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         if ( gene_tree.getRoot().getNumberOfDescendants() == 3 ) {
  63             gene_tree.reRoot( gene_tree.getRoot().getChildNode( 2 ) );
  64         }
  65         final NodesLinkingResult nodes_linking_result = linkNodesOfG( gene_tree,
  66                                                                       species_tree,
  67                                                                       null,
  68                                                                       strip_gene_tree,
  69                                                                       strip_species_tree );
  70         _stripped_gene_tree_nodes = nodes_linking_result.getStrippedGeneTreeNodes();
  71         _stripped_species_tree_nodes = nodes_linking_result.getStrippedSpeciesTreeNodes();
  72         _mapped_species_tree_nodes = nodes_linking_result.getMappedSpeciesTreeNodes();
  73         _scientific_names_mapped_to_reduced_specificity = nodes_linking_result
  74                 .getScientificNamesMappedToReducedSpecificity();
  75         _tax_comp_base = nodes_linking_result.getTaxCompBase();
  76         PhylogenyMethods.preOrderReId( species_tree );
  77         final GSDIsummaryResult gsdi_summary_result = geneTreePostOrderTraversal( gene_tree,
  78                                                                                   _most_parsimonious_duplication_model );
  79         _speciation_or_duplication_events_sum = gsdi_summary_result.getSpeciationOrDuplicationEventsSum();
  80         _speciations_sum = gsdi_summary_result.getSpeciationsSum();
  81         _duplications_sum = gsdi_summary_result.getDuplicationsSum();
  82     }
  83
  84     public int getDuplicationsSum() {
  85         return _duplications_sum;
  86     }
  87
  88     @Override
  89     public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {
  90         return _mapped_species_tree_nodes;
  91     }
  92
  93     @Override
  94     public final SortedSet<String> getReMappedScientificNamesFromGeneTree() {
  95         return _scientific_names_mapped_to_reduced_specificity;
  96     }
  97
  98     public final int getSpeciationOrDuplicationEventsSum() {
  99         return _speciation_or_duplication_events_sum;
 100     }
 101
 102     @Override
 103     public final int getSpeciationsSum() {
 104         return _speciations_sum;
 105     }
 106
 107     @Override
 108     public List<PhylogenyNode> getStrippedExternalGeneTreeNodes() {
 109         return _stripped_gene_tree_nodes;
 110     }
 111
 112     @Override
 113     public List<PhylogenyNode> getStrippedSpeciesTreeNodes() {
 114         return _stripped_species_tree_nodes;
 115     }
 116
 117     @Override
 118     public TaxonomyComparisonBase getTaxCompBase() {
 119         return _tax_comp_base;
 120     }
 121
 122     @Override
 123     public final String toString() {
 124         final StringBuffer sb = new StringBuffer();
 125         sb.append( "Most parsimonious duplication model: " + _most_parsimonious_duplication_model );
 126         sb.append( ForesterUtil.getLineSeparator() );
 127         sb.append( "Speciations sum                    : " + getSpeciationsSum() );
 128         sb.append( ForesterUtil.getLineSeparator() );
 129         sb.append( "Duplications sum                   : " + getDuplicationsSum() );
 130         sb.append( ForesterUtil.getLineSeparator() );
 131         if ( !_most_parsimonious_duplication_model ) {
 132             sb.append( "Speciation or duplications sum     : " + getSpeciationOrDuplicationEventsSum() );
 133             sb.append( ForesterUtil.getLineSeparator() );
 134         }
 135         return sb.toString();
 136     }
 137
 138     /**
 139      * Traverses the subtree of PhylogenyNode g in postorder, calculating the
 140      * mapping function M, and determines which nodes represent speciation
 141      * events and which ones duplication events.
 142      * <p>
 143      * Preconditions: Mapping M for external nodes must have been calculated and
 144      * the species tree must be labeled in preorder.
