JAL-1953 JAL-2852 added public "paintFile" method

[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 f444ff7..81fd861 100644 (file)
--- a/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java
@@ -32,33 +32,30 @@ import java.util.SortedSet;
 
 import org.forester.protein.BinaryDomainCombination;
 import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
-import org.forester.protein.DomainId;
 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();
-
     /**
-     * This should return a statistic for per domain 
+     * This should return a statistic for per domain
      * promiscuity in a genome.
-     * 
+     *
      * @return descriptive statistics for per domain promiscuity in a genome
      */
     public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics();
@@ -69,14 +66,16 @@ public interface GenomeWideCombinableDomains {
 
     /**
      * This should return all binary domain combinations present in the genome.
-     * 
+     *
      * @return a sorted set of binary domain combinations
      */
     public SortedSet<BinaryDomainCombination> toBinaryDomainCombinations();
 
     public StringBuilder toStringBuilder( GenomeWideCombinableDomainsSortOrder order );
 
+    SortedSet<String> getMostPromiscuosDomain();
+
     public static enum GenomeWideCombinableDomainsSortOrder {
-        ALPHABETICAL_KEY_ID, KEY_DOMAIN_PROTEINS_COUNT, KEY_DOMAIN_COUNT, COMBINATIONS_COUNT
+        ALPHABETICAL_KEY_ID, COMBINATIONS_COUNT, KEY_DOMAIN_COUNT, KEY_DOMAIN_PROTEINS_COUNT
     }
 }