X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FSurfacingUtil.java;h=ea51d190da7ae4d2cc19980eabf460ac71157233;hb=e572f0142daf64409db0461f15215288137603f8;hp=599fd73c30b52856ef3ed6df734a132e09b0ebed;hpb=0fc3bc32fc5be907e3f91a780af68c6baff79db1;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 599fd73..ea51d19 100644
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -26,6 +26,7 @@
 
 package org.forester.surfacing;
 
+import java.awt.Color;
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileWriter;
@@ -84,9 +85,9 @@ import org.forester.protein.BinaryDomainCombination;
 import org.forester.protein.Domain;
 import org.forester.protein.Protein;
 import org.forester.species.Species;
+import org.forester.surfacing.DomainSimilarity.PRINT_OPTION;
 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
-import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
 import org.forester.util.AsciiHistogram;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.BasicTable;
@@ -94,49 +95,36 @@ import org.forester.util.BasicTableParser;
 import org.forester.util.CommandLineArguments;
 import org.forester.util.DescriptiveStatistics;
 import org.forester.util.ForesterUtil;
+import org.forester.util.TaxonomyColors;
 
 public final class SurfacingUtil {
 
-    final static class DomainComparator implements Comparator<Domain> {
-
-        final private boolean _ascending;
-
-        public DomainComparator( final boolean ascending ) {
-            _ascending = ascending;
-        }
+    public final static Pattern              PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
+    private final static Map<String, String> _TAXCODE_HEXCOLORSTRING_MAP      = new HashMap<String, String>();
+    private final static Map<String, String> _TAXCODE_TAXGROUP_MAP            = new HashMap<String, String>();
+    private static final Comparator<Domain>  ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
 
         @Override
-        public final int compare( final Domain d0, final Domain d1 ) {
-            if ( d0.getFrom() < d1.getFrom() ) {
-                return _ascending ? -1 : 1;
+        public int compare( final Domain d1,
+                            final Domain d2 ) {
+            if ( d1.getPerDomainEvalue() < d2
+                    .getPerDomainEvalue() ) {
+                return -1;
             }
-            else if ( d0.getFrom() > d1.getFrom() ) {
-                return _ascending ? 1 : -1;
+            else if ( d1.getPerDomainEvalue() > d2
+                    .getPerDomainEvalue() ) {
+                return 1;
+            }
+            else {
+                return d1.compareTo( d2 );
             }
-            return 0;
         }
+    };
+    private final static NumberFormat        FORMATTER_3                      = new DecimalFormat( "0.000" );
+
+    private SurfacingUtil() {
+        // Hidden constructor.
     }
-    private final static NumberFormat       FORMATTER_3                      = new DecimalFormat( "0.000" );
-    private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
-
-                                                                                 @Override
-                                                                                 public int compare( final Domain d1,
-                                                                                                     final Domain d2 ) {
-                                                                                     if ( d1.getPerSequenceEvalue() < d2
-                                                                                             .getPerSequenceEvalue() ) {
-                                                                                         return -1;
-                                                                                     }
-                                                                                     else if ( d1
-                                                                                             .getPerSequenceEvalue() > d2
-                                                                                             .getPerSequenceEvalue() ) {
-                                                                                         return 1;
-                                                                                     }
-                                                                                     else {
-                                                                                         return d1.compareTo( d2 );
-                                                                                     }
-                                                                                 }
-                                                                             };
-    public final static Pattern             PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
 
     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
@@ -154,63 +142,6 @@ public final class SurfacingUtil {
         }
     }
 
-    public static void addHtmlHead( final Writer w, final String title ) throws IOException {
-        w.write( SurfacingConstants.NL );
-        w.write( "<head>" );
-        w.write( "<title>" );
-        w.write( title );
-        w.write( "</title>" );
-        w.write( SurfacingConstants.NL );
-        w.write( "<style>" );
-        w.write( SurfacingConstants.NL );
-        w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
-        w.write( SurfacingConstants.NL );
-        w.write( "a:link { color : #6633FF; text-decoration : none; }" );
-        w.write( SurfacingConstants.NL );
-        w.write( "a:active { color : #99FF00; text-decoration : none; }" );
-        w.write( SurfacingConstants.NL );
-        w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
-        w.write( SurfacingConstants.NL );
-        //
-        w.write( "a.pl:visited { color : #505050; text-decoration : none; font-size: 7pt;}" );
-        w.write( SurfacingConstants.NL );
-        w.write( "a.pl:link { color : #505050; text-decoration : none; font-size: 7pt;}" );
-        w.write( SurfacingConstants.NL );
-        w.write( "a.pl:active { color : #505050; text-decoration : none; font-size: 7pt;}" );
-        w.write( SurfacingConstants.NL );
-        w.write( "a.pl:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; font-size: 7pt;}" );
-        w.write( SurfacingConstants.NL );
-        //
-        w.write( "a.ps:visited { color : #707070; text-decoration : none; font-size: 7pt;}" );
-        w.write( SurfacingConstants.NL );
-        w.write( "a.ps:link { color : #707070; text-decoration : none; font-size: 7pt;}" );
-        w.write( SurfacingConstants.NL );
-        w.write( "a.ps:active { color : #707070; text-decoration : none; font-size: 7pt;}" );
-        w.write( SurfacingConstants.NL );
-        w.write( "a.ps:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; font-size: 7pt;}" );
-        w.write( SurfacingConstants.NL );
-        //
-        w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
-        w.write( SurfacingConstants.NL );
-        w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
-        w.write( SurfacingConstants.NL );
-        w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
-        w.write( SurfacingConstants.NL );
-        w.write( "</style>" );
-        w.write( SurfacingConstants.NL );
-        w.write( "</head>" );
-        w.write( SurfacingConstants.NL );
-    }
-
-    private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
-        if ( map.containsKey( s ) ) {
-            map.put( s, map.get( s ) + 1 );
-        }
-        else {
-            map.put( s, 1 );
-        }
-    }
-
     public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final DomainSimilarity similarity : similarities ) {
@@ -219,501 +150,115 @@ public final class SurfacingUtil {
         return stats;
     }
 
