X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fcommands%2FOrderCommand.java;h=5758e19aa1e4a14dc0f2110f7774c9f77df8993f;hb=a23cc416cd520ac6dec6052591575b264f5d25bc;hp=e45aaa1ca2f60c4f6f62d764b49d25d405defc89;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/commands/OrderCommand.java b/src/jalview/commands/OrderCommand.java
index e45aaa1..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 2.7)
- * Copyright (C) 2011 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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;
+ }
}