in progress (special coloring is still true)

[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 8ada705..52620a2 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
@@ -66,28 +67,33 @@ public class GSDIR implements GSDII {
         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
-            if ( !n.isRoot() /*&& !( n.getParent().isRoot() && n.isFirstChildNode() )*/) {\r
+            if ( !n.isRoot() && !( n.getParent().isRoot() && ( gene_tree.getRoot().getNumberOfDescendants() == 2 ) ) ) {\r
                 gene_tree_branches_post_order.add( new PhylogenyBranch( n, n.getParent() ) );\r
             }\r
         }\r
+        if ( gene_tree.getRoot().getNumberOfDescendants() == 2 ) {\r
+            gene_tree_branches_post_order.add( new PhylogenyBranch( gene_tree.getRoot().getChildNode1(), gene_tree\r
+                    .getRoot().getChildNode2() ) );\r
+        }\r
         int min_duplications_sum = Integer.MAX_VALUE;\r
         int speciations_sum = 0;\r
         _duplications_sum_stats = new BasicDescriptiveStatistics();\r
         for( final PhylogenyBranch branch : gene_tree_branches_post_order ) {\r
-            gene_tree.reRoot( branch );\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, true );\r
+            final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree,\r
+                                                                                   true,\r
+                                                                                   min_duplications_sum );\r
+            if ( gsdi_result == null ) {\r
+                continue;\r
+            }\r
             if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {\r
                 min_duplications_sum = gsdi_result.getDuplicationsSum();\r
                 speciations_sum = gsdi_result.getSpeciationsSum();\r
                 _min_duplications_sum_gene_tree = gene_tree.copy();\r
+                if ( transfer_taxonomy ) {\r
+                    transferTaxonomy( _min_duplications_sum_gene_tree );\r
+                }\r
             }\r
             else if ( gsdi_result.getDuplicationsSum() == min_duplications_sum ) {\r
                 final List<Phylogeny> l = new ArrayList<Phylogeny>();\r
@@ -96,6 +102,9 @@ public class GSDIR implements GSDII {
                 final int index = getIndexesOfShortestTree( l ).get( 0 );\r
                 if ( index == 1 ) {\r
                     _min_duplications_sum_gene_tree = gene_tree.copy();\r
+                    if ( transfer_taxonomy ) {\r
+                        transferTaxonomy( _min_duplications_sum_gene_tree );\r
+                    }\r
                 }\r
             }\r
             _duplications_sum_stats.addValue( gsdi_result.getDuplicationsSum() );\r
@@ -175,4 +184,40 @@ public class GSDIR implements GSDII {
         }\r
         return shortests;\r
     }\r
+\r
+    /**\r
+     * Places the root of this Phylogeny on Branch b. The new root is always\r
+     * placed on the middle of the branch b.\r
+     * \r
+     */\r
+    static final void reRoot( final PhylogenyBranch b, final Phylogeny phy ) {\r
+        final PhylogenyNode n1 = b.getFirstNode();\r
+        final PhylogenyNode n2 = b.getSecondNode();\r
+        if ( n1.isExternal() ) {\r
+            phy.reRoot( n1 );\r
+        }\r
+        else if ( n2.isExternal() ) {\r
+            phy.reRoot( n2 );\r
+        }\r
+        else if ( ( n2 == n1.getChildNode1() ) || ( n2 == n1.getChildNode2() ) ) {\r
+            phy.reRoot( n2 );\r
+        }\r
+        else if ( ( n1 == n2.getChildNode1() ) || ( n1 == n2.getChildNode2() ) ) {\r
+            phy.reRoot( n1 );\r
+        }\r
+        //        else if ( ( n1.getParent() != null ) && n1.getParent().isRoot()\r
+        //                && ( ( n1.getParent().getChildNode1() == n2 ) || ( n1.getParent().getChildNode2() == n2 ) ) ) {\r
+        //            phy.reRoot( n1 );\r
+        //           \r
+        //        }\r
+        else {\r
+            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