in progress

[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 b1abfeb..8439f4c 100644 (file)
--- a/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java
@@ -7,7 +7,7 @@
 // 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
@@ -17,20 +17,20 @@
 // 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).
@@ -39,27 +39,28 @@ public class CountsBasedPairwiseDomainSimilarity implements PairwiseDomainSimila
      * @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 ) );
     }
 }