From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 2 Jul 2013 02:09:51 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=87d34f343d0262cd0c009c6f1da058a5a217bc64;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/application/pfam2go_extractor.java b/forester/java/src/org/forester/application/pfam2go_extractor.java
index d9f4cd3..6852d05 100644
--- a/forester/java/src/org/forester/application/pfam2go_extractor.java
+++ b/forester/java/src/org/forester/application/pfam2go_extractor.java
@@ -39,7 +39,6 @@ import org.forester.go.GoUtils;
 import org.forester.go.OBOparser;
 import org.forester.go.PfamToGoMapping;
 import org.forester.go.PfamToGoParser;
-import org.forester.protein.DomainId;
 
 public class pfam2go_extractor {
 
@@ -79,7 +78,7 @@ public class pfam2go_extractor {
         }
         final SortedSet<String> pfams = new TreeSet<String>();
         for( final PfamToGoMapping pfam_to_go_mapping : pfam2go ) {
-            final DomainId domain_id = pfam_to_go_mapping.getKey();
+            final String domain_id = pfam_to_go_mapping.getKey();
             final GoId go_id = pfam_to_go_mapping.getValue();
             final Set<GoId> supers = GoUtils.getAllSuperGoIds( go_id, goid_to_term_map );
             supers.add( go_id );
diff --git a/forester/java/src/org/forester/application/pfam_go.java b/forester/java/src/org/forester/application/pfam_go.java
index 475b5d4..0da8a2d 100644
--- a/forester/java/src/org/forester/application/pfam_go.java
+++ b/forester/java/src/org/forester/application/pfam_go.java
@@ -78,7 +78,7 @@ public class pfam_go {
                     encountered_domains.add( line );
                     boolean found = false;
                     for( final PfamToGoMapping mapping : mappings ) {
-                        if ( mapping.getKey().getId().equals( line ) ) {
+                        if ( mapping.getKey().equals( line ) ) {
                             System.out.println( mapping.getValue() );
                             found = true;
                         }
diff --git a/forester/java/src/org/forester/application/pfamacc2go.java b/forester/java/src/org/forester/application/pfamacc2go.java
index ce34dc7..82ff0b8 100644
--- a/forester/java/src/org/forester/application/pfamacc2go.java
+++ b/forester/java/src/org/forester/application/pfamacc2go.java
@@ -82,7 +82,7 @@ public class pfamacc2go {
                         total_pfam_ids++;
                         boolean mapped = false;
                         for( final PfamToGoMapping pfam_to_go_mapping : pfam2go ) {
-                            if ( pfam_to_go_mapping.getKey().getId().equals( pfam_id ) ) {
+                            if ( pfam_to_go_mapping.getKey().equals( pfam_id ) ) {
                                 mapped = true;
                                 System.out.println( pfam_to_go_mapping.getValue().toString() );
                             }
diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index dbba361..d83fdf7 100644
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -63,7 +63,6 @@ import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.protein.BinaryDomainCombination;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.species.BasicSpecies;
 import org.forester.species.Species;
@@ -229,8 +228,8 @@ public class surfacing {
     final static private String                               INPUT_GENOMES_FILE_OPTION                                                     = "genomes";
     final static private String                               INPUT_SPECIES_TREE_OPTION                                                     = "species_tree";
     final static private String                               SEQ_EXTRACT_OPTION                                                            = "prot_extract";
-    final static private String                               PRG_VERSION                                                                   = "2.270";
-    final static private String                               PRG_DATE                                                                      = "130628";
+    final static private String                               PRG_VERSION                                                                   = "2.280";
+    final static private String                               PRG_DATE                                                                      = "130701";
     final static private String                               E_MAIL                                                                        = "czmasek@burnham.org";
     final static private String                               WWW                                                                           = "www.phylosoft.org/forester/applications/surfacing";
     final static private boolean                              IGNORE_DUFS_DEFAULT                                                           = true;
@@ -369,8 +368,8 @@ public class surfacing {
         final Writer out = ForesterUtil.createBufferedWriter( output_file );
         final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
                 .listToSortedCountsMap( all_bin_domain_combinations_changed );
-        final SortedSet<DomainId> all_domains_in_combination_changed_more_than_once = new TreeSet<DomainId>();
-        final SortedSet<DomainId> all_domains_in_combination_changed_only_once = new TreeSet<DomainId>();
+        final SortedSet<String> all_domains_in_combination_changed_more_than_once = new TreeSet<String>();
+        final SortedSet<String> all_domains_in_combination_changed_only_once = new TreeSet<String>();
         int above_one = 0;
         int one = 0;
         for( final Object bdc_object : bdc_to_counts.keySet() ) {
@@ -438,7 +437,7 @@ public class surfacing {
                                                   final List<String> plus_minus_analysis_low_copy,
                                                   final List<GenomeWideCombinableDomains> gwcd_list,
                                                   final SortedMap<Species, List<Protein>> protein_lists_per_species,
-                                                  final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+                                                  final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                   final Map<GoId, GoTerm> go_id_to_term_map,
                                                   final List<Object> plus_minus_analysis_numbers ) {
         final Set<String> all_spec = new HashSet<String>();
@@ -1048,7 +1047,7 @@ public class surfacing {
             SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
         }
         File pfam_to_go_file = null;
-        Map<DomainId, List<GoId>> domain_id_to_go_ids_map = null;
+        Map<String, List<GoId>> domain_id_to_go_ids_map = null;
         int domain_id_to_go_ids_count = 0;
         if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
             if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
@@ -1237,10 +1236,10 @@ public class surfacing {
             }
             radomize_fitch_parsimony = true;
         }
-        SortedSet<DomainId> filter = null;
+        SortedSet<String> filter = null;
         if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
                 || ( negative_domains_filter_file != null ) ) {
-            filter = new TreeSet<DomainId>();
+            filter = new TreeSet<String>();
             if ( positive_filter_file != null ) {
                 processFilter( positive_filter_file, filter );
             }
@@ -1251,7 +1250,7 @@ public class surfacing {
                 processFilter( negative_domains_filter_file, filter );
             }
         }
-        Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps = null;
+        Map<String, Set<String>>[] domain_id_to_secondary_features_maps = null;
         File[] secondary_features_map_files = null;
         final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
                 + DOMAIN_LENGTHS_ANALYSIS_SUFFIX );
@@ -1606,8 +1605,8 @@ public class surfacing {
                     if ( VERBOSE ) {
                         System.out.println();
                         System.out.println( "Domain ids to secondary features map:" );
-                        for( final DomainId domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
-                            System.out.print( domain_id.getId() );
+                        for( final String domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
+                            System.out.print( domain_id );
                             System.out.print( " => " );
                             for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) {
                                 System.out.print( sec );
@@ -1623,7 +1622,7 @@ public class surfacing {
         html_desc.append( "<tr><td>Command line:</td><td>\n" + cla.getCommandLineArgsAsString() + "\n</td></tr>" + nl );
         System.out.println( "Command line                : " + cla.getCommandLineArgsAsString() );
         BufferedWriter[] query_domains_writer_ary = null;
-        List<DomainId>[] query_domain_ids_array = null;
+        List<String>[] query_domain_ids_array = null;
         if ( query_domain_ids != null ) {
             final String[] query_domain_ids_str_array = query_domain_ids.split( "#" );
             query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ];
@@ -1631,9 +1630,9 @@ public class surfacing {
             for( int i = 0; i < query_domain_ids_str_array.length; i++ ) {
                 String query_domain_ids_str = query_domain_ids_str_array[ i ];
                 final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" );
-                final List<DomainId> query = new ArrayList<DomainId>();
+                final List<String> query = new ArrayList<String>();
                 for( final String element : query_domain_ids_str_ary ) {
-                    query.add( new DomainId( element ) );
+                    query.add( element );
                 }
                 query_domain_ids_array[ i ] = query;
                 query_domain_ids_str = query_domain_ids_str.replace( '~', '_' );
@@ -1659,7 +1658,7 @@ public class surfacing {
             protein_lists_per_species = new TreeMap<Species, List<Protein>>();
         }
         final List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
-        final SortedSet<DomainId> all_domains_encountered = new TreeSet<DomainId>();
+        final SortedSet<String> all_domains_encountered = new TreeSet<String>();
         final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
         List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
         List<BinaryDomainCombination> all_bin_domain_combinations_lost_fitch = null;
@@ -2283,7 +2282,7 @@ public class surfacing {
                 if ( ( domain_id_to_secondary_features_maps != null )
                         && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
                     int j = 0;
-                    for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
+                    for( final Map<String, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
                         final Map<Species, MappingResults> mapping_results_map = new TreeMap<Species, MappingResults>();
                         final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator
                                 .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map );
@@ -2604,7 +2603,7 @@ public class surfacing {
         System.out.println();
     }
 
-    private static void processFilter( final File filter_file, final SortedSet<DomainId> filter ) {
+    private static void processFilter( final File filter_file, final SortedSet<String> filter ) {
         SortedSet<String> filter_str = null;
         try {
             filter_str = ForesterUtil.file2set( filter_file );
@@ -2614,13 +2613,13 @@ public class surfacing {
         }
         if ( filter_str != null ) {
             for( final String string : filter_str ) {
-                filter.add( new DomainId( string ) );
+                filter.add( string );
             }
         }
         if ( VERBOSE ) {
             System.out.println( "Filter:" );
-            for( final DomainId domainId : filter ) {
-                System.out.println( domainId.getId() );
+            for( final String domainId : filter ) {
+                System.out.println( domainId );
             }
         }
     }
@@ -2760,7 +2759,7 @@ public class surfacing {
 
     private static void writePresentToNexus( final File output_file,
                                              final File positive_filter_file,
-                                             final SortedSet<DomainId> filter,
+                                             final SortedSet<String> filter,
                                              final List<GenomeWideCombinableDomains> gwcd_list ) {
         try {
             SurfacingUtil
@@ -2780,11 +2779,11 @@ public class surfacing {
                                                         final SortedMap<Species, List<Protein>> protein_lists_per_species,
                                                         final List<GenomeWideCombinableDomains> gwcd_list,
                                                         final double domain_e_cutoff ) {
-        final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
+        final SortedSet<String> all_domains = new TreeSet<String>();
         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
             all_domains.addAll( gwcd.getAllDomainIds() );
         }
-        for( final DomainId domain : all_domains ) {
+        for( final String domain : all_domains ) {
             final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
             SurfacingUtil.checkForOutputFileWriteability( out );
             try {
diff --git a/forester/java/src/org/forester/go/PfamToGoMapping.java b/forester/java/src/org/forester/go/PfamToGoMapping.java
index e11fde1..33815ab 100644
--- a/forester/java/src/org/forester/go/PfamToGoMapping.java
+++ b/forester/java/src/org/forester/go/PfamToGoMapping.java
@@ -25,14 +25,12 @@
 
 package org.forester.go;
 
-import org.forester.protein.DomainId;
-
 public class PfamToGoMapping implements Mapping {
 
-    private final DomainId _pfam_domain_id;
-    private final GoId     _go_id;
+    private final String _pfam_domain_id;
+    private final GoId   _go_id;
 
-    public PfamToGoMapping( final DomainId pfam_domain_id, final GoId go_id ) {
+    public PfamToGoMapping( final String pfam_domain_id, final GoId go_id ) {
         _pfam_domain_id = pfam_domain_id;
         _go_id = go_id;
     }
@@ -42,7 +40,7 @@ public class PfamToGoMapping implements Mapping {
         if ( this == m ) {
             return 0;
         }
-        return getKey().compareTo( ( DomainId ) m.getKey() );
+        return getKey().compareTo( ( String ) m.getKey() );
     }
 
     /**
@@ -69,7 +67,7 @@ public class PfamToGoMapping implements Mapping {
     }
 
     @Override
-    public DomainId getKey() {
+    public String getKey() {
         return _pfam_domain_id;
     }
 
diff --git a/forester/java/src/org/forester/go/PfamToGoParser.java b/forester/java/src/org/forester/go/PfamToGoParser.java
index 8840b96..ca55c12 100644
--- a/forester/java/src/org/forester/go/PfamToGoParser.java
+++ b/forester/java/src/org/forester/go/PfamToGoParser.java
@@ -10,7 +10,6 @@ import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.forester.protein.DomainId;
 import org.forester.util.ForesterUtil;
 
 public class PfamToGoParser {
@@ -78,7 +77,7 @@ public class PfamToGoParser {
                     if ( ForesterUtil.isEmpty( pfam ) || ForesterUtil.isEmpty( go ) ) {
                         throw new IOException( "unexpected format [\"" + line + "\"]" );
                     }
-                    final PfamToGoMapping map = new PfamToGoMapping( new DomainId( pfam ), new GoId( go ) );
+                    final PfamToGoMapping map = new PfamToGoMapping( pfam, new GoId( go ) );
                     ++_mapping_count;
                     mappings.add( map );
                 }
diff --git a/forester/java/src/org/forester/go/TestGo.java b/forester/java/src/org/forester/go/TestGo.java
index f8197ee..9d5f0c7 100644
--- a/forester/java/src/org/forester/go/TestGo.java
+++ b/forester/java/src/org/forester/go/TestGo.java
@@ -31,7 +31,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.SortedSet;
 
-import org.forester.protein.DomainId;
 import org.forester.util.ForesterUtil;
 
 public class TestGo {
@@ -356,11 +355,11 @@ public class TestGo {
 
     private static boolean testPfamToGoMapping() {
         try {
-            final PfamToGoMapping pg0 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000001" ) );
-            final PfamToGoMapping pg1 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000001" ) );
-            final PfamToGoMapping pg2 = new PfamToGoMapping( new DomainId( "B" ), new GoId( "GO:0000001" ) );
-            final PfamToGoMapping pg3 = new PfamToGoMapping( new DomainId( "A" ), new GoId( "GO:0000002" ) );
-            final PfamToGoMapping pg4 = new PfamToGoMapping( new DomainId( "B" ), new GoId( "GO:0000002" ) );
+            final PfamToGoMapping pg0 = new PfamToGoMapping( "A", new GoId( "GO:0000001" ) );
+            final PfamToGoMapping pg1 = new PfamToGoMapping( "A", new GoId( "GO:0000001" ) );
+            final PfamToGoMapping pg2 = new PfamToGoMapping( "B", new GoId( "GO:0000001" ) );
+            final PfamToGoMapping pg3 = new PfamToGoMapping( "A", new GoId( "GO:0000002" ) );
+            final PfamToGoMapping pg4 = new PfamToGoMapping( "B", new GoId( "GO:0000002" ) );
             if ( !pg0.equals( pg0 ) ) {
                 return false;
             }
@@ -412,55 +411,55 @@ public class TestGo {
             final PfamToGoMapping m5 = mappings.get( 5 );
             final PfamToGoMapping m424 = mappings.get( 424 );
             final PfamToGoMapping m425 = mappings.get( 425 );
-            if ( !m0.getKey().equals( new DomainId( "7tm_1" ) ) ) {
+            if ( !m0.getKey().equals( "7tm_1" ) ) {
                 return false;
             }
             if ( !m0.getValue().equals( new GoId( "GO:0001584" ) ) ) {
                 return false;
             }
-            if ( m0.getKey().equals( new DomainId( "7tm_x" ) ) ) {
+            if ( m0.getKey().equals( "7tm_x" ) ) {
                 return false;
             }
             if ( m0.getValue().equals( new GoId( "GO:0001585" ) ) ) {
                 return false;
             }
-            if ( !m1.getKey().equals( new DomainId( "7tm_1" ) ) ) {
+            if ( !m1.getKey().equals( "7tm_1" ) ) {
                 return false;
             }
             if ( !m1.getValue().equals( new GoId( "GO:0007186" ) ) ) {
                 return false;
             }
-            if ( !m2.getKey().equals( new DomainId( "7tm_1" ) ) ) {
+            if ( !m2.getKey().equals( "7tm_1" ) ) {
                 return false;
             }
             if ( !m2.getValue().equals( new GoId( "GO:0016021" ) ) ) {
                 return false;
             }
-            if ( !m3.getKey().equals( new DomainId( "7tm_2" ) ) ) {
+            if ( !m3.getKey().equals( "7tm_2" ) ) {
                 return false;
             }
             if ( !m3.getValue().equals( new GoId( "GO:0004930" ) ) ) {
                 return false;
             }
-            if ( !m4.getKey().equals( new DomainId( "7tm_2" ) ) ) {
+            if ( !m4.getKey().equals( "7tm_2" ) ) {
                 return false;
             }
             if ( !m4.getValue().equals( new GoId( "GO:0016020" ) ) ) {
                 return false;
             }
-            if ( !m5.getKey().equals( new DomainId( "7tm_3" ) ) ) {
+            if ( !m5.getKey().equals( "7tm_3" ) ) {
                 return false;
             }
             if ( !m5.getValue().equals( new GoId( "GO:0008067" ) ) ) {
                 return false;
             }
-            if ( !m424.getKey().equals( new DomainId( "OMPdecase" ) ) ) {
+            if ( !m424.getKey().equals( "OMPdecase" ) ) {
                 return false;
             }
             if ( !m424.getValue().equals( new GoId( "GO:0006207" ) ) ) {
                 return false;
             }
-            if ( !m425.getKey().equals( new DomainId( "Bac_DNA_binding" ) ) ) {
+            if ( !m425.getKey().equals( "Bac_DNA_binding" ) ) {
                 return false;
             }
             if ( !m425.getValue().equals( new GoId( "GO:0003677" ) ) ) {
diff --git a/forester/java/src/org/forester/go/etc/MetaOntologizer.java b/forester/java/src/org/forester/go/etc/MetaOntologizer.java
index 32f841d..98bf943 100644
--- a/forester/java/src/org/forester/go/etc/MetaOntologizer.java
+++ b/forester/java/src/org/forester/go/etc/MetaOntologizer.java
@@ -51,7 +51,6 @@ import org.forester.go.GoTerm;
 import org.forester.go.GoUtils;
 import org.forester.go.OBOparser;
 import org.forester.go.PfamToGoMapping;
-import org.forester.protein.DomainId;
 import org.forester.species.BasicSpecies;
 import org.forester.species.Species;
 import org.forester.surfacing.SurfacingConstants;
@@ -85,12 +84,12 @@ public class MetaOntologizer {
     }
 
     private static StringBuilder obtainDomainsForGoId( final List<PfamToGoMapping> pfam_to_go,
-                                                       final SortedSet<DomainId> domains_per_species,
+                                                       final SortedSet<String> domains_per_species,
                                                        final Map<GoId, GoTerm> all_go_terms,
                                                        final GoId query_go_id,
-                                                       final Set<DomainId> found_domain_ids ) {
+                                                       final Set<String> found_domain_ids ) {
         final StringBuilder sb = new StringBuilder();
-        D: for( final DomainId domain_id : domains_per_species ) {
+        D: for( final String domain_id : domains_per_species ) {
             for( final PfamToGoMapping ptg : pfam_to_go ) {
                 if ( ptg.getKey().equals( domain_id ) ) {
                     final GoId go_id = ptg.getValue();
@@ -128,13 +127,12 @@ public class MetaOntologizer {
         return species;
     }
 
-    private static SortedMap<Species, SortedSet<DomainId>> parseDomainGainLossFile( final File input )
-            throws IOException {
+    private static SortedMap<Species, SortedSet<String>> parseDomainGainLossFile( final File input ) throws IOException {
         final String error = ForesterUtil.isReadableFile( input );
         if ( !ForesterUtil.isEmpty( error ) ) {
             throw new IOException( error );
         }
-        final SortedMap<Species, SortedSet<DomainId>> speciesto_to_domain_id = new TreeMap<Species, SortedSet<DomainId>>();
+        final SortedMap<Species, SortedSet<String>> speciesto_to_domain_id = new TreeMap<Species, SortedSet<String>>();
         final BufferedReader br = new BufferedReader( new FileReader( input ) );
         String line;
         int line_number = 0;
@@ -148,7 +146,7 @@ public class MetaOntologizer {
                 }
                 else if ( line.startsWith( "#" ) ) {
                     current_species = new BasicSpecies( line.substring( 1 ) );
-                    speciesto_to_domain_id.put( current_species, new TreeSet<DomainId>() );
+                    speciesto_to_domain_id.put( current_species, new TreeSet<String>() );
                     if ( VERBOSE ) {
                         ForesterUtil.programMessage( PRG_NAME, "saw " + current_species );
                     }
@@ -157,7 +155,7 @@ public class MetaOntologizer {
                     if ( current_species == null ) {
                         throw new IOException( "parsing problem [at line " + line_number + "] in [" + input + "]" );
                     }
-                    speciesto_to_domain_id.get( current_species ).add( new DomainId( line ) );
+                    speciesto_to_domain_id.get( current_species ).add( new String( line ) );
                 }
             }
         }
@@ -178,9 +176,9 @@ public class MetaOntologizer {
                                            final SortedMap<String, SortedSet<OntologizerResult>> species_to_results_map,
                                            final String species,
                                            final double p_adjusted_upper_limit,
-                                           final SortedSet<DomainId> domains_per_species,
+                                           final SortedSet<String> domains_per_species,
                                            final List<PfamToGoMapping> pfam_to_go,
-                                           final Set<DomainId> domain_ids_with_go_annot ) throws IOException {
+                                           final Set<String> domain_ids_with_go_annot ) throws IOException {
         final SortedSet<OntologizerResult> ontologizer_results = species_to_results_map.get( species );
         for( final OntologizerResult ontologizer_result : ontologizer_results ) {
             final GoTerm go_term = go_id_to_terms.get( ontologizer_result.getGoId() );
@@ -230,7 +228,7 @@ public class MetaOntologizer {
             throw new IllegalArgumentException( "adjusted P values limit [" + p_adjusted_upper_limit
                     + "] is out of range" );
         }
-        SortedMap<Species, SortedSet<DomainId>> speciesto_to_domain_id = null;
+        SortedMap<Species, SortedSet<String>> speciesto_to_domain_id = null;
         if ( domain_gain_loss_file != null ) {
             if ( !domain_gain_loss_file.exists() ) {
                 throw new IllegalArgumentException( "[" + domain_gain_loss_file + "] does not exist" );
@@ -333,11 +331,11 @@ public class MetaOntologizer {
                                        GoNameSpace.GoNamespaceType.MOLECULAR_FUNCTION ) ) {
                 writeHtmlSpecies( m_html_writer, species );
             }
-            SortedSet<DomainId> domains_per_species = null;
+            SortedSet<String> domains_per_species = null;
             if ( ( speciesto_to_domain_id != null ) && ( speciesto_to_domain_id.size() > 0 ) ) {
                 domains_per_species = speciesto_to_domain_id.get( new BasicSpecies( species ) );
             }
-            final Set<DomainId> domain_ids_with_go_annot = new HashSet<DomainId>();
+            final Set<String> domain_ids_with_go_annot = new HashSet<String>();
             processOneSpecies( go_id_to_terms,
                                b_html_writer,
                                b_tab_writer,
@@ -398,12 +396,12 @@ public class MetaOntologizer {
     }
 
     private static void writeHtmlDomains( final Writer writer,
-                                          final SortedSet<DomainId> domains,
-                                          final Set<DomainId> domain_ids_with_go_annot ) throws IOException {
+                                          final SortedSet<String> domains,
+                                          final Set<String> domain_ids_with_go_annot ) throws IOException {
         writer.write( "<tr>" );
         writer.write( "<td colspan=\"10\">" );
         if ( domains != null ) {
-            for( final DomainId domain : domains ) {
+            for( final String domain : domains ) {
                 if ( !domain_ids_with_go_annot.contains( domain ) ) {
                     writer.write( "[<a class=\"new_type\" href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain
                             + "\">" + domain + "</a>] " );
@@ -555,9 +553,9 @@ public class MetaOntologizer {
                                                  final double p_adjusted_upper_limit,
                                                  final String species,
                                                  final Map<GoId, GoTerm> go_id_to_terms,
-                                                 final SortedSet<DomainId> domains_per_species,
+                                                 final SortedSet<String> domains_per_species,
                                                  final List<PfamToGoMapping> pfam_to_go,
-                                                 final Set<DomainId> domain_ids_with_go_annot ) throws IOException {
+                                                 final Set<String> domain_ids_with_go_annot ) throws IOException {
         final Color p_adj_color = ForesterUtil.calcColor( ontologizer_result.getPAdjusted(),
                                                           0,
                                                           p_adjusted_upper_limit,
diff --git a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
index 090a052..2fae940 100644
--- a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
@@ -43,7 +43,6 @@ import java.util.TreeSet;
 import org.forester.protein.BasicDomain;
 import org.forester.protein.BasicProtein;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.surfacing.SurfacingUtil;
 import org.forester.util.ForesterUtil;
@@ -62,7 +61,7 @@ public final class HmmPfamOutputParser {
     private static final ReturnType RETURN_TYPE_DEFAULT         = ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN;
     private static final boolean    IGNORE_DUFS_DEFAULT         = false;
     private static final int        MAX_ALLOWED_OVERLAP_DEFAULT = -1;
-    private final Set<DomainId>     _filter;
+    private final Set<String>       _filter;
     private final FilterType        _filter_type;
     private final File              _input_file;
     private final String            _species;
@@ -85,7 +84,7 @@ public final class HmmPfamOutputParser {
     private int                     _domains_ignored_due_to_e_value;
     private int                     _domains_ignored_due_to_individual_score_cutoff;
     private int                     _domains_stored;
-    private SortedSet<DomainId>     _domains_stored_set;
+    private SortedSet<String>       _domains_stored_set;
     private long                    _time;
     private int                     _domains_ignored_due_to_negative_domain_filter;
     private Map<String, Integer>    _domains_ignored_due_to_negative_domain_filter_counts_map;
@@ -104,7 +103,7 @@ public final class HmmPfamOutputParser {
     public HmmPfamOutputParser( final File input_file,
                                 final String species,
                                 final String model_type,
-                                final Set<DomainId> filter,
+                                final Set<String> filter,
                                 final FilterType filter_type ) {
         _input_file = input_file;
         _species = species;
@@ -125,7 +124,7 @@ public final class HmmPfamOutputParser {
 
     private void addProtein( final List<Protein> proteins, final Protein current_protein ) {
         if ( ( getFilterType() == FilterType.POSITIVE_PROTEIN ) || ( getFilterType() == FilterType.NEGATIVE_PROTEIN ) ) {
-            final Set<DomainId> domain_ids_in_protein = new HashSet<DomainId>();
+            final Set<String> domain_ids_in_protein = new HashSet<String>();
             for( final Domain d : current_protein.getProteinDomains() ) {
                 domain_ids_in_protein.add( d.getDomainId() );
             }
@@ -192,7 +191,7 @@ public final class HmmPfamOutputParser {
         return _domains_stored;
     }
 
