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