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 \r
  24 \r
  25 public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener\r
  26 {\r
  27   public static JDesktopPane desktop;\r
  28   static int openFrameCount = 0;\r
  29   static final int xOffset = 30, yOffset = 30;\r
  30 \r
  31   public Desktop()\r
  32   {\r
  33     Image image =null;\r
  34     try{\r
  35       java.net.URL url = getClass().getResource("/images/logo.gif");\r
  36       if(url!=null)\r
  37       {\r
  38         image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
  39         MediaTracker mt = new MediaTracker(this);\r
  40         mt.addImage(image, 0);\r
  41         mt.waitForID(0);\r
  42         setIconImage(image);\r
  43       }\r
  44 \r
  45     }catch(Exception ex){}\r
  46 \r
  47     setTitle("Jalview 2005");\r
  48     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
  49     desktop = new JDesktopPane();\r
  50     desktop.setBackground(new Color(220,220,230));\r
  51     setContentPane(desktop);\r
  52     desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
  53     desktop.setDesktopManager( new DefaultDesktopManager() );\r
  54 \r
  55     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
  56     String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
  57     String y = jalview.bin.Cache.getProperty("SCREEN_Y");\r
  58     String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
  59     String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
  60 \r
  61     if(x!=null && y!=null && width!=null && height!=null)\r
  62     {\r
  63       setBounds( Integer.parseInt(x), Integer.parseInt(y),\r
  64                  Integer.parseInt(width), Integer.parseInt(height));\r
  65     }\r
  66     else\r
  67       setBounds( (int)(screenSize.width-900)/2,\r
  68            (int)(screenSize.height-650)/2,\r
  69           900 ,\r
  70           650);\r
  71 \r
  72 this.addWindowListener(new WindowAdapter()\r
  73 {\r
  74 public void windowClosing(WindowEvent evt)\r
  75 {\r
  76  jalview.bin.Cache.setProperty("SCREEN_X",\r
  77                                getBounds().x + "");\r
  78  jalview.bin.Cache.setProperty("SCREEN_Y",\r
  79                                getBounds().y + "");\r
  80  jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
  81  jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
  82 }\r
  83 });\r
  84 setVisible(true);\r
  85 \r
  86 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
  87 \r
  88 \r
  89    /////////Add a splashscreen on startup\r
  90     JInternalFrame frame = new JInternalFrame();\r
  91 \r
  92     SplashScreen splash = new SplashScreen(frame, image);\r
  93     frame.setContentPane(splash);\r
  94     desktop.add(frame);\r
  95 \r
  96     openFrameCount++;\r
  97     try\r
  98     {\r
  99       frame.setSelected(true);\r
 100     }\r
 101     catch (java.beans.PropertyVetoException e)\r
 102     {}\r
 103     frame.setResizable(true);\r
 104     frame.setSize(750, 160);\r
 105     frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));\r
 106     frame.setClosable(false);\r
 107     frame.setIconifiable(false);\r
 108     frame.setMaximizable(false);\r
 109     frame.setFrameIcon(null);\r
 110     frame.setVisible(true);\r
 111 \r
 112   }\r
 113 \r
 114   public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
 115   {\r
 116    desktop.add(frame);\r
 117    openFrameCount++;\r
 118    try {\r
 119        frame.setSelected(true);\r
 120    } catch (java.beans.PropertyVetoException e) {}\r
 121    frame.setTitle(title);\r
 122    frame.setResizable(true);\r
 123    frame.setSize(w,h);\r
 124    frame.setClosable(true);\r
 125    frame.setMaximizable(true);\r
 126    frame.setIconifiable(true);\r
 127    frame.setFrameIcon(null);\r
 128    frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
 129    frame.toFront();\r
 130    final JMenuItem menuItem = new JMenuItem(title);\r
 131    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 132                                    { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 133                                      {\r
 134                                        openFrameCount--;\r
 135                                        windowMenu.remove(menuItem);\r
 136                                      };\r
 137                                    });\r
 138 \r
 139    menuItem.addActionListener(new ActionListener()\r
 140     {\r
 141       public void actionPerformed(ActionEvent e)\r
 142       {\r
 143         try{  frame.setSelected(true);   frame.setIcon(false); }\r
 144         catch(java.beans.PropertyVetoException ex){};\r
 145       }\r
 146     });\r
 147 \r
 148    frame.setVisible(true);\r
 149    windowMenu.add(menuItem);\r
 150  }\r
 151 \r
