X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=7057e3c01afaa2edd7e0c9d614f72bb1f4da11ad;hb=b1f3b63568afc23462caff32f3001ecb36ff2a57;hp=8f4838580d1059d2f34cd42e319c9c4fbe397358;hpb=937fb5ceb241d72ce5e829bf36a1382d6e13510c;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 8f48385..7057e3c 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -43,7 +43,8 @@ public class JalviewLite extends Applet
     boolean fileFound = true;
     String file = "No file";
     Button launcher = new Button("Start Jalview");
-    public static boolean AWT1 = false;
+
+    AlignFrame currentAlignFrame;
 
 
     /**
@@ -51,10 +52,6 @@ public class JalviewLite extends Applet
      */
     public void init()
     {
-        String version = System.getProperty("java.version");
-        if (version.indexOf("1.1") == 0)
-          AWT1 = true;
-
         int r = 255;
         int g = 255;
         int b = 255;
@@ -162,6 +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>
@@ -210,12 +230,12 @@ public class JalviewLite extends Applet
 
             if ((sequences != null) && (sequences.length > 0))
             {
-                AlignFrame af = new AlignFrame(new Alignment(sequences),
+                currentAlignFrame = new AlignFrame(new Alignment(sequences),
                         applet, file);
-                af.statusBar.setText("Successfully loaded file " + file);
+                currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
 
                 if(featuresFile!=null)
-                  af.parseFeaturesFile(featuresFile);
+                  currentAlignFrame.parseFeaturesFile(featuresFile);
             }
             else
             {