GPL license added

[jalview.git] / src / jalview / analysis / AlignmentSorter.java

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 8274768..53eb1dd 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,3 +1,22 @@
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+\r
 package jalview.analysis;\r
 \r
 import jalview.datamodel.*;\r
@@ -35,13 +54,7 @@ public class AlignmentSorter {
 \r
     QuickSort.sort(arr,s);\r
 \r
-    Vector newg = new Vector(nGroup);\r
-\r
-    for (int i=nGroup-1; i >= 0; i--) {\r
-      newg.addElement(s[i]);\r
-    }\r
-\r
-    //    align.setGroups(newg);\r
+    //  align..setGroups(newg);\r
   }\r
 \r
   /**\r
@@ -122,7 +135,6 @@ public class AlignmentSorter {
   static boolean sortGroupAscending = true;\r
 \r
   public static void sortByGroup(AlignmentI align) {\r
-    int    nSeq = align.getHeight();\r
     Vector groups = align.getGroups();\r
     if (groups.hashCode()!=lastGroupHash) {\r
       sortGroupAscending=true;\r