2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
9 // This library is free software; you can redistribute it and/or
10 // modify it under the terms of the GNU Lesser General Public
11 // License as published by the Free Software Foundation; either
12 // version 2.1 of the License, or (at your option) any later version.
14 // This library is distributed in the hope that it will be useful,
15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 // Lesser General Public License for more details.
19 // You should have received a copy of the GNU Lesser General Public
20 // License along with this library; if not, write to the Free Software
21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.pccx;
28 import java.util.List;
30 import org.forester.phylogeny.Phylogeny;
33 * @author Christian M. Zmasek
35 public class CoverageCalculator {
37 private final CoverageCalculationMethod _method;
38 private final CoverageCalculationOptions _options;
40 private CoverageCalculator( final CoverageCalculationMethod method, final CoverageCalculationOptions options ) {
45 public Coverage calculateCoverage( final List<Phylogeny> phylogenies,
46 final List<String> names,
47 final boolean annotate_phylogenies ) {
48 return getMethod().calculateCoverage( phylogenies, names, getOptions(), annotate_phylogenies );
51 private CoverageCalculationMethod getMethod() {
55 private CoverageCalculationOptions getOptions() {
59 public static CoverageCalculator getInstance( final CoverageCalculationMethod method,
60 final CoverageCalculationOptions options ) {
61 return new CoverageCalculator( method, options );