forester/java/src/org/forester/sdi/GSDI.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: www.phylosoft.org/forester
  25
  26 package org.forester.sdi;
  27
  28 import java.util.ArrayList;
  29 import java.util.HashMap;
  30 import java.util.HashSet;
  31 import java.util.List;
  32 import java.util.Map;
  33 import java.util.Set;
  34 import java.util.SortedSet;
  35
  36 import org.forester.phylogeny.Phylogeny;
  37 import org.forester.phylogeny.PhylogenyMethods;
  38 import org.forester.phylogeny.PhylogenyNode;
  39 import org.forester.phylogeny.data.Event;
  40 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  41 import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
  42 import org.forester.util.ForesterUtil;
  43
  44 public final class GSDI implements GSDII {
  45
  46     private final boolean                _most_parsimonious_duplication_model;
  47     private final int                    _speciation_or_duplication_events_sum;
  48     private final int                    _speciations_sum;
  49     private final int                    _duplications_sum;
  50     private final List<PhylogenyNode>    _stripped_gene_tree_nodes;
  51     private final List<PhylogenyNode>    _stripped_species_tree_nodes;
  52     private final Set<PhylogenyNode>     _mapped_species_tree_nodes;
  53     private final TaxonomyComparisonBase _tax_comp_base;
  54     private final SortedSet<String>      _scientific_names_mapped_to_reduced_specificity;
  55
  56     public GSDI( final Phylogeny gene_tree,
  57                  final Phylogeny species_tree,
  58                  final boolean most_parsimonious_duplication_model,
  59                  final boolean strip_gene_tree,
  60                  final boolean strip_species_tree ) throws SDIException {
  61         _most_parsimonious_duplication_model = most_parsimonious_duplication_model;
  62         final NodesLinkingResult nodes_linking_result = linkNodesOfG( gene_tree,
  63                                                                       species_tree,
  64                                                                       null,
  65                                                                       strip_gene_tree,
  66                                                                       strip_species_tree );
  67         _stripped_gene_tree_nodes = nodes_linking_result.getStrippedGeneTreeNodes();
  68         _stripped_species_tree_nodes = nodes_linking_result.getStrippedSpeciesTreeNodes();
  69         _mapped_species_tree_nodes = nodes_linking_result.getMappedSpeciesTreeNodes();
  70         _scientific_names_mapped_to_reduced_specificity = nodes_linking_result
  71                 .getScientificNamesMappedToReducedSpecificity();
  72         _tax_comp_base = nodes_linking_result.getTaxCompBase();
  73         PhylogenyMethods.preOrderReId( species_tree );
  74         final GSDIsummaryResult gsdi_summary_result = geneTreePostOrderTraversal( gene_tree,
  75                                                                                   _most_parsimonious_duplication_model );
  76         _speciation_or_duplication_events_sum = gsdi_summary_result.getSpeciationOrDuplicationEventsSum();
  77         _speciations_sum = gsdi_summary_result.getSpeciationsSum();
  78         _duplications_sum = gsdi_summary_result.getDuplicationsSum();
  79     }
  80
  81     public int getDuplicationsSum() {
  82         return _duplications_sum;
  83     }
  84
  85     @Override
  86     public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {
  87         return _mapped_species_tree_nodes;
  88     }
  89
  90     @Override
  91     public final SortedSet<String> getReMappedScientificNamesFromGeneTree() {
  92         return _scientific_names_mapped_to_reduced_specificity;
  93     }
  94
  95     public final int getSpeciationOrDuplicationEventsSum() {
  96         return _speciation_or_duplication_events_sum;
  97     }
  98
  99     @Override
 100     public final int getSpeciationsSum() {
 101         return _speciations_sum;
 102     }
 103
 104     @Override
 105     public List<PhylogenyNode> getStrippedExternalGeneTreeNodes() {
 106         return _stripped_gene_tree_nodes;
 107     }
 108
 109     @Override
 110     public List<PhylogenyNode> getStrippedSpeciesTreeNodes() {
 111         return _stripped_species_tree_nodes;
 112     }
 113
 114     @Override
 115     public TaxonomyComparisonBase getTaxCompBase() {
 116         return _tax_comp_base;
 117     }
 118
 119     @Override
 120     public final String toString() {
 121         final StringBuffer sb = new StringBuffer();
 122         sb.append( "Most parsimonious duplication model: " + _most_parsimonious_duplication_model );
 123         sb.append( ForesterUtil.getLineSeparator() );
 124         sb.append( "Speciations sum                    : " + getSpeciationsSum() );
 125         sb.append( ForesterUtil.getLineSeparator() );
 126         sb.append( "Duplications sum                   : " + getDuplicationsSum() );
 127         sb.append( ForesterUtil.getLineSeparator() );
 128         if ( !_most_parsimonious_duplication_model ) {
 129             sb.append( "Speciation or duplications sum     : " + getSpeciationOrDuplicationEventsSum() );
 130             sb.append( ForesterUtil.getLineSeparator() );
 131         }
 132         return sb.toString();
 133     }
 134
 135     /**
 136      * Traverses the subtree of PhylogenyNode g in postorder, calculating the
 137      * mapping function M, and determines which nodes represent speciation
 138      * events and which ones duplication events.
