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("/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     setContentPane(desktop);\r
  48     desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
  49 \r
  50     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
  51     int width = 1200, height = 800;\r
  52     if(screenSize.getWidth()<width)\r
  53       width = screenSize.width;\r
  54     if(screenSize.getHeight()<height)\r
  55       height = screenSize.height;\r
  56 \r
  57     setBounds( (int)(screenSize.width-width)/2,\r
  58                (int)(screenSize.height-height)/2,\r
  59               width ,\r
  60               height);\r
  61 \r
  62 \r
  63    /////////Add a splashscreen on startup\r
  64     JInternalFrame frame = new JInternalFrame();\r
  65 \r
  66     SplashScreen splash = new SplashScreen(frame, image);\r
  67     frame.setContentPane(splash);\r
  68     desktop.add(frame);\r
  69     frame.setVisible(true);\r
  70     openFrameCount++;\r
  71     try\r
  72     {\r
  73       frame.setSelected(true);\r
  74     }\r
  75     catch (java.beans.PropertyVetoException e)\r
  76     {}\r
  77     frame.setResizable(true);\r
  78     frame.setSize(845, 200);\r
  79     frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /2));\r
  80     frame.setClosable(false);\r
  81     frame.setIconifiable(false);\r
  82     frame.setMaximizable(false);\r
  83     frame.setFrameIcon(null);\r
  84 \r
  85   }\r
  86 \r
  87   public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
  88   {\r
  89    desktop.add(frame);\r
  90    frame.setVisible(true);\r
  91    openFrameCount++;\r
  92    try {\r
  93        frame.setSelected(true);\r
  94    } catch (java.beans.PropertyVetoException e) {}\r
  95    frame.setTitle(title);\r
  96    frame.setResizable(true);\r
  97    frame.setSize(w,h);\r
  98    frame.setClosable(true);\r
  99    frame.setMaximizable(true);\r
 100    frame.setIconifiable(true);\r
 101    frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
 102    frame.toFront();\r
 103    final JMenuItem menuItem = new JMenuItem(title);\r
 104    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 105                                    { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 106                                      {\r
 107                                        openFrameCount--;\r
 108                                        windowMenu.remove(menuItem);\r
 109                                      };\r
 110                                    });\r
 111 \r
 112    menuItem.addActionListener(new ActionListener()\r
 113     {\r
 114       public void actionPerformed(ActionEvent e)\r
 115       {\r
 116         try{  frame.setSelected(true);   frame.setIcon(false); }\r
 117         catch(java.beans.PropertyVetoException ex){};\r
 118       }\r
 119     });\r
 120 \r
 121    windowMenu.add(menuItem);\r
 122  }\r
 123 \r
 124 \r
 125 \r
 126  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
 127  {\r
 128    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
 129    chooser.setDialogTitle("Open local file");\r
 130    chooser.setToolTipText("Open");\r
 131    int value = chooser.showOpenDialog(this);\r
 132    if(value == JFileChooser.APPROVE_OPTION)\r
 133    {\r
 134      String choice =  chooser.getSelectedFile().getPath();\r
 135      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 136      String format = IdentifyFile.Identify(choice, "File");\r
 137      LoadFile(choice, "File", format);\r
 138    }\r
 139  }\r
 140 \r
 141  public void LoadFile(String file, String protocol,  String format)\r
 142  {\r
 143    SequenceI [] sequences = null;\r
 144 \r
 145    if (FormatProperties.contains(format))\r
 146        sequences = FormatAdapter.read(file, protocol, format);\r
 147 \r
 148    if (sequences != null)\r
 149    {\r
 150      AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 151      addInternalFrame(af, file, 700, 500);\r
 152      af.statusBar.setText("Successfully loaded file " + file);\r
 153 \r
 154 \r
 155    }\r
 156    else\r
 157      JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"\r
 158                           + "Formats currently supported are\n"\r
 159                           + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"\r
 160                           ,"Error loading file",\r
 161                                    JOptionPane.WARNING_MESSAGE);\r
 162 \r
 163  }\r
 164 \r
 165  public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
 166  {\r
 167    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
 168                                             "Input alignment from URL",\r
 169                                             JOptionPane.QUESTION_MESSAGE);\r
 170    if (url == null)\r
 171      return;\r
 172 \r
 173    String format = IdentifyFile.Identify(url, "URL");\r
 174 \r
 175    System.out.println(format +" format");\r
 176    if (format.equals("URL NOT FOUND"))\r
 177    {\r
 178      JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
 179                                    "URL not found",\r
 180                                    JOptionPane.WARNING_MESSAGE);\r
 181      return;\r
 182    }\r
 183 \r
 184     LoadFile(url, "URL", format);\r
 185  }\r
 186 \r
 187  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
 188  {\r
 189    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 190    int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
