2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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.
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.
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
23 // Contact: phylosoft @ gmail . com
24 // WWW: www.phylosoft.org/forester
26 package org.forester.sdi;
28 import java.util.ArrayList;
29 import java.util.HashMap;
30 import java.util.HashSet;
31 import java.util.List;
34 import java.util.SortedSet;
35 import java.util.TreeSet;
37 import org.forester.phylogeny.Phylogeny;
38 import org.forester.phylogeny.PhylogenyNode;
39 import org.forester.phylogeny.data.Event;
40 import org.forester.phylogeny.data.Taxonomy;
41 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
42 import org.forester.util.ForesterUtil;
45 * Implements our algorithm for speciation - duplication inference (SDI). <p>
46 * The initialization is accomplished by: </p> <ul> <li>method
47 * "linkExtNodesOfG()" of class SDI: setting the links for the external nodes of
48 * the gene tree <li>"preorderReID(int)" from class Phylogeny: numbering of
49 * nodes of the species tree in preorder <li>the optional stripping of the
50 * species tree is accomplished by method "stripTree(Phylogeny,Phylogeny)" of
51 * class Phylogeny </ul> <p> The recursion part is accomplished by this class'
52 * method "geneTreePostOrderTraversal(PhylogenyNode)". <p> Requires JDK 1.5 or
55 * @see SDI#linkNodesOfG()
57 * @see Phylogeny#preorderReID(int)
60 * PhylogenyMethods#taxonomyBasedDeletionOfExternalNodes(Phylogeny,Phylogeny)
62 * @see #geneTreePostOrderTraversal(PhylogenyNode)
64 * @author Christian M. Zmasek
66 public final class GSDI extends SDI {
68 private final boolean _most_parsimonious_duplication_model;
69 private final boolean _strip_gene_tree;
70 private final boolean _strip_species_tree;
71 private int _speciation_or_duplication_events_sum;
72 private int _speciations_sum;
73 private final List<PhylogenyNode> _stripped_gene_tree_nodes;
74 private final List<PhylogenyNode> _stripped_species_tree_nodes;
75 private final Set<PhylogenyNode> _mapped_species_tree_nodes;
76 private TaxonomyComparisonBase _tax_comp_base;
77 private final SortedSet<String> _scientific_names_mapped_to_reduced_specificity;
79 public GSDI( final Phylogeny gene_tree,
80 final Phylogeny species_tree,
81 final boolean most_parsimonious_duplication_model,
82 final boolean strip_gene_tree,
83 final boolean strip_species_tree ) throws SDIException {
84 super( gene_tree, species_tree );
85 _speciation_or_duplication_events_sum = 0;
87 _most_parsimonious_duplication_model = most_parsimonious_duplication_model;
88 _duplications_sum = 0;
89 _strip_gene_tree = strip_gene_tree;
90 _strip_species_tree = strip_species_tree;
91 _stripped_gene_tree_nodes = new ArrayList<PhylogenyNode>();
92 _stripped_species_tree_nodes = new ArrayList<PhylogenyNode>();
93 _mapped_species_tree_nodes = new HashSet<PhylogenyNode>();
94 _scientific_names_mapped_to_reduced_specificity = new TreeSet<String>();
96 getSpeciesTree().preOrderReId();
97 geneTreePostOrderTraversal();
100 GSDI( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean most_parsimonious_duplication_model )
101 throws SDIException {
102 this( gene_tree, species_tree, most_parsimonious_duplication_model, false, false );
105 // s is the node on the species tree g maps to.
106 private final void determineEvent( final PhylogenyNode s, final PhylogenyNode g ) {
107 boolean oyako = false;
108 if ( ( g.getChildNode1().getLink() == s ) || ( g.getChildNode2().getLink() == s ) ) {
111 if ( g.getLink().getNumberOfDescendants() == 2 ) {
113 g.getNodeData().setEvent( createDuplicationEvent() );
116 g.getNodeData().setEvent( createSpeciationEvent() );
121 final Set<PhylogenyNode> set = new HashSet<PhylogenyNode>();
122 for( PhylogenyNode n : g.getChildNode1().getAllExternalDescendants() ) {
124 while ( n.getParent() != s ) {
132 boolean multiple = false;
133 for( PhylogenyNode n : g.getChildNode2().getAllExternalDescendants() ) {
135 while ( n.getParent() != s ) {
141 if ( set.contains( n ) ) {
147 g.getNodeData().setEvent( createDuplicationEvent() );
150 if ( _most_parsimonious_duplication_model ) {
151 g.getNodeData().setEvent( createSpeciationEvent() );
154 g.getNodeData().setEvent( createSingleSpeciationOrDuplicationEvent() );
159 g.getNodeData().setEvent( createSpeciationEvent() );
165 * Traverses the subtree of PhylogenyNode g in postorder, calculating the
166 * mapping function M, and determines which nodes represent speciation
167 * events and which ones duplication events.
