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(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 151        new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");\r
 152    chooser.setFileView(new JalviewFileView());\r
 153    chooser.setDialogTitle("Open local file");\r
 154    chooser.setToolTipText("Open");\r
 155    int value = chooser.showOpenDialog(this);\r
 156    if(value == JalviewFileChooser.APPROVE_OPTION)\r
 157    {\r
 158      String choice =  chooser.getSelectedFile().getPath();\r
 159      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 160      String format = IdentifyFile.Identify(choice, "File");\r
 161      LoadFile(choice, "File", format);\r
 162    }\r
 163  }\r
 164 \r
 165  public void LoadFile(String file, String protocol,  String format)\r
 166  {\r
 167    SequenceI [] sequences = null;\r
 168 \r
 169    if (FormatProperties.contains(format))\r
 170        sequences = FormatAdapter.read(file, protocol, format);\r
 171 \r
 172    if (sequences != null)\r
 173    {\r
 174      AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 175      addInternalFrame(af, file, 700, 500);\r
 176      af.statusBar.setText("Successfully loaded file " + file);\r
 177 \r
 178 \r
 179    }\r
 180    else\r
 181      JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"\r
 182                           + "Formats currently supported are\n"\r
 183                           + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"\r
 184                           ,"Error loading file",\r
 185                                    JOptionPane.WARNING_MESSAGE);\r
 186 \r
 187  }\r
 188 \r
 189  public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
 190  {\r
 191    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
 192                                             "Input alignment from URL",\r
 193                                             JOptionPane.QUESTION_MESSAGE);\r
 194    if (url == null)\r
 195      return;\r
 196 \r
 197    String format = IdentifyFile.Identify(url, "URL");\r
 198 \r
 199    System.out.println(format +" format");\r
 200    if (format.equals("URL NOT FOUND"))\r
 201    {\r
 202      JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
 203                                    "URL not found",\r
 204                                    JOptionPane.WARNING_MESSAGE);\r
 205      return;\r
 206    }\r
 207 \r
 208     LoadFile(url, "URL", format);\r
 209  }\r
 210 \r
 211  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
 212  {\r
 213    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 214    int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
 215                                        JOptionPane.YES_NO_CANCEL_OPTION,\r
 216                                        JOptionPane.PLAIN_MESSAGE,\r
 217                                        null,\r
 218                                        new Object[]{"Accept", "Cancel", }, null);\r
 219 \r
 220 \r
 221   if(accept == JOptionPane.YES_OPTION)\r
 222   {\r
 223     String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
 224     SequenceI [] sequences = null;\r
 225 \r
 226     if (FormatProperties.contains( format ))\r
 227       sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
 228 \r
 229 \r
 230       if(sequences!=null)\r
 231       {\r
 232         AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 233         addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);\r
 234         af.statusBar.setText("Successfully pasted alignment file");\r
 235       }\r
 236       else\r
 237         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
 238                                       +"Formats currently supported are\n"\r
 239                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
 240                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
 241 \r
 242    }\r
 243  }\r
 244 \r
 245 /*\r
 246 * Exit the program\r
 247 */\r
 248  public void quit_actionPerformed(ActionEvent e)\r
 249  {\r
 250    if(jalview.bin.Jalview.applet!=null)\r
 251      jalview.bin.Jalview.applet.destroy();\r
 252     else\r
 253       System.exit(0);\r
 254  }\r
 255 \r
 256 \r
 257 \r
 258  public void aboutMenuItem_actionPerformed(ActionEvent e)\r
 259  {\r
 260    JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 261                                          "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE\r
 262                                        +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
 263                                        +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
 264                                        +"\nIf  you use JalView, please cite:  \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
 265                                          "About Jalview",\r
 266                                          JOptionPane.INFORMATION_MESSAGE);\r
 267  }\r
 268 \r
 269  public void documentationMenuItem_actionPerformed(ActionEvent e)\r
 270  {\r
 271    try\r
 272    {\r
 273       ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
 274       java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
 275       javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
 276 \r
 277       javax.help.HelpBroker hb = hs.createHelpBroker();\r
 278       hb.setLocation(new Point(200, 50));\r
 279       hb.setSize(new Dimension(800,700));\r
 280       hb.setCurrentID("home");\r
 281       hb.setDisplayed(true);\r
 282    }\r
 283    catch (Exception ex)\r
 284    {\r
 285      ex.printStackTrace();\r
 286    }\r
 287  }\r
 288 \r
 289  static JInternalFrame conservationSlider;\r
 290  static JInternalFrame PIDSlider;\r
 291  public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 292  {\r
 293    SliderPanel sp = null;\r
 294 \r
 295    if(conservationSlider == null)\r
 296    {\r
 297      sp = new SliderPanel(ap, 30, true, cs);\r
 298      conservationSlider = new JInternalFrame();\r
 299      conservationSlider.setContentPane(sp);\r
 300      conservationSlider.setResizable(false);\r
 301      addInternalFrame(conservationSlider, "Conservation Colour Increment  ("+source+")", 420, 90);\r
 302      conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 303                   {\r
 304                     public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
 305                     {\r
 306                       conservationSlider = null;\r
 307                     }\r
 308                   });\r
 309    }\r
 310    else\r
 311    {\r
 312        conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");\r
 313        sp = (SliderPanel)conservationSlider.getContentPane();\r
 314        sp.cs = cs;\r
 315    }\r
 316 \r
 317    if(ap.av.alignment.getGroups()!=null)\r
 318      sp.setAllGroupsCheckEnabled( true );\r
 319    else\r
 320      sp.setAllGroupsCheckEnabled( false);\r
 321 \r
 322    return sp.getValue();\r
 323 \r
 324  }\r
 325 \r
 326  public static void hideConservationSlider()\r
 327  {\r
 328   try{\r
 329     conservationSlider.setClosed(true);\r
 330     conservationSlider = null;\r
 331   }catch(Exception ex){}\r
 332 }\r
 333 \r
 334 \r
 335  public static void hidePIDSlider()\r
 336  {\r
 337    try{\r
 338      PIDSlider.setClosed(true);\r
 339      PIDSlider = null;\r
 340    }catch(Exception ex){}\r
 341  }\r
 342 \r
 343  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 344  {\r
 345    SliderPanel pid = null;\r
 346    if(PIDSlider == null)\r
 347    {\r
 348      pid = new SliderPanel(ap, 50, false, cs);\r
 349      PIDSlider = new JInternalFrame();\r
 350      PIDSlider.setContentPane(pid);\r
 351      PIDSlider.setResizable(false);\r
 352      addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);\r
 353    }\r
 354    else\r
 355    {\r
 356        PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
 357        pid = (SliderPanel)PIDSlider.getContentPane();\r
 358        pid.cs = cs;\r
 359    }\r
 360 \r
 361    if (ap.av.alignment.getGroups() != null)\r
 362      pid.setAllGroupsCheckEnabled(true);\r
 363    else\r
 364      pid.setAllGroupsCheckEnabled(false);\r
 365 \r
 366 \r
 367    return pid.getValue();\r
 368 \r
 369  }\r
 370 \r
 371 }\r