2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 import java.awt.datatransfer.*;
25 import java.awt.dnd.*;
26 import java.awt.event.*;
27 import java.io.BufferedInputStream;
28 import java.io.BufferedOutputStream;
30 import java.io.FileOutputStream;
31 import java.io.InputStream;
32 import java.lang.reflect.Constructor;
34 import java.net.URLConnection;
35 import java.nio.channels.ReadableByteChannel;
39 import javax.swing.event.MenuEvent;
40 import javax.swing.event.MenuListener;
48 public class Desktop extends jalview.jbgui.GDesktop implements
49 DropTargetListener, ClipboardOwner, IProgressIndicator
52 public static Desktop instance;
54 // Need to decide if the Memory Usage is to be included in
55 // Next release or not.
56 public static MyDesktopPane desktop;
58 // public static JDesktopPane desktop;
60 static int openFrameCount = 0;
62 static final int xOffset = 30;
64 static final int yOffset = 30;
66 public static jalview.ws.Discoverer discoverer;
68 public static Object[] jalviewClipboard;
70 public static boolean internalCopy = false;
72 static int fileLoadingCount = 0;
75 * Creates a new Desktop object.
80 * A note to implementors. It is ESSENTIAL that any activities that might
81 * block are spawned off as threads rather than waited for during this
85 doVamsasClientCheck();
88 setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
89 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
90 boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
92 desktop = new MyDesktopPane(selmemusage);
93 showMemusage.setSelected(selmemusage);
94 desktop.setBackground(Color.white);
95 getContentPane().setLayout(new BorderLayout());
96 getContentPane().add(desktop, BorderLayout.CENTER);
97 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
99 // This line prevents Windows Look&Feel resizing all new windows to maximum
100 // if previous window was maximised
101 desktop.setDesktopManager(new DefaultDesktopManager());
103 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
104 String x = jalview.bin.Cache.getProperty("SCREEN_X");
105 String y = jalview.bin.Cache.getProperty("SCREEN_Y");
106 String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
107 String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
109 if ((x != null) && (y != null) && (width != null) && (height != null))
111 setBounds(Integer.parseInt(x), Integer.parseInt(y), Integer
112 .parseInt(width), Integer.parseInt(height));
116 setBounds((int) (screenSize.width - 900) / 2,
117 (int) (screenSize.height - 650) / 2, 900, 650);
120 this.addWindowListener(new WindowAdapter()
122 public void windowClosing(WindowEvent evt)
128 this.addMouseListener(new MouseAdapter()
130 public void mousePressed(MouseEvent evt)
132 if (SwingUtilities.isRightMouseButton(evt))
134 showPasteMenu(evt.getX(), evt.getY());
139 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
140 // Spawn a thread that shows the splashscreen
143 discoverer = new jalview.ws.Discoverer(); // Only gets started if gui is
147 private void doVamsasClientCheck()
149 if (jalview.bin.Cache.vamsasJarsPresent())
151 setupVamsasDisconnectedGui();
152 VamsasMenu.setVisible(true);
153 final Desktop us = this;
154 VamsasMenu.addMenuListener(new MenuListener()
156 // this listener remembers when the menu was first selected, and
157 // doesn't rebuild the session list until it has been cleared and
159 boolean refresh = true;
161 public void menuCanceled(MenuEvent e)
166 public void menuDeselected(MenuEvent e)
171 public void menuSelected(MenuEvent e)
175 us.buildVamsasStMenu();
180 vamsasStart.setVisible(true);
184 void showPasteMenu(int x, int y)
186 JPopupMenu popup = new JPopupMenu();
187 JMenuItem item = new JMenuItem("Paste To New Window");
188 item.addActionListener(new ActionListener()
190 public void actionPerformed(ActionEvent evt)
197 popup.show(this, x, y);
204 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
205 Transferable contents = c.getContents(this);
207 if (contents != null)
209 String file = (String) contents
210 .getTransferData(DataFlavor.stringFlavor);
212 String format = new IdentifyFile().Identify(file,
213 FormatAdapter.PASTE);
215 new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
218 } catch (Exception ex)
221 .println("Unable to paste alignment from system clipboard:\n"
238 public static synchronized void addInternalFrame(
239 final JInternalFrame frame, String title, int w, int h)
