src/jalview/gui/Desktop.java

   1 /********************\r
   2  * 2004 Jalview Reengineered\r
   3  * Barton Group\r
   4  * Dundee University\r
   5  *\r
   6  * AM Waterhouse\r
   7  *******************/\r
   8 \r
   9 \r
  10 package jalview.gui;\r
  11 \r
  12 import jalview.gui.*;\r
  13 import jalview.io.*;\r
  14 import jalview.datamodel.*;\r
  15 import javax.swing.*;\r
  16 import java.awt.*;\r
  17 import java.awt.event.*;\r
  18 import java.awt.dnd.*;\r
  19 import javax.swing.*;\r
  20 import java.awt.datatransfer.*;\r
  21 import jalview.bin.Cache;\r
  22 \r
  23 \r
  24 public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener\r
  25 {\r
  26   public static JDesktopPane desktop;\r
  27   static int openFrameCount = 0;\r
  28   static final int xOffset = 30, yOffset = 30;\r
  29 \r
  30   public Desktop()\r
  31   {\r
  32     Image image =null;\r
  33     try{\r
  34       java.net.URL url = getClass().getResource("/images/logo.gif");\r
  35       if(url!=null)\r
  36       {\r
  37         image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
  38         MediaTracker mt = new MediaTracker(this);\r
  39         mt.addImage(image, 0);\r
  40         mt.waitForID(0);\r
  41         setIconImage(image);\r
  42       }\r
  43 \r
  44     }catch(Exception ex){}\r
  45 \r
  46     setTitle("Jalview 2005");\r
  47     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
  48     desktop = new JDesktopPane();\r
  49     desktop.setBackground(Color.white);\r
  50     setContentPane(desktop);\r
  51     desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
  52 \r
  53 \r
  54     // This line prevents Windows Look&Feel resizing all new windows to maximum\r
  55     // if previous window was maximised\r
  56     desktop.setDesktopManager( new DefaultDesktopManager() );\r
  57 \r
  58 \r
  59     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
  60     String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
  61     String y = jalview.bin.Cache.getProperty("SCREEN_Y");\r
  62     String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
  63     String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
  64 \r
  65     if(x!=null && y!=null && width!=null && height!=null)\r
  66     {\r
  67       setBounds( Integer.parseInt(x), Integer.parseInt(y),\r
  68                  Integer.parseInt(width), Integer.parseInt(height));\r
  69     }\r
  70     else\r
  71       setBounds( (int)(screenSize.width-900)/2,\r
  72            (int)(screenSize.height-650)/2,\r
  73           900 ,\r
  74           650);\r
  75 \r
  76 this.addWindowListener(new WindowAdapter()\r
  77 {\r
  78 public void windowClosing(WindowEvent evt)\r
  79 {\r
  80  jalview.bin.Cache.setProperty("SCREEN_X",\r
  81                                getBounds().x + "");\r
  82  jalview.bin.Cache.setProperty("SCREEN_Y",\r
  83                                getBounds().y + "");\r
  84  jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
  85  jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
  86 }\r
  87 });\r
  88 setVisible(true);\r
  89 \r
  90 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
  91 \r
  92 /////////Add a splashscreen on startup\r
  93    /////////Add a splashscreen on startup\r
  94     JInternalFrame frame = new JInternalFrame();\r
  95 \r
  96     SplashScreen splash = new SplashScreen(frame, image);\r
  97     frame.setContentPane(splash);\r
  98     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
  99     addInternalFrame(frame, "", 750,160, false);\r
 100     frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));\r
 101   }\r
 102   public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
 103   {\r
 104     addInternalFrame(frame, title, w, h, true);\r
 105   }\r
 106 \r
 107   public static void addInternalFrame(final JInternalFrame frame, String title,\r
 108                                       int w,\r
 109                                       int h,\r
 110                                       boolean resizable )\r
 111   {\r
 112    desktop.add(frame);\r
 113    openFrameCount++;\r
 114    try {\r
 115        frame.setSelected(true);\r
 116    } catch (java.beans.PropertyVetoException e) {}\r
 117    frame.setTitle(title);\r
 118    frame.setSize(w,h);\r
 119    frame.setClosable(true);\r
 120    frame.setResizable(resizable);\r
 121    frame.setMaximizable(resizable);\r
 122    frame.setIconifiable(resizable);\r
 123    frame.setFrameIcon(null);\r
 124    frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
 125    frame.toFront();\r
 126    final JMenuItem menuItem = new JMenuItem(title);\r
 127    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 128    {\r
 129      public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 130      {\r
 131        openFrameCount--;\r
 132        windowMenu.remove(menuItem);\r
 133      };\r
 134    });\r
 135 \r
 136    menuItem.addActionListener(new ActionListener()\r
 137     {\r
 138       public void actionPerformed(ActionEvent e)\r
 139       {\r
