- public LoadingThread(String file, String protocol, String format, JalviewLite applet)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
- this.jlapplet = applet;\r
- }\r
- public void run()\r
- {\r
- SequenceI [] sequences = null;\r
- sequences = FormatAdapter.readFile(file, protocol, format);\r
-\r
- if (sequences != null && sequences.length>0)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences), jlapplet );\r
- addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, 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
+ /**\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
+ if(currentAlignFrame == frame)\r
+ {\r
+ currentAlignFrame = null;\r
+ }\r
+ lastFrameX -=40;\r
+ lastFrameY -=40;\r
+ frame.setMenuBar(null);\r
+ frame.dispose();\r
+ }\r
+ public void windowActivated(WindowEvent e)\r
+ {\r
+ if(frame instanceof AlignFrame)\r
+ currentAlignFrame = (AlignFrame)frame;\r
+ }\r
+\r
+ });\r
+ frame.setVisible(true);\r
+ }\r
+\r
+ public String getSelectedSequences()\r
+ {\r
+ StringBuffer result = new StringBuffer("");\r
+\r
+ if(initialAlignFrame.viewport.getSelectionGroup()!=null)\r
+ {\r
+ SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().\r
+ getSequencesInOrder(\r
+ initialAlignFrame.viewport.getAlignment());\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ result.append(seqs[i].getName() + "¬");\r
+ }\r
+\r
+ return result.toString();\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
+ {\r
+ ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\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
+ else if(embedded)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.setFont(new Font("Arial", Font.BOLD, 24));\r
+ g.drawString("Jalview Applet", 50, this.size().height/2 -30);\r
+ g.drawString("Loading Data...", 50, this.size().height/2);\r
+ }\r
+\r
+\r
+ }\r
+\r
+ class LoadingThread extends Thread\r
+ {\r
+ String file;\r
+ String protocol;\r
+ String format;\r
+ JalviewLite applet;\r
+\r
+ public LoadingThread(String _file,\r
+ JalviewLite _applet)\r
+ {\r
+ file = _file;\r
+ if(inArchive(file))\r
+ protocol = AppletFormatAdapter.CLASSLOADER;\r
+ else\r
+ {\r
+ file = addProtocol(file);\r
+ protocol = AppletFormatAdapter.URL;\r
+ }\r
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
+ applet = _applet;\r
+ }\r