 139      * <p>
 140      * Preconditions: Mapping M for external nodes must have been calculated and
 141      * the species tree must be labeled in preorder.
 142      * <p>
 143      * @return
 144      *
 145      */
 146     final static GSDIsummaryResult geneTreePostOrderTraversal( final Phylogeny gene_tree,
 147                                                                final boolean most_parsimonious_duplication_model ) {
 148         final GSDIsummaryResult res = new GSDIsummaryResult();
 149         for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {
 150             final PhylogenyNode g = it.next();
 151             if ( g.isInternal() ) {
 152                 PhylogenyNode s1 = g.getChildNode1().getLink();
 153                 PhylogenyNode s2 = g.getChildNode2().getLink();
 154                 while ( s1 != s2 ) {
 155                     if ( s1.getId() > s2.getId() ) {
 156                         s1 = s1.getParent();
 157                     }
 158                     else {
 159                         s2 = s2.getParent();
 160                     }
 161                 }
 162                 g.setLink( s1 );
 163                 determineEvent( s1, g, most_parsimonious_duplication_model, res );
 164             }
 165         }
 166         return res;
 167     }
 168
 169     /**
 170      * This allows for linking of internal nodes of the species tree (as opposed
 171      * to just external nodes, as in the method it overrides.
 172      * If TaxonomyComparisonBase is null, it will try to determine it.
 173      * @throws SDIException
 174      *
 175      */
 176     final static NodesLinkingResult linkNodesOfG( final Phylogeny gene_tree,
 177                                                   final Phylogeny species_tree,
 178                                                   final TaxonomyComparisonBase tax_comp_base,
 179                                                   final boolean strip_gene_tree,
 180                                                   final boolean strip_species_tree ) throws SDIException {
 181         final Map<String, PhylogenyNode> species_to_node_map = new HashMap<String, PhylogenyNode>();
 182         final List<PhylogenyNode> species_tree_ext_nodes = new ArrayList<PhylogenyNode>();
 183         final NodesLinkingResult res = new NodesLinkingResult();
 184         if ( tax_comp_base == null ) {
 185             res.setTaxCompBase( SDIutil.determineTaxonomyComparisonBase( gene_tree ) );
 186         }
 187         else {
 188             res.setTaxCompBase( tax_comp_base );
 189         }
 190         // Stringyfied taxonomy is the key, node is the value.
 191         for( final PhylogenyNodeIterator iter = species_tree.iteratorExternalForward(); iter.hasNext(); ) {
 192             final PhylogenyNode s = iter.next();
 193             species_tree_ext_nodes.add( s );
 194             if ( s.getNodeData().isHasTaxonomy() ) {
 195                 final String tax_str = SDIutil.taxonomyToString( s, res.getTaxCompBase() );
 196                 if ( !ForesterUtil.isEmpty( tax_str ) ) {
 197                     if ( species_to_node_map.containsKey( tax_str ) ) {
 198                         throw new SDIException( "taxonomy \"" + tax_str + "\" is not unique in species tree (using "
 199                                 + res.getTaxCompBase() + " for linking to gene tree)" );
 200                     }
 201                     species_to_node_map.put( tax_str, s );
 202                 }
 203             }
 204         }
 205         // Retrieve the reference to the node with a matching stringyfied taxonomy.
