return nodes;
}
- public static void deleteExternalNodesNegativeSelection( final Set<Integer> to_delete, final Phylogeny phy ) {
- phy.clearHashIdToNodeMap();
- for( final Integer id : to_delete ) {
+ public static void deleteExternalNodesNegativeSelection( final Set<Long> to_delete, final Phylogeny phy ) {
+ for( final Long id : to_delete ) {
phy.deleteSubtree( phy.getNode( id ), true );
}
phy.clearHashIdToNodeMap();
p.externalNodesHaveChanged();
}
- public static void deleteExternalNodesPositiveSelection( final Set<Taxonomy> species_to_keep, final Phylogeny phy ) {
- // final Set<Integer> to_delete = new HashSet<Integer>();
- for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( n.getNodeData().isHasTaxonomy() ) {
- if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {
- //to_delete.add( n.getNodeId() );
- phy.deleteSubtree( n, true );
- }
- }
- else {
- throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
- }
- }
- phy.clearHashIdToNodeMap();
- phy.externalNodesHaveChanged();
- }
-
public static List<String> deleteExternalNodesPositiveSelection( final String[] node_names_to_keep,
final Phylogeny p ) {
final PhylogenyNodeIterator it = p.iteratorExternalForward();
return deleted;
}
+ public static void deleteExternalNodesPositiveSelectionT( final List<Taxonomy> species_to_keep, final Phylogeny phy ) {
+ final Set<Long> to_delete = new HashSet<Long>();
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getNodeData().isHasTaxonomy() ) {
+ if ( !species_to_keep.contains( n.getNodeData().getTaxonomy() ) ) {
+ to_delete.add( n.getId() );
+ }
+ }
+ else {
+ throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
+ }
+ }
+ deleteExternalNodesNegativeSelection( to_delete, phy );
+ }
+
final public static void deleteInternalNodesWithOnlyOneDescendent( final Phylogeny phy ) {
final ArrayList<PhylogenyNode> to_delete = new ArrayList<PhylogenyNode>();
for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {