X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=778142c24fed58fc045634860caf4029f5be35ee;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=938aa6aedd1f92e7b1cfc3aec460705e79c6f42d;hpb=9d69f0b2ad93d854ae2f85ec86e59c322d925d09;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 938aa6a..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);
         }
 
@@ -113,11 +113,24 @@ public class AlignmentSorter
     {
         // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
         Vector algn = align.getSequences();
+        Vector tmp = new Vector();
 
         for (int i = 0; i < seqs.length; i++)
         {
-            algn.setElementAt(seqs[i], i);
+          if(algn.contains(seqs[i]))
+            tmp.addElement(seqs[i]);
+        }
+
+        algn.removeAllElements();
+        //User may have hidden seqs, then clicked undo or redo
+        for (int i = 0; i < tmp.size(); i++)
+        {
+          algn.addElement(tmp.elementAt(i));
         }
+
+
+
+
     }
 
     /**
@@ -185,7 +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);