241 addInternalFrame(frame, title, w, h, true);
258 public static synchronized void addInternalFrame(
259 final JInternalFrame frame, String title, int w, int h,
263 // TODO: consider fixing method to update entries in the window submenu with
264 // the current window title
266 frame.setTitle(title);
267 if (frame.getWidth() < 1 || frame.getHeight() < 1)
271 // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
272 // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
273 // IF JALVIEW IS RUNNING HEADLESS
274 // ///////////////////////////////////////////////
275 if (System.getProperty("java.awt.headless") != null
276 && System.getProperty("java.awt.headless").equals("true"))
283 frame.setVisible(true);
284 frame.setClosable(true);
285 frame.setResizable(resizable);
286 frame.setMaximizable(resizable);
287 frame.setIconifiable(resizable);
288 frame.setFrameIcon(null);
290 if (frame.getX() < 1 && frame.getY() < 1)
292 frame.setLocation(xOffset * openFrameCount, yOffset
293 * ((openFrameCount - 1) % 10) + yOffset);
296 final JMenuItem menuItem = new JMenuItem(title);
298 .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
300 public void internalFrameActivated(
301 javax.swing.event.InternalFrameEvent evt)
303 JInternalFrame itf = desktop.getSelectedFrame();
311 public void internalFrameClosed(
312 javax.swing.event.InternalFrameEvent evt)
314 PaintRefresher.RemoveComponent(frame);
316 windowMenu.remove(menuItem);
317 JInternalFrame itf = desktop.getSelectedFrame();
326 menuItem.addActionListener(new ActionListener()
328 public void actionPerformed(ActionEvent e)
332 frame.setSelected(true);
333 frame.setIcon(false);
334 } catch (java.beans.PropertyVetoException ex)
341 windowMenu.add(menuItem);
347 frame.setSelected(true);
348 frame.requestFocus();
349 } catch (java.beans.PropertyVetoException ve)
354 public void lostOwnership(Clipboard clipboard, Transferable contents)
358 Desktop.jalviewClipboard = null;
361 internalCopy = false;
364 public void dragEnter(DropTargetDragEvent evt)
368 public void dragExit(DropTargetEvent evt)
372 public void dragOver(DropTargetDragEvent evt)
376 public void dropActionChanged(DropTargetDragEvent evt)
386 public void drop(DropTargetDropEvent evt)
388 Transferable t = evt.getTransferable();
389 java.util.List files = null;
393 DataFlavor uriListFlavor = new DataFlavor(
394 "text/uri-list;class=java.lang.String");
395 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
397 // Works on Windows and MacOSX
398 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
399 files = (java.util.List) t
400 .getTransferData(DataFlavor.javaFileListFlavor);
402 else if (t.isDataFlavorSupported(uriListFlavor))
404 // This is used by Unix drag system
405 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
406 String data = (String) t.getTransferData(uriListFlavor);
407 files = new java.util.ArrayList(1);
408 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
409 data, "\r\n"); st.hasMoreTokens();)
411 String s = st.nextToken();
412 if (s.startsWith("#"))
414 // the line is a comment (as per the RFC 2483)
418 java.net.URI uri = new java.net.URI(s);
419 java.io.File file = new java.io.File(uri);
423 } catch (Exception e)
431 for (int i = 0; i < files.size(); i++)
433 String file = files.get(i).toString();
434 String protocol = FormatAdapter.FILE;
435 String format = null;
437 if (file.endsWith(".jar"))
444 format = new IdentifyFile().Identify(file, protocol);
447 new FileLoader().LoadFile(file, protocol, format);
450 } catch (Exception ex)
462 public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
464 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
465 .getProperty("LAST_DIRECTORY"),
466 jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
467 jalview.io.AppletFormatAdapter.READABLE_FNAMES,
468 jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
470 chooser.setFileView(new JalviewFileView());
471 chooser.setDialogTitle("Open local file");
472 chooser.setToolTipText("Open");
474 int value = chooser.showOpenDialog(this);
476 if (value == JalviewFileChooser.APPROVE_OPTION)
478 String choice = chooser.getSelectedFile().getPath();
479 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
480 .getSelectedFile().getParent());
482 String format = null;
483 if (chooser.getSelectedFormat().equals("Jalview"))
489 format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
