import java.util.ArrayList;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
-import java.util.SortedSet;
-import java.util.TreeSet;
+import java.util.Set;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
*/
public final class GSDI extends SDI {
- private final HashMap<PhylogenyNode, Integer> _transversal_counts;
- private final boolean _most_parsimonious_duplication_model;
- private final boolean _strip_gene_tree;
- private final boolean _strip_species_tree;
- private int _speciation_or_duplication_events_sum;
- private int _speciations_sum;
- private final List<PhylogenyNode> _stripped_gene_tree_nodes;
- private final List<PhylogenyNode> _stripped_species_tree_nodes;
- private final SortedSet<PhylogenyNode> _mapped_species_tree_nodes;
+ private final boolean _most_parsimonious_duplication_model;
+ private final boolean _strip_gene_tree;
+ private final boolean _strip_species_tree;
+ private int _speciation_or_duplication_events_sum;
+ private int _speciations_sum;
+ private final List<PhylogenyNode> _stripped_gene_tree_nodes;
+ private final List<PhylogenyNode> _stripped_species_tree_nodes;
+ private final Set<PhylogenyNode> _mapped_species_tree_nodes;
- /**
- * Constructor which sets the gene tree and the species tree to be compared.
- * species_tree is the species tree to which the gene tree gene_tree will be
- * compared to - with method "infer(boolean)". Both Trees must be completely
- * binary and rooted. The actual inference is accomplished with method
- * "infer(boolean)". The mapping cost L can then be calculated with method
- * "computeMappingCost()".
- * <p>
- *
- * @see #infer(boolean)
- * @see SDI#computeMappingCostL()
- * @param gene_tree
- * reference to a rooted gene tree to which assign duplication vs
- * speciation, must have species names in the species name fields
- * for all external nodes
- * @param species_tree
- * reference to a rooted binary species tree which might get
- * stripped in the process, must have species names in the
- * species name fields for all external nodes
- *
- * @param most_parsimonious_duplication_model
- * set to true to assign nodes as speciations which would
- * otherwise be assiged as unknown because of polytomies in the
- * species tree.
- * @throws SdiException
- *
- */
public GSDI( final Phylogeny gene_tree,
final Phylogeny species_tree,
final boolean most_parsimonious_duplication_model,
_speciation_or_duplication_events_sum = 0;
_speciations_sum = 0;
_most_parsimonious_duplication_model = most_parsimonious_duplication_model;
- _transversal_counts = new HashMap<PhylogenyNode, Integer>();
_duplications_sum = 0;
_strip_gene_tree = strip_gene_tree;
_strip_species_tree = strip_species_tree;
_stripped_gene_tree_nodes = new ArrayList<PhylogenyNode>();
_stripped_species_tree_nodes = new ArrayList<PhylogenyNode>();
- _mapped_species_tree_nodes = new TreeSet<PhylogenyNode>();
+ _mapped_species_tree_nodes = new HashSet<PhylogenyNode>();
getSpeciesTree().preOrderReId();
linkNodesOfG();
- geneTreePostOrderTraversal( getGeneTree().getRoot() );
+ geneTreePostOrderTraversal();
}
GSDI( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean most_parsimonious_duplication_model )
this( gene_tree, species_tree, most_parsimonious_duplication_model, false, false );
}
- private final Event createDuplicationEvent() {
- final Event event = Event.createSingleDuplicationEvent();
- ++_duplications_sum;
- return event;
- }
-
- private final Event createSingleSpeciationOrDuplicationEvent() {
- final Event event = Event.createSingleSpeciationOrDuplicationEvent();
- ++_speciation_or_duplication_events_sum;
- return event;
- }
-
- private final Event createSpeciationEvent() {
- final Event event = Event.createSingleSpeciationEvent();
- ++_speciations_sum;
- return event;
- }
-
// s is the node on the species tree g maps to.
private final void determineEvent( final PhylogenyNode s, final PhylogenyNode g ) {
- Event event = null;
- // Determine how many children map to same node as parent.