169 * Preconditions: Mapping M for external nodes must have been calculated and
170 * the species tree must be labeled in preorder.
174 final void geneTreePostOrderTraversal() {
175 for( final PhylogenyNodeIterator it = getGeneTree().iteratorPostorder(); it.hasNext(); ) {
176 final PhylogenyNode g = it.next();
177 if ( g.isInternal() ) {
178 PhylogenyNode s1 = g.getChildNode1().getLink();
179 PhylogenyNode s2 = g.getChildNode2().getLink();
181 if ( s1.getId() > s2.getId() ) {
189 determineEvent( s1, g );
194 private final Event createDuplicationEvent() {
195 final Event event = Event.createSingleDuplicationEvent();
200 private final Event createSingleSpeciationOrDuplicationEvent() {
201 final Event event = Event.createSingleSpeciationOrDuplicationEvent();
202 ++_speciation_or_duplication_events_sum;
206 private final Event createSpeciationEvent() {
207 final Event event = Event.createSingleSpeciationEvent();
212 public final int getSpeciationOrDuplicationEventsSum() {
213 return _speciation_or_duplication_events_sum;
216 public final int getSpeciationsSum() {
217 return _speciations_sum;
221 * This allows for linking of internal nodes of the species tree (as opposed
222 * to just external nodes, as in the method it overrides.
223 * @throws SDIException
227 final void linkNodesOfG() throws SDIException {
228 final Map<String, PhylogenyNode> species_to_node_map = new HashMap<String, PhylogenyNode>();
229 final List<PhylogenyNode> species_tree_ext_nodes = new ArrayList<PhylogenyNode>();
230 _tax_comp_base = determineTaxonomyComparisonBase( _gene_tree );
231 // Stringyfied taxonomy is the key, node is the value.
232 for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) {
233 final PhylogenyNode s = iter.next();
234 species_tree_ext_nodes.add( s );
235 if ( s.getNodeData().isHasTaxonomy() ) {
236 final String tax_str = taxonomyToString( s, _tax_comp_base );
237 if ( !ForesterUtil.isEmpty( tax_str ) ) {
238 if ( species_to_node_map.containsKey( tax_str ) ) {
239 throw new SDIException( "taxonomy \"" + s + "\" is not unique in species tree" );
241 species_to_node_map.put( tax_str, s );
245 // Retrieve the reference to the node with a matching stringyfied taxonomy.
246 for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
247 final PhylogenyNode g = iter.next();
248 if ( !g.getNodeData().isHasTaxonomy() ) {
249 if ( _strip_gene_tree ) {
250 _stripped_gene_tree_nodes.add( g );
253 throw new SDIException( "gene tree node \"" + g + "\" has no taxonomic data" );
257 final String tax_str = taxonomyToString( g, _tax_comp_base );
258 if ( ForesterUtil.isEmpty( tax_str ) ) {
259 if ( _strip_gene_tree ) {
260 _stripped_gene_tree_nodes.add( g );
263 throw new SDIException( "gene tree node \"" + g + "\" has no appropriate taxonomic data" );
267 PhylogenyNode s = species_to_node_map.get( tax_str );
268 if ( ( _tax_comp_base == TaxonomyComparisonBase.SCIENTIFIC_NAME ) && ( s == null )
269 && ( ForesterUtil.countChars( tax_str, ' ' ) > 1 ) ) {
270 s = tryMapByRemovingOverlySpecificData( species_to_node_map, tax_str );
273 if ( _strip_gene_tree ) {
274 _stripped_gene_tree_nodes.add( g );
277 throw new SDIException( "taxonomy \"" + g.getNodeData().getTaxonomy()
278 + "\" not present in species tree" );
283 _mapped_species_tree_nodes.add( s );
288 if ( _strip_gene_tree ) {
290 if ( getGeneTree().isEmpty() || ( getGeneTree().getNumberOfExternalNodes() < 2 ) ) {
291 throw new SDIException( "species could not be mapped between gene tree and species tree" );
294 if ( _strip_species_tree ) {
295 stripSpeciesTree( species_tree_ext_nodes );
299 private final PhylogenyNode tryMapByRemovingOverlySpecificData( final Map<String, PhylogenyNode> species_to_node_map,
300 final String tax_str ) {
301 PhylogenyNode s = tryMapByRemovingOverlySpecificData( species_to_node_map, tax_str, " (" );
303 if ( ForesterUtil.countChars( tax_str, ' ' ) == 2 ) {
