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     int width = 900, height = 650;\r
  53     if(screenSize.getWidth()<width)\r
  54       width = screenSize.width;\r
  55     if(screenSize.getHeight()<height)\r
  56       height = screenSize.height;\r
  57 \r
  58     setBounds( (int)(screenSize.width-width)/2,\r
  59                (int)(screenSize.height-height)/2,\r
  60               width ,\r
  61               height);\r
  62 \r
  63 \r
  64    /////////Add a splashscreen on startup\r
  65     JInternalFrame frame = new JInternalFrame();\r
  66 \r
  67     SplashScreen splash = new SplashScreen(frame, image);\r
  68     frame.setContentPane(splash);\r
  69     desktop.add(frame);\r
  70     frame.setVisible(true);\r
  71     openFrameCount++;\r
  72     try\r
  73     {\r
  74       frame.setSelected(true);\r
  75     }\r
  76     catch (java.beans.PropertyVetoException e)\r
  77     {}\r
  78     frame.setResizable(true);\r
  79     frame.setSize(845, 200);\r
  80     frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /2));\r
  81     frame.setClosable(false);\r
  82     frame.setIconifiable(false);\r
  83     frame.setMaximizable(false);\r
  84     frame.setFrameIcon(null);\r
  85 \r
  86   }\r
  87 \r
  88   public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
  89   {\r
  90    desktop.add(frame);\r
  91    frame.setVisible(true);\r
  92    openFrameCount++;\r
  93    try {\r
  94        frame.setSelected(true);\r
  95    } catch (java.beans.PropertyVetoException e) {}\r
  96    frame.setTitle(title);\r
  97    frame.setResizable(true);\r
  98    frame.setSize(w,h);\r
  99    frame.setClosable(true);\r
 100    frame.setMaximizable(true);\r
 101    frame.setIconifiable(true);\r
 102    frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
 103    frame.toFront();\r
 104    final JMenuItem menuItem = new JMenuItem(title);\r
 105    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 106                                    { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 107                                      {\r
 108                                        openFrameCount--;\r
 109                                        windowMenu.remove(menuItem);\r
 110                                      };\r
 111                                    });\r
 112 \r
 113    menuItem.addActionListener(new ActionListener()\r
 114     {\r
 115       public void actionPerformed(ActionEvent e)\r
 116       {\r
 117         try{  frame.setSelected(true);   frame.setIcon(false); }\r
 118         catch(java.beans.PropertyVetoException ex){};\r
 119       }\r
 120     });\r
 121 \r
 122    windowMenu.add(menuItem);\r
 123  }\r
 124 \r
 125 \r
 126 \r
 127  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
 128  {\r
 129    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
 130    chooser.setFileView(new JalviewFileView());\r
 131    chooser.setDialogTitle("Open local file");\r
 132    chooser.setToolTipText("Open");\r
 133    int value = chooser.showOpenDialog(this);\r
 134    if(value == JFileChooser.APPROVE_OPTION)\r
 135    {\r
 136      String choice =  chooser.getSelectedFile().getPath();\r
 137      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 138      String format = IdentifyFile.Identify(choice, "File");\r
 139      LoadFile(choice, "File", format);\r
 140    }\r
 141  }\r
 142 \r
 143  public void LoadFile(String file, String protocol,  String format)\r
 144  {\r
 145    SequenceI [] sequences = null;\r
 146 \r
 147    if (FormatProperties.contains(format))\r
 148        sequences = FormatAdapter.read(file, protocol, format);\r
 149 \r
 150    if (sequences != null)\r
 151    {\r
 152      AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 153      addInternalFrame(af, file, 700, 500);\r
 154      af.statusBar.setText("Successfully loaded file " + file);\r
 155 \r
 156 \r
 157    }\r
 158    else\r
 159      JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"\r
 160                           + "Formats currently supported are\n"\r
 161                           + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"\r
 162                           ,"Error loading file",\r
 163                                    JOptionPane.WARNING_MESSAGE);\r
 164 \r
 165  }\r
 166 \r
 167  public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
 168  {\r
 169    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
 170                                             "Input alignment from URL",\r
 171                                             JOptionPane.QUESTION_MESSAGE);\r
 172    if (url == null)\r
 173      return;\r
 174 \r
 175    String format = IdentifyFile.Identify(url, "URL");\r
 176 \r
 177    System.out.println(format +" format");\r
 178    if (format.equals("URL NOT FOUND"))\r
 179    {\r
 180      JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
 181                                    "URL not found",\r
 182                                    JOptionPane.WARNING_MESSAGE);\r
 183      return;\r
 184    }\r
 185 \r
 186     LoadFile(url, "URL", format);\r
 187  }\r
 188 \r
 189  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
 190  {\r
 191    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 192    int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
 193                                        JOptionPane.YES_NO_CANCEL_OPTION,\r
 194                                        JOptionPane.PLAIN_MESSAGE,\r