- int sum_g_childs_mapping_to_s = 0;
- for( final PhylogenyNodeIterator iter = g.iterateChildNodesForward(); iter.hasNext(); ) {
- if ( iter.next().getLink() == s ) {
- ++sum_g_childs_mapping_to_s;
- }
+ boolean oyako = false;
+ if ( ( g.getChildNode1().getLink() == s ) || ( g.getChildNode2().getLink() == s ) ) {
+ oyako = true;
}
- // Determine the sum of traversals.
- int traversals_sum = 0;
- int max_traversals = 0;
- PhylogenyNode max_traversals_node = null;
- if ( !s.isExternal() ) {
- for( final PhylogenyNodeIterator iter = s.iterateChildNodesForward(); iter.hasNext(); ) {
- final PhylogenyNode current_node = iter.next();
- final int traversals = getTraversalCount( current_node );
- traversals_sum += traversals;
- if ( traversals > max_traversals ) {
- max_traversals = traversals;
- max_traversals_node = current_node;
- }
+ if ( g.getLink().getNumberOfDescendants() == 2 ) {
+ if ( oyako ) {
+ g.getNodeData().setEvent( createDuplicationEvent() );
}
- }
- // System.out.println( " sum=" + traversals_sum );
- // System.out.println( " max=" + max_traversals );
- // System.out.println( " m=" + sum_g_childs_mapping_to_s );
- if ( sum_g_childs_mapping_to_s > 0 ) {
- if ( traversals_sum == 2 ) {
- event = createDuplicationEvent();
+ else {
+ g.getNodeData().setEvent( createSpeciationEvent() );
}
- else if ( traversals_sum > 2 ) {
- if ( max_traversals <= 1 ) {
- if ( _most_parsimonious_duplication_model ) {
- event = createSpeciationEvent();
+ }
+ else {
+ if ( oyako ) {
+ final Set<PhylogenyNode> set = new HashSet<PhylogenyNode>();
+ for( PhylogenyNode n : g.getChildNode1().getAllExternalDescendants() ) {
+ n = n.getLink();
+ while ( n.getParent() != s ) {
+ n = n.getParent();
+ if ( n.isRoot() ) {
+ break;
+ }
}
- else {
- event = createSingleSpeciationOrDuplicationEvent();
+ set.add( n );
+ }
+ boolean multiple = false;
+ for( PhylogenyNode n : g.getChildNode2().getAllExternalDescendants() ) {
+ n = n.getLink();
+ while ( n.getParent() != s ) {
+ n = n.getParent();
+ if ( n.isRoot() ) {
+ break;
+ }
}
+ if ( set.contains( n ) ) {
+ multiple = true;
+ break;
+ }
+ }
+ if ( multiple ) {
+ g.getNodeData().setEvent( createDuplicationEvent() );
}
else {
- event = createDuplicationEvent();
- _transversal_counts.put( max_traversals_node, 1 );
+ g.getNodeData().setEvent( createSingleSpeciationOrDuplicationEvent() );
}
}
else {
- event = createDuplicationEvent();
+ g.getNodeData().setEvent( createSpeciationEvent() );
}
}
- else {
- event = createSpeciationEvent();
- }
- g.getNodeData().setEvent( event );
}
/**
* the species tree must be labeled in preorder.
