refactored do and undo() method to take array of alignments for operations that resul...

[jalview.git] / src / jalview / commands / OrderCommand.java

diff --git a/src/jalview/commands/OrderCommand.java b/src/jalview/commands/OrderCommand.java
index 57097c0..b331690 100644 (file)
--- a/src/jalview/commands/OrderCommand.java
+++ b/src/jalview/commands/OrderCommand.java
@@ -1,62 +1,62 @@
-/*\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
+ * 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(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);
+  }
+}