X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=27d1e7b4064ef42986f0b28cc3dfd7a2a863ca53;hb=4a62141371fa3ab28aa2e21bab95399e97382142;hp=c2814b894a65b2a9f3a6c92274e3b932b94ee724;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index c2814b8..27d1e7b 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -52,7 +52,8 @@ public class AlignmentSorter
 
         for (int i = 0; i < nSeq; i++)
         {
-            scores[i] = Comparison.PID(align.getSequenceAt(i), s);
+            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),
+                                       s.getSequence());
             seqs[i] = align.getSequenceAt(i);
         }