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 6c4d267..c211c42 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -37,13 +37,17 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.sdi.SDIutil.TaxonomyComparisonBase;\r
 import org.forester.util.BasicDescriptiveStatistics;\r
 \r
-public class GSDIR {\r
+public class GSDIR implements GSDII {\r
 \r
-    private int                              _min_duplications_sum;\r
+    private final int _min_duplications_sum;\r
+    private final int _speciations_sum;\r
+\r
+    @Override\r
+    public int getSpeciationsSum() {\r
+        return _speciations_sum;\r
+    }\r
     private final BasicDescriptiveStatistics _duplications_sum_stats;\r
     private final List<Phylogeny>            _min_duplications_sum_gene_trees;\r
-    protected int                            _speciations_sum;\r
-    protected int                            _duplications_sum;\r
     private final List<PhylogenyNode>        _stripped_gene_tree_nodes;\r
     private final List<PhylogenyNode>        _stripped_species_tree_nodes;\r
     private final Set<PhylogenyNode>         _mapped_species_tree_nodes;\r
@@ -54,8 +58,6 @@ public class GSDIR {
                   final Phylogeny species_tree,\r
                   final boolean strip_gene_tree,\r
                   final boolean strip_species_tree ) throws SDIException {\r
-        _speciations_sum = 0;\r
-        _duplications_sum = 0;\r
         final NodesLinkingResult nodes_linking_result = GSDI.linkNodesOfG( gene_tree,\r
                                                                            species_tree,\r
                                                                            null,\r
@@ -70,16 +72,15 @@ public class GSDIR {
         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() && n.isFirstChildNode() )*/) {\r
                 gene_tree_branches_post_order.add( new PhylogenyBranch( n, n.getParent() ) );\r
             }\r
         }\r
-        _min_duplications_sum = Integer.MAX_VALUE;\r
+        int min_duplications_sum = Integer.MAX_VALUE;\r
+        int speciations_sum = 0;\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
-            _speciations_sum = 0;\r
             gene_tree.reRoot( branch );\r
             PhylogenyMethods.preOrderReId( species_tree );\r
             //TEST, remove later\r
@@ -89,19 +90,21 @@ public class GSDIR {
             //                    g.setLink( null );\r
             //                }\r
             //            }\r
-            final GSDIsummaryResult gsdi_summary_result = new GSDIsummaryResult();\r
-            GSDI.geneTreePostOrderTraversal( gene_tree, true, gsdi_summary_result );\r
-            if ( _duplications_sum < _min_duplications_sum ) {\r
-                _min_duplications_sum = _duplications_sum;\r
+            final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree, true );\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_trees.clear();\r
                 _min_duplications_sum_gene_trees.add( gene_tree.copy() );\r
                 //_speciations_sum\r
             }\r
-            else if ( _duplications_sum == _min_duplications_sum ) {\r
+            else if ( gsdi_result.getDuplicationsSum() == min_duplications_sum ) {\r
                 _min_duplications_sum_gene_trees.add( gene_tree.copy() );\r
             }\r
-            _duplications_sum_stats.addValue( _duplications_sum );\r
+            _duplications_sum_stats.addValue( gsdi_result.getDuplicationsSum() );\r
         }\r
+        _min_duplications_sum = min_duplications_sum;\r
+        _speciations_sum = speciations_sum;\r
     }\r
 \r
     public int getMinDuplicationsSum() {\r
@@ -116,23 +119,58 @@ public class GSDIR {
         return _duplications_sum_stats;\r
     }\r
 \r
+    @Override\r
     public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {\r
         return _mapped_species_tree_nodes;\r
     }\r
 \r
+    @Override\r
     public final SortedSet<String> getReMappedScientificNamesFromGeneTree() {\r
         return _scientific_names_mapped_to_reduced_specificity;\r
     }\r
 \r
+    @Override\r
     public List<PhylogenyNode> getStrippedExternalGeneTreeNodes() {\r
         return _stripped_gene_tree_nodes;\r
     }\r
 \r
+    @Override\r
     public List<PhylogenyNode> getStrippedSpeciesTreeNodes() {\r
         return _stripped_species_tree_nodes;\r
     }\r
 \r
+    @Override\r
     public TaxonomyComparisonBase getTaxCompBase() {\r
         return _tax_comp_base;\r
     }\r
+\r
+    public final static List<Integer> getIndexesOfShortestTree( final List<Phylogeny> assigned_trees ) {\r
+        final List<Integer> shortests = new ArrayList<Integer>();\r
+        boolean depth = true;\r
+        double x = Double.MAX_VALUE;\r
+        for( int i = 0; i < assigned_trees.size(); ++i ) {\r
+            final Phylogeny phy = assigned_trees.get( i );\r
+            if ( i == 0 ) {\r
+                if ( PhylogenyMethods.calculateMaxDistanceToRoot( phy ) > 0 ) {\r
+                    depth = false;\r
+                }\r
+            }\r
+            final double d;\r
+            if ( depth ) {\r
+                d = PhylogenyMethods.calculateMaxDepth( phy );\r
+            }\r
+            else {\r
+                d = PhylogenyMethods.calculateMaxDistanceToRoot( phy );\r
+            }\r
+            if ( d < x ) {\r
+                x = d;\r
+                shortests.clear();\r
+                shortests.add( i );\r
+            }\r
+            else if ( d == x ) {\r
+                shortests.add( i );\r
+            }\r
+        }\r
+        return shortests;\r
+    }\r
 }\r