X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FCombinableDomains.java;h=307da8e3374e2207fe2b9080711c009a57ffee55;hb=5cad5dbd4f9e8cf09a123d4ee490cf314c05fd2f;hp=58b055d93e138e64c42df4365dfc1d904df8d13b;hpb=87d34f343d0262cd0c009c6f1da058a5a217bc64;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/CombinableDomains.java b/forester/java/src/org/forester/surfacing/CombinableDomains.java
index 58b055d..307da8e 100644
--- a/forester/java/src/org/forester/surfacing/CombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/CombinableDomains.java
@@ -27,37 +27,26 @@
 package org.forester.surfacing;
 
 import java.util.List;
+import java.util.Set;
 import java.util.SortedMap;
 
 import org.forester.protein.BinaryDomainCombination;
 import org.forester.species.Species;
-import org.forester.util.DescriptiveStatistics;
 
 public interface CombinableDomains {
 
     /**
      * To add a new combinable domain.
-     * 
+     *
      * @param protein_domain
      */
     public void addCombinableDomain( final String protein_domain );
 
     /**
-     * 
-     * This must return all domains in this set of combinable domains (i.e.
-     * the key domain and all domains which can combine with the key domain).
-     * 
-     *  @return all domains
-     */
-    List<String> getAllDomains();
-
-    List<String> getCombinableDomains();
-
-    /**
      * Returns the combinable domain identifiers sorted in alphabetical manner: -
      * keys are the combinable domain identifiers - values are the counts of
      * proteins exhibiting a particular combination
-     * 
+     *
      * @return combining domain identifiers sorted in alphabetical manner
      */
     public SortedMap<String, Integer> getCombinableDomainsIds();
@@ -67,32 +56,25 @@ public interface CombinableDomains {
     /**
      * Returns the domain whose combinable domains are in stored in this
      * combinable domains.
-     * 
+     *
      * @return the domain identifier
      */
     public String getKeyDomain();
 
     /**
-     * Gets descriptive statistics for the confidence (i.e. E-values) of the key
-     * domain.
-     * 
-     * 
-     * @return descriptive statistics for the confidence of the key domain
-     */
-    public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics();
-
-    /**
      * Returns how many times the key domain is present in a given species
      * genome.
-     * 
+     *
      * @return key domain count in species
      */
     public int getKeyDomainCount();
 
+    public Set<String> getKeyDomainProteins();
+
     /**
      * Returns how many proteins with the key domain are present in a given
      * species genome.
-     * 
+     *
      * @return key domain proteins count in species
      */
     public int getKeyDomainProteinsCount();
@@ -103,38 +85,33 @@ public interface CombinableDomains {
 
     /**
      * Returns the species of this combinable domains.
-     * 
+     *
      * @return the species
      */
     public Species getSpecies();
 
     public boolean isCombinable( final String protein_domain );
 
+    public List<BinaryDomainCombination> toBinaryDomainCombinations();
+
+    void addKeyDomainProtein( String protein );
+
     /**
-     * This is to set descriptive statistics for the confidence (i.e. E-values)
-     * of the key domain.
-     * 
-     * 
-     * @param statistics
+     *
+     * This must return all domains in this set of combinable domains (i.e.
+     * the key domain and all domains which can combine with the key domain).
+     *
+     *  @return all domains
      */
-    void setKeyDomainConfidenceDescriptiveStatistics( final DescriptiveStatistics statistics );
+    List<String> getAllDomains();
+
+    List<String> getCombinableDomains();
 
     /**
      * Sets how many times the key domain is present in a given species genome.
-     * 
+     *
      * @param key_domain_count
      *            key domain count in species
      */
     void setKeyDomainCount( final int key_domain_count );
-
-    /**
-     * Sets how many proteins with the key domain are present in a given species
-     * genome.
-     * 
-     * @param key_domain_proteins_count
-     *            key domain protein count in species
-     */
-    void setKeyDomainProteinsCount( final int key_domain_proteins_count );
-
-    public List<BinaryDomainCombination> toBinaryDomainCombinations();
 }
\ No newline at end of file