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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
surfacing
/
CountsBasedPairwiseDomainSimilarity.java
diff --git
a/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java
b/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java
index
a037ed5
..
f4bfd16
100644
(file)
--- a/
forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java
+++ b/
forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java
@@
-23,37
+23,36
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// 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 {
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).
/**
* 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
*/
* @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 );
}
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" );
}
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).
}
/**
* Returns (counts for domain 1) minus (counts for domain 2).
- *
+ *
*/
@Override
public int getDifferenceInCounts() {
*/
@Override
public int getDifferenceInCounts() {
@@
-62,6
+61,6
@@
public class CountsBasedPairwiseDomainSimilarity implements PairwiseDomainSimila
@Override
public double getSimilarityScore() {
@Override
public double getSimilarityScore() {
- return _score;
+ return ( 1.0 - ( ( double ) Math.abs( _copy_number_difference ) / _counts_sum ) );
}
}
}
}