-    private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
-                                                                    final String outfilename_for_counts,
-                                                                    final String outfilename_for_dc,
-                                                                    final String outfilename_for_dc_for_go_mapping,
-                                                                    final String outfilename_for_dc_for_go_mapping_unique,
-                                                                    final String outfilename_for_rank_counts,
-                                                                    final String outfilename_for_ancestor_species_counts,
-                                                                    final String outfilename_for_protein_stats,
-                                                                    final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
-                                                                    final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
-                                                                    final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
-        try {
-            //
-            //            if ( protein_length_stats_by_dc != null ) {
-            //                for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
-            //                    System.out.print( entry.getKey().toString() );
-            //                    System.out.print( ": " );
-            //                    double[] a = entry.getValue().getDataAsDoubleArray();
-            //                    for( int i = 0; i < a.length; i++ ) {
-            //                        System.out.print( a[ i ] + " " );
-            //                    }
-            //                    System.out.println();
-            //                }
-            //            }
-            //            if ( domain_number_stats_by_dc != null ) {
-            //                for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
-            //                    System.out.print( entry.getKey().toString() );
-            //                    System.out.print( ": " );
-            //                    double[] a = entry.getValue().getDataAsDoubleArray();
-            //                    for( int i = 0; i < a.length; i++ ) {
-            //                        System.out.print( a[ i ] + " " );
-            //                    }
-            //                    System.out.println();
-            //                }
-            //            }
-            //
-            final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
-            final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
-            final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
-            final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
-            final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
-            for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
-                final PhylogenyNode n = it.next();
-                final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
-                for( final String dc : gained_dc ) {
-                    if ( dc_gain_counts.containsKey( dc ) ) {
-                        dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
-                    }
-                    else {
-                        dc_gain_counts.put( dc, 1 );
-                    }
-                }
-            }
-            final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
-            final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
-            final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
-            final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
-            final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
-            final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
-            final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
-            final Set<String> dcs = dc_gain_counts.keySet();
-            final SortedSet<String> more_than_once = new TreeSet<String>();
-            DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
-            DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
-            DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
-            final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
-            long gained_multiple_times_domain_length_sum = 0;
-            long gained_once_domain_length_sum = 0;
-            long gained_multiple_times_domain_length_count = 0;
-            long gained_once_domain_length_count = 0;
-            for( final String dc : dcs ) {
-                final int count = dc_gain_counts.get( dc );
-                if ( histogram.containsKey( count ) ) {
-                    histogram.put( count, histogram.get( count ) + 1 );
-                    domain_lists.get( count ).append( ", " + dc );
-                    domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
-                    domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
-                }
-                else {
-                    histogram.put( count, 1 );
-                    domain_lists.put( count, new StringBuilder( dc ) );
-                    final PriorityQueue<String> q = new PriorityQueue<String>();
-                    q.addAll( splitDomainCombination( dc ) );
-                    domain_lists_go.put( count, q );
-                    final SortedSet<String> set = new TreeSet<String>();
-                    set.addAll( splitDomainCombination( dc ) );
-                    domain_lists_go_unique.put( count, set );
-                }
-                if ( protein_length_stats_by_dc != null ) {
-                    if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
-                        dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
-                    }
-                    dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
-                            .arithmeticMean() );
-                }
-                if ( domain_number_stats_by_dc != null ) {
-                    if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
-                        dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
-                    }
-                    dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
-                            .arithmeticMean() );
+    public static void checkForOutputFileWriteability( final File outfile ) {
+        final String error = ForesterUtil.isWritableFile( outfile );
+        if ( !ForesterUtil.isEmpty( error ) ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+        }
+    }
+
+    public static void checkWriteabilityForPairwiseComparisons( final DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+                                                                final String[][] input_file_properties,
+                                                                final String automated_pairwise_comparison_suffix,
+                                                                final File outdir ) {
+        for( int i = 0; i < input_file_properties.length; ++i ) {
+            for( int j = 0; j < i; ++j ) {
+                final String species_i = input_file_properties[ i ][ 1 ];
+                final String species_j = input_file_properties[ j ][ 1 ];
+                String pairwise_similarities_output_file_str = surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i
+                        + "_" + species_j + automated_pairwise_comparison_suffix;
+                switch ( domain_similarity_print_option ) {
+                    case HTML:
+                        if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
+                            pairwise_similarities_output_file_str += ".html";
+                        }
+                        break;
                 }
-                if ( domain_length_stats_by_domain != null ) {
-                    if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
-                        dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
-                    }
-                    final String[] ds = dc.split( "=" );
-                    dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
-                            .get( ds[ 0 ] ).arithmeticMean() );
-                    dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
-                            .get( ds[ 1 ] ).arithmeticMean() );
+                final String error = ForesterUtil
+                        .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
+                                + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
+                if ( !ForesterUtil.isEmpty( error ) ) {
+                    ForesterUtil.fatalError( surfacing.PRG_NAME, error );
                 }
-                if ( count > 1 ) {
-                    more_than_once.add( dc );
-                    if ( protein_length_stats_by_dc != null ) {
-                        final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
-                        for( final double element : s.getData() ) {
-                            gained_multiple_times_lengths_stats.addValue( element );
-                        }
+            }
+        }
+    }
+
+    public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
+                                                                                           final BinaryDomainCombination.DomainCombinationType dc_type,
+                                                                                           final List<BinaryDomainCombination> all_binary_domains_combination_gained,
+                                                                                           final boolean get_gains ) {
+        final SortedSet<String> sorted_ids = new TreeSet<String>();
+        for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
+            sorted_ids.add( matrix.getIdentifier( i ) );
+        }
+        for( final String id : sorted_ids ) {
+            for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
+                if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
+                        || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
+                    if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
+                        all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
+                                                                   .obtainInstance( matrix.getCharacter( c ) ) );
                     }
-                    if ( domain_number_stats_by_dc != null ) {
-                        final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
-                        for( final double element : s.getData() ) {
-                            gained_multiple_times_domain_count_stats.addValue( element );
-                        }
+                    else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
+                        all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
+                                                                   .obtainInstance( matrix.getCharacter( c ) ) );
                     }
-                    if ( domain_length_stats_by_domain != null ) {
-                        final String[] ds = dc.split( "=" );
-                        final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
-                        final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
-                        for( final double element : s0.getData() ) {
-                            gained_multiple_times_domain_length_sum += element;
-                            ++gained_multiple_times_domain_length_count;
-                        }
-                        for( final double element : s1.getData() ) {
-                            gained_multiple_times_domain_length_sum += element;
-                            ++gained_multiple_times_domain_length_count;
-                        }
+                    else {
+                        all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.obtainInstance( matrix
+                                                                                                                .getCharacter( c ) ) );
                     }
                 }
-                else {
-                    if ( protein_length_stats_by_dc != null ) {
-                        final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
-                        for( final double element : s.getData() ) {
-                            gained_once_lengths_stats.addValue( element );
-                        }
-                    }
-                    if ( domain_number_stats_by_dc != null ) {
-                        final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
-                        for( final double element : s.getData() ) {
-                            gained_once_domain_count_stats.addValue( element );
-                        }
-                    }
-                    if ( domain_length_stats_by_domain != null ) {
-                        final String[] ds = dc.split( "=" );
-                        final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
-                        final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
-                        for( final double element : s0.getData() ) {
-                            gained_once_domain_length_sum += element;
-                            ++gained_once_domain_length_count;
-                        }
-                        for( final double element : s1.getData() ) {
-                            gained_once_domain_length_sum += element;
-                            ++gained_once_domain_length_count;
-                        }
-                    }
-                }
-            }
-            final Set<Integer> histogram_keys = histogram.keySet();
-            for( final Integer histogram_key : histogram_keys ) {
-                final int count = histogram.get( histogram_key );
-                final StringBuilder dc = domain_lists.get( histogram_key );
-                out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
-                out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
-                out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
-                final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
-                Arrays.sort( sorted );
-                for( final Object domain : sorted ) {
-                    out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
-                }
-                out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
-                for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
-                    out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
-                }
-            }
-            out_counts.close();
-            out_dc.close();
-            out_dc_for_go_mapping.close();
-            out_dc_for_go_mapping_unique.close();
-            final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
-            final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
-            for( final String dc : more_than_once ) {
-                final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
-                for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
-                    final PhylogenyNode n = it.next();
-                    if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
-                        nodes.add( n );
-                    }
-                }
-                for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
-                    for( int j = i + 1; j < nodes.size(); ++j ) {
-                        final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
-                        String rank = "unknown";
-                        if ( lca.getNodeData().isHasTaxonomy()
-                                && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
-                            rank = lca.getNodeData().getTaxonomy().getRank();
-                        }
-                        addToCountMap( lca_rank_counts, rank );
-                        String lca_species;
-                        if ( lca.getNodeData().isHasTaxonomy()
-                                && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
-                            lca_species = lca.getNodeData().getTaxonomy().getScientificName();
-                        }
-                        else if ( lca.getNodeData().isHasTaxonomy()
-                                && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
-                            lca_species = lca.getNodeData().getTaxonomy().getCommonName();
-                        }
-                        else {
-                            lca_species = lca.getName();
-                        }
-                        addToCountMap( lca_ancestor_species_counts, lca_species );
-                    }
-                }
-            }
-            final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
-            final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
-            ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
-            ForesterUtil.map2writer( out_for_ancestor_species_counts,
-                                     lca_ancestor_species_counts,
-                                     "\t",
-                                     ForesterUtil.LINE_SEPARATOR );
-            out_for_rank_counts.close();
-            out_for_ancestor_species_counts.close();
-            if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
-                    && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
-                final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
-                w.write( "Domain Lengths: " );
-                w.write( "\n" );
-                if ( domain_length_stats_by_domain != null ) {
-                    for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
-                            .entrySet() ) {
-                        w.write( entry.getKey().toString() );
-                        w.write( "\t" + entry.getValue().arithmeticMean() );
-                        w.write( "\t" + entry.getValue().median() );
-                        w.write( "\n" );
-                    }
-                }
-                w.flush();
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "Protein Lengths: " );
-                w.write( "\n" );
-                if ( protein_length_stats_by_dc != null ) {
-                    for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
-                            .entrySet() ) {
-                        w.write( entry.getKey().toString() );
-                        w.write( "\t" + entry.getValue().arithmeticMean() );
-                        w.write( "\t" + entry.getValue().median() );
-                        w.write( "\n" );
-                    }
-                }
-                w.flush();
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "Number of domains: " );
-                w.write( "\n" );
-                if ( domain_number_stats_by_dc != null ) {
-                    for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
-                            .entrySet() ) {
-                        w.write( entry.getKey().toString() );
-                        w.write( "\t" + entry.getValue().arithmeticMean() );
-                        w.write( "\t" + entry.getValue().median() );
-                        w.write( "\n" );
-                    }
-                }
-                w.flush();
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "Gained once, domain lengths:" );
-                w.write( "\n" );
-                w.write( "N: " + gained_once_domain_length_count );
-                w.write( "\n" );
-                w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "Gained multiple times, domain lengths:" );
-                w.write( "\n" );
-                w.write( "N: " + gained_multiple_times_domain_length_count );
-                w.write( "\n" );
-                w.write( "Avg: "
-                        + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "Gained once, protein lengths:" );
-                w.write( "\n" );
-                w.write( gained_once_lengths_stats.toString() );
-                gained_once_lengths_stats = null;
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "Gained once, domain counts:" );
-                w.write( "\n" );
-                w.write( gained_once_domain_count_stats.toString() );
-                gained_once_domain_count_stats = null;
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "Gained multiple times, protein lengths:" );
-                w.write( "\n" );
-                w.write( gained_multiple_times_lengths_stats.toString() );
-                gained_multiple_times_lengths_stats = null;
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "Gained multiple times, domain counts:" );
-                w.write( "\n" );
-                w.write( gained_multiple_times_domain_count_stats.toString() );
-                w.flush();
-                w.close();
             }
         }
-        catch ( final IOException e ) {
-            ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
-        }
-        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
-                + outfilename_for_counts + "]" );
-        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
-                + outfilename_for_dc + "]" );
-        ForesterUtil.programMessage( surfacing.PRG_NAME,
-                                     "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
-                                             + outfilename_for_dc_for_go_mapping + "]" );
-        ForesterUtil.programMessage( surfacing.PRG_NAME,
-                                     "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
-                                             + outfilename_for_dc_for_go_mapping_unique + "]" );
     }
 
-    public static void checkForOutputFileWriteability( final File outfile ) {
-        final String error = ForesterUtil.isWritableFile( outfile );
-        if ( !ForesterUtil.isEmpty( error ) ) {
-            ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+    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>() );
+            }
+            domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
         }
+        return domain_id_to_go_ids_map;
     }
 
-    public static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
-                                                                final String[][] input_file_properties,
-                                                                final String automated_pairwise_comparison_suffix,
-                                                                final File outdir ) {
-        for( int i = 0; i < input_file_properties.length; ++i ) {
-            for( int j = 0; j < i; ++j ) {
-                final String species_i = input_file_properties[ i ][ 1 ];
-                final String species_j = input_file_properties[ j ][ 1 ];
-                String pairwise_similarities_output_file_str = surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i
-                        + "_" + species_j + automated_pairwise_comparison_suffix;
-                switch ( domain_similarity_print_option ) {
-                    case HTML:
-                        if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
-                            pairwise_similarities_output_file_str += ".html";
-                        }
-                        break;
-                }
-                final String error = ForesterUtil
-                        .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
-                                + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
-                if ( !ForesterUtil.isEmpty( error ) ) {
-                    ForesterUtil.fatalError( surfacing.PRG_NAME, error );
-                }
+    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<String, Set<String>> map = new TreeMap<String, Set<String>>();
+        for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
+            final String domain_id = primary_table.getValue( 0, r );
+            if ( !map.containsKey( domain_id ) ) {
+                map.put( domain_id, new HashSet<String>() );
             }
+            map.get( domain_id ).add( primary_table.getValue( 1, r ) );
         }
+        return map;
     }
 
-    private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
-                                                                        final boolean get_gains ) {
-        final SortedSet<String> domains = new TreeSet<String>();
-        for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
-            final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
-            if ( get_gains ) {
-                domains.addAll( chars.getGainedCharacters() );
-            }
-            else {
-                domains.addAll( chars.getLostCharacters() );
-            }
-        }
-        return domains;
+    public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
+        checkForOutputFileWriteability( nj_tree_outfile );
+        final NeighborJoining nj = NeighborJoining.createInstance();
+        final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
+        phylogeny.setName( nj_tree_outfile.getName() );
+        writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
+        return phylogeny;
     }
 
-    public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
-                                                                                           final BinaryDomainCombination.DomainCombinationType dc_type,
-                                                                                           final List<BinaryDomainCombination> all_binary_domains_combination_gained,
-                                                                                           final boolean get_gains ) {
-        final SortedSet<String> sorted_ids = new TreeSet<String>();
-        for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
-            sorted_ids.add( matrix.getIdentifier( i ) );
-        }
-        for( final String id : sorted_ids ) {
-            for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
-                if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
-                        || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
-                    if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
-                        all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
-                                .createInstance( matrix.getCharacter( c ) ) );
-                    }
-                    else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
-                        all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
-                                .createInstance( matrix.getCharacter( c ) ) );
-                    }
-                    else {
-                        all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
-                                .getCharacter( c ) ) );
-                    }
-                }
-            }
-        }
-    }
-
-    private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
-                                                            final boolean domain_combinations,
-                                                            final CharacterStateMatrix.GainLossStates state,
-                                                            final String outfile ) {
-        File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
-                + ForesterUtil.FILE_SEPARATOR + base_dir );
-        if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
-            per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
-        }
-        if ( domain_combinations ) {
-            per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
-                    + ForesterUtil.FILE_SEPARATOR + "DC" );
-        }
-        else {
-            per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
-                    + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
-        }
-        if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
-            per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
-        }
-        if ( state == GainLossStates.GAIN ) {
-            per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
-                    + ForesterUtil.FILE_SEPARATOR + "GAINS" );
-        }
-        else if ( state == GainLossStates.LOSS ) {
-            per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
-                    + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
-        }
-        else {
-            per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
-                    + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
-        }
-        if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
-            per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
-        }
-        return per_node_go_mapped_domain_gain_loss_files_base_dir;
-    }
-
-    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>() );
-            }
-            domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
-        }
-        return domain_id_to_go_ids_map;
-    }
-
-    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<String, Set<String>> map = new TreeMap<String, Set<String>>();
-        for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
-            final String domain_id = primary_table.getValue( 0, r );
-            if ( !map.containsKey( domain_id ) ) {
-                map.put( domain_id, new HashSet<String>() );
-            }
-            map.get( domain_id ).add( primary_table.getValue( 1, r ) );
-        }
-        return map;
-    }
-
-    public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
-        checkForOutputFileWriteability( nj_tree_outfile );
-        final NeighborJoining nj = NeighborJoining.createInstance();
-        final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
-        phylogeny.setName( nj_tree_outfile.getName() );
-        writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
-        return phylogeny;
-    }
-
-    public static StringBuilder createParametersAsString( final boolean ignore_dufs,
-                                                          final double e_value_max,
-                                                          final int max_allowed_overlap,
-                                                          final boolean no_engulfing_overlaps,
-                                                          final File cutoff_scores_file,
-                                                          final BinaryDomainCombination.DomainCombinationType dc_type ) {
-        final StringBuilder parameters_sb = new StringBuilder();
-        parameters_sb.append( "E-value: " + e_value_max );
-        if ( cutoff_scores_file != null ) {
-            parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
+    public static StringBuilder createParametersAsString( final boolean ignore_dufs,
+                                                          final double ie_value_max,
+                                                          final double fs_e_value_max,
+                                                          final int max_allowed_overlap,
+                                                          final boolean no_engulfing_overlaps,
+                                                          final File cutoff_scores_file,
+                                                          final BinaryDomainCombination.DomainCombinationType dc_type ) {
+        final StringBuilder parameters_sb = new StringBuilder();
+        parameters_sb.append( "iE-value: " + ie_value_max );
+        parameters_sb.append( ", FS E-value: " + fs_e_value_max );
+        if ( cutoff_scores_file != null ) {
+            parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
         }
         else {
             parameters_sb.append( ", Cutoff-scores-file: not-set" );
@@ -740,73 +285,63 @@ public final class SurfacingUtil {
         return parameters_sb;
     }
 