* <p>
*
- * @param g
- * starting node of a gene tree - normally the root
*/
- final void geneTreePostOrderTraversal( final PhylogenyNode g ) {
- if ( !g.isExternal() ) {
- for( final PhylogenyNodeIterator iter = g.iterateChildNodesForward(); iter.hasNext(); ) {
- geneTreePostOrderTraversal( iter.next() );
- }
- final PhylogenyNode[] linked_nodes = new PhylogenyNode[ g.getNumberOfDescendants() ];
- for( int i = 0; i < linked_nodes.length; ++i ) {
- if ( g.getChildNode( i ).getLink() == null ) {
- System.out.println( "link is null for " + g.getChildNode( i ) );
- System.exit( -1 );
+ final void geneTreePostOrderTraversal() {
+ for( final PhylogenyNodeIterator it = getGeneTree().iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode g = it.next();
+ if ( g.isInternal() ) {
+ PhylogenyNode s1 = g.getChildNode1().getLink();
+ PhylogenyNode s2 = g.getChildNode2().getLink();
+ while ( s1 != s2 ) {
+ if ( s1.getId() > s2.getId() ) {
+ s1 = s1.getParent();
+ }
+ else {
+ s2 = s2.getParent();
+ }
}
- linked_nodes[ i ] = g.getChildNode( i ).getLink();
- }
- final int[] min_max = obtainMinMaxIdIndices( linked_nodes );
- int min_i = min_max[ 0 ];
- int max_i = min_max[ 1 ];
- // initTransversalCounts();
- while ( linked_nodes[ min_i ] != linked_nodes[ max_i ] ) {
- increaseTraversalCount( linked_nodes[ max_i ] );
- linked_nodes[ max_i ] = linked_nodes[ max_i ].getParent();
- final int[] min_max_ = obtainMinMaxIdIndices( linked_nodes );
- min_i = min_max_[ 0 ];
- max_i = min_max_[ 1 ];
+ g.setLink( s1 );
+ determineEvent( s1, g );
}
- final PhylogenyNode s = linked_nodes[ max_i ];
- g.setLink( s );
- // Determines whether dup. or spec.
- determineEvent( s, g );
- // _transversal_counts.clear();
}
}
- public final int getSpeciationOrDuplicationEventsSum() {
- return _speciation_or_duplication_events_sum;
+ private final Event createDuplicationEvent() {
+ final Event event = Event.createSingleDuplicationEvent();
+ ++_duplications_sum;
+ return event;
}
- public final int getSpeciationsSum() {
- return _speciations_sum;
+ private final Event createSingleSpeciationOrDuplicationEvent() {
+ final Event event = Event.createSingleSpeciationOrDuplicationEvent();
+ ++_speciation_or_duplication_events_sum;
+ return event;
}
- private final int getTraversalCount( final PhylogenyNode node ) {
- if ( _transversal_counts.containsKey( node ) ) {
- return _transversal_counts.get( node );
- }
- return 0;
+ private final Event createSpeciationEvent() {
+ final Event event = Event.createSingleSpeciationEvent();
+ ++_speciations_sum;
+ return event;
}
- private final void increaseTraversalCount( final PhylogenyNode node ) {
- if ( _transversal_counts.containsKey( node ) ) {
- _transversal_counts.put( node, _transversal_counts.get( node ) + 1 );
- }
- else {
- _transversal_counts.put( node, 1 );
- }
- // System.out.println( "count for node " + node.getID() + " is now "
- // + getTraversalCount( node ) );
+ public final int getSpeciationOrDuplicationEventsSum() {
+ return _speciation_or_duplication_events_sum;
+ }
+
+ public final int getSpeciationsSum() {
+ return _speciations_sum;
}
/**
*
*/
@Override
- // final void linkNodesOfG() {
- // final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes = createTaxonomyToNodeMap();
- // if ( _strip_gene_tree ) {
- // stripGeneTree( speciestree_ext_nodes );
- // if ( ( _gene_tree == null ) || ( _gene_tree.getNumberOfExternalNodes() < 2 ) ) {
- // throw new IllegalArgumentException( "species tree does not contain any"
- // + " nodes matching species in the gene tree" );
- // }
- // }
- // // Retrieve the reference to the PhylogenyNode with a matching species.
