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