2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
21 import jalview.io.*;
\r
24 import java.awt.datatransfer.*;
\r
25 import java.awt.dnd.*;
\r
26 import java.awt.event.*;
\r
28 import javax.swing.*;
\r
30 import org.vamsas.test.simpleclient.ArchiveClient;
\r
37 * @version $Revision$
\r
39 public class Desktop extends jalview.jbgui.GDesktop
\r
40 implements DropTargetListener
\r
42 /** DOCUMENT ME!! */
\r
43 public static JDesktopPane desktop;
\r
44 static int openFrameCount = 0;
\r
45 static final int xOffset = 30;
\r
46 static final int yOffset = 30;
\r
47 public static jalview.ws.Discoverer discoverer;
\r
49 public static Object [] jalviewClipboard;
\r
53 * Creates a new Desktop object.
\r
62 java.net.URL url = getClass().getResource("/images/logo.gif");
\r
66 image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
\r
68 MediaTracker mt = new MediaTracker(this);
\r
69 mt.addImage(image, 0);
\r
71 setIconImage(image);
\r
74 catch (Exception ex)
\r
78 setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
\r
79 setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
\r
80 desktop = new JDesktopPane();
\r
81 desktop.setBackground(Color.white);
\r
82 setContentPane(desktop);
\r
83 desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
\r
85 // This line prevents Windows Look&Feel resizing all new windows to maximum
\r
86 // if previous window was maximised
\r
87 desktop.setDesktopManager(new DefaultDesktopManager());
\r
89 Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
\r
90 String x = jalview.bin.Cache.getProperty("SCREEN_X");
\r
91 String y = jalview.bin.Cache.getProperty("SCREEN_Y");
\r
92 String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");
\r
93 String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");
\r
95 if ((x != null) && (y != null) && (width != null) && (height != null))
\r
97 setBounds(Integer.parseInt(x), Integer.parseInt(y),
\r
98 Integer.parseInt(width), Integer.parseInt(height));
\r
102 setBounds((int) (screenSize.width - 900) / 2,
\r
103 (int) (screenSize.height - 650) / 2, 900, 650);
\r
106 this.addWindowListener(new WindowAdapter()
\r
108 public void windowClosing(WindowEvent evt)
\r
114 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
\r
116 /////////Add a splashscreen on startup
\r
117 /////////Add a splashscreen on startup
\r
118 JInternalFrame frame = new JInternalFrame();
\r
120 SplashScreen splash = new SplashScreen(frame, image);
\r
121 frame.setContentPane(splash);
\r
122 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
123 frame.setLocation((int) ((getWidth() - 750) / 2),
\r
124 (int) ((getHeight() - 160) / 2));
\r
126 addInternalFrame(frame, "", 750, 160, false);
\r
128 discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
\r
135 * @param frame DOCUMENT ME!
\r
136 * @param title DOCUMENT ME!
\r
137 * @param w DOCUMENT ME!
\r
138 * @param h DOCUMENT ME!
\r
140 public static synchronized void addInternalFrame(final JInternalFrame frame,
\r
141 String title, int w, int h)
\r
143 addInternalFrame(frame, title, w, h, true);
\r
149 * @param frame DOCUMENT ME!
\r
150 * @param title DOCUMENT ME!
\r
151 * @param w DOCUMENT ME!
\r
152 * @param h DOCUMENT ME!
\r
153 * @param resizable DOCUMENT ME!
\r
155 public static synchronized void addInternalFrame(final JInternalFrame frame,
\r
156 String title, int w, int h, boolean resizable)
\r
159 frame.setTitle(title);
\r
160 if(frame.getWidth()<1 || frame.getHeight()<1)
\r
162 frame.setSize(w, h);
\r
164 // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
\r
165 // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
\r
166 // IF JALVIEW IS RUNNING HEADLESS
\r
167 /////////////////////////////////////////////////
\r
168 if (System.getProperty("java.awt.headless") != null
\r
169 && System.getProperty("java.awt.headless").equals("true"))
\r
177 frame.setVisible(true);
\r
178 frame.setClosable(true);
\r
179 frame.setResizable(resizable);
\r
180 frame.setMaximizable(resizable);
\r
181 frame.setIconifiable(resizable);
\r
182 frame.setFrameIcon(null);
\r
184 if (frame.getX()<1 && frame.getY()<1)
\r
186 frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);
\r
189 final JMenuItem menuItem = new JMenuItem(title);
\r
190 frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
\r
192 public void internalFrameActivated(javax.swing.event.