 206         for( final PhylogenyNodeIterator iter = gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
 207             final PhylogenyNode g = iter.next();
 208             if ( !g.getNodeData().isHasTaxonomy() ) {
 209                 if ( strip_gene_tree ) {
 210                     res.getStrippedGeneTreeNodes().add( g );
 211                 }
 212                 else {
 213                     throw new SDIException( "gene tree node \"" + g + "\" has no taxonomic data" );
 214                 }
 215             }
 216             else {
 217                 final String tax_str = SDIutil.taxonomyToString( g, res.getTaxCompBase() );
 218                 if ( ForesterUtil.isEmpty( tax_str ) ) {
 219                     if ( strip_gene_tree ) {
 220                         res.getStrippedGeneTreeNodes().add( g );
 221                     }
 222                     else {
 223                         throw new SDIException( "gene tree node \"" + g + "\" has no appropriate taxonomic data" );
 224                     }
 225                 }
 226                 else {
 227                     PhylogenyNode s = species_to_node_map.get( tax_str );
 228                     if ( ( res.getTaxCompBase() == TaxonomyComparisonBase.SCIENTIFIC_NAME ) && ( s == null )
 229                             && ( ForesterUtil.countChars( tax_str, ' ' ) > 1 ) ) {
 230                         s = tryMapByRemovingOverlySpecificData( species_to_node_map,
 231                                                                 tax_str,
 232                                                                 res.getScientificNamesMappedToReducedSpecificity() );
 233                     }
 234                     if ( s == null ) {
 235                         if ( strip_gene_tree ) {
 236                             res.getStrippedGeneTreeNodes().add( g );
 237                         }
 238                         else {
 239                             throw new SDIException( "taxonomy \"" + g.getNodeData().getTaxonomy()
 240                                     + "\" not present in species tree" );
 241                         }
 242                     }
 243                     else {
 244                         g.setLink( s );
 245                         res.getMappedSpeciesTreeNodes().add( s );
 246                     }
 247                 }
 248             }
 249         } // for loop
 250         if ( strip_gene_tree ) {
 251             stripTree( gene_tree, res.getStrippedGeneTreeNodes() );
 252             if ( gene_tree.isEmpty() || ( gene_tree.getNumberOfExternalNodes() < 2 ) ) {
 253                 throw new SDIException( "species could not be mapped between gene tree and species tree" );
 254             }
 255         }
 256         if ( strip_species_tree ) {
 257             stripSpeciesTree( species_tree, species_tree_ext_nodes, res );
 258         }
 259         return res;
 260     }
 261
 262     private final static void addScientificNamesMappedToReducedSpecificity( final String s1,
 263                                                                             final String s2,
 264                                                                             final SortedSet<String> scientific_names_mapped_to_reduced_specificity ) {
 265         scientific_names_mapped_to_reduced_specificity.add( s1 + " -> " + s2 );
 266     }
 267
 268     private final static void determineEvent( final PhylogenyNode s,
 269                                               final PhylogenyNode g,
 270                                               final boolean most_parsimonious_duplication_model,
 271                                               final GSDIsummaryResult res ) {
 272         boolean oyako = false;
 273         if ( ( g.getChildNode1().getLink() == s ) || ( g.getChildNode2().getLink() == s ) ) {
 274             oyako = true;
 275         }
 276         if ( g.getLink().getNumberOfDescendants() == 2 ) {
 277             if ( oyako ) {
 278                 g.getNodeData().setEvent( Event.createSingleDuplicationEvent() );
 279                 res.increaseDuplicationsSum();
 280             }
 281             else {
 282                 g.getNodeData().setEvent( Event.createSingleSpeciationEvent() );
 283                 res.increaseSpeciationsSum();
 284             }
 285         }
 286         else {
 287             if ( oyako ) {
 288                 final Set<PhylogenyNode> set = new HashSet<PhylogenyNode>();
 289                 for( PhylogenyNode n : g.getChildNode1().getAllExternalDescendants() ) {
 290                     n = n.getLink();
 291                     while ( n.getParent() != s ) {
 292                         n = n.getParent();
 293                         if ( n.isRoot() ) {
 294                             break;
 295                         }
 296                     }
 297                     set.add( n );
 298                 }
 299                 boolean multiple = false;
 300                 for( PhylogenyNode n : g.getChildNode2().getAllExternalDescendants() ) {
 301                     n = n.getLink();
 302                     while ( n.getParent() != s ) {
 303                         n = n.getParent();
 304                         if ( n.isRoot() ) {
 305                             break;
 306                         }
 307                     }
 308                     if ( set.contains( n ) ) {
