in progress

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

diff --git a/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java b/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java
index 537f44f..4dbe718 100644 (file)
--- a/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java
@@ -23,34 +23,36 @@
 // 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;
 
 import java.util.SortedMap;
 import java.util.SortedSet;
 
-import org.forester.surfacing.BinaryDomainCombination.DomainCombinationType;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
+import org.forester.species.Species;
 import org.forester.util.DescriptiveStatistics;
 
 public interface GenomeWideCombinableDomains {
 
-    public boolean contains( DomainId key_id );
+    public boolean contains( String key_id );
 
-    public CombinableDomains get( DomainId key_id );
+    public CombinableDomains get( String key_id );
 
-    public SortedMap<DomainId, CombinableDomains> getAllCombinableDomainsIds();
+    public SortedMap<String, CombinableDomains> getAllCombinableDomainsIds();
 
     /**
      * This should return all domains ids present in the genome.
      * 
      * @return a sorted set of domains ids
      */
-    public SortedSet<DomainId> getAllDomainIds();
+    public SortedSet<String> getAllDomainIds();
 
     public DomainCombinationType getDomainCombinationType();
 
-    SortedSet<DomainId> getMostPromiscuosDomain();
+    SortedSet<String> getMostPromiscuosDomain();
 
     /**
      * This should return a statistic for per domain