From 323176a27b0f2de09034435e0531ec181390eaf1 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 11 Feb 2005 11:03:47 +0000
Subject: [PATCH] update start and end res when copying

---
 src/jalview/gui/AlignFrame.java |    5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 83f7ba0..7f8b8e9 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -210,7 +210,8 @@ public class AlignFrame extends GAlignFrame
        for(int i=0; i<sg.getSize(); i++)
        {
          SequenceI seq = sg.getSequenceAt(i);
-         buffer.append( seq.getName()+"\t"+seq.getStart() +"\t"+seq.getEnd()+"\t"
+         buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
+                        +seq.findPosition( sg.getEndRes() )+ "\t"
                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
        }
      c.setContents( new StringSelection( buffer.toString()) , null ) ;
@@ -244,8 +245,8 @@ public class AlignFrame extends GAlignFrame
         String name = st.nextToken();
         int start = Integer.parseInt(st.nextToken());
         int end = Integer.parseInt(st.nextToken());
+        Sequence sequence = new Sequence(name,st.nextToken(), start, end);
 
-        Sequence sequence = new Sequence(name, st.nextToken(), start, end);
         if(!newAlignment)
           viewport.alignment.addSequence(sequence);
         else
-- 
1.7.10.2