inprogress

[jalview.git] / forester / java / src / org / forester / surfacing / BasicDomainSimilarityCalculator.java

diff --git a/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java
index 5b5a91e..846aa7a 100644 (file)
--- a/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.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
@@ -17,13 +17,13 @@
 // 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;
 
@@ -34,6 +34,7 @@ import java.util.SortedSet;
 import java.util.TreeMap;
 import java.util.TreeSet;
 
+import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
 
@@ -51,6 +52,7 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
         _treat_as_binary_comparison = treat_as_binary_comparison;
     }
 
+    @Override
     public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
                                                               final List<GenomeWideCombinableDomains> cdc_list,
                                                               final boolean ignore_domains_without_combinations_in_any_genome,
@@ -59,11 +61,11 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
             throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinale domains collections" );
         }
         final SortedSet<DomainSimilarity> similarities = new TreeSet<DomainSimilarity>();
-        final SortedSet<DomainId> keys = new TreeSet<DomainId>();
+        final SortedSet<String> keys = new TreeSet<String>();
         for( final GenomeWideCombinableDomains cdc : cdc_list ) {
             keys.addAll( ( cdc ).getAllCombinableDomainsIds().keySet() );
         }
-        for( final DomainId key : keys ) {
+        for( final String key : keys ) {
             final List<CombinableDomains> same_id_cd_list = new ArrayList<CombinableDomains>( cdc_list.size() );
             final List<Species> species_with_key_id_domain = new ArrayList<Species>();
             for( final GenomeWideCombinableDomains cdc : cdc_list ) {
@@ -142,8 +144,8 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
         }
         final DescriptiveStatistics stat = new BasicDescriptiveStatistics();
         final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data = new TreeMap<Species, SpeciesSpecificDomainSimilariyData>();
-        species_data.put( domains_list.get( 0 ).getSpecies(), createSpeciesSpecificDomainSimilariyData( domains_list
-                .get( 0 ) ) );
+        species_data.put( domains_list.get( 0 ).getSpecies(),
+                          createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
         int max_difference_in_counts = 0;
         int max_difference = 0;
         final boolean is_domain_combination_based = pairwise_calculator instanceof CombinationsBasedPairwiseDomainSimilarityCalculator;
@@ -231,10 +233,11 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
     }
 
     private static SpeciesSpecificDomainSimilariyData createSpeciesSpecificDomainSimilariyData( final CombinableDomains cd ) {
-        final SpeciesSpecificDomainSimilariyData sd = new PrintableSpeciesSpecificDomainSimilariyData( cd
-                .getKeyDomainProteinsCount(), cd.getKeyDomainCount(), cd.getNumberOfCombinableDomains(), cd
-                .getKeyDomainConfidenceDescriptiveStatistics() );
-        for( final DomainId domain : cd.getCombinableDomains() ) {
+        final SpeciesSpecificDomainSimilariyData sd = new PrintableSpeciesSpecificDomainSimilariyData( cd.getKeyDomainProteinsCount(),
+                                                                                                       cd.getKeyDomainCount(),
+                                                                                                       cd.getNumberOfCombinableDomains(),
+                                                                                                       cd.getKeyDomainConfidenceDescriptiveStatistics() );
+        for( final String domain : cd.getCombinableDomains() ) {
             sd.addProteinsExhibitingCombinationCount( domain, cd.getNumberOfProteinsExhibitingCombination( domain ) );
         }
         return sd;