X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FCombinableDomains.java;h=307da8e3374e2207fe2b9080711c009a57ffee55;hb=b6366fd2ac865514d2ceacb63432dac532147a85;hp=028810edf7e95b6abe06db7176e4357d08ce733d;hpb=08a92c65e8b969a3ce2a4b511055cd6029357831;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/CombinableDomains.java b/forester/java/src/org/forester/surfacing/CombinableDomains.java
index 028810e..307da8e 100644
--- a/forester/java/src/org/forester/surfacing/CombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/CombinableDomains.java
@@ -37,27 +37,16 @@ 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();
@@ -67,7 +56,7 @@ public interface CombinableDomains {
     /**
      * Returns the domain whose combinable domains are in stored in this
      * combinable domains.
-     * 
+     *
      * @return the domain identifier
      */
     public String getKeyDomain();
@@ -75,43 +64,54 @@ public interface CombinableDomains {
     /**
      * 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();
 
-    public Set<String> getKeyDomainProteins();
-
     public int getNumberOfCombinableDomains();
 
     public int getNumberOfProteinsExhibitingCombination( final String protein_domain );
 
     /**
      * 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 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();
+
     /**
      * 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 );
-
-    public List<BinaryDomainCombination> toBinaryDomainCombinations();
-
-    void addKeyDomainProtein( String protein );
 }
\ No newline at end of file