X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fgene_tree_preprocess.java;h=f755d910d2df81bfdba6dc86cf1dd13f60f914be;hb=4acc1443d8c6c6f47c26a7c57357bdcdad27ecf8;hp=840c33558c0aa357448a2c9cb7e566b1cb610dcd;hpb=755675533024c40e69c0b3a4f93e5f19d87cab79;p=jalview.git

diff --git a/forester/java/src/org/forester/application/gene_tree_preprocess.java b/forester/java/src/org/forester/application/gene_tree_preprocess.java
index 840c335..f755d91 100644
--- a/forester/java/src/org/forester/application/gene_tree_preprocess.java
+++ b/forester/java/src/org/forester/application/gene_tree_preprocess.java
@@ -82,10 +82,12 @@ public class gene_tree_preprocess {
                 ForesterUtil.fatalError( PRG_NAME, "phylogeny has " + phy.getNumberOfExternalNodes()
                         + " external node(s), aborting" );
             }
-            final SortedSet<String> not_found = SequenceDataRetriver.obtainSeqInformation( phy, true , false);
+            final SortedSet<String> not_found = SequenceDataRetriver.obtainSeqInformation( phy, true, false );
             for( final String remove_me : not_found ) {
                 phy.deleteSubtree( phy.getNode( remove_me ), true );
             }
+            phy.clearHashIdToNodeMap();
+            phy.externalNodesHaveChanged();
             if ( phy.getNumberOfExternalNodes() < 2 ) {
                 ForesterUtil.fatalError( PRG_NAME,
                                          "after removal of unresolvable external nodes, phylogeny has "