// $Id: // 22:43:35 cmzmasek Exp $ // // FORESTER -- software libraries and applications // for evolutionary biology research and applications. // // Copyright (C) 2008-2009 Christian M. Zmasek // Copyright (C) 2008-2009 Burnham Institute for Medical Research // All rights reserved // // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public // License as published by the Free Software Foundation; either // version 2.1 of the License, or (at your option) any later version. // // This library is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. // // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com // WWW: www.phylosoft.org/forester package org.forester.surfacing; import java.util.List; public class CombinationsBasedPairwiseDomainSimilarityCalculator implements PairwiseDomainSimilarityCalculator { @Override public PairwiseDomainSimilarity calculateSimilarity( final CombinableDomains domains_1, final CombinableDomains domains_2 ) { if ( !domains_1.getKeyDomain().equals( domains_2.getKeyDomain() ) ) { throw new IllegalArgumentException( "attempt to calculate similarity between domain collection with different keys" ); } final List d1 = domains_1.getCombinableDomains(); final List d2 = domains_2.getCombinableDomains(); int same = 0; int different = 0; for( final DomainId domain : d1 ) { if ( d2.contains( domain ) ) { same++; } else { different++; } } for( final DomainId domain : d2 ) { if ( !( d1.contains( domain ) ) ) { different++; } } final int difference = domains_1.getNumberOfCombinableDomains() - domains_2.getNumberOfCombinableDomains(); return new CombinationsBasedPairwiseDomainSimilarity( same, different, difference ); } }