import java.awt.event.*;\r
\r
\r
-public class JalviewLite extends Applet {\r
+/**\r
+ * Jalview Applet. Runs in Java 1.18 runtime\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class JalviewLite extends Applet\r
+{\r
static int lastFrameX = 200;\r
static int lastFrameY = 200;\r
static Applet applet;\r
String file = "No file";\r
Button launcher = new Button("Start Jalview");\r
\r
- public void init() {\r
+ /**\r
+ * init method for Jalview Applet\r
+ */\r
+ public void init()\r
+ {\r
applet = this;\r
\r
- int r=255,g=255,b=255;\r
+ int r = 255;\r
+ int g = 255;\r
+ int b = 255;\r
String param = getParameter("RGB");\r
- if(param!=null)\r
+\r
+ if (param != null)\r
{\r
- try\r
- {\r
- r = Integer.parseInt(param.substring(0,2),16);\r
- g = Integer.parseInt(param.substring(2,4),16);\r
- b = Integer.parseInt(param.substring(4,6),16);\r
- }\r
- catch (Exception ex)\r
- { r=255;g=255;b=255; }\r
+ try\r
+ {\r
+ r = Integer.parseInt(param.substring(0, 2), 16);\r
+ g = Integer.parseInt(param.substring(2, 4), 16);\r
+ b = Integer.parseInt(param.substring(4, 6), 16);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ r = 255;\r
+ g = 255;\r
+ b = 255;\r
+ }\r
}\r
\r
- this.setBackground(new Color(r,g,b));\r
+ this.setBackground(new Color(r, g, b));\r
\r
file = getParameter("file");\r
\r
- if (file != null) {\r
+ if (file != null)\r
+ {\r
add(launcher);\r
file = applet.getCodeBase() + file;\r
- launcher.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
+ launcher.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
String format = jalview.io.IdentifyFile.Identify(file,\r
"URL");\r
LoadFile(file, "URL", format);\r
}\r
});\r
- } else {\r
+ }\r
+ else\r
+ {\r
file = "NO FILE";\r
fileFound = false;\r
}\r
}\r
\r
- public static void showURL(String url) {\r
- try {\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
+ try\r
+ {\r
applet.getAppletContext().showDocument(new java.net.URL(url),\r
"HELP_WINDOW");\r
- } catch (Exception ex) {\r
+ }\r
+ catch (Exception ex)\r
+ {\r
}\r
}\r
\r
- public void LoadFile(String file, String protocol, String format) {\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
+ 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
- public void windowClosing(WindowEvent e) {\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 void paint(Graphics g) {\r
- if (!fileFound) {\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
}\r
}\r
\r
- class LoadingThread extends Thread {\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
+ 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
+ public void run()\r
+ {\r
SequenceI[] sequences = null;\r
sequences = FormatAdapter.readFile(file, protocol, format);\r
\r
- if ((sequences != null) && (sequences.length > 0)) {\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
- } else {\r
+ }\r
+ else\r
+ {\r
fileFound = false;\r
remove(launcher);\r
repaint();\r
git://source.jalview.org / jalview.git / blobdiff