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