 140         try{  frame.setSelected(true);   frame.setIcon(false); }\r
 141         catch(java.beans.PropertyVetoException ex){};\r
 142       }\r
 143     });\r
 144 \r
 145    frame.setVisible(true);\r
 146    windowMenu.add(menuItem);\r
 147  }\r
 148 \r
 149  public void dragEnter(DropTargetDragEvent evt){}\r
 150  public void dragExit(DropTargetEvent evt){}\r
 151  public void dragOver(DropTargetDragEvent evt){}\r
 152  public void dropActionChanged(DropTargetDragEvent evt){}\r
 153  public void drop(DropTargetDropEvent evt)\r
 154 {\r
 155    Transferable t = evt.getTransferable();\r
 156    if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
 157      return;\r
 158 \r
 159    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
 160    try{\r
 161      java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
 162 \r
 163      for (int i = 0; i < files.size(); i++)\r
 164      {\r
 165        String file = files.get(i).toString();\r
 166        String protocol = "File";\r
 167        if(file.endsWith(".jar"))\r
 168                 Jalview2XML.LoadJalviewAlign(file);\r
 169       else\r
 170       {\r
 171         String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
 172         LoadFile(file, protocol, format);\r
 173       }\r
 174      }\r
 175 \r
 176    }catch(Exception ex){ex.printStackTrace();}\r
 177   }\r
 178 \r
 179 \r
 180  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
 181  {\r
 182    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 183        new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},\r
 184        new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}\r
 185        ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
 186 \r
 187    chooser.setFileView(new JalviewFileView());\r
 188    chooser.setDialogTitle("Open local file");\r
 189    chooser.setToolTipText("Open");\r
 190    int value = chooser.showOpenDialog(this);\r
 191    if(value == JalviewFileChooser.APPROVE_OPTION)\r
 192    {\r
 193      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());\r
 194      String choice =  chooser.getSelectedFile().getPath();\r
 195      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
 196      if(chooser.getSelectedFormat().equals("Jalview"))\r
 197      {\r
 198        Jalview2XML.LoadJalviewAlign(choice);\r
 199      }\r
 200      else\r
 201      {\r
 202        String format = IdentifyFile.Identify(choice, "File");\r
 203        LoadFile(choice, "File", format);\r
 204      }\r
 205    }\r
 206  }\r
 207 \r
 208  public void LoadFile(String file, String protocol,  String format)\r
 209  {\r
 210    LoadingThread loader = new LoadingThread(file, protocol, format);\r
 211    loader.start();\r
 212  }\r
 213 \r
 214  class LoadingThread extends Thread\r
 215  {\r
 216    String file, protocol, format;\r
 217 \r
 218    public LoadingThread(String file, String protocol,  String format)\r
 219    {\r
 220      this.file = file;\r
 221      this.protocol = protocol;\r
 222      this.format = format;\r
 223    }\r
 224    public void run()\r
 225    {\r
 226      SequenceI [] sequences = null;\r
 227 \r
 228      if (FormatAdapter.formats.contains(format))\r
 229          sequences = FormatAdapter.readFile(file, protocol, format);\r
 230 \r
 231      if (sequences != null && sequences.length>0)\r
 232      {\r
 233        AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 234        addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
 235        af.currentFileFormat = format;\r
 236        af.statusBar.setText("Successfully loaded file " + file);\r
 237        try{\r
 238            af.setMaximum(Preferences.showFullscreen);\r
 239        }catch(Exception ex){}\r
 240 \r
 241      }\r
 242      else\r
 243        JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"\r
 244                             + "Formats currently supported are\n"\r
 245                             + "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!\r
 246                             ,"Error loading file",\r
 247                                      JOptionPane.WARNING_MESSAGE);\r
 248 \r
 249    }\r
 250  }\r
 251 \r
 252 \r
 253  public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
 254  {\r
 255    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
 256                                             "Input alignment from URL",\r
 257                                             JOptionPane.QUESTION_MESSAGE,\r
 258                                             null, null,\r
 259                                             "http://www.").toString();\r
 260    if (url == null)\r
 261      return;\r
 262 \r
 263    String format = IdentifyFile.Identify(url, "URL");\r
 264 \r
 265    if (format.equals("URL NOT FOUND"))\r
 266    {\r
 267      JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
 268                                    "URL not found",\r
 269                                    JOptionPane.WARNING_MESSAGE);\r
 270      return;\r
 271    }\r
 272 \r
 273     LoadFile(url, "URL", format);\r
