X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FRemoveGapColCommand.java;h=80a0dd58374af2434e069de6d8973cf64599b994;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=a874f7181c487ed89b3cd246638c6a5d6070016f;hpb=fa93bb578999b13c0364a712ae368ca8841012a1;p=jalview.git

diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index a874f71..80a0dd5 100644
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -1,33 +1,50 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
+ *  
+ * 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/>.
+ * 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
+ * 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.*;
 
-public class RemoveGapColCommand
-    extends EditCommand
+public class RemoveGapColCommand extends EditCommand
 {
   int columnsDeleted;
-  public RemoveGapColCommand(String description,
-                             SequenceI[] seqs,
-                             int start, int end, AlignmentI al)
+
+  public RemoveGapColCommand(String description, SequenceI[] seqs,
+          int start, int end, AlignmentI al)
   {
     this.description = description;
 
@@ -67,11 +84,8 @@ public class RemoveGapColCommand
 
       if (!delete && startCol > -1)
       {
-        this.appendEdit(DELETE_GAP, seqs,
-                        startCol - columnsDeleted,
-                        endCol - startCol,
-                        al,
-                        false,null);
+        this.appendEdit(DELETE_GAP, seqs, startCol - columnsDeleted, endCol
+                - startCol, al, false, null);
 
         columnsDeleted += (endCol - startCol);
         startCol = -1;
@@ -81,25 +95,22 @@ public class RemoveGapColCommand
 
     if (delete && startCol > -1)
     {
-      //This is for empty columns at the
-      //end of the alignment
+      // 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(DELETE_GAP, seqs, startCol - columnsDeleted, end
+              - startCol + 1, al, false, null);
 
       columnsDeleted += (end - startCol + 1);
     }
 
-    performEdit(0,null);
+    performEdit(0, null);
   }
 
   public int getSize()
   {
-    //We're interested in the number of columns deleted,
-    //Not the number of sequence edits.
+    // We're interested in the number of columns deleted,
+    // Not the number of sequence edits.
     return columnsDeleted;
   }