-    public SortedSet<DomainId> getDomainsStoredSet() {
+    public SortedSet<String> getDomainsStoredSet() {
         return _domains_stored_set;
     }
 
@@ -200,7 +199,7 @@ public final class HmmPfamOutputParser {
         return _e_value_maximum;
     }
 
-    private Set<DomainId> getFilter() {
+    private Set<String> getFilter() {
         return _filter;
     }
 
@@ -262,7 +261,7 @@ public final class HmmPfamOutputParser {
     }
 
     private void intitCounts() {
-        setDomainsStoredSet( new TreeSet<DomainId>() );
+        setDomainsStoredSet( new TreeSet<String>() );
         setDomainsEncountered( 0 );
         setProteinsEncountered( 0 );
         setProteinsIgnoredDueToFilter( 0 );
@@ -539,8 +538,7 @@ public final class HmmPfamOutputParser {
                     ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToVirusLikeIdCountsMap(), id );
                     ++_domains_ignored_due_to_virus_like_id;
                 }
-                else if ( ( getFilterType() == FilterType.NEGATIVE_DOMAIN )
-                        && getFilter().contains( new DomainId( id ) ) ) {
+                else if ( ( getFilterType() == FilterType.NEGATIVE_DOMAIN ) && getFilter().contains( id ) ) {
                     ++_domains_ignored_due_to_negative_domain_filter;
                     ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToNegativeDomainFilterCountsMap(), id );
                 }
@@ -608,7 +606,7 @@ public final class HmmPfamOutputParser {
         _domains_stored = domains_stored;
     }
 
-    private void setDomainsStoredSet( final SortedSet<DomainId> _storeddomains_stored ) {
+    private void setDomainsStoredSet( final SortedSet<String> _storeddomains_stored ) {
         _domains_stored_set = _storeddomains_stored;
     }
 
diff --git a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
index ada802a..4495009 100644
--- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
@@ -44,7 +44,6 @@ import java.util.TreeSet;
 import org.forester.protein.BasicDomain;
 import org.forester.protein.BasicProtein;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.surfacing.SurfacingUtil;
 import org.forester.util.ForesterUtil;
@@ -65,7 +64,7 @@ public final class HmmscanPerDomainTableParser {
     private static final boolean          IGNORE_DUFS_DEFAULT         = false;
     private static final int              MAX_ALLOWED_OVERLAP_DEFAULT = -1;
     private static final boolean          IGNORE_REPLACED_RRMS        = false;
-    private final Set<DomainId>           _filter;
+    private final Set<String>             _filter;
     private final FilterType              _filter_type;
     private final File                    _input_file;
     private final String                  _species;
@@ -85,7 +84,7 @@ public final class HmmscanPerDomainTableParser {
     private int                           _domains_ignored_due_to_e_value;
     private int                           _domains_ignored_due_to_individual_score_cutoff;
     private int                           _domains_stored;
-    private SortedSet<DomainId>           _domains_stored_set;
+    private SortedSet<String>             _domains_stored_set;
     private long                          _time;
     private int                           _domains_ignored_due_to_negative_domain_filter;
     private Map<String, Integer>          _domains_ignored_due_to_negative_domain_filter_counts_map;
@@ -121,7 +120,7 @@ public final class HmmscanPerDomainTableParser {
 
     public HmmscanPerDomainTableParser( final File input_file,
                                         final String species,
-                                        final Set<DomainId> filter,
+                                        final Set<String> filter,
                                         final FilterType filter_type,
                                         final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) {
         _input_file = input_file;
@@ -135,7 +134,7 @@ public final class HmmscanPerDomainTableParser {
 
     public HmmscanPerDomainTableParser( final File input_file,
                                         final String species,
-                                        final Set<DomainId> filter,
+                                        final Set<String> filter,
                                         final FilterType filter_type,
                                         final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to,
                                         final boolean allow_proteins_with_same_name ) {
@@ -173,7 +172,7 @@ public final class HmmscanPerDomainTableParser {
             _domains_ignored_due_to_overlap += domains_removed;
         }
         if ( ( getFilterType() == FilterType.POSITIVE_PROTEIN ) || ( getFilterType() == FilterType.NEGATIVE_PROTEIN ) ) {
-            final Set<DomainId> domain_ids_in_protein = new HashSet<DomainId>();
+            final Set<String> domain_ids_in_protein = new HashSet<String>();
             for( final Domain d : current_protein.getProteinDomains() ) {
                 domain_ids_in_protein.add( d.getDomainId() );
             }
@@ -240,7 +239,7 @@ public final class HmmscanPerDomainTableParser {
         return _domains_stored;
     }
 
-    public SortedSet<DomainId> getDomainsStoredSet() {
+    public SortedSet<String> getDomainsStoredSet() {
         return _domains_stored_set;
     }
 
@@ -248,7 +247,7 @@ public final class HmmscanPerDomainTableParser {
         return _e_value_maximum;
     }
 
-    private Set<DomainId> getFilter() {
+    private Set<String> getFilter() {
         return _filter;
     }
 
@@ -308,7 +307,7 @@ public final class HmmscanPerDomainTableParser {
     }
 
     private void intitCounts() {
-        setDomainsStoredSet( new TreeSet<DomainId>() );
+        setDomainsStoredSet( new TreeSet<String>() );
         setDomainsEncountered( 0 );
         setProteinsEncountered( 0 );
         setProteinsIgnoredDueToFilter( 0 );
@@ -459,8 +458,7 @@ public final class HmmscanPerDomainTableParser {
                 ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToVirusLikeIdCountsMap(), target_id );
                 ++_domains_ignored_due_to_virus_like_id;
             }
-            else if ( ( getFilterType() == FilterType.NEGATIVE_DOMAIN )
-                    && getFilter().contains( new DomainId( target_id ) ) ) {
+            else if ( ( getFilterType() == FilterType.NEGATIVE_DOMAIN ) && getFilter().contains( target_id ) ) {
                 ++_domains_ignored_due_to_negative_domain_filter;
                 ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToNegativeDomainFilterCountsMap(), target_id );
             }
@@ -556,7 +554,7 @@ public final class HmmscanPerDomainTableParser {
         _domains_stored = domains_stored;
     }
 
-    private void setDomainsStoredSet( final SortedSet<DomainId> _storeddomains_stored ) {
+    private void setDomainsStoredSet( final SortedSet<String> _storeddomains_stored ) {
         _domains_stored_set = _storeddomains_stored;
     }
 
diff --git a/forester/java/src/org/forester/protein/BasicDomain.java b/forester/java/src/org/forester/protein/BasicDomain.java
index 0232b91..171b0d0 100644
--- a/forester/java/src/org/forester/protein/BasicDomain.java
+++ b/forester/java/src/org/forester/protein/BasicDomain.java
@@ -26,26 +26,25 @@
 
 package org.forester.protein;
 
-import org.forester.go.GoId;
 import org.forester.util.ForesterUtil;
 
 public class BasicDomain implements Domain {
 
-    final private DomainId _id;
-    final private int      _from;
-    final private int      _to;
-    final private short    _number;
-    final private short    _total_count;
-    final private double   _per_sequence_evalue;
-    final private double   _per_sequence_score;
-    final private double   _per_domain_evalue;
-    final private double   _per_domain_score;
-
-    public BasicDomain( final String id_str ) {
-        if ( ForesterUtil.isEmpty( id_str ) ) {
+    final private String _id;
+    final private int    _from;
+    final private int    _to;
+    final private short  _number;
+    final private short  _total_count;
+    final private double _per_sequence_evalue;
+    final private double _per_sequence_score;
+    final private double _per_domain_evalue;
+    final private double _per_domain_score;
+
+    public BasicDomain( final String id ) {
+        if ( ForesterUtil.isEmpty( id ) ) {
             throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
         }
-        _id = new DomainId( id_str );
+        _id = id;
         _from = -1;
         _to = -1;
         _number = -1;
@@ -56,17 +55,17 @@ public class BasicDomain implements Domain {
         _per_domain_score = -1;
     }
 
-    public BasicDomain( final String id_str,
+    public BasicDomain( final String id,
                         final int from,
                         final int to,
                         final short number,
                         final short total_count,
                         final double per_sequence_evalue,
                         final double per_sequence_score ) {
-        this( id_str, from, to, number, total_count, per_sequence_evalue, per_sequence_score, 0, 0 );
+        this( id, from, to, number, total_count, per_sequence_evalue, per_sequence_score, 0, 0 );
     }
 
-    public BasicDomain( final String id_str,
+    public BasicDomain( final String id,
                         final int from,
                         final int to,
                         final short number,
@@ -78,7 +77,7 @@ public class BasicDomain implements Domain {
         if ( ( from >= to ) || ( from < 0 ) ) {
             throw new IllegalArgumentException( "attempt to create protein domain from " + from + " to " + to );
         }
-        if ( ForesterUtil.isEmpty( id_str ) ) {
+        if ( ForesterUtil.isEmpty( id ) ) {
             throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
         }
         if ( ( number > total_count ) || ( number < 0 ) ) {
@@ -88,7 +87,7 @@ public class BasicDomain implements Domain {
         if ( ( per_sequence_evalue < 0.0 ) || ( per_domain_evalue < 0.0 ) ) {
             throw new IllegalArgumentException( "attempt to create protein domain with negative E-value" );
         }
-        _id = new DomainId( id_str );
+        _id = id;
         _from = from;
         _to = to;
         _number = number;
@@ -99,11 +98,10 @@ public class BasicDomain implements Domain {
         _per_domain_score = per_domain_score;
     }
 
-    @Override
-    public void addGoId( final GoId go_id ) {
-        getDomainId().getGoIds().add( go_id );
-    }
-
+    // ^^     @Override
+    // ^^    public void addGoId( final GoId go_id ) {
+    // ^^       getDomainId().getGoIds().add( go_id );
+    // ^^   }
     /**
      * Basic domains are compared/sorted based upon their identifiers (case
      * insensitive) and their numbers.
@@ -144,7 +142,7 @@ public class BasicDomain implements Domain {
     }
 
     @Override
-    public DomainId getDomainId() {
+    public String getDomainId() {
         return _id;
     }
 
@@ -153,21 +151,19 @@ public class BasicDomain implements Domain {
         return _from;
     }
 
-    @Override
-    public GoId getGoId( final int i ) {
-        return getDomainId().getGoIds().get( i );
-    }
-
+    // ^^  @Override
+    // ^^   public GoId getGoId( final int i ) {
+    // ^^       return getDomainId().getGoIds().get( i );
+    // ^^   }
     @Override
     public short getNumber() {
         return _number;
     }
 
-    @Override
-    public int getNumberOfGoIds() {
-        return getDomainId().getGoIds().size();
-    }
-
+    // ^^  @Override
+    // ^^    public int getNumberOfGoIds() {
+    // ^^        return getDomainId().getGoIds().size();
+    // ^^   }
     @Override
     public double getPerDomainEvalue() {
         return _per_domain_evalue;
@@ -200,16 +196,16 @@ public class BasicDomain implements Domain {
 
     @Override
     public int hashCode() {
-        return getDomainId().getId().hashCode();
+        return getDomainId().hashCode();
     }
 
     @Override
     public String toString() {
-        return toStringBuffer().toString();
+        return getDomainId();
     }
 
     public StringBuffer toStringBuffer() {
-        return new StringBuffer( getDomainId().getId() );
+        return new StringBuffer( getDomainId() );
     }
 
     @Override
diff --git a/forester/java/src/org/forester/protein/BasicProtein.java b/forester/java/src/org/forester/protein/BasicProtein.java
index e17862f..c793c15 100644
--- a/forester/java/src/org/forester/protein/BasicProtein.java
+++ b/forester/java/src/org/forester/protein/BasicProtein.java
@@ -56,8 +56,8 @@ public class BasicProtein implements Protein {
                                                                          final int m1 = ( d1.getTo() + d1.getFrom() );
                                                                          final int m2 = ( d2.getTo() + d2.getFrom() );
                                                                          return m1 < m2 ? -1 : m1 > m2 ? 1 : d1
-                                                                                 .getDomainId().getId()
-                                                                                 .compareTo( d2.getDomainId().getId() );
+                                                                                 .getDomainId()
+                                                                                 .compareTo( d2.getDomainId() );
                                                                      }
                                                                  };
 
@@ -96,9 +96,9 @@ public class BasicProtein implements Protein {
      * @param in_nc_order to consider order
      * @return
      */
-    public boolean contains( final List<DomainId> query_domain_ids, final boolean in_nc_order ) {
+    public boolean contains( final List<String> query_domain_ids, final boolean in_nc_order ) {
         if ( !in_nc_order ) {
-            for( final DomainId query_domain_id : query_domain_ids ) {
+            for( final String query_domain_id : query_domain_ids ) {
                 if ( !getProteinDomainIds().contains( query_domain_id ) ) {
                     return false;
                 }
@@ -107,7 +107,7 @@ public class BasicProtein implements Protein {
         }
         else {
             int current_start_position = -1;
-            I: for( final DomainId query_domain_id : query_domain_ids ) {
+            I: for( final String query_domain_id : query_domain_ids ) {
                 if ( getProteinDomainIds().contains( query_domain_id ) ) {
                     final List<Domain> found_domains = getProteinDomains( query_domain_id );
                     final SortedSet<Integer> ordered_start_positions = new TreeSet<Integer>();
@@ -171,7 +171,7 @@ public class BasicProtein implements Protein {
     }
 
     @Override
-    public int getProteinDomainCount( final DomainId domain_id ) {
+    public int getProteinDomainCount( final String domain_id ) {
         return getProteinDomains( domain_id ).size();
     }
 
@@ -181,7 +181,7 @@ public class BasicProtein implements Protein {
     }
 
     @Override
-    public List<Domain> getProteinDomains( final DomainId domain_id ) {
+    public List<Domain> getProteinDomains( final String domain_id ) {
         final List<Domain> domains = new ArrayList<Domain>();
         for( final Domain domain : getProteinDomains() ) {
             if ( domain.getDomainId().equals( domain_id ) ) {
@@ -223,7 +223,7 @@ public class BasicProtein implements Protein {
             else {
                 sb.append( separator );
             }
-            sb.append( d.getDomainId().getId() );
+            sb.append( d.getDomainId() );
         }
         return sb.toString();
     }
@@ -239,7 +239,7 @@ public class BasicProtein implements Protein {
         String prev_id = "";
         int counter = 1;
         for( final Domain d : getDomainsSortedByPosition() ) {
-            final String id = d.getDomainId().getId();
+            final String id = d.getDomainId();
             if ( prev_id.equals( id ) ) {
                 counter++;
             }
@@ -272,8 +272,8 @@ public class BasicProtein implements Protein {
         return toDomainArchitectureString( "~" );
     }
 
-    private List<DomainId> getProteinDomainIds() {
-        final List<DomainId> ids = new ArrayList<DomainId>( getProteinDomains().size() );
+    private List<String> getProteinDomainIds() {
+        final List<String> ids = new ArrayList<String>( getProteinDomains().size() );
         for( final Domain domain : getProteinDomains() ) {
             ids.add( domain.getDomainId() );
         }
diff --git a/forester/java/src/org/forester/protein/BinaryDomainCombination.java b/forester/java/src/org/forester/protein/BinaryDomainCombination.java
index 1098644..191e51b 100644
--- a/forester/java/src/org/forester/protein/BinaryDomainCombination.java
+++ b/forester/java/src/org/forester/protein/BinaryDomainCombination.java
@@ -29,9 +29,9 @@ public interface BinaryDomainCombination extends Comparable<BinaryDomainCombinat
 
     public static final String SEPARATOR = "=";
 
-    public DomainId getId0();
+    public String getId0();
 
-    public DomainId getId1();
+    public String getId1();
 
     public abstract StringBuffer toGraphDescribingLanguage( final OutputFormat format,
                                                             final String node_attribute,
diff --git a/forester/java/src/org/forester/protein/Domain.java b/forester/java/src/org/forester/protein/Domain.java
index 3ede985..a4ab80e 100644
--- a/forester/java/src/org/forester/protein/Domain.java
+++ b/forester/java/src/org/forester/protein/Domain.java
@@ -26,24 +26,19 @@
 
 package org.forester.protein;
 
-import org.forester.go.GoId;
-
 public interface Domain extends Comparable<Domain> {
 
-    public void addGoId( GoId go_id );
-
-    public DomainId getDomainId();
+    // ^^  public void addGoId( GoId go_id );
+    public String getDomainId();
 
     public int getLength();
 
     public int getFrom();
 
-    public GoId getGoId( int i );
-
+    // ^^   public GoId getGoId( int i );
     public short getNumber();
 
-    public int getNumberOfGoIds();
-
+    // ^^  public int getNumberOfGoIds();
     public double getPerDomainEvalue();
 
     public double getPerDomainScore();
diff --git a/forester/java/src/org/forester/protein/DomainId.java b/forester/java/src/org/forester/protein/DomainId.java
index 89a23cf..8802283 100644
--- a/forester/java/src/org/forester/protein/DomainId.java
+++ b/forester/java/src/org/forester/protein/DomainId.java
@@ -26,18 +26,14 @@
 
 package org.forester.protein;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import org.forester.go.GoId;
 import org.forester.util.ForesterUtil;
 
 public class DomainId implements Comparable<DomainId> {
 
     final private String _id;
-    private List<GoId>   _go_ids;
 
-    public DomainId( final String id ) {
+    //  private List<GoId>   _go_ids;
+    private DomainId( final String id ) {
         if ( ForesterUtil.isEmpty( id ) ) {
             throw new IllegalArgumentException( "attempt to create domain id from empty or null string" );
         }
@@ -50,16 +46,15 @@ public class DomainId implements Comparable<DomainId> {
             throw new IllegalArgumentException( "attempt to create domain id from string containing the separator character ["
                     + BinaryDomainCombination.SEPARATOR + "] for domain combinations [" + _id + "]" );
         }
-        setGoIds( null );
-    }
-
-    public void addGoId( final GoId go_id ) {
-        if ( getGoIds() == null ) {
-            setGoIds( new ArrayList<GoId>() );
-        }
-        getGoIds().add( go_id );
+        ///////////////////////////// //      setGoIds( null );
     }
 
+    //  public void addGoId( final GoId go_id ) {
+    //       if ( getGoIds() == null ) {
+    //           setGoIds( new ArrayList<GoId>() );
+    //      }
+    //      getGoIds().add( go_id );
+    //  }
     @Override
     public int compareTo( final DomainId domain_id ) {
         if ( this == domain_id ) {
@@ -85,10 +80,9 @@ public class DomainId implements Comparable<DomainId> {
         }
     }
 
-    public GoId getGoId( final int i ) {
-        return getGoIds().get( i );
-    }
-
+    // public GoId getGoId( final int i ) {
+    //     return getGoIds().get( i );
+    //}
     // Note.
     // The fact that equals and compareTo do not behave the same in cases where ids only differ by their case
     // is not ideal. From Sun regarding Interface SortedSet<E>:
@@ -100,30 +94,27 @@ public class DomainId implements Comparable<DomainId> {
     // so two elements that are deemed equal by this method are, from the standpoint of the sorted set,
     // equal. The behavior of a sorted set is well-defined even if its ordering is inconsistent with equals; 
     // it just fails to obey the general contract of the Set interface."
-    public List<GoId> getGoIds() {
-        return _go_ids;
-    }
-
-    public String getId() {
+    // public List<GoId> getGoIds() {
+    //     return _go_ids;
+    // }
+    private String getId() {
         return _id;
     }
 
-    public int getNumberOfGoIds() {
-        if ( getGoIds() == null ) {
-            return 0;
-        }
-        return getGoIds().size();
-    }
-
+    // public int getNumberOfGoIds() {
+    //     if ( getGoIds() == null ) {
+    //         return 0;
+    //     }
+    //     return getGoIds().size();
+    // }
     @Override
     public int hashCode() {
         return getId().hashCode();
     }
 
-    private void setGoIds( final List<GoId> go_ids ) {
-        _go_ids = go_ids;
-    }
-
+    // private void setGoIds( final List<GoId> go_ids ) {
+    //     _go_ids = go_ids;
+    // }
     @Override
     public String toString() {
         return getId();
diff --git a/forester/java/src/org/forester/protein/Protein.java b/forester/java/src/org/forester/protein/Protein.java
index 6616361..4b81f46 100644
--- a/forester/java/src/org/forester/protein/Protein.java
+++ b/forester/java/src/org/forester/protein/Protein.java
@@ -46,7 +46,7 @@ public interface Protein {
      * @param in_nc_order to consider order
      * @return
      */
-    public boolean contains( final List<DomainId> domains, final boolean in_nc_order );
+    public boolean contains( final List<String> domains, final boolean in_nc_order );
 
     public String getAccession();
 
@@ -58,11 +58,11 @@ public interface Protein {
 
     public Domain getProteinDomain( final int index );
 
-    public int getProteinDomainCount( final DomainId domain_id );
+    public int getProteinDomainCount( final String domain_id );
 
     public List<Domain> getProteinDomains();
 
-    public List<Domain> getProteinDomains( final DomainId domain_id );
+    public List<Domain> getProteinDomains( final String domain_id );
 
     public ProteinId getProteinId();
 
diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
index 81cdf08..1bcbc60 100644
--- a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
@@ -27,24 +27,16 @@
 package org.forester.surfacing;
 
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 
 public class AdjactantDirectedBinaryDomainCombination extends BasicBinaryDomainCombination {
 
-    public AdjactantDirectedBinaryDomainCombination( final DomainId n_terminal, final DomainId c_terminal ) {
-        super();
-        if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
-            throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
-        }
-        _data = n_terminal.getId() + BinaryDomainCombination.SEPARATOR + c_terminal.getId();
-    }
-
     public AdjactantDirectedBinaryDomainCombination( final String n_terminal, final String c_terminal ) {
         super();
         if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        _data = n_terminal + BinaryDomainCombination.SEPARATOR + c_terminal;
+        _id0 = n_terminal;
+        _id1 = c_terminal;
     }
 
     public static AdjactantDirectedBinaryDomainCombination createInstance( final String ids ) {
diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java
index 20d88d9..eb4f9f1 100644
--- a/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java
@@ -31,19 +31,18 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 
 public class AdjactantDirectedCombinableDomains extends BasicCombinableDomains {
 
-    public AdjactantDirectedCombinableDomains( final DomainId n_terminal_key_domain, final Species species ) {
+    public AdjactantDirectedCombinableDomains( final String n_terminal_key_domain, final Species species ) {
         super( n_terminal_key_domain, species );
     }
 
     @Override
     public List<BinaryDomainCombination> toBinaryDomainCombinations() {
         final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
-        for( final DomainId domain : getCombiningDomains().keySet() ) {
+        for( final String domain : getCombiningDomains().keySet() ) {
             // Precondition (!): key domain is most upstream domain.
             //TODO ensure this is true.
             binary_combinations.add( new AdjactantDirectedBinaryDomainCombination( getKeyDomain(), domain ) );
diff --git a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
index da009b5..1413feb 100644
--- a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
@@ -27,33 +27,41 @@
 package org.forester.surfacing;
 
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 import org.forester.util.ForesterUtil;
 
 public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
-    String _data;
+    String _id0;
+    String _id1;
+    String _str;
 
     BasicBinaryDomainCombination() {
-        _data = null;
+        _id0 = null;
+        _id1 = null;
+        _str = null;
     }
 
-    public BasicBinaryDomainCombination( final String id_0, final String id_1 ) {
-        if ( ( id_0 == null ) || ( id_1 == null ) ) {
+    private String getAsStr() {
+        if ( _str == null ) {
+            _str = _id0 + SEPARATOR + _id1;
+        }
+        return _str;
+    }
+
+    public BasicBinaryDomainCombination( final String id0, final String id1 ) {
+        if ( ( id0 == null ) || ( id1 == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        if ( id_0.toLowerCase().compareTo( id_1.toLowerCase() ) < 0 ) {
-            _data = id_0 + BinaryDomainCombination.SEPARATOR + id_1;
+        if ( id0.toLowerCase().compareTo( id1.toLowerCase() ) < 0 ) {
+            _id0 = id0;
+            _id1 = id1;
         }
         else {
-            _data = id_1 + BinaryDomainCombination.SEPARATOR + id_0;
+            _id0 = id1;
+            _id1 = id0;
         }
     }
 
-    public BasicBinaryDomainCombination( final DomainId id_0, final DomainId id_1 ) {
-        this( id_0.getId(), id_1.getId() );
-    }
-
     @Override
     public int compareTo( final BinaryDomainCombination binary_domain_combination ) {
         if ( binary_domain_combination.getClass() != this.getClass() ) {
@@ -91,18 +99,18 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
     }
 
     @Override
-    public DomainId getId0() {
-        return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 0 ] );
+    public String getId0() {
+        return _id0;
     }
 
     @Override
-    public DomainId getId1() {
-        return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 1 ] );
+    public String getId1() {
+        return _id1;
     }
 
     @Override
     public int hashCode() {
-        return _data.hashCode();
+        return getAsStr().hashCode();
     }
 
     @Override
@@ -151,7 +159,7 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
     @Override
     public String toString() {
-        return _data;
+        return getAsStr();
     }
 
     public static BinaryDomainCombination createInstance( final String ids ) {
diff --git a/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java b/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java
index 300a4ed..84408dc 100644
--- a/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java
@@ -33,28 +33,27 @@ import java.util.SortedMap;
 import java.util.TreeMap;
 
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.util.DescriptiveStatistics;
 
 public class BasicCombinableDomains implements CombinableDomains {
 
-    final private DomainId                   _key_domain;
-    private int                              _key_domain_count;
-    private int                              _key_domain_proteins_count;
-    final private Species                    _species;
-    final private TreeMap<DomainId, Integer> _combining_domains;
-    private DescriptiveStatistics            _key_domain_confidence_statistics;
+    final private String                   _key_domain;
+    private int                            _key_domain_count;
+    private int                            _key_domain_proteins_count;
+    final private Species                  _species;
+    final private TreeMap<String, Integer> _combining_domains;
+    private DescriptiveStatistics          _key_domain_confidence_statistics;
 
-    public BasicCombinableDomains( final DomainId key_domain, final Species species ) {
+    public BasicCombinableDomains( final String key_domain, final Species species ) {
         _key_domain = key_domain;
         _species = species;
-        _combining_domains = new TreeMap<DomainId, Integer>();
+        _combining_domains = new TreeMap<String, Integer>();
         init();
     }
 
     @Override
-    public void addCombinableDomain( final DomainId protein_domain ) {
+    public void addCombinableDomain( final String protein_domain ) {
         if ( getCombiningDomains().containsKey( protein_domain ) ) {
             getCombiningDomains().put( protein_domain, getCombiningDomains().get( protein_domain ) + 1 );
         }
@@ -64,8 +63,8 @@ public class BasicCombinableDomains implements CombinableDomains {
     }
 
     @Override
-    public List<DomainId> getAllDomains() {
-        final List<DomainId> domains = getCombinableDomains();
+    public List<String> getAllDomains() {
+        final List<String> domains = getCombinableDomains();
         if ( !domains.contains( getKeyDomain() ) ) {
             domains.add( getKeyDomain() );
         }
@@ -73,19 +72,19 @@ public class BasicCombinableDomains implements CombinableDomains {
     }
 
     @Override
-    public List<DomainId> getCombinableDomains() {
-        final List<DomainId> domains = new ArrayList<DomainId>( getNumberOfCombinableDomains() );
-        for( final DomainId domain : getCombiningDomains().keySet() ) {
+    public List<String> getCombinableDomains() {
+        final List<String> domains = new ArrayList<String>( getNumberOfCombinableDomains() );
+        for( final String domain : getCombiningDomains().keySet() ) {
             domains.add( domain );
         }
         return domains;
     }
 
     @Override
-    public SortedMap<DomainId, Integer> getCombinableDomainsIds() {
-        final SortedMap<DomainId, Integer> ids = new TreeMap<DomainId, Integer>();
-        for( final DomainId domain : getCombiningDomains().keySet() ) {
-            final DomainId pd = domain;
+    public SortedMap<String, Integer> getCombinableDomainsIds() {
+        final SortedMap<String, Integer> ids = new TreeMap<String, Integer>();
+        for( final String domain : getCombiningDomains().keySet() ) {
+            final String pd = domain;
             ids.put( pd, getCombiningDomains().get( pd ) );
         }
         return ids;
@@ -94,8 +93,8 @@ public class BasicCombinableDomains implements CombinableDomains {
     @Override
     public StringBuilder getCombiningDomainIdsAsStringBuilder() {
         final StringBuilder sb = new StringBuilder();
-        for( final Iterator<DomainId> iter = getCombiningDomains().keySet().iterator(); iter.hasNext(); ) {
-            final DomainId key = iter.next();
+        for( final Iterator<String> iter = getCombiningDomains().keySet().iterator(); iter.hasNext(); ) {
+            final String key = iter.next();
             sb.append( key.toString() );
             sb.append( " [" );
             final int count = getCombiningDomains().get( key );
@@ -108,12 +107,12 @@ public class BasicCombinableDomains implements CombinableDomains {
         return sb;
     }
 
-    protected TreeMap<DomainId, Integer> getCombiningDomains() {
+    protected TreeMap<String, Integer> getCombiningDomains() {
         return _combining_domains;
     }
 
     @Override
-    public DomainId getKeyDomain() {
+    public String getKeyDomain() {
         return _key_domain;
     }
 
@@ -138,7 +137,7 @@ public class BasicCombinableDomains implements CombinableDomains {
     }
 
     @Override
-    public int getNumberOfProteinsExhibitingCombination( final DomainId protein_domain ) {
+    public int getNumberOfProteinsExhibitingCombination( final String protein_domain ) {
         if ( getCombiningDomains().containsKey( protein_domain ) ) {
             return getCombiningDomains().get( protein_domain );
         }
@@ -159,7 +158,7 @@ public class BasicCombinableDomains implements CombinableDomains {
     }
 
     @Override
-    public boolean isCombinable( final DomainId protein_domain ) {
+    public boolean isCombinable( final String protein_domain ) {
         return getCombiningDomains().containsKey( protein_domain );
     }
 
@@ -181,7 +180,7 @@ public class BasicCombinableDomains implements CombinableDomains {
     @Override
     public List<BinaryDomainCombination> toBinaryDomainCombinations() {
         final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
-        for( final DomainId domain : getCombiningDomains().keySet() ) {
+        for( final String domain : getCombiningDomains().keySet() ) {
             binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
         }
         return binary_combinations;
diff --git a/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java
index 9a9bbfb..846aa7a 100644
--- a/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java
@@ -34,7 +34,6 @@ import java.util.SortedSet;
 import java.util.TreeMap;
 import java.util.TreeSet;
 
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
@@ -62,11 +61,11 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
             throw new IllegalArgumentException( "attempt to calculate multiple combinable domains similarity for less than two combinale domains collections" );
         }
         final SortedSet<DomainSimilarity> similarities = new TreeSet<DomainSimilarity>();
-        final SortedSet<DomainId> keys = new TreeSet<DomainId>();
+        final SortedSet<String> keys = new TreeSet<String>();
         for( final GenomeWideCombinableDomains cdc : cdc_list ) {
             keys.addAll( ( cdc ).getAllCombinableDomainsIds().keySet() );
         }
-        for( final DomainId key : keys ) {
+        for( final String key : keys ) {
             final List<CombinableDomains> same_id_cd_list = new ArrayList<CombinableDomains>( cdc_list.size() );
             final List<Species> species_with_key_id_domain = new ArrayList<Species>();
             for( final GenomeWideCombinableDomains cdc : cdc_list ) {
@@ -238,7 +237,7 @@ public class BasicDomainSimilarityCalculator implements DomainSimilarityCalculat
                                                                                                        cd.getKeyDomainCount(),
                                                                                                        cd.getNumberOfCombinableDomains(),
                                                                                                        cd.getKeyDomainConfidenceDescriptiveStatistics() );
-        for( final DomainId domain : cd.getCombinableDomains() ) {
+        for( final String domain : cd.getCombinableDomains() ) {
             sd.addProteinsExhibitingCombinationCount( domain, cd.getNumberOfProteinsExhibitingCombination( domain ) );
         }
         return sd;
diff --git a/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java b/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java
index ef98751..c6d205f 100644
--- a/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/BasicGenomeWideCombinableDomains.java
@@ -20,7 +20,6 @@ import org.forester.go.GoId;
 import org.forester.protein.BinaryDomainCombination;
 import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
@@ -29,115 +28,109 @@ import org.forester.util.ForesterUtil;
 
 public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDomains {
 
-    private final static NumberFormat                    FORMATTER                                  = new DecimalFormat( "0.0E0" );
-    private static final Comparator<CombinableDomains>   DESCENDING_KEY_DOMAIN_COUNT_ORDER          = new Comparator<CombinableDomains>() {
+    private final static NumberFormat                  FORMATTER                                  = new DecimalFormat( "0.0E0" );
+    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.getKeyDomainCount() < d2
-                                                                                                                    .getKeyDomainCount() ) {
-                                                                                                                return 1;
-                                                                                                            }
-                                                                                                            else if ( d1
-                                                                                                                    .getKeyDomainCount() > d2
-                                                                                                                    .getKeyDomainCount() ) {
-                                                                                                                return -1;
-                                                                                                            }
-                                                                                                            else {
-                                                                                                                return d1
-                                                                                                                        .getKeyDomain()
-                                                                                                                        .getId()
-                                                                                                                        .compareTo( d2
-                                                                                                                                .getKeyDomain()
-                                                                                                                                .getId() );
-                                                                                                            }
-                                                                                                        }
-                                                                                                    };
-    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.getKeyDomainCount() < d2
+                                                                                                                  .getKeyDomainCount() ) {
+                                                                                                              return 1;
+                                                                                                          }
+                                                                                                          else if ( d1
+                                                                                                                  .getKeyDomainCount() > d2
+                                                                                                                  .getKeyDomainCount() ) {
+                                                                                                              return -1;
+                                                                                                          }
+                                                                                                          else {
+                                                                                                              return d1
+                                                                                                                      .getKeyDomain()
+                                                                                                                      .compareTo( d2
+                                                                                                                              .getKeyDomain() );
+                                                                                                          }
+                                                                                                      }
+                                                                                                  };
+    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.getKeyDomainProteinsCount() < d2
-                                                                                                                    .getKeyDomainProteinsCount() ) {
-                                                                                                                return 1;
-                                                                                                            }
-                                                                                                            else if ( d1
-                                                                                                                    .getKeyDomainProteinsCount() > d2
-                                                                                                                    .getKeyDomainProteinsCount() ) {
-                                                                                                                return -1;
-                                                                                                            }
-                                                                                                            else {
-                                                                                                                return d1
-                                                                                                                        .getKeyDomain()
-                                                                                                                        .getId()
-                                                                                                                        .compareTo( d2
-                                                                                                                                .getKeyDomain()
-                                                                                                                                .getId() );
-                                                                                                            }
-                                                                                                        }
-                                                                                                    };
-    private static final Comparator<CombinableDomains>   DESCENDING_COMBINATIONS_COUNT_ORDER        = new Comparator<CombinableDomains>() {
+                                                                                                      @Override
+                                                                                                      public int compare( final CombinableDomains d1,
+                                                                                                                          final CombinableDomains d2 ) {
+                                                                                                          if ( d1.getKeyDomainProteinsCount() < d2
+                                                                                                                  .getKeyDomainProteinsCount() ) {
+                                                                                                              return 1;
+                                                                                                          }
+                                                                                                          else if ( d1
+                                                                                                                  .getKeyDomainProteinsCount() > d2
+                                                                                                                  .getKeyDomainProteinsCount() ) {
+                                                                                                              return -1;
+                                                                                                          }
+                                                                                                          else {
+                                                                                                              return d1
+                                                                                                                      .getKeyDomain()
+                                                                                                                      .compareTo( d2
+                                                                                                                              .getKeyDomain() );
+                                                                                                          }
+                                                                                                      }
+                                                                                                  };
+    private static final Comparator<CombinableDomains> DESCENDING_COMBINATIONS_COUNT_ORDER        = new Comparator<CombinableDomains>() {
 
-                                                                                                        @Override
-                                                                                                        public int compare( final CombinableDomains d1,
-                                                                                                                            final CombinableDomains d2 ) {
-                                                                                                            if ( d1.getNumberOfCombinableDomains() < d2
-                                                                                                                    .getNumberOfCombinableDomains() ) {
-                                                                                                                return 1;
-                                                                                                            }
-                                                                                                            else if ( d1
-                                                                                                                    .getNumberOfCombinableDomains() > d2
-                                                                                                                    .getNumberOfCombinableDomains() ) {
-                                                                                                                return -1;
-                                                                                                            }
-                                                                                                            else {
-                                                                                                                return d1
-                                                                                                                        .getKeyDomain()
-                                                                                                                        .getId()
-                                                                                                                        .compareTo( d2
-                                                                                                                                .getKeyDomain()
-                                                                                                                                .getId() );
-                                                                                                            }
-                                                                                                        }
-                                                                                                    };
-    final private SortedMap<DomainId, CombinableDomains> _combinable_domains_map;
-    final private Species                                _species;
-    final private DomainCombinationType                  _dc_type;
+                                                                                                      @Override
+                                                                                                      public int compare( final CombinableDomains d1,
+                                                                                                                          final CombinableDomains d2 ) {
+                                                                                                          if ( d1.getNumberOfCombinableDomains() < d2
+                                                                                                                  .getNumberOfCombinableDomains() ) {
+                                                                                                              return 1;
+                                                                                                          }
+                                                                                                          else if ( d1
+                                                                                                                  .getNumberOfCombinableDomains() > d2
+                                                                                                                  .getNumberOfCombinableDomains() ) {
+                                                                                                              return -1;
+                                                                                                          }
+                                                                                                          else {
+                                                                                                              return d1
+                                                                                                                      .getKeyDomain()
+                                                                                                                      .compareTo( d2
+                                                                                                                              .getKeyDomain() );
+                                                                                                          }
+                                                                                                      }
+                                                                                                  };
+    final private SortedMap<String, CombinableDomains> _combinable_domains_map;
+    final private Species                              _species;
+    final private DomainCombinationType                _dc_type;
 
     private BasicGenomeWideCombinableDomains( final Species species, final DomainCombinationType dc_type ) {
-        _combinable_domains_map = new TreeMap<DomainId, CombinableDomains>();
+        _combinable_domains_map = new TreeMap<String, CombinableDomains>();
         _species = species;
         _dc_type = dc_type;
     }
 
-    private void add( final DomainId key, final CombinableDomains cdc ) {
+    private void add( final String key, final CombinableDomains cdc ) {
         _combinable_domains_map.put( key, cdc );
     }
 
     @Override
-    public boolean contains( final DomainId key_id ) {
+    public boolean contains( final String key_id ) {
         return _combinable_domains_map.containsKey( key_id );
     }
 
     @Override
-    public CombinableDomains get( final DomainId key_id ) {
+    public CombinableDomains get( final String key_id ) {
         return _combinable_domains_map.get( key_id );
     }
 
     @Override
-    public SortedMap<DomainId, CombinableDomains> getAllCombinableDomainsIds() {
+    public SortedMap<String, CombinableDomains> getAllCombinableDomainsIds() {
         return _combinable_domains_map;
     }
 
     @Override
-    public SortedSet<DomainId> getAllDomainIds() {
-        final SortedSet<DomainId> domains = new TreeSet<DomainId>();
-        for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
+    public SortedSet<String> getAllDomainIds() {
+        final SortedSet<String> domains = new TreeSet<String>();
+        for( final String key : getAllCombinableDomainsIds().keySet() ) {
             final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
-            final List<DomainId> ds = cb.getAllDomains();
-            for( final DomainId d : ds ) {
+            final List<String> ds = cb.getAllDomains();
+            for( final String d : ds ) {
                 domains.add( d );
             }
         }
@@ -150,10 +143,10 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
     }
 
     @Override
-    public SortedSet<DomainId> getMostPromiscuosDomain() {
-        final SortedSet<DomainId> doms = new TreeSet<DomainId>();
+    public SortedSet<String> getMostPromiscuosDomain() {
+        final SortedSet<String> doms = new TreeSet<String>();
         final int max = ( int ) getPerGenomeDomainPromiscuityStatistics().getMax();
-        for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
+        for( final String key : getAllCombinableDomainsIds().keySet() ) {
             final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
             if ( cb.getNumberOfCombinableDomains() == max ) {
                 doms.add( key );
@@ -165,7 +158,7 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
     @Override
     public DescriptiveStatistics getPerGenomeDomainPromiscuityStatistics() {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
-        for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
+        for( final String key : getAllCombinableDomainsIds().keySet() ) {
             final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
             stats.addValue( cb.getNumberOfCombinableDomains() );
         }
@@ -185,7 +178,7 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
     @Override
     public SortedSet<BinaryDomainCombination> toBinaryDomainCombinations() {
         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
-        for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
+        for( final String key : getAllCombinableDomainsIds().keySet() ) {
             final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
             for( final BinaryDomainCombination b : cb.toBinaryDomainCombinations() ) {
                 binary_combinations.add( b );
@@ -205,7 +198,7 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
     public StringBuilder toStringBuilder( final GenomeWideCombinableDomainsSortOrder sort_order ) {
         final StringBuilder sb = new StringBuilder();
         final List<CombinableDomains> combinable_domains = new ArrayList<CombinableDomains>();
-        for( final DomainId key : getAllCombinableDomainsIds().keySet() ) {
+        for( final String key : getAllCombinableDomainsIds().keySet() ) {
             final CombinableDomains cb = getAllCombinableDomainsIds().get( key );
             combinable_domains.add( cb );
         }
@@ -236,11 +229,11 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
         return sb;
     }
 
-    private static void countDomains( final Map<DomainId, Integer> domain_counts,
-                                      final Map<DomainId, Integer> domain_protein_counts,
-                                      final Map<DomainId, DescriptiveStatistics> stats,
-                                      final Set<DomainId> saw_c,
-                                      final DomainId id_i,
+    private static void countDomains( final Map<String, Integer> domain_counts,
+                                      final Map<String, Integer> domain_protein_counts,
+                                      final Map<String, DescriptiveStatistics> stats,
+                                      final Set<String> saw_c,
+                                      final String id_i,
                                       final double support ) {
         if ( domain_counts.containsKey( id_i ) ) {
             domain_counts.put( id_i, 1 + domain_counts.get( ( id_i ) ) );
@@ -279,24 +272,24 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
     public static BasicGenomeWideCombinableDomains createInstance( final List<Protein> protein_list,
                                                                    final boolean ignore_combination_with_same_domain,
                                                                    final Species species,
-                                                                   final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+                                                                   final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                                    final DomainCombinationType dc_type,
                                                                    final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
                                                                    final Map<String, DescriptiveStatistics> domain_number_stats_by_dc ) {
         final BasicGenomeWideCombinableDomains instance = new BasicGenomeWideCombinableDomains( species, dc_type );
-        final Map<DomainId, Integer> domain_counts = new HashMap<DomainId, Integer>();
-        final Map<DomainId, Integer> domain_protein_counts = new HashMap<DomainId, Integer>();
-        final Map<DomainId, DescriptiveStatistics> stats = new HashMap<DomainId, DescriptiveStatistics>();
+        final Map<String, Integer> domain_counts = new HashMap<String, Integer>();
+        final Map<String, Integer> domain_protein_counts = new HashMap<String, Integer>();
+        final Map<String, DescriptiveStatistics> stats = new HashMap<String, DescriptiveStatistics>();
         for( final Protein protein : protein_list ) {
             if ( !protein.getSpecies().equals( species ) ) {
                 throw new IllegalArgumentException( "species (" + protein.getSpecies()
                         + ") does not match species of combinable domains collection (" + species + ")" );
             }
-            final Set<DomainId> saw_i = new HashSet<DomainId>();
-            final Set<DomainId> saw_c = new HashSet<DomainId>();
+            final Set<String> saw_i = new HashSet<String>();
+            final Set<String> saw_c = new HashSet<String>();
             for( int i = 0; i < protein.getProteinDomains().size(); ++i ) {
                 final Domain pd_i = protein.getProteinDomain( i );
-                final DomainId id_i = pd_i.getDomainId();
+                final String id_i = pd_i.getDomainId();
                 final int current_start = pd_i.getFrom();
                 BasicGenomeWideCombinableDomains.countDomains( domain_counts,
                                                                domain_protein_counts,
@@ -322,16 +315,16 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
                         else {
                             domain_combination = new BasicCombinableDomains( pd_i.getDomainId(), species );
                         }
-                        if ( ( domain_id_to_go_ids_map != null )
-                                && domain_id_to_go_ids_map.containsKey( pd_i.getDomainId() ) ) {
-                            final List<GoId> go_ids = domain_id_to_go_ids_map.get( pd_i.getDomainId() );
-                            for( final GoId go_id : go_ids ) {
-                                domain_combination.getKeyDomain().addGoId( go_id );
-                            }
-                        }
+                        // ^^       if ( ( domain_id_to_go_ids_map != null )
+                        // ^^             && domain_id_to_go_ids_map.containsKey( pd_i.getDomainId() ) ) {
+                        // ^^        final List<GoId> go_ids = domain_id_to_go_ids_map.get( pd_i.getDomainId() );
+                        // ^^        for( final GoId go_id : go_ids ) {
+                        // ^^           domain_combination.getKeyDomain().addGoId( go_id );
+                        // ^^       }
+                        // ^^  }
                         instance.add( id_i, domain_combination );
                     }
-                    final Set<DomainId> saw_j = new HashSet<DomainId>();
+                    final Set<String> saw_j = new HashSet<String>();
                     if ( ignore_combination_with_same_domain ) {
                         saw_j.add( id_i );
                     }
@@ -342,7 +335,7 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
                             continue;
                         }
                         if ( i != j ) {
-                            final DomainId id = protein.getProteinDomain( j ).getDomainId();
+                            final String id = protein.getProteinDomain( j ).getDomainId();
                             if ( !saw_j.contains( id ) ) {
                                 saw_j.add( id );
                                 if ( dc_type != DomainCombinationType.DIRECTED_ADJACTANT ) {
@@ -389,7 +382,7 @@ public class BasicGenomeWideCombinableDomains implements GenomeWideCombinableDom
                 }
             }
         }
-        for( final DomainId key_id : domain_counts.keySet() ) {
+        for( final String key_id : domain_counts.keySet() ) {
             instance.get( key_id ).setKeyDomainCount( domain_counts.get( key_id ) );
             instance.get( key_id ).setKeyDomainProteinsCount( domain_protein_counts.get( key_id ) );
             instance.get( key_id ).setKeyDomainConfidenceDescriptiveStatistics( stats.get( key_id ) );
diff --git a/forester/java/src/org/forester/surfacing/CombinableDomains.java b/forester/java/src/org/forester/surfacing/CombinableDomains.java
index 28ca259..58b055d 100644
--- a/forester/java/src/org/forester/surfacing/CombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/CombinableDomains.java
@@ -30,7 +30,6 @@ import java.util.List;
 import java.util.SortedMap;
 
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.util.DescriptiveStatistics;
 
@@ -41,7 +40,7 @@ public interface CombinableDomains {
      * 
      * @param protein_domain
      */
-    public void addCombinableDomain( final DomainId protein_domain );
+    public void addCombinableDomain( final String protein_domain );
 
     /**
      * 
@@ -50,9 +49,9 @@ public interface CombinableDomains {
      * 
      *  @return all domains
      */
-    List<DomainId> getAllDomains();
+    List<String> getAllDomains();
 
-    List<DomainId> getCombinableDomains();
+    List<String> getCombinableDomains();
 
     /**
      * Returns the combinable domain identifiers sorted in alphabetical manner: -
@@ -61,7 +60,7 @@ public interface CombinableDomains {
      * 
      * @return combining domain identifiers sorted in alphabetical manner
      */
-    public SortedMap<DomainId, Integer> getCombinableDomainsIds();
+    public SortedMap<String, Integer> getCombinableDomainsIds();
 
     public StringBuilder getCombiningDomainIdsAsStringBuilder();
 
@@ -71,7 +70,7 @@ public interface CombinableDomains {
      * 
      * @return the domain identifier
      */
-    public DomainId getKeyDomain();
+    public String getKeyDomain();
 
     /**
      * Gets descriptive statistics for the confidence (i.e. E-values) of the key
@@ -100,7 +99,7 @@ public interface CombinableDomains {
 
     public int getNumberOfCombinableDomains();
 
-    public int getNumberOfProteinsExhibitingCombination( final DomainId protein_domain );
+    public int getNumberOfProteinsExhibitingCombination( final String protein_domain );
 
     /**
      * Returns the species of this combinable domains.
@@ -109,7 +108,7 @@ public interface CombinableDomains {
      */
     public Species getSpecies();
 
-    public boolean isCombinable( final DomainId protein_domain );
+    public boolean isCombinable( final String protein_domain );
 
     /**
      * This is to set descriptive statistics for the confidence (i.e. E-values)
diff --git a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
index 27327b6..feda0bc 100644
--- a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
@@ -29,8 +29,6 @@ package org.forester.surfacing;
 
 import java.util.List;
 
-import org.forester.protein.DomainId;
-
 public class CombinationsBasedPairwiseDomainSimilarityCalculator implements PairwiseDomainSimilarityCalculator {
 
     @Override
@@ -39,11 +37,11 @@ public class CombinationsBasedPairwiseDomainSimilarityCalculator implements Pair
         if ( !domains_1.getKeyDomain().equals( domains_2.getKeyDomain() ) ) {
             throw new IllegalArgumentException( "attempt to calculate similarity between domain collection with different keys" );
         }
-        final List<DomainId> d1 = domains_1.getCombinableDomains();
-        final List<DomainId> d2 = domains_2.getCombinableDomains();
+        final List<String> d1 = domains_1.getCombinableDomains();
+        final List<String> d2 = domains_2.getCombinableDomains();
         int same = 0;
         int different = 0;
-        for( final DomainId domain : d1 ) {
+        for( final String domain : d1 ) {
             if ( d2.contains( domain ) ) {
                 same++;
             }
@@ -51,7 +49,7 @@ public class CombinationsBasedPairwiseDomainSimilarityCalculator implements Pair
                 different++;
             }
         }
-        for( final DomainId domain : d2 ) {
+        for( final String domain : d2 ) {
             if ( !( d1.contains( domain ) ) ) {
                 different++;
             }
diff --git a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
index bfd7b2e..4716be8 100644
--- a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
@@ -27,24 +27,16 @@
 package org.forester.surfacing;
 
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 
 public class DirectedBinaryDomainCombination extends BasicBinaryDomainCombination {
 
-    public DirectedBinaryDomainCombination( final DomainId n_terminal, final DomainId c_terminal ) {
-        super();
-        if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
-            throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
-        }
-        _data = n_terminal.getId() + BinaryDomainCombination.SEPARATOR + c_terminal.getId();
-    }
-
     public DirectedBinaryDomainCombination( final String n_terminal, final String c_terminal ) {
         super();
         if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        _data = n_terminal + BinaryDomainCombination.SEPARATOR + c_terminal;
+        _id0 = n_terminal;
+        _id1 = c_terminal;
     }
 
     public static BinaryDomainCombination createInstance( final String ids ) {
diff --git a/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java b/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
index 16c2940..9955eec 100644
--- a/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
@@ -30,19 +30,18 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 
 public class DirectedCombinableDomains extends BasicCombinableDomains {
 
-    public DirectedCombinableDomains( final DomainId n_terminal_key_domain, final Species species ) {
+    public DirectedCombinableDomains( final String n_terminal_key_domain, final Species species ) {
         super( n_terminal_key_domain, species );
     }
 
     @Override
     public List<BinaryDomainCombination> toBinaryDomainCombinations() {
         final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
-        for( final DomainId domain : getCombiningDomains().keySet() ) {
+        for( final String domain : getCombiningDomains().keySet() ) {
             // Precondition (!): key domain is most upstream domain.
             //TODO ensure this is true.
             binary_combinations.add( new DirectedBinaryDomainCombination( getKeyDomain(), domain ) );
diff --git a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
index cdc9416..caf6cb0 100644
--- a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java
@@ -30,7 +30,6 @@ import java.util.HashSet;
 import java.util.Set;
 
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 
 public class DomainArchitectureBasedGenomeSimilarityCalculator {
 
@@ -38,12 +37,12 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
     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;
@@ -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 );
     }
@@ -113,7 +112,7 @@ public class DomainArchitectureBasedGenomeSimilarityCalculator {
 
     public void deleteAllDomainIdsToIgnore() {
         forceRecalculation();
-        setDomainIdsToIgnore( new HashSet<DomainId>() );
+        setDomainIdsToIgnore( new HashSet<String>() );
     }
 
     private void forceRecalculation() {
@@ -155,9 +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() ) {
@@ -216,23 +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 );
                 }
@@ -244,14 +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 );
         }
@@ -276,12 +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 );
                 }
@@ -314,9 +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 );
             }
@@ -329,7 +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;
     }
diff --git a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
index 20a25d4..08f3989 100644
--- a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
+++ b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java
@@ -48,7 +48,6 @@ import org.forester.application.surfacing;
 import org.forester.go.GoId;
 import org.forester.go.GoTerm;
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
@@ -86,8 +85,8 @@ public final class DomainCountsDifferenceUtil {
         }
     }
 
-    private static void addCounts( final SortedMap<DomainId, List<Integer>> copy_counts,
-                                   final DomainId domain,
+    private static void addCounts( final SortedMap<String, List<Integer>> copy_counts,
+                                   final String domain,
                                    final GenomeWideCombinableDomains genome ) {
         if ( !copy_counts.containsKey( domain ) ) {
             copy_counts.put( domain, new ArrayList<Integer>() );
@@ -100,8 +99,8 @@ public final class DomainCountsDifferenceUtil {
         }
     }
 
-    private static StringBuilder addGoInformation( final DomainId d,
-                                                   final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+    private static StringBuilder addGoInformation( final String d,
+                                                   final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                    final Map<GoId, GoTerm> go_id_to_term_map ) {
         final StringBuilder sb = new StringBuilder();
         if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty()
@@ -116,7 +115,7 @@ public final class DomainCountsDifferenceUtil {
                 sb.append( "<br>" );
             }
             else {
-                sb.append( "go id \"" + go_id + "\" not found [" + d.getId() + "]" );
+                sb.append( "go id \"" + go_id + "\" not found [" + d + "]" );
             }
         }
         return sb;
@@ -143,7 +142,7 @@ public final class DomainCountsDifferenceUtil {
                                                        final File plain_output_dom,
                                                        final File html_output_dom,
                                                        final File html_output_dc,
-                                                       final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+                                                       final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                        final Map<GoId, GoTerm> go_id_to_term_map,
                                                        final File all_domains_go_ids_out_dom,
                                                        final File passing_domains_go_ids_out_dom,
@@ -175,13 +174,13 @@ public final class DomainCountsDifferenceUtil {
         final Writer html_writer_dc = new BufferedWriter( new FileWriter( html_output_dc ) );
         final Writer all_gos_writer = new BufferedWriter( new FileWriter( all_domains_go_ids_out_dom ) );
         final Writer passing_gos_writer = new BufferedWriter( new FileWriter( passing_domains_go_ids_out_dom ) );
-        final SortedMap<DomainId, Double> high_copy_base_values = new TreeMap<DomainId, Double>();
-        final SortedMap<DomainId, Double> high_copy_target_values = new TreeMap<DomainId, Double>();
-        final SortedMap<DomainId, Double> low_copy_values = new TreeMap<DomainId, Double>();
-        final SortedMap<DomainId, List<Integer>> high_copy_base_copy_counts = new TreeMap<DomainId, List<Integer>>();
-        final SortedMap<DomainId, List<Integer>> high_copy_target_copy_counts = new TreeMap<DomainId, List<Integer>>();
-        final SortedMap<DomainId, List<Integer>> low_copy_copy_counts = new TreeMap<DomainId, List<Integer>>();
-        final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
+        final SortedMap<String, Double> high_copy_base_values = new TreeMap<String, Double>();
+        final SortedMap<String, Double> high_copy_target_values = new TreeMap<String, Double>();
+        final SortedMap<String, Double> low_copy_values = new TreeMap<String, Double>();
+        final SortedMap<String, List<Integer>> high_copy_base_copy_counts = new TreeMap<String, List<Integer>>();
+        final SortedMap<String, List<Integer>> high_copy_target_copy_counts = new TreeMap<String, List<Integer>>();
+        final SortedMap<String, List<Integer>> low_copy_copy_counts = new TreeMap<String, List<Integer>>();
+        final SortedSet<String> all_domains = new TreeSet<String>();
         final SortedMap<BinaryDomainCombination, Double> high_copy_base_values_dc = new TreeMap<BinaryDomainCombination, Double>();
         final SortedMap<BinaryDomainCombination, Double> high_copy_target_values_dc = new TreeMap<BinaryDomainCombination, Double>();
         final SortedMap<BinaryDomainCombination, Double> low_copy_values_dc = new TreeMap<BinaryDomainCombination, Double>();
@@ -193,11 +192,11 @@ public final class DomainCountsDifferenceUtil {
         final SortedSet<GoId> go_ids_of_passing_domains = new TreeSet<GoId>();
         final SortedSet<GoId> go_ids_all = new TreeSet<GoId>();
         for( final GenomeWideCombinableDomains genome : genomes ) {
-            final SortedSet<DomainId> domains = genome.getAllDomainIds();
+            final SortedSet<String> domains = genome.getAllDomainIds();
             final SortedSet<BinaryDomainCombination> dcs = genome.toBinaryDomainCombinations();
             final String species = genome.getSpecies().getSpeciesId();
             bdcs_per_genome.put( species, genome.toBinaryDomainCombinations() );
-            for( final DomainId d : domains ) {
+            for( final String d : domains ) {
                 all_domains.add( d );
                 if ( domain_id_to_go_ids_map.containsKey( d ) ) {
                     go_ids_all.addAll( domain_id_to_go_ids_map.get( d ) );
@@ -207,7 +206,7 @@ public final class DomainCountsDifferenceUtil {
                 all_dcs.add( dc );
             }
         }
-        for( final DomainId domain : all_domains ) {
+        for( final String domain : all_domains ) {
             for( final GenomeWideCombinableDomains genome : genomes ) {
                 final String species = genome.getSpecies().getSpeciesId();
                 if ( high_copy_base_species.contains( species ) ) {
@@ -244,7 +243,7 @@ public final class DomainCountsDifferenceUtil {
                 }
             }
         }
-        for( final DomainId domain : all_domains ) {
+        for( final String domain : all_domains ) {
             calculateDomainCountsBasedValue( high_copy_target_values,
                                              high_copy_target_copy_counts,
                                              domain,
@@ -332,9 +331,9 @@ public final class DomainCountsDifferenceUtil {
         }
     }
 
-    private static void calculateDomainCountsBasedValue( final SortedMap<DomainId, Double> copy_values,
-                                                         final SortedMap<DomainId, List<Integer>> copy_counts,
-                                                         final DomainId domain,
+    private static void calculateDomainCountsBasedValue( final SortedMap<String, Double> copy_values,
+                                                         final SortedMap<String, List<Integer>> copy_counts,
+                                                         final String domain,
                                                          final COPY_CALCULATION_MODE copy_calc_mode ) {
         if ( copy_counts.containsKey( domain ) ) {
             switch ( copy_calc_mode ) {
@@ -372,9 +371,9 @@ public final class DomainCountsDifferenceUtil {
         results.put( bdc, ( double ) max );
     }
 
-    private static void calculateMaxCount( final SortedMap<DomainId, Double> results,
-                                           final SortedMap<DomainId, List<Integer>> copy_counts,
-                                           final DomainId domain ) {
+    private static void calculateMaxCount( final SortedMap<String, Double> results,
+                                           final SortedMap<String, List<Integer>> copy_counts,
+                                           final String domain ) {
         final List<Integer> counts = copy_counts.get( domain );
         int max = 0;
         for( final Integer count : counts ) {
@@ -396,9 +395,9 @@ public final class DomainCountsDifferenceUtil {
         results.put( bdc, ( ( double ) sum ) / ( ( double ) counts.size() ) );
     }
 
-    private static void calculateMeanCount( final SortedMap<DomainId, Double> results,
-                                            final SortedMap<DomainId, List<Integer>> copy_counts,
-                                            final DomainId domain ) {
+    private static void calculateMeanCount( final SortedMap<String, Double> results,
+                                            final SortedMap<String, List<Integer>> copy_counts,
+                                            final String domain ) {
         final List<Integer> counts = copy_counts.get( domain );
         int sum = 0;
         for( final Integer count : counts ) {
@@ -418,9 +417,9 @@ public final class DomainCountsDifferenceUtil {
         results.put( bdc, stats.median() );
     }
 
-    private static void calculateMedianCount( final SortedMap<DomainId, Double> results,
-                                              final SortedMap<DomainId, List<Integer>> copy_counts,
-                                              final DomainId domain ) {
+    private static void calculateMedianCount( final SortedMap<String, Double> results,
+                                              final SortedMap<String, List<Integer>> copy_counts,
+                                              final String domain ) {
         final List<Integer> counts = copy_counts.get( domain );
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final Integer count : counts ) {
@@ -442,9 +441,9 @@ public final class DomainCountsDifferenceUtil {
         results.put( bdc, ( double ) min );
     }
 
-    private static void calculateMinCount( final SortedMap<DomainId, Double> results,
-                                           final SortedMap<DomainId, List<Integer>> copy_counts,
-                                           final DomainId domain ) {
+    private static void calculateMinCount( final SortedMap<String, Double> results,
+                                           final SortedMap<String, List<Integer>> copy_counts,
+                                           final String domain ) {
         final List<Integer> counts = copy_counts.get( domain );
         int min = Integer.MAX_VALUE;
         for( final Integer count : counts ) {
@@ -506,8 +505,8 @@ public final class DomainCountsDifferenceUtil {
         html_writer.write( "</td>" );
     }
 
-    private static void writeCopyNumberValues( final SortedMap<DomainId, Double> copy_means,
-                                               final DomainId domain,
+    private static void writeCopyNumberValues( final SortedMap<String, Double> copy_means,
+                                               final String domain,
                                                final GenomeWideCombinableDomains genome,
                                                final String species,
                                                final Writer plain_writer,
@@ -660,15 +659,15 @@ public final class DomainCountsDifferenceUtil {
                                                   final List<String> low_copy_species,
                                                   final int min_diff,
                                                   final Double factor,
-                                                  final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+                                                  final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                   final Map<GoId, GoTerm> go_id_to_term_map,
                                                   final Writer plain_writer,
                                                   final Writer html_writer,
                                                   final File proteins_file_base,
-                                                  final SortedMap<DomainId, Double> high_copy_base_values,
-                                                  final SortedMap<DomainId, Double> high_copy_target_values,
-                                                  final SortedMap<DomainId, Double> low_copy_values,
-                                                  final SortedSet<DomainId> all_domains,
+                                                  final SortedMap<String, Double> high_copy_base_values,
+                                                  final SortedMap<String, Double> high_copy_target_values,
+                                                  final SortedMap<String, Double> low_copy_values,
+                                                  final SortedSet<String> all_domains,
                                                   final SortedSet<GoId> go_ids_of_passing_domains,
                                                   final SortedMap<Species, List<Protein>> protein_lists_per_species )
             throws IOException {
@@ -677,7 +676,7 @@ public final class DomainCountsDifferenceUtil {
         int not_total_absense_counter = 0;
         SurfacingUtil.addHtmlHead( html_writer, "Domain Copy Differences" );
         html_writer.write( "<body><table>" );
-        for( final DomainId domain_id : all_domains ) {
+        for( final String domain_id : all_domains ) {
             if ( ( high_copy_base_values.get( domain_id ) > 0 ) && ( high_copy_target_values.get( domain_id ) > 0 )
                     && ( high_copy_base_values.get( domain_id ) >= low_copy_values.get( domain_id ) ) ) {
                 if ( high_copy_target_values.get( domain_id ) >= ( min_diff + ( factor * low_copy_values
@@ -693,10 +692,10 @@ public final class DomainCountsDifferenceUtil {
                     if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
                         go_ids_of_passing_domains.addAll( domain_id_to_go_ids_map.get( domain_id ) );
                     }
-                    plain_writer.write( domain_id.getId() );
+                    plain_writer.write( domain_id );
                     plain_writer.write( SurfacingConstants.NL );
-                    html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK
-                            + domain_id.getId() + "\">" + domain_id.getId() + "</a></td><td>" );
+                    html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id
+                            + "\">" + domain_id + "</a></td><td>" );
                     html_writer.write( addGoInformation( domain_id, domain_id_to_go_ids_map, go_id_to_term_map )
                             .toString() );
                     html_writer.write( "</td><td>" );
@@ -820,7 +819,7 @@ public final class DomainCountsDifferenceUtil {
 
     private static void writeProteinsToFile( final File proteins_file_base,
                                              final SortedMap<Species, List<Protein>> protein_lists_per_species,
-                                             final DomainId domain_id ) throws IOException {
+                                             final String domain_id ) throws IOException {
         final File my_proteins_file = new File( proteins_file_base.getParentFile() + ForesterUtil.FILE_SEPARATOR
                 + domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
         SurfacingUtil.checkForOutputFileWriteability( my_proteins_file );
diff --git a/forester/java/src/org/forester/surfacing/DomainLengths.java b/forester/java/src/org/forester/surfacing/DomainLengths.java
index 7e628ce..1018aea 100644
--- a/forester/java/src/org/forester/surfacing/DomainLengths.java
+++ b/forester/java/src/org/forester/surfacing/DomainLengths.java
@@ -31,17 +31,16 @@ import java.util.List;
 import java.util.SortedMap;
 import java.util.TreeMap;
 
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
 
 public class DomainLengths {
 
-    final DomainId                                  _domain_id;
+    final String                                    _domain_id;
     final SortedMap<Species, DescriptiveStatistics> _length_statistics;
 
-    public DomainLengths( final DomainId domain_id ) {
+    public DomainLengths( final String domain_id ) {
         _domain_id = domain_id;
         _length_statistics = new TreeMap<Species, DescriptiveStatistics>();
     }
@@ -91,7 +90,7 @@ public class DomainLengths {
         return ( species_mean - population_mean ) / population_sd;
     }
 
-    public DomainId getDomainId() {
+    public String getDomainId() {
         return _domain_id;
     }
 
diff --git a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
index 9a9e0a7..44b6247 100644
--- a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
+++ b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java
@@ -33,7 +33,6 @@ import java.util.SortedMap;
 import java.util.TreeMap;
 
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.species.Species;
 import org.forester.util.BasicDescriptiveStatistics;
@@ -42,12 +41,12 @@ import org.forester.util.ForesterUtil;
 
 public class DomainLengthsTable {
 
-    private final static DecimalFormat       DF = new DecimalFormat( "#.0" );
-    final SortedMap<DomainId, DomainLengths> _domain_lengths;
-    final List<Species>                      _species;
+    private final static DecimalFormat     DF = new DecimalFormat( "#.0" );
+    final SortedMap<String, DomainLengths> _domain_lengths;
+    final List<Species>                    _species;
 
     public DomainLengthsTable() {
-        _domain_lengths = new TreeMap<DomainId, DomainLengths>();
+        _domain_lengths = new TreeMap<String, DomainLengths>();
         _species = new ArrayList<Species>();
     }
 
@@ -59,7 +58,7 @@ public class DomainLengthsTable {
         getDomainLengths().put( domain_lengths.getDomainId(), domain_lengths );
     }
 
-    private void addLength( final DomainId domain_id, final Species species, final int domain_length ) {
+    private void addLength( final String domain_id, final Species species, final int domain_length ) {
         if ( !getDomainLengths().containsKey( domain_id ) ) {
             addDomainLengths( new DomainLengths( domain_id ) );
         }
@@ -87,7 +86,7 @@ public class DomainLengthsTable {
         return stats;
     }
 
-    public DescriptiveStatistics calculateMeanBasedStatisticsForDomain( final DomainId domain_id ) {
+    public DescriptiveStatistics calculateMeanBasedStatisticsForDomain( final String domain_id ) {
         return getDomainLengths( domain_id ).calculateMeanBasedStatistics();
     }
 
@@ -143,11 +142,11 @@ public class DomainLengthsTable {
         return sb;
     }
 
-    private SortedMap<DomainId, DomainLengths> getDomainLengths() {
+    private SortedMap<String, DomainLengths> getDomainLengths() {
         return _domain_lengths;
     }
 
-    public DomainLengths getDomainLengths( final DomainId domain_id ) {
+    public DomainLengths getDomainLengths( final String domain_id ) {
         return getDomainLengths().get( domain_id );
     }
 
@@ -159,7 +158,7 @@ public class DomainLengthsTable {
         return list;
     }
 
-    public DescriptiveStatistics getLengthStatistic( final DomainId domain_id, final Species species ) {
+    public DescriptiveStatistics getLengthStatistic( final String domain_id, final Species species ) {
         return getDomainLengths( domain_id ).getLengthStatistic( species );
     }
 
diff --git a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
index e2e0af3..e2db537 100644
--- a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
@@ -49,7 +49,6 @@ import org.forester.phylogeny.data.BinaryCharacters;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.protein.BinaryDomainCombination;
 import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.util.ForesterUtil;
 
@@ -64,8 +63,8 @@ public final class DomainParsimonyCalculator {
     private int                                     _total_gains;
     private int                                     _total_unchanged;
     private int                                     _cost;
-    private Map<DomainId, Set<String>>              _domain_id_to_secondary_features_map;
-    private SortedSet<DomainId>                     _positive_filter;
+    private Map<String, Set<String>>                _domain_id_to_secondary_features_map;
+    private SortedSet<String>                       _positive_filter;
 
     private DomainParsimonyCalculator( final Phylogeny phylogeny ) {
         init();
@@ -81,7 +80,7 @@ public final class DomainParsimonyCalculator {
 
     private DomainParsimonyCalculator( final Phylogeny phylogeny,
                                        final List<GenomeWideCombinableDomains> gwcd_list,
-                                       final Map<DomainId, Set<String>> domain_id_to_secondary_features_map ) {
+                                       final Map<String, Set<String>> domain_id_to_secondary_features_map ) {
         init();
         _phylogeny = phylogeny;
         _gwcd_list = gwcd_list;
@@ -160,7 +159,7 @@ public final class DomainParsimonyCalculator {
         executeDolloParsimony( true );
     }
 
-    public void executeDolloParsimonyOnDomainPresence( final SortedSet<DomainId> positive_filter ) {
+    public void executeDolloParsimonyOnDomainPresence( final SortedSet<String> positive_filter ) {
         setPositiveFilter( positive_filter );
         executeDolloParsimony( true );
         setPositiveFilter( null );
@@ -231,14 +230,13 @@ public final class DomainParsimonyCalculator {
         fitch.setUseLast( use_last );
         fitch.setReturnGainLossMatrix( true );
         fitch.setReturnInternalStates( true );
-        final Map<DomainId, Set<String>> map = getDomainIdToSecondaryFeaturesMap();
-        final Map<DomainId, String> newmap = new HashMap<DomainId, String>();
-        final Iterator<Entry<DomainId, Set<String>>> it = map.entrySet().iterator();
+        final Map<String, Set<String>> map = getDomainIdToSecondaryFeaturesMap();
+        final Map<String, String> newmap = new HashMap<String, String>();
+        final Iterator<Entry<String, Set<String>>> it = map.entrySet().iterator();
         while ( it.hasNext() ) {
-            final Map.Entry<DomainId, Set<String>> pair = it.next();
+            final Map.Entry<String, Set<String>> pair = it.next();
             if ( pair.getValue().size() != 1 ) {
-                throw new IllegalArgumentException( pair.getKey().getId() + " mapps to " + pair.getValue().size()
-                        + " items" );
+                throw new IllegalArgumentException( pair.getKey() + " mapps to " + pair.getValue().size() + " items" );
             }
             newmap.put( pair.getKey(), ( String ) pair.getValue().toArray()[ 0 ] );
         }
@@ -350,7 +348,7 @@ public final class DomainParsimonyCalculator {
         return _cost;
     }
 
-    private Map<DomainId, Set<String>> getDomainIdToSecondaryFeaturesMap() {
+    private Map<String, Set<String>> getDomainIdToSecondaryFeaturesMap() {
         return _domain_id_to_secondary_features_map;
     }
 
@@ -415,7 +413,7 @@ public final class DomainParsimonyCalculator {
         return _phylogeny;
     }
 
-    private SortedSet<DomainId> getPositiveFilter() {
+    private SortedSet<String> getPositiveFilter() {
         return _positive_filter;
     }
 
@@ -500,7 +498,7 @@ public final class DomainParsimonyCalculator {
         _cost = cost;
     }
 
-    private void setDomainIdToSecondaryFeaturesMap( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map ) {
+    private void setDomainIdToSecondaryFeaturesMap( final Map<String, Set<String>> domain_id_to_secondary_features_map ) {
         _domain_id_to_secondary_features_map = domain_id_to_secondary_features_map;
     }
 
@@ -508,7 +506,7 @@ public final class DomainParsimonyCalculator {
         _gain_loss_matrix = gain_loss_matrix;
     }
 
-    private void setPositiveFilter( final SortedSet<DomainId> positive_filter ) {
+    private void setPositiveFilter( final SortedSet<String> positive_filter ) {
         _positive_filter = positive_filter;
     }
 
@@ -539,7 +537,7 @@ public final class DomainParsimonyCalculator {
 
     public static DomainParsimonyCalculator createInstance( final Phylogeny phylogeny,
                                                             final List<GenomeWideCombinableDomains> gwcd_list,
-                                                            final Map<DomainId, Set<String>> domain_id_to_secondary_features_map ) {
+                                                            final Map<String, Set<String>> domain_id_to_secondary_features_map ) {
         if ( phylogeny.getNumberOfExternalNodes() != gwcd_list.size() ) {
             throw new IllegalArgumentException( "size of external nodes does not equal size of genome wide combinable domains list" );
         }
@@ -554,7 +552,7 @@ public final class DomainParsimonyCalculator {
      * @return
      */
     static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeaturePresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
-                                                                                               final Map<DomainId, Set<String>> domain_id_to_second_features_map,
+                                                                                               final Map<String, Set<String>> domain_id_to_second_features_map,
                                                                                                final Map<Species, MappingResults> mapping_results_map ) {
         if ( gwcd_list.isEmpty() ) {
             throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
@@ -567,7 +565,7 @@ public final class DomainParsimonyCalculator {
         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
             int mapped = 0;
             int not_mapped = 0;
-            for( final DomainId domain : gwcd.getAllDomainIds() ) {
+            for( final String domain : gwcd.getAllDomainIds() ) {
                 if ( domain_id_to_second_features_map.containsKey( domain ) ) {
                     all_secondary_features.addAll( domain_id_to_second_features_map.get( domain ) );
                     mapped++;
@@ -601,7 +599,7 @@ public final class DomainParsimonyCalculator {
             all_identifiers.add( species_id );
             matrix.setIdentifier( identifier_index, species_id );
             final Set<String> all_second_per_gwcd = new HashSet<String>();
-            for( final DomainId domain : gwcd.getAllDomainIds() ) {
+            for( final String domain : gwcd.getAllDomainIds() ) {
                 if ( domain_id_to_second_features_map.containsKey( domain ) ) {
                     all_second_per_gwcd.addAll( domain_id_to_second_features_map.get( domain ) );
                 }
@@ -620,7 +618,7 @@ public final class DomainParsimonyCalculator {
     }
 
     public static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
-                                                                                                                             final Map<DomainId, String> domain_id_to_second_features_map ) {
+                                                                                                                             final Map<String, String> domain_id_to_second_features_map ) {
         if ( gwcd_list.isEmpty() ) {
             throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
         }
@@ -689,21 +687,21 @@ public final class DomainParsimonyCalculator {
         return matrix;
     }
 
-    private static BinaryDomainCombination mapBinaryDomainCombination( final Map<DomainId, String> domain_id_to_second_features_map,
+    private static BinaryDomainCombination mapBinaryDomainCombination( final Map<String, String> domain_id_to_second_features_map,
                                                                        final BinaryDomainCombination bc,
                                                                        final SortedSet<String> no_mappings ) {
         String id0 = "";
         String id1 = "";
         if ( !domain_id_to_second_features_map.containsKey( bc.getId0() ) ) {
-            no_mappings.add( bc.getId0().getId() );
-            id0 = bc.getId0().getId();
+            no_mappings.add( bc.getId0() );
+            id0 = bc.getId0();
         }
         else {
             id0 = domain_id_to_second_features_map.get( bc.getId0() );
         }
         if ( !domain_id_to_second_features_map.containsKey( bc.getId1() ) ) {
-            no_mappings.add( bc.getId1().getId() );
-            id1 = bc.getId1().getId();
+            no_mappings.add( bc.getId1() );
+            id1 = bc.getId1();
         }
         else {
             id1 = domain_id_to_second_features_map.get( bc.getId1() );
@@ -771,7 +769,7 @@ public final class DomainParsimonyCalculator {
     }
 
     public static CharacterStateMatrix<BinaryStates> createMatrixOfDomainPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
-                                                                                            final SortedSet<DomainId> positive_filter ) {
+                                                                                            final SortedSet<String> positive_filter ) {
         if ( gwcd_list.isEmpty() ) {
             throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
         }
@@ -779,9 +777,9 @@ public final class DomainParsimonyCalculator {
             throw new IllegalArgumentException( "positive filter is empty" );
         }
         final int number_of_identifiers = gwcd_list.size();
-        final SortedSet<DomainId> all_domain_ids = new TreeSet<DomainId>();
+        final SortedSet<String> all_domain_ids = new TreeSet<String>();
         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
-            for( final DomainId domain : gwcd.getAllDomainIds() ) {
+            for( final String domain : gwcd.getAllDomainIds() ) {
                 all_domain_ids.add( domain );
             }
         }
@@ -789,7 +787,7 @@ public final class DomainParsimonyCalculator {
         if ( positive_filter != null ) {
             //number_of_characters = positive_filter.size(); -- bad if doms in filter but not in genomes 
             number_of_characters = 0;
-            for( final DomainId id : all_domain_ids ) {
+            for( final String id : all_domain_ids ) {
                 if ( positive_filter.contains( id ) ) {
                     number_of_characters++;
                 }
@@ -798,13 +796,13 @@ public final class DomainParsimonyCalculator {
         final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> matrix = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( number_of_identifiers,
                                                                                                                                                  number_of_characters );
         int character_index = 0;
-        for( final DomainId id : all_domain_ids ) {
+        for( final String id : all_domain_ids ) {
             if ( positive_filter == null ) {
-                matrix.setCharacter( character_index++, id.getId() );
+                matrix.setCharacter( character_index++, id );
             }
             else {
                 if ( positive_filter.contains( id ) ) {
-                    matrix.setCharacter( character_index++, id.getId() );
+                    matrix.setCharacter( character_index++, id );
                 }
             }
         }
@@ -821,7 +819,7 @@ public final class DomainParsimonyCalculator {
                 if ( ForesterUtil.isEmpty( matrix.getCharacter( ci ) ) ) {
                     throw new RuntimeException( "this should not have happened: problem with character #" + ci );
                 }
-                final DomainId id = new DomainId( matrix.getCharacter( ci ) );
+                final String id = matrix.getCharacter( ci );
                 if ( gwcd.contains( id ) ) {
                     matrix.setState( identifier_index, ci, CharacterStateMatrix.BinaryStates.PRESENT );
                 }
diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarity.java b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
index b6ae576..0787439 100644
--- a/forester/java/src/org/forester/surfacing/DomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/DomainSimilarity.java
@@ -30,7 +30,6 @@ import java.util.Map;
 import java.util.SortedMap;
 import java.util.SortedSet;
 
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
 
@@ -48,9 +47,9 @@ public interface DomainSimilarity extends Comparable<DomainSimilarity> {
         MIN, MAX, SD, MEAN, ABS_MAX_COUNTS_DIFFERENCE, MAX_COUNTS_DIFFERENCE, MAX_DIFFERENCE, SPECIES_COUNT, DOMAIN_ID,
     }
 
-    public SortedSet<DomainId> getCombinableDomainIds( final Species species_of_combinable_domain );;
+    public SortedSet<String> getCombinableDomainIds( final Species species_of_combinable_domain );;
 
-    public DomainId getDomainId();
+    public String getDomainId();
 
     /**
      * For pairwise similarities, this should return the "difference"; for example the difference in counts
diff --git a/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java b/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java
index f444ff7..4dbe718 100644
--- a/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java
@@ -32,28 +32,27 @@ import java.util.SortedSet;
 
 import org.forester.protein.BinaryDomainCombination;
 import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.util.DescriptiveStatistics;
 
 public interface GenomeWideCombinableDomains {
 
-    public boolean contains( DomainId key_id );
+    public boolean contains( String key_id );
 
-    public CombinableDomains get( DomainId key_id );
+    public CombinableDomains get( String key_id );
 
-    public SortedMap<DomainId, CombinableDomains> getAllCombinableDomainsIds();
+    public SortedMap<String, CombinableDomains> getAllCombinableDomainsIds();
 
     /**
      * This should return all domains ids present in the genome.
      * 
      * @return a sorted set of domains ids
      */
-    public SortedSet<DomainId> getAllDomainIds();
+    public SortedSet<String> getAllDomainIds();
 
     public DomainCombinationType getDomainCombinationType();
 
-    SortedSet<DomainId> getMostPromiscuosDomain();
+    SortedSet<String> getMostPromiscuosDomain();
 
     /**
      * This should return a statistic for per domain 
diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
index a811450..0fd6c6d 100644
--- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
+++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java
@@ -43,7 +43,6 @@ import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.go.GoId;
 import org.forester.go.GoNameSpace;
 import org.forester.go.GoTerm;
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
 import org.forester.util.DescriptiveStatistics;
@@ -90,7 +89,7 @@ public class PairwiseGenomeComparator {
                                             final DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field,
                                             final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
                                             final DomainSimilarity.DomainSimilarityScoring scoring,
-                                            final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+                                            final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                             final Map<GoId, GoTerm> go_id_to_term_map,
                                             final GoNameSpace go_namespace_limit,
                                             final Species[] species,
@@ -268,7 +267,7 @@ public class PairwiseGenomeComparator {
         else if ( jacknife_ratio >= 1.0 ) {
             throw new IllegalArgumentException( "attempt to perform jacknife resampling with jacknife ratio 1.0 or more" );
         }
-        final DomainId[] all_unique_domain_ids = getAllUniqueDomainIdAsArray( list_of_genome_wide_combinable_domains );
+        final String[] all_unique_domain_ids = getAllUniqueDomainIdAsArray( list_of_genome_wide_combinable_domains );
         if ( verbose ) {
             System.out.println();
             System.out.println( "Jacknife: total of domains: " + all_unique_domain_ids.length );
@@ -281,9 +280,9 @@ public class PairwiseGenomeComparator {
             if ( verbose ) {
                 System.out.print( " " + r );
             }
-            final SortedSet<DomainId> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
-                                                                                    jacknife_ratio,
-                                                                                    generator );
+            final SortedSet<String> domain_ids_to_ignore = randomlyPickDomainIds( all_unique_domain_ids,
+                                                                                  jacknife_ratio,
+                                                                                  generator );
             final BasicSymmetricalDistanceMatrix shared_domains_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
             final BasicSymmetricalDistanceMatrix shared_binary_combinations_based_distances = new BasicSymmetricalDistanceMatrix( number_of_genomes );
             for( int i = 0; i < number_of_genomes; ++i ) {
@@ -314,28 +313,28 @@ public class PairwiseGenomeComparator {
         }
     }
 
-    static private DomainId[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
-        DomainId[] all_domain_ids_array;
-        final SortedSet<DomainId> all_domain_ids = new TreeSet<DomainId>();
+    static private String[] getAllUniqueDomainIdAsArray( final List<GenomeWideCombinableDomains> list_of_genome_wide_combinable_domains ) {
+        String[] all_domain_ids_array;
+        final SortedSet<String> all_domain_ids = new TreeSet<String>();
         for( final GenomeWideCombinableDomains genome_wide_combinable_domains : list_of_genome_wide_combinable_domains ) {
-            final SortedSet<DomainId> all_domains = genome_wide_combinable_domains.getAllDomainIds();
-            for( final DomainId domain : all_domains ) {
+            final SortedSet<String> all_domains = genome_wide_combinable_domains.getAllDomainIds();
+            for( final String domain : all_domains ) {
                 all_domain_ids.add( domain );
             }
         }
-        all_domain_ids_array = new DomainId[ all_domain_ids.size() ];
+        all_domain_ids_array = new String[ all_domain_ids.size() ];
         int n = 0;
-        for( final DomainId domain_id : all_domain_ids ) {
+        for( final String domain_id : all_domain_ids ) {
             all_domain_ids_array[ n++ ] = domain_id;
         }
         return all_domain_ids_array;
     }
 
-    static private SortedSet<DomainId> randomlyPickDomainIds( final DomainId[] all_domain_ids_array,
-                                                              final double jacknife_ratio,
-                                                              final Random generator ) {
+    static private SortedSet<String> randomlyPickDomainIds( final String[] all_domain_ids_array,
+                                                            final double jacknife_ratio,
+                                                            final Random generator ) {
         final int size = all_domain_ids_array.length;
-        final SortedSet<DomainId> random_domain_ids = new TreeSet<DomainId>();
+        final SortedSet<String> random_domain_ids = new TreeSet<String>();
         final int number_of_ids_pick = ForesterUtil.roundToInt( jacknife_ratio * size );
         while ( random_domain_ids.size() < number_of_ids_pick ) {
             final int r = generator.nextInt( size );
diff --git a/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java b/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java
index 31d0e55..2cf1a91 100644
--- a/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java
@@ -36,7 +36,6 @@ import org.forester.go.GoId;
 import org.forester.go.GoNameSpace;
 import org.forester.go.GoTerm;
 import org.forester.go.GoXRef;
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
@@ -139,52 +138,51 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
         }
     }
 
-    private void addGoInformation( final StringBuffer sb, final boolean for_table, final boolean html ) {
-        if ( !for_table ) {
-            sb.append( "<" );
-        }
-        switch ( getGoAnnotationOutput() ) {
-            case ALL: {
-                final int go_ids = getCombinableDomains().getKeyDomain().getNumberOfGoIds();
-                boolean first = true;
-                for( int i = 0; i < go_ids; ++i ) {
-                    final GoId go_id = getCombinableDomains().getKeyDomain().getGoId( i );
-                    if ( getGoIdToTermMap() != null ) {
-                        if ( getGoIdToTermMap().containsKey( go_id ) ) {
-                            first = appendGoTerm( sb, getGoIdToTermMap().get( go_id ), first, html );
-                        }
-                        else {
-                            sb.append( "go id \"" + go_id + "\" not found ["
-                                    + getCombinableDomains().getKeyDomain().getId() + "]" );
-                        }
-                    }
-                    else {
-                        if ( !first ) {
-                            sb.append( ", " );
-                        }
-                        if ( html ) {
-                            sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id
-                                    + "\" target=\"amigo_window\">" + go_id + "</a>" );
-                        }
-                        else {
-                            sb.append( go_id );
-                        }
-                        first = false;
-                    }
-                }
-                break;
-            }
-            case NONE: {
-                break;
-            }
-            default:
-                throw new RuntimeException( "unknown " + getGoAnnotationOutput() );
-        }
-        if ( !for_table ) {
-            sb.append( ">: " );
-        }
-    }
-
+    //    private void addGoInformation( final StringBuffer sb, final boolean for_table, final boolean html ) {
+    //        if ( !for_table ) {
+    //            sb.append( "<" );
+    //        }
+    //        switch ( getGoAnnotationOutput() ) {
+    //            case ALL: {
+    //                final int go_ids = getCombinableDomains().getKeyDomain().getNumberOfGoIds();
+    //                boolean first = true;
+    //                for( int i = 0; i < go_ids; ++i ) {
+    //                    final GoId go_id = getCombinableDomains().getKeyDomain().getGoId( i );
+    //                    if ( getGoIdToTermMap() != null ) {
+    //                        if ( getGoIdToTermMap().containsKey( go_id ) ) {
+    //                            first = appendGoTerm( sb, getGoIdToTermMap().get( go_id ), first, html );
+    //                        }
+    //                        else {
+    //                            sb.append( "go id \"" + go_id + "\" not found ["
+    //                                    + getCombinableDomains().getKeyDomain().getId() + "]" );
+    //                        }
+    //                    }
+    //                    else {
+    //                        if ( !first ) {
+    //                            sb.append( ", " );
+    //                        }
+    //                        if ( html ) {
+    //                            sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id
+    //                                    + "\" target=\"amigo_window\">" + go_id + "</a>" );
+    //                        }
+    //                        else {
+    //                            sb.append( go_id );
+    //                        }
+    //                        first = false;
+    //                    }
+    //                }
+    //                break;
+    //            }
+    //            case NONE: {
+    //                break;
+    //            }
+    //            default:
+    //                throw new RuntimeException( "unknown " + getGoAnnotationOutput() );
+    //        }
+    //        if ( !for_table ) {
+    //            sb.append( ">: " );
+    //        }
+    //    }
     private void addSpeciesSpecificDomainData( final StringBuffer sb,
                                                final Species species,
                                                final boolean html,
@@ -426,10 +424,10 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
     }
 
     @Override
-    public SortedSet<DomainId> getCombinableDomainIds( final Species species_of_combinable_domain ) {
-        final SortedSet<DomainId> sorted_ids = new TreeSet<DomainId>();
+    public SortedSet<String> getCombinableDomainIds( final Species species_of_combinable_domain ) {
+        final SortedSet<String> sorted_ids = new TreeSet<String>();
         if ( getSpeciesData().containsKey( species_of_combinable_domain ) ) {
-            for( final DomainId id : getSpeciesData().get( species_of_combinable_domain )
+            for( final String id : getSpeciesData().get( species_of_combinable_domain )
                     .getCombinableDomainIdToCountsMap().keySet() ) {
                 sorted_ids.add( id );
             }
@@ -446,7 +444,7 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
     }
 
     @Override
-    public DomainId getDomainId() {
+    public String getDomainId() {
         return getCombinableDomains().getKeyDomain();
     }
 
@@ -662,11 +660,11 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
             }
             sb.append( "</td>" );
         }
-        if ( getGoAnnotationOutput() != DomainSimilarityCalculator.GoAnnotationOutput.NONE ) {
-            sb.append( "<td>" );
-            addGoInformation( sb, true, true );
-            sb.append( "</td>" );
-        }
+        // ^^     if ( getGoAnnotationOutput() != DomainSimilarityCalculator.GoAnnotationOutput.NONE ) {
+        // ^^         sb.append( "<td>" );
+        // ^^         addGoInformation( sb, true, true );
+        // ^^         sb.append( "</td>" );
+        // ^^     }
         if ( ( getSpeciesCustomOrder() == null ) || getSpeciesCustomOrder().isEmpty() ) {
             sb.append( "<td>" );
             sb.append( getSpeciesDataInAlphabeticalOrder( true, tax_code_to_id_map ) );
@@ -723,10 +721,10 @@ public class PrintableDomainSimilarity implements DomainSimilarity {
             default:
                 throw new AssertionError( "Unknown sort method: " + getSortField() );
         }
-        if ( getGoAnnotationOutput() != DomainSimilarityCalculator.GoAnnotationOutput.NONE ) {
-            sb.append( TAB );
-            addGoInformation( sb, true, false );
-        }
+        // ^^     if ( getGoAnnotationOutput() != DomainSimilarityCalculator.GoAnnotationOutput.NONE ) {
+        // ^^       sb.append( TAB );
+        // ^^       addGoInformation( sb, true, false );
+        // ^^   }
         return sb;
     }
 
diff --git a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java
index 28ca512..d361573 100644
--- a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java
+++ b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java
@@ -33,13 +33,12 @@ import java.util.Set;
 import java.util.SortedMap;
 import java.util.TreeMap;
 
-import org.forester.protein.DomainId;
 import org.forester.util.DescriptiveStatistics;
 
 class PrintableSpeciesSpecificDomainSimilariyData implements SpeciesSpecificDomainSimilariyData {
 
     private final static NumberFormat   FORMATTER = new DecimalFormat( "0.0E0" );
-    final SortedMap<DomainId, Integer>  _combinable_domain_id_to_count_map;
+    final SortedMap<String, Integer>    _combinable_domain_id_to_count_map;
     final private int                   _key_domain_proteins_count;
     final private int                   _key_domain_domains_count;
     final private int                   _combinable_domains_count;
@@ -53,11 +52,11 @@ class PrintableSpeciesSpecificDomainSimilariyData implements SpeciesSpecificDoma
         _key_domain_domains_count = key_domain_domains_count;
         _combinable_domains_count = combinable_domains;
         _key_domain_confidence_descriptive_statistics = key_domain_confidence_descriptive_statistics;
-        _combinable_domain_id_to_count_map = new TreeMap<DomainId, Integer>();
+        _combinable_domain_id_to_count_map = new TreeMap<String, Integer>();
     }
 
     @Override
-    public void addProteinsExhibitingCombinationCount( final DomainId domain_id, final int count ) {
+    public void addProteinsExhibitingCombinationCount( final String domain_id, final int count ) {
         if ( getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
             throw new IllegalArgumentException( "Domain with id " + domain_id + " already exists" );
         }
@@ -65,7 +64,7 @@ class PrintableSpeciesSpecificDomainSimilariyData implements SpeciesSpecificDoma
     }
 
     @Override
-    public SortedMap<DomainId, Integer> getCombinableDomainIdToCountsMap() {
+    public SortedMap<String, Integer> getCombinableDomainIdToCountsMap() {
         return _combinable_domain_id_to_count_map;
     }
 
@@ -86,7 +85,7 @@ class PrintableSpeciesSpecificDomainSimilariyData implements SpeciesSpecificDoma
     }
 
     @Override
-    public int getNumberOfProteinsExhibitingCombinationWith( final DomainId domain_id ) {
+    public int getNumberOfProteinsExhibitingCombinationWith( final String domain_id ) {
         if ( !getCombinableDomainIdToCountsMap().containsKey( domain_id ) ) {
             throw new IllegalArgumentException( "Domain with id " + domain_id + " not found" );
         }
@@ -121,17 +120,17 @@ class PrintableSpeciesSpecificDomainSimilariyData implements SpeciesSpecificDoma
                 sb.append( ":" );
             }
         }
-        final Set<DomainId> ids = getCombinableDomainIdToCountsMap().keySet();
+        final Set<String> ids = getCombinableDomainIdToCountsMap().keySet();
         int i = 0;
-        for( final DomainId domain_id : ids ) {
+        for( final String domain_id : ids ) {
             ++i;
             sb.append( " " );
             if ( html ) {
-                sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id.getId() + "\">"
-                        + domain_id.getId() + "</a>" );
+                sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id + "\">" + domain_id
+                        + "</a>" );
             }
             else {
-                sb.append( domain_id.getId() );
+                sb.append( domain_id );
             }
             if ( detailedness == DomainSimilarityCalculator.Detailedness.PUNCTILIOUS ) {
                 sb.append( ":" );
diff --git a/forester/java/src/org/forester/surfacing/SimpleDomain.java b/forester/java/src/org/forester/surfacing/SimpleDomain.java
index 5182865..2d1826e 100644
--- a/forester/java/src/org/forester/surfacing/SimpleDomain.java
+++ b/forester/java/src/org/forester/surfacing/SimpleDomain.java
@@ -26,9 +26,7 @@
 
 package org.forester.surfacing;
 
-import org.forester.go.GoId;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.util.ForesterUtil;
 
 /*
@@ -37,20 +35,19 @@ import org.forester.util.ForesterUtil;
  */
 public class SimpleDomain implements Domain {
 
-    final private DomainId _id;
+    final private String _id;
 
-    public SimpleDomain( final String id_str ) {
-        if ( ForesterUtil.isEmpty( id_str ) ) {
+    public SimpleDomain( final String id ) {
+        if ( ForesterUtil.isEmpty( id ) ) {
             throw new IllegalArgumentException( "attempt to create protein domain with null or empty id" );
         }
-        _id = new DomainId( id_str );
-    }
-
-    @Override
-    public void addGoId( final GoId go_id ) {
-        throw new RuntimeException( "method not implemented" );
+        _id = id;
     }
 
+    // ^^  @Override
+    // ^^  public void addGoId( final GoId go_id ) {
+    // ^^     throw new RuntimeException( "method not implemented" );
+    // ^^ }
     @Override
     public int compareTo( final Domain domain ) {
         if ( this == domain ) {
@@ -60,7 +57,7 @@ public class SimpleDomain implements Domain {
     }
 
     @Override
-    public DomainId getDomainId() {
+    public String getDomainId() {
         return _id;
     }
 
@@ -69,11 +66,10 @@ public class SimpleDomain implements Domain {
         throw new RuntimeException( "method not implemented" );
     }
 
-    @Override
-    public GoId getGoId( final int i ) {
-        throw new RuntimeException( "method not implemented" );
-    }
-
+    // ^^   @Override
+    // ^^   public GoId getGoId( final int i ) {
+    // ^^      throw new RuntimeException( "method not implemented" );
+    // ^^  }
     @Override
     public int getLength() {
         throw new RuntimeException( "method not implemented" );
@@ -84,11 +80,10 @@ public class SimpleDomain implements Domain {
         throw new RuntimeException( "method not implemented" );
     }
 
-    @Override
-    public int getNumberOfGoIds() {
-        throw new RuntimeException( "method not implemented" );
-    }
-
+    // ^^   @Override
+    // ^^  public int getNumberOfGoIds() {
+    // ^^      throw new RuntimeException( "method not implemented" );
+    // ^^ }
     @Override
     public double getPerDomainEvalue() {
         throw new RuntimeException( "method not implemented" );
diff --git a/forester/java/src/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java b/forester/java/src/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java
index d605344..0e45491 100644
--- a/forester/java/src/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java
+++ b/forester/java/src/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java
@@ -29,14 +29,12 @@ package org.forester.surfacing;
 
 import java.util.SortedMap;
 
-import org.forester.protein.DomainId;
-
 /*
  * A helper class for PrintableDomainSimilarity.
  */
 interface SpeciesSpecificDomainSimilariyData {
 
-    public void addProteinsExhibitingCombinationCount( final DomainId domain_id, final int count );
+    public void addProteinsExhibitingCombinationCount( final String domain_id, final int count );
 
     /**
      * This should return a sorted map mapping domain ids to their corresponding
@@ -44,9 +42,9 @@ interface SpeciesSpecificDomainSimilariyData {
      * 
      * @return a sorted map mapping domain ids to their corresponding counts
      */
-    public SortedMap<DomainId, Integer> getCombinableDomainIdToCountsMap();
+    public SortedMap<String, Integer> getCombinableDomainIdToCountsMap();
 
-    public int getNumberOfProteinsExhibitingCombinationWith( final DomainId domain_id );
+    public int getNumberOfProteinsExhibitingCombinationWith( final String domain_id );
 
     public StringBuffer toStringBuffer( final DomainSimilarityCalculator.Detailedness detailedness, boolean html );
 }
diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index ebce1cc..49991d0 100644
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -79,7 +79,6 @@ import org.forester.protein.BasicDomain;
 import org.forester.protein.BasicProtein;
 import org.forester.protein.BinaryDomainCombination;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.species.Species;
 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
@@ -123,16 +122,16 @@ public final class SurfacingUtil {
 
     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
-        final SortedMap<DomainId, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
-        for( final DomainId domain_id : all_cd.keySet() ) {
+        final SortedMap<String, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
+        for( final String domain_id : all_cd.keySet() ) {
             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
         }
     }
 
     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
-                                             final SortedSet<DomainId> domain_ids ) {
-        final SortedSet<DomainId> domains = genome.getAllDomainIds();
-        for( final DomainId domain : domains ) {
+                                             final SortedSet<String> domain_ids ) {
+        final SortedSet<String> domains = genome.getAllDomainIds();
+        for( final String domain : domains ) {
             domain_ids.add( domain );
         }
     }
@@ -220,9 +219,8 @@ public final class SurfacingUtil {
         }
     }
 
-    public static Map<DomainId, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
-        final Map<DomainId, List<GoId>> domain_id_to_go_ids_map = new HashMap<DomainId, List<GoId>>( pfam_to_go_mappings
-                .size() );
+    public static Map<String, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
+        final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings.size() );
         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
@@ -232,12 +230,12 @@ public final class SurfacingUtil {
         return domain_id_to_go_ids_map;
     }
 
-    public static Map<DomainId, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
+    public static Map<String, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
             throws IOException {
         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' );
-        final Map<DomainId, Set<String>> map = new TreeMap<DomainId, Set<String>>();
+        final Map<String, Set<String>> map = new TreeMap<String, Set<String>>();
         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
-            final DomainId domain_id = new DomainId( primary_table.getValue( 0, r ) );
+            final String domain_id = primary_table.getValue( 0, r );
             if ( !map.containsKey( domain_id ) ) {
                 map.put( domain_id, new HashSet<String>() );
             }
@@ -307,7 +305,7 @@ public final class SurfacingUtil {
     }
 
     public static void doit( final List<Protein> proteins,
-                             final List<DomainId> query_domain_ids_nc_order,
+                             final List<String> query_domain_ids_nc_order,
                              final Writer out,
                              final String separator,
                              final String limit_to_species,
@@ -321,7 +319,7 @@ public final class SurfacingUtil {
                     out.write( protein.getProteinId().getId() );
                     out.write( separator );
                     out.write( "[" );
-                    final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
+                    final Set<String> visited_domain_ids = new HashSet<String>();
                     boolean first = true;
                     for( final Domain domain : protein.getProteinDomains() ) {
                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
@@ -332,7 +330,7 @@ public final class SurfacingUtil {
                             else {
                                 out.write( " " );
                             }
-                            out.write( domain.getDomainId().getId() );
+                            out.write( domain.getDomainId() );
                             out.write( " {" );
                             out.write( "" + domain.getTotalCount() );
                             out.write( "}" );
@@ -378,7 +376,7 @@ public final class SurfacingUtil {
                                                           1 + all_genomes_domains_per_potein_histo.get( domains ) );
             }
             if ( domains == 1 ) {
-                final String domain = protein.getProteinDomain( 0 ).getDomainId().getId();
+                final String domain = protein.getProteinDomain( 0 ).getDomainId();
                 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
                     if ( domains_which_never_single.contains( domain ) ) {
                         domains_which_never_single.remove( domain );
@@ -391,7 +389,7 @@ public final class SurfacingUtil {
             }
             else if ( domains > 1 ) {
                 for( final Domain d : protein.getProteinDomains() ) {
-                    final String domain = d.getDomainId().getId();
+                    final String domain = d.getDomainId();
                     // System.out.println( domain );
                     if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
                         if ( domains_which_are_always_single.contains( domain ) ) {
@@ -526,12 +524,12 @@ public final class SurfacingUtil {
                                                  final String outfile_name,
                                                  final DomainParsimonyCalculator domain_parsimony,
                                                  final Phylogeny phylogeny,
-                                                 final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+                                                 final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                  final Map<GoId, GoTerm> go_id_to_term_map,
                                                  final GoNameSpace go_namespace_limit,
                                                  final String parameters_str,
-                                                 final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
-                                                 final SortedSet<DomainId> positive_filter,
+                                                 final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
+                                                 final SortedSet<String> positive_filter,
                                                  final boolean output_binary_domain_combinations_for_graphs,
                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
@@ -856,7 +854,7 @@ public final class SurfacingUtil {
     }
 
     public static void extractProteinNames( final List<Protein> proteins,
-                                            final List<DomainId> query_domain_ids_nc_order,
+                                            final List<String> query_domain_ids_nc_order,
                                             final Writer out,
                                             final String separator,
                                             final String limit_to_species ) throws IOException {
@@ -869,7 +867,7 @@ public final class SurfacingUtil {
                     out.write( protein.getProteinId().getId() );
                     out.write( separator );
                     out.write( "[" );
-                    final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
+                    final Set<String> visited_domain_ids = new HashSet<String>();
                     boolean first = true;
                     for( final Domain domain : protein.getProteinDomains() ) {
                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
@@ -880,7 +878,7 @@ public final class SurfacingUtil {
                             else {
                                 out.write( " " );
                             }
-                            out.write( domain.getDomainId().getId() );
+                            out.write( domain.getDomainId() );
                             out.write( " {" );
                             out.write( "" + domain.getTotalCount() );
                             out.write( "}" );
@@ -905,7 +903,7 @@ public final class SurfacingUtil {
     }
 
     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
-                                            final DomainId domain_id,
+                                            final String domain_id,
                                             final Writer out,
                                             final String separator,
                                             final String limit_to_species,
@@ -980,10 +978,10 @@ public final class SurfacingUtil {
         out.flush();
     }
 
-    public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
-        final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
+    public static SortedSet<String> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
+        final SortedSet<String> all_domains_ids = new TreeSet<String>();
         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
-            final Set<DomainId> all_domains = gwcd.getAllDomainIds();
+            final Set<String> all_domains = gwcd.getAllDomainIds();
             //    for( final Domain domain : all_domains ) {
             all_domains_ids.addAll( all_domains );
             //    }
@@ -996,7 +994,7 @@ public final class SurfacingUtil {
         for( final Protein protein_domain_collection : protein_domain_collections ) {
             for( final Object name : protein_domain_collection.getProteinDomains() ) {
                 final BasicDomain protein_domain = ( BasicDomain ) name;
-                final String id = protein_domain.getDomainId().getId();
+                final String id = protein_domain.getDomainId();
                 if ( map.containsKey( id ) ) {
                     map.put( id, map.get( id ) + 1 );
                 }
@@ -1136,7 +1134,7 @@ public final class SurfacingUtil {
         if ( domains.size() > 1 ) {
             final Map<String, Integer> counts = new HashMap<String, Integer>();
             for( final Domain domain : domains ) {
-                final String id = domain.getDomainId().getId();
+                final String id = domain.getDomainId();
                 if ( counts.containsKey( id ) ) {
                     counts.put( id, counts.get( id ) + 1 );
                 }
@@ -1153,24 +1151,24 @@ public final class SurfacingUtil {
                         domain_n = domains.get( j );
                         domain_c = domains.get( i );
                     }
-                    final String dc = domain_n.getDomainId().getId() + domain_c.getDomainId().getId();
+                    final String dc = domain_n.getDomainId() + domain_c.getDomainId();
                     if ( !dcs.contains( dc ) ) {
                         dcs.add( dc );
                         sb.append( protein.getSpecies() );
                         sb.append( separator );
                         sb.append( protein_id );
                         sb.append( separator );
-                        sb.append( domain_n.getDomainId().getId() );
+                        sb.append( domain_n.getDomainId() );
                         sb.append( separator );
-                        sb.append( domain_c.getDomainId().getId() );
+                        sb.append( domain_c.getDomainId() );
                         sb.append( separator );
                         sb.append( domain_n.getPerDomainEvalue() );
                         sb.append( separator );
                         sb.append( domain_c.getPerDomainEvalue() );
                         sb.append( separator );
-                        sb.append( counts.get( domain_n.getDomainId().getId() ) );
+                        sb.append( counts.get( domain_n.getDomainId() ) );
                         sb.append( separator );
-                        sb.append( counts.get( domain_c.getDomainId().getId() ) );
+                        sb.append( counts.get( domain_c.getDomainId() ) );
                         sb.append( ForesterUtil.LINE_SEPARATOR );
                     }
                 }
@@ -1181,7 +1179,7 @@ public final class SurfacingUtil {
             sb.append( separator );
             sb.append( protein_id );
             sb.append( separator );
-            sb.append( domains.get( 0 ).getDomainId().getId() );
+            sb.append( domains.get( 0 ).getDomainId() );
             sb.append( separator );
             sb.append( separator );
             sb.append( domains.get( 0 ).getPerDomainEvalue() );
@@ -1432,7 +1430,7 @@ public final class SurfacingUtil {
         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
     }
 
-    public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+    public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                       final Map<GoId, GoTerm> go_id_to_term_map,
                                                       final GoNameSpace go_namespace_limit,
                                                       final boolean domain_combinations,
@@ -1443,7 +1441,7 @@ public final class SurfacingUtil {
                                                       final String character_separator,
                                                       final String title_for_html,
                                                       final String prefix_for_html,
-                                                      final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
+                                                      final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
                                                       final SortedSet<String> all_pfams_encountered,
                                                       final SortedSet<String> pfams_gained_or_lost,
                                                       final String suffix_for_per_node_events_file,
@@ -1648,9 +1646,9 @@ public final class SurfacingUtil {
             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
-            final SortedSet<DomainId> mpds = gwcd.getMostPromiscuosDomain();
-            for( final DomainId mpd : mpds ) {
-                per_genome_domain_promiscuity_statistics_writer.write( mpd.getId() + " " );
+            final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
+            for( final String mpd : mpds ) {
+                per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
             }
             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
         }
@@ -1872,18 +1870,20 @@ public final class SurfacingUtil {
             }
             if ( single_writer != null ) {
                 single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
+                single_writer.write( SurfacingConstants.NL );
             }
             else {
-                Writer local_writer = split_writers.get( ( similarity.getDomainId().getId().charAt( 0 ) + "" )
-                        .toLowerCase().charAt( 0 ) );
+                Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
+                        .charAt( 0 ) );
                 if ( local_writer == null ) {
                     local_writer = split_writers.get( '0' );
                 }
                 local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
+                local_writer.write( SurfacingConstants.NL );
             }
-            for( final Writer w : split_writers.values() ) {
-                w.write( SurfacingConstants.NL );
-            }
+            // for( final Writer w : split_writers.values() ) {
+            //w.write( SurfacingConstants.NL );
+            // }
         }
         switch ( print_option ) {
             case HTML:
@@ -2370,9 +2370,9 @@ public final class SurfacingUtil {
     }
 
     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
-        final SortedMap<DomainId, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
+        final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
-        for( final DomainId domain_id : cds.keySet() ) {
+        for( final String domain_id : cds.keySet() ) {
             final CombinableDomains cd = cds.get( domain_id );
             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
         }
@@ -2392,7 +2392,7 @@ public final class SurfacingUtil {
         return l;
     }
 
-    private static void writeAllEncounteredPfamsToFile( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+    private static void writeAllEncounteredPfamsToFile( final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                         final Map<GoId, GoTerm> go_id_to_term_map,
                                                         final String outfile_name,
                                                         final SortedSet<String> all_pfams_encountered ) {
@@ -2420,7 +2420,7 @@ public final class SurfacingUtil {
             for( final String pfam : all_pfams_encountered ) {
                 all_pfams_encountered_writer.write( pfam );
                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
-                final DomainId domain_id = new DomainId( pfam );
+                final String domain_id = new String( pfam );
                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
                     ++pfams_with_mappings_counter;
                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
@@ -2530,7 +2530,7 @@ public final class SurfacingUtil {
         }
     }
 
-    private static void writeDomainData( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+    private static void writeDomainData( final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                          final Map<GoId, GoTerm> go_id_to_term_map,
                                          final GoNameSpace go_namespace_limit,
                                          final Writer out,
@@ -2538,7 +2538,7 @@ public final class SurfacingUtil {
                                          final String domain_1,
                                          final String prefix_for_html,
                                          final String character_separator_for_non_html_output,
-                                         final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
+                                         final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
                                          final Set<GoId> all_go_ids ) throws IOException {
         boolean any_go_annotation_present = false;
         boolean first_has_no_go = false;
@@ -2551,22 +2551,20 @@ public final class SurfacingUtil {
             List<GoId> go_ids = null;
             boolean go_annotation_present = false;
             if ( d == 0 ) {
-                final DomainId domain_id = new DomainId( domain_0 );
-                if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
+                if ( domain_id_to_go_ids_map.containsKey( domain_0 ) ) {
                     go_annotation_present = true;
                     any_go_annotation_present = true;
-                    go_ids = domain_id_to_go_ids_map.get( domain_id );
+                    go_ids = domain_id_to_go_ids_map.get( domain_0 );
                 }
                 else {
                     first_has_no_go = true;
                 }
             }
             else {
-                final DomainId domain_id = new DomainId( domain_1 );
-                if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
+                if ( domain_id_to_go_ids_map.containsKey( domain_1 ) ) {
                     go_annotation_present = true;
                     any_go_annotation_present = true;
-                    go_ids = domain_id_to_go_ids_map.get( domain_id );
+                    go_ids = domain_id_to_go_ids_map.get( domain_1 );
                 }
             }
             if ( go_annotation_present ) {
@@ -2639,7 +2637,7 @@ public final class SurfacingUtil {
                                               final String domain_0,
                                               final String domain_1,
                                               final String prefix_for_detailed_html,
-                                              final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
+                                              final Map<String, Set<String>>[] domain_id_to_secondary_features_maps )
             throws IOException {
         out.write( "<td>" );
         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java
index 3efaccb..4ab0fb0 100644
--- a/forester/java/src/org/forester/surfacing/TestSurfacing.java
+++ b/forester/java/src/org/forester/surfacing/TestSurfacing.java
@@ -53,7 +53,6 @@ import org.forester.protein.BasicProtein;
 import org.forester.protein.BinaryDomainCombination;
 import org.forester.protein.BinaryDomainCombination.DomainCombinationType;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.protein.ProteinId;
 import org.forester.species.BasicSpecies;
@@ -336,7 +335,7 @@ public class TestSurfacing {
                                             true );
             final Iterator<DomainSimilarity> sims_it = sims.iterator();
             final DomainSimilarity sa = sims_it.next();
-            if ( !sa.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa.getDomainId().equals( "A" ) ) {
                 return false;
             }
             if ( sa.getSpeciesData().size() != 4 ) {
@@ -377,7 +376,7 @@ public class TestSurfacing {
                 return false;
             }
             final DomainSimilarity sb = sims_it.next();
-            if ( !sb.getDomainId().getId().equals( "B" ) ) {
+            if ( !sb.getDomainId().equals( "B" ) ) {
                 return false;
             }
             if ( sb.getSpeciesData().size() != 2 ) {
@@ -411,7 +410,7 @@ public class TestSurfacing {
                 return false;
             }
             final DomainSimilarity sc = sims_it.next();
-            if ( !sc.getDomainId().getId().equals( "C" ) ) {
+            if ( !sc.getDomainId().equals( "C" ) ) {
                 return false;
             }
             if ( sc.getSpeciesData().size() != 3 ) {
@@ -486,7 +485,7 @@ public class TestSurfacing {
                                             true );
             final Iterator<DomainSimilarity> sims_it2 = sims2.iterator();
             final DomainSimilarity sa2 = sims_it2.next();
-            if ( !sa2.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa2.getDomainId().equals( "A" ) ) {
                 return false;
             }
             if ( sa2.getSpeciesData().size() != 4 ) {
@@ -573,23 +572,23 @@ public class TestSurfacing {
                                             true );
             final Iterator<DomainSimilarity> sims_it3 = sims3.iterator();
             final DomainSimilarity sa3 = sims_it3.next();
-            if ( !sa3.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa3.getDomainId().equals( "A" ) ) {
                 return false;
             }
             final SpeciesSpecificDomainSimilariyData ssdsd = sa3.getSpeciesData().get( new BasicSpecies( "ciona" ) );
             if ( ssdsd.getCombinableDomainIdToCountsMap().size() != 4 ) {
                 return false;
             }
-            if ( ssdsd.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "B" ) ) != 2 ) {
+            if ( ssdsd.getNumberOfProteinsExhibitingCombinationWith( "B" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "F" ) ) != 2 ) {
+            if ( ssdsd.getNumberOfProteinsExhibitingCombinationWith( "F" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "G" ) ) != 2 ) {
+            if ( ssdsd.getNumberOfProteinsExhibitingCombinationWith( "G" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "X" ) ) != 3 ) {
+            if ( ssdsd.getNumberOfProteinsExhibitingCombinationWith( "X" ) != 3 ) {
                 return false;
             }
             final List<GenomeWideCombinableDomains> cdc_list4 = new ArrayList<GenomeWideCombinableDomains>();
@@ -616,33 +615,33 @@ public class TestSurfacing {
                                             true );
             final Iterator<DomainSimilarity> sims_it4 = sims4.iterator();
             final DomainSimilarity sa4 = sims_it4.next();
-            if ( !sa4.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa4.getDomainId().equals( "A" ) ) {
                 return false;
             }
             final SpeciesSpecificDomainSimilariyData ssdsd4 = sa4.getSpeciesData().get( new BasicSpecies( "ciona" ) );
             if ( ssdsd4.getCombinableDomainIdToCountsMap().size() != 5 ) {
                 return false;
             }
-            if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "A" ) ) != 3 ) {
+            if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( "A" ) != 3 ) {
                 return false;
             }
-            if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "B" ) ) != 2 ) {
+            if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( "B" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "F" ) ) != 2 ) {
+            if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( "F" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "G" ) ) != 2 ) {
+            if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( "G" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "X" ) ) != 3 ) {
+            if ( ssdsd4.getNumberOfProteinsExhibitingCombinationWith( "X" ) != 3 ) {
                 return false;
             }
             final SortedSet<DomainSimilarity> sims4_d = calc4
                     .calculateSimilarities( new DomainCountsBasedPairwiseSimilarityCalculator(), cdc_list4, false, true );
             final Iterator<DomainSimilarity> sims_it4_d = sims4_d.iterator();
             final DomainSimilarity sa4_d = sims_it4_d.next();
-            if ( !sa4_d.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa4_d.getDomainId().equals( "A" ) ) {
                 return false;
             }
             if ( sa4_d.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).size() != 5 ) {
@@ -669,25 +668,25 @@ public class TestSurfacing {
                                             true );
             final Iterator<DomainSimilarity> sims_it4_p = sims4_p.iterator();
             final DomainSimilarity sa4_p = sims_it4_p.next();
-            if ( !sa4_p.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa4_p.getDomainId().equals( "A" ) ) {
                 return false;
             }
             if ( sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).size() != 5 ) {
                 return false;
             }
-            if ( !sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).contains( new DomainId( "A" ) ) ) {
+            if ( !sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).contains( "A" ) ) {
                 return false;
             }
-            if ( !sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).contains( new DomainId( "B" ) ) ) {
+            if ( !sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).contains( "B" ) ) {
                 return false;
             }
-            if ( !sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).contains( new DomainId( "F" ) ) ) {
+            if ( !sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).contains( "F" ) ) {
                 return false;
             }
-            if ( !sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).contains( new DomainId( "G" ) ) ) {
+            if ( !sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).contains( "G" ) ) {
                 return false;
             }
-            if ( !sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).contains( new DomainId( "X" ) ) ) {
+            if ( !sa4_p.getCombinableDomainIds( new BasicSpecies( "ciona" ) ).contains( "X" ) ) {
                 return false;
             }
             if ( !TestSurfacing
@@ -731,38 +730,38 @@ public class TestSurfacing {
             if ( ssdsd5.getCombinableDomainIdToCountsMap().size() != 4 ) {
                 return false;
             }
-            if ( ssdsd5.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "B" ) ) != 2 ) {
+            if ( ssdsd5.getNumberOfProteinsExhibitingCombinationWith( "B" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd5.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "F" ) ) != 2 ) {
+            if ( ssdsd5.getNumberOfProteinsExhibitingCombinationWith( "F" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd5.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "G" ) ) != 2 ) {
+            if ( ssdsd5.getNumberOfProteinsExhibitingCombinationWith( "G" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd5.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "X" ) ) != 3 ) {
+            if ( ssdsd5.getNumberOfProteinsExhibitingCombinationWith( "X" ) != 3 ) {
                 return false;
             }
-            if ( !sa5_d.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa5_d.getDomainId().equals( "A" ) ) {
                 return false;
             }
             final Species ciona = new BasicSpecies( "ciona" );
             if ( sa5_d.getCombinableDomainIds( ciona ).size() != 4 ) {
                 return false;
             }
-            if ( sa5_d.getCombinableDomainIds( ciona ).contains( new DomainId( "A" ) ) ) {
+            if ( sa5_d.getCombinableDomainIds( ciona ).contains( "A" ) ) {
                 return false;
             }
-            if ( !sa5_d.getCombinableDomainIds( ciona ).contains( new DomainId( "B" ) ) ) {
+            if ( !sa5_d.getCombinableDomainIds( ciona ).contains( "B" ) ) {
                 return false;
             }
-            if ( !sa5_d.getCombinableDomainIds( ciona ).contains( new DomainId( "F" ) ) ) {
+            if ( !sa5_d.getCombinableDomainIds( ciona ).contains( "F" ) ) {
                 return false;
             }
-            if ( !sa5_d.getCombinableDomainIds( ciona ).contains( new DomainId( "G" ) ) ) {
+            if ( !sa5_d.getCombinableDomainIds( ciona ).contains( "G" ) ) {
                 return false;
             }
-            if ( !sa5_d.getCombinableDomainIds( ciona ).contains( new DomainId( "X" ) ) ) {
+            if ( !sa5_d.getCombinableDomainIds( ciona ).contains( "X" ) ) {
                 return false;
             }
             if ( !TestSurfacing
@@ -795,25 +794,25 @@ public class TestSurfacing {
                                             true );
             final Iterator<DomainSimilarity> sims_it5_p = sims5_p.iterator();
             final DomainSimilarity sa5_p = sims_it5_p.next();
-            if ( !sa5_p.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa5_p.getDomainId().equals( "A" ) ) {
                 return false;
             }
             if ( sa5_p.getCombinableDomainIds( ciona ).size() != 4 ) {
                 return false;
             }
-            if ( sa5_p.getCombinableDomainIds( ciona ).contains( new DomainId( "A" ) ) ) {
+            if ( sa5_p.getCombinableDomainIds( ciona ).contains( "A" ) ) {
                 return false;
             }
-            if ( !sa5_p.getCombinableDomainIds( ciona ).contains( new DomainId( "B" ) ) ) {
+            if ( !sa5_p.getCombinableDomainIds( ciona ).contains( "B" ) ) {
                 return false;
             }
-            if ( !sa5_p.getCombinableDomainIds( ciona ).contains( new DomainId( "F" ) ) ) {
+            if ( !sa5_p.getCombinableDomainIds( ciona ).contains( "F" ) ) {
                 return false;
             }
-            if ( !sa5_p.getCombinableDomainIds( ciona ).contains( new DomainId( "G" ) ) ) {
+            if ( !sa5_p.getCombinableDomainIds( ciona ).contains( "G" ) ) {
                 return false;
             }
-            if ( !sa5_p.getCombinableDomainIds( ciona ).contains( new DomainId( "X" ) ) ) {
+            if ( !sa5_p.getCombinableDomainIds( ciona ).contains( "X" ) ) {
                 return false;
             }
             if ( !TestSurfacing
@@ -866,38 +865,38 @@ public class TestSurfacing {
             if ( ssdsd6.getCombinableDomainIdToCountsMap().size() != 5 ) {
                 return false;
             }
-            if ( ssdsd6.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "B" ) ) != 2 ) {
+            if ( ssdsd6.getNumberOfProteinsExhibitingCombinationWith( "B" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd6.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "F" ) ) != 2 ) {
+            if ( ssdsd6.getNumberOfProteinsExhibitingCombinationWith( "F" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd6.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "G" ) ) != 2 ) {
+            if ( ssdsd6.getNumberOfProteinsExhibitingCombinationWith( "G" ) != 2 ) {
                 return false;
             }
-            if ( ssdsd6.getNumberOfProteinsExhibitingCombinationWith( new DomainId( "X" ) ) != 3 ) {
+            if ( ssdsd6.getNumberOfProteinsExhibitingCombinationWith( "X" ) != 3 ) {
                 return false;
             }
-            if ( !sa5_d.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa5_d.getDomainId().equals( "A" ) ) {
                 return false;
             }
             final Species ciona6 = new BasicSpecies( "ciona" );
             if ( sa6_d.getCombinableDomainIds( ciona6 ).size() != 5 ) {
                 return false;
             }
-            if ( !sa6_d.getCombinableDomainIds( ciona6 ).contains( new DomainId( "A" ) ) ) {
+            if ( !sa6_d.getCombinableDomainIds( ciona6 ).contains( "A" ) ) {
                 return false;
             }
-            if ( !sa6_d.getCombinableDomainIds( ciona6 ).contains( new DomainId( "B" ) ) ) {
+            if ( !sa6_d.getCombinableDomainIds( ciona6 ).contains( "B" ) ) {
                 return false;
             }
-            if ( !sa6_d.getCombinableDomainIds( ciona6 ).contains( new DomainId( "F" ) ) ) {
+            if ( !sa6_d.getCombinableDomainIds( ciona6 ).contains( "F" ) ) {
                 return false;
             }
-            if ( !sa6_d.getCombinableDomainIds( ciona6 ).contains( new DomainId( "G" ) ) ) {
+            if ( !sa6_d.getCombinableDomainIds( ciona6 ).contains( "G" ) ) {
                 return false;
             }
-            if ( !sa6_d.getCombinableDomainIds( ciona6 ).contains( new DomainId( "X" ) ) ) {
+            if ( !sa6_d.getCombinableDomainIds( ciona6 ).contains( "X" ) ) {
                 return false;
             }
             if ( !TestSurfacing
@@ -930,25 +929,25 @@ public class TestSurfacing {
                                             true );
             final Iterator<DomainSimilarity> sims_it6_p = sims6_p.iterator();
             final DomainSimilarity sa6_p = sims_it6_p.next();
-            if ( !sa6_p.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa6_p.getDomainId().equals( "A" ) ) {
                 return false;
             }
             if ( sa6_p.getCombinableDomainIds( ciona ).size() != 5 ) {
                 return false;
             }
-            if ( !sa6_p.getCombinableDomainIds( ciona ).contains( new DomainId( "A" ) ) ) {
+            if ( !sa6_p.getCombinableDomainIds( ciona ).contains( "A" ) ) {
                 return false;
             }
-            if ( !sa6_p.getCombinableDomainIds( ciona ).contains( new DomainId( "B" ) ) ) {
+            if ( !sa6_p.getCombinableDomainIds( ciona ).contains( "B" ) ) {
                 return false;
             }
-            if ( !sa6_p.getCombinableDomainIds( ciona ).contains( new DomainId( "F" ) ) ) {
+            if ( !sa6_p.getCombinableDomainIds( ciona ).contains( "F" ) ) {
                 return false;
             }
-            if ( !sa6_p.getCombinableDomainIds( ciona ).contains( new DomainId( "G" ) ) ) {
+            if ( !sa6_p.getCombinableDomainIds( ciona ).contains( "G" ) ) {
                 return false;
             }
-            if ( !sa6_p.getCombinableDomainIds( ciona ).contains( new DomainId( "X" ) ) ) {
+            if ( !sa6_p.getCombinableDomainIds( ciona ).contains( "X" ) ) {
                 return false;
             }
             if ( !TestSurfacing
@@ -1047,7 +1046,7 @@ public class TestSurfacing {
                                             false );
             final Iterator<DomainSimilarity> sims_it = sims.iterator();
             final DomainSimilarity sa = sims_it.next();
-            if ( !sa.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa.getDomainId().equals( "A" ) ) {
                 return false;
             }
             if ( sa.getSpeciesData().size() != 1 ) {
@@ -1078,7 +1077,7 @@ public class TestSurfacing {
                 return false;
             }
             final DomainSimilarity sb = sims_it.next();
-            if ( !sb.getDomainId().getId().equals( "B" ) ) {
+            if ( !sb.getDomainId().equals( "B" ) ) {
                 return false;
             }
             if ( sb.getSpeciesData().size() != 1 ) {
@@ -1094,7 +1093,7 @@ public class TestSurfacing {
                                             true );
             final Iterator<DomainSimilarity> sims_it2 = sims2.iterator();
             final DomainSimilarity sa2 = sims_it2.next();
-            if ( !sa2.getDomainId().getId().equals( "D" ) ) {
+            if ( !sa2.getDomainId().equals( "D" ) ) {
                 return false;
             }
             if ( sa2.getSpeciesData().size() != 2 ) {
@@ -1158,7 +1157,7 @@ public class TestSurfacing {
             }
             final Iterator<DomainSimilarity> sims_it = sims.iterator();
             final DomainSimilarity sa = sims_it.next();
-            if ( !sa.getDomainId().getId().equals( "A" ) ) {
+            if ( !sa.getDomainId().equals( "A" ) ) {
                 return false;
             }
             if ( sa.getSpeciesData().size() != 4 ) {
@@ -1277,17 +1276,18 @@ public class TestSurfacing {
             final SortedSet<BasicBinaryDomainCombination> sorted = new TreeSet<BasicBinaryDomainCombination>();
             sorted.add( s0 );
             sorted.add( s1 );
-            sorted.add( s2 );
+            sorted.add( s2 );//
             sorted.add( s3 );
-            sorted.add( s3 );
-            sorted.add( s3 );
-            sorted.add( s4 );
+            sorted.add( s3 );//
+            sorted.add( s3 );//
+            sorted.add( s4 );//
             sorted.add( s5 );
             sorted.add( s6 );
             sorted.add( s7 );
-            sorted.add( s7 );
+            sorted.add( s7 );//
             sorted.add( s8 );
-            if ( sorted.size() != 6 ) {
+            if ( sorted.size() != 7 ) {
+                System.out.println( sorted.size() );
                 return false;
             }
             final DirectedBinaryDomainCombination aa = new DirectedBinaryDomainCombination( "a", "a" );
@@ -2751,7 +2751,7 @@ public class TestSurfacing {
             if ( !calc_i.getSharedDomains().contains( f.getDomainId() ) ) {
                 return false;
             }
-            final Set<DomainId> all = calc_ni.getAllDomains();
+            final Set<String> all = calc_ni.getAllDomains();
             if ( !all.contains( a.getDomainId() ) ) {
                 return false;
             }
@@ -3226,8 +3226,8 @@ public class TestSurfacing {
             }
             calc_u.setAllowDomainsToBeIgnored( true );
             calc_u.addDomainIdToIgnore( u.getDomainId() );
-            calc_u.addDomainIdToIgnore( new DomainId( "other" ) );
-            calc_u.addDomainIdToIgnore( new DomainId( "other_too" ) );
+            calc_u.addDomainIdToIgnore( "other" );
+            calc_u.addDomainIdToIgnore( "other_too" );
             if ( calc_u.getAllDomains().size() != 5 ) {
                 return false;
             }
@@ -3331,10 +3331,10 @@ public class TestSurfacing {
             //------------
             calc_u.setAllowDomainsToBeIgnored( true );
             calc_u.deleteAllDomainIdsToIgnore();
-            calc_u.addDomainIdToIgnore( new DomainId( "v" ) );
-            calc_u.addDomainIdToIgnore( new DomainId( "w" ) );
-            calc_u.addDomainIdToIgnore( new DomainId( "other" ) );
-            calc_u.addDomainIdToIgnore( new DomainId( "other_too" ) );
+            calc_u.addDomainIdToIgnore( "v" );
+            calc_u.addDomainIdToIgnore( "w" );
+            calc_u.addDomainIdToIgnore( "other" );
+            calc_u.addDomainIdToIgnore( "other_too" );
             if ( calc_u.getAllDomains().size() != 4 ) {
                 return false;
             }
@@ -3453,7 +3453,7 @@ public class TestSurfacing {
             final List<Protein> domain_collections = parser.parse();
             final BasicGenomeWideCombinableDomains cdcc = BasicGenomeWideCombinableDomains
                     .createInstance( domain_collections, false, new BasicSpecies( "human" ) );
-            CombinableDomains cd = cdcc.get( new DomainId( "A" ) );
+            CombinableDomains cd = cdcc.get( "A" );
             if ( cd.getKeyDomainCount() != 9 ) {
                 return false;
             }
@@ -3502,7 +3502,7 @@ public class TestSurfacing {
             if ( cd.getKeyDomainCount() != 9 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "B" ) );
+            cd = cdcc.get( "B" );
             if ( cd.getKeyDomainCount() != 12 ) {
                 return false;
             }
@@ -3551,7 +3551,7 @@ public class TestSurfacing {
             if ( cd.getKeyDomainCount() != 12 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "C" ) );
+            cd = cdcc.get( "C" );
             if ( cd.getKeyDomainCount() != 10 ) {
                 return false;
             }
@@ -3597,7 +3597,7 @@ public class TestSurfacing {
             if ( cd.getNumberOfProteinsExhibitingCombination( new SimpleDomain( "NN" ).getDomainId() ) != 0 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "D" ) );
+            cd = cdcc.get( "D" );
             if ( cd.getKeyDomainCount() != 15 ) {
                 return false;
             }
@@ -3607,7 +3607,7 @@ public class TestSurfacing {
             if ( cd.getNumberOfCombinableDomains() != 11 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "E" ) );
+            cd = cdcc.get( "E" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
@@ -3617,7 +3617,7 @@ public class TestSurfacing {
             if ( cd.getKeyDomainProteinsCount() != 1 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "U" ) );
+            cd = cdcc.get( "U" );
             if ( cd.getNumberOfCombinableDomains() != 11 ) {
                 return false;
             }
@@ -3627,7 +3627,7 @@ public class TestSurfacing {
             if ( cd.getKeyDomainProteinsCount() != 3 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "V" ) );
+            cd = cdcc.get( "V" );
             if ( cd.getNumberOfCombinableDomains() != 11 ) {
                 return false;
             }
@@ -3637,7 +3637,7 @@ public class TestSurfacing {
             if ( cd.getKeyDomainProteinsCount() != 2 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "W" ) );
+            cd = cdcc.get( "W" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
@@ -3647,22 +3647,22 @@ public class TestSurfacing {
             if ( cd.getKeyDomainProteinsCount() != 2 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "X" ) );
+            cd = cdcc.get( "X" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
             if ( cd.getKeyDomainCount() != 2 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "Y" ) );
+            cd = cdcc.get( "Y" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "Z" ) );
+            cd = cdcc.get( "Z" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "NN" ) );
+            cd = cdcc.get( "NN" );
             if ( cd.getKeyDomainCount() != 1 ) {
                 return false;
             }
@@ -3675,7 +3675,7 @@ public class TestSurfacing {
             if ( cd.getNumberOfProteinsExhibitingCombination( new SimpleDomain( "NN" ).getDomainId() ) != 0 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "MM" ) );
+            cd = cdcc.get( "MM" );
             if ( cd.getNumberOfCombinableDomains() != 1 ) {
                 return false;
             }
@@ -3685,7 +3685,7 @@ public class TestSurfacing {
             if ( cd.getNumberOfProteinsExhibitingCombination( new SimpleDomain( "OO" ).getDomainId() ) != 1 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "OO" ) );
+            cd = cdcc.get( "OO" );
             if ( cd.getNumberOfCombinableDomains() != 2 ) {
                 return false;
             }
@@ -3695,7 +3695,7 @@ public class TestSurfacing {
             if ( cd.getNumberOfProteinsExhibitingCombination( new SimpleDomain( "MM" ).getDomainId() ) != 1 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "QQ" ) );
+            cd = cdcc.get( "QQ" );
             if ( cd.getNumberOfCombinableDomains() != 1 ) {
                 return false;
             }
@@ -3708,7 +3708,7 @@ public class TestSurfacing {
             if ( cd.getNumberOfProteinsExhibitingCombination( new SimpleDomain( "QQ" ).getDomainId() ) != 3 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "PP" ) );
+            cd = cdcc.get( "PP" );
             if ( cd.getNumberOfCombinableDomains() != 0 ) {
                 return false;
             }
@@ -3718,7 +3718,7 @@ public class TestSurfacing {
             if ( cd.getKeyDomainProteinsCount() != 2 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "singlet" ) );
+            cd = cdcc.get( "singlet" );
             if ( cd.getKeyDomainCount() != 1 ) {
                 return false;
             }
@@ -3731,7 +3731,7 @@ public class TestSurfacing {
             if ( cd.getNumberOfProteinsExhibitingCombination( new SimpleDomain( "singlet" ).getDomainId() ) != 0 ) {
                 return false;
             }
-            cd = cdcc.get( new DomainId( "three" ) );
+            cd = cdcc.get( "three" );
             if ( cd.getKeyDomainCount() != 3 ) {
                 return false;
             }
@@ -3741,10 +3741,10 @@ public class TestSurfacing {
             if ( cd.getNumberOfCombinableDomains() != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "three" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "three" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "so_far_so_bad" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "so_far_so_bad" ) != 0 ) {
                 return false;
             }
             // Ignore combinations with same:
@@ -3756,7 +3756,7 @@ public class TestSurfacing {
                                      DomainCombinationType.BASIC,
                                      null,
                                      null );
-            cd = cdcc2.get( new DomainId( "A" ) );
+            cd = cdcc2.get( "A" );
             if ( cd.getKeyDomainCount() != 9 ) {
                 return false;
             }
@@ -3781,28 +3781,28 @@ public class TestSurfacing {
             if ( cd.getNumberOfProteinsExhibitingCombination( new SimpleDomain( "E" ).getDomainId() ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "U" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "U" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "V" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "V" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "W" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "W" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "X" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "X" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "Y" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "Y" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "Z" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "Z" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "NN" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "NN" ) != 0 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "B" ) );
+            cd = cdcc2.get( "B" );
             if ( cd.getKeyDomainCount() != 12 ) {
                 return false;
             }
@@ -3812,43 +3812,43 @@ public class TestSurfacing {
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "A" ) ) != 6 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "A" ) != 6 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "B" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "B" ) != 0 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "C" ) ) != 4 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "C" ) != 4 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "D" ) ) != 3 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "D" ) != 3 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "E" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "E" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "U" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "U" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "V" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "V" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "W" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "W" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "X" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "X" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "Y" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "Y" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "Z" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "Z" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "NN" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "NN" ) != 0 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "C" ) );
+            cd = cdcc2.get( "C" );
             if ( cd.getKeyDomainCount() != 10 ) {
                 return false;
             }
@@ -3858,112 +3858,112 @@ public class TestSurfacing {
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "A" ) ) != 4 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "A" ) != 4 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "B" ) ) != 4 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "B" ) != 4 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "C" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "C" ) != 0 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "D" ) ) != 3 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "D" ) != 3 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "E" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "E" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "U" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "U" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "V" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "V" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "W" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "W" ) != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "X" ) ) != 2 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "X" ) != 2 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "Y" ) ) != 2 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "Y" ) != 2 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "Z" ) ) != 2 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "Z" ) != 2 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "NN" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "NN" ) != 0 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "D" ) );
+            cd = cdcc2.get( "D" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "E" ) );
+            cd = cdcc2.get( "E" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
             if ( cd.getKeyDomainCount() != 1 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "U" ) );
+            cd = cdcc2.get( "U" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "V" ) );
+            cd = cdcc2.get( "V" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "W" ) );
+            cd = cdcc2.get( "W" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "X" ) );
+            cd = cdcc2.get( "X" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "Y" ) );
+            cd = cdcc2.get( "Y" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "Z" ) );
+            cd = cdcc2.get( "Z" );
             if ( cd.getNumberOfCombinableDomains() != 10 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "NN" ) );
+            cd = cdcc2.get( "NN" );
             if ( cd.getNumberOfCombinableDomains() != 0 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "NN" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "NN" ) != 0 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "MM" ) );
+            cd = cdcc2.get( "MM" );
             if ( cd.getNumberOfCombinableDomains() != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "MM" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "MM" ) != 0 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "OO" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "OO" ) != 1 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "OO" ) );
+            cd = cdcc2.get( "OO" );
             if ( cd.getNumberOfCombinableDomains() != 1 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "OO" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "OO" ) != 0 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "MM" ) ) != 1 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "MM" ) != 1 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "QQ" ) );
+            cd = cdcc2.get( "QQ" );
             if ( cd.getNumberOfCombinableDomains() != 0 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "QQ" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "QQ" ) != 0 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "singlet" ) );
+            cd = cdcc2.get( "singlet" );
             if ( cd.getKeyDomainCount() != 1 ) {
                 return false;
             }
@@ -3973,10 +3973,10 @@ public class TestSurfacing {
             if ( cd.getNumberOfCombinableDomains() != 0 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "singlet" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "singlet" ) != 0 ) {
                 return false;
             }
-            cd = cdcc2.get( new DomainId( "three" ) );
+            cd = cdcc2.get( "three" );
             if ( cd.getKeyDomainCount() != 3 ) {
                 return false;
             }
@@ -3986,10 +3986,10 @@ public class TestSurfacing {
             if ( cd.getNumberOfCombinableDomains() != 0 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "three" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "three" ) != 0 ) {
                 return false;
             }
-            if ( cd.getNumberOfProteinsExhibitingCombination( new DomainId( "so_far_so_bad" ) ) != 0 ) {
+            if ( cd.getNumberOfProteinsExhibitingCombination( "so_far_so_bad" ) != 0 ) {
                 return false;
             }
         }
@@ -4045,73 +4045,73 @@ public class TestSurfacing {
             if ( sorted.size() != 17 ) {
                 return false;
             }
-            if ( !sorted.get( 0 ).getDomainId().getId().equals( "A" ) ) {
+            if ( !sorted.get( 0 ).getDomainId().equals( "A" ) ) {
                 return false;
             }
             if ( sorted.get( 0 ).getNumber() != 1 ) {
                 return false;
             }
-            if ( !sorted.get( 1 ).getDomainId().getId().equals( "B" ) ) {
+            if ( !sorted.get( 1 ).getDomainId().equals( "B" ) ) {
                 return false;
             }
             if ( sorted.get( 1 ).getNumber() != 1 ) {
                 return false;
             }
-            if ( !sorted.get( 2 ).getDomainId().getId().equals( "C" ) ) {
+            if ( !sorted.get( 2 ).getDomainId().equals( "C" ) ) {
                 return false;
             }
             if ( sorted.get( 2 ).getNumber() != 1 ) {
                 return false;
             }
-            if ( !sorted.get( 3 ).getDomainId().getId().equals( "D" ) ) {
+            if ( !sorted.get( 3 ).getDomainId().equals( "D" ) ) {
                 return false;
             }
             if ( sorted.get( 3 ).getNumber() != 1 ) {
                 return false;
             }
-            if ( !sorted.get( 4 ).getDomainId().getId().equals( "E" ) ) {
+            if ( !sorted.get( 4 ).getDomainId().equals( "E" ) ) {
                 return false;
             }
             if ( sorted.get( 4 ).getNumber() != 1 ) {
                 return false;
             }
-            if ( !sorted.get( 5 ).getDomainId().getId().equals( "F" ) ) {
+            if ( !sorted.get( 5 ).getDomainId().equals( "F" ) ) {
                 return false;
             }
             if ( sorted.get( 5 ).getNumber() != 1 ) {
                 return false;
             }
-            if ( !sorted.get( 6 ).getDomainId().getId().equals( "G" ) ) {
+            if ( !sorted.get( 6 ).getDomainId().equals( "G" ) ) {
                 return false;
             }
             if ( sorted.get( 6 ).getNumber() != 1 ) {
                 return false;
             }
-            if ( !sorted.get( 7 ).getDomainId().getId().equals( "H" ) ) {
+            if ( !sorted.get( 7 ).getDomainId().equals( "H" ) ) {
                 return false;
             }
             if ( sorted.get( 7 ).getNumber() != 5 ) {
                 return false;
             }
-            if ( !sorted.get( 8 ).getDomainId().getId().equals( "H" ) ) {
+            if ( !sorted.get( 8 ).getDomainId().equals( "H" ) ) {
                 return false;
             }
             if ( sorted.get( 8 ).getNumber() != 2 ) {
                 return false;
             }
-            if ( !sorted.get( 9 ).getDomainId().getId().equals( "H" ) ) {
+            if ( !sorted.get( 9 ).getDomainId().equals( "H" ) ) {
                 return false;
             }
             if ( sorted.get( 9 ).getNumber() != 6 ) {
                 return false;
             }
-            if ( !sorted.get( 10 ).getDomainId().getId().equals( "H" ) ) {
+            if ( !sorted.get( 10 ).getDomainId().equals( "H" ) ) {
                 return false;
             }
             if ( sorted.get( 10 ).getNumber() != 4 ) {
                 return false;
             }
-            if ( !sorted.get( 11 ).getDomainId().getId().equals( "H" ) ) {
+            if ( !sorted.get( 11 ).getDomainId().equals( "H" ) ) {
                 return false;
             }
             if ( sorted.get( 11 ).getNumber() != 1 ) {
@@ -4120,25 +4120,25 @@ public class TestSurfacing {
             if ( sorted.get( 11 ).getTotalCount() != 5 ) {
                 return false;
             }
-            if ( !sorted.get( 12 ).getDomainId().getId().equals( "H" ) ) {
+            if ( !sorted.get( 12 ).getDomainId().equals( "H" ) ) {
                 return false;
             }
             if ( sorted.get( 12 ).getNumber() != 3 ) {
                 return false;
             }
-            if ( !sorted.get( 13 ).getDomainId().getId().equals( "H7" ) ) {
+            if ( !sorted.get( 13 ).getDomainId().equals( "H7" ) ) {
                 return false;
             }
             if ( sorted.get( 13 ).getNumber() != 5 ) {
                 return false;
             }
-            if ( !sorted.get( 14 ).getDomainId().getId().equals( "H7" ) ) {
+            if ( !sorted.get( 14 ).getDomainId().equals( "H7" ) ) {
                 return false;
             }
             if ( sorted.get( 14 ).getNumber() != 5 ) {
                 return false;
             }
-            if ( !sorted.get( 15 ).getDomainId().getId().equals( "H7" ) ) {
+            if ( !sorted.get( 15 ).getDomainId().equals( "H7" ) ) {
                 return false;
             }
             if ( sorted.get( 15 ).getNumber() != 5 ) {
@@ -4146,7 +4146,7 @@ public class TestSurfacing {
             }
             // To check if sorting is stable [as claimed by Sun for
             // Collections.sort( List )]
-            if ( !sorted.get( 16 ).getDomainId().getId().equals( "H7" ) ) {
+            if ( !sorted.get( 16 ).getDomainId().equals( "H7" ) ) {
                 return false;
             }
             if ( sorted.get( 16 ).getNumber() != 5 ) {
@@ -4221,10 +4221,10 @@ public class TestSurfacing {
             if ( abc_r2.getNumberOfProteinDomains() != 2 ) {
                 return false;
             }
-            if ( !abc_r2.getProteinDomain( 0 ).getDomainId().getId().equals( "a" ) ) {
+            if ( !abc_r2.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
                 return false;
             }
-            if ( !abc_r2.getProteinDomain( 1 ).getDomainId().getId().equals( "b" ) ) {
+            if ( !abc_r2.getProteinDomain( 1 ).getDomainId().equals( "b" ) ) {
                 return false;
             }
             final Domain d = new BasicDomain( "d", 0, 10, ( short ) 1, ( short ) 1, 0.1, 1 );
@@ -4245,13 +4245,13 @@ public class TestSurfacing {
             if ( def_r2.getNumberOfProteinDomains() != 3 ) {
                 return false;
             }
-            if ( !def_r2.getProteinDomain( 0 ).getDomainId().getId().equals( "d" ) ) {
+            if ( !def_r2.getProteinDomain( 0 ).getDomainId().equals( "d" ) ) {
                 return false;
             }
-            if ( !def_r2.getProteinDomain( 1 ).getDomainId().getId().equals( "f" ) ) {
+            if ( !def_r2.getProteinDomain( 1 ).getDomainId().equals( "f" ) ) {
                 return false;
             }
-            if ( !def_r2.getProteinDomain( 2 ).getDomainId().getId().equals( "e" ) ) {
+            if ( !def_r2.getProteinDomain( 2 ).getDomainId().equals( "e" ) ) {
                 return false;
             }
         }
@@ -4311,58 +4311,58 @@ public class TestSurfacing {
                     .createInstance( protein_list_eel, false, new BasicSpecies( "eel" ) );
             final BasicGenomeWideCombinableDomains eel_ignore = BasicGenomeWideCombinableDomains
                     .createInstance( protein_list_eel, true, new BasicSpecies( "eel" ) );
-            if ( !eel_not_ignore.contains( new DomainId( "a" ) ) ) {
+            if ( !eel_not_ignore.contains( "a" ) ) {
                 return false;
             }
-            if ( !eel_not_ignore.contains( new DomainId( "b" ) ) ) {
+            if ( !eel_not_ignore.contains( "b" ) ) {
                 return false;
             }
-            if ( !eel_not_ignore.contains( new DomainId( "c" ) ) ) {
+            if ( !eel_not_ignore.contains( "c" ) ) {
                 return false;
             }
-            if ( !eel_not_ignore.contains( new DomainId( "d" ) ) ) {
+            if ( !eel_not_ignore.contains( "d" ) ) {
                 return false;
             }
-            if ( !eel_not_ignore.contains( new DomainId( "e" ) ) ) {
+            if ( !eel_not_ignore.contains( "e" ) ) {
                 return false;
             }
-            if ( !eel_not_ignore.contains( new DomainId( "f" ) ) ) {
+            if ( !eel_not_ignore.contains( "f" ) ) {
                 return false;
             }
-            if ( !eel_not_ignore.contains( new DomainId( "g" ) ) ) {
+            if ( !eel_not_ignore.contains( "g" ) ) {
                 return false;
             }
-            if ( !eel_not_ignore.contains( new DomainId( "h" ) ) ) {
+            if ( !eel_not_ignore.contains( "h" ) ) {
                 return false;
             }
-            if ( eel_not_ignore.contains( new DomainId( "x" ) ) ) {
+            if ( eel_not_ignore.contains( "x" ) ) {
                 return false;
             }
-            if ( !eel_ignore.contains( new DomainId( "a" ) ) ) {
+            if ( !eel_ignore.contains( "a" ) ) {
                 return false;
             }
-            if ( !eel_ignore.contains( new DomainId( "b" ) ) ) {
+            if ( !eel_ignore.contains( "b" ) ) {
                 return false;
             }
-            if ( !eel_ignore.contains( new DomainId( "c" ) ) ) {
+            if ( !eel_ignore.contains( "c" ) ) {
                 return false;
             }
-            if ( !eel_ignore.contains( new DomainId( "d" ) ) ) {
+            if ( !eel_ignore.contains( "d" ) ) {
                 return false;
             }
-            if ( !eel_ignore.contains( new DomainId( "e" ) ) ) {
+            if ( !eel_ignore.contains( "e" ) ) {
                 return false;
             }
-            if ( !eel_ignore.contains( new DomainId( "f" ) ) ) {
+            if ( !eel_ignore.contains( "f" ) ) {
                 return false;
             }
-            if ( !eel_ignore.contains( new DomainId( "g" ) ) ) {
+            if ( !eel_ignore.contains( "g" ) ) {
                 return false;
             }
-            if ( !eel_ignore.contains( new DomainId( "h" ) ) ) {
+            if ( !eel_ignore.contains( "h" ) ) {
                 return false;
             }
-            if ( eel_ignore.contains( new DomainId( "x" ) ) ) {
+            if ( eel_ignore.contains( "x" ) ) {
                 return false;
             }
             if ( eel_not_ignore.getSize() != 8 ) {
@@ -4371,52 +4371,52 @@ public class TestSurfacing {
             if ( eel_ignore.getSize() != 8 ) {
                 return false;
             }
-            if ( eel_not_ignore.get( new DomainId( "a" ) ).getCombinableDomainsIds().size() != 5 ) {
+            if ( eel_not_ignore.get( "a" ).getCombinableDomainsIds().size() != 5 ) {
                 return false;
             }
-            if ( eel_not_ignore.get( new DomainId( "b" ) ).getCombinableDomainsIds().size() != 4 ) {
+            if ( eel_not_ignore.get( "b" ).getCombinableDomainsIds().size() != 4 ) {
                 return false;
             }
-            if ( eel_not_ignore.get( new DomainId( "c" ) ).getCombinableDomainsIds().size() != 4 ) {
+            if ( eel_not_ignore.get( "c" ).getCombinableDomainsIds().size() != 4 ) {
                 return false;
             }
-            if ( eel_not_ignore.get( new DomainId( "d" ) ).getCombinableDomainsIds().size() != 4 ) {
+            if ( eel_not_ignore.get( "d" ).getCombinableDomainsIds().size() != 4 ) {
                 return false;
             }
-            if ( eel_not_ignore.get( new DomainId( "e" ) ).getCombinableDomainsIds().size() != 6 ) {
+            if ( eel_not_ignore.get( "e" ).getCombinableDomainsIds().size() != 6 ) {
                 return false;
             }
-            if ( eel_not_ignore.get( new DomainId( "f" ) ).getCombinableDomainsIds().size() != 2 ) {
+            if ( eel_not_ignore.get( "f" ).getCombinableDomainsIds().size() != 2 ) {
                 return false;
             }
-            if ( eel_not_ignore.get( new DomainId( "g" ) ).getCombinableDomainsIds().size() != 1 ) {
+            if ( eel_not_ignore.get( "g" ).getCombinableDomainsIds().size() != 1 ) {
                 return false;
             }
-            if ( eel_not_ignore.get( new DomainId( "h" ) ).getCombinableDomainsIds().size() != 1 ) {
+            if ( eel_not_ignore.get( "h" ).getCombinableDomainsIds().size() != 1 ) {
                 return false;
             }
-            if ( eel_ignore.get( new DomainId( "a" ) ).getCombinableDomainsIds().size() != 4 ) {
+            if ( eel_ignore.get( "a" ).getCombinableDomainsIds().size() != 4 ) {
                 return false;
             }
-            if ( eel_ignore.get( new DomainId( "b" ) ).getCombinableDomainsIds().size() != 4 ) {
+            if ( eel_ignore.get( "b" ).getCombinableDomainsIds().size() != 4 ) {
                 return false;
             }
-            if ( eel_ignore.get( new DomainId( "c" ) ).getCombinableDomainsIds().size() != 4 ) {
+            if ( eel_ignore.get( "c" ).getCombinableDomainsIds().size() != 4 ) {
                 return false;
             }
-            if ( eel_ignore.get( new DomainId( "d" ) ).getCombinableDomainsIds().size() != 4 ) {
+            if ( eel_ignore.get( "d" ).getCombinableDomainsIds().size() != 4 ) {
                 return false;
             }
-            if ( eel_ignore.get( new DomainId( "e" ) ).getCombinableDomainsIds().size() != 5 ) {
+            if ( eel_ignore.get( "e" ).getCombinableDomainsIds().size() != 5 ) {
                 return false;
             }
-            if ( eel_ignore.get( new DomainId( "f" ) ).getCombinableDomainsIds().size() != 1 ) {
+            if ( eel_ignore.get( "f" ).getCombinableDomainsIds().size() != 1 ) {
                 return false;
             }
-            if ( eel_ignore.get( new DomainId( "g" ) ).getCombinableDomainsIds().size() != 1 ) {
+            if ( eel_ignore.get( "g" ).getCombinableDomainsIds().size() != 1 ) {
                 return false;
             }
-            if ( eel_ignore.get( new DomainId( "h" ) ).getCombinableDomainsIds().size() != 1 ) {
+            if ( eel_ignore.get( "h" ).getCombinableDomainsIds().size() != 1 ) {
                 return false;
             }
             if ( eel_not_ignore.getAllDomainIds().size() != 8 ) {
@@ -4660,9 +4660,9 @@ public class TestSurfacing {
                     .equals( "pep:known chromosome:NCBI36:21:16024215:16174248:1 gene:ENSG00000155313 transcript:ENST00000285681" ) ) {
                 return false;
             }
-            final List<Domain> uba = pdc.getProteinDomains( new DomainId( "UBA" ) );
-            final List<Domain> uim = pdc.getProteinDomains( new DomainId( "UIM" ) );
-            final List<Domain> uch = pdc.getProteinDomains( new DomainId( "UCH" ) );
+            final List<Domain> uba = pdc.getProteinDomains( "UBA" );
+            final List<Domain> uim = pdc.getProteinDomains( "UIM" );
+            final List<Domain> uch = pdc.getProteinDomains( "UCH" );
             if ( uba.size() != 1 ) {
                 return false;
             }
@@ -4673,14 +4673,14 @@ public class TestSurfacing {
                 return false;
             }
             final BasicDomain uim_domain = ( BasicDomain ) uim.get( 1 );
-            if ( !uim_domain.getDomainId().equals( new DomainId( "UIM" ) ) ) {
+            if ( !uim_domain.getDomainId().equals( "UIM" ) ) {
                 return false;
             }
             if ( uim_domain.getTotalCount() != 2 ) {
                 return false;
             }
             final BasicDomain uba_domain = ( BasicDomain ) uba.get( 0 );
-            if ( !uba_domain.getDomainId().equals( new DomainId( "UBA" ) ) ) {
+            if ( !uba_domain.getDomainId().equals( "UBA" ) ) {
                 return false;
             }
             if ( uba_domain.getNumber() != 1 ) {
@@ -4747,9 +4747,9 @@ public class TestSurfacing {
             if ( pdc2.getNumberOfProteinDomains() != 3 ) {
                 return false;
             }
-            final List<Domain> uba2 = pdc2.getProteinDomains( new DomainId( "UBA" ) );
-            final List<Domain> uim2 = pdc2.getProteinDomains( new DomainId( "UIM" ) );
-            final List<Domain> uch2 = pdc2.getProteinDomains( new DomainId( "UCH" ) );
+            final List<Domain> uba2 = pdc2.getProteinDomains( "UBA" );
+            final List<Domain> uim2 = pdc2.getProteinDomains( "UIM" );
+            final List<Domain> uch2 = pdc2.getProteinDomains( "UCH" );
             if ( uba2.size() != 1 ) {
                 return false;
             }
@@ -4760,14 +4760,14 @@ public class TestSurfacing {
                 return false;
             }
             final BasicDomain uim_domain2 = ( BasicDomain ) uim2.get( 1 );
-            if ( !uim_domain2.getDomainId().getId().equals( "UIM" ) ) {
+            if ( !uim_domain2.getDomainId().equals( "UIM" ) ) {
                 return false;
             }
             if ( uim_domain2.getTotalCount() != 2 ) {
                 return false;
             }
             final BasicDomain uba_domain2 = ( BasicDomain ) uba2.get( 0 );
-            if ( !uba_domain2.getDomainId().getId().equals( "UBA" ) ) {
+            if ( !uba_domain2.getDomainId().equals( "UBA" ) ) {
                 return false;
             }
             if ( uba_domain2.getNumber() != 1 ) {
@@ -4809,9 +4809,9 @@ public class TestSurfacing {
                 return false;
             }
             //
-            Set<DomainId> filter = new TreeSet<DomainId>();
-            filter.add( new DomainId( "beauty" ) );
-            filter.add( new DomainId( "strange" ) );
+            Set<String> filter = new TreeSet<String>();
+            filter.add( "beauty" );
+            filter.add( "strange" );
             parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
                                               "human",
                                               "ls",
@@ -4829,9 +4829,9 @@ public class TestSurfacing {
                 return false;
             }
             //
-            filter = new TreeSet<DomainId>();
-            filter.add( new DomainId( "beauty" ) );
-            filter.add( new DomainId( "strange" ) );
+            filter = new TreeSet<String>();
+            filter.add( "beauty" );
+            filter.add( "strange" );
             parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
                                               "human",
                                               "ls",
@@ -4849,10 +4849,10 @@ public class TestSurfacing {
                 return false;
             }
             //
-            filter = new TreeSet<DomainId>();
-            filter.add( new DomainId( "UIM" ) );
-            filter.add( new DomainId( "A" ) );
-            filter.add( new DomainId( "C" ) );
+            filter = new TreeSet<String>();
+            filter.add( "UIM" );
+            filter.add( "A" );
+            filter.add( "C" );
             parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
                                               "human",
                                               "ls",
@@ -4870,11 +4870,11 @@ public class TestSurfacing {
                 return false;
             }
             //
-            filter = new TreeSet<DomainId>();
-            filter.add( new DomainId( "UIM" ) );
-            filter.add( new DomainId( "A" ) );
-            filter.add( new DomainId( "C" ) );
-            filter.add( new DomainId( "X" ) );
+            filter = new TreeSet<String>();
+            filter.add( "UIM" );
+            filter.add( "A" );
+            filter.add( "C" );
+            filter.add( "X" );
             parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
                                               "human",
                                               "ls",
@@ -4892,10 +4892,10 @@ public class TestSurfacing {
                 return false;
             }
             //
-            filter = new TreeSet<DomainId>();
-            filter.add( new DomainId( "UIM" ) );
-            filter.add( new DomainId( "A" ) );
-            filter.add( new DomainId( "C" ) );
+            filter = new TreeSet<String>();
+            filter.add( "UIM" );
+            filter.add( "A" );
+            filter.add( "C" );
             parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
                                               "human",
                                               "ls",
@@ -4913,8 +4913,8 @@ public class TestSurfacing {
                 return false;
             }
             //
-            filter = new TreeSet<DomainId>();
-            filter.add( new DomainId( "UIM" ) );
+            filter = new TreeSet<String>();
+            filter.add( "UIM" );
             parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
                                               "human",
                                               "ls",
@@ -4935,8 +4935,8 @@ public class TestSurfacing {
                 return false;
             }
             //
-            filter = new TreeSet<DomainId>();
-            filter.add( new DomainId( "UIM" ) );
+            filter = new TreeSet<String>();
+            filter.add( "UIM" );
             parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
                                               "human",
                                               "ls",
@@ -4957,9 +4957,9 @@ public class TestSurfacing {
                 return false;
             }
             //
-            filter = new TreeSet<DomainId>();
-            filter.add( new DomainId( "A" ) );
-            filter.add( new DomainId( "C" ) );
+            filter = new TreeSet<String>();
+            filter.add( "A" );
+            filter.add( "C" );
             parser = new HmmPfamOutputParser( new File( test_dir + ForesterUtil.getFileSeparator() + "hmmpfam_output3" ),
                                               "human",
                                               "ls",
@@ -5037,7 +5037,7 @@ public class TestSurfacing {
             if ( ab_s0.getNumberOfProteinDomains() != 1 ) {
                 return false;
             }
-            if ( !ab_s0.getProteinDomain( 0 ).getDomainId().getId().equals( "a" ) ) {
+            if ( !ab_s0.getProteinDomain( 0 ).getDomainId().equals( "a" ) ) {
                 return false;
             }
             final Protein ab_s1 = SurfacingUtil.removeOverlappingDomains( 4, false, ab );
@@ -5087,7 +5087,7 @@ public class TestSurfacing {
             if ( fghi_s0.getNumberOfProteinDomains() != 1 ) {
                 return false;
             }
-            if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().getId().equals( "h" ) ) {
+            if ( !fghi_s0.getProteinDomain( 0 ).getDomainId().equals( "h" ) ) {
                 return false;
             }
             final Protein fghi_s1 = SurfacingUtil.removeOverlappingDomains( 11, false, fghi );
@@ -5119,7 +5119,7 @@ public class TestSurfacing {
             if ( jklm_s0.getNumberOfProteinDomains() != 1 ) {
                 return false;
             }
-            if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().getId().equals( "l" ) ) {
+            if ( !jklm_s0.getProteinDomain( 0 ).getDomainId().equals( "l" ) ) {
                 return false;
             }
             final Protein jklm_s1 = SurfacingUtil.removeOverlappingDomains( 11, false, jklm );
@@ -5554,7 +5554,7 @@ public class TestSurfacing {
             gwcd_list.add( two );
             gwcd_list.add( three );
             gwcd_list.add( four );
-            final Map<DomainId, Set<String>> map_same = new HashMap<DomainId, Set<String>>();
+            final Map<String, Set<String>> map_same = new HashMap<String, Set<String>>();
             final HashSet<String> a_s = new HashSet<String>();
             a_s.add( "AAA" );
             final HashSet<String> b_s = new HashSet<String>();
diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 8f9341d..9a6afc0 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -91,7 +91,6 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.protein.BasicDomain;
 import org.forester.protein.BasicProtein;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.protein.ProteinId;
 import org.forester.rio.TestRIO;
@@ -172,15 +171,6 @@ public final class Test {
             System.exit( -1 );
         }
         final long start_time = new Date().getTime();
-        System.out.print( "Domain id: " );
-        if ( !testDomainId() ) {
-            System.out.println( "failed." );
-            failed++;
-        }
-        else {
-            succeeded++;
-        }
-        System.out.println( "OK." );
         System.out.print( "Protein id: " );
         if ( !testProteinId() ) {
             System.out.println( "failed." );
@@ -953,7 +943,7 @@ public final class Test {
     private static boolean testBasicDomain() {
         try {
             final Domain pd = new BasicDomain( "id", 23, 25, ( short ) 1, ( short ) 4, 0.1, -12 );
-            if ( !pd.getDomainId().getId().equals( "id" ) ) {
+            if ( !pd.getDomainId().equals( "id" ) ) {
                 return false;
             }
             if ( pd.getNumber() != 1 ) {
@@ -997,7 +987,7 @@ public final class Test {
             if ( a1.compareTo( a2 ) != 0 ) {
                 return false;
             }
-            if ( a1.compareTo( a3 ) != 0 ) {
+            if ( a1.compareTo( a3 ) == 0 ) {
                 return false;
             }
         }
@@ -1856,238 +1846,78 @@ public final class Test {
             p.addProteinDomain( A20 );
             p.addProteinDomain( B25 );
             p.addProteinDomain( D80 );
-            List<DomainId> domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "C" ) );
+            List<String> domains_ids = new ArrayList<String>();
+            domains_ids.add( "A" );
+            domains_ids.add( "B" );
+            domains_ids.add( "C" );
             if ( !p.contains( domains_ids, false ) ) {
                 return false;
             }
             if ( !p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids.add( new DomainId( "X" ) );
+            domains_ids.add( "X" );
             if ( p.contains( domains_ids, false ) ) {
                 return false;
             }
             if ( p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "D" ) );
+            domains_ids = new ArrayList<String>();
+            domains_ids.add( "A" );
+            domains_ids.add( "C" );
+            domains_ids.add( "D" );
             if ( !p.contains( domains_ids, false ) ) {
                 return false;
             }
             if ( !p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "D" ) );
-            domains_ids.add( new DomainId( "C" ) );
+            domains_ids = new ArrayList<String>();
+            domains_ids.add( "A" );
+            domains_ids.add( "D" );
+            domains_ids.add( "C" );
             if ( !p.contains( domains_ids, false ) ) {
                 return false;
             }
             if ( p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            if ( !p.contains( domains_ids, false ) ) {
-                return false;
-            }
-            if ( !p.contains( domains_ids, true ) ) {
-                return false;
-            }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            if ( !p.contains( domains_ids, false ) ) {
-                return false;
-            }
-            if ( !p.contains( domains_ids, true ) ) {
-                return false;
-            }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
+            domains_ids = new ArrayList<String>();
+            domains_ids.add( "A" );
+            domains_ids.add( "A" );
+            domains_ids.add( "B" );
             if ( !p.contains( domains_ids, false ) ) {
                 return false;
             }
             if ( !p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            if ( !p.contains( domains_ids, false ) ) {
-                return false;
-            }
-            if ( p.contains( domains_ids, true ) ) {
-                return false;
-            }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "D" ) );
+            domains_ids = new ArrayList<String>();
+            domains_ids.add( "A" );
+            domains_ids.add( "A" );
+            domains_ids.add( "A" );
+            domains_ids.add( "B" );
+            domains_ids.add( "B" );
             if ( !p.contains( domains_ids, false ) ) {
                 return false;
             }
             if ( !p.contains( domains_ids, true ) ) {
                 return false;
             }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "D" ) );
-            if ( !p.contains( domains_ids, false ) ) {
-                return false;
-            }
-            if ( !p.contains( domains_ids, true ) ) {
-                return false;
-            }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "D" ) );
-            if ( !p.contains( domains_ids, false ) ) {
-                return false;
-            }
-            if ( p.contains( domains_ids, true ) ) {
-                return false;
-            }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "D" ) );
-            if ( !p.contains( domains_ids, false ) ) {
-                return false;
-            }
-            if ( p.contains( domains_ids, true ) ) {
-                return false;
-            }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "D" ) );
-            if ( !p.contains( domains_ids, false ) ) {
-                return false;
-            }
-            if ( !p.contains( domains_ids, true ) ) {
-                return false;
-            }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "D" ) );
-            domains_ids.add( new DomainId( "X" ) );
-            if ( p.contains( domains_ids, false ) ) {
-                return false;
-            }
-            if ( p.contains( domains_ids, true ) ) {
-                return false;
-            }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "X" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "D" ) );
-            if ( p.contains( domains_ids, false ) ) {
-                return false;
-            }
-            if ( p.contains( domains_ids, true ) ) {
-                return false;
-            }
-            domains_ids = new ArrayList<DomainId>();
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "B" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "A" ) );
-            domains_ids.add( new DomainId( "C" ) );
-            domains_ids.add( new DomainId( "D" ) );
+            domains_ids = new ArrayList<String>();
+            domains_ids.add( "A" );
+            domains_ids.add( "A" );
+            domains_ids.add( "B" );
+            domains_ids.add( "A" );
+            domains_ids.add( "B" );
+            domains_ids.add( "B" );
+            domains_ids.add( "A" );
+            domains_ids.add( "B" );
+            domains_ids.add( "C" );
+            domains_ids.add( "A" );
+            domains_ids.add( "C" );
+            domains_ids.add( "D" );
             if ( !p.contains( domains_ids, false ) ) {
                 return false;
             }
@@ -3461,69 +3291,6 @@ public final class Test {
         return true;
     }
 
-    private static boolean testDomainId() {
-        try {
-            final DomainId id1 = new DomainId( "a" );
-            final DomainId id2 = new DomainId( "a" );
-            final DomainId id3 = new DomainId( "A" );
-            final DomainId id4 = new DomainId( "b" );
-            if ( !id1.equals( id1 ) ) {
-                return false;
-            }
-            if ( id1.getId().equals( "x" ) ) {
-                return false;
-            }
-            if ( id1.getId().equals( null ) ) {
-                return false;
-            }
-            if ( !id1.equals( id2 ) ) {
-                return false;
-            }
-            if ( id1.equals( id3 ) ) {
-                return false;
-            }
-            if ( id1.hashCode() != id1.hashCode() ) {
-                return false;
-            }
-            if ( id1.hashCode() != id2.hashCode() ) {
-                return false;
-            }
-            if ( id1.hashCode() == id3.hashCode() ) {
-                return false;
-            }
-            if ( id1.compareTo( id1 ) != 0 ) {
-                return false;
-            }
-            if ( id1.compareTo( id2 ) != 0 ) {
-                return false;
-            }
-            if ( id1.compareTo( id3 ) != 0 ) {
-                return false;
-            }
-            if ( id1.compareTo( id4 ) >= 0 ) {
-                return false;
-            }
-            if ( id4.compareTo( id1 ) <= 0 ) {
-                return false;
-            }
-            if ( !id4.getId().equals( "b" ) ) {
-                return false;
-            }
-            final DomainId id5 = new DomainId( " C " );
-            if ( !id5.getId().equals( "C" ) ) {
-                return false;
-            }
-            if ( id5.equals( id1 ) ) {
-                return false;
-            }
-        }
-        catch ( final Exception e ) {
-            e.printStackTrace( System.out );
-            return false;
-        }
-        return true;
-    }
-
     private static boolean testEmblEntryRetrieval() {
         //The format for GenBank Accession numbers are:
         //Nucleotide: 1 letter + 5 numerals OR 2 letters + 6 numerals