From 5aca821095eac17ed013a04b66256d5db7df69b7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Nov 2005 18:35:52 +0000
Subject: [PATCH] Add getAlignment function

---
 src/jalview/bin/JalviewLite.java |   31 ++++++++++++++++++++++++++++---
 1 file changed, 28 insertions(+), 3 deletions(-)

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
             {
-- 
1.7.10.2