+ /** DOCUMENT ME!! */\r
+ public static JDesktopPane desktop;\r
+ static int openFrameCount = 0;\r
+ static final int xOffset = 30;\r
+ static final int yOffset = 30;\r
+\r
+ /**\r
+ * Creates a new Desktop object.\r
+ */\r
+ public Desktop()\r
+ {\r
+ Image image = null;\r
+\r
+ try\r
+ {\r
+ java.net.URL url = getClass().getResource("/images/logo.gif");\r
+\r
+ if (url != null)\r
+ {\r
+ image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+\r
+ MediaTracker mt = new MediaTracker(this);\r
+ mt.addImage(image, 0);\r
+ mt.waitForID(0);\r
+ // setIconImage(image);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ setTitle("Jalview 2005");\r
+ setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
+ desktop = new JDesktopPane();\r
+ desktop.setBackground(Color.white);\r
+ setContentPane(desktop);\r
+ desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
+\r
+ // This line prevents Windows Look&Feel resizing all new windows to maximum\r
+ // if previous window was maximised\r
+ desktop.setDesktopManager(new DefaultDesktopManager());\r
+\r
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
+ String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
+ String y = jalview.bin.Cache.getProperty("SCREEN_Y");\r
+ String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
+ String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
+\r
+ if ((x != null) && (y != null) && (width != null) && (height != null))\r
+ {\r
+ setBounds(Integer.parseInt(x), Integer.parseInt(y),\r
+ Integer.parseInt(width), Integer.parseInt(height));\r
+ }\r
+ else\r
+ {\r
+ setBounds((int) (screenSize.width - 900) / 2,\r
+ (int) (screenSize.height - 650) / 2, 900, 650);\r
+ }\r
+\r
+ this.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ quit();\r
+ }\r
+ });\r
+\r
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
+\r
+ /////////Add a splashscreen on startup\r
+ /////////Add a splashscreen on startup\r
+ JInternalFrame frame = new JInternalFrame();\r
+\r
+ SplashScreen splash = new SplashScreen(frame, image);\r
+ frame.setContentPane(splash);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ addInternalFrame(frame, "", 750, 160, false);\r
+ frame.setLocation((int) ((getWidth() - 750) / 2),\r
+ (int) ((getHeight() - 160) / 2));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param frame DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ * @param w DOCUMENT ME!\r
+ * @param h DOCUMENT ME!\r
+ */\r
+ public static void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h)\r
+ {\r
+ addInternalFrame(frame, title, w, h, true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param frame DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ * @param w DOCUMENT ME!\r
+ * @param h DOCUMENT ME!\r
+ * @param resizable DOCUMENT ME!\r
+ */\r
+ public static void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h, boolean resizable)\r
+ {\r
+ desktop.add(frame);\r
+ openFrameCount++;\r
+\r
+ try\r
+ {\r
+ frame.setSelected(true);\r
+ }\r
+ catch (java.beans.PropertyVetoException e)\r
+ {\r
+ }\r
+\r
+ frame.setTitle(title);\r
+ frame.setSize(w, h);\r
+ frame.setClosable(true);\r
+ frame.setResizable(resizable);\r
+ frame.setMaximizable(resizable);\r
+ frame.setIconifiable(resizable);\r
+ frame.setFrameIcon(null);\r
+ frame.setLocation(xOffset * openFrameCount, yOffset * openFrameCount);\r
+ frame.toFront();\r
+\r
+ final JMenuItem menuItem = new JMenuItem(title);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ openFrameCount--;\r
+ windowMenu.remove(menuItem);\r
+ }\r
+ ;\r
+ });\r
+\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ frame.setSelected(true);\r
+ frame.setIcon(false);\r
+ }\r
+ catch (java.beans.PropertyVetoException ex)\r
+ {\r
+ }\r
+\r
+ ;\r
+ }\r
+ });\r
+\r
+ frame.setVisible(true);\r
+ windowMenu.add(menuItem);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void dragEnter(DropTargetDragEvent evt)\r
+ {\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void dragExit(DropTargetEvent evt)\r
+ {\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void dragOver(DropTargetDragEvent evt)\r
+ {\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void dropActionChanged(DropTargetDragEvent evt)\r
+ {\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void drop(DropTargetDropEvent evt)\r
+ {\r
+ Transferable t = evt.getTransferable();\r
+\r
+ if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+ {\r
+ return;\r
+ }\r
+\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+\r
+ try\r
+ {\r
+ java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
+\r
+ for (int i = 0; i < files.size(); i++)\r
+ {\r
+ String file = files.get(i).toString();\r
+ String protocol = "File";\r
+ String format = null;\r
+\r
+ if (file.endsWith(".jar"))\r
+ {\r
+ format = "Jalview";\r
+\r
+ }\r
+ else\r
+ {\r
+ format = jalview.io.IdentifyFile.Identify(file,\r
+ protocol);\r
+ }\r
+ LoadFile(file, protocol, format);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"),\r
+ new String[]\r
+ {\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\r
+ {\r
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Open local file");\r
+ chooser.setToolTipText("Open");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ String format = null;\r
+ if (chooser.getSelectedFormat().equals("Jalview"))\r
+ {\r
+ format = "Jalview";\r
+ }\r
+ else\r
+ {\r
+ format = IdentifyFile.Identify(choice, "File");\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
+ LoadFile(choice, "File", format);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ * @param protocol DOCUMENT ME!\r
+ * @param format DOCUMENT ME!\r
+ */\r
+ public void LoadFile(String file, String protocol, String format)\r
+ {\r
+ LoadingThread loader = new LoadingThread(file, protocol, format);\r
+ loader.start();\r
+ }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ * @param protocol DOCUMENT ME!\r
+ * @param format DOCUMENT ME!\r
+ */\r
+ public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, String format)\r
+ {\r
+ LoadingThread loader = new LoadingThread(file, protocol, format);\r
+ loader.start();\r
+\r
+ while (loader.isAlive())\r
+ {\r
+ try\r
+ {\r
+ Thread.sleep(50);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+ }\r
+\r
+ return loader.af;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ String url = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Enter url of input file", "Input alignment from URL",\r
+ JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")\r
+ .toString();\r
+\r
+ if (url == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (url.trim().toLowerCase().endsWith(".jar"))\r
+ {\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");\r
+ Jalview2XML.LoadJalviewAlign(url);\r
+ }\r
+ else\r
+ {\r
+\r
+ String format = IdentifyFile.Identify(url, "URL");\r
+\r
+ if (format.equals("URL NOT FOUND"))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't locate " + url,\r
+ "URL not found",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ LoadFile(url, "URL", format);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput();\r
+ Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
+ }\r
+\r
+ /*\r
+ * Exit the program\r
+ */\r
+ public void quit()\r
+ {\r
+ jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
+ System.exit(0);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void aboutMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ StringBuffer message = new StringBuffer("JalView 2005 version " +\r
+ jalview.bin.Cache.getProperty(\r
+ "VERSION") +\r
+ "; last updated: " +\r
+ jalview.bin.\r
+ Cache.getProperty("BUILD_DATE"));\r
+\r
+ if (!jalview.bin.Cache.getProperty("jalview.version").equals(\r
+ jalview.bin.Cache.getProperty("VERSION")))\r