+ String format = jalview.io.IdentifyFile.Identify(args[0],"File");\r
+ SequenceI[] sequences = new FormatAdapter().readFile(args[0], "File", format);\r
+\r
+ if ( (sequences != null) && (sequences.length > 0))\r
+ {\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences), null);\r
+ addFrame(af, args[0], AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.statusBar.setText("Successfully loaded file " + args[0]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Displays the given URL in a new browser window\r
+ *\r
+ * @param url URL to display in browser window.\r
+ * <br>New window will be named "HELP_WINDOW"\r
+ */\r
+ public static void showURL(String url)\r
+ {\r
+ showURL(url, "HELP");\r
+ }\r
+\r
+ public static void showURL(String url, String target)\r
+ {\r
+ if(applet==null)\r
+ {\r
+ System.out.println("Not running as applet - no browser available.");\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ applet.getAppletContext().showDocument(new java.net.URL(url),\r
+ target);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ /**\r
+ * Starts a new LoadingThread for loading an alignment file\r
+ *\r
+ * @param file file name including full path to file\r
+ * @param protocol file or URL or paste\r
+ * @param format Fasta, Clustal, PFAM, MSF, PIR, BLC, Jalview\r
+ */\r
+ public void LoadFile(String file, String protocol, String format)\r
+ {\r
+ LoadingThread loader = new LoadingThread(file, protocol, format, this);\r
+ loader.start();\r
+ }\r
+\r
+ /**\r
+ * Initialises and displays a new java.awt.Frame\r
+ *\r
+ * @param frame java.awt.Frame to be displayed\r
+ * @param title title of new frame\r
+ * @param width width if new frame\r
+ * @param height height of new frame\r
+ */\r
+ public static void addFrame(final Frame frame, String title, int width,\r
+ int height)\r
+ {\r
+ frame.setLocation(lastFrameX, lastFrameY);\r
+ lastFrameX += 40;\r
+ lastFrameY += 40;\r
+ frame.setSize(width, height);\r
+ frame.setTitle(title);\r
+ frame.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ frame.dispose();\r
+ }\r
+ });\r
+ frame.setVisible(true);\r
+ }\r
+\r
+ /**\r
+ * This paints the background surrounding the "Launch Jalview button"\r
+ * <br>\r
+ * <br>If file given in parameter not found, displays error message\r
+ *\r
+ * @param g graphics context\r
+ */\r
+ public void paint(Graphics g)\r
+ {\r
+ if (!fileFound)\r
+ {\r
+ g.setColor(new Color(200, 200, 200));\r
+ g.setColor(Color.cyan);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setColor(Color.red);\r
+ g.drawString("Jalview can't open file", 5, 15);\r
+ g.drawString("\"" + file + "\"", 5, 30);\r
+ }\r
+ }\r
+\r
+ class LoadingThread extends Thread\r
+ {\r
+ String file;\r
+ String protocol;\r
+ String format;\r
+ JalviewLite jlapplet;\r
+\r
+ public LoadingThread(String file, String protocol, String format,\r
+ JalviewLite applet)\r
+ {\r
+ this.file = file;\r
+ this.protocol = protocol;\r
+ this.format = format;\r
+ this.jlapplet = applet;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ SequenceI[] sequences = null;\r
+ sequences = new FormatAdapter().readFile(file, protocol, format);\r
+\r
+ if ((sequences != null) && (sequences.length > 0))\r
+ {\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences),\r
+ jlapplet);\r
+ addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.statusBar.setText("Successfully loaded file " + file);\r
+ }\r
+ else\r
+ {\r
+ fileFound = false;\r
+ remove(launcher);\r
+ repaint();\r
+ }\r
+ }\r
+ }\r
+}\r