X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=a26b9d05b83c26ac560cbbeb3f33fb2dccdc5537;hb=a87f4c6fd568ccf29aaf3af0ad528da442ea921d;hp=2a411f743fbc04394f6b4c22d714a998b0c89dc7;hpb=a5dc530b8530620b5a879f66caf5f7d76f07ee2f;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 2a411f7..a26b9d0 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -28,83 +28,187 @@ import java.applet.*;
 
 import java.awt.*;
 import java.awt.event.*;
+import jalview.appletgui.TreePanel;
 
 
-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;
     boolean fileFound = true;
     String file = "No file";
     Button launcher = new Button("Start Jalview");
 
-    public void init() {
-        applet = this;
+    static AlignFrame currentAlignFrame;
+    boolean embedded = false;
 
-        int r=255,g=255,b=255;
+
+    /**
+     * init method for Jalview Applet
+     */
+    public void init()
+    {
+        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));
+        param = getParameter("label");
+        if(param != null)
+          launcher.setLabel(param);
+
+        this.setBackground(new Color(r, g, b));
 
         file = getParameter("file");
+        if(file.indexOf("://")==-1)
+               file = getCodeBase() + file;
 
-        if (file != null) {
+        final JalviewLite applet = this;
+        if(getParameter("embedded")!=null
+           && getParameter("embedded").equalsIgnoreCase("true"))
+        {
+          embedded = true;
+          LoadingThread loader = new LoadingThread(file,
+                            "URL",
+                            applet);
+          loader.start();
+        }
+        else if (file != null)
+        {
             add(launcher);
-            file = applet.getCodeBase() + file;
-            launcher.addActionListener(new java.awt.event.ActionListener() {
-                    public void actionPerformed(ActionEvent e) {
-                        String format = jalview.io.IdentifyFile.Identify(file,
-                                "URL");
-                        LoadFile(file, "URL", format);
-                    }
+
+            launcher.addActionListener(new java.awt.event.ActionListener()
+                {
+                    public void actionPerformed(ActionEvent e)
+                    {
+                        LoadingThread loader = new LoadingThread(file,
+                            "URL",
+                            applet);
+                        loader.start();
+                      }
                 });
-        } 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 void LoadFile(String file, String protocol, String format) {
-        LoadingThread loader = new LoadingThread(file, protocol, format, this);
-        loader.start();
+    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 = new AppletFormatAdapter().readFile(args[0], "File", format);
+
+      if ( (sequences != null) && (sequences.length > 0))
+      {
+        AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);
+        af.statusBar.setText("Successfully loaded file " + args[0]);
+      }
     }
 
+
+    /**
+     * 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)
+                {
+                    if(currentAlignFrame == frame)
+                    {
+                      currentAlignFrame = null;
+                    }
+                    lastFrameX -=40;
+                    lastFrameY-=40;
+                    frame.setMenuBar(null);
                     frame.dispose();
                 }
+                public void windowActivated(WindowEvent e)
+                {
+                  if(frame instanceof AlignFrame)
+                    currentAlignFrame = (AlignFrame)frame;
+                }
+
             });
         frame.setVisible(true);
     }
 
-    public void paint(Graphics g) {
-        if (!fileFound) {
+    public String getAlignment(String format)
+    {
+      return getAlignment(format, "true");
+    }
+
+    public String getAlignment(String format, String suffix)
+    {
+      try
+      {
+        boolean seqlimits = suffix.equalsIgnoreCase("true");
+
+        String reply = new AppletFormatAdapter().formatSequences(format,
+            currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);
+        return reply;
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+        return "Error retrieving alignment in " + format + " format. ";
+      }
+    }
+
+    /**
+     * 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);
@@ -112,33 +216,119 @@ public class JalviewLite extends Applet {
             g.drawString("Jalview can't open file", 5, 15);
             g.drawString("\"" + file + "\"", 5, 30);
         }
+        else if(embedded)
+        {
+          g.setColor(Color.black);
+          g.setFont(new Font("Arial", Font.BOLD, 24));
+          g.drawString("Jalview Applet", 50, this.size().height/2 -30);
+          g.drawString("Loading Data...", 50, this.size().height/2);
+        }
+
+
     }
 
-    class LoadingThread extends Thread {
+    class LoadingThread extends Thread
+    {
         String file;
         String protocol;
         String format;
-        JalviewLite jlapplet;
+        JalviewLite applet;
 
-        public LoadingThread(String file, String protocol, String format,
-            JalviewLite applet) {
+        public LoadingThread(String file,
+                             String protocol,
+                             JalviewLite applet)
+        {
             this.file = file;
             this.protocol = protocol;
-            this.format = format;
-            this.jlapplet = applet;
+            format = jalview.io.IdentifyFile.Identify(file, "URL");
+            this.applet = applet;
         }
 
-        public void run() {
+        public void run()
+        {
             SequenceI[] sequences = null;
-            sequences = FormatAdapter.readFile(file, protocol, format);
-
-            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 {
+            sequences = new AppletFormatAdapter().readFile(file, protocol, format);
+
+            if ((sequences != null) && (sequences.length > 0))
+            {
+              currentAlignFrame = new AlignFrame(new Alignment(sequences),
+                                                 applet, file);
+              if (embedded)
+                currentAlignFrame.setEmbedded();
+
+              currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
+
+
+                String treeFile = applet.getParameter("treeFile");
+                if (treeFile != null)
+                {
+                  if (treeFile.indexOf("://") == -1)
+                  treeFile = getCodeBase() + treeFile;
+
+                  try
+                  {
+                    jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
+                        getCodeBase() + treeFile, "URL");
+                    fin.parse();
+
+                    if (fin.getTree() != null)
+                    {
+                      TreePanel tp = null;
+                      tp = new TreePanel(currentAlignFrame.viewport,
+                                         currentAlignFrame.viewport.getAlignment().getSequences(),
+                                         fin, "FromFile", applet.getCodeBase() + treeFile);
+                      addFrame(tp, treeFile, 600, 500);
+                      currentAlignFrame.addTreeMenuItem(tp, treeFile);
+                    }
+                  }
+                  catch (Exception ex)
+                  {
+                    ex.printStackTrace();
+                  }
+              }
+
+              String param = getParameter("features");
+              if (param != null)
+              {
+                if (param.indexOf("://") == -1)
+                  param = getCodeBase() + param;
+
+                currentAlignFrame.parseFeaturesFile(param);
+              }
+
+             param = getParameter("annotations");
+             if (param != null)
+             {
+               if (param.indexOf("://") == -1)
+                 param = getCodeBase() + param;
+
+               new AnnotationReader().readAnnotationFile(
+                   currentAlignFrame.viewport.getAlignment(),
+                   param);
+
+               currentAlignFrame.alignPanel.fontChanged();
+             }
+
+
+                String pdbfile = applet.getParameter("PDBFILE");
+                if(pdbfile!=null)
+                {
+                  if(pdbfile.indexOf("://")==-1)
+                       pdbfile = getCodeBase() + pdbfile;
+
+                  String sequence = applet.getParameter("PDBSEQ");
+
+                  if(sequence!=null)
+                  {
+                    new MCview.AppletPDBViewer(pdbfile, "URL",
+                                               (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
+                                               currentAlignFrame.getSeqcanvas());
+                  }
+
+                }
+            }
+            else
+            {
                 fileFound = false;
                 remove(launcher);
                 repaint();