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