inprogress

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

diff --git a/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java
index 81cef33..b245cbc 100644 (file)
--- a/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java
@@ -43,9 +43,9 @@ import org.forester.util.ForesterUtil;
 public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculator {
 
     final DomainSimilarity.DomainSimilaritySortField _sort;
+    private final boolean                            _calc_similarity_score;
     private final boolean                            _sort_by_species_count_first;
     private final boolean                            _treat_as_binary_comparison;
-    private final boolean                            _calc_similarity_score;
 
     public BasicDomainSimilarityCalculator( final DomainSimilarity.DomainSimilaritySortField sort,
                                             final boolean sort_by_species_count_first,
@@ -57,10 +57,6 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
         _calc_similarity_score = calc_similarity_score;
     }
 
-    public boolean isCalcSimilarityScore() {
-        return _calc_similarity_score;
-    }
-
     @Override
     public SortedSet<DomainSimilarity> calculateSimilarities( final PairwiseDomainSimilarityCalculator pairwise_calculator,
                                                               final List<GenomeWideCombinableDomains> cdc_list,
@@ -119,6 +115,10 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
         return similarities;
     }
 
+    public boolean isCalcSimilarityScore() {
+        return _calc_similarity_score;
+    }
+
     private DomainSimilarity calculateSimilarity( final PairwiseDomainSimilarityCalculator pairwise_calculator,
                                                   final List<CombinableDomains> domains_list ) {
         if ( domains_list.size() == 1 ) {
@@ -126,26 +126,26 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
             species_data.put( domains_list.get( 0 ).getSpecies(),
                               createSpeciesSpecificDomainSimilariyData( domains_list.get( 0 ) ) );
             if ( !isCalcSimilarityScore() ) {
-                return new PrintableDomainSimilarity( domains_list.get( 0 ),
-                                                      0,
-                                                      0,
-                                                      species_data,
-                                                      isSortBySpeciesCountFirst(),
-                                                      isTreatAsBinaryComparison() );
+                return new DomainSimilarity( domains_list.get( 0 ),
+                                             0,
+                                             0,
+                                             species_data,
+                                             isSortBySpeciesCountFirst(),
+                                             isTreatAsBinaryComparison() );
             }
             else {
-                return new PrintableDomainSimilarity( domains_list.get( 0 ),
-                                                      1.0,
-                                                      1.0,
-                                                      1.0,
-                                                      1.0,
-                                                      0.0,
-                                                      0,
-                                                      0,
-                                                      0,
-                                                      species_data,
-                                                      isSortBySpeciesCountFirst(),
-                                                      isTreatAsBinaryComparison() );
+                return new DomainSimilarity( domains_list.get( 0 ),
+                                             1.0,
+                                             1.0,
+                                             1.0,
+                                             1.0,
+                                             0.0,
+                                             0,
+                                             0,
+                                             0,
+                                             species_data,
+                                             isSortBySpeciesCountFirst(),
+                                             isTreatAsBinaryComparison() );
             }
         }
         DescriptiveStatistics stat = null;
@@ -201,41 +201,41 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
         }
         DomainSimilarity similarity = null;
         if ( !isCalcSimilarityScore() ) {
-            similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
-                                                        max_difference_in_counts,
-                                                        max_difference,
-                                                        species_data,
-                                                        isSortBySpeciesCountFirst(),
-                                                        isTreatAsBinaryComparison() );
+            similarity = new DomainSimilarity( domains_list.get( 0 ),
+                                               max_difference_in_counts,
+                                               max_difference,
+                                               species_data,
+                                               isSortBySpeciesCountFirst(),
+                                               isTreatAsBinaryComparison() );
         }
         else {
             if ( stat.getN() == 1 ) {
-                similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
-                                                            stat.getMin(),
-                                                            stat.getMax(),
-                                                            stat.arithmeticMean(),
-                                                            stat.median(),
-                                                            0.0,
-                                                            stat.getN(),
-                                                            max_difference_in_counts,
-                                                            max_difference,
-                                                            species_data,
-                                                            isSortBySpeciesCountFirst(),
-                                                            isTreatAsBinaryComparison() );
+                similarity = new DomainSimilarity( domains_list.get( 0 ),
+                                                   stat.getMin(),
+                                                   stat.getMax(),
+                                                   stat.arithmeticMean(),
+                                                   stat.median(),
+                                                   0.0,
+                                                   stat.getN(),
+                                                   max_difference_in_counts,
+                                                   max_difference,
+                                                   species_data,
+                                                   isSortBySpeciesCountFirst(),
+                                                   isTreatAsBinaryComparison() );
             }
             else {
-                similarity = new PrintableDomainSimilarity( domains_list.get( 0 ),
-                                                            stat.getMin(),
-                                                            stat.getMax(),
-                                                            stat.arithmeticMean(),
-                                                            stat.median(),
-                                                            stat.sampleStandardDeviation(),
-                                                            stat.getN(),
-                                                            max_difference_in_counts,
-                                                            max_difference,
-                                                            species_data,
-                                                            isSortBySpeciesCountFirst(),
-                                                            isTreatAsBinaryComparison() );
+                similarity = new DomainSimilarity( domains_list.get( 0 ),
+                                                   stat.getMin(),
+                                                   stat.getMax(),
+                                                   stat.arithmeticMean(),
+                                                   stat.median(),
+                                                   stat.sampleStandardDeviation(),
+                                                   stat.getN(),
+                                                   max_difference_in_counts,
+                                                   max_difference,
+                                                   species_data,
+                                                   isSortBySpeciesCountFirst(),
+                                                   isTreatAsBinaryComparison() );
             }
         }
         return similarity;