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 \r
 119   public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
 120   {\r
 121    desktop.add(frame);\r
 122    openFrameCount++;\r
 123    try {\r
 124        frame.setSelected(true);\r
 125    } catch (java.beans.PropertyVetoException e) {}\r
 126    frame.setTitle(title);\r
 127    frame.setResizable(true);\r
 128    frame.setSize(w,h);\r
 129    frame.setClosable(true);\r
 130    frame.setMaximizable(true);\r
 131    frame.setIconifiable(true);\r
 132    frame.setFrameIcon(null);\r
 133    frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
 134    frame.toFront();\r
 135    final JMenuItem menuItem = new JMenuItem(title);\r
 136    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 137                                    { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 138                                      {\r
 139                                        openFrameCount--;\r
 140                                        windowMenu.remove(menuItem);\r
 141                                      };\r
 142                                    });\r
 143 \r
 144    menuItem.addActionListener(new ActionListener()\r
 145     {\r
 146       public void actionPerformed(ActionEvent e)\r
 147       {\r
 148         try{  frame.setSelected(true);   frame.setIcon(false); }\r
 149         catch(java.beans.PropertyVetoException ex){};\r
 150       }\r
 151     });\r
 152 \r
 153    frame.setVisible(true);\r
 154    windowMenu.add(menuItem);\r
 155  }\r
 156 \r
 157  public void dragEnter(DropTargetDragEvent evt){}\r
 158  public void dragExit(DropTargetEvent evt){}\r
 159  public void dragOver(DropTargetDragEvent evt){}\r
 160  public void dropActionChanged(DropTargetDragEvent evt){}\r
 161  public void drop(DropTargetDropEvent evt)\r
 162 {\r
 163    Transferable t = evt.getTransferable();\r
 164    if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
 165      return;\r
 166 \r
 167    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
 168    try{\r
 169      java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
 170 \r
 171      for (int i = 0; i < files.size(); i++)\r
 172      {\r
 173        String file = files.get(i).toString();\r
 174        String protocol = "File";\r
 175        String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
 176        LoadFile(file, protocol, format);\r
 177      }\r
 178 \r
 179    }catch(Exception ex){ex.printStackTrace();}\r
 180   }\r
 181 \r
 182  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
 183  {\r
 184    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 185        new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");\r
 186    chooser.setFileView(new JalviewFileView());\r
 187    chooser.setDialogTitle("Open local file");\r
 188    chooser.setToolTipText("Open");\r
 189    int value = chooser.showOpenDialog(this);\r
 190    if(value == JalviewFileChooser.APPROVE_OPTION)\r
 191    {\r
 192      String choice =  chooser.getSelectedFile().getPath();\r
 193      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 194      String format = IdentifyFile.Identify(choice, "File");\r
 195      LoadFile(choice, "File", format);\r
 196    }\r
 197  }\r
 198 \r
 199  public void LoadFile(String file, String protocol,  String format)\r
 200  {\r
 201    SequenceI [] sequences = null;\r
 202 \r
 203    if (FormatProperties.contains(format))\r
 204        sequences = FormatAdapter.read(file, protocol, format);\r
 205 \r
 206    if (sequences != null && sequences.length>0)\r
 207    {\r
 208      AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 209      addInternalFrame(af, file, 700, 500);\r
 210      af.statusBar.setText("Successfully loaded file " + file);\r
 211 \r
 212    }\r
 213    else\r
 214      JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"\r
 215                           + "Formats currently supported are\n"\r
 216                           + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" // JBPNote - message should be generated through FormatAdapter!\r
 217                           ,"Error loading file",\r
 218                                    JOptionPane.WARNING_MESSAGE);\r
 219 \r
 220  }\r
 221 \r
 222  public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
 223  {\r
 224    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
 225                                             "Input alignment from URL",\r
 226                                             JOptionPane.QUESTION_MESSAGE);\r
 227    if (url == null)\r
 228      return;\r
 229 \r
 230    String format = IdentifyFile.Identify(url, "URL");\r
 231 \r
 232    if (format.equals("URL NOT FOUND"))\r
 233    {\r
 234      JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
 235                                    "URL not found",\r
 236                                    JOptionPane.WARNING_MESSAGE);\r
 237      return;\r
 238    }\r
 239 \r
 240     LoadFile(url, "URL", format);\r
 241  }\r
 242 \r
 243  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
 244  {\r
 245    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 246    int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
 247                                        JOptionPane.YES_NO_CANCEL_OPTION,\r
 248                                        JOptionPane.PLAIN_MESSAGE,\r
 249                                        null,\r
 250                                        new Object[]{"Accept", "Cancel", }, null);\r
 251 \r
 252 \r
 253   if(accept == JOptionPane.YES_OPTION)\r