-    private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
-        final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
-        final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
-        for( final String domain_id : cds.keySet() ) {
-            final CombinableDomains cd = cds.get( domain_id );
-            binary_combinations.addAll( cd.toBinaryDomainCombinations() );
-        }
-        return binary_combinations;
-    }
-
     public static void createSplitWriters( final File out_dir,
                                            final String my_outfile,
                                            final Map<Character, Writer> split_writers ) throws IOException {
         split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_A.html" ) ) );
+                                                                    + "_domains_A.html" ) ) );
         split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_B.html" ) ) );
+                                                                    + "_domains_B.html" ) ) );
         split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_C.html" ) ) );
+                                                                    + "_domains_C.html" ) ) );
         split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_D.html" ) ) );
+                                                                    + "_domains_D.html" ) ) );
         split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_E.html" ) ) );
+                                                                    + "_domains_E.html" ) ) );
         split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_F.html" ) ) );
+                                                                    + "_domains_F.html" ) ) );
         split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_G.html" ) ) );
+                                                                    + "_domains_G.html" ) ) );
         split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_H.html" ) ) );
+                                                                    + "_domains_H.html" ) ) );
         split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_I.html" ) ) );
+                                                                    + "_domains_I.html" ) ) );
         split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_J.html" ) ) );
+                                                                    + "_domains_J.html" ) ) );
         split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_K.html" ) ) );
+                                                                    + "_domains_K.html" ) ) );
         split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_L.html" ) ) );
+                                                                    + "_domains_L.html" ) ) );
         split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_M.html" ) ) );
+                                                                    + "_domains_M.html" ) ) );
         split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_N.html" ) ) );
+                                                                    + "_domains_N.html" ) ) );
         split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_O.html" ) ) );
+                                                                    + "_domains_O.html" ) ) );
         split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_P.html" ) ) );
+                                                                    + "_domains_P.html" ) ) );
         split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_Q.html" ) ) );
+                                                                    + "_domains_Q.html" ) ) );
         split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_R.html" ) ) );
+                                                                    + "_domains_R.html" ) ) );
         split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_S.html" ) ) );
+                                                                    + "_domains_S.html" ) ) );
         split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_T.html" ) ) );
+                                                                    + "_domains_T.html" ) ) );
         split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_U.html" ) ) );
+                                                                    + "_domains_U.html" ) ) );
         split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_V.html" ) ) );
+                                                                    + "_domains_V.html" ) ) );
         split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_W.html" ) ) );
+                                                                    + "_domains_W.html" ) ) );
         split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_X.html" ) ) );
+                                                                    + "_domains_X.html" ) ) );
         split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_Y.html" ) ) );
+                                                                    + "_domains_Y.html" ) ) );
         split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_Z.html" ) ) );
+                                                                    + "_domains_Z.html" ) ) );
         split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_domains_0.html" ) ) );
+                                                                    + "_domains_0.html" ) ) );
     }
 
     public static Map<String, Integer> createTaxCodeToIdMap( final Phylogeny phy ) {
@@ -844,8 +379,8 @@ public final class SurfacingUtil {
     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
                                                             final Detailedness detailedness ) {
         for( final DomainSimilarity domain_similarity : domain_similarities ) {
-            if ( domain_similarity instanceof PrintableDomainSimilarity ) {
-                final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
+            if ( domain_similarity instanceof DomainSimilarity ) {
+                final DomainSimilarity printable_domain_similarity = domain_similarity;
                 printable_domain_similarity.setDetailedness( detailedness );
             }
         }
@@ -1047,14 +582,14 @@ public final class SurfacingUtil {
 
     /**
      * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
-     * 
-     * 
+     *
+     *
      * @param output_file
      * @param all_bin_domain_combinations_changed
      * @param sum_of_all_domains_encountered
      * @param all_bin_domain_combinations_encountered
      * @param is_gains_analysis
-     * @param protein_length_stats_by_dc 
+     * @param protein_length_stats_by_dc
      * @throws IOException
      */
     public static void executeFitchGainsAnalysis( final File output_file,
@@ -1099,9 +634,9 @@ public final class SurfacingUtil {
         }
         if ( is_gains_analysis ) {
             out.write( "Sum of all distinct domain combinations appearing once               : " + one
-                    + ForesterUtil.LINE_SEPARATOR );
+                       + ForesterUtil.LINE_SEPARATOR );
             out.write( "Sum of all distinct domain combinations appearing more than once     : " + above_one
-                    + ForesterUtil.LINE_SEPARATOR );
+                       + ForesterUtil.LINE_SEPARATOR );
             out.write( "Sum of all distinct domains in combinations apppearing only once     : "
                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
             out.write( "Sum of all distinct domains in combinations apppearing more than once: "
@@ -1109,31 +644,32 @@ public final class SurfacingUtil {
         }
         else {
             out.write( "Sum of all distinct domain combinations never lost                   : " + never_lost
-                    + ForesterUtil.LINE_SEPARATOR );
+                       + ForesterUtil.LINE_SEPARATOR );
             out.write( "Sum of all distinct domain combinations lost once                    : " + one
-                    + ForesterUtil.LINE_SEPARATOR );
+                       + ForesterUtil.LINE_SEPARATOR );
             out.write( "Sum of all distinct domain combinations lost more than once          : " + above_one
-                    + ForesterUtil.LINE_SEPARATOR );
+                       + ForesterUtil.LINE_SEPARATOR );
             out.write( "Sum of all distinct domains in combinations lost only once           : "
                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
             out.write( "Sum of all distinct domains in combinations lost more than once: "
                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
         }
         out.write( "All binary combinations                                              : " + all
-                + ForesterUtil.LINE_SEPARATOR );
+                   + ForesterUtil.LINE_SEPARATOR );
         out.write( "All domains                                                          : "
                 + sum_of_all_domains_encountered );
         out.close();
         ForesterUtil.programMessage( surfacing.PRG_NAME,
                                      "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
-                                             + "\"" );
+                                     + "\"" );
     }
 
     /**
-     * 
-     * @param all_binary_domains_combination_lost_fitch 
-     * @param use_last_in_fitch_parsimony 
-     * @param consider_directedness_and_adjacency_for_bin_combinations 
+     *
+     * @param all_binary_domains_combination_lost_fitch
+     * @param use_last_in_fitch_parsimony
+     * @param perform_dc_fich
+     * @param consider_directedness_and_adjacency_for_bin_combinations
      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
      * which were gained under unweighted (Fitch) parsimony.
      */
@@ -1157,7 +693,8 @@ public final class SurfacingUtil {
                                                  final Map<String, DescriptiveStatistics> domain_length_stats_by_domain,
                                                  final Map<String, Integer> tax_code_to_id_map,
                                                  final boolean write_to_nexus,
-                                                 final boolean use_last_in_fitch_parsimony ) {
+                                                 final boolean use_last_in_fitch_parsimony,
+                                                 final boolean perform_dc_fich ) {
         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
         final String date_time = ForesterUtil.getCurrentDateTime();
         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
@@ -1178,9 +715,9 @@ public final class SurfacingUtil {
             domain_parsimony.executeDolloParsimonyOnDomainPresence();
         }
         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
-                + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
+                                         + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
-                + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
+                                         + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
                                                            CharacterStateMatrix.GainLossStates.GAIN,
                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
@@ -1194,7 +731,7 @@ public final class SurfacingUtil {
                                                            ForesterUtil.LINE_SEPARATOR,
                                                            null );
         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
-                + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
+                                                           + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
         //HTML:
         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
                                        go_id_to_term_map,
@@ -1251,7 +788,7 @@ public final class SurfacingUtil {
                           "dollo_on_domains_" + outfile_name,
                           parameters_str );
         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
-                + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+                                            + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
         try {
             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
@@ -1260,7 +797,7 @@ public final class SurfacingUtil {
             e.printStackTrace();
             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
         }
-        if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
+        if ( perform_dc_fich && ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) ) {
             // FITCH DOMAIN COMBINATIONS
             // -------------------------
             local_phylogeny_l = phylogeny.copy();
@@ -1273,25 +810,25 @@ public final class SurfacingUtil {
                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( use_last_in_fitch_parsimony );
             }
             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
-                    + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
+                                             + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
-                    + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
+                                             + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
             SurfacingUtil
-                    .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
-                                                          CharacterStateMatrix.GainLossStates.GAIN,
-                                                          outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
-                                                          sep,
-                                                          ForesterUtil.LINE_SEPARATOR,
-                                                          null );
+            .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
+                                                  CharacterStateMatrix.GainLossStates.GAIN,
+                                                  outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
+                                                  sep,
+                                                  ForesterUtil.LINE_SEPARATOR,
+                                                  null );
             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
                                                                CharacterStateMatrix.GainLossStates.LOSS,
                                                                outfile_name
-                                                                       + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
+                                                               + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
                                                                sep,
                                                                ForesterUtil.LINE_SEPARATOR,
                                                                null );
             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
-                    + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
+                                                               + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
             if ( all_binary_domains_combination_gained_fitch != null ) {
                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
                                                                                     dc_type,
@@ -1306,14 +843,14 @@ public final class SurfacingUtil {
             }
             if ( output_binary_domain_combinations_for_graphs ) {
                 SurfacingUtil
-                        .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
-                                                                                                           .getGainLossMatrix(),
-                                                                                                   null,
-                                                                                                   outfile_name
-                                                                                                           + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
-                                                                                                   sep,
-                                                                                                   ForesterUtil.LINE_SEPARATOR,
-                                                                                                   BinaryDomainCombination.OutputFormat.DOT );
+                .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
+                                                                                           .getGainLossMatrix(),
+                                                                                           null,
+                                                                                           outfile_name
+                                                                                           + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
+                                                                                           sep,
+                                                                                           ForesterUtil.LINE_SEPARATOR,
+                                                                                           BinaryDomainCombination.OutputFormat.DOT );
             }
             // HTML:
             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
@@ -1378,19 +915,19 @@ public final class SurfacingUtil {
                               date_time,
                               "Fitch parsimony on binary domain combination presence/absence randomization: "
                                       + randomization,
-                              "fitch_on_binary_domain_combinations_" + outfile_name,
-                              parameters_str );
+                                      "fitch_on_binary_domain_combinations_" + outfile_name,
+                                      parameters_str );
             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
-                    + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
+                                                + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
             calculateIndependentDomainCombinationGains( local_phylogeny_l,
                                                         outfile_name
-                                                                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
+                                                        + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
                                                         outfile_name
-                                                                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
+                                                        + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
                                                         outfile_name
-                                                                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
+                                                        + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
                                                         outfile_name
-                                                                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
+                                                        + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
                                                         outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
                                                         outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
                                                         outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
@@ -1415,33 +952,33 @@ public final class SurfacingUtil {
         Phylogeny local_phylogeny_copy = phylogeny.copy();
         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
-                + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
+                                         + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
-                + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
+                                         + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
         SurfacingUtil
-                .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
-                                                      CharacterStateMatrix.GainLossStates.GAIN,
-                                                      outfile_name
-                                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
-                                                      sep,
-                                                      ForesterUtil.LINE_SEPARATOR,
-                                                      null );
+        .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
+                                              CharacterStateMatrix.GainLossStates.GAIN,
+                                              outfile_name
+                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
+                                              sep,
+                                              ForesterUtil.LINE_SEPARATOR,
+                                              null );
         SurfacingUtil
-                .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
-                                                      CharacterStateMatrix.GainLossStates.LOSS,
-                                                      outfile_name
-                                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
-                                                      sep,
-                                                      ForesterUtil.LINE_SEPARATOR,
-                                                      null );
+        .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
+                                              CharacterStateMatrix.GainLossStates.LOSS,
+                                              outfile_name
+                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
+                                              sep,
+                                              ForesterUtil.LINE_SEPARATOR,
+                                              null );
         SurfacingUtil
-                .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
-                                                      null,
-                                                      outfile_name
-                                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
-                                                      sep,
-                                                      ForesterUtil.LINE_SEPARATOR,
-                                                      null );
+        .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
+                                              null,
+                                              outfile_name
+                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
+                                              sep,
+                                              ForesterUtil.LINE_SEPARATOR,
+                                              null );
         preparePhylogeny( local_phylogeny_copy,
                           secondary_features_parsimony,
                           date_time,
@@ -1449,29 +986,29 @@ public final class SurfacingUtil {
                           "dollo_on_secondary_features_" + outfile_name,
                           parameters_str );
         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
-                + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+                                            + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
         // FITCH DOMAIN COMBINATIONS
         // -------------------------
         local_phylogeny_copy = phylogeny.copy();
         final String randomization = "no";
         secondary_features_parsimony
-                .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony );
+        .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony );
         preparePhylogeny( local_phylogeny_copy,
                           secondary_features_parsimony,
                           date_time,
                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
                                   + randomization,
-                          "fitch_on_binary_domain_combinations_" + outfile_name,
-                          parameters_str );
+                                  "fitch_on_binary_domain_combinations_" + outfile_name,
+                                  parameters_str );
         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
-                + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
+                                            + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
-                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
-                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
-                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
-                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
-                + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
-                + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
+                                                    + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
+                                                    + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
+                                                    + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
+                                                    + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
+                                                    + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
+                                                    + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
     }
 
