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 import java.awt.dnd.*;\r
  20 import javax.swing.*;\r
  21 import java.awt.datatransfer.*;\r
  22 import java.io.*;\r
  23 \r
  24 \r
  25 public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener\r
  26 {\r
  27   public static JDesktopPane desktop;\r
  28   static int openFrameCount = 0;\r
  29   static final int xOffset = 30, yOffset = 30;\r
  30 \r
  31   public Desktop()\r
  32   {\r
  33     Image image =null;\r
  34     try{\r
  35       java.net.URL url = getClass().getResource("/images/logo.gif");\r
  36       if(url!=null)\r
  37       {\r
  38         image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
  39         MediaTracker mt = new MediaTracker(this);\r
  40         mt.addImage(image, 0);\r
  41         mt.waitForID(0);\r
  42         setIconImage(image);\r
  43       }\r
  44 \r
  45     }catch(Exception ex){}\r
  46 \r
  47     setTitle("Jalview 2005");\r
  48     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
  49     desktop = new JDesktopPane();\r
  50  //   desktop.setBackground(Color.white);\r
  51     setContentPane(desktop);\r
  52     desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
  53 \r
  54 \r
  55     // This line prevents Windows Look&Feel resizing all new windows to maximum\r
  56     // if previous window was maximised\r
  57     desktop.setDesktopManager( new DefaultDesktopManager() );\r
  58 \r
  59 \r
  60     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
  61     String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
  62     String y = jalview.bin.Cache.getProperty("SCREEN_Y");\r
  63     String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
  64     String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
  65 \r
  66     if(x!=null && y!=null && width!=null && height!=null)\r
  67     {\r
  68       setBounds( Integer.parseInt(x), Integer.parseInt(y),\r
  69                  Integer.parseInt(width), Integer.parseInt(height));\r
  70     }\r
  71     else\r
  72       setBounds( (int)(screenSize.width-900)/2,\r
  73            (int)(screenSize.height-650)/2,\r
  74           900 ,\r
  75           650);\r
  76 \r
  77 this.addWindowListener(new WindowAdapter()\r
  78 {\r
  79 public void windowClosing(WindowEvent evt)\r
  80 {\r
  81  jalview.bin.Cache.setProperty("SCREEN_X",\r
  82                                getBounds().x + "");\r
  83  jalview.bin.Cache.setProperty("SCREEN_Y",\r
  84                                getBounds().y + "");\r
  85  jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
  86  jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
  87 }\r
  88 });\r
  89 setVisible(true);\r
  90 \r
  91 this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
  92 \r
  93 /////////Add a splashscreen on startup\r
  94    /////////Add a splashscreen on startup\r
  95     JInternalFrame frame = new JInternalFrame();\r
  96 \r
  97     SplashScreen splash = new SplashScreen(frame, image);\r
  98     frame.setContentPane(splash);\r
  99     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
 100     addInternalFrame(frame, "", 750,160, false);\r
 101     frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));\r
 102   }\r
 103   public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
 104   {\r
 105     addInternalFrame(frame, title, w, h, true);\r
 106   }\r
 107 \r
 108   public static void addInternalFrame(final JInternalFrame frame, String title,\r
 109                                       int w,\r
 110                                       int h,\r
 111                                       boolean resizable )\r
 112   {\r
 113    desktop.add(frame);\r
 114    openFrameCount++;\r
 115    try {\r
 116        frame.setSelected(true);\r
 117    } catch (java.beans.PropertyVetoException e) {}\r
 118    frame.setTitle(title);\r
 119    frame.setSize(w,h);\r
 120    frame.setClosable(true);\r
 121    frame.setResizable(resizable);\r
 122    frame.setMaximizable(resizable);\r
 123    frame.setIconifiable(resizable);\r
 124    frame.setFrameIcon(null);\r
 125    frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
 126    frame.toFront();\r
 127    final JMenuItem menuItem = new JMenuItem(title);\r
 128    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
 129                                    { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
 130                                      {\r
 131                                        openFrameCount--;\r
 132                                        windowMenu.remove(menuItem);\r
 133                                      };\r
 134                                    });\r
 135 \r
 136    menuItem.addActionListener(new ActionListener()\r
 137     {\r
 138       public void actionPerformed(ActionEvent e)\r
 139       {\r
 140         try{  frame.setSelected(true);   frame.setIcon(false); }\r
 141         catch(java.beans.PropertyVetoException ex){};\r
 142       }\r
 143     });\r
 144 \r
 145    frame.setVisible(true);\r
 146    windowMenu.add(menuItem);\r
 147  }\r
 148 \r
 149  public void dragEnter(DropTargetDragEvent evt){}\r
 150  public void dragExit(DropTargetEvent evt){}\r
 151  public void dragOver(DropTargetDragEvent evt){}\r
 152  public void dropActionChanged(DropTargetDragEvent evt){}\r
 153  public void drop(DropTargetDropEvent evt)\r
 154 {\r
 155    Transferable t = evt.getTransferable();\r
 156    if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
 157      return;\r
 158 \r
 159    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
 160    try{\r
 161      java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
 162 \r
 163      for (int i = 0; i < files.size(); i++)\r
 164      {\r
 165        String file = files.get(i).toString();\r
 166        String protocol = "File";\r
 167        String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
 168        LoadFile(file, protocol, format);\r
 169      }\r
 170 \r
 171    }catch(Exception ex){ex.printStackTrace();}\r
 172   }\r
 173 \r
