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 \r
  45     \r
  46     @Override\r
  47     public int getSpeciationsSum() {\r
  48         return _speciations_sum;\r
  49     }\r
  50 \r
  51     private final BasicDescriptiveStatistics _duplications_sum_stats;\r
  52     private final List<Phylogeny>            _min_duplications_sum_gene_trees;\r
  53   \r
  54     private final List<PhylogenyNode>        _stripped_gene_tree_nodes;\r
  55     private final List<PhylogenyNode>        _stripped_species_tree_nodes;\r
  56     private final Set<PhylogenyNode>         _mapped_species_tree_nodes;\r
  57     private final TaxonomyComparisonBase     _tax_comp_base;\r
  58     private final SortedSet<String>          _scientific_names_mapped_to_reduced_specificity;\r
  59    \r
  60     public GSDIR( final Phylogeny gene_tree,\r
  61                   final Phylogeny species_tree,\r
  62                   final boolean strip_gene_tree,\r
  63                   final boolean strip_species_tree ) throws SDIException {\r
  64       \r
  65         final NodesLinkingResult nodes_linking_result = GSDI.linkNodesOfG( gene_tree,\r
  66                                                                            species_tree,\r
  67                                                                            null,\r
  68                                                                            strip_gene_tree,\r
  69                                                                            strip_species_tree );\r
  70         _stripped_gene_tree_nodes = nodes_linking_result.getStrippedGeneTreeNodes();\r
  71         _stripped_species_tree_nodes = nodes_linking_result.getStrippedSpeciesTreeNodes();\r
  72         _mapped_species_tree_nodes = nodes_linking_result.getMappedSpeciesTreeNodes();\r
  73         _scientific_names_mapped_to_reduced_specificity = nodes_linking_result\r
  74                 .getScientificNamesMappedToReducedSpecificity();\r
  75         _tax_comp_base = nodes_linking_result.getTaxCompBase();\r
  76         final List<PhylogenyBranch> gene_tree_branches_post_order = new ArrayList<PhylogenyBranch>();\r
  77         for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
  78             final PhylogenyNode n = it.next();\r
  79             if ( !n.isRoot() && !( n.getParent().isRoot() && n.isFirstChildNode() ) ) {\r
  80                 gene_tree_branches_post_order.add( new PhylogenyBranch( n, n.getParent() ) );\r
  81             }\r
  82         }\r
  83         int min_duplications_sum = Integer.MAX_VALUE;\r
  84         int speciations_sum = 0;\r
  85         _min_duplications_sum_gene_trees = new ArrayList<Phylogeny>();\r
  86         _duplications_sum_stats = new BasicDescriptiveStatistics();\r
  87         for( final PhylogenyBranch branch : gene_tree_branches_post_order ) {\r
  88            \r
  89             gene_tree.reRoot( branch );\r
  90             PhylogenyMethods.preOrderReId( species_tree );\r
  91             //TEST, remove later\r
  92             //            for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
  93             //                final PhylogenyNode g = it.next();\r
  94             //                if ( g.isInternal() ) {\r
  95             //                    g.setLink( null );\r
  96             //                }\r
  97             //            }\r
  98             final GSDIsummaryResult gsdi_result = GSDI.geneTreePostOrderTraversal( gene_tree, true );\r
  99             if ( gsdi_result.getDuplicationsSum() < min_duplications_sum ) {\r
 100                 min_duplications_sum = gsdi_result.getDuplicationsSum();\r
 101                 speciations_sum =  gsdi_result.getSpeciationsSum();\r
 102                 _min_duplications_sum_gene_trees.clear();\r
 103                 _min_duplications_sum_gene_trees.add( gene_tree.copy() );\r
 104                 //_speciations_sum\r
 105             }\r
 106             else if ( gsdi_result.getDuplicationsSum()== min_duplications_sum ) {\r
 107                 _min_duplications_sum_gene_trees.add( gene_tree.copy() );\r
 108             }\r
 109             _duplications_sum_stats.addValue( gsdi_result.getDuplicationsSum() );\r
 110            \r
 111         }\r
 112         _min_duplications_sum = min_duplications_sum; \r
 113         _speciations_sum =  speciations_sum;\r
 114     }\r
 115 \r
 116     public int getMinDuplicationsSum() {\r
 117         return _min_duplications_sum;\r
 118     }\r
 119 \r
 120     public List<Phylogeny> getMinDuplicationsSumGeneTrees() {\r
 121         return _min_duplications_sum_gene_trees;\r
 122     }\r
 123 \r
 124     public BasicDescriptiveStatistics getDuplicationsSumStats() {\r
 125         return _duplications_sum_stats;\r
 126     }\r
 127 \r
 128     @Override\r
 129     public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {\r
 130         return _mapped_species_tree_nodes;\r
 131     }\r
 132 \r
 133     @Override\r
 134     public final SortedSet<String> getReMappedScientificNamesFromGeneTree() {\r
 135         return _scientific_names_mapped_to_reduced_specificity;\r
 136     }\r
 137 \r
 138     @Override\r
 139     public List<PhylogenyNode> getStrippedExternalGeneTreeNodes() {\r
 140         return _stripped_gene_tree_nodes;\r
 141     }\r
 142 \r
 143     @Override\r
 144     public List<PhylogenyNode> getStrippedSpeciesTreeNodes() {\r
 145         return _stripped_species_tree_nodes;\r
 146     }\r
 147 \r
 148     @Override\r
 149     public TaxonomyComparisonBase getTaxCompBase() {\r
 150         return _tax_comp_base;\r
 151     }\r
 152 }\r