2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2005 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.*;
37 public class Desktop extends jalview.jbgui.GDesktop
38 implements DropTargetListener
41 public static JDesktopPane desktop;
42 static int openFrameCount = 0;
43 static final int xOffset = 30;
44 static final int yOffset = 30;
45 public static jalview.ws.Discoverer discoverer;
47 public static Object [] jalviewClipboard;
51 * Creates a new Desktop object.
60 java.net.URL url = getClass().getResource("/images/logo.gif");
64 image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
66 MediaTracker mt = new MediaTracker(this);
67 mt.addImage(image, 0);
76 setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
77 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
78 desktop = new JDesktopPane();
79 desktop.setBackground(Color.white);
80 setContentPane(desktop);
81 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
83 // This line prevents Windows Look&Feel resizing all new windows to maximum
84 // if previous window was maximised
85 desktop.setDesktopManager(new DefaultDesktopManager());
87 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
88 String x = jalview.bin.Cache.getProperty("SCREEN_X");
89 String y = jalview.bin.Cache.getProperty("SCREEN_Y");
90 String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
91 String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
93 if ((x != null) && (y != null) && (width != null) && (height != null))
95 setBounds(Integer.parseInt(x), Integer.parseInt(y),
96 Integer.parseInt(width), Integer.parseInt(height));
100 setBounds((int) (screenSize.width - 900) / 2,
101 (int) (screenSize.height - 650) / 2, 900, 650);
104 this.addWindowListener(new WindowAdapter()
106 public void windowClosing(WindowEvent evt)
112 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
114 /////////Add a splashscreen on startup
115 /////////Add a splashscreen on startup
116 JInternalFrame frame = new JInternalFrame();
118 SplashScreen splash = new SplashScreen(frame, image);
119 frame.setContentPane(splash);
120 frame.setLayer(JLayeredPane.PALETTE_LAYER);
121 frame.setLocation((int) ((getWidth() - 750) / 2),
122 (int) ((getHeight() - 160) / 2));
124 addInternalFrame(frame, "", 750, 160, false);
126 discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
133 * @param frame DOCUMENT ME!
134 * @param title DOCUMENT ME!
135 * @param w DOCUMENT ME!
136 * @param h DOCUMENT ME!
138 public static synchronized void addInternalFrame(final JInternalFrame frame,
139 String title, int w, int h)
141 addInternalFrame(frame, title, w, h, true);
147 * @param frame DOCUMENT ME!
148 * @param title DOCUMENT ME!
149 * @param w DOCUMENT ME!
150 * @param h DOCUMENT ME!
151 * @param resizable DOCUMENT ME!
153 public static synchronized void addInternalFrame(final JInternalFrame frame,
154 String title, int w, int h, boolean resizable)
157 frame.setTitle(title);
158 if(frame.getWidth()<1 || frame.getHeight()<1)
162 // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
163 // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
164 // IF JALVIEW IS RUNNING HEADLESS
165 /////////////////////////////////////////////////
166 if (System.getProperty("java.awt.headless") != null
167 && System.getProperty("java.awt.headless").equals("true"))
175 frame.setVisible(true);
176 frame.setClosable(true);
177 frame.setResizable(resizable);
178 frame.setMaximizable(resizable);
179 frame.setIconifiable(resizable);
180 frame.setFrameIcon(null);
182 if (frame.getX()<1 && frame.getY()<1)
184 frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
187 final JMenuItem menuItem = new JMenuItem(title);
188 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
190 public void internalFrameActivated(javax.swing.event.
191 InternalFrameEvent evt)
193 JInternalFrame itf = desktop.getSelectedFrame();
199 public void internalFrameClosed(
200 javax.swing.event.InternalFrameEvent evt)
203 windowMenu.remove(menuItem);
204 JInternalFrame itf = desktop.getSelectedFrame();
211 menuItem.addActionListener(new ActionListener()
213 public void actionPerformed(ActionEvent e)
217 frame.setSelected(true);
218 frame.setIcon(false);
220 catch (java.beans.PropertyVetoException ex)
227 windowMenu.add(menuItem);
232 frame.setSelected(true);
233 frame.requestFocus();
234 }catch(java.beans.PropertyVetoException ve)
238 public void dragEnter(DropTargetDragEvent evt)
241 public void dragExit(DropTargetEvent evt)
244 public void dragOver(DropTargetDragEvent evt)
247 public void dropActionChanged(DropTargetDragEvent evt)
253 * @param evt DOCUMENT ME!
255 public void drop(DropTargetDropEvent evt)
257 Transferable t = evt.getTransferable();
258 java.util.List files = null;
262 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
263 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
265 //Works on Windows and MacOSX
266 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
267 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
269 else if (t.isDataFlavorSupported(uriListFlavor))
271 // This is used by Unix drag system
272 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
273 String data = (String) t.getTransferData(uriListFlavor);
274 files = new java.util.ArrayList(1);
275 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
278 st.hasMoreTokens(); )
280 String s = st.nextToken();
281 if (s.startsWith("#"))
283 // the line is a comment (as per the RFC 2483)
287 java.net.URI uri = new java.net.URI(s);
288 java.io.File file = new java.io.File(uri);
302 for (int i = 0; i < files.size(); i++)
304 String file = files.get(i).toString();
305 String protocol = "File";
306 String format = null;
308 if (file.endsWith(".jar"))
315 format = jalview.io.IdentifyFile.Identify(file,
318 LoadFile(file, protocol, format);
323 ex.printStackTrace();
331 * @param e DOCUMENT ME!