 254   {\r
 255     String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
 256     SequenceI [] sequences = null;\r
 257 \r
 258     if (FormatProperties.contains( format ))\r
 259       sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
 260 \r
 261 \r
 262       if(sequences!=null)\r
 263       {\r
 264         AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 265         addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);\r
 266         af.statusBar.setText("Successfully pasted alignment file");\r
 267       }\r
 268       else\r
 269         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
 270                                       +"Formats currently supported are\n"\r
 271                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
 272                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
 273 \r
 274    }\r
 275  }\r
 276 \r
 277 /*\r
 278 * Exit the program\r
 279 */\r
 280  public void quit_actionPerformed(ActionEvent e)\r
 281  {\r
 282    if(jalview.bin.Jalview.applet!=null)\r
 283      jalview.bin.Jalview.applet.destroy();\r
 284     else\r
 285       System.exit(0);\r
 286  }\r
 287 \r
 288 \r
 289 \r
 290  public void aboutMenuItem_actionPerformed(ActionEvent e)\r
 291  {\r
 292    JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 293                                          "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE\r
 294                                        +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
 295                                        +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
 296                                        +"\nIf  you use JalView, please cite:  Bioinformatics,  2004 12;426-7."\r
 297                                        +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
 298                                          "About Jalview",\r
 299                                          JOptionPane.INFORMATION_MESSAGE);\r
 300  }\r
 301 \r
 302  public void documentationMenuItem_actionPerformed(ActionEvent e)\r
 303  {\r
 304    try\r
 305    {\r
 306       ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
 307       java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
 308       javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
 309 \r
 310       javax.help.HelpBroker hb = hs.createHelpBroker();\r
 311       hb.setLocation(new Point(200, 50));\r
 312       hb.setSize(new Dimension(800,700));\r
 313       hb.setCurrentID("home");\r
 314       hb.setDisplayed(true);\r
 315    }\r
 316    catch (Exception ex)\r
 317    {\r
 318      ex.printStackTrace();\r
 319    }\r
 320  }\r
 321 \r
 322  static JInternalFrame conservationSlider;\r
 323  static JInternalFrame PIDSlider;\r
 324  public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 325  {\r
 326    SliderPanel sp = null;\r
 327    ConservationColourScheme ccs = (ConservationColourScheme)cs;\r
 328    int value = ccs.inc;\r
 329 \r
 330    if(conservationSlider == null)\r
 331    {\r
 332      sp = new SliderPanel(ap, value, true, cs);\r
 333      conservationSlider = new JInternalFrame();\r
 334      conservationSlider.setContentPane(sp);\r
 335      addInternalFrame(conservationSlider, "Conservation Colour Increment  ("+source+")", 420, 90);\r
 336      conservationSlider.setResizable(false);\r
 337      conservationSlider.setMaximizable(false);\r
 338      conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 339                   {\r
 340                     public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
 341                     {\r
 342                       conservationSlider = null;\r
 343                     }\r
 344                   });\r
 345    }\r
 346    else\r
 347    {\r
 348 \r
 349        conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");\r
 350        sp = (SliderPanel)conservationSlider.getContentPane();\r
 351        sp.cs = cs;\r
 352        sp.setValue(value);\r
 353    }\r
 354 \r
 355    if(ap.av.alignment.getGroups()!=null)\r
 356      sp.setAllGroupsCheckEnabled( true );\r
 357    else\r
 358      sp.setAllGroupsCheckEnabled( false);\r
 359 \r
 360    return sp.getValue();\r
 361 \r
 362  }\r
 363 \r
 364  public static void hideConservationSlider()\r
 365  {\r
 366   try{\r
 367     conservationSlider.setClosed(true);\r
 368     conservationSlider = null;\r
 369   }catch(Exception ex){}\r
 370 }\r
 371 \r
 372 \r
 373  public static void hidePIDSlider()\r
 374  {\r
 375    try{\r
 376      PIDSlider.setClosed(true);\r
 377      PIDSlider = null;\r
 378    }catch(Exception ex){}\r
 379  }\r
 380 \r
 381  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 382  {\r
 383    SliderPanel pid = null;\r
 384    if(PIDSlider == null)\r
 385    {\r
 386      pid = new SliderPanel(ap, 50, false, cs);\r
 387      PIDSlider = new JInternalFrame();\r
 388      PIDSlider.setContentPane(pid);\r
 389      addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);\r
 390      PIDSlider.setResizable(false);\r
 391      PIDSlider.setMaximizable(false);\r
 392    }\r
 393    else\r
 394    {\r
 395        PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
 396        pid = (SliderPanel)PIDSlider.getContentPane();\r
 397        pid.cs = cs;\r
 398    }\r
 399 \r
 400    if (ap.av.alignment.getGroups() != null)\r
 401      pid.setAllGroupsCheckEnabled(true);\r
 402    else\r
 403      pid.setAllGroupsCheckEnabled(false);\r
 404 \r
 405 \r
 406    return pid.getValue();\r
 407 \r
 408  }\r
 409 \r
 410 }\r