred
2843 if (discoverer == null)
2845 discoverer = new jalview.ws.jws1.Discoverer();
2846 // register PCS handler for desktop.
2847 discoverer.addPropertyChangeListener(changeSupport);
2849 // JAL-940 - disabled JWS1 service configuration - always start discoverer
2850 // until we phase out completely
2851 (t0 = new Thread(discoverer)).start();
2854 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
2856 t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
2857 .startDiscoverer(changeSupport);
2861 // TODO: do rest service discovery
2870 } catch (Exception e)
2873 alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
2874 || (t3 != null && t3.isAlive())
2875 || (t0 != null && t0.isAlive());
2881 * called to check if the service discovery process completed successfully.
2885 protected void JalviewServicesChanged(PropertyChangeEvent evt)
2887 if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
2889 final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
2890 .getErrorMessages();
2893 if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
2895 if (serviceChangedDialog == null)
2897 // only run if we aren't already displaying one of these.
2898 addDialogThread(serviceChangedDialog = new Runnable()
2905 * JalviewDialog jd =new JalviewDialog() {
2907 * @Override protected void cancelPressed() { // TODO
2908 * Auto-generated method stub
2910 * }@Override protected void okPressed() { // TODO
2911 * Auto-generated method stub
2913 * }@Override protected void raiseClosed() { // TODO
2914 * Auto-generated method stub
2916 * } }; jd.initDialogFrame(new
2917 * JLabel("<html><table width=\"450\"><tr><td>" + ermsg +
2918 * "<br/>It may be that you have invalid JABA URLs in your web service preferences,"
2919 * + " or mis-configured HTTP proxy settings.<br/>" +
2920 * "Check the <em>Connections</em> and <em>Web services</em> tab of the"
2922 * " Tools->Preferences dialog box to change them.</td></tr></table></html>"
2923 * ), true, true, "Web Service Configuration Problem", 450,
2926 * jd.waitForInput();
2928 JvOptionPane.showConfirmDialog(Desktop.desktop,
2929 new JLabel("<html><table width=\"450\"><tr><td>"
2930 + ermsg + "</td></tr></table>"
2931 + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
2932 + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
2933 + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
2934 + " Tools->Preferences dialog box to change them.</p></html>"),
2935 "Web Service Configuration Problem",
2936 JvOptionPane.DEFAULT_OPTION,
2937 JvOptionPane.ERROR_MESSAGE);
2938 serviceChangedDialog = null;
2947 "Errors reported by JABA discovery service. Check web services preferences.\n"
2954 private Runnable serviceChangedDialog = null;
2957 * start a thread to open a URL in the configured browser. Pops up a warning
2958 * dialog to the user if there is an exception when calling out to the browser
2963 public static void showUrl(final String url)
2965 showUrl(url, Desktop.instance);
2969 * Like showUrl but allows progress handler to be specified
2973 * (null) or object implementing IProgressIndicator
2975 public static void showUrl(final String url,
2976 final IProgressIndicator progress)
2978 new Thread(new Runnable()
2985 if (progress != null)
2987 progress.setProgressBar(MessageManager
2988 .formatMessage("status.opening_params", new Object[]
2989 { url }), this.hashCode());
2991 jalview.util.BrowserLauncher.openURL(url);
2992 } catch (Exception ex)
2994 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
2996 .getString("label.web_browser_not_found_unix"),
2997 MessageManager.getString("label.web_browser_not_found"),
2998 JvOptionPane.WARNING_MESSAGE);
3000 ex.printStackTrace();
3002 if (progress != null)
3004 progress.setProgressBar(null, this.hashCode());
3010 public static WsParamSetManager wsparamManager = null;
3012 public static ParamManager getUserParameterStore()
3014 if (wsparamManager == null)
3016 wsparamManager = new WsParamSetManager();
3018 return wsparamManager;
3022 * static hyperlink handler proxy method for use by Jalview's internal windows
3026 public static void hyperlinkUpdate(HyperlinkEvent e)
3028 if (e.getEventType() == EventType.ACTIVATED)
3033 url = e.getURL().toString();
3034 Desktop.showUrl(url);
3035 } catch (Exception x)
3039 if (Cache.log != null)
3041 Cache.log.error("Couldn't handle string " + url + " as a URL.");
3046 "Couldn't handle string " + url + " as a URL.");
3049 // ignore any exceptions due to dud links.
3056 * single thread that handles display of dialogs to user.