333 public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
335 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
339 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
344 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
345 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
347 chooser.setFileView(new JalviewFileView());
348 chooser.setDialogTitle("Open local file");
349 chooser.setToolTipText("Open");
351 int value = chooser.showOpenDialog(this);
353 if (value == JalviewFileChooser.APPROVE_OPTION)
355 String choice = chooser.getSelectedFile().getPath();
356 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
357 chooser.getSelectedFile().getParent());
359 String format = null;
360 if (chooser.getSelectedFormat().equals("Jalview"))
366 format = IdentifyFile.Identify(choice, "File");
369 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
370 LoadFile(choice, "File", format);
377 * @param file DOCUMENT ME!
378 * @param protocol DOCUMENT ME!
379 * @param format DOCUMENT ME!
381 public void LoadFile(String file, String protocol, String format)
383 FileLoader fileLoader = new FileLoader();
384 fileLoader.LoadFile(file, protocol, format);
390 * @param e DOCUMENT ME!
392 public void inputURLMenuItem_actionPerformed(ActionEvent e)
394 // This construct allows us to have a wider textfield
396 JLabel label = new JLabel("Enter URL of Input File");
397 JTextField textinput = new JTextField("http://www.", 40);
398 JPanel panel = new JPanel(new BorderLayout());
399 panel.add(label, BorderLayout.NORTH);
400 panel.add(textinput, BorderLayout.SOUTH);
403 int reply = JOptionPane.showInternalConfirmDialog(desktop,
404 panel, "Input Alignment From URL",
405 JOptionPane.OK_CANCEL_OPTION );
408 if (reply != JOptionPane.OK_OPTION )
413 String url = textinput.getText();
415 if (url.toLowerCase().endsWith(".jar"))
417 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
418 Jalview2XML.LoadJalviewAlign(url);
423 String format = IdentifyFile.Identify(url, "URL");
425 if (format.equals("URL NOT FOUND"))
427 JOptionPane.showInternalMessageDialog(Desktop.desktop,
428 "Couldn't locate " + url,
430 JOptionPane.WARNING_MESSAGE);
435 LoadFile(url, "URL", format);
442 * @param e DOCUMENT ME!
444 public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
446 CutAndPasteTransfer cap = new CutAndPasteTransfer();
448 Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
456 jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
457 jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
458 jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
459 jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
466 * @param e DOCUMENT ME!
468 public void aboutMenuItem_actionPerformed(ActionEvent e)
470 StringBuffer message = new StringBuffer("JalView version " +
471 jalview.bin.Cache.getProperty(
475 Cache.getDefault("BUILD_DATE", "unknown"));
477 if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
478 jalview.bin.Cache.getProperty("VERSION")))
480 message.append("\n\n!! Jalview version "
481 + jalview.bin.Cache.getProperty("LATEST_VERSION")
482 + " is available for download from http://www.jalview.org !!\n");
486 message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
487 "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
488 "\nFor all issues relating to Jalview, email help@jalview.org" +
489 "\n\nIf you use JalView, please cite:" +
490 "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
491 "\nBioinformatics, 2004 12;426-7.");
493 JOptionPane.showInternalMessageDialog(Desktop.desktop,
495 message.toString(), "About Jalview",
496 JOptionPane.INFORMATION_MESSAGE);
502 * @param e DOCUMENT ME!
504 public void documentationMenuItem_actionPerformed(ActionEvent e)
508 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
509 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
510 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
512 javax.help.HelpBroker hb = hs.createHelpBroker();
513 hb.setCurrentID("home");
514 hb.setDisplayed(true);
518 ex.printStackTrace();
525 * @param e DOCUMENT ME!
527 protected void preferences_actionPerformed(ActionEvent e)
535 * @param e DOCUMENT ME!
537 public void saveState_actionPerformed(ActionEvent e)
539 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
540 "LAST_DIRECTORY"), new String[] { "jar" },
541 new String[] { "Jalview Project" }, "Jalview Project");
543 chooser.setFileView(new JalviewFileView());
544 chooser.setDialogTitle("Save State");
546 int value = chooser.showSaveDialog(this);
548 if (value == JalviewFileChooser.APPROVE_OPTION)
550 java.io.File choice = chooser.getSelectedFile();
551 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
552 Jalview2XML.SaveState(choice);
559 * @param e DOCUMENT ME!
561 public void loadState_actionPerformed(ActionEvent e)
563 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
564 "LAST_DIRECTORY"), new String[] { "jar" },
565 new String[] { "Jalview Project" }, "Jalview Project");
566 chooser.setFileView(new JalviewFileView());
567 chooser.setDialogTitle("Restore state");
569 int value = chooser.showOpenDialog(this);
571 if (value == JalviewFileChooser.APPROVE_OPTION)
573 String choice = chooser.getSelectedFile().getAbsolutePath();
574 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
575 chooser.getSelectedFile().getParent());
576 Jalview2XML.LoadJalviewAlign(choice);
580 /* public void vamsasLoad_actionPerformed(ActionEvent e)
582 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
583 getProperty("LAST_DIRECTORY"));
585 chooser.setFileView(new JalviewFileView());
586 chooser.setDialogTitle("Load Vamsas file");
587 chooser.setToolTipText("Import");
589 int value = chooser.showOpenDialog(this);
591 if (value == JalviewFileChooser.APPROVE_OPTION)
593 jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
595 chooser.getSelectedFile().getAbsolutePath()
602 public void inputSequence_actionPerformed(ActionEvent e)
604 SequenceFetcher sf = new SequenceFetcher(null);