added transfer of taxonomy for GSDI

diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java
index 44fb856..b9fa794 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDI.java
+++ b/forester/java/src/org/forester/sdi/GSDI.java
@@ -182,7 +182,7 @@ public final class GSDI implements GSDII {
 
     private static final void transferTaxonomy( final PhylogenyNode g, final PhylogenyNode s ) {
         if ( s.getNodeData().isHasTaxonomy() ) {
-            g.getNodeData().setTaxonomy(  s.getNodeData().getTaxonomy() );
+            g.getNodeData().setTaxonomy( s.getNodeData().getTaxonomy() );
             if ( g.isInternal() ) {
                 if ( g.getChildNode1().isInternal() ) {
                     if ( g.getChildNode1().getNodeData().isHasTaxonomy() && g.getChildNode1().getNodeData().getTaxonomy() == s.getNodeData().getTaxonomy() ) {
@@ -201,12 +201,12 @@ public final class GSDI implements GSDII {
             if ( g.isInternal() ) {
                 if ( g.getChildNode1().isInternal() ) {
                     if ( g.getChildNode1().getName() == s.getName() ) {
-                        g.getChildNode1().setName(  "" );
+                        g.getChildNode1().setName( "" );
                     }
                 }
                 if ( g.getChildNode2().isInternal() ) {
                     if ( g.getChildNode2().getName() == s.getName() ) {
-                        g.getChildNode2().setName(  "" );
+                        g.getChildNode2().setName( "" );
                     }
                 }
             }

diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java
index 3615f31..6b170d9 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -80,13 +80,7 @@ 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
+          \r
             final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree,\r
                                                                                    true,\r
                                                                                    min_duplications_sum );\r