X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainSimilarity.java;h=bf9cef44cd3f65e57e9509e40d7a6ee96168bb7e;hb=f47b5de663d2ca59a4d53587ea8d5cd20c594db2;hp=724aa70542ef57a0531cca17f52f2ad758953c27;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarity.java b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
index 724aa70..bf9cef4 100644
--- a/forester/java/src/org/forester/surfacing/DomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
@@ -22,22 +22,34 @@
 // 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.Map;
 import java.util.SortedMap;
 import java.util.SortedSet;
 
+import org.forester.species.Species;
+import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
+
 /*
  * This is to represent a measure of similarity between two or more domains from
  * different genomes.
  */
 public interface DomainSimilarity extends Comparable<DomainSimilarity> {
 
-    public SortedSet<DomainId> getCombinableDomainIds( final Species species_of_combinable_domain );;
+    static public enum DomainSimilarityScoring {
+        DOMAINS, PROTEINS, COMBINATIONS;
+    }
+
+    public static enum DomainSimilaritySortField {
+        MIN, MAX, SD, MEAN, ABS_MAX_COUNTS_DIFFERENCE, MAX_COUNTS_DIFFERENCE, MAX_DIFFERENCE, SPECIES_COUNT, DOMAIN_ID,
+    }
+
+    public SortedSet<String> getCombinableDomainIds( final Species species_of_combinable_domain );
 
-    public DomainId getDomainId();
+    public String getDomainId();
 
     /**
      * For pairwise similarities, this should return the "difference"; for example the difference in counts
@@ -85,17 +97,9 @@ public interface DomainSimilarity extends Comparable<DomainSimilarity> {
      * 
      * @return SortedMap<String, SpeciesSpecificDomainSimilariyData>
      */
-    public SortedMap<Species, SpeciesSpecificDomainSimilariyData> getSpeciesData();
+    public SortedMap<Species, SpeciesSpecificDcData> getSpeciesData();
 
     public double getStandardDeviationOfSimilarityScore();
 
-    public StringBuffer toStringBuffer( final PrintableDomainSimilarity.PRINT_OPTION print_option );
-
-    static public enum DomainSimilarityScoring {
-        DOMAINS, PROTEINS, COMBINATIONS;
-    }
-
-    public static enum DomainSimilaritySortField {
-        MIN, MAX, SD, MEAN, ABS_MAX_COUNTS_DIFFERENCE, MAX_COUNTS_DIFFERENCE, MAX_DIFFERENCE, SPECIES_COUNT, DOMAIN_ID,
-    }
+    public StringBuffer toStringBuffer( PRINT_OPTION print_option, Map<String, Integer> tax_code_to_id_map );
 }