     public static void executePlusMinusAnalysis( final File output_file,
@@ -1492,7 +1029,7 @@ public final class SurfacingUtil {
         final File html_out_dc = new File( output_file + surfacing.PLUS_MINUS_DC_SUFFIX_HTML );
         final File all_domains_go_ids_out_dom = new File( output_file + surfacing.PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
         final File passing_domains_go_ids_out_dom = new File( output_file
-                + surfacing.PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
+                                                              + surfacing.PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
         final File proteins_file_base = new File( output_file + "" );
         final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
         final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
@@ -1521,7 +1058,7 @@ public final class SurfacingUtil {
         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
                 + plain_out_dom + "\"" );
         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc
-                + "\"" );
+                                     + "\"" );
         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \""
                 + passing_domains_go_ids_out_dom + "\"" );
         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
@@ -1688,9 +1225,9 @@ public final class SurfacingUtil {
             final PhylogenyNode n = it.next();
             if ( ForesterUtil.isEmpty( n.getName() )
                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
-                            .getScientificName() ) )
-                    && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
-                            .getCommonName() ) ) ) {
+                                                                                   .getScientificName() ) )
+                                                                                   && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
+                                                                                                                                                  .getCommonName() ) ) ) {
                 if ( n.getParent() != null ) {
                     names.append( " " );
                     names.append( n.getParent().getName() );
@@ -1732,17 +1269,17 @@ public final class SurfacingUtil {
                         .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
                 if ( p_array.length < 1 ) {
                     ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
-                            + "] does not contain any phylogeny in phyloXML format" );
+                                             + "] does not contain any phylogeny in phyloXML format" );
                 }
                 else if ( p_array.length > 1 ) {
                     ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
-                            + "] contains more than one phylogeny in phyloXML format" );
+                                             + "] contains more than one phylogeny in phyloXML format" );
                 }
                 intree = p_array[ 0 ];
             }
             catch ( final Exception e ) {
                 ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
-                        + "]: " + error );
+                                         + "]: " + error );
             }
             if ( ( intree == null ) || intree.isEmpty() ) {
                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
@@ -1753,9 +1290,9 @@ public final class SurfacingUtil {
             if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
                 ForesterUtil.fatalError( surfacing.PRG_NAME,
                                          "number of external nodes [" + intree.getNumberOfExternalNodes()
-                                                 + "] of input tree [" + intree_file
-                                                 + "] is smaller than the number of genomes the be analyzed ["
-                                                 + number_of_genomes + "]" );
+                                         + "] of input tree [" + intree_file
+                                         + "] is smaller than the number of genomes the be analyzed ["
+                                         + number_of_genomes + "]" );
             }
             final StringBuilder parent_names = new StringBuilder();
             final int nodes_lacking_name = getNumberOfNodesLackingName( intree, parent_names );
@@ -1766,7 +1303,7 @@ public final class SurfacingUtil {
             preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
             if ( !intree.isCompletelyBinary() ) {
                 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
-                        + "] is not completely binary" );
+                                                  + "] is not completely binary" );
             }
             intrees[ i++ ] = intree;
         }
@@ -1784,11 +1321,11 @@ public final class SurfacingUtil {
                     .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
             if ( phys.length < 1 ) {
                 ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
-                        + "] does not contain any phylogeny in phyloXML format" );
+                                         + "] does not contain any phylogeny in phyloXML format" );
             }
             else if ( phys.length > 1 ) {
                 ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
-                        + "] contains more than one phylogeny in phyloXML format" );
+                                         + "] contains more than one phylogeny in phyloXML format" );
             }
             intree = phys[ 0 ];
         }
@@ -1805,6 +1342,90 @@ public final class SurfacingUtil {
         return intree;
     }
 
+    public static String obtainHexColorStringDependingOnTaxonomyGroup( final String tax_code, final Phylogeny phy )
+            throws IllegalArgumentException {
+        if ( !_TAXCODE_HEXCOLORSTRING_MAP.containsKey( tax_code ) ) {
+            if ( ( phy != null ) && !phy.isEmpty() ) {
+                //                final List<PhylogenyNode> nodes = phy.getNodesViaTaxonomyCode( tax_code );
+                //                Color c = null;
+                //                if ( ( nodes == null ) || nodes.isEmpty() ) {
+                //                    throw new IllegalArgumentException( "code " + tax_code + " is not found" );
+                //                }
+                //                if ( nodes.size() != 1 ) {
+                //                    throw new IllegalArgumentException( "code " + tax_code + " is not unique" );
+                //                }
+                //                PhylogenyNode n = nodes.get( 0 );
+                //                while ( n != null ) {
+                //                    if ( n.getNodeData().isHasTaxonomy()
+                //                            && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+                //                        c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getNodeData().getTaxonomy()
+                //                                .getScientificName(), tax_code );
+                //                    }
+                //                    if ( ( c == null ) && !ForesterUtil.isEmpty( n.getName() ) ) {
+                //                        c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getName(), tax_code );
+                //                    }
+                //                    if ( c != null ) {
+                //                        break;
+                //                    }
+                //                    n = n.getParent();
+                //                }
+                final String group = obtainTaxonomyGroup( tax_code, phy );
+                final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+                if ( c == null ) {
+                    throw new IllegalArgumentException( "no color found for taxonomy group \"" + group
+                                                        + "\" for code \"" + tax_code + "\"" );
+                }
+                final String hex = String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() );
+                _TAXCODE_HEXCOLORSTRING_MAP.put( tax_code, hex );
+            }
+            else {
+                throw new IllegalArgumentException( "unable to obtain color for code " + tax_code
+                                                    + " (tree is null or empty and code is not in map)" );
+            }
+        }
+        return _TAXCODE_HEXCOLORSTRING_MAP.get( tax_code );
+    }
+
+    public static String obtainTaxonomyGroup( final String tax_code, final Phylogeny species_tree )
+            throws IllegalArgumentException {
+        if ( !_TAXCODE_TAXGROUP_MAP.containsKey( tax_code ) ) {
+            if ( ( species_tree != null ) && !species_tree.isEmpty() ) {
+                final List<PhylogenyNode> nodes = species_tree.getNodesViaTaxonomyCode( tax_code );
+                if ( ( nodes == null ) || nodes.isEmpty() ) {
+                    throw new IllegalArgumentException( "code " + tax_code + " is not found" );
+                }
+                if ( nodes.size() != 1 ) {
+                    throw new IllegalArgumentException( "code " + tax_code + " is not unique" );
+                }
+                PhylogenyNode n = nodes.get( 0 );
+                String group = null;
+                while ( n != null ) {
+                    if ( n.getNodeData().isHasTaxonomy()
+                            && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+                        group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getNodeData().getTaxonomy()
+                                                                            .getScientificName() );
+                    }
+                    if ( ForesterUtil.isEmpty( group ) && !ForesterUtil.isEmpty( n.getName() ) ) {
+                        group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getName() );
+                    }
+                    if ( !ForesterUtil.isEmpty( group ) ) {
+                        break;
+                    }
+                    n = n.getParent();
+                }
+                if ( ForesterUtil.isEmpty( group ) ) {
+                    throw new IllegalArgumentException( "no group found for taxonomy code \"" + tax_code + "\"" );
+                }
+                _TAXCODE_TAXGROUP_MAP.put( tax_code, group );
+            }
+            else {
+                throw new IllegalArgumentException( "unable to obtain group for code " + tax_code
+                                                    + " (tree is null or empty and code is not in map)" );
+            }
+        }
+        return _TAXCODE_TAXGROUP_MAP.get( tax_code );
+    }
+
     public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
                                                           final SortedMap<String, Integer> domain_architecuture_counts,
                                                           final int min_count,
@@ -1902,8 +1523,8 @@ public final class SurfacingUtil {
                 }
                 else {
                     ForesterUtil
-                            .fatalError( surfacing.PRG_NAME,
-                                         "node with no name, scientific name, common name, or taxonomy code present" );
+                    .fatalError( surfacing.PRG_NAME,
+                                 "node with no name, scientific name, common name, or taxonomy code present" );
                 }
             }
         }
@@ -1938,42 +1559,6 @@ public final class SurfacingUtil {
         log( "Percentage of multidomain proteins:            : " + percentage + "%", log_writer );
     }
 
-    private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
-            throws IOException {
-        w.write( "<hr>" );
-        w.write( "<br>" );
-        w.write( SurfacingConstants.NL );
-        w.write( "<tt><pre>" );
-        w.write( SurfacingConstants.NL );
-        if ( histo != null ) {
-            w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
-            w.write( SurfacingConstants.NL );
-        }
-        w.write( "</pre></tt>" );
-        w.write( SurfacingConstants.NL );
-        w.write( "<table>" );
-        w.write( SurfacingConstants.NL );
-        w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
-        w.write( SurfacingConstants.NL );
-        w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
-        w.write( SurfacingConstants.NL );
-        w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
-        w.write( SurfacingConstants.NL );
-        w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
-        w.write( SurfacingConstants.NL );
-        if ( stats.getN() > 1 ) {
-            w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
-        }
-        else {
-            w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
-        }
-        w.write( SurfacingConstants.NL );
-        w.write( "</table>" );
-        w.write( SurfacingConstants.NL );
-        w.write( "<br>" );
-        w.write( SurfacingConstants.NL );
-    }
-
     public static void processFilter( final File filter_file, final SortedSet<String> filter ) {
         SortedSet<String> filter_str = null;
         try {
@@ -2115,9 +1700,9 @@ public final class SurfacingUtil {
                 }
                 else {
                     ForesterUtil
-                            .fatalError( surfacing.PRG_NAME,
-                                         "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
-                                                 + species + "\"" );
+                    .fatalError( surfacing.PRG_NAME,
+                                 "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
+                                         + species + "\"" );
                 }
                 numbers.add( new Integer( min_diff + "" ) );
                 numbers.add( new Double( factor + "" ) );
@@ -2130,8 +1715,8 @@ public final class SurfacingUtil {
 
     /*
      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
-     * 
-     * 
+     *
+     *
      */
     static public StringBuffer proteinToDomainCombinations( final Protein protein,
                                                             final String protein_id,
@@ -2226,19 +1811,6 @@ public final class SurfacingUtil {
         return domains;
     }
 
-    private static List<String> splitDomainCombination( final String dc ) {
-        final String[] s = dc.split( "=" );
-        if ( s.length != 2 ) {
-            ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
-                    + dc );
-            System.exit( -1 );
-        }
-        final List<String> l = new ArrayList<String>( 2 );
-        l.add( s[ 0 ] );
-        l.add( s[ 1 ] );
-        return l;
-    }
-
     public static int storeDomainArchitectures( final String genome,
                                                 final SortedMap<String, Set<String>> domain_architecutures,
                                                 final List<Protein> protein_list,
@@ -2279,7 +1851,7 @@ public final class SurfacingUtil {
                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
                 if ( domains.size() > 0 ) {
                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
-                            + node.getName() + suffix_for_filename );
+                                                                             + node.getName() + suffix_for_filename );
                     for( final String domain : domains ) {
                         writer.write( domain );
                         writer.write( ForesterUtil.LINE_SEPARATOR );
@@ -2290,171 +1862,40 @@ public final class SurfacingUtil {
         }
     }
 
