X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=83e44174ba49be74307137bd15c2349ab57da63d;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=7218115323f4e4994994b814cd173b1ccbe42560;hpb=91d2b7cf873f1437a3e21049c5aa6c7a7117e820;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 7218115..83e4417 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -99,6 +99,11 @@ public class EditCommand implements CommandI
     return edits==null?0:edits.length;
   }
 
+  public AlignmentI getAlignment()
+  {
+    return edits[0].al;
+  }
+
 
   public void appendEdit(String command,
                          SequenceI[] seqs,
@@ -235,6 +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;
       }
@@ -274,6 +290,7 @@ public class EditCommand implements CommandI
          int number,
          AlignmentI al)
     {
+      this.gapChar = al.getGapCharacter();
       this.command = command;
       this.seqs = seqs;
       this.position = position;