X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDomainArchitectureBasedGenomeSimilarityCalculator.java;h=a61ba305a8bce02ff46b0666e5e21bdc9238997e;hb=bf4f34e0511813622f68e54ffb783e4e6d92bfa4;hp=cdc9416369471d8f281e587cead369accbdbfcc4;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
index cdc9416..a61ba30 100644
--- a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
@@ -30,24 +30,23 @@ import java.util.HashSet;
 import java.util.Set;
 
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 
 public class DomainArchitectureBasedGenomeSimilarityCalculator {
 
     public static final double                MAX_SIMILARITY_SCORE = 1.0;
     public static final double                MIN_SIMILARITY_SCORE = 0.0;
-    final private GenomeWideCombinableDomains _combinable_domains_genome_0;
-    final private GenomeWideCombinableDomains _combinable_domains_genome_1;
-    private Set<DomainId>                     _domain_ids_to_ignore;
-    private boolean                           _allow_domains_to_be_ignored;
-    private Set<DomainId>                     _all_domains;
-    private Set<DomainId>                     _shared_domains;
-    private Set<DomainId>                     _domains_specific_to_0;
-    private Set<DomainId>                     _domains_specific_to_1;
     private Set<BinaryDomainCombination>      _all_binary_domain_combinations;
-    private Set<BinaryDomainCombination>      _shared_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 Set<String>                       _domains_specific_to_0;
+    private Set<String>                       _domains_specific_to_1;
+    private Set<BinaryDomainCombination>      _shared_binary_domain_combinations;
+    private Set<String>                       _shared_domains;
 
     public DomainArchitectureBasedGenomeSimilarityCalculator( final GenomeWideCombinableDomains combinable_domains_genome_0,
                                                               final GenomeWideCombinableDomains combinable_domains_genome_1 ) {
@@ -64,7 +63,7 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         forceRecalculation();
     }
 
-    public void addDomainIdToIgnore( final DomainId domain_id_to_ignore ) {
+    public void addDomainIdToIgnore( final String domain_id_to_ignore ) {
         forceRecalculation();
         getDomainIdsToIgnore().add( domain_id_to_ignore );
     }
@@ -113,18 +112,7 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
 
     public void deleteAllDomainIdsToIgnore() {
         forceRecalculation();
-        setDomainIdsToIgnore( new HashSet<DomainId>() );
-    }
-
-    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;
+        setDomainIdsToIgnore( new HashSet<String>() );
     }
 
     /**
@@ -155,9 +143,9 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
      * 
      * @return
      */
-    public Set<DomainId> getAllDomains() {
+    public Set<String> getAllDomains() {
         if ( _all_domains == null ) {
-            final Set<DomainId> all = new HashSet<DomainId>();
+            final Set<String> all = new HashSet<String>();
             all.addAll( getCombinableDomainsGenome0().getAllDomainIds() );
             all.addAll( getCombinableDomainsGenome1().getAllDomainIds() );
             if ( isAllowDomainsToBeIgnored() && !getDomainIdsToIgnore().isEmpty() ) {
@@ -170,30 +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 );
@@ -208,50 +172,14 @@ 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<DomainId> getDomainIdsToIgnore() {
-        return _domain_ids_to_ignore;
-    }
-
-    private Set<DomainId> getDomainsSpecificToGenome( final boolean specific_to_genome_0 ) {
-        final Set<DomainId> specific = new HashSet<DomainId>();
-        final Set<DomainId> d0 = getCombinableDomainsGenome0().getAllDomainIds();
-        final Set<DomainId> d1 = getCombinableDomainsGenome1().getAllDomainIds();
-        if ( specific_to_genome_0 ) {
-            for( final DomainId domain0 : d0 ) {
-                if ( !d1.contains( domain0 ) ) {
-                    specific.add( domain0 );
-                }
-            }
-        }
-        else {
-            for( final DomainId domain1 : d1 ) {
-                if ( !d0.contains( domain1 ) ) {
-                    specific.add( domain1 );
-                }
-            }
-        }
-        if ( isAllowDomainsToBeIgnored() && !getDomainIdsToIgnore().isEmpty() ) {
-            return pruneDomains( specific );
-        }
-        return specific;
-    }
-
-    public Set<DomainId> getDomainsSpecificToGenome0() {
+    public Set<String> getDomainsSpecificToGenome0() {
         if ( _domains_specific_to_0 == null ) {
             _domains_specific_to_0 = getDomainsSpecificToGenome( true );
         }
         return _domains_specific_to_0;
     }
 
-    public Set<DomainId> getDomainsSpecificToGenome1() {
+    public Set<String> getDomainsSpecificToGenome1() {
         if ( _domains_specific_to_1 == null ) {
             _domains_specific_to_1 = getDomainsSpecificToGenome( false );
         }
@@ -276,12 +204,12 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         return _shared_binary_domain_combinations;
     }
 
-    public Set<DomainId> getSharedDomains() {
+    public Set<String> getSharedDomains() {
         if ( _shared_domains == null ) {
-            final Set<DomainId> shared = new HashSet<DomainId>();
-            final Set<DomainId> d0 = getCombinableDomainsGenome0().getAllDomainIds();
-            final Set<DomainId> d1 = getCombinableDomainsGenome1().getAllDomainIds();
-            for( final DomainId domain0 : d0 ) {
+            final Set<String> shared = new HashSet<String>();
+            final Set<String> d0 = getCombinableDomainsGenome0().getAllDomainIds();
+            final Set<String> d1 = getCombinableDomainsGenome1().getAllDomainIds();
+            for( final String domain0 : d0 ) {
                 if ( d1.contains( domain0 ) ) {
                     shared.add( domain0 );
                 }
@@ -294,6 +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 );
@@ -314,23 +323,13 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         return pruned;
     }
 
-    private Set<DomainId> pruneDomains( final Set<DomainId> all ) {
-        final Set<DomainId> pruned = new HashSet<DomainId>();
-        for( final DomainId d : all ) {
+    private Set<String> pruneDomains( final Set<String> all ) {
+        final Set<String> pruned = new HashSet<String>();
+        for( final String d : all ) {
             if ( !getDomainIdsToIgnore().contains( d ) ) {
                 pruned.add( d );
             }
         }
         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<DomainId> domain_ids_to_ignore ) {
-        forceRecalculation();
-        _domain_ids_to_ignore = domain_ids_to_ignore;
-    }
 }
\ No newline at end of file