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/BartonGroupBanner.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(845, 200);\r
 100     frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /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.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
 123    frame.toFront();\r
 124    final JMenuItem menuItem = new JMenuItem(title);\r
 125    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 126                                    { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 127                                      {\r
 128                                        openFrameCount--;\r
 129                                        windowMenu.remove(menuItem);\r
 130                                      };\r
 131                                    });\r
 132 \r
 133    menuItem.addActionListener(new ActionListener()\r
 134     {\r
 135       public void actionPerformed(ActionEvent e)\r
 136       {\r
 137         try{  frame.setSelected(true);   frame.setIcon(false); }\r
 138         catch(java.beans.PropertyVetoException ex){};\r
 139       }\r
 140     });\r
 141 \r
 142    windowMenu.add(menuItem);\r
 143  }\r
 144 \r
 145 \r
 146 \r
 147  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
 148  {\r
 149    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
 150    chooser.setFileView(new JalviewFileView());\r
 151    chooser.setDialogTitle("Open local file");\r
 152    chooser.setToolTipText("Open");\r
 153    int value = chooser.showOpenDialog(this);\r
 154    if(value == JFileChooser.APPROVE_OPTION)\r
 155    {\r
 156      String choice =  chooser.getSelectedFile().getPath();\r
 157      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 158      String format = IdentifyFile.Identify(choice, "File");\r
 159      LoadFile(choice, "File", format);\r
 160    }\r
 161  }\r
 162 \r
 163  public void LoadFile(String file, String protocol,  String format)\r
 164  {\r
 165    SequenceI [] sequences = null;\r
 166 \r
 167    if (FormatProperties.contains(format))\r
 168        sequences = FormatAdapter.read(file, protocol, format);\r
 169 \r
 170    if (sequences != null)\r
 171    {\r
 172      AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 173      addInternalFrame(af, file, 700, 500);\r
 174      af.statusBar.setText("Successfully loaded file " + file);\r
 175 \r
 176 \r
 177    }\r
 178    else\r
 179      JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"\r
 180                           + "Formats currently supported are\n"\r
 181                           + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"\r
 182                           ,"Error loading file",\r
 183                                    JOptionPane.WARNING_MESSAGE);\r
 184 \r
 185  }\r
 186 \r
 187  public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
 188  {\r
 189    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
 190                                             "Input alignment from URL",\r
 191                                             JOptionPane.QUESTION_MESSAGE);\r
 192    if (url == null)\r
 193      return;\r
 194 \r
 195    String format = IdentifyFile.Identify(url, "URL");\r
 196 \r
 197    System.out.println(format +" format");\r
 198    if (format.equals("URL NOT FOUND"))\r
 199    {\r
 200      JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
 201                                    "URL not found",\r
 202                                    JOptionPane.WARNING_MESSAGE);\r
 203      return;\r
 204    }\r
 205 \r
 206     LoadFile(url, "URL", format);\r
 207  }\r
 208 \r
 209  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
 210  {\r
 211    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 212    int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
 213                                        JOptionPane.YES_NO_CANCEL_OPTION,\r
 214                                        JOptionPane.PLAIN_MESSAGE,\r
 215                                        null,\r
 216                                        new Object[]{"Accept", "Cancel", }, null);\r
 217 \r
 218 \r
 219   if(accept == JOptionPane.YES_OPTION)\r
 220   {\r
 221     String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
 222     SequenceI [] sequences = null;\r
 223 \r
 224     if (FormatProperties.contains( format ))\r
 225       sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
 226 \r
 227 \r
 228       if(sequences!=null)\r
 229       {\r
 230         AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 231         addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);\r
 232         af.statusBar.setText("Successfully pasted alignment file");\r
