X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FGSDIR.java;h=80a0d3aa7e2cc5a489eb2f2d89ea846e8b29737a;hb=0bcaf88108ac7d33e5a76df7fa49bf22d01c6798;hp=6c4d26797e88f2a445dbc80a9b273a9b96f17eb8;hpb=9bad57b1ba0f75075ab8c6bda1dedb906f8c6280;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java
index 6c4d267..80a0d3a 100644
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -37,13 +37,12 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
 import org.forester.util.BasicDescriptiveStatistics;
 
-public class GSDIR {
+public class GSDIR implements GSDII {
 
-    private int                              _min_duplications_sum;
+    private final int                        _min_duplications_sum;
+    private final int                        _speciations_sum;
     private final BasicDescriptiveStatistics _duplications_sum_stats;
-    private final List<Phylogeny>            _min_duplications_sum_gene_trees;
-    protected int                            _speciations_sum;
-    protected int                            _duplications_sum;
+    private Phylogeny                        _min_duplications_sum_gene_tree;
     private final List<PhylogenyNode>        _stripped_gene_tree_nodes;
     private final List<PhylogenyNode>        _stripped_species_tree_nodes;
     private final Set<PhylogenyNode>         _mapped_species_tree_nodes;
@@ -54,11 +53,8 @@ public class GSDIR {
                   final Phylogeny species_tree,
                   final boolean strip_gene_tree,
                   final boolean strip_species_tree ) throws SDIException {
-        _speciations_sum = 0;
-        _duplications_sum = 0;
         final NodesLinkingResult nodes_linking_result = GSDI.linkNodesOfG( gene_tree,
                                                                            species_tree,
-                                                                           null,
                                                                            strip_gene_tree,
                                                                            strip_species_tree );
         _stripped_gene_tree_nodes = nodes_linking_result.getStrippedGeneTreeNodes();
@@ -70,69 +66,118 @@ public class GSDIR {
         final List<PhylogenyBranch> gene_tree_branches_post_order = new ArrayList<PhylogenyBranch>();
         for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();
-            if ( !n.isRoot() && !( n.getParent().isRoot() && n.isFirstChildNode() ) ) {
+            if ( !n.isRoot() /*&& !( n.getParent().isRoot() && n.isFirstChildNode() )*/) {
                 gene_tree_branches_post_order.add( new PhylogenyBranch( n, n.getParent() ) );
             }
         }
-        _min_duplications_sum = Integer.MAX_VALUE;
-        _min_duplications_sum_gene_trees = new ArrayList<Phylogeny>();
+        int min_duplications_sum = Integer.MAX_VALUE;
+        int speciations_sum = 0;
         _duplications_sum_stats = new BasicDescriptiveStatistics();
         for( final PhylogenyBranch branch : gene_tree_branches_post_order ) {
-            _duplications_sum = 0;
-            _speciations_sum = 0;
             gene_tree.reRoot( branch );
             PhylogenyMethods.preOrderReId( species_tree );
             //TEST, remove later
-            //            for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {
+            //            for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {
             //                final PhylogenyNode g = it.next();
             //                if ( g.isInternal() ) {
             //                    g.setLink( null );
             //                }
             //            }
-            final GSDIsummaryResult gsdi_summary_result = new GSDIsummaryResult();
-            GSDI.geneTreePostOrderTraversal( gene_tree, true, gsdi_summary_result );
-            if ( _duplications_sum < _min_duplications_sum ) {
-                _min_duplications_sum = _duplications_sum;
-                _min_duplications_sum_gene_trees.clear();
-                _min_duplications_sum_gene_trees.add( gene_tree.copy() );
-                //_speciations_sum
+            final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree,
+                                                                                   true,
+                                                                                   min_duplications_sum );
+            if ( gsdi_result == null ) {
+                continue;
             }
-            else if ( _duplications_sum == _min_duplications_sum ) {
-                _min_duplications_sum_gene_trees.add( gene_tree.copy() );
+            if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {
+                min_duplications_sum = gsdi_result.getDuplicationsSum();
+                speciations_sum = gsdi_result.getSpeciationsSum();
+                _min_duplications_sum_gene_tree = gene_tree.copy();
             }
-            _duplications_sum_stats.addValue( _duplications_sum );
+            else if ( gsdi_result.getDuplicationsSum() == min_duplications_sum ) {
+                final List<Phylogeny> l = new ArrayList<Phylogeny>();
+                l.add( _min_duplications_sum_gene_tree );
+                l.add( gene_tree );
+                final int index = getIndexesOfShortestTree( l ).get( 0 );
+                if ( index == 1 ) {
+                    _min_duplications_sum_gene_tree = gene_tree.copy();
+                }
+            }
+            _duplications_sum_stats.addValue( gsdi_result.getDuplicationsSum() );
         }
-    }
-
-    public int getMinDuplicationsSum() {
-        return _min_duplications_sum;
-    }
-
-    public List<Phylogeny> getMinDuplicationsSumGeneTrees() {
-        return _min_duplications_sum_gene_trees;
+        _min_duplications_sum = min_duplications_sum;
+        _speciations_sum = speciations_sum;
     }
 
     public BasicDescriptiveStatistics getDuplicationsSumStats() {
         return _duplications_sum_stats;
     }
 
+    @Override
     public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {
         return _mapped_species_tree_nodes;
     }
 
+    public int getMinDuplicationsSum() {
+        return _min_duplications_sum;
+    }
+
+    public Phylogeny getMinDuplicationsSumGeneTree() {
+        return _min_duplications_sum_gene_tree;
+    }
+
+    @Override
     public final SortedSet<String> getReMappedScientificNamesFromGeneTree() {
         return _scientific_names_mapped_to_reduced_specificity;
     }
 
+    @Override
+    public int getSpeciationsSum() {
+        return _speciations_sum;
+    }
+
+    @Override
     public List<PhylogenyNode> getStrippedExternalGeneTreeNodes() {
         return _stripped_gene_tree_nodes;
     }
 
+    @Override
     public List<PhylogenyNode> getStrippedSpeciesTreeNodes() {
         return _stripped_species_tree_nodes;
     }
 
+    @Override
     public TaxonomyComparisonBase getTaxCompBase() {
         return _tax_comp_base;
     }
+
+    public final static List<Integer> getIndexesOfShortestTree( final List<Phylogeny> assigned_trees ) {
+        final List<Integer> shortests = new ArrayList<Integer>();
+        boolean depth = true;
+        double x = Double.MAX_VALUE;
+        for( int i = 0; i < assigned_trees.size(); ++i ) {
+            final Phylogeny phy = assigned_trees.get( i );
+            if ( i == 0 ) {
+                if ( PhylogenyMethods.calculateMaxDistanceToRoot( phy ) > 0 ) {
+                    depth = false;
+                }
+            }
+            final double d;
+            if ( depth ) {
+                d = PhylogenyMethods.calculateMaxDepth( phy );
+            }
+            else {
+                d = PhylogenyMethods.calculateMaxDistanceToRoot( phy );
+            }
+            if ( d < x ) {
+                x = d;
+                shortests.clear();
+                shortests.add( i );
+            }
+            else if ( d == x ) {
+                shortests.add( i );
+            }
+        }
+        return shortests;
+    }
 }