304 final String new_tax_str = tax_str.substring( 0, tax_str.lastIndexOf( ' ' ) ).trim();
305 s = species_to_node_map.get( new_tax_str );
307 addScientificNamesMappedToReducedSpecificity( tax_str, new_tax_str );
312 for( final String t : new String[] { " subspecies ", " strain ", " variety ", " varietas ", " subvariety ",
313 " form ", " subform ", " cultivar ", " section ", " subsection " } ) {
314 s = tryMapByRemovingOverlySpecificData( species_to_node_map, tax_str, t );
323 private final PhylogenyNode tryMapByRemovingOverlySpecificData( final Map<String, PhylogenyNode> species_to_node_map,
324 final String tax_str,
325 final String term ) {
326 final int i = tax_str.indexOf( term );
328 final String new_tax_str = tax_str.substring( 0, i ).trim();
329 final PhylogenyNode s = species_to_node_map.get( new_tax_str );
331 addScientificNamesMappedToReducedSpecificity( tax_str, new_tax_str );
338 private final void addScientificNamesMappedToReducedSpecificity( final String s1, final String s2 ) {
339 _scientific_names_mapped_to_reduced_specificity.add( s1 + " -> " + s2 );
342 public final SortedSet<String> getReMappedScientificNamesFromGeneTree() {
343 return _scientific_names_mapped_to_reduced_specificity;
346 public TaxonomyComparisonBase getTaxCompBase() {
347 return _tax_comp_base;
350 private void stripSpeciesTree( final List<PhylogenyNode> species_tree_ext_nodes ) {
351 for( final PhylogenyNode s : species_tree_ext_nodes ) {
352 if ( !_mapped_species_tree_nodes.contains( s ) ) {
353 _species_tree.deleteSubtree( s, true );
354 _stripped_species_tree_nodes.add( s );
359 public List<PhylogenyNode> getStrippedSpeciesTreeNodes() {
360 return _stripped_species_tree_nodes;
363 private void stripGeneTree() {
364 for( final PhylogenyNode g : _stripped_gene_tree_nodes ) {
365 _gene_tree.deleteSubtree( g, true );
369 public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {
370 return _mapped_species_tree_nodes;
373 public static TaxonomyComparisonBase determineTaxonomyComparisonBase( final Phylogeny gene_tree ) {
374 int with_id_count = 0;
375 int with_code_count = 0;
376 int with_sn_count = 0;
378 for( final PhylogenyNodeIterator iter = gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
379 final PhylogenyNode g = iter.next();
380 if ( g.getNodeData().isHasTaxonomy() ) {
381 final Taxonomy tax = g.getNodeData().getTaxonomy();
382 if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) {
383 if ( ++with_id_count > max ) {
387 if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
388 if ( ++with_code_count > max ) {
389 max = with_code_count;
392 if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
393 if ( ++with_sn_count > max ) {
400 throw new IllegalArgumentException( "gene tree has no taxonomic data" );
402 else if ( max == 1 ) {
403 throw new IllegalArgumentException( "gene tree has only one node with taxonomic data" );
405 else if ( max == with_id_count ) {
406 return SDI.TaxonomyComparisonBase.ID;
408 else if ( max == with_sn_count ) {
409 return SDI.TaxonomyComparisonBase.SCIENTIFIC_NAME;
412 return SDI.TaxonomyComparisonBase.CODE;
416 public List<PhylogenyNode> getStrippedExternalGeneTreeNodes() {
417 return _stripped_gene_tree_nodes;
421 public final String toString() {
422 final StringBuffer sb = new StringBuffer();
423 sb.append( "Most parsimonious duplication model: " + _most_parsimonious_duplication_model );
424 sb.append( ForesterUtil.getLineSeparator() );
425 sb.append( "Speciations sum : " + getSpeciationsSum() );
426 sb.append( ForesterUtil.getLineSeparator() );
427 sb.append( "Duplications sum : " + getDuplicationsSum() );
428 sb.append( ForesterUtil.getLineSeparator() );
429 if ( !_most_parsimonious_duplication_model ) {
430 sb.append( "Speciation or duplications sum : " + getSpeciationOrDuplicationEventsSum() );
431 sb.append( ForesterUtil.getLineSeparator() );
433 sb.append( "mapping cost L : " + computeMappingCostL() );
434 return sb.toString();