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                                    { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 129                                      {\r
 130                                        openFrameCount--;\r
 131                                        windowMenu.remove(menuItem);\r
 132                                      };\r
 133                                    });\r
 134 \r
 135    menuItem.addActionListener(new ActionListener()\r
 136     {\r
 137       public void actionPerformed(ActionEvent e)\r
 138       {\r
 139         try{  frame.setSelected(true);   frame.setIcon(false); }\r
 140         catch(java.beans.PropertyVetoException ex){};\r
 141       }\r
 142     });\r
 143 \r
 144    frame.setVisible(true);\r
 145    windowMenu.add(menuItem);\r
 146  }\r
 147 \r
 148  public void dragEnter(DropTargetDragEvent evt){}\r
 149  public void dragExit(DropTargetEvent evt){}\r
 150  public void dragOver(DropTargetDragEvent evt){}\r
 151  public void dropActionChanged(DropTargetDragEvent evt){}\r
 152  public void drop(DropTargetDropEvent evt)\r
 153 {\r
 154    Transferable t = evt.getTransferable();\r
 155    if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
 156      return;\r
 157 \r
 158    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
 159    try{\r
 160      java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
 161 \r
 162      for (int i = 0; i < files.size(); i++)\r
 163      {\r
 164        String file = files.get(i).toString();\r
 165        String protocol = "File";\r
 166        String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
 167        LoadFile(file, protocol, format);\r
 168      }\r
 169 \r
 170    }catch(Exception ex){ex.printStackTrace();}\r
 171   }\r
 172 \r
 173 \r
 174  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
 175  {\r
 176    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 177        new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");\r
 178    chooser.setFileView(new JalviewFileView());\r
 179    chooser.setDialogTitle("Open local file");\r
 180    chooser.setToolTipText("Open");\r
 181    int value = chooser.showOpenDialog(this);\r
 182    if(value == JalviewFileChooser.APPROVE_OPTION)\r
 183    {\r
 184      String choice =  chooser.getSelectedFile().getPath();\r
 185      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 186      String format = IdentifyFile.Identify(choice, "File");\r
 187      LoadFile(choice, "File", format);\r
 188    }\r
 189  }\r
 190 \r
 191  public void LoadFile(String file, String protocol,  String format)\r
 192  {\r
 193    LoadingThread loader = new LoadingThread(file, protocol, format);\r
 194    loader.start();\r
 195  }\r
 196 \r
 197  class LoadingThread extends Thread\r
 198  {\r
 199    String file, protocol, format;\r
 200 \r
 201    public LoadingThread(String file, String protocol,  String format)\r
 202    {\r
 203      this.file = file;\r
 204      this.protocol = protocol;\r
 205      this.format = format;\r
 206    }\r
 207    public void run()\r
 208    {\r
 209      SequenceI [] sequences = null;\r
 210 \r
 211      if (FormatAdapter.formats.contains(format))\r
 212          sequences = FormatAdapter.readFile(file, protocol, format);\r
 213 \r
 214      if (sequences != null && sequences.length>0)\r
 215      {\r
 216        AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 217        addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
 218        af.statusBar.setText("Successfully loaded file " + file);\r
 219        try{\r
 220            af.setMaximum(Preferences.showFullscreen);\r
 221        }catch(Exception ex){}\r
 222 \r
 223      }\r
 224      else\r
 225        JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"\r
 226                             + "Formats currently supported are\n"\r
 227                             + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" // JBPNote - message should be generated through FormatAdapter!\r
 228                             ,"Error loading file",\r
 229                                      JOptionPane.WARNING_MESSAGE);\r
 230 \r
 231    }\r
 232  }\r
 233 \r
 234 \r
 235  public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
 236  {\r
 237    JOptionPane op = new JOptionPane();\r
 238 \r
 239    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
 240                                             "Input alignment from URL",\r
 241                                             JOptionPane.QUESTION_MESSAGE,\r
 242                                             null, null,\r
 243                                             "http://www.").toString();\r
 244    if (url == null)\r
 245      return;\r
 246 \r
 247    String format = IdentifyFile.Identify(url, "URL");\r
 248 \r
 249    if (format.equals("URL NOT FOUND"))\r
 250    {\r
 251      JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
 252                                    "URL not found",\r
 253                                    JOptionPane.WARNING_MESSAGE);\r
 254      return;\r
 255    }\r
 256 \r
 257     LoadFile(url, "URL", format);\r
 258  }\r
 259 \r
 260  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
 261  {\r
 262    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 263    int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
 264                                        JOptionPane.YES_NO_CANCEL_OPTION,\r
 265                                        JOptionPane.PLAIN_MESSAGE,\r
 266                                        null,\r
 267                                        new Object[]{"Accept", "Cancel", }, null);\r
 268 \r
 269 \r
 270   if(accept == JOptionPane.YES_OPTION)\r
 271   {\r
 272     String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
 273     SequenceI [] sequences = null;\r
 274 \r
 275     if (FormatAdapter.formats.contains( format ))\r
 276       sequences = FormatAdapter.readFile(cap.getText(), "Paste", format);\r
 277 \r
 278 \r
 279       if(sequences!=null)\r
 280       {\r
 281         AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 282         addInternalFrame(af, "Cut & Paste input - "+format,\r
 283                          AlignFrame.NEW_WINDOW_WIDTH,\r
 284                          AlignFrame.NEW_WINDOW_HEIGHT);\r
 285         af.statusBar.setText("Successfully pasted alignment file");\r
 286       }\r
 287       else\r
 288         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
 289                                       +"Formats currently supported are\n"\r
 290                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
 291                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
 292 \r
 293    }\r
 294  }\r
 295 \r
 296 /*\r
 297 * Exit the program\r
 298 */\r
 299  public void quit_actionPerformed(ActionEvent e)\r
 300  {\r
 301    if(jalview.bin.Jalview.applet!=null)\r
 302      jalview.bin.Jalview.applet.destroy();\r
 303     else\r
 304       System.exit(0);\r
 305  }\r
 306 \r
 307 \r
 308 \r
 309  public void aboutMenuItem_actionPerformed(ActionEvent e)\r
 310  {\r
 311    JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 312                                          "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE\r
 313                                        +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
 314                                        +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
 315                                        +"\nIf  you use JalView, please cite:"\r
 316                                        +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""\r
 317                                        +"\nBioinformatics,  2004 12;426-7.",\r
 318                                          "About Jalview",\r
 319                                          JOptionPane.INFORMATION_MESSAGE);\r
 320  }\r
 321 \r
 322  public void documentationMenuItem_actionPerformed(ActionEvent e)\r
 323  {\r
 324    try\r
 325    {\r
 326       ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
 327       java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
 328       javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
 329 \r
 330       javax.help.HelpBroker hb = hs.createHelpBroker();\r
 331       hb.setLocation(new Point(200, 50));\r
 332       hb.setSize(new Dimension(800,700));\r
 333       hb.setCurrentID("home");\r
 334       hb.setDisplayed(true);\r
 335    }\r
 336    catch (Exception ex)\r
 337    {\r
 338      ex.printStackTrace();\r
 339    }\r
 340  }\r
 341 \r
 342  protected void preferences_actionPerformed(ActionEvent e)\r
 343  {\r
 344    Preferences pref = new Preferences();\r
 345  }\r
 346 \r
 347 }\r
 348 \r
 349 \r