X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FGSDIR.java;h=651383d424183139b07d68dd4d4e5e3c9779be6e;hb=eb22dac14771c467104f57362e3a624d0140f897;hp=7ca8dca5e490411d96f5dddf454e310b4e8f8587;hpb=b819fa043cac2722618af63f0d4752ffa1a40890;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java
index 7ca8dca..651383d 100644
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -73,7 +73,7 @@ public class GSDIR implements GSDII {
         }
         if ( gene_tree.getRoot().getNumberOfDescendants() == 2 ) {
             gene_tree_branches_post_order.add( new PhylogenyBranch( gene_tree.getRoot().getChildNode1(), gene_tree
-                    .getRoot().getChildNode2() ) );
+                                                                    .getRoot().getChildNode2() ) );
         }
         int min_duplications_sum = Integer.MAX_VALUE;
         int speciations_sum = 0;
@@ -90,10 +90,10 @@ public class GSDIR implements GSDII {
             if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {
                 min_duplications_sum = gsdi_result.getDuplicationsSum();
                 speciations_sum = gsdi_result.getSpeciationsSum();
+                _min_duplications_sum_gene_tree = gene_tree.copy();
                 if ( transfer_taxonomy ) {
-                    transferTaxonomy( gene_tree );
+                    transferTaxonomy( _min_duplications_sum_gene_tree );
                 }
-                _min_duplications_sum_gene_tree = gene_tree.copy();
             }
             else if ( gsdi_result.getDuplicationsSum() == min_duplications_sum ) {
                 final List<Phylogeny> l = new ArrayList<Phylogeny>();
@@ -101,10 +101,10 @@ public class GSDIR implements GSDII {
                 l.add( gene_tree );
                 final int index = getIndexesOfShortestTree( l ).get( 0 );
                 if ( index == 1 ) {
+                    _min_duplications_sum_gene_tree = gene_tree.copy();
                     if ( transfer_taxonomy ) {
-                        transferTaxonomy( gene_tree );
+                        transferTaxonomy( _min_duplications_sum_gene_tree );
                     }
-                    _min_duplications_sum_gene_tree = gene_tree.copy();
                 }
             }
             _duplications_sum_stats.addValue( gsdi_result.getDuplicationsSum() );
@@ -188,7 +188,7 @@ public class GSDIR implements GSDII {
     /**
      * Places the root of this Phylogeny on Branch b. The new root is always
      * placed on the middle of the branch b.
-     * 
+     *
      */
     static final void reRoot( final PhylogenyBranch b, final Phylogeny phy ) {
         final PhylogenyNode n1 = b.getFirstNode();
@@ -208,7 +208,7 @@ public class GSDIR implements GSDII {
         //        else if ( ( n1.getParent() != null ) && n1.getParent().isRoot()
         //                && ( ( n1.getParent().getChildNode1() == n2 ) || ( n1.getParent().getChildNode2() == n2 ) ) ) {
         //            phy.reRoot( n1 );
-        //           
+        //
         //        }
         else {
             throw new IllegalArgumentException( "reRoot( Branch b ): b is not a branch." );