492 if (viewport != null)
494 new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
499 new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
510 public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
512 // This construct allows us to have a wider textfield
514 JLabel label = new JLabel("Enter URL of Input File");
515 final JComboBox history = new JComboBox();
517 JPanel panel = new JPanel(new GridLayout(2, 1));
520 history.setPreferredSize(new Dimension(400, 20));
521 history.setEditable(true);
522 history.addItem("http://www.");
524 String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
528 if (historyItems != null)
530 st = new StringTokenizer(historyItems, "\t");
532 while (st.hasMoreTokens())
534 history.addItem(st.nextElement());
538 int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
539 "Input Alignment From URL", JOptionPane.OK_CANCEL_OPTION);
541 if (reply != JOptionPane.OK_OPTION)
546 String url = history.getSelectedItem().toString();
548 if (url.toLowerCase().endsWith(".jar"))
550 if (viewport != null)
552 new FileLoader().LoadFile(viewport, url, FormatAdapter.URL,
557 new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
562 String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
564 if (format.equals("URL NOT FOUND"))
566 JOptionPane.showInternalMessageDialog(Desktop.desktop,
567 "Couldn't locate " + url, "URL not found",
568 JOptionPane.WARNING_MESSAGE);
573 if (viewport != null)
575 new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
579 new FileLoader().LoadFile(url, FormatAdapter.URL, format);
590 public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
592 CutAndPasteTransfer cap = new CutAndPasteTransfer();
593 cap.setForInput(viewport);
594 Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
602 jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
603 jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
604 jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
605 jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
615 public void aboutMenuItem_actionPerformed(ActionEvent e)
617 StringBuffer message = new StringBuffer("Jalview version "
618 + jalview.bin.Cache.getProperty("VERSION") + "; last updated: "
619 + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
621 if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
622 jalview.bin.Cache.getProperty("VERSION")))
625 .append("\n\n!! Jalview version "
626 + jalview.bin.Cache.getProperty("LATEST_VERSION")
627 + " is available for download from http://www.jalview.org !!\n");
630 // TODO: update this text for each release or centrally store it for lite
633 .append("\nAuthors: Andrew Waterhouse, Jim Procter, Michele Clamp, James Cuff, Steve Searle,\n David Martin & Geoff Barton."
634 + "\nDevelopment managed by The Barton Group, University of Dundee, Scotland, UK.\n"
635 + "\nFor help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list\n"
636 + "\nIf you use Jalview, please cite:"
637 + "\nWaterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
638 + "\nJalview Version 2 - a multiple sequence alignment editor and analysis workbench"
639 + "\nBioinformatics doi: 10.1093/bioinformatics/btp033");
640 JOptionPane.showInternalMessageDialog(Desktop.desktop,
642 message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
651 public void documentationMenuItem_actionPerformed(ActionEvent e)
655 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
656 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
657 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
659 javax.help.HelpBroker hb = hs.createHelpBroker();
660 hb.setCurrentID("home");
661 hb.setDisplayed(true);
662 } catch (Exception ex)
667 public void closeAll_actionPerformed(ActionEvent e)
669 JInternalFrame[] frames = desktop.getAllFrames();
670 for (int i = 0; i < frames.length; i++)
674 frames[i].setClosed(true);
675 } catch (java.beans.PropertyVetoException ex)
679 System.out.println("ALL CLOSED");
680 if (v_client != null)
682 // TODO clear binding to vamsas document objects on close_all
687 public void raiseRelated_actionPerformed(ActionEvent e)
689 reorderAssociatedWindows(false, false);
692 public void minimizeAssociated_actionPerformed(ActionEvent e)
694 reorderAssociatedWindows(true, false);
697 void closeAssociatedWindows()
699 reorderAssociatedWindows(false, true);
705 * @seejalview.jbgui.GDesktop#garbageCollect_actionPerformed(java.awt.event.
