inprogress

[jalview.git] / forester / java / src / org / forester / surfacing / BasicGenomeWideCombinableDomains.java

diff --git a/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java b/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java
index 3e59603..1d115b2 100644 (file)
--- a/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java
@@ -26,18 +26,18 @@ import org.forester.util.ForesterUtil;
 
 public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDomains {
 
-    private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_COUNT_ORDER          = new Comparator<CombinableDomains>() {
+    private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER        = new Comparator<CombinableDomains>() {
 
                                                                                                       @Override
                                                                                                       public int compare( final CombinableDomains d1,
                                                                                                                           final CombinableDomains d2 ) {
-                                                                                                          if ( d1.getKeyDomainCount() < d2
-                                                                                                                  .getKeyDomainCount() ) {
+                                                                                                          if ( d1.getNumberOfCombinableDomains() < d2
+                                                                                                                  .getNumberOfCombinableDomains() ) {
                                                                                                               return 1;
                                                                                                           }
                                                                                                           else if ( d1
-                                                                                                                  .getKeyDomainCount() > d2
-                                                                                                                  .getKeyDomainCount() ) {
+                                                                                                                  .getNumberOfCombinableDomains() > d2
+                                                                                                                  .getNumberOfCombinableDomains() ) {
                                                                                                               return -1;
                                                                                                           }
                                                                                                           else {
@@ -48,18 +48,18 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
                                                                                                           }
                                                                                                       }
                                                                                                   };
-    private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER = new Comparator<CombinableDomains>() {
+    private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_COUNT_ORDER          = new Comparator<CombinableDomains>() {
 
                                                                                                       @Override
                                                                                                       public int compare( final CombinableDomains d1,
                                                                                                                           final CombinableDomains d2 ) {
-                                                                                                          if ( d1.getKeyDomainProteinsCount() < d2
-                                                                                                                  .getKeyDomainProteinsCount() ) {
+                                                                                                          if ( d1.getKeyDomainCount() < d2
+                                                                                                                  .getKeyDomainCount() ) {
                                                                                                               return 1;
                                                                                                           }
                                                                                                           else if ( d1
-                                                                                                                  .getKeyDomainProteinsCount() > d2
-                                                                                                                  .getKeyDomainProteinsCount() ) {
+                                                                                                                  .getKeyDomainCount() > d2
+                                                                                                                  .getKeyDomainCount() ) {
                                                                                                               return -1;
                                                                                                           }
                                                                                                           else {
@@ -70,18 +70,18 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
                                                                                                           }
                                                                                                       }
                                                                                                   };
-    private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER        = new Comparator<CombinableDomains>() {
+    private static final Comparator<CombinableDomains> DESCENDING_KEY_DOMAIN_PROTEINS_COUNT_ORDER = new Comparator<CombinableDomains>() {
 
                                                                                                       @Override
                                                                                                       public int compare( final CombinableDomains d1,
                                                                                                                           final CombinableDomains d2 ) {
-                                                                                                          if ( d1.getNumberOfCombinableDomains() < d2
-                                                                                                                  .getNumberOfCombinableDomains() ) {
+                                                                                                          if ( d1.getKeyDomainProteinsCount() < d2
+                                                                                                                  .getKeyDomainProteinsCount() ) {
                                                                                                               return 1;
                                                                                                           }
                                                                                                           else if ( d1
-                                                                                                                  .getNumberOfCombinableDomains() > d2
-                                                                                                                  .getNumberOfCombinableDomains() ) {
+                                                                                                                  .getKeyDomainProteinsCount() > d2
+                                                                                                                  .getKeyDomainProteinsCount() ) {
                                                                                                               return -1;
                                                                                                           }
                                                                                                           else {
@@ -93,8 +93,8 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
                                                                                                       }
                                                                                                   };
     final private SortedMap<String, CombinableDomains> _combinable_domains_map;
-    final private Species                              _species;
     final private DomainCombinationType                _dc_type;
+    final private Species                              _species;
 
     private BasicGenomeWideCombinableDomains( final Species species, final DomainCombinationType dc_type ) {
         _combinable_domains_map = new TreeMap<String, CombinableDomains>();
@@ -102,10 +102,6 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
         _dc_type = dc_type;
     }
 
-    private void add( final String key, final CombinableDomains cdc ) {
-        _combinable_domains_map.put( key, cdc );
-    }
-
     @Override
     public boolean contains( final String key_id ) {
         return _combinable_domains_map.containsKey( key_id );
@@ -220,16 +216,8 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
         return sb;
     }
 
-    private static void countDomains( final Map<String, Integer> domain_counts,
-                                      final Set<String> saw_c,
-                                      final String id_i ) {
-        if ( domain_counts.containsKey( id_i ) ) {
-            domain_counts.put( id_i, 1 + domain_counts.get( ( id_i ) ) );
-        }
-        else {
-            domain_counts.put( id_i, 1 );
-        }
-        saw_c.add( id_i );
+    private void add( final String key, final CombinableDomains cdc ) {
+        _combinable_domains_map.put( key, cdc );
     }
 
     public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
@@ -355,4 +343,16 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
         }
         return instance;
     }
+
+    private static void countDomains( final Map<String, Integer> domain_counts,
+                                      final Set<String> saw_c,
+                                      final String id_i ) {
+        if ( domain_counts.containsKey( id_i ) ) {
+            domain_counts.put( id_i, 1 + domain_counts.get( ( id_i ) ) );
+        }
+        else {
+            domain_counts.put( id_i, 1 );
+        }
+        saw_c.add( id_i );
+    }
 }