-    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 ) {
-        final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
-        final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
-                + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
-        final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
-        int biological_process_counter = 0;
-        int cellular_component_counter = 0;
-        int molecular_function_counter = 0;
-        int pfams_with_mappings_counter = 0;
-        int pfams_without_mappings_counter = 0;
-        int pfams_without_mappings_to_bp_or_mf_counter = 0;
-        int pfams_with_mappings_to_bp_or_mf_counter = 0;
+    public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
+                                                                          final File output_dir,
+                                                                          final GenomeWideCombinableDomains gwcd,
+                                                                          final int i,
+                                                                          final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
+        File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
+                + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
+        if ( output_dir != null ) {
+            dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
+        }
+        checkForOutputFileWriteability( dc_outfile_dot );
+        final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
         try {
-            final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
-            final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
-            final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
-            summary_writer.write( "# Pfam to GO mapping summary" );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.write( "# Actual summary is at the end of this file." );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.write( "# Encountered Pfams without a GO mapping:" );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            for( final String pfam : all_pfams_encountered ) {
-                all_pfams_encountered_writer.write( pfam );
-                all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
-                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 );
-                    all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
-                    final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
-                    boolean maps_to_bp = false;
-                    boolean maps_to_cc = false;
-                    boolean maps_to_mf = false;
-                    for( final GoId go_id : go_ids ) {
-                        final GoTerm go_term = go_id_to_term_map.get( go_id );
-                        if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
-                            maps_to_bp = true;
-                        }
-                        else if ( go_term.getGoNameSpace().isCellularComponent() ) {
-                            maps_to_cc = true;
-                        }
-                        else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
-                            maps_to_mf = true;
-                        }
-                    }
-                    if ( maps_to_bp ) {
-                        ++biological_process_counter;
-                    }
-                    if ( maps_to_cc ) {
-                        ++cellular_component_counter;
-                    }
-                    if ( maps_to_mf ) {
-                        ++molecular_function_counter;
-                    }
-                    if ( maps_to_bp || maps_to_mf ) {
-                        ++pfams_with_mappings_to_bp_or_mf_counter;
-                    }
-                    else {
-                        ++pfams_without_mappings_to_bp_or_mf_counter;
-                    }
-                }
-                else {
-                    ++pfams_without_mappings_to_bp_or_mf_counter;
-                    ++pfams_without_mappings_counter;
-                    summary_writer.write( pfam );
-                    summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-                }
-            }
-            all_pfams_encountered_writer.close();
-            all_pfams_encountered_with_go_annotation_writer.close();
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
-                    + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
-                    + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
-                    + "\"" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
-                    + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
-                    + encountered_pfams_summary_file + "\"" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
-                    + all_pfams_encountered.size() );
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
-                    + pfams_without_mappings_counter + " ["
-                    + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
-                    + pfams_without_mappings_to_bp_or_mf_counter + " ["
-                    + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping                    : "
-                    + pfams_with_mappings_counter + " ["
-                    + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
-                    + pfams_with_mappings_to_bp_or_mf_counter + " ["
-                    + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
-                    + biological_process_counter + " ["
-                    + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
-                    + molecular_function_counter + " ["
-                    + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
-                    + cellular_component_counter + " ["
-                    + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
-                    + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.write( "# Pfams without mapping to proc. or func. : "
-                    + pfams_without_mappings_to_bp_or_mf_counter + " ["
-                    + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
-                    + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
-                    + pfams_with_mappings_to_bp_or_mf_counter + " ["
-                    + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
-                    + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
-                    + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
-                    + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
-            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
-            summary_writer.close();
-        }
-        catch ( final IOException e ) {
-            ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
-        }
-    }
-
-    public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
-                                                                          final File output_dir,
-                                                                          final GenomeWideCombinableDomains gwcd,
-                                                                          final int i,
-                                                                          final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
-        File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
-                + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
-        if ( output_dir != null ) {
-            dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
-        }
-        checkForOutputFileWriteability( dc_outfile_dot );
-        final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
-        try {
-            final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
-            for( final BinaryDomainCombination bdc : binary_combinations ) {
-                out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
-                        .toString() );
-                out_dot.write( SurfacingConstants.NL );
+            final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
+            for( final BinaryDomainCombination bdc : binary_combinations ) {
+                out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
+                               .toString() );
+                out_dot.write( SurfacingConstants.NL );
             }
             out_dot.close();
         }
         catch ( final IOException e ) {
             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
         }
-        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
-                + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
-                + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
+        if ( input_file_properties[ i ].length == 3 ) {
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
+                    + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+                    + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
+        }
+        else {
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
+                    + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
+                    + dc_outfile_dot + "\"" );
+        }
     }
 