708 protected void garbageCollect_actionPerformed(ActionEvent e)
710 // We simply collect the garbage
711 jalview.bin.Cache.log.debug("Collecting garbage...");
713 jalview.bin.Cache.log.debug("Finished garbage collection.");
720 * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
723 protected void showMemusage_actionPerformed(ActionEvent e)
725 desktop.showMemoryUsage(showMemusage.isSelected());
728 void reorderAssociatedWindows(boolean minimize, boolean close)
730 JInternalFrame[] frames = desktop.getAllFrames();
731 if (frames == null || frames.length < 1)
736 AlignViewport source = null, target = null;
737 if (frames[0] instanceof AlignFrame)
739 source = ((AlignFrame) frames[0]).getCurrentView();
741 else if (frames[0] instanceof TreePanel)
743 source = ((TreePanel) frames[0]).getViewPort();
745 else if (frames[0] instanceof PCAPanel)
747 source = ((PCAPanel) frames[0]).av;
749 else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
751 source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
756 for (int i = 0; i < frames.length; i++)
759 if (frames[i] == null)
763 if (frames[i] instanceof AlignFrame)
765 target = ((AlignFrame) frames[i]).getCurrentView();
767 else if (frames[i] instanceof TreePanel)
769 target = ((TreePanel) frames[i]).getViewPort();
771 else if (frames[i] instanceof PCAPanel)
773 target = ((PCAPanel) frames[i]).av;
775 else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
777 target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
780 if (source == target)
786 frames[i].setClosed(true);
790 frames[i].setIcon(minimize);
797 } catch (java.beans.PropertyVetoException ex)
811 protected void preferences_actionPerformed(ActionEvent e)
822 public void saveState_actionPerformed(ActionEvent e)
824 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
825 .getProperty("LAST_DIRECTORY"), new String[]
826 { "jar" }, new String[]
827 { "Jalview Project" }, "Jalview Project");
829 chooser.setFileView(new JalviewFileView());
830 chooser.setDialogTitle("Save State");
832 int value = chooser.showSaveDialog(this);
834 if (value == JalviewFileChooser.APPROVE_OPTION)
836 java.io.File choice = chooser.getSelectedFile();
837 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
838 new Jalview2XML().SaveState(choice);
848 public void loadState_actionPerformed(ActionEvent e)
850 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
851 .getProperty("LAST_DIRECTORY"), new String[]
852 { "jar" }, new String[]
853 { "Jalview Project" }, "Jalview Project");
854 chooser.setFileView(new JalviewFileView());
855 chooser.setDialogTitle("Restore state");
857 int value = chooser.showOpenDialog(this);
859 if (value == JalviewFileChooser.APPROVE_OPTION)
861 String choice = chooser.getSelectedFile().getAbsolutePath();
862 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
863 .getSelectedFile().getParent());
864 new Jalview2XML().LoadJalviewAlign(choice);
868 public void inputSequence_actionPerformed(ActionEvent e)
870 new SequenceFetcher(this);
873 JPanel progressPanel;
875 public void startLoading(final String fileName)
877 if (fileLoadingCount == 0)
879 addProgressPanel("Loading File: " + fileName + " ");
885 private JProgressBar addProgressPanel(String string)
887 if (progressPanel == null)
889 progressPanel = new JPanel(new BorderLayout());
890 totalProgressCount = 0;
892 JProgressBar progressBar = new JProgressBar();
893 progressBar.setIndeterminate(true);
895 progressPanel.add(new JLabel(string), BorderLayout.WEST);
897 progressPanel.add(progressBar, BorderLayout.CENTER);
899 instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
900 totalProgressCount++;
905 int totalProgressCount = 0;
907 private void removeProgressPanel(JProgressBar progbar)
909 if (progressPanel != null)
911 progressPanel.remove(progbar);
912 if (--totalProgressCount < 1)
914 this.getContentPane().remove(progressPanel);
915 progressPanel = null;
921 public void stopLoading()
924 if (fileLoadingCount < 1)
926 if (progressPanel != null)
928 this.getContentPane().remove(progressPanel);
929 progressPanel = null;
931 fileLoadingCount = 0;
936 public static int getViewCount(String viewId)
938 AlignViewport[] aps = getViewports(viewId);
939 return (aps == null) ? 0 : aps.length;
945 * @return all AlignmentPanels concerning the viewId sequence set
947 public static AlignmentPanel[] getAlignmentPanels(String viewId)
950 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
951 ArrayList aps = new ArrayList();
952 for (int t = 0; t < frames.length; t++)
954 if (frames[t] instanceof AlignFrame)
956 AlignFrame af = (AlignFrame) frames[t];
957 for (int a = 0; a < af.alignPanels.size(); a++)
960 .equals(((AlignmentPanel) af.alignPanels.elementAt(a)).av
961 .getSequenceSetId()))
963 aps.add(af.alignPanels.elementAt(a));
972 AlignmentPanel[] vap = new AlignmentPanel[aps.size()];
973 for (int t = 0; t < vap.length; t++)
975 vap[t] = (AlignmentPanel) aps.get(t);
981 * get all the viewports on an alignment.