 195                                        null,\r
 196                                        new Object[]{"Accept", "Cancel", }, null);\r
 197 \r
 198 \r
 199   if(accept == JOptionPane.YES_OPTION)\r
 200   {\r
 201     String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
 202     SequenceI [] sequences = null;\r
 203 \r
 204     if (FormatProperties.contains( format ))\r
 205       sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
 206 \r
 207 \r
 208       if(sequences!=null)\r
 209       {\r
 210         AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 211         addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);\r
 212         af.statusBar.setText("Successfully pasted alignment file");\r
 213       }\r
 214       else\r
 215         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
 216                                       +"Formats currently supported are\n"\r
 217                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
 218                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
 219 \r
 220    }\r
 221  }\r
 222 \r
 223 /*\r
 224 * Exit the program\r
 225 */\r
 226  public void quit_actionPerformed(ActionEvent e)\r
 227  {\r
 228    if(jalview.bin.Jalview.applet!=null)\r
 229      jalview.bin.Jalview.applet.destroy();\r
 230     else\r
 231       System.exit(0);\r
 232  }\r
 233 \r
 234 \r
 235 \r
 236  public void aboutMenuItem_actionPerformed(ActionEvent e)\r
 237  {\r
 238    JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 239                                          "JalView 2005"\r
 240                                        +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
 241                                        +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
 242                                        +"\nIf  you use JalView, please cite:  \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
 243                                          "About Jalview",\r
 244                                          JOptionPane.INFORMATION_MESSAGE);\r
 245  }\r
 246 \r
 247  public void documentationMenuItem_actionPerformed(ActionEvent e)\r
 248  {\r
 249    try\r
 250    {\r
 251       ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
 252       java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
 253       javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
 254 \r
 255       javax.help.HelpBroker hb = hs.createHelpBroker();\r
 256       hb.setLocation(new Point(200, 50));\r
 257       hb.setSize(new Dimension(800,700));\r
 258       hb.setCurrentID("home");\r
 259       hb.setDisplayed(true);\r
 260    }\r
 261    catch (Exception ex)\r
 262    {\r
 263      ex.printStackTrace();\r
 264    }\r
 265  }\r
 266 \r
 267  static JInternalFrame conservationSlider;\r
 268  static JInternalFrame PIDSlider;\r
 269  public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 270  {\r
 271    SliderPanel sp = null;\r
 272 \r
 273    if(conservationSlider == null)\r
 274    {\r
 275      sp = new SliderPanel(ap, 30, true, cs);\r
 276      conservationSlider = new JInternalFrame();\r
 277      conservationSlider.setContentPane(sp);\r
 278      conservationSlider.setResizable(false);\r
 279      addInternalFrame(conservationSlider, "Conservation Colour Increment  ("+source+")", 420, 90);\r
 280      conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 281                   {\r
 282                     public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
 283                     {\r
 284                       conservationSlider = null;\r
 285                     }\r
 286                   });\r
 287    }\r
 288    else\r
 289    {\r
 290        conservationSlider.setTitle("Conservation Colour Increment  ("+source+")");\r
 291        sp = (SliderPanel)conservationSlider.getContentPane();\r
 292        sp.cs = cs;\r
 293    }\r
 294 \r
 295    if(ap.av.alignment.getGroups()!=null)\r
 296      sp.setAllGroupsCheckEnabled( true );\r
 297    else\r
 298      sp.setAllGroupsCheckEnabled( false);\r
 299 \r
 300    return sp.getValue();\r
 301 \r
 302  }\r
 303 \r
 304  public static void hideConservationSlider()\r
 305  {\r
 306   try{\r
 307     conservationSlider.setClosed(true);\r
 308     conservationSlider = null;\r
 309   }catch(Exception ex){}\r
 310 }\r
 311 \r
 312 \r
 313  public static void hidePIDSlider()\r
 314  {\r
 315    try{\r
 316      PIDSlider.setClosed(true);\r
 317      PIDSlider = null;\r
 318    }catch(Exception ex){}\r
 319  }\r
 320 \r
 321  public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
 322  {\r
 323    SliderPanel pid = null;\r
 324    if(PIDSlider == null)\r
 325    {\r
 326      pid = new SliderPanel(ap, 50, false, cs);\r
 327      PIDSlider = new JInternalFrame();\r
 328      PIDSlider.setContentPane(pid);\r
 329      PIDSlider.setResizable(false);\r
 330      addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);\r
 331    }\r
 332    else\r
 333    {\r
 334        PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
 335        pid = (SliderPanel)PIDSlider.getContentPane();\r
 336        pid.cs = cs;\r
 337    }\r
 338 \r
 339    if (ap.av.alignment.getGroups() != null)\r
 340      pid.setAllGroupsCheckEnabled(true);\r
 341    else\r
 342      pid.setAllGroupsCheckEnabled(false);\r
 343 \r
 344 \r
 345    return pid.getValue();\r
 346 \r
 347  }\r
 348 \r
 349 }\r