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 69adcb9..846aa7a 100644 (file)
--- a/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java
@@ -23,7 +23,7 @@
 // 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;
 
@@ -34,7 +34,6 @@ import java.util.SortedSet;
 import java.util.TreeMap;
 import java.util.TreeSet;
 
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
@@ -62,11 +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 ) {
@@ -238,7 +237,7 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
                                                                                                        cd.getKeyDomainCount(),
                                                                                                        cd.getNumberOfCombinableDomains(),
                                                                                                        cd.getKeyDomainConfidenceDescriptiveStatistics() );
-        for( final DomainId domain : cd.getCombinableDomains() ) {
+        for( final String domain : cd.getCombinableDomains() ) {
             sd.addProteinsExhibitingCombinationCount( domain, cd.getNumberOfProteinsExhibitingCombination( domain ) );
         }
         return sd;