 309                         multiple = true;
 310                         break;
 311                     }
 312                 }
 313                 if ( multiple ) {
 314                     g.getNodeData().setEvent( Event.createSingleDuplicationEvent() );
 315                     res.increaseDuplicationsSum();
 316                 }
 317                 else {
 318                     if ( most_parsimonious_duplication_model ) {
 319                         g.getNodeData().setEvent( Event.createSingleSpeciationEvent() );
 320                         res.increaseSpeciationsSum();
 321                     }
 322                     else {
 323                         g.getNodeData().setEvent( Event.createSingleSpeciationOrDuplicationEvent() );
 324                         res.increaseSpeciationOrDuplicationEventsSum();
 325                     }
 326                 }
 327             }
 328             else {
 329                 g.getNodeData().setEvent( Event.createSingleSpeciationEvent() );
 330                 res.increaseSpeciationsSum();
 331             }
 332         }
 333     }
 334
 335     private final static void stripSpeciesTree( final Phylogeny species_tree,
 336                                                 final List<PhylogenyNode> species_tree_ext_nodes,
 337                                                 final NodesLinkingResult res ) {
 338         for( final PhylogenyNode s : species_tree_ext_nodes ) {
 339             if ( !res.getMappedSpeciesTreeNodes().contains( s ) ) {
 340                 species_tree.deleteSubtree( s, true );
 341                 res.getStrippedSpeciesTreeNodes().add( s );
 342             }
 343         }
 344         species_tree.clearHashIdToNodeMap();
 345         species_tree.externalNodesHaveChanged();
 346     }
 347
 348     private final static void stripTree( final Phylogeny phy, final List<PhylogenyNode> strip_nodes ) {
 349         for( final PhylogenyNode g : strip_nodes ) {
 350             phy.deleteSubtree( g, true );
 351         }
 352         phy.clearHashIdToNodeMap();
 353         phy.externalNodesHaveChanged();
 354     }
 355
 356     private final static PhylogenyNode tryMapByRemovingOverlySpecificData( final Map<String, PhylogenyNode> species_to_node_map,
 357                                                                            final String tax_str,
 358                                                                            final SortedSet<String> scientific_names_mapped_to_reduced_specificity ) {
 359         PhylogenyNode s = tryMapByRemovingOverlySpecificData( species_to_node_map,
 360                                                               tax_str,
 361                                                               " (",
 362                                                               scientific_names_mapped_to_reduced_specificity );
 363         if ( s == null ) {
 364             if ( ForesterUtil.countChars( tax_str, ' ' ) == 2 ) {
 365                 final String new_tax_str = tax_str.substring( 0, tax_str.lastIndexOf( ' ' ) ).trim();
 366                 s = species_to_node_map.get( new_tax_str );
 367                 if ( s != null ) {
 368                     addScientificNamesMappedToReducedSpecificity( tax_str,
 369                                                                   new_tax_str,
 370                                                                   scientific_names_mapped_to_reduced_specificity );
 371                 }
 372             }
 373         }
 374         if ( s == null ) {
 375             for( final String t : new String[] { " subspecies ", " strain ", " variety ", " varietas ", " subvariety ",
 376                     " form ", " subform ", " cultivar ", " section ", " subsection " } ) {
 377                 s = tryMapByRemovingOverlySpecificData( species_to_node_map,
 378                                                         tax_str,
 379                                                         t,
 380                                                         scientific_names_mapped_to_reduced_specificity );
 381                 if ( s != null ) {
 382                     break;
 383                 }
 384             }
 385         }
 386         return s;
 387     }
 388
 389     private final static PhylogenyNode tryMapByRemovingOverlySpecificData( final Map<String, PhylogenyNode> species_to_node_map,
 390                                                                            final String tax_str,
 391                                                                            final String term,
 392                                                                            final SortedSet<String> scientific_names_mapped_to_reduced_specificity ) {
 393         final int i = tax_str.indexOf( term );
 394         if ( i > 4 ) {
 395             final String new_tax_str = tax_str.substring( 0, i ).trim();
 396             final PhylogenyNode s = species_to_node_map.get( new_tax_str );
 397             if ( s != null ) {
 398                 addScientificNamesMappedToReducedSpecificity( tax_str,
 399                                                               new_tax_str,
 400                                                               scientific_names_mapped_to_reduced_specificity );
 401             }
 402             return s;
 403         }
 404         return null;
 405     }
 406 }