\r
193 InternalFrameEvent evt)
\r
195 JInternalFrame itf = desktop.getSelectedFrame();
\r
197 itf.requestFocus();
\r
201 public void internalFrameClosed(
\r
202 javax.swing.event.InternalFrameEvent evt)
\r
205 windowMenu.remove(menuItem);
\r
206 JInternalFrame itf = desktop.getSelectedFrame();
\r
208 itf.requestFocus();
\r
213 menuItem.addActionListener(new ActionListener()
\r
215 public void actionPerformed(ActionEvent e)
\r
219 frame.setSelected(true);
\r
220 frame.setIcon(false);
\r
222 catch (java.beans.PropertyVetoException ex)
\r
229 windowMenu.add(menuItem);
\r
231 desktop.add(frame);
\r
234 frame.setSelected(true);
\r
235 frame.requestFocus();
\r
236 }catch(java.beans.PropertyVetoException ve)
\r
240 public void dragEnter(DropTargetDragEvent evt)
\r
243 public void dragExit(DropTargetEvent evt)
\r
246 public void dragOver(DropTargetDragEvent evt)
\r
249 public void dropActionChanged(DropTargetDragEvent evt)
\r
255 * @param evt DOCUMENT ME!
\r
257 public void drop(DropTargetDropEvent evt)
\r
259 Transferable t = evt.getTransferable();
\r
260 java.util.List files = null;
\r
264 DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");
\r
265 if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
\r
267 //Works on Windows and MacOSX
\r
268 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
\r
269 files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);
\r
271 else if (t.isDataFlavorSupported(uriListFlavor))
\r
273 // This is used by Unix drag system
\r
274 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
\r
275 String data = (String) t.getTransferData(uriListFlavor);
\r
276 files = new java.util.ArrayList(1);
\r
277 for (java.util.StringTokenizer st = new java.util.StringTokenizer(
\r
280 st.hasMoreTokens(); )
\r
282 String s = st.nextToken();
\r
283 if (s.startsWith("#"))
\r
285 // the line is a comment (as per the RFC 2483)
\r
289 java.net.URI uri = new java.net.URI(s);
\r
290 java.io.File file = new java.io.File(uri);
\r
295 catch (Exception e)
\r
297 e.printStackTrace();
\r
304 for (int i = 0; i < files.size(); i++)
\r
306 String file = files.get(i).toString();
\r
307 String protocol = FormatAdapter.FILE;
\r
308 String format = null;
\r
310 if (file.endsWith(".jar"))
\r
312 format = "Jalview";
\r
317 format = new IdentifyFile().Identify(file,
\r
320 LoadFile(file, protocol, format);
\r
323 catch (Exception ex)
\r
325 ex.printStackTrace();
\r
333 * @param e DOCUMENT ME!
\r
335 public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
\r
337 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
341 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
\r
346 "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
\r
347 }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
\r
349 chooser.setFileView(new JalviewFileView());
\r
350 chooser.setDialogTitle("Open local file");
\r
351 chooser.setToolTipText("Open");
\r
353 int value = chooser.showOpenDialog(this);
\r
355 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
357 String choice = chooser.getSelectedFile().getPath();
\r
358 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
\r
359 chooser.getSelectedFile().getParent());
\r
361 String format = null;
\r
362 if (chooser.getSelectedFormat().equals("Jalview"))
\r
364 format = "Jalview";
\r
368 format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
\r
371 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
\r
372 LoadFile(choice, FormatAdapter.FILE, format);
\r
379 * @param file DOCUMENT ME!
\r
380 * @param protocol DOCUMENT ME!
\r
381 * @param format DOCUMENT ME!
\r
383 public void LoadFile(String file, String protocol, String format)
\r
385 FileLoader fileLoader = new FileLoader();
\r
386 fileLoader.LoadFile(file, protocol, format);
\r
392 * @param e DOCUMENT ME!
\r
394 public void inputURLMenuItem_actionPerformed(ActionEvent e)
\r
396 // This construct allows us to have a wider textfield
\r
398 JLabel label = new JLabel("Enter URL of Input File");
\r
399 JTextField textinput = new JTextField("http://www.", 40);
\r
400 JPanel panel = new JPanel(new BorderLayout());
\r
401 panel.add(label, BorderLayout.NORTH);
\r
402 panel.add(textinput, BorderLayout.SOUTH);
\r
405 int reply = JOptionPane.showInternalConfirmDialog(desktop,
\r
406 panel, "Input Alignment From URL",
\r
407 JOptionPane.OK_CANCEL_OPTION );
\r
410 if (reply != JOptionPane.OK_OPTION )
\r
415 String url = textinput.getText();
\r
417 if (url.toLowerCase().endsWith(".jar"))
\r
419 jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
\r
420 Jalview2XML.LoadJalviewAlign(url);
\r
425 String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
\r
427 if (format.equals("URL NOT FOUND"))
\r
429 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
430 "Couldn't locate " + url,
\r
432 JOptionPane.WARNING_MESSAGE);
\r
437 LoadFile(url, FormatAdapter.URL, format);
\r
444 * @param e DOCUMENT ME!