     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
@@ -2526,7 +1967,7 @@ public final class SurfacingUtil {
                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
                         BinaryDomainCombination bdc = null;
                         try {
-                            bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
+                            bdc = BasicBinaryDomainCombination.obtainInstance( matrix.getCharacter( c ) );
                         }
                         catch ( final Exception e ) {
                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
@@ -2587,7 +2028,7 @@ public final class SurfacingUtil {
             int per_node_counter = 0;
             out.write( "<html>" );
             out.write( SurfacingConstants.NL );
-            addHtmlHead( out, title_for_html );
+            writeHtmlHead( out, title_for_html );
             out.write( SurfacingConstants.NL );
             out.write( "<body>" );
             out.write( SurfacingConstants.NL );
@@ -2643,7 +2084,7 @@ public final class SurfacingUtil {
                 per_node_counter = 0;
                 if ( matrix.getNumberOfCharacters() > 0 ) {
                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
-                            + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
+                                                                            + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
@@ -2712,7 +2153,7 @@ public final class SurfacingUtil {
                 out.write( SurfacingConstants.NL );
                 out.write( "<hr>" );
                 out.write( SurfacingConstants.NL );
-            } // for( final String id : sorted_ids ) {  
+            } // for( final String id : sorted_ids ) {
             out.write( "</body>" );
             out.write( SurfacingConstants.NL );
             out.write( "</html>" );
@@ -2755,7 +2196,7 @@ public final class SurfacingUtil {
             }
             else {
                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
-                        .sampleStandardDeviation() ) + "\t" );
+                                                                                           .sampleStandardDeviation() ) + "\t" );
             }
             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
@@ -2768,20 +2209,970 @@ public final class SurfacingUtil {
             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
         }
         catch ( final IOException e ) {
-            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
-        }
-        if ( input_file_properties[ i ].length == 3 ) {
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
-                    + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
-                    + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
-        }
-        else {
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
-                    + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
-                    + dc_outfile + "\"" );
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+        }
+        if ( input_file_properties[ i ].length == 3 ) {
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
+                    + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+                    + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
+        }
+        else {
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
+                    + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
+                    + dc_outfile + "\"" );
+        }
+    }
+
+    public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
+                                                      final StringBuilder html_title,
+                                                      final Writer simple_tab_writer,
+                                                      final Writer single_writer,
+                                                      Map<Character, Writer> split_writers,
+                                                      final SortedSet<DomainSimilarity> similarities,
+                                                      final boolean treat_as_binary,
+                                                      final List<Species> species_order,
+                                                      final DomainSimilarity.PRINT_OPTION print_option,
+                                                      final DomainSimilarity.DomainSimilarityScoring scoring,
+                                                      final boolean verbose,
+                                                      final Map<String, Integer> tax_code_to_id_map,
+                                                      final Phylogeny phy,
+                                                      final Set<String> pos_filter_doms ) throws IOException {
+        if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
+            split_writers = new HashMap<Character, Writer>();
+            split_writers.put( '_', single_writer );
+        }
+        switch ( print_option ) {
+            case SIMPLE_TAB_DELIMITED:
+                break;
+            case HTML:
+                for( final Character key : split_writers.keySet() ) {
+                    final Writer w = split_writers.get( key );
+                    w.write( "<html>" );
+                    w.write( SurfacingConstants.NL );
+                    if ( key != '_' ) {
+                        writeHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
+                    }
+                    else {
+                        writeHtmlHead( w, "DC analysis (" + html_title + ")" );
+                    }
+                    w.write( SurfacingConstants.NL );
+                    w.write( "<body>" );
+                    w.write( SurfacingConstants.NL );
+                    w.write( html_desc.toString() );
+                    w.write( SurfacingConstants.NL );
+                    w.write( "<hr>" );
+                    w.write( SurfacingConstants.NL );
+                    w.write( "<br>" );
+                    w.write( SurfacingConstants.NL );
+                    w.write( "<table>" );
+                    w.write( SurfacingConstants.NL );
+                    w.write( "<tr><td><b>Domains:</b></td></tr>" );
+                    w.write( SurfacingConstants.NL );
+                }
+                break;
+        }
+        //
+        for( final DomainSimilarity similarity : similarities ) {
+            if ( ( species_order != null ) && !species_order.isEmpty() ) {
+                ( similarity ).setSpeciesOrder( species_order );
+            }
+            if ( single_writer != null ) {
+                if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) {
+                    single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId()
+                                         + "\"><span style=\"color:#00ff00\">" + similarity.getDomainId()
+                                         + "</span></a></b></td></tr>" );
+                }
+                else {
+                    single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+                            + similarity.getDomainId() + "</a></b></td></tr>" );
+                }
+                single_writer.write( SurfacingConstants.NL );
+            }
+            else {
+                Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
+                                                         .charAt( 0 ) );
+                if ( local_writer == null ) {
+                    local_writer = split_writers.get( '0' );
+                }
+                if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) {
+                    local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId()
+                                        + "\"><span style=\"color:#00ff00\">" + similarity.getDomainId()
+                                        + "</span></a></b></td></tr>" );
+                }
+                else {
+                    local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+                            + similarity.getDomainId() + "</a></b></td></tr>" );
+                }
+                local_writer.write( SurfacingConstants.NL );
+            }
+        }
+        for( final Writer w : split_writers.values() ) {
+            w.write( "</table>" );
+            w.write( SurfacingConstants.NL );
+            w.write( "<hr>" );
+            w.write( SurfacingConstants.NL );
+            //
+            w.write( "<table>" );
+            w.write( SurfacingConstants.NL );
+            w.write( "<tr><td><b>" );
+            w.write( "Species group colors:" );
+            w.write( "</b></td></tr>" );
+            w.write( SurfacingConstants.NL );
+            writeColorLabels( "Deuterostomia", TaxonomyColors.DEUTEROSTOMIA_COLOR, w );
+            writeColorLabels( "Protostomia", TaxonomyColors.PROTOSTOMIA_COLOR, w );
+            writeColorLabels( "Cnidaria", TaxonomyColors.CNIDARIA_COLOR, w );
+            writeColorLabels( "Placozoa", TaxonomyColors.PLACOZOA_COLOR, w );
+            writeColorLabels( "Ctenophora (comb jellies)", TaxonomyColors.CTENOPHORA_COLOR, w );
+            writeColorLabels( "Porifera (sponges)", TaxonomyColors.PORIFERA_COLOR, w );
+            writeColorLabels( "Choanoflagellida", TaxonomyColors.CHOANOFLAGELLIDA, w );
+            writeColorLabels( "Ichthyosporea & Filasterea", TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA, w );
+            writeColorLabels( "Dikarya (Ascomycota & Basidiomycota, so-called \"higher fungi\")",
+                              TaxonomyColors.DIKARYA_COLOR,
+                              w );
+            writeColorLabels( "other Fungi", TaxonomyColors.OTHER_FUNGI_COLOR, w );
+            writeColorLabels( "Nucleariidae and Fonticula group",
+                              TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR,
+                              w );
+            writeColorLabels( "Amoebozoa", TaxonomyColors.AMOEBOZOA_COLOR, w );
+            writeColorLabels( "Embryophyta (plants)", TaxonomyColors.EMBRYOPHYTA_COLOR, w );
+            writeColorLabels( "Chlorophyta (green algae)", TaxonomyColors.CHLOROPHYTA_COLOR, w );
+            writeColorLabels( "Rhodophyta (red algae)", TaxonomyColors.RHODOPHYTA_COLOR, w );
+            writeColorLabels( "Glaucocystophyce (Glaucophyta)", TaxonomyColors.GLAUCOPHYTA_COLOR, w );
+            writeColorLabels( "Hacrobia (Cryptophyta & Haptophyceae & Centroheliozoa)",
+                              TaxonomyColors.HACROBIA_COLOR,
+                              w );
+            writeColorLabels( "Stramenopiles (Chromophyta, heterokonts)", TaxonomyColors.STRAMENOPILES_COLOR, w );
+            writeColorLabels( "Alveolata", TaxonomyColors.ALVEOLATA_COLOR, w );
+            writeColorLabels( "Rhizaria", TaxonomyColors.RHIZARIA_COLOR, w );
+            writeColorLabels( "Excavata", TaxonomyColors.EXCAVATA_COLOR, w );
+            writeColorLabels( "Apusozoa", TaxonomyColors.APUSOZOA_COLOR, w );
+            writeColorLabels( "Archaea", TaxonomyColors.ARCHAEA_COLOR, w );
+            writeColorLabels( "Bacteria", TaxonomyColors.BACTERIA_COLOR, w );
+            w.write( "</table>" );
+            w.write( SurfacingConstants.NL );
+            //
+            w.write( "<hr>" );
+            w.write( SurfacingConstants.NL );
+            w.write( "<table>" );
+            w.write( SurfacingConstants.NL );
+        }
+        //
+        for( final DomainSimilarity similarity : similarities ) {
+            if ( ( species_order != null ) && !species_order.isEmpty() ) {
+                ( similarity ).setSpeciesOrder( species_order );
+            }
+            if ( simple_tab_writer != null ) {
+                simple_tab_writer.write( similarity.toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED,
+                                                                    tax_code_to_id_map,
+                                                                    null ).toString() );
+            }
+            if ( single_writer != null ) {
+                single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
+                single_writer.write( SurfacingConstants.NL );
+            }
+            else {
+                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, phy ).toString() );
+                local_writer.write( SurfacingConstants.NL );
+            }
+        }
+        switch ( print_option ) {
+            case HTML:
+                for( final Writer w : split_writers.values() ) {
+                    w.write( SurfacingConstants.NL );
+                    w.write( "</table>" );
+                    w.write( SurfacingConstants.NL );
+                    w.write( "</font>" );
+                    w.write( SurfacingConstants.NL );
+                    w.write( "</body>" );
+                    w.write( SurfacingConstants.NL );
+                    w.write( "</html>" );
+                    w.write( SurfacingConstants.NL );
+                }
+                break;
+            default:
+                break;
+        }
+        for( final Writer w : split_writers.values() ) {
+            w.close();
+        }
+    }
+
+    public static void writeHtmlHead( final Writer w, final String title ) throws IOException {
+        w.write( SurfacingConstants.NL );
+        w.write( "<head>" );
+        w.write( "<title>" );
+        w.write( title );
+        w.write( "</title>" );
+        w.write( SurfacingConstants.NL );
+        w.write( "<style>" );
+        w.write( SurfacingConstants.NL );
+        w.write( "a:visited { color : #000066; text-decoration : none; }" );
+        w.write( SurfacingConstants.NL );
+        w.write( "a:link { color : #000066; text-decoration : none; }" );
+        w.write( SurfacingConstants.NL );
+        w.write( "a:active { color : ##000066; text-decoration : none; }" );
+        w.write( SurfacingConstants.NL );
+        w.write( "a:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; }" );
+        w.write( SurfacingConstants.NL );
+        //
+        w.write( "a.pl:visited { color : #505050; text-decoration : none; font-size: 7px;}" );
+        w.write( SurfacingConstants.NL );
+        w.write( "a.pl:link { color : #505050; text-decoration : none; font-size: 7px;}" );
+        w.write( SurfacingConstants.NL );
+        w.write( "a.pl:active { color : #505050; text-decoration : none; font-size: 7px;}" );
+        w.write( SurfacingConstants.NL );
+        w.write( "a.pl:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; font-size: 7px;}" );
+        w.write( SurfacingConstants.NL );
+        //
+        w.write( "a.ps:visited { color : #707070; text-decoration : none; font-size: 7px;}" );
+        w.write( SurfacingConstants.NL );
+        w.write( "a.ps:link { color : #707070; text-decoration : none; font-size: 7px;}" );
+        w.write( SurfacingConstants.NL );
+        w.write( "a.ps:active { color : #707070; text-decoration : none; font-size: 7px;}" );
+        w.write( SurfacingConstants.NL );
+        w.write( "a.ps:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; font-size: 7px;}" );
+        w.write( SurfacingConstants.NL );
+        //
+        w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
+        w.write( SurfacingConstants.NL );
+        w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
+        w.write( SurfacingConstants.NL );
+        w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
+        w.write( SurfacingConstants.NL );
+        w.write( "</style>" );
+        w.write( SurfacingConstants.NL );
+        w.write( "</head>" );
+        w.write( SurfacingConstants.NL );
+    }
+
+    public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
+                                          final String filename,
+                                          final Format format ) {
+        final File outfile = new File( filename );
+        checkForOutputFileWriteability( outfile );
+        try {
+            final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
+            matrix.toWriter( out, format );
+            out.flush();
+            out.close();
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+        }
+        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
+    }
+
+    public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
+        checkForOutputFileWriteability( matrix_outfile );
+        try {
+            final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
+            for( final DistanceMatrix distance_matrix : matrices ) {
+                out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
+                out.write( ForesterUtil.LINE_SEPARATOR );
+                out.flush();
+            }
+            out.close();
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+        }
+        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
+    }
+
+    public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
+        final PhylogenyWriter writer = new PhylogenyWriter();
+        try {
+            writer.toPhyloXML( new File( filename ), phylogeny, 1 );
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
+                    + e );
+        }
+        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
+    }
+
+    public static void writePresentToNexus( final File output_file,
+                                            final File positive_filter_file,
+                                            final SortedSet<String> filter,
+                                            final List<GenomeWideCombinableDomains> gwcd_list ) {
+        try {
+            writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence( gwcd_list,
+                                                                                                positive_filter_file == null ? null
+                                                                                                        : filter ),
+                                                                                                        output_file + surfacing.DOMAINS_PRESENT_NEXUS,
+                                                                                                        Format.NEXUS_BINARY );
+            writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ),
+                               output_file + surfacing.BDC_PRESENT_NEXUS,
+                               Format.NEXUS_BINARY );
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+        }
+    }
+
+    public static void writeProteinListsForAllSpecies( final File output_dir,
+                                                       final SortedMap<Species, List<Protein>> protein_lists_per_species,
+                                                       final List<GenomeWideCombinableDomains> gwcd_list,
+                                                       final double domain_e_cutoff,
+                                                       final Set<String> pos_filter_doms ) {
+        final SortedSet<String> all_domains = new TreeSet<String>();
+        for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+            all_domains.addAll( gwcd.getAllDomainIds() );
+        }
+        for( final String domain : all_domains ) {
+            if ( !ForesterUtil.isEmpty( pos_filter_doms ) && !pos_filter_doms.contains( domain ) ) {
+                continue;
+            }
+            final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + surfacing.SEQ_EXTRACT_SUFFIX );
+            checkForOutputFileWriteability( out );
+            try {
+                final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
+                extractProteinNames( protein_lists_per_species,
+                                     domain,
+                                     proteins_file_writer,
+                                     "\t",
+                                     surfacing.LIMIT_SPEC_FOR_PROT_EX,
+                                     domain_e_cutoff );
+                proteins_file_writer.close();
+            }
+            catch ( final IOException e ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+            }
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
+        }
+    }
+
+    public static void writeTaxonomyLinks( final Writer writer,
+                                           final String species,
+                                           final Map<String, Integer> tax_code_to_id_map ) throws IOException {
+        if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
+            writer.write( " [" );
+            if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
+                writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
+                              + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot</a>" );
+            }
+            else {
+                writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
+                              + "\" target=\"taxonomy_window\">eol</a>" );
+                writer.write( "|" );
+                writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
+                              + "\" target=\"taxonomy_window\">scholar</a>" );
+                writer.write( "|" );
+                writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
+                              + "\" target=\"taxonomy_window\">google</a>" );
+            }
+            writer.write( "]" );
+        }
+    }
+
+    private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
+        if ( map.containsKey( s ) ) {
+            map.put( s, map.get( s ) + 1 );
+        }
+        else {
+            map.put( s, 1 );
+        }
+    }
+
+    private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
+                                                                    final String outfilename_for_counts,
+                                                                    final String outfilename_for_dc,
+                                                                    final String outfilename_for_dc_for_go_mapping,
+                                                                    final String outfilename_for_dc_for_go_mapping_unique,
+                                                                    final String outfilename_for_rank_counts,
+                                                                    final String outfilename_for_ancestor_species_counts,
+                                                                    final String outfilename_for_protein_stats,
+                                                                    final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
+                                                                    final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
+                                                                    final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
+        try {
+            //
+            //            if ( protein_length_stats_by_dc != null ) {
+            //                for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
+            //                    System.out.print( entry.getKey().toString() );
+            //                    System.out.print( ": " );
+            //                    double[] a = entry.getValue().getDataAsDoubleArray();
+            //                    for( int i = 0; i < a.length; i++ ) {
+            //                        System.out.print( a[ i ] + " " );
+            //                    }
+            //                    System.out.println();
+            //                }
+            //            }
+            //            if ( domain_number_stats_by_dc != null ) {
+            //                for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
+            //                    System.out.print( entry.getKey().toString() );
+            //                    System.out.print( ": " );
+            //                    double[] a = entry.getValue().getDataAsDoubleArray();
+            //                    for( int i = 0; i < a.length; i++ ) {
+            //                        System.out.print( a[ i ] + " " );
+            //                    }
+            //                    System.out.println();
+            //                }
+            //            }
+            //
+            final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
+            final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
+            final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
+            final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
+            final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
+            for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
+                final PhylogenyNode n = it.next();
+                final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
+                for( final String dc : gained_dc ) {
+                    if ( dc_gain_counts.containsKey( dc ) ) {
+                        dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
+                    }
+                    else {
+                        dc_gain_counts.put( dc, 1 );
+                    }
+                }
+            }
+            final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
+            final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
+            final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
+            final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
+            final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
+            final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
+            final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
+            final Set<String> dcs = dc_gain_counts.keySet();
+            final SortedSet<String> more_than_once = new TreeSet<String>();
+            DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
+            DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
+            DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
+            final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
+            long gained_multiple_times_domain_length_sum = 0;
+            long gained_once_domain_length_sum = 0;
+            long gained_multiple_times_domain_length_count = 0;
+            long gained_once_domain_length_count = 0;
+            for( final String dc : dcs ) {
+                final int count = dc_gain_counts.get( dc );
+                if ( histogram.containsKey( count ) ) {
+                    histogram.put( count, histogram.get( count ) + 1 );
+                    domain_lists.get( count ).append( ", " + dc );
+                    domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
+                    domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
+                }
+                else {
+                    histogram.put( count, 1 );
+                    domain_lists.put( count, new StringBuilder( dc ) );
+                    final PriorityQueue<String> q = new PriorityQueue<String>();
+                    q.addAll( splitDomainCombination( dc ) );
+                    domain_lists_go.put( count, q );
+                    final SortedSet<String> set = new TreeSet<String>();
+                    set.addAll( splitDomainCombination( dc ) );
+                    domain_lists_go_unique.put( count, set );
+                }
+                if ( protein_length_stats_by_dc != null ) {
+                    if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
+                        dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
+                    }
+                    dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
+                                                                                   .arithmeticMean() );
+                }
+                if ( domain_number_stats_by_dc != null ) {
+                    if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
+                        dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
+                    }
+                    dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
+                                                                                  .arithmeticMean() );
+                }
+                if ( domain_length_stats_by_domain != null ) {
+                    if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
+                        dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
+                    }
+                    final String[] ds = dc.split( "=" );
+                    dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
+                                                                                   .get( ds[ 0 ] ).arithmeticMean() );
+                    dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
+                                                                                   .get( ds[ 1 ] ).arithmeticMean() );
+                }
+                if ( count > 1 ) {
+                    more_than_once.add( dc );
+                    if ( protein_length_stats_by_dc != null ) {
+                        final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
+                        for( final double element : s.getData() ) {
+                            gained_multiple_times_lengths_stats.addValue( element );
+                        }
+                    }
+                    if ( domain_number_stats_by_dc != null ) {
+                        final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
+                        for( final double element : s.getData() ) {
+                            gained_multiple_times_domain_count_stats.addValue( element );
+                        }
+                    }
+                    if ( domain_length_stats_by_domain != null ) {
+                        final String[] ds = dc.split( "=" );
+                        final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
+                        final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
+                        for( final double element : s0.getData() ) {
+                            gained_multiple_times_domain_length_sum += element;
+                            ++gained_multiple_times_domain_length_count;
+                        }
+                        for( final double element : s1.getData() ) {
+                            gained_multiple_times_domain_length_sum += element;
+                            ++gained_multiple_times_domain_length_count;
+                        }
+                    }
+                }
+                else {
+                    if ( protein_length_stats_by_dc != null ) {
+                        final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
+                        for( final double element : s.getData() ) {
+                            gained_once_lengths_stats.addValue( element );
+                        }
+                    }
+                    if ( domain_number_stats_by_dc != null ) {
+                        final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
+                        for( final double element : s.getData() ) {
+                            gained_once_domain_count_stats.addValue( element );
+                        }
+                    }
+                    if ( domain_length_stats_by_domain != null ) {
+                        final String[] ds = dc.split( "=" );
+                        final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
+                        final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
+                        for( final double element : s0.getData() ) {
+                            gained_once_domain_length_sum += element;
+                            ++gained_once_domain_length_count;
+                        }
+                        for( final double element : s1.getData() ) {
+                            gained_once_domain_length_sum += element;
+                            ++gained_once_domain_length_count;
+                        }
+                    }
+                }
+            }
+            final Set<Integer> histogram_keys = histogram.keySet();
+            for( final Integer histogram_key : histogram_keys ) {
+                final int count = histogram.get( histogram_key );
+                final StringBuilder dc = domain_lists.get( histogram_key );
+                out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
+                out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
+                out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
+                final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
+                Arrays.sort( sorted );
+                for( final Object domain : sorted ) {
+                    out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
+                }
+                out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
+                for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
+                    out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
+                }
+            }
+            out_counts.close();
+            out_dc.close();
+            out_dc_for_go_mapping.close();
+            out_dc_for_go_mapping_unique.close();
+            final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
+            final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
+            for( final String dc : more_than_once ) {
+                final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+                for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
+                    final PhylogenyNode n = it.next();
+                    if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
+                        nodes.add( n );
+                    }
+                }
+                for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
+                    for( int j = i + 1; j < nodes.size(); ++j ) {
+                        final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
+                        String rank = "unknown";
+                        if ( lca.getNodeData().isHasTaxonomy()
+                                && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
+                            rank = lca.getNodeData().getTaxonomy().getRank();
+                        }
+                        addToCountMap( lca_rank_counts, rank );
+                        String lca_species;
+                        if ( lca.getNodeData().isHasTaxonomy()
+                                && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
+                            lca_species = lca.getNodeData().getTaxonomy().getScientificName();
+                        }
+                        else if ( lca.getNodeData().isHasTaxonomy()
+                                && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
+                            lca_species = lca.getNodeData().getTaxonomy().getCommonName();
+                        }
+                        else {
+                            lca_species = lca.getName();
+                        }
+                        addToCountMap( lca_ancestor_species_counts, lca_species );
+                    }
+                }
+            }
+            final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
+            final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
+            ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
+            ForesterUtil.map2writer( out_for_ancestor_species_counts,
+                                     lca_ancestor_species_counts,
+                                     "\t",
+                                     ForesterUtil.LINE_SEPARATOR );
+            out_for_rank_counts.close();
+            out_for_ancestor_species_counts.close();
+            if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
+                    && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
+                final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
+                w.write( "Domain Lengths: " );
+                w.write( "\n" );
+                if ( domain_length_stats_by_domain != null ) {
+                    for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
+                            .entrySet() ) {
+                        w.write( entry.getKey().toString() );
+                        w.write( "\t" + entry.getValue().arithmeticMean() );
+                        w.write( "\t" + entry.getValue().median() );
+                        w.write( "\n" );
+                    }
+                }
+                w.flush();
+                w.write( "\n" );
+                w.write( "\n" );
+                w.write( "Protein Lengths: " );
+                w.write( "\n" );
+                if ( protein_length_stats_by_dc != null ) {
+                    for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
+                            .entrySet() ) {
+                        w.write( entry.getKey().toString() );
+                        w.write( "\t" + entry.getValue().arithmeticMean() );
+                        w.write( "\t" + entry.getValue().median() );
+                        w.write( "\n" );
+                    }
+                }
+                w.flush();
+                w.write( "\n" );
+                w.write( "\n" );
+                w.write( "Number of domains: " );
+                w.write( "\n" );
+                if ( domain_number_stats_by_dc != null ) {
+                    for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
+                            .entrySet() ) {
+                        w.write( entry.getKey().toString() );
+                        w.write( "\t" + entry.getValue().arithmeticMean() );
+                        w.write( "\t" + entry.getValue().median() );
+                        w.write( "\n" );
+                    }
+                }
+                w.flush();
+                w.write( "\n" );
+                w.write( "\n" );
+                w.write( "Gained once, domain lengths:" );
+                w.write( "\n" );
+                w.write( "N: " + gained_once_domain_length_count );
+                w.write( "\n" );
+                w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
+                w.write( "\n" );
+                w.write( "\n" );
+                w.write( "Gained multiple times, domain lengths:" );
+                w.write( "\n" );
+                w.write( "N: " + gained_multiple_times_domain_length_count );
+                w.write( "\n" );
+                w.write( "Avg: "
+                        + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
+                w.write( "\n" );
+                w.write( "\n" );
+                w.write( "\n" );
+                w.write( "\n" );
+                w.write( "Gained once, protein lengths:" );
+                w.write( "\n" );
+                w.write( gained_once_lengths_stats.toString() );
+                gained_once_lengths_stats = null;
+                w.write( "\n" );
+                w.write( "\n" );
+                w.write( "Gained once, domain counts:" );
+                w.write( "\n" );
+                w.write( gained_once_domain_count_stats.toString() );
+                gained_once_domain_count_stats = null;
+                w.write( "\n" );
+                w.write( "\n" );
+                w.write( "Gained multiple times, protein lengths:" );
+                w.write( "\n" );
+                w.write( gained_multiple_times_lengths_stats.toString() );
+                gained_multiple_times_lengths_stats = null;
+                w.write( "\n" );
+                w.write( "\n" );
+                w.write( "Gained multiple times, domain counts:" );
+                w.write( "\n" );
+                w.write( gained_multiple_times_domain_count_stats.toString() );
+                w.flush();
+                w.close();
+            }
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
+        }
+        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
+                + outfilename_for_counts + "]" );
+        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
+                + outfilename_for_dc + "]" );
+        ForesterUtil.programMessage( surfacing.PRG_NAME,
+                                     "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
+                                             + outfilename_for_dc_for_go_mapping + "]" );
+        ForesterUtil.programMessage( surfacing.PRG_NAME,
+                                     "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
+                                             + outfilename_for_dc_for_go_mapping_unique + "]" );
+    }
+
+    private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
+                                                                        final boolean get_gains ) {
+        final SortedSet<String> domains = new TreeSet<String>();
+        for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
+            final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
+            if ( get_gains ) {
+                domains.addAll( chars.getGainedCharacters() );
+            }
+            else {
+                domains.addAll( chars.getLostCharacters() );
+            }
+        }
+        return domains;
+    }
+
+    private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
+                                                            final boolean domain_combinations,
+                                                            final CharacterStateMatrix.GainLossStates state,
+                                                            final String outfile ) {
+        File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
+                                                                            + ForesterUtil.FILE_SEPARATOR + base_dir );
+        if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
+            per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
+        }
+        if ( domain_combinations ) {
+            per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+                                                                           + ForesterUtil.FILE_SEPARATOR + "DC" );
+        }
+        else {
+            per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+                                                                           + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
+        }
+        if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
+            per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
+        }
+        if ( state == GainLossStates.GAIN ) {
+            per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+                                                                           + ForesterUtil.FILE_SEPARATOR + "GAINS" );
+        }
+        else if ( state == GainLossStates.LOSS ) {
+            per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+                                                                           + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
+        }
+        else {
+            per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
+                                                                           + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
+        }
+        if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
+            per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
+        }
+        return per_node_go_mapped_domain_gain_loss_files_base_dir;
+    }
+
+    private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
+        final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
+        final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
+        for( final String domain_id : cds.keySet() ) {
+            final CombinableDomains cd = cds.get( domain_id );
+            binary_combinations.addAll( cd.toBinaryDomainCombinations() );
+        }
+        return binary_combinations;
+    }
+
+    private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
+            throws IOException {
+        w.write( "<hr>" );
+        w.write( "<br>" );
+        w.write( SurfacingConstants.NL );
+        w.write( "<tt><pre>" );
+        w.write( SurfacingConstants.NL );
+        if ( histo != null ) {
+            w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
+            w.write( SurfacingConstants.NL );
+        }
+        w.write( "</pre></tt>" );
+        w.write( SurfacingConstants.NL );
+        w.write( "<table>" );
+        w.write( SurfacingConstants.NL );
+        w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
+        w.write( SurfacingConstants.NL );
+        w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
+        w.write( SurfacingConstants.NL );
+        w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
+        w.write( SurfacingConstants.NL );
+        w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
+        w.write( SurfacingConstants.NL );
+        if ( stats.getN() > 1 ) {
+            w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
+        }
+        else {
+            w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
+        }
+        w.write( SurfacingConstants.NL );
+        w.write( "</table>" );
+        w.write( SurfacingConstants.NL );
+        w.write( "<br>" );
+        w.write( SurfacingConstants.NL );
+    }
+
+    private static List<String> splitDomainCombination( final String dc ) {
+        final String[] s = dc.split( "=" );
+        if ( s.length != 2 ) {
+            ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
+                    + dc );
+            System.exit( -1 );
+        }
+        final List<String> l = new ArrayList<String>( 2 );
+        l.add( s[ 0 ] );
+        l.add( s[ 1 ] );
+        return l;
+    }
+
+    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 ) {
+        final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
+        final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
+                                                                             + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
+        final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
+        int biological_process_counter = 0;
+        int cellular_component_counter = 0;
+        int molecular_function_counter = 0;
+        int pfams_with_mappings_counter = 0;
+        int pfams_without_mappings_counter = 0;
+        int pfams_without_mappings_to_bp_or_mf_counter = 0;
+        int pfams_with_mappings_to_bp_or_mf_counter = 0;
+        try {
+            final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
+            final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
+            final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
+            summary_writer.write( "# Pfam to GO mapping summary" );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.write( "# Actual summary is at the end of this file." );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.write( "# Encountered Pfams without a GO mapping:" );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            for( final String pfam : all_pfams_encountered ) {
+                all_pfams_encountered_writer.write( pfam );
+                all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
+                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 );
+                    all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
+                    final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
+                    boolean maps_to_bp = false;
+                    boolean maps_to_cc = false;
+                    boolean maps_to_mf = false;
+                    for( final GoId go_id : go_ids ) {
+                        final GoTerm go_term = go_id_to_term_map.get( go_id );
+                        if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
+                            maps_to_bp = true;
+                        }
+                        else if ( go_term.getGoNameSpace().isCellularComponent() ) {
+                            maps_to_cc = true;
+                        }
+                        else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
+                            maps_to_mf = true;
+                        }
+                    }
+                    if ( maps_to_bp ) {
+                        ++biological_process_counter;
+                    }
+                    if ( maps_to_cc ) {
+                        ++cellular_component_counter;
+                    }
+                    if ( maps_to_mf ) {
+                        ++molecular_function_counter;
+                    }
+                    if ( maps_to_bp || maps_to_mf ) {
+                        ++pfams_with_mappings_to_bp_or_mf_counter;
+                    }
+                    else {
+                        ++pfams_without_mappings_to_bp_or_mf_counter;
+                    }
+                }
+                else {
+                    ++pfams_without_mappings_to_bp_or_mf_counter;
+                    ++pfams_without_mappings_counter;
+                    summary_writer.write( pfam );
+                    summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+                }
+            }
+            all_pfams_encountered_writer.close();
+            all_pfams_encountered_with_go_annotation_writer.close();
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
+                                         + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
+                                         + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
+                                         + "\"" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
+                    + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
+                    + encountered_pfams_summary_file + "\"" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
+                    + all_pfams_encountered.size() );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
+                    + pfams_without_mappings_counter + " ["
+                    + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
+                    + pfams_without_mappings_to_bp_or_mf_counter + " ["
+                    + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping                    : "
+                    + pfams_with_mappings_counter + " ["
+                    + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
+                    + pfams_with_mappings_to_bp_or_mf_counter + " ["
+                    + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
+                    + biological_process_counter + " ["
+                    + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
+                    + molecular_function_counter + " ["
+                    + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
+                    + cellular_component_counter + " ["
+                    + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
+                                  + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.write( "# Pfams without mapping to proc. or func. : "
+                    + pfams_without_mappings_to_bp_or_mf_counter + " ["
+                    + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
+                    + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
+                    + pfams_with_mappings_to_bp_or_mf_counter + " ["
+                    + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
+                    + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
+                    + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
+                    + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
+            summary_writer.write( ForesterUtil.LINE_SEPARATOR );
+            summary_writer.close();
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
         }
     }
 