 274  }\r
 275 \r
 276  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
 277  {\r
 278    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 279    int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
 280                                        JOptionPane.YES_NO_CANCEL_OPTION,\r
 281                                        JOptionPane.PLAIN_MESSAGE,\r
 282                                        null,\r
 283                                        new Object[]{"Accept", "Cancel", }, null);\r
 284 \r
 285 \r
 286   if(accept == JOptionPane.YES_OPTION)\r
 287   {\r
 288     String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
 289     SequenceI [] sequences = null;\r
 290 \r
 291     if (FormatAdapter.formats.contains( format ))\r
 292       sequences = FormatAdapter.readFile(cap.getText(), "Paste", format);\r
 293 \r
 294 \r
 295       if(sequences!=null)\r
 296       {\r
 297         AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 298         af.currentFileFormat = format;\r
 299         addInternalFrame(af, "Cut & Paste input - "+format,\r
 300                          AlignFrame.NEW_WINDOW_WIDTH,\r
 301                          AlignFrame.NEW_WINDOW_HEIGHT);\r
 302         af.statusBar.setText("Successfully pasted alignment file");\r
 303       }\r
 304       else\r
 305         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
 306                                       +"Formats currently supported are\n"\r
 307                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",\r
 308                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
 309 \r
 310    }\r
 311  }\r
 312 \r
 313 /*\r
 314 * Exit the program\r
 315 */\r
 316  public void quit_actionPerformed(ActionEvent e)\r
 317  {\r
 318    if(jalview.bin.Jalview.applet!=null)\r
 319      jalview.bin.Jalview.applet.destroy();\r
 320     else\r
 321       System.exit(0);\r
 322  }\r
 323 \r
 324 \r
 325 \r
 326  public void aboutMenuItem_actionPerformed(ActionEvent e)\r
 327  {\r
 328    JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 329                                          "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE\r
 330                                        +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
 331                                        +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
 332                                        +"\nIf  you use JalView, please cite:"\r
 333                                        +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""\r
 334                                        +"\nBioinformatics,  2004 12;426-7.",\r
 335                                          "About Jalview",\r
 336                                          JOptionPane.INFORMATION_MESSAGE);\r
 337  }\r
 338 \r
 339  public void documentationMenuItem_actionPerformed(ActionEvent e)\r
 340  {\r
 341    try\r
 342    {\r
 343       ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
 344       java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
 345       javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
 346 \r
 347       javax.help.HelpBroker hb = hs.createHelpBroker();\r
 348       hb.setLocation(new Point(200, 50));\r
 349       hb.setSize(new Dimension(800,700));\r
 350       hb.setCurrentID("home");\r
 351       hb.setDisplayed(true);\r
 352    }\r
 353    catch (Exception ex)\r
 354    {\r
 355      ex.printStackTrace();\r
 356    }\r
 357  }\r
 358 \r
 359  protected void preferences_actionPerformed(ActionEvent e)\r
 360  {\r
 361    Preferences pref = new Preferences();\r
 362  }\r
 363 \r
 364  public void saveState_actionPerformed(ActionEvent e)\r
 365  {\r
 366    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
 367        getProperty("LAST_DIRECTORY"),\r
 368        new String[]\r
 369        {"xml"}, new String[]{"Jalview Project"}, "Jalview Project");\r
 370 \r
 371    chooser.setFileView(new JalviewFileView());\r
 372    chooser.setDialogTitle("Save State");\r
 373    int value = chooser.showSaveDialog(this);\r
 374    if (value == JalviewFileChooser.APPROVE_OPTION)\r
 375    {\r
 376      java.io.File choice = chooser.getSelectedFile();\r
 377      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
 378      Jalview2XML.SaveState(choice);\r
 379    }\r
 380 \r
 381  }\r
 382 \r
 383 \r
 384  public void loadState_actionPerformed(ActionEvent e)\r
 385  {\r
 386    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 387        new String[]{"xml"}, new String[]{"Jalview Project"}, "Jalview Project");\r
 388    chooser.setFileView(new JalviewFileView());\r
 389    chooser.setDialogTitle("Restore state");\r
 390    int value = chooser.showOpenDialog(this);\r
 391    if(value == JalviewFileChooser.APPROVE_OPTION)\r
 392    {\r
 393      String choice =  chooser.getSelectedFile().getAbsolutePath();\r
 394      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
 395      Jalview2XML.LoadState(choice);\r
 396    }\r
 397  }\r
 398 }\r
 399 \r
 400 \r