- // for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- // final PhylogenyNode g = iter.next();
- // if ( !g.getNodeData().isHasTaxonomy() ) {
- // throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" );
- // }
- // final PhylogenyNode s = speciestree_ext_nodes.get( g.getNodeData().getTaxonomy() );
- // if ( s == null ) {
- // throw new IllegalArgumentException( "species " + g.getNodeData().getTaxonomy()
- // + " not present in species tree" );
- // }
- // g.setLink( s );
- // }
- // }
final void linkNodesOfG() throws SdiException {
final Map<String, PhylogenyNode> species_to_node_map = new HashMap<String, PhylogenyNode>();
final List<PhylogenyNode> species_tree_ext_nodes = new ArrayList<PhylogenyNode>();
final TaxonomyComparisonBase tax_comp_base = determineTaxonomyComparisonBase( _gene_tree );
- System.out.println( "comp base is: " + tax_comp_base );
+ // System.out.println( "comp base is: " + tax_comp_base );
// Stringyfied taxonomy is the key, node is the value.
for( final PhylogenyNodeIterator iter = _species_tree.iteratorExternalForward(); iter.hasNext(); ) {
final PhylogenyNode s = iter.next();
else {
g.setLink( s );
_mapped_species_tree_nodes.add( s );
- System.out.println( "setting link of " + g + " to " + s );
+ // System.out.println( "setting link of " + g + " to " + s );
}
}
}
}
}
if ( _strip_species_tree ) {
- for( PhylogenyNode x : _mapped_species_tree_nodes ) {
- System.out.println( ">>" + x );
- }
for( final PhylogenyNode s : species_tree_ext_nodes ) {
- System.out.print( ">>>>>>>>>" + s );
if ( !_mapped_species_tree_nodes.contains( s ) ) {
_species_tree.deleteSubtree( s, true );
- System.out.println( " DELETING" );
}
- else {
- System.out.println();
- }
- }
- for( PhylogenyNode x : _mapped_species_tree_nodes ) {
- System.out.println( ">>" + x );
}
}
}
- public SortedSet<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {
+ public Set<PhylogenyNode> getMappedExternalSpeciesTreeNodes() {
return _mapped_species_tree_nodes;
}
- // final private HashMap<Taxonomy, PhylogenyNode> createTaxonomyToNodeMap() {
- // final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes = new HashMap<Taxonomy, PhylogenyNode>();
- // for( final PhylogenyNodeIterator iter = _species_tree.iteratorLevelOrder(); iter.hasNext(); ) {
- // final PhylogenyNode n = iter.next();
- // if ( n.getNodeData().isHasTaxonomy() ) {
- // if ( speciestree_ext_nodes.containsKey( n.getNodeData().getTaxonomy() ) ) {
- // throw new IllegalArgumentException( "taxonomy [" + n.getNodeData().getTaxonomy()
- // + "] is not unique in species phylogeny" );
- // }
- // speciestree_ext_nodes.put( n.getNodeData().getTaxonomy(), n );
- // }
- // }
- // return speciestree_ext_nodes;
- // }
- // private final void stripGeneTree( final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes ) {
- // // final Set<PhylogenyNode> to_delete = new HashSet<PhylogenyNode>();
- // for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- // final PhylogenyNode g = iter.next();
- // if ( !g.getNodeData().isHasTaxonomy() ) {
- // throw new IllegalArgumentException( "gene tree node " + g + " has no taxonomic data" );
- // }
- // if ( !speciestree_ext_nodes.containsKey( g.getNodeData().getTaxonomy() ) ) {
- // _stripped_gene_tree_nodes.add( g );
- // }
- // }
- // for( final PhylogenyNode n : _stripped_gene_tree_nodes ) {
- // _gene_tree.deleteSubtree( n, true );
- // }
- // }
- // private final void stripGeneTree2( final HashMap<Taxonomy, PhylogenyNode> speciestree_ext_nodes ) {
- // // final Set<PhylogenyNode> to_delete = new HashSet<PhylogenyNode>();
- // for( final PhylogenyNodeIterator iter = _gene_tree.iteratorExternalForward(); iter.hasNext(); ) {
