*/
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 Set<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.
_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;
_mapped_species_tree_nodes = new HashSet<PhylogenyNode>();
getSpeciesTree().preOrderReId();
linkNodesOfG();
- geneTreePostOrderTraversal( getGeneTree().getRoot() );
+ //geneTreePostOrderTraversal( getGeneTree().getRoot(), null );
+ 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;
++sum_g_childs_mapping_to_s;
}
}
- // Determine the sum of traversals.
- int traversals_sum = 0;
- int max_traversals = 0;
- PhylogenyNode max_traversals_node = null;
- if ( !s.isExternal() ) {
- for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode current_node = s.getChildNode( i );
- final int traversals = getTraversalCount( current_node );
- traversals_sum += traversals;
- if ( traversals > max_traversals ) {
- max_traversals = traversals;
- max_traversals_node = current_node;
- }
- }
- }
- // 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 ) {
+ if ( g.getLink().getNumberOfDescendants() == 2 ) {
+ if ( sum_g_childs_mapping_to_s > 0 ) {
event = createDuplicationEvent();
- System.out.print( g.toString() );
- System.out.println( " : ==2" );
- // _transversal_counts.clear();
}
- else if ( traversals_sum > 2 ) {
- if ( max_traversals <= 1 ) {
- if ( _most_parsimonious_duplication_model ) {
- event = createSpeciationEvent();
- }
- else {
- event = createSingleSpeciationOrDuplicationEvent();
+ else {
+ event = createSpeciationEvent();
+ }
+ }
+ else {
+ if ( sum_g_childs_mapping_to_s > 0 ) {
+ boolean multiple = false;
+ Set<PhylogenyNode> set = new HashSet<PhylogenyNode>();
+ for( PhylogenyNode n : g.getChildNode1().getLink().getAllExternalDescendants() ) {
+ set.add( n );
+ }
+ for( PhylogenyNode n : g.getChildNode2().getLink().getAllExternalDescendants() ) {
+ if ( set.contains( n ) ) {
+ multiple = true;
+ break;
}
+ // else {
+ // set.add( n );
+ // }
}
- else {
+ if ( multiple ) {
event = createDuplicationEvent();
- //System.out.println( g.toString() );
- _transversal_counts.put( max_traversals_node, 1 );
- // _transversal_counts.clear();
+ }
+ else {
+ event = createSingleSpeciationOrDuplicationEvent();
}
}
else {
- event = createDuplicationEvent();
- // _transversal_counts.clear();
+ event = createSpeciationEvent();
}
- normalizeTcounts( s );
- }
- else {
- event = createSpeciationEvent();
}
g.getNodeData().setEvent( event );
}
- private void normalizeTcounts( final PhylogenyNode s ) {
- int min_traversals = Integer.MAX_VALUE;
- for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode current_node = s.getChildNode( i );
- final int traversals = getTraversalCount( current_node );
- if ( traversals < min_traversals ) {
- min_traversals = traversals;
- }
- }
- for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
- final PhylogenyNode current_node = s.getChildNode( i );
- _transversal_counts.put( current_node, getTraversalCount( current_node ) - min_traversals );
- }
- }
-
+ // private final void determineEvent2( 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( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
+ // final PhylogenyNode c = g.getChildNode( i );
+ // if ( c.getLink() == s ) {
+ // ++sum_g_childs_mapping_to_s;
+ // }
+ // }
+ // // Determine the sum of traversals.
+ // int traversals_sum = 0;
+ // int max_traversals = 0;
+ // PhylogenyNode max_traversals_node = null;
+ // if ( !s.isExternal() ) {
+ // for( int i = 0; i < s.getNumberOfDescendants(); ++i ) {
+ // final PhylogenyNode current_node = s.getChildNode( i );
+ // final int traversals = getTraversalCount( current_node );
+ // traversals_sum += traversals;
+ // if ( traversals > max_traversals ) {
+ // max_traversals = traversals;
+ // max_traversals_node = current_node;
+ // }
+ // }
+ // }
+ // // System.out.println( " sum=" + traversals_sum );
+ // // System.out.println( " max=" + max_traversals );
+ // // System.out.println( " m=" + sum_g_childs_mapping_to_s );
+ // if ( s.getNumberOfDescendants() == 2 ) {
+ // if ( sum_g_childs_mapping_to_s == 0 ) {
+ // event = createSpeciationEvent();
+ // }
+ // else {
+ // event = createDuplicationEvent();
+ // }
+ // }
+ // else {
+ // if ( sum_g_childs_mapping_to_s == 2 ) {
+ // event = createDuplicationEvent();
+ // }
+ // else if ( sum_g_childs_mapping_to_s == 1 ) {
+ // event = createSingleSpeciationOrDuplicationEvent();
+ // }
+ // else {
+ // event = createSpeciationEvent();
+ // }
+ // }
+ // g.getNodeData().setEvent( event );
+ // }
/**
* Traverses the subtree of PhylogenyNode g in postorder, calculating the
* mapping function M, and determines which nodes represent speciation
* @param g
* starting node of a gene tree - normally the root
*/
- final void geneTreePostOrderTraversal( final PhylogenyNode g ) {
- if ( !g.isExternal() ) {
- boolean all_ext = true;
- for( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
- if ( g.getChildNode( i ).isInternal() ) {
- all_ext = false;
- break;
+ final void geneTreePostOrderTraversal() {
+ for( PhylogenyNodeIterator it = getGeneTree().iteratorPostorder(); it.hasNext(); ) {
+ PhylogenyNode g = it.next();
+ if ( !g.isExternal() ) {
+ 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 );
+ }
+ linked_nodes[ i ] = g.getChildNode( i ).getLink();
}
- }
- if ( all_ext ) {
- //_transversal_counts.clear();
- }
- for( int i = 0; i < g.getNumberOfDescendants(); ++i ) {
- geneTreePostOrderTraversal( g.getChildNode( i ) );
- }
- 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 int[] min_max = obtainMinMaxIdIndices( linked_nodes );
+ int min_i = min_max[ 0 ];
+ int max_i = min_max[ 1 ];
+ while ( linked_nodes[ min_i ] != 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 ];
}
- 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 ];
+ final PhylogenyNode s = linked_nodes[ max_i ];
+ g.setLink( s );
+ // Determines whether dup. or spec.
+ determineEvent( s, g );
}
- final PhylogenyNode s = linked_nodes[ max_i ];
- g.setLink( s );
- // Determines whether dup. or spec.
- determineEvent( s, g );
}
}
- 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;
}
/**
git://source.jalview.org / jalview.git / blobdiff