+    private final static void writeColorLabels( final String l, final Color c, final Writer w ) throws IOException {
+        w.write( "<tr><td><b><span style=\"color:" );
+        w.write( String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() ) );
+        w.write( "\">" );
+        w.write( l );
+        w.write( "</span></b></td></tr>" );
+        w.write( SurfacingConstants.NL );
+    }
+
     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,
@@ -2798,7 +3189,7 @@ public final class SurfacingUtil {
         if ( ForesterUtil.isEmpty( domain_1 ) ) {
             domain_count = 1;
         }
-        // The following has a difficult to understand logic.  
+        // The following has a difficult to understand logic.
         for( int d = 0; d < domain_count; ++d ) {
             List<GoId> go_ids = null;
             boolean go_annotation_present = false;
@@ -2843,7 +3234,7 @@ public final class SurfacingUtil {
                         final String go_id_str = go_id.getId();
                         out.write( "<td>" );
                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
-                                + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
+                                   + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
                         out.write( "</td><td>" );
                         out.write( go_term.getName() );
                         if ( domain_count == 2 ) {
@@ -2871,7 +3262,7 @@ public final class SurfacingUtil {
                     out.write( SurfacingConstants.NL );
                 }
             }
-        } //  for( int d = 0; d < domain_count; ++d ) 
+        } //  for( int d = 0; d < domain_count; ++d )
         if ( !any_go_annotation_present ) {
             out.write( "<tr>" );
             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
@@ -2890,7 +3281,7 @@ public final class SurfacingUtil {
                                               final String domain_1,
                                               final String prefix_for_detailed_html,
                                               final Map<String, Set<String>>[] domain_id_to_secondary_features_maps )
-            throws IOException {
+                                                      throws IOException {
         out.write( "<td>" );
         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
             out.write( prefix_for_detailed_html );
@@ -2900,126 +3291,6 @@ public final class SurfacingUtil {
         out.write( "</td>" );
     }
 
