From 2c0ef17f9ede3abaa49b661fe5113412002378dd Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 21 Nov 2006 16:02:23 +0000
Subject: [PATCH] Undo cut from end of alignment, padding on

---
 src/jalview/commands/EditCommand.java |   12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 97448e0..83e4417 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -240,6 +240,17 @@ public class EditCommand implements CommandI
 
       if(command.string!=null && command.string[i]!=null)
       {
+        if(command.position>=tmp.length())
+        {
+          //This occurs if padding is on, and residues
+          //are removed from end of alignment
+          int length = command.position-tmp.length();
+          while (length > 0)
+          {
+            tmp.append(command.gapChar);
+            length--;
+          }
+        }
         tmp.insert(command.position, command.string[i]);
         command.string[i] = null;
       }
@@ -279,6 +290,7 @@ public class EditCommand implements CommandI
          int number,
          AlignmentI al)
     {
+      this.gapChar = al.getGapCharacter();
       this.command = command;
       this.seqs = seqs;
       this.position = position;
-- 
1.7.10.2