X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Ftools%2FSupportCount.java;h=283668ca09cbdd254f74f6e89f0cdc0f77f0a7e3;hb=01d681ced8f186561a3dd76715d950bd0eabd82d;hp=a3c7fa8e0f362652110b1bf7787cc06b37e903d2;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/tools/SupportCount.java b/forester/java/src/org/forester/tools/SupportCount.java
index a3c7fa8..283668c 100644
--- a/forester/java/src/org/forester/tools/SupportCount.java
+++ b/forester/java/src/org/forester/tools/SupportCount.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,13 +15,13 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.tools;
 
@@ -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;
 
@@ -63,7 +64,7 @@ public final class SupportCount {
             phylogeny.reRoot( phylogeny.getNode( child0_name ) );
             evaluator_phylogeny.reRoot( evaluator_phylogeny.getNode( child0_name ) );
         }
-        final Map<Integer, ArrayList<String>> phylogeny_external_names_per_node = SupportCount
+        final Map<Long, ArrayList<String>> phylogeny_external_names_per_node = SupportCount
                 .extractExternalNamesPerNode( phylogeny );
         return ( SupportCount.compare( phylogeny,
                                        evaluator_phylogeny,
@@ -96,7 +97,7 @@ public final class SupportCount {
      */
     private static double compare( final Phylogeny phylogeny,
                                    final Phylogeny evaluator_phylogeny,
-                                   final Map<Integer, ArrayList<String>> phylogeny_external_names_per_node,
+                                   final Map<Long, ArrayList<String>> phylogeny_external_names_per_node,
                                    final boolean update_support_in_phylogeny,
                                    final double similarity_threshold ) {
         int matching_branches = 0;
@@ -113,7 +114,7 @@ public final class SupportCount {
             for( final Object element : evaluator_phylogeny_it.next().getAllExternalDescendants() ) {
                 c1.add( ( ( PhylogenyNode ) element ).getName() );
             }
-            for( final Integer id : phylogeny_external_names_per_node.keySet() ) {
+            for( final Long id : phylogeny_external_names_per_node.keySet() ) {
                 final List<String> c2 = phylogeny_external_names_per_node.get( id );
                 if ( ( c2.size() == c1.size() ) && c2.containsAll( c1 ) ) {
                     if ( c2.size() > 1 ) {
@@ -180,7 +181,7 @@ public final class SupportCount {
         }
         final String child0_name = phylogeny.getFirstExternalNode().getName();
         phylogeny.reRoot( phylogeny.getNode( child0_name ) );
-        final Map<Integer, ArrayList<String>> phylogeny_external_names_per_node = SupportCount
+        final Map<Long, ArrayList<String>> phylogeny_external_names_per_node = SupportCount
                 .extractExternalNamesPerNode( phylogeny );
         if ( verbose ) {
             System.out.println();
@@ -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 ) {
@@ -229,14 +239,14 @@ public final class SupportCount {
         return evaluator_phylogenies_above_threshold;
     }
 
-    private static Map<Integer, ArrayList<String>> extractExternalNamesPerNode( final Phylogeny phylogeny )
+    private static Map<Long, ArrayList<String>> extractExternalNamesPerNode( final Phylogeny phylogeny )
             throws NoSuchElementException {
-        final HashMap<Integer, ArrayList<String>> phylogeny_external_names_per_node = new HashMap<Integer, ArrayList<String>>();
+        final HashMap<Long, ArrayList<String>> phylogeny_external_names_per_node = new HashMap<Long, ArrayList<String>>();
         for( final PhylogenyNodeIterator it = phylogeny.iteratorPostorder(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();
             final List<PhylogenyNode> l = n.getAllExternalDescendants();
             final ArrayList<String> c = new ArrayList<String>();
-            phylogeny_external_names_per_node.put( new Integer( n.getId() ), c );
+            phylogeny_external_names_per_node.put( new Long( n.getId() ), c );
             for( final PhylogenyNode phylogenyNode : l ) {
                 c.add( phylogenyNode.getName() );
             }