X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=b99d642ecc6128158bb6e57445f53696f5ed6319;hb=74e4d71835fd0031dd7c309e37ec6bf934e4de4a;hp=2a411f743fbc04394f6b4c22d714a998b0c89dc7;hpb=a5dc530b8530620b5a879f66caf5f7d76f07ee2f;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 2a411f7..b99d642 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -30,7 +30,14 @@ import java.awt.*;
import java.awt.event.*;
-public class JalviewLite extends Applet {
+/**
+ * Jalview Applet. Runs in Java 1.18 runtime
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class JalviewLite extends Applet
+{
static int lastFrameX = 200;
static int lastFrameY = 200;
static Applet applet;
@@ -38,73 +45,134 @@ public class JalviewLite extends Applet {
String file = "No file";
Button launcher = new Button("Start Jalview");
- public void init() {
+ /**
+ * init method for Jalview Applet
+ */
+ public void init()
+ {
applet = this;
- int r=255,g=255,b=255;
+ int r = 255;
+ int g = 255;
+ int b = 255;
String param = getParameter("RGB");
- if(param!=null)
+
+ if (param != null)
{
- try
- {
- r = Integer.parseInt(param.substring(0,2),16);
- g = Integer.parseInt(param.substring(2,4),16);
- b = Integer.parseInt(param.substring(4,6),16);
- }
- catch (Exception ex)
- { r=255;g=255;b=255; }
+ try
+ {
+ r = Integer.parseInt(param.substring(0, 2), 16);
+ g = Integer.parseInt(param.substring(2, 4), 16);
+ b = Integer.parseInt(param.substring(4, 6), 16);
+ }
+ catch (Exception ex)
+ {
+ r = 255;
+ g = 255;
+ b = 255;
+ }
}
- this.setBackground(new Color(r,g,b));
+ this.setBackground(new Color(r, g, b));
file = getParameter("file");
- if (file != null) {
+ if (file != null)
+ {
add(launcher);
file = applet.getCodeBase() + file;
- launcher.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent e) {
+ launcher.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
String format = jalview.io.IdentifyFile.Identify(file,
"URL");
LoadFile(file, "URL", format);
}
});
- } else {
+ }
+ else
+ {
file = "NO FILE";
fileFound = false;
}
}
- public static void showURL(String url) {
- try {
- applet.getAppletContext().showDocument(new java.net.URL(url),
- "HELP_WINDOW");
- } catch (Exception ex) {
- }
+ /**
+ * Displays the given URL in a new browser window
+ *
+ * @param url URL to display in browser window.
+ *
New window will be named "HELP_WINDOW"
+ */
+ public static void showURL(String url)
+ {
+ showURL(url, "HELP");
}
- public void LoadFile(String file, String protocol, String format) {
+ public static void showURL(String url, String target)
+ {
+ try
+ {
+ applet.getAppletContext().showDocument(new java.net.URL(url),
+ target);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+
+ /**
+ * Starts a new LoadingThread for loading an alignment file
+ *
+ * @param file file name including full path to file
+ * @param protocol file or URL or paste
+ * @param format Fasta, Clustal, PFAM, MSF, PIR, BLC, Jalview
+ */
+ public void LoadFile(String file, String protocol, String format)
+ {
LoadingThread loader = new LoadingThread(file, protocol, format, this);
loader.start();
}
+ /**
+ * Initialises and displays a new java.awt.Frame
+ *
+ * @param frame java.awt.Frame to be displayed
+ * @param title title of new frame
+ * @param width width if new frame
+ * @param height height of new frame
+ */
public static void addFrame(final Frame frame, String title, int width,
- int height) {
+ int height)
+ {
frame.setLocation(lastFrameX, lastFrameY);
lastFrameX += 40;
lastFrameY += 40;
frame.setSize(width, height);
frame.setTitle(title);
- frame.addWindowListener(new WindowAdapter() {
- public void windowClosing(WindowEvent e) {
+ frame.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent e)
+ {
frame.dispose();
}
});
frame.setVisible(true);
}
- public void paint(Graphics g) {
- if (!fileFound) {
+ /**
+ * This paints the background surrounding the "Launch Jalview button"
+ *
+ *
If file given in parameter not found, displays error message
+ *
+ * @param g graphics context
+ */
+ public void paint(Graphics g)
+ {
+ if (!fileFound)
+ {
g.setColor(new Color(200, 200, 200));
g.setColor(Color.cyan);
g.fillRect(0, 0, getSize().width, getSize().height);
@@ -114,31 +182,37 @@ public class JalviewLite extends Applet {
}
}
- class LoadingThread extends Thread {
+ class LoadingThread extends Thread
+ {
String file;
String protocol;
String format;
JalviewLite jlapplet;
public LoadingThread(String file, String protocol, String format,
- JalviewLite applet) {
+ JalviewLite applet)
+ {
this.file = file;
this.protocol = protocol;
this.format = format;
this.jlapplet = applet;
}
- public void run() {
+ public void run()
+ {
SequenceI[] sequences = null;
sequences = FormatAdapter.readFile(file, protocol, format);
- if ((sequences != null) && (sequences.length > 0)) {
+ if ((sequences != null) && (sequences.length > 0))
+ {
AlignFrame af = new AlignFrame(new Alignment(sequences),
jlapplet);
addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
AlignFrame.NEW_WINDOW_HEIGHT);
af.statusBar.setText("Successfully loaded file " + file);
- } else {
+ }
+ else
+ {
fileFound = false;
remove(launcher);
repaint();