X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainArchitectureBasedGenomeSimilarityCalculator.java;h=a61ba305a8bce02ff46b0666e5e21bdc9238997e;hb=1556760e353eae5745f1ae9471a64f0089554639;hp=caf6cb06c68d722c1af567b927e10d73322d6c4f;hpb=87d34f343d0262cd0c009c6f1da058a5a217bc64;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
index caf6cb0..a61ba30 100644
--- a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
@@ -35,18 +35,18 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
 
     public static final double                MAX_SIMILARITY_SCORE = 1.0;
     public static final double                MIN_SIMILARITY_SCORE = 0.0;
+    private Set<BinaryDomainCombination>      _all_binary_domain_combinations;
+    private Set<String>                       _all_domains;
+    private boolean                           _allow_domains_to_be_ignored;
+    private Set<BinaryDomainCombination>      _binary_domain_combinations_specific_to_0;
+    private Set<BinaryDomainCombination>      _binary_domain_combinations_specific_to_1;
     final private GenomeWideCombinableDomains _combinable_domains_genome_0;
     final private GenomeWideCombinableDomains _combinable_domains_genome_1;
     private Set<String>                       _domain_ids_to_ignore;
-    private boolean                           _allow_domains_to_be_ignored;
-    private Set<String>                       _all_domains;
-    private Set<String>                       _shared_domains;
     private Set<String>                       _domains_specific_to_0;
     private Set<String>                       _domains_specific_to_1;
-    private Set<BinaryDomainCombination>      _all_binary_domain_combinations;
     private Set<BinaryDomainCombination>      _shared_binary_domain_combinations;
-    private Set<BinaryDomainCombination>      _binary_domain_combinations_specific_to_0;
-    private Set<BinaryDomainCombination>      _binary_domain_combinations_specific_to_1;
+    private Set<String>                       _shared_domains;
 
     public DomainArchitectureBasedGenomeSimilarityCalculator( final GenomeWideCombinableDomains combinable_domains_genome_0,
                                                               final GenomeWideCombinableDomains combinable_domains_genome_1 ) {
@@ -115,17 +115,6 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         setDomainIdsToIgnore( new HashSet<String>() );
     }
 
-    private void forceRecalculation() {
-        _all_domains = null;
-        _shared_domains = null;
-        _domains_specific_to_0 = null;
-        _domains_specific_to_1 = null;
-        _all_binary_domain_combinations = null;
-        _shared_binary_domain_combinations = null;
-        _binary_domain_combinations_specific_to_0 = null;
-        _binary_domain_combinations_specific_to_1 = null;
-    }
-
     /**
      * Does not return binary combinations which contain one or two domains
      * to be ignored -- if ignoring is allowed.
@@ -169,30 +158,6 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         return _all_domains;
     }
 
-    private Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome( final boolean specific_to_genome_0 ) {
-        final Set<BinaryDomainCombination> specific = new HashSet<BinaryDomainCombination>();
-        final Set<BinaryDomainCombination> bc0 = getCombinableDomainsGenome0().toBinaryDomainCombinations();
-        final Set<BinaryDomainCombination> bc1 = getCombinableDomainsGenome1().toBinaryDomainCombinations();
-        if ( specific_to_genome_0 ) {
-            for( final BinaryDomainCombination binary_domain_combination0 : bc0 ) {
-                if ( !bc1.contains( binary_domain_combination0 ) ) {
-                    specific.add( binary_domain_combination0 );
-                }
-            }
-        }
-        else {
-            for( final BinaryDomainCombination binary_domain_combination1 : bc1 ) {
-                if ( !bc0.contains( binary_domain_combination1 ) ) {
-                    specific.add( binary_domain_combination1 );
-                }
-            }
-        }
-        if ( isAllowDomainsToBeIgnored() && !getDomainIdsToIgnore().isEmpty() ) {
-            return pruneBinaryCombinations( specific );
-        }
-        return specific;
-    }
-
     public Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome0() {
         if ( _binary_domain_combinations_specific_to_0 == null ) {
             _binary_domain_combinations_specific_to_0 = getBinaryDomainCombinationsSpecificToGenome( true );
@@ -207,42 +172,6 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         return _binary_domain_combinations_specific_to_1;
     }
 
