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 CountsBasedPairwiseDomainSimilarity implements PairwiseDomainSimilarity {
32 private final short _copy_number_difference;
33 private final short _counts_sum;
36 * counts_difference: (counts for domain 1) minus (counts for domain 2).
39 * @param counts_difference value of domain_1 minus value of domain_2
42 public CountsBasedPairwiseDomainSimilarity( final short counts_difference, final short counts_sum ) {
43 if ( counts_sum <= 0 ) {
44 throw new IllegalArgumentException( "attempt to use copy sum of less than or equal to 0: " + counts_sum );
46 if ( Math.abs( counts_difference ) > counts_sum ) {
47 throw new IllegalArgumentException( "attempt to use absolute copy number difference larger than copy number sum" );
49 _copy_number_difference = counts_difference;
50 _counts_sum = counts_sum;
54 * Returns (counts for domain 1) minus (counts for domain 2).
58 public int getDifferenceInCounts() {
59 return _copy_number_difference;
63 public double getSimilarityScore() {
64 return ( 1.0 - ( ( double ) Math.abs( _copy_number_difference ) / _counts_sum ) );