983 * @param sequenceSetId
984 * unique alignment id
985 * @return all viewports on the alignment bound to sequenceSetId
987 public static AlignViewport[] getViewports(String sequenceSetId)
989 Vector viewp = new Vector();
992 javax.swing.JInternalFrame[] frames = instance.getAllFrames();
994 for (int t = 0; t < frames.length; t++)
996 if (frames[t] instanceof AlignFrame)
998 AlignFrame afr = ((AlignFrame) frames[t]);
999 if (afr.getViewport().getSequenceSetId().equals(sequenceSetId))
1001 if (afr.alignPanels != null)
1003 for (int a = 0; a < afr.alignPanels.size(); a++)
1005 if (sequenceSetId.equals(((AlignmentPanel) afr.alignPanels
1006 .elementAt(a)).av.getSequenceSetId()))
1008 viewp.addElement(((AlignmentPanel) afr.alignPanels
1015 viewp.addElement(((AlignFrame) frames[t]).getViewport());
1020 if (viewp.size() > 0)
1022 AlignViewport[] vp = new AlignViewport[viewp.size()];
1030 public void explodeViews(AlignFrame af)
1032 int size = af.alignPanels.size();
1038 for (int i = 0; i < size; i++)
1040 AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(i);
1041 AlignFrame newaf = new AlignFrame(ap);
1042 if (ap.av.explodedPosition != null
1043 && !ap.av.explodedPosition.equals(af.getBounds()))
1045 newaf.setBounds(ap.av.explodedPosition);
1048 ap.av.gatherViewsHere = false;
1050 addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
1051 AlignFrame.DEFAULT_HEIGHT);
1054 af.alignPanels.clear();
1055 af.closeMenuItem_actionPerformed(true);
1059 public void gatherViews(AlignFrame source)
1061 source.viewport.gatherViewsHere = true;
1062 source.viewport.explodedPosition = source.getBounds();
1063 JInternalFrame[] frames = desktop.getAllFrames();
1064 String viewId = source.viewport.sequenceSetID;
1066 for (int t = 0; t < frames.length; t++)
1068 if (frames[t] instanceof AlignFrame && frames[t] != source)
1070 AlignFrame af = (AlignFrame) frames[t];
1071 boolean gatherThis = false;
1072 for (int a = 0; a < af.alignPanels.size(); a++)
1074 AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
1075 if (viewId.equals(ap.av.getSequenceSetId()))
1078 ap.av.gatherViewsHere = false;
1079 ap.av.explodedPosition = af.getBounds();
1080 source.addAlignmentPanel(ap, false);
1086 af.alignPanels.clear();
1087 af.closeMenuItem_actionPerformed(true);
1094 jalview.gui.VamsasApplication v_client = null;
1096 public void vamsasImport_actionPerformed(ActionEvent e)
1098 if (v_client == null)
1100 // Load and try to start a session.
1101 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1102 .getProperty("LAST_DIRECTORY"));
1104 chooser.setFileView(new JalviewFileView());
1105 chooser.setDialogTitle("Open a saved VAMSAS session");
1107 .setToolTipText("select a vamsas session to be opened as a new vamsas session.");
1109 int value = chooser.showOpenDialog(this);
1111 if (value == JalviewFileChooser.APPROVE_OPTION)
1113 String fle = chooser.getSelectedFile().toString();
1114 if (!vamsasImport(chooser.getSelectedFile()))
1116 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1117 "Couldn't import '" + fle + "' as a new vamsas session.",
1118 "Vamsas Document Import Failed",
1119 JOptionPane.ERROR_MESSAGE);
1125 jalview.bin.Cache.log
1126 .error("Implementation error - load session from a running session is not supported.");
1131 * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
1133 * @return true if import was a success and a session was started.
1135 public boolean vamsasImport(URL url)
1137 // TODO: create progress bar
1138 if (v_client != null)
1141 jalview.bin.Cache.log
1142 .error("Implementation error - load session from a running session is not supported.");
1148 // copy the URL content to a temporary local file
1149 // TODO: be a bit cleverer here with nio (?!)
