// 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
// 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
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.surfacing;
public class CountsBasedPairwiseDomainSimilarity implements PairwiseDomainSimilarity {
- private final double _score;
- private final int _copy_number_difference;
+ private final short _copy_number_difference;
+ private final short _counts_sum;
/**
* counts_difference: (counts for domain 1) minus (counts for domain 2).
* @param counts_difference value of domain_1 minus value of domain_2
* @param counts_sum
*/
- public CountsBasedPairwiseDomainSimilarity( final int counts_difference, final int counts_sum ) {
+ public CountsBasedPairwiseDomainSimilarity( final short counts_difference, final short counts_sum ) {
if ( counts_sum <= 0 ) {
throw new IllegalArgumentException( "attempt to use copy sum of less than or equal to 0: " + counts_sum );
}
- _copy_number_difference = counts_difference;
- final int abs_copy_number_difference = Math.abs( counts_difference );
- if ( abs_copy_number_difference > counts_sum ) {
+ if ( Math.abs( counts_difference ) > counts_sum ) {
throw new IllegalArgumentException( "attempt to use absolute copy number difference larger than copy number sum" );
}
- _score = 1.0 - ( double ) abs_copy_number_difference / counts_sum;
+ _copy_number_difference = counts_difference;
+ _counts_sum = counts_sum;
}
/**
* Returns (counts for domain 1) minus (counts for domain 2).
*
*/
+ @Override
public int getDifferenceInCounts() {
return _copy_number_difference;
}
+ @Override
public double getSimilarityScore() {
- return _score;
+ return ( 1.0 - ( ( double ) Math.abs( _copy_number_difference ) / _counts_sum ) );
}
}