X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=c9ec3918e3f65231aced553aeaf2cc9372c6ed6d;hb=9344c308a62c48e2ddedd12247edab74e581c2e7;hp=35ebecc5d8e2a577f20d32ecb53be0c2ae301cd1;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 35ebecc..c9ec391 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;
@@ -38,58 +45,161 @@ 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;
- this.setBackground(Color.white);
+
+ int r = 255;
+ int g = 255;
+ int b = 255;
+ String param = getParameter("RGB");
+
+ 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;
+ }
+ }
+
+ 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) {
- }
+ public static void main(String [] args)
+ {
+ if(args.length!=1)
+ {
+ System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
+ System.exit(1);
+ }
+
+ String format = jalview.io.IdentifyFile.Identify(args[0],"File");
+ SequenceI[] sequences = FormatAdapter.readFile(args[0], "File", format);
+
+ if ( (sequences != null) && (sequences.length > 0))
+ {
+ AlignFrame af = new AlignFrame(new Alignment(sequences), null);
+ addFrame(af, args[0], AlignFrame.NEW_WINDOW_WIDTH,
+ AlignFrame.NEW_WINDOW_HEIGHT);
+ af.statusBar.setText("Successfully loaded file " + args[0]);
+ }
+ }
+
+ /**
+ * 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)
+ {
+ if(applet==null)
+ {
+ System.out.println("Not running as applet - no browser available.");
+ }
+ else
+ {
+ 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);
@@ -99,31 +209,37 @@ 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();