-    private GenomeWideCombinableDomains getCombinableDomainsGenome0() {
-        return _combinable_domains_genome_0;
-    }
-
-    private GenomeWideCombinableDomains getCombinableDomainsGenome1() {
-        return _combinable_domains_genome_1;
-    }
-
-    private Set<String> getDomainIdsToIgnore() {
-        return _domain_ids_to_ignore;
-    }
-
-    private Set<String> getDomainsSpecificToGenome( final boolean specific_to_genome_0 ) {
-        final Set<String> specific = new HashSet<String>();
-        final Set<String> d0 = getCombinableDomainsGenome0().getAllDomainIds();
-        final Set<String> d1 = getCombinableDomainsGenome1().getAllDomainIds();
-        if ( specific_to_genome_0 ) {
-            for( final String domain0 : d0 ) {
-                if ( !d1.contains( domain0 ) ) {
-                    specific.add( domain0 );
-                }
-            }
-        }
-        else {
-            for( final String domain1 : d1 ) {
-                if ( !d0.contains( domain1 ) ) {
-                    specific.add( domain1 );
-                }
-            }
-        }
-        if ( isAllowDomainsToBeIgnored() && !getDomainIdsToIgnore().isEmpty() ) {
-            return pruneDomains( specific );
-        }
-        return specific;
-    }
-
     public Set<String> getDomainsSpecificToGenome0() {
         if ( _domains_specific_to_0 == null ) {
             _domains_specific_to_0 = getDomainsSpecificToGenome( true );
@@ -293,6 +222,87 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         return _shared_domains;
     }
 
+    public void setAllowDomainsToBeIgnored( final boolean allow_domains_to_be_ignored ) {
+        forceRecalculation();
+        _allow_domains_to_be_ignored = allow_domains_to_be_ignored;
+    }
+
+    void setDomainIdsToIgnore( final Set<String> domain_ids_to_ignore ) {
+        forceRecalculation();
+        _domain_ids_to_ignore = domain_ids_to_ignore;
+    }
+
+    private void forceRecalculation() {
+        _all_domains = null;
+        _shared_domains = null;
+        _domains_specific_to_0 = null;
+        _domains_specific_to_1 = null;
+        _all_binary_domain_combinations = null;
+        _shared_binary_domain_combinations = null;
+        _binary_domain_combinations_specific_to_0 = null;
+        _binary_domain_combinations_specific_to_1 = null;
+    }
+
+    private Set<BinaryDomainCombination> getBinaryDomainCombinationsSpecificToGenome( final boolean specific_to_genome_0 ) {
+        final Set<BinaryDomainCombination> specific = new HashSet<BinaryDomainCombination>();
+        final Set<BinaryDomainCombination> bc0 = getCombinableDomainsGenome0().toBinaryDomainCombinations();
+        final Set<BinaryDomainCombination> bc1 = getCombinableDomainsGenome1().toBinaryDomainCombinations();
+        if ( specific_to_genome_0 ) {
+            for( final BinaryDomainCombination binary_domain_combination0 : bc0 ) {
+                if ( !bc1.contains( binary_domain_combination0 ) ) {
+                    specific.add( binary_domain_combination0 );
+                }
+            }
+        }
+        else {
+            for( final BinaryDomainCombination binary_domain_combination1 : bc1 ) {
+                if ( !bc0.contains( binary_domain_combination1 ) ) {
+                    specific.add( binary_domain_combination1 );
+                }
+            }
+        }
+        if ( isAllowDomainsToBeIgnored() && !getDomainIdsToIgnore().isEmpty() ) {
+            return pruneBinaryCombinations( specific );
+        }
+        return specific;
+    }
+
+    private GenomeWideCombinableDomains getCombinableDomainsGenome0() {
+        return _combinable_domains_genome_0;
+    }
+
+    private GenomeWideCombinableDomains getCombinableDomainsGenome1() {
+        return _combinable_domains_genome_1;
+    }
+
+    private Set<String> getDomainIdsToIgnore() {
+        return _domain_ids_to_ignore;
+    }
+
+    private Set<String> getDomainsSpecificToGenome( final boolean specific_to_genome_0 ) {
+        final Set<String> specific = new HashSet<String>();
+        final Set<String> d0 = getCombinableDomainsGenome0().getAllDomainIds();
+        final Set<String> d1 = getCombinableDomainsGenome1().getAllDomainIds();
+        if ( specific_to_genome_0 ) {
+            for( final String domain0 : d0 ) {
+                if ( !d1.contains( domain0 ) ) {
+                    specific.add( domain0 );
+                }
+            }
+        }
+        else {
+            for( final String domain1 : d1 ) {
+                if ( !d0.contains( domain1 ) ) {
+                    specific.add( domain1 );
+                }
+            }
+        }
+        if ( isAllowDomainsToBeIgnored() && !getDomainIdsToIgnore().isEmpty() ) {
+            return pruneDomains( specific );
+        }
+        return specific;
+    }
+
     private void init() {
         deleteAllDomainIdsToIgnore();
         setAllowDomainsToBeIgnored( false );
@@ -322,14 +332,4 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         }
         return pruned;
     }
-
-    public void setAllowDomainsToBeIgnored( final boolean allow_domains_to_be_ignored ) {
-        forceRecalculation();
-        _allow_domains_to_be_ignored = allow_domains_to_be_ignored;
-    }
-
-    void setDomainIdsToIgnore( final Set<String> domain_ids_to_ignore ) {
-        forceRecalculation();
-        _domain_ids_to_ignore = domain_ids_to_ignore;
-    }
 }
\ No newline at end of file