From f7209385ed929337d8a4259981700f2bd7a8bbba Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 10 Oct 2006 14:11:53 +0000
Subject: [PATCH] No need to find index when deleting

---
 src/jalview/gui/AlignFrame.java |   10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 27503f9..fe6f4cf 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1292,8 +1292,6 @@ public class AlignFrame
     for (int i = 0; i < sg.getSize(false); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.getAlignment().findIndex(seq);
-
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
       // If the cut affects all sequences, remove highlighted columns
@@ -1308,10 +1306,6 @@ public class AlignFrame
         viewport.getAlignment().deleteSequence(seq);
         PaintRefresher.Refresh(alignPanel,alignPanel.av.getSequenceSetId(),seq,null);
       }
-      else
-      {
-        viewport.getAlignment().getSequences().setElementAt(seq, index);
-      }
     }
 
     viewport.setSelectionGroup(null);
@@ -2759,7 +2753,7 @@ public class AlignFrame
     return ShowNewickTree(nf, title, null, w, h, x, y);
   }
   /**
-   * Add a treeviewer for the tree extracted from a newick file object to the current alignment view 
+   * Add a treeviewer for the tree extracted from a newick file object to the current alignment view
    *
    * @param nf the tree
    * @param title tree viewer title
@@ -3224,4 +3218,4 @@ public void drop(DropTargetDropEvent evt)
   {
     return viewport;
   }
-}
\ No newline at end of file
+}
-- 
1.7.10.2