X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=797af0c068c0c2b3558c0064dd55136ba0f2e76d;hb=d6c464dcc3c70d07a756ceef49971e212e8b5876;hp=158fe8195dfd436e87e66350c9d29f09b39e42d0;hpb=6403068c0c328cfb63af451f7fa1bd568fa0fdd3;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 158fe81..797af0c 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -456,15 +456,15 @@ public class AlignmentSorter
       // TODO: JBPNote - decide if this is always an error
       // (eg. not when a tree is associated to another alignment which has more
       // sequences)
-      if (tmp.size() < nSeq)
+      if (tmp.size() != nSeq)
       {
         addStrays(align, tmp);
       }
 
       if (tmp.size() != nSeq)
       {
-        System.err.println("ERROR: tmp.size()=" + tmp.size() + " != nseq="
-                + nSeq + " in getOrderByTree");
+        System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+                + nSeq + " in getOrderByTree - tree contains sequences not in alignment");
       }
     }
 
@@ -560,7 +560,7 @@ public class AlignmentSorter
       {
         if (node.element() instanceof SequenceI)
         {
-          if (!tmp.contains(node.element()))
+          if (!tmp.contains(node.element())) //  && (seqset==null || seqset.size()==0 || seqset.contains(tmp)))
           {
             tmp.addElement((SequenceI) node.element());
           }