X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftools%2FSupportCount.java;h=5c8e924b4448ac12314856b912ddeae9f6f03467;hb=f3578c8bca780191d23d36d3791d2ec2c0bf38ad;hp=001491581ad43dbe1d4afa69e3ab7700d0fa020c;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/tools/SupportCount.java b/forester/java/src/org/forester/tools/SupportCount.java
index 0014915..5c8e924 100644
--- a/forester/java/src/org/forester/tools/SupportCount.java
+++ b/forester/java/src/org/forester/tools/SupportCount.java
@@ -33,6 +33,7 @@ import java.util.NoSuchElementException;
 
 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.iterators.PhylogenyNodeIterator;
 
@@ -195,11 +196,17 @@ public final class SupportCount {
             if ( strip_evaluator_phylogenies ) {
                 unstripped_evaluator_phylogeny = evaluator_phylogeny.copy();
                 SupportCount.strip( seq_names_to_keep, evaluator_phylogeny );
-                evaluator_phylogeny.orderAppearance( true ); // This is for
+                PhylogenyMethods.orderAppearance( evaluator_phylogeny.getRoot(),
+                                                  true,
+                                                  true,
+                                                  DESCENDANT_SORT_PRIORITY.TAXONOMY ); // This is for
                 // easer
                 // comparison if
                 // phylos are saved
                 // to file.
+                evaluator_phylogeny.externalNodesHaveChanged();
+                evaluator_phylogeny.clearHashIdToNodeMap();
+                evaluator_phylogeny.recalculateNumberOfExternalDescendants( true );
             }
             final double s = SupportCount.compare( phylogeny,
                                                    evaluator_phylogenies[ i ],
@@ -207,7 +214,10 @@ public final class SupportCount {
                                                    true,
                                                    similarity_threshold );
             if ( ( similarity_threshold < 0.0 ) || ( s >= similarity_threshold ) ) {
-                unstripped_evaluator_phylogeny.orderAppearance( true );
+                PhylogenyMethods.orderAppearance( unstripped_evaluator_phylogeny.getRoot(),
+                                                  true,
+                                                  true,
+                                                  DESCENDANT_SORT_PRIORITY.TAXONOMY );
                 evaluator_phylogenies_above_threshold.add( unstripped_evaluator_phylogeny );
             }
             if ( verbose ) {