forester/java/src/org/forester/sdi/GSDIR.java

   1 // $Id:\r
   2 // FORESTER -- software libraries and applications\r
   3 // for evolutionary biology research and applications.\r
   4 //\r
   5 // Copyright (C) 2008-2013 Christian M. Zmasek\r
   6 // All rights reserved\r
   7 //\r
   8 // This library is free software; you can redistribute it and/or\r
   9 // modify it under the terms of the GNU Lesser General Public\r
  10 // License as published by the Free Software Foundation; either\r
  11 // version 2.1 of the License, or (at your option) any later version.\r
  12 //\r
  13 // This library is distributed in the hope that it will be useful,\r
  14 // but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  15 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\r
  16 // Lesser General Public License for more details.\r
  17 //\r
  18 // You should have received a copy of the GNU Lesser General Public\r
  19 // License along with this library; if not, write to the Free Software\r
  20 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
  21 //\r
  22 // Contact: phylosoft @ gmail . com\r
  23 // WWW: www.phylosoft.org\r
  24 \r
  25 package org.forester.sdi;\r
  26 \r
  27 import java.util.ArrayList;\r
  28 import java.util.List;\r
  29 import java.util.Set;\r
  30 import java.util.SortedSet;\r
  31 \r
  32 import org.forester.phylogeny.Phylogeny;\r
  33 import org.forester.phylogeny.PhylogenyBranch;\r
  34 import org.forester.phylogeny.PhylogenyMethods;\r
  35 import org.forester.phylogeny.PhylogenyNode;\r
  36 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
  37 import org.forester.sdi.SDIutil.TaxonomyComparisonBase;\r
  38 import org.forester.util.BasicDescriptiveStatistics;\r
  39 \r
  40 public class GSDIR implements GSDII {\r
  41 \r
  42     private final int                        _min_duplications_sum;\r
  43     private final int                        _speciations_sum;\r
  44     private final BasicDescriptiveStatistics _duplications_sum_stats;\r
  45     private Phylogeny                        _min_duplications_sum_gene_tree;\r
  46     private final List<PhylogenyNode>        _stripped_gene_tree_nodes;\r
  47     private final List<PhylogenyNode>        _stripped_species_tree_nodes;\r
  48     private final Set<PhylogenyNode>         _mapped_species_tree_nodes;\r
  49     private final TaxonomyComparisonBase     _tax_comp_base;\r
  50     private final SortedSet<String>          _scientific_names_mapped_to_reduced_specificity;\r
  51 \r
  52     public GSDIR( final Phylogeny gene_tree,\r
  53                   final Phylogeny species_tree,\r
  54                   final boolean strip_gene_tree,\r
  55                   final boolean strip_species_tree ) throws SDIException {\r
  56         final NodesLinkingResult nodes_linking_result = GSDI.linkNodesOfG( gene_tree,\r
  57                                                                            species_tree,\r
  58                                                                            strip_gene_tree,\r
  59                                                                            strip_species_tree );\r
  60         _stripped_gene_tree_nodes = nodes_linking_result.getStrippedGeneTreeNodes();\r
  61         _stripped_species_tree_nodes = nodes_linking_result.getStrippedSpeciesTreeNodes();\r
  62         _mapped_species_tree_nodes = nodes_linking_result.getMappedSpeciesTreeNodes();\r
  63         _scientific_names_mapped_to_reduced_specificity = nodes_linking_result\r
  64                 .getScientificNamesMappedToReducedSpecificity();\r
  65         _tax_comp_base = nodes_linking_result.getTaxCompBase();\r
  66         final List<PhylogenyBranch> gene_tree_branches_post_order = new ArrayList<PhylogenyBranch>();\r
  67         for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
  68             final PhylogenyNode n = it.next();\r
  69             if ( !n.isRoot() /*&& !( n.getParent().isRoot() && n.isFirstChildNode() )*/) {\r
  70                 gene_tree_branches_post_order.add( new PhylogenyBranch( n, n.getParent() ) );\r
  71             }\r
  72         }\r
  73         int min_duplications_sum = Integer.MAX_VALUE;\r
  74         int speciations_sum = 0;\r
  75         _duplications_sum_stats = new BasicDescriptiveStatistics();\r
  76         for( final PhylogenyBranch branch : gene_tree_branches_post_order ) {\r
  77             gene_tree.reRoot( branch );\r
  78             PhylogenyMethods.preOrderReId( species_tree );\r