1150 File file = File.createTempFile("vdocfromurl", ".vdj");
1151 FileOutputStream fos = new FileOutputStream(file);
1152 BufferedInputStream bis = new BufferedInputStream(url.openStream());
1153 byte[] buffer = new byte[2048];
1155 while ((ln = bis.read(buffer))>-1)
1157 fos.write(buffer,0,ln);
1161 v_client = new jalview.gui.VamsasApplication(this, file, url.toExternalForm());
1162 } catch (Exception ex)
1164 jalview.bin.Cache.log.error(
1165 "Failed to create new vamsas session from contents of URL "+url,ex);
1168 setupVamsasConnectedGui();
1169 v_client.initial_update(); // TODO: thread ?
1170 return v_client.inSession();
1174 * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
1176 * @return true if import was a success and a session was started.
1178 public boolean vamsasImport(File file)
1180 // TODO: create progress bar
1181 if (v_client != null)
1184 jalview.bin.Cache.log
1185 .error("Implementation error - load session from a running session is not supported.");
1191 v_client = new jalview.gui.VamsasApplication(this, file,null);
1192 } catch (Exception ex)
1194 jalview.bin.Cache.log.error(
1195 "New vamsas session from existing session file failed:", ex);
1198 setupVamsasConnectedGui();
1199 v_client.initial_update(); // TODO: thread ?
1200 return v_client.inSession();
1202 public boolean joinVamsasSession(String mysesid) {
1205 throw new Error("Trying to join a vamsas session when another is already connected.");
1209 throw new Error("Invalid vamsas session id.");
1211 v_client = new VamsasApplication(this, mysesid);
1212 setupVamsasConnectedGui();
1213 v_client.initial_update();
1214 return (v_client.inSession());
1217 public void vamsasStart_actionPerformed(ActionEvent e)
1219 if (v_client == null)
1222 // we just start a default session for moment.
1224 * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
1225 * getProperty("LAST_DIRECTORY"));
1227 * chooser.setFileView(new JalviewFileView());
1228 * chooser.setDialogTitle("Load Vamsas file");
1229 * chooser.setToolTipText("Import");
1231 * int value = chooser.showOpenDialog(this);
1233 * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
1234 * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
1236 v_client = new VamsasApplication(this);
1237 setupVamsasConnectedGui();
1238 v_client.initial_update(); // TODO: thread ?
1242 // store current data in session.
1243 v_client.push_update(); // TODO: thread
1247 protected void setupVamsasConnectedGui()
1249 vamsasStart.setText("Session Update");
1250 vamsasSave.setVisible(true);
1251 vamsasStop.setVisible(true);
1252 vamsasImport.setVisible(false); // Document import to existing session is
1253 // not possible for vamsas-client-1.0.
1256 protected void setupVamsasDisconnectedGui()
1258 vamsasSave.setVisible(false);
1259 vamsasStop.setVisible(false);
1260 vamsasImport.setVisible(true);
1261 vamsasStart.setText("New Vamsas Session");
1264 public void vamsasStop_actionPerformed(ActionEvent e)
1266 if (v_client != null)
1268 v_client.end_session();
1270 setupVamsasDisconnectedGui();
1274 protected void buildVamsasStMenu()
1276 if (v_client == null)
1278 String[] sess = null;
1281 sess = VamsasApplication.getSessionList();
1282 } catch (Exception e)
1284 jalview.bin.Cache.log.warn(
1285 "Problem getting current sessions list.", e);
1290 jalview.bin.Cache.log.debug("Got current sessions list: "
1291 + sess.length + " entries.");
1292 VamsasStMenu.removeAll();
1293 for (int i = 0; i < sess.length; i++)
1295 JMenuItem sessit = new JMenuItem();
1296 sessit.setText(sess[i]);
1297 sessit.setToolTipText("Connect to session " + sess[i]);
1298 final Desktop dsktp = this;
1299 final String mysesid = sess[i];
1300 sessit.addActionListener(new ActionListener()
1303 public void actionPerformed(ActionEvent e)
1305 if (dsktp.v_client == null)
1307 Thread rthr = new Thread(new Runnable()
1312 dsktp.v_client = new VamsasApplication(dsktp, mysesid);
1313 dsktp.setupVamsasConnectedGui();
1314 dsktp.v_client.initial_update();
1322 VamsasStMenu.add(sessit);
1324 // don't show an empty menu.
1325 VamsasStMenu.setVisible(sess.length > 0);
1330 jalview.bin.Cache.log.debug("No current vamsas sessions.");
1331 VamsasStMenu.removeAll();
1332 VamsasStMenu.setVisible(false);
1337 // Not interested in the content. Just hide ourselves.
