JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 2d3a8d8..1cd6fcc 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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -307,8 +307,7 @@ public class EditCommand implements CommandI
    * @param performEdit
    */
   final public void appendEdit(Action command, SequenceI[] seqs,
-          int position,
-          int number, AlignmentI al, boolean performEdit)
+          int position, int number, AlignmentI al, boolean performEdit)
   {
     appendEdit(command, seqs, position, number, al, performEdit, null);
   }
@@ -326,8 +325,8 @@ public class EditCommand implements CommandI
    * @param views
    */
   final public void appendEdit(Action command, SequenceI[] seqs,
-          int position,
-          int number, AlignmentI al, boolean performEdit, AlignmentI[] views)
+          int position, int number, AlignmentI al, boolean performEdit,
+          AlignmentI[] views)
   {
     Edit edit = new Edit(command, seqs, position, number,
             al.getGapCharacter());
@@ -432,7 +431,7 @@ public class EditCommand implements CommandI
    */
   @Override
   final public void undoCommand(AlignmentI[] views)
-  { 
+  {
     ListIterator<Edit> iterator = edits.listIterator(edits.size());
     while (iterator.hasPrevious())
     {
@@ -474,8 +473,8 @@ public class EditCommand implements CommandI
 
     for (int s = 0; s < command.seqs.length; s++)
     {
-      command.seqs[s].insertCharAt(command.position,
-              command.number, command.gapChar);
+      command.seqs[s].insertCharAt(command.position, command.number,
+              command.gapChar);
       // System.out.println("pos: "+command.position+" number: "+command.number);
     }
 
@@ -560,8 +559,8 @@ public class EditCommand implements CommandI
                     command,
                     i,
                     sequence.findPosition(command.position),
-                    sequence.findPosition(command.position
-                            + command.number), false);
+                    sequence.findPosition(command.position + command.number),
+                    false);
           }
         }
       }
@@ -1045,7 +1044,7 @@ public class EditCommand implements CommandI
           int copylen = Math.min(command.position,
                   annotations[a].annotations.length);
           if (copylen > 0)
-           {
+          {
             System.arraycopy(annotations[a].annotations, 0, temp, 0,
                     copylen); // command.position);
           }
@@ -1117,8 +1116,7 @@ public class EditCommand implements CommandI
       if (command.editedFeatures != null
               && command.editedFeatures.containsKey(seq))
       {
-        sequence.setSequenceFeatures(command.editedFeatures
-                .get(seq));
+        sequence.setSequenceFeatures(command.editedFeatures.get(seq));
       }
 
       return;
@@ -1265,8 +1263,7 @@ public class EditCommand implements CommandI
           if (action == Action.DELETE_GAP)
           {
             preEdit.setSequence(new String(StringUtils.insertCharAt(
-                    preEdit.getSequence(), position,
-                    number, gap)));
+                    preEdit.getSequence(), position, number, gap)));
           }
           else if (action == Action.INSERT_GAP)
           {