 191                                        JOptionPane.YES_NO_CANCEL_OPTION,\r
 192                                        JOptionPane.PLAIN_MESSAGE,\r
 193                                        null,\r
 194                                        new Object[]{"Accept", "Cancel", }, null);\r
 195 \r
 196 \r
 197   if(accept == JOptionPane.YES_OPTION)\r
 198   {\r
 199     String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
 200     SequenceI [] sequences = null;\r
 201 \r
 202     if (FormatProperties.contains( format ))\r
 203       sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
 204 \r
 205 \r
 206       if(sequences!=null)\r
 207       {\r
 208         AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 209         addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);\r
 210         af.statusBar.setText("Successfully pasted alignment file");\r
 211       }\r
 212       else\r
 213         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
 214                                       +"Formats currently supported are\n"\r
 215                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
 216                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
 217 \r
 218    }\r
 219  }\r
 220 \r
 221 /*\r
 222 * Exit the program\r
 223 */\r
 224  public void quit_actionPerformed(ActionEvent e)\r
 225  {\r
 226    if(jalview.bin.Jalview.applet!=null)\r
 227      jalview.bin.Jalview.applet.destroy();\r
 228     else\r
 229       System.exit(0);\r
 230  }\r
 231 \r
 232 \r
 233 \r
 234  public void aboutMenuItem_actionPerformed(ActionEvent e)\r
 235  {\r
 236    JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 237                                          "JalView 2005"\r
 238                                        +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
 239                                        +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
 240                                        +"\nIf  you use JalView, please cite:  \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
 241                                          "About Jalview",\r
 242                                          JOptionPane.INFORMATION_MESSAGE);\r
 243  }\r
 244 \r
 245  public void documentationMenuItem_actionPerformed(ActionEvent e)\r
 246  {\r
 247    try\r
 248    {\r
 249       ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
 250       java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
 251       javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
 252 \r
 253       javax.help.HelpBroker hb = hs.createHelpBroker();\r
 254       hb.setLocation(new Point(200, 50));\r
 255       hb.setSize(new Dimension(800,700));\r
 256       hb.setCurrentID("home");\r
 257       hb.setDisplayed(true);\r
 258    }\r
 259    catch (Exception ex)\r
 260    {\r
 261      ex.printStackTrace();\r
 262    }\r
 263  }\r
 264 \r
 265  static JInternalFrame conservationSlider;\r
 266  static JInternalFrame PIDSlider;\r
 267  public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 268  {\r
 269    SliderPanel sp = null;\r
 270 \r
 271    if(conservationSlider == null)\r
 272    {\r
 273      sp = new SliderPanel(ap, 30, true, cs);\r
 274      conservationSlider = new JInternalFrame();\r
 275      conservationSlider.setContentPane(sp);\r
 276      conservationSlider.setResizable(false);\r
 277      addInternalFrame(conservationSlider, "Conservation Colour Increment  ("+source+")", 420, 90);\r
 278      conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 279                   {\r
 280                     public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
 281                     {\r
 282                       conservationSlider = null;\r
 283                     }\r
 284                   });\r
 285    }\r
 286    else\r
 287    {\r
 288        conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");\r
 289        sp = (SliderPanel)conservationSlider.getContentPane();\r
 290        sp.cs = cs;\r
 291    }\r
 292 \r
 293    if(ap.av.alignment.getGroups()!=null)\r
 294      sp.setAllGroupsCheckEnabled( true );\r
 295    else\r
 296      sp.setAllGroupsCheckEnabled( false);\r
 297 \r
 298    return sp.getValue();\r
 299 \r
 300  }\r
 301 \r
 302  public static void hideConservationSlider()\r
 303  {\r
 304   try{\r
 305     conservationSlider.setClosed(true);\r
 306     conservationSlider = null;\r
 307   }catch(Exception ex){}\r
 308 }\r
 309 \r
 310 \r
 311  public static void hidePIDSlider()\r
 312  {\r
 313    try{\r
 314      PIDSlider.setClosed(true);\r
 315      PIDSlider = null;\r
 316    }catch(Exception ex){}\r
 317  }\r
 318 \r
 319  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 320  {\r
 321    SliderPanel pid = null;\r
 322    if(PIDSlider == null)\r
 323    {\r
 324      pid = new SliderPanel(ap, 50, false, cs);\r
 325      PIDSlider = new JInternalFrame();\r
 326      PIDSlider.setContentPane(pid);\r
 327      PIDSlider.setResizable(false);\r
 328      addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);\r
 329    }\r
 330    else\r
 331    {\r
 332        PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
 333        pid = (SliderPanel)PIDSlider.getContentPane();\r
 334        pid.cs = cs;\r
 335    }\r
 336 \r
 337    if (ap.av.alignment.getGroups() != null)\r
 338      pid.setAllGroupsCheckEnabled(true);\r
 339    else\r
 340      pid.setAllGroupsCheckEnabled(false);\r
 341 \r
 342 \r
 343    return pid.getValue();\r
 344 \r
 345  }\r
 346 \r
 347 }\r