X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FOrderCommand.java;h=5758e19aa1e4a14dc0f2110f7774c9f77df8993f;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=57097c01bf4a48cff1afad1ef910aa58caca43dc;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/commands/OrderCommand.java b/src/jalview/commands/OrderCommand.java
index 57097c0..5758e19 100644
--- a/src/jalview/commands/OrderCommand.java
+++ b/src/jalview/commands/OrderCommand.java
@@ -1,62 +1,102 @@
-/*
- * 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
- */
-package jalview.commands;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-
-public class OrderCommand
-    implements CommandI
-{
-  String description;
-  SequenceI[] seqs;
-  SequenceI[] seqs2;
-  AlignmentI al;
-
-  public OrderCommand(String description,
-                      SequenceI[] seqs,
-                      AlignmentI al)
-  {
-    this.description = description;
-    this.seqs = seqs;
-    this.seqs2 = al.getSequencesArray();
-    this.al = al;
-    doCommand();
-  }
-
-  public String getDescription()
-  {
-    return description;
-  }
-
-  public int getSize()
-  {
-    return 1;
-  }
-
-  public void doCommand()
-  {
-    AlignmentSorter.setOrder(al, seqs2);
-  }
-
-  public void undoCommand()
-  {
-    AlignmentSorter.setOrder(al, seqs);
-  }
-}
+/*
+ * 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.
+ *  
+ * 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;
+
+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;
+    this.seqs = seqs;
+    this.seqs2 = al.getSequencesArray();
+    this.al = al;
+    doCommand(null);
+  }
+
+  public String getDescription()
+  {
+    return description;
+  }
+
+  public int getSize()
+  {
+    return 1;
+  }
+
+  public void doCommand(AlignmentI[] views)
+  {
+    AlignmentSorter.setOrder(al, seqs2);
+  }
+
+  public void undoCommand(AlignmentI[] views)
+  {
+    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;
+  }
+}