X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=24f2ddfa2f62f7596e5b33b2db4f3b8d6cd3cfe2;hb=3f9c1d052c8fe2e92ae0d7a1c3088ccb82c58ba5;hp=c80c3260c85a7a0d7b9c8d98ddc76b08660f49b1;hpb=256f99fa9de8ee5a2f206163a6a55be69b35e00c;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index c80c326..24f2ddf 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++)
         {