X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FGSDIR.java;h=80a0d3aa7e2cc5a489eb2f2d89ea846e8b29737a;hb=0bcaf88108ac7d33e5a76df7fa49bf22d01c6798;hp=8ada70598ce963fcd16195e50cd3dbeeb2f8b35c;hpb=8f8bbd46b51ab6778da479b6fa2a444b46ac3a60;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java
index 8ada705..80a0d3a 100644
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -77,13 +77,18 @@ public class GSDIR implements GSDII {
             gene_tree.reRoot( branch );
             PhylogenyMethods.preOrderReId( species_tree );
             //TEST, remove later
-            //            for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {
+            //            for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {
             //                final PhylogenyNode g = it.next();
             //                if ( g.isInternal() ) {
             //                    g.setLink( null );
             //                }
             //            }
-            final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree, true );
+            final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree,
+                                                                                   true,
+                                                                                   min_duplications_sum );
+            if ( gsdi_result == null ) {
+                continue;
+            }
             if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {
                 min_duplications_sum = gsdi_result.getDuplicationsSum();
                 speciations_sum = gsdi_result.getSpeciationsSum();