3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: www.phylosoft.org/forester
27 package org.forester.pccx;
29 public class ExternalNodeBasedCoverageMethodOptions implements CoverageCalculationOptions {
31 final private String _scoring_method;
34 * This constructor sets the class name for the scoring method e.g.
35 * "org.forester.tools.modeling.BranchCountingBasedScoringMethod"
37 * @param scoring_method
38 * class name for the scoring method
40 public ExternalNodeBasedCoverageMethodOptions( final String scoring_method ) {
41 _scoring_method = scoring_method;
45 public String asString() {
46 final StringBuffer sb = new StringBuffer();
47 sb.append( "scoring method: " );
48 BranchCountingBasedScoringMethod scoring_method;
50 scoring_method = ( BranchCountingBasedScoringMethod ) ( Class.forName( getScoringMethod() ) ).newInstance();
52 catch ( final Exception e ) {
56 sb.append( scoring_method.getDesciption() );
60 public String getScoringMethod() {
61 return _scoring_method;