in progress

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

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 (file)
--- 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 "