X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainSimilarity.java;h=5a0735e3a162489a05c4b164eb368e6e1a260ca2;hb=eae9b4d545845ccc94c1465c1664086b22188ad1;hp=bdf227cbf4bd27d966852c1937fc00c672aecc57;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarity.java b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
index bdf227c..5a0735e 100644
--- a/forester/java/src/org/forester/surfacing/DomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
@@ -6,7 +6,7 @@
 // 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
@@ -16,28 +16,41 @@
 // 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;
 
+import java.util.Map;
 import java.util.SortedMap;
 import java.util.SortedSet;
 
+import org.forester.phylogeny.Phylogeny;
+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 DomainId getDomainId();
+    public SortedSet<String> getCombinableDomainIds( final Species species_of_combinable_domain );
+
+    public String getDomainId();
 
     /**
      * For pairwise similarities, this should return the "difference"; for example the difference in counts
@@ -85,17 +98,11 @@ 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,
+                                        Phylogeny phy );
 }