1338 VamsasStMenu.setVisible(false);
1342 public void vamsasSave_actionPerformed(ActionEvent e)
1344 if (v_client != null)
1346 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
1347 .getProperty("LAST_DIRECTORY"), new String[]
1348 { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
1350 { "Vamsas Document" }, "Vamsas Document");
1352 chooser.setFileView(new JalviewFileView());
1353 chooser.setDialogTitle("Save Vamsas Document Archive");
1355 int value = chooser.showSaveDialog(this);
1357 if (value == JalviewFileChooser.APPROVE_OPTION)
1359 java.io.File choice = chooser.getSelectedFile();
1360 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
1361 String warnmsg = null;
1362 String warnttl = null;
1365 v_client.vclient.storeDocument(choice);
1368 warnttl = "Serious Problem saving Vamsas Document";
1369 warnmsg = ex.toString();
1370 jalview.bin.Cache.log.error("Error Whilst saving document to "
1373 } catch (Exception ex)
1375 warnttl = "Problem saving Vamsas Document.";
1376 warnmsg = ex.toString();
1377 jalview.bin.Cache.log.warn("Exception Whilst saving document to "
1381 if (warnmsg != null)
1383 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1385 warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
1391 JProgressBar vamUpdate = null;
1394 * hide vamsas user gui bits when a vamsas document event is being handled.
1397 * true to hide gui, false to reveal gui
1399 public void setVamsasUpdate(boolean b)
1401 jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
1402 + (b ? "in progress" : "finished"));
1404 if (vamUpdate != null)
1406 this.removeProgressPanel(vamUpdate);
1410 vamUpdate = this.addProgressPanel("Updating vamsas session");
1412 vamsasStart.setVisible(!b);
1413 vamsasStop.setVisible(!b);
1414 vamsasSave.setVisible(!b);
1417 public JInternalFrame[] getAllFrames()
1419 return desktop.getAllFrames();
1423 * Checks the given url to see if it gives a response indicating that the user
1424 * should be informed of a new questionnaire.
1428 public void checkForQuestionnaire(String url)
1430 UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
1431 // javax.swing.SwingUtilities.invokeLater(jvq);
1432 new Thread(jvq).start();
1436 * Proxy class for JDesktopPane which optionally displays the current memory
1437 * usage and highlights the desktop area with a red bar if free memory runs
1442 public class MyDesktopPane extends JDesktopPane implements Runnable
1445 boolean showMemoryUsage = false;
1449 java.text.NumberFormat df;
1451 float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
1454 public MyDesktopPane(boolean showMemoryUsage)
1456 showMemoryUsage(showMemoryUsage);
1459 public void showMemoryUsage(boolean showMemoryUsage)
1461 this.showMemoryUsage = showMemoryUsage;
1462 if (showMemoryUsage)
1464 Thread worker = new Thread(this);
1469 public boolean isShowMemoryUsage()
1471 return showMemoryUsage;
1476 df = java.text.NumberFormat.getNumberInstance();
1477 df.setMaximumFractionDigits(2);
1478 runtime = Runtime.getRuntime();
1480 while (showMemoryUsage)
1485 maxMemory = runtime.maxMemory() / 1048576f;
1486 allocatedMemory = runtime.totalMemory() / 1048576f;
1487 freeMemory = runtime.freeMemory() / 1048576f;
1488 totalFreeMemory = freeMemory + (maxMemory - allocatedMemory);
1490 percentUsage = (totalFreeMemory / maxMemory) * 100;
1492 // if (percentUsage < 20)
1494 // border1 = BorderFactory.createMatteBorder(12, 12, 12, 12,
1496 // instance.set.setBorder(border1);
1500 } catch (Exception ex)
1502 ex.printStackTrace();
1507 public void paintComponent(Graphics g)
1509 if (showMemoryUsage)
1511 if (percentUsage < 20)
1512 g.setColor(Color.red);
1514 g.drawString("Total Free Memory: " + df.format(totalFreeMemory)
1515 + "MB; Max Memory: " + df.format(maxMemory) + "MB; "
1516 + df.format(percentUsage) + "%", 10, getHeight()
1517 - g.getFontMetrics().getHeight());
1523 protected JMenuItem groovyShell;
1525 public void doGroovyCheck()
1527 if (jalview.bin.Cache.groovyJarsPresent())
1529 groovyShell = new JMenuItem();
1530 groovyShell.setText("Groovy Console...");
1531 groovyShell.addActionListener(new ActionListener()
1533 public void actionPerformed(ActionEvent e)
1535 groovyShell_actionPerformed(e);
1538 toolsMenu.add(groovyShell);
1539 groovyShell.setVisible(true);
1544 * Accessor method to quickly get all the AlignmentFrames loaded.
