From 98f4db4c56ddbffb5690d9311b1e25bd9150f9c0 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 19 Jul 2006 08:11:16 +0000
Subject: [PATCH] Copy works with selection area

---
 src/jalview/gui/AlignFrame.java |   16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 05ba50c..0edc578 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -362,6 +362,7 @@ public class AlignFrame
           omitHidden) ;
 
 
+
       if (output == null)
       {
         return false;
@@ -667,15 +668,8 @@ public class AlignFrame
     {
       return;
     }
-    SequenceI [] seqs;
-    if(viewport.getSelectionGroup()==null)
-    {
-      seqs = viewport.alignment.getSequencesArray();
-    }
-    else
-    {
-      seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.alignment);
-    }
+
+    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
 
     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
 
@@ -2385,9 +2379,9 @@ public class AlignFrame
       if (nf.getTree() != null)
       {
         tp = new TreePanel(viewport,
-                           nf,
                            "FromFile",
-                           title);
+                           title,
+                           nf);
 
         tp.setSize(w,h);
 
-- 
1.7.10.2