"rio" work

[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 8179811..70cc009 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -40,13 +40,12 @@ public class GSDIR extends GSDI {
     private final BasicDescriptiveStatistics _duplications_sum_stats;\r
     private final List<Phylogeny>            _min_duplications_sum_gene_trees;\r
 \r
-    public GSDIR( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean strip_gene_tree, final int x )\r
-            throws SDIException {\r
-        super( gene_tree.copy(), species_tree, true, strip_gene_tree, true, 1 );\r
-        _min_duplications_sum = Integer.MAX_VALUE;\r
-        _min_duplications_sum_gene_trees = new ArrayList<Phylogeny>();\r
-        _duplications_sum_stats = new BasicDescriptiveStatistics();\r
-        linkNodesOfG();\r
+    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
+        super( gene_tree.copy(), species_tree, strip_gene_tree );\r
+        linkNodesOfG( null, strip_gene_tree, strip_species_tree );\r
         final List<PhylogenyBranch> gene_tree_branches_post_order = new ArrayList<PhylogenyBranch>();\r
         for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
             final PhylogenyNode n = it.next();\r
@@ -54,9 +53,11 @@ public class GSDIR extends GSDI {
                 gene_tree_branches_post_order.add( new PhylogenyBranch( n, n.getParent() ) );\r
             }\r
         }\r
+        _min_duplications_sum = Integer.MAX_VALUE;\r
+        _min_duplications_sum_gene_trees = new ArrayList<Phylogeny>();\r
+        _duplications_sum_stats = new BasicDescriptiveStatistics();\r
         for( final PhylogenyBranch branch : gene_tree_branches_post_order ) {\r
             _duplications_sum = 0;\r
-            _speciation_or_duplication_events_sum = 0;\r
             _speciations_sum = 0;\r
             _gene_tree.reRoot( branch );\r
             PhylogenyMethods.preOrderReId( getSpeciesTree() );\r
@@ -78,7 +79,7 @@ public class GSDIR extends GSDI {
             }\r
             _duplications_sum_stats.addValue( _duplications_sum );\r
         }\r
-        System.out.println( _duplications_sum_stats.getSummaryAsString() );\r
+        //System.out.println( _duplications_sum_stats.getSummaryAsString() );\r
     }\r
 \r
     public int getMinDuplicationsSum() {\r