4 // FORESTER -- software libraries and applications
5 // for evolutionary biology research and applications.
7 // Copyright (C) 2008-2009 Christian M. Zmasek
8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
11 // This library is free software; you can redistribute it and/or
12 // modify it under the terms of the GNU Lesser General Public
13 // License as published by the Free Software Foundation; either
14 // version 2.1 of the License, or (at your option) any later version.
16 // This library is distributed in the hope that it will be useful,
17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 // Lesser General Public License for more details.
21 // You should have received a copy of the GNU Lesser General Public
22 // License along with this library; if not, write to the Free Software
23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
25 // Contact: phylosoft @ gmail . com
26 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
28 package org.forester.surfacing;
30 public class CombinationsBasedPairwiseDomainSimilarity implements PairwiseDomainSimilarity {
32 private final int _same_domains;
33 private final int _different_domains;
34 private final int _difference_in_counts;
35 private final double _score;
37 public CombinationsBasedPairwiseDomainSimilarity( final int same_domains,
38 final int different_domains,
39 final int difference_in_counts ) {
40 if ( ( same_domains < 0 ) || ( different_domains < 0 ) ) {
41 throw new IllegalArgumentException( "attempt to use domain counts less than 0" );
43 _difference_in_counts = difference_in_counts;
44 _same_domains = same_domains;
45 _different_domains = different_domains;
46 if ( _different_domains == 0 ) {
50 _score = ( double ) _same_domains / ( _different_domains + _same_domains );
55 public int getDifferenceInCounts() {
56 return _difference_in_counts;
59 public int getNumberOfDifferentDomains() {
60 return _different_domains;
63 public int getNumberOfSameDomains() {
68 public double getSimilarityScore() {