JAL-2675 source license

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

diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index 6172ce8..32e5fb4 100644 (file)
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,26 +20,8 @@
  */
 package jalview.commands;
 
-/*
- * Jalview - A Sequence Alignment Editor and Viewer Copyright (C) 2007 AM
- * Waterhouse, J Procter, G Barton, M Clamp, S Searle
- * 
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU General Public License as published by the Free Software
- * Foundation; either version 2 of the License, or (at your option) any later
- * version.
- * 
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
- * 
- * You should have received a copy of the GNU General Public License along with
- * this program; if not, write to the Free Software Foundation, Inc., 51
- * Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 
 public class RemoveGapColCommand extends EditCommand
 {
@@ -55,7 +37,7 @@ public class RemoveGapColCommand extends EditCommand
     int startCol = -1, endCol = -1;
     columnsDeleted = 0;
 
-    edits = new Edit[0];
+    clearEdits();
 
     boolean delete = true;
     for (int i = start; i <= end; i++)
@@ -86,8 +68,8 @@ public class RemoveGapColCommand extends EditCommand
 
       if (!delete && startCol > -1)
       {
-        this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, endCol
-                - startCol, al, false, null);
+        this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
+                endCol - startCol, al, false, null);
 
         columnsDeleted += (endCol - startCol);
         startCol = -1;
@@ -100,8 +82,8 @@ public class RemoveGapColCommand extends EditCommand
       // This is for empty columns at the
       // end of the alignment
 
-      this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, end
-              - startCol + 1, al, false, null);
+      this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
+              end - startCol + 1, al, false, null);
 
       columnsDeleted += (end - startCol + 1);
     }
@@ -109,6 +91,7 @@ public class RemoveGapColCommand extends EditCommand
     performEdit(0, null);
   }
 
+  @Override
   public int getSize()
   {
     // We're interested in the number of columns deleted,