X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=4e4f943d268cbb6743ea5df95300878e6d0d9ef2;hb=a0d1b1826f8ab0792c589946746d52ad0316fc99;hp=8f4838580d1059d2f34cd42e319c9c4fbe397358;hpb=937fb5ceb241d72ce5e829bf36a1382d6e13510c;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 8f48385..4e4f943 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -45,6 +45,8 @@ public class JalviewLite extends Applet
     Button launcher = new Button("Start Jalview");
     public static boolean AWT1 = false;
 
+    AlignFrame currentAlignFrame;
+
 
     /**
      * init method for Jalview Applet
@@ -162,6 +164,29 @@ 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 +235,12 @@ 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
             {