 152  public void dragEnter(DropTargetDragEvent evt){}\r
 153  public void dragExit(DropTargetEvent evt){}\r
 154  public void dragOver(DropTargetDragEvent evt){}\r
 155  public void dropActionChanged(DropTargetDragEvent evt){}\r
 156  public void drop(DropTargetDropEvent evt)\r
 157 {\r
 158    Transferable t = evt.getTransferable();\r
 159    if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
 160      return;\r
 161 \r
 162    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
 163    try{\r
 164      java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
 165 \r
 166      for (int i = 0; i < files.size(); i++)\r
 167      {\r
 168        String file = files.get(i).toString();\r
 169        String protocol = "File";\r
 170        String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
 171        LoadFile(file, protocol, format);\r
 172      }\r
 173 \r
 174    }catch(Exception ex){ex.printStackTrace();}\r
 175   }\r
 176 \r
 177  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
 178  {\r
 179    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 180        new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");\r
 181    chooser.setFileView(new JalviewFileView());\r
 182    chooser.setDialogTitle("Open local file");\r
 183    chooser.setToolTipText("Open");\r
 184    int value = chooser.showOpenDialog(this);\r
 185    if(value == JalviewFileChooser.APPROVE_OPTION)\r
 186    {\r
 187      String choice =  chooser.getSelectedFile().getPath();\r
 188      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 189      String format = IdentifyFile.Identify(choice, "File");\r
 190      LoadFile(choice, "File", format);\r
 191    }\r
 192  }\r
 193 \r
 194  public void LoadFile(String file, String protocol,  String format)\r
 195  {\r
 196    SequenceI [] sequences = null;\r
 197 \r
 198    if (FormatProperties.contains(format))\r
 199        sequences = FormatAdapter.read(file, protocol, format);\r
 200 \r
 201    if (sequences != null && sequences.length>0)\r
 202    {\r
 203      AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 204      addInternalFrame(af, file, 700, 500);\r
 205      af.statusBar.setText("Successfully loaded file " + file);\r
 206 \r
 207    }\r
 208    else\r
 209      JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"\r
 210                           + "Formats currently supported are\n"\r
 211                           + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" // JBPNote - message should be generated through FormatAdapter!\r
 212                           ,"Error loading file",\r
 213                                    JOptionPane.WARNING_MESSAGE);\r
 214 \r
 215  }\r
 216 \r
 217  public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
 218  {\r
 219    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
 220                                             "Input alignment from URL",\r
 221                                             JOptionPane.QUESTION_MESSAGE);\r
 222    if (url == null)\r
 223      return;\r
 224 \r
 225    String format = IdentifyFile.Identify(url, "URL");\r
 226 \r
 227    if (format.equals("URL NOT FOUND"))\r
 228    {\r
 229      JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
 230                                    "URL not found",\r
 231                                    JOptionPane.WARNING_MESSAGE);\r
 232      return;\r
 233    }\r
 234 \r
 235     LoadFile(url, "URL", format);\r
 236  }\r
 237 \r
 238  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
 239  {\r
 240    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 241    int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
 242                                        JOptionPane.YES_NO_CANCEL_OPTION,\r
 243                                        JOptionPane.PLAIN_MESSAGE,\r
 244                                        null,\r
 245                                        new Object[]{"Accept", "Cancel", }, null);\r
 246 \r
 247 \r
 248   if(accept == JOptionPane.YES_OPTION)\r
 249   {\r
 250     String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
 251     SequenceI [] sequences = null;\r
 252 \r
 253     if (FormatProperties.contains( format ))\r
 254       sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
 255 \r
 256 \r
 257       if(sequences!=null)\r
 258       {\r
 259         AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 260         addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);\r
 261         af.statusBar.setText("Successfully pasted alignment file");\r
 262       }\r
 263       else\r
 264         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
 265                                       +"Formats currently supported are\n"\r
 266                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
 267                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
 268 \r
 269    }\r
 270  }\r
 271 \r
 272 /*\r
 273 * Exit the program\r
 274 */\r
 275  public void quit_actionPerformed(ActionEvent e)\r
 276  {\r
 277    if(jalview.bin.Jalview.applet!=null)\r
 278      jalview.bin.Jalview.applet.destroy();\r
 279     else\r
 280       System.exit(0);\r
 281  }\r
 282 \r
 283 \r
 284 \r
 285  public void aboutMenuItem_actionPerformed(ActionEvent e)\r
 286  {\r
 287    JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 288                                          "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE\r
 289                                        +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
 290                                        +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
 291                                        +"\nIf  you use JalView, please cite:  Bioinformatics,  2004 12;426-7."\r
 292                                        +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
 293                                          "About Jalview",\r
 294                                          JOptionPane.INFORMATION_MESSAGE);\r
 295  }\r
 296 \r
 297  public void documentationMenuItem_actionPerformed(ActionEvent e)\r
 298  {\r
 299    try\r
 300    {\r
 301       ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
 302       java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
 303       javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
 304 \r
 305       javax.help.HelpBroker hb = hs.createHelpBroker();\r
 306       hb.setLocation(new Point(200, 50));\r
 307       hb.setSize(new Dimension(800,700));\r
 308       hb.setCurrentID("home");\r
 309       hb.setDisplayed(true);\r
 310    }\r
 311    catch (Exception ex)\r
 312    {\r
 313      ex.printStackTrace();\r
 314    }\r
 315  }\r
 316 \r
 317  static JInternalFrame conservationSlider;\r
 318  static JInternalFrame PIDSlider;\r
 319  public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 320  {\r
 321    SliderPanel sp = null;\r
 322    ConservationColourScheme ccs = (ConservationColourScheme)cs;\r
 323    int value = ccs.inc;\r
 324 \r
 325    if(conservationSlider == null)\r
 326    {\r
 327      sp = new SliderPanel(ap, value, true, cs);\r
 328      conservationSlider = new JInternalFrame();\r
 329      conservationSlider.setContentPane(sp);\r
 330      addInternalFrame(conservationSlider, "Conservation Colour Increment  ("+source+")", 420, 90);\r
 331      conservationSlider.setResizable(false);\r
 332      conservationSlider.setMaximizable(false);\r
 333      conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 334                   {\r
 335                     public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
 336                     {\r
 337                       conservationSlider = null;\r
 338                     }\r
 339                   });\r
 340    }\r
 341    else\r
 342    {\r
 343 \r
 344        conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");\r
 345        sp = (SliderPanel)conservationSlider.getContentPane();\r
 346        sp.cs = cs;\r
 347        sp.setValue(value);\r
 348    }\r
 349 \r
 350    if(ap.av.alignment.getGroups()!=null)\r
 351      sp.setAllGroupsCheckEnabled( true );\r
 352    else\r
 353      sp.setAllGroupsCheckEnabled( false);\r
 354 \r
 355    return sp.getValue();\r
 356 \r
 357  }\r
 358 \r
 359  public static void hideConservationSlider()\r
 360  {\r
 361   try{\r
 362     conservationSlider.setClosed(true);\r
 363     conservationSlider = null;\r
 364   }catch(Exception ex){}\r
 365 }\r
 366 \r
 367 \r
 368  public static void hidePIDSlider()\r
 369  {\r
 370    try{\r
 371      PIDSlider.setClosed(true);\r
 372      PIDSlider = null;\r
 373    }catch(Exception ex){}\r
 374  }\r
 375 \r
 376  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 377  {\r
 378    SliderPanel pid = null;\r
 379    if(PIDSlider == null)\r
 380    {\r
 381      pid = new SliderPanel(ap, 50, false, cs);\r
 382      PIDSlider = new JInternalFrame();\r
 383      PIDSlider.setContentPane(pid);\r
 384      addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);\r
 385      PIDSlider.setResizable(false);\r
 386      PIDSlider.setMaximizable(false);\r
 387    }\r
 388    else\r
 389    {\r
 390        PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
 391        pid = (SliderPanel)PIDSlider.getContentPane();\r
 392        pid.cs = cs;\r
 393    }\r
 394 \r
 395    if (ap.av.alignment.getGroups() != null)\r
 396      pid.setAllGroupsCheckEnabled(true);\r
 397    else\r
 398      pid.setAllGroupsCheckEnabled(false);\r
 399 \r
 400 \r
 401    return pid.getValue();\r
 402 \r
 403  }\r
 404 \r
 405 }\r