inprogress

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

diff --git a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
index 317bec3..caf6cb0 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
@@ -6,7 +6,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -16,31 +16,33 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.surfacing;
 
 import java.util.HashSet;
 import java.util.Set;
 
+import org.forester.protein.BinaryDomainCombination;
+
 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 Set<String>                       _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<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;
@@ -61,7 +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 );
     }
@@ -110,7 +112,7 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
 
     public void deleteAllDomainIdsToIgnore() {
         forceRecalculation();
-        setDomainIdsToIgnore( new HashSet<DomainId>() );
+        setDomainIdsToIgnore( new HashSet<String>() );
     }
 
     private void forceRecalculation() {
@@ -152,9 +154,9 @@ 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() ) {
@@ -213,23 +215,23 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         return _combinable_domains_genome_1;
     }
 
-    private Set<DomainId> getDomainIdsToIgnore() {
+    private Set<String> 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();
+    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 DomainId domain0 : d0 ) {
+            for( final String domain0 : d0 ) {
                 if ( !d1.contains( domain0 ) ) {
                     specific.add( domain0 );
                 }
             }
         }
         else {
-            for( final DomainId domain1 : d1 ) {
+            for( final String domain1 : d1 ) {
                 if ( !d0.contains( domain1 ) ) {
                     specific.add( domain1 );
                 }
@@ -241,14 +243,14 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         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 );
         }
@@ -273,12 +275,12 @@ 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 );
                 }
@@ -311,9 +313,9 @@ 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 );
             }
@@ -326,7 +328,7 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
         _allow_domains_to_be_ignored = allow_domains_to_be_ignored;
     }
 
-    void setDomainIdsToIgnore( final Set<DomainId> domain_ids_to_ignore ) {
+    void setDomainIdsToIgnore( final Set<String> domain_ids_to_ignore ) {
         forceRecalculation();
         _domain_ids_to_ignore = domain_ids_to_ignore;
     }