update author list in license for (JAL-826)

[jalview.git] / src / jalview / commands / EditCommand.java

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index d556442..76ddbac 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
-      }
+       }
     }
   }
 
@@ -234,10 +240,23 @@ 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);
+//  }
 
   final void deleteGap(Edit command)
   {
@@ -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;