2 package org.forester.sdi;
4 import java.util.ArrayList;
5 import java.util.HashSet;
8 import java.util.SortedSet;
9 import java.util.TreeSet;
11 import org.forester.phylogeny.PhylogenyNode;
12 import org.forester.sdi.SDIutil.TaxonomyComparisonBase;
14 final class NodesLinkingResult {
16 private final List<PhylogenyNode> _stripped_gene_tree_nodes;
17 private final List<PhylogenyNode> _stripped_species_tree_nodes;
18 private final Set<PhylogenyNode> _mapped_species_tree_nodes;
19 private TaxonomyComparisonBase _tax_comp_base;
20 private final SortedSet<String> _scientific_names_mapped_to_reduced_specificity;
22 NodesLinkingResult() {
23 _stripped_gene_tree_nodes = new ArrayList<PhylogenyNode>();
24 _stripped_species_tree_nodes = new ArrayList<PhylogenyNode>();
25 _mapped_species_tree_nodes = new HashSet<PhylogenyNode>();
26 _scientific_names_mapped_to_reduced_specificity = new TreeSet<String>();
27 _tax_comp_base = null;
30 final Set<PhylogenyNode> getMappedSpeciesTreeNodes() {
31 return _mapped_species_tree_nodes;
34 final SortedSet<String> getScientificNamesMappedToReducedSpecificity() {
35 return _scientific_names_mapped_to_reduced_specificity;
38 final List<PhylogenyNode> getStrippedGeneTreeNodes() {
39 return _stripped_gene_tree_nodes;
42 final List<PhylogenyNode> getStrippedSpeciesTreeNodes() {
43 return _stripped_species_tree_nodes;
46 final TaxonomyComparisonBase getTaxCompBase() {
47 return _tax_comp_base;
50 final void setTaxCompBase( final TaxonomyComparisonBase tax_comp_base ) {
51 _tax_comp_base = tax_comp_base;