\r
446 public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
\r
448 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
450 Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
\r
458 jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");
\r
459 jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");
\r
460 jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");
\r
461 jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");
\r
468 * @param e DOCUMENT ME!
\r
470 public void aboutMenuItem_actionPerformed(ActionEvent e)
\r
472 StringBuffer message = new StringBuffer("JalView version " +
\r
473 jalview.bin.Cache.getProperty(
\r
475 "; last updated: " +
\r
477 Cache.getDefault("BUILD_DATE", "unknown"));
\r
479 if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(
\r
480 jalview.bin.Cache.getProperty("VERSION")))
\r
482 message.append("\n\n!! Jalview version "
\r
483 + jalview.bin.Cache.getProperty("LATEST_VERSION")
\r
484 + " is available for download from http://www.jalview.org !!\n");
\r
488 message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +
\r
489 "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +
\r
490 "\nFor all issues relating to Jalview, email help@jalview.org" +
\r
491 "\n\nIf you use JalView, please cite:" +
\r
492 "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
\r
493 "\nBioinformatics, 2004 12;426-7.");
\r
495 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
497 message.toString(), "About Jalview",
\r
498 JOptionPane.INFORMATION_MESSAGE);
\r
504 * @param e DOCUMENT ME!
\r
506 public void documentationMenuItem_actionPerformed(ActionEvent e)
\r
510 ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
\r
511 java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");
\r
512 javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
\r
514 javax.help.HelpBroker hb = hs.createHelpBroker();
\r
515 hb.setCurrentID("home");
\r
516 hb.setDisplayed(true);
\r
518 catch (Exception ex)
\r
520 ex.printStackTrace();
\r
527 * @param e DOCUMENT ME!
\r
529 protected void preferences_actionPerformed(ActionEvent e)
\r
537 * @param e DOCUMENT ME!
\r
539 public void saveState_actionPerformed(ActionEvent e)
\r
541 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
542 "LAST_DIRECTORY"), new String[] { "jar" },
\r
543 new String[] { "Jalview Project" }, "Jalview Project");
\r
545 chooser.setFileView(new JalviewFileView());
\r
546 chooser.setDialogTitle("Save State");
\r
548 int value = chooser.showSaveDialog(this);
\r
550 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
552 java.io.File choice = chooser.getSelectedFile();
\r
553 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
\r
554 Jalview2XML.SaveState(choice);
\r
561 * @param e DOCUMENT ME!
\r
563 public void loadState_actionPerformed(ActionEvent e)
\r
565 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
\r
566 "LAST_DIRECTORY"), new String[] { "jar" },
\r
567 new String[] { "Jalview Project" }, "Jalview Project");
\r
568 chooser.setFileView(new JalviewFileView());
\r
569 chooser.setDialogTitle("Restore state");
\r
571 int value = chooser.showOpenDialog(this);
\r
573 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
575 String choice = chooser.getSelectedFile().getAbsolutePath();
\r
576 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
\r
577 chooser.getSelectedFile().getParent());
\r
578 Jalview2XML.LoadJalviewAlign(choice);
\r
581 jalview.io.VamsasClient v_client=null;
\r
582 public void vamsasLoad_actionPerformed(ActionEvent e)
\r
584 if (v_client==null) {
\r
585 // Start a session.
\r
586 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
587 getProperty("LAST_DIRECTORY"));
\r
589 chooser.setFileView(new JalviewFileView());
\r
590 chooser.setDialogTitle("Load Vamsas file");
\r
591 chooser.setToolTipText("Import");
\r
593 int value = chooser.showOpenDialog(this);
\r
595 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
597 v_client = new jalview.io.VamsasClient(this,
\r
598 chooser.getSelectedFile().getAbsolutePath()
\r
600 this.vamsasLoad.setText("Session Update");
\r
601 this.vamsasStop.setVisible(true);
\r
602 v_client.initial_update();
\r
605 // store current data in session.
\r
606 v_client.push_update();
\r
609 public void vamsasStop_actionPerformed(ActionEvent e) {
\r
610 if (v_client!=null) {
\r
611 v_client.end_session();
\r
613 this.vamsasStop.setVisible(false);
\r
614 this.vamsasLoad.setText("Start Vamsas Session...");
\r
618 public void inputSequence_actionPerformed(ActionEvent e)
\r
620 SequenceFetcher sf = new SequenceFetcher(null);
\r