 145      * <p>
 146      * @return
 147      * @throws SDIException
 148      *
 149      */
 150     final static GSDIsummaryResult geneTreePostOrderTraversal( final Phylogeny gene_tree,
 151                                                                final boolean most_parsimonious_duplication_model )
 152             throws SDIException {
 153         final GSDIsummaryResult res = new GSDIsummaryResult();
 154         for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {
 155             final PhylogenyNode g = it.next();
 156             if ( g.isInternal() ) {
 157                 if ( g.getNumberOfDescendants() != 2 ) {
 158                     throw new SDIException( "gene tree contains internal node with " + g.getNumberOfDescendants()
 159                             + " descendents" );
 160                 }
 161                 PhylogenyNode s1 = g.getChildNode1().getLink();
 162                 PhylogenyNode s2 = g.getChildNode2().getLink();
 163                 while ( s1 != s2 ) {
 164                     if ( s1.getId() > s2.getId() ) {
 165                         s1 = s1.getParent();
 166                     }
 167                     else {
 168                         s2 = s2.getParent();
 169                     }
 170                 }
 171                 g.setLink( s1 );
 172                 determineEvent( s1, g, most_parsimonious_duplication_model, res );
 173             }
 174         }
 175         return res;
 176     }
 177
 178     /**
 179      * This allows for linking of internal nodes of the species tree (as opposed
 180      * to just external nodes, as in the method it overrides.
 181      * If TaxonomyComparisonBase is null, it will try to determine it.
 182      * @throws SDIException
 183      *
 184      */
 185     final static NodesLinkingResult linkNodesOfG( final Phylogeny gene_tree,
 186                                                   final Phylogeny species_tree,
 187                                                   final TaxonomyComparisonBase tax_comp_base,
 188                                                   final boolean strip_gene_tree,
 189                                                   final boolean strip_species_tree ) throws SDIException {
 190         final Map<String, PhylogenyNode> species_to_node_map = new HashMap<String, PhylogenyNode>();
 191         final List<PhylogenyNode> species_tree_ext_nodes = new ArrayList<PhylogenyNode>();
 192         final NodesLinkingResult res = new NodesLinkingResult();
 193         if ( tax_comp_base == null ) {
 194             res.setTaxCompBase( SDIutil.determineTaxonomyComparisonBase( gene_tree ) );
 195         }
 196         else {
 197             res.setTaxCompBase( tax_comp_base );
 198         }
 199         // Stringyfied taxonomy is the key, node is the value.
 200         for( final PhylogenyNodeIterator iter = species_tree.iteratorExternalForward(); iter.hasNext(); ) {
 201             final PhylogenyNode s = iter.next();
 202             species_tree_ext_nodes.add( s );
 203             if ( s.getNodeData().isHasTaxonomy() ) {
 204                 final String tax_str = SDIutil.taxonomyToString( s, res.getTaxCompBase() );
 205                 if ( !ForesterUtil.isEmpty( tax_str ) ) {
 206                     if ( species_to_node_map.containsKey( tax_str ) ) {
 207                         throw new SDIException( "taxonomy \"" + tax_str + "\" is not unique in species tree (using "
 208                                 + res.getTaxCompBase() + " for linking to gene tree)" );
 209                     }
 210                     species_to_node_map.put( tax_str, s );
 211                 }
 212             }
 213         }
 214         // Retrieve the reference to the node with a matching stringyfied taxonomy.
