X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=7057e3c01afaa2edd7e0c9d614f72bb1f4da11ad;hb=4232f0a5699af84c5361e6cea446a97e7bcc788e;hp=a263ed45b834df90e516a4b1b3b06b5c2854bee1;hpb=783520af519c958e10a2af29f1d4242e1ab890a3;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index a263ed4..7057e3c 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -40,18 +40,18 @@ 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");
 
+    AlignFrame currentAlignFrame;
+
+
     /**
      * init method for Jalview Applet
      */
     public void init()
     {
-        applet = this;
-
         int r = 255;
         int g = 255;
         int b = 255;
@@ -75,13 +75,22 @@ public class JalviewLite extends Applet
 
         this.setBackground(new Color(r, g, b));
 
-        file = getParameter("file");
 
+        param = getParameter("features");
+        if(param!=null)
+        {
+          if(param.indexOf("://")==-1)
+               param = getCodeBase() + param;
+        }
+        final String featuresFile = param;
+
+        file = getParameter("file");
+        final JalviewLite applet = this;
         if (file != null)
         {
             add(launcher);
-            if(!file.startsWith("http://") && !file.startsWith("file://"))
-               file = applet.getCodeBase() + file;
+            if(file.indexOf("://")==-1)
+               file = getCodeBase() + file;
 
             launcher.addActionListener(new java.awt.event.ActionListener()
                 {
@@ -89,8 +98,13 @@ public class JalviewLite extends Applet
                     {
                         String format = jalview.io.IdentifyFile.Identify(file,
                                 "URL");
-                        LoadFile(file, "URL", format);
-                    }
+                        LoadingThread loader = new LoadingThread(file,
+                            "URL",
+                            format,
+                            featuresFile,
+                            applet);
+                        loader.start();
+                      }
                 });
         }
         else
@@ -108,7 +122,6 @@ public class JalviewLite extends Applet
         System.exit(1);
       }
 
-
       String format = jalview.io.IdentifyFile.Identify(args[0],"File");
       SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);
 
@@ -119,50 +132,6 @@ public class JalviewLite extends Applet
       }
     }
 
-    /**
-     * 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 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
@@ -190,6 +159,29 @@ public class JalviewLite extends Applet
         frame.setVisible(true);
     }
 
+    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(),
+            true, 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>
@@ -215,15 +207,20 @@ public class JalviewLite extends Applet
         String file;
         String protocol;
         String format;
-        JalviewLite jlapplet;
-
-        public LoadingThread(String file, String protocol, String format,
-            JalviewLite applet)
+        String featuresFile;
+        JalviewLite applet;
+
+        public LoadingThread(String file,
+                             String protocol,
+                             String format,
+                             String features,
+                             JalviewLite applet)
         {
             this.file = file;
             this.protocol = protocol;
             this.format = format;
-            this.jlapplet = applet;
+            featuresFile = features;
+            this.applet = applet;
         }
 
         public void run()
@@ -233,9 +230,12 @@ public class JalviewLite extends Applet
 
             if ((sequences != null) && (sequences.length > 0))
             {
-                AlignFrame af = new AlignFrame(new Alignment(sequences),
-                        jlapplet, file);
-                af.statusBar.setText("Successfully loaded file " + file);
+                currentAlignFrame = new AlignFrame(new Alignment(sequences),
+                        applet, file);
+                currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
+
+                if(featuresFile!=null)
+                  currentAlignFrame.parseFeaturesFile(featuresFile);
             }
             else
             {