transfer of taxonomy in GSDI and RIO

[jalview.git] / forester / java / src / org / forester / sdi / GSDIR.java

diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java
index 3615f31..7ca8dca 100644 (file)
--- 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,\r
                   final Phylogeny species_tree,\r
                   final boolean strip_gene_tree,\r
-                  final boolean strip_species_tree ) throws SDIException {\r
+                  final boolean strip_species_tree,\r
+                  final boolean transfer_taxonomy ) throws SDIException {\r
         final NodesLinkingResult nodes_linking_result = GSDI.linkNodesOfG( gene_tree,\r
                                                                            species_tree,\r
                                                                            strip_gene_tree,\r
@@ -80,13 +81,6 @@ public class GSDIR implements GSDII {
         for( final PhylogenyBranch branch : gene_tree_branches_post_order ) {\r
             reRoot( branch, gene_tree );\r
             PhylogenyMethods.preOrderReId( species_tree );\r
-            //TEST, remove later\r
-            //            for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
-            //                final PhylogenyNode g = it.next();\r
-            //                if ( g.isInternal() ) {\r
-            //                    g.setLink( null );\r
-            //                }\r
-            //            }\r
             final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree,\r
                                                                                    true,\r
                                                                                    min_duplications_sum );\r
@@ -96,6 +90,9 @@ public class GSDIR implements GSDII {
             if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {\r
                 min_duplications_sum = gsdi_result.getDuplicationsSum();\r
                 speciations_sum = gsdi_result.getSpeciationsSum();\r
+                if ( transfer_taxonomy ) {\r
+                    transferTaxonomy( gene_tree );\r
+                }\r
                 _min_duplications_sum_gene_tree = gene_tree.copy();\r
             }\r
             else if ( gsdi_result.getDuplicationsSum() == min_duplications_sum ) {\r
@@ -104,6 +101,9 @@ public class GSDIR implements GSDII {
                 l.add( gene_tree );\r
                 final int index = getIndexesOfShortestTree( l ).get( 0 );\r
                 if ( index == 1 ) {\r
+                    if ( transfer_taxonomy ) {\r
+                        transferTaxonomy( gene_tree );\r
+                    }\r
                     _min_duplications_sum_gene_tree = gene_tree.copy();\r
                 }\r
             }\r
@@ -214,4 +214,10 @@ public class GSDIR implements GSDII {
             throw new IllegalArgumentException( "reRoot( Branch b ): b is not a branch." );\r
         }\r
     }\r
+\r
+    private final static void transferTaxonomy( final Phylogeny gt ) {\r
+        for( final PhylogenyNodeIterator it = gt.iteratorPostorder(); it.hasNext(); ) {\r
+            GSDI.transferTaxonomy( it.next() );\r
+        }\r
+    }\r
 }\r