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;
}
/**
@Override
public double getSimilarityScore() {
- return _score;
+ return ( 1.0 - ( ( double ) Math.abs( _copy_number_difference ) / _counts_sum ) );
}
}