-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.commands;\r
-\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-\r
-public class OrderCommand\r
- implements CommandI\r
-{\r
- String description;\r
- SequenceI[] seqs;\r
- SequenceI[] seqs2;\r
- AlignmentI al;\r
-\r
- public OrderCommand(String description,\r
- SequenceI[] seqs,\r
- AlignmentI al)\r
- {\r
- this.description = description;\r
- this.seqs = seqs;\r
- this.seqs2 = al.getSequencesArray();\r
- this.al = al;\r
- doCommand();\r
- }\r
-\r
- public String getDescription()\r
- {\r
- return description;\r
- }\r
-\r
- public int getSize()\r
- {\r
- return 1;\r
- }\r
-\r
- public void doCommand()\r
- {\r
- AlignmentSorter.setOrder(al, seqs2);\r
- }\r
-\r
- public void undoCommand()\r
- {\r
- AlignmentSorter.setOrder(al, seqs);\r
- }\r
-}\r
+/*
+ * 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;
+ }
+}