X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FGSDIR.java;h=651383d424183139b07d68dd4d4e5e3c9779be6e;hb=c0439ed8b088887ffea2faf11bc7897333287cb3;hp=6b170d99159f2f450982b298842479ae7fa8f212;hpb=49d24119c8c55614fb78fba64333c02d3b4c52ae;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java
index 6b170d9..651383d 100644
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -52,7 +52,8 @@ public class GSDIR implements GSDII {
     public GSDIR( final Phylogeny gene_tree,
                   final Phylogeny species_tree,
                   final boolean strip_gene_tree,
-                  final boolean strip_species_tree ) throws SDIException {
+                  final boolean strip_species_tree,
+                  final boolean transfer_taxonomy ) throws SDIException {
         final NodesLinkingResult nodes_linking_result = GSDI.linkNodesOfG( gene_tree,
                                                                            species_tree,
                                                                            strip_gene_tree,
@@ -72,7 +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;
@@ -80,7 +81,6 @@ public class GSDIR implements GSDII {
         for( final PhylogenyBranch branch : gene_tree_branches_post_order ) {
             reRoot( branch, gene_tree );
             PhylogenyMethods.preOrderReId( species_tree );
-          
             final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree,
                                                                                    true,
                                                                                    min_duplications_sum );
@@ -91,6 +91,9 @@ public class GSDIR implements GSDII {
                 min_duplications_sum = gsdi_result.getDuplicationsSum();
                 speciations_sum = gsdi_result.getSpeciationsSum();
                 _min_duplications_sum_gene_tree = gene_tree.copy();
+                if ( transfer_taxonomy ) {
+                    transferTaxonomy( _min_duplications_sum_gene_tree );
+                }
             }
             else if ( gsdi_result.getDuplicationsSum() == min_duplications_sum ) {
                 final List<Phylogeny> l = new ArrayList<Phylogeny>();
@@ -99,6 +102,9 @@ public class GSDIR implements GSDII {
                 final int index = getIndexesOfShortestTree( l ).get( 0 );
                 if ( index == 1 ) {
                     _min_duplications_sum_gene_tree = gene_tree.copy();
+                    if ( transfer_taxonomy ) {
+                        transferTaxonomy( _min_duplications_sum_gene_tree );
+                    }
                 }
             }
             _duplications_sum_stats.addValue( gsdi_result.getDuplicationsSum() );
@@ -182,7 +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();
@@ -202,10 +208,16 @@ 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." );
         }
     }
+
+    private final static void transferTaxonomy( final Phylogeny gt ) {
+        for( final PhylogenyNodeIterator it = gt.iteratorPostorder(); it.hasNext(); ) {
+            GSDI.transferTaxonomy( it.next() );
+        }
+    }
 }