+ if ( (sequences != null) && (sequences.length > 0))\r
+ {\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);\r
+ af.statusBar.setText("Successfully loaded file " + args[0]);\r
+ }\r
+ }\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
+ public String getAlignment(String format)\r
+ {\r
+ return getAlignment(format, "true");\r
+ }\r
+\r
+ public String getAlignment(String format, String suffix)\r
+ {\r
+ try\r
+ {\r
+ boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+\r
+ String reply = new AppletFormatAdapter().formatSequences(format,\r
+ currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);\r
+ return reply;\r
+ }\r
+ catch (Exception ex)\r
+ {ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+\r
+ }\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
+ String featuresFile;\r
+ JalviewLite applet;\r
+\r
+ public LoadingThread(String file,\r
+ String protocol,\r
+ String format,\r
+ String features,\r
+ JalviewLite applet)\r
+ {\r
+ this.file = file;\r
+ this.protocol = protocol;\r
+ this.format = format;\r
+ featuresFile = features;\r
+ this.applet = applet;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ SequenceI[] sequences = null;\r
+ sequences = new AppletFormatAdapter().readFile(file, protocol, format);\r
+\r
+ if ((sequences != null) && (sequences.length > 0))\r
+ {\r
+ currentAlignFrame = new AlignFrame(new Alignment(sequences),\r
+ applet, file);\r
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
+\r
+ if(featuresFile!=null)\r
+ currentAlignFrame.parseFeaturesFile(featuresFile);\r
+ }\r
+ else\r
+ {\r
+ fileFound = false;\r
+ remove(launcher);\r
+ repaint();\r
+ }\r
+ }\r
+ }\r
+}\r