X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FRemoveGapColCommand.java;h=32e5fb41017ee0fcc4e0c31d18d3b99c599de777;hb=45bf1ca88efba1a6510947bbad6667a210ccd752;hp=c5e12f50ceca6b1ff76049e44f0cd44ffafe4f19;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index c5e12f5..32e5fb4 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -1,43 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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
 {
@@ -53,7 +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++)
@@ -84,8 +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;
@@ -98,8 +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);
     }
@@ -107,6 +91,7 @@ public class RemoveGapColCommand extends EditCommand
     performEdit(0, null);
   }
 
+  @Override
   public int getSize()
   {
     // We're interested in the number of columns deleted,