X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FRemoveGapColCommand.java;h=3e0023de7604564a465d4e5ddfbbb196efae86eb;hb=refs%2Fheads%2Fj2s%2Fdevelop;hp=88203aecbafdd12278dcd6d41c48c2b163f7db7f;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index 88203ae..3e0023d 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * 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.
- * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.commands;
 
@@ -36,7 +39,9 @@ package jalview.commands;
  * Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  */
 
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 public class RemoveGapColCommand extends EditCommand
 {
@@ -52,7 +57,7 @@ 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++)
@@ -63,7 +68,7 @@ public class RemoveGapColCommand extends EditCommand
       {
         if (seqs[j].getLength() > i)
         {
-          if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
+          if (!Comparison.isGap(seqs[j].getCharAt(i)))
           {
             if (delete)
             {
@@ -83,7 +88,8 @@ public class RemoveGapColCommand extends EditCommand
 
       if (!delete && startCol > -1)
       {
-        this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, endCol
+        this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
+                endCol
                 - startCol, al, false, null);
 
         columnsDeleted += (endCol - startCol);
@@ -97,7 +103,8 @@ public class RemoveGapColCommand extends EditCommand
       // This is for empty columns at the
       // end of the alignment
 
-      this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, end
+      this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted,
+              end
               - startCol + 1, al, false, null);
 
       columnsDeleted += (end - startCol + 1);