 233       }\r
 234       else\r
 235         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
 236                                       +"Formats currently supported are\n"\r
 237                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
 238                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
 239 \r
 240    }\r
 241  }\r
 242 \r
 243 /*\r
 244 * Exit the program\r
 245 */\r
 246  public void quit_actionPerformed(ActionEvent e)\r
 247  {\r
 248    if(jalview.bin.Jalview.applet!=null)\r
 249      jalview.bin.Jalview.applet.destroy();\r
 250     else\r
 251       System.exit(0);\r
 252  }\r
 253 \r
 254 \r
 255 \r
 256  public void aboutMenuItem_actionPerformed(ActionEvent e)\r
 257  {\r
 258    JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 259                                          "JalView 2005"\r
 260                                        +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
 261                                        +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
 262                                        +"\nIf  you use JalView, please cite:  \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
 263                                          "About Jalview",\r
 264                                          JOptionPane.INFORMATION_MESSAGE);\r
 265  }\r
 266 \r
 267  public void documentationMenuItem_actionPerformed(ActionEvent e)\r
 268  {\r
 269    try\r
 270    {\r
 271       ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
 272       java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
 273       javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
 274 \r
 275       javax.help.HelpBroker hb = hs.createHelpBroker();\r
 276       hb.setLocation(new Point(200, 50));\r
 277       hb.setSize(new Dimension(800,700));\r
 278       hb.setCurrentID("home");\r
 279       hb.setDisplayed(true);\r
 280    }\r
 281    catch (Exception ex)\r
 282    {\r
 283      ex.printStackTrace();\r
 284    }\r
 285  }\r
 286 \r
 287  static JInternalFrame conservationSlider;\r
 288  static JInternalFrame PIDSlider;\r
 289  public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 290  {\r
 291    SliderPanel sp = null;\r
 292 \r
 293    if(conservationSlider == null)\r
 294    {\r
 295      sp = new SliderPanel(ap, 30, true, cs);\r
 296      conservationSlider = new JInternalFrame();\r
 297      conservationSlider.setContentPane(sp);\r
 298      conservationSlider.setResizable(false);\r
 299      addInternalFrame(conservationSlider, "Conservation Colour Increment  ("+source+")", 420, 90);\r
 300      conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 301                   {\r
 302                     public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
 303                     {\r
 304                       conservationSlider = null;\r
 305                     }\r
 306                   });\r
 307    }\r
 308    else\r
 309    {\r
 310        conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");\r
 311        sp = (SliderPanel)conservationSlider.getContentPane();\r
 312        sp.cs = cs;\r
 313    }\r
 314 \r
 315    if(ap.av.alignment.getGroups()!=null)\r
 316      sp.setAllGroupsCheckEnabled( true );\r
 317    else\r
 318      sp.setAllGroupsCheckEnabled( false);\r
 319 \r
 320    return sp.getValue();\r
 321 \r
 322  }\r
 323 \r
 324  public static void hideConservationSlider()\r
 325  {\r
 326   try{\r
 327     conservationSlider.setClosed(true);\r
 328     conservationSlider = null;\r
 329   }catch(Exception ex){}\r
 330 }\r
 331 \r
 332 \r
 333  public static void hidePIDSlider()\r
 334  {\r
 335    try{\r
 336      PIDSlider.setClosed(true);\r
 337      PIDSlider = null;\r
 338    }catch(Exception ex){}\r
 339  }\r
 340 \r
 341  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 342  {\r
 343    SliderPanel pid = null;\r
 344    if(PIDSlider == null)\r
 345    {\r
 346      pid = new SliderPanel(ap, 50, false, cs);\r
 347      PIDSlider = new JInternalFrame();\r
 348      PIDSlider.setContentPane(pid);\r
 349      PIDSlider.setResizable(false);\r
 350      addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);\r
 351    }\r
 352    else\r
 353    {\r
 354        PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
 355        pid = (SliderPanel)PIDSlider.getContentPane();\r
 356        pid.cs = cs;\r
 357    }\r
 358 \r
 359    if (ap.av.alignment.getGroups() != null)\r
 360      pid.setAllGroupsCheckEnabled(true);\r
 361    else\r
 362      pid.setAllGroupsCheckEnabled(false);\r
 363 \r
 364 \r
 365    return pid.getValue();\r
 366 \r
 367  }\r
 368 \r
 369 }\r