X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=778142c24fed58fc045634860caf4029f5be35ee;hb=3d9d1f6c1c1da3b2657f9ebb95430d0bc8dde873;hp=c80c3260c85a7a0d7b9c8d98ddc76b08660f49b1;hpb=256f99fa9de8ee5a2f206163a6a55be69b35e00c;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index c80c326..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);
         }
 
@@ -121,7 +121,7 @@ public class AlignmentSorter
             tmp.addElement(seqs[i]);
         }
 
-        algn.clear();
+        algn.removeAllElements();
         //User may have hidden seqs, then clicked undo or redo
         for (int i = 0; i < tmp.size(); 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);