phylotastic hackathon at NESCENT 120606

[jalview.git] / forester / java / src / org / forester / application / phyloxml_converter.java

diff --git a/forester/java/src/org/forester/application/phyloxml_converter.java b/forester/java/src/org/forester/application/phyloxml_converter.java
index afa7dd7..6d45207 100644 (file)
--- a/forester/java/src/org/forester/application/phyloxml_converter.java
+++ b/forester/java/src/org/forester/application/phyloxml_converter.java
@@ -38,6 +38,7 @@ import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
@@ -253,7 +254,10 @@ public class phyloxml_converter {
         }
         if ( order_subtrees ) {
             for( final Phylogeny phy : phys ) {
-                phy.orderAppearance( true );
+                PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.TAXONOMY );
+                phy.externalNodesHaveChanged();
+                phy.hashIDs();
+                phy.recalculateNumberOfExternalDescendants( true );
             }
         }
         try {