 174  public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
 175  {\r
 176    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
 177        new String[]{"fa", "fasta", "fastq", "blc", "msf", "pfam", "aln", "pir"}, "Alignment files");\r
 178    chooser.setFileView(new JalviewFileView());\r
 179    chooser.setDialogTitle("Open local file");\r
 180    chooser.setToolTipText("Open");\r
 181    int value = chooser.showOpenDialog(this);\r
 182    if(value == JalviewFileChooser.APPROVE_OPTION)\r
 183    {\r
 184      String choice =  chooser.getSelectedFile().getPath();\r
 185      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
 186      String format = IdentifyFile.Identify(choice, "File");\r
 187      LoadFile(choice, "File", format);\r
 188    }\r
 189  }\r
 190 \r
 191  public void LoadFile(String file, String protocol,  String format)\r
 192  {\r
 193    SequenceI [] sequences = null;\r
 194 \r
 195    if (FormatProperties.contains(format))\r
 196        sequences = FormatAdapter.read(file, protocol, format);\r
 197 \r
 198    if (sequences != null && sequences.length>0)\r
 199    {\r
 200      AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 201      addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
 202      af.statusBar.setText("Successfully loaded file " + file);\r
 203 \r
 204    }\r
 205    else\r
 206      JOptionPane.showInternalMessageDialog(Desktop.desktop,  "Couldn't open file.\n"\r
 207                           + "Formats currently supported are\n"\r
 208                           + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM" // JBPNote - message should be generated through FormatAdapter!\r
 209                           ,"Error loading file",\r
 210                                    JOptionPane.WARNING_MESSAGE);\r
 211 \r
 212  }\r
 213 \r
 214  public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
 215  {\r
 216    String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
 217                                             "Input alignment from URL",\r
 218                                             JOptionPane.QUESTION_MESSAGE);\r
 219    if (url == null)\r
 220      return;\r
 221 \r
 222    String format = IdentifyFile.Identify(url, "URL");\r
 223 \r
 224    if (format.equals("URL NOT FOUND"))\r
 225    {\r
 226      JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
 227                                    "URL not found",\r
 228                                    JOptionPane.WARNING_MESSAGE);\r
 229      return;\r
 230    }\r
 231 \r
 232     LoadFile(url, "URL", format);\r
 233  }\r
 234 \r
 235  public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
 236  {\r
 237    CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
 238    int accept =  JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
 239                                        JOptionPane.YES_NO_CANCEL_OPTION,\r
 240                                        JOptionPane.PLAIN_MESSAGE,\r
 241                                        null,\r
 242                                        new Object[]{"Accept", "Cancel", }, null);\r
 243 \r
 244 \r
 245   if(accept == JOptionPane.YES_OPTION)\r
 246   {\r
 247     String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
 248     SequenceI [] sequences = null;\r
 249 \r
 250     if (FormatProperties.contains( format ))\r
 251       sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
 252 \r
 253 \r
 254       if(sequences!=null)\r
 255       {\r
 256         AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 257         addInternalFrame(af, "Cut & Paste input - "+format,\r
 258                          AlignFrame.NEW_WINDOW_WIDTH,\r
 259                          AlignFrame.NEW_WINDOW_HEIGHT);\r
 260         af.statusBar.setText("Successfully pasted alignment file");\r
 261       }\r
 262       else\r
 263         JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
 264                                       +"Formats currently supported are\n"\r
 265                                       +"Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM",\r
 266                                       "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
 267 \r
 268    }\r
 269  }\r
 270 \r
 271 /*\r
 272 * Exit the program\r
 273 */\r
 274  public void quit_actionPerformed(ActionEvent e)\r
 275  {\r
 276    if(jalview.bin.Jalview.applet!=null)\r
 277      jalview.bin.Jalview.applet.destroy();\r
 278     else\r
 279       System.exit(0);\r
 280  }\r
 281 \r
 282 \r
 283 \r
 284  public void aboutMenuItem_actionPerformed(ActionEvent e)\r
 285  {\r
 286    JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 287                                          "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE\r
 288                                        +"\nAuthors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
 289                                        +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
 290                                        +"\nIf  you use JalView, please cite:"\r
 291                                        +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""\r
 292                                        +"\nBioinformatics,  2004 12;426-7.",\r
 293                                          "About Jalview",\r
 294                                          JOptionPane.INFORMATION_MESSAGE);\r
 295  }\r
 296 \r
 297  public void documentationMenuItem_actionPerformed(ActionEvent e)\r
 298  {\r
 299    try\r
 300    {\r
 301       ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
 302       java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
 303       javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
 304 \r
 305       javax.help.HelpBroker hb = hs.createHelpBroker();\r
 306       hb.setLocation(new Point(200, 50));\r
 307       hb.setSize(new Dimension(800,700));\r
 308       hb.setCurrentID("home");\r
 309       hb.setDisplayed(true);\r
 310    }\r
 311    catch (Exception ex)\r
 312    {\r
 313      ex.printStackTrace();\r
 314    }\r
 315  }\r
 316 }\r