header updated

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

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 20101dc..bfe8f1e 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 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
@@ -52,7 +52,8 @@ public class AlignmentSorter
 \r
         for (int i = 0; i < nSeq; i++)\r
         {\r
-            scores[i] = Comparison.PID(align.getSequenceAt(i), s);\r
+            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),\r
+                                       s.getSequence());\r
             seqs[i] = align.getSequenceAt(i);\r
         }\r
 \r
@@ -184,7 +185,7 @@ public class AlignmentSorter
             {\r
                 SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);\r
 \r
-                if (sg.getSize() > sg2.getSize())\r
+                if (sg.getSize(false) > sg2.getSize(false))\r
                 {\r
                     groups.insertElementAt(sg, j);\r
 \r