X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;fp=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=0f3edfd8c9a9fc3bd65ac6e938d10780caca3d78;hb=4c2789fc5d5f3ccc8ef55d833d3c87dcb45956c2;hp=81bddc2ebd637e7908687360a56e373447ce83e1;hpb=be87ee66ed7952a13c1b402257b8a270ba9168e0;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 81bddc2..0f3edfd 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -25,6 +25,7 @@ import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.BinaryNode;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -534,7 +535,7 @@ public class AlignmentSorter
    * 
    * @return DOCUMENT ME!
    */
-  private static List<SequenceI> _sortByTree(SequenceNode node,
+  private static List<SequenceI> _sortByTree(BinaryNode node,
           List<SequenceI> tmp, List<SequenceI> seqset)
   {
     if (node == null)
@@ -542,12 +543,12 @@ public class AlignmentSorter
       return tmp;
     }
 
-    SequenceNode left = (SequenceNode) node.left();
-    SequenceNode right = (SequenceNode) node.right();
+    BinaryNode left = (BinaryNode) node.left();
+    BinaryNode right = (BinaryNode) node.right();
 
     if ((left == null) && (right == null))
     {
-      if (!node.isPlaceholder() && (node.element() != null))
+      if (!(node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder()) && (node.element() != null))
       {
         if (node.element() instanceof SequenceI)
         {