From 39e87aa4cc011c4e23286fcd6432d23334cb4cdc Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 12 Dec 2005 18:00:26 +0000
Subject: [PATCH] GetAlignment uses active alignment window

---
 src/jalview/bin/JalviewLite.java |   18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index be4675f..7838755 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -45,7 +45,7 @@ public class JalviewLite extends Applet
     String file = "No file";
     Button launcher = new Button("Start Jalview");
 
-    AlignFrame currentAlignFrame;
+    static AlignFrame currentAlignFrame;
 
 
     /**
@@ -159,10 +159,20 @@ public class JalviewLite extends Applet
             {
                 public void windowClosing(WindowEvent e)
                 {
+                    if(currentAlignFrame == frame)
+                    {
+                      currentAlignFrame = null;
+                    }
                     lastFrameX -=40;
                     lastFrameY-=40;
                     frame.dispose();
                 }
+                public void windowActivated(WindowEvent e)
+                {
+                  if(frame instanceof AlignFrame)
+                    currentAlignFrame = (AlignFrame)frame;
+                }
+
             });
         frame.setVisible(true);
     }
@@ -183,9 +193,9 @@ public class JalviewLite extends Applet
         return reply;
       }
       catch (Exception ex)
-      {ex.printStackTrace();
+      {
+        ex.printStackTrace();
         return "Error retrieving alignment in " + format + " format. ";
-
       }
     }
 
@@ -259,7 +269,7 @@ public class JalviewLite extends Applet
                       tp = new TreePanel(currentAlignFrame.viewport,
                                          currentAlignFrame.viewport.getAlignment().getSequences(),
                                          fin, "FromFile", applet.getCodeBase() + treeFile);
-                      jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+                      addFrame(tp, treeFile, 600, 500);
                       currentAlignFrame.addTreeMenuItem(tp, treeFile);
                     }
                   }
-- 
1.7.10.2