X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FOrderCommand.java;h=5758e19aa1e4a14dc0f2110f7774c9f77df8993f;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=bacca28c759b6569270c6c6001817cfdfa53c2ad;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/commands/OrderCommand.java b/src/jalview/commands/OrderCommand.java
index bacca28..5758e19 100644
--- a/src/jalview/commands/OrderCommand.java
+++ b/src/jalview/commands/OrderCommand.java
@@ -1,35 +1,65 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import jalview.analysis.AlignmentSorter;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 
+/**
+ * An undoable command to reorder the sequences in an alignment.
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class OrderCommand implements CommandI
 {
   String description;
 
+  /*
+   * The sequence order before sorting (target order for an undo)
+   */
   SequenceI[] seqs;
 
+  /*
+   * The sequence order specified by this command
+   */
   SequenceI[] seqs2;
 
+  /*
+   * The alignment the command acts on
+   */
   AlignmentI al;
 
+  /**
+   * Constructor given the 'undo' sequence order, and the (already) sorted
+   * alignment.
+   * 
+   * @param description
+   *          a text label for the 'undo' menu option
+   * @param seqs
+   *          the sequence order for undo
+   * @param al
+   *          the alignment as ordered by this command
+   */
   public OrderCommand(String description, SequenceI[] seqs, AlignmentI al)
   {
     this.description = description;
@@ -58,4 +88,15 @@ public class OrderCommand implements CommandI
   {
     AlignmentSorter.setOrder(al, seqs);
   }
+
+  /**
+   * Returns the sequence order used to sort, or before sorting if undo=true.
+   * 
+   * @param undo
+   * @return
+   */
+  public SequenceI[] getSequenceOrder(boolean undo)
+  {
+    return undo ? seqs : seqs2;
+  }
 }