X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=778142c24fed58fc045634860caf4029f5be35ee;hb=a2497c9a753e13eeb17d33f73a697b4ad7ebdbc3;hp=bf18b70e69440be632de857667494430165842a7;hpb=083196ff5de0d570ee70420a15aa6ff1c2dd03bf;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index bf18b70..778142c 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -52,8 +52,8 @@ public class AlignmentSorter
 
         for (int i = 0; i < nSeq; i++)
         {
-            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),
-                                       s.getSequence());
+            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
+                                       s.getSequenceAsString());
             seqs[i] = align.getSequenceAt(i);
         }
 
@@ -198,7 +198,7 @@ public class AlignmentSorter
             {
                 SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
 
-                if (sg.getSize(false) > sg2.getSize(false))
+                if (sg.getSize() > sg2.getSize())
                 {
                     groups.insertElementAt(sg, j);