 215         for( final PhylogenyNodeIterator iter = gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
 216             final PhylogenyNode g = iter.next();
 217             if ( !g.getNodeData().isHasTaxonomy() ) {
 218                 if ( strip_gene_tree ) {
 219                     res.getStrippedGeneTreeNodes().add( g );
 220                 }
 221                 else {
 222                     throw new SDIException( "gene tree node \"" + g + "\" has no taxonomic data" );
 223                 }
 224             }
 225             else {
 226                 final String tax_str = SDIutil.taxonomyToString( g, res.getTaxCompBase() );
 227                 if ( ForesterUtil.isEmpty( tax_str ) ) {
 228                     if ( strip_gene_tree ) {
 229                         res.getStrippedGeneTreeNodes().add( g );
 230                     }
 231                     else {
 232                         throw new SDIException( "gene tree node \"" + g + "\" has no appropriate taxonomic data" );
 233                     }
 234                 }
 235                 else {
 236                     PhylogenyNode s = species_to_node_map.get( tax_str );
 237                     if ( ( res.getTaxCompBase() == TaxonomyComparisonBase.SCIENTIFIC_NAME ) && ( s == null )
 238                             && ( ForesterUtil.countChars( tax_str, ' ' ) > 1 ) ) {
 239                         s = tryMapByRemovingOverlySpecificData( species_to_node_map,
 240                                                                 tax_str,
 241                                                                 res.getScientificNamesMappedToReducedSpecificity() );
 242                     }
 243                     if ( s == null ) {
 244                         if ( strip_gene_tree ) {
 245                             res.getStrippedGeneTreeNodes().add( g );
 246                         }
 247                         else {
 248                             throw new SDIException( "taxonomy \"" + g.getNodeData().getTaxonomy()
 249                                     + "\" not present in species tree" );
 250                         }
 251                     }
 252                     else {
 253                         g.setLink( s );
 254                         res.getMappedSpeciesTreeNodes().add( s );
 255                     }
 256                 }
 257             }
 258         } // for loop
 259         if ( strip_gene_tree ) {
 260             stripTree( gene_tree, res.getStrippedGeneTreeNodes() );
 261             if ( gene_tree.isEmpty() || ( gene_tree.getNumberOfExternalNodes() < 2 ) ) {
 262                 throw new SDIException( "species could not be mapped between gene tree and species tree" );
 263             }
 264         }
 265         if ( strip_species_tree ) {
 266             stripSpeciesTree( species_tree, species_tree_ext_nodes, res );
 267         }
 268         return res;
 269     }
 270
 271     private final static void addScientificNamesMappedToReducedSpecificity( final String s1,
 272                                                                             final String s2,
 273                                                                             final SortedSet<String> scientific_names_mapped_to_reduced_specificity ) {
 274         scientific_names_mapped_to_reduced_specificity.add( s1 + " -> " + s2 );
 275     }
 276
 277     private final static void determineEvent( final PhylogenyNode s,
 278                                               final PhylogenyNode g,
 279                                               final boolean most_parsimonious_duplication_model,
 280                                               final GSDIsummaryResult res ) {
 281         boolean oyako = false;
 282         if ( ( g.getChildNode1().getLink() == s ) || ( g.getChildNode2().getLink() == s ) ) {
 283             oyako = true;
 284         }
 285         if ( g.getLink().getNumberOfDescendants() == 2 ) {
 286             if ( oyako ) {
 287                 g.getNodeData().setEvent( Event.createSingleDuplicationEvent() );
 288                 res.increaseDuplicationsSum();
 289             }
 290             else {
 291                 g.getNodeData().setEvent( Event.createSingleSpeciationEvent() );
 292                 res.increaseSpeciationsSum();
 293             }
 294         }
 295         else {
 296             if ( oyako ) {
 297                 final Set<PhylogenyNode> set = new HashSet<PhylogenyNode>();
 298                 for( PhylogenyNode n : g.getChildNode1().getAllExternalDescendants() ) {
 299                     n = n.getLink();
 300                     while ( n.getParent() != s ) {
 301                         n = n.getParent();
 302                         if ( n.isRoot() ) {
 303                             break;
 304                         }
 305                     }
 306                     set.add( n );
 307                 }
 308                 boolean multiple = false;
 309                 for( PhylogenyNode n : g.getChildNode2().getAllExternalDescendants() ) {
 310                     n = n.getLink();
 311                     while ( n.getParent() != s ) {
 312                         n = n.getParent();
 313                         if ( n.isRoot() ) {
 314                             break;
 315                         }
 316                     }
 317                     if ( set.contains( n ) ) {