- // final PhylogenyNode g = iter.next();
- // if ( !g.getNodeData().isHasTaxonomy() ) {
- // _stripped_gene_tree_nodes.add( g );
- // }
- // else {
- // if ( !speciestree_ext_nodes.containsKey( g.getNodeData().getTaxonomy() ) ) {
- // _stripped_gene_tree_nodes.add( g );
- // }
- // }
- // }
- // for( final PhylogenyNode n : _stripped_gene_tree_nodes ) {
- // _gene_tree.deleteSubtree( n, true );
- // }
- // }
public static TaxonomyComparisonBase determineTaxonomyComparisonBase( final Phylogeny gene_tree ) {
int with_id_count = 0;
int with_code_count = 0;
sb.append( "mapping cost L : " + computeMappingCostL() );
return sb.toString();
}
-
- static final int[] obtainMinMaxIdIndices( final PhylogenyNode[] linked_nodes ) {
- int max_i = 0;
- int min_i = 0;
- int max_i_id = -Integer.MAX_VALUE;
- int min_i_id = Integer.MAX_VALUE;
- for( int i = 0; i < linked_nodes.length; ++i ) {
- final int id_i = linked_nodes[ i ].getId();
- if ( id_i > max_i_id ) {
- max_i = i;
- max_i_id = linked_nodes[ max_i ].getId();
- }
- if ( id_i < min_i_id ) {
- min_i = i;
- min_i_id = linked_nodes[ min_i ].getId();
- }
- }
- return new int[] { min_i, max_i };
- }
- /**
- * Updates the mapping function M after the root of the gene tree has been
- * moved by one branch. It calculates M for the root of the gene tree and
- * one of its two children.
- * <p>
- * To be used ONLY by method "SDIunrooted.fastInfer(Phylogeny,Phylogeny)".
- * <p>
- * (Last modfied: )
- *
- * @param prev_root_was_dup
- * true if the previous root was a duplication, false otherwise
- * @param prev_root_c1
- * child 1 of the previous root
- * @param prev_root_c2
- * child 2 of the previous root
- * @return number of duplications which have been assigned in gene tree
- */
- // int updateM( final boolean prev_root_was_dup,
- // final PhylogenyNode prev_root_c1, final PhylogenyNode prev_root_c2 ) {
- // final PhylogenyNode root = getGeneTree().getRoot();
- // if ( ( root.getChildNode1() == prev_root_c1 )
- // || ( root.getChildNode2() == prev_root_c1 ) ) {
- // calculateMforNode( prev_root_c1 );
- // }
- // else {
- // calculateMforNode( prev_root_c2 );
- // }
- // Event event = null;
- // if ( prev_root_was_dup ) {
- // event = Event.createSingleDuplicationEvent();
- // }
- // else {
- // event = Event.createSingleSpeciationEvent();
- // }
- // root.getPhylogenyNodeData().setEvent( event );
- // calculateMforNode( root );
- // return getDuplications();
- // } // updateM( boolean, PhylogenyNode, PhylogenyNode )
- // Helper method for updateM( boolean, PhylogenyNode, PhylogenyNode )
- // Calculates M for PhylogenyNode n, given that M for the two children
- // of n has been calculated.
- // (Last modified: 10/02/01)
- // private void calculateMforNode( final PhylogenyNode n ) {
- // if ( !n.isExternal() ) {
- // boolean was_duplication = n.isDuplication();
- // PhylogenyNode a = n.getChildNode1().getLink(), b = n
- // .getChildNode2().getLink();
- // while ( a != b ) {
- // if ( a.getID() > b.getID() ) {
- // a = a.getParent();
- // }
- // else {
- // b = b.getParent();
- // }
- // }
- // n.setLink( a );
- // Event event = null;
- // if ( ( a == n.getChildNode1().getLink() )
- // || ( a == n.getChildNode2().getLink() ) ) {
- // event = Event.createSingleDuplicationEvent();
- // if ( !was_duplication ) {
- // increaseDuplications();
- // }
- // }
- // else {
- // event = Event.createSingleSpeciationEvent();
- // if ( was_duplication ) {
- // decreaseDuplications();
- // }
- // }
- // n.getPhylogenyNodeData().setEvent( event );
- // }
- // } // calculateMforNode( PhylogenyNode )
}
git://source.jalview.org / jalview.git / blobdiff