Merge remote-tracking branch 'origin/bug/JAL-2722' into portforward/JAL-2675_2102b1to2103

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

diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index 631d50a..27831dd 100644 (file)
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -1,42 +1,27 @@
 /*
- * 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;
 
-/*
- * 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 RemoveGapsCommand extends EditCommand
 {
@@ -71,7 +56,7 @@ public class RemoveGapsCommand extends EditCommand
 
     int j, jSize;
 
-    edits = new Edit[0];
+    clearEdits();
 
     boolean delete = true;
     char[] sequence;
@@ -105,9 +90,10 @@ public class RemoveGapsCommand extends EditCommand
 
         if (!delete && startCol > -1)
         {
-          this.appendEdit(DELETE_GAP, new SequenceI[]
-          { seqs[s] }, start + startCol - deletedCols, endCol - startCol,
-                  al, false, null);
+          this.appendEdit(
+                  Action.DELETE_GAP, new SequenceI[]
+                  { seqs[s] }, start + startCol - deletedCols,
+                  endCol - startCol, al, false, null);
 
           deletedCols += (endCol - startCol);
           startCol = -1;
@@ -116,9 +102,10 @@ public class RemoveGapsCommand extends EditCommand
       }
       if (delete && startCol > -1)
       {
-        this.appendEdit(DELETE_GAP, new SequenceI[]
-        { seqs[s] }, start + startCol - deletedCols, jSize - startCol, al,
-                false, null);
+        this.appendEdit(
+                Action.DELETE_GAP, new SequenceI[]
+                { seqs[s] }, start + startCol - deletedCols,
+                jSize - startCol, al, false, null);
       }
 
     }