X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=83e44174ba49be74307137bd15c2349ab57da63d;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=a53798ac9ae24c3a8b3c9beb9b480599fcc71bc2;hpb=ebb678af128304dc13e1b6ec9e0961489bf83d39;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index a53798a..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,
@@ -200,11 +205,14 @@ public class EditCommand implements CommandI
 
     for(int i=0; i<command.seqs.length; i++)
     {
-      command.string[i] = command.seqs[i].getSequence(command.position,
-                                           command.position + command.number);
+      if(command.seqs[i].getLength()>command.position)
+      {
+        command.string[i] = command.seqs[i].getSequence(command.position,
+            command.position + command.number);
 
-      command.seqs[i].deleteChars(command.position,
-                                  command.position+command.number);
+        command.seqs[i].deleteChars(command.position,
+                                    command.position + command.number);
+      }
 
       if(command.seqs[i].getLength()<1)
       {
@@ -229,8 +237,20 @@ public class EditCommand implements CommandI
           command.al.addSequence(command.seqs[i]);
       }
       tmp = new StringBuffer(command.seqs[i].getSequence());
-      if(command.string!=null)
+
+      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;
       }
@@ -270,6 +290,7 @@ public class EditCommand implements CommandI
          int number,
          AlignmentI al)
     {
+      this.gapChar = al.getGapCharacter();
       this.command = command;
       this.seqs = seqs;
       this.position = position;