X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fgene_tree_preprocess.java;h=f755d910d2df81bfdba6dc86cf1dd13f60f914be;hb=63d3280463d0864203eda0fa5fc9dd5479e18957;hp=41f6a473d0e20825db4495153947edee73fcb1f9;hpb=f0c947ea4c0fba2ef9b688b9e6523952ca6c6110;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 41f6a47..f755d91 100644
--- a/forester/java/src/org/forester/application/gene_tree_preprocess.java
+++ b/forester/java/src/org/forester/application/gene_tree_preprocess.java
@@ -52,7 +52,7 @@ public class gene_tree_preprocess {
     final static private String PRG_VERSION   = "1.01";
     final static private String PRG_DATE      = "2012.06.07";
     final static private String E_MAIL        = "phylosoft@gmail.com";
-    final static private String WWW           = "www.phylosoft.org/forester/";
+    final static private String WWW           = "www.phylosoft.org/forester";
 
     public static void main( final String[] args ) {
         try {
@@ -82,11 +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 );
+            final SortedSet<String> not_found = SequenceDataRetriver.obtainSeqInformation( phy, true, false );
             for( final String remove_me : not_found ) {
-                //PhylogenyMethods.removeNode( phy.getNode( remove_me ), phy );
                 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 "