X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=25717d03bcfc77f8842648e3cbe2f6395e56eb4f;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=0ea479dd07671da35efe3dc112d86f8ad3754e0f;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 0ea479d..25717d0 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -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());
           }
@@ -798,9 +798,8 @@ public class AlignmentSorter
         // filter for selection criteria
         if (
         // ignore features outwith alignment start-stop positions.
-        (sf[f].end < sstart || sf[f].begin > sstop)
-                ||
-                // or ignore based on selection criteria
+        (sf[f].end < sstart || sf[f].begin > sstop) ||
+        // or ignore based on selection criteria
                 (featureLabels != null && !AlignmentSorter
                         .containsIgnoreCase(sf[f].type, featureLabels))
                 || (groupLabels != null