-    public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
-                                                      final StringBuilder html_title,
-                                                      final Writer simple_tab_writer,
-                                                      final Writer single_writer,
-                                                      Map<Character, Writer> split_writers,
-                                                      final SortedSet<DomainSimilarity> similarities,
-                                                      final boolean treat_as_binary,
-                                                      final List<Species> species_order,
-                                                      final PrintableDomainSimilarity.PRINT_OPTION print_option,
-                                                      final DomainSimilarity.DomainSimilarityScoring scoring,
-                                                      final boolean verbose,
-                                                      final Map<String, Integer> tax_code_to_id_map,
-                                                      Phylogeny phy ) throws IOException {
-        if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
-            split_writers = new HashMap<Character, Writer>();
-            split_writers.put( '_', single_writer );
-        }
-        switch ( print_option ) {
-            case SIMPLE_TAB_DELIMITED:
-                break;
-            case HTML:
-                for( final Character key : split_writers.keySet() ) {
-                    final Writer w = split_writers.get( key );
-                    w.write( "<html>" );
-                    w.write( SurfacingConstants.NL );
-                    if ( key != '_' ) {
-                        addHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
-                    }
-                    else {
-                        addHtmlHead( w, "DC analysis (" + html_title + ")" );
-                    }
-                    w.write( SurfacingConstants.NL );
-                    w.write( "<body>" );
-                    w.write( SurfacingConstants.NL );
-                    w.write( html_desc.toString() );
-                    w.write( SurfacingConstants.NL );
-                    w.write( "<hr>" );
-                    w.write( SurfacingConstants.NL );
-                    w.write( "<br>" );
-                    w.write( SurfacingConstants.NL );
-                    w.write( "<table>" );
-                    w.write( SurfacingConstants.NL );
-                    w.write( "<tr><td><b>Domains:</b></td></tr>" );
-                    w.write( SurfacingConstants.NL );
-                }
-                break;
-        }
-        //
-        for( final DomainSimilarity similarity : similarities ) {
-            if ( ( species_order != null ) && !species_order.isEmpty() ) {
-                ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
-            }
-            if ( single_writer != null ) {
-                single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
-                        + similarity.getDomainId() + "</a></b></td></tr>" );
-                single_writer.write( SurfacingConstants.NL );
-            }
-            else {
-                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( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
-                        + similarity.getDomainId() + "</a></b></td></tr>" );
-                local_writer.write( SurfacingConstants.NL );
-            }
-        }
-        for( final Writer w : split_writers.values() ) {
-            w.write( "</table>" );
-            w.write( SurfacingConstants.NL );
-            w.write( "<hr>" );
-            w.write( SurfacingConstants.NL );
-            w.write( "<table>" );
-            w.write( SurfacingConstants.NL );
-        }
-        //
-        for( final DomainSimilarity similarity : similarities ) {
-            if ( ( species_order != null ) && !species_order.isEmpty() ) {
-                ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
-            }
-            if ( simple_tab_writer != null ) {
-                simple_tab_writer.write( similarity.toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED,
-                                                                    tax_code_to_id_map,
-                                                                    null ).toString() );
-            }
-            if ( single_writer != null ) {
-                single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
-                single_writer.write( SurfacingConstants.NL );
-            }
-            else {
-                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, phy ).toString() );
-                local_writer.write( SurfacingConstants.NL );
-            }
-        }
-        switch ( print_option ) {
-            case HTML:
-                for( final Writer w : split_writers.values() ) {
-                    w.write( SurfacingConstants.NL );
-                    w.write( "</table>" );
-                    w.write( SurfacingConstants.NL );
-                    w.write( "</font>" );
-                    w.write( SurfacingConstants.NL );
-                    w.write( "</body>" );
-                    w.write( SurfacingConstants.NL );
-                    w.write( "</html>" );
-                    w.write( SurfacingConstants.NL );
-                }
-                break;
-        }
-        for( final Writer w : split_writers.values() ) {
-            w.close();
-        }
-    }
-
     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
                                                                  final String domain_0,
                                                                  final String domain_1 ) throws IOException {
@@ -3031,40 +3302,6 @@ public final class SurfacingUtil {
         }
     }
 
-    public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
-                                          final String filename,
-                                          final Format format ) {
-        final File outfile = new File( filename );
-        checkForOutputFileWriteability( outfile );
-        try {
-            final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
-            matrix.toWriter( out, format );
-            out.flush();
-            out.close();
-        }
-        catch ( final IOException e ) {
-            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
-        }
-        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
-    }
-
-    public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
-        checkForOutputFileWriteability( matrix_outfile );
-        try {
-            final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
-            for( final DistanceMatrix distance_matrix : matrices ) {
-                out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
-                out.write( ForesterUtil.LINE_SEPARATOR );
-                out.flush();
-            }
-            out.close();
-        }
-        catch ( final IOException e ) {
-            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
-        }
-        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
-    }
-
     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
         try {
             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
@@ -3074,101 +3311,19 @@ public final class SurfacingUtil {
             }
             writer.close();
             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
-                    + "]" );
+                                         + "]" );
         }
         catch ( final IOException e ) {
             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
         }
     }
 
-    public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
-        final PhylogenyWriter writer = new PhylogenyWriter();
-        try {
-            writer.toPhyloXML( new File( filename ), phylogeny, 1 );
-        }
-        catch ( final IOException e ) {
-            ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
-                    + e );
-        }
-        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
-    }
-
-    public static void writePresentToNexus( final File output_file,
-                                            final File positive_filter_file,
-                                            final SortedSet<String> filter,
-                                            final List<GenomeWideCombinableDomains> gwcd_list ) {
-        try {
-            writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence( gwcd_list,
-                                                                                                positive_filter_file == null ? null
-                                                                                                        : filter ),
-                               output_file + surfacing.DOMAINS_PRESENT_NEXUS,
-                               Format.NEXUS_BINARY );
-            writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ),
-                               output_file + surfacing.BDC_PRESENT_NEXUS,
-                               Format.NEXUS_BINARY );
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
-        }
-    }
-
-    public static void writeProteinListsForAllSpecies( final File output_dir,
-                                                       final SortedMap<Species, List<Protein>> protein_lists_per_species,
-                                                       final List<GenomeWideCombinableDomains> gwcd_list,
-                                                       final double domain_e_cutoff ) {
-        final SortedSet<String> all_domains = new TreeSet<String>();
-        for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
-            all_domains.addAll( gwcd.getAllDomainIds() );
-        }
-        for( final String domain : all_domains ) {
-            final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + surfacing.SEQ_EXTRACT_SUFFIX );
-            checkForOutputFileWriteability( out );
-            try {
-                final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
-                extractProteinNames( protein_lists_per_species,
-                                     domain,
-                                     proteins_file_writer,
-                                     "\t",
-                                     surfacing.LIMIT_SPEC_FOR_PROT_EX,
-                                     domain_e_cutoff );
-                proteins_file_writer.close();
-            }
-            catch ( final IOException e ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
-            }
-            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
-        }
-    }
-
-    public static void writeTaxonomyLinks( final Writer writer,
-                                           final String species,
-                                           final Map<String, Integer> tax_code_to_id_map ) throws IOException {
-        if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
-            writer.write( " [" );
-            if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
-                writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
-                        + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot</a>" );
-            }
-            else {
-                writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
-                        + "\" target=\"taxonomy_window\">eol</a>" );
-                writer.write( "|" );
-                writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
-                        + "\" target=\"taxonomy_window\">scholar</a>" );
-                writer.write( "|" );
-                writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
-                        + "\" target=\"taxonomy_window\">google</a>" );
-            }
-            writer.write( "]" );
-        }
-    }
-
     private static void writeToNexus( final String outfile_name,
                                       final CharacterStateMatrix<BinaryStates> matrix,
                                       final Phylogeny phylogeny ) {
         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
-                    + "] to nexus" );
+                                                + "] to nexus" );
         }
         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
@@ -3200,7 +3355,23 @@ public final class SurfacingUtil {
                       phylogeny );
     }
 
-    private SurfacingUtil() {
-        // Hidden constructor.
+    final static class DomainComparator implements Comparator<Domain> {
+
+        final private boolean _ascending;
+
+        public DomainComparator( final boolean ascending ) {
+            _ascending = ascending;
+        }
+
+        @Override
+        public final int compare( final Domain d0, final Domain d1 ) {
+            if ( d0.getFrom() < d1.getFrom() ) {
+                return _ascending ? -1 : 1;
+            }
+            else if ( d0.getFrom() > d1.getFrom() ) {
+                return _ascending ? 1 : -1;
+            }
+            return 0;
+        }
     }
 }