 318                         multiple = true;
 319                         break;
 320                     }
 321                 }
 322                 if ( multiple ) {
 323                     g.getNodeData().setEvent( Event.createSingleDuplicationEvent() );
 324                     res.increaseDuplicationsSum();
 325                 }
 326                 else {
 327                     if ( most_parsimonious_duplication_model ) {
 328                         g.getNodeData().setEvent( Event.createSingleSpeciationEvent() );
 329                         res.increaseSpeciationsSum();
 330                     }
 331                     else {
 332                         g.getNodeData().setEvent( Event.createSingleSpeciationOrDuplicationEvent() );
 333                         res.increaseSpeciationOrDuplicationEventsSum();
 334                     }
 335                 }
 336             }
 337             else {
 338                 g.getNodeData().setEvent( Event.createSingleSpeciationEvent() );
 339                 res.increaseSpeciationsSum();
 340             }
 341         }
 342     }
 343
 344     private final static void stripSpeciesTree( final Phylogeny species_tree,
 345                                                 final List<PhylogenyNode> species_tree_ext_nodes,
 346                                                 final NodesLinkingResult res ) {
 347         for( final PhylogenyNode s : species_tree_ext_nodes ) {
 348             if ( !res.getMappedSpeciesTreeNodes().contains( s ) ) {
 349                 species_tree.deleteSubtree( s, true );
 350                 res.getStrippedSpeciesTreeNodes().add( s );
 351             }
 352         }
 353         species_tree.clearHashIdToNodeMap();
 354         species_tree.externalNodesHaveChanged();
 355     }
 356
 357     private final static void stripTree( final Phylogeny phy, final List<PhylogenyNode> strip_nodes ) {
 358         for( final PhylogenyNode g : strip_nodes ) {
 359             phy.deleteSubtree( g, true );
 360         }
 361         phy.clearHashIdToNodeMap();
 362         phy.externalNodesHaveChanged();
 363     }
 364
 365     private final static PhylogenyNode tryMapByRemovingOverlySpecificData( final Map<String, PhylogenyNode> species_to_node_map,
 366                                                                            final String tax_str,
 367                                                                            final SortedSet<String> scientific_names_mapped_to_reduced_specificity ) {
 368         PhylogenyNode s = tryMapByRemovingOverlySpecificData( species_to_node_map,
 369                                                               tax_str,
 370                                                               " (",
 371                                                               scientific_names_mapped_to_reduced_specificity );
 372         if ( s == null ) {
 373             if ( ForesterUtil.countChars( tax_str, ' ' ) == 2 ) {
 374                 final String new_tax_str = tax_str.substring( 0, tax_str.lastIndexOf( ' ' ) ).trim();
 375                 s = species_to_node_map.get( new_tax_str );
 376                 if ( s != null ) {
 377                     addScientificNamesMappedToReducedSpecificity( tax_str,
 378                                                                   new_tax_str,
 379                                                                   scientific_names_mapped_to_reduced_specificity );
 380                 }
 381             }
 382         }
 383         if ( s == null ) {
 384             for( final String t : new String[] { " subspecies ", " strain ", " variety ", " varietas ", " subvariety ",
 385                     " form ", " subform ", " cultivar ", " section ", " subsection " } ) {
 386                 s = tryMapByRemovingOverlySpecificData( species_to_node_map,
 387                                                         tax_str,
 388                                                         t,
 389                                                         scientific_names_mapped_to_reduced_specificity );
 390                 if ( s != null ) {
 391                     break;
 392                 }
 393             }
 394         }
 395         return s;
 396     }
 397
 398     private final static PhylogenyNode tryMapByRemovingOverlySpecificData( final Map<String, PhylogenyNode> species_to_node_map,
 399                                                                            final String tax_str,
 400                                                                            final String term,
 401                                                                            final SortedSet<String> scientific_names_mapped_to_reduced_specificity ) {
 402         final int i = tax_str.indexOf( term );
 403         if ( i > 4 ) {
 404             final String new_tax_str = tax_str.substring( 0, i ).trim();
 405             final PhylogenyNode s = species_to_node_map.get( new_tax_str );
 406             if ( s != null ) {
 407                 addScientificNamesMappedToReducedSpecificity( tax_str,
 408                                                               new_tax_str,
 409                                                               scientific_names_mapped_to_reduced_specificity );
 410             }
 411             return s;
 412         }
 413         return null;
 414     }
 415 }