1546 public static AlignFrame[] getAlignframes()
1548 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1554 Vector avp = new Vector();
1558 for (int i = frames.length - 1; i > -1; i--)
1560 if (frames[i] instanceof AlignFrame)
1562 AlignFrame af = (AlignFrame) frames[i];
1566 } catch (Exception ex)
1568 ex.printStackTrace();
1570 if (avp.size() == 0)
1574 AlignFrame afs[] = new AlignFrame[avp.size()];
1575 for (int i = 0, j = avp.size(); i < j; i++)
1577 afs[i] = (AlignFrame) avp.elementAt(i);
1584 * Add Groovy Support to Jalview
1586 public void groovyShell_actionPerformed(ActionEvent e)
1588 // use reflection to avoid creating compilation dependency.
1589 if (!jalview.bin.Cache.groovyJarsPresent())
1592 "Implementation Error. Cannot create groovyShell without Groovy on the classpath!");
1596 Class gcClass = Desktop.class.getClassLoader().loadClass(
1597 "groovy.ui.Console");
1598 Constructor gccons = gcClass.getConstructor(null);
1599 java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
1601 { String.class, Object.class });
1602 java.lang.reflect.Method run = gcClass.getMethod("run", null);
1603 Object gc = gccons.newInstance(null);
1604 setvar.invoke(gc, new Object[]
1605 { "Jalview", this });
1606 run.invoke(gc, null);
1607 } catch (Exception ex)
1609 jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
1611 .showInternalMessageDialog(
1614 "Couldn't create the groovy Shell. Check the error log for the details of what went wrong.",
1615 "Jalview Groovy Support Failed",
1616 JOptionPane.ERROR_MESSAGE);
1621 * Progress bars managed by the IProgressIndicator method.
1623 private Hashtable progressBars, progressBarHandlers;
1628 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
1630 public void setProgressBar(String message, long id)
1632 if (progressBars == null)
1634 progressBars = new Hashtable();
1635 progressBarHandlers = new Hashtable();
1638 if (progressBars.get(new Long(id)) != null)
1640 JProgressBar progressPanel = (JProgressBar) progressBars
1641 .remove(new Long(id));
1642 if (progressBarHandlers.contains(new Long(id)))
1644 progressBarHandlers.remove(new Long(id));
1646 removeProgressPanel(progressPanel);
1650 progressBars.put(new Long(id), addProgressPanel(message));
1657 * @see jalview.gui.IProgressIndicator#registerHandler(long,
1658 * jalview.gui.IProgressIndicatorHandler)
1660 public void registerHandler(final long id,
1661 final IProgressIndicatorHandler handler)
1663 if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
1666 "call setProgressBar before registering the progress bar's handler.");
1668 progressBarHandlers.put(new Long(id), handler);
1669 final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
1670 if (handler.canCancel())
1672 JButton cancel = new JButton("Cancel");
1673 final IProgressIndicator us = this;
1674 cancel.addActionListener(new ActionListener()
1677 public void actionPerformed(ActionEvent e)
1679 handler.cancelActivity(id);
1680 us.setProgressBar("Cancelled "
1681 + ((JLabel) progressPanel.getComponent(0)).getText(), id);
1684 progressPanel.add(cancel, BorderLayout.EAST);
1689 * This will return the first AlignFrame viewing AlignViewport av. It will
1690 * break if there are more than one AlignFrames viewing a particular av. This
1693 * @return alignFrame for av
1695 public static AlignFrame getAlignFrameFor(AlignViewport av)
1697 if (desktop != null)
1699 AlignmentPanel[] aps = getAlignmentPanels(av.getSequenceSetId());
1700 for (int panel = 0; aps != null && panel < aps.length; panel++)
1702 if (aps[panel] != null && aps[panel].av == av)
1704 return aps[panel].alignFrame;
1711 public VamsasApplication getVamsasApplication()