Examples with TaxonSet beast.evolution.alignment.TaxonSet used on opensource projects

Example 36 with TaxonSet

use of beast.evolution.alignment.TaxonSet in project beast2 by CompEvol.

the class GeneTreeForSpeciesTreeDistribution method getSetID.

/**
 * @param lineageID
 * @return species ID to which the lineage ID belongs according to the TaxonSets
 */
String getSetID(final String lineageID) {
    final TaxonSet taxonSuperset = speciesTreePriorInput.get().taxonSetInput.get();
    final List<Taxon> taxonSets = taxonSuperset.taxonsetInput.get();
    for (final Taxon taxonSet : taxonSets) {
        final List<Taxon> taxa = ((TaxonSet) taxonSet).taxonsetInput.get();
        for (final Taxon aTaxa : taxa) {
            if (aTaxa.getID().equals(lineageID)) {
                return taxonSet.getID();
            }
        }
    }
    return null;
}