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