Remove static refs to applet

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index a263ed4..8f48385 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -40,17 +40,20 @@ public class JalviewLite extends Applet
 {\r
     static int lastFrameX = 200;\r
     static int lastFrameY = 200;\r
-    static Applet applet;\r
     boolean fileFound = true;\r
     String file = "No file";\r
     Button launcher = new Button("Start Jalview");\r
+    public static boolean AWT1 = false;\r
+\r
 \r
     /**\r
      * init method for Jalview Applet\r
      */\r
     public void init()\r
     {\r
-        applet = this;\r
+        String version = System.getProperty("java.version");\r
+        if (version.indexOf("1.1") == 0)\r
+          AWT1 = true;\r
 \r
         int r = 255;\r
         int g = 255;\r
@@ -75,13 +78,22 @@ public class JalviewLite extends Applet
 \r
         this.setBackground(new Color(r, g, b));\r
 \r
-        file = getParameter("file");\r
 \r
+        param = getParameter("features");\r
+        if(param!=null)\r
+        {\r
+          if(param.indexOf("://")==-1)\r
+               param = getCodeBase() + param;\r
+        }\r
+        final String featuresFile = param;\r
+\r
+        file = getParameter("file");\r
+        final JalviewLite applet = this;\r
         if (file != null)\r
         {\r
             add(launcher);\r
-            if(!file.startsWith("http://") && !file.startsWith("file://"))\r
-               file = applet.getCodeBase() + file;\r
+            if(file.indexOf("://")==-1)\r
+               file = getCodeBase() + file;\r
 \r
             launcher.addActionListener(new java.awt.event.ActionListener()\r
                 {\r
@@ -89,8 +101,13 @@ public class JalviewLite extends Applet
                     {\r
                         String format = jalview.io.IdentifyFile.Identify(file,\r
                                 "URL");\r
-                        LoadFile(file, "URL", format);\r
-                    }\r
+                        LoadingThread loader = new LoadingThread(file,\r
+                            "URL",\r
+                            format,\r
+                            featuresFile,\r
+                            applet);\r
+                        loader.start();\r
+                      }\r
                 });\r
         }\r
         else\r
@@ -108,7 +125,6 @@ public class JalviewLite extends Applet
         System.exit(1);\r
       }\r
 \r
-\r
       String format = jalview.io.IdentifyFile.Identify(args[0],"File");\r
       SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);\r
 \r
@@ -119,50 +135,6 @@ public class JalviewLite extends Applet
       }\r
     }\r
 \r
-    /**\r
-     * Displays the given URL in a new browser window\r
-     *\r
-     * @param url URL to display in browser window.\r
-     * <br>New window will be named "HELP_WINDOW"\r
-     */\r
-    public static void showURL(String url)\r
-    {\r
-      showURL(url, "HELP");\r
-    }\r
-\r
-      public static void showURL(String url, String target)\r
-      {\r
-        if(applet==null)\r
-        {\r
-          System.out.println("Not running as applet - no browser available.");\r
-        }\r
-        else\r
-        {\r
-          try\r
-          {\r
-            applet.getAppletContext().showDocument(new java.net.URL(url),\r
-                target);\r
-          }\r
-          catch (Exception ex)\r
-          {\r
-            ex.printStackTrace();\r
-          }\r
-        }\r
-      }\r
-\r
-\r
-    /**\r
-     * Starts a new LoadingThread for loading an alignment file\r
-     *\r
-     * @param file file name including full path to file\r
-     * @param protocol file or URL or paste\r
-     * @param format Fasta, Clustal, PFAM, MSF, PIR, BLC, Jalview\r
-     */\r
-    public void LoadFile(String file, String protocol, String format)\r
-    {\r
-        LoadingThread loader = new LoadingThread(file, protocol, format, this);\r
-        loader.start();\r
-    }\r
 \r
     /**\r
      * Initialises and displays a new java.awt.Frame\r
@@ -215,15 +187,20 @@ public class JalviewLite extends Applet
         String file;\r
         String protocol;\r
         String format;\r
-        JalviewLite jlapplet;\r
-\r
-        public LoadingThread(String file, String protocol, String format,\r
-            JalviewLite applet)\r
+        String featuresFile;\r
+        JalviewLite applet;\r
+\r
+        public LoadingThread(String file,\r
+                             String protocol,\r
+                             String format,\r
+                             String features,\r
+                             JalviewLite applet)\r
         {\r
             this.file = file;\r
             this.protocol = protocol;\r
             this.format = format;\r
-            this.jlapplet = applet;\r
+            featuresFile = features;\r
+            this.applet = applet;\r
         }\r
 \r
         public void run()\r
@@ -234,8 +211,11 @@ public class JalviewLite extends Applet
             if ((sequences != null) && (sequences.length > 0))\r
             {\r
                 AlignFrame af = new AlignFrame(new Alignment(sequences),\r
-                        jlapplet, file);\r
+                        applet, file);\r
                 af.statusBar.setText("Successfully loaded file " + file);\r
+\r
+                if(featuresFile!=null)\r
+                  af.parseFeaturesFile(featuresFile);\r
             }\r
             else\r
             {\r