3058 ExecutorService dialogExecutor = Executors.newSingleThreadExecutor();
3061 * flag indicating if dialogExecutor should try to acquire a permit
3063 private volatile boolean dialogPause = true;
3068 private java.util.concurrent.Semaphore block = new Semaphore(0);
3070 private static groovy.ui.Console groovyConsole;
3073 * add another dialog thread to the queue
3077 public void addDialogThread(final Runnable prompter)
3079 dialogExecutor.submit(new Runnable()
3089 } catch (InterruptedException x)
3094 if (instance == null)
3100 SwingUtilities.invokeAndWait(prompter);
3101 } catch (Exception q)
3103 Cache.log.warn("Unexpected Exception in dialog thread.", q);
3109 public void startDialogQueue()
3111 // set the flag so we don't pause waiting for another permit and semaphore
3112 // the current task to begin
3113 dialogPause = false;
3118 protected void snapShotWindow_actionPerformed(ActionEvent e)
3122 ImageMaker im = new jalview.util.ImageMaker(
3123 this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(),
3124 getHeight(), of = new File("Jalview_snapshot"
3125 + System.currentTimeMillis() + ".eps"),
3126 "View of desktop", null, 0, false);
3129 paintAll(im.getGraphics());
3131 } catch (Exception q)
3133 Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
3137 Cache.log.info("Successfully written snapshot to file "
3138 + of.getAbsolutePath());
3142 * Explode the views in the given SplitFrame into separate SplitFrame windows.
3143 * This respects (remembers) any previous 'exploded geometry' i.e. the size
3144 * and location last time the view was expanded (if any). However it does not
3145 * remember the split pane divider location - this is set to match the
3146 * 'exploding' frame.
3150 public void explodeViews(SplitFrame sf)
3152 AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame();
3153 AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame();
3154 List<? extends AlignmentViewPanel> topPanels = oldTopFrame
3156 List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame
3158 int viewCount = topPanels.size();
3165 * Processing in reverse order works, forwards order leaves the first panels
3166 * not visible. I don't know why!
3168 for (int i = viewCount - 1; i >= 0; i--)
3171 * Make new top and bottom frames. These take over the respective
3172 * AlignmentPanel objects, including their AlignmentViewports, so the
3173 * cdna/protein relationships between the viewports is carried over to the
3176 * explodedGeometry holds the (x, y) position of the previously exploded
3177 * SplitFrame, and the (width, height) of the AlignFrame component
3179 AlignmentPanel topPanel = (AlignmentPanel) topPanels.get(i);
3180 AlignFrame newTopFrame = new AlignFrame(topPanel);
3181 newTopFrame.setSize(oldTopFrame.getSize());
3182 newTopFrame.setVisible(true);
3183 Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
3184 .getExplodedGeometry();
3185 if (geometry != null)
3187 newTopFrame.setSize(geometry.getSize());
3190 AlignmentPanel bottomPanel = (AlignmentPanel) bottomPanels.get(i);
3191 AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
3192 newBottomFrame.setSize(oldBottomFrame.getSize());
3193 newBottomFrame.setVisible(true);
3194 geometry = ((AlignViewport) bottomPanel.getAlignViewport())
3195 .getExplodedGeometry();
3196 if (geometry != null)
3198 newBottomFrame.setSize(geometry.getSize());
3201 topPanel.av.setGatherViewsHere(false);
3202 bottomPanel.av.setGatherViewsHere(false);
3203 JInternalFrame splitFrame = new SplitFrame(newTopFrame,
3205 if (geometry != null)
3207 splitFrame.setLocation(geometry.getLocation());
3209 Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
3213 * Clear references to the panels (now relocated in the new SplitFrames)
3214 * before closing the old SplitFrame.
3217 bottomPanels.clear();
3222 * Gather expanded split frames, sharing the same pairs of sequence set ids,
3223 * back into the given SplitFrame as additional views. Note that the gathered
3224 * frames may themselves have multiple views.
3228 public void gatherViews(GSplitFrame source)
3231 * special handling of explodedGeometry for a view within a SplitFrame: - it
3232 * holds the (x, y) position of the enclosing SplitFrame, and the (width,
3233 * height) of the AlignFrame component
3235 AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
3236 AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
3237 myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
3238 source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
3239 myBottomFrame.viewport
3240 .setExplodedGeometry(new Rectangle(source.getX(), source.getY(),
3241 myBottomFrame.getWidth(), myBottomFrame.getHeight()));
3242 myTopFrame.viewport.setGatherViewsHere(true);
3243 myBottomFrame.viewport.setGatherViewsHere(true);
3244 String topViewId = myTopFrame.viewport.getSequenceSetId();
3245 String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
3247 JInternalFrame[] frames = desktop.getAllFrames();
3248 for (JInternalFrame frame : frames)
3250 if (frame instanceof SplitFrame && frame != source)
3252 SplitFrame sf = (SplitFrame) frame;
3253 AlignFrame topFrame = (AlignFrame) sf.getTopFrame();
3254 AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame();
3255 boolean gatherThis = false;
3256 for (int a = 0; a < topFrame.alignPanels.size(); a++)
3258 AlignmentPanel topPanel = topFrame.alignPanels.get(a);
3259 AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a);
3260 if (topViewId.equals(topPanel.av.getSequenceSetId())
3261 && bottomViewId.equals(bottomPanel.av.getSequenceSetId()))
3264 topPanel.av.setGatherViewsHere(false);
3265 bottomPanel.av.setGatherViewsHere(false);
3266 topPanel.av.setExplodedGeometry(
3267 new Rectangle(sf.getLocation(), topFrame.getSize()));
3268 bottomPanel.av.setExplodedGeometry(
3269 new Rectangle(sf.getLocation(), bottomFrame.getSize()));
3270 myTopFrame.addAlignmentPanel(topPanel, false);
3271 myBottomFrame.addAlignmentPanel(bottomPanel, false);
3277 topFrame.getAlignPanels().clear();
3278 bottomFrame.getAlignPanels().clear();
3285 * The dust settles...give focus to the tab we did this from.
3287 myTopFrame.setDisplayedView(myTopFrame.alignPanel);
3290 public static groovy.ui.Console getGroovyConsole()
3292 return groovyConsole;
3295 public static void transferFromDropTarget(List<String> files,
3296 List<DataSourceType> protocols, DropTargetDropEvent evt,
3297 Transferable t) throws Exception
3300 DataFlavor uriListFlavor = new DataFlavor(
3301 "text/uri-list;class=java.lang.String");
3302 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
3304 // Works on Windows and MacOSX
3305 Cache.log.debug("Drop handled as javaFileListFlavor");
3306 for (Object file : (List) t
3307 .getTransferData(DataFlavor.javaFileListFlavor))
3309 files.add(((File) file).toString());
3310 protocols.add(DataSourceType.FILE);
3315 // Unix like behaviour
3316 boolean added = false;
3318 if (t.isDataFlavorSupported(uriListFlavor))
3320 Cache.log.debug("Drop handled as uriListFlavor");
3321 // This is used by Unix drag system
3322 data = (String) t.getTransferData(uriListFlavor);
3326 // fallback to text: workaround - on OSX where there's a JVM bug
3327 Cache.log.debug("standard URIListFlavor failed. Trying text");
3328 // try text fallback
3329 data = (String) t.getTransferData(
3330 new DataFlavor("text/plain;class=java.lang.String"));
3331 if (Cache.log.isDebugEnabled())
3333 Cache.log.debug("fallback returned " + data);
3336 while (protocols.size() < files.size())
3338 Cache.log.debug("Adding missing FILE protocol for "
3339 + files.get(protocols.size()));
3340 protocols.add(DataSourceType.FILE);
3342 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
3343 data, "\r\n"); st.hasMoreTokens();)
3346 String s = st.nextToken();
3347 if (s.startsWith("#"))
3349 // the line is a comment (as per the RFC 2483)
3352 java.net.URI uri = new java.net.URI(s);
3353 if (uri.getScheme().toLowerCase().startsWith("http"))
3355 protocols.add(DataSourceType.URL);
3356 files.add(uri.toString());
3360 // otherwise preserve old behaviour: catch all for file objects
3361 java.io.File file = new java.io.File(uri);
3362 protocols.add(DataSourceType.FILE);
3363 files.add(file.toString());
3366 if (Cache.log.isDebugEnabled())
3368 if (data == null || !added)
3371 "Couldn't resolve drop data. Here are the supported flavors:");
3372 for (DataFlavor fl : t.getTransferDataFlavors())
3375 "Supported transfer dataflavor: " + fl.toString());
3376 Object df = t.getTransferData(fl);
3379 Cache.log.debug("Retrieves: " + df);
3383 Cache.log.debug("Retrieved nothing");
3392 * Sets the Preferences property for experimental features to True or False
3393 * depending on the state of the controlling menu item
3396 protected void showExperimental_actionPerformed(boolean selected)
3398 Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));