X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=c2814b894a65b2a9f3a6c92274e3b932b94ee724;hb=df9b85c1cf39894039018499fe802406cc37f209;hp=20101dc908c91448b86c396dc648548c6024b45c;hpb=bf2bf43c980b18a26b724d2a2d51dddc1a79a185;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 20101dc..c2814b8 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -184,7 +184,7 @@ public class AlignmentSorter
             {
                 SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
 
-                if (sg.getSize() > sg2.getSize())
+                if (sg.getSize(false) > sg2.getSize(false))
                 {
                     groups.insertElementAt(sg, j);