  79             //TEST, remove later\r
  80             //            for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
  81             //                final PhylogenyNode g = it.next();\r
  82             //                if ( g.isInternal() ) {\r
  83             //                    g.setLink( null );\r
  84             //                }\r
  85             //            }\r
  86             final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree,\r
  87                                                                                    true,\r
  88                                                                                    min_duplications_sum );\r
  89             if ( gsdi_result == null ) {\r
  90                 continue;\r
  91             }\r
  92             if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {\r
  93                 min_duplications_sum = gsdi_result.getDuplicationsSum();\r
  94                 speciations_sum = gsdi_result.getSpeciationsSum();\r
  95                 _min_duplications_sum_gene_tree = gene_tree.copy();\r
  96             }\r
  97             else if ( gsdi_result.getDuplicationsSum() == min_duplications_sum ) {\r
  98                 final List<Phylogeny> l = new ArrayList<Phylogeny>();\r
  99                 l.add( _min_duplications_sum_gene_tree );\r
 100                 l.add( gene_tree );\r
 101                 final int index = getIndexesOfShortestTree( l ).get( 0 );\r
 102                 if ( index == 1 ) {\r
 103                     _min_duplications_sum_gene_tree = gene_tree.copy();\r
 104                 }\r
 105             }\r
 106             _duplications_sum_stats.addValue( gsdi_result.getDuplicationsSum() );\r
 107         }\r
 108         _min_duplications_sum = min_duplications_sum;\r
 109         _speciations_sum = speciations_sum;\r
 110     }\r
 111 \r
 112     public BasicDescriptiveStatistics getDuplicationsSumStats() {\r
 113         return _duplications_sum_stats;\r
 114     }\r
 115 \r
 116     @Override\r
 117     public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {\r
 118         return _mapped_species_tree_nodes;\r
 119     }\r
 120 \r
 121     public int getMinDuplicationsSum() {\r
 122         return _min_duplications_sum;\r
 123     }\r
 124 \r
 125     public Phylogeny getMinDuplicationsSumGeneTree() {\r
 126         return _min_duplications_sum_gene_tree;\r
 127     }\r
 128 \r
 129     @Override\r
 130     public final SortedSet<String> getReMappedScientificNamesFromGeneTree() {\r
 131         return _scientific_names_mapped_to_reduced_specificity;\r
 132     }\r
 133 \r
 134     @Override\r
 135     public int getSpeciationsSum() {\r
 136         return _speciations_sum;\r
 137     }\r
 138 \r
 139     @Override\r
 140     public List<PhylogenyNode> getStrippedExternalGeneTreeNodes() {\r
 141         return _stripped_gene_tree_nodes;\r
 142     }\r
 143 \r
 144     @Override\r
 145     public List<PhylogenyNode> getStrippedSpeciesTreeNodes() {\r
 146         return _stripped_species_tree_nodes;\r
 147     }\r
 148 \r
 149     @Override\r
 150     public TaxonomyComparisonBase getTaxCompBase() {\r
 151         return _tax_comp_base;\r
 152     }\r
 153 \r
 154     public final static List<Integer> getIndexesOfShortestTree( final List<Phylogeny> assigned_trees ) {\r
 155         final List<Integer> shortests = new ArrayList<Integer>();\r
 156         boolean depth = true;\r
 157         double x = Double.MAX_VALUE;\r
 158         for( int i = 0; i < assigned_trees.size(); ++i ) {\r
 159             final Phylogeny phy = assigned_trees.get( i );\r
 160             if ( i == 0 ) {\r
 161                 if ( PhylogenyMethods.calculateMaxDistanceToRoot( phy ) > 0 ) {\r
 162                     depth = false;\r
 163                 }\r
 164             }\r
 165             final double d;\r
 166             if ( depth ) {\r
 167                 d = PhylogenyMethods.calculateMaxDepth( phy );\r
 168             }\r
 169             else {\r
 170                 d = PhylogenyMethods.calculateMaxDistanceToRoot( phy );\r
 171             }\r
 172             if ( d < x ) {\r
 173                 x = d;\r
 174                 shortests.clear();\r
 175                 shortests.add( i );\r
 176             }\r
 177             else if ( d == x ) {\r
 178                 shortests.add( i );\r
 179             }\r
 180         }\r
 181         return shortests;\r
 182     }\r
 183 }\r