X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=b99d642ecc6128158bb6e57445f53696f5ed6319;hb=ac233160f70bacfd484e371af9433a7ed226ceb4;hp=35ebecc5d8e2a577f20d32ecb53be0c2ae301cd1;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 35ebecc..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;
@@ -38,58 +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;
-        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) {
-        }
+    /**
+     * Displays the given URL in a new browser window
+     *
+     * @param url URL to display in browser window.
+     * <br>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"
+     * <br>
+     * <br>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 +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();