X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=83e44174ba49be74307137bd15c2349ab57da63d;hb=97acc4fa0742948992abd1f3ca982c6df4eff653;hp=97448e0c38f73ed2046895da678bed845825da74;hpb=4aad2f3624613cfc4d883f40c0470debd8f699b6;p=jalview.git

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;