X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsdi%2FGSDIR.java;h=7ca8dca5e490411d96f5dddf454e310b4e8f8587;hb=b819fa043cac2722618af63f0d4752ffa1a40890;hp=5fd0a3b605575a2868a59c2aace0f24707af59e0;hpb=bb367671ad9b009584da301ad4591c2f1e8f0901;p=jalview.git

diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java
index 5fd0a3b..7ca8dca 100644
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -26,70 +26,198 @@ package org.forester.sdi;
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Set;
+import java.util.SortedSet;
 
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyBranch;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
 import org.forester.util.BasicDescriptiveStatistics;
 
-public class GSDIR extends GSDI {
+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;
+    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;
+    private final TaxonomyComparisonBase     _tax_comp_base;
+    private final SortedSet<String>          _scientific_names_mapped_to_reduced_specificity;
 
     public GSDIR( final Phylogeny gene_tree,
                   final Phylogeny species_tree,
                   final boolean strip_gene_tree,
-                  final boolean strip_species_tree ) throws SDIException {
-        super( gene_tree.copy(), species_tree, strip_gene_tree );
-        linkNodesOfG( null, strip_gene_tree, strip_species_tree );
+                  final boolean strip_species_tree,
+                  final boolean transfer_taxonomy ) throws SDIException {
+        final NodesLinkingResult nodes_linking_result = GSDI.linkNodesOfG( gene_tree,
+                                                                           species_tree,
+                                                                           strip_gene_tree,
+                                                                           strip_species_tree );
+        _stripped_gene_tree_nodes = nodes_linking_result.getStrippedGeneTreeNodes();
+        _stripped_species_tree_nodes = nodes_linking_result.getStrippedSpeciesTreeNodes();
+        _mapped_species_tree_nodes = nodes_linking_result.getMappedSpeciesTreeNodes();
+        _scientific_names_mapped_to_reduced_specificity = nodes_linking_result
+                .getScientificNamesMappedToReducedSpecificity();
+        _tax_comp_base = nodes_linking_result.getTaxCompBase();
         final List<PhylogenyBranch> gene_tree_branches_post_order = new ArrayList<PhylogenyBranch>();
-        for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {
+        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() && ( gene_tree.getRoot().getNumberOfDescendants() == 2 ) ) ) {
                 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>();
+        if ( gene_tree.getRoot().getNumberOfDescendants() == 2 ) {
+            gene_tree_branches_post_order.add( new PhylogenyBranch( gene_tree.getRoot().getChildNode1(), gene_tree
+                    .getRoot().getChildNode2() ) );
+        }
+        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( getSpeciesTree() );
-            //TEST, remove later
-            //            for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {
-            //                final PhylogenyNode g = it.next();
-            //                if ( g.isInternal() ) {
-            //                    g.setLink( null );
-            //                }
-            //            }
-            geneTreePostOrderTraversal();
-            if ( _duplications_sum < _min_duplications_sum ) {
-                _min_duplications_sum = _duplications_sum;
-                _min_duplications_sum_gene_trees.clear();
-                _min_duplications_sum_gene_trees.add( getGeneTree().copy() );
+            reRoot( branch, gene_tree );
+            PhylogenyMethods.preOrderReId( species_tree );
+            final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree,
+                                                                                   true,
+                                                                                   min_duplications_sum );
+            if ( gsdi_result == null ) {
+                continue;
+            }
+            if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {
+                min_duplications_sum = gsdi_result.getDuplicationsSum();
+                speciations_sum = gsdi_result.getSpeciationsSum();
+                if ( transfer_taxonomy ) {
+                    transferTaxonomy( gene_tree );
+                }
+                _min_duplications_sum_gene_tree = gene_tree.copy();
             }
-            else if ( _duplications_sum == _min_duplications_sum ) {
-                _min_duplications_sum_gene_trees.add( getGeneTree().copy() );
+            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 ) {
+                    if ( transfer_taxonomy ) {
+                        transferTaxonomy( gene_tree );
+                    }
+                    _min_duplications_sum_gene_tree = gene_tree.copy();
+                }
             }
-            _duplications_sum_stats.addValue( _duplications_sum );
+            _duplications_sum_stats.addValue( gsdi_result.getDuplicationsSum() );
         }
+        _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 List<Phylogeny> getMinDuplicationsSumGeneTrees() {
-        return _min_duplications_sum_gene_trees;
+    public Phylogeny getMinDuplicationsSumGeneTree() {
+        return _min_duplications_sum_gene_tree;
     }
 
-    public BasicDescriptiveStatistics getDuplicationsSumStats() {
-        return _duplications_sum_stats;
+    @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;
+    }
+
+    /**
+     * Places the root of this Phylogeny on Branch b. The new root is always
+     * placed on the middle of the branch b.
+     * 
+     */
+    static final void reRoot( final PhylogenyBranch b, final Phylogeny phy ) {
+        final PhylogenyNode n1 = b.getFirstNode();
+        final PhylogenyNode n2 = b.getSecondNode();
+        if ( n1.isExternal() ) {
+            phy.reRoot( n1 );
+        }
+        else if ( n2.isExternal() ) {
+            phy.reRoot( n2 );
+        }
+        else if ( ( n2 == n1.getChildNode1() ) || ( n2 == n1.getChildNode2() ) ) {
+            phy.reRoot( n2 );
+        }
+        else if ( ( n1 == n2.getChildNode1() ) || ( n1 == n2.getChildNode2() ) ) {
+            phy.reRoot( n1 );
+        }
+        //        else if ( ( n1.getParent() != null ) && n1.getParent().isRoot()
+        //                && ( ( n1.getParent().getChildNode1() == n2 ) || ( n1.getParent().getChildNode2() == n2 ) ) ) {
+        //            phy.reRoot( n1 );
+        //           
+        //        }
+        else {
+            throw new IllegalArgumentException( "reRoot( Branch b ): b is not a branch." );
+        }
+    }
+
+    private final static void transferTaxonomy( final Phylogeny gt ) {
+        for( final PhylogenyNodeIterator it = gt.iteratorPostorder(); it.hasNext(); ) {
+            GSDI.transferTaxonomy( it.next() );
+        }
     }
 }