X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=03b94d3ca6dcfe7921526636ea6f90fad7b353c5;hb=be415b56e8ce1bc00f5004c64793ce5d0cb17be8;hp=414cea71832a0d7e2d78174e6d08a51116fb62f5;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 414cea7..03b94d3 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -54,6 +54,8 @@ public class EditCommand implements CommandI
   public static final int PASTE = 3;
 
   public static final int REPLACE = 4;
+  
+  public static final int INSERT_NUC=5;
 
   Edit[] edits;
 
@@ -143,8 +145,8 @@ public class EditCommand implements CommandI
   final public void appendEdit(int command, SequenceI[] seqs, int position,
           int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
   {
-    Edit edit = new Edit(command, seqs, position, number, al
-            .getGapCharacter());
+    Edit edit = new Edit(command, seqs, position, number,
+            al.getGapCharacter());
     if (al.getHeight() == seqs.length)
     {
       edit.al = al;
@@ -192,6 +194,10 @@ public class EditCommand implements CommandI
       case REPLACE:
         replace(edits[e]);
         break;
+        //TODO:add deleteNuc for UNDO
+      case INSERT_NUC:
+    	insertNuc(edits[e]);
+    	break;
       }
     }
   }
@@ -223,7 +229,7 @@ public class EditCommand implements CommandI
       case REPLACE:
         replace(edits[e]);
         break;
-      }
+       }
     }
   }
 
@@ -234,6 +240,19 @@ public class EditCommand implements CommandI
     {
       command.seqs[s].insertCharAt(command.position, command.number,
               command.gapChar);
+      System.out.println("pos: "+command.position+" number: "+command.number);
+    }
+
+    adjustAnnotations(command, true, false, null);
+  }
+  
+  final void insertNuc(Edit command)
+  {
+
+    for (int s = 0; s < command.seqs.length; s++)
+    {
+        System.out.println("pos: "+command.position+" number: "+command.number);
+    	command.seqs[s].insertCharAt(command.position, command.number,'A');
     }
 
     adjustAnnotations(command, true, false, null);
@@ -286,9 +305,12 @@ public class EditCommand implements CommandI
               command.oldds = new SequenceI[command.seqs.length];
             }
             command.oldds[i] = oldds;
-            adjustFeatures(command, i, command.seqs[i]
-                    .findPosition(command.position), command.seqs[i]
-                    .findPosition(command.position + command.number), false);
+            adjustFeatures(
+                    command,
+                    i,
+                    command.seqs[i].findPosition(command.position),
+                    command.seqs[i].findPosition(command.position
+                            + command.number), false);
           }
         }
       }
@@ -781,9 +803,8 @@ public class EditCommand implements CommandI
       if (command.editedFeatures != null
               && command.editedFeatures.containsKey(seq))
       {
-        sequence
-                .setSequenceFeatures((SequenceFeature[]) command.editedFeatures
-                        .get(seq));
+        sequence.setSequenceFeatures((SequenceFeature[